Merge branch 'releases/v0.12'v0.12.0

3856 files changed, 100268 insertions, 89099 deletions

diff --git a/.dockerignore b/.dockerignore
new file mode 100644
index 0000000000..7dc5a44b2e
--- /dev/null
+++ b/.dockerignore
@@ -0,0 +1,6 @@
+.git
+opt/spack
+share/spack/docker/Dockerfile
+share/spack/docker/build-image.sh
+share/spack/docker/run-image.sh
+share/spack/docker/push-image.sh
diff --git a/.flake8 b/.flake8
index 49199b35c8..9188f8efa5 100644
--- a/.flake8
+++ b/.flake8
@@ -16,6 +16,9 @@
 # These are required to get the package.py files to test clean:
 # - F999: syntax error in doctest
 #
+# Exempt to allow decorator classes to be lowercase, but follow otherwise:
+# - N801: CapWords for class names.
+#
 [flake8]
-ignore = E129,E221,E241,E272,E731,F999
+ignore = E129,E221,E241,E272,E731,F999,N801,W503,W504
 max-line-length = 79
diff --git a/.flake8_packages b/.flake8_packages
index 9fcc3b86d4..74b42293af 100644
--- a/.flake8_packages
+++ b/.flake8_packages
@@ -18,5 +18,5 @@
 # - F821: undefined name `name` (needed for cmake, configure, etc.)
 #
 [flake8]
-ignore = E129,E221,E241,E272,E731,F999,F405,F821
+ignore = E129,E221,E241,E272,E731,F999,F405,F821,W503,W504
 max-line-length = 79
diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
new file mode 100644
index 0000000000..d9512c06c3
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -0,0 +1,49 @@
+---
+name: Bug report 
+about: Report a bug in the core of Spack (command not working as expected, etc.) 
+
+---
+
+
+*Explain, in a clear and concise way, the command you ran and the result you were trying to achieve.
+Example: "I ran Spack find to list all the installed packages and..."*
+
+
+
+### Steps to reproduce the issue
+
+```console
+$ spack <command1> <spec>
+$ spack <command2> <spec>
+...
+```
+
+### Error Message
+
+If Spack reported an error, provide the error message. If it did not report an error
+but the output appears incorrect, provide the incorrect output. If there was no error
+message and no output but the result is incorrect, describe how it does not match
+what you expect. To provide more information you might re-run the commands with 
+the additional -sd flags:
+```console
+$ spack -sd <command1> <spec>
+$ spack -sd <command2> <spec>
+...
+```
+that activate the full debug output. 
+
+
+### Information on your system
+
+This includes:
+
+ 1. which platform you are using
+ 2. any relevant configuration detail (custom `packages.yaml` or `modules.yaml`, etc.)
+
+-----
+
+We encourage you to try, as much as possible, to reduce your problem to the minimal example that still reproduces the issue. That would help us a lot in fixing it quickly and effectively!
+
+If you want to ask a question about the tool (how to use it, what it can currently do, etc.), try the `#general` channel on our Slack first. We have a welcoming community and chances are you'll get your reply faster and without opening an issue.
+
+Other than that, thanks for taking the time to contribute to Spack!
\ No newline at end of file
diff --git a/.github/ISSUE_TEMPLATE/build_error.md b/.github/ISSUE_TEMPLATE/build_error.md
new file mode 100644
index 0000000000..ae47b2338d
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/build_error.md
@@ -0,0 +1,78 @@
+---
+name: Build error 
+about: Some package in Spack didn't build correctly  
+
+---
+
+*Thanks for taking the time to report this build failure. To proceed with the
+report please:*
+1. Title the issue "Installation issue: <name-of-the-package>".
+2. Provide the information required below.
+3. Remove the template instructions before posting the issue.
+
+We encourage you to try, as much as possible, to reduce your problem to the minimal example that still reproduces the issue. That would help us a lot in fixing it quickly and effectively!
+
+
+---
+
+### Steps to reproduce the issue
+
+```console
+$ spack install <spec> # Fill in the exact spec you are using
+... # and the relevant part of the error message
+```
+
+### Platform and user environment
+
+Please report your OS here:
+```commandline
+$ uname -a 
+Linux nuvolari 4.15.0-29-generic #31-Ubuntu SMP Tue Jul 17 15:39:52 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
+$ lsb_release -d
+Description:	Ubuntu 18.04.1 LTS
+``` 
+and, if relevant, post or attach:
+
+- `packages.yaml`
+- `compilers.yaml`
+
+to the issue
+
+### Additional information
+
+Sometimes the issue benefits from additional details. In these cases there are
+a few things we can suggest doing. First of all, you can post the full output of:
+```console
+$ spack spec --install-status <spec>
+...
+```
+to show people whether Spack installed a faulty software or if it was not able to
+build it at all. 
+
+If your build didn't make it past the configure stage, Spack as also commands to parse 
+logs and report error and warning messages:
+```console
+$ spack log-parse --show=errors,warnings <file-to-parse>
+```
+You might want to run this command on the `config.log` or any other similar file
+found in the stage directory: 
+```console
+$ spack location -s <spec>
+```
+In case in `config.log` there are other settings that you think might be the cause 
+of the build failure, you can consider attaching the file to this issue.
+
+Rebuilding the package with the following options:
+```console
+$ spack -d install -j 1 <spec>
+...
+```
+will provide additional debug information. After the failure you will find two files in the current directory:
+
+1. `spack-cc-<spec>.in`, which contains details on the command given in input 
+    to Spack's compiler wrapper  
+1. `spack-cc-<spec>.out`, which contains the command used to compile / link the 
+    failed object after Spack's compiler wrapper did its processing 
+
+You can post or attach those files to provide maintainers with more information on what
+is causing the failure.
diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md
new file mode 100644
index 0000000000..d1c44df48c
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/feature_request.md
@@ -0,0 +1,27 @@
+---
+name: Feature request 
+about: Suggest adding a feature that is not yet in Spack  
+
+---
+
+*Please add a concise summary of your suggestion here.*
+
+### Rationale
+
+*Is your feature request related to a problem? Please describe it!*
+
+### Description
+
+*Describe the solution you'd like and the alternatives you have considered.*
+
+
+### Additional information
+*Add any other context about the feature request here.*
+
+
+-----
+
+
+If you want to ask a question about the tool (how to use it, what it can currently do, etc.), try the `#general` channel on our Slack first. We have a welcoming community and chances are you'll get your reply faster and without opening an issue.
+
+Other than that, thanks for taking the time to contribute to Spack!
\ No newline at end of file
diff --git a/.gitignore b/.gitignore
index 49bc74063e..ee71398e44 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,6 +1,7 @@
 /db
 /var/spack/stage
 /var/spack/cache
+/var/spack/environments
 /var/spack/repos/*/index.yaml
 /var/spack/repos/*/lock
 *.pyc
@@ -21,5 +22,7 @@
 .coverage
 #*
 .#*
-/.cache
+lib/spack/spack/test/.cache
 /bin/spackc
+*.in.log
+*.out.log
diff --git a/.mailmap b/.mailmap
index df0a82a197..f6f781e891 100644
--- a/.mailmap
+++ b/.mailmap
@@ -3,6 +3,7 @@ Adam Moody            <moody20@llnl.gov>                Adam T. Moody
 Alfredo Gimenez       <gimenez1@llnl.gov>               Alfredo Gimenez         <alfredo.gimenez@gmail.com>
 Alfredo Gimenez       <gimenez1@llnl.gov>               Alfredo Adolfo Gimenez  <alfredo.gimenez@gmail.com>
 Andrew Williams       <williamsa89@cardiff.ac.uk>       Andrew Williams         <andrew@alshain.org.uk>
+Axel Huebl            <a.huebl@hzdr.de>                 Axel Huebl              <axel.huebl@plasma.ninja>
 Ben Boeckel           <ben.boeckel@kitware.com>         Ben Boeckel             <mathstuf@gmail.com>
 Ben Boeckel           <ben.boeckel@kitware.com>         Ben Boeckel             <mathstuf@users.noreply.github.com>
 Benedikt Hegner       <hegner@cern.ch>                  Benedikt Hegner         <benedikt.hegner@cern.ch>
@@ -48,6 +49,7 @@ Robert D. French      <frenchrd@ornl.gov>               Robert D. French
 Robert D. French      <frenchrd@ornl.gov>               Robert.French           <frenchrd@ornl.gov>
 Robert D. French      <frenchrd@ornl.gov>               robertdfrench           <frenchrd@ornl.gov>
 Saravan Pantham       <saravan.pantham@gmail.com>       Saravan Pantham         <pantham1@surface86.llnl.gov>
+Sergey Kosukhin       <sergey.kosukhin@mpimet.mpg.de>   Sergey Kosukhin         <skosukhin@gmail.com>
 Stephen Herbein       <sherbein@udel.edu>               Stephen Herbein         <stephen272@gmail.com>
 Todd Gamblin          <tgamblin@llnl.gov>               George Todd Gamblin     <gamblin2@llnl.gov>
 Todd Gamblin          <tgamblin@llnl.gov>               Todd Gamblin            <gamblin2@llnl.gov>
diff --git a/.travis.yml b/.travis.yml
index 3b55797beb..1db49e476f 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -11,11 +11,19 @@ branches:
 #=============================================================================
 # Build matrix
 #=============================================================================
+
+# Adding the keyword dist to permit an `allow_failures` section
+# under `matrix.include`. More information here:
+#
+# https://docs.travis-ci.com/user/customizing-the-build/#Rows-that-are-Allowed-to-Fail
+dist: trusty
+
 jobs:
   fast_finish: true
   include:
-    - stage: 'flake8 + documentation'
+    - stage: 'style checks'
       python: '2.7'
+      sudo: required
       os: linux
       language: python
       env: TEST_SUITE=flake8
@@ -26,74 +34,103 @@ jobs:
       env: TEST_SUITE=doc
     - stage: 'unit tests'
       python: '2.6'
+      sudo: required
       os: linux
       language: python
       env: TEST_SUITE=unit
     - python: '2.7'
-      os: linux
-      language: python
-      env: [ TEST_SUITE=unit, COVERAGE=true ]
-    - python: '3.3'
+      sudo: required
       os: linux
       language: python
       env: TEST_SUITE=unit
     - python: '3.4'
+      sudo: required
       os: linux
       language: python
       env: TEST_SUITE=unit
     - python: '3.5'
+      sudo: required
+      os: linux
+      language: python
+      env: TEST_SUITE=unit
+    - python: '3.6'
+      sudo: required
+      os: linux
+      language: python
+      env: TEST_SUITE=unit
+    - python: '3.7'
+      sudo: required
       os: linux
+      dist: xenial
       language: python
       env: TEST_SUITE=unit
     - python: '3.6'
+      sudo: required
       os: linux
       language: python
-      env: [ TEST_SUITE=unit, COVERAGE=true ]
-    - stage: 'unit tests - osx'
-      os: osx
+      env: TEST_SUITE=doc
+    - os: osx
       language: generic
-      env: [ TEST_SUITE=unit, PYTHON_VERSION=2.7, COVERAGE=true ]
+      env: [ TEST_SUITE=unit, PYTHON_VERSION=2.7 ]
 # mpich (AutotoolsPackage)
     - stage: 'build tests'
       python: '2.7'
       os: linux
       language: python
-      env: [ TEST_SUITE=build, COVERAGE=true, 'SPEC=mpich' ]
+      env: [ TEST_SUITE=build, 'SPEC=mpich' ]
 # astyle (MakefilePackage)
     - python: '2.7'
       os: linux
       language: python
-      env: [ TEST_SUITE=build, COVERAGE=true, 'SPEC=astyle' ]
+      env: [ TEST_SUITE=build, 'SPEC=astyle' ]
 # tut (WafPackage)
     - python: '2.7'
       os: linux
       language: python
-      env: [ TEST_SUITE=build, COVERAGE=true, 'SPEC=tut' ]
+      env: [ TEST_SUITE=build, 'SPEC=tut' ]
 # py-setuptools (PythonPackage)
     - python: '2.7'
       os: linux
       language: python
-      env: [ TEST_SUITE=build, COVERAGE=true, 'SPEC=py-setuptools' ]
+      env: [ TEST_SUITE=build, 'SPEC=py-setuptools' ]
 # perl-dbi (PerlPackage)
 #    - python: '2.7'
 #      os: linux
 #      language: python
-#      env: [ TEST_SUITE=build, COVERAGE=true, 'SPEC=perl-dbi' ]
+#      env: [ TEST_SUITE=build, 'SPEC=perl-dbi' ]
 # openjpeg (CMakePackage + external cmake)
     - python: '2.7'
       os: linux
       language: python
-      env: [ TEST_SUITE=build, COVERAGE=true, 'SPEC=openjpeg' ]
+      env: [ TEST_SUITE=build, 'SPEC=openjpeg' ]
 # r-rcpp (RPackage + external R)
     - python: '2.7'
       os: linux
       language: python
-      env: [ TEST_SUITE=build, COVERAGE=true, 'SPEC=r-rcpp' ]
+      env: [ TEST_SUITE=build, 'SPEC=r-rcpp' ]
 # mpich (AutotoolsPackage)
     - python: '3.6'
       os: linux
       language: python
-      env: [ TEST_SUITE=build, COVERAGE=true, 'SPEC=mpich' ]
+      env: [ TEST_SUITE=build, 'SPEC=mpich' ]
+    - stage: 'docker build'
+      sudo: required
+      os: linux
+      language: generic
+      env: TEST_SUITE=docker
+  allow_failures:
+    - dist: xenial
+    - env: TEST_SUITE=docker
+    # temporary Python 2.6 exception while we figure out why Travis is hanging
+    - python: '2.6'
+
+stages:
+  - 'style checks'
+  - 'unit tests + documentation'
+  - 'build tests'
+  - name: 'docker build'
+    if: type = push AND branch IN (develop, master)
+
 
 stages:
   - 'flake8 + documentation'
@@ -118,23 +155,32 @@ addons:
       - graphviz
       - gnupg2
       - cmake
+      - ninja-build
       - r-base
       - r-base-core
       - r-base-dev
       - perl
       - perl-base
 
-cache: pip
+cache:
+  pip: true
+  directories:
+    - ~/.mirror
 
 # Work around Travis's lack of support for Python on OSX
 before_install:
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew update; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew ls --versions python > /dev/null || brew install python; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then rm /usr/local/include/c++ ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew ls --versions gcc    > /dev/null || brew install gcc;    fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew ls --versions gnupg2 > /dev/null || brew install gnupg2; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then virtualenv venv; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then source venv/bin/activate; fi
+  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
+        brew update;
+        export HOMEBREW_NO_AUTO_UPDATE=1;
+        rm /usr/local/include/c++ ;
+        brew ls --versions python@2 > /dev/null || brew install python@2;
+        brew ls --versions gcc      > /dev/null || brew install gcc;
+        brew ls --versions gnupg2   > /dev/null || brew install gnupg2;
+        pip2 install --upgrade pip;
+        pip2 install virtualenv;
+        virtualenv venv;
+        source venv/bin/activate;
+    fi
 
 # Install various dependencies
 install:
@@ -143,7 +189,10 @@ install:
   - pip install --upgrade setuptools
   - pip install --upgrade codecov
   - pip install --upgrade flake8
-  - if [[ "$TEST_SUITE" == "doc" ]]; then pip install --upgrade -r lib/spack/docs/requirements.txt; fi
+  - pip install --upgrade pep8-naming
+  - if [[ "$TEST_SUITE" == "doc" ]]; then
+        pip install --upgrade -r lib/spack/docs/requirements.txt;
+    fi
 
 before_script:
   # Need this for the git tests to succeed.
@@ -153,15 +202,41 @@ before_script:
   # Need this to be able to compute the list of changed files
   - git fetch origin develop:develop
 
-  # Set up external dependencies for build tests, because the take too long to compile
-  - if [[ "$TEST_SUITE" == "build" ]]; then cp share/spack/qa/configuration/packages.yaml etc/spack/packages.yaml; fi
+  # Set up external deps for build tests, b/c they take too long to compile
+  - if [[ "$TEST_SUITE" == "build" ]]; then cp
+        share/spack/qa/configuration/packages.yaml etc/spack/packages.yaml;
+    fi
 
 #=============================================================================
 # Building
 #=============================================================================
+services:
+  - docker
+
 script:
   - share/spack/qa/run-$TEST_SUITE-tests
-  - if [[ "$COVERAGE" == "true" ]]; then codecov --env PYTHON_VERSION --required --flags "${TEST_SUITE}${TRAVIS_OS_NAME}"; fi
+  - if [[ "$TEST_SUITE" == "docker build" ]]; then
+        login_attempted=0; login_success=0;
+        for config in share/spack/docker/config/* ; do
+            source "$config" ;
+            ./share/spack/docker/build-image.sh;
+            if [ "$TRAVIS_EVENT_TYPE" != "pull_request" ]; then
+                if [ "$login_attempted" '=' '0' ]; then
+                    if echo "$DOCKER_PASSWORD" | docker login -u "$DOCKER_USERNAME" --password-stdin; then
+                        login_success=1;
+                    fi;
+                    login_attempted=1;
+                fi;
+                if [ "$login_success" '=' '1' ]; then
+                    ./share/spack/docker/push-image.sh;
+                fi
+            fi
+        done;
+    fi
+  - if [[ "$TEST_SUITE" == "unit" || "$TEST_SUITE" == "build" ]]; then
+        codecov --env PYTHON_VERSION
+                --required --flags "${TEST_SUITE}${TRAVIS_OS_NAME}";
+    fi
 
 #=============================================================================
 # Notifications
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index b72967ae54..b7feeb5c68 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -1,5 +1,8 @@
 # Contributing to Spack
 
-Before contributing to Spack you should read the
+All contributions to Spack must be made under both the Apache License,
+Version 2.0 (Apache-2.0) and the MIT license (MIT).
+
+Before contributing to Spack, you should read the
 [Contribution Guide](https://spack.readthedocs.io/en/latest/contribution_guide.html),
 which is maintained as part of Spack's documentation.
diff --git a/COPYRIGHT b/COPYRIGHT
new file mode 100644
index 0000000000..d2cdb2a0f4
--- /dev/null
+++ b/COPYRIGHT
@@ -0,0 +1,85 @@
+Intellectual Property Notice
+------------------------------
+
+Spack is licensed under the Apache License, Version 2.0 (LICENSE-APACHE
+or http://www.apache.org/licenses/LICENSE-2.0) or the MIT license,
+(LICENSE-MIT or http://opensource.org/licenses/MIT), at your option.
+
+Copyrights and patents in the Spack project are retained by contributors.
+No copyright assignment is required to contribute to Spack.
+
+Spack was originally distributed under the LGPL-2.1 license. Consent from
+contributors to relicense to Apache-2.0/MIT is documented at
+https://github.com/spack/spack/issues/9137.
+
+
+SPDX usage
+------------
+
+Individual files contain SPDX tags instead of the full license text.
+This enables machine processing of license information based on the SPDX
+License Identifiers that are available here: https://spdx.org/licenses/
+
+Files that are dual-licensed as Apache-2.0 OR MIT contain the following
+text in the license header:
+
+    SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+External Packages
+-------------------
+Spack bundles its external dependencies in lib/spack/external.  These
+packages are covered by various permissive licenses.  A summary listing
+follows.  See the license included with each package for full details.
+
+PackageName: argparse
+PackageHomePage: https://pypi.python.org/pypi/argparse
+PackageLicenseDeclared: Python-2.0
+
+PackageName: ctest_log_parser
+PackageHomePage: https://github.com/Kitware/CMake
+PackageLicenseDeclared: BSD-3-Clause
+
+PackageName: distro
+PackageHomePage: https://pypi.python.org/pypi/distro
+PackageLicenseDeclared: Apache-2.0
+
+PackageName: functools
+PackageHomePage: https://github.com/python/cpython/blob/2.7/Lib/functools.py
+PackageLicenseDeclared: Python-2.0
+
+PackageName: jinja2
+PackageHomePage: https://pypi.python.org/pypi/Jinja2
+PackageLicenseDeclared: BSD-3-Clause
+
+PackageName: jsonschema
+PackageHomePage: https://pypi.python.org/pypi/jsonschema
+PackageLicenseDeclared: MIT
+
+PackageName: markupsafe
+PackageHomePage: https://pypi.python.org/pypi/MarkupSafe
+PackageLicenseDeclared: BSD-3-Clause
+
+PackageName: orderddict
+Homepage: https://pypi.org/project/ordereddict/
+PackageLicenseDeclared: MIT
+
+PackageName: py
+PackageHomePage: https://pypi.python.org/pypi/py
+PackageLicenseDeclared: MIT
+
+PackageName: pyqver
+PackageHomePage: https://github.com/ghewgill/pyqver
+PackageLicenseDeclared: BSD-3-Clause
+
+PackageName: pytest
+PackageHomePage: https://pypi.python.org/pypi/pytest
+PackageLicenseDeclared: MIT
+
+PackageName: ruamel.yaml
+PackageHomePage: https://yaml.readthedocs.io/
+PackageLicenseDeclared: MIT
+
+PackageName: six
+PackageHomePage: https://pypi.python.org/pypi/six
+PackageLicenseDeclared: MIT
diff --git a/LICENSE b/LICENSE
deleted file mode 100644
index 744bb9f3b5..0000000000
--- a/LICENSE
+++ /dev/null
@@ -1,503 +0,0 @@
-		  GNU LESSER GENERAL PUBLIC LICENSE
-		       Version 2.1, February 1999
-
- Copyright (C) 1991, 1999 Free Software Foundation, Inc.
- 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
- Everyone is permitted to copy and distribute verbatim copies
- of this license document, but changing it is not allowed.
-
-[This is the first released version of the Lesser GPL.  It also counts
- as the successor of the GNU Library Public License, version 2, hence
- the version number 2.1.]
-
-			    Preamble
-
-  The licenses for most software are designed to take away your
-freedom to share and change it.  By contrast, the GNU General Public
-Licenses are intended to guarantee your freedom to share and change
-free software--to make sure the software is free for all its users.
-
-  This license, the Lesser General Public License, applies to some
-specially designated software packages--typically libraries--of the
-Free Software Foundation and other authors who decide to use it.  You
-can use it too, but we suggest you first think carefully about whether
-this license or the ordinary General Public License is the better
-strategy to use in any particular case, based on the explanations below.
-
-  When we speak of free software, we are referring to freedom of use,
-not price.  Our General Public Licenses are designed to make sure that
-you have the freedom to distribute copies of free software (and charge
-for this service if you wish); that you receive source code or can get
-it if you want it; that you can change the software and use pieces of
-it in new free programs; and that you are informed that you can do
-these things.
-
-  To protect your rights, we need to make restrictions that forbid
-distributors to deny you these rights or to ask you to surrender these
-rights.  These restrictions translate to certain responsibilities for
-you if you distribute copies of the library or if you modify it.
-
-  For example, if you distribute copies of the library, whether gratis
-or for a fee, you must give the recipients all the rights that we gave
-you.  You must make sure that they, too, receive or can get the source
-code.  If you link other code with the library, you must provide
-complete object files to the recipients, so that they can relink them
-with the library after making changes to the library and recompiling
-it.  And you must show them these terms so they know their rights.
-
-  We protect your rights with a two-step method: (1) we copyright the
-library, and (2) we offer you this license, which gives you legal
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diff --git a/LICENSE-APACHE b/LICENSE-APACHE
new file mode 100644
index 0000000000..d645695673
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+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
+      except as required for reasonable and customary use in describing the
+      origin of the Work and reproducing the content of the NOTICE file.
+
+   7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
+      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+      implied, including, without limitation, any warranties or conditions
+      of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+      PARTICULAR PURPOSE. You are solely responsible for determining the
+      appropriateness of using or redistributing the Work and assume any
+      risks associated with Your exercise of permissions under this License.
+
+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
+      incidental, or consequential damages of any character arising as a
+      result of this License or out of the use or inability to use the
+      Work (including but not limited to damages for loss of goodwill,
+      work stoppage, computer failure or malfunction, or any and all
+      other commercial damages or losses), even if such Contributor
+      has been advised of the possibility of such damages.
+
+   9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
+      and charge a fee for, acceptance of support, warranty, indemnity,
+      or other liability obligations and/or rights consistent with this
+      License. However, in accepting such obligations, You may act only
+      on Your own behalf and on Your sole responsibility, not on behalf
+      of any other Contributor, and only if You agree to indemnify,
+      defend, and hold each Contributor harmless for any liability
+      incurred by, or claims asserted against, such Contributor by reason
+      of your accepting any such warranty or additional liability.
+
+   END OF TERMS AND CONDITIONS
+
+   APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
+      boilerplate notice, with the fields enclosed by brackets "[]"
+      replaced with your own identifying information. (Don't include
+      the brackets!)  The text should be enclosed in the appropriate
+      comment syntax for the file format. We also recommend that a
+      file or class name and description of purpose be included on the
+      same "printed page" as the copyright notice for easier
+      identification within third-party archives.
+
+   Copyright [yyyy] [name of copyright owner]
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.
diff --git a/LICENSE-MIT b/LICENSE-MIT
new file mode 100644
index 0000000000..f7a9b81fd0
--- /dev/null
+++ b/LICENSE-MIT
@@ -0,0 +1,20 @@
+Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+Permission is hereby granted, free of charge, to any person obtaining a
+copy of this software and associated documentation files (the "Software"),
+to deal in the Software without restriction, including without limitation
+the rights to use, copy, modify, merge, publish, distribute, sublicense,
+and/or sell copies of the Software, and to permit persons to whom the
+Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.
diff --git a/NOTICE b/NOTICE
index ed0d0df792..3737d5a86d 100644
--- a/NOTICE
+++ b/NOTICE
@@ -1,32 +1,21 @@
-########################################################################
-LLNL NOTICE AND TERMS AND CONDITIONS OF THE GNU LGPL
-########################################################################
+This work was produced under the auspices of the U.S. Department of
+Energy by Lawrence Livermore National Laboratory under Contract
+DE-AC52-07NA27344.
 
-LLNL Preamble Notice
+This work was prepared as an account of work sponsored by an agency of
+the United States Government. Neither the United States Government nor
+Lawrence Livermore National Security, LLC, nor any of their employees
+makes any warranty, expressed or implied, or assumes any legal liability
+or responsibility for the accuracy, completeness, or usefulness of any
+information, apparatus, product, or process disclosed, or represents that
+its use would not infringe privately owned rights.
 
-A. This notice is required to be provided under LLNL's contract with
-   the U.S. Department of Energy (DOE). This work was produced at the
-   Lawrence Livermore National Laboratory under Contract
-   No. DE-AC52-07NA27344 with the DOE.
+Reference herein to any specific commercial product, process, or service
+by trade name, trademark, manufacturer, or otherwise does not necessarily
+constitute or imply its endorsement, recommendation, or favoring by the
+United States Government or Lawrence Livermore National Security, LLC.
 
-B. Neither the United States Government nor Lawrence Livermore
-   National Security, LLC nor any of their employees, makes any
-   warranty, express or implied, or assumes any liability or
-   responsibility for the accuracy, completeness, or usefulness of any
-   information, apparatus, product, or process disclosed, or
-   represents that its use would not infringe privately-owned rights.
-
-C. Also, reference herein to any specific commercial products,
-   process, or services by trade name, trademark, manufacturer or
-   otherwise does not necessarily constitute or imply its endorsement,
-   recommendation, or favoring by the United States Government or
-   Lawrence Livermore National Security, LLC. The views and opinions
-   of authors expressed herein do not necessarily state or reflect
-   those of the United States Government or Lawrence Livermore
-   National Security, LLC, and shall not be used for advertising or
-   product endorsement purposes.
-
-See the LICENSE file for the precise terms and conditions for copying,
-distribution and modification.
-
-########################################################################
+The views and opinions of authors expressed herein do not necessarily
+state or reflect those of the United States Government or Lawrence
+Livermore National Security, LLC, and shall not be used for advertising
+or product endorsement purposes.
diff --git a/README.md b/README.md
index 04b047f722..d1a3a1240f 100644
--- a/README.md
+++ b/README.md
@@ -67,6 +67,12 @@ Spack has a Slack channel where you can chat about all things Spack:
 [Sign up here](https://spackpm.herokuapp.com) to get an invitation mailed
 to you.
 
+### Twitter
+
+You can follow [@spackpm](https://twitter.com/spackpm) on Twitter for
+updates. Also, feel free to `@mention` us in in questions or comments
+about your own experience with Spack.
+
 ### Contributions
 
 Contributing to Spack is relatively easy.  Just send us a
@@ -101,11 +107,21 @@ If you are referencing Spack in a publication, please cite the following paper:
    [**The Spack Package Manager: Bringing Order to HPC Software Chaos**](http://www.computer.org/csdl/proceedings/sc/2015/3723/00/2807623.pdf).
    In *Supercomputing 2015 (SC’15)*, Austin, Texas, November 15-20 2015. LLNL-CONF-669890.
 
-Release
+License
 ----------------
-Spack is released under an LGPL license.  For more details see the
-NOTICE and LICENSE files.
 
-``LLNL-CODE-647188``
+Spack is distributed under the terms of both the MIT license and the
+Apache License (Version 2.0). Users may choose either license, at their
+option.
+
+All new contributions must be made under both the MIT and Apache-2.0
+licenses.
 
-![Analytics](https://ga-beacon.appspot.com/UA-101208306-3/welcome-page?pixel)
+See [LICENSE-MIT](https://github.com/spack/spack/blob/develop/LICENSE-MIT),
+[LICENSE-APACHE](https://github.com/spack/spack/blob/develop/LICENSE-APACHE),
+[COPYRIGHT](https://github.com/spack/spack/blob/develop/COPYRIGHT), and
+[NOTICE](https://github.com/spack/spack/blob/develop/NOTICE) for details.
+
+`SPDX-License-Identifier: (Apache-2.0 OR MIT)`
+
+``LLNL-CODE-647188``
diff --git a/bin/sbang b/bin/sbang
index f7182c0f23..b3d74ef48f 100755
--- a/bin/sbang
+++ b/bin/sbang
@@ -1,28 +1,10 @@
 #!/bin/bash
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+#
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 # `sbang`: Run scripts with long shebang lines.
 #
diff --git a/bin/spack b/bin/spack
index 51dbce695b..171ee0f724 100755
--- a/bin/spack
+++ b/bin/spack
@@ -1,28 +1,10 @@
 #!/usr/bin/env python
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from __future__ import print_function
 
 import os
@@ -43,38 +25,23 @@ sys.path.insert(0, spack_lib_path)
 
 # Add external libs
 spack_external_libs = os.path.join(spack_lib_path, "external")
-sys.path.insert(0, spack_external_libs)
 
-# Handle vendoring of YAML specially, as it has two versions.
-if sys.version_info[0] == 2:
-    spack_yaml_libs = os.path.join(spack_external_libs, "yaml/lib")
-else:
-    spack_yaml_libs = os.path.join(spack_external_libs, "yaml/lib3")
-sys.path.insert(0, spack_yaml_libs)
+if sys.version_info[:2] == (2, 6):
+    sys.path.insert(0, os.path.join(spack_external_libs, 'py26'))
 
-# Quick and dirty check to clean orphaned .pyc files left over from
-# previous revisions.  These files were present in earlier versions of
-# Spack, were removed, but shadow system modules that Spack still
-# imports.  If we leave them, Spack will fail in mysterious ways.
-# TODO: more elegant solution for orphaned pyc files.
-orphaned_pyc_files = [
-    os.path.join(spack_external_libs, 'functools.pyc'),
-    os.path.join(spack_external_libs, 'ordereddict.pyc'),
-    os.path.join(spack_lib_path, 'spack', 'platforms', 'cray_xc.pyc'),
-    os.path.join(spack_lib_path, 'spack', 'cmd', 'package-list.pyc'),
-    os.path.join(spack_lib_path, 'spack', 'cmd', 'test-install.pyc'),
-    os.path.join(spack_lib_path, 'spack', 'cmd', 'url-parse.pyc'),
-    os.path.join(spack_lib_path, 'spack', 'test', 'yaml.pyc')
-]
+sys.path.insert(0, spack_external_libs)
 
-for pyc_file in orphaned_pyc_files:
-    if not os.path.exists(pyc_file):
-        continue
-    try:
-        os.remove(pyc_file)
-    except OSError as e:
-        print("WARNING: Spack may fail mysteriously. "
-              "Couldn't remove orphaned .pyc file: %s" % pyc_file)
+# Here we delete ruamel.yaml in case it has been already imported from site
+# (see #9206 for a broader description of the issue).
+#
+# Briefly: ruamel.yaml produces a .pth file when installed with pip that
+# makes the site installed package the preferred one, even tough sys.path
+# is modified to point to another version of ruamel.yaml.
+if 'ruamel.yaml' in sys.modules:
+    del sys.modules['ruamel.yaml']
+
+if 'ruamel' in sys.modules:
+    del sys.modules['ruamel']
 
 # Once we've set up the system path, run the spack main method
 import spack.main  # noqa
diff --git a/bin/spack-python b/bin/spack-python
index 2a717025bf..e4487e3464 100755
--- a/bin/spack-python
+++ b/bin/spack-python
@@ -1,28 +1,10 @@
 #!/bin/sh
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+#
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 # spack-python
 #
diff --git a/etc/spack/defaults/config.yaml b/etc/spack/defaults/config.yaml
index b6a09a7738..8525947fbd 100644
--- a/etc/spack/defaults/config.yaml
+++ b/etc/spack/defaults/config.yaml
@@ -18,9 +18,15 @@ config:
   # You can use $spack here to refer to the root of the spack instance.
   install_tree: $spack/opt/spack
 
+
   # Locations where templates should be found
   template_dirs:
-    - $spack/templates
+    - $spack/share/spack/templates
+
+
+  # Default directory layout
+  install_path_scheme: "${ARCHITECTURE}/${COMPILERNAME}-${COMPILERVER}/${PACKAGE}-${VERSION}-${HASH}"
+
 
   # Locations where different types of modules should be installed.
   module_roots:
@@ -39,20 +45,20 @@ config:
   # builds directly inside its install directory without staging them in
   # temporary space.
   #
-  # The build stage can be purged with `spack purge --stage`.
+  # The build stage can be purged with `spack clean --stage`.
   build_stage:
     - $tempdir
     - /nfs/tmp2/$user
     - $spack/var/spack/stage
 
 
-  # Cache directory already downloaded source tarballs and archived
-  # repositories. This can be purged with `spack purge --downloads`.
+  # Cache directory for already downloaded source tarballs and archived
+  # repositories. This can be purged with `spack clean --downloads`.
   source_cache: $spack/var/spack/cache
 
 
   # Cache directory for miscellaneous files, like the package index.
-  # This can be purged with `spack purge --misc-cache`
+  # This can be purged with `spack clean --misc-cache`
   misc_cache: ~/.spack/cache
 
 
@@ -71,7 +77,43 @@ config:
   dirty: false
 
 
+  # The language the build environment will use. This will produce English
+  # compiler messages by default, so the log parser can highlight errors.
+  # If set to C, it will use English (see man locale).
+  # If set to the empty string (''), it will use the language from the
+  # user's environment.
+  build_language: C
+
+
+  # When set to true, concurrent instances of Spack will use locks to
+  # avoid modifying the install tree, database file, etc. If false, Spack
+  # will disable all locking, but you must NOT run concurrent instances
+  # of Spack.  For filesystems that don't support locking, you should set
+  # this to false and run one Spack at a time, but otherwise we recommend
+  # enabling locks.
+  locks: true
+
+
   # The default number of jobs to use when running `make` in parallel.
   # If set to 4, for example, `spack install` will run `make -j4`.
   # If not set, all available cores are used by default.
   # build_jobs: 4
+
+
+  # If set to true, Spack will use ccache to cache C compiles.
+  ccache: false
+
+
+  # How long to wait to lock the Spack installation database. This lock is used
+  # when Spack needs to manage its own package metadata and all operations are
+  # expected to complete within the default time limit. The timeout should
+  # therefore generally be left untouched.
+  db_lock_timeout: 120
+
+
+  # How long to wait when attempting to modify a package (e.g. to install it).
+  # This value should typically be 'null' (never time out) unless the Spack
+  # instance only ever has a single user at a time, and only if the user
+  # anticipates that a significant delay indicates that the lock attempt will
+  # never succeed.
+  package_lock_timeout: null
diff --git a/etc/spack/defaults/darwin/modules.yaml b/etc/spack/defaults/darwin/modules.yaml
new file mode 100644
index 0000000000..570aec2e84
--- /dev/null
+++ b/etc/spack/defaults/darwin/modules.yaml
@@ -0,0 +1,23 @@
+# -------------------------------------------------------------------------
+# This is the default configuration for Spack's module file generation.
+#
+# Settings here are versioned with Spack and are intended to provide
+# sensible defaults out of the box. Spack maintainers should edit this
+# file to keep it current.
+#
+# Users can override these settings by editing the following files.
+#
+# Per-spack-instance settings (overrides defaults):
+#   $SPACK_ROOT/etc/spack/modules.yaml
+#
+# Per-user settings (overrides default and site settings):
+#   ~/.spack/modules.yaml
+# -------------------------------------------------------------------------
+modules:
+  prefix_inspections:
+    lib:
+      - DYLD_LIBRARY_PATH
+      - DYLD_FALLBACK_LIBRARY_PATH
+    lib64:
+      - DYLD_LIBRARY_PATH
+      - DYLD_FALLBACK_LIBRARY_PATH
diff --git a/etc/spack/defaults/darwin/packages.yaml b/etc/spack/defaults/darwin/packages.yaml
index 24a08809db..1150f6bab7 100644
--- a/etc/spack/defaults/darwin/packages.yaml
+++ b/etc/spack/defaults/darwin/packages.yaml
@@ -16,3 +16,12 @@
 packages:
   all:
     compiler: [clang, gcc, intel]
+    providers:
+      elf: [libelf]
+      unwind: [apple-libunwind]
+  apple-libunwind:
+    paths:
+    # Apple bundles libunwind version 35.3 with macOS 10.9 and later,
+    # although the version number used here isn't critical
+      apple-libunwind@35.3: /usr
+    buildable: False
diff --git a/etc/spack/defaults/linux/modules.yaml b/etc/spack/defaults/linux/modules.yaml
new file mode 100644
index 0000000000..a86a4794f1
--- /dev/null
+++ b/etc/spack/defaults/linux/modules.yaml
@@ -0,0 +1,21 @@
+# -------------------------------------------------------------------------
+# This is the default configuration for Spack's module file generation.
+#
+# Settings here are versioned with Spack and are intended to provide
+# sensible defaults out of the box. Spack maintainers should edit this
+# file to keep it current.
+#
+# Users can override these settings by editing the following files.
+#
+# Per-spack-instance settings (overrides defaults):
+#   $SPACK_ROOT/etc/spack/modules.yaml
+#
+# Per-user settings (overrides default and site settings):
+#   ~/.spack/modules.yaml
+# -------------------------------------------------------------------------
+modules:
+  prefix_inspections:
+    lib:
+      - LD_LIBRARY_PATH
+    lib64:
+      - LD_LIBRARY_PATH
diff --git a/etc/spack/defaults/modules.yaml b/etc/spack/defaults/modules.yaml
index 8b6f1b40af..b5ea65da95 100644
--- a/etc/spack/defaults/modules.yaml
+++ b/etc/spack/defaults/modules.yaml
@@ -28,10 +28,8 @@ modules:
       - ACLOCAL_PATH
     lib:
       - LIBRARY_PATH
-      - LD_LIBRARY_PATH
     lib64:
       - LIBRARY_PATH
-      - LD_LIBRARY_PATH
     include:
       - CPATH
     lib/pkgconfig:
diff --git a/etc/spack/defaults/packages.yaml b/etc/spack/defaults/packages.yaml
index 2cfdd399df..aaab12b3ef 100644
--- a/etc/spack/defaults/packages.yaml
+++ b/etc/spack/defaults/packages.yaml
@@ -17,13 +17,18 @@ packages:
   all:
     compiler: [gcc, intel, pgi, clang, xl, nag]
     providers:
+      D: [ldc]
       awk: [gawk]
       blas: [openblas]
       daal: [intel-daal]
       elf: [elfutils]
+      fftw-api: [fftw]
+      gl: [mesa, opengl]
+      glu: [mesa-glu, openglu]
       golang: [gcc]
       ipp: [intel-ipp]
       java: [jdk]
+      jpeg: [libjpeg-turbo, libjpeg]
       lapack: [openblas]
       mkl: [intel-mkl]
       mpe: [mpe2]
@@ -31,7 +36,11 @@ packages:
       opencl: [pocl]
       openfoam: [openfoam-com, openfoam-org, foam-extend]
       pil: [py-pillow]
+      pkgconfig: [pkgconf, pkg-config]
       scalapack: [netlib-scalapack]
       szip: [libszip, libaec]
       tbb: [intel-tbb]
-      jpeg: [libjpeg-turbo, libjpeg]
+      unwind: [libunwind]
+    permissions:
+      read: world
+      write: user
diff --git a/lib/spack/docs/.gitignore b/lib/spack/docs/.gitignore
index 9afb658706..0b6258af50 100644
--- a/lib/spack/docs/.gitignore
+++ b/lib/spack/docs/.gitignore
@@ -1,4 +1,4 @@
-package_list.rst
+package_list.html
 command_index.rst
 spack*.rst
 llnl*.rst
diff --git a/lib/spack/docs/Makefile b/lib/spack/docs/Makefile
index 3503794021..1ce5c1910c 100644
--- a/lib/spack/docs/Makefile
+++ b/lib/spack/docs/Makefile
@@ -17,7 +17,7 @@ ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
 # the i18n builder cannot share the environment and doctrees with the others
 I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
 
-.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext apidoc
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext apidoc dashdoc
 
 all: html
 
@@ -83,7 +83,7 @@ help:
 	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
 
 clean:
-	-rm -f package_list.rst command_index.rst
+	-rm -f command_index.rst
 	-rm -rf $(BUILDDIR)/* $(APIDOC_FILES)
 
 html:
@@ -196,3 +196,9 @@ doctest:
 	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
 	@echo "Testing of doctests in the sources finished, look at the " \
 	      "results in $(BUILDDIR)/doctest/output.txt."
+
+dashdoc:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/dashdoc
+	doc2dash -A -v -n spack -d $(BUILDDIR)/ -f -I index.html -j $(BUILDDIR)/dashdoc
+	@echo
+	@echo "Build finished. The Docset is in $(BUILDDIR)/dashdoc."
diff --git a/lib/spack/docs/_themes/sphinx_rtd_theme/__init__.py b/lib/spack/docs/_themes/sphinx_rtd_theme/__init__.py
deleted file mode 100644
index 95ddc52ae0..0000000000
--- a/lib/spack/docs/_themes/sphinx_rtd_theme/__init__.py
+++ /dev/null
@@ -1,17 +0,0 @@
-"""Sphinx ReadTheDocs theme.
-
-From https://github.com/ryan-roemer/sphinx-bootstrap-theme.
-
-"""
-import os
-
-VERSION = (0, 1, 8)
-
-__version__ = ".".join(str(v) for v in VERSION)
-__version_full__ = __version__
-
-
-def get_html_theme_path():
-    """Return list of HTML theme paths."""
-    cur_dir = os.path.abspath(os.path.dirname(os.path.dirname(__file__)))
-    return cur_dir
diff --git a/lib/spack/docs/_themes/sphinx_rtd_theme/breadcrumbs.html b/lib/spack/docs/_themes/sphinx_rtd_theme/breadcrumbs.html
deleted file mode 100644
index 0028421e1c..0000000000
--- a/lib/spack/docs/_themes/sphinx_rtd_theme/breadcrumbs.html
+++ /dev/null
@@ -1,23 +0,0 @@
-<div role="navigation" aria-label="breadcrumbs navigation">
-  <ul class="wy-breadcrumbs">
-    <li><a href="{{ pathto(master_doc) }}">Docs</a> &raquo;</li>
-      {% for doc in parents %}
-          <li><a href="{{ doc.link|e }}">{{ doc.title }}</a> &raquo;</li>
-      {% endfor %}
-    <li>{{ title }}</li>
-      <li class="wy-breadcrumbs-aside">
-        {% if pagename != "search" %}
-          {% if display_github %}
-            <a href="https://{{ github_host|default("github.com") }}/{{ github_user }}/{{ github_repo }}/blob/{{ github_version }}{{ conf_py_path }}{{ pagename }}{{ source_suffix }}" class="fa fa-github"> Edit on GitHub</a>
-          {% elif display_bitbucket %}
-            <a href="https://bitbucket.org/{{ bitbucket_user }}/{{ bitbucket_repo }}/src/{{ bitbucket_version}}{{ conf_py_path }}{{ pagename }}{{ source_suffix }}" class="fa fa-bitbucket"> Edit on Bitbucket</a>
-          {% elif show_source and source_url_prefix %}
-            <a href="{{ source_url_prefix }}{{ pagename }}{{ source_suffix }}">View page source</a>
-          {% elif show_source and has_source and sourcename %}
-            <a href="{{ pathto('_sources/' + sourcename, true)|e }}" rel="nofollow"> View page source</a>
-          {% endif %}
-        {% endif %}
-      </li>
-  </ul>
-  <hr/>
-</div>
diff --git a/lib/spack/docs/_themes/sphinx_rtd_theme/footer.html b/lib/spack/docs/_themes/sphinx_rtd_theme/footer.html
deleted file mode 100644
index 958ebbd2f7..0000000000
--- a/lib/spack/docs/_themes/sphinx_rtd_theme/footer.html
+++ /dev/null
@@ -1,40 +0,0 @@
-<footer>
-  {% if next or prev %}
-    <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
-      {% if next %}
-        <a href="{{ next.link|e }}" class="btn btn-neutral float-right" title="{{ next.title|striptags|e }}" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
-      {% endif %}
-      {% if prev %}
-        <a href="{{ prev.link|e }}" class="btn btn-neutral" title="{{ prev.title|striptags|e }}" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
-      {% endif %}
-    </div>
-  {% endif %}
-
-  <hr/>
-
-  <div role="contentinfo">
-    <p>
-    {%- if show_copyright %}
-      {%- if hasdoc('copyright') %}
-        {% trans path=pathto('copyright'), copyright=copyright|e %}&copy; <a href="{{ path }}">Copyright</a> {{ copyright }}.{% endtrans %}
-      {%- else %}
-        {% trans copyright=copyright|e %}&copy; Copyright {{ copyright }}.{% endtrans %}
-      {%- endif %}
-    {%- endif %}
-
-    <br/>
-    Written by Todd Gamblin (<a href="mailto:tgamblin@llnl.gov">tgamblin@llnl.gov</a>) and
-    many <a href="https://github.com/spack/spack/graphs/contributors">contributors.</a> LLNL-CODE-647188.
-
-    {%- if last_updated %}
-      <br/>
-      {% trans last_updated=last_updated|e %}Last updated on {{ last_updated }}.{% endtrans %}
-    {%- endif %}
-    </p>
-  </div>
-
-  {%- if show_sphinx %}
-  {% trans %}Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>{% endtrans %}.
-  {%- endif %}
-
-</footer>
diff --git a/lib/spack/docs/_themes/sphinx_rtd_theme/layout.html b/lib/spack/docs/_themes/sphinx_rtd_theme/layout.html
deleted file mode 100644
index 9481d8b426..0000000000
--- a/lib/spack/docs/_themes/sphinx_rtd_theme/layout.html
+++ /dev/null
@@ -1,181 +0,0 @@
-{# TEMPLATE VAR SETTINGS #}
-{%- set url_root = pathto('', 1) %}
-{%- if url_root == '#' %}{% set url_root = '' %}{% endif %}
-{%- if not embedded and docstitle %}
-  {%- set titlesuffix = " &mdash; "|safe + docstitle|e %}
-{%- else %}
-  {%- set titlesuffix = "" %}
-{%- endif %}
-
-<!DOCTYPE html>
-<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
-<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
-<head>
-  <meta charset="utf-8">
-  {{ metatags }}
-  <meta name="viewport" content="width=device-width, initial-scale=1.0">
-  {% block htmltitle %}
-  <title>{{ title|striptags|e }}{{ titlesuffix }}</title>
-  {% endblock %}
-
-  {# FAVICON #}
-  {% if favicon %}
-    <link rel="shortcut icon" href="{{ pathto('_static/' + favicon, 1) }}"/>
-  {% endif %}
-
-  {# CSS #}
-
-  {# OPENSEARCH #}
-  {% if not embedded %}
-    {% if use_opensearch %}
-      <link rel="search" type="application/opensearchdescription+xml" title="{% trans docstitle=docstitle|e %}Search within {{ docstitle }}{% endtrans %}" href="{{ pathto('_static/opensearch.xml', 1) }}"/>
-    {% endif %}
-
-  {% endif %}
-
-  {# RTD hosts this file, so just load on non RTD builds #}
-  {% if not READTHEDOCS %}
-    <link rel="stylesheet" href="{{ pathto('_static/' + style, 1) }}" type="text/css" />
-  {% endif %}
-
-  {% for cssfile in css_files %}
-    <link rel="stylesheet" href="{{ pathto(cssfile, 1) }}" type="text/css" />
-  {% endfor %}
-
-  {% for cssfile in extra_css_files %}
-    <link rel="stylesheet" href="{{ pathto(cssfile, 1) }}" type="text/css" />
-  {% endfor %}
-
-  {%- block linktags %}
-    {%- if hasdoc('about') %}
-        <link rel="author" title="{{ _('About these documents') }}"
-              href="{{ pathto('about') }}"/>
-    {%- endif %}
-    {%- if hasdoc('genindex') %}
-        <link rel="index" title="{{ _('Index') }}"
-              href="{{ pathto('genindex') }}"/>
-    {%- endif %}
-    {%- if hasdoc('search') %}
-        <link rel="search" title="{{ _('Search') }}" href="{{ pathto('search') }}"/>
-    {%- endif %}
-    {%- if hasdoc('copyright') %}
-        <link rel="copyright" title="{{ _('Copyright') }}" href="{{ pathto('copyright') }}"/>
-    {%- endif %}
-    <link rel="top" title="{{ docstitle|e }}" href="{{ pathto('index') }}"/>
-    {%- if parents %}
-        <link rel="up" title="{{ parents[-1].title|striptags|e }}" href="{{ parents[-1].link|e }}"/>
-    {%- endif %}
-    {%- if next %}
-        <link rel="next" title="{{ next.title|striptags|e }}" href="{{ next.link|e }}"/>
-    {%- endif %}
-    {%- if prev %}
-        <link rel="prev" title="{{ prev.title|striptags|e }}" href="{{ prev.link|e }}"/>
-    {%- endif %}
-  {%- endblock %}
-  {%- block extrahead %} {% endblock %}
-
-  {# Keep modernizr in head - http://modernizr.com/docs/#installing #}
-  <script src="_static/js/modernizr.min.js"></script>
-
-</head>
-
-<body class="wy-body-for-nav" role="document">
-
-  <div class="wy-grid-for-nav">
-
-    {# SIDE NAV, TOGGLES ON MOBILE #}
-    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
-      <div class="wy-side-nav-search">
-        {% block sidebartitle %}
-
-        {% if logo and theme_logo_only %}
-          <a href="{{ pathto(master_doc) }}">
-        {% else %}
-          <a href="{{ pathto(master_doc) }}" class="icon icon-home"> {{ project }}
-        {% endif %}
-
-        {% if logo %}
-          {# Not strictly valid HTML, but it's the only way to display/scale it properly, without weird scripting or heaps of work #}
-          <img src="{{ pathto('_static/' + logo, 1) }}" class="logo" />
-        {% endif %}
-        </a>
-
-        {% include "searchbox.html" %}
-
-        {% endblock %}
-      </div>
-
-      <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
-        {% block menu %}
-          {% set toctree = toctree(maxdepth=4, collapse=False, includehidden=True) %}
-          {% if toctree %}
-              {{ toctree }}
-          {% else %}
-              <!-- Local TOC -->
-              <div class="local-toc">{{ toc }}</div>
-          {% endif %}
-        {% endblock %}
-      </div>
-      &nbsp;
-    </nav>
-
-    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
-
-      {# MOBILE NAV, TRIGGLES SIDE NAV ON TOGGLE #}
-      <nav class="wy-nav-top" role="navigation" aria-label="top navigation">
-        <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
-        <a href="{{ pathto(master_doc) }}">{{ project }}</a>
-      </nav>
-
-
-      {# PAGE CONTENT #}
-      <div class="wy-nav-content">
-        <div class="rst-content">
-          {% include "breadcrumbs.html" %}
-          <div role="main" class="document">
-            {% block body %}{% endblock %}
-          </div>
-          {% include "footer.html" %}
-        </div>
-      </div>
-
-    </section>
-
-  </div>
-  {% include "versions.html" %}
-
-  {% if not embedded %}
-
-    <script type="text/javascript">
-        var DOCUMENTATION_OPTIONS = {
-            URL_ROOT:'{{ url_root }}',
-            VERSION:'{{ release|e }}',
-            COLLAPSE_INDEX:false,
-            FILE_SUFFIX:'{{ '' if no_search_suffix else file_suffix }}',
-            HAS_SOURCE:  {{ has_source|lower }}
-        };
-    </script>
-    {%- for scriptfile in script_files %}
-      <script type="text/javascript" src="{{ pathto(scriptfile, 1) }}"></script>
-    {%- endfor %}
-
-  {% endif %}
-
-  {# RTD hosts this file, so just load on non RTD builds #}
-  {% if not READTHEDOCS %}
-    <script type="text/javascript" src="{{ pathto('_static/js/theme.js', 1) }}"></script>
-  {% endif %}
-
-  {# STICKY NAVIGATION #}
-  {% if theme_sticky_navigation %}
-  <script type="text/javascript">
-      jQuery(function () {
-          SphinxRtdTheme.StickyNav.enable();
-      });
-  </script>
-  {% endif %}
-
-  {%- block footer %} {% endblock %}
-
-</body>
-</html>
diff --git a/lib/spack/docs/_themes/sphinx_rtd_theme/layout_old.html b/lib/spack/docs/_themes/sphinx_rtd_theme/layout_old.html
deleted file mode 100644
index deb8df2a1a..0000000000
--- a/lib/spack/docs/_themes/sphinx_rtd_theme/layout_old.html
+++ /dev/null
@@ -1,205 +0,0 @@
-{#
-    basic/layout.html
-    ~~~~~~~~~~~~~~~~~
-
-    Master layout template for Sphinx themes.
-
-    :copyright: Copyright 2007-2013 by the Sphinx team, see AUTHORS.
-    :license: BSD, see LICENSE for details.
-#}
-{%- block doctype -%}
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-{%- endblock %}
-{%- set reldelim1 = reldelim1 is not defined and ' &raquo;' or reldelim1 %}
-{%- set reldelim2 = reldelim2 is not defined and ' |' or reldelim2 %}
-{%- set render_sidebar = (not embedded) and (not theme_nosidebar|tobool) and
-                         (sidebars != []) %}
-{%- set url_root = pathto('', 1) %}
-{# XXX necessary? #}
-{%- if url_root == '#' %}{% set url_root = '' %}{% endif %}
-{%- if not embedded and docstitle %}
-  {%- set titlesuffix = " &mdash; "|safe + docstitle|e %}
-{%- else %}
-  {%- set titlesuffix = "" %}
-{%- endif %}
-
-{%- macro relbar() %}
-    <div class="related">
-      <h3>{{ _('Navigation') }}</h3>
-      <ul>
-        {%- for rellink in rellinks %}
-        <li class="right" {% if loop.first %}style="margin-right: 10px"{% endif %}>
-          <a href="{{ pathto(rellink[0]) }}" title="{{ rellink[1]|striptags|e }}"
-             {{ accesskey(rellink[2]) }}>{{ rellink[3] }}</a>
-          {%- if not loop.first %}{{ reldelim2 }}{% endif %}</li>
-        {%- endfor %}
-        {%- block rootrellink %}
-        <li><a href="{{ pathto(master_doc) }}">{{ shorttitle|e }}</a>{{ reldelim1 }}</li>
-        {%- endblock %}
-        {%- for parent in parents %}
-          <li><a href="{{ parent.link|e }}" {% if loop.last %}{{ accesskey("U") }}{% endif %}>{{ parent.title }}</a>{{ reldelim1 }}</li>
-        {%- endfor %}
-        {%- block relbaritems %} {% endblock %}
-      </ul>
-    </div>
-{%- endmacro %}
-
-{%- macro sidebar() %}
-      {%- if render_sidebar %}
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-          {%- block sidebarlogo %}
-          {%- if logo %}
-            <p class="logo"><a href="{{ pathto(master_doc) }}">
-              <img class="logo" src="{{ pathto('_static/' + logo, 1) }}" alt="Logo"/>
-            </a></p>
-          {%- endif %}
-          {%- endblock %}
-          {%- if sidebars != None %}
-            {#- new style sidebar: explicitly include/exclude templates #}
-            {%- for sidebartemplate in sidebars %}
-            {%- include sidebartemplate %}
-            {%- endfor %}
-          {%- else %}
-            {#- old style sidebars: using blocks -- should be deprecated #}
-            {%- block sidebartoc %}
-            {%- include "localtoc.html" %}
-            {%- endblock %}
-            {%- block sidebarrel %}
-            {%- include "relations.html" %}
-            {%- endblock %}
-            {%- block sidebarsourcelink %}
-            {%- include "sourcelink.html" %}
-            {%- endblock %}
-            {%- if customsidebar %}
-            {%- include customsidebar %}
-            {%- endif %}
-            {%- block sidebarsearch %}
-            {%- include "searchbox.html" %}
-            {%- endblock %}
-          {%- endif %}
-        </div>
-      </div>
-      {%- endif %}
-{%- endmacro %}
-
-{%- macro script() %}
-    <script type="text/javascript">
-      var DOCUMENTATION_OPTIONS = {
-        URL_ROOT:    '{{ url_root }}',
-        VERSION:     '{{ release|e }}',
-        COLLAPSE_INDEX: false,
-        FILE_SUFFIX: '{{ '' if no_search_suffix else file_suffix }}',
-        HAS_SOURCE:  {{ has_source|lower }}
-      };
-    </script>
-    {%- for scriptfile in script_files %}
-    <script type="text/javascript" src="{{ pathto(scriptfile, 1) }}"></script>
-    {%- endfor %}
-{%- endmacro %}
-
-{%- macro css() %}
-    <link rel="stylesheet" href="{{ pathto('_static/' + style, 1) }}" type="text/css" />
-    <link rel="stylesheet" href="{{ pathto('_static/pygments.css', 1) }}" type="text/css" />
-    {%- for cssfile in css_files %}
-    <link rel="stylesheet" href="{{ pathto(cssfile, 1) }}" type="text/css" />
-    {%- endfor %}
-{%- endmacro %}
-
-<html xmlns="http://www.w3.org/1999/xhtml">
-  <head>
-    <meta http-equiv="Content-Type" content="text/html; charset={{ encoding }}" />
-    {{ metatags }}
-    {%- block htmltitle %}
-    <title>{{ title|striptags|e }}{{ titlesuffix }}</title>
-    {%- endblock %}
-    {{ css() }}
-    {%- if not embedded %}
-    {{ script() }}
-    {%- if use_opensearch %}
-    <link rel="search" type="application/opensearchdescription+xml"
-          title="{% trans docstitle=docstitle|e %}Search within {{ docstitle }}{% endtrans %}"
-          href="{{ pathto('_static/opensearch.xml', 1) }}"/>
-    {%- endif %}
-    {%- if favicon %}
-    <link rel="shortcut icon" href="{{ pathto('_static/' + favicon, 1) }}"/>
-    {%- endif %}
-    {%- endif %}
-{%- block linktags %}
-    {%- if hasdoc('about') %}
-    <link rel="author" title="{{ _('About these documents') }}" href="{{ pathto('about') }}" />
-    {%- endif %}
-    {%- if hasdoc('genindex') %}
-    <link rel="index" title="{{ _('Index') }}" href="{{ pathto('genindex') }}" />
-    {%- endif %}
-    {%- if hasdoc('search') %}
-    <link rel="search" title="{{ _('Search') }}" href="{{ pathto('search') }}" />
-    {%- endif %}
-    {%- if hasdoc('copyright') %}
-    <link rel="copyright" title="{{ _('Copyright') }}" href="{{ pathto('copyright') }}" />
-    {%- endif %}
-    <link rel="top" title="{{ docstitle|e }}" href="{{ pathto('index') }}" />
-    {%- if parents %}
-    <link rel="up" title="{{ parents[-1].title|striptags|e }}" href="{{ parents[-1].link|e }}" />
-    {%- endif %}
-    {%- if next %}
-    <link rel="next" title="{{ next.title|striptags|e }}" href="{{ next.link|e }}" />
-    {%- endif %}
-    {%- if prev %}
-    <link rel="prev" title="{{ prev.title|striptags|e }}" href="{{ prev.link|e }}" />
-    {%- endif %}
-{%- endblock %}
-{%- block extrahead %} {% endblock %}
-  </head>
-  <body>
-{%- block header %}{% endblock %}
-
-{%- block relbar1 %}{{ relbar() }}{% endblock %}
-
-{%- block content %}
-  {%- block sidebar1 %} {# possible location for sidebar #} {% endblock %}
-
-    <div class="document">
-  {%- block document %}
-      <div class="documentwrapper">
-      {%- if render_sidebar %}
-        <div class="bodywrapper">
-      {%- endif %}
-          <div class="body">
-            {% block body %} {% endblock %}
-          </div>
-      {%- if render_sidebar %}
-        </div>
-      {%- endif %}
-      </div>
-  {%- endblock %}
-
-  {%- block sidebar2 %}{{ sidebar() }}{% endblock %}
-      <div class="clearer"></div>
-    </div>
-{%- endblock %}
-
-{%- block relbar2 %}{{ relbar() }}{% endblock %}
-
-{%- block footer %}
-    <div class="footer">
-    {%- if show_copyright %}
-      {%- if hasdoc('copyright') %}
-        {% trans path=pathto('copyright'), copyright=copyright|e %}&copy; <a href="{{ path }}">Copyright</a> {{ copyright }}.{% endtrans %}
-      {%- else %}
-        {% trans copyright=copyright|e %}&copy; Copyright {{ copyright }}.{% endtrans %}
-      {%- endif %}
-    {%- endif %}
-    {%- if last_updated %}
-      {% trans last_updated=last_updated|e %}Last updated on {{ last_updated }}.{% endtrans %}
-    {%- endif %}
-    {%- if show_sphinx %}
-      {% trans sphinx_version=sphinx_version|e %}Created using <a href="http://sphinx-doc.org/">Sphinx</a> {{ sphinx_version }}.{% endtrans %}
-    {%- endif %}
-    </div>
-    <p>asdf asdf asdf asdf 22</p>
-{%- endblock %}
-  </body>
-</html>
-
diff --git a/lib/spack/docs/_themes/sphinx_rtd_theme/search.html b/lib/spack/docs/_themes/sphinx_rtd_theme/search.html
deleted file mode 100644
index e3aa9b5c6e..0000000000
--- a/lib/spack/docs/_themes/sphinx_rtd_theme/search.html
+++ /dev/null
@@ -1,50 +0,0 @@
-{#
-    basic/search.html
-    ~~~~~~~~~~~~~~~~~
-
-    Template for the search page.
-
-    :copyright: Copyright 2007-2013 by the Sphinx team, see AUTHORS.
-    :license: BSD, see LICENSE for details.
-#}
-{%- extends "layout.html" %}
-{% set title = _('Search') %}
-{% set script_files = script_files + ['_static/searchtools.js'] %}
-{% block footer %}
-  <script type="text/javascript">
-    jQuery(function() { Search.loadIndex("{{ pathto('searchindex.js', 1) }}"); });
-  </script>
-  {# this is used when loading the search index using $.ajax fails,
-     such as on Chrome for documents on localhost #}
-  <script type="text/javascript" id="searchindexloader"></script>
-  {{ super() }}
-{% endblock %}
-{% block body %}
-  <noscript>
-  <div id="fallback" class="admonition warning">
-    <p class="last">
-      {% trans %}Please activate JavaScript to enable the search
-      functionality.{% endtrans %}
-    </p>
-  </div>
-  </noscript>
-
-  {% if search_performed %}
-    <h2>{{ _('Search Results') }}</h2>
-    {% if not search_results %}
-      <p>{{ _('Your search did not match any documents. Please make sure that all words are spelled correctly and that you\'ve selected enough categories.') }}</p>
-    {% endif %}
-  {% endif %}
-  <div id="search-results">
-  {% if search_results %}
-    <ul>
-    {% for href, caption, context in search_results %}
-      <li>
-        <a href="{{ pathto(item.href) }}">{{ caption }}</a>
-        <p class="context">{{ context|e }}</p>
-      </li>
-    {% endfor %}
-    </ul>
-  {% endif %}
-  </div>
-{% endblock %}
diff --git a/lib/spack/docs/_themes/sphinx_rtd_theme/searchbox.html b/lib/spack/docs/_themes/sphinx_rtd_theme/searchbox.html
deleted file mode 100644
index 35ad52c5f6..0000000000
--- a/lib/spack/docs/_themes/sphinx_rtd_theme/searchbox.html
+++ /dev/null
@@ -1,9 +0,0 @@
-{%- if builder != 'singlehtml' %}
-<div role="search">
-  <form id="rtd-search-form" class="wy-form" action="{{ pathto('search') }}" method="get">
-    <input type="text" name="q" placeholder="Search docs" />
-    <input type="hidden" name="check_keywords" value="yes" />
-    <input type="hidden" name="area" value="default" />
-  </form>
-</div>
-{%- endif %}
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deleted file mode 100644
index 7e17fb148c..0000000000
--- a/lib/spack/docs/_themes/sphinx_rtd_theme/static/css/badge_only.css
+++ /dev/null
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deleted file mode 100644
index b09cc628bf..0000000000
--- a/lib/spack/docs/_themes/sphinx_rtd_theme/static/css/badge_only.css.map
+++ /dev/null
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diff --git a/lib/spack/docs/_themes/sphinx_rtd_theme/static/css/theme.css b/lib/spack/docs/_themes/sphinx_rtd_theme/static/css/theme.css
deleted file mode 100644
index 57b98fe6af..0000000000
--- a/lib/spack/docs/_themes/sphinx_rtd_theme/static/css/theme.css
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deleted file mode 100644
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diff --git a/lib/spack/docs/_themes/sphinx_rtd_theme/static/js/theme.js b/lib/spack/docs/_themes/sphinx_rtd_theme/static/js/theme.js
deleted file mode 100644
index 749e58f400..0000000000
--- a/lib/spack/docs/_themes/sphinx_rtd_theme/static/js/theme.js
+++ /dev/null
@@ -1,113 +0,0 @@
-function toggleCurrent (elem) {
-    var parent_li = elem.closest('li');
-    parent_li.siblings('li.current').removeClass('current');
-    parent_li.siblings().find('li.current').removeClass('current');
-    parent_li.find('> ul li.current').removeClass('current');
-    parent_li.toggleClass('current');
-}
-
-$(document).ready(function() {
-    // Shift nav in mobile when clicking the menu.
-    $(document).on('click', "[data-toggle='wy-nav-top']", function() {
-        $("[data-toggle='wy-nav-shift']").toggleClass("shift");
-        $("[data-toggle='rst-versions']").toggleClass("shift");
-    });
-    // Nav menu link click operations
-    $(document).on('click', ".wy-menu-vertical .current ul li a", function() {
-        var target = $(this);
-        // Close menu when you click a link.
-        $("[data-toggle='wy-nav-shift']").removeClass("shift");
-        $("[data-toggle='rst-versions']").toggleClass("shift");
-        // Handle dynamic display of l3 and l4 nav lists
-        toggleCurrent(target);
-        if (typeof(window.SphinxRtdTheme) != 'undefined') {
-            window.SphinxRtdTheme.StickyNav.hashChange();
-        }
-    });
-    $(document).on('click', "[data-toggle='rst-current-version']", function() {
-        $("[data-toggle='rst-versions']").toggleClass("shift-up");
-    });
-    // Make tables responsive
-    $("table.docutils:not(.field-list)").wrap("<div class='wy-table-responsive'></div>");
-
-    // Add expand links to all parents of nested ul
-    $('.wy-menu-vertical ul').siblings('a').each(function () {
-        var link = $(this);
-            expand = $('<span class="toctree-expand"></span>');
-        expand.on('click', function (ev) {
-            toggleCurrent(link);
-            ev.stopPropagation();
-            return false;
-        });
-        link.prepend(expand);
-    });
-});
-
-// Sphinx theme state
-window.SphinxRtdTheme = (function (jquery) {
-    var stickyNav = (function () {
-        var navBar,
-            win,
-            winScroll = false,
-            linkScroll = false,
-            winPosition = 0,
-            enable = function () {
-                init();
-                reset();
-                win.on('hashchange', reset);
-
-                // Set scrolling
-                win.on('scroll', function () {
-                    if (!linkScroll) {
-                        winScroll = true;
-                    }
-                });
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-                            navPosition = navBar.scrollTop(),
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-                    }
-                    catch (err) {
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-            hashChange = function () {
-                linkScroll = true;
-                win.one('hashchange', function () {
-                    linkScroll = false;
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-        jquery(init);
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-            hashChange: hashChange
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-    return {
-        StickyNav: stickyNav
-    };
-}($));
diff --git a/lib/spack/docs/_themes/sphinx_rtd_theme/theme.conf b/lib/spack/docs/_themes/sphinx_rtd_theme/theme.conf
deleted file mode 100644
index b71548b2af..0000000000
--- a/lib/spack/docs/_themes/sphinx_rtd_theme/theme.conf
+++ /dev/null
@@ -1,9 +0,0 @@
-[theme]
-inherit = basic
-stylesheet = css/theme.css
-
-[options]
-typekit_id = hiw1hhg
-analytics_id = 
-sticky_navigation = False
-logo_only =
diff --git a/lib/spack/docs/_themes/sphinx_rtd_theme/versions.html b/lib/spack/docs/_themes/sphinx_rtd_theme/versions.html
deleted file mode 100644
index 8b3eb79d25..0000000000
--- a/lib/spack/docs/_themes/sphinx_rtd_theme/versions.html
+++ /dev/null
@@ -1,37 +0,0 @@
-{% if READTHEDOCS %}
-{# Add rst-badge after rst-versions for small badge style. #}
-  <div class="rst-versions" data-toggle="rst-versions" role="note" aria-label="versions">
-    <span class="rst-current-version" data-toggle="rst-current-version">
-      <span class="fa fa-book"> Read the Docs</span>
-      v: {{ current_version }}
-      <span class="fa fa-caret-down"></span>
-    </span>
-    <div class="rst-other-versions">
-      <dl>
-        <dt>Versions</dt>
-        {% for slug, url in versions %}
-          <dd><a href="{{ url }}">{{ slug }}</a></dd>
-        {% endfor %}
-      </dl>
-      <dl>
-        <dt>Downloads</dt>
-        {% for type, url in downloads %}
-          <dd><a href="{{ url }}">{{ type }}</a></dd>
-        {% endfor %}
-      </dl>
-      <dl>
-        <dt>On Read the Docs</dt>
-          <dd>
-            <a href="//{{ PRODUCTION_DOMAIN }}/projects/{{ slug }}/?fromdocs={{ slug }}">Project Home</a>
-          </dd>
-          <dd>
-            <a href="//{{ PRODUCTION_DOMAIN }}/builds/{{ slug }}/?fromdocs={{ slug }}">Builds</a>
-          </dd>
-      </dl>
-      <hr/>
-      Free document hosting provided by <a href="http://www.readthedocs.org">Read the Docs</a>.
-
-    </div>
-  </div>
-{% endif %}
-
diff --git a/lib/spack/docs/basic_usage.rst b/lib/spack/docs/basic_usage.rst
index bb426b4378..7eda320029 100644
--- a/lib/spack/docs/basic_usage.rst
+++ b/lib/spack/docs/basic_usage.rst
@@ -1,3 +1,8 @@
+.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 .. _basic-usage:
 
 ===========
@@ -596,6 +601,9 @@ name or compiler specifier to their left in the spec.
 If the compiler spec is omitted, Spack will choose a default compiler
 based on site policies.
 
+
+.. _basic-variants:
+
 ^^^^^^^^
 Variants
 ^^^^^^^^
@@ -681,11 +689,12 @@ Compiler environment variables and additional RPATHs
 
 In the exceptional case a compiler requires setting special environment
 variables, like an explicit library load path. These can bet set in an
-extra section in the compiler configuration.  The user can also specify
-additional ``RPATHs`` that the compiler will add to all executables
-generated by that compiler.  This is useful for forcing certain compilers
-to RPATH their own runtime libraries, so that executables will run
-without the need to set ``LD_LIBRARY_PATH``.
+extra section in the compiler configuration (the supported environment
+modification commands are: ``set``, ``unset``, ``append-path``, and
+``prepend-path``). The user can also specify additional ``RPATHs`` that the
+compiler will add to all executables generated by that compiler.  This is
+useful for forcing certain compilers to RPATH their own runtime libraries, so
+that executables will run without the need to set ``LD_LIBRARY_PATH``.
 
 .. code-block:: yaml
 
@@ -698,12 +707,29 @@ without the need to set ``LD_LIBRARY_PATH``.
           f77: /opt/gcc/bin/gfortran
           fc: /opt/gcc/bin/gfortran
         environment:
+          unset:
+            BAD_VARIABLE: # The colon is required but the value must be empty
           set:
-            LD_LIBRARY_PATH : /opt/gcc/lib
+            GOOD_VARIABLE_NUM: 1
+            GOOD_VARIABLE_STR: good
+          prepend-path:
+            PATH: /path/to/binutils
+          append-path:
+            LD_LIBRARY_PATH: /opt/gcc/lib
         extra_rpaths:
         - /path/to/some/compiler/runtime/directory
         - /path/to/some/other/compiler/runtime/directory
 
+
+.. note::
+
+   The section `environment` is interpreted as an ordered dictionary, which
+   means two things. First, environment modification are applied in the order
+   they are specified in the configuration file. Second, you cannot express
+   environment modifications that require mixing different commands, i.e. you
+   cannot `set` one variable, than `prepend-path` to another one, and than
+   again `set` a third one.
+
 ^^^^^^^^^^^^^^^^^^^^^^^
 Architecture specifiers
 ^^^^^^^^^^^^^^^^^^^^^^^
@@ -950,11 +976,11 @@ directly when you run ``python``:
    ImportError: No module named numpy
    >>>
 
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Extensions & Environment Modules
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+^^^^^^^^^^^^^^^^
+Using Extensions
+^^^^^^^^^^^^^^^^
 
-There are two ways to get ``numpy`` working in Python.  The first is
+There are three ways to get ``numpy`` working in Python.  The first is
 to use :ref:`shell-support`.  You can simply ``use`` or ``load`` the
 module for the extension, and it will be added to the ``PYTHONPATH``
 in your current shell.
@@ -976,15 +1002,26 @@ or, for dotkit:
 Now ``import numpy`` will succeed for as long as you keep your current
 session open.
 
-^^^^^^^^^^^^^^^^^^^^^
-Activating Extensions
-^^^^^^^^^^^^^^^^^^^^^
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Activating Extensions in a View
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The second way to use extensions is to create a view, which merges the
+python installation along with the extensions into a single prefix.
+See :ref:`filesystem-views` for a more in-depth description of views and
+:ref:`cmd-spack-view` for usage of the ``spack view`` command.
 
-It is often desirable to have certain packages *always* available as
-part of a Python installation.  Spack offers a more permanent solution
-for this case.  Instead of requiring users to load particular
-environment modules, you can *activate* the package within the Python
-installation:
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Activating Extensions Globally
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+As an alternative to creating a merged prefix with Python and its extensions,
+and prior to support for views, Spack has provided a means to install the
+extension into the Spack installation prefix for the extendee. This has
+typically been useful since extendable packages typically search their own
+installation path for addons by default.
+
+Global activations are performed with the ``spack activate`` command:
 
 .. _cmd-spack-activate:
 
@@ -1044,11 +1081,11 @@ the ``py-numpy`` into the prefix of the ``python`` package.  To the
 python interpreter, it looks like ``numpy`` is installed in the
 ``site-packages`` directory.
 
-The only limitation of activation is that you can only have a *single*
+The only limitation of global activation is that you can only have a *single*
 version of an extension activated at a time.  This is because multiple
 versions of the same extension would conflict if symbolically linked
 into the same prefix.  Users who want a different version of a package
-can still get it by using environment modules, but they will have to
+can still get it by using environment modules or views, but they will have to
 explicitly load their preferred version.
 
 ^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -1093,22 +1130,43 @@ several variants:
 Filesystem requirements
 -----------------------
 
-Spack currently needs to be run from a filesystem that supports
+By default, Spack needs to be run from a filesystem that supports
 ``flock`` locking semantics.  Nearly all local filesystems and recent
-versions of NFS support this, but parallel filesystems may be mounted
-without ``flock`` support enabled.  You can determine how your
-filesystems are mounted with ``mount -p``.  The output for a Lustre
+versions of NFS support this, but parallel filesystems or NFS volumes may
+be configured without ``flock`` support enabled.  You can determine how
+your filesystems are mounted with ``mount``.  The output for a Lustre
 filesystem might look like this:
 
 .. code-block:: console
 
-   $ mount -l | grep lscratch
-   pilsner-mds1-lnet0@o2ib100:/lsd on /p/lscratchd type lustre (rw,nosuid,noauto,_netdev,lazystatfs,flock)
-   porter-mds1-lnet0@o2ib100:/lse on /p/lscratche type lustre (rw,nosuid,noauto,_netdev,lazystatfs,flock)
+   $ mount | grep lscratch
+   mds1-lnet0@o2ib100:/lsd on /p/lscratchd type lustre (rw,nosuid,lazystatfs,flock)
+   mds2-lnet0@o2ib100:/lse on /p/lscratche type lustre (rw,nosuid,lazystatfs,flock)
+
+Note the ``flock`` option on both Lustre mounts.
+
+If you do not see this or a similar option for your filesystem, you have
+a few options. First, you can move your Spack installation to a
+filesystem that supports locking. Second, you could ask your system
+administrator to enable ``flock`` for your filesystem.
+
+If none of those work, you can disable locking in one of two ways:
+
+  1. Run Spack with the ``-L`` or ``--disable-locks`` option to disable
+     locks on a call-by-call basis.
+  2. Edit :ref:`config.yaml <config-yaml>` and set the ``locks`` option
+     to ``false`` to always disable locking.
+
+.. warning::
+
+   If you disable locking, concurrent instances of Spack will have no way
+   to avoid stepping on each other.  You must ensure that there is only
+   **one** instance of Spack running at a time.  Otherwise, Spack may end
+   up with a corrupted database file, or you may not be able to see all
+   installed packages in commands like ``spack find``.
 
-Note the ``flock`` option on both Lustre mounts.  If you do not see
-this or a similar option for your filesystem, you may need ot ask your
-system administrator to enable ``flock``.
+   If you are unfortunate enough to run into this situation, you may be
+   able to fix it by running ``spack reindex``.
 
 This issue typically manifests with the error below:
 
diff --git a/lib/spack/docs/binary_caches.rst b/lib/spack/docs/binary_caches.rst
index c7eed69a6e..1400b0c9f7 100644
--- a/lib/spack/docs/binary_caches.rst
+++ b/lib/spack/docs/binary_caches.rst
@@ -1,7 +1,12 @@
+.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 .. _binary_caches:
 
 ============
-Build caches
+Build Caches
 ============
 
 Some sites may encourage users to set up their own test environments
diff --git a/lib/spack/docs/build_settings.rst b/lib/spack/docs/build_settings.rst
index 0f935aa1ce..da2730baa1 100644
--- a/lib/spack/docs/build_settings.rst
+++ b/lib/spack/docs/build_settings.rst
@@ -1,14 +1,20 @@
+.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 .. _build-settings:
 
-======================================
-Build customization
-======================================
+===================
+Build Customization
+===================
 
 Spack allows you to customize how your software is built through the
 ``packages.yaml`` file.  Using it, you can make Spack prefer particular
-implementations of virtual dependencies (e.g., compilers, MPI, or BLAS),
+implementations of virtual dependencies (e.g., MPI or BLAS/LAPACK),
 or you can make it prefer to build with particular compilers.  You can
-also tell Spack to use *external* installations of certain software.
+also tell Spack to use *external* software installations already
+present on your system.
 
 At a high level, the ``packages.yaml`` file is structured like this:
 
@@ -23,14 +29,14 @@ At a high level, the ``packages.yaml`` file is structured like this:
      all:
        # settings that apply to all packages.
 
-So you can either set build preferences *specifically* for one package,
-or you can specify that certain settings should apply to all packages.
+So you can either set build preferences specifically for *one* package,
+or you can specify that certain settings should apply to *all* packages.
 The types of settings you can customize are described in detail below.
 
 Spack's build defaults are in the default
 ``etc/spack/defaults/packages.yaml`` file.  You can override them in
 ``~/.spack/packages.yaml`` or ``etc/spack/packages.yaml``. For more
-details on how this works, see :ref:`configuration-scopes`
+details on how this works, see :ref:`configuration-scopes`.
 
 .. _sec-external-packages:
 
@@ -56,11 +62,12 @@ directory. Here's an example of an external configuration:
          openmpi@1.4.3%gcc@4.4.7 arch=linux-x86_64-debian7+debug: /opt/openmpi-1.4.3-debug
          openmpi@1.6.5%intel@10.1 arch=linux-x86_64-debian7: /opt/openmpi-1.6.5-intel
 
-This example lists three installations of OpenMPI, one built with gcc,
-one built with gcc and debug information, and another built with Intel.
+This example lists three installations of OpenMPI, one built with GCC,
+one built with GCC and debug information, and another built with Intel.
 If Spack is asked to build a package that uses one of these MPIs as a
-dependency, it will use the the pre-installed OpenMPI in
-the given directory. Packages.yaml can also be used to specify modules
+dependency, it will use the pre-installed OpenMPI in
+the given directory. ``packages.yaml`` can also be used to specify modules
+to load instead of the installation prefixes.
 
 Each ``packages.yaml`` begins with a ``packages:`` token, followed
 by a list of package names.  To specify externals, add a ``paths`` or ``modules``
@@ -77,9 +84,9 @@ though the package and compiler may not ever be built.
 
 The packages configuration can tell Spack to use an external location
 for certain package versions, but it does not restrict Spack to using
-external packages.  In the above example, if an OpenMPI 1.8.4 became
-available Spack may choose to start building and linking with that version
-rather than continue using the pre-installed OpenMPI versions.
+external packages.  In the above example, since newer versions of OpenMPI
+are available, Spack will choose to start building and linking with the
+latest version rather than continue using the pre-installed OpenMPI versions.
 
 To prevent this, the ``packages.yaml`` configuration also allows packages
 to be flagged as non-buildable.  The previous example could be modified to
@@ -115,12 +122,12 @@ Concretization Preferences
 --------------------------
 
 Spack can be configured to prefer certain compilers, package
-versions, depends_on, and variants during concretization.
+versions, dependencies, and variants during concretization.
 The preferred configuration can be controlled via the
-``~/.spack/packages.yaml`` file for user configuations, or the
+``~/.spack/packages.yaml`` file for user configurations, or the
 ``etc/spack/packages.yaml`` site configuration.
 
-Here's an example packages.yaml file that sets preferred packages:
+Here's an example ``packages.yaml`` file that sets preferred packages:
 
 .. code-block:: yaml
 
@@ -133,17 +140,17 @@ Here's an example packages.yaml file that sets preferred packages:
      all:
        compiler: [gcc@4.4.7, gcc@4.6:, intel, clang, pgi]
        providers:
-         mpi: [mvapich, mpich, openmpi]
+         mpi: [mvapich2, mpich, openmpi]
 
 At a high level, this example is specifying how packages should be
-concretized.  The opencv package should prefer using gcc 4.9 and
+concretized.  The opencv package should prefer using GCC 4.9 and
 be built with debug options.  The gperftools package should prefer version
-2.2 over 2.4.  Every package on the system should prefer mvapich for
-its MPI and gcc 4.4.7 (except for opencv, which overrides this by preferring gcc 4.9).
+2.2 over 2.4.  Every package on the system should prefer mvapich2 for
+its MPI and GCC 4.4.7 (except for opencv, which overrides this by preferring GCC 4.9).
 These options are used to fill in implicit defaults.  Any of them can be overwritten
 on the command line if explicitly requested.
 
-Each packages.yaml file begins with the string ``packages:`` and
+Each ``packages.yaml`` file begins with the string ``packages:`` and
 package names are specified on the next level. The special string ``all``
 applies settings to each package. Underneath each package name is
 one or more components: ``compiler``, ``variants``, ``version``,
@@ -164,5 +171,54 @@ gcc to pgi will thus be preferred over the xlc compiler.
 
 The syntax for the ``provider`` section differs slightly from other
 concretization rules.  A provider lists a value that packages may
-``depend_on`` (e.g, mpi) and a list of rules for fulfilling that
+``depend_on`` (e.g, MPI) and a list of rules for fulfilling that
 dependency.
+
+.. _package_permissions:
+
+-------------------
+Package Permissions
+-------------------
+
+Spack can be configured to assign permissions to the files installed
+by a package.
+
+In the ``packages.yaml`` file under ``permissions``, the attributes
+``read``, ``write``, and ``group`` control the package
+permissions. These attributes can be set per-package, or for all
+packages under ``all``. If permissions are set under ``all`` and for a
+specific package, the package-specific settings take precedence.
+
+The ``read`` and ``write`` attributes take one of ``user``, ``group``,
+and ``world``.
+
+.. code-block:: yaml
+
+  packages:
+    all:
+      permissions:
+        write: group
+        group: spack
+    my_app:
+      permissions:
+        read: group
+        group: my_team
+
+The permissions settings describe the broadest level of access to
+installations of the specified packages. The execute permissions of
+the file are set to the same level as read permissions for those files
+that are executable. The default setting for ``read`` is ``world``,
+and for ``write`` is ``user``. In the example above, installations of
+``my_app`` will be installed with user and group permissions but no
+world permissions, and owned by the group ``my_team``. All other
+packages will be installed with user and group write privileges, and
+world read privileges. Those packages will be owned by the group
+``spack``.
+
+The ``group`` attribute assigns a Unix-style group to a package. All
+files installed by the package will be owned by the assigned group,
+and the sticky group bit will be set on the install prefix and all
+directories inside the install prefix. This will ensure that even
+manually placed files within the install prefix are owned by the
+assigned group. If no group is assigned, Spack will allow the OS
+default behavior to go as expected.
diff --git a/lib/spack/docs/build_systems.rst b/lib/spack/docs/build_systems.rst
new file mode 100644
index 0000000000..eb8d3f6ab2
--- /dev/null
+++ b/lib/spack/docs/build_systems.rst
@@ -0,0 +1,89 @@
+.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+.. _build-systems:
+
+=============
+Build Systems
+=============
+
+Spack defines a number of classes which understand how to use common
+`build systems  <https://en.wikipedia.org/wiki/List_of_build_automation_software>`_
+(Makefiles, CMake, etc.). Spack package definitions can inherit these
+classes in order to streamline their builds.
+
+This guide provides information specific to each particular build system.
+It assumes that you've read the :ref:`packaging-guide` and expands
+on these ideas for each distinct build system that Spack supports:
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Make-based
+
+   build_systems/makefilepackage
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Make-incompatible
+
+   build_systems/sconspackage
+   build_systems/wafpackage
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Build-script generation
+
+   build_systems/autotoolspackage
+   build_systems/cmakepackage
+   build_systems/mesonpackage
+   build_systems/qmakepackage
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Language-specific
+
+   build_systems/octavepackage
+   build_systems/perlpackage
+   build_systems/pythonpackage
+   build_systems/rpackage
+   build_systems/rubypackage
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Other
+
+   build_systems/cudapackage
+   build_systems/intelpackage
+   build_systems/custompackage
+
+For reference, the :py:mod:`Build System API docs <spack.build_systems>`
+provide a list of build systems and methods/attributes that can be
+overridden. If you are curious about the implementation of a particular
+build system, you can view the source code by running:
+
+.. code-block:: console
+
+   $ spack edit --build-system autotools
+
+
+This will open up the ``AutotoolsPackage`` definition in your favorite
+editor. In addition, if you are working with a less common build system
+like QMake, SCons, or Waf, it may be useful to see examples of other
+packages. You can quickly find examples by running:
+
+.. code-block:: console
+
+   $ cd var/spack/repos/builtin/packages
+   $ grep -l QMakePackage */package.py
+
+
+You can then view these packages with ``spack edit``.
+
+This guide is intended to supplement the
+:py:mod:`Build System API docs <spack.build_systems>` with examples of
+how to override commonly used methods. It also provides rules of thumb
+and suggestions for package developers who are unfamiliar with a
+particular build system.
diff --git a/lib/spack/docs/build_systems/Autoconf-automake-process.svg b/lib/spack/docs/build_systems/Autoconf-automake-process.svg
new file mode 100644
index 0000000000..13eb36a80e
--- /dev/null
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+    <path
+       style="fill:none;stroke:#000000;stroke-width:2"
+       inkscape:connector-curvature="0"
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+       style="font-size:14px;text-anchor:middle;font-family:Liberation Sans"
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diff --git a/lib/spack/docs/build_systems/autotoolspackage.rst b/lib/spack/docs/build_systems/autotoolspackage.rst
new file mode 100644
index 0000000000..ce22fd832b
--- /dev/null
+++ b/lib/spack/docs/build_systems/autotoolspackage.rst
@@ -0,0 +1,305 @@
+.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+.. _autotoolspackage:
+
+----------------
+AutotoolsPackage
+----------------
+
+Autotools is a GNU build system that provides a build-script generator.
+By running the platform-independent ``./configure`` script that comes
+with the package, you can generate a platform-dependent Makefile.
+
+^^^^^^
+Phases
+^^^^^^
+
+The ``AutotoolsPackage`` base class comes with the following phases:
+
+#. ``autoreconf`` - generate the configure script
+#. ``configure`` - generate the Makefiles
+#. ``build`` - build the package
+#. ``install`` - install the package
+
+Most of the time, the ``autoreconf`` phase will do nothing, but if the
+package is missing a ``configure`` script, ``autoreconf`` will generate
+one for you.
+
+The other phases run:
+
+.. code-block:: console
+
+   $ ./configure --prefix=/path/to/installation/prefix
+   $ make
+   $ make check  # optional
+   $ make install
+   $ make installcheck  # optional
+
+
+Of course, you may need to add a few arguments to the ``./configure``
+line.
+
+^^^^^^^^^^^^^^^
+Important files
+^^^^^^^^^^^^^^^
+
+The most important file for an Autotools-based package is the ``configure``
+script. This script is automatically generated by Autotools and generates
+the appropriate Makefile when run.
+
+.. warning::
+
+   Watch out for fake Autotools packages!
+
+   Autotools is a very popular build system, and many people are used to the
+   classic steps to install a package:
+
+   .. code-block:: console
+
+      $ ./configure
+      $ make
+      $ make install
+
+
+   For this reason, some developers will write their own ``configure``
+   scripts that have nothing to do with Autotools. These packages may
+   not accept the same flags as other Autotools packages, so it is
+   better to use the ``Package`` base class and create a
+   :ref:`custom build system <custompackage>`. You can tell if a package
+   uses Autotools by running ``./configure --help`` and comparing the output
+   to other known Autotools packages. You should also look for files like:
+
+   * ``configure.ac``
+   * ``configure.in``
+   * ``Makefile.am``
+
+   Packages that don't use Autotools aren't likely to have these files.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^
+Build system dependencies
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Whether or not your package requires Autotools to install depends on
+how the source code is distributed. Most of the time, when developers
+distribute tarballs, they will already contain the ``configure`` script
+necessary for installation. If this is the case, your package does not
+require any Autotools dependencies.
+
+However, a basic rule of version control systems is to never commit
+code that can be generated. The source code repository itself likely
+does not have a ``configure`` script. Developers typically write
+(or auto-generate) a ``configure.ac`` script that contains configuration
+preferences and a ``Makefile.am`` script that contains build instructions.
+Then, ``autoconf`` is used to convert ``configure.ac`` into ``configure``,
+while ``automake`` is used to convert ``Makefile.am`` into ``Makefile.in``.
+``Makefile.in`` is used by ``configure`` to generate a platform-dependent
+``Makefile`` for you. The following diagram provides a high-level overview
+of the process:
+
+.. figure:: Autoconf-automake-process.*
+   :target: https://commons.wikimedia.org/w/index.php?curid=15581407
+
+   `GNU autoconf and automake process for generating makefiles <https://commons.wikimedia.org/wiki/File:Autoconf-automake-process.svg>`_
+   by `Jdthood` under `CC BY-SA 3.0 <https://creativecommons.org/licenses/by-sa/3.0/deed.en>`_
+
+If a ``configure`` script is not present in your tarball, you will
+need to generate one yourself. Luckily, Spack already has an ``autoreconf``
+phase to do most of the work for you. By default, the ``autoreconf``
+phase runs:
+
+.. code-block:: console
+
+   $ libtoolize
+   $ aclocal
+   $ autoreconf --install --verbose --force
+
+All you need to do is add a few Autotools dependencies to the package.
+Most stable releases will come with a ``configure`` script, but if you
+check out a commit from the ``develop`` branch, you would want to add:
+
+.. code-block:: python
+
+   depends_on('autoconf', type='build', when='@develop')
+   depends_on('automake', type='build', when='@develop')
+   depends_on('libtool',  type='build', when='@develop')
+   depends_on('m4',       type='build', when='@develop')
+
+In some cases, developers might need to distribute a patch that modifies
+one of the files used to generate ``configure`` or ``Makefile.in``.
+In this case, these scripts will need to be regenerated. It is
+preferable to regenerate these manually using the patch, and then
+create a new patch that directly modifies ``configure``. That way,
+Spack can use the secondary patch and additional build system
+dependencies aren't necessary.
+
+""""""""""""""""
+force_autoreconf
+""""""""""""""""
+
+If for whatever reason you really want to add the original patch
+and tell Spack to regenerate ``configure``, you can do so using the
+following setting:
+
+.. code-block:: python
+
+   force_autoreconf = True
+
+This line tells Spack to wipe away the existing ``configure`` script
+and generate a new one. If you only need to do this for a single
+version, this can be done like so:
+
+.. code-block:: python
+
+   @property
+   def force_autoreconf(self):
+       return self.version == Version('1.2.3'):
+
+^^^^^^^^^^^^^^^^^^^^^^^
+Finding configure flags
+^^^^^^^^^^^^^^^^^^^^^^^
+
+Once you have a ``configure`` script present, the next step is to
+determine what option flags are available. These flags can be found
+by running:
+
+.. code-block:: console
+
+   $ ./configure --help
+
+``configure`` will display a list of valid flags separated into
+some or all of the following sections:
+
+* Configuration
+* Installation directories
+* Fine tuning of the installation directories
+* Program names
+* X features
+* System types
+* **Optional Features**
+* **Optional Packages**
+* **Some influential environment variables**
+
+For the most part, you can ignore all but the last 3 sections.
+The "Optional Features" sections lists flags that enable/disable
+features you may be interested in. The "Optional Packages" section
+often lists dependencies and the flags needed to locate them. The
+"environment variables" section lists environment variables that the
+build system uses to pass flags to the compiler and linker.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+Addings flags to configure
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+For most of the flags you encounter, you will want a variant to
+optionally enable/disable them. You can then optionally pass these
+flags to the ``configure`` call by overriding the ``configure_args``
+function like so:
+
+.. code-block:: python
+
+   def configure_args(self):
+       args = []
+
+       if '+mpi' in self.spec:
+           args.append('--enable-mpi')
+       else:
+           args.append('--disable-mpi')
+
+       return args
+
+Note that we are explicitly disabling MPI support if it is not
+requested. This is important, as many Autotools packages will enable
+options by default if the dependencies are found, and disable them
+otherwise. We want Spack installations to be as deterministic as possible.
+If two users install a package with the same variants, the goal is that
+both installations work the same way. See `here <https://www.linux.com/news/best-practices-autotools>`__
+and `here <https://wiki.gentoo.org/wiki/Project:Quality_Assurance/Automagic_dependencies>`__
+for a rationale as to why these so-called "automagic" dependencies
+are a problem.
+
+By default, Autotools installs packages to ``/usr``. We don't want this,
+so Spack automatically adds ``--prefix=/path/to/installation/prefix``
+to your list of ``configure_args``. You don't need to add this yourself.
+
+^^^^^^^^^^^^^^^^
+Helper functions
+^^^^^^^^^^^^^^^^
+
+You may have noticed that most of the Autotools flags are of the form
+``--enable-foo``, ``--disable-bar``, ``--with-baz=<prefix>``, or
+``--without-baz``. Since these flags are so common, Spack provides a
+couple of helper functions to make your life easier.
+
+TODO: document ``with_or_without`` and ``enable_or_disable``.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Configure script in a sub-directory
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Occasionally, developers will hide their source code and ``configure``
+script in a subdirectory like ``src``. If this happens, Spack won't
+be able to automatically detect the build system properly when running
+``spack create``. You will have to manually change the package base
+class and tell Spack where the ``configure`` script resides. You can
+do this like so:
+
+.. code-block:: python
+
+   configure_directory = 'src'
+
+^^^^^^^^^^^^^^^^^^^^^^
+Building out of source
+^^^^^^^^^^^^^^^^^^^^^^
+
+Some packages like ``gcc`` recommend building their software in a
+different directory than the source code to prevent build pollution.
+This can be done using the ``build_directory`` variable:
+
+.. code-block:: python
+
+   build_directory = 'spack-build'
+
+By default, Spack will build the package in the same directory that
+contains the ``configure`` script
+
+^^^^^^^^^^^^^^^^^^^^^^^^^
+Build and install targets
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+For most Autotools packages, the usual:
+
+.. code-block:: console
+
+   $ configure
+   $ make
+   $ make install
+
+is sufficient to install the package. However, if you need to run
+make with any other targets, for example, to build an optional
+library or build the documentation, you can add these like so:
+
+.. code-block:: python
+
+   build_targets = ['all', 'docs']
+   install_targets = ['install', 'docs']
+
+^^^^^^^
+Testing
+^^^^^^^
+
+Autotools-based packages typically provide unit testing via the
+``check`` and ``installcheck`` targets. If you build your software
+with ``spack install --test=root``, Spack will check for the presence
+of a ``check`` or ``test`` target in the Makefile and run
+``make check`` for you. After installation, it will check for an
+``installcheck`` target and run ``make installcheck`` if it finds one.
+
+^^^^^^^^^^^^^^^^^^^^^^
+External documentation
+^^^^^^^^^^^^^^^^^^^^^^
+
+For more information on the Autotools build system, see:
+https://www.gnu.org/software/automake/manual/html_node/Autotools-Introduction.html
diff --git a/lib/spack/docs/build_systems/cmakepackage.rst b/lib/spack/docs/build_systems/cmakepackage.rst
new file mode 100644
index 0000000000..b627ddb84b
--- /dev/null
+++ b/lib/spack/docs/build_systems/cmakepackage.rst
@@ -0,0 +1,279 @@
+.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+.. _cmakepackage:
+
+------------
+CMakePackage
+------------
+
+Like Autotools, CMake is a widely-used build-script generator. Designed
+by Kitware, CMake is the most popular build system for new C, C++, and
+Fortran projects, and many older projects are switching to it as well.
+
+Unlike Autotools, CMake can generate build scripts for builders other
+than Make: Ninja, Visual Studio, etc. It is therefore cross-platform,
+whereas Autotools is Unix-only.
+
+^^^^^^
+Phases
+^^^^^^
+
+The ``CMakePackage`` base class comes with the following phases:
+
+#. ``cmake`` - generate the Makefile
+#. ``build`` - build the package
+#. ``install`` - install the package
+
+By default, these phases run:
+
+.. code-block:: console
+
+   $ mkdir spack-build
+   $ cd spack-build
+   $ cmake .. -DCMAKE_INSTALL_PREFIX=/path/to/installation/prefix
+   $ make
+   $ make test  # optional
+   $ make install
+
+
+A few more flags are passed to ``cmake`` by default, including flags
+for setting the build type and flags for locating dependencies. Of
+course, you may need to add a few arguments yourself.
+
+^^^^^^^^^^^^^^^
+Important files
+^^^^^^^^^^^^^^^
+
+A CMake-based package can be identified by the presence of a
+``CMakeLists.txt`` file. This file defines the build flags that can be
+passed to the cmake invocation, as well as linking instructions. If
+you are familiar with CMake, it can prove very useful for determining
+dependencies and dependency version requirements.
+
+One thing to look for is the ``cmake_minimum_required`` function:
+
+.. code-block:: cmake
+
+   cmake_minimum_required(VERSION 2.8.12)
+
+
+This means that CMake 2.8.12 is the earliest release that will work.
+You should specify this in a ``depends_on`` statement.
+
+CMake-based packages may also contain ``CMakeLists.txt`` in subdirectories.
+This modularization helps to manage complex builds in a hierarchical
+fashion. Sometimes these nested ``CMakeLists.txt`` require additional
+dependencies not mentioned in the top-level file.
+
+There's also usually a ``cmake`` or ``CMake`` directory containing
+additional macros, find scripts, etc. These may prove useful in
+determining dependency version requirements.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^
+Build system dependencies
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Every package that uses the CMake build system requires a ``cmake``
+dependency. Since this is always the case, the ``CMakePackage`` base
+class already contains:
+
+.. code-block:: python
+
+   depends_on('cmake', type='build')
+
+
+If you need to specify a particular version requirement, you can
+override this in your package:
+
+.. code-block:: python
+
+   depends_on('cmake@2.8.12:', type='build')
+
+
+^^^^^^^^^^^^^^^^^^^
+Finding cmake flags
+^^^^^^^^^^^^^^^^^^^
+
+To get a list of valid flags that can be passed to ``cmake``, run the
+following command in the directory that contains ``CMakeLists.txt``:
+
+.. code-block:: console
+
+   $ cmake . -LAH
+
+
+CMake will start by checking for compilers and dependencies. Eventually
+it will begin to list build options. You'll notice that most of the
+build options at the top are prefixed with ``CMAKE_``. You can safely
+ignore most of these options as Spack already sets them for you. This
+includes flags needed to locate dependencies, RPATH libraries, set the
+installation directory, and set the build type.
+
+The rest of the flags are the ones you should consider adding to your
+package. They often include flags to enable/disable support for certain
+features and locate specific dependencies. One thing you'll notice that
+makes CMake different from Autotools is that CMake has an understanding
+of build flag hierarchy. That is, certain flags will not display unless
+their parent flag has been selected. For example, flags to specify the
+``lib`` and ``include`` directories for a package might not appear
+unless CMake found the dependency it was looking for. You may need to
+manually specify certain flags to explore the full depth of supported
+build flags, or check the ``CMakeLists.txt`` yourself.
+
+^^^^^^^^^^^^^^^^^^^^^
+Adding flags to cmake
+^^^^^^^^^^^^^^^^^^^^^
+
+To add additional flags to the ``cmake`` call, simply override the
+``cmake_args`` function:
+
+.. code-block:: python
+
+   def cmake_args(self):
+       args = []
+
+       if '+hdf5' in self.spec:
+           args.append('-DDETECT_HDF5=ON')
+       else:
+           args.append('-DDETECT_HDF5=OFF')
+
+       return args
+
+
+^^^^^^^^^^
+Generators
+^^^^^^^^^^
+
+CMake and Autotools are build-script generation tools; they "generate"
+the Makefiles that are used to build a software package. CMake actually
+supports multiple generators, not just Makefiles. Another common
+generator is Ninja. To switch to the Ninja generator, simply add:
+
+.. code-block:: python
+
+   generator = 'Ninja'
+
+
+``CMakePackage`` defaults to "Unix Makefiles". If you switch to the
+Ninja generator, make sure to add:
+
+.. code-block:: python
+
+   depends_on('ninja', type='build')
+
+to the package as well. Aside from that, you shouldn't need to do
+anything else. Spack will automatically detect that you are using
+Ninja and run:
+
+.. code-block:: console
+
+   $ cmake .. -G Ninja
+   $ ninja
+   $ ninja install
+
+Spack currently only supports "Unix Makefiles" and "Ninja" as valid
+generators, but it should be simple to add support for alternative
+generators. For more information on CMake generators, see:
+https://cmake.org/cmake/help/latest/manual/cmake-generators.7.html
+
+^^^^^^^^^^^^^^^^
+CMAKE_BUILD_TYPE
+^^^^^^^^^^^^^^^^
+
+Every CMake-based package accepts a ``-DCMAKE_BUILD_TYPE`` flag to
+dictate which level of optimization to use. In order to ensure
+uniformity across packages, the ``CMakePackage`` base class adds
+a variant to control this:
+
+.. code-block:: python
+
+   variant('build_type', default='RelWithDebInfo',
+           description='CMake build type',
+           values=('Debug', 'Release', 'RelWithDebInfo', 'MinSizeRel'))
+
+However, not every CMake package accepts all four of these options.
+Grep the ``CMakeLists.txt`` file to see if the default values are
+missing or replaced. For example, the
+`dealii <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/dealii/package.py>`_
+package overrides the default variant with:
+
+.. code-block:: python
+
+   variant('build_type', default='DebugRelease',
+           description='The build type to build',
+           values=('Debug', 'Release', 'DebugRelease'))
+
+For more information on ``CMAKE_BUILD_TYPE``, see:
+https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+CMakeLists.txt in a sub-directory
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Occasionally, developers will hide their source code and ``CMakeLists.txt``
+in a subdirectory like ``src``. If this happens, Spack won't
+be able to automatically detect the build system properly when running
+``spack create``. You will have to manually change the package base
+class and tell Spack where ``CMakeLists.txt`` resides. You can do this
+like so:
+
+.. code-block:: python
+
+   root_cmakelists_dir = 'src'
+
+
+Note that this path is relative to the root of the extracted tarball,
+not to the ``build_directory``. It defaults to the current directory.
+
+^^^^^^^^^^^^^^^^^^^^^^
+Building out of source
+^^^^^^^^^^^^^^^^^^^^^^
+
+By default, Spack builds every ``CMakePackage`` in a ``spack-build``
+sub-directory. If, for whatever reason, you would like to build in a
+different sub-directory, simply override ``build_directory`` like so:
+
+.. code-block:: python
+
+   build_directory = 'my-build'
+
+^^^^^^^^^^^^^^^^^^^^^^^^^
+Build and install targets
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+For most CMake packages, the usual:
+
+.. code-block:: console
+
+   $ cmake
+   $ make
+   $ make install
+
+is sufficient to install the package. However, if you need to run
+make with any other targets, for example, to build an optional
+library or build the documentation, you can add these like so:
+
+.. code-block:: python
+
+   build_targets = ['all', 'docs']
+   install_targets = ['install', 'docs']
+
+^^^^^^^
+Testing
+^^^^^^^
+
+CMake-based packages typically provide unit testing via the
+``test`` target. If you build your software with ``--test=root``,
+Spack will check for the presence of a ``test`` target in the
+Makefile and run ``make test`` for you. If you want to run a
+different test instead, simply override the ``check`` method.
+
+^^^^^^^^^^^^^^^^^^^^^^
+External documentation
+^^^^^^^^^^^^^^^^^^^^^^
+
+For more information on the CMake build system, see:
+https://cmake.org/cmake/help/latest/
diff --git a/lib/spack/docs/build_systems/cudapackage.rst b/lib/spack/docs/build_systems/cudapackage.rst
new file mode 100644
index 0000000000..1eed57e669
--- /dev/null
+++ b/lib/spack/docs/build_systems/cudapackage.rst
@@ -0,0 +1,43 @@
+.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+.. _cudapackage:
+
+-----------
+CudaPackage
+-----------
+
+Different from other packages, ``CudaPackage`` does not represent a build
+system. Instead its goal is to simplify and unify usage of ``CUDA`` in other
+packages.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Provided variants and dependencies
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+``CudaPackage`` provides ``cuda`` variant (default to ``off``) to enable/disable
+``CUDA``, and ``cuda_arch`` variant to optionally specify the architecture.
+It also declares dependencies on the ``CUDA`` package ``depends_on('cuda@...')``
+based on the architecture as well as specifies conflicts for certain compiler versions.
+
+^^^^^
+Usage
+^^^^^
+
+In order to use it, just add another base class to your package, for example:
+
+.. code-block:: python
+
+    class MyPackage(CMakePackage, CudaPackage):
+        ...
+        def cmake_args(self):
+            spec = self.spec
+            if '+cuda' in spec:
+                options.append('-DWITH_CUDA=ON')
+                cuda_arch = spec.variants['cuda_arch'].value
+                if cuda_arch is not None:
+                    options.append('-DCUDA_FLAGS=-arch=sm_{0}'.format(cuda_arch[0]))
+            else:
+                options.append('-DWITH_CUDA=OFF')
diff --git a/lib/spack/docs/build_systems/custompackage.rst b/lib/spack/docs/build_systems/custompackage.rst
new file mode 100644
index 0000000000..d02c9c1a0a
--- /dev/null
+++ b/lib/spack/docs/build_systems/custompackage.rst
@@ -0,0 +1,209 @@
+.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+.. _custompackage:
+
+--------------------
+Custom Build Systems
+--------------------
+
+While the build systems listed above should meet your needs for the
+vast majority of packages, some packages provide custom build scripts.
+This guide is intended for the following use cases:
+
+* Packaging software with its own custom build system
+* Adding support for new build systems
+
+If you want to add support for a new build system, a good place to
+start is to look at the definitions of other build systems. This guide
+focuses mostly on how Spack's build systems work.
+
+In this guide, we will be using the
+`perl <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/perl/package.py>`_ and
+`cmake <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/cmake/package.py>`_
+packages as examples. ``perl``'s build system is a hand-written
+``Configure`` shell script, while ``cmake`` bootstraps itself during
+installation. Both of these packages require custom build systems.
+
+^^^^^^^^^^
+Base class
+^^^^^^^^^^
+
+If your package does not belong to any of the aforementioned build
+systems that Spack already supports, you should inherit from the
+``Package`` base class. ``Package`` is a simple base class with a
+single phase: ``install``. If your package is simple, you may be able
+to simply write an ``install`` method that gets the job done. However,
+if your package is more complex and installation involves multiple
+steps, you should add separate phases as mentioned in the next section.
+
+If you are creating a new build system base class, you should inherit
+from ``PackageBase``. This is the superclass for all build systems in
+Spack.
+
+^^^^^^
+Phases
+^^^^^^
+
+The most important concept in Spack's build system support is the idea
+of phases. Each build system defines a set of phases that are necessary
+to install the package. They usually follow some sort of "configure",
+"build", "install" guideline, but any of those phases may be missing
+or combined with another phase.
+
+If you look at the ``perl`` package, you'll see:
+
+.. code-block:: python
+
+   phases = ['configure', 'build', 'install']
+
+Similarly, ``cmake`` defines:
+
+.. code-block:: python
+
+   phases = ['bootstrap', 'build', 'install']
+
+If we look at the ``cmake`` example, this tells Spack's ``PackageBase``
+class to run the ``bootstrap``, ``build``, and ``install`` functions
+in that order. It is now up to you to define these methods.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Phase and phase_args functions
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+If we look at ``perl``, we see that it defines a ``configure`` method:
+
+.. code-block:: python
+
+   def configure(self, spec, prefix):
+       configure = Executable('./Configure')
+       configure(*self.configure_args())
+
+There is also a corresponding ``configure_args`` function that handles
+all of the arguments to pass to ``Configure``, just like in
+``AutotoolsPackage``. Comparatively, the ``build`` and ``install``
+phases are pretty simple:
+
+.. code-block:: python
+
+   def build(self, spec, prefix):
+       make()
+
+   def install(self, spec, prefix):
+       make('install')
+
+The ``cmake`` package looks very similar, but with a ``bootstrap``
+function instead of ``configure``:
+
+.. code-block:: python
+
+   def bootstrap(self, spec, prefix):
+       bootstrap = Executable('./bootstrap')
+       bootstrap(*self.bootstrap_args())
+
+   def build(self, spec, prefix):
+       make()
+
+   def install(self, spec, prefix):
+       make('install')
+
+Again, there is a ``boostrap_args`` function that determines the
+correct bootstrap flags to use.
+
+^^^^^^^^^^^^^^^^^^^^
+run_before/run_after
+^^^^^^^^^^^^^^^^^^^^
+
+Occasionally, you may want to run extra steps either before or after
+a given phase. This applies not just to custom build systems, but to
+existing build systems as well. You may need to patch a file that is
+generated by configure, or install extra files in addition to what
+``make install`` copies to the installation prefix. This is where
+``@run_before`` and ``@run_after`` come in.
+
+These Python decorators allow you to write functions that are called
+before or after a particular phase. For example, in ``perl``, we see:
+
+.. code-block:: python
+
+   @run_after('install')
+   def install_cpanm(self):
+       spec = self.spec
+
+       if '+cpanm' in spec:
+           with working_dir(join_path('cpanm', 'cpanm')):
+               perl = spec['perl'].command
+               perl('Makefile.PL')
+               make()
+               make('install')
+
+This extra step automatically installs ``cpanm`` in addition to the
+base Perl installation.
+
+^^^^^^^^^^^^^^^^^^^^^
+on_package_attributes
+^^^^^^^^^^^^^^^^^^^^^
+
+The ``run_before``/``run_after`` logic discussed above becomes
+particularly powerful when combined with the ``@on_package_attributes``
+decorator. This decorator allows you to conditionally run certain
+functions depending on the attributes of that package. The most
+common example is conditional testing. Many unit tests are prone to
+failure, even when there is nothing wrong with the installation.
+Unfortunately, non-portable unit tests and tests that are
+"supposed to fail" are more common than we would like. Instead of
+always running unit tests on installation, Spack lets users
+conditionally run tests with the ``--test=root`` flag.
+
+If we wanted to define a function that would conditionally run
+if and only if this flag is set, we would use the following line:
+
+.. code-block:: python
+
+   @on_package_attributes(run_tests=True)
+
+^^^^^^^
+Testing
+^^^^^^^
+
+Let's put everything together and add unit tests to our package.
+In the ``perl`` package, we can see:
+
+.. code-block:: python
+
+   @run_after('build')
+   @on_package_attributes(run_tests=True)
+   def test(self):
+       make('test')
+
+As you can guess, this runs ``make test`` *after* building the package,
+if and only if testing is requested. Again, this is not specific to
+custom build systems, it can be added to existing build systems as well.
+
+Ideally, every package in Spack will have some sort of test to ensure
+that it was built correctly. It is up to the package authors to make
+sure this happens. If you are adding a package for some software and
+the developers list commands to test the installation, please add these
+tests to your ``package.py``.
+
+.. warning::
+
+   The order of decorators matters. The following ordering:
+
+   .. code-block:: python
+
+      @run_after('install')
+      @on_package_attributes(run_tests=True)
+
+   works as expected. However, if you reverse the ordering:
+
+   .. code-block:: python
+
+      @on_package_attributes(run_tests=True)
+      @run_after('install')
+
+   the tests will always be run regardless of whether or not
+   ``--test=root`` is requested. See https://github.com/spack/spack/issues/3833
+   for more information
diff --git a/lib/spack/docs/build_systems/intelpackage.rst b/lib/spack/docs/build_systems/intelpackage.rst
new file mode 100644
index 0000000000..6a1be0519b
--- /dev/null
+++ b/lib/spack/docs/build_systems/intelpackage.rst
@@ -0,0 +1,1060 @@
+.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+.. _intelpackage:
+
+------------
+IntelPackage
+------------
+
+.. contents::
+
+^^^^^^^^^^^^^^^^^^^^^^^^
+Intel packages in Spack
+^^^^^^^^^^^^^^^^^^^^^^^^
+
+Spack can install and use several software development products offered by Intel.
+Some of these are available under no-cost terms, others require a paid license.
+All share the same basic steps for configuration, installation, and, where
+applicable, license management. The Spack Python class ``IntelPackage`` implements
+these steps.
+
+Spack interacts with Intel tools in several routes, like it does for any
+other package:
+
+.. _`route 1`:
+
+1. Accept system-provided tools after you declare them to Spack as *external packages*.
+
+.. _`route 2`:
+
+2. Install the products for you as *internal packages* in Spack.
+
+.. _`route 3`:
+
+3. *Use* the packages, regardless of installation route, to install what we'll
+   call *client packages* for you, this being Spack's primary purpose.
+
+An auxiliary route follows from route 2, as it would for most Spack
+packages, namely:
+
+.. _`route 4`:
+
+4. Make Spack-installed Intel tools available outside of Spack for ad-hoc use,
+   typically through Spack-managed modulefiles.
+
+This document covers routes 1 through 3.
+
+
+""""""""""""""""""""""""""""""""""
+Packages under no-cost license
+""""""""""""""""""""""""""""""""""
+
+Intel's standalone performance library products, notably MKL and MPI, are
+available for use under a `simplified license
+<https://software.intel.com/en-us/license/intel-simplified-software-license>`_
+since 2017 [fn1]_. They are packaged in Spack as:
+
+* ``intel-mkl`` -- Math Kernel Library (linear algebra and FFT),
+* ``intel-mpi`` -- The Intel-MPI implementation (derived from MPICH),
+* ``intel-ipp`` -- Primitives for image-, signal-, and data-processing,
+* ``intel-daal`` -- Machine learning and data analytics.
+
+Some earlier versions of these libraries were released under a paid license.
+For these older versions, the license must be available at installation time of
+the products and during compilation of client packages.
+
+The library packages work well with the Intel compilers but do not require them
+-- those packages can just as well be used with other compilers.  The Intel
+compiler invocation commands offer custom options to simplify linking Intel
+libraries (sometimes considerably), but Spack always uses fairly explicit
+linkage anyway.
+
+
+""""""""""""""""""
+Licensed packages
+""""""""""""""""""
+
+Intel's core software development products that provide compilers, analyzers,
+and optimizers do require a paid license.  In Spack, they are packaged as:
+
+* ``intel-parallel-studio`` -- the entire suite of compilers and libraries,
+* ``intel`` -- a subset containing just the compilers and the Intel-MPI runtime [fn2]_.
+
+..
+    TODO: Confirm and possible change(!) the scope of MPI components (runtime
+    vs. devel) in current (and previous?) *cluster/professional/composer*
+    editions, i.e., presence in downloads, possibly subject to license
+    coverage(!); see `disussion in PR #4300
+    <https://github.com/spack/spack/pull/4300#issuecomment-305582898>`_.  [NB:
+    An "mpi" subdirectory is not indicative of the full MPI SDK being present
+    (i.e., ``mpicc``, ..., and header files).  The directory may just as well
+    contain only the MPI runtime (``mpirun`` and shared libraries) .]
+    See also issue #8632.
+
+The license is needed at installation time and to compile client packages, but
+never to merely run any resulting binaries. The license status for a given
+Spack package is normally specified in the *package code* through directives like
+`license_required` (see :ref:`Licensed software <license>`).
+For the Intel packages, however, the *class code* provides these directives (in
+exchange of forfeiting a measure of OOP purity) and takes care of idiosyncasies
+like historic version dependence.
+
+The libraries that are provided in the standalone packages are also included in the
+all-encompassing ``intel-parallel-studio``. To complicate matters a bit, that
+package is sold in 3 "editions", of which only the upper-tier ``cluster``
+edition supports *compiling* MPI applications, and hence only that edition can
+provide the ``mpi`` virtual package.  (As mentioned [fn2]_, all editions
+provide support for *running* MPI applications.)
+
+The edition forms the leading part of the version number for Spack's
+``intel*`` packages discussed here. This differs from the primarily numeric
+version numbers seen with most other Spack packages. For example, we have:
+
+
+.. code-block:: console
+
+   $ spack info intel-parallel-studio
+   ...
+   Preferred version:
+       professional.2018.3    http:...
+  
+   Safe versions:
+       professional.2018.3    http:...
+       ...
+       composer.2018.3        http:...
+       ...
+       cluster.2018.3         http:...
+       ...
+   ...
+
+The full studio suite, capable of compiling MPI applications, currently
+requires about 12 GB of disk space when installed (see section `Install steps
+for packages with compilers and libraries`_ for detailed instructions).
+If you need to save disk space or installation time, you could install the
+``intel`` compilers-only subset (0.6 GB) and just the library packages you
+need, for example ``intel-mpi`` (0.5 GB) and ``intel-mkl`` (2.5 GB).
+
+
+""""""""""""""""""""
+Unrelated packages
+""""""""""""""""""""
+
+The following packages do not use the Intel installer and are not in class ``IntelPackage``
+that is discussed here:
+
+* ``intel-gpu-tools`` -- Test suite and low-level tools for the Linux `Direct
+  Rendering Manager <https://en.wikipedia.org/wiki/Direct_Rendering_Manager>`_
+* ``intel-mkl-dnn`` -- Math Kernel Library for Deep Neural Networks (``CMakePackage``)
+* ``intel-xed`` -- X86 machine instructions encoder/decoder
+* ``intel-tbb`` -- Standalone version of Intel Threading Building Blocks. Note that
+  a TBB runtime version is included with ``intel-mkl``, and development
+  versions are provided by the packages ``intel-parallel-studio`` (all
+  editions) and its ``intel`` subset.
+
+""""""""""""""""""""""""""""""""""""""""""
+Configuring Spack to use Intel licenses
+""""""""""""""""""""""""""""""""""""""""""
+
+If you wish to integrate licensed Intel products into Spack as external packages
+(`route 1`_ above) we assume that their license configuration is in place and
+is working [fn3]_. In this case, skip to section `Integration of Intel tools
+installed external to Spack`_.
+
+If you plan to have Spack install licensed products for you (`route 2`_ above),
+the Intel product installer that Spack will run underneath must have access to
+a license that is either provided by a *license server* or as a *license file*.
+The installer may be able to locate a license that is already configured on
+your system.  If it cannot, you must configure Spack to provide either the
+server location or the license file.
+
+For authoritative information on Intel licensing, see:
+
+* https://software.intel.com/en-us/faq/licensing
+* https://software.intel.com/en-us/articles/how-do-i-manage-my-licenses
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Pointing to an existing license server
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Installing and configuring a license server is outside the scope of Spack. We
+assume that:
+
+* Your system administrator has a license server running.
+* The license server offers valid licenses for the Intel packages of interest.
+* You can access these licenses under the user id running Spack.
+
+Be aware of the difference between (a) installing and configuring a license
+server, and (b) configuring client software to *use* a server's
+so-called floating licenses.  We are concerned here with (b) only. The
+process of obtaining a license from a server for temporary use is called
+"checking out a license".  For that, a client application such as the Intel
+package installer or a compiler needs to know the host name and port number of
+one or more license servers that it may query [fn4]_.
+
+Follow one of three methods to `point client software to a floating license server
+<https://software.intel.com/en-us/articles/licensing-setting-up-the-client-floating-license>`_.
+Ideally, your license administrator will already have implemented one that can
+be used unchanged in Spack: Look for the environment variable
+``INTEL_LICENSE_FILE`` or for files
+``/opt/intel/licenses/*.lic`` that contain::
+
+  SERVER  hostname  hostid_or_ANY  portnum
+  USE_SERVER
+
+The relevant tokens, among possibly others, are the ``USE_SERVER`` line,
+intended specifically for clients, and one or more ``SERVER`` lines above it
+which give the network address.
+
+If you cannot find pre-existing ``/opt/intel/licenses/*.lic`` files and the
+``INTEL_LICENSE_FILE`` environment variable is not set (even after you loaded
+any relevant modulefiles), ask your license administrator for the server
+address(es) and place them in a "global" license file within your Spack
+directory tree `as shown below <Spack-managed file_>`_).
+
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Installing a standalone license file
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+If you purchased a user-specific license, follow `Intel's instructions
+<https://software.intel.com/en-us/faq/licensing#license-management>`_
+to "activate" it for your serial number, then download the resulting license file.
+If needed, `request to have the file re-sent
+<https://software.intel.com/en-us/articles/resend-license-file>`_ to you.
+
+Intel's license files are text files that contain tokens in the proprietary
+"FLEXlm" format and whose name ends in ``.lic``.
+Intel installers and compilers look for license files in several locations when they run.
+Place your license by one of the following means, in order of decreasing preference:
+
+* Default directory
+
+  Install your license file in the directory ``/opt/intel/licenses/`` if you
+  have write permission to it. This directory is inspected by all Intel tools
+  and is therefore preferred, as no further configuration will be needed.
+  Create the directory if it does not yet exist.  For the file name, either
+  keep the downloaded name or use another suitably plain yet descriptive
+  name that ends in ``.lic``. Adjust file permissions for access by licensed
+  users.
+
+
+* Directory given in environment variable
+
+  If you cannot use the default directory, but your system already has set the
+  environment variable ``INTEL_LICENSE_FILE`` independent from Spack [fn5]_,
+  then, if you have the necessary write permissions, place your license file in
+  one of the directories mentioned in this environment variable.  Adjust file
+  permissions to match licensed users.
+
+  .. tip::
+
+      If your system has not yet set and used the environment variable
+      ``INTEL_LICENSE_FILE``, you could start using it with the ``spack
+      install`` stage of licensed tools and subsequent client packages. You
+      would, however, be in a bind to always set that variable in the same
+      manner, across updates and re-installations, and perhaps accommodate
+      additions to it. As this may be difficult in the long run, we recommend
+      that you do *not* attempt to start using the variable solely for Spack.
+
+.. _`Spack-managed file`:
+
+* Spack-managed file
+
+  The first time Spack encounters an Intel package that requires a license, it
+  will initialize a Spack-global Intel-specific license file for you, as a
+  template with instructional comments, and bring up an editor [fn6]_.  Spack
+  will do this *even if you have a working license elsewhere* on the system.
+
+  * To proceed with an externally configured license, leave the newly templated
+    file as is (containing comments only) and close the editor. You do not need
+    to touch the file again.
+
+  * To configure your own standalone license, copy the contents of your
+    downloaded license file into the opened file, save it, and close the editor.
+
+  * To use a license server (i.e., a floating network license) that is not
+    already configured elsewhere on the system, supply your license server
+    address(es) in the form of ``SERVER`` and ``USE_SERVER`` lines at the
+    *beginning of the file* [fn7]_, in the format shown in section `Pointing to
+    an existing license server`_. Save the file and close the editor.
+
+  To revisit and manually edit this file, such as prior to a subsequent
+  installation attempt, find it at
+  ``$SPACK_ROOT/etc/spack/licenses/intel/intel.lic`` .
+
+  Spack will place symbolic links to this file in each directory where licensed
+  Intel binaries were installed.  If you kept the template unchanged, Intel tools
+  will simply ignore it.
+
+
+.. _integrate-external-intel:
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Integration of Intel tools installed *external* to Spack
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+This section discusses `route 1`_ from the introduction.
+
+A site that already uses Intel tools, especially licensed ones, will likely
+have some versions already installed on the system, especially at a time when
+Spack is just being introduced. It will be useful to make such previously
+installed tools available for use by Spack as they are. How to do this varies
+depending on the type of the tools:
+
+""""""""""""""""""""""""""""""""""
+Integrating external compilers
+""""""""""""""""""""""""""""""""""
+
+For Spack to use external Intel compilers, you must tell it both *where* to
+find them and *when* to use them.  The present section documents the "where"
+aspect, involving ``compilers.yaml`` and, in most cases, long absolute paths.
+The "when" aspect actually relates to `route 3`_ and requires explicitly
+stating the compiler as a spec component (in the form ``foo %intel`` or ``foo
+%intel@compilerversion``) when installing client packages or altering Spack's
+compiler default in ``packages.yaml``.
+See section `Selecting Intel compilers <Selecting Intel compilers_>`_ for details.
+
+To integrate a new set of externally installed Intel compilers into Spack
+follow section
+:ref:`Compiler configuration <compiler-config>`.
+Briefly, prepare your shell environment like you would if you were to use these
+compilers normally, i.e., typically by a ``module load ...`` or a shell
+``source ...`` command, then use ``spack compiler find`` to make Spack aware of
+these compilers.  This will create a new entry in a suitably scoped and possibly new
+``compilers.yaml`` file. You could certainly create such a compiler entry
+manually, but this is error-prone due to the indentation and different data
+types involved.
+
+The Intel compilers need and use the system's native GCC compiler (``gcc`` on
+most systems, ``clang`` on macOS) to provide certain functionality, notably to
+support C++. To provide a different GCC compiler for the Intel tools, or more
+generally set persistent flags for all invocations of the Intel compilers, locate
+the ``compilers.yaml`` entry that defines your Intel compiler, and, using a
+text editor, change one or both of the following:
+
+1. At the ``modules:`` tag, add a ``gcc`` module to the list.
+2. At the ``flags:`` tag, add ``cflags:``, ``cxxflags:``, and ``fflags:`` key-value entries.
+
+Consult the examples under
+:ref:`Compiler configuration <compiler-config>`
+and
+:ref:`Vendor-Specific Compiler Configuration <vendor-specific-compiler-configuration>`
+in the Spack documentation.
+When done, validate your compiler definition by running
+``spack compiler info intel@compilerversion`` (replacing ``compilerversion`` by
+the version that you defined).
+
+Be aware that both the GCC integration and persistent compiler flags can also be
+affected by an advanced third method:
+
+3. A modulefile that provides the Intel compilers for you
+   could, for the benefit of users outside of Spack, implicitly
+   integrate a specific ``gcc`` version via compiler flag environment variables
+   or (hopefully not) via a sneaky extra ``PATH`` addition.
+
+Next, visit section `Selecting Intel Compilers`_ to learn how to tell
+Spack to use the newly configured compilers.
+
+""""""""""""""""""""""""""""""""""
+Integrating external libraries
+""""""""""""""""""""""""""""""""""
+
+Configure external library-type packages (as opposed to compilers)
+in the files ``$SPACK_ROOT/etc/spack/packages.yaml`` or
+``~/.spack/packages.yaml``, following the Spack documentation under
+:ref:`External Packages <sec-external-packages>`.
+
+Similar to ``compilers.yaml``, the ``packages.yaml`` files define a package
+external to Spack in terms of a Spack spec and resolve each such spec via
+either the ``paths`` or ``modules`` tokens to a specific pre-installed package
+version on the system.  Since Intel tools generally need environment variables
+to interoperate, which cannot be conveyed in a mere ``paths`` specification,
+the ``modules`` token will be more sensible to use. It resolves the Spack-side
+spec to a modulefile generated and managed outside of Spack's purview,
+which Spack will load internally and transiently when the corresponding spec is
+called upon to compile client packages.
+
+Unlike for compilers, where ``spack find compilers [spec]`` generates an entry
+in an existing or new ``compilers.yaml`` file, Spack does not offer a command
+to generate an entirely new ``packages.yaml`` entry.  You must create
+new entries yourself in a text editor, though the command ``spack config
+[--scope=...] edit packages`` can help with selecting the proper file.
+See section
+:ref:`Configuration Scopes <configuration-scopes>`
+for an explanation about the different files
+and section
+:ref:`Build customization <build-settings>`
+for specifics and examples for ``packages.yaml`` files.
+
+.. If your system administrator did not provide modules for pre-installed Intel
+   tools, you could do well to ask for them, because installing multiple copies
+   of the Intel tools, as is wont to happen once Spack is in the picture, is
+   bound to stretch disk space and patience thin. If you *are* the system
+   administrator and are still new to modules, then perhaps it's best to follow
+   the `next section <Installing Intel tools within Spack_>`_ and install the tools
+   solely within Spack.
+
+The following example integrates packages embodied by hypothetical
+external modulefiles ``intel-mkl/18/...`` into
+Spack as packages ``intel-mkl@...``:
+
+.. code-block:: console
+
+   $ spack config edit packages
+
+Make sure the file begins with:
+
+.. code-block:: yaml
+
+   packages:
+
+Adapt the following example. Be sure to maintain the indentation:
+
+.. code-block:: yaml
+
+   # other content ...
+
+     intel-mkl:
+       modules:
+         intel-mkl@2018.2.199  arch=linux-centos6-x86_64:  intel-mkl/18/18.0.2
+         intel-mkl@2018.3.222  arch=linux-centos6-x86_64:  intel-mkl/18/18.0.3
+
+The version numbers for the ``intel-mkl`` specs defined here correspond to file
+and directory names that Intel uses for its products because they were adopted
+and declared as such within Spack's package repository. You can inspect the
+versions known to your current Spack installation by:
+
+.. code-block:: console
+
+   $ spack info intel-mkl
+
+Using the same version numbers for external packages as for packages known
+internally is useful for clarity, but not strictly necessary.  Moreover, with a
+``packages.yaml`` entry, you can go beyond internally known versions.
+
+.. _compiler-neutral-package:
+
+Note that the Spack spec in the example does not contain a compiler
+specification. This is intentional, as the Intel library packages can be used
+unmodified with different compilers.
+
+A slightly more advanced example illustrates how to provide
+:ref:`variants <basic-variants>`
+and how to use the ``buildable: False`` directive to prevent Spack from installing
+other versions or variants of the named package through its normal internal
+mechanism.
+
+.. code-block:: yaml
+
+   packages:
+     intel-parallel-studio:
+       modules:
+         intel-parallel-studio@cluster.2018.2.199 +mkl+mpi+ipp+tbb+daal  arch=linux-centos6-x86_64:  intel/18/18.0.2
+         intel-parallel-studio@cluster.2018.3.222 +mkl+mpi+ipp+tbb+daal  arch=linux-centos6-x86_64:  intel/18/18.0.3
+       buildable: False
+
+One additional example illustrates the use of ``paths:`` instead of
+``modules:``, useful when external modulefiles are not available or not
+suitable:
+
+.. code-block:: yaml
+
+   packages:
+     intel-parallel-studio:
+       paths:
+         intel-parallel-studio@cluster.2018.2.199 +mkl+mpi+ipp+tbb+daal: /opt/intel
+         intel-parallel-studio@cluster.2018.3.222 +mkl+mpi+ipp+tbb+daal: /opt/intel
+       buildable: False
+
+Note that for the Intel packages discussed here, the directory values in the
+``paths:`` entries must be the high-level and typically version-less
+"installation directory" that has been used by Intel's product installer.
+Such a directory will typically accumulate various product versions.  Amongst
+them, Spack will select the correct version-specific product directory based on
+the ``@version`` spec component that each path is being defined for.
+
+For further background and details, see
+:ref:`External Packages <sec-external-packages>`.
+
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Installing Intel tools *within* Spack
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+This section discusses `route 2`_ from the introduction.
+
+When a system does not yet have Intel tools installed already, or the installed
+versions are undesirable, Spack can install these tools like any regular Spack
+package for you and, with appropriate pre- and post-install configuration, use its
+compilers and/or libraries to install client packages.
+
+.. _intel-install-studio:
+
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+Install steps for packages with compilers and libraries
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+The packages ``intel-parallel-studio`` and ``intel`` (which is a subset of the
+former) are many-in-one products that contain both compilers and a set of
+library packages whose scope depends on the edition.
+Because they are general products geared towards shell environments,
+it can be somewhat involved to integrate these packages at their full extent
+into Spack.
+
+Note: To install library-only packages like ``intel-mkl``, ``intel-mpi``, and ``intel-daal``
+follow `the next section <intel-install-libs_>`_ instead.
+
+1. Review the section `Configuring spack to use intel licenses`_.
+
+.. _intel-compiler-anticipation:
+
+2. To install a version of ``intel-parallel-studio`` that provides Intel
+   compilers at a version that you have *not yet declared in Spack*,
+   the following preparatory steps are recommended:
+
+   A. Determine the compiler spec that the new ``intel-parallel-studio`` package
+      will provide, as follows: From the package version, combine the last two
+      digits of the version year, a literal "0" (zero), and the version component
+      that immediately follows the year.
+
+      ==========================================  ======================
+      Package version                             Compiler spec provided
+      ------------------------------------------  ----------------------
+       ``intel-parallel-studio@edition.YYyy.u``   ``intel@yy.0.u``
+      ==========================================  ======================
+
+      Example: The package ``intel-parallel-studio@cluster.2018.3`` will provide
+      the compiler with spec ``intel@18.0.3``.
+
+   .. _`config-compiler-anticipated`:
+
+   B. Add a new compiler section with the newly anticipated version at the
+      end of a ``compilers.yaml`` file in a suitable scope.  For example, run:
+
+      .. code-block:: console
+
+         $ spack config --scope=user/linux edit compilers
+
+      and append a stub entry:
+
+      .. code-block:: yaml
+
+         - compiler:
+             target:     x86_64
+             operating_system:   centos6
+             modules:    []
+             spec:       intel@18.0.3
+             paths:
+               cc:       stub
+               cxx:      stub
+               f77:      stub
+               fc:       stub
+
+      Replace ``18.0.3`` with the version that you determined in the preceeding
+      step. The contents under ``paths:`` do not matter yet.
+
+   You are right to ask: "Why on earth is that necessary?" [fn8]_.
+   The answer lies in Spack striving for strict compiler consistency.
+   Consider what happens without such a pre-declared compiler stub:
+   Say, you ask Spack to install a particular version
+   ``intel-parallel-studio@edition.V``.  Spack will apply an unrelated compiler
+   spec to concretize and install your request, resulting in
+   ``intel-parallel-studio@edition.V %X``. That compiler ``%X`` is not going to
+   be the version that this new package itself provides. Rather, it would
+   typically be ``%gcc@...`` in a default Spack installation or possibly indeed
+   ``%intel@...``, but at a version that precedes ``V``.
+
+   The problem comes to the fore as soon as you try to use any virtual ``mkl``
+   or ``mpi`` packages that you would expect to now be provided by
+   ``intel-parallel-studio@edition.V``.  Spack will indeed see those virtual
+   packages, but only as being tied to the compiler that the package
+   ``intel-parallel-studio@edition.V`` was concretized with *at installation*.
+   If you were to install a client package with the new compilers now available
+   to you, you would naturally run ``spack install foo +mkl %intel@V``, yet
+   Spack will either complain about ``mkl%intel@V`` being missing (because it
+   only knows about ``mkl%X``) or it will go and attempt to install *another
+   instance* of ``intel-parallel-studio@edition.V %intel@V`` so as to match the
+   compiler spec ``%intel@V`` that you gave for your client package ``foo``.
+   This will be unexpected and will quickly get annoying because each
+   reinstallation takes up time and extra disk space.
+
+   To escape this trap, put the compiler stub declaration shown here in place,
+   then use that pre-declared compiler spec to install the actual package, as
+   shown next.  This approach works because during installation only the
+   package's own self-sufficient installer will be used, not any compiler.
+
+   .. _`verify-compiler-anticipated`:
+
+3. Verify that the compiler version provided by the new ``studio`` version
+   would be used as expected if you were to compile a client package:
+
+   .. code-block:: console
+
+      $ spack spec zlib %intel
+
+   If the version does not match, explicitly state the anticipated compiler version, e.g.:
+
+   .. code-block:: console
+
+      $ spack spec zlib %intel@18.0.3
+
+   if there are problems, review and correct the compiler's ``compilers.yaml``
+   entry, be it still in stub form or already complete (as it would be for a
+   re-installation).
+
+4. Install the new ``studio`` package using Spack's regular ``install``
+   command.
+   It may be wise to provide the anticipated compiler (`see above
+   <verify-compiler-anticipated_>`_) as an explicit concretization
+   element:
+
+   .. code-block:: console
+
+      $ spack install intel-parallel-studio@cluster.2018.3  %intel@18.0.3
+
+5. Follow the same steps as under `Integrating external compilers`_ to tell
+   Spack the minutiae for actually using those compilers with client packages.
+   If you placed a stub entry in a ``compilers.yaml`` file, now is the time to
+   edit it and fill in the particulars.
+
+   * Under ``paths:``, give the full paths to the actual compiler binaries (``icc``,
+     ``ifort``, etc.) located within the Spack installation tree, in all their
+     unsightly length [fn9]_.
+
+     To determine the full path to the C compiler, adapt and run:
+
+     .. code-block:: console
+
+        $ find `spack location -i intel-parallel-studio@cluster.2018.3` \
+               -name icc -type f -ls
+
+     If you get hits for both ``intel64`` and ``ia32``, you almost certainly will
+     want to use the ``intel64`` variant.  The ``icpc`` and ``ifort`` compilers
+     will be located in the same directory as ``icc``.
+
+   * Use the ``modules:`` and/or ``cflags:`` tokens to specify a suitable accompanying
+     ``gcc`` version to help pacify picky client packages that ask for C++
+     standards more recent than supported by your system-provided ``gcc`` and its
+     ``libstdc++.so``.
+
+   * To set the Intel compilers for default use in Spack, instead of the usual ``%gcc``,
+     follow section `Selecting Intel compilers`_.
+
+.. tip::
+
+   Compiler packages like ``intel-parallel-studio`` can easily be above 10 GB
+   in size, which can tax the disk space available for temporary files on
+   small, busy, or restricted systems (like virtual machines). The Intel
+   installer will stop and report insufficient space as::
+
+       ==> './install.sh' '--silent' 'silent.cfg'
+       ...
+       Missing critical prerequisite
+       -- Not enough disk space
+
+   As first remedy, clean Spack's existing staging area:
+
+   .. code-block:: console
+
+      $ spack clean --stage
+
+   then retry installing the large package. Spack normally cleans staging
+   directories but certain failures may prevent it from doing so.
+
+   If the error persists, tell Spack to use an alternative location for
+   temporary files:
+
+   1. Run ``df -h`` to identify an alternative location on your system.
+
+   2. Tell Spack to use that location for staging. Do **one** of the following:
+
+      * Run Spack with the environment variable ``TMPDIR`` altered for just a
+        single command. For example, to use your ``$HOME`` directory:
+
+        .. code-block:: console
+
+           $ TMPDIR="$HOME/spack-stage"  spack install ....
+
+        This example uses Bourne shell syntax. Adapt for other shells as needed.
+
+      * Alternatively, customize
+        Spack's ``build_stage`` :ref:`configuration setting <config-overrides>`.
+
+        .. code-block:: console
+
+           $ spack config edit config
+
+        Append:
+
+        .. code-block:: yaml
+
+           config:
+             build_stage:
+             - /home/$user/spack-stage
+
+        Do not duplicate the ``config:`` line if it already is present.
+        Adapt the location, which here is the same as in the preceeding example.
+
+   3. Retry installing the large package.
+
+
+.. _intel-install-libs:
+
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+Install steps for library-only packages
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+To install library-only packages like ``intel-mkl``, ``intel-mpi``, and ``intel-daal``
+follow the steps given here.
+For packages that contain a compiler, follow `the previous section
+<intel-install-studio_>`_ instead.
+
+1. For pre-2017 product releases, review the section `Configuring Spack to use Intel licenses`_.
+
+2. Inspect the package spec. Specify an explicit compiler if necessary, e.g.:
+
+   .. code-block:: console
+
+      $ spack spec intel-mpi@2018.3.199
+      $ spack spec intel-mpi@2018.3.199  %intel
+
+   Check that the package will use the compiler flavor and version that you expect.
+
+3. Install the package normally within Spack. Use the same spec as in the
+   previous command, i.e., as general or as specific as needed:
+
+   .. code-block:: console
+
+      $ spack install intel-mpi@2018.3.199 
+      $ spack install intel-mpi@2018.3.199  %intel@18
+
+4. To prepare the new packages for use with client packages,
+   follow `Selecting libraries to satisfy virtual packages`_.
+
+
+""""""""""""""""
+Debug notes
+""""""""""""""""
+
+* You can trigger a wall of additional diagnostics using Spack options, e.g.:
+
+  .. code-block:: console
+
+     $ spack --debug -v install intel-mpi
+
+  The ``--debug`` option can also be useful while installing client
+  packages `(see below) <Using Intel tools in Spack to install client
+  packages_>`_ to confirm the integration of the Intel tools in Spack, notably
+  MKL and MPI.
+
+* The ``.spack/`` subdirectory of an installed ``IntelPackage`` will contain,
+  besides Spack's usual archival items, a copy of the ``silent.cfg`` file that
+  was passed to the Intel installer:
+
+  .. code-block:: console
+
+     $ grep COMPONENTS ...intel-mpi...<hash>/.spack/silent.cfg
+     COMPONENTS=ALL
+
+* If an installation error occurs, Spack will normally clean up and remove a
+  partially installed target directory. You can direct Spack to keep it using
+  ``--keep-prefix``, e.g.:
+
+  .. code-block:: console
+
+     $ spack install --keep-prefix  intel-mpi
+
+  You must, however, *remove such partial installations* prior to subsequent
+  installation attempts. Otherwise, the Intel installer will behave
+  incorrectly.
+
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Using Intel tools in Spack to install client packages
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Finally, this section pertains to `route 3`_ from the introduction.
+
+Once Intel tools are installed within Spack as external or internal packages
+they can be used as intended for installing client packages.
+
+
+.. _`select-intel-compilers`:
+
+""""""""""""""""""""""""""
+Selecting Intel compilers
+""""""""""""""""""""""""""
+
+Select Intel compilers to compile client packages, like any compiler in Spack,
+by one of the following means:
+
+* Request the Intel compilers explicitly in the client spec, e.g.:
+
+  .. code-block:: console
+
+     $ spack install libxc@3.0.0%intel
+
+
+* Alternatively, request Intel compilers implicitly by concretization preferences.
+  Configure the order of compilers in the appropriate ``packages.yaml`` file,
+  under either an ``all:`` or client-package-specific entry, in a
+  ``compiler:`` list. Consult the Spack documentation for
+  :ref:`Configuring Package Preferences <configs-tutorial-package-prefs>`
+  and
+  :ref:`Concretization Preferences <concretization-preferences>`.
+
+Example: ``etc/spack/packages.yaml`` might simply contain:
+
+.. code-block:: yaml
+
+  packages:
+    all:
+      compiler: [ intel, gcc, ]
+
+To be more specific, you can state partial or full compiler version numbers,
+for example:
+
+.. code-block:: yaml
+
+  packages:
+    all:
+      compiler: [ intel@18, intel@17, gcc@4.4.7, gcc@4.9.3, gcc@7.3.0, ]
+
+
+
+""""""""""""""""""""""""""""""""""""""""""""""""
+Selecting libraries to satisfy virtual packages
+""""""""""""""""""""""""""""""""""""""""""""""""
+
+Intel packages, whether integrated into Spack as external packages or
+installed within Spack, can be called upon to satisfy the requirement of a
+client package for a library that is available from different providers.
+The relevant virtual packages for Intel are ``blas``, ``lapack``,
+``scalapack``, and ``mpi``.
+
+In both integration routes, Intel packages can have optional
+:ref:`variants <basic-variants>`
+which alter the list of virtual packages they can satisfy.  For Spack-external
+packages, the active variants are a combination of the defaults declared in
+Spack's package repository and the spec it is declared as in ``packages.yaml``.
+Needless to say, those should match the components that are actually present in
+the external product installation. Likewise, for Spack-internal packages, the
+active variants are determined, persistently at installation time, from the
+defaults in the repository and the spec selected to be installed.
+
+To have Intel packages satisfy virtual package requests for all or selected
+client packages, edit the ``packages.yaml`` file.  Customize, either in the
+``all:`` or a more specific entry, a ``providers:`` dictionary whose keys are
+the virtual packages and whose values are the Spack specs that satisfy the
+virtual package, in order of decreasing preference.  To learn more about the
+``providers:`` settings, see the Spack tutorial for
+:ref:`Configuring Package Preferences <configs-tutorial-package-prefs>`
+and the section
+:ref:`Concretization Preferences <concretization-preferences>`.
+
+Example: The following fairly minimal example for ``packages.yaml`` shows how
+to exclusively use the standalone ``intel-mkl`` package for all the linear
+algebra virtual packages in Spack, and ``intel-mpi`` as the preferred MPI
+implementation. Other providers can still be chosen on a per-package basis.
+
+.. code-block:: yaml
+
+  packages:
+    all:
+      providers:
+        mpi:       [intel-mpi]
+        blas:      [intel-mkl]
+        lapack:    [intel-mkl]
+        scalapack: [intel-mkl]
+
+If you have access to the ``intel-parallel-studio@cluster`` edition, you can
+use instead:
+
+.. code-block:: yaml
+
+    all:
+      providers:
+        mpi:       [intel-parallel-studio+mpi]
+        # Note: +mpi vs. +mkl
+        blas:      [intel-parallel-studio+mkl]
+        lapack:    [intel-parallel-studio+mkl]
+        scalapack: [intel-parallel-studio+mkl]
+
+If you installed ``intel-parallel-studio`` within Spack ("`route 2`_"), make
+sure you followed the `special installation step
+<intel-compiler-anticipation_>`_ to ensure that its virtual packages match the
+compilers it provides.
+
+
+""""""""""""""""""""""""""""""""""""""""""""
+Using Intel tools as explicit dependency
+""""""""""""""""""""""""""""""""""""""""""""
+
+With the proper installation as detailed above, no special steps should be
+required when a client package specifically (and thus deliberately) requests an
+Intel package as dependency, this being one of the target use cases for Spack.
+
+
+"""""""""""""""""""""""""""""""""""""""""""""""
+Tips for configuring client packages to use MKL
+"""""""""""""""""""""""""""""""""""""""""""""""
+
+The Math Kernel Library (MKL) is provided by several Intel packages, currently
+``intel-parallel-studio`` when variant ``+mkl`` is active (it is by default)
+and the standalone ``intel-mkl``. Because of these different provider packages,
+a *virtual* ``mkl`` package is declared in Spack.
+
+* To use MKL-specific APIs in a client package:
+
+  Declare a dependency on ``mkl``, rather than a specific provider like
+  ``intel-mkl``.  Declare the dependency either absolutely or conditionally
+  based on variants that your package might have declared:
+
+  .. code-block:: python
+
+     # Examples for absolute and conditional dependencies:
+     depends_on('mkl')
+     depends_on('mkl', when='+mkl')
+     depends_on('mkl', when='fftw=mkl')
+
+  The ``MKLROOT`` environment variable (part of the documented API) will be set
+  during all stages of client package installation, and is available to both
+  the Spack packaging code and the client code.
+
+* To use MKL as provider for BLAS, LAPACK, or ScaLAPACK:
+
+  The packages that provide ``mkl`` also provide the narrower
+  virtual ``blas``, ``lapack``, and ``scalapack`` packages.
+  See the relevant :ref:`Packaging Guide section <blas_lapack_scalapack>`
+  for an introduction.
+  To portably use these virtual packages, construct preprocessor and linker
+  option strings in your package configuration code using the package functions
+  ``.headers`` and ``.libs`` in conjunction with utility functions from the
+  following classes:
+
+  * :py:class:`llnl.util.filesystem.FileList`,
+  * :py:class:`llnl.util.filesystem.HeaderList`,
+  * :py:class:`llnl.util.filesystem.LibraryList`.
+
+  .. tip::
+     *Do not* use constructs like ``.prefix.include`` or ``.prefix.lib``, with
+     Intel or any other implementation of ``blas``, ``lapack``, and
+     ``scalapack``.
+
+  For example, for an
+  :ref:`AutotoolsPackage <autotoolspackage>`
+  use ``.libs.ld_flags`` to transform the library file list into linker options
+  passed to ``./configure``:
+
+  .. code-block:: python
+
+      def configure_args(self):
+          args = []
+          ...
+          args.append('--with-blas=%s' % self.spec['blas'].libs.ld_flags)
+          args.append('--with-lapack=%s' % self.spec['lapack'].libs.ld_flags)
+          ...
+
+  .. tip::
+     Even though ``.ld_flags`` will return a string of multiple words, *do not*
+     use quotes for options like ``--with-blas=...`` because Spack passes them
+     to ``./configure`` without invoking a shell.
+
+  Likewise, in a
+  :ref:`MakefilePackage <makefilepackage>`
+  or similiar package that does not use AutoTools you may need to provide include
+  and link options for use on command lines or in environment variables.
+  For example, to generate an option string of the form ``-I<dir>``, use:
+
+  .. code-block:: python
+
+    self.spec['blas'].headers.include_flags
+    
+  and to generate linker options (``-L<dir> -llibname ...``), use the same as above,
+
+  .. code-block:: python
+
+    self.spec['blas'].libs.ld_flags
+
+  See
+  :ref:`MakefilePackage <makefilepackage>`
+  and more generally the
+  :ref:`Packaging Guide <blas_lapack_scalapack>`
+  for background and further examples.
+
+
+^^^^^^^^^^
+Footnotes
+^^^^^^^^^^
+
+.. [fn1] Strictly speaking, versions from ``2017.2`` onward.
+
+.. [fn2] The package ``intel`` intentionally does not have a ``+mpi`` variant since
+   it is meant to be small. The native installer will always add MPI *runtime*
+   components because it follows defaults defined in the download package, even
+   when ``intel-parallel-studio ~mpi`` has been requested.
+
+   For ``intel-parallel-studio +mpi``, the class function
+   :py:func:``.IntelPackage.pset_components``
+   will include ``"intel-mpi intel-imb"`` in a list of component patterns passed
+   to the Intel installer. The installer will extend each pattern word with an
+   implied glob-like ``*`` to resolve it to package names that are
+   *actually present in the product BOM*.
+   As a side effect, this pattern approach accommodates occasional package name
+   changes, e.g., capturing both ``intel-mpirt`` and ``intel-mpi-rt`` .
+
+.. [fn3] How could the external installation have succeeded otherwise?
+
+.. [fn4] According to Intel's documentation, there is supposedly a way to install a
+   product using a network license even `when a FLEXlm server is not running
+   <https://software.intel.com/en-us/articles/licensing-setting-up-the-client-floating-license>`_:
+   Specify the license in the form ``port@serverhost`` in the
+   ``INTEL_LICENSE_FILE`` environment variable. All other means of specifying a
+   network license require that the license server be up.
+
+.. [fn5]  Despite the name, ``INTEL_LICENSE_FILE`` can hold several and diverse entries.
+   They  can be either directories (presumed to contain ``*.lic`` files), file
+   names, or network locations in the form ``port@host`` (on Linux and Mac),
+   with all items separated by ":" (on Linux and Mac).
+
+.. [fn6] Should said editor turn out to be ``vi``, you better be in a position
+   to know how to use it.
+
+.. [fn7] Comment lines in FLEXlm files, indicated by ``#`` as the first
+   non-whitespace character on the line, are generally allowed anywhere in the file.
+   There `have been reports <https://github.com/spack/spack/issues/6534>`_,
+   however, that as of 2018, ``SERVER`` and ``USE_SERVER`` lines must precede
+   any comment lines.
+
+..
+    .. [fnX] The name component ``intel`` of the compiler spec is separate from (in
+       a different namespace than) the names of the Spack packages
+       ``intel-parallel-studio`` and ``intel``. Both of the latter provide the former.
+
+.. [fn8] Spack's close coupling of installed packages to compilers, which both
+   necessitates the detour for installing ``intel-parallel-studio``, and
+   largely limits any of its provided virtual packages to a single compiler, heavily
+   favors `recommending to install Intel Parallel Studio outside of Spack
+   <integrate-external-intel_>`_ and declare it for Spack in ``packages.yaml``
+   by a `compiler-less spec <compiler-neutral-package_>`_.
+
+.. [fn9] With some effort, you can convince Spack to use shorter paths.
+
+   .. warning:: Altering the naming scheme means that Spack will lose track of
+      all packages it has installed for you so far.
+      That said, the time is right for this kind of customization
+      when you are defining a new set of compilers.
+
+   The relevant tunables are:
+
+   1. Set the ``install_tree`` location in ``config.yaml``
+      (:ref:`see doc <config-yaml>`).
+   2. Set the hash length in ``install-path-scheme``, also in ``config.yaml``
+      (:ref:`q.v. <config-yaml>`).
+   3. You will want to set the *same* hash length for
+      :ref:`tcl module files <modules-naming-scheme>`
+      if you have Spack produce them for you, under ``naming_scheme`` in
+      ``modules.yaml``.  Other module dialects cannot be altered in this manner.
diff --git a/lib/spack/docs/build_systems/makefilepackage.rst b/lib/spack/docs/build_systems/makefilepackage.rst
new file mode 100644
index 0000000000..dbb8686cc3
--- /dev/null
+++ b/lib/spack/docs/build_systems/makefilepackage.rst
@@ -0,0 +1,309 @@
+.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+.. _makefilepackage:
+
+---------------
+MakefilePackage
+---------------
+
+The most primitive build system a package can use is a plain Makefile.
+Makefiles are simple to write for small projects, but they usually
+require you to edit the Makefile to set platform and compiler-specific
+variables.
+
+^^^^^^
+Phases
+^^^^^^
+
+The ``MakefilePackage`` base class comes with 3 phases:
+
+#. ``edit`` - edit the Makefile
+#. ``build`` - build the project
+#. ``install`` - install the project
+
+By default, ``edit`` does nothing, but you can override it to replace
+hard-coded Makefile variables. The ``build`` and ``install`` phases
+run:
+
+.. code-block:: console
+
+   $ make
+   $ make install
+
+
+^^^^^^^^^^^^^^^
+Important files
+^^^^^^^^^^^^^^^
+
+The main file that matters for a ``MakefilePackage`` is the Makefile.
+This file will be named one of the following ways:
+
+* GNUmakefile (only works with GNU Make)
+* Makefile (most common)
+* makefile
+
+Some Makefiles also *include* other configuration files. Check for an
+``include`` directive in the Makefile.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^
+Build system dependencies
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Spack assumes that the operating system will have a valid ``make`` utility
+installed already, so you don't need to add a dependency on ``make``.
+However, if the package uses a ``GNUmakefile`` or the developers recommend
+using GNU Make, you should add a dependency on ``gmake``:
+
+.. code-block:: python
+
+   depends_on('gmake', type='build')
+
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+Types of Makefile packages
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Most of the work involved in packaging software that uses Makefiles
+involves overriding or replacing hard-coded variables. Many packages
+make the mistake of hard-coding compilers, usually for GCC or Intel.
+This is fine if you happen to be using that particular compiler, but
+Spack is designed to work with *any* compiler, and you need to ensure
+that this is the case.
+
+Depending on how the Makefile is designed, there are 4 common strategies
+that can be used to set or override the appropriate variables:
+
+"""""""""""""""""""""
+Environment variables
+"""""""""""""""""""""
+
+Make has multiple types of
+`assignment operators <https://www.gnu.org/software/make/manual/make.html#Setting>`_.
+Some Makefiles use ``=`` to assign variables. The only way to override
+these variables is to edit the Makefile or override them on the
+command-line. However, Makefiles that use ``?=`` for assignment honor
+environment variables. Since Spack already sets ``CC``, ``CXX``, ``F77``,
+and ``FC``, you won't need to worry about setting these variables. If
+there are any other variables you need to set, you can do this in the
+``edit`` method:
+
+.. code-block:: python
+
+   def edit(self, spec, prefix):
+       env['PREFIX'] = prefix
+       env['BLASLIB'] = spec['blas'].libs.ld_flags
+
+
+`cbench <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/cbench/package.py>`_
+is a good example of a simple package that does this, while
+`esmf <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/esmf/package.py>`_
+is a good example of a more complex package.
+
+""""""""""""""""""""""
+Command-line arguments
+""""""""""""""""""""""
+
+If the Makefile ignores environment variables, the next thing to try
+is command-line arguments. You can do this by overriding the
+``build_targets`` attribute. If you don't need access to the spec,
+you can do this like so:
+
+.. code-block:: python
+
+   build_targets = ['CC=cc']
+
+
+If you do need access to the spec, you can create a property like so:
+
+.. code-block:: python
+
+   @property
+   def build_targets(self):
+       spec = self.spec
+
+       return [
+           'CC=cc',
+           'BLASLIB={0}'.format(spec['blas'].libs.ld_flags),
+       ]
+
+
+`cloverleaf <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/cloverleaf/package.py>`_
+is a good example of a package that uses this strategy.
+
+"""""""""""""
+Edit Makefile
+"""""""""""""
+
+Some Makefiles are just plain stubborn and will ignore command-line
+variables. The only way to ensure that these packages build correctly
+is to directly edit the Makefile. Spack provides a ``FileFilter`` class
+and a ``filter_file`` method to help with this. For example:
+
+.. code-block:: python
+
+   def edit(self, spec, prefix):
+       makefile = FileFilter('Makefile')
+
+       makefile.filter('CC = gcc',  'CC = cc')
+       makefile.filter('CXX = g++', 'CC = c++')
+
+
+`stream <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/stream/package.py>`_
+is a good example of a package that involves editing a Makefile to set
+the appropriate variables.
+
+"""""""""""
+Config file
+"""""""""""
+
+More complex packages often involve Makefiles that *include* a
+configuration file. These configuration files are primarily composed
+of variables relating to the compiler, platform, and the location of
+dependencies or names of libraries. Since these config files are
+dependent on the compiler and platform, you will often see entire
+directories of examples for common compilers and architectures. Use
+these examples to help determine what possible values to use.
+
+If the config file is long and only contains one or two variables
+that need to be modified, you can use the technique above to edit
+the config file. However, if you end up needing to modify most of
+the variables, it may be easier to write a new file from scratch.
+
+If each variable is independent of each other, a dictionary works
+well for storing variables:
+
+.. code-block:: python
+
+   def edit(self, spec, prefix):
+       config = {
+           'CC': 'cc',
+           'MAKE': 'make',
+       }
+
+       if '+blas' in spec:
+           config['BLAS_LIBS'] = spec['blas'].libs.joined()
+
+       with open('make.inc', 'w') as inc:
+           for key in config:
+               inc.write('{0} = {1}\n'.format(key, config[key]))
+
+
+`elk <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/elk/package.py>`_
+is a good example of a package that uses a dictionary to store
+configuration variables.
+
+If the order of variables is important, it may be easier to store
+them in a list:
+
+.. code-block:: python
+
+   def edit(self, spec, prefix):
+       config = [
+           'INSTALL_DIR = {0}'.format(prefix),
+           'INCLUDE_DIR = $(INSTALL_DIR)/include',
+           'LIBRARY_DIR = $(INSTALL_DIR)/lib',
+       ]
+
+       with open('make.inc', 'w') as inc:
+           for var in config:
+               inc.write('{0}\n'.format(var))
+
+
+`hpl <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/hpl/package.py>`_
+is a good example of a package that uses a list to store
+configuration variables.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+Variables to watch out for
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The following is a list of common variables to watch out for. The first
+two sections are
+`implicit variables <https://www.gnu.org/software/make/manual/html_node/Implicit-Variables.html>`_
+defined by Make and will always use the same name, while the rest are
+user-defined variables and may vary from package to package.
+
+* **Compilers**
+
+  This includes variables such as ``CC``, ``CXX``, ``F77``, ``F90``,
+  and ``FC``, as well as variables related to MPI compiler wrappers,
+  like ``MPICC`` and friends.
+
+* **Compiler flags**
+
+  This includes variables for specific compilers, like ``CFLAGS``,
+  ``CXXFLAGS``, ``F77FLAGS``, ``F90FLAGS``, ``FCFLAGS``, and ``CPPFLAGS``.
+  These variables are often hard-coded to contain flags specific to a
+  certain compiler. If these flags don't work for every compiler,
+  you may want to consider filtering them.
+
+* **Variables that enable or disable features**
+
+  This includes variables like ``MPI``, ``OPENMP``, ``PIC``, and
+  ``DEBUG``. These flags often require you to create a variant
+  so that you can either build with or without MPI support, for
+  example. These flags are often compiler-dependent. You should
+  replace them with the appropriate compiler flags, such as
+  ``self.compiler.openmp_flag`` or ``self.compiler.pic_flag``.
+
+* **Platform flags**
+
+  These flags control the type of architecture that the executable
+  is compiler for. Watch out for variables like ``PLAT`` or ``ARCH``.
+
+* **Dependencies**
+
+  Look out for variables that sound like they could be used to
+  locate dependencies, such as ``JAVA_HOME``, ``JPEG_ROOT``, or
+  ``ZLIBDIR``. Also watch out for variables that control linking,
+  such as ``LIBS``, ``LDFLAGS``, and ``INCLUDES``. These variables
+  need to be set to the installation prefix of a dependency, or
+  to the correct linker flags to link to that dependency.
+
+* **Installation prefix**
+
+  If your Makefile has an ``install`` target, it needs some way of
+  knowing where to install. By default, many packages install to
+  ``/usr`` or ``/usr/local``. Since many Spack users won't have
+  sudo privileges, it is imperative that each package is installed
+  to the proper prefix. Look for variables like ``PREFIX`` or
+  ``INSTALL``.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Makefiles in a sub-directory
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Not every package places their Makefile in the root of the package
+tarball. If the Makefile is in a sub-directory like ``src``, you
+can tell Spack where to locate it like so:
+
+.. code-block:: python
+
+   build_directory = 'src'
+
+
+^^^^^^^^^^^^^^^^^^^
+Manual installation
+^^^^^^^^^^^^^^^^^^^
+
+Not every Makefile includes an ``install`` target. If this is the
+case, you can override the default ``install`` method to manually
+install the package:
+
+.. code-block:: python
+
+   def install(self, spec, prefix):
+       mkdir(prefix.bin)
+       install('foo', prefix.bin)
+       install_tree('lib', prefix.lib)
+
+
+^^^^^^^^^^^^^^^^^^^^^^
+External documentation
+^^^^^^^^^^^^^^^^^^^^^^
+
+For more information on reading and writing Makefiles, see:
+https://www.gnu.org/software/make/manual/make.html
diff --git a/lib/spack/docs/build_systems/mesonpackage.rst b/lib/spack/docs/build_systems/mesonpackage.rst
new file mode 100644
index 0000000000..4b30ac5df0
--- /dev/null
+++ b/lib/spack/docs/build_systems/mesonpackage.rst
@@ -0,0 +1,90 @@
+.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+.. _mesonpackage:
+
+------------
+MesonPackage
+------------
+
+Much like Autotools and CMake, Meson is a build system.  But it is
+meant to be both fast and as user friendly as possible.  GNOME's goal
+is to port modules to use the Meson build system.
+
+^^^^^^
+Phases
+^^^^^^
+
+The ``MesonPackage`` base class comes with the following phases:
+
+#. ``meson`` - generate ninja files
+#. ``build`` - build the project
+#. ``install`` - install the project
+
+By default, these phases run:
+
+.. code-block:: console
+
+   $ mkdir spack-build
+   $ cd spack-build
+   $ meson .. --prefix=/path/to/installation/prefix
+   $ ninja
+   $ ninja test  # optional
+   $ ninja install
+
+
+Any of these phases can be overridden in your package as necessary.
+There is also a ``check`` method that looks for a ``test`` target
+in the build file. If a ``test`` target exists and the user runs:
+
+.. code-block:: console
+
+   $ spack install --test=root <meson-package>
+
+
+Spack will run ``ninja test`` after the build phase.
+
+^^^^^^^^^^^^^^^
+Important files
+^^^^^^^^^^^^^^^
+
+Packages that use the Meson build system can be identified by the
+presence of a ``meson.build`` file. This file declares things
+like build instructions and dependencies.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^
+Build system dependencies
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+At the bare minimum, packages that use the Meson build system need
+``meson`` and ```ninja``` dependencies. Since this is always the case,
+the ``MesonPackage`` base class already contains:
+
+.. code-block:: python
+
+   depends_on('meson', type='build')
+   depends_on('ninja', type='build')
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+Passing arguments to meson
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+If you need to pass any arguments to the ``meson`` call, you can
+override the ``meson_args`` method like so:
+
+.. code-block:: python
+
+   def meson_args(self):
+       return ['--default-library=both']
+
+
+This method can be used to pass flags as well as variables.
+
+^^^^^^^^^^^^^^^^^^^^^^
+External documentation
+^^^^^^^^^^^^^^^^^^^^^^
+
+For more information on the Meson build system, see:
+https://mesonbuild.com/index.html
diff --git a/lib/spack/docs/build_systems/octavepackage.rst b/lib/spack/docs/build_systems/octavepackage.rst
new file mode 100644
index 0000000000..f63089406c
--- /dev/null
+++ b/lib/spack/docs/build_systems/octavepackage.rst
@@ -0,0 +1,52 @@
+.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+.. _octavepackage:
+
+-------------
+OctavePackage
+-------------
+
+Octave has its own build system for installing packages.
+
+^^^^^^
+Phases
+^^^^^^
+
+The ``OctavePackage`` base class has a single phase:
+
+#. ``install`` - install the package
+
+By default, this phase runs the following command:
+
+.. code-block:: console
+
+   $ octave '--eval' 'pkg prefix <prefix>; pkg install <archive_file>'
+
+
+Beware that uninstallation is not implemented at the moment. After uninstalling
+a package via Spack, you also need to manually uninstall it from Octave via
+``pkg uninstall <package_name>``.
+
+^^^^^^^^^^^^^^^^^^^^^^^
+Finding Octave packages
+^^^^^^^^^^^^^^^^^^^^^^^
+
+Most Octave packages are listed at https://octave.sourceforge.io/packages.php.
+
+^^^^^^^^^^^^
+Dependencies
+^^^^^^^^^^^^
+
+Usually, the homepage of a package will list dependencies, i.e.
+``Dependencies:	Octave >= 3.6.0 struct >= 1.0.12``. The same information should
+be available in the ``DESCRIPTION`` file in the root of each archive.
+
+^^^^^^^^^^^^^^^^^^^^^^
+External Documentation
+^^^^^^^^^^^^^^^^^^^^^^
+
+For more information on the Octave build system, see:
+https://octave.org/doc/v4.4.0/Installing-and-Removing-Packages.html
diff --git a/lib/spack/docs/build_systems/perlpackage.rst b/lib/spack/docs/build_systems/perlpackage.rst
new file mode 100644
index 0000000000..3f36a4eb2f
--- /dev/null
+++ b/lib/spack/docs/build_systems/perlpackage.rst
@@ -0,0 +1,212 @@
+.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+.. _perlpackage:
+
+-----------
+PerlPackage
+-----------
+
+Much like Octave, Perl has its own language-specific
+build system.
+
+^^^^^^
+Phases
+^^^^^^
+
+The ``PerlPackage`` base class comes with 3 phases that can be overridden:
+
+#. ``configure`` - configure the package
+#. ``build`` - build the package
+#. ``install`` - install the package
+
+Perl packages have 2 common modules used for module installation:
+
+"""""""""""""""""""""""
+``ExtUtils::MakeMaker``
+"""""""""""""""""""""""
+
+The ``ExtUtils::MakeMaker`` module is just what it sounds like, a module
+designed to generate Makefiles. It can be identified by the presence of
+a ``Makefile.PL`` file, and has the following installation steps:
+
+.. code-block:: console
+
+   $ perl Makefile.PL INSTALL_BASE=/path/to/installation/prefix
+   $ make
+   $ make test  # optional
+   $ make install
+
+
+"""""""""""""""""
+``Module::Build``
+"""""""""""""""""
+
+The ``Module::Build`` module is a pure-Perl build system, and can be
+identified by the presence of a ``Build.PL`` file. It has the following
+installation steps:
+
+.. code-block:: console
+
+   $ perl Build.PL --install_base /path/to/installation/prefix
+   $ ./Build
+   $ ./Build test  # optional
+   $ ./Build install
+
+
+If both ``Makefile.PL`` and ``Build.PL`` files exist in the package,
+Spack will use ``Makefile.PL`` by default. If your package uses a
+different module, ``PerlPackage`` will need to be extended to support
+it.
+
+``PerlPackage`` automatically detects which build steps to use, so there
+shouldn't be much work on the package developer's side to get things
+working.
+
+^^^^^^^^^^^^^^^^^^^^^
+Finding Perl packages
+^^^^^^^^^^^^^^^^^^^^^
+
+Most Perl modules are hosted on CPAN - The Comprehensive Perl Archive
+Network. If you need to find a package for ``XML::Parser``, for example,
+you should search for "CPAN XML::Parser".
+
+Some CPAN pages are versioned. Check for a link to the
+"Latest Release" to make sure you have the latest version.
+
+^^^^^^^^^^^^
+Package name
+^^^^^^^^^^^^
+
+When you use ``spack create`` to create a new Perl package, Spack will
+automatically prepend ``perl-`` to the front of the package name. This
+helps to keep Perl modules separate from other packages. The same
+naming scheme is used for other language extensions, like Python and R.
+
+^^^^^^^^^^^
+Description
+^^^^^^^^^^^
+
+Most CPAN pages have a short description under "NAME" and a longer
+description under "DESCRIPTION". Use whichever you think is more
+useful while still being succinct.
+
+^^^^^^^^
+Homepage
+^^^^^^^^
+
+In the top-right corner of the CPAN page, you'll find a "permalink"
+for the package. This should be used instead of the current URL, as
+it doesn't contain the version number and will always link to the
+latest release.
+
+^^^
+URL
+^^^
+
+If you haven't found it already, the download URL is on the right
+side of the page below the permalink. Search for "Download".
+
+^^^^^^^^^^^^^^^^^^^^^^^^^
+Build system dependencies
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Every ``PerlPackage`` obviously depends on Perl at build and run-time,
+so ``PerlPackage`` contains:
+
+.. code-block:: python
+
+   extends('perl')
+
+   depends_on('perl', type=('build', 'run'))
+
+
+If your package requires a specific version of Perl, you should
+specify this.
+
+Although newer versions of Perl include ``ExtUtils::MakeMaker`` and
+``Module::Build`` as "core" modules, you may want to add dependencies
+on ``perl-extutils-makemaker`` and ``perl-module-build`` anyway. Many
+people add Perl as an external package, and we want the build to work
+properly. If your package uses ``Makefile.PL`` to build, add:
+
+.. code-block:: python
+
+   depends_on('perl-extutils-makemaker', type='build')
+
+
+If your package uses ``Build.PL`` to build, add:
+
+.. code-block:: python
+
+   depends_on('perl-module-build', type='build')
+
+
+^^^^^^^^^^^^^^^^^
+Perl dependencies
+^^^^^^^^^^^^^^^^^
+
+Below the download URL, you will find a "Dependencies" link, which
+takes you to a page listing all of the dependencies of the package.
+Packages listed as "Core module" don't need to be added as dependencies,
+but all direct dependencies should be added. Don't add dependencies of
+dependencies. These should be added as dependencies to the dependency,
+not to your package.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Passing arguments to configure
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Packages that have non-Perl dependencies often use command-line
+variables to specify their installation directory. You can pass
+arguments to ``Makefile.PL`` or ``Build.PL`` by overriding
+``configure_args`` like so:
+
+.. code-block:: python
+
+   def configure_args(self):
+       expat = self.spec['expat'].prefix
+
+       return [
+           'EXPATLIBPATH={0}'.format(expat.lib),
+           'EXPATINCPATH={0}'.format(expat.include),
+       ]
+
+
+^^^^^^^^^^^^^^^^^^^^^
+Alternatives to Spack
+^^^^^^^^^^^^^^^^^^^^^
+
+If you need to maintain a stack of Perl modules for a user and don't
+want to add all of them to Spack, a good alternative is ``cpanm``.
+If Perl is already installed on your system, it should come with a
+``cpan`` executable. To install ``cpanm``, run the following command:
+
+.. code-block:: console
+
+   $ cpan App::cpanminus
+
+
+Now, you can install any Perl module you want by running:
+
+.. code-block:: console
+
+   $ cpanm Module::Name
+
+
+Obviously, these commands can only be run if you have root privileges.
+Furthermore, ``cpanm`` is not capable of installing non-Perl dependencies.
+If you need to install to your home directory or need to install a module
+with non-Perl dependencies, Spack is a better option.
+
+^^^^^^^^^^^^^^^^^^^^^^
+External documentation
+^^^^^^^^^^^^^^^^^^^^^^
+
+You can find more information on installing Perl modules from source
+at: http://www.perlmonks.org/?node_id=128077
+
+More generic Perl module installation instructions can be found at:
+http://www.cpan.org/modules/INSTALL.html
diff --git a/lib/spack/docs/build_systems/pythonpackage.rst b/lib/spack/docs/build_systems/pythonpackage.rst
new file mode 100644
index 0000000000..61aef00c50
--- /dev/null
+++ b/lib/spack/docs/build_systems/pythonpackage.rst
@@ -0,0 +1,747 @@
+.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+.. _pythonpackage:
+
+-------------
+PythonPackage
+-------------
+
+Python packages and modules have their own special build system.
+
+^^^^^^
+Phases
+^^^^^^
+
+The ``PythonPackage`` base class provides the following phases that
+can be overridden:
+
+* ``build``
+* ``build_py``
+* ``build_ext``
+* ``build_clib``
+* ``build_scripts``
+* ``clean``
+* ``install``
+* ``install_lib``
+* ``install_headers``
+* ``install_scripts``
+* ``install_data``
+* ``sdist``
+* ``register``
+* ``bdist``
+* ``bdist_dumb``
+* ``bdist_rpm``
+* ``bdist_wininst``
+* ``upload``
+* ``check``
+
+These are all standard ``setup.py`` commands and can be found by running:
+
+.. code-block:: console
+
+   $ python setup.py --help-commands
+
+
+By default, only the ``build`` and ``install`` phases are run:
+
+#. ``build`` - build everything needed to install
+#. ``install`` - install everything from build directory
+
+If for whatever reason you need to run more phases, simply modify your
+``phases`` list like so:
+
+.. code-block:: python
+
+   phases = ['build_ext', 'install', 'bdist']
+
+
+Each phase provides a function ``<phase>`` that runs:
+
+.. code-block:: console
+
+   $ python -s setup.py --no-user-cfg <phase>
+
+
+Each phase also has a ``<phase_args>`` function that can pass arguments to
+this call. All of these functions are empty except for the ``install_args``
+function, which passes ``--prefix=/path/to/installation/prefix``. There is
+also some additional logic specific to setuptools and eggs.
+
+If you need to run a phase that is not a standard ``setup.py`` command,
+you'll need to define a function for it like so:
+
+.. code-block:: python
+
+   phases = ['configure', 'build', 'install']
+
+   def configure(self, spec, prefix):
+       self.setup_py('configure')
+
+
+^^^^^^^^^^^^^^^
+Important files
+^^^^^^^^^^^^^^^
+
+Python packages can be identified by the presence of a ``setup.py`` file.
+This file is used by package managers like ``pip`` to determine a
+package's dependencies and the version of dependencies required, so if
+the ``setup.py`` file is not accurate, the package will not build properly.
+For this reason, the ``setup.py`` file should be fairly reliable. If the
+documentation and ``setup.py`` disagree on something, the ``setup.py``
+file should be considered to be the truth. As dependencies are added or
+removed, the documentation is much more likely to become outdated than
+the ``setup.py``.
+
+^^^^^^^^^^^^^^^^^^^^^^^
+Finding Python packages
+^^^^^^^^^^^^^^^^^^^^^^^
+
+The vast majority of Python packages are hosted on PyPI - The Python
+Package Index. ``pip`` only supports packages hosted on PyPI, making
+it the only option for developers who want a simple installation.
+Search for "PyPI <package-name>" to find the download page. Note that
+some pages are versioned, and the first result may not be the newest
+version. Click on the "Latest Version" button to the top right to see
+if a newer version is available. The download page is usually at:
+https://pypi.org/project/<package-name>
+
+^^^^^^^^^^^
+Description
+^^^^^^^^^^^
+
+The top of the PyPI downloads page contains a description of the
+package. The first line is usually a short description, while there
+may be a several line "Project Description" that follows. Choose whichever
+is more useful. You can also get these descriptions on the command-line
+using:
+
+.. code-block:: console
+
+   $ python setup.py --description
+   $ python setup.py --long-description
+
+
+^^^^^^^^
+Homepage
+^^^^^^^^
+
+Package developers use ``setup.py`` to upload new versions to PyPI.
+The ``setup`` method often passes metadata like ``homepage`` to PyPI.
+This metadata is displayed on the left side of the download page.
+Search for the text "Homepage" under "Project links" to find it. You
+should use this page instead of the PyPI page if they differ. You can
+also get the homepage on the command-line by running:
+
+.. code-block:: console
+
+   $ python setup.py --url
+
+
+^^^
+URL
+^^^
+
+You may have noticed that Spack allows you to add multiple versions of
+the same package without adding multiple versions of the download URL.
+It does this by guessing what the version string in the URL is and
+replacing this with the requested version. Obviously, if Spack cannot
+guess the version correctly, or if non-version-related things change
+in the URL, Spack cannot substitute the version properly.
+
+Once upon a time, PyPI offered nice, simple download URLs like:
+https://pypi.python.org/packages/source/n/numpy/numpy-1.13.1.zip
+
+As you can see, the version is 1.13.1. It probably isn't hard to guess
+what URL to use to download version 1.12.0, and Spack was perfectly
+capable of performing this calculation.
+
+However, PyPI switched to a new download URL format:
+https://pypi.python.org/packages/c0/3a/40967d9f5675fbb097ffec170f59c2ba19fc96373e73ad47c2cae9a30aed/numpy-1.13.1.zip#md5=2c3c0f4edf720c3a7b525dacc825b9ae
+
+and more recently:
+https://files.pythonhosted.org/packages/b0/2b/497c2bb7c660b2606d4a96e2035e92554429e139c6c71cdff67af66b58d2/numpy-1.14.3.zip
+
+As you can imagine, it is impossible for Spack to guess what URL to
+use to download version 1.12.0 given this URL. There is a solution,
+however. PyPI offers a new hidden interface for downloading
+Python packages that does not include a hash in the URL:
+https://pypi.io/packages/source/n/numpy/numpy-1.13.1.zip
+
+This URL redirects to the files.pythonhosted.org URL. The general syntax for
+this pypi.io URL is:
+https://pypi.io/packages/source/<first-letter-of-name>/<name>/<name>-<version>.<extension>
+
+Please use the pypi.io URL instead of the pypi.python.org URL. If both
+``.tar.gz`` and ``.zip`` versions are available, ``.tar.gz`` is preferred.
+If some releases offer both ``.tar.gz`` and ``.zip`` versions, but some
+only offer ``.zip`` versions, use ``.zip``.
+
+"""""""""""""""
+PyPI vs. GitHub
+"""""""""""""""
+
+Many packages are hosted on PyPI, but are developed on GitHub and other
+version control systems. The tarball can be downloaded from either
+location, but PyPI is preferred for the following reasons:
+
+#. PyPI contains the bare minimum of files to install the package.
+
+   You may notice that the tarball you download from PyPI does not
+   have the same checksum as the tarball you download from GitHub.
+   When a developer uploads a new release to PyPI, it doesn't contain
+   every file in the repository, only the files necessary to install
+   the package. PyPI tarballs are therefore smaller.
+
+#. PyPI is the official source for package managers like ``pip``.
+
+   Let's be honest, ``pip`` is much more popular than Spack. If the
+   GitHub tarball contains a file not present in the PyPI tarball that
+   causes a bug, the developers may not realize this for quite some
+   time. If the bug was in a file contained in the PyPI tarball, users
+   would notice the bug much more quickly.
+
+#. GitHub release may be a beta version.
+
+   When a developer releases a new version of a package on GitHub,
+   it may not be intended for most users. Until that release also
+   makes its way to PyPI, it should be assumed that the release is
+   not yet ready for general use.
+
+#. The checksum for a GitHub release may change.
+
+   Unfortunately, some developers have a habit of patching releases
+   without incrementing the version number. This results in a change
+   in tarball checksum. Package managers like Spack that use checksums
+   to verify the integrity of a download tarball grind to a halt when
+   the checksum for a known version changes. Most of the time, the
+   change is intentional, and contains a needed bug fix. However,
+   sometimes the change indicates a download source that has been
+   compromised, and a tarball that contains a virus. If this happens,
+   you must contact the developers to determine which is the case.
+   PyPI is nice because it makes it physically impossible to
+   re-release the same version of a package with a different checksum.
+
+There are some reasons to prefer downloading from GitHub:
+
+#. The GitHub tarball may contain unit tests
+
+   As previously mentioned, the PyPI tarball contains the bare minimum
+   of files to install the package. Unless explicitly specified by the
+   developers, it will not contain development files like unit tests.
+   If you desire to run the unit tests during installation, you should
+   use the GitHub tarball instead.
+
+#. Spack does not yet support ``spack versions`` and ``spack checksum``
+   with PyPI URLs
+
+   These commands work just fine with GitHub URLs. This is a minor
+   annoyance, not a reason to prefer GitHub over PyPI.
+
+If you really want to run these unit tests, no one will stop you from
+submitting a PR for a new package that downloads from GitHub.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^
+Build system dependencies
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+There are a few dependencies common to the ``PythonPackage`` build system.
+
+""""""
+Python
+""""""
+
+Obviously, every ``PythonPackage`` needs Python at build-time to run
+``python setup.py build && python setup.py install``. Python is also
+needed at run-time if you want to import the module. Due to backwards
+incompatible changes between Python 2 and 3, it is very important to
+specify which versions of Python are supported. If the documentation
+mentions that Python 3 is required, this can be specified as:
+
+.. code-block:: python
+
+   depends_on('python@3:', type=('build', 'run')
+
+
+If Python 2 is required, this would look like:
+
+.. code-block:: python
+
+   depends_on('python@:2', type=('build', 'run')
+
+
+If Python 2.7 is the only version that works, you can use:
+
+.. code-block:: python
+
+   depends_on('python@2.7:2.8', type=('build', 'run')
+
+
+The documentation may not always specify supported Python versions.
+Another place to check is in the ``setup.py`` file. Look for a line
+containing ``python_requires``. An example from
+`py-numpy <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/py-numpy/package.py>`_
+looks like:
+
+.. code-block:: python
+
+   python_requires='>=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*'
+
+
+More commonly, you will find a version check at the top of the file:
+
+.. code-block:: python
+
+   if sys.version_info[:2] < (2, 7) or (3, 0) <= sys.version_info[:2] < (3, 4):
+       raise RuntimeError("Python version 2.7 or >= 3.4 required.")
+
+
+This can be converted to Spack's spec notation like so:
+
+.. code-block:: python
+
+   depends_on('python@2.7:2.8,3.4:', type=('build', 'run'))
+
+
+""""""""""
+setuptools
+""""""""""
+
+Originally, the Python language had a single build system called
+distutils, which is built into Python. Distutils provided a common
+framework for package authors to describe their project and how it
+should be built. However, distutils was not without limitations.
+Most notably, there was no way to list a project's dependencies
+with distutils. Along came setuptools, a non-builtin build system
+designed to overcome the limitations of distutils. Both projects
+use a similar API, making the transition easy while adding much
+needed functionality. Today, setuptools is used in around 75% of
+the Python packages in Spack.
+
+Since setuptools isn't built-in to Python, you need to add it as a
+dependency. To determine whether or not a package uses setuptools,
+search the file for an import statement like:
+
+.. code-block:: python
+
+   import setuptools
+
+
+or:
+
+.. code-block:: python
+
+   from setuptools import setup
+
+
+Some packages are designed to work with both setuptools and distutils,
+so you may find something like:
+
+.. code-block:: python
+
+   try:
+       from setuptools import setup
+   except ImportError:
+       from distutils.core import setup
+
+
+This uses setuptools if available, and falls back to distutils if not.
+In this case, you would still want to add a setuptools dependency, as
+it offers us more control over the installation.
+
+Unless specified otherwise, setuptools is usually a build-only dependency.
+That is, it is needed to install the software, but is not needed at
+run-time. This can be specified as:
+
+.. code-block:: python
+
+   depends_on('py-setuptools', type='build')
+
+
+""""""
+cython
+""""""
+
+Compared to compiled languages, interpreted languages like Python can
+be quite a bit slower. To work around this, some Python developers
+rewrite computationally demanding sections of code in C, a process
+referred to as "cythonizing". In order to build these package, you
+need to add a build dependency on cython:
+
+.. code-block:: python
+
+   depends_on('py-cython', type='build')
+
+
+Look for references to "cython" in the ``setup.py`` to determine
+whether or not this is necessary. Cython may be optional, but
+even then you should list it as a required dependency. Spack is
+designed to compile software, and is meant for HPC facilities
+where speed is crucial. There is no reason why someone would not
+want an optimized version of a library instead of the pure-Python
+version.
+
+^^^^^^^^^^^^^^^^^^^
+Python dependencies
+^^^^^^^^^^^^^^^^^^^
+
+When you install a package with ``pip``, it reads the ``setup.py``
+file in order to determine the dependencies of the package.
+If the dependencies are not yet installed, ``pip`` downloads them
+and installs them for you. This may sound convenient, but Spack
+cannot rely on this behavior for two reasons:
+
+#. Spack needs to be able to install packages on air-gapped networks.
+
+   If there is no internet connection, ``pip`` can't download the
+   package dependencies. By explicitly listing every dependency in
+   the ``package.py``, Spack knows what to download ahead of time.
+
+#. Duplicate installations of the same dependency may occur.
+
+   Spack supports *activation* of Python extensions, which involves
+   symlinking the package installation prefix to the Python installation
+   prefix. If your package is missing a dependency, that dependency
+   will be installed to the installation directory of the same package.
+   If you try to activate the package + dependency, it may cause a
+   problem if that package has already been activated.
+
+For these reasons, you must always explicitly list all dependencies.
+Although the documentation may list the package's dependencies,
+often the developers assume people will use ``pip`` and won't have to
+worry about it. Always check the ``setup.py`` to find the true
+dependencies.
+
+If the package relies on ``distutils``, it may not explicitly list its
+dependencies. Check for statements like:
+
+.. code-block:: python
+
+   try:
+       import numpy
+   except ImportError:
+       raise ImportError("numpy must be installed prior to installation")
+
+
+Obviously, this means that ``py-numpy`` is a dependency.
+
+If the package uses ``setuptools``, check for the following clues:
+
+* ``install_requires``
+
+  These packages are required for installation.
+
+* ``extra_requires``
+
+  These packages are optional dependencies that enable additional
+  functionality. You should add a variant that optionally adds these
+  dependencies.
+
+* ``test_requires``
+
+  These are packages that are required to run the unit tests for the
+  package. These dependencies can be specified using the
+  ``type='test'`` dependency type.
+
+In the root directory of the package, you may notice a
+``requirements.txt`` file. It may look like this file contains a list
+of all of the package's dependencies. Don't be fooled. This file is
+used by tools like Travis to install the pre-requisites for the
+package... and a whole bunch of other things. It often contains
+dependencies only needed for unit tests, like:
+
+* mock
+* nose
+* pytest
+
+It can also contain dependencies for building the documentation, like
+sphinx. If you can't find any information about the package's
+dependencies, you can take a look in ``requirements.txt``, but be sure
+not to add test or documentation dependencies.
+
+""""""""""
+setuptools
+""""""""""
+
+Setuptools is a bit of a special case. If a package requires setuptools
+at run-time, how do they express this? They could add it to
+``install_requires``, but setuptools is imported long before this and
+needed to read this line. And since you can't install the package
+without setuptools, the developers assume that setuptools will already
+be there, so they never mention when it is required. We don't want to
+add run-time dependencies if they aren't needed, so you need to
+determine whether or not setuptools is needed. Grep the installation
+directory for any files containing a reference to ``setuptools`` or
+``pkg_resources``. Both modules come from ``py-setuptools``.
+``pkg_resources`` is particularly common in scripts in ``prefix/bin``.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Passing arguments to setup.py
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The default build and install phases should be sufficient to install
+most packages. However, you may want to pass additional flags to
+either phase.
+
+You can view the available options for a particular phase with:
+
+.. code-block:: console
+
+   $ python setup.py <phase> --help
+
+
+Each phase provides a ``<phase_args>`` function that can be used to
+pass arguments to that phase. For example,
+`py-numpy <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/py-numpy/package.py>`_
+adds:
+
+.. code-block:: python
+
+   def build_args(self, spec, prefix):
+       args = []
+
+       # From NumPy 1.10.0 on it's possible to do a parallel build.
+       if self.version >= Version('1.10.0'):
+           # But Parallel build in Python 3.5+ is broken.  See:
+           # https://github.com/spack/spack/issues/7927
+           # https://github.com/scipy/scipy/issues/7112
+           if spec['python'].version < Version('3.5'):
+               args = ['-j', str(make_jobs)]
+
+       return args
+
+
+^^^^^^^
+Testing
+^^^^^^^
+
+``PythonPackage`` provides a couple of options for testing packages.
+
+""""""""""""
+Import tests
+""""""""""""
+
+Just because a package successfully built does not mean that it built
+correctly. The most reliable test of whether or not the package was
+correctly installed is to attempt to import all of the modules that
+get installed. To get a list of modules, run the following command
+in the source directory:
+
+.. code-block:: console
+
+   $ python
+   >>> import setuptools
+   >>> setuptools.find_packages()
+   ['numpy', 'numpy._build_utils', 'numpy.compat', 'numpy.core', 'numpy.distutils', 'numpy.doc', 'numpy.f2py', 'numpy.fft', 'numpy.lib', 'numpy.linalg', 'numpy.ma', 'numpy.matrixlib', 'numpy.polynomial', 'numpy.random', 'numpy.testing', 'numpy.core.code_generators', 'numpy.distutils.command', 'numpy.distutils.fcompiler']
+
+
+Large, complex packages like ``numpy`` will return a long list of
+packages, while other packages like ``six`` will return an empty list.
+``py-six`` installs a single ``six.py`` file. In Python packaging lingo,
+a "package" is a directory containing files like:
+
+.. code-block:: none
+
+   foo/__init__.py
+   foo/bar.py
+   foo/baz.py
+
+
+whereas a "module" is a single Python file. Since ``find_packages``
+only returns packages, you'll have to determine the correct module
+names yourself. You can now add these packages and modules to the
+package like so:
+
+.. code-block:: python
+
+   import_modules = ['six']
+
+
+When you run ``spack install --test=root py-six``, Spack will attempt
+to import the ``six`` module after installation.
+
+These tests most often catch missing dependencies and non-RPATHed
+libraries. Make sure not to add modules/packages containing the word
+"test", as these likely won't end up in installation directory.
+
+""""""""""
+Unit tests
+""""""""""
+
+The package you want to install may come with additional unit tests.
+By default, Spack runs:
+
+.. code-block:: console
+
+   $ python setup.py test
+
+
+if it detects that the ``setup.py`` file supports a ``test`` phase.
+You can add additional build-time or install-time tests by overriding
+``test`` and ``installtest``, respectively. For example, ``py-numpy``
+adds:
+
+.. code-block:: python
+
+   def install_test(self):
+        with working_dir('..'):
+            python('-c', 'import numpy; numpy.test("full", verbose=2)')
+
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Setup file in a sub-directory
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+In order to be compatible with package managers like ``pip``, the package
+is required to place its ``setup.py`` in the root of the tarball. However,
+not every Python package cares about ``pip`` or PyPI. If you are installing
+a package that is not hosted on PyPI, you may find that it places its
+``setup.py`` in a sub-directory. To handle this, add the directory containing
+``setup.py`` to the package like so:
+
+.. code-block:: python
+
+   build_directory = 'source'
+
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Alternate names for setup.py
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+As previously mentioned, packages need to call their setup script ``setup.py``
+in order to be compatible with package managers like ``pip``. However, some
+packages like
+`py-meep <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/py-meep/package.py>`_  and
+`py-adios <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/py-adios/package.py>`_
+come with multiple setup scripts, one for a serial build and another for a
+parallel build. You can override the default name to use like so:
+
+.. code-block:: python
+
+   def setup_file(self):
+       return 'setup-mpi.py' if '+mpi' in self.spec else 'setup.py'
+
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+PythonPackage vs. packages that use Python
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+There are many packages that make use of Python, but packages that depend
+on Python are not necessarily ``PythonPackages``.
+
+"""""""""""""""""""""""
+Choosing a build system
+"""""""""""""""""""""""
+
+First of all, you need to select a build system. ``spack create`` usually
+does this for you, but if for whatever reason you need to do this manually,
+choose ``PythonPackage`` if and only if the package contains a ``setup.py``
+file.
+
+"""""""""""""""""""""""
+Choosing a package name
+"""""""""""""""""""""""
+
+Selecting the appropriate package name is a little more complicated
+than choosing the build system. By default, ``spack create`` will
+prepend ``py-`` to the beginning of the package name if it detects
+that the package uses the ``PythonPackage`` build system. However, there
+are occasionally packages that use ``PythonPackage`` that shouldn't
+start with ``py-``. For example:
+
+* busco
+* easybuild
+* httpie
+* mercurial
+* scons
+* snakemake
+
+The thing these packages have in common is that they are command-line
+tools that just so happen to be written in Python. Someone who wants
+to install ``mercurial`` with Spack isn't going to realize that it is
+written in Python, and they certainly aren't going to assume the package
+is called ``py-mercurial``. For this reason, we manually renamed the
+package to ``mercurial``.
+
+Likewise, there are occasionally packages that don't use the
+``PythonPackage`` build system but should still be prepended with ``py-``.
+For example:
+
+* py-genders
+* py-py2cairo
+* py-pygobject
+* py-pygtk
+* py-pyqt
+* py-pyserial
+* py-sip
+* py-xpyb
+
+These packages are primarily used as Python libraries, not as
+command-line tools. You may see C/C++ packages that have optional
+Python language-bindings, such as:
+
+* antlr
+* cantera
+* conduit
+* pagmo
+* vtk
+
+Don't prepend these kind of packages with ``py-``. When in doubt,
+think about how this package will be used. Is it primarily a Python
+library that will be imported in other Python scripts? Or is it a
+command-line tool, or C/C++/Fortran program with optional Python
+modules? The former should be prepended with ``py-``, while the
+latter should not.
+
+""""""""""""""""""""""
+extends vs. depends_on
+""""""""""""""""""""""
+
+This is very similar to the naming dilemma above, with a slight twist.
+As mentioned in the :ref:`Packaging Guide <packaging_extensions>`,
+``extends`` and ``depends_on`` are very similar, but ``extends`` adds
+the ability to *activate* the package. Activation involves symlinking
+everything in the installation prefix of the package to the installation
+prefix of Python. This allows the user to import a Python module without
+having to add that module to ``PYTHONPATH``.
+
+When deciding between ``extends`` and ``depends_on``, the best rule of
+thumb is to check the installation prefix. If Python libraries are
+installed to ``prefix/lib/python2.7/site-packages`` (where 2.7 is the
+MAJOR.MINOR version of Python you used to install the package), then
+you should use ``extends``. If Python libraries are installed elsewhere
+or the only files that get installed reside in ``prefix/bin``, then
+don't use ``extends``, as symlinking the package wouldn't be useful.
+
+^^^^^^^^^^^^^^^^^^^^^
+Alternatives to Spack
+^^^^^^^^^^^^^^^^^^^^^
+
+PyPI has hundreds of thousands of packages that are not yet in Spack,
+and ``pip`` may be a perfectly valid alternative to using Spack. The
+main advantage of Spack over ``pip`` is its ability to compile
+non-Python dependencies. It can also build cythonized versions of a
+package or link to an optimized BLAS/LAPACK library like MKL,
+resulting in calculations that run orders of magnitude faster.
+Spack does not offer a significant advantage to other python-management
+systems for installing and using tools like flake8 and sphinx.
+But if you need packages with non-Python dependencies like
+numpy and scipy, Spack will be very valuable to you.
+
+Anaconda is another great alternative to Spack, and comes with its own
+``conda`` package manager. Like Spack, Anaconda is capable of compiling
+non-Python dependencies. Anaconda contains many Python packages that
+are not yet in Spack, and Spack contains many Python packages that are
+not yet in Anaconda. The main advantage of Spack over Anaconda is its
+ability to choose a specific compiler and BLAS/LAPACK or MPI library.
+Spack also has better platform support for supercomputers. On the
+other hand, Anaconda offers Windows support.
+
+^^^^^^^^^^^^^^^^^^^^^^
+External documentation
+^^^^^^^^^^^^^^^^^^^^^^
+
+For more information on Python packaging, see:
+https://packaging.python.org/
diff --git a/lib/spack/docs/build_systems/qmakepackage.rst b/lib/spack/docs/build_systems/qmakepackage.rst
new file mode 100644
index 0000000000..f54b80f8d3
--- /dev/null
+++ b/lib/spack/docs/build_systems/qmakepackage.rst
@@ -0,0 +1,116 @@
+.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+.. _qmakepackage:
+
+------------
+QMakePackage
+------------
+
+Much like Autotools and CMake, QMake is a build-script generator
+designed by the developers of Qt. In its simplest form, Spack's
+``QMakePackage`` runs the following steps:
+
+.. code-block:: console
+
+   $ qmake
+   $ make
+   $ make check  # optional
+   $ make install
+
+
+QMake does not appear to have a standardized way of specifying
+the installation directory, so you may have to set environment
+variables or edit ``*.pro`` files to get things working properly.
+
+^^^^^^
+Phases
+^^^^^^
+
+The ``QMakePackage`` base class comes with the following phases:
+
+#. ``qmake`` - generate Makefiles
+#. ``build`` - build the project
+#. ``install`` - install the project
+
+By default, these phases run:
+
+.. code-block:: console
+
+   $ qmake
+   $ make
+   $ make install
+
+
+Any of these phases can be overridden in your package as necessary.
+There is also a ``check`` method that looks for a ``check`` target
+in the Makefile. If a ``check`` target exists and the user runs:
+
+.. code-block:: console
+
+   $ spack install --test=root <qmake-package>
+
+
+Spack will run ``make check`` after the build phase.
+
+^^^^^^^^^^^^^^^
+Important files
+^^^^^^^^^^^^^^^
+
+Packages that use the QMake build system can be identified by the
+presence of a ``<project-name>.pro`` file. This file declares things
+like build instructions and dependencies.
+
+One thing to look for is the ``minQtVersion`` function:
+
+.. code-block:: none
+
+   minQtVersion(5, 6, 0)
+
+
+This means that Qt 5.6.0 is the earliest release that will work.
+You should specify this in a ``depends_on`` statement.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^
+Build system dependencies
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+At the bare minimum, packages that use the QMake build system need a
+``qt`` dependency. Since this is always the case, the ``QMakePackage``
+base class already contains:
+
+.. code-block:: python
+
+   depends_on('qt', type='build')
+
+
+If you want to specify a particular version requirement, or need to
+link to the ``qt`` libraries, you can override this in your package:
+
+.. code-block:: python
+
+   depends_on('qt@5.6.0:')
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+Passing arguments to qmake
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+If you need to pass any arguments to the ``qmake`` call, you can
+override the ``qmake_args`` method like so:
+
+.. code-block:: python
+
+   def qmake_args(self):
+       return ['-recursive']
+
+
+This method can be used to pass flags as well as variables.
+
+^^^^^^^^^^^^^^^^^^^^^^
+External documentation
+^^^^^^^^^^^^^^^^^^^^^^
+
+For more information on the QMake build system, see:
+http://doc.qt.io/qt-5/qmake-manual.html
diff --git a/lib/spack/docs/build_systems/rpackage.rst b/lib/spack/docs/build_systems/rpackage.rst
new file mode 100644
index 0000000000..5e44b2135e
--- /dev/null
+++ b/lib/spack/docs/build_systems/rpackage.rst
@@ -0,0 +1,346 @@
+.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+.. _rpackage:
+
+--------
+RPackage
+--------
+
+Like Python, R has its own built-in build system.
+
+The R build system is remarkably uniform and well-tested.
+This makes it one of the easiest build systems to create
+new Spack packages for.
+
+^^^^^^
+Phases
+^^^^^^
+
+The ``RPackage`` base class has a single phase:
+
+#. ``install`` - install the package
+
+By default, this phase runs the following command:
+
+.. code-block:: console
+
+   $ R CMD INSTALL --library=/path/to/installation/prefix/rlib/R/library .
+
+
+^^^^^^^^^^^^^^^^^^
+Finding R packages
+^^^^^^^^^^^^^^^^^^
+
+The vast majority of R packages are hosted on CRAN - The Comprehensive
+R Archive Network. If you are looking for a particular R package, search
+for "CRAN <package-name>" and you should quickly find what you want.
+If it isn't on CRAN, try Bioconductor, another common R repository.
+
+For the purposes of this tutorial, we will be walking through
+`r-caret <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/r-caret/package.py>`_
+as an example. If you search for "CRAN caret", you will quickly find what
+you are looking for at https://cran.r-project.org/web/packages/caret/index.html.
+If you search for "Package source", you will find the download URL for
+the latest release. Use this URL with ``spack create`` to create a new
+package.
+
+^^^^^^^^^^^^
+Package name
+^^^^^^^^^^^^
+
+The first thing you'll notice is that Spack prepends ``r-`` to the front
+of the package name. This is how Spack separates R package extensions
+from the rest of the packages in Spack. Without this, we would end up
+with package name collisions more frequently than we would like. For
+instance, there are already packages for both:
+
+* ``ape`` and ``r-ape``
+* ``curl`` and ``r-curl``
+* ``gmp`` and ``r-gmp``
+* ``jpeg`` and ``r-jpeg``
+* ``openssl`` and ``r-openssl``
+* ``uuid`` and ``r-uuid``
+* ``xts`` and ``r-xts``
+
+Many popular programs written in C/C++ are later ported to R as a
+separate project.
+
+^^^^^^^^^^^
+Description
+^^^^^^^^^^^
+
+The first thing you'll need to add to your new package is a description.
+The top of the homepage for ``caret`` lists the following description:
+
+   caret: Classification and Regression Training
+
+   Misc functions for training and plotting classification and regression models.
+
+You can either use the short description (first line), long description
+(second line), or both depending on what you feel is most appropriate.
+
+^^^^^^^^
+Homepage
+^^^^^^^^
+
+If you look at the bottom of the page, you'll see:
+
+   Linking:
+
+   Please use the canonical form https://CRAN.R-project.org/package=caret to link to this page.
+
+Please uphold the wishes of the CRAN admins and use
+https://CRAN.R-project.org/package=caret as the homepage instead of
+https://cran.r-project.org/web/packages/caret/index.html. The latter may
+change without notice.
+
+^^^
+URL
+^^^
+
+As previously mentioned, the download URL for the latest release can be
+found by searching "Package source" on the homepage.
+
+^^^^^^^^
+List URL
+^^^^^^^^
+
+CRAN maintains a single webpage containing the latest release of every
+single package: https://cran.r-project.org/src/contrib/
+
+Of course, as soon as a new release comes out, the version you were using
+in your package is no longer available at that URL. It is moved to an
+archive directory. If you search for "Old sources", you will find:
+https://cran.r-project.org/src/contrib/Archive/caret
+
+If you only specify the URL for the latest release, your package will
+no longer be able to fetch that version as soon as a new release comes
+out. To get around this, add the archive directory as a ``list_url``.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^
+Build system dependencies
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+As an extension of the R ecosystem, your package will obviously depend
+on R to build and run. Normally, we would use ``depends_on`` to express
+this, but for R packages, we use ``extends``. ``extends`` is similar to
+``depends_on``, but adds an additional feature: the ability to "activate"
+the package by symlinking it to the R installation directory. Since
+every R package needs this, the ``RPackage`` base class contains:
+
+.. code-block:: python
+
+   extends('r')
+   depends_on('r', type=('build', 'run'))
+
+
+Take a close look at the homepage for ``caret``. If you look at the
+"Depends" section, you'll notice that ``caret`` depends on "R (≥ 2.10)".
+You should add this to your package like so:
+
+.. code-block:: python
+
+   depends_on('r@2.10:', type=('build', 'run'))
+
+
+^^^^^^^^^^^^^^
+R dependencies
+^^^^^^^^^^^^^^
+
+R packages are often small and follow the classic Unix philosophy
+of doing one thing well. They are modular and usually depend on
+several other packages. You may find a single package with over a
+hundred dependencies. Luckily, CRAN packages are well-documented
+and list all of their dependencies in the following sections:
+
+* Depends
+* Imports
+* LinkingTo
+
+As far as Spack is concerned, all 3 of these dependency types
+correspond to ``type=('build', 'run')``, so you don't have to worry
+about them. If you are curious what they mean,
+https://github.com/spack/spack/issues/2951 has a pretty good summary:
+
+   ``Depends`` is required and will cause those R packages to be *attached*,
+   that is, their APIs are exposed to the user. ``Imports`` *loads* packages
+   so that *the package* importing these packages can access their APIs,
+   while *not* being exposed to the user. When a user calls ``library(foo)``
+   s/he *attaches* package ``foo`` and all of the packages under ``Depends``.
+   Any function in one of these package can be called directly as ``bar()``.
+   If there are conflicts, user can also specify ``pkgA::bar()`` and
+   ``pkgB::bar()`` to distinguish between them. Historically, there was only
+   ``Depends`` and ``Suggests``, hence the confusing names. Today, maybe
+   ``Depends`` would have been named ``Attaches``.
+
+   The ``LinkingTo`` is not perfect and there was recently an extensive
+   discussion about API/ABI among other things on the R-devel mailing
+   list among very skilled R developers:
+
+   * https://stat.ethz.ch/pipermail/r-devel/2016-December/073505.html
+   * https://stat.ethz.ch/pipermail/r-devel/2017-January/073647.html
+
+Some packages also have a fourth section:
+
+* Suggests
+
+These are optional, rarely-used dependencies that a user might find
+useful. You should **NOT** add these dependencies to your package.
+R packages already have enough dependencies as it is, and adding
+optional dependencies can really slow down the concretization
+process. They can also introduce circular dependencies.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Core, recommended, and non-core packages
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+If you look at "Depends", "Imports", and "LinkingTo", you will notice
+3 different types of packages:
+
+"""""""""""""
+Core packages
+"""""""""""""
+
+If you look at the ``caret`` homepage, you'll notice a few dependencies
+that don't have a link to the package, like ``methods``, ``stats``, and
+``utils``. These packages are part of the core R distribution and are
+tied to the R version installed. You can basically consider these to be
+"R itself". These are so essential to R so it would not make sense that
+they could be updated via CRAN. If so, you would basically get a different
+version of R. Thus, they're updated when R is updated.
+
+You can find a list of these core libraries at:
+https://github.com/wch/r-source/tree/trunk/src/library
+
+""""""""""""""""""""
+Recommended packages
+""""""""""""""""""""
+
+When you install R, there is an option called ``--with-recommended-packages``.
+This flag causes the R installation to include a few "Recommended" packages
+(legacy term). They are for historical reasons quite tied to the core R
+distribution, developed by the R core team or people closely related to it.
+The R core distribution "knows" about these package, but they are indeed
+distributed via CRAN. Because they're distributed via CRAN, they can also be
+updated between R version releases.
+
+Spack explicitly adds the ``--without-recommended-packages`` flag to prevent
+the installation of these packages. Due to the way Spack handles package
+activation (symlinking packages to the R installation directory),
+pre-existing recommended packages will cause conflicts for already-existing
+files. We could either not include these recommended packages in Spack and
+require them to be installed through ``--with-recommended-packages``, or
+we could not install them with R and let users choose the version of the
+package they want to install. We chose the latter.
+
+Since these packages are so commonly distributed with the R system, many
+developers may assume these packages exist and fail to list them as
+dependencies. Watch out for this.
+
+You can find a list of these recommended packages at:
+https://github.com/wch/r-source/blob/trunk/share/make/vars.mk
+
+"""""""""""""""""
+Non-core packages
+"""""""""""""""""
+
+These are packages that are neither "core" nor "recommended". There are more
+than 10,000 of these packages hosted on CRAN alone.
+
+For each of these package types, if you see that a specific version is
+required, for example, "lattice (≥ 0.20)", please add this information to
+the dependency:
+
+.. code-block:: python
+
+   depends_on('r-lattice@0.20:', type=('build', 'run'))
+
+
+^^^^^^^^^^^^^^^^^^
+Non-R dependencies
+^^^^^^^^^^^^^^^^^^
+
+Some packages depend on non-R libraries for linking. Check out the
+`r-stringi <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/r-stringi/package.py>`_
+package for an example: https://CRAN.R-project.org/package=stringi.
+If you search for the text "SystemRequirements", you will see:
+
+   ICU4C (>= 52, optional)
+
+This is how non-R dependencies are listed. Make sure to add these
+dependencies. The default dependency type should suffice.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Passing arguments to the installation
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Some R packages provide additional flags that can be passed to
+``R CMD INSTALL``, often to locate non-R dependencies.
+`r-rmpi <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/r-rmpi/package.py>`_
+is an example of this, and flags for linking to an MPI library. To pass
+these to the installation command, you can override ``configure_args``
+like so:
+
+.. code-block:: python
+
+   def configure_args(self, spec, prefix):
+       mpi_name = spec['mpi'].name
+
+       # The type of MPI. Supported values are:
+       # OPENMPI, LAM, MPICH, MPICH2, or CRAY
+       if mpi_name == 'openmpi':
+           Rmpi_type = 'OPENMPI'
+       elif mpi_name == 'mpich':
+           Rmpi_type = 'MPICH2'
+       else:
+           raise InstallError('Unsupported MPI type')
+
+       return [
+           '--with-Rmpi-type={0}'.format(Rmpi_type),
+           '--with-mpi={0}'.format(spec['mpi'].prefix),
+       ]
+
+
+There is a similar ``configure_vars`` function that can be overridden
+to pass variables to the build.
+
+^^^^^^^^^^^^^^^^^^^^^
+Alternatives to Spack
+^^^^^^^^^^^^^^^^^^^^^
+
+CRAN hosts over 10,000 R packages, most of which are not in Spack. Many
+users may not need the advanced features of Spack, and may prefer to
+install R packages the normal way:
+
+.. code-block:: console
+
+   $ R
+   > install.packages("ggplot2")
+
+
+R will search CRAN for the ``ggplot2`` package and install all necessary
+dependencies for you. If you want to update all installed R packages to
+the latest release, you can use:
+
+.. code-block:: console
+
+   > update.packages(ask = FALSE)
+
+
+This works great for users who have internet access, but those on an
+air-gapped cluster will find it easier to let Spack build a download
+mirror and install these packages for you.
+
+Where Spack really shines is its ability to install non-R dependencies
+and link to them properly, something the R installation mechanism
+cannot handle.
+
+^^^^^^^^^^^^^^^^^^^^^^
+External documentation
+^^^^^^^^^^^^^^^^^^^^^^
+
+For more information on installing R packages, see:
+https://stat.ethz.ch/R-manual/R-devel/library/utils/html/INSTALL.html
diff --git a/lib/spack/docs/build_systems/rubypackage.rst b/lib/spack/docs/build_systems/rubypackage.rst
new file mode 100644
index 0000000000..70e23f6d50
--- /dev/null
+++ b/lib/spack/docs/build_systems/rubypackage.rst
@@ -0,0 +1,16 @@
+.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+.. _rubypackage:
+
+-----------
+RubyPackage
+-----------
+
+Like Perl, Python, and R, Ruby has its own build system for
+installing Ruby gems.
+
+This build system is a work-in-progress. See
+https://github.com/spack/spack/pull/3127 for more information.
diff --git a/lib/spack/docs/build_systems/sconspackage.rst b/lib/spack/docs/build_systems/sconspackage.rst
new file mode 100644
index 0000000000..d87702b9dc
--- /dev/null
+++ b/lib/spack/docs/build_systems/sconspackage.rst
@@ -0,0 +1,306 @@
+.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+.. _sconspackage:
+
+------------
+SConsPackage
+------------
+
+SCons is a general-purpose build system that does not rely on
+Makefiles to build software. SCons is written in Python, and handles
+all building and linking itself.
+
+As far as build systems go, SCons is very non-uniform. It provides a
+common framework for developers to write build scripts, but the build
+scripts themselves can vary drastically. Some developers add subcommands
+like:
+
+.. code-block:: console
+
+   $ scons clean
+   $ scons build
+   $ scons test
+   $ scons install
+
+
+Others don't add any subcommands. Some have configuration options that
+can be specified through variables on the command line. Others don't.
+
+^^^^^^
+Phases
+^^^^^^
+
+As previously mentioned, SCons allows developers to add subcommands like
+``build`` and ``install``, but by default, installation usually looks like:
+
+.. code-block:: console
+
+   $ scons
+   $ scons install
+
+
+To facilitate this, the ``SConsPackage`` base class provides the
+following phases:
+
+#. ``build`` - build the package
+#. ``install`` - install the package
+
+Package developers often add unit tests that can be invoked with
+``scons test`` or ``scons check``. Spack provides a ``test`` method
+to handle this. Since we don't know which one the package developer
+chose, the ``test`` method does nothing by default, but can be easily
+overridden like so:
+
+.. code-block:: python
+
+   def test(self):
+       scons('check')
+
+
+^^^^^^^^^^^^^^^
+Important files
+^^^^^^^^^^^^^^^
+
+SCons packages can be identified by their ``SConstruct`` files. These
+files handle everything from setting up subcommands and command-line
+options to linking and compiling.
+
+One thing to look for is the ``EnsureSConsVersion`` function:
+
+.. code-block:: none
+
+   EnsureSConsVersion(2, 3, 0)
+
+
+This means that SCons 2.3.0 is the earliest release that will work.
+You should specify this in a ``depends_on`` statement.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^
+Build system dependencies
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+At the bare minimum, packages that use the SCons build system need a
+``scons`` dependency. Since this is always the case, the ``SConsPackage``
+base class already contains:
+
+.. code-block:: python
+
+   depends_on('scons', type='build')
+
+
+If you want to specify a particular version requirement, you can override
+this in your package:
+
+.. code-block:: python
+
+   depends_on('scons@2.3.0:', type='build')
+
+
+^^^^^^^^^^^^^^^^^^^^^^^^^
+Finding available options
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The first place to start when looking for a list of valid options to
+build a package is ``scons --help``. Some packages like
+`kahip <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/kahip/package.py>`_
+don't bother overwriting the default SCons help message, so this isn't
+very useful, but other packages like
+`serf <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/serf/package.py>`_
+print a list of valid command-line variables:
+
+.. code-block:: console
+
+   $ scons --help
+   scons: Reading SConscript files ...
+   Checking for GNU-compatible C compiler...yes
+   scons: done reading SConscript files.
+
+   PREFIX: Directory to install under ( /path/to/PREFIX )
+       default: /usr/local
+       actual: /usr/local
+
+   LIBDIR: Directory to install architecture dependent libraries under ( /path/to/LIBDIR )
+       default: $PREFIX/lib
+       actual: /usr/local/lib
+
+   APR: Path to apr-1-config, or to APR's install area ( /path/to/APR )
+       default: /usr
+       actual: /usr
+
+   APU: Path to apu-1-config, or to APR's install area ( /path/to/APU )
+       default: /usr
+       actual: /usr
+
+   OPENSSL: Path to OpenSSL's install area ( /path/to/OPENSSL )
+       default: /usr
+       actual: /usr
+
+   ZLIB: Path to zlib's install area ( /path/to/ZLIB )
+       default: /usr
+       actual: /usr
+
+   GSSAPI: Path to GSSAPI's install area ( /path/to/GSSAPI )
+       default: None
+       actual: None
+
+   DEBUG: Enable debugging info and strict compile warnings (yes|no)
+       default: False
+       actual: False
+
+   APR_STATIC: Enable using a static compiled APR (yes|no)
+       default: False
+       actual: False
+
+   CC: Command name or path of the C compiler
+       default: None
+       actual: gcc
+
+   CFLAGS: Extra flags for the C compiler (space-separated)
+       default: None
+       actual:
+
+   LIBS: Extra libraries passed to the linker, e.g. "-l<library1> -l<library2>" (space separated)
+       default: None
+       actual: None
+
+   LINKFLAGS: Extra flags for the linker (space-separated)
+       default: None
+       actual:
+
+   CPPFLAGS: Extra flags for the C preprocessor (space separated)
+       default: None
+       actual: None
+
+   Use scons -H for help about command-line options.
+
+
+More advanced packages like
+`cantera <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/cantera/package.py>`_
+use ``scons --help`` to print a list of subcommands:
+
+.. code-block:: console
+
+   $ scons --help
+   scons: Reading SConscript files ...
+
+   SCons build script for Cantera
+
+   Basic usage:
+       'scons help' - print a description of user-specifiable options.
+
+       'scons build' - Compile Cantera and the language interfaces using
+                       default options.
+
+       'scons clean' - Delete files created while building Cantera.
+
+       '[sudo] scons install' - Install Cantera.
+
+       '[sudo] scons uninstall' - Uninstall Cantera.
+
+       'scons test' - Run all tests which did not previously pass or for which the
+                      results may have changed.
+
+       'scons test-reset' - Reset the passing status of all tests.
+
+       'scons test-clean' - Delete files created while running the tests.
+
+       'scons test-help' - List available tests.
+
+       'scons test-NAME' - Run the test named "NAME".
+
+       'scons <command> dump' - Dump the state of the SCons environment to the
+                                screen instead of doing <command>, e.g.
+                                'scons build dump'. For debugging purposes.
+
+       'scons samples' - Compile the C++ and Fortran samples.
+
+       'scons msi' - Build a Windows installer (.msi) for Cantera.
+
+       'scons sphinx' - Build the Sphinx documentation
+
+       'scons doxygen' - Build the Doxygen documentation
+
+
+You'll notice that cantera provides a ``scons help`` subcommand. Running
+``scons help`` prints a list of valid command-line variables.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+Passing arguments to scons
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Now that you know what arguments the project accepts, you can add them to
+the package build phase. This is done by overriding ``build_args`` like so:
+
+.. code-block:: python
+
+   def build_args(self, spec, prefix):
+       args = [
+         'PREFIX={0}'.format(prefix),
+         'ZLIB={0}'.format(spec['zlib'].prefix),
+       ]
+
+       if '+debug' in spec:
+           args.append('DEBUG=yes')
+       else:
+           args.append('DEBUG=no')
+
+       return args
+
+
+``SConsPackage`` also provides an ``install_args`` function that you can
+override to pass additional arguments to ``scons install``.
+
+^^^^^^^^^^^^^^^^^
+Compiler wrappers
+^^^^^^^^^^^^^^^^^
+
+By default, SCons builds all packages in a separate execution environment,
+and doesn't pass any environment variables from the user environment.
+Even changes to ``PATH`` are not propagated unless the package developer
+does so.
+
+This is particularly troublesome for Spack's compiler wrappers, which depend
+on environment variables to manage dependencies and linking flags. In many
+cases, SCons packages are not compatible with Spack's compiler wrappers,
+and linking must be done manually.
+
+First of all, check the list of valid options for anything relating to
+environment variables. For example, cantera has the following option:
+
+.. code-block:: none
+
+   * env_vars: [ string ]
+       Environment variables to propagate through to SCons. Either the
+       string "all" or a comma separated list of variable names, e.g.
+       'LD_LIBRARY_PATH,HOME'.
+       - default: 'LD_LIBRARY_PATH,PYTHONPATH'
+
+
+In the case of cantera, using ``env_vars=all`` allows us to use
+Spack's compiler wrappers. If you don't see an option related to
+environment variables, try using Spack's compiler wrappers by passing
+``spack_cc``, ``spack_cxx``, and ``spack_fc`` via the ``CC``, ``CXX``,
+and ``FC`` arguments, respectively. If you pass them to the build and
+you see an error message like:
+
+.. code-block:: none
+
+   Spack compiler must be run from Spack! Input 'SPACK_PREFIX' is missing.
+
+
+you'll know that the package isn't compatible with Spack's compiler
+wrappers. In this case, you'll have to use the path to the actual
+compilers, which are stored in ``self.compiler.cc`` and friends.
+Note that this may involve passing additional flags to the build to
+locate dependencies, a task normally done by the compiler wrappers.
+serf is an example of a package with this limitation.
+
+^^^^^^^^^^^^^^^^^^^^^^
+External documentation
+^^^^^^^^^^^^^^^^^^^^^^
+
+For more information on the SCons build system, see:
+http://scons.org/documentation.html
diff --git a/lib/spack/docs/build_systems/wafpackage.rst b/lib/spack/docs/build_systems/wafpackage.rst
new file mode 100644
index 0000000000..10a458f59e
--- /dev/null
+++ b/lib/spack/docs/build_systems/wafpackage.rst
@@ -0,0 +1,129 @@
+.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+.. _wafpackage:
+
+----------
+WafPackage
+----------
+
+Like SCons, Waf is a general-purpose build system that does not rely
+on Makefiles to build software.
+
+^^^^^^
+Phases
+^^^^^^
+
+The ``WafPackage`` base class comes with the following phases:
+
+#. ``configure`` - configure the project
+#. ``build`` - build the project
+#. ``install`` - install the project
+
+By default, these phases run:
+
+.. code-block:: console
+
+   $ python waf configure --prefix=/path/to/installation/prefix
+   $ python waf build
+   $ python waf install
+
+
+Each of these are standard Waf commands and can be found by running:
+
+.. code-block:: console
+
+   $ python waf --help
+
+
+Each phase provides a ``<phase>`` function that runs:
+
+.. code-block:: console
+
+   $ python waf -j<jobs> <phase>
+
+
+where ``<jobs>`` is the number of parallel jobs to build with. Each phase
+also has a ``<phase_args>`` function that can pass arguments to this call.
+All of these functions are empty except for the ``configure_args``
+function, which passes ``--prefix=/path/to/installation/prefix``.
+
+^^^^^^^
+Testing
+^^^^^^^
+
+``WafPackage`` also provides ``test`` and ``installtest`` methods,
+which are run after the ``build`` and ``install`` phases, respectively.
+By default, these phases do nothing, but you can override them to
+run package-specific unit tests. For example, the
+`py-py2cairo <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/py-py2cairo/package.py>`_
+package uses:
+
+.. code-block:: python
+
+   def installtest(self):
+       with working_dir('test'):
+           pytest = which('py.test')
+           pytest()
+
+
+^^^^^^^^^^^^^^^
+Important files
+^^^^^^^^^^^^^^^
+
+Each Waf package comes with a custom ``waf`` build script, written in
+Python. This script contains instructions to build the project.
+
+The package also comes with a ``wscript`` file. This file is used to
+override the default ``configure``, ``build``, and ``install`` phases
+to customize the Waf project. It also allows developers to override
+the default ``./waf --help`` message. Check this file to find useful
+information about dependencies and the minimum versions that are
+supported.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^
+Build system dependencies
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+``WafPackage`` does not require ``waf`` to build. ``waf`` is only
+needed to create the ``./waf`` script. Since ``./waf`` is a Python
+script, Python is needed to build the project. ``WafPackage`` adds
+the following dependency automatically:
+
+.. code-block:: python
+
+   depends_on('python@2.5:', type='build')
+
+
+Waf only supports Python 2.5 and up.
+
+^^^^^^^^^^^^^^^^^^^^^^^^
+Passing arguments to waf
+^^^^^^^^^^^^^^^^^^^^^^^^
+
+As previously mentioned, each phase comes with a ``<phase_args>``
+function that can be used to pass arguments to that particular
+phase. For example, if you need to pass arguments to the build
+phase, you can use:
+
+.. code-block:: python
+
+   def build_args(self, spec, prefix):
+       args = []
+
+       if self.run_tests:
+           args.append('--test')
+
+       return args
+
+
+A list of valid options can be found by running ``./waf --help``.
+
+^^^^^^^^^^^^^^^^^^^^^^
+External documentation
+^^^^^^^^^^^^^^^^^^^^^^
+
+For more information on the Waf build system, see:
+https://waf.io/book/
diff --git a/lib/spack/docs/command_index.in b/lib/spack/docs/command_index.in
index 6520352b42..7f1f35c744 100644
--- a/lib/spack/docs/command_index.in
+++ b/lib/spack/docs/command_index.in
@@ -1,9 +1,9 @@
-=============
-Command Index
-=============
+=================
+Command Reference
+=================
 
-This is an alphabetical list of commands with links to the places they
-appear in the documentation.
+This is a reference for all commands in the Spack command line interface.
+The same information is available through :ref:`spack-help`.
 
-.. hlist::
-   :columns: 3
+Commands that also have sections in the main documentation have a link to
+"More documentation".
diff --git a/lib/spack/docs/conf.py b/lib/spack/docs/conf.py
index 94d301f6d9..5212b4cc30 100644
--- a/lib/spack/docs/conf.py
+++ b/lib/spack/docs/conf.py
@@ -1,28 +1,9 @@
-# flake8: noqa
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+# flake8: noqa
 # -*- coding: utf-8 -*-
 #
 # Spack documentation build configuration file, created by
@@ -42,7 +23,13 @@ import re
 import shutil
 import subprocess
 from glob import glob
-from sphinx.apidoc import main as sphinx_apidoc
+
+# Since Sphinx 1.7, sphinx.apidoc has been moved to sphinx.ext.apidoc
+# sphinx.apidoc is deprecated and will be removed in Sphinx 2.0
+try:
+    from sphinx.ext.apidoc import main as sphinx_apidoc
+except ImportError:
+    from sphinx.apidoc import main as sphinx_apidoc
 
 # -- Spack customizations -----------------------------------------------------
 
@@ -68,26 +55,32 @@ os.environ['COLIFY_SIZE'] = '25x120'
 #
 # Generate package list using spack command
 #
-with open('package_list.rst', 'w') as plist_file:
+with open('package_list.html', 'w') as plist_file:
     subprocess.Popen(
-        [spack_root + '/bin/spack', 'list', '--format=rst'], stdout=plist_file)
+        [spack_root + '/bin/spack', 'list', '--format=html'],
+        stdout=plist_file)
 
 #
 # Find all the `cmd-spack-*` references and add them to a command index
 #
-command_names = []
+import spack
+import spack.cmd
+command_names = spack.cmd.all_commands()
+documented_commands = set()
 for filename in glob('*rst'):
     with open(filename) as f:
         for line in f:
-            match = re.match('.. _(cmd-spack-.*):', line)
+            match = re.match('.. _cmd-(spack-.*):', line)
             if match:
-                command_names.append(match.group(1).strip())
+                documented_commands.add(match.group(1).strip())
 
+os.environ['COLUMNS'] = '120'
 shutil.copy('command_index.in', 'command_index.rst')
 with open('command_index.rst', 'a') as index:
-    index.write('\n')
-    for cmd in sorted(command_names):
-        index.write('   * :ref:`%s`\n' % cmd)
+    subprocess.Popen(
+        [spack_root + '/bin/spack', 'commands', '--format=rst'] + list(
+            documented_commands),
+        stdout=index)
 
 #
 # Run sphinx-apidoc
@@ -105,28 +98,6 @@ apidoc_args = [
 sphinx_apidoc(apidoc_args + ['../spack'])
 sphinx_apidoc(apidoc_args + ['../llnl'])
 
-#
-# Exclude everything in spack.__all__ from indexing.  All of these
-# symbols are imported from elsewhere in spack; their inclusion in
-# __all__ simply allows package authors to use `from spack import *`.
-# Excluding them ensures they're only documented in their "real" module.
-#
-# This also avoids issues where some of these symbols shadow core spack
-# modules.  Sphinx will complain about duplicate docs when this happens.
-#
-import fileinput, spack
-handling_spack = False
-for line in fileinput.input('spack.rst', inplace=1):
-    if handling_spack:
-        if not line.startswith('    :noindex:'):
-            print('    :noindex: %s' % ' '.join(spack.__all__))
-        handling_spack = False
-
-    if line.startswith('.. automodule::'):
-        handling_spack = (line == '.. automodule:: spack\n')
-
-    sys.stdout.write(line)
-
 # Enable todo items
 todo_include_todos = True
 
@@ -180,16 +151,16 @@ master_doc = 'index'
 
 # General information about the project.
 project = u'Spack'
-copyright = u'2013-2017, Lawrence Livermore National Laboratory.'
+copyright = u'2013-2018, Lawrence Livermore National Laboratory.'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = str(spack.spack_version.up_to(2))
+version = '.'.join(str(s) for s in spack.spack_version_info[:2])
 # The full version, including alpha/beta/rc tags.
-release = str(spack.spack_version.up_to(2))
+release = spack.spack_version
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -238,7 +209,7 @@ html_theme = 'sphinx_rtd_theme'
 html_theme_options = { 'logo_only' : True }
 
 # Add any paths that contain custom themes here, relative to this directory.
-html_theme_path = ["_themes"]
+# html_theme_path = ["_themes"]
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
diff --git a/lib/spack/docs/config_yaml.rst b/lib/spack/docs/config_yaml.rst
index da760f05e3..c02929d8c1 100644
--- a/lib/spack/docs/config_yaml.rst
+++ b/lib/spack/docs/config_yaml.rst
@@ -1,8 +1,13 @@
+.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 .. _config-yaml:
 
-====================================
-Basic settings in ``config.yaml``
-====================================
+==============
+Basic Settings
+==============
 
 Spack's basic configuration options are set in ``config.yaml``.  You can
 see the default settings by looking at
@@ -79,8 +84,8 @@ See :ref:`modules` for details.
 --------------------
 
 Spack is designed to run out of a user home directory, and on many
-systems the home directory is a (slow) network filesystem.  On most systems,
-building in a temporary filesystem results in faster builds than building
+systems the home directory is a (slow) network file system.  On most systems,
+building in a temporary file system results in faster builds than building
 in the home directory.  Usually, there is also more space available in
 the temporary location than in the home directory. So, Spack tries to
 create build stages in temporary space.
@@ -151,6 +156,17 @@ to ``false`` to disable these checks.  Disabling this can expose you to
 attacks.  Use at your own risk.
 
 --------------------
+``locks``
+--------------------
+
+When set to ``true``, concurrent instances of Spack will use locks to
+avoid modifying the install tree, database file, etc. If false, Spack
+will disable all locking, but you must **not** run concurrent instances
+of Spack.  For file systems that don't support locking, you should set
+this to ``false`` and run one Spack at a time, but otherwise we recommend
+enabling locks.
+
+--------------------
 ``dirty``
 --------------------
 
@@ -180,3 +196,22 @@ to 4, for example, commands like ``spack install`` will run ``make -j4``
 instead of hogging every core.
 
 To build all software in serial, set ``build_jobs`` to 1.
+
+--------------------
+``ccache``
+--------------------
+
+When set to ``true`` Spack will use ccache to cache compiles. This is
+useful specifically in two cases: (1) when using ``spack setup``, and (2)
+when building the same package with many different variants. The default is
+``false``.
+
+When enabled, Spack will look inside your ``PATH`` for a ``ccache``
+executable and stop if it is not found. Some systems come with
+``ccache``, but it can also be installed using ``spack install
+ccache``. ``ccache`` comes with reasonable defaults for cache size
+and location. (See the *Configuration settings* section of ``man
+ccache`` to learn more about the default settings and how to change
+them). Please note that we currently disable ccache's ``hash_dir``
+feature to avoid an issue with the stage directory (see
+https://github.com/LLNL/spack/pull/3761#issuecomment-294352232).
diff --git a/lib/spack/docs/configuration.rst b/lib/spack/docs/configuration.rst
index f1648eb4e0..2ff1987ba8 100644
--- a/lib/spack/docs/configuration.rst
+++ b/lib/spack/docs/configuration.rst
@@ -1,8 +1,13 @@
+.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 .. _configuration:
 
-==============================
-Configuration Files in Spack
-==============================
+===================
+Configuration Files
+===================
 
 Spack has many configuration files.  Here is a quick list of them, in
 case you want to skip directly to specific docs:
@@ -14,9 +19,9 @@ case you want to skip directly to specific docs:
 * :ref:`packages.yaml <build-settings>`
 * :ref:`repos.yaml <repositories>`
 
--------------------------
+-----------
 YAML Format
--------------------------
+-----------
 
 Spack configuration files are written in YAML.  We chose YAML because
 it's human readable, but also versatile in that it supports dictionaries,
@@ -29,44 +34,52 @@ Here is an example ``config.yaml`` file:
    config:
      install_tree: $spack/opt/spack
      module_roots:
-       lmod:   $spack/share/spack/lmod
+       lmod: $spack/share/spack/lmod
      build_stage:
        - $tempdir
        - /nfs/tmp2/$user
 
-Each spack configuration files is nested under a top-level section
+Each Spack configuration file is nested under a top-level section
 corresponding to its name. So, ``config.yaml`` starts with ``config:``,
-and ``mirrors.yaml`` starts with ``mirrors:``, etc.
+``mirrors.yaml`` starts with ``mirrors:``, etc.
 
 .. _configuration-scopes:
 
--------------------------
+--------------------
 Configuration Scopes
--------------------------
+--------------------
 
 Spack pulls configuration data from files in several directories. There
-are four configuration scopes.  From lowest to highest:
+are six configuration scopes. From lowest to highest:
 
 #. **defaults**: Stored in ``$(prefix)/etc/spack/defaults/``. These are
    the "factory" settings. Users should generally not modify the settings
    here, but should override them in other configuration scopes. The
    defaults here will change from version to version of Spack.
 
-#. **system**: Stored in ``/etc/spack``. These are settings for this
+#. **system**: Stored in ``/etc/spack/``. These are settings for this
    machine, or for all machines on which this file system is
    mounted. The site scope can be used for settings idiosyncratic to a
    particular machine, such as the locations of compilers or external
    packages. These settings are presumably controlled by someone with
-   root access on the machine.
+   root access on the machine. They override the defaults scope.
 
-#. **site**: Stored in ``$(prefix)/etc/spack/``.  Settings here affect
-   only *this instance* of Spack, and they override defaults.  The site
-   scope can can be used for per-project settings (one spack instance per
-   project) or for site-wide settings on a multi-user machine (e.g., for
-   a common spack instance).
+#. **site**: Stored in ``$(prefix)/etc/spack/``. Settings here affect
+   only *this instance* of Spack, and they override the defaults and system
+   scopes.  The site scope can can be used for per-project settings (one
+   Spack instance per project) or for site-wide settings on a multi-user
+   machine (e.g., for a common Spack instance).
 
 #. **user**: Stored in the home directory: ``~/.spack/``. These settings
-   affect all instances of Spack and take the highest precedence.
+   affect all instances of Spack and take higher precedence than site,
+   system, or defaults scopes.
+
+#. **custom**: Stored in a custom directory specified by ``--config-scope``.
+   If multiple scopes are listed on the command line, they are ordered
+   from lowest to highest precedence.
+
+#. **command line**: Build settings specified on the command line take
+   precedence over all other scopes.
 
 Each configuration directory may contain several configuration files,
 such as ``config.yaml``, ``compilers.yaml``, or ``mirrors.yaml``.  When
@@ -75,76 +88,175 @@ lower-precedence settings.
 
 Commands that modify scopes (e.g., ``spack compilers``, ``spack repo``,
 etc.) take a ``--scope=<name>`` parameter that you can use to control
-which scope is modified.  By default they modify the highest-precedence
+which scope is modified.  By default, they modify the highest-precedence
 scope.
 
+.. _custom-scopes:
+
+^^^^^^^^^^^^^
+Custom scopes
+^^^^^^^^^^^^^
+
+In addition to the ``defaults``, ``system``, ``site``, and ``user``
+scopes, you may add configuration scopes directly on the command
+line with the ``--config-scope`` argument, or ``-C`` for short.
+
+For example, the following adds two configuration scopes, named
+``scopea`` and ``scopeb``, to a ``spack spec`` command:
+
+.. code-block:: console
+
+   $ spack -C ~/myscopes/scopea -C ~/myscopes/scopeb spec ncurses
+
+Custom scopes come *after* the ``spack`` command and *before* the
+subcommand, and they specify a single path to a directory full of
+configuration files. You can add the same configuration files to that
+directory that you can add to any other scope (``config.yaml``,
+``packages.yaml``, etc.).
+
+If multiple scopes are provided:
+
+#. Each must be preceded with the ``--config-scope`` or ``-C`` flag.
+#. They must be ordered from lowest to highest precedence.
+
+"""""""""""""""""""""""""""""""""""""""""""
+Example: scopes for release and development
+"""""""""""""""""""""""""""""""""""""""""""
+
+Suppose that you need to support simultaneous building of release and
+development versions of ``mypackage``, where ``mypackage`` -> ``A`` -> ``B``.
+You could create The following files:
+
+.. code-block:: yaml
+   :caption: ~/myscopes/release/packages.yaml
+
+   packages:
+       mypackage:
+           version: [1.7]
+       A:
+           version: [2.3]
+       B:
+           version: [0.8]
+
+.. code-block:: yaml
+   :caption: ~/myscopes/develop/packages.yaml
+
+   packages:
+       mypackage:
+           version: [develop]
+       A:
+           version: [develop]
+       B:
+           version: [develop]
+
+You can switch between ``release`` and ``develop`` configurations using
+configuration arguments.  You would type ``spack -C ~/myscopes/release``
+when you want to build the designated release versions of ``mypackage``,
+``A``, and ``B``, and you would type ``spack -C ~/myscopes/develop`` when
+you want to build all of these packages at the ``develop`` version.
+
+"""""""""""""""""""""""""""""""
+Example: swapping MPI providers
+"""""""""""""""""""""""""""""""
+
+Suppose that you need to build two software packages, ``packagea`` and
+``packageb``. ``packagea`` is Python 2-based and ``packageb`` is Python
+3-based. ``packagea`` only builds with OpenMPI and ``packageb`` only builds
+with MPICH. You can create different configuration scopes for use with
+``packagea`` and ``packageb``:
+
+.. code-block:: yaml
+   :caption: ~/myscopes/packgea/packages.yaml
+
+   packages:
+       python:
+           version: [2.7.11]
+       all:
+           providers:
+               mpi: [openmpi]
+
+.. code-block:: yaml
+   :caption: ~/myscopes/packageb/packages.yaml
+
+   packages:
+       python:
+           version: [3.5.2]
+       all:
+           providers:
+               mpi: [mpich]
+
+
 .. _platform-scopes:
 
--------------------------
-Platform-specific scopes
--------------------------
-
-For each scope above, there can *also* be platform-specific settings.
-For example, on Blue Gene/Q machines, Spack needs to know the location
-of cross-compilers for the compute nodes.  This configuration is in
-``etc/spack/defaults/bgq/compilers.yaml``.  It will take precedence
-over settings in the ``defaults`` scope, but can still be overridden
-by settings in ``system``, ``system/bgq``, ``site``, ``site/bgq``,
-``user``, or ``user/bgq``. So, the full scope precedence is:
-
-1. ``defaults``
-2. ``defaults/<platform>``
-3. ``system``
-4. ``system/<platform>``
-5. ``site``
-6. ``site/<platform>``
-7. ``user``
-8. ``user/<platform>``
+------------------------
+Platform-specific Scopes
+------------------------
+
+For each scope above, there can also be platform-specific settings.
+For example, on most platforms, GCC is the preferred compiler.
+However, on macOS (darwin), Clang often works for more packages,
+and is set as the default compiler. This configuration is set in
+``$(prefix)/etc/spack/defaults/darwin/packages.yaml``. It will take
+precedence over settings in the ``defaults`` scope, but can still be
+overridden by settings in ``system``, ``system/darwin``, ``site``,
+``site/darwin``, ``user``, ``user/darwin``, ``custom``, or
+``custom/darwin``. So, the full scope precedence is:
+
+#. ``defaults``
+#. ``defaults/<platform>``
+#. ``system``
+#. ``system/<platform>``
+#. ``site``
+#. ``site/<platform>``
+#. ``user``
+#. ``user/<platform>``
+#. ``custom``
+#. ``custom/<platform>``
 
 You can get the name to use for ``<platform>`` by running ``spack arch
 --platform``. The system config scope has a ``<platform>`` section for
 sites at which ``/etc`` is mounted on multiple heterogeneous machines.
 
--------------------------
-Scope precedence
--------------------------
+----------------
+Scope Precedence
+----------------
 
 When spack queries for configuration parameters, it searches in
-higher-precedence scopes first.  So, settings in a higher-precedence file
-can override those with the same key in a lower-precedence one.  For
+higher-precedence scopes first. So, settings in a higher-precedence file
+can override those with the same key in a lower-precedence one. For
 list-valued settings, Spack *prepends* higher-precedence settings to
 lower-precedence settings. Completely ignoring higher-level configuration
 options is supported with the ``::`` notation for keys (see
 :ref:`config-overrides` below).
 
-^^^^^^^^^^^^^^^^^^^^^^^^
+^^^^^^^^^^^
 Simple keys
-^^^^^^^^^^^^^^^^^^^^^^^^
+^^^^^^^^^^^
 
-Let's look at an example of overriding a single key in a Spack file.  If
+Let's look at an example of overriding a single key in a Spack file. If
 your configurations look like this:
 
-**defaults** scope:
-
 .. code-block:: yaml
+   :caption: $(prefix)/etc/spack/defaults/config.yaml
 
    config:
      install_tree: $spack/opt/spack
      module_roots:
-       lmod:   $spack/share/spack/lmod
+       lmod: $spack/share/spack/lmod
      build_stage:
        - $tempdir
        - /nfs/tmp2/$user
 
-**site** scope:
 
 .. code-block:: yaml
+   :caption: ~/.spack/config.yaml
 
    config:
      install_tree: /some/other/directory
 
+
 Spack will only override ``install_tree`` in the ``config`` section, and
-will take the site preferences for other settings.  You can see the
+will take the site preferences for other settings. You can see the
 final, combined configuration with the ``spack config get <configtype>``
 command:
 
@@ -155,11 +267,11 @@ command:
    config:
      install_tree: /some/other/directory
      module_roots:
-       lmod:   $spack/share/spack/lmod
+       lmod: $spack/share/spack/lmod
      build_stage:
        - $tempdir
        - /nfs/tmp2/$user
-   $ _
+
 
 .. _config-overrides:
 
@@ -167,14 +279,14 @@ command:
 Overriding entire sections
 ^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Above, the site ``config.yaml`` only overrides specific settings in the
-default ``config.yaml``.  Sometimes, it is useful to *completely*
-override lower-precedence settings.  To do this, you can use *two* colons
-at the end of a key in a configuration file.  For example, if the
-**site** ``config.yaml`` above looks like this:
+Above, the user ``config.yaml`` only overrides specific settings in the
+default ``config.yaml``. Sometimes, it is useful to *completely*
+override lower-precedence settings. To do this, you can use *two* colons
+at the end of a key in a configuration file. For example:
 
 .. code-block:: yaml
    :emphasize-lines: 1
+   :caption: ~/.spack/config.yaml
 
    config::
      install_tree: /some/other/directory
@@ -188,35 +300,36 @@ Spack will ignore all lower-precedence configuration under the
    config:
      install_tree: /some/other/directory
 
-^^^^^^^^^^^^^^^^^^^^^^
+
+^^^^^^^^^^^^^^^^^^^^
 List-valued settings
-^^^^^^^^^^^^^^^^^^^^^^
+^^^^^^^^^^^^^^^^^^^^
 
-Let's revisit the ``config.yaml`` example one more time.  The
+Let's revisit the ``config.yaml`` example one more time. The
 ``build_stage`` setting's value is an ordered list of directories:
 
-**defaults**
-
 .. code-block:: yaml
+   :caption: $(prefix)/etc/spack/defaults/config.yaml
 
    build_stage:
      - $tempdir
      - /nfs/tmp2/$user
 
+
 Suppose the user configuration adds its *own* list of ``build_stage``
 paths:
 
-**user**
-
 .. code-block:: yaml
+   :caption: ~/.spack/config.yaml
 
    build_stage:
      - /lustre-scratch/$user
      - ~/mystage
 
-Spack will first look at the paths in the site ``config.yaml``, then the
-paths in the user's ``~/.spack/config.yaml``.  The list in the
-higher-precedence scope is *prepended* to the defaults.  ``spack config
+
+Spack will first look at the paths in the defaults ``config.yaml``, then the
+paths in the user's ``~/.spack/config.yaml``. The list in the
+higher-precedence scope is *prepended* to the defaults. ``spack config
 get config`` shows the result:
 
 .. code-block:: console
@@ -226,27 +339,27 @@ get config`` shows the result:
    config:
      install_tree: /some/other/directory
      module_roots:
-       lmod:   $spack/share/spack/lmod
+       lmod: $spack/share/spack/lmod
      build_stage:
        - /lustre-scratch/$user
        - ~/mystage
        - $tempdir
        - /nfs/tmp2/$user
-   $ _
+
 
 As in :ref:`config-overrides`, the higher-precedence scope can
-*completely* override the lower-precedence scope using `::`.  So if the
+*completely* override the lower-precedence scope using ``::``. So if the
 user config looked like this:
 
-**user**
-
 .. code-block:: yaml
    :emphasize-lines: 1
+   :caption: ~/.spack/config.yaml
 
    build_stage::
      - /lustre-scratch/$user
      - ~/mystage
 
+
 The merged configuration would look like this:
 
 .. code-block:: console
@@ -256,57 +369,163 @@ The merged configuration would look like this:
    config:
      install_tree: /some/other/directory
      module_roots:
-       lmod:   $spack/share/spack/lmod
+       lmod: $spack/share/spack/lmod
      build_stage:
        - /lustre-scratch/$user
        - ~/mystage
-   $ _
+
 
 .. _config-file-variables:
 
-------------------------------
-Config file variables
-------------------------------
+---------------------
+Config File Variables
+---------------------
 
-Spack understands several variables which can be used in config file paths
-where ever they appear. There are three sets of these variables, Spack specific 
-variables, environment variables, and user path variables. Spack specific
-variables and environment variables both are indicated by prefixing the variable
-name with ``$``. User path variables are indicated at the start of the path with
-``~`` or ``~user``. Let's discuss each in turn.
+Spack understands several variables which can be used in config file
+paths wherever they appear. There are three sets of these variables:
+Spack-specific variables, environment variables, and user path
+variables. Spack-specific variables and environment variables are both
+indicated by prefixing the variable name with ``$``. User path variables
+are indicated at the start of the path with ``~`` or ``~user``.
 
 ^^^^^^^^^^^^^^^^^^^^^^^^
-Spack Specific Variables
+Spack-specific variables
 ^^^^^^^^^^^^^^^^^^^^^^^^
 
 Spack understands several special variables. These are:
 
-  * ``$spack``: path to the prefix of this spack installation
-  * ``$tempdir``: default system temporary directory (as specified in
-    Python's `tempfile.tempdir
-    <https://docs.python.org/2/library/tempfile.html#tempfile.tempdir>`_
-    variable.
-  * ``$user``: name of the current user
+* ``$spack``: path to the prefix of this Spack installation
+* ``$tempdir``: default system temporary directory (as specified in
+  Python's `tempfile.tempdir
+  <https://docs.python.org/2/library/tempfile.html#tempfile.tempdir>`_
+  variable.
+* ``$user``: name of the current user
 
 Note that, as with shell variables, you can write these as ``$varname``
 or with braces to distinguish the variable from surrounding characters:
-``${varname}``. Their names are also case insensitive meaning that ``$SPACK``
-works just as well as ``$spack``. These special variables are also
-substituted first, so any environment variables with the same name will not
-be used.
+``${varname}``. Their names are also case insensitive, meaning that
+``$SPACK`` works just as well as ``$spack``. These special variables are
+substituted first, so any environment variables with the same name will
+not be used.
+
+^^^^^^^^^^^^^^^^^^^^^
+Environment variables
+^^^^^^^^^^^^^^^^^^^^^
+
+After Spack-specific variables are evaluated, environment variables are
+expanded. These are formatted like Spack-specific variables, e.g.,
+``${varname}``. You can use this to insert environment variables in your
+Spack configuration.
 
 ^^^^^^^^^^^^^^^^^^^^^
-Environment Variables
+User home directories
 ^^^^^^^^^^^^^^^^^^^^^
 
-Spack then uses ``os.path.expandvars`` to expand any remaining environment
-variables.
+Spack performs Unix-style tilde expansion on paths in configuration
+files. This means that tilde (``~``) will expand to the current user's
+home directory, and ``~user`` will expand to a specified user's home
+directory. The ``~`` must appear at the beginning of the path, or Spack
+will not expand it.
+
+----------------------------
+Seeing Spack's Configuration
+----------------------------
+
+With so many scopes overriding each other, it can sometimes be difficult
+to understand what Spack's final configuration looks like.
 
-^^^^^^^^^^^^^^
-User Variables
-^^^^^^^^^^^^^^
+Spack provides two useful ways to view the final "merged" version of any
+configuration file: ``spack config get`` and ``spack config blame``.
+
+.. _cmd-spack-config-get:
+
+^^^^^^^^^^^^^^^^^^^^
+``spack config get``
+^^^^^^^^^^^^^^^^^^^^
+
+``spack config get`` shows a fully merged configuration file, taking into
+account all scopes. For example, to see the fully merged
+``config.yaml``, you can type:
+
+.. code-block:: console
+
+   $ spack config get config
+   config:
+     debug: false
+     checksum: true
+     verify_ssl: true
+     dirty: false
+     build_jobs: 8
+     install_tree: $spack/opt/spack
+     template_dirs:
+     - $spack/templates
+     directory_layout: ${ARCHITECTURE}/${COMPILERNAME}-${COMPILERVER}/${PACKAGE}-${VERSION}-${HASH}
+     module_roots:
+       tcl: $spack/share/spack/modules
+       lmod: $spack/share/spack/lmod
+       dotkit: $spack/share/spack/dotkit
+     build_stage:
+     - $tempdir
+     - /nfs/tmp2/$user
+     - $spack/var/spack/stage
+     source_cache: $spack/var/spack/cache
+     misc_cache: ~/.spack/cache
+     locks: true
+
+Likewise, this will show the fully merged ``packages.yaml``:
+
+.. code-block:: console
+
+   $ spack config get packages
+
+You can use this in conjunction with the ``-C`` / ``--config-scope`` argument to
+see how your scope will affect Spack's configuration:
+
+.. code-block:: console
+
+   $ spack -C /path/to/my/scope config get packages
+
+
+.. _cmd-spack-config-blame:
+
+^^^^^^^^^^^^^^^^^^^^^^
+``spack config blame``
+^^^^^^^^^^^^^^^^^^^^^^
+
+``spack config blame`` functions much like ``spack config get``, but it
+shows exactly which configuration file each preference came from. If you
+do not know why Spack is behaving a certain way, this can help you track
+down the problem:
+
+.. code-block:: console
 
-Spack also uses the ``os.path.expanduser`` function on the path to expand
-any user tilde paths such as ``~`` or ``~user``. These tilde paths must appear
-at the beginning of the path or ``os.path.expanduser`` will not properly
-expand them.
+   $ spack --insecure -C ./my-scope -C ./my-scope-2 config blame config
+   ==> Warning: You asked for --insecure. Will NOT check SSL certificates.
+   ---                                                   config:
+   _builtin                                                debug: False
+   /home/myuser/spack/etc/spack/defaults/config.yaml:72    checksum: True
+   command_line                                            verify_ssl: False
+   ./my-scope-2/config.yaml:2                              dirty: False
+   _builtin                                                build_jobs: 8
+   ./my-scope/config.yaml:2                                install_tree: /path/to/some/tree
+   /home/myuser/spack/etc/spack/defaults/config.yaml:23    template_dirs:
+   /home/myuser/spack/etc/spack/defaults/config.yaml:24    - $spack/templates
+   /home/myuser/spack/etc/spack/defaults/config.yaml:28    directory_layout: ${ARCHITECTURE}/${COMPILERNAME}-${COMPILERVER}/${PACKAGE}-${VERSION}-${HASH}
+   /home/myuser/spack/etc/spack/defaults/config.yaml:32    module_roots:
+   /home/myuser/spack/etc/spack/defaults/config.yaml:33      tcl: $spack/share/spack/modules
+   /home/myuser/spack/etc/spack/defaults/config.yaml:34      lmod: $spack/share/spack/lmod
+   /home/myuser/spack/etc/spack/defaults/config.yaml:35      dotkit: $spack/share/spack/dotkit
+   /home/myuser/spack/etc/spack/defaults/config.yaml:49    build_stage:
+   /home/myuser/spack/etc/spack/defaults/config.yaml:50    - $tempdir
+   /home/myuser/spack/etc/spack/defaults/config.yaml:51    - /nfs/tmp2/$user
+   /home/myuser/spack/etc/spack/defaults/config.yaml:52    - $spack/var/spack/stage
+   /home/myuser/spack/etc/spack/defaults/config.yaml:57    source_cache: $spack/var/spack/cache
+   /home/myuser/spack/etc/spack/defaults/config.yaml:62    misc_cache: ~/.spack/cache
+   /home/myuser/spack/etc/spack/defaults/config.yaml:86    locks: True
+
+You can see above that the ``build_jobs`` and ``debug`` settings are
+built in and are not overridden by a configuration file. The
+``verify_ssl`` setting comes from the ``--insceure`` option on the
+command line. ``dirty`` and ``install_tree`` come from the custom
+scopes ``./my-scope`` and ``./my-scope-2``, and all other configuration
+options come from the default configuration files that ship with Spack.
diff --git a/lib/spack/docs/contribution_guide.rst b/lib/spack/docs/contribution_guide.rst
index 6ee55c2f66..11b826da13 100644
--- a/lib/spack/docs/contribution_guide.rst
+++ b/lib/spack/docs/contribution_guide.rst
@@ -1,3 +1,8 @@
+.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 .. _contribution-guide:
 
 ==================
@@ -34,13 +39,30 @@ Continuous Integration
 
 Spack uses `Travis CI <https://travis-ci.org/spack/spack>`_ for Continuous Integration
 testing. This means that every time you submit a pull request, a series of tests will
-be run to make sure you didn't accidentally introduce any bugs into Spack. Your PR
-will not be accepted until it passes all of these tests. While you can certainly wait
+be run to make sure you didn't accidentally introduce any bugs into Spack. **Your PR
+will not be accepted until it passes all of these tests.** While you can certainly wait
 for the results of these tests after submitting a PR, we recommend that you run them
 locally to speed up the review process.
 
+.. note::
+
+   Oftentimes, Travis will fail for reasons other than a problem with your PR.
+   For example, apt-get, pip, or homebrew will fail to download one of the
+   dependencies for the test suite, or a transient bug will cause the unit tests
+   to timeout. If Travis fails, click the "Details" link and click on the test(s)
+   that is failing. If it doesn't look like it is failing for reasons related to
+   your PR, you have two options. If you have write permissions for the Spack
+   repository, you should see a "Restart job" button on the right-hand side. If
+   not, you can close and reopen your PR to rerun all of the tests. If the same
+   test keeps failing, there may be a problem with your PR. If you notice that
+   every recent PR is failing with the same error message, it may be that Travis
+   is down or one of Spack's dependencies put out a new release that is causing
+   problems. If this is the case, please file an issue.
+
+
 If you take a look in ``$SPACK_ROOT/.travis.yml``, you'll notice that we test
-against Python 2.6, 2.7, and 3.3-3.6. We currently perform 3 types of tests:
+against Python 2.6, 2.7, and 3.4-3.7 on both macOS and Linux. We currently
+perform 3 types of tests:
 
 ^^^^^^^^^^
 Unit Tests
@@ -80,6 +102,13 @@ tests, run:
 A more detailed list of available unit tests can be found by running
 ``spack test --long-list``.
 
+By default, ``pytest`` captures the output of all unit tests. If you add print
+statements to a unit test and want to see the output, simply run:
+
+.. code-block:: console
+
+   $ spack test -s -k architecture
+
 Unit tests are crucial to making sure bugs aren't introduced into Spack. If you
 are modifying core Spack libraries or adding new functionality, please consider
 adding new unit tests or strengthening existing tests.
@@ -87,7 +116,7 @@ adding new unit tests or strengthening existing tests.
 .. note::
 
    There is also a ``run-unit-tests`` script in ``share/spack/qa`` that
-   runs the unit tests. Afterwards, it reports back to Coverage with the
+   runs the unit tests. Afterwards, it reports back to Codecov with the
    percentage of Spack that is covered by unit tests. This script is
    designed for Travis CI. If you want to run the unit tests yourself, we
    suggest you use ``spack test``.
@@ -154,20 +183,27 @@ However, if you aren't compliant with PEP 8, flake8 will complain:
 
 Most of the error messages are straightforward, but if you don't understand what
 they mean, just ask questions about them when you submit your PR. The line numbers
-will change if you add or delete lines, so simply run ``run-flake8-tests`` again
+will change if you add or delete lines, so simply run ``spack flake8`` again
 to update them.
 
 .. tip::
 
    Try fixing flake8 errors in reverse order. This eliminates the need for
-   multiple runs of ``flake8`` just to re-compute line numbers and makes it
-   much easier to fix errors directly off of the Travis output.
+   multiple runs of ``spack flake8`` just to re-compute line numbers and
+   makes it much easier to fix errors directly off of the Travis output.
 
 .. warning::
 
-   Flake8 requires setuptools in order to run. If you installed ``py-flake8``
-   with Spack, make sure to add ``py-setuptools`` to your ``PYTHONPATH``.
-   Otherwise, you will get an error message like:
+   Flake8 and ``pep8-naming`` require a number of dependencies in order
+   to run.  If you installed ``py-flake8`` and ``py-pep8-naming``, the
+   easiest way to ensure the right packages are on your ``PYTHONPATH`` is
+   to run::
+
+     spack activate py-flake8
+     spack activate pep8-naming
+
+   so that all of the dependencies are symlinked to a central
+   location. If you see an error message like:
 
    .. code-block:: console
 
@@ -176,6 +212,8 @@ to update them.
           from pkg_resources import load_entry_point
       ImportError: No module named pkg_resources
 
+   that means Flake8 couldn't find setuptools in your ``PYTHONPATH``.
+
 ^^^^^^^^^^^^^^^^^^^
 Documentation Tests
 ^^^^^^^^^^^^^^^^^^^
@@ -190,6 +228,7 @@ installed with Spack:
 
 * sphinx
 * sphinxcontrib-programoutput
+* sphinx-rtd-theme
 * graphviz
 * git
 * mercurial
@@ -199,18 +238,25 @@ installed with Spack:
 
    Sphinx has `several required dependencies <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/py-sphinx/package.py>`_.
    If you installed ``py-sphinx`` with Spack, make sure to add all of these
-   dependencies to your ``PYTHONPATH``. The easiest way to do this is to run
-   ``spack activate py-sphinx`` so that all of the dependencies are symlinked
-   to a central location. If you see an error message like:
+   dependencies to your ``PYTHONPATH``. The easiest way to do this is to run:
 
    .. code-block:: console
 
-      Traceback (most recent call last):
-        File: "/usr/bin/flake8", line 5, in <module>
-          from pkg_resources import load_entry_point
-      ImportError: No module named pkg_resources
+      $ spack activate py-sphinx
+      $ spack activate py-sphinx-rtd-theme
+      $ spack activate py-sphinxcontrib-programoutput
 
-   that means Sphinx couldn't find setuptools in your ``PYTHONPATH``.
+   so that all of the dependencies are symlinked to a central location.
+   If you see an error message like:
+
+   .. code-block:: console
+
+      Extension error:
+      Could not import extension sphinxcontrib.programoutput (exception: No module named sphinxcontrib.programoutput)
+      make: *** [html] Error 1
+
+   that means Sphinx couldn't find ``py-sphinxcontrib-programoutput`` in your
+   ``PYTHONPATH``.
 
 Once all of the dependencies are installed, you can try building the documentation:
 
@@ -225,11 +271,11 @@ your PR is accepted.
 
 .. note::
 
-   There is also a ``run-doc-tests`` script in the Quality Assurance directory.
-   The only difference between running this script and running ``make`` by hand
-   is that the script will exit immediately if it encounters an error or warning.
-   This is necessary for Travis CI. If you made a lot of documentation changes, it
-   is much quicker to run ``make`` by hand so that you can see all of the warnings
+   There is also a ``run-doc-tests`` script in ``share/spack/qa``. The only
+   difference between running this script and running ``make`` by hand is that
+   the script will exit immediately if it encounters an error or warning. This
+   is necessary for Travis CI. If you made a lot of documentation changes, it is
+   much quicker to run ``make`` by hand so that you can see all of the warnings
    at once.
 
 If you are editing the documentation, you should obviously be running the
@@ -277,6 +323,37 @@ Documentation changes can result in much more obfuscated warning messages.
 If you don't understand what they mean, feel free to ask when you submit
 your PR.
 
+--------
+Coverage
+--------
+
+Spack uses `Codecov <https://codecov.io/>`_ to generate and report unit test
+coverage. This helps us tell what percentage of lines of code in Spack are
+covered by unit tests. Although code covered by unit tests can still contain
+bugs, it is much less error prone than code that is not covered by unit tests.
+
+Codecov provides `browser extensions <https://github.com/codecov/browser-extension>`_
+for Google Chrome, Firefox, and Opera. These extensions integrate with GitHub
+and allow you to see coverage line-by-line when viewing the Spack repository.
+If you are new to Spack, a great way to get started is to write unit tests to
+increase coverage!
+
+Unlike with Travis, Codecov tests are not required to pass in order for your
+PR to be merged. If you modify core Spack libraries, we would greatly
+appreciate unit tests that cover these changed lines. Otherwise, we have no
+way of knowing whether or not your changes introduce a bug. If you make
+substantial changes to the core, we may request unit tests to increase coverage.
+
+.. note::
+
+   If the only files you modified are package files, we do not care about
+   coverage on your PR. You may notice that the Codecov tests fail even though
+   you didn't modify any core files. This means that Spack's overall coverage
+   has increased since you branched off of develop. This is a good thing!
+   If you really want to get the Codecov tests to pass, you can rebase off of
+   the latest develop, but again, this is not required.
+
+
 -------------
 Git Workflows
 -------------
diff --git a/lib/spack/docs/developer_guide.rst b/lib/spack/docs/developer_guide.rst
index 96b4436683..926d2a360d 100644
--- a/lib/spack/docs/developer_guide.rst
+++ b/lib/spack/docs/developer_guide.rst
@@ -1,3 +1,8 @@
+.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 .. _developer_guide:
 
 ===============
@@ -119,7 +124,7 @@ etc.) but we wanted to make Spack *very* easy to use.  The simple layout
 spares users from the need to install Spack into a Python environment.
 Many users don't have write access to a Python installation, and installing
 an entire new instance of Python to bootstrap Spack would be very complicated.
-Users should not have to install install a big, complicated package to
+Users should not have to install a big, complicated package to
 use the thing that's supposed to spare them from the details of big,
 complicated packages.  The end result is that Spack works out of the
 box: clone it and add ``bin`` to your PATH and you're ready to go.
@@ -314,7 +319,7 @@ See the `Argparse documentation <https://docs.python.org/2.7/library/argparse.ht
 for more details on how to add arguments.
 
 Some commands have a set of subcommands, like ``spack compiler find`` or
-``spack module refresh``. You can add subparsers to your parser to handle
+``spack module lmod refresh``. You can add subparsers to your parser to handle
 this. Check out ``spack edit --command compiler`` for an example of this.
 
 A lot of commands take the same arguments and flags. These arguments should
diff --git a/lib/spack/docs/docker_for_developers.rst b/lib/spack/docs/docker_for_developers.rst
new file mode 100644
index 0000000000..2f1b5a949a
--- /dev/null
+++ b/lib/spack/docs/docker_for_developers.rst
@@ -0,0 +1,41 @@
+.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+.. _docker_for_developers:
+
+=====================
+Docker for Developers
+=====================
+
+This guide is intended for people who want to use our prepared docker
+environments to work on developing Spack or working on spack packages. It is
+meant to serve as the companion documentation for the :ref:`packaging-guide`.
+
+--------
+Overview
+--------
+
+To get started, all you need is the latest version of ``docker``.
+
+.. code-block:: console
+
+    $ cd share/spack/docker
+    $ source config/ubuntu.bash
+    $ ./run-image.sh
+
+This command should drop you into an interactive shell where you can run spack
+within an isolated docker container running ubuntu.  The copy of spack being
+used should be tied to the working copy of your cloned git repo, so any changes
+you make should be immediately reflected in the running docker container.  Feel
+free to add or modify any packages or to hack on spack, itself.  Your contained
+copy of spack should immediately reflect all changes.
+
+To work within a container running a different linux distro, source one of the
+other environment files under ``config``.
+
+.. code-block:: console
+
+    $ source config/fedora.bash
+    $ ./run-image.sh
diff --git a/lib/spack/docs/features.rst b/lib/spack/docs/features.rst
index 8d7c1ec0cd..dce20d51d6 100644
--- a/lib/spack/docs/features.rst
+++ b/lib/spack/docs/features.rst
@@ -1,3 +1,8 @@
+.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 ================
 Feature Overview
 ================
@@ -126,7 +131,7 @@ It doesn't take much python coding to get from there to a working
 package:
 
 .. literalinclude:: ../../../var/spack/repos/builtin/packages/libelf/package.py
-   :lines: 25-
+   :lines: 6-
 
 Spack also provides wrapper functions around common commands like
 ``configure``, ``make``, and ``cmake`` to make writing packages
diff --git a/lib/spack/docs/getting_started.rst b/lib/spack/docs/getting_started.rst
index 9e59b28dac..8fd0840e35 100644
--- a/lib/spack/docs/getting_started.rst
+++ b/lib/spack/docs/getting_started.rst
@@ -1,3 +1,8 @@
+.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 .. _getting_started:
 
 ===============
@@ -11,7 +16,7 @@ Prerequisites
 Spack has the following minimum requirements, which must be installed
 before Spack is run:
 
-1. Python 2 (2.6 or 2.7) or 3 (3.3 - 3.6)
+1. Python 2 (2.6 or 2.7) or 3 (3.4 - 3.7)
 2. A C/C++ compiler
 3. The ``git`` and ``curl`` commands.
 4. If using the ``gpg`` subcommand, ``gnupg2`` is required.
@@ -163,7 +168,7 @@ compilers`` or ``spack compiler list``:
 Any of these compilers can be used to build Spack packages.  More on
 how this is done is in :ref:`sec-specs`.
 
-.. _spack-compiler-add:
+.. _cmd-spack-compiler-add:
 
 ^^^^^^^^^^^^^^^^^^^^^^
 ``spack compiler add``
@@ -171,7 +176,7 @@ how this is done is in :ref:`sec-specs`.
 
 An alias for ``spack compiler find``.
 
-.. _spack-compiler-find:
+.. _cmd-spack-compiler-find:
 
 ^^^^^^^^^^^^^^^^^^^^^^^
 ``spack compiler find``
@@ -202,7 +207,14 @@ installed, but you know that new compilers have been added to your
 This loads the environment module for gcc-4.9.0 to add it to
 ``PATH``, and then it adds the compiler to Spack.
 
-.. _spack-compiler-info:
+.. note::
+
+   By default, spack does not fill in the ``modules:`` field in the
+   ``compilers.yaml`` file.  If you are using a compiler from a
+   module, then you should add this field manually.
+   See the section on :ref:`compilers-requiring-modules`.
+
+.. _cmd-spack-compiler-info:
 
 ^^^^^^^^^^^^^^^^^^^^^^^
 ``spack compiler info``
@@ -320,6 +332,7 @@ by adding the following to your ``packages.yaml`` file:
      all:
        compiler: [gcc@4.9.3]
 
+.. _compilers-requiring-modules:
 
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
 Compilers Requiring Modules
@@ -484,6 +497,9 @@ simple package.  For example:
 
    $ spack install zlib%gcc@5.3.0
 
+
+.. _vendor-specific-compiler-configuration:
+
 --------------------------------------
 Vendor-Specific Compiler Configuration
 --------------------------------------
@@ -805,7 +821,7 @@ encountered on a Macintosh during ``spack install julia-master``:
 
 .. code-block:: console
 
-   ==> Trying to clone git repository:
+   ==> Cloning git repository:
      https://github.com/JuliaLang/julia.git
      on branch master
    Cloning into 'julia'...
@@ -816,7 +832,7 @@ This problem is related to OpenSSL, and in some cases might be solved
 by installing a new version of ``git`` and ``openssl``:
 
 #. Run ``spack install git``
-#. Add the output of ``spack module loads git`` to your ``.bashrc``.
+#. Add the output of ``spack module tcl loads git`` to your ``.bashrc``.
 
 If this doesn't work, it is also possible to disable checking of SSL
 certificates by using:
@@ -861,7 +877,7 @@ or alternately:
 
 .. code-block:: console
 
-    $ spack module loads curl >>~/.bashrc
+    $ spack module tcl loads curl >>~/.bashrc
 
 or if environment modules don't work:
 
@@ -926,75 +942,38 @@ Once ``curl`` has been installed, you can similarly install the others.
 Environment Modules
 """""""""""""""""""
 
-In order to use Spack's generated environment modules, you must have
-installed one of *Environment Modules* or *Lmod*.  On many Linux
-distributions, this can be installed from the vendor's repository.  For
-example: ``yum install environment-modules`` (Fedora/RHEL/CentOS). If
-your Linux distribution does not have Environment Modules, Spack can
-build it for you!
-
-What follows are three steps describing how to install and use environment-modules with spack.
-
-#. Install ``environment-modules``.
-
-   * ``spack bootstrap`` will build ``environment-modules`` for you (and may build
-     other packages that are useful to the operation of Spack)
-
-   * Install ``environment-modules`` using ``spack install`` with
-     ``spack install environment-modules~X`` (The ``~X`` variant builds without Xorg
-     dependencies, but ``environment-modules`` works fine too.)
-
-#. Add ``modulecmd`` to ``PATH`` and create a ``module`` command. 
-
-   * If you are using ``bash`` or ``ksh``, Spack can currently do this for you as well.
-     After installing ``environment-modules`` following the step
-     above, source Spack's shell integration script. This will automatically
-     detect the lack of ``modulecmd`` and ``module``, and use the installed
-     ``environment-modules`` from ``spack bootstrap`` or ``spack install``.
-     
-     .. code-block:: console
-
-        # For bash/zsh users
-        $ export SPACK_ROOT=/path/to/spack
-        $ . $SPACK_ROOT/share/spack/setup-env.sh
+In order to use Spack's generated module files, you must have
+installed ``environment-modules`` or ``lmod``. The simplest way
+to get the latest version of either of these tools is installing
+it as part of Spack's bootstrap procedure:
 
+.. code-block:: console
 
-   * If you prefer to do it manually,  you can activate with the following 
-     script (or apply the updates to your ``.bashrc`` file manually):
+   $ spack bootstrap
 
-         .. code-block:: sh
+.. warning::
+   At the moment ``spack bootstrap`` is only able to install ``environment-modules``.
+   Extending its capabilities to prefer ``lmod`` where possible is in the roadmap,
+   and likely to happen before the next release.
 
-            TMP=`tempfile`
-            echo >$TMP
-            MODULE_HOME=`spack location --install-dir environment-modules`
-            MODULE_VERSION=`ls -1 $MODULE_HOME/Modules | head -1`
-            ${MODULE_HOME}/Modules/${MODULE_VERSION}/bin/add.modules <$TMP
-            cp .bashrc $TMP
-            echo "MODULE_VERSION=${MODULE_VERSION}" > .bashrc
-            cat $TMP >>.bashrc
+Alternatively, on many Linux distributions, you can install a pre-built binary
+from the vendor's repository. On Fedora/RHEL/CentOS, for example, this can be
+done with the command:
 
-      This is added to your ``.bashrc`` (or similar) files, enabling Environment
-      Modules when you log in.
-        
-#. Test that the ``module`` command is found with:
+.. code-block:: console
 
-   .. code-block:: console
+   $ yum install environment-modules
 
-      $ module avail
+Once you have the tool installed and available in your path, you can source
+Spack's setup file:
 
+.. code-block:: console
 
-If ``tcl`` 8.0 or later is installed on  your system, you can prevent
-spack from rebuilding ``tcl`` as part of the ``environment-modules`` dependency
-stack by adding the following to your ``~/.spack/packages.yaml`` replacing
-version 8.5 with whatever version is installed on your system:
+   $ source share/spack/setup-env.sh
 
-   .. code-block:: yaml
+This activates :ref:`shell support <shell-support>` and makes commands like
+``spack load`` available for use.
 
-      packages:
-          tcl:
-              paths:
-                  tcl@8.5: /usr
-              buildable: False
 
 ^^^^^^^^^^^^^^^^^
 Package Utilities
@@ -1096,6 +1075,37 @@ they may use packages you have signed using the ``--export <keyfile>`` flag.
 Secret keys may also be later exported using the
 ``spack gpg export <location> [<key>...]`` command.
 
+.. note::
+
+   Key creation speed
+      The creation of a new GPG key requires generating a lot of random numbers.
+      Depending on the entropy produced on your system, the entire process may
+      take a long time (*even appearing to hang*). Virtual machines and cloud
+      instances are particularly likely to display this behavior.
+
+      To speed it up you may install tools like ``rngd``, which is
+      usually available as a package in the host OS.  On e.g. an
+      Ubuntu machine you need to give the following commands:
+
+      .. code-block:: console
+
+         $ sudo apt-get install rng-tools
+         $ sudo rngd -r /dev/urandom
+
+      before generating the keys.
+
+      Another alternative is ``haveged``, which can be installed on
+      RHEL/CentOS machines as follows:
+
+      .. code-block:: console
+
+         $ sudo yum install haveged
+         $ sudo chkconfig haveged on
+
+      `This Digital Ocean tutorial
+      <https://www.digitalocean.com/community/tutorials/how-to-setup-additional-entropy-for-cloud-servers-using-haveged>`_
+      provides a good overview of sources of randomness.
+
 ^^^^^^^^^^^^
 Listing keys
 ^^^^^^^^^^^^
@@ -1226,6 +1236,13 @@ cray-mpich module into the environment. You can then be able to use whatever
 environment variables, libraries, etc, that are brought into the environment
 via module load.
 
+.. note::
+
+    For Cray-provided packages, it is best to use ``modules:`` instead of ``paths:``
+    in ``packages.yaml``, because the Cray Programming Environment heavily relies on
+    modules (e.g., loading the ``cray-mpich`` module adds MPI libraries to the
+    compiler wrapper link line).
+
 You can set the default compiler that Spack can use for each compiler type.
 If you want to use the Cray defaults, then set them under ``all:`` in packages.yaml.
 In the compiler field, set the compiler specs in your order of preference.
@@ -1262,3 +1279,17 @@ for each compiler type for each cray modules. This ensures that for each
 compiler on our system we can use that external module.
 
 For more on external packages check out the section :ref:`sec-external-packages`.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Using Linux containers on Cray machines
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Spack uses environment variables particular to the Cray programming
+environment to determine which systems are Cray platforms. These
+environment variables may be propagated into containers that are not
+using the Cray programming environment.
+
+To ensure that Spack does not autodetect the Cray programming
+environment, unset the environment variable ``CRAYPE_VERSION``. This
+will cause Spack to treat a linux container on a Cray system as a base
+linux distro.
diff --git a/lib/spack/docs/index.rst b/lib/spack/docs/index.rst
index 2ca737bb72..c2d8a28b89 100644
--- a/lib/spack/docs/index.rst
+++ b/lib/spack/docs/index.rst
@@ -1,3 +1,8 @@
+.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 .. Spack documentation master file, created by
    sphinx-quickstart on Mon Dec  9 15:32:41 2013.
    You can adapt this file completely to your liking, but it should at least
@@ -73,7 +78,9 @@ or refer to the full manual below.
 
    contribution_guide
    packaging_guide
+   build_systems
    developer_guide
+   docker_for_developers
    Spack API Docs <spack>
    LLNL API Docs <llnl>
 
diff --git a/lib/spack/docs/known_issues.rst b/lib/spack/docs/known_issues.rst
index c45ababc4f..9e64cd63b4 100644
--- a/lib/spack/docs/known_issues.rst
+++ b/lib/spack/docs/known_issues.rst
@@ -1,3 +1,8 @@
+.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 ============
 Known Issues
 ============
@@ -5,38 +10,6 @@ Known Issues
 This is a list of known bugs in Spack. It provides ways of getting around these
 problems if you encounter them.
 
------------------------------------------------------------------
-Default variants are not taken into account during concretization
------------------------------------------------------------------
-
-**Status:** Expected to be fixed in the next release
-
-Current concretization algorithm does not take into account default values
-of variants when adding extra constraints to the spec via CLI. For example
-you may encounter the following error when trying to specify which MPI provider
-to use:
-
-.. code-block:: console
-
-   $ spack install hdf5 ^openmpi
-   ==> Error: hdf5 does not depend on openmpi
-
-although the hdf5 package contains:
-
-.. code-block:: python
-
-   variant('mpi', default=True, description='Enable MPI support')
-   depends_on('mpi', when='+mpi')
-
-A workaround is to explicitly activate the variant related to the dependency:
-
-.. code-block:: console
-
-   $ spack install hdf5+mpi ^openmpi
-
-See https://github.com/spack/spack/issues/397 for further details.
-
-
 ---------------------------------------------------
 Variants are not properly forwarded to dependencies
 ---------------------------------------------------
@@ -77,26 +50,6 @@ See https://github.com/spack/spack/issues/267 and
 https://github.com/spack/spack/issues/2546 for further details.
 
 
----------------------------------
-``spack extensions`` doesn't work
----------------------------------
-
-**Status:** Up for grabs if you want to try to fix it
-
-Spack provides an ``extensions`` command that lists all available extensions
-of a package, the ones that are installed, and the ones that are already
-activated. This is very useful in conjunction with ``spack activate``.
-Unfortunately, this command no longer works:
-
-.. code-block:: console
-
-   $ spack extensions python
-   ==> python@2.7.13%clang@8.0.0-apple~tk~ucs4 arch=darwin-sierra-x86_64 -ckrr4mg has no extensions.
-
-
-See https://github.com/spack/spack/issues/2895 for further details.
-
-
 ----------------------------
 ``spack setup`` doesn't work
 ----------------------------
diff --git a/lib/spack/docs/mirrors.rst b/lib/spack/docs/mirrors.rst
index 4075421e12..d273e330d0 100644
--- a/lib/spack/docs/mirrors.rst
+++ b/lib/spack/docs/mirrors.rst
@@ -1,3 +1,8 @@
+.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 .. _mirrors:
 
 =======
@@ -69,7 +74,7 @@ packages from the internet and checksumming them.
 The other three commands are for managing mirror configuration.  They
 control the URL(s) from which Spack downloads its packages.
 
-.. _spack-mirror-create:
+.. _cmd-spack-mirror-create:
 
 -----------------------
 ``spack mirror create``
@@ -154,7 +159,7 @@ can supply a file with specs in it, one per line:
 This is useful if there is a specific suite of software managed by
 your site.
 
-.. _spack-mirror-add:
+.. _cmd-spack-mirror-add:
 
 --------------------
 ``spack mirror add``
@@ -166,7 +171,7 @@ a directory, you can use a file URL like this one:
 
 .. code-block:: none
 
-   file://~/spack-mirror-2014-06-24
+   file://$HOME/spack-mirror-2014-06-24
 
 That points to the directory on the local filesystem.  If it were on a
 web server, you could use a URL like this one:
@@ -178,11 +183,11 @@ You can tell your Spack installation to use that mirror like this:
 
 .. code-block:: console
 
-   $ spack mirror add local_filesystem file://~/spack-mirror-2014-06-24
+   $ spack mirror add local_filesystem file://$HOME/spack-mirror-2014-06-24
 
 Each mirror has a name so that you can refer to it again later.
 
-.. _spack-mirror-list:
+.. _cmd-spack-mirror-list:
 
 ---------------------
 ``spack mirror list``
@@ -193,9 +198,9 @@ To see all the mirrors Spack knows about, run ``spack mirror list``:
 .. code-block:: console
 
    $ spack mirror list
-   local_filesystem    file://~/spack-mirror-2014-06-24
+   local_filesystem    file:///home/username/spack-mirror-2014-06-24
 
-.. _spack-mirror-remove:
+.. _cmd-spack-mirror-remove:
 
 -----------------------
 ``spack mirror remove``
@@ -218,7 +223,7 @@ Adding a mirror really adds a line in ``~/.spack/mirrors.yaml``:
 .. code-block:: yaml
 
    mirrors:
-     local_filesystem: file://~/spack-mirror-2014-06-24
+     local_filesystem: file:///home/username/spack-mirror-2014-06-24
      remote_server: https://example.com/some/web-hosted/directory/spack-mirror-2014-06-24
 
 If you want to change the order in which mirrors are searched for
diff --git a/lib/spack/docs/module_file_support.rst b/lib/spack/docs/module_file_support.rst
index 6b874fbe97..37dd03547f 100644
--- a/lib/spack/docs/module_file_support.rst
+++ b/lib/spack/docs/module_file_support.rst
@@ -1,3 +1,8 @@
+.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 .. _modules:
 
 =======
@@ -113,8 +118,10 @@ Modules                    Dotkit
 =========================  ==========================
 
 And you can use the same shortened names you use everywhere else in
-Spack.  For example, this will add the ``mpich`` package built with
-``gcc`` to your path:
+Spack.
+
+For example, if you are using dotkit, this will add the ``mpich``
+package built with ``gcc`` to your path:
 
 .. code-block:: console
 
@@ -122,16 +129,16 @@ Spack.  For example, this will add the ``mpich`` package built with
 
    # ... wait for install ...
 
-   $ spack use mpich %gcc@4.4.7
+   $ spack use mpich %gcc@4.4.7     # dotkit
    Prepending: mpich@3.0.4%gcc@4.4.7 (ok)
    $ which mpicc
    ~/spack/opt/linux-debian7-x86_64/gcc@4.4.7/mpich@3.0.4/bin/mpicc
 
-Or, similarly with modules, you could type:
+Or, similarly if you are using modules, you could type:
 
 .. code-block:: console
 
-   $ spack load mpich %gcc@4.4.7
+   $ spack load mpich %gcc@4.4.7    # modules
 
 These commands will add appropriate directories to your ``PATH``,
 ``MANPATH``, ``CPATH``, and ``LD_LIBRARY_PATH``.  When you no longer
@@ -178,9 +185,9 @@ To identify just the one built with the Intel compiler.
 
 .. _cmd-spack-module-loads:
 
-^^^^^^^^^^^^^^^^^^^^^^
-``spack module loads``
-^^^^^^^^^^^^^^^^^^^^^^
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+``spack module tcl loads``
+^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 In some cases, it is desirable to load not just a module, but also all
 the modules it depends on.  This is not required for most modules
@@ -193,21 +200,13 @@ Scripts to load modules recursively may be made with the command:
 
 .. code-block:: console
 
-    $ spack module loads --dependencies <spec>
+    $ spack module tcl loads --dependencies <spec>
 
 An equivalent alternative using `process substitution <http://tldp.org/LDP/abs/html/process-sub.html>`_ is:
 
 .. code-block :: console
 
-    $ source <( spack module loads --dependencies <spec> )
-
-.. warning::
-
-    The ``spack load`` command does not currently accept the
-    ``--dependencies`` flag.  Use ``spack module loads`` instead, for
-    now.
-
-.. See #1662
+    $ source <( spack module tcl loads --dependencies <spec> )
 
 
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -217,12 +216,12 @@ Module Commands for Shell Scripts
 Although Spack is flexible, the ``module`` command is much faster.
 This could become an issue when emitting a series of ``spack load``
 commands inside a shell script.  By adding the ``--shell`` flag,
-``spack module find`` may also be used to generate code that can be
+``spack module tcl find`` may also be used to generate code that can be
 cut-and-pasted into a shell script.  For example:
 
 .. code-block:: console
 
-    $ spack module loads --dependencies py-numpy git
+    $ spack module tcl loads --dependencies py-numpy git
     # bzip2@1.0.6%gcc@4.9.3=linux-x86_64
     module load bzip2-1.0.6-gcc-4.9.3-ktnrhkrmbbtlvnagfatrarzjojmkvzsx
     # ncurses@6.0%gcc@4.9.3=linux-x86_64
@@ -262,9 +261,9 @@ Module Prefixes
 ^^^^^^^^^^^^^^^
 
 On some systems, modules are automatically prefixed with a certain
-string; ``spack module loads`` needs to know about that prefix when it
+string; ``spack module tcl loads`` needs to know about that prefix when it
 issues ``module load`` commands.  Add the ``--prefix`` option to your
-``spack module loads`` commands if this is necessary.
+``spack module tcl loads`` commands if this is necessary.
 
 For example, consider the following on one system:
 
@@ -273,11 +272,11 @@ For example, consider the following on one system:
     $ module avail
     linux-SuSE11-x86_64/antlr-2.7.7-gcc-5.3.0-bdpl46y
 
-    $ spack module loads antlr    # WRONG!
+    $ spack module tcl loads antlr    # WRONG!
     # antlr@2.7.7%gcc@5.3.0~csharp+cxx~java~python arch=linux-SuSE11-x86_64
     module load antlr-2.7.7-gcc-5.3.0-bdpl46y
 
-    $ spack module loads --prefix linux-SuSE11-x86_64/ antlr
+    $ spack module tcl loads --prefix linux-SuSE11-x86_64/ antlr
     # antlr@2.7.7%gcc@5.3.0~csharp+cxx~java~python arch=linux-SuSE11-x86_64
     module load linux-SuSE11-x86_64/antlr-2.7.7-gcc-5.3.0-bdpl46y
 
@@ -290,15 +289,15 @@ installation of a package. The table below summarizes the essential
 information associated with the different file formats
 that can be generated by Spack:
 
-  +-----------------------------+--------------------+-------------------------------+----------------------------------+----------------------+
-  |                             | **Hook name**      |  **Default root directory**   | **Default template file**        | **Compatible tools** |
-  +=============================+====================+===============================+==================================+======================+
-  |  **Dotkit**                 | ``dotkit``         |  share/spack/dotkit           | templates/modules/modulefile.dk  | DotKit               |
-  +-----------------------------+--------------------+-------------------------------+----------------------------------+----------------------+
-  |  **TCL - Non-Hierarchical** | ``tcl``            |  share/spack/modules          | templates/modules/modulefile.tcl | Env. Modules/LMod    |
-  +-----------------------------+--------------------+-------------------------------+----------------------------------+----------------------+
-  |  **Lua - Hierarchical**     | ``lmod``           |  share/spack/lmod             | templates/modules/modulefile.lua | LMod                 |
-  +-----------------------------+--------------------+-------------------------------+----------------------------------+----------------------+
+  +-----------------------------+--------------------+-------------------------------+----------------------------------------------+----------------------+
+  |                             | **Hook name**      |  **Default root directory**   | **Default template file**                    | **Compatible tools** |
+  +=============================+====================+===============================+==============================================+======================+
+  |  **Dotkit**                 | ``dotkit``         |  share/spack/dotkit           | share/spack/templates/modules/modulefile.dk  | DotKit               |
+  +-----------------------------+--------------------+-------------------------------+----------------------------------------------+----------------------+
+  |  **TCL - Non-Hierarchical** | ``tcl``            |  share/spack/modules          | share/spack/templates/modules/modulefile.tcl | Env. Modules/LMod    |
+  +-----------------------------+--------------------+-------------------------------+----------------------------------------------+----------------------+
+  |  **Lua - Hierarchical**     | ``lmod``           |  share/spack/lmod             | share/spack/templates/modules/modulefile.lua | LMod                 |
+  +-----------------------------+--------------------+-------------------------------+----------------------------------------------+----------------------+
 
 
 Spack ships with sensible defaults for the generation of module files, but
@@ -485,6 +484,9 @@ you will prevent the generation of module files for any package that
 is compiled with ``gcc@4.4.7``, with the only exception of any ``gcc``
 or any ``llvm`` installation.
 
+
+.. _modules-naming-scheme:
+
 """""""""""""""""""""""""""
 Customize the naming scheme
 """""""""""""""""""""""""""
@@ -629,39 +631,38 @@ The allowed values for the ``autoload`` statement are either ``none``,
 Maintaining Module Files
 ------------------------
 
-Spack not only provides great flexibility in the generation of module files
-and in the customization of both their layout and content, but also ships with
-a tool to ease the burden of their maintenance in production environments.
-This tool is the ``spack module`` command:
+Each type of module file has a command with the same name associated
+with it. The actions these commands permit are usually associated
+with the maintenance of a production environment. Here's, for instance,
+a sample of the features of the ``spack module tcl`` command:
 
-.. command-output:: spack module --help
+.. command-output:: spack module tcl --help
 
 .. _cmd-spack-module-refresh:
 
-^^^^^^^^^^^^^^^^^^^^^^^^
-``spack module refresh``
-^^^^^^^^^^^^^^^^^^^^^^^^
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+Refresh the set of modules
+^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-The command that regenerates module files to update their content or
-their layout is ``module refresh``:
+The subcommand that regenerates module files to update their content or
+their layout is ``refresh``:
 
-.. command-output:: spack module refresh --help
+.. command-output:: spack module tcl refresh --help
 
 A set of packages can be selected using anonymous specs for the optional
-``constraint`` positional argument. The argument ``--module-type`` identifies
-the type of module files to refresh. Optionally the entire tree can be deleted
+``constraint`` positional argument. Optionally the entire tree can be deleted
 before regeneration if the change in layout is radical.
 
 .. _cmd-spack-module-rm:
 
 ^^^^^^^^^^^^^^^^^^^
-``spack module rm``
+Delete module files
 ^^^^^^^^^^^^^^^^^^^
 
 If instead what you need is just to delete a few module files, then the right
-command is ``module rm``:
+subcommand is ``rm``:
 
-.. command-output:: spack module rm --help
+.. command-output:: spack module tcl rm --help
 
 .. note::
   We care about your module files!
diff --git a/lib/spack/docs/package_list.rst b/lib/spack/docs/package_list.rst
new file mode 100644
index 0000000000..f112525d52
--- /dev/null
+++ b/lib/spack/docs/package_list.rst
@@ -0,0 +1,17 @@
+.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+.. _package-list:
+
+============
+Package List
+============
+
+This is a list of things you can install using Spack.  It is
+automatically generated based on the packages in the latest Spack
+release.
+
+.. raw:: html
+   :file: package_list.html
diff --git a/lib/spack/docs/packaging_guide.rst b/lib/spack/docs/packaging_guide.rst
index a066aa96df..17d7cffed4 100644
--- a/lib/spack/docs/packaging_guide.rst
+++ b/lib/spack/docs/packaging_guide.rst
@@ -1,3 +1,8 @@
+.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 .. _packaging-guide:
 
 ===============
@@ -413,27 +418,26 @@ The most straightforward way to add new versions to your package is to
 add a line like this in the package class:
 
 .. code-block:: python
-   :linenos:
 
    class Foo(Package):
-       url = 'http://example.com/foo-1.0.tar.gz'
+
+       url = "http://example.com/foo-1.0.tar.gz"
+
        version('8.2.1', '4136d7b4c04df68b686570afa26988ac')
-       ...
+       version('8.2.0', '1c9f62f0778697a09d36121ead88e08e')
+       version('8.1.2', 'd47dd09ed7ae6e7fd6f9a816d7f5fdf6')
 
-Versions should be listed with the newest version first.
+Versions should be listed in descending order, from newest to oldest.
 
 ^^^^^^^^^^^^^
 Date Versions
 ^^^^^^^^^^^^^
 
 If you wish to use dates as versions, it is best to use the format
-``@date-yyyy-mm-dd``.  This will ensure they sort in the correct
-order.  If you want your date versions to be numeric (assuming they
-don't conflict with other numeric versions), you can use just
-``yyyy.mm.dd``.
+``@yyyy-mm-dd``.  This will ensure they sort in the correct order.
 
 Alternately, you might use a hybrid release-version / date scheme.
-For example, ``@1.3.2016.08.31`` would mean the version from the
+For example, ``@1.3_2016-08-31`` would mean the version from the
 ``1.3`` branch, as of August 31, 2016.
 
 ^^^^^^^^^^^^
@@ -442,7 +446,7 @@ Version URLs
 
 By default, each version's URL is extrapolated from the ``url`` field
 in the package.  For example, Spack is smart enough to download
-version ``8.2.1.`` of the ``Foo`` package above from
+version ``8.2.1`` of the ``Foo`` package above from
 http://example.com/foo-8.2.1.tar.gz.
 
 If the URL is particularly complicated or changes based on the release,
@@ -515,44 +519,28 @@ of its versions, you can add an explicit URL for a particular version:
 
 
 When you supply a custom URL for a version, Spack uses that URL
-*verbatim* and does not perform extrapolation.
-
-^^^^^^^^^^^^^^^^^^^^^
-PyPI and version URLs
-^^^^^^^^^^^^^^^^^^^^^
-
-In addition to their developer websites, many python packages are hosted at the
-`Python Package Index (PyPi) <https://pypi.python.org/pypi>`_. Although links to
-these individual files are typically `generated using a hash
-<https://bitbucket.org/pypa/pypi/issues/438>`_ it is often possible to find a
-reliable link of the format
-
-.. code-block:: sh
+*verbatim* and does not perform extrapolation. The order of precedence
+of these methods is:
 
-  https://pypi.python.org/packages/source/<first letter of package>/<package>/<package>-<version>.<extension>
+#. package-level ``url``
+#. ``url_for_version()``
+#. version-specific ``url``
 
-Packages hosted on GitHub and the like are often developer versions that do not
-contain all of the files (e.g. configuration scripts) necessary to support
-compilation. For this reason it is ideal to link to a repository such as PyPi
-if possible.
-
-More recently, sources are being indexed at `pypi.io <https://pypi.io>`_ as
-well. Links obtained from this site follow a similar pattern, namely
-
-.. code-block:: sh
-
-  https://pypi.io/packages/source/<first letter of package>/<package>/<package>-<version>.<extension>
-
-These links currently redirect back to `pypi.python.org
-<https://pypi.python.org>`_, but this `may change in the future
-<https://bitbucket.org/pypa/pypi/issues/438#comment-27243225>`_.
+so if your package contains a ``url_for_version()``, it can be overridden
+by a version-specific ``url``.
 
+If your package does not contain a package-level ``url`` or ``url_for_version()``,
+Spack can determine which URL to download from even if only some of the versions
+specify their own ``url``. Spack will use the nearest URL *before* the requested
+version. This is useful for packages that have an easy to extrapolate URL, but
+keep changing their URL format every few releases. With this method, you only
+need to specify the ``url`` when the URL changes.
 
 ^^^^^^^^^^^^^^^^^^^^^^^^
 Skipping the expand step
 ^^^^^^^^^^^^^^^^^^^^^^^^
 
-Spack normally expands archives (e.g. `*.tar.gz` and `*.zip`) automatically
+Spack normally expands archives (e.g. ``*.tar.gz`` and ``*.zip``) automatically
 after downloading them. If you want to skip this step (e.g., for
 self-extracting executables and other custom archive types), you can add
 ``expand=False`` to a ``version`` directive.
@@ -560,7 +548,7 @@ self-extracting executables and other custom archive types), you can add
 .. code-block:: python
 
    version('8.2.1', '4136d7b4c04df68b686570afa26988ac',
-           url='http://example.com/foo-8.2.1-special-version.tar.gz', expand=False)
+           url='http://example.com/foo-8.2.1-special-version.sh', expand=False)
 
 When ``expand`` is set to ``False``, Spack sets the current working
 directory to the directory containing the downloaded archive before it
@@ -605,7 +593,7 @@ here will suffice; for example, ``@develop``, ``@master``, ``@local``.
 The following rules determine the sort order of numeric
 vs. non-numeric versions:
 
-#. The non-numeric versions ``@develop`` is considered greatest (newest).
+#. The non-numeric version ``@develop`` is considered greatest (newest).
 
 #. Numeric versions are all less than ``@develop`` version, and are
    sorted numerically.
@@ -617,7 +605,7 @@ The logic behind this sort order is two-fold:
 
 #. Non-numeric versions are usually used for special cases while
    developing or debugging a piece of software.  Keeping most of them
-   less than numeric versions ensures that Spack choose numeric
+   less than numeric versions ensures that Spack chooses numeric
    versions by default whenever possible.
 
 #. The most-recent development version of a package will usually be
@@ -652,34 +640,6 @@ use:
 #. If all else fails and ``@develop`` is the only matching version, it
    will be used.
 
-^^^^^^^^^^^^^
-``spack md5``
-^^^^^^^^^^^^^
-
-If you have one or more files to checksum, you can use the ``spack md5``
-command to do it:
-
-.. code-block:: console
-
-   $ spack md5 foo-8.2.1.tar.gz foo-8.2.2.tar.gz
-   ==> 2 MD5 checksums:
-   4136d7b4c04df68b686570afa26988ac  foo-8.2.1.tar.gz
-   1586b70a49dfe05da5fcc29ef239dce0  foo-8.2.2.tar.gz
-
-``spack md5`` also accepts one or more URLs and automatically downloads
-the files for you:
-
-.. code-block:: console
-
-   $ spack md5 http://example.com/foo-8.2.1.tar.gz
-   ==> Trying to fetch from http://example.com/foo-8.2.1.tar.gz
-   ######################################################################## 100.0%
-   ==> 1 MD5 checksum:
-   4136d7b4c04df68b686570afa26988ac  foo-8.2.1.tar.gz
-
-Doing this for lots of files, or whenever a new package version is
-released, is tedious.  See ``spack checksum`` below for an automated
-version of this process.
 
 .. _cmd-spack-checksum:
 
@@ -707,7 +667,7 @@ example for ``libelf``:
      ...
      0.5.2     http://www.mr511.de/software/libelf-0.5.2.tar.gz
 
-   How many would you like to checksum? (default is 5, q to abort)
+   How many would you like to checksum? (default is 1, q to abort)
 
 This does the same thing that ``spack create`` does, but it allows you
 to go back and add new versions easily as you need them (e.g., as
@@ -833,12 +793,12 @@ But its downloads are in many different subdirectories of
        homepage   = "http://www.mpich.org"
        url        = "http://www.mpich.org/static/downloads/3.0.4/mpich-3.0.4.tar.gz"
        list_url   = "http://www.mpich.org/static/downloads/"
-       list_depth = 2
+       list_depth = 1
 
 By default, Spack only looks at the top-level page available at
-``list_url``.  ``list_depth`` tells it to follow up to 2 levels of
-links from the top-level page.  Note that here, this implies two
-levels of subdirectories, as the ``mpich`` website is structured much
+``list_url``.  ``list_depth = 1`` tells it to follow up to 1 level of
+links from the top-level page.  Note that here, this implies 1
+level of subdirectories, as the ``mpich`` website is structured much
 like a filesystem.  But ``list_depth`` really refers to link depth
 when spidering the page.
 
@@ -851,13 +811,57 @@ Fetching from code repositories
 For some packages, source code is provided in a Version Control System
 (VCS) repository rather than in a tarball.  Spack can fetch packages
 from VCS repositories. Currently, Spack supports fetching with `Git
-<git-fetch_>`_, `Mercurial (hg) <hg-fetch_>`_, and `Subversion (SVN)
-<svn-fetch_>`_.
+<git-fetch_>`_, `Mercurial (hg) <hg-fetch_>`_, `Subversion (svn)
+<svn-fetch_>`_, and `Go <go-fetch_>`_.
+
+To fetch a package from a source repository, Spack needs to know which
+VCS to use and where to download from. Much like with ``url``, package
+authors can specify a class-level ``git``, ``hg``, ``svn``, or ``go``
+attribute containing the correct download location.
+
+Many packages developed with Git have both a Git repository as well as
+release tarballs available for download. Packages can define both a
+class-level tarball URL and VCS. For example:
+
+.. code-block:: python
+
+   class Trilinos(CMakePackage):
+
+       homepage = "https://trilinos.org/"
+       url      = "https://github.com/trilinos/Trilinos/archive/trilinos-release-12-12-1.tar.gz"
+       git      = "https://github.com/trilinos/Trilinos.git"
+
+       version('develop', branch='develop')
+       version('master',  branch='master')
+       version('12.12.1', 'ecd4606fa332212433c98bf950a69cc7')
+       version('12.10.1', '667333dbd7c0f031d47d7c5511fd0810')
+       version('12.8.1',  '9f37f683ee2b427b5540db8a20ed6b15')
+
+If a package contains both a ``url`` and ``git`` class-level attribute,
+Spack decides which to use based on the arguments to the ``version()``
+directive. Versions containing a specific branch, tag, or revision are
+assumed to be for VCS download methods, while versions containing a
+checksum are assumed to be for URL download methods.
+
+Like ``url``, if a specific version downloads from a different repository
+than the default repo, it can be overridden with a version-specific argument.
+
+.. note::
+
+   In order to reduce ambiguity, each package can only have a single VCS
+   top-level attribute in addition to ``url``. In the rare case that a
+   package uses multiple VCS, a fetch strategy can be specified for each
+   version. For example, the ``rockstar`` package contains:
+
+   .. code-block:: python
+
+      class Rockstar(MakefilePackage):
+
+          homepage = "https://bitbucket.org/gfcstanford/rockstar"
+
+          version('develop', git='https://bitbucket.org/gfcstanford/rockstar.git')
+          version('yt', hg='https://bitbucket.org/MatthewTurk/rockstar')
 
-To fetch a package from a source repository, you add a ``version()``
-call to your package with parameters indicating the repository URL and
-any branch, tag, or revision to fetch.  See below for the parameters
-you'll need for each VCS system.
 
 .. _git-fetch:
 
@@ -865,11 +869,11 @@ you'll need for each VCS system.
 Git
 ^^^
 
-Git fetching is enabled with the following parameters to ``version``:
+Git fetching supports the following parameters to ``version``:
 
-* ``git``: URL of the git repository.
-* ``tag``: name of a tag to fetch.
-* ``branch``: name of a branch to fetch.
+* ``git``: URL of the git repository, if different than the class-level ``git``.
+* ``branch``: Name of a branch to fetch.
+* ``tag``: Name of a tag to fetch.
 * ``commit``: SHA hash (or prefix) of a commit to fetch.
 * ``submodules``: Also fetch submodules recursively when checking out this repository.
 
@@ -881,66 +885,72 @@ Default branch
   .. code-block:: python
 
      class Example(Package):
-         ...
-         version('develop', git='https://github.com/example-project/example.git')
 
-  This download method is untrusted, and is not recommended.
+         git = "https://github.com/example-project/example.git"
 
-Tags
-  To fetch from a particular tag, use the ``tag`` parameter along with
-  ``git``:
+         version('develop')
+
+  This download method is untrusted, and is not recommended. Aside from HTTPS,
+  there is no way to verify that the repository has not been compromised, and
+  the commit you get when you install the package likely won't be the same
+  commit that was used when the package was first written. Additionally, the
+  default branch may change. It is best to at least specify a branch name.
+
+Branches
+  To fetch a particular branch, use the ``branch`` parameter:
 
   .. code-block:: python
 
-     version('1.0.1', git='https://github.com/example-project/example.git',
-             tag='v1.0.1')
+     version('experimental', branch='experimental')
 
-  This download method is untrusted, and is not recommended.
+  This download method is untrusted, and is not recommended. Branches are
+  moving targets, so the commit you get when you install the package likely
+  won't be the same commit that was used when the package was first written.
 
-Branches
-  To fetch a particular branch, use ``branch`` instead:
+Tags
+  To fetch from a particular tag, use ``tag`` instead:
 
   .. code-block:: python
 
-     version('experimental', git='https://github.com/example-project/example.git',
-             branch='experimental')
+     version('1.0.1', tag='v1.0.1')
 
-  This download method is untrusted, and is not recommended.
+  This download method is untrusted, and is not recommended. Although tags
+  are generally more stable than branches, Git allows tags to be moved.
+  Many developers use tags to denote rolling releases, and may move the
+  tag when a bug is patched.
 
 Commits
   Finally, to fetch a particular commit, use ``commit``:
 
   .. code-block:: python
 
-     version('2014-10-08', git='https://github.com/example-project/example.git',
-             commit='9d38cd4e2c94c3cea97d0e2924814acc')
+     version('2014-10-08', commit='9d38cd4e2c94c3cea97d0e2924814acc')
 
   This doesn't have to be a full hash; you can abbreviate it as you'd
   expect with git:
 
   .. code-block:: python
 
-     version('2014-10-08', git='https://github.com/example-project/example.git',
-             commit='9d38cd')
+     version('2014-10-08', commit='9d38cd')
 
   This download method *is trusted*.  It is the recommended way to
   securely download from a Git repository.
 
   It may be useful to provide a saner version for commits like this,
-  e.g. you might use the date as the version, as done above.  Or you
-  could just use the abbreviated commit hash.  It's up to the package
-  author to decide what makes the most sense.
+  e.g. you might use the date as the version, as done above. Or, if you
+  know the commit at which a release was cut, you can use the release
+  version. It's up to the package author to decide what makes the most
+  sense. Although you can use the commit hash as the version number,
+  this is not recommended, as it won't sort properly.
 
 Submodules
-
   You can supply ``submodules=True`` to cause Spack to fetch submodules
   recursively along with the repository at fetch time. For more information
   about git submodules see the manpage of git: ``man git-submodule``.
 
   .. code-block:: python
 
-     version('1.0.1', git='https://github.com/example-project/example.git',
-             tag='v1.0.1', submodules=True)
+     version('1.0.1', tag='v1.0.1', submodules=True)
 
 
 .. _github-fetch:
@@ -949,7 +959,7 @@ Submodules
 GitHub
 ^^^^^^
 
-If a project is hosted on GitHub, *any* valid Git branch, tag or hash
+If a project is hosted on GitHub, *any* valid Git branch, tag, or hash
 may be downloaded as a tarball.  This is accomplished simply by
 constructing an appropriate URL.  Spack can checksum any package
 downloaded this way, thereby producing a trusted download.  For
@@ -959,7 +969,7 @@ checksum.
 .. code-block:: python
 
        version('1.9.5.1.1', 'd035e4bc704d136db79b43ab371b27d2',
-           url='https://www.github.com/jswhit/pyproj/tarball/0be612cc9f972e38b50a90c946a9b353e2ab140f')
+               url='https://www.github.com/jswhit/pyproj/tarball/0be612cc9f972e38b50a90c946a9b353e2ab140f')
 
 .. _hg-fetch:
 
@@ -967,34 +977,38 @@ checksum.
 Mercurial
 ^^^^^^^^^
 
-Fetching with mercurial works much like `git <git-fetch>`_, but you
+Fetching with Mercurial works much like `Git <git-fetch>`_, but you
 use the ``hg`` parameter.
 
-Default
-  Add the ``hg`` parameter with no ``revision``:
+Default branch
+  Add the ``hg`` attribute with no ``revision`` passed to ``version``:
 
   .. code-block:: python
 
-     version('develop', hg='https://jay.grs.rwth-aachen.de/hg/example')
+     class Example(Package):
 
-  This download method is untrusted, and is not recommended.
+         hg = "https://bitbucket.org/example-project/example"
+
+         version('develop')
+
+  This download method is untrusted, and is not recommended. As with
+  Git's default fetching strategy, there is no way to verify the
+  integrity of the download.
 
 Revisions
-  Add ``hg`` and ``revision`` parameters:
+  To fetch a particular revision, use the ``revision`` parameter:
 
   .. code-block:: python
 
-     version('1.0', hg='https://jay.grs.rwth-aachen.de/hg/example',
-             revision='v1.0')
-
-  This download method is untrusted, and is not recommended.
+     version('1.0', revision='v1.0')
 
   Unlike ``git``, which has special parameters for different types of
   revisions, you can use ``revision`` for branches, tags, and commits
-  when you fetch with Mercurial.
+  when you fetch with Mercurial. Like Git, fetching specific branches
+  or tags is an untrusted download method, and is not recommended.
+  The recommended fetch strategy is to specify a particular commit
+  hash as the revision.
 
-As with git, you can fetch these versions using the ``spack install
-example@<version>`` command-line syntax.
 
 .. _svn-fetch:
 
@@ -1002,34 +1016,70 @@ example@<version>`` command-line syntax.
 Subversion
 ^^^^^^^^^^
 
-To fetch with subversion, use the ``svn`` and ``revision`` parameters:
+To fetch with subversion, use the ``svn`` and ``revision`` parameters.
 
 Fetching the head
-  Simply add an ``svn`` parameter to ``version``:
+  Simply add an ``svn`` parameter to the package:
 
   .. code-block:: python
 
-     version('develop', svn='https://outreach.scidac.gov/svn/libmonitor/trunk')
+     class Example(Package):
 
-  This download method is untrusted, and is not recommended.
+         svn = "https://outreach.scidac.gov/svn/example/trunk"
+
+         version('develop')
+
+  This download method is untrusted, and is not recommended for the
+  same reasons as mentioned above.
 
 Fetching a revision
-  To fetch a particular revision, add a ``revision`` to the
-  version call:
+  To fetch a particular revision, add a ``revision`` argument to the
+  version directive:
 
   .. code-block:: python
 
-     version('develop', svn='https://outreach.scidac.gov/svn/libmonitor/trunk',
-             revision=128)
+     version('develop', revision=128)
 
   This download method is untrusted, and is not recommended.
 
+  Unfortunately, Subversion has no commit hashing scheme like Git and
+  Mercurial do, so there is no way to guarantee that the download you
+  get is the same as the download used when the package was created.
+  Use at your own risk.
+
 Subversion branches are handled as part of the directory structure, so
-you can check out a branch or tag by changing the ``url``.
+you can check out a branch or tag by changing the URL. If you want to
+package multiple branches, simply add a ``svn`` argument to each
+version directive.
+
+.. _go-fetch:
 
--------------------------------------------------
+^^
+Go
+^^
+
+Go isn't a VCS, it is a programming language with a builtin command,
+`go get <https://golang.org/cmd/go/#hdr-Download_and_install_packages_and_dependencies>`_,
+that fetches packages and their dependencies automatically.
+It can clone a Git repository, or download from another source location.
+For example:
+
+.. code-block:: python
+
+   class ThePlatinumSearcher(Package):
+
+       homepage = "https://github.com/monochromegane/the_platinum_searcher"
+       go       = "github.com/monochromegane/the_platinum_searcher/..."
+
+       version('head')
+
+Go cannot be used to fetch a particular commit or branch, it always
+downloads the head of the repository. This download method is untrusted,
+and is not recommended. Use another fetch strategy whenever possible.
+
+------------------------------------
 Resources (expanding extra tarballs)
--------------------------------------------------
+------------------------------------
 
 Some packages (most notably compilers) provide optional features if additional
 resources are expanded within their source tree before building. In Spack it is
@@ -1593,6 +1643,14 @@ correct way to specify this would be:
 
    depends_on('python@2.6.0:2.6.999')
 
+A spec can contain multiple version ranges separated by commas.
+For example, if you need Boost 1.59.0 or newer, but there are known
+issues with 1.64.0, 1.65.0, and 1.66.0, you can say:
+
+.. code-block:: python
+
+   depends_on('boost@1.59.0:1.63,1.65.1,1.67.0:')
+
 
 ^^^^^^^^^^^^^^^^
 Dependency types
@@ -1874,18 +1932,38 @@ from being linked in at activation time.
    ``depends_on('python')`` and ``extends(python)`` in the same
    package.  ``extends`` implies ``depends_on``.
 
+-----
+Views
+-----
+
+As covered in :ref:`filesystem-views`, the ``spack view`` command can be
+used to symlink a number of packages into a merged prefix. The methods of
+``PackageViewMixin`` can be overridden to customize how packages are added
+to views. Generally this can be used to create copies of specific files rather
+than symlinking them when symlinking does not work. For example, ``Python``
+overrides ``add_files_to_view`` in order to create a copy of the ``python``
+binary since the real path of the Python executable is used to detect
+extensions; as a consequence python extension packages (those inheriting from
+``PythonPackage``) likewise override ``add_files_to_view`` in order to rewrite
+shebang lines which point to the Python interpreter.
+
 ^^^^^^^^^^^^^^^^^^^^^^^^^
 Activation & deactivation
 ^^^^^^^^^^^^^^^^^^^^^^^^^
 
+Adding an extension to a view is referred to as an activation. If the view is
+maintained in the Spack installation prefix of the extendee this is called a
+global activation. Activations may involve updating some centralized state
+that is maintained by the extendee package, so there can be additional work
+for adding extensions compared with non-extension packages.
+
 Spack's ``Package`` class has default ``activate`` and ``deactivate``
 implementations that handle symbolically linking extensions' prefixes
-into the directory of the parent package.  However, extendable
-packages can override these methods to add custom activate/deactivate
-logic of their own.  For example, the ``activate`` and ``deactivate``
-methods in the Python class use the symbolic linking, but they also
-handle details surrounding Python's ``.pth`` files, and other aspects
-of Python packaging.
+into a specified view. Extendable packages can override these methods
+to add custom activate/deactivate logic of their own.  For example,
+the ``activate`` and ``deactivate`` methods in the Python class handle
+symbolic linking of extensions, but they also handle details surrounding
+Python's ``.pth`` files, and other aspects of Python packaging.
 
 Spack's extensions mechanism is designed to be extensible, so that
 other packages (like Ruby, R, Perl, etc.)  can provide their own
@@ -1900,7 +1978,7 @@ Let's look at Python's activate function:
 
 This function is called on the *extendee* (Python).  It first calls
 ``activate`` in the superclass, which handles symlinking the
-extension package's prefix into this package's prefix.  It then does
+extension package's prefix into the specified view.  It then does
 some special handling of the ``easy-install.pth`` file, part of
 Python's setuptools.
 
@@ -2268,6 +2346,10 @@ The classes that are currently provided by Spack are:
     | :py:class:`.CMakePackage`     | Specialized class for packages   |
     |                               | built using CMake                |
     +-------------------------------+----------------------------------+
+    | :py:class:`.CudaPackage`      | A helper class for packages that |
+    |                               | use CUDA. It is intended to be   |
+    |                               | used in combination with others  |
+    +-------------------------------+----------------------------------+
     | :py:class:`.QMakePackage`     | Specialized class for packages   |
     |                               | build using QMake                |
     +-------------------------------+----------------------------------+
@@ -2280,6 +2362,9 @@ The classes that are currently provided by Spack are:
     | :py:class:`.RPackage`         | Specialized class for            |
     |                               | :py:class:`.R` extensions        |
     +-------------------------------+----------------------------------+
+    | :py:class:`.OctavePackage`    | Specialized class for            |
+    |                               | :py:class:`.Octave` packages     |
+    +-------------------------------+----------------------------------+
     | :py:class:`.PythonPackage`    | Specialized class for            |
     |                               | :py:class:`.Python` extensions   |
     +-------------------------------+----------------------------------+
@@ -2607,15 +2692,16 @@ as arguments.
 
 Here are the definitions of the three built-in flag handlers:
 
-.. code-block:: python
+   def build_system_flags(self, name, flags):
+       return (None, None, flags)
 
-   def inject_flags(self, name, flags):
+   def inject_flags(pkg, name, flags):
        return (flags, None, None)
 
-   def env_flags(self, name, flags):
+   def env_flags(pkg, name, flags):
        return (None, flags, None)
 
-   def build_system_flags(self, name, flags):
+   def build_system_flags(pkg, name, flags):
        return (None, None, flags)
 
 .. note::
@@ -2628,10 +2714,7 @@ the built-in flag handlers,
 
 .. code-block:: python
 
-   flag_handler = <PackageClass>.env_flags
-
-where ``<PackageClass>`` can be any of the subclasses of PackageBase
-discussed in :ref:`installation_procedure`,
+   flag_handler = env_flags
 
 or by implementing the flag_handler method. Suppose for a package
 ``Foo`` we need to pass ``cflags``, ``cxxflags``, and ``cppflags``
@@ -2657,7 +2740,7 @@ method of the ``EnvironmentModifications`` class to append values to a
 list of flags whenever the flag handler is ``env_flags``. If the
 package passes flags through the environment or the build system
 manually (in the install method, for example), we recommend using the
-default flag handler, or removind manual references and implementing a
+default flag handler, or removing manual references and implementing a
 custom flag handler method that adds the desired flags to export as
 environment variables or pass to the build system. Manual flag passing
 is likely to interfere with the ``env_flags`` and
@@ -2667,8 +2750,8 @@ In rare circumstances such as compiling and running small unit tests, a
 package developer may need to know what are the appropriate compiler
 flags to enable features like ``OpenMP``, ``c++11``, ``c++14`` and
 alike. To that end the compiler classes in ``spack`` implement the
-following **properties**: ``openmp_flag``, ``cxx11_flag``,
-``cxx14_flag``, which can be accessed in a package by
+following **properties**: ``openmp_flag``, ``cxx98_flag``, ``cxx11_flag``,
+``cxx14_flag``, and ``cxx17_flag``, which can be accessed in a package by
 ``self.compiler.cxx11_flag`` and alike. Note that the implementation is
 such that if a given compiler version does not support this feature, an
 error will be produced. Therefore package developers can also use these
@@ -2679,6 +2762,8 @@ is handy when a package supports additional variants like
 
    variant('openmp', default=True, description="Enable OpenMP support.")
 
+.. _blas_lapack_scalapack:
+
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 Blas, Lapack and ScaLapack libraries
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -2776,11 +2861,11 @@ Prefix Attribute        Location
 
 Of course, this only works if your file or directory is a valid Python
 variable name. If your file or directory contains dashes or dots, use
-``join_path`` instead:
+``join`` instead:
 
 .. code-block:: python
 
-   join_path(prefix.lib, 'libz.a')
+   prefix.lib.join('libz.a')
 
 
 .. _spec-objects:
diff --git a/lib/spack/docs/repositories.rst b/lib/spack/docs/repositories.rst
index 5e722e2139..699fe4a7ed 100644
--- a/lib/spack/docs/repositories.rst
+++ b/lib/spack/docs/repositories.rst
@@ -1,3 +1,8 @@
+.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 .. _repositories:
 
 =============================
@@ -36,7 +41,7 @@ Package repositories allow you to:
 
 1. Maintain your own packages separately from Spack;
 
-2. Share your packages (e.g. by hosting them in a shared file system),
+2. Share your packages (e.g., by hosting them in a shared file system),
    without committing them to the built-in Spack package repository; and
 
 3. Override built-in Spack packages with your own implementation.
@@ -72,7 +77,7 @@ paths to repositories. Each path is on a separate line starting with
   - /opt/local-repo
   - $spack/var/spack/repos/builtin
 
-When Spack interprets a spec, e.g. ``mpich`` in ``spack install mpich``,
+When Spack interprets a spec, e.g., ``mpich`` in ``spack install mpich``,
 it searches these repositories in order (first to last) to resolve each
 package name.  In this example, Spack will look for the following
 packages and use the first valid file:
@@ -142,7 +147,7 @@ packages created by the Computation directorate might use ``llnl.comp``.
 Spack cannot ensure that every repository is named uniquely, but it will
 prevent you from registering two repositories with the same namespace at
 the same time.  If you try to add a repository that has the same name as
-an existing one, e.g. ``builtin``, Spack will print a warning message.
+an existing one, e.g., ``builtin``, Spack will print a warning message.
 
 .. _namespace-example:
 
@@ -445,7 +450,7 @@ Spack repo namespaces are actually Python namespaces tacked on under
 ``spack.pkg``.  The search semantics of ``repos.yaml`` are actually
 implemented using Python's built-in `sys.path
 <https://docs.python.org/2/library/sys.html#sys.path>`_ search.  The
-:py:mod:`spack.repository` module implements a custom `Python importer
+:py:mod:`spack.repo` module implements a custom `Python importer
 <https://docs.python.org/2/library/imp.html>`_.
 
 .. warning::
diff --git a/lib/spack/docs/requirements.txt b/lib/spack/docs/requirements.txt
index d3fe0d18d7..592060a89e 100644
--- a/lib/spack/docs/requirements.txt
+++ b/lib/spack/docs/requirements.txt
@@ -1,5 +1,6 @@
 # These dependencies should be installed using pip in order
 # to build the documentation.
 
-sphinx
+sphinx==1.7.0
 sphinxcontrib-programoutput
+sphinx-rtd-theme
diff --git a/lib/spack/docs/tutorial.rst b/lib/spack/docs/tutorial.rst
index ff2a2f6870..c41f8c87d2 100644
--- a/lib/spack/docs/tutorial.rst
+++ b/lib/spack/docs/tutorial.rst
@@ -1,12 +1,17 @@
+.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 .. _spack-101:
 
 =============================
 Tutorial: Spack 101
 =============================
 
-This is a 3-hour introduction to Spack with lectures and live demos.  It
-was presented as a tutorial at `Supercomputing 2016
-<http://sc16.supercomputing.org>`_.  You can use these materials to teach
+This is a full-day introduction to Spack with lectures and live demos.  It
+was presented as a tutorial at `Supercomputing 2018
+<http://sc18.supercomputing.org>`_.  You can use these materials to teach
 a course on Spack at your own site, or you can just skip ahead and read
 the live demo scripts to see how Spack is used in practice.
 
@@ -15,19 +20,18 @@ the live demo scripts to see how Spack is used in practice.
 .. rubric:: Slides
 
 .. figure:: tutorial/sc16-tutorial-slide-preview.png
-   :target: http://llnl.github.io/spack/files/Spack-SC16-Tutorial.pdf
+   :target: http://spack.io/slides/Spack-SC18-Tutorial.pdf
    :height: 72px
    :align: left
    :alt: Slide Preview
 
-`Download Slides <http://llnl.github.io/spack/files/Spack-SC16-Tutorial.pdf>`_.
+`Download Slides <http://spack.io/slides/Spack-SC18-Tutorial.pdf>`_.
 
-**Full citation:** Todd Gamblin, Massimiliano Culpo, Gregory Becker, Matt
-Legendre, Greg Lee, Elizabeth Fischer, and Benedikt Hegner.
+**Full citation:** Todd Gamblin, Gregory Becker, Massimiliano Culpo, Matt
+Legendre, Mario Melara, Peter Scheibel, and Adam Stewart.
 `Managing HPC Software Complexity with Spack
-<http://sc16.supercomputing.org/presentation/?id=tut166&sess=sess209>`_.
-Tutorial presented at Supercomputing 2016. November 13, 2016, Salt Lake
-City, UT, USA.
+<https://sc18.supercomputing.org/presentation/?id=tut165&sess=sess252>`_.
+Tutorial presented at Supercomputing 2018. November 12, 2018, Dallas, TX, USA.
 
 .. _sc16-live-demos:
 
@@ -39,9 +43,10 @@ correspond to sections in the slides above.
   1. :ref:`basics-tutorial`
   2. :ref:`configs-tutorial`
   3. :ref:`packaging-tutorial`
-  4. :ref:`build-systems-tutorial`
-  5. :ref:`advanced-packaging-tutorial`
-  6. :ref:`modules-tutorial`
+  4. :ref:`environments-tutorial`
+  5. :ref:`modules-tutorial`
+  6. :ref:`build-systems-tutorial`
+  7. :ref:`advanced-packaging-tutorial`
 
 Full contents:
 
@@ -49,6 +54,7 @@ Full contents:
    tutorial_basics
    tutorial_configuration
    tutorial_packaging
+   tutorial_environments
+   tutorial_modules
    tutorial_buildsystems
    tutorial_advanced_packaging
-   tutorial_modules
diff --git a/lib/spack/docs/tutorial/examples/0.package.py b/lib/spack/docs/tutorial/examples/0.package.py
index 0a42cdc802..cdc8f6a6e4 100644
--- a/lib/spack/docs/tutorial/examples/0.package.py
+++ b/lib/spack/docs/tutorial/examples/0.package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 # This is a template package file for Spack.  We've put "FIXME"
 # next to all the things you'll want to change. Once you've handled
diff --git a/lib/spack/docs/tutorial/examples/1.package.py b/lib/spack/docs/tutorial/examples/1.package.py
index 308779d016..a6af7ed3e4 100644
--- a/lib/spack/docs/tutorial/examples/1.package.py
+++ b/lib/spack/docs/tutorial/examples/1.package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/lib/spack/docs/tutorial/examples/2.package.py b/lib/spack/docs/tutorial/examples/2.package.py
index 7980768e06..c2687a95cd 100644
--- a/lib/spack/docs/tutorial/examples/2.package.py
+++ b/lib/spack/docs/tutorial/examples/2.package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/lib/spack/docs/tutorial/examples/3.package.py b/lib/spack/docs/tutorial/examples/3.package.py
index b30dd900ae..1a9d76f050 100644
--- a/lib/spack/docs/tutorial/examples/3.package.py
+++ b/lib/spack/docs/tutorial/examples/3.package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/lib/spack/docs/tutorial/examples/4.package.py b/lib/spack/docs/tutorial/examples/4.package.py
index 116a11a0fa..c90c14b836 100644
--- a/lib/spack/docs/tutorial/examples/4.package.py
+++ b/lib/spack/docs/tutorial/examples/4.package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/lib/spack/docs/tutorial/examples/5.package.py b/lib/spack/docs/tutorial/examples/5.package.py
index 3e7a1f83cb..18cb846d34 100644
--- a/lib/spack/docs/tutorial/examples/5.package.py
+++ b/lib/spack/docs/tutorial/examples/5.package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/lib/spack/docs/tutorial/examples/Autotools/0.package.py b/lib/spack/docs/tutorial/examples/Autotools/0.package.py
index 44a157b36a..b9d2f2ca43 100644
--- a/lib/spack/docs/tutorial/examples/Autotools/0.package.py
+++ b/lib/spack/docs/tutorial/examples/Autotools/0.package.py
@@ -1,31 +1,12 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/llnl/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class Mpileaks(AutoToolsPackage):
+class Mpileaks(AutotoolsPackage):
     """Tool to detect and report leaked MPI objects like MPI_Requests and
        MPI_Datatypes."""
 
diff --git a/lib/spack/docs/tutorial/examples/Autotools/1.package.py b/lib/spack/docs/tutorial/examples/Autotools/1.package.py
index bc12c70b7f..cebe14f91b 100644
--- a/lib/spack/docs/tutorial/examples/Autotools/1.package.py
+++ b/lib/spack/docs/tutorial/examples/Autotools/1.package.py
@@ -1,31 +1,12 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/llnl/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class Mpileaks(AutoToolsPackage):
+class Mpileaks(AutotoolsPackage):
     """Tool to detect and report leaked MPI objects like MPI_Requests and
        MPI_Datatypes."""
 
diff --git a/lib/spack/docs/tutorial/examples/Cmake/0.package.py b/lib/spack/docs/tutorial/examples/Cmake/0.package.py
index 724b3fdf94..2cdf06fd69 100644
--- a/lib/spack/docs/tutorial/examples/Cmake/0.package.py
+++ b/lib/spack/docs/tutorial/examples/Cmake/0.package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/llnl/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 # This is a template package file for Spack.  We've put "FIXME"
 # next to all the things you'll want to change. Once you've handled
diff --git a/lib/spack/docs/tutorial/examples/Cmake/1.package.py b/lib/spack/docs/tutorial/examples/Cmake/1.package.py
index dcb44260d2..4b8c35b5a3 100644
--- a/lib/spack/docs/tutorial/examples/Cmake/1.package.py
+++ b/lib/spack/docs/tutorial/examples/Cmake/1.package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/llnl/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/lib/spack/docs/tutorial/examples/Cmake/2.package.py b/lib/spack/docs/tutorial/examples/Cmake/2.package.py
index 126a841ce9..2fbff1ce08 100644
--- a/lib/spack/docs/tutorial/examples/Cmake/2.package.py
+++ b/lib/spack/docs/tutorial/examples/Cmake/2.package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/llnl/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/lib/spack/docs/tutorial/examples/Makefile/0.package.py b/lib/spack/docs/tutorial/examples/Makefile/0.package.py
index 641b6ccb8f..c6be060420 100644
--- a/lib/spack/docs/tutorial/examples/Makefile/0.package.py
+++ b/lib/spack/docs/tutorial/examples/Makefile/0.package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/llnl/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/lib/spack/docs/tutorial/examples/Makefile/1.package.py b/lib/spack/docs/tutorial/examples/Makefile/1.package.py
index 709bc71afa..184a8a137a 100644
--- a/lib/spack/docs/tutorial/examples/Makefile/1.package.py
+++ b/lib/spack/docs/tutorial/examples/Makefile/1.package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/llnl/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/lib/spack/docs/tutorial/examples/Makefile/2.package.py b/lib/spack/docs/tutorial/examples/Makefile/2.package.py
index 10aba473e3..fda0d8aae6 100644
--- a/lib/spack/docs/tutorial/examples/Makefile/2.package.py
+++ b/lib/spack/docs/tutorial/examples/Makefile/2.package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/llnl/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/lib/spack/docs/tutorial/examples/Makefile/3.package.py b/lib/spack/docs/tutorial/examples/Makefile/3.package.py
index 269ab2c454..7520ad5c27 100644
--- a/lib/spack/docs/tutorial/examples/Makefile/3.package.py
+++ b/lib/spack/docs/tutorial/examples/Makefile/3.package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/llnl/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -43,11 +24,13 @@ class Bowtie(MakefilePackage):
         makefile.filter('CC= .*', 'CC = ' + env['CC'])
         makefile.filter('CXX = .*', 'CXX = ' + env['CXX'])
 
-    def build(self, spec, prefix):
+    @property
+    def build_targets(self):
         if "+tbb" in spec:
-            make()
+            return []
         else:
-            make("NO_TBB=1")
+            return ["NO_TBB=1"]
 
-    def install(self, spec, prefix):
-        make('prefix={0}'.format(self.prefix), 'install')
+    @property
+    def install_targets(self):
+        return ['prefix={0}'.format(self.prefix), 'install']
diff --git a/lib/spack/docs/tutorial/examples/PyPackage/0.package.py b/lib/spack/docs/tutorial/examples/PyPackage/0.package.py
index 48114075a7..e06546ae9a 100644
--- a/lib/spack/docs/tutorial/examples/PyPackage/0.package.py
+++ b/lib/spack/docs/tutorial/examples/PyPackage/0.package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/llnl/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 # This is a template package file for Spack.  We've put "FIXME"
 # next to all the things you'll want to change. Once you've handled
diff --git a/lib/spack/docs/tutorial/examples/PyPackage/1.package.py b/lib/spack/docs/tutorial/examples/PyPackage/1.package.py
index a9cbff00e2..40402a824e 100644
--- a/lib/spack/docs/tutorial/examples/PyPackage/1.package.py
+++ b/lib/spack/docs/tutorial/examples/PyPackage/1.package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/llnl/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/lib/spack/docs/tutorial_advanced_packaging.rst b/lib/spack/docs/tutorial_advanced_packaging.rst
index 901e75bfd7..dafc095f5b 100644
--- a/lib/spack/docs/tutorial_advanced_packaging.rst
+++ b/lib/spack/docs/tutorial_advanced_packaging.rst
@@ -1,104 +1,238 @@
+.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 .. _advanced-packaging-tutorial:
 
 ============================
 Advanced Topics in Packaging
 ============================
 
-While you can quickly accomplish most common tasks with what
-was covered in :ref:`packaging-tutorial`, there are times when such
-knowledge won't suffice. Usually this happens for libraries that provide
-more than one API and need to let dependents decide which one to use
-or for packages that provide tools that are invoked at build-time,
-or in other similar situations.
+Spack tries to automatically configure packages with information from
+dependencies such that all you need to do is to list the dependencies
+(i.e., with the ``depends_on`` directive) and the build system (for example
+by deriving from :code:`CmakePackage`).
 
-In the following we'll dig into some of the details of package
-implementation that help us deal with these rare, but important,
-occurrences. You can rest assured that in every case Spack remains faithful to
-its philosophy: keep simple things simple, but be flexible enough when
-complex requests arise!
+However, there are many special cases. Often you need to retrieve details
+about dependencies to set package-specific configuration options, or to
+define package-specific environment variables used by the package's build
+system. This tutorial covers how to retrieve build information from
+dependencies, and how you can automatically provide important information to
+dependents in your package.
 
 ----------------------
 Setup for the tutorial
 ----------------------
 
-The simplest way to follow along with this tutorial is to use our Docker image,
-which comes with Spack and various packages pre-installed:
+.. note::
 
-.. code-block:: console
+  If you are not using the tutorial docker image, it is recommended that you
+  do this section of the tutorial in a fresh clone of Spack
 
-  $ docker pull alalazo/spack:advanced_packaging_tutorial
-  $ docker run --rm -h advanced-packaging-tutorial -it alalazo/spack:advanced_packaging_tutorial
-  root@advanced-packaging-tutorial:/#
-  root@advanced-packaging-tutorial:/# spack find
-  ==> 20 installed packages.
-  -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
-  arpack-ng@3.5.0  hdf5@1.10.1   libpciaccess@0.13.5  libtool@2.4.6  m4@1.4.18  ncurses@6.0          openblas@0.2.20  openssl@1.0.2k     superlu@5.2.1       xz@5.2.3
-  cmake@3.9.4      hwloc@1.11.8  libsigsegv@2.11      libxml2@2.9.4  mpich@3.2  netlib-lapack@3.6.1  openmpi@3.0.0    pkg-config@0.29.2  util-macros@1.19.1  zlib@1.2.11
+The tutorial uses custom package definitions with missing sections that
+will be filled in during the tutorial. These package definitions are stored
+in a separate package repository, which can be enabled with:
 
-If you already started the image, you can set the ``EDITOR`` environment
-variable to your preferred editor (``vi``, ``emacs``, and ``nano`` are included in the image)
-and move directly to :ref:`specs_build_interface_tutorial`.
+.. code-block:: console
 
-If you choose not to use the Docker image, you can clone the Spack repository
-and build the necessary bits yourself:
+  $ spack repo add --scope=site var/spack/repos/tutorial
 
-.. code-block:: console
+This section of the tutorial may also require a newer version of gcc, which
+you can add with:
 
-  $ git clone https://github.com/spack/spack.git
-  Cloning into 'spack'...
-  remote: Counting objects: 92731, done.
-  remote: Compressing objects: 100% (1108/1108), done.
-  remote: Total 92731 (delta 1964), reused 4186 (delta 1637), pack-reused 87932
-  Receiving objects: 100% (92731/92731), 33.31 MiB | 64.00 KiB/s, done.
-  Resolving deltas: 100% (43557/43557), done.
-  Checking connectivity... done.
+.. code-block:: console
 
-  $ cd spack
-  $ git checkout tutorials/advanced_packaging
-  Branch tutorials/advanced_packaging set up to track remote branch tutorials/advanced_packaging from origin.
-  Switched to a new branch 'tutorials/advanced_packaging'
+  $ spack install gcc@7.2.0
+  $ spack compiler add --scope=site path/to/spack-installed-gcc/bin
 
-At this point you can install the software that will be used
-during the rest of the tutorial (the output of the commands is omitted
-for the sake of brevity):
+If you are using the tutorial docker image, all dependency packages
+will have been installed. Otherwise, to install these packages you can use
+the following commands:
 
 .. code-block:: console
 
   $ spack install openblas
   $ spack install netlib-lapack
   $ spack install mpich
-  $ spack install openmpi
-  $ spack install --only=dependencies armadillo ^openblas
-  $ spack install --only=dependencies netcdf
-  $ spack install --only=dependencies elpa
 
 Now, you are ready to set your preferred ``EDITOR`` and continue with
 the rest of the tutorial.
 
+.. note::
+
+  Several of these packages depend on an MPI implementation. You can use
+  OpenMPI if you install it from scratch, but this is slow (>10 min.).
+  A binary cache of MPICH may be provided, in which case you can force
+  the package to use it and install quickly. All tutorial examples with
+  packages that depend on MPICH include the spec syntax for building with it
 
-.. _specs_build_interface_tutorial:
+.. _adv_pkg_tutorial_start:
 
-----------------------
-Spec's build interface
-----------------------
+---------------------------------------
+Modifying a package's build environment
+---------------------------------------
+
+Spack sets up several environment variables like ``PATH`` by default to aid in
+building a package, but many packages make use of environment variables which
+convey specific information about their dependencies (e.g., ``MPICC``).
+This section covers how to update your Spack packages so that package-specific
+environment variables are defined at build-time.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Set environment variables in dependent packages at build-time
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Dependencies can set environment variables that are required when their
+dependents build. For example, when a package depends on a python extension
+like py-numpy, Spack's ``python`` package will add it to ``PYTHONPATH``
+so it is available at build time; this is required because the default setup
+that spack does is not sufficient for python to import modules.
+
+To provide environment setup for a dependent, a package can implement the
+:py:func:`setup_dependent_environment <spack.package.PackageBase.setup_dependent_environment>`
+function. This function takes as a parameter a :py:class:`EnvironmentModifications <spack.util.environment.EnvironmentModifications>`
+object which includes convenience methods to update the environment. For
+example, an MPI implementation can set ``MPICC`` for packages that depend on it:
+
+.. code-block:: python
+
+  def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+      spack_env.set('MPICC', join_path(self.prefix.bin, 'mpicc'))
+
+In this case packages that depend on ``mpi`` will have ``MPICC`` defined in
+their environment when they build. This section is focused on modifying the
+build-time environment represented by ``spack_env``, but it's worth noting that
+modifications to ``run_env`` are included in Spack's automatically-generated
+module files.
+
+We can practice by editing the ``mpich`` package to set the ``MPICC``
+environment variable in the build-time environment of dependent packages.
+
+.. code-block:: console
+
+  root@advanced-packaging-tutorial:/# spack edit mpich
+
+Once you're finished, the method should look like this:
+
+.. code-block:: python
+
+  def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+      spack_env.set('MPICC',  join_path(self.prefix.bin, 'mpicc'))
+      spack_env.set('MPICXX', join_path(self.prefix.bin, 'mpic++'))
+      spack_env.set('MPIF77', join_path(self.prefix.bin, 'mpif77'))
+      spack_env.set('MPIF90', join_path(self.prefix.bin, 'mpif90'))
+
+      spack_env.set('MPICH_CC', spack_cc)
+      spack_env.set('MPICH_CXX', spack_cxx)
+      spack_env.set('MPICH_F77', spack_f77)
+      spack_env.set('MPICH_F90', spack_fc)
+      spack_env.set('MPICH_FC', spack_fc)
+
+At this point we can, for instance, install ``netlib-scalapack`` with
+``mpich``:
+
+.. code-block:: console
+
+  root@advanced-packaging-tutorial:/# spack install netlib-scalapack ^mpich
+  ...
+  ==> Created stage in /usr/local/var/spack/stage/netlib-scalapack-2.0.2-km7tsbgoyyywonyejkjoojskhc5knz3z
+  ==> No patches needed for netlib-scalapack
+  ==> Building netlib-scalapack [CMakePackage]
+  ==> Executing phase: 'cmake'
+  ==> Executing phase: 'build'
+  ==> Executing phase: 'install'
+  ==> Successfully installed netlib-scalapack
+    Fetch: 0.01s.  Build: 3m 59.86s.  Total: 3m 59.87s.
+  [+] /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netlib-scalapack-2.0.2-km7tsbgoyyywonyejkjoojskhc5knz3z
+
+
+and double check the environment logs to verify that every variable was
+set to the correct value.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Set environment variables in your own package
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Packages can modify their own build-time environment by implementing the
+:py:func:`setup_environment <spack.package.PackageBase.setup_environment>` function.
+For ``qt`` this looks like:
+
+.. code-block:: python
+
+    def setup_environment(self, spack_env, run_env):
+        spack_env.set('MAKEFLAGS', '-j{0}'.format(make_jobs))
+        run_env.set('QTDIR', self.prefix)
+
+When ``qt`` builds, ``MAKEFLAGS`` will be defined in the environment.
+
+To contrast with ``qt``'s :py:func:`setup_dependent_environment <spack.package.PackageBase.setup_dependent_environment>`
+function:
+
+.. code-block:: python
 
-Spack is designed with an emphasis on assigning responsibilities
-to the appropriate entities, as this results in a clearer and more intuitive interface
-for the users.
-When it comes to packaging, one of the most fundamental guideline that
-emerged from this tenet is that:
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        spack_env.set('QTDIR', self.prefix)
 
-  *It is a package's responsibility to know
-  every software it directly depends on and to expose to others how to
-  use the services it provides*.
+Let's see how it works by completing the ``elpa`` package:
 
-Spec's build interface is a protocol-like implementation of this guideline
-that allows packages to easily query their dependencies,
-and prescribes how they should expose their own build information.
+.. code-block:: console
+
+  root@advanced-packaging-tutorial:/# spack edit elpa
+
+In the end your method should look like:
 
-^^^^^^^^^^^^^^^^^^^^
-A motivating example
-^^^^^^^^^^^^^^^^^^^^
+.. code-block:: python
+
+  def setup_environment(self, spack_env, run_env):
+      spec = self.spec
+
+      spack_env.set('CC', spec['mpi'].mpicc)
+      spack_env.set('FC', spec['mpi'].mpifc)
+      spack_env.set('CXX', spec['mpi'].mpicxx)
+      spack_env.set('SCALAPACK_LDFLAGS', spec['scalapack'].libs.joined())
+
+      spack_env.append_flags('LDFLAGS', spec['lapack'].libs.search_flags)
+      spack_env.append_flags('LIBS', spec['lapack'].libs.link_flags)
+
+At this point it's possible to proceed with the installation of ``elpa ^mpich``
+
+------------------------------
+Retrieving library information
+------------------------------
+
+Although Spack attempts to help packages locate their dependency libraries
+automatically (e.g. by setting ``PKG_CONFIG_PATH`` and ``CMAKE_PREFIX_PATH``),
+a package may have unique configuration options that are required to locate
+libraries. When a package needs information about dependency libraries, the
+general approach in Spack is to query the dependencies for the locations of
+their libraries and set configuration options accordingly. By default most
+Spack packages know how to automatically locate their libraries. This section
+covers how to retrieve library information from dependencies and how to locate
+libraries when the default logic doesn't work.
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Accessing dependency libraries
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+If you need to access the libraries of a dependency, you can do so
+via the ``libs`` property of the spec, for example in the ``arpack-ng``
+package:
+
+.. code-block:: python
+
+    def install(self, spec, prefix):
+        lapack_libs = spec['lapack'].libs.joined(';')
+        blas_libs = spec['blas'].libs.joined(';')
+
+        cmake(*[
+            '-DLAPACK_LIBRARIES={0}'.format(lapack_libs),
+            '-DBLAS_LIBRARIES={0}'.format(blas_libs)
+        ], '.')
+
+Note that ``arpack-ng`` is querying virtual dependencies, which Spack
+automatically resolves to the installed implementation (e.g. ``openblas``
+for ``blas``).
 
 We've started work on a package for ``armadillo``. You should open it,
 read through the comment that starts with ``# TUTORIAL:`` and complete
@@ -135,11 +269,11 @@ is as easy as accessing the their ``libs`` attribute. Furthermore, the interface
 remains the same whether you are querying regular or virtual dependencies.
 
 At this point you can complete the installation of ``armadillo`` using ``openblas``
-as a LAPACK provider:
+as a LAPACK provider (``armadillo ^openblas ^mpich``):
 
 .. code-block:: console
 
-  root@advanced-packaging-tutorial:/# spack install armadillo ^openblas
+  root@advanced-packaging-tutorial:/# spack install armadillo ^openblas ^mpich
   ==> pkg-config is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pkg-config-0.29.2-ae2hwm7q57byfbxtymts55xppqwk7ecj
   ...
   ==> superlu is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/superlu-5.2.1-q2mbtw2wo4kpzis2e2n227ip2fquxrno
@@ -160,12 +294,36 @@ Hopefully the installation went fine and the code we added expanded to the right
 of semicolon separated libraries (you are encouraged to open ``armadillo``'s
 build logs to double check).
 
-If we try to build another version tied to ``netlib-lapack`` we'll
-notice that this time the installation won't complete:
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Providing libraries to dependents
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Spack provides a default implementation for ``libs`` which often works
+out of the box. A user can write a package definition without having to
+implement a ``libs`` property and dependents can retrieve its libraries
+as shown in the above section. However, the default implementation assumes that
+libraries follow the naming scheme ``lib<package name>.so`` (or e.g.
+``lib<package name>.a`` for static libraries). Packages which don't
+follow this naming scheme must implement this function themselves, e.g.
+``opencv``:
+
+.. code-block:: python
+
+    @property
+    def libs(self):
+        shared = "+shared" in self.spec
+        return find_libraries(
+            "libopencv_*", root=self.prefix, shared=shared, recurse=True
+        )
+
+This issue is common for packages which implement an interface (i.e.
+virtual package providers in Spack). If we try to build another version of
+``armadillo`` tied to ``netlib-lapack`` (``armadillo ^netlib-lapack ^mpich``)
+we'll notice that this time the installation won't complete:
 
 .. code-block:: console
 
-  root@advanced-packaging-tutorial:/# spack install  armadillo ^netlib-lapack
+  root@advanced-packaging-tutorial:/# spack install  armadillo ^netlib-lapack ^mpich
   ==> pkg-config is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pkg-config-0.29.2-ae2hwm7q57byfbxtymts55xppqwk7ecj
   ...
   ==> openmpi is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f
@@ -190,8 +348,9 @@ notice that this time the installation won't complete:
   See build log for details:
     /usr/local/var/spack/stage/arpack-ng-3.5.0-bloz7cqirpdxj33pg7uj32zs5likz2un/arpack-ng-3.5.0/spack-build.out
 
-This is because ``netlib-lapack`` requires extra work, compared to ``openblas``,
-to expose its build information to other packages. Let's edit it:
+Unlike ``openblas`` which provides a library named ``libopenblas.so``,
+``netlib-lapack`` provides ``liblapack.so``, so it needs to implement
+customized library search logic. Let's edit it:
 
 .. code-block:: console
 
@@ -206,15 +365,21 @@ What we need to implement is:
   def lapack_libs(self):
       shared = True if '+shared' in self.spec else False
       return find_libraries(
-          'liblapack', root=self.prefix, shared=shared, recurse=True
+          'liblapack', root=self.prefix, shared=shared, recursive=True
       )
 
-i.e. a property that returns the correct list of libraries for the LAPACK interface.
-Now we can finally install ``armadillo ^netlib-lapack``:
+i.e., a property that returns the correct list of libraries for the LAPACK interface.
+
+We use the name ``lapack_libs`` rather than ``libs`` because
+``netlib-lapack`` can also provide ``blas``, and when it does it is provided
+as a separate library file. Using this name ensures that when
+dependents ask for ``lapack`` libraries, ``netlib-lapack`` will retrieve only
+the libraries associated with the ``lapack`` interface. Now we can finally
+install ``armadillo ^netlib-lapack ^mpich``:
 
 .. code-block:: console
 
-  root@advanced-packaging-tutorial:/# spack install  armadillo ^netlib-lapack
+  root@advanced-packaging-tutorial:/# spack install  armadillo ^netlib-lapack ^mpich
   ...
 
   ==> Building armadillo [CMakePackage]
@@ -225,62 +390,43 @@ Now we can finally install ``armadillo ^netlib-lapack``:
     Fetch: 0.01s.  Build: 3.75s.  Total: 3.76s.
   [+] /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/armadillo-8.100.1-sxmpu5an4dshnhickh6ykchyfda7jpyn
 
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-What happens at subscript time?
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Since each implementation of a virtual package is responsible for locating the
+libraries associated with the interfaces it provides, dependents do not need
+to include special-case logic for different implementations and for example
+need only ask for :code:`spec['blas'].libs`.
 
-The example above leaves us with a few questions. How could it be that the
-attribute:
-
-.. code-block:: python
+----------------------
+Other Packaging Topics
+----------------------
 
-  spec['lapack'].libs
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Attach attributes to other packages
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-stems from a property of the ``netlib-lapack`` package that has a different name?
-How is it even computed for ``openblas``, given that in its package there's no code
-that deals with finding libraries?
-The answer is that ``libs`` is one of the few properties of specs that follow the
-*build-interface protocol*. The others are currently ``command`` and ``headers``.
-These properties exist only on concrete specs that have been retrieved via the
-subscript notation.
+Build tools usually also provide a set of executables that can be used
+when another package is being installed. Spack gives you the opportunity
+to monkey-patch dependent modules and attach attributes to them. This
+helps make the packager experience as similar as possible to what would
+have been the manual installation of the same package.
 
-What happens is that, whenever you retrieve a spec using subscripts:
+An example here is the ``automake`` package, which overrides
+:py:func:`setup_dependent_package <spack.package.PackageBase.setup_dependent_package>`:
 
 .. code-block:: python
 
-  lapack = spec['lapack']
-
-the key that appears in the query (in this case ``'lapack'``) is attached to the
-returned item. When, later on, you access any of the build-interface attributes, this
-key is used to compute the result according to the following algorithm:
-
-.. code-block:: none
-
-  Given any pair of <query-key> and <build-attribute>:
-
-    1. If <query-key> is the name of a virtual spec and the package
-       providing it has an attribute named '<query-key>_<build-attribute>'
-       return it
-
-    2. Otherwise if the package has an attribute named '<build-attribute>'
-       return that
-
-    3. Otherwise use the default handler for <build-attribute>
+  def setup_dependent_package(self, module, dependent_spec):
+      # Automake is very likely to be a build dependency,
+      # so we add the tools it provides to the dependent module
+      executables = ['aclocal', 'automake']
+      for name in executables:
+          setattr(module, name, self._make_executable(name))
 
-Going back to our concrete case this means that, if the spec providing LAPACK
-is ``netlib-lapack``, we are returning the value computed in the ``lapack_libs``
-property. If it is ``openblas``, we are instead resorting to the default handler
-for ``libs`` (which searches for the presence of ``libopenblas`` in the
-installation prefix).
+so that every other package that depends on it can use directly ``aclocal``
+and ``automake`` with the usual function call syntax of :py:class:`Executable <spack.util.executable.Executable>`:
 
-.. note::
+.. code-block:: python
 
-  Types commonly returned by build-interface attributes
-    Even though there's no enforcement on it, the type of the objects returned most often when
-    asking for the ``libs`` attributes is :py:class:`LibraryList <llnl.util.filesystem.LibraryList>`.
-    Similarly the usual type returned for ``headers`` is :py:class:`HeaderList <llnl.util.filesystem.HeaderList>`,
-    while for ``command`` is :py:class:`Executable <spack.util.executable.Executable>`. You can refer to
-    these objects' API documentation to discover more about them.
+  aclocal('--force')
 
 ^^^^^^^^^^^^^^^^^^^^^^^
 Extra query parameters
@@ -288,14 +434,14 @@ Extra query parameters
 
 An advanced feature of the Spec's build-interface protocol is the support
 for extra parameters after the subscript key. In fact, any of the keys used in the query
-can be followed by a comma separated list of extra parameters which can be
+can be followed by a comma-separated list of extra parameters which can be
 inspected by the package receiving the request to fine-tune a response.
 
-Let's look at an example and try to install ``netcdf``:
+Let's look at an example and try to install ``netcdf ^mpich``:
 
 .. code-block:: console
 
-  root@advanced-packaging-tutorial:/# spack install netcdf
+  root@advanced-packaging-tutorial:/# spack install netcdf ^mpich
   ==> libsigsegv is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libsigsegv-2.11-fypapcprssrj3nstp6njprskeyynsgaz
   ==> m4 is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/m4-1.4.18-r5envx3kqctwwflhd4qax4ahqtt6x43a
   ...
@@ -336,12 +482,12 @@ If you followed the instructions correctly, the code added to the
       libraries, root=self.prefix, shared=shared, recurse=True
   )
 
-where we highlighted the line retrieving  the extra parameters. Now we can successfully
-complete the installation of ``netcdf``:
+where we highlighted the line retrieving the extra parameters. Now we can successfully
+complete the installation of ``netcdf ^mpich``:
 
 .. code-block:: console
 
-  root@advanced-packaging-tutorial:/# spack install netcdf
+  root@advanced-packaging-tutorial:/# spack install netcdf ^mpich
   ==> libsigsegv is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libsigsegv-2.11-fypapcprssrj3nstp6njprskeyynsgaz
   ==> m4 is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/m4-1.4.18-r5envx3kqctwwflhd4qax4ahqtt6x43a
   ...
@@ -357,207 +503,3 @@ complete the installation of ``netcdf``:
   ==> Successfully installed netcdf
     Fetch: 0.01s.  Build: 24.61s.  Total: 24.62s.
   [+] /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netcdf-4.4.1.1-gk2xxhbqijnrdwicawawcll4t3c7dvoj
-
-
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Single package providing multiple virtual specs
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-At the close of this tutorial's subsection, it may be useful to see where the
-build-interface protocol shines the most i.e. when it comes to manage packages
-that provide more than one virtual spec. An example of a package of this kind is
-``intel-parallel-studio``, and due to its complexity we'll limit our discussion
-here to just a few considerations (without any hands-on). You can open
-the related ``package.py`` in the usual way:
-
-.. code-block:: console
-
-  root@advanced-packaging-tutorial:/# spack edit intel-parallel-studio
-
-As you can see this package provides a lot of virtual specs, and thus it has
-more than one function that enters into the build-interface protocol. These
-functions will be invoked for *exactly the same spec* according to the key used
-by its dependents in the subscript query.
-
-So, for instance, the ``blas_libs`` property will be returned when
-``intel-parallel-studio`` is the BLAS provider in the current DAG and
-is retrieved by a dependent with:
-
-.. code-block:: python
-
-  blas = self.spec['blas']
-  blas_libs = blas.libs
-
-Within the property we inspect various aspects of the current spec:
-
-.. code-block:: python
-
-  @property
-  def blas_libs(self):
-     spec = self.spec
-     prefix = self.prefix
-     shared = '+shared' in spec
-
-     if '+ilp64' in spec:
-         mkl_integer = ['libmkl_intel_ilp64']
-     else:
-         mkl_integer = ['libmkl_intel_lp64']
-     ...
-
-and construct the list of library we need to return accordingly.
-
-What we achieved is that the complexity of dealing with ``intel-parallel-studio``
-is now gathered in the package itself, instead of being spread
-all over its possible dependents.
-Thus, a package that uses MPI or LAPACK doesn't care which implementation it uses,
-as each virtual dependency has
-*a uniform interface* to ask for libraries or headers and manipulate them.
-The packages that provide this virtual spec, on the other hand, have a clear
-way to differentiate their answer to the query [#uniforminterface]_.
-
-.. [#uniforminterface] Before this interface was added, each package that
-   depended on MPI or LAPACK had dozens of lines of code copied from other
-   packages telling it where to find the libraries and what they are called.
-   With the addition of this interface, the virtual dependency itself tells
-   other packages that depend on it where it can find its libraries.
-
----------------------------
-Package's build environment
----------------------------
-
-Besides Spec's build interface, Spack provides means to set environment
-variables, either for yourself or for your dependent packages, and to
-attach attributes to your dependents. We'll see them next with the help
-of a few real use cases.
-
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Set variables at build-time for yourself
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Spack provides a way to manipulate a package's build time and
-run time environments using the
-:py:func:`setup_environment <spack.package.PackageBase.setup_environment>` function.
-Let's try to see how it works by completing the ``elpa`` package:
-
-.. code-block:: console
-
-  root@advanced-packaging-tutorial:/# spack edit elpa
-
-In the end your method should look like:
-
-.. code-block:: python
-
-  def setup_environment(self, spack_env, run_env):
-      spec = self.spec
-
-      spack_env.set('CC', spec['mpi'].mpicc)
-      spack_env.set('FC', spec['mpi'].mpifc)
-      spack_env.set('CXX', spec['mpi'].mpicxx)
-      spack_env.set('SCALAPACK_LDFLAGS', spec['scalapack'].libs.joined())
-
-      spack_env.append_flags('LDFLAGS', spec['lapack'].libs.search_flags)
-      spack_env.append_flags('LIBS', spec['lapack'].libs.link_flags)
-
-The two arguments, ``spack_env`` and ``run_env``, are both instances of
-:py:class:`EnvironmentModifications <spack.environment.EnvironmentModifications>` and
-permit you to register modifications to either the build-time or the run-time
-environment of the package, respectively.
-At this point it's possible to proceed with the installation of ``elpa``:
-
-.. code-block:: console
-
-  root@advanced-packaging-tutorial:/# spack install elpa
-  ==> pkg-config is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pkg-config-0.29.2-ae2hwm7q57byfbxtymts55xppqwk7ecj
-  ==> ncurses is already installed in /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/ncurses-6.0-ukq4tccptm2rxd56d2bumqthnpcjzlez
-  ...
-  ==> Executing phase: 'build'
-  ==> Executing phase: 'install'
-  ==> Successfully installed elpa
-    Fetch: 3.94s.  Build: 41.93s.  Total: 45.87s.
-  [+] /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/elpa-2016.05.004-sdbfhwcexg7s2zqf52vssb762ocvklbu
-
-If you had modifications to ``run_env``, those would have appeared e.g. in the module files
-generated for the package.
-
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Set variables in dependencies at build-time
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Another common occurrence, particularly for packages like ``r`` and ``python``
-that support extensions and for packages that provide build tools,
-is to require *their dependents* to have some environment variables set.
-
-The mechanism is similar to what we just saw, except that we override the
-:py:func:`setup_dependent_environment <spack.package.PackageBase.setup_dependent_environment>`
-function, which takes one additional argument, i.e. the dependent spec that needs the modified
-environment. Let's practice completing the ``mpich`` package:
-
-.. code-block:: console
-
-  root@advanced-packaging-tutorial:/# spack edit mpich
-
-Once you're finished the method should look like this:
-
-.. code-block:: python
-
-  def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
-      spack_env.set('MPICC',  join_path(self.prefix.bin, 'mpicc'))
-      spack_env.set('MPICXX', join_path(self.prefix.bin, 'mpic++'))
-      spack_env.set('MPIF77', join_path(self.prefix.bin, 'mpif77'))
-      spack_env.set('MPIF90', join_path(self.prefix.bin, 'mpif90'))
-
-      spack_env.set('MPICH_CC', spack_cc)
-      spack_env.set('MPICH_CXX', spack_cxx)
-      spack_env.set('MPICH_F77', spack_f77)
-      spack_env.set('MPICH_F90', spack_fc)
-      spack_env.set('MPICH_FC', spack_fc)
-
-At this point we can, for instance, install ``netlib-scalapack``:
-
-.. code-block:: console
-
-  root@advanced-packaging-tutorial:/# spack install netlib-scalapack ^mpich
-  ...
-  ==> Created stage in /usr/local/var/spack/stage/netlib-scalapack-2.0.2-km7tsbgoyyywonyejkjoojskhc5knz3z
-  ==> No patches needed for netlib-scalapack
-  ==> Building netlib-scalapack [CMakePackage]
-  ==> Executing phase: 'cmake'
-  ==> Executing phase: 'build'
-  ==> Executing phase: 'install'
-  ==> Successfully installed netlib-scalapack
-    Fetch: 0.01s.  Build: 3m 59.86s.  Total: 3m 59.87s.
-  [+] /usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netlib-scalapack-2.0.2-km7tsbgoyyywonyejkjoojskhc5knz3z
-
-
-and double check the environment logs to verify that every variable was
-set to the correct value. More complicated examples of the use of this function
-may be found in the ``r`` and ``python`` package.
-
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Attach attributes to other packages
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Build tools usually also provide a set of executables that can be used
-when another package is being installed. Spack gives the opportunity
-to monkey-patch dependent modules and attach attributes to them. This
-helps make the packager experience as similar as possible to what would
-have been the manual installation of the same package.
-
-An example here is the ``automake`` package, which overrides
-:py:func:`setup_dependent_package <spack.package.PackageBase.setup_dependent_package>`:
-
-.. code-block:: python
-
-  def setup_dependent_package(self, module, dependent_spec):
-      # Automake is very likely to be a build dependency,
-      # so we add the tools it provides to the dependent module
-      executables = ['aclocal', 'automake']
-      for name in executables:
-          setattr(module, name, self._make_executable(name))
-
-so that every other package that depends on it can use directly ``aclocal``
-and ``automake`` with the usual function call syntax of :py:class:`Executable <spack.util.executable.Executable>`:
-
-.. code-block:: python
-
-  aclocal('--force')
\ No newline at end of file
diff --git a/lib/spack/docs/tutorial_basics.rst b/lib/spack/docs/tutorial_basics.rst
index d74159d7f6..50c072c08e 100644
--- a/lib/spack/docs/tutorial_basics.rst
+++ b/lib/spack/docs/tutorial_basics.rst
@@ -1,3 +1,8 @@
+.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 .. _basics-tutorial:
 
 =========================================
@@ -23,22 +28,24 @@ Installing Spack
 ----------------
 
 Spack works out of the box. Simply clone spack and get going. We will
-clone Spack and immediately checkout the most recent release, v0.11.0.
+clone Spack and immediately checkout the most recent release, v0.12.
 
 .. code-block:: console
 
   $ git clone https://github.com/spack/spack
+  git clone https://github.com/spack/spack
   Cloning into 'spack'...
-  remote: Counting objects: 94561, done.
-  remote: Compressing objects: 100% (121/121), done.
-  remote: Total 94561 (delta 91), reused 121 (delta 48), pack-reused 94368
-  Receiving objects: 100% (94561/94561), 32.44 MiB | 31.88 MiB/s, done.
-  Resolving deltas: 100% (44914/44914), done.
+  remote: Enumerating objects: 68, done.
+  remote: Counting objects: 100% (68/68), done.
+  remote: Compressing objects: 100% (56/56), done.
+  remote: Total 135389 (delta 40), reused 16 (delta 9), pack-reused 135321
+  Receiving objects: 100% (135389/135389), 47.31 MiB | 1.01 MiB/s, done.
+  Resolving deltas: 100% (64414/64414), done.
   Checking connectivity... done.
   $ cd spack
-  $ git checkout releases/v0.11.0
-  Branch releases/v0.11.0 set up to track remote branch releases/v0.11.0 from origin.
-  Switched to a new branch 'releases/v0.11.0'
+  $ git checkout releases/v0.12
+  Branch releases/v0.12 set up to track remote branch releases/v0.12 from origin.
+  Switched to a new branch 'releases/v0.12'
 
 Next add Spack to your path. Spack has some nice command line
 integration tools, so instead of simply appending to your ``PATH``
@@ -59,10 +66,10 @@ The ``spack list`` command shows available packages.
 .. code-block:: console
 
   $ spack list
-  ==> 2177 packages.
-  abinit                           libepoxy                               py-html5lib                     r-ncdf4
-  abyss                            libevent                               py-httpbin                      r-network
-  ack                              libevpath                              py-hypothesis                   r-networkd3abinit
+  ==> 2907 packages.
+  abinit                           libgpuarray                            py-espresso                     r-mlrmbo
+  abyss                            libgridxc                              py-espressopp                   r-mmwrweek
+  accfft                           libgtextutils                          py-et-xmlfile                   r-mnormt
   ...
 
 The ``spack list`` command can also take a query string. Spack
@@ -72,10 +79,10 @@ we can view all available python packages.
 .. code-block:: console
 
   $ spack list py-
-  ==> 356 packages.
-  py-3to2                                py-functools32       py-numpydoc         py-pywavelets
-  py-4suite-xml                          py-future            py-olefile          py-pyyaml
-  py-abipy                               py-futures           py-ont-fast5-api    py-qtawesome
+  ==> 479 packages.
+  lumpy-sv                               py-funcsigs          py-numpydoc         py-utililib
+  perl-file-copy-recursive               py-functools32       py-olefile          py-pywavelets
+  py-3to2                                py-future            py-ont-fast5-api    py-pyyaml
   ...
 
 -------------------
@@ -89,43 +96,42 @@ software, simply type ``spack install <package_name>``.
 
   $ spack install zlib
   ==> Installing zlib
-  ==> Fetching file:///home/ubuntu/becker/buildcache/zlib/zlib-1.2.11.tar.gz
-  curl: (37) Couldn't open file /home/ubuntu/becker/buildcache/zlib/zlib-1.2.11.tar.gz
-  ==> Fetching from file:///home/ubuntu/becker/buildcache/zlib/zlib-1.2.11.tar.gz failed.
+  ==> Searching for binary cache of zlib
+  ==> Warning: No Spack mirrors are currently configured
+  ==> No binary for zlib found: installing from source
   ==> Fetching http://zlib.net/fossils/zlib-1.2.11.tar.gz
   ######################################################################## 100.0%
-  ==> Staging archive: /home/ubuntu/test/spack/var/spack/stage/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb/zlib-1.2.11.tar.gz
-  ==> Created stage in /home/ubuntu/test/spack/var/spack/stage/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
+  ==> Staging archive: /home/spack1/spack/var/spack/stage/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb/zlib-1.2.11.tar.gz
+  ==> Created stage in /home/spack1/spack/var/spack/stage/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
   ==> No patches needed for zlib
   ==> Building zlib [Package]
   ==> Executing phase: 'install'
   ==> Successfully installed zlib
-    Fetch: 0.58s.  Build: 1.15s.  Total: 1.73s.
-    [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
+    Fetch: 3.27s.  Build: 2.18s.  Total: 5.44s.
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
 
 Spack can install software either from source or from a binary
 cache. Packages in the binary cache are signed with GPG for
 security. For the tutorial we have prepared a binary cache so you
 don't have to wait on slow compilation from source. To be able to
-install from the binary cache, we will need to trust the GPG key that
-the binary cache was prepared with.
+install from the binary cache, we will need to configure Spack with
+the location of the binary cache and trust the GPG key that the binary
+cache was signed with.
 
 .. code-block:: console
 
-  $ spack gpg trust ~/public.key
-  gpg: keybox '/home/ubuntu/test/spack/opt/spack/gpg/pubring.kbx' created
-  gpg: /home/ubuntu/test/spack/opt/spack/gpg/trustdb.gpg: trustdb created
+  $ spack mirror add tutorial /mirror
+  $ spack gpg trust /mirror/public.key
+  gpg: keybox '/home/spack1/spack/opt/spack/gpg/pubring.kbx' created
+  gpg: /home/spack1/spack/opt/spack/gpg/trustdb.gpg: trustdb created
   gpg: key 3B7C69B2: public key "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" imported
   gpg: Total number processed: 1
   gpg:               imported: 1
 
-The AWS instances and Docker images we use for the tutorial already
-have configuration files in place so that Spack knows where to look
-for binary packages (and that's the only change we've made). You'll
-learn more about configuring Spack later in the tutorial, but for now
-you will be able to install the rest of the packages in the tutorial
-from a binary cache by specifying ``spack install --use-cache
-<package_name>``. This will install the binary cached version if it
+You'll learn more about configuring Spack later in the tutorial, but
+for now you will be able to install the rest of the packages in the
+tutorial from a binary cache using the same ``spack install``
+command. By default this will install the binary cached version if it
 exists and fall back on installing from source.
 
 Spack's spec syntax is the interface by which we can request specific
@@ -134,24 +140,28 @@ compilers.
 
 .. code-block:: console
 
-  $ spack install --use-cache zlib %clang
-  ...
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64-gcc-4.7-libsigsegv-2.11-eaqxu5mka32jpjif32rttiwebimrr2kb.spec.yaml
+  $ spack install zlib %clang
+  ==> Installing zlib
+  ==> Searching for binary cache of zlib
+  ==> Finding buildcaches in /mirror/build_cache
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64-gcc-7.2.0-texinfo-6.5-cuqnfgfhhmudqp5f7upmld6ax7pratzw.spec.yaml
+  ######################################################################## 100.0%
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64-gcc-4.7-zlib-1.2.11-bq2wtdxakpjytk2tjr7qu23i4py2fi2r.spec.yaml
   ######################################################################## 100.0%
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64-gcc-5.4.0-util-macros-1.19.1-milz7fmttmptcic2qdk5cnel7ll5sybr.spec.yaml
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64-gcc-5.4.0-dyninst-9.3.2-bu6s2jzievsjkwtcnrtimc5b625j5omf.spec.yaml
   ######################################################################## 100.0%
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64-gcc-7.2.0-openmpi-3.1.3-do5xfer2whhk7gc26atgs3ozr3ljbvs4.spec.yaml
+  ...
   ==> Installing zlib from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/clang-3.8.0-2ubuntu4/zlib-1.2.11/linux-ubuntu16.04-x86_64-clang-3.8.0-2ubuntu4-zlib-1.2.11-4pt75q7qq6lygf3hgnona4lyc2uwedul.spack
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/clang-3.8.0-2ubuntu4/zlib-1.2.11/linux-ubuntu16.04-x86_64-clang-3.8.0-2ubuntu4-zlib-1.2.11-4pt75q7qq6lygf3hgnona4lyc2uwedul.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 01:05:02 AM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:08:01 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
   ==> Successfully installed zlib from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/clang-3.8.0-2ubuntu4/zlib-1.2.11-4pt75q7qq6lygf3hgnona4lyc2uwedul
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/clang-3.8.0-2ubuntu4/zlib-1.2.11-4pt75q7qq6lygf3hgnona4lyc2uwedul
 
 Note that this installation is located separately from the previous
 one. We will discuss this in more detail later, but this is part of what
@@ -175,43 +185,35 @@ compilers.
 
 .. code-block:: console
 
-  $ spack install --use-cache zlib@1.2.8
+  $ spack install zlib@1.2.8
   ==> Installing zlib
   ==> Searching for binary cache of zlib
-  ==> Finding buildcaches in /home/ubuntu/becker/buildcache/build_cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64-clang-3.8.0-2ubuntu4-zlib-1.2.11-4pt75q7qq6lygf3hgnona4lyc2uwedul.spec.yaml
-  ######################################################################## 100.0%
+  ==> Finding buildcaches in /mirror/build_cache
   ==> Installing zlib from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.8/linux-ubuntu16.04-x86_64-gcc-5.4.0-zlib-1.2.8-bkyl5bhuep6fmhuxzkmhqy25qefjcvzc.spack
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.8/linux-ubuntu16.04-x86_64-gcc-5.4.0-zlib-1.2.8-bkyl5bhuep6fmhuxzkmhqy25qefjcvzc.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 01:05:03 AM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:18:30 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
   ==> Successfully installed zlib from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.8-bkyl5bhuep6fmhuxzkmhqy25qefjcvzc
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.8-bkyl5bhuep6fmhuxzkmhqy25qefjcvzc
 
-  $ spack install --use-cache zlib %gcc@4.7
+  $ spack install zlib %gcc@4.7
   ==> Installing zlib
   ==> Searching for binary cache of zlib
-  ==> Finding buildcaches in /home/ubuntu/becker/buildcache/build_cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64-gcc-5.4.0-zlib-1.2.8-bkyl5bhuep6fmhuxzkmhqy25qefjcvzc.spec.yaml
-  ######################################################################## 100.0%
+  ==> Finding buildcaches in /mirror/build_cache
   ==> Installing zlib from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-4.7/zlib-1.2.11/linux-ubuntu16.04-x86_64-gcc-4.7-zlib-1.2.11-bq2wtdxakpjytk2tjr7qu23i4py2fi2r.spack
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-4.7/zlib-1.2.11/linux-ubuntu16.04-x86_64-gcc-4.7-zlib-1.2.11-bq2wtdxakpjytk2tjr7qu23i4py2fi2r.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 01:03:00 AM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 04:55:30 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
   ==> Successfully installed zlib from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-4.7/zlib-1.2.11-bq2wtdxakpjytk2tjr7qu23i4py2fi2r
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-4.7/zlib-1.2.11-bq2wtdxakpjytk2tjr7qu23i4py2fi2r
 
 The spec syntax also includes compiler flags. Spack accepts
 ``cppflags``, ``cflags``, ``cxxflags``, ``fflags``, ``ldflags``, and
@@ -221,24 +223,20 @@ into the compile line automatically by the Spack compiler wrappers.
 
 .. code-block:: console
 
-  $ spack install --use-cache zlib @1.2.8 cppflags=-O3
+  $ spack install zlib @1.2.8 cppflags=-O3
   ==> Installing zlib
   ==> Searching for binary cache of zlib
-  ==> Finding buildcaches in /home/ubuntu/becker/buildcache/build_cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64-gcc-4.7-zlib-1.2.11-bq2wtdxakpjytk2tjr7qu23i4py2fi2r.spec.yaml
-  ######################################################################## 100.0%
+  ==> Finding buildcaches in /mirror/build_cache
   ==> Installing zlib from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.8/linux-ubuntu16.04-x86_64-gcc-5.4.0-zlib-1.2.8-64mns5mvdacqvlashkf7v6lqrxixhmxu.spack
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.8/linux-ubuntu16.04-x86_64-gcc-5.4.0-zlib-1.2.8-64mns5mvdacqvlashkf7v6lqrxixhmxu.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 01:03:00 AM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:31:54 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
   ==> Successfully installed zlib from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.8-64mns5mvdacqvlashkf7v6lqrxixhmxu
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.8-64mns5mvdacqvlashkf7v6lqrxixhmxu
 
 The ``spack find`` command is used to query installed packages. Note that
 some packages appear identical with the default output. The ``-l`` flag
@@ -286,25 +284,21 @@ existing package's hash matches the desired spec.
 
 .. code-block:: console
 
-  $ spack install --use-cache openssl
-  ==> zlib is already installed in /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
-  ==> Installing openssl
-  ==> Searching for binary cache of openssl
-  ==> Finding buildcaches in /home/ubuntu/becker/buildcache/build_cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64-gcc-5.4.0-zlib-1.2.8-64mns5mvdacqvlashkf7v6lqrxixhmxu.spec.yaml
+  $ spack install tcl
+  ==> zlib is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
+  ==> Installing tcl
+  ==> Searching for binary cache of tcl
+  ==> Finding buildcaches in /mirror/build_cache
+  ==> Installing tcl from binary cache
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/tcl-8.6.8/linux-ubuntu16.04-x86_64-gcc-5.4.0-tcl-8.6.8-qhwyccywhx2i6s7ob2gvjrjtj3rnfuqt.spack
   ######################################################################## 100.0%
-  ==> Installing openssl from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/openssl-1.0.2k/linux-ubuntu16.04-x86_64-gcc-5.4.0-openssl-1.0.2k-2woov64m3n4gjtnfp722qcyemzf2qtom.spack
-  ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 01:03:18 AM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:07:15 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
-  ==> Successfully installed openssl from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openssl-1.0.2k-2woov64m3n4gjtnfp722qcyemzf2qtom
+  ==> Successfully installed tcl from binary cache
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/tcl-8.6.8-qhwyccywhx2i6s7ob2gvjrjtj3rnfuqt
 
 Dependencies can be explicitly requested using the ``^`` sigil. Note that
 the spec syntax is recursive. Anything we could specify about the
@@ -312,38 +306,32 @@ top-level package, we can also specify about a dependency using ``^``.
 
 .. code-block:: console
 
-  $ spack install --use-cache openssl ^zlib @1.2.8 %clang
+  $ spack install tcl ^zlib @1.2.8 %clang
   ==> Installing zlib
   ==> Searching for binary cache of zlib
-  ==> Finding buildcaches in /home/ubuntu/becker/buildcache/build_cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64-gcc-5.4.0-openssl-1.0.2k-2woov64m3n4gjtnfp722qcyemzf2qtom.spec.yaml
-  ######################################################################## 100.0%
+  ==> Finding buildcaches in /mirror/build_cache
   ==> Installing zlib from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/clang-3.8.0-2ubuntu4/zlib-1.2.8/linux-ubuntu16.04-x86_64-clang-3.8.0-2ubuntu4-zlib-1.2.8-i426yu3o6lyau5fv5ljwsajfkqxj5rl5.spack
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/clang-3.8.0-2ubuntu4/zlib-1.2.8/linux-ubuntu16.04-x86_64-clang-3.8.0-2ubuntu4-zlib-1.2.8-i426yu3o6lyau5fv5ljwsajfkqxj5rl5.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 01:03:06 AM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:09:01 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
   ==> Successfully installed zlib from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/clang-3.8.0-2ubuntu4/zlib-1.2.8-i426yu3o6lyau5fv5ljwsajfkqxj5rl5
-  ==> Installing openssl
-  ==> Searching for binary cache of openssl
-  ==> Installing openssl from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/clang-3.8.0-2ubuntu4/openssl-1.0.2k/linux-ubuntu16.04-x86_64-clang-3.8.0-2ubuntu4-openssl-1.0.2k-ufruk7kj2fz3oupuat2jbgc2y7hg37vy.spack
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/clang-3.8.0-2ubuntu4/zlib-1.2.8-i426yu3o6lyau5fv5ljwsajfkqxj5rl5
+  ==> Installing tcl
+  ==> Searching for binary cache of tcl
+  ==> Installing tcl from binary cache
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/clang-3.8.0-2ubuntu4/tcl-8.6.8/linux-ubuntu16.04-x86_64-clang-3.8.0-2ubuntu4-tcl-8.6.8-6wc66etr7y6hgibp2derrdkf763exwvc.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 01:03:23 AM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:10:21 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
-  ==> Successfully installed openssl from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/clang-3.8.0-2ubuntu4/openssl-1.0.2k-ufruk7kj2fz3oupuat2jbgc2y7hg37vy
+  ==> Successfully installed tcl from binary cache
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/clang-3.8.0-2ubuntu4/tcl-8.6.8-6wc66etr7y6hgibp2derrdkf763exwvc
 
 Packages can also be referred to from the command line by their package
 hash. Using the ``spack find -lf`` command earlier we saw that the hash
@@ -357,27 +345,21 @@ packages share the prefix) then spack will report an error.
 
 .. code-block:: console
 
-  $ spack install --use-cache openssl ^/64mn
-  ==> zlib is already installed in /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.8-64mns5mvdacqvlashkf7v6lqrxixhmxu
-  ==> Installing openssl
-  ==> Searching for binary cache of openssl
-  ==> Finding buildcaches in /home/ubuntu/becker/buildcache/build_cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64-clang-3.8.0-2ubuntu4-zlib-1.2.8-i426yu3o6lyau5fv5ljwsajfkqxj5rl5.spec.yaml
-  ######################################################################## 100.0%
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64-clang-3.8.0-2ubuntu4-openssl-1.0.2k-ufruk7kj2fz3oupuat2jbgc2y7hg37vy.spec.yaml
-  ######################################################################## 100.0%
-  ==> Installing openssl from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/openssl-1.0.2k/linux-ubuntu16.04-x86_64-gcc-5.4.0-openssl-1.0.2k-gyxmhgbam26d7y42omb7xrvkjjgmzwio.spack
+  $ spack install tcl ^/64mn
+  ==> zlib is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.8-64mns5mvdacqvlashkf7v6lqrxixhmxu
+  ==> Installing tcl
+  ==> Searching for binary cache of tcl
+  ==> Finding buildcaches in /mirror/build_cache
+  ==> Installing tcl from binary cache
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/tcl-8.6.8/linux-ubuntu16.04-x86_64-gcc-5.4.0-tcl-8.6.8-am4pbatrtga3etyusg2akmsvrswwxno2.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 01:03:12 AM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:11:53 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
-  ==> Successfully installed openssl from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openssl-1.0.2k-gyxmhgbam26d7y42omb7xrvkjjgmzwio
+  ==> Successfully installed tcl from binary cache
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/tcl-8.6.8-am4pbatrtga3etyusg2akmsvrswwxno2
 
 The ``spack find`` command can also take a ``-d`` flag, which can show
 dependency information. Note that each package has a top-level entry,
@@ -386,9 +368,9 @@ even if it also appears as a dependency.
 .. code-block:: console
 
   $ spack find -ldf
-  ==> 9 installed packages.
+  ==> 9 installed packages
   -- linux-ubuntu16.04-x86_64 / clang@3.8.0-2ubuntu4 --------------
-  ufruk7k    openssl@1.0.2k%clang
+  6wc66et    tcl@8.6.8%clang
   i426yu3        ^zlib@1.2.8%clang
 
   i426yu3    zlib@1.2.8%clang
@@ -401,10 +383,10 @@ even if it also appears as a dependency.
 
 
   -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
-  gyxmhgb    openssl@1.0.2k%gcc
+  am4pbat    tcl@8.6.8%gcc
   64mns5m        ^zlib@1.2.8%gcc cppflags="-O3"
 
-  2woov64    openssl@1.0.2k%gcc
+  qhwyccy    tcl@8.6.8%gcc
   5nus6kn        ^zlib@1.2.11%gcc
 
   bkyl5bh    zlib@1.2.8%gcc
@@ -420,197 +402,250 @@ we install it "out of the box," it will build with ``openmpi``.
 
 .. code-block:: console
 
-  $ spack install --use-cache hdf5
+  $ spack install hdf5
   ==> Installing libsigsegv
   ==> Searching for binary cache of libsigsegv
-  ==> Finding buildcaches in /home/ubuntu/becker/buildcache/build_cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64-gcc-5.4.0-openssl-1.0.2k-gyxmhgbam26d7y42omb7xrvkjjgmzwio.spec.yaml
-  ######################################################################## 100.0%
+  ==> Finding buildcaches in /mirror/build_cache
   ==> Installing libsigsegv from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/libsigsegv-2.11/linux-ubuntu16.04-x86_64-gcc-5.4.0-libsigsegv-2.11-fypapcprssrj3nstp6njprskeyynsgaz.spack
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/libsigsegv-2.11/linux-ubuntu16.04-x86_64-gcc-5.4.0-libsigsegv-2.11-fypapcprssrj3nstp6njprskeyynsgaz.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 01:21:10 AM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:08:01 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
   ==> Successfully installed libsigsegv from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libsigsegv-2.11-fypapcprssrj3nstp6njprskeyynsgaz
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libsigsegv-2.11-fypapcprssrj3nstp6njprskeyynsgaz
   ==> Installing m4
   ==> Searching for binary cache of m4
   ==> Installing m4 from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/m4-1.4.18/linux-ubuntu16.04-x86_64-gcc-5.4.0-m4-1.4.18-r5envx3kqctwwflhd4qax4ahqtt6x43a.spack
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/m4-1.4.18/linux-ubuntu16.04-x86_64-gcc-5.4.0-m4-1.4.18-suf5jtcfehivwfesrc5hjy72r4nukyel.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 01:22:03 AM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:24:11 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
   ==> Successfully installed m4 from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/m4-1.4.18-r5envx3kqctwwflhd4qax4ahqtt6x43a
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/m4-1.4.18-suf5jtcfehivwfesrc5hjy72r4nukyel
   ==> Installing libtool
   ==> Searching for binary cache of libtool
   ==> Installing libtool from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/libtool-2.4.6/linux-ubuntu16.04-x86_64-gcc-5.4.0-libtool-2.4.6-o2pfwjf44353ajgr42xqtvzyvqsazkgu.spack
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/libtool-2.4.6/linux-ubuntu16.04-x86_64-gcc-5.4.0-libtool-2.4.6-o2pfwjf44353ajgr42xqtvzyvqsazkgu.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 01:29:09 AM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:12:47 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
   ==> Successfully installed libtool from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libtool-2.4.6-o2pfwjf44353ajgr42xqtvzyvqsazkgu
-  ==> Installing pkg-config
-  ==> Searching for binary cache of pkg-config
-  ==> Installing pkg-config from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/pkg-config-0.29.2/linux-ubuntu16.04-x86_64-gcc-5.4.0-pkg-config-0.29.2-ae2hwm7q57byfbxtymts55xppqwk7ecj.spack
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libtool-2.4.6-o2pfwjf44353ajgr42xqtvzyvqsazkgu
+  ==> Installing pkgconf
+  ==> Searching for binary cache of pkgconf
+  ==> Installing pkgconf from binary cache
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/pkgconf-1.4.2/linux-ubuntu16.04-x86_64-gcc-5.4.0-pkgconf-1.4.2-fovrh7alpft646n6mhis5mml6k6e5f4v.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 01:30:13 AM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:00:47 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
-  ==> Successfully installed pkg-config from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pkg-config-0.29.2-ae2hwm7q57byfbxtymts55xppqwk7ecj
+  ==> Successfully installed pkgconf from binary cache
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pkgconf-1.4.2-fovrh7alpft646n6mhis5mml6k6e5f4v
   ==> Installing util-macros
   ==> Searching for binary cache of util-macros
   ==> Installing util-macros from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/util-macros-1.19.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-util-macros-1.19.1-milz7fmttmptcic2qdk5cnel7ll5sybr.spack
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/util-macros-1.19.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-util-macros-1.19.1-milz7fmttmptcic2qdk5cnel7ll5sybr.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 01:30:12 AM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:31:54 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
   ==> Successfully installed util-macros from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/util-macros-1.19.1-milz7fmttmptcic2qdk5cnel7ll5sybr
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/util-macros-1.19.1-milz7fmttmptcic2qdk5cnel7ll5sybr
   ==> Installing libpciaccess
   ==> Searching for binary cache of libpciaccess
   ==> Installing libpciaccess from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/libpciaccess-0.13.5/linux-ubuntu16.04-x86_64-gcc-5.4.0-libpciaccess-0.13.5-5urc6tcjae26fbbd2wyfohoszhgxtbmc.spack
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/libpciaccess-0.13.5/linux-ubuntu16.04-x86_64-gcc-5.4.0-libpciaccess-0.13.5-5urc6tcjae26fbbd2wyfohoszhgxtbmc.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 12:30:23 AM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:09:34 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
   ==> Successfully installed libpciaccess from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libpciaccess-0.13.5-5urc6tcjae26fbbd2wyfohoszhgxtbmc
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libpciaccess-0.13.5-5urc6tcjae26fbbd2wyfohoszhgxtbmc
   ==> Installing xz
   ==> Searching for binary cache of xz
   ==> Installing xz from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/xz-5.2.3/linux-ubuntu16.04-x86_64-gcc-5.4.0-xz-5.2.3-htnq7wqdrqtof6uxqicdj3f7oe3xz6pw.spack
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/xz-5.2.4/linux-ubuntu16.04-x86_64-gcc-5.4.0-xz-5.2.4-teneqii2xv5u6zl5r6qi3pwurc6pmypz.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 12:30:34 AM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:05:03 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
   ==> Successfully installed xz from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/xz-5.2.3-htnq7wqdrqtof6uxqicdj3f7oe3xz6pw
-  ==> zlib is already installed in /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/xz-5.2.4-teneqii2xv5u6zl5r6qi3pwurc6pmypz
+  ==> zlib is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
   ==> Installing libxml2
   ==> Searching for binary cache of libxml2
   ==> Installing libxml2 from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/libxml2-2.9.4/linux-ubuntu16.04-x86_64-gcc-5.4.0-libxml2-2.9.4-sxk64lvcxhqjflzesnf3ye4wakovwi45.spack
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/libxml2-2.9.8/linux-ubuntu16.04-x86_64-gcc-5.4.0-libxml2-2.9.8-wpexsphdmfayxqxd4up5vgwuqgu5woo7.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 12:30:23 AM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 04:56:04 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
   ==> Successfully installed libxml2 from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libxml2-2.9.4-sxk64lvcxhqjflzesnf3ye4wakovwi45
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libxml2-2.9.8-wpexsphdmfayxqxd4up5vgwuqgu5woo7
+  ==> Installing ncurses
+  ==> Searching for binary cache of ncurses
+  ==> Installing ncurses from binary cache
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/ncurses-6.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-ncurses-6.1-3o765ourmesfrji6yeclb4wb5w54aqbh.spack
+  ######################################################################## 100.0%
+  gpg: Signature made Sat Nov 10 05:04:49 2018 UTC using RSA key ID 3B7C69B2
+  gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
+  gpg: WARNING: This key is not certified with a trusted signature!
+  gpg:          There is no indication that the signature belongs to the owner.
+  Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
+  ==> Successfully installed ncurses from binary cache
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/ncurses-6.1-3o765ourmesfrji6yeclb4wb5w54aqbh
+  ==> Installing readline
+  ==> Searching for binary cache of readline
+  ==> Installing readline from binary cache
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/readline-7.0/linux-ubuntu16.04-x86_64-gcc-5.4.0-readline-7.0-nxhwrg7xwc6nbsm2v4ezwe63l6nfidbi.spack
+  ######################################################################## 100.0%
+  gpg: Signature made Sat Nov 10 05:04:56 2018 UTC using RSA key ID 3B7C69B2
+  gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
+  gpg: WARNING: This key is not certified with a trusted signature!
+  gpg:          There is no indication that the signature belongs to the owner.
+  Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
+  ==> Successfully installed readline from binary cache
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/readline-7.0-nxhwrg7xwc6nbsm2v4ezwe63l6nfidbi
+  ==> Installing gdbm
+  ==> Searching for binary cache of gdbm
+  ==> Installing gdbm from binary cache
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/gdbm-1.14.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-gdbm-1.14.1-q4fpyuo7ouhkeq6d3oabtrppctpvxmes.spack
+  ######################################################################## 100.0%
+  gpg: Signature made Sat Nov 10 05:18:34 2018 UTC using RSA key ID 3B7C69B2
+  gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
+  gpg: WARNING: This key is not certified with a trusted signature!
+  gpg:          There is no indication that the signature belongs to the owner.
+  Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
+  ==> Successfully installed gdbm from binary cache
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gdbm-1.14.1-q4fpyuo7ouhkeq6d3oabtrppctpvxmes
+  ==> Installing perl
+  ==> Searching for binary cache of perl
+  ==> Installing perl from binary cache
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/perl-5.26.2/linux-ubuntu16.04-x86_64-gcc-5.4.0-perl-5.26.2-ic2kyoadgp3dxfejcbllyplj2wf524fo.spack
+  ######################################################################## 100.0%
+  gpg: Signature made Sat Nov 10 05:12:45 2018 UTC using RSA key ID 3B7C69B2
+  gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
+  gpg: WARNING: This key is not certified with a trusted signature!
+  gpg:          There is no indication that the signature belongs to the owner.
+  Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
+  ==> Successfully installed perl from binary cache
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/perl-5.26.2-ic2kyoadgp3dxfejcbllyplj2wf524fo
+  ==> Installing autoconf
+  ==> Searching for binary cache of autoconf
+  ==> Installing autoconf from binary cache
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/autoconf-2.69/linux-ubuntu16.04-x86_64-gcc-5.4.0-autoconf-2.69-3sx2gxeibc4oasqd4o5h6lnwpcpsgd2q.spack
+  ######################################################################## 100.0%
+  gpg: Signature made Sat Nov 10 05:24:03 2018 UTC using RSA key ID 3B7C69B2
+  gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
+  gpg: WARNING: This key is not certified with a trusted signature!
+  gpg:          There is no indication that the signature belongs to the owner.
+  Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
+  ==> Successfully installed autoconf from binary cache
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/autoconf-2.69-3sx2gxeibc4oasqd4o5h6lnwpcpsgd2q
+  ==> Installing automake
+  ==> Searching for binary cache of automake
+  ==> Installing automake from binary cache
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/automake-1.16.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-automake-1.16.1-rymw7imfehycqxzj4nuy2oiw3abegooy.spack
+  ######################################################################## 100.0%
+  gpg: Signature made Sat Nov 10 05:12:03 2018 UTC using RSA key ID 3B7C69B2
+  gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
+  gpg: WARNING: This key is not certified with a trusted signature!
+  gpg:          There is no indication that the signature belongs to the owner.
+  Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
+  ==> Successfully installed automake from binary cache
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/automake-1.16.1-rymw7imfehycqxzj4nuy2oiw3abegooy
+  ==> Installing numactl
+  ==> Searching for binary cache of numactl
+  ==> Installing numactl from binary cache
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/numactl-2.0.11/linux-ubuntu16.04-x86_64-gcc-5.4.0-numactl-2.0.11-ft463odrombnxlc3qew4omckhlq7tqgc.spack
+  ######################################################################## 100.0%
+  gpg: Signature made Sat Nov 10 05:30:34 2018 UTC using RSA key ID 3B7C69B2
+  gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
+  gpg: WARNING: This key is not certified with a trusted signature!
+  gpg:          There is no indication that the signature belongs to the owner.
+  Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
+  ==> Successfully installed numactl from binary cache
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/numactl-2.0.11-ft463odrombnxlc3qew4omckhlq7tqgc
   ==> Installing hwloc
   ==> Searching for binary cache of hwloc
   ==> Installing hwloc from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/hwloc-1.11.8/linux-ubuntu16.04-x86_64-gcc-5.4.0-hwloc-1.11.8-ivg4d2e6anxwin4zbld2g4qlrbuquoyg.spack
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/hwloc-1.11.9/linux-ubuntu16.04-x86_64-gcc-5.4.0-hwloc-1.11.9-43tkw5mt6huhv37vqnybqgxtkodbsava.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 12:30:32 AM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:08:00 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
   ==> Successfully installed hwloc from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hwloc-1.11.8-ivg4d2e6anxwin4zbld2g4qlrbuquoyg
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hwloc-1.11.9-43tkw5mt6huhv37vqnybqgxtkodbsava
   ==> Installing openmpi
   ==> Searching for binary cache of openmpi
   ==> Installing openmpi from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0/linux-ubuntu16.04-x86_64-gcc-5.4.0-openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f.spack
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.1.3/linux-ubuntu16.04-x86_64-gcc-5.4.0-openmpi-3.1.3-3njc4q5pqdpptq6jvqjrezkffwokv2sx.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 12:43:34 AM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:01:54 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
   ==> Successfully installed openmpi from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.1.3-3njc4q5pqdpptq6jvqjrezkffwokv2sx
   ==> Installing hdf5
   ==> Searching for binary cache of hdf5
   ==> Installing hdf5 from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-hdf5-1.10.1-bovz45ms24pmfr7hlckf56bxegfc4rea.spack
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4/linux-ubuntu16.04-x86_64-gcc-5.4.0-hdf5-1.10.4-ozyvmhzdew66byarohm4p36ep7wtcuiw.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 12:53:08 AM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:23:04 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
   ==> Successfully installed hdf5 from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.1-bovz45ms24pmfr7hlckf56bxegfc4rea
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4-ozyvmhzdew66byarohm4p36ep7wtcuiw
 
-Spack packages can also have variants. Boolean variants can be specified
-using the ``+`` and ``~`` or ``-`` sigils. There are two sigils for
-``False`` to avoid conflicts with shell parsing in different
-situations. Variants (boolean or otherwise) can also be specified using
-the same syntax as compiler flags.  Here we can install HDF5 without MPI
-support.
+Spack packages can also have build options, called variants. Boolean
+variants can be specified using the ``+`` and ``~`` or ``-``
+sigils. There are two sigils for ``False`` to avoid conflicts with
+shell parsing in different situations. Variants (boolean or otherwise)
+can also be specified using the same syntax as compiler flags.  Here
+we can install HDF5 without MPI support.
 
 .. code-block:: console
 
-   $ spack install --use-cache hdf5~mpi
-   ==> zlib is already installed in /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
+   $ spack install hdf5~mpi
+   ==> zlib is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
    ==> Installing hdf5
    ==> Searching for binary cache of hdf5
-   ==> Finding buildcaches in /home/ubuntu/becker/buildcache/build_cache
-   ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64-gcc-5.4.0-openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f.spec.yaml
-   ######################################################################## 100.0%
-   ...
-   ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64-gcc-5.4.0-util-macros-1.19.1-milz7fmttmptcic2qdk5cnel7ll5sybr.spec.yaml
-   ######################################################################## 100.0%
+   ==> Finding buildcaches in /mirror/build_cache
    ==> Installing hdf5 from binary cache
-   ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-hdf5-1.10.1-pa6oqzfeqzkqkzqr2375fqyt3qggx3tr.spack
+   ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4/linux-ubuntu16.04-x86_64-gcc-5.4.0-hdf5-1.10.4-5vcv5r67vpjzenq4apyebshclelnzuja.spack
    ######################################################################## 100.0%
-   gpg: Signature made Sat 11 Nov 2017 12:53:40 AM UTC using RSA key ID 3B7C69B2
+   gpg: Signature made Sat Nov 10 05:23:24 2018 UTC using RSA key ID 3B7C69B2
    gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
    gpg: WARNING: This key is not certified with a trusted signature!
    gpg:          There is no indication that the signature belongs to the owner.
    Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-   ==> Relocating package from
-     /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
    ==> Successfully installed hdf5 from binary cache
-   [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.1-pa6oqzfeqzkqkzqr2375fqyt3qggx3tr
+   [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4-5vcv5r67vpjzenq4apyebshclelnzuja
 
 We might also want to install HDF5 with a different MPI
 implementation. While MPI is not a package itself, packages can depend on
@@ -627,48 +662,76 @@ by any of several providers.
 
 .. code-block:: console
 
-  $ spack install --use-cache hdf5+hl+mpi ^mpich
+  $ spack install hdf5+hl+mpi ^mpich
+  ==> libsigsegv is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libsigsegv-2.11-fypapcprssrj3nstp6njprskeyynsgaz
+  ==> m4 is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/m4-1.4.18-suf5jtcfehivwfesrc5hjy72r4nukyel
+  ==> pkgconf is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pkgconf-1.4.2-fovrh7alpft646n6mhis5mml6k6e5f4v
+  ==> ncurses is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/ncurses-6.1-3o765ourmesfrji6yeclb4wb5w54aqbh
+  ==> readline is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/readline-7.0-nxhwrg7xwc6nbsm2v4ezwe63l6nfidbi
+  ==> gdbm is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gdbm-1.14.1-q4fpyuo7ouhkeq6d3oabtrppctpvxmes
+  ==> perl is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/perl-5.26.2-ic2kyoadgp3dxfejcbllyplj2wf524fo
+  ==> autoconf is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/autoconf-2.69-3sx2gxeibc4oasqd4o5h6lnwpcpsgd2q
+  ==> automake is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/automake-1.16.1-rymw7imfehycqxzj4nuy2oiw3abegooy
+  ==> libtool is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libtool-2.4.6-o2pfwjf44353ajgr42xqtvzyvqsazkgu
+  ==> Installing texinfo
+  ==> Searching for binary cache of texinfo
+  ==> Finding buildcaches in /mirror/build_cache
+  ==> Installing texinfo from binary cache
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/texinfo-6.5/linux-ubuntu16.04-x86_64-gcc-5.4.0-texinfo-6.5-zs7a2pcwhq6ho2cj2x26uxfktwkpyucn.spack
+  ######################################################################## 100.0%
+  gpg: Signature made Sat Nov 10 05:18:29 2018 UTC using RSA key ID 3B7C69B2
+  gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
+  gpg: WARNING: This key is not certified with a trusted signature!
+  gpg:          There is no indication that the signature belongs to the owner.
+  Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
+  ==> Successfully installed texinfo from binary cache
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/texinfo-6.5-zs7a2pcwhq6ho2cj2x26uxfktwkpyucn
+  ==> Installing findutils
+  ==> Searching for binary cache of findutils
+  ==> Installing findutils from binary cache
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/findutils-4.6.0/linux-ubuntu16.04-x86_64-gcc-5.4.0-findutils-4.6.0-d4iajxsopzrlcjtasahxqeyjkjv5jx4v.spack
+  ######################################################################## 100.0%
+  gpg: Signature made Sat Nov 10 05:07:17 2018 UTC using RSA key ID 3B7C69B2
+  gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
+  gpg: WARNING: This key is not certified with a trusted signature!
+  gpg:          There is no indication that the signature belongs to the owner.
+  Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
+  ==> Successfully installed findutils from binary cache
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/findutils-4.6.0-d4iajxsopzrlcjtasahxqeyjkjv5jx4v
   ==> Installing mpich
   ==> Searching for binary cache of mpich
-  ==> Finding buildcaches in /home/ubuntu/becker/buildcache/build_cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64-gcc-5.4.0-hdf5-1.10.1-pa6oqzfeqzkqkzqr2375fqyt3qggx3tr.spec.yaml
-  ######################################################################## 100.0%
   ==> Installing mpich from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpich-3.2/linux-ubuntu16.04-x86_64-gcc-5.4.0-mpich-3.2-cymrnoowcc4vdyvdnf5ypvob4cmdadk5.spack
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpich-3.2.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-mpich-3.2.1-p3f7p2r5ntrynqibosglxvhwyztiwqs5.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 12:45:26 AM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:23:57 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
   ==> Successfully installed mpich from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpich-3.2-cymrnoowcc4vdyvdnf5ypvob4cmdadk5
-  ==> zlib is already installed in /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpich-3.2.1-p3f7p2r5ntrynqibosglxvhwyztiwqs5
+  ==> zlib is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
   ==> Installing hdf5
   ==> Searching for binary cache of hdf5
   ==> Installing hdf5 from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-hdf5-1.10.1-e4gz6f2l5ik3ijuk3alwsqplex4tbvin.spack
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4/linux-ubuntu16.04-x86_64-gcc-5.4.0-hdf5-1.10.4-xxd7syhgej6onpyfyewxqcqe7ltkt7ob.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 12:49:45 AM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:07:32 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
   ==> Successfully installed hdf5 from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.1-e4gz6f2l5ik3ijuk3alwsqplex4tbvin
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4-xxd7syhgej6onpyfyewxqcqe7ltkt7ob
 
 We'll do a quick check in on what we have installed so far.
 
 .. code-block:: console
 
   $ spack find -ldf
-  ==> 23 installed packages.
+  ==> 32 installed packages
   -- linux-ubuntu16.04-x86_64 / clang@3.8.0-2ubuntu4 --------------
-  ufruk7k    openssl@1.0.2k%clang
+  6wc66et    tcl@8.6.8%clang
   i426yu3        ^zlib@1.2.8%clang
 
   i426yu3    zlib@1.2.8%clang
@@ -681,26 +744,48 @@ We'll do a quick check in on what we have installed so far.
 
 
   -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
-  pa6oqzf    hdf5@1.10.1%gcc
+  3sx2gxe    autoconf@2.69%gcc
+  suf5jtc        ^m4@1.4.18%gcc
+  fypapcp            ^libsigsegv@2.11%gcc
+  ic2kyoa        ^perl@5.26.2%gcc
+  q4fpyuo            ^gdbm@1.14.1%gcc
+  nxhwrg7                ^readline@7.0%gcc
+  3o765ou                    ^ncurses@6.1%gcc
+
+  rymw7im    automake@1.16.1%gcc
+  ic2kyoa        ^perl@5.26.2%gcc
+  q4fpyuo            ^gdbm@1.14.1%gcc
+  nxhwrg7                ^readline@7.0%gcc
+  3o765ou                    ^ncurses@6.1%gcc
+
+  d4iajxs    findutils@4.6.0%gcc
+
+  q4fpyuo    gdbm@1.14.1%gcc
+  nxhwrg7        ^readline@7.0%gcc
+  3o765ou            ^ncurses@6.1%gcc
+
+  5vcv5r6    hdf5@1.10.4%gcc
   5nus6kn        ^zlib@1.2.11%gcc
 
-  bovz45m    hdf5@1.10.1%gcc
-  yo5qkfv        ^openmpi@3.0.0%gcc
-  ivg4d2e            ^hwloc@1.11.8%gcc
+  ozyvmhz    hdf5@1.10.4%gcc
+  3njc4q5        ^openmpi@3.1.3%gcc
+  43tkw5m            ^hwloc@1.11.9%gcc
   5urc6tc                ^libpciaccess@0.13.5%gcc
-  sxk64lv                ^libxml2@2.9.4%gcc
-  htnq7wq                    ^xz@5.2.3%gcc
+  wpexsph                ^libxml2@2.9.8%gcc
+  teneqii                    ^xz@5.2.4%gcc
   5nus6kn                    ^zlib@1.2.11%gcc
+  ft463od                ^numactl@2.0.11%gcc
 
-  e4gz6f2    hdf5@1.10.1%gcc
-  cymrnoo        ^mpich@3.2%gcc
+  xxd7syh    hdf5@1.10.4%gcc
+  p3f7p2r        ^mpich@3.2.1%gcc
   5nus6kn        ^zlib@1.2.11%gcc
 
-  ivg4d2e    hwloc@1.11.8%gcc
+  43tkw5m    hwloc@1.11.9%gcc
   5urc6tc        ^libpciaccess@0.13.5%gcc
-  sxk64lv        ^libxml2@2.9.4%gcc
-  htnq7wq            ^xz@5.2.3%gcc
+  wpexsph        ^libxml2@2.9.8%gcc
+  teneqii            ^xz@5.2.4%gcc
   5nus6kn            ^zlib@1.2.11%gcc
+  ft463od        ^numactl@2.0.11%gcc
 
   5urc6tc    libpciaccess@0.13.5%gcc
 
@@ -708,33 +793,52 @@ We'll do a quick check in on what we have installed so far.
 
   o2pfwjf    libtool@2.4.6%gcc
 
-  sxk64lv    libxml2@2.9.4%gcc
-  htnq7wq        ^xz@5.2.3%gcc
+  wpexsph    libxml2@2.9.8%gcc
+  teneqii        ^xz@5.2.4%gcc
   5nus6kn        ^zlib@1.2.11%gcc
 
-  r5envx3    m4@1.4.18%gcc
+  suf5jtc    m4@1.4.18%gcc
   fypapcp        ^libsigsegv@2.11%gcc
 
-  cymrnoo    mpich@3.2%gcc
+  p3f7p2r    mpich@3.2.1%gcc
 
-  yo5qkfv    openmpi@3.0.0%gcc
-  ivg4d2e        ^hwloc@1.11.8%gcc
+  3o765ou    ncurses@6.1%gcc
+
+  ft463od    numactl@2.0.11%gcc
+
+  3njc4q5    openmpi@3.1.3%gcc
+  43tkw5m        ^hwloc@1.11.9%gcc
   5urc6tc            ^libpciaccess@0.13.5%gcc
-  sxk64lv            ^libxml2@2.9.4%gcc
-  htnq7wq                ^xz@5.2.3%gcc
+  wpexsph            ^libxml2@2.9.8%gcc
+  teneqii                ^xz@5.2.4%gcc
   5nus6kn                ^zlib@1.2.11%gcc
+  ft463od            ^numactl@2.0.11%gcc
+
+  ic2kyoa    perl@5.26.2%gcc
+  q4fpyuo        ^gdbm@1.14.1%gcc
+  nxhwrg7            ^readline@7.0%gcc
+  3o765ou                ^ncurses@6.1%gcc
 
-  gyxmhgb    openssl@1.0.2k%gcc
+  fovrh7a    pkgconf@1.4.2%gcc
+
+  nxhwrg7    readline@7.0%gcc
+  3o765ou        ^ncurses@6.1%gcc
+
+  am4pbat    tcl@8.6.8%gcc
   64mns5m        ^zlib@1.2.8%gcc cppflags="-O3"
 
-  2woov64    openssl@1.0.2k%gcc
+  qhwyccy    tcl@8.6.8%gcc
   5nus6kn        ^zlib@1.2.11%gcc
 
-  ae2hwm7    pkg-config@0.29.2%gcc
+  zs7a2pc    texinfo@6.5%gcc
+  ic2kyoa        ^perl@5.26.2%gcc
+  q4fpyuo            ^gdbm@1.14.1%gcc
+  nxhwrg7                ^readline@7.0%gcc
+  3o765ou                    ^ncurses@6.1%gcc
 
   milz7fm    util-macros@1.19.1%gcc
 
-  htnq7wq    xz@5.2.3%gcc
+  teneqii    xz@5.2.4%gcc
 
   bkyl5bh    zlib@1.2.8%gcc
 
@@ -756,6 +860,30 @@ DAG as a graph.
   o |  zlib
    /
   o  mpich
+  o  findutils
+  |\
+  | |\
+  | | |\
+  | | | |\
+  o | | | |  texinfo
+  | | | o |  automake
+  | |_|/| |
+  |/| | | |
+  | | | |/
+  | | | o  autoconf
+  | |_|/|
+  |/| |/
+  | |/|
+  o | |  perl
+  o | |  gdbm
+  o | |  readline
+  o | |  ncurses
+  o | |  pkgconf
+   / /
+  | o  libtool
+  |/
+  o  m4
+  o  libsigsegv
 
 You may also have noticed that there are some packages shown in the
 ``spack find -d`` output that we didn't install explicitly. These are
@@ -777,270 +905,237 @@ let's look at an even more complicated package.
 
 .. code-block:: console
 
-  $ spack install --use-cache trilinos
+  $ spack install trilinos
+  ==> Installing diffutils
+  ==> Searching for binary cache of diffutils
+  ==> Finding buildcaches in /mirror/build_cache
+  ==> Installing diffutils from binary cache
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/diffutils-3.6/linux-ubuntu16.04-x86_64-gcc-5.4.0-diffutils-3.6-2rhuivgjrna2nrxhntyde6md2khcvs34.spack
+  ######################################################################## 100.0%
+  gpg: Signature made Sat Nov 10 05:30:17 2018 UTC using RSA key ID 3B7C69B2
+  gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
+  gpg: WARNING: This key is not certified with a trusted signature!
+  gpg:          There is no indication that the signature belongs to the owner.
+  Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
+  ==> Successfully installed diffutils from binary cache
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/diffutils-3.6-2rhuivgjrna2nrxhntyde6md2khcvs34
   ==> Installing bzip2
   ==> Searching for binary cache of bzip2
-  ==> Finding buildcaches in /home/ubuntu/becker/buildcache/build_cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64-gcc-5.4.0-hdf5-1.10.1-e4gz6f2l5ik3ijuk3alwsqplex4tbvin.spec.yaml
-  ######################################################################## 100.0%
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64-gcc-5.4.0-mpich-3.2-cymrnoowcc4vdyvdnf5ypvob4cmdadk5.spec.yaml
-  ######################################################################## 100.0%
   ==> Installing bzip2 from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/bzip2-1.0.6/linux-ubuntu16.04-x86_64-gcc-5.4.0-bzip2-1.0.6-ufczdvsqt6edesm36xiucyry7myhj7e7.spack
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/bzip2-1.0.6/linux-ubuntu16.04-x86_64-gcc-5.4.0-bzip2-1.0.6-ufczdvsqt6edesm36xiucyry7myhj7e7.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 12:39:37 AM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:34:37 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
   ==> Successfully installed bzip2 from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/bzip2-1.0.6-ufczdvsqt6edesm36xiucyry7myhj7e7
-  ==> zlib is already installed in /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/bzip2-1.0.6-ufczdvsqt6edesm36xiucyry7myhj7e7
+  ==> zlib is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
   ==> Installing boost
   ==> Searching for binary cache of boost
   ==> Installing boost from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/boost-1.65.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-boost-1.65.1-xxqnbqql5nup7rujer2ury3hsdgcumzb.spack
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/boost-1.68.0/linux-ubuntu16.04-x86_64-gcc-5.4.0-boost-1.68.0-zbgfxapchxa4awxdwpleubfuznblxzvt.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 12:43:14 AM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 04:58:55 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
   ==> Successfully installed boost from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/boost-1.65.1-xxqnbqql5nup7rujer2ury3hsdgcumzb
-  ==> pkg-config is already installed in /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pkg-config-0.29.2-ae2hwm7q57byfbxtymts55xppqwk7ecj
-  ==> Installing ncurses
-  ==> Searching for binary cache of ncurses
-  ==> Installing ncurses from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/ncurses-6.0/linux-ubuntu16.04-x86_64-gcc-5.4.0-ncurses-6.0-ukq4tccptm2rxd56d2bumqthnpcjzlez.spack
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/boost-1.68.0-zbgfxapchxa4awxdwpleubfuznblxzvt
+  ==> pkgconf is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pkgconf-1.4.2-fovrh7alpft646n6mhis5mml6k6e5f4v
+  ==> ncurses is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/ncurses-6.1-3o765ourmesfrji6yeclb4wb5w54aqbh
+  ==> readline is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/readline-7.0-nxhwrg7xwc6nbsm2v4ezwe63l6nfidbi
+  ==> gdbm is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gdbm-1.14.1-q4fpyuo7ouhkeq6d3oabtrppctpvxmes
+  ==> perl is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/perl-5.26.2-ic2kyoadgp3dxfejcbllyplj2wf524fo
+  ==> Installing openssl
+  ==> Searching for binary cache of openssl
+  ==> Installing openssl from binary cache
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/openssl-1.0.2o/linux-ubuntu16.04-x86_64-gcc-5.4.0-openssl-1.0.2o-b4y3w3bsyvjla6eesv4vt6aplpfrpsha.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 01:06:38 AM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:24:10 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
-  ==> Successfully installed ncurses from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/ncurses-6.0-ukq4tccptm2rxd56d2bumqthnpcjzlez
-  ==> openssl is already installed in /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openssl-1.0.2k-2woov64m3n4gjtnfp722qcyemzf2qtom
+  ==> Successfully installed openssl from binary cache
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openssl-1.0.2o-b4y3w3bsyvjla6eesv4vt6aplpfrpsha
   ==> Installing cmake
   ==> Searching for binary cache of cmake
   ==> Installing cmake from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/cmake-3.9.4/linux-ubuntu16.04-x86_64-gcc-5.4.0-cmake-3.9.4-a2lyofsoxutyy4ihvzopizpbjubtdoem.spack
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/cmake-3.12.3/linux-ubuntu16.04-x86_64-gcc-5.4.0-cmake-3.12.3-otafqzhh4xnlq2mpakch7dr3tjfsrjnx.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 01:22:03 AM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:33:15 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
   ==> Successfully installed cmake from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/cmake-3.9.4-a2lyofsoxutyy4ihvzopizpbjubtdoem
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/cmake-3.12.3-otafqzhh4xnlq2mpakch7dr3tjfsrjnx
   ==> Installing glm
   ==> Searching for binary cache of glm
   ==> Installing glm from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/glm-0.9.7.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-glm-0.9.7.1-jnw622jwcbsymzj2fsx22omjl7tmvaws.spack
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/glm-0.9.7.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-glm-0.9.7.1-jnw622jwcbsymzj2fsx22omjl7tmvaws.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 12:30:38 AM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:30:33 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
   ==> Successfully installed glm from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/glm-0.9.7.1-jnw622jwcbsymzj2fsx22omjl7tmvaws
-  ==> libsigsegv is already installed in /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libsigsegv-2.11-fypapcprssrj3nstp6njprskeyynsgaz
-  ==> m4 is already installed in /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/m4-1.4.18-r5envx3kqctwwflhd4qax4ahqtt6x43a
-  ==> libtool is already installed in /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libtool-2.4.6-o2pfwjf44353ajgr42xqtvzyvqsazkgu
-  ==> util-macros is already installed in /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/util-macros-1.19.1-milz7fmttmptcic2qdk5cnel7ll5sybr
-  ==> libpciaccess is already installed in /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libpciaccess-0.13.5-5urc6tcjae26fbbd2wyfohoszhgxtbmc
-  ==> xz is already installed in /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/xz-5.2.3-htnq7wqdrqtof6uxqicdj3f7oe3xz6pw
-  ==> libxml2 is already installed in /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libxml2-2.9.4-sxk64lvcxhqjflzesnf3ye4wakovwi45
-  ==> hwloc is already installed in /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hwloc-1.11.8-ivg4d2e6anxwin4zbld2g4qlrbuquoyg
-  ==> openmpi is already installed in /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/glm-0.9.7.1-jnw622jwcbsymzj2fsx22omjl7tmvaws
+  ==> libsigsegv is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libsigsegv-2.11-fypapcprssrj3nstp6njprskeyynsgaz
+  ==> m4 is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/m4-1.4.18-suf5jtcfehivwfesrc5hjy72r4nukyel
+  ==> libtool is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libtool-2.4.6-o2pfwjf44353ajgr42xqtvzyvqsazkgu
+  ==> util-macros is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/util-macros-1.19.1-milz7fmttmptcic2qdk5cnel7ll5sybr
+  ==> libpciaccess is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libpciaccess-0.13.5-5urc6tcjae26fbbd2wyfohoszhgxtbmc
+  ==> xz is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/xz-5.2.4-teneqii2xv5u6zl5r6qi3pwurc6pmypz
+  ==> libxml2 is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libxml2-2.9.8-wpexsphdmfayxqxd4up5vgwuqgu5woo7
+  ==> autoconf is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/autoconf-2.69-3sx2gxeibc4oasqd4o5h6lnwpcpsgd2q
+  ==> automake is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/automake-1.16.1-rymw7imfehycqxzj4nuy2oiw3abegooy
+  ==> numactl is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/numactl-2.0.11-ft463odrombnxlc3qew4omckhlq7tqgc
+  ==> hwloc is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hwloc-1.11.9-43tkw5mt6huhv37vqnybqgxtkodbsava
+  ==> openmpi is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.1.3-3njc4q5pqdpptq6jvqjrezkffwokv2sx
   ==> Installing hdf5
   ==> Searching for binary cache of hdf5
   ==> Installing hdf5 from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-hdf5-1.10.1-d73xxpvfxgd2z2ypmuuwtxhoxmzdglez.spack
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4/linux-ubuntu16.04-x86_64-gcc-5.4.0-hdf5-1.10.4-oqwnui7wtovuf2id4vjwcxfmxlzjus6y.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 12:39:36 AM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:09:10 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-  /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
   ==> Successfully installed hdf5 from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.1-d73xxpvfxgd2z2ypmuuwtxhoxmzdglez
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4-oqwnui7wtovuf2id4vjwcxfmxlzjus6y
   ==> Installing openblas
   ==> Searching for binary cache of openblas
   ==> Installing openblas from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/openblas-0.2.20/linux-ubuntu16.04-x86_64-gcc-5.4.0-openblas-0.2.20-4dahl6ltbpojei4s3stbqbq5iuuqlaxo.spack
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/openblas-0.3.3/linux-ubuntu16.04-x86_64-gcc-5.4.0-openblas-0.3.3-cyeg2yiitpuqglhvbox5gtbgsim2v5vn.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 12:43:22 AM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:32:04 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
   ==> Successfully installed openblas from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openblas-0.2.20-4dahl6ltbpojei4s3stbqbq5iuuqlaxo
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openblas-0.3.3-cyeg2yiitpuqglhvbox5gtbgsim2v5vn
   ==> Installing hypre
   ==> Searching for binary cache of hypre
   ==> Installing hypre from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/hypre-2.12.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-hypre-2.12.1-z3rgfzqc4gu4u4qvveyo2dqqzl2j463z.spack
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/hypre-2.15.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-hypre-2.15.1-fshksdpecwiq7r6vawfswpboedhbisju.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 12:30:17 AM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:07:34 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
   ==> Successfully installed hypre from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hypre-2.12.1-z3rgfzqc4gu4u4qvveyo2dqqzl2j463z
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hypre-2.15.1-fshksdpecwiq7r6vawfswpboedhbisju
   ==> Installing matio
   ==> Searching for binary cache of matio
   ==> Installing matio from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/matio-1.5.9/linux-ubuntu16.04-x86_64-gcc-5.4.0-matio-1.5.9-4ajrcuhdf5uktotnrfzufufy5vbd6any.spack
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/matio-1.5.9/linux-ubuntu16.04-x86_64-gcc-5.4.0-matio-1.5.9-lmzdgssvobdljw52mtahelu2ju7osh6h.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 12:30:24 AM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:05:13 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
   ==> Successfully installed matio from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/matio-1.5.9-4ajrcuhdf5uktotnrfzufufy5vbd6any
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/matio-1.5.9-lmzdgssvobdljw52mtahelu2ju7osh6h
   ==> Installing metis
   ==> Searching for binary cache of metis
   ==> Installing metis from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/metis-5.1.0/linux-ubuntu16.04-x86_64-gcc-5.4.0-metis-5.1.0-m34qytcqsvsaduxyh3wevf3kj6pbzyw6.spack
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/metis-5.1.0/linux-ubuntu16.04-x86_64-gcc-5.4.0-metis-5.1.0-3wnvp4ji3wwu4v4vymszrhx6naehs6jc.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 12:39:28 AM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:31:42 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-  /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
   ==> Successfully installed metis from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/metis-5.1.0-m34qytcqsvsaduxyh3wevf3kj6pbzyw6
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/metis-5.1.0-3wnvp4ji3wwu4v4vymszrhx6naehs6jc
   ==> Installing netlib-scalapack
   ==> Searching for binary cache of netlib-scalapack
   ==> Installing netlib-scalapack from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/netlib-scalapack-2.0.2/linux-ubuntu16.04-x86_64-gcc-5.4.0-netlib-scalapack-2.0.2-xudg7xypr63nte6ifrdsmllilxbrfiar.spack
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/netlib-scalapack-2.0.2/linux-ubuntu16.04-x86_64-gcc-5.4.0-netlib-scalapack-2.0.2-wotpfwfctgfkzzn2uescucxvvbg3tm6b.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 12:30:28 AM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:07:22 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
   ==> Successfully installed netlib-scalapack from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netlib-scalapack-2.0.2-xudg7xypr63nte6ifrdsmllilxbrfiar
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netlib-scalapack-2.0.2-wotpfwfctgfkzzn2uescucxvvbg3tm6b
   ==> Installing mumps
   ==> Searching for binary cache of mumps
   ==> Installing mumps from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/mumps-5.1.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-mumps-5.1.1-5a7hgodxoze47xqd32jcxhvzctex4ezx.spack
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/mumps-5.1.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-mumps-5.1.1-acsg2dzroox2swssgc5cwgkvdy6jcm5q.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 12:30:15 AM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:18:32 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
   ==> Successfully installed mumps from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/mumps-5.1.1-5a7hgodxoze47xqd32jcxhvzctex4ezx
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/mumps-5.1.1-acsg2dzroox2swssgc5cwgkvdy6jcm5q
   ==> Installing netcdf
   ==> Searching for binary cache of netcdf
   ==> Installing netcdf from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/netcdf-4.4.1.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-netcdf-4.4.1.1-gk2xxhbqijnrdwicawawcll4t3c7dvoj.spack
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/netcdf-4.6.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-netcdf-4.6.1-mhm4izpogf4mrjidyskb6ewtzxdi7t6g.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 12:43:37 AM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:11:57 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
   ==> Successfully installed netcdf from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netcdf-4.4.1.1-gk2xxhbqijnrdwicawawcll4t3c7dvoj
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netcdf-4.6.1-mhm4izpogf4mrjidyskb6ewtzxdi7t6g
   ==> Installing parmetis
   ==> Searching for binary cache of parmetis
   ==> Installing parmetis from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/parmetis-4.0.3/linux-ubuntu16.04-x86_64-gcc-5.4.0-parmetis-4.0.3-o4qdo7aylhejov2e5ii7tagrnw6qrrlo.spack
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/parmetis-4.0.3/linux-ubuntu16.04-x86_64-gcc-5.4.0-parmetis-4.0.3-uv6h3sqx6quqg22hxesi2mw2un3kw6b7.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 12:39:37 AM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:12:04 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-  /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
   ==> Successfully installed parmetis from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/parmetis-4.0.3-o4qdo7aylhejov2e5ii7tagrnw6qrrlo
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/parmetis-4.0.3-uv6h3sqx6quqg22hxesi2mw2un3kw6b7
   ==> Installing suite-sparse
   ==> Searching for binary cache of suite-sparse
   ==> Installing suite-sparse from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/suite-sparse-4.5.5/linux-ubuntu16.04-x86_64-gcc-5.4.0-suite-sparse-4.5.5-bg67crx4ltmxulnumuxjxqzrcobpmyzg.spack
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/suite-sparse-5.3.0/linux-ubuntu16.04-x86_64-gcc-5.4.0-suite-sparse-5.3.0-zaau4kifha2enpdcn3mjlrqym7hm7yon.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 12:30:31 AM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:22:54 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
   ==> Successfully installed suite-sparse from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/suite-sparse-4.5.5-bg67crx4ltmxulnumuxjxqzrcobpmyzg
-  ==> Installing superlu-dist
-  ==> Searching for binary cache of superlu-dist
-  ==> Installing superlu-dist from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/superlu-dist-5.2.2/linux-ubuntu16.04-x86_64-gcc-5.4.0-superlu-dist-5.2.2-gggsamgizi2dwmwxglgzbxvg6hkamhol.spack
-  ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 12:43:35 AM UTC using RSA key ID 3B7C69B2
-  gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
-  gpg: WARNING: This key is not certified with a trusted signature!
-  gpg:          There is no indication that the signature belongs to the owner.
-  Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
-  ==> Successfully installed superlu-dist from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/superlu-dist-5.2.2-gggsamgizi2dwmwxglgzbxvg6hkamhol
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/suite-sparse-5.3.0-zaau4kifha2enpdcn3mjlrqym7hm7yon
   ==> Installing trilinos
   ==> Searching for binary cache of trilinos
   ==> Installing trilinos from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/trilinos-12.12.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-trilinos-12.12.1-istwe3b43b7etgtrhcuzjem3p5gonc6h.spack
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/trilinos-12.12.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-trilinos-12.12.1-rlsruavxqvwk2tgxzxboclbo6ykjf54r.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 11:47:19 PM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:18:10 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
   ==> Successfully installed trilinos from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/trilinos-12.12.1-istwe3b43b7etgtrhcuzjem3p5gonc6h
 
-Now we're starting to see the power of Spack. Trilinos has 11 top
-level dependecies, many of which have dependencies of their
-own. Installing more complex packages can take days or weeks even for
-an experienced user. Although we've done a binary installation for the
-tutorial, a source installation of trilinos using Spack takes about 3
-hours (depending on the system), but only 20 seconds of programmer
-time.
+Now we're starting to see the power of Spack. Trilinos in its default
+configuration has 23 top level dependecies, many of which have
+dependencies of their own. Installing more complex packages can take
+days or weeks even for an experienced user. Although we've done a
+binary installation for the tutorial, a source installation of
+trilinos using Spack takes about 3 hours (depending on the system),
+but only 20 seconds of programmer time.
 
 Spack manages constistency of the entire DAG. Every MPI dependency will
 be satisfied by the same configuration of MPI, etc. If we install
@@ -1049,142 +1144,116 @@ with ``mpich``:
 
 .. code-block:: console
 
-  $ spack install --use-cache trilinos +hdf5 ^hdf5+hl+mpi ^mpich
-  ==> bzip2 is already installed in /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/bzip2-1.0.6-ufczdvsqt6edesm36xiucyry7myhj7e7
-  ==> zlib is already installed in /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
-  ==> boost is already installed in /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/boost-1.65.1-xxqnbqql5nup7rujer2ury3hsdgcumzb
-  ==> pkg-config is already installed in /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pkg-config-0.29.2-ae2hwm7q57byfbxtymts55xppqwk7ecj
-  ==> ncurses is already installed in /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/ncurses-6.0-ukq4tccptm2rxd56d2bumqthnpcjzlez
-  ==> openssl is already installed in /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openssl-1.0.2k-2woov64m3n4gjtnfp722qcyemzf2qtom
-  ==> cmake is already installed in /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/cmake-3.9.4-a2lyofsoxutyy4ihvzopizpbjubtdoem
-  ==> glm is already installed in /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/glm-0.9.7.1-jnw622jwcbsymzj2fsx22omjl7tmvaws
-  ==> mpich is already installed in /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpich-3.2-cymrnoowcc4vdyvdnf5ypvob4cmdadk5
-  ==> hdf5 is already installed in /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.1-e4gz6f2l5ik3ijuk3alwsqplex4tbvin
-  ==> openblas is already installed in /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openblas-0.2.20-4dahl6ltbpojei4s3stbqbq5iuuqlaxo
+  $ spack install trilinos +hdf5 ^hdf5+hl+mpi ^mpich
+  ==> diffutils is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/diffutils-3.6-2rhuivgjrna2nrxhntyde6md2khcvs34
+  ==> bzip2 is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/bzip2-1.0.6-ufczdvsqt6edesm36xiucyry7myhj7e7
+  ==> zlib is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
+  ==> boost is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/boost-1.68.0-zbgfxapchxa4awxdwpleubfuznblxzvt
+  ==> pkgconf is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pkgconf-1.4.2-fovrh7alpft646n6mhis5mml6k6e5f4v
+  ==> ncurses is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/ncurses-6.1-3o765ourmesfrji6yeclb4wb5w54aqbh
+  ==> readline is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/readline-7.0-nxhwrg7xwc6nbsm2v4ezwe63l6nfidbi
+  ==> gdbm is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gdbm-1.14.1-q4fpyuo7ouhkeq6d3oabtrppctpvxmes
+  ==> perl is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/perl-5.26.2-ic2kyoadgp3dxfejcbllyplj2wf524fo
+  ==> openssl is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openssl-1.0.2o-b4y3w3bsyvjla6eesv4vt6aplpfrpsha
+  ==> cmake is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/cmake-3.12.3-otafqzhh4xnlq2mpakch7dr3tjfsrjnx
+  ==> glm is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/glm-0.9.7.1-jnw622jwcbsymzj2fsx22omjl7tmvaws
+  ==> libsigsegv is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libsigsegv-2.11-fypapcprssrj3nstp6njprskeyynsgaz
+  ==> m4 is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/m4-1.4.18-suf5jtcfehivwfesrc5hjy72r4nukyel
+  ==> autoconf is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/autoconf-2.69-3sx2gxeibc4oasqd4o5h6lnwpcpsgd2q
+  ==> automake is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/automake-1.16.1-rymw7imfehycqxzj4nuy2oiw3abegooy
+  ==> libtool is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libtool-2.4.6-o2pfwjf44353ajgr42xqtvzyvqsazkgu
+  ==> texinfo is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/texinfo-6.5-zs7a2pcwhq6ho2cj2x26uxfktwkpyucn
+  ==> findutils is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/findutils-4.6.0-d4iajxsopzrlcjtasahxqeyjkjv5jx4v
+  ==> mpich is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpich-3.2.1-p3f7p2r5ntrynqibosglxvhwyztiwqs5
+  ==> hdf5 is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4-xxd7syhgej6onpyfyewxqcqe7ltkt7ob
+  ==> openblas is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openblas-0.3.3-cyeg2yiitpuqglhvbox5gtbgsim2v5vn
   ==> Installing hypre
   ==> Searching for binary cache of hypre
-  ==> Finding buildcaches in /home/ubuntu/becker/buildcache/build_cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64-gcc-5.4.0-netcdf-4.4.1.1-gk2xxhbqijnrdwicawawcll4t3c7dvoj.spec.yaml
-  ######################################################################## 100.0%
-  ...
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64-gcc-5.4.0-bzip2-1.0.6-ufczdvsqt6edesm36xiucyry7myhj7e7.spec.yaml
-  ######################################################################## 100.0%
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64-gcc-5.4.0-boost-1.65.1-xxqnbqql5nup7rujer2ury3hsdgcumzb.spec.yaml
-  ######################################################################## 100.0%
+  ==> Finding buildcaches in /mirror/build_cache
   ==> Installing hypre from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/hypre-2.12.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-hypre-2.12.1-3psjg2ka2qa26jtgitlil4vglqr67anj.spack
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/hypre-2.15.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-hypre-2.15.1-obewuozolon7tkdg4cfxc6ae2tzkronb.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 12:49:37 AM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:34:36 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
   ==> Successfully installed hypre from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hypre-2.12.1-3psjg2ka2qa26jtgitlil4vglqr67anj
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hypre-2.15.1-obewuozolon7tkdg4cfxc6ae2tzkronb
   ==> Installing matio
   ==> Searching for binary cache of matio
   ==> Installing matio from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/matio-1.5.9/linux-ubuntu16.04-x86_64-gcc-5.4.0-matio-1.5.9-3ibrutc6cs7x6ybyt5ni5n6djtq5okm2.spack
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/matio-1.5.9/linux-ubuntu16.04-x86_64-gcc-5.4.0-matio-1.5.9-gvyqldhifflmvcrtui3b6s64jcczsxxh.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 12:45:26 AM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:25:11 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
   ==> Successfully installed matio from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/matio-1.5.9-3ibrutc6cs7x6ybyt5ni5n6djtq5okm2
-  ==> metis is already installed in /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/metis-5.1.0-m34qytcqsvsaduxyh3wevf3kj6pbzyw6
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/matio-1.5.9-gvyqldhifflmvcrtui3b6s64jcczsxxh
+  ==> metis is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/metis-5.1.0-3wnvp4ji3wwu4v4vymszrhx6naehs6jc
   ==> Installing netlib-scalapack
   ==> Searching for binary cache of netlib-scalapack
   ==> Installing netlib-scalapack from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/netlib-scalapack-2.0.2/linux-ubuntu16.04-x86_64-gcc-5.4.0-netlib-scalapack-2.0.2-km7tsbgoyyywonyejkjoojskhc5knz3z.spack
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/netlib-scalapack-2.0.2/linux-ubuntu16.04-x86_64-gcc-5.4.0-netlib-scalapack-2.0.2-p7iln2pcosw2ipyqoyr7ie6lpva2oj7r.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 12:49:49 AM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:32:20 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
   ==> Successfully installed netlib-scalapack from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netlib-scalapack-2.0.2-km7tsbgoyyywonyejkjoojskhc5knz3z
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netlib-scalapack-2.0.2-p7iln2pcosw2ipyqoyr7ie6lpva2oj7r
   ==> Installing mumps
   ==> Searching for binary cache of mumps
   ==> Installing mumps from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/mumps-5.1.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-mumps-5.1.1-phvk6yhkzqed6gjsbah6dnhlesdclild.spack
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/mumps-5.1.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-mumps-5.1.1-cumcj5a75cagsznpjrgretxdg6okxaur.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 12:45:28 AM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:33:18 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
   ==> Successfully installed mumps from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/mumps-5.1.1-phvk6yhkzqed6gjsbah6dnhlesdclild
-  ==> libsigsegv is already installed in /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libsigsegv-2.11-fypapcprssrj3nstp6njprskeyynsgaz
-  ==> m4 is already installed in /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/m4-1.4.18-r5envx3kqctwwflhd4qax4ahqtt6x43a
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/mumps-5.1.1-cumcj5a75cagsznpjrgretxdg6okxaur
   ==> Installing netcdf
   ==> Searching for binary cache of netcdf
   ==> Installing netcdf from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/netcdf-4.4.1.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-netcdf-4.4.1.1-rmx4uppnhpv6kq7bh7r46zfqevgdkkgw.spack
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/netcdf-4.6.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-netcdf-4.6.1-wmmx5sgwfds34v7bkkhiduar5yecrnnd.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 12:49:38 AM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:24:01 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
   ==> Successfully installed netcdf from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netcdf-4.4.1.1-rmx4uppnhpv6kq7bh7r46zfqevgdkkgw
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/netcdf-4.6.1-wmmx5sgwfds34v7bkkhiduar5yecrnnd
   ==> Installing parmetis
   ==> Searching for binary cache of parmetis
   ==> Installing parmetis from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/parmetis-4.0.3/linux-ubuntu16.04-x86_64-gcc-5.4.0-parmetis-4.0.3-qk77g6aiqr3f2hsykg54zzuhlxcpdcmv.spack
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/parmetis-4.0.3/linux-ubuntu16.04-x86_64-gcc-5.4.0-parmetis-4.0.3-jehtatan4y2lcobj6waoqv66jj4libtz.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 12:45:14 AM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:07:41 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
   ==> Successfully installed parmetis from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/parmetis-4.0.3-qk77g6aiqr3f2hsykg54zzuhlxcpdcmv
-  ==> suite-sparse is already installed in /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/suite-sparse-4.5.5-bg67crx4ltmxulnumuxjxqzrcobpmyzg
-  ==> Installing superlu-dist
-  ==> Searching for binary cache of superlu-dist
-  ==> Installing superlu-dist from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/superlu-dist-5.2.2/linux-ubuntu16.04-x86_64-gcc-5.4.0-superlu-dist-5.2.2-65vot2le3ezooz7tj6eveovly725o44x.spack
-  ######################################################################## 100.0%
-  gpg: Signature made Sat 11 Nov 2017 12:45:14 AM UTC using RSA key ID 3B7C69B2
-  gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
-  gpg: WARNING: This key is not certified with a trusted signature!
-  gpg:          There is no indication that the signature belongs to the owner.
-  Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
-  ==> Successfully installed superlu-dist from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/superlu-dist-5.2.2-65vot2le3ezooz7tj6eveovly725o44x
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/parmetis-4.0.3-jehtatan4y2lcobj6waoqv66jj4libtz
+  ==> suite-sparse is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/suite-sparse-5.3.0-zaau4kifha2enpdcn3mjlrqym7hm7yon
   ==> Installing trilinos
   ==> Searching for binary cache of trilinos
   ==> Installing trilinos from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/trilinos-12.12.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-trilinos-12.12.1-xupifcp5d4f53cobm6g3xzao577uzezs.spack
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/trilinos-12.12.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-trilinos-12.12.1-kqc52moweigxqxzwzfqajc6ocxwdwn4w.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sun 12 Nov 2017 12:04:58 AM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:30:15 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
   ==> Successfully installed trilinos from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/trilinos-12.12.1-xupifcp5d4f53cobm6g3xzao577uzezs
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/trilinos-12.12.1-kqc52moweigxqxzwzfqajc6ocxwdwn4w
 
 
 We see that every package in the trilinos DAG that depends on MPI now
@@ -1193,47 +1262,47 @@ uses ``mpich``.
 .. code-block:: console
 
   $ spack find -d trilinos
-  ==> 2 installed packages.
+  ==> 2 installed packages
   -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
       trilinos@12.12.1
-          ^boost@1.65.1
+          ^boost@1.68.0
               ^bzip2@1.0.6
               ^zlib@1.2.11
           ^glm@0.9.7.1
-          ^hdf5@1.10.1
-              ^openmpi@3.0.0
-                  ^hwloc@1.11.8
+          ^hdf5@1.10.4
+              ^openmpi@3.1.3
+                  ^hwloc@1.11.9
                       ^libpciaccess@0.13.5
-                      ^libxml2@2.9.4
-                          ^xz@5.2.3
-          ^hypre@2.12.1
-              ^openblas@0.2.20
+                      ^libxml2@2.9.8
+                          ^xz@5.2.4
+                      ^numactl@2.0.11
+          ^hypre@2.15.1
+              ^openblas@0.3.3
           ^matio@1.5.9
           ^metis@5.1.0
           ^mumps@5.1.1
               ^netlib-scalapack@2.0.2
-          ^netcdf@4.4.1.1
+          ^netcdf@4.6.1
           ^parmetis@4.0.3
-          ^suite-sparse@4.5.5
-          ^superlu-dist@5.2.2
+          ^suite-sparse@5.3.0
 
       trilinos@12.12.1
-          ^boost@1.65.1
+          ^boost@1.68.0
               ^bzip2@1.0.6
               ^zlib@1.2.11
           ^glm@0.9.7.1
-          ^hdf5@1.10.1
-              ^mpich@3.2
-          ^hypre@2.12.1
-              ^openblas@0.2.20
+          ^hdf5@1.10.4
+              ^mpich@3.2.1
+          ^hypre@2.15.1
+              ^openblas@0.3.3
           ^matio@1.5.9
           ^metis@5.1.0
           ^mumps@5.1.1
               ^netlib-scalapack@2.0.2
-          ^netcdf@4.4.1.1
+          ^netcdf@4.6.1
           ^parmetis@4.0.3
-          ^suite-sparse@4.5.5
-          ^superlu-dist@5.2.2
+          ^suite-sparse@5.3.0
+
 
 As we discussed before, the ``spack find -d`` command shows the
 dependency information as a tree. While that is often sufficient, many
@@ -1258,95 +1327,111 @@ command shows the full DAG of the dependency information.
   | | | | | | | | | | |\
   | | | | | | | | | | | |\
   | | | | | | | | | | | | |\
-  | | | | | | | | | | | | | |\
-  o | | | | | | | | | | | | | |  superlu-dist
-  |\ \ \ \ \ \ \ \ \ \ \ \ \ \ \
-  | |_|/ / / / / / / / / / / / /
-  |/| | | | | | | | | | | | | |
-  | |\ \ \ \ \ \ \ \ \ \ \ \ \ \
-  | | |_|/ / / / / / / / / / / /
-  | |/| | | | | | | | | | | | |
-  | | |\ \ \ \ \ \ \ \ \ \ \ \ \
-  | | | |_|/ / / / / / / / / / /
-  | | |/| | | | | | | | | | | |
-  | | | | |_|_|/ / / / / / / /
-  | | | |/| | | | | | | | | |
-  | | | | o | | | | | | | | |  suite-sparse
-  | | | |/| | | | | | | | | |
-  | | |/|/ / / / / / / / / /
-  o | | | | | | | | | | | |  parmetis
-  |\| | | | | | | | | | | |
-  |\ \ \ \ \ \ \ \ \ \ \ \ \
-  | |_|_|/ / / / / / / / / /
-  |/| | | | | | | | | | | |
-  | | |_|_|_|_|_|_|_|/ / /
-  | |/| | | | | | | | | |
+  o | | | | | | | | | | | | |  suite-sparse
+  |\ \ \ \ \ \ \ \ \ \ \ \ \ \
+  | |_|_|/ / / / / / / / / / /
+  |/| | | | | | | | | | | | |
+  | |\ \ \ \ \ \ \ \ \ \ \ \ \
+  | | |_|_|_|_|_|/ / / / / / /
+  | |/| | | | | | | | | | | |
+  | | | |_|_|_|_|_|_|_|/ / /
+  | | |/| | | | | | | | | |
+  | | | o | | | | | | | | |  parmetis
+  | | |/| | | | | | | | | |
+  | |/|/| | | | | | | | | |
+  | | | |/ / / / / / / / /
   | | | | | | o | | | | |  mumps
-  | | | |_|_|/| | | | | |
-  | | |/| |_|/| | | | | |
+  | |_|_|_|_|/| | | | | |
+  |/| | | |_|/| | | | | |
   | | | |/| |/ / / / / /
   | | | | |/| | | | | |
   | | | | o | | | | | |  netlib-scalapack
-  | | |_|/| | | | | | |
-  | |/| |/| | | | | | |
+  | |_|_|/| | | | | | |
+  |/| | |/| | | | | | |
   | | |/|/ / / / / / /
-  o | | | | | | | | |  metis
-  |/ / / / / / / / /
+  | o | | | | | | | |  metis
+  | |/ / / / / / / /
   | | | | | | | o |  glm
-  | |_|_|_|_|_|/ /
-  |/| | | | | | |
-  o | | | | | | |  cmake
-  |\ \ \ \ \ \ \ \
-  o | | | | | | | |  openssl
-  | | | | o | | | |  netcdf
-  | |_|_|/| | | | |
-  |/| | |/| | | | |
-  | | |/| | | | | |
-  | | | | |\ \ \ \ \
-  | | | | | | |_|/ /
-  | | | | | |/| | |
-  | | | | | | o | |  matio
-  | |_|_|_|_|/| | |
-  |/| | | | |/ / /
-  | | | | | | o |  hypre
-  | | | |_|_|/| |
-  | | |/| |_|/ /
+  | | |_|_|_|_|/ /
+  | |/| | | | | |
+  | o | | | | | |  cmake
+  | |\ \ \ \ \ \ \
+  | o | | | | | | |  openssl
+  | |\ \ \ \ \ \ \ \
+  | | | | | o | | | |  netcdf
+  | | |_|_|/| | | | |
+  | |/| | |/| | | | |
+  | | | | | |\ \ \ \ \
+  | | | | | | | |_|/ /
+  | | | | | | |/| | |
+  | | | | | | | o | |  matio
+  | | |_|_|_|_|/| | |
+  | |/| | | | |/ / /
+  | | | | | | | o |  hypre
+  | |_|_|_|_|_|/| |
+  |/| | | | |_|/ /
+  | | | | |/| | |
+  | | | | | | o |  hdf5
+  | | |_|_|_|/| |
+  | |/| | | |/ /
+  | | | | |/| |
+  | | | | o | |  openmpi
+  | | |_|/| | |
+  | |/| | | | |
+  | | | | |\ \ \
+  | | | | | o | |  hwloc
+  | | | | |/| | |
+  | | | | | |\ \ \
+  | | | | | | |\ \ \
+  | | | | | | o | | |  libxml2
+  | | |_|_|_|/| | | |
+  | |/| | | |/| | | |
+  | | | | | | | | | o  boost
+  | | |_|_|_|_|_|_|/|
+  | |/| | | | | | | |
+  | o | | | | | | | |  zlib
+  |  / / / / / / / /
+  | | | | | o | | |  xz
+  | | | | |  / / /
+  | | | | | o | |  libpciaccess
+  | | | | |/| | |
+  | | | | | |\ \ \
+  | | | | | o | | |  util-macros
+  | | | | |  / / /
+  | | | o | | | |  numactl
+  | | | |\ \ \ \ \
+  | | | | |_|_|/ /
+  | | | |/| | | |
+  | | | | |\ \ \ \
+  | | | | | |_|/ /
+  | | | | |/| | |
+  | | | | | |\ \ \
+  | | | | | o | | |  automake
+  | | |_|_|/| | | |
+  | |/| | | | | | |
+  | | | | | |/ / /
+  | | | | | o | |  autoconf
+  | | |_|_|/| | |
+  | |/| | |/ / /
   | | | |/| | |
-  | | | | | o |  hdf5
-  | |_|_|_|/| |
-  |/| | |_|/ /
-  | | |/| | |
-  | | o | | |  openmpi
-  | | o | | |  hwloc
-  | | |\ \ \ \
-  | | | |\ \ \ \
-  | | | o | | | |  libxml2
-  | |_|/| | | | |
-  |/| |/| | | | |
-  | | | | | | | o  boost
-  | |_|_|_|_|_|/|
-  |/| | | | | | |
-  o | | | | | | |  zlib
-   / / / / / / /
-   | | o | | | |  xz
-   | |  / / / /
-   | | o | | |  libpciaccess
-   | |/| | | |
-   | | |\ \ \ \
-   | | o | | | |  util-macros
-   | |  / / / /
-   o | | | | |  ncurses
-   |/ / / / /
-   o | | | |  pkg-config
-    / / / /
-    | o | |  openblas
-    |  / /
-    o | |  libtool
-    |/ /
-    o |  m4
-    o |  libsigsegv
-     /
-     o  bzip2
+  | o | | | | |  perl
+  | o | | | | |  gdbm
+  | o | | | | |  readline
+  | |/ / / / /
+  | o | | | |  ncurses
+  | | |_|/ /
+  | |/| | |
+  | o | | |  pkgconf
+  |  / / /
+  o | | |  openblas
+   / / /
+   | o |  libtool
+   |/ /
+   o |  m4
+   o |  libsigsegv
+    /
+    o  bzip2
+    o  diffutils
 
 You can control how the output is displayed with a number of options.
 
@@ -1364,25 +1449,27 @@ complicated packages. The output can be changed to the ``graphviz``
 Uninstalling Packages
 ---------------------
 
-Earlier we installed many configurations each of zlib and
-openssl. Now we will go through and uninstall some of those packages
-that we didn't really need.
+Earlier we installed many configurations each of zlib and tcl. Now we
+will go through and uninstall some of those packages that we didn't
+really need.
 
 .. code-block:: console
 
-  $ spack find -d openssl
-  ==> 3 installed packages.
+  $ spack find -d tcl
+  ==> 3 installed packages
   -- linux-ubuntu16.04-x86_64 / clang@3.8.0-2ubuntu4 --------------
-      openssl@1.0.2k
+      tcl@8.6.8
           ^zlib@1.2.8
 
+
   -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
-      openssl@1.0.2k
+      tcl@8.6.8
           ^zlib@1.2.8
 
-      openssl@1.0.2k
+      tcl@8.6.8
           ^zlib@1.2.11
 
+
   $ spack find zlib
   ==> 6 installed packages.
   -- linux-ubuntu16.04-x86_64 / clang@3.8.0-2ubuntu4 --------------
@@ -1411,15 +1498,12 @@ We can uninstall packages by spec using the same syntax as install.
   ==> 5 installed packages.
   -- linux-ubuntu16.04-x86_64 / clang@3.8.0-2ubuntu4 --------------
   i426yu3 zlib@1.2.8%clang
-
   4pt75q7 zlib@1.2.11%clang
 
 
   -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
   bkyl5bh zlib@1.2.8%gcc
-
   64mns5m zlib@1.2.8%gcc cppflags="-O3"
-
   5nus6kn zlib@1.2.11%gcc
 
 We can also uninstall packages by referring only to their hash.
@@ -1433,22 +1517,19 @@ remove packages that are required by another installed package.
   ==> Error: Will not uninstall zlib@1.2.8%clang@3.8.0-2ubuntu4/i426yu3
 
   The following packages depend on it:
-  -- linux-ubuntu16.04-x86_64 / clang@3.8.0-2ubuntu4 --------------
-  ufruk7k openssl@1.0.2k%clang
-
+      -- linux-ubuntu16.04-x86_64 / clang@3.8.0-2ubuntu4 --------------
+      6wc66et tcl@8.6.8%clang
 
   ==> Error: Use \`spack uninstall --dependents\` to uninstall these dependencies as well.
 
   $ spack uninstall -R zlib/i426
   ==> The following packages will be uninstalled:
 
-  -- linux-ubuntu16.04-x86_64 / clang@3.8.0-2ubuntu4 --------------
-  ufruk7k openssl@1.0.2k%clang
-
-  i426yu3 zlib@1.2.8%clang+optimize+pic+shared
-
+      -- linux-ubuntu16.04-x86_64 / clang@3.8.0-2ubuntu4 --------------
+      6wc66et tcl@8.6.8%clang
+      i426yu3 zlib@1.2.8%clang+optimize+pic+shared
   ==> Do you want to proceed? [y/N] y
-  ==> Successfully uninstalled openssl@1.0.2k%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64 /ufruk7k
+  ==> Successfully uninstalled tcl@8.6.8%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64 /6wc66et
   ==> Successfully uninstalled zlib@1.2.8%clang@3.8.0-2ubuntu4+optimize+pic+shared arch=linux-ubuntu16.04-x86_64 /i426yu3
 
 Spack will not uninstall packages that are not sufficiently
@@ -1460,25 +1541,22 @@ packages at once.
   $ spack uninstall trilinos
   ==> Error: trilinos matches multiple packages:
 
-  -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
-  istwe3b trilinos@12.12.1%gcc~alloptpkgs+amesos+amesos2+anasazi+aztec+belos+boost build_type=RelWithDebInfo ~dtk+epetra+epetraext+exodus+fortran~fortrilinos+gtest+hdf5+hypre+ifpack+ifpack2+instantiate~instantiate_cmplx~intrepid~intrepid2+metis+ml+muelu+mumps~nox~openmp~pnetcdf~python~rol+sacado~shards+shared~stk+suite-sparse~superlu+superlu-dist+teuchos+tpetra~x11~xsdkflags~zlib+zoltan+zoltan2
-
-  xupifcp trilinos@12.12.1%gcc~alloptpkgs+amesos+amesos2+anasazi+aztec+belos+boost build_type=RelWithDebInfo ~dtk+epetra+epetraext+exodus+fortran~fortrilinos+gtest+hdf5+hypre+ifpack+ifpack2+instantiate~instantiate_cmplx~intrepid~intrepid2+metis+ml+muelu+mumps~nox~openmp~pnetcdf~python~rol+sacado~shards+shared~stk+suite-sparse~superlu+superlu-dist+teuchos+tpetra~x11~xsdkflags~zlib+zoltan+zoltan2
-
+      -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
+      rlsruav trilinos@12.12.1%gcc~alloptpkgs+amesos+amesos2+anasazi+aztec+belos+boost build_type=RelWithDebInfo ~cgns~complex~dtk+epetra+epetraext+exodus+explicit_template_instantiation~float+fortran~fortrilinos+gtest+hdf5+hypre+ifpack+ifpack2~intrepid~intrepid2~isorropia+kokkos+metis~minitensor+ml+muelu+mumps~nox~openmp~phalanx~piro~pnetcdf~python~rol~rythmos+sacado~shards+shared~stk+suite-sparse~superlu~superlu-dist~teko~tempus+teuchos+tpetra~x11~xsdkflags~zlib+zoltan+zoltan2
+      kqc52mo trilinos@12.12.1%gcc~alloptpkgs+amesos+amesos2+anasazi+aztec+belos+boost build_type=RelWithDebInfo ~cgns~complex~dtk+epetra+epetraext+exodus+explicit_template_instantiation~float+fortran~fortrilinos+gtest+hdf5+hypre+ifpack+ifpack2~intrepid~intrepid2~isorropia+kokkos+metis~minitensor+ml+muelu+mumps~nox~openmp~phalanx~piro~pnetcdf~python~rol~rythmos+sacado~shards+shared~stk+suite-sparse~superlu~superlu-dist~teko~tempus+teuchos+tpetra~x11~xsdkflags~zlib+zoltan+zoltan2
 
   ==> Error: You can either:
       a) use a more specific spec, or
       b) use `spack uninstall --all` to uninstall ALL matching specs.
 
 
-  $ spack uninstall /istw
+  $ spack uninstall /rlsr
   ==> The following packages will be uninstalled:
 
-  -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
-  istwe3b trilinos@12.12.1%gcc~alloptpkgs+amesos+amesos2+anasazi+aztec+belos+boost build_type=RelWithDebInfo ~dtk+epetra+epetraext+exodus+fortran~fortrilinos+gtest+hdf5+hypre+ifpack+ifpack2+instantiate~instantiate_cmplx~intrepid~intrepid2+metis+ml+muelu+mumps~nox~openmp~pnetcdf~python~rol+sacado~shards+shared~stk+suite-sparse~superlu+superlu-dist+teuchos+tpetra~x11~xsdkflags~zlib+zoltan+zoltan2
-
+      -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
+      rlsruav trilinos@12.12.1%gcc~alloptpkgs+amesos+amesos2+anasazi+aztec+belos+boost build_type=RelWithDebInfo ~cgns~complex~dtk+epetra+epetraext+exodus+explicit_template_instantiation~float+fortran~fortrilinos+gtest+hdf5+hypre+ifpack+ifpack2~intrepid~intrepid2~isorropia+kokkos+metis~minitensor+ml+muelu+mumps~nox~openmp~phalanx~piro~pnetcdf~python~rol~rythmos+sacado~shards+shared~stk+suite-sparse~superlu~superlu-dist~teko~tempus+teuchos+tpetra~x11~xsdkflags~zlib+zoltan+zoltan2
   ==> Do you want to proceed? [y/N] y
-  ==> Successfully uninstalled trilinos@12.12.1%gcc@5.4.0~alloptpkgs+amesos+amesos2+anasazi+aztec+belos+boost build_type=RelWithDebInfo ~dtk+epetra+epetraext+exodus+fortran~fortrilinos+gtest+hdf5+hypre+ifpack+ifpack2+instantiate~instantiate_cmplx~intrepid~intrepid2+metis+ml+muelu+mumps~nox~openmp~pnetcdf~python~rol+sacado~shards+shared~stk+suite-sparse~superlu+superlu-dist+teuchos+tpetra~x11~xsdkflags~zlib+zoltan+zoltan2 arch=linux-ubuntu16.04-x86_64 /istwe3b
+  ==> Successfully uninstalled trilinos@12.12.1%gcc@5.4.0~alloptpkgs+amesos+amesos2+anasazi+aztec+belos+boost build_type=RelWithDebInfo ~cgns~complex~dtk+epetra+epetraext+exodus+explicit_template_instantiation~float+fortran~fortrilinos+gtest+hdf5+hypre+ifpack+ifpack2~intrepid~intrepid2~isorropia+kokkos+metis~minitensor+ml+muelu+mumps~nox~openmp~phalanx~piro~pnetcdf~python~rol~rythmos+sacado~shards+shared~stk+suite-sparse~superlu~superlu-dist~teko~tempus+teuchos+tpetra~x11~xsdkflags~zlib+zoltan+zoltan2 arch=linux-ubuntu16.04-x86_64 /rlsruav
 
 -----------------------------
 Advanced ``spack find`` Usage
@@ -1497,10 +1575,10 @@ return every package which was built with ``cppflags="-O3"``.
 .. code-block:: console
 
   $ spack find ^mpich
-  ==> 9 installed packages.
+  ==> 8 installed packages
   -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
-  hdf5@1.10.1  hypre@2.12.1  matio@1.5.9  mumps@5.1.1  netcdf@4.4.1.1  netlib-scalapack@2.0.2  parmetis@4.0.3  superlu-dist@5.2.2  trilinos@12.12.1
-
+  hdf5@1.10.4   matio@1.5.9  netcdf@4.6.1            parmetis@4.0.3
+  hypre@2.15.1  mumps@5.1.1  netlib-scalapack@2.0.2  trilinos@12.12.1
 
   $ spack find cppflags=-O3
   ==> 1 installed packages.
@@ -1508,28 +1586,28 @@ return every package which was built with ``cppflags="-O3"``.
   zlib@1.2.8
 
 The ``find`` command can also show which packages were installed
-explicitly (rather than pulled in as a dependency) using the ``-e``
-flag. The ``-E`` flag shows implicit installs only. The ``find`` command can
+explicitly (rather than pulled in as a dependency) using the ``-x``
+flag. The ``-X`` flag shows implicit installs only. The ``find`` command can
 also show the path to which a spack package was installed using the ``-p``
 command.
 
 .. code-block:: console
 
-  $ spack find -pe
-  ==> 10 installed packages.
+  $ spack find -px
+  ==> 10 installed packages
   -- linux-ubuntu16.04-x86_64 / clang@3.8.0-2ubuntu4 --------------
-      zlib@1.2.11  /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/clang-3.8.0-2ubuntu4/zlib-1.2.11-4pt75q7qq6lygf3hgnona4lyc2uwedul
+      zlib@1.2.11  /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/clang-3.8.0-2ubuntu4/zlib-1.2.11-4pt75q7qq6lygf3hgnona4lyc2uwedul
 
   -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
-      hdf5@1.10.1       /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.1-pa6oqzfeqzkqkzqr2375fqyt3qggx3tr
-      hdf5@1.10.1       /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.1-bovz45ms24pmfr7hlckf56bxegfc4rea
-      hdf5@1.10.1       /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.1-e4gz6f2l5ik3ijuk3alwsqplex4tbvin
-      openssl@1.0.2k    /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openssl-1.0.2k-gyxmhgbam26d7y42omb7xrvkjjgmzwio
-      openssl@1.0.2k    /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openssl-1.0.2k-2woov64m3n4gjtnfp722qcyemzf2qtom
-      trilinos@12.12.1  /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/trilinos-12.12.1-xupifcp5d4f53cobm6g3xzao577uzezs
-      zlib@1.2.8        /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.8-bkyl5bhuep6fmhuxzkmhqy25qefjcvzc
-      zlib@1.2.8        /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.8-64mns5mvdacqvlashkf7v6lqrxixhmxu
-      zlib@1.2.11       /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
+      hdf5@1.10.4       /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4-5vcv5r67vpjzenq4apyebshclelnzuja
+      hdf5@1.10.4       /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4-ozyvmhzdew66byarohm4p36ep7wtcuiw
+      hdf5@1.10.4       /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4-xxd7syhgej6onpyfyewxqcqe7ltkt7ob
+      tcl@8.6.8         /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/tcl-8.6.8-am4pbatrtga3etyusg2akmsvrswwxno2
+      tcl@8.6.8         /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/tcl-8.6.8-qhwyccywhx2i6s7ob2gvjrjtj3rnfuqt
+      trilinos@12.12.1  /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/trilinos-12.12.1-kqc52moweigxqxzwzfqajc6ocxwdwn4w
+      zlib@1.2.8        /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.8-bkyl5bhuep6fmhuxzkmhqy25qefjcvzc
+      zlib@1.2.8        /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.8-64mns5mvdacqvlashkf7v6lqrxixhmxu
+      zlib@1.2.11       /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
 
 ---------------------
 Customizing Compilers
@@ -1557,175 +1635,86 @@ added to the configuration.
 
 .. code-block:: console
 
-  $ spack install --use-cache gcc
-  ==> libsigsegv is already installed in /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libsigsegv-2.11-fypapcprssrj3nstp6njprskeyynsgaz
-  ==> m4 is already installed in /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/m4-1.4.18-r5envx3kqctwwflhd4qax4ahqtt6x43a
-  ==> pkg-config is already installed in /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pkg-config-0.29.2-ae2hwm7q57byfbxtymts55xppqwk7ecj
-  ==> ncurses is already installed in /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/ncurses-6.0-ukq4tccptm2rxd56d2bumqthnpcjzlez
-  ==> Installing readline
-  ==> Searching for binary cache of readline
-  ==> Finding buildcaches in /home/ubuntu/becker/buildcache/build_cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64-gcc-5.4.0-matio-1.5.9-3ibrutc6cs7x6ybyt5ni5n6djtq5okm2.spec.yaml
-  ######################################################################## 100.0%
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64-gcc-5.4.0-trilinos-12.12.1-xupifcp5d4f53cobm6g3xzao577uzezs.spec.yaml
-  ######################################################################## 100.0%
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64-gcc-5.4.0-parmetis-4.0.3-qk77g6aiqr3f2hsykg54zzuhlxcpdcmv.spec.yaml
-  ######################################################################## 100.0%
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64-gcc-5.4.0-superlu-dist-5.2.2-65vot2le3ezooz7tj6eveovly725o44x.spec.yaml
-  ######################################################################## 100.0%
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64-gcc-5.4.0-hypre-2.12.1-3psjg2ka2qa26jtgitlil4vglqr67anj.spec.yaml
-  ######################################################################## 100.0%
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64-gcc-5.4.0-mumps-5.1.1-phvk6yhkzqed6gjsbah6dnhlesdclild.spec.yaml
-  ######################################################################## 100.0%
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64-gcc-5.4.0-netcdf-4.4.1.1-rmx4uppnhpv6kq7bh7r46zfqevgdkkgw.spec.yaml
-  ######################################################################## 100.0%
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64-gcc-5.4.0-netlib-scalapack-2.0.2-km7tsbgoyyywonyejkjoojskhc5knz3z.spec.yaml
-  ######################################################################## 100.0%
-  ==> Installing readline from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/readline-7.0/linux-ubuntu16.04-x86_64-gcc-5.4.0-readline-7.0-gizxpch53zv5ufa62a2tb5lalcqgxbuc.spack
-  ######################################################################## 100.0%
-  gpg: Signature made Sun 12 Nov 2017 10:26:53 PM UTC using RSA key ID 3B7C69B2
-  gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
-  gpg: WARNING: This key is not certified with a trusted signature!
-  gpg:          There is no indication that the signature belongs to the owner.
-  Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
-  ==> Successfully installed readline from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/readline-7.0-gizxpch53zv5ufa62a2tb5lalcqgxbuc
-  ==> Installing gdbm
-  ==> Searching for binary cache of gdbm
-  ==> Installing gdbm from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/gdbm-1.13/linux-ubuntu16.04-x86_64-gcc-5.4.0-gdbm-1.13-vdhoris6wdzzb2ykax2hz7qzgizk5h3t.spack
-  ######################################################################## 100.0%
-  gpg: Signature made Sun 12 Nov 2017 10:26:51 PM UTC using RSA key ID 3B7C69B2
-  gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
-  gpg: WARNING: This key is not certified with a trusted signature!
-  gpg:          There is no indication that the signature belongs to the owner.
-  Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
-  ==> Successfully installed gdbm from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gdbm-1.13-vdhoris6wdzzb2ykax2hz7qzgizk5h3t
-  ==> Installing perl
-  ==> Searching for binary cache of perl
-  ==> Installing perl from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/perl-5.24.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-perl-5.24.1-mfzwy6y5mlbqpqvti4etpe3cgkmxkpi2.spack
-  ######################################################################## 100.0%
-  gpg: Signature made Sun 12 Nov 2017 10:27:19 PM UTC using RSA key ID 3B7C69B2
-  gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
-  gpg: WARNING: This key is not certified with a trusted signature!
-  gpg:          There is no indication that the signature belongs to the owner.
-  Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
-  ==> Successfully installed perl from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/perl-5.24.1-mfzwy6y5mlbqpqvti4etpe3cgkmxkpi2
-  ==> Installing autoconf
-  ==> Searching for binary cache of autoconf
-  ==> Installing autoconf from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/autoconf-2.69/linux-ubuntu16.04-x86_64-gcc-5.4.0-autoconf-2.69-bvabhjiklhi7c5742ixzs7hubhid3ax2.spack
-  ######################################################################## 100.0%
-  gpg: Signature made Sun 12 Nov 2017 10:27:22 PM UTC using RSA key ID 3B7C69B2
-  gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
-  gpg: WARNING: This key is not certified with a trusted signature!
-  gpg:          There is no indication that the signature belongs to the owner.
-  Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
-  ==> Successfully installed autoconf from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/autoconf-2.69-bvabhjiklhi7c5742ixzs7hubhid3ax2
-  ==> Installing automake
-  ==> Searching for binary cache of automake
-  ==> Installing automake from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/automake-1.15.1/linux-ubuntu16.04-x86_64-gcc-5.4.0-automake-1.15.1-kaiefe4j2lsq6b32ncrclmbeoa5z25a5.spack
-  ######################################################################## 100.0%
-  gpg: Signature made Sun 12 Nov 2017 10:27:21 PM UTC using RSA key ID 3B7C69B2
-  gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
-  gpg: WARNING: This key is not certified with a trusted signature!
-  gpg:          There is no indication that the signature belongs to the owner.
-  Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
-  ==> Successfully installed automake from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/automake-1.15.1-kaiefe4j2lsq6b32ncrclmbeoa5z25a5
-  ==> libtool is already installed in /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libtool-2.4.6-o2pfwjf44353ajgr42xqtvzyvqsazkgu
+  $ spack install gcc
+  ==> libsigsegv is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libsigsegv-2.11-fypapcprssrj3nstp6njprskeyynsgaz
+  ==> m4 is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/m4-1.4.18-suf5jtcfehivwfesrc5hjy72r4nukyel
+  ==> pkgconf is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/pkgconf-1.4.2-fovrh7alpft646n6mhis5mml6k6e5f4v
+  ==> ncurses is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/ncurses-6.1-3o765ourmesfrji6yeclb4wb5w54aqbh
+  ==> readline is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/readline-7.0-nxhwrg7xwc6nbsm2v4ezwe63l6nfidbi
+  ==> gdbm is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gdbm-1.14.1-q4fpyuo7ouhkeq6d3oabtrppctpvxmes
+  ==> perl is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/perl-5.26.2-ic2kyoadgp3dxfejcbllyplj2wf524fo
+  ==> autoconf is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/autoconf-2.69-3sx2gxeibc4oasqd4o5h6lnwpcpsgd2q
+  ==> automake is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/automake-1.16.1-rymw7imfehycqxzj4nuy2oiw3abegooy
+  ==> libtool is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libtool-2.4.6-o2pfwjf44353ajgr42xqtvzyvqsazkgu
   ==> Installing gmp
   ==> Searching for binary cache of gmp
+  ==> Finding buildcaches in /mirror/build_cache
   ==> Installing gmp from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/gmp-6.1.2/linux-ubuntu16.04-x86_64-gcc-5.4.0-gmp-6.1.2-qc4qcfz4monpllc3nqupdo7vwinf73sw.spack
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/gmp-6.1.2/linux-ubuntu16.04-x86_64-gcc-5.4.0-gmp-6.1.2-qc4qcfz4monpllc3nqupdo7vwinf73sw.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sun 12 Nov 2017 10:12:29 PM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:18:16 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
   ==> Successfully installed gmp from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gmp-6.1.2-qc4qcfz4monpllc3nqupdo7vwinf73sw
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gmp-6.1.2-qc4qcfz4monpllc3nqupdo7vwinf73sw
   ==> Installing isl
   ==> Searching for binary cache of isl
   ==> Installing isl from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/isl-0.18/linux-ubuntu16.04-x86_64-gcc-5.4.0-isl-0.18-vttqoutnsmjpm3ogb52rninksc7hq5ax.spack
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/isl-0.18/linux-ubuntu16.04-x86_64-gcc-5.4.0-isl-0.18-vttqoutnsmjpm3ogb52rninksc7hq5ax.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sun 12 Nov 2017 10:12:28 PM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:05:19 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
   ==> Successfully installed isl from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/isl-0.18-vttqoutnsmjpm3ogb52rninksc7hq5ax
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/isl-0.18-vttqoutnsmjpm3ogb52rninksc7hq5ax
   ==> Installing mpfr
   ==> Searching for binary cache of mpfr
   ==> Installing mpfr from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpfr-3.1.5/linux-ubuntu16.04-x86_64-gcc-5.4.0-mpfr-3.1.5-mdi6irzvxcbemt7yredzr36dvo6ty4sl.spack
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpfr-3.1.6/linux-ubuntu16.04-x86_64-gcc-5.4.0-mpfr-3.1.6-jnt2nnp5pmvikbw7opueajlbwbhmjxyv.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sun 12 Nov 2017 10:12:30 PM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:32:07 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
   ==> Successfully installed mpfr from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpfr-3.1.5-mdi6irzvxcbemt7yredzr36dvo6ty4sl
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpfr-3.1.6-jnt2nnp5pmvikbw7opueajlbwbhmjxyv
   ==> Installing mpc
   ==> Searching for binary cache of mpc
   ==> Installing mpc from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpc-1.0.3/linux-ubuntu16.04-x86_64-gcc-5.4.0-mpc-1.0.3-tumbpshu5hjxwextoudk5hmic6nspb3z.spack
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpc-1.1.0/linux-ubuntu16.04-x86_64-gcc-5.4.0-mpc-1.1.0-iuf3gc3zpgr4n4mditnxhff6x3joxi27.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sun 12 Nov 2017 10:12:29 PM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:30:35 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
   ==> Successfully installed mpc from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpc-1.0.3-tumbpshu5hjxwextoudk5hmic6nspb3z
-  ==> zlib is already installed in /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
-  ==> Installing gcc
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpc-1.1.0-iuf3gc3zpgr4n4mditnxhff6x3joxi27
+  ==> zlib is already installed in /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
+  Installing gcc
   ==> Searching for binary cache of gcc
+  ==> Finding buildcaches in /mirror/build_cache
   ==> Installing gcc from binary cache
-  ==> Fetching file:///home/ubuntu/becker/buildcache/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0/linux-ubuntu16.04-x86_64-gcc-5.4.0-gcc-7.2.0-k3vy57euyeuyvpotwf4wezfmpo3mrtrj.spack
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0/linux-ubuntu16.04-x86_64-gcc-5.4.0-gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs.spack
   ######################################################################## 100.0%
-  gpg: Signature made Sun 12 Nov 2017 10:16:31 PM UTC using RSA key ID 3B7C69B2
+  gpg: Signature made Sat Nov 10 05:22:47 2018 UTC using RSA key ID 3B7C69B2
   gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
   gpg: WARNING: This key is not certified with a trusted signature!
   gpg:          There is no indication that the signature belongs to the owner.
   Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
-  ==> Relocating package from
-    /home/ubuntu/becker/spack/opt/spack to /home/ubuntu/test/spack/opt/spack.
   ==> Successfully installed gcc from binary cache
-  [+] /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-k3vy57euyeuyvpotwf4wezfmpo3mrtrj
+  [+] /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs
 
   $ spack find -p gcc
-  ==> 1 installed packages.
+  spack find -p gcc
+  ==> 1 installed package
   -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
-      gcc@7.2.0  /home/ubuntu/test/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-k3vy57euyeuyvpotwf4wezfmpo3mrtrj
+      gcc@7.2.0  /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs
 
 We can add gcc to Spack as an available compiler using the ``spack
 compiler add`` command. This will allow future packages to build with
@@ -1733,7 +1722,7 @@ gcc@7.2.0.
 
 .. code-block:: console
 
-  $ spack compiler add /home/ubuntu/becker/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-k3vy57euyeuyvpotwf4wezfmpo3mrtrj
+  $ spack compiler add `spack location -i gcc@7.2.0`
   ==> Added 1 new compiler to /home/ubuntu/.spack/linux/compilers.yaml
       gcc@7.2.0
   ==> Compilers are defined in the following files:
diff --git a/lib/spack/docs/tutorial_buildsystems.rst b/lib/spack/docs/tutorial_buildsystems.rst
index d92db13062..db31f318df 100644
--- a/lib/spack/docs/tutorial_buildsystems.rst
+++ b/lib/spack/docs/tutorial_buildsystems.rst
@@ -1,3 +1,8 @@
+.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 .. _build-systems-tutorial:
 
 ==============================
@@ -105,8 +110,8 @@ This will open the :code:`AutotoolsPackage` file in your text editor.
 
 .. literalinclude:: ../../../lib/spack/spack/build_systems/autotools.py
     :language: python
-    :emphasize-lines: 42,45,62
-    :lines: 40-95,259-267
+    :emphasize-lines: 33,36,54
+    :lines: 30-76,240-248
     :linenos:
 
 
@@ -151,7 +156,7 @@ build system. Although this package is acceptable let's make this into an
 
 .. literalinclude:: tutorial/examples/Autotools/0.package.py
    :language: python
-   :emphasize-lines: 28
+   :emphasize-lines: 9
    :linenos:
 
 We first inherit from the :code:`AutotoolsPackage` class.
@@ -163,7 +168,7 @@ to be overridden is :code:`configure_args()`.
 
 .. literalinclude:: tutorial/examples/Autotools/1.package.py
    :language: python
-   :emphasize-lines: 42,43
+   :emphasize-lines: 25,26,27,28,29,30,31,32
    :linenos:
 
 Since Spack takes care of setting the prefix for us we can exclude that as
@@ -204,8 +209,8 @@ Take note of the following:
 
 .. literalinclude:: ../../../lib/spack/spack/build_systems/makefile.py
    :language: python
-   :lines: 33-79,89-107
-   :emphasize-lines: 48,54,61
+   :lines: 14,43-61,70-88
+   :emphasize-lines: 21,27,34
    :linenos:
 
 Similar to :code:`Autotools`, :code:`MakefilePackage` class has properties
@@ -247,7 +252,7 @@ Let's add in the rest of our details for our package:
 
 .. literalinclude:: tutorial/examples/Makefile/1.package.py
    :language: python
-   :emphasize-lines: 29,30,32,33,37,39
+   :emphasize-lines: 10,11,13,14,18,20
    :linenos:
 
 As we mentioned earlier, most packages using a :code:`Makefile` have hard-coded
@@ -289,7 +294,7 @@ To fix this, we need to use the :code:`edit()` method to write our custom
 
 .. literalinclude:: tutorial/examples/Makefile/2.package.py
    :language: python
-   :emphasize-lines: 42,43,44
+   :emphasize-lines: 23,24,25
    :linenos:
 
 Here we use a :code:`FileFilter` object to edit our :code:`Makefile`. It takes
@@ -302,7 +307,7 @@ Let's change the build and install phases of our package:
 
 .. literalinclude:: tutorial/examples/Makefile/3.package.py
    :language: python
-   :emphasize-lines: 46, 52
+   :emphasize-lines: 28,29,30,31,32,35,36
    :linenos:
 
 Here demonstrate another strategy that we can use to manipulate our package
@@ -318,23 +323,36 @@ Let's look at a couple of other examples and go through them:
 
 .. code-block:: console
 
-    $ spack edit cbench
+    $ spack edit esmf
 
 Some packages allow environment variables to be set and will honor them.
 Packages that use :code:`?=` for assignment in their :code:`Makefile`
-can be set using environment variables. In our :code:`cbench` example we
+can be set using environment variables. In our :code:`esmf` example we
 set two environment variables in our :code:`edit()` method:
 
 .. code-block:: python
 
     def edit(self, spec, prefix):
-        # The location of the Cbench source tree
-        env['CBENCHHOME'] = self.stage.source_path
-
-        # The location that will contain all your tests and your results
-        env['CBENCHTEST'] = prefix
-
-        # ... more code
+        for var in os.environ:
+            if var.startswith('ESMF_'):
+                os.environ.pop(var)
+
+        # More code ...
+
+        if self.compiler.name == 'gcc':
+            os.environ['ESMF_COMPILER'] = 'gfortran'
+        elif self.compiler.name == 'intel':
+            os.environ['ESMF_COMPILER'] = 'intel'
+        elif self.compiler.name == 'clang':
+            os.environ['ESMF_COMPILER'] = 'gfortranclang'
+        elif self.compiler.name == 'nag':
+            os.environ['ESMF_COMPILER'] = 'nag'
+        elif self.compiler.name == 'pgi':
+            os.environ['ESMF_COMPILER'] = 'pgi'
+        else:
+            msg  = "The compiler you are building with, "
+            msg += "'{0}', is not supported by ESMF."
+            raise InstallError(msg.format(self.compiler.name))
 
 As you may have noticed, we didn't really write anything to the :code:`Makefile`
 but rather we set environment variables that will override variables set in
@@ -355,7 +373,7 @@ Let's look at an example of this in the :code:`elk` package:
 .. code-block:: python
 
         def edit(self, spec, prefix):
-        # Dictionary of configuration options
+            # Dictionary of configuration options
             config = {
                 'MAKE': 'make',
                 'AR':   'ar'
@@ -470,20 +488,16 @@ In the :code:`CMakePackage` class we can override the following phases:
 The :code:`CMakePackage` class also provides sensible defaults so we only need to
 override :code:`cmake_args()`.
 
-Let's look at these defaults in the :code:`CMakePackage` class:
+Let's look at these defaults in the :code:`CMakePackage` class in the :code:`_std_args()` method:
 
 .. code-block:: console
 
     $ spack edit --build-system cmake
 
-
-And go into a bit of detail on the highlighted sections:
-
-
 .. literalinclude:: ../../../lib/spack/spack/build_systems/cmake.py
    :language: python
-   :lines: 37-92, 94-155, 174-211
-   :emphasize-lines: 57,68,86,94,96,99,100,101,102,111,117,135,136
+   :lines: 102-147
+   :emphasize-lines: 10,18,24,36,37,38,44
    :linenos:
 
 Some :code:`CMake` packages use different generators. Spack is able to support
@@ -492,16 +506,16 @@ Unix-Makefile_ generators as well as Ninja_ generators.
 .. _Unix-Makefile: https://cmake.org/cmake/help/v3.4/generator/Unix%20Makefiles.html
 .. _Ninja: https://cmake.org/cmake/help/v3.4/generator/Ninja.html
 
-Default generator is :code:`Unix Makefile`.
+If no generator is specified Spack will default to :code:`Unix Makefiles`.
 
 Next we setup the build type. In :code:`CMake` you can specify the build type
 that you want. Options include:
 
-1. empty
-2. Debug
-3. Release
-4. RelWithDebInfo
-5. MinSizeRel
+1. :code:`empty`
+2. :code:`Debug`
+3. :code:`Release`
+4. :code:`RelWithDebInfo`
+5. :code:`MinSizeRel`
 
 With these options you can specify whether you want your executable to have
 the debug version only, release version or the release with debug information.
@@ -509,7 +523,7 @@ Release executables tend to be more optimized than Debug. In Spack, we set
 the default as RelWithDebInfo unless otherwise specified through a variant.
 
 Spack then automatically sets up the :code:`-DCMAKE_INSTALL_PREFIX` path,
-appends the build type (RelDebInfo default), and then specifies a verbose
+appends the build type (:code:`RelWithDebInfo` default), and then specifies a verbose
 :code:`Makefile`.
 
 Next we add the :code:`rpaths` to :code:`-DCMAKE_INSTALL_RPATH:STRING`.
@@ -524,9 +538,8 @@ In the end our :code:`cmake` line will look like this (example is :code:`xrootd`
 
     $ cmake $HOME/spack/var/spack/stage/xrootd-4.6.0-4ydm74kbrp4xmcgda5upn33co5pwddyk/xrootd-4.6.0 -G Unix Makefiles -DCMAKE_INSTALL_PREFIX:PATH=$HOME/spack/opt/spack/darwin-sierra-x86_64/clang-9.0.0-apple/xrootd-4.6.0-4ydm74kbrp4xmcgda5upn33co5pwddyk -DCMAKE_BUILD_TYPE:STRING=RelWithDebInfo -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_FIND_FRAMEWORK:STRING=LAST -DCMAKE_INSTALL_RPATH_USE_LINK_PATH:BOOL=FALSE -DCMAKE_INSTALL_RPATH:STRING=$HOME/spack/opt/spack/darwin-sierra-x86_64/clang-9.0.0-apple/xrootd-4.6.0-4ydm74kbrp4xmcgda5upn33co5pwddyk/lib:$HOME/spack/opt/spack/darwin-sierra-x86_64/clang-9.0.0-apple/xrootd-4.6.0-4ydm74kbrp4xmcgda5upn33co5pwddyk/lib64 -DCMAKE_PREFIX_PATH:STRING=$HOME/spack/opt/spack/darwin-sierra-x86_64/clang-9.0.0-apple/cmake-3.9.4-hally3vnbzydiwl3skxcxcbzsscaasx5
 
-
-Saves a lot of typing doesn't it?
-
+We can see now how :code:`CMake` takes care of a lot of the boilerplate code
+that would have to be otherwise typed in.
 
 Let's try to recreate callpath_:
 
@@ -564,7 +577,7 @@ Again we fill in the details:
 .. literalinclude:: tutorial/examples/Cmake/1.package.py
    :language: python
    :linenos:
-   :emphasize-lines: 28,32,33,37,38,39,40,41,42
+   :emphasize-lines: 9,13,14,18,19,20,21,22,23
 
 As mentioned earlier, Spack will use sensible defaults to prevent repeated code
 and to make writing :code:`CMake` package files simpler.
@@ -575,7 +588,7 @@ compiler flags. We add the following options like so:
 .. literalinclude:: tutorial/examples/Cmake/2.package.py
    :language: python
    :linenos:
-   :emphasize-lines: 45,49,50
+   :emphasize-lines: 26,30,31
 
 Now we can control our build options using :code:`cmake_args()`. If defaults are
 sufficient enough for the package, we can leave this method out.
@@ -590,7 +603,7 @@ different location is found in :code:`spades`.
 
 .. code-block:: console
 
-    $ spack edit spade
+    $ spack edit spades
 
 .. code-block:: python
 
@@ -665,6 +678,12 @@ list you can run:
         check             perform some checks on the package
 
 
+We can write package files for Python packages using the :code:`Package` class,
+but the class brings with it a lot of methods that are useless for Python packages.
+Instead, Spack has a :code:`PythonPackage` subclass that allows packagers
+of Python modules to be able to invoke :code:`setup.py` and use :code:`Distutils`,
+which is much more familiar to a typical python user.
+
 To see the defaults that Spack has for each a methods, we will take a look
 at the :code:`PythonPackage` class:
 
@@ -677,18 +696,11 @@ We see the following:
 
 .. literalinclude:: ../../../lib/spack/spack/build_systems/python.py
    :language: python
-   :lines: 35, 161-364
+   :lines: 19,146-357
    :linenos:
 
 Each of these methods have sensible defaults or they can be overridden.
 
-We can write package files for Python packages using the :code:`Package` class,
-but the class brings with it a lot of methods that are useless for Python packages.
-Instead, Spack has a :code: `PythonPackage` subclass that allows packagers
-of Python modules to be able to invoke :code:`setup.py` and use :code:`Distutils`,
-which is much more familiar to a typical python user.
-
-
 We will write a package file for Pandas_:
 
 .. _pandas: https://pandas.pydata.org
@@ -783,7 +795,7 @@ for the following build systems:
 3. :code:`WafPackage`
 4. :code:`RPackage`
 5. :code:`PerlPackage`
-6. :code:`QMake`
+6. :code:`QMakePackage`
 
 
 Each of these classes have their own abstractions to help assist in writing
diff --git a/lib/spack/docs/tutorial_configuration.rst b/lib/spack/docs/tutorial_configuration.rst
index f9221be9b4..4c2ce6a314 100644
--- a/lib/spack/docs/tutorial_configuration.rst
+++ b/lib/spack/docs/tutorial_configuration.rst
@@ -1,3 +1,8 @@
+.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 .. _configs-tutorial:
 
 ======================
@@ -8,7 +13,7 @@ This tutorial will guide you through various configuration options
 that allow you to customize Spack's behavior with respect to
 software installation. We will first cover the configuration file
 hierarchy. Then, we will cover configuration options for compilers,
-focusing on how it can be used to extend Spack's compiler auto-detection.
+focusing on how they can be used to extend Spack's compiler auto-detection.
 Next, we will cover the packages configuration file, focusing on
 how it can be used to override default build options as well as
 specify external package installations to use. Finally, we will
@@ -31,17 +36,19 @@ Configuration Scopes
 Depending on your use case, you may want to provide configuration
 settings common to everyone on your team, or you may want to set
 default behaviors specific to a single user account. Spack provides
-4 configuration *scopes* to handle this customization. These scopes,
+six configuration *scopes* to handle this customization. These scopes,
 in order of decreasing priority, are:
 
-======================   ==================================
-Scope                    Directory
-======================   ==================================
-User configurations      ``~/.spack``
-Project configurations   ``$SPACK_ROOT/etc/spack``
-System configurations    ``/etc/spack``
-Default configurations   ``$SPACK_ROOT/etc/spack/defaults``
-======================   ==================================
+============   ===================================================
+Scope          Directory
+============   ===================================================
+Command-line   N/A
+Custom         Custom directory, specified with ``--config-scope``
+User           ``~/.spack/``
+Site           ``$SPACK_ROOT/etc/spack/``
+System         ``/etc/spack/``
+Defaults       ``$SPACK_ROOT/etc/spack/defaults/``
+============   ===================================================
 
 Spack's default configuration settings reside in
 ``$SPACK_ROOT/etc/spack/defaults``. These are useful for reference,
@@ -60,24 +67,40 @@ configuration files to the ``~/.spack`` directory. When Spack first
 checked for compilers on your system, you may have noticed that it
 placed your compiler configuration in this directory.
 
+Configuration settings can also be placed in a custom location,
+which is then specified on the command line via ``--config-scope``.
+An example use case is managing two sets of configurations, one for
+development and another for production preferences.
+
+Settings specified on the command line have precedence over all
+other configuration scopes.
+
+^^^^^^^^^^^^^^^^^^^^^^^^
+Platform-specific Scopes
+^^^^^^^^^^^^^^^^^^^^^^^^
+
 Some facilities manage multiple platforms from a single shared
-filesystem. In order to handle this, each of the configuration
+file system. In order to handle this, each of the configuration
 scopes listed above has two *sub-scopes*: platform-specific and
 platform-independent. For example, compiler settings can be stored
 in ``compilers.yaml`` configuration files in the following locations:
 
-- ``~/.spack/<platform>/compilers.yaml``
-- ``~/.spack/compilers.yaml``
-- ``$SPACK_ROOT/etc/spack/<platform>/compilers.yaml``
-- ``$SPACK_ROOT/etc/spack/compilers.yaml``
-- ``/etc/spack/<platform>/compilers.yaml``
-- ``/etc/spack/compilers.yaml``
-- ``$SPACK_ROOT/etc/defaults/<platform>/compilers.yaml``
-- ``$SPACK_ROOT/etc/defaults/compilers.yaml``
+#. ``~/.spack/<platform>/compilers.yaml``
+#. ``~/.spack/compilers.yaml``
+#. ``$SPACK_ROOT/etc/spack/<platform>/compilers.yaml``
+#. ``$SPACK_ROOT/etc/spack/compilers.yaml``
+#. ``/etc/spack/<platform>/compilers.yaml``
+#. ``/etc/spack/compilers.yaml``
+#. ``$SPACK_ROOT/etc/defaults/<platform>/compilers.yaml``
+#. ``$SPACK_ROOT/etc/defaults/compilers.yaml``
 
 These files are listed in decreasing order of precedence, so files in
 ``~/.spack/<platform>`` will override settings in ``~/.spack``.
 
+-----------
+YAML Format
+-----------
+
 Spack configurations are YAML dictionaries. Every configuration file
 begins with a top-level dictionary that tells Spack which
 configuration set it modifies. When Spack checks it's configuration,
@@ -112,7 +135,7 @@ ensures that no other compilers are used, as the user configuration
 scope is the last scope searched and the ``compilers::`` line replaces
 all previous configuration files information. If the same
 configuration file had a single colon instead of the double colon, it
-would add the gcc version 5.4.0 compiler to whatever other compilers
+would add the GCC version 5.4.0 compiler to whatever other compilers
 were listed in other configuration files.
 
 .. _configs-tutorial-compilers:
@@ -122,8 +145,8 @@ Compiler Configuration
 ----------------------
 
 For most tasks, we can use Spack with the compilers auto-detected the
-first time Spack runs on a system. As we discussed in the basic
-installation section, we can also tell Spack where compilers are
+first time Spack runs on a system. As discussed in the basic
+installation tutorial, we can also tell Spack where compilers are
 located using the ``spack compiler add`` command. However, in some
 circumstances we want even more fine-grained control over the
 compilers available. This section will teach you how to exercise that
@@ -146,6 +169,19 @@ We will start by opening the compilers configuration file
        modules: []
        operating_system: ubuntu16.04
        paths:
+         cc: /usr/bin/clang-3.7
+         cxx: /usr/bin/clang++-3.7
+         f77: null
+         fc: null
+       spec: clang@3.7.1-2ubuntu2
+       target: x86_64
+   - compiler:
+       environment: {}
+       extra_rpaths: []
+       flags: {}
+       modules: []
+       operating_system: ubuntu16.04
+       paths:
          cc: /usr/bin/clang
          cxx: /usr/bin/clang++
          f77: null
@@ -159,6 +195,19 @@ We will start by opening the compilers configuration file
        modules: []
        operating_system: ubuntu16.04
        paths:
+         cc: /usr/bin/gcc-4.7
+         cxx: /usr/bin/g++-4.7
+         f77: /usr/bin/gfortran-4.7
+         fc: /usr/bin/gfortran-4.7
+       spec: gcc@4.7
+       target: x86_64
+   - compiler:
+       environment: {}
+       extra_rpaths: []
+       flags: {}
+       modules: []
+       operating_system: ubuntu16.04
+       paths:
          cc: /usr/bin/gcc
          cxx: /usr/bin/g++
          f77: /usr/bin/gfortran
@@ -167,27 +216,27 @@ We will start by opening the compilers configuration file
        target: x86_64
 
 
-This specifies one version of the gcc compiler and one version of the
-clang compiler with no flang compiler. Now suppose we have a code that
-we want to compile with the clang compiler for C/C++ code, but with
+This specifies two versions of the GCC compiler and two versions of the
+Clang compiler with no Flang compiler. Now suppose we have a code that
+we want to compile with the Clang compiler for C/C++ code, but with
 gfortran for Fortran components. We can do this by adding another entry
 to the ``compilers.yaml`` file.
 
 .. code-block:: yaml
 
    - compiler:
-     environment: {}
-     extra_rpaths: []
-     flags: {}
-     modules: []
-     operating_system: ubuntu16.04
-     paths:
-       cc: /usr/bin/clang
-       cxx: /usr/bin/clang++
-       f77: /usr/bin/gfortran
-       fc: /usr/bin/gfortran
-     spec: clang@3.8.0-gfortran
-     target: x86_64
+       environment: {}
+       extra_rpaths: []
+       flags: {}
+       modules: []
+       operating_system: ubuntu16.04
+       paths:
+         cc: /usr/bin/clang
+         cxx: /usr/bin/clang++
+         f77: /usr/bin/gfortran
+         fc: /usr/bin/gfortran
+       spec: clang@3.8.0-gfortran
+       target: x86_64
 
 
 Let's talk about the sections of this compiler entry that we've changed.
@@ -198,7 +247,7 @@ compiler for both specifications of Fortran. We've also changed the
 ``spec`` entry for this compiler. The ``spec`` entry is effectively the
 name of the compiler for Spack. It consists of a name and a version
 number, separated by the ``@`` sigil. The name must be one of the supported
-compiler names in Spack (gcc, intel, pgi, xl, xl_r, clang, nag, cce).
+compiler names in Spack (gcc, intel, pgi, xl, xl_r, clang, nag, cce, arm).
 The version number can be an arbitrary string of alphanumeric characters,
 as well as ``-``, ``.``, and ``_``. The ``target`` and ``operating_system``
 sections we leave unchanged. These sections specify when Spack can use
@@ -209,7 +258,7 @@ We can verify that our new compiler works by invoking it now:
 
 .. code-block:: console
 
-   $ spack install zlib %clang@3.8.0-gfortran
+   $ spack install --no-cache zlib %clang@3.8.0-gfortran
    ...
 
 
@@ -217,7 +266,7 @@ This new compiler also works on Fortran codes:
 
 .. code-block:: console
 
-   $ spack install cfitsio %clang@3.8.0-gfortran
+   $ spack install --no-cache cfitsio %clang@3.8.0-gfortran -bzip2
    ...
 
 
@@ -238,19 +287,19 @@ Let's open our compilers configuration file again and add a compiler flag.
 .. code-block:: yaml
 
    - compiler:
-     environment: {}
-     extra_rpaths: []
-     flags:
-       cppflags: -g
-     modules: []
-     operating_system: ubuntu16.04
-     paths:
-       cc: /usr/bin/clang
-       cxx: /usr/bin/clang++
-       f77: /usr/bin/gfortran
-       fc: /usr/bin/gfortran
-     spec: clang@3.8.0-gfortran
-     target: x86_64
+       environment: {}
+       extra_rpaths: []
+       flags:
+         cppflags: -g
+       modules: []
+       operating_system: ubuntu16.04
+       paths:
+         cc: /usr/bin/clang
+         cxx: /usr/bin/clang++
+         f77: /usr/bin/gfortran
+         fc: /usr/bin/gfortran
+       spec: clang@3.8.0-gfortran
+       target: x86_64
 
 
 We can test this out using the ``spack spec`` command to show how the
@@ -273,14 +322,14 @@ spec is concretized.
        ^bzip2@1.0.6%clang@3.8.0-gfortran cppflags="-g" +shared arch=linux-ubuntu16.04-x86_64
 
 
-We can see that "cppflags=-g" has been added to every node in the DAG.
+We can see that ``cppflags="-g"`` has been added to every node in the DAG.
 
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 Advanced Compiler Configuration
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 There are three fields of the compiler configuration entry that we
-have not talked about yet.
+have not yet talked about.
 
 The ``modules`` field of the compiler is used primarily on Cray systems,
 but can be useful on any system that has compilers that are only
@@ -290,21 +339,45 @@ of the build environment for packages using that compiler.
 
 The ``extra_rpaths`` field of the compiler configuration is used for
 compilers that do not rpath all of their dependencies by
-default. Since compilers are generally installed externally to Spack,
+default. Since compilers are often installed externally to Spack,
 Spack is unable to manage compiler dependencies and enforce
 rpath usage. This can lead to packages not finding link dependencies
 imposed by the compiler properly. For compilers that impose link
 dependencies on the resulting executables that are not rpath'ed into
-the executable automatically, the ``extra_rpath`` field of the compiler
+the executable automatically, the ``extra_rpaths`` field of the compiler
 configuration tells Spack which dependencies to rpath into every
 executable created by that compiler. The executables will then be able
-to find the link dependencies imposed by the compiler.
+to find the link dependencies imposed by the compiler. As an example,
+this field can be set by
+
+.. code-block:: yaml
+
+   - compiler:
+     ...
+     extra_rpaths:
+      - /apps/intel/ComposerXE2017/compilers_and_libraries_2017.5.239/linux/compiler/lib/intel64_lin
+     ...
+
 
 The ``environment`` field of the compiler configuration is used for
 compilers that require environment variables to be set during build
 time. For example, if your Intel compiler suite requires the
 ``INTEL_LICENSE_FILE`` environment variable to point to the proper
-license server, you can set this in ``compilers.yaml``.
+license server, you can set this in ``compilers.yaml`` as follows:
+
+.. code-block:: yaml
+
+  - compiler:
+      environment:
+        set:
+          INTEL_LICENSE_FILE: 1713@license4
+      ...
+
+
+In addition to ``set``, ``environment`` also supports ``unset``,
+``prepend-path``, and ``append-path``.
+
+.. _configs-tutorial-package-prefs:
 
 -------------------------------
 Configuring Package Preferences
@@ -325,8 +398,8 @@ configuration file. First, we will look at the default
 
 This sets the default preferences for compilers and for providers of
 virtual packages. To illustrate how this works, suppose we want to
-change the preferences to prefer the clang compiler and to prefer
-mpich over openmpi. Currently, we prefer gcc and openmpi
+change the preferences to prefer the Clang compiler and to prefer
+MPICH over OpenMPI. Currently, we prefer GCC and OpenMPI.
 
 .. code-block:: console
 
@@ -335,20 +408,27 @@ mpich over openmpi. Currently, we prefer gcc and openmpi
    --------------------------------
    hdf5
 
-   Normalized
-   --------------------------------
-   hdf5
-       ^zlib@1.1.2:
-
    Concretized
    --------------------------------
-   hdf5@1.10.1%gcc@5.4.0+cxx~debug+fortran+mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
-       ^openmpi@3.0.0%gcc@5.4.0~cuda fabrics= ~java schedulers= ~sqlite3~thread_multiple+vt arch=linux-ubuntu16.04-x86_64
-           ^hwloc@1.11.7%gcc@5.4.0~cuda+libxml2~pci arch=linux-ubuntu16.04-x86_64
-               ^libxml2@2.9.4%gcc@5.4.0~python arch=linux-ubuntu16.04-x86_64
-                   ^pkg-config@0.29.2%gcc@5.4.0+internal_glib arch=linux-ubuntu16.04-x86_64
-                   ^xz@5.2.3%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
-                   ^zlib@1.2.11%gcc@5.4.0+pic+shared arch=linux-ubuntu16.04-x86_64
+   hdf5@1.10.4%gcc@5.4.0~cxx~debug~fortran~hl+mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
+       ^openmpi@3.1.3%gcc@5.4.0~cuda+cxx_exceptions fabrics= ~java~legacylaunchers~memchecker~pmi schedulers= ~sqlite3~thread_multiple+vt arch=linux-ubuntu16.04-x86_64
+           ^hwloc@1.11.9%gcc@5.4.0~cairo~cuda+libxml2+pci+shared arch=linux-ubuntu16.04-x86_64
+               ^libpciaccess@0.13.5%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+                   ^libtool@2.4.6%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+                       ^m4@1.4.18%gcc@5.4.0 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64
+                           ^libsigsegv@2.11%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+                   ^pkgconf@1.4.2%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+                   ^util-macros@1.19.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+               ^libxml2@2.9.8%gcc@5.4.0~python arch=linux-ubuntu16.04-x86_64
+                   ^xz@5.2.4%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+                   ^zlib@1.2.11%gcc@5.4.0+optimize+pic+shared arch=linux-ubuntu16.04-x86_64
+               ^numactl@2.0.11%gcc@5.4.0 patches=592f30f7f5f757dfc239ad0ffd39a9a048487ad803c26b419e0f96b8cda08c1a arch=linux-ubuntu16.04-x86_64
+                   ^autoconf@2.69%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+                       ^perl@5.26.2%gcc@5.4.0+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-ubuntu16.04-x86_64
+                           ^gdbm@1.14.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+                               ^readline@7.0%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+                                   ^ncurses@6.1%gcc@5.4.0~symlinks~termlib arch=linux-ubuntu16.04-x86_64
+                   ^automake@1.16.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
 
 
 Now we will open the packages configuration file and update our
@@ -378,16 +458,23 @@ overrides the default settings just for these two items.
    --------------------------------
    hdf5
 
-   Normalized
-   --------------------------------
-   hdf5
-       ^zlib@1.1.2:
-
    Concretized
    --------------------------------
-   hdf5@1.10.1%clang@3.8.0-2ubuntu4+cxx~debug~fortran~hl+mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
-       ^mpich@3.2%clang@3.8.0-2ubuntu4 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-ubuntu16.04-x86_64
-       ^zlib@1.2.11%clang@3.8.0-2ubuntu4+pic+shared arch=linux-ubuntu16.04-x86_64
+   hdf5@1.10.4%clang@3.8.0-2ubuntu4~cxx~debug~fortran~hl+mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
+       ^mpich@3.2.1%clang@3.8.0-2ubuntu4 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-ubuntu16.04-x86_64
+           ^findutils@4.6.0%clang@3.8.0-2ubuntu4 patches=84b916c0bf8c51b7e7b28417692f0ad3e7030d1f3c248ba77c42ede5c1c5d11e,bd9e4e5cc280f9753ae14956c4e4aa17fe7a210f55dd6c84aa60b12d106d47a2 arch=linux-ubuntu16.04-x86_64
+               ^autoconf@2.69%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
+                   ^m4@1.4.18%clang@3.8.0-2ubuntu4 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64
+                       ^libsigsegv@2.11%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
+                   ^perl@5.26.2%clang@3.8.0-2ubuntu4+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-ubuntu16.04-x86_64
+                       ^gdbm@1.14.1%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
+                           ^readline@7.0%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
+                               ^ncurses@6.1%clang@3.8.0-2ubuntu4~symlinks~termlib arch=linux-ubuntu16.04-x86_64
+                                   ^pkgconf@1.4.2%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
+               ^automake@1.16.1%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
+               ^libtool@2.4.6%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
+               ^texinfo@6.5%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
+       ^zlib@1.2.11%clang@3.8.0-2ubuntu4+optimize+pic+shared arch=linux-ubuntu16.04-x86_64
 
 
 ^^^^^^^^^^^^^^^^^^^
@@ -418,16 +505,23 @@ We can check the effect of this command with ``spack spec hdf5`` again.
    --------------------------------
    hdf5
 
-   Normalized
-   --------------------------------
-   hdf5
-       ^zlib@1.1.2:
-
    Concretized
    --------------------------------
-   hdf5@1.10.1%clang@3.8.0-2ubuntu4+cxx~debug~fortran~hl+mpi+pic~shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
-       ^mpich@3.2%clang@3.8.0-2ubuntu4 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-ubuntu16.04-x86_64
-       ^zlib@1.2.11%clang@3.8.0-2ubuntu4+pic~shared arch=linux-ubuntu16.04-x86_64
+   hdf5@1.10.4%clang@3.8.0-2ubuntu4~cxx~debug~fortran~hl+mpi+pic~shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
+       ^mpich@3.2.1%clang@3.8.0-2ubuntu4 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-ubuntu16.04-x86_64
+           ^findutils@4.6.0%clang@3.8.0-2ubuntu4 patches=84b916c0bf8c51b7e7b28417692f0ad3e7030d1f3c248ba77c42ede5c1c5d11e,bd9e4e5cc280f9753ae14956c4e4aa17fe7a210f55dd6c84aa60b12d106d47a2 arch=linux-ubuntu16.04-x86_64
+               ^autoconf@2.69%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
+                   ^m4@1.4.18%clang@3.8.0-2ubuntu4 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64
+                       ^libsigsegv@2.11%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
+                   ^perl@5.26.2%clang@3.8.0-2ubuntu4+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac ~shared+threads arch=linux-ubuntu16.04-x86_64
+                       ^gdbm@1.14.1%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
+                           ^readline@7.0%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
+                               ^ncurses@6.1%clang@3.8.0-2ubuntu4~symlinks~termlib arch=linux-ubuntu16.04-x86_64
+                                   ^pkgconf@1.4.2%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
+               ^automake@1.16.1%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
+               ^libtool@2.4.6%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
+               ^texinfo@6.5%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
+       ^zlib@1.2.11%clang@3.8.0-2ubuntu4+optimize+pic~shared arch=linux-ubuntu16.04-x86_64
 
 
 So far we have only made global changes to the package preferences. As
@@ -458,15 +552,10 @@ Now hdf5 will concretize without an MPI dependency by default.
    --------------------------------
    hdf5
 
-   Normalized
-   --------------------------------
-   hdf5
-       ^zlib@1.1.2:
-
    Concretized
    --------------------------------
-   hdf5@1.10.1%clang@3.8.0-2ubuntu4+cxx~debug~fortran~hl+mpi+pic~shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
-       ^zlib@1.2.11%clang@3.8.0-2ubuntu4+pic~shared arch=linux-ubuntu16.04-x86_64
+   hdf5@1.10.4%clang@3.8.0-2ubuntu4~cxx~debug~fortran~hl~mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
+       ^zlib@1.2.11%clang@3.8.0-2ubuntu4+optimize+pic~shared arch=linux-ubuntu16.04-x86_64
 
 
 In general, every attribute that we can set for all packages we can
@@ -507,14 +596,9 @@ okay.
    --------------------------------
    hdf5
 
-   Normalized
-   --------------------------------
-   hdf5
-       ^zlib@1.1.2:
-
    Concretized
    --------------------------------
-   hdf5@1.10.1%gcc@5.4.0~cxx~debug~fortran~hl~mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
+   hdf5@1.10.4%gcc@5.4.0~cxx~debug~fortran~hl~mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
        ^zlib@1.2.8%gcc@5.4.0+optimize+pic~shared arch=linux-ubuntu16.04-x86_64
 
 
@@ -529,14 +613,9 @@ preference of clang. If we explicitly specify clang:
    --------------------------------
    hdf5%clang
 
-   Normalized
-   --------------------------------
-   hdf5%clang
-       ^zlib@1.1.2:
-
    Concretized
    --------------------------------
-   hdf5@1.10.1%clang@3.8.0-2ubuntu4~cxx~debug~fortran~hl~mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
+   hdf5@1.10.4%clang@3.8.0-2ubuntu4~cxx~debug~fortran~hl~mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
        ^zlib@1.2.11%clang@3.8.0-2ubuntu4+optimize+pic~shared arch=linux-ubuntu16.04-x86_64
 
 
@@ -571,14 +650,9 @@ Now Spack will be forced to choose the external zlib.
    --------------------------------
    hdf5%clang
 
-   Normalized
-   --------------------------------
-   hdf5%clang
-       ^zlib@1.1.2:
-
    Concretized
    --------------------------------
-   hdf5@1.10.1%clang@3.8.0-2ubuntu4~cxx~debug~fortran~hl~mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
+   hdf5@1.10.4%clang@3.8.0-2ubuntu4~cxx~debug~fortran~hl~mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
        ^zlib@1.2.8%gcc@5.4.0+optimize+pic~shared arch=linux-ubuntu16.04-x86_64
 
 
@@ -616,31 +690,32 @@ build with an alternate MPI implementation.
    --------------------------------
    hdf5%clang+mpi
 
-   Normalized
-   --------------------------------
-   hdf5%clang+mpi
-       ^mpi
-       ^zlib@1.1.2:
-
    Concretized
    --------------------------------
-   hdf5@1.10.1%clang@3.8.0-2ubuntu4~cxx~debug~fortran~hl+mpi+pic~shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
-       ^openmpi@3.0.0%clang@3.8.0-2ubuntu4~cuda fabrics=verbs ~java schedulers= ~sqlite3~thread_multiple+vt arch=linux-ubuntu16.04-x86_64
-           ^hwloc@1.11.8%clang@3.8.0-2ubuntu4~cuda+libxml2+pci arch=linux-ubuntu16.04-x86_64
+   hdf5@1.10.4%clang@3.8.0-2ubuntu4~cxx~debug~fortran~hl+mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
+       ^openmpi@3.1.3%clang@3.8.0-2ubuntu4~cuda+cxx_exceptions fabrics= ~java~legacylaunchers~memchecker~pmi schedulers= ~sqlite3~thread_multiple+vt arch=linux-ubuntu16.04-x86_64
+           ^hwloc@1.11.9%clang@3.8.0-2ubuntu4~cairo~cuda+libxml2+pci~shared arch=linux-ubuntu16.04-x86_64
                ^libpciaccess@0.13.5%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
                    ^libtool@2.4.6%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
-                       ^m4@1.4.18%clang@3.8.0-2ubuntu4 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00 +sigsegv arch=linux-ubuntu16.04-x86_64
+                       ^m4@1.4.18%clang@3.8.0-2ubuntu4 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64
                            ^libsigsegv@2.11%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
-                   ^pkg-config@0.29.2%clang@3.8.0-2ubuntu4+internal_glib arch=linux-ubuntu16.04-x86_64
+                   ^pkgconf@1.4.2%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
                    ^util-macros@1.19.1%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
-               ^libxml2@2.9.4%clang@3.8.0-2ubuntu4~python arch=linux-ubuntu16.04-x86_64
-                   ^xz@5.2.3%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
-                   ^zlib@1.2.8%gcc@5.4.0+optimize+pic+shared arch=linux-ubuntu16.04-x86_64
+               ^libxml2@2.9.8%clang@3.8.0-2ubuntu4~python arch=linux-ubuntu16.04-x86_64
+                   ^xz@5.2.4%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
+                   ^zlib@1.2.8%gcc@5.4.0+optimize+pic~shared arch=linux-ubuntu16.04-x86_64
+               ^numactl@2.0.11%clang@3.8.0-2ubuntu4 patches=592f30f7f5f757dfc239ad0ffd39a9a048487ad803c26b419e0f96b8cda08c1a arch=linux-ubuntu16.04-x86_64
+                   ^autoconf@2.69%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
+                       ^perl@5.26.2%clang@3.8.0-2ubuntu4+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac ~shared+threads arch=linux-ubuntu16.04-x86_64
+                           ^gdbm@1.14.1%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
+                               ^readline@7.0%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
+                                   ^ncurses@6.1%clang@3.8.0-2ubuntu4~symlinks~termlib arch=linux-ubuntu16.04-x86_64
+                   ^automake@1.16.1%clang@3.8.0-2ubuntu4 arch=linux-ubuntu16.04-x86_64
 
 
 We have only expressed a preference for mpich over other MPI
 implementations, and Spack will happily build with one we haven't
-forbid it from using. We could resolve this by requesting
+forbid it from building. We could resolve this by requesting
 ``hdf5%clang+mpi^mpich`` explicitly, or we can configure Spack not to
 use any other MPI implementation. Since we're focused on
 configurations here and the former can get tedious, we'll need to
@@ -671,10 +746,17 @@ again.
        buildable: False
      intel-mpi:
        buildable: False
+     intel-parallel-studio:
+       buildable: False
      spectrum-mpi:
        buildable: False
-     intel-parallel-studio:
+     mpilander:
+       buildable: False
+     charm:
        buildable: False
+     charmpp:
+       buildable: False
+
 
 Now that we have configured Spack not to build any of the possible
 providers for MPI we can try again.
@@ -686,17 +768,11 @@ providers for MPI we can try again.
    --------------------------------
    hdf5%clang
 
-   Normalized
-   --------------------------------
-   hdf5%clang
-       ^mpi
-       ^zlib@1.1.2:
-
    Concretized
    --------------------------------
-   hdf5@1.10.1%clang@3.8.0-2ubuntu4+cxx~debug~fortran~hl+mpi+pic~shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
+   hdf5@1.10.4%clang@3.8.0-2ubuntu4~cxx~debug~fortran~hl+mpi+pic~shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
        ^mpich@3.2%gcc@5.4.0 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-ubuntu16.04-x86_64
-       ^zlib@1.2.8%gcc@5.4.0+pic+shared arch=linux-ubuntu16.04-x86_64
+       ^zlib@1.2.8%gcc@5.4.0+optimize+pic~shared arch=linux-ubuntu16.04-x86_64
 
 
 By configuring most of our package preferences in ``packages.yaml``,
@@ -706,6 +782,31 @@ preferences, we can specify version preferences as well. Anything
 that you can specify on the command line can be specified in
 ``packages.yaml`` with the exact same spec syntax.
 
+^^^^^^^^^^^^^^^^^^^^^^^^
+Installation Permissions
+^^^^^^^^^^^^^^^^^^^^^^^^
+
+The ``packages.yaml`` file also controls the default permissions
+to use when installing a package. You'll notice that by default,
+the installation prefix will be world readable but only user writable.
+
+Let's say we need to install ``converge``, a licensed software package.
+Since a specific research group, ``fluid_dynamics``, pays for this
+license, we want to ensure that only members of this group can access
+the software. We can do this like so:
+
+.. code-block:: yaml
+
+   packages:
+     converge:
+       permissions:
+         read: group
+         group: fluid_dynamics
+
+
+Now, only members of the ``fluid_dynamics`` group can use any
+``converge`` installations.
+
 .. warning::
 
    Make sure to delete or move the ``packages.yaml`` you have been
@@ -736,8 +837,8 @@ As you can see, many of the directories Spack uses can be customized.
 For example, you can tell Spack to install packages to a prefix
 outside of the ``$SPACK_ROOT`` hierarchy. Module files can be
 written to a central location if you are using multiple Spack
-instances. If you have a fast scratch filesystem, you can run builds
-from this filesystem with the following ``config.yaml``:
+instances. If you have a fast scratch file system, you can run builds
+from this file system with the following ``config.yaml``:
 
 .. code-block:: yaml
 
@@ -762,39 +863,31 @@ into the build.
 One last setting that may be of interest to many users is the ability
 to customize the parallelism of Spack builds. By default, Spack
 installs all packages in parallel with the number of jobs equal to the
-number of cores on the node. For example, on a node with 36 cores,
+number of cores on the node. For example, on a node with 16 cores,
 this will look like:
 
 .. code-block:: console
 
-   $ spack install --verbose zlib
+   $ spack install --no-cache --verbose zlib
    ==> Installing zlib
-   ==> Using cached archive: ~/spack/var/spack/cache/zlib/zlib-1.2.11.tar.gz
-   ==> Staging archive: ~/spack/var/spack/stage/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb/zlib-1.2.11.tar.gz
-   ==> Created stage in ~/spack/var/spack/stage/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
+   ==> Using cached archive: /home/user/spack/var/spack/cache/zlib/zlib-1.2.11.tar.gz
+   ==> Staging archive: /home/user/spack/var/spack/stage/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb/zlib-1.2.11.tar.gz
+   ==> Created stage in /home/user/spack/var/spack/stage/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
    ==> No patches needed for zlib
    ==> Building zlib [Package]
    ==> Executing phase: 'install'
-   ==> './configure' '--prefix=~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb'
-   Checking for shared library support...
-   Building shared library libz.so.1.2.11 with ~/spack/lib/spack/env/gcc/gcc.
-   Checking for size_t... Yes.
-   Checking for off64_t... Yes.
-   Checking for fseeko... Yes.
-   Checking for strerror... Yes.
-   Checking for unistd.h... Yes.
-   Checking for stdarg.h... Yes.
-   Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf().
-   Checking for vsnprintf() in stdio.h... Yes.
-   Checking for return value of vsnprintf()... Yes.
-   Checking for attribute(visibility) support... Yes.
-   ==> 'make' '-j36'
+   ==> './configure' '--prefix=/home/user/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb'
    ...
-   ==> 'make' '-j36' 'install'
+   ==> 'make' '-j16'
    ...
+   ==> 'make' '-j16' 'install'
+   ...
+   ==> Successfully installed zlib
+     Fetch: 0.00s.  Build: 1.03s.  Total: 1.03s.
+   [+] /home/user/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
 
 
-As you can see, we are building with all 36 cores on the node. If you are
+As you can see, we are building with all 16 cores on the node. If you are
 on a shared login node, this can slow down the system for other users. If
 you have a strict ulimit or restriction on the number of available licenses,
 you may not be able to build at all with this many cores. On nodes with 64+
@@ -811,33 +904,32 @@ If we uninstall and reinstall zlib, we see that it now uses only 4 cores:
 
 .. code-block:: console
 
-   $ spack install -v zlib
+   $ spack install --no-cache --verbose zlib
    ==> Installing zlib
-   ==> Using cached archive: ~/spack/var/spack/cache/zlib/zlib-1.2.11.tar.gz
-   ==> Staging archive: ~/spack/var/spack/stage/zlib-1.2.11-ezuwp4pa52e75v6iweawzwymmf4ahxxn/zlib-1.2.11.tar.gz
-   ==> Created stage in ~/spack/var/spack/stage/zlib-1.2.11-ezuwp4pa52e75v6iweawzwymmf4ahxxn
+   ==> Using cached archive: /home/user/spack/var/spack/cache/zlib/zlib-1.2.11.tar.gz
+   ==> Staging archive: /home/user/spack/var/spack/stage/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb/zlib-1.2.11.tar.gz
+   ==> Created stage in /home/user/spack/var/spack/stage/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
    ==> No patches needed for zlib
    ==> Building zlib [Package]
    ==> Executing phase: 'install'
-   ==> './configure' '--prefix=~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/zlib-1.2.11-ezuwp4pa52e75v6iweawzwymmf4ahxxn'
-   Checking for shared library support...
-   Building shared library libz.so.1.2.11 with ~/spack/lib/spack/env/gcc/gcc.
-   Checking for size_t... Yes.
-   Checking for off64_t... Yes.
-   Checking for fseeko... Yes.
-   Checking for strerror... Yes.
-   Checking for unistd.h... Yes.
-   Checking for stdarg.h... Yes.
-   Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf().
-   Checking for vsnprintf() in stdio.h... Yes.
-   Checking for return value of vsnprintf()... Yes.
-   Checking for attribute(visibility) support... Yes.
+   ==> './configure' '--prefix=/home/user/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb'
+   ...
    ==> 'make' '-j4'
    ...
    ==> 'make' '-j4' 'install'
    ...
+   ==> Successfully installed zlib
+     Fetch: 0.00s.  Build: 1.03s.  Total: 1.03s.
+   [+] /home/user/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb
 
 
 Obviously, if you want to build everything in serial for whatever reason,
 you would set ``build_jobs`` to 1.
 
+--------
+Examples
+--------
+
+For examples of how other sites configure Spack, see
+https://github.com/spack/spack-configs. If you use Spack at your site
+and want to share your config files, feel free to submit a pull request!
diff --git a/lib/spack/docs/tutorial_environments.rst b/lib/spack/docs/tutorial_environments.rst
new file mode 100644
index 0000000000..9ad2e9567c
--- /dev/null
+++ b/lib/spack/docs/tutorial_environments.rst
@@ -0,0 +1,815 @@
+.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+.. _environments-tutorial:
+
+================================================
+Environments, ``spack.yaml``, and ``spack.lock``
+================================================
+
+We've shown you how to install and remove packages with Spack.  You can
+use :ref:`cmd-spack-install` to install packages,
+:ref:`cmd-spack-uninstall` to remove them, and :ref:`cmd-spack-find` to
+look at and query what is installed.  We've also shown you how to
+customize Spack's installation with configuration files like
+:ref:`packages.yaml <build-settings>`.
+
+If you build a lot of software, or if you work on multiple projects,
+managing everything in one place can be overwhelming. The default ``spack
+find`` output may contain many packages, but you may want to *just* focus
+on packages a particular project.  Moreover, you may want to include
+special configuration with your package groups, e.g., to build all the
+packages in the same group the same way.
+
+Spack **environments** provide a way to handle these problems.
+
+-------------------
+Environment basics
+-------------------
+
+Let's look at the output of ``spack find`` at this point in the tutorial.
+
+.. code-block:: console
+
+   $ bin/spack find
+   ==> 70 installed packages
+   -- linux-ubuntu16.04-x86_64 / clang@3.8.0-2ubuntu4 --------------
+   tcl@8.6.8  zlib@1.2.8  zlib@1.2.11
+
+   -- linux-ubuntu16.04-x86_64 / gcc@4.7 ---------------------------
+   zlib@1.2.11
+
+   -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
+   adept-utils@1.0.1  hdf5@1.10.4          mpc@1.1.0               perl@5.26.2
+   autoconf@2.69      hdf5@1.10.4          mpfr@3.1.6              pkgconf@1.4.2
+   automake@1.16.1    hdf5@1.10.4          mpich@3.2.1             readline@7.0
+   boost@1.68.0       hwloc@1.11.9         mpileaks@1.0            suite-sparse@5.3.0
+   bzip2@1.0.6        hypre@2.15.1         mumps@5.1.1             tar@1.30
+   callpath@1.0.4     hypre@2.15.1         mumps@5.1.1             tcl@8.6.8
+   cmake@3.12.3       isl@0.18             ncurses@6.1             tcl@8.6.8
+   diffutils@3.6      libdwarf@20180129    netcdf@4.6.1            texinfo@6.5
+   dyninst@9.3.2      libiberty@2.31.1     netcdf@4.6.1            trilinos@12.12.1
+   elfutils@0.173     libpciaccess@0.13.5  netlib-scalapack@2.0.2  trilinos@12.12.1
+   findutils@4.6.0    libsigsegv@2.11      netlib-scalapack@2.0.2  util-macros@1.19.1
+   gcc@7.2.0          libtool@2.4.6        numactl@2.0.11          xz@5.2.4
+   gdbm@1.14.1        libxml2@2.9.8        openblas@0.3.3          zlib@1.2.8
+   gettext@0.19.8.1   m4@1.4.18            openmpi@3.1.3           zlib@1.2.8
+   glm@0.9.7.1        matio@1.5.9          openssl@1.0.2o          zlib@1.2.11
+   gmp@6.1.2          matio@1.5.9          parmetis@4.0.3
+   hdf5@1.10.4        metis@5.1.0          parmetis@4.0.3
+
+
+This is a complete, but cluttered view.  There are packages built with
+both ``openmpi`` and ``mpich``, as well as multiple variants of other
+packages, like ``zlib``.  The query mechanism we learned about in ``spack
+find`` can help, but it would be nice if we could start from a clean
+slate without losing what we've already done.
+
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Creating and activating environments
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The ``spack env`` command can help.  Let's create a new environment:
+
+.. code-block:: console
+
+   $ spack env create myproject
+   ==> Created environment 'myproject' in ~/spack/var/spack/environments/myproject
+
+An environment is a virtualized ``spack`` instance that you can use for a
+specific purpose.  You can see the environments we've created so far like this:
+
+.. code-block:: console
+
+   $ spack env list
+   ==> 1 environments
+       myproject
+
+And you can **activate** an environment with ``spack env activate``:
+
+.. code-block:: console
+
+   $ spack env activate myproject
+
+Once you enter an environment, ``spack find`` shows only what is in the
+current environment.  That's nothing, so far:
+
+.. code-block:: console
+
+   $ spack find
+   ==> In environment myproject
+   ==> No root specs
+
+   ==> 0 installed packages
+
+The ``spack find`` output is still *slightly* different.  It tells you
+that you're in the ``myproject`` environment, so that you don't panic
+when you see that there is nothing installed.  It also says that there
+are *no root specs*.  We'll get back to what that means later.
+
+If you *only* want to check what environment you are in, you can use
+``spack env status``:
+
+.. code-block:: console
+
+   $ spack env status
+   ==> In environment myproject
+
+And, if you want to leave this environment and go back to normal Spack,
+you can use ``spack env deactivate``.  We like to use the
+``despacktivate`` alias (which Spack sets up automatically) for short:
+
+.. code-block:: console
+
+   $ despacktivate     # short alias for `spack env deactivate`
+   $ spack env status
+   ==> No active environment
+   $ spack find
+   netcdf@4.6.1            readline@7.0        zlib@1.2.11
+   diffutils@3.6      hdf5@1.10.4       m4@1.4.18            netcdf@4.6.1            suite-sparse@5.3.0
+   dyninst@10.0.0     hwloc@1.11.9      matio@1.5.9          netlib-scalapack@2.0.2  tar@1.30
+   elfutils@0.173     hypre@2.15.1      matio@1.5.9          netlib-scalapack@2.0.2  tcl@8.6.8
+   findutils@4.6.0    hypre@2.15.1      metis@5.1.0          numactl@2.0.11          tcl@8.6.8
+   gcc@7.2.0          intel-tbb@2019    mpc@1.1.0            openblas@0.3.3          texinfo@6.5~
+
+
+^^^^^^^^^^^^^^^^^^^
+Installing packages
+^^^^^^^^^^^^^^^^^^^
+
+Ok, now that we understand how creation and activation work, let's go
+back to ``myproject`` and *install* a few packages:
+
+.. code-block:: console
+
+   $ spack env activate myproject
+   $ spack install tcl
+   ==> tcl is already installed in ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/tcl-8.6.8-qhwyccywhx2i6s7ob2gvjrjtj3rnfuqt
+   $ spack install trilinos
+   ==> trilinos is already installed in ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/trilinos-12.12.1-rlsruavxqvwk2tgxzxboclbo6ykjf54r
+   $ spack find
+   ==> In environment myproject
+   ==> Root specs
+   tcl  trilinos
+
+   ==> 22 installed packages
+   -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
+   boost@1.68.0  hwloc@1.11.9         matio@1.5.9   netlib-scalapack@2.0.2  parmetis@4.0.3      xz@5.2.4
+   bzip2@1.0.6   hypre@2.15.1         metis@5.1.0   numactl@2.0.11          suite-sparse@5.3.0  zlib@1.2.11
+   glm@0.9.7.1   libpciaccess@0.13.5  mumps@5.1.1   openblas@0.3.3          tcl@8.6.8
+   hdf5@1.10.4   libxml2@2.9.8        netcdf@4.6.1  openmpi@3.1.3           trilinos@12.12.1
+
+We've installed ``tcl`` and ``trilinos`` in our environment, along with
+all of their dependencies.  We call ``tcl`` and ``trilinos`` the
+**roots** because we asked for them explicitly.  The other 20 packages
+listed under "installed packages" are present because they were needed as
+dependencies.  So, these are the roots of the packages' dependency graph.
+
+The "<package> is already installed" messages above are generated because
+we already installed these packages in previous steps of the tutorial,
+and we don't have to rebuild them to put them in an environment.
+
+Now let's create *another* project.  We'll call this one ``myproject2``:
+
+.. code-block:: console
+
+   $ spack env create myproject2
+   ==> Created environment 'myproject2' in ~/spack/var/spack/environments/myproject2
+   $ spack env activate myproject2
+   $ spack install hdf5
+   ==> hdf5 is already installed in ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4-ozyvmhzdew66byarohm4p36ep7wtcuiw
+   $ spack install trilinos
+   ==> trilinos is already installed in ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/trilinos-12.12.1-rlsruavxqvwk2tgxzxboclbo6ykjf54r
+   $ spack find
+   ==> In environment myproject2
+   ==> Root specs
+   hdf5  trilinos
+
+   ==> 22 installed packages
+   -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
+   boost@1.68.0  hdf5@1.10.4          libxml2@2.9.8  netcdf@4.6.1            openmpi@3.1.3       xz@5.2.4
+   bzip2@1.0.6   hwloc@1.11.9         matio@1.5.9    netlib-scalapack@2.0.2  parmetis@4.0.3      zlib@1.2.11
+   glm@0.9.7.1   hypre@2.15.1         metis@5.1.0    numactl@2.0.11          suite-sparse@5.3.0
+   hdf5@1.10.4   libpciaccess@0.13.5  mumps@5.1.1    openblas@0.3.3          trilinos@12.12.1
+
+Now we have two environments: one with ``tcl`` and ``trilinos``, and
+another with ``hdf5`` and ``trilinos``.
+
+We can uninstall trilinos from ``myproject2`` as you would expect:
+
+.. code-block:: console
+
+   $ spack uninstall trilinos
+   ==> The following packages will be uninstalled:
+
+       -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
+       rlsruav trilinos@12.12.1%gcc~alloptpkgs+amesos+amesos2+anasazi+aztec+belos+boost build_type=RelWithDebInfo ~cgns~complex~dtk+epetra+epetraext+exodus+explicit_template_instantiation~float+fortran~fortrilinos+gtest+hdf5+hypre+ifpack+ifpack2~intrepid~intrepid2~isorropia+kokkos+metis~minitensor+ml+muelu+mumps~nox~openmp~phalanx~piro~pnetcdf~python~rol~rythmos+sacado~shards+shared~stk+suite-sparse~superlu~superlu-dist~teko~tempus+teuchos+tpetra~x11~xsdkflags~zlib+zoltan+zoltan2
+   ==> Do you want to proceed? [y/N] y
+   $ spack find
+   ==> In environment myproject2
+   ==> Root specs
+   hdf5
+
+   ==> 8 installed packages
+   -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
+   hdf5@1.10.4   libpciaccess@0.13.5  numactl@2.0.11  xz@5.2.4
+   hwloc@1.11.9  libxml2@2.9.8        openmpi@3.1.3   zlib@1.2.11
+
+Now there is only one root spec, ``hdf5``, which requires fewer
+additional dependencies.
+
+However, we still needed ``trilinos`` for the ``myproject`` environment!
+What happened to it?  Let's switch back and see.
+
+.. code-block:: console
+
+   $ despacktivate
+   $ spack env activate myproject
+   $ spack find
+   ==> In environment myproject
+   ==> Root specs
+   tcl  trilinos
+
+   ==> 22 installed packages
+   -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
+   boost@1.68.0  hwloc@1.11.9         matio@1.5.9   netlib-scalapack@2.0.2  parmetis@4.0.3      xz@5.2.4
+   bzip2@1.0.6   hypre@2.15.1         metis@5.1.0   numactl@2.0.11          suite-sparse@5.3.0  zlib@1.2.11
+   glm@0.9.7.1   libpciaccess@0.13.5  mumps@5.1.1   openblas@0.3.3          tcl@8.6.8
+   hdf5@1.10.4   libxml2@2.9.8        netcdf@4.6.1  openmpi@3.1.3           trilinos@12.12.1
+
+
+Spack is smart enough to realize that ``trilinos`` is still present in
+the other environment.  Trilinos won't *actually* be uninstalled unless
+it is no longer needed by any environments or packages.  If it is still
+needed, it is only removed from the environment.
+
+-------------------------------
+Dealing with many specs at once
+-------------------------------
+
+In the above examples, we just used ``install`` and ``uninstall``.  There
+are other ways to deal with groups of packages, as well.
+
+^^^^^^^^^^^^^
+Adding specs
+^^^^^^^^^^^^^
+
+Let's go back to our first ``myproject`` environment and *add* a few specs instead of installing them:
+
+.. code-block:: console
+
+   $ spack add hdf5
+   ==> Adding hdf5 to environment myproject
+   $ spack add gmp
+   ==> Adding mumps to environment myproject
+   $ spack find
+   ==> In environment myproject
+   ==> Root specs
+   gmp  hdf5  tcl  trilinos
+
+   ==> 22 installed packages
+   -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
+   boost@1.68.0  hwloc@1.11.9         matio@1.5.9   netlib-scalapack@2.0.2  parmetis@4.0.3      xz@5.2.4
+   bzip2@1.0.6   hypre@2.15.1         metis@5.1.0   numactl@2.0.11          suite-sparse@5.3.0  zlib@1.2.11
+   glm@0.9.7.1   libpciaccess@0.13.5  mumps@5.1.1   openblas@0.3.3          tcl@8.6.8
+   hdf5@1.10.4   libxml2@2.9.8        netcdf@4.6.1  openmpi@3.1.3           trilinos@12.12.1
+
+Let's take a close look at what happened.  The two packages we added,
+``hdf5`` and ``gmp``, are present, but they're not installed in the
+environment yet.  ``spack add`` just adds *roots* to the environment, but
+it does not automatically install them.
+
+We can install *all* the as-yet uninstalled packages in an environment by
+simply running ``spack install`` with no arguments:
+
+.. code-block:: console
+
+   $ spack install
+   ==> Concretizing hdf5
+   [+]  ozyvmhz  hdf5@1.10.4%gcc@5.4.0~cxx~debug~fortran~hl+mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
+   [+]  3njc4q5      ^openmpi@3.1.3%gcc@5.4.0~cuda+cxx_exceptions fabrics= ~java~legacylaunchers~memchecker~pmi schedulers= ~sqlite3~thread_multiple+vt arch=linux-ubuntu16.04-x86_64
+   [+]  43tkw5m          ^hwloc@1.11.9%gcc@5.4.0~cairo~cuda+libxml2+pci+shared arch=linux-ubuntu16.04-x86_64
+   [+]  5urc6tc              ^libpciaccess@0.13.5%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  o2pfwjf                  ^libtool@2.4.6%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  suf5jtc                      ^m4@1.4.18%gcc@5.4.0 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64
+   [+]  fypapcp                          ^libsigsegv@2.11%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  fovrh7a                  ^pkgconf@1.4.2%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  milz7fm                  ^util-macros@1.19.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  wpexsph              ^libxml2@2.9.8%gcc@5.4.0~python arch=linux-ubuntu16.04-x86_64
+   [+]  teneqii                  ^xz@5.2.4%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  5nus6kn                  ^zlib@1.2.11%gcc@5.4.0+optimize+pic+shared arch=linux-ubuntu16.04-x86_64
+   [+]  ft463od              ^numactl@2.0.11%gcc@5.4.0 patches=592f30f7f5f757dfc239ad0ffd39a9a048487ad803c26b419e0f96b8cda08c1a arch=linux-ubuntu16.04-x86_64
+   [+]  3sx2gxe                  ^autoconf@2.69%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  ic2kyoa                      ^perl@5.26.2%gcc@5.4.0+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-ubuntu16.04-x86_64
+   [+]  q4fpyuo                          ^gdbm@1.14.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  nxhwrg7                              ^readline@7.0%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  3o765ou                                  ^ncurses@6.1%gcc@5.4.0~symlinks~termlib arch=linux-ubuntu16.04-x86_64
+   [+]  rymw7im                  ^automake@1.16.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   ==> Concretizing gmp
+   [+]  qc4qcfz  gmp@6.1.2%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  3sx2gxe      ^autoconf@2.69%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  suf5jtc          ^m4@1.4.18%gcc@5.4.0 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64
+   [+]  fypapcp              ^libsigsegv@2.11%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  ic2kyoa          ^perl@5.26.2%gcc@5.4.0+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-ubuntu16.04-x86_64
+   [+]  q4fpyuo              ^gdbm@1.14.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  nxhwrg7                  ^readline@7.0%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  3o765ou                      ^ncurses@6.1%gcc@5.4.0~symlinks~termlib arch=linux-ubuntu16.04-x86_64
+   [+]  fovrh7a                          ^pkgconf@1.4.2%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  rymw7im      ^automake@1.16.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  o2pfwjf      ^libtool@2.4.6%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   ==> Installing environment myproject
+   ==> tcl is already installed in ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/tcl-8.6.8-qhwyccywhx2i6s7ob2gvjrjtj3rnfuqt
+   ==> trilinos is already installed in ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/trilinos-12.12.1-rlsruavxqvwk2tgxzxboclbo6ykjf54r
+   ==> hdf5 is already installed in ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/hdf5-1.10.4-ozyvmhzdew66byarohm4p36ep7wtcuiw
+   ==> gmp is already installed in ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gmp-6.1.2-qc4qcfz4monpllc3nqupdo7vwinf73sw
+
+Spack will concretize the new roots, and install everything you added to
+the environment.  Now we can see the installed roots in the output of
+``spack find``:
+
+.. code-block:: console
+
+   $ spack find
+   ==> In environment myproject
+   ==> Root specs
+   gmp  hdf5  tcl  trilinos
+
+   ==> 24 installed packages
+   -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
+   boost@1.68.0  hdf5@1.10.4   libpciaccess@0.13.5  mumps@5.1.1             openblas@0.3.3      tcl@8.6.8
+   bzip2@1.0.6   hdf5@1.10.4   libxml2@2.9.8        netcdf@4.6.1            openmpi@3.1.3       trilinos@12.12.1
+   glm@0.9.7.1   hwloc@1.11.9  matio@1.5.9          netlib-scalapack@2.0.2  parmetis@4.0.3      xz@5.2.4
+   gmp@6.1.2     hypre@2.15.1  metis@5.1.0          numactl@2.0.11          suite-sparse@5.3.0  zlib@1.2.11
+
+We can build whole environments this way, by adding specs and installing
+all at once, or we can install them with the usual ``install`` and
+``uninstall`` portions.  The advantage to doing them all at once is that
+we don't have to write a script outside of Spack to automate this, and we
+can kick off a large build of many packages easily.
+
+^^^^^^^^^^^^^^^^^^^^^
+Configuration
+^^^^^^^^^^^^^^^^^^^^^
+
+So far, ``myproject`` does not have any special configuration associated
+with it.  The specs concretize using Spack's defaults:
+
+.. code-block:: console
+
+   $ spack spec hypre
+   Input spec
+   --------------------------------
+   hypre
+
+   Concretized
+   --------------------------------
+   hypre@2.15.1%gcc@5.4.0~debug~int64+internal-superlu+mpi+shared arch=linux-ubuntu16.04-x86_64
+       ^openblas@0.3.3%gcc@5.4.0 cpu_target= ~ilp64 patches=47cfa7a952ac7b2e4632c73ae199d69fb54490627b66a62c681e21019c4ddc9d,714aea33692304a50bd0ccde42590c176c82ded4a8ac7f06e573dc8071929c33 +pic+shared threads=none ~virtual_machine arch=linux-ubuntu16.04-x86_64
+       ^openmpi@3.1.3%gcc@5.4.0~cuda+cxx_exceptions fabrics= ~java~legacylaunchers~memchecker~pmi schedulers= ~sqlite3~thread_multiple+vt arch=linux-ubuntu16.04-x86_64
+           ^hwloc@1.11.9%gcc@5.4.0~cairo~cuda+libxml2+pci+shared arch=linux-ubuntu16.04-x86_64
+               ^libpciaccess@0.13.5%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+                   ^libtool@2.4.6%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+                       ^m4@1.4.18%gcc@5.4.0 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64
+                           ^libsigsegv@2.11%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+                   ^pkgconf@1.4.2%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+                   ^util-macros@1.19.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+               ^libxml2@2.9.8%gcc@5.4.0~python arch=linux-ubuntu16.04-x86_64
+                   ^xz@5.2.4%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+                   ^zlib@1.2.11%gcc@5.4.0+optimize+pic+shared arch=linux-ubuntu16.04-x86_64
+               ^numactl@2.0.11%gcc@5.4.0 patches=592f30f7f5f757dfc239ad0ffd39a9a048487ad803c26b419e0f96b8cda08c1a arch=linux-ubuntu16.04-x86_64
+                   ^autoconf@2.69%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+                       ^perl@5.26.2%gcc@5.4.0+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-ubuntu16.04-x86_64
+                           ^gdbm@1.14.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+                               ^readline@7.0%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+                                   ^ncurses@6.1%gcc@5.4.0~symlinks~termlib arch=linux-ubuntu16.04-x86_64
+                   ^automake@1.16.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+
+You may want to add extra configuration to your environment.  You can see
+how your environment is configured using ``spack config get``:
+
+.. code-block:: console
+
+   $ spack config get
+   # This is a Spack Environment file.
+   #
+   # It describes a set of packages to be installed, along with
+   # configuration settings.
+   spack:
+     # add package specs to the `specs` list
+     specs: [tcl, trilinos, hdf5, gmp]
+
+It turns out that this is a special configuration format where Spack
+stores the state for the environment. Currently, the file is just a
+``spack:`` header and a list of ``specs``.  These are the roots.
+
+You can edit this file to add your own custom configuration.  Spack
+provides a shortcut to do that:
+
+.. code-block:: console
+
+   spack config edit
+
+You should now see the same file, and edit it to look like this:
+
+.. code-block:: yaml
+
+   # This is a Spack Environment file.
+   #
+   # It describes a set of packages to be installed, along with
+   # configuration settings.
+   spack:
+     packages:
+       all:
+         providers:
+           mpi: [mpich]
+
+     # add package specs to the `specs` list
+     specs: [tcl, trilinos, hdf5, gmp]
+
+Now if we run ``spack spec`` again in the environment, specs will concretize with ``mpich`` as the MPI implementation:
+
+.. code-block:: console
+
+   $ spack spec hypre
+   Input spec
+   --------------------------------
+   hypre
+
+   Concretized
+   --------------------------------
+   hypre@2.15.1%gcc@5.4.0~debug~int64+internal-superlu+mpi+shared arch=linux-ubuntu16.04-x86_64
+       ^mpich@3.2.1%gcc@5.4.0 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-ubuntu16.04-x86_64
+           ^findutils@4.6.0%gcc@5.4.0 patches=84b916c0bf8c51b7e7b28417692f0ad3e7030d1f3c248ba77c42ede5c1c5d11e,bd9e4e5cc280f9753ae14956c4e4aa17fe7a210f55dd6c84aa60b12d106d47a2 arch=linux-ubuntu16.04-x86_64
+               ^autoconf@2.69%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+                   ^m4@1.4.18%gcc@5.4.0 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64
+                       ^libsigsegv@2.11%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+                   ^perl@5.26.2%gcc@5.4.0+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-ubuntu16.04-x86_64
+                       ^gdbm@1.14.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+                           ^readline@7.0%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+                               ^ncurses@6.1%gcc@5.4.0~symlinks~termlib arch=linux-ubuntu16.04-x86_64
+                                   ^pkgconf@1.4.2%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+               ^automake@1.16.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+               ^libtool@2.4.6%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+               ^texinfo@6.5%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+       ^openblas@0.3.3%gcc@5.4.0 cpu_target= ~ilp64 patches=47cfa7a952ac7b2e4632c73ae199d69fb54490627b66a62c681e21019c4ddc9d,714aea33692304a50bd0ccde42590c176c82ded4a8ac7f06e573dc8071929c33 +pic+shared threads=none ~virtual_machine arch=linux-ubuntu16.04-x86_64
+
+In addition to the ``specs`` section, an environment's configuration can
+contain any of the configuration options from Spack's various config
+sections. You can add custom repositories, a custom install location,
+custom compilers, or custom external packages, in addition to the ``package``
+preferences we show here.
+
+But now we have a problem.  We already installed part of this environment
+with openmpi, but now we want to install it with ``mpich``.
+
+You can run ``spack concretize`` inside of an environment to concretize
+all of its specs.  We can run it here:
+
+.. code-block:: console
+
+   $ spack concretize -f
+   ==> Concretizing tcl
+   [+]  qhwyccy  tcl@8.6.8%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  5nus6kn      ^zlib@1.2.11%gcc@5.4.0+optimize+pic+shared arch=linux-ubuntu16.04-x86_64
+   ==> Concretizing trilinos
+   [+]  kqc52mo  trilinos@12.12.1%gcc@5.4.0~alloptpkgs+amesos+amesos2+anasazi+aztec+belos+boost build_type=RelWithDebInfo ~cgns~complex~dtk+epetra+epetraext+exodus+explicit_template_instantiation~float+fortran~fortrilinos+gtest+hdf5+hypre+ifpack+ifpack2~intrepid~intrepid2~isorropia+kokkos+metis~minitensor+ml+muelu+mumps~nox~openmp~phalanx~piro~pnetcdf~python~rol~rythmos+sacado~shards+shared~stk+suite-sparse~superlu~superlu-dist~teko~tempus+teuchos+tpetra~x11~xsdkflags~zlib+zoltan+zoltan2 arch=linux-ubuntu16.04-x86_64
+   [+]  zbgfxap      ^boost@1.68.0%gcc@5.4.0+atomic+chrono~clanglibcpp cxxstd=default +date_time~debug+exception+filesystem+graph~icu+iostreams+locale+log+math~mpi+multithreaded~numpy patches=2ab6c72d03dec6a4ae20220a9dfd5c8c572c5294252155b85c6874d97c323199 +program_options~python+random+regex+serialization+shared+signals~singlethreaded+system~taggedlayout+test+thread+timer~versionedlayout+wave arch=linux-ubuntu16.04-x86_64
+   [+]  ufczdvs          ^bzip2@1.0.6%gcc@5.4.0+shared arch=linux-ubuntu16.04-x86_64
+   [+]  2rhuivg              ^diffutils@3.6%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  5nus6kn          ^zlib@1.2.11%gcc@5.4.0+optimize+pic+shared arch=linux-ubuntu16.04-x86_64
+   [+]  otafqzh      ^cmake@3.12.3%gcc@5.4.0~doc+ncurses+openssl+ownlibs patches=dd3a40d4d92f6b2158b87d6fb354c277947c776424aa03f6dc8096cf3135f5d0 ~qt arch=linux-ubuntu16.04-x86_64
+   [+]  3o765ou          ^ncurses@6.1%gcc@5.4.0~symlinks~termlib arch=linux-ubuntu16.04-x86_64
+   [+]  fovrh7a              ^pkgconf@1.4.2%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  b4y3w3b          ^openssl@1.0.2o%gcc@5.4.0+systemcerts arch=linux-ubuntu16.04-x86_64
+   [+]  ic2kyoa              ^perl@5.26.2%gcc@5.4.0+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-ubuntu16.04-x86_64
+   [+]  q4fpyuo                  ^gdbm@1.14.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  nxhwrg7                      ^readline@7.0%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  jnw622j      ^glm@0.9.7.1%gcc@5.4.0 build_type=RelWithDebInfo arch=linux-ubuntu16.04-x86_64
+   [+]  xxd7syh      ^hdf5@1.10.4%gcc@5.4.0~cxx~debug~fortran+hl+mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
+   [+]  p3f7p2r          ^mpich@3.2.1%gcc@5.4.0 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-ubuntu16.04-x86_64
+   [+]  d4iajxs              ^findutils@4.6.0%gcc@5.4.0 patches=84b916c0bf8c51b7e7b28417692f0ad3e7030d1f3c248ba77c42ede5c1c5d11e,bd9e4e5cc280f9753ae14956c4e4aa17fe7a210f55dd6c84aa60b12d106d47a2 arch=linux-ubuntu16.04-x86_64
+   [+]  3sx2gxe                  ^autoconf@2.69%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  suf5jtc                      ^m4@1.4.18%gcc@5.4.0 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64
+   [+]  fypapcp                          ^libsigsegv@2.11%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  rymw7im                  ^automake@1.16.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  o2pfwjf                  ^libtool@2.4.6%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  zs7a2pc                  ^texinfo@6.5%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  obewuoz      ^hypre@2.15.1%gcc@5.4.0~debug~int64~internal-superlu+mpi+shared arch=linux-ubuntu16.04-x86_64
+   [+]  cyeg2yi          ^openblas@0.3.3%gcc@5.4.0 cpu_target= ~ilp64 patches=47cfa7a952ac7b2e4632c73ae199d69fb54490627b66a62c681e21019c4ddc9d,714aea33692304a50bd0ccde42590c176c82ded4a8ac7f06e573dc8071929c33 +pic+shared threads=none ~virtual_machine arch=linux-ubuntu16.04-x86_64
+   [+]  gvyqldh      ^matio@1.5.9%gcc@5.4.0+hdf5+shared+zlib arch=linux-ubuntu16.04-x86_64
+   [+]  3wnvp4j      ^metis@5.1.0%gcc@5.4.0 build_type=Release ~gdb~int64 patches=4991da938c1d3a1d3dea78e49bbebecba00273f98df2a656e38b83d55b281da1 ~real64+shared arch=linux-ubuntu16.04-x86_64
+   [+]  cumcj5a      ^mumps@5.1.1%gcc@5.4.0+complex+double+float~int64~metis+mpi~parmetis~ptscotch~scotch+shared arch=linux-ubuntu16.04-x86_64
+   [+]  p7iln2p          ^netlib-scalapack@2.0.2%gcc@5.4.0 build_type=RelWithDebInfo ~pic+shared arch=linux-ubuntu16.04-x86_64
+   [+]  wmmx5sg      ^netcdf@4.6.1%gcc@5.4.0~dap~hdf4 maxdims=1024 maxvars=8192 +mpi~parallel-netcdf+shared arch=linux-ubuntu16.04-x86_64
+   [+]  jehtata      ^parmetis@4.0.3%gcc@5.4.0 build_type=RelWithDebInfo ~gdb patches=4f892531eb0a807eb1b82e683a416d3e35154a455274cf9b162fb02054d11a5b,50ed2081bc939269689789942067c58b3e522c269269a430d5d34c00edbc5870,704b84f7c7444d4372cb59cca6e1209df4ef3b033bc4ee3cf50f369bce972a9d +shared arch=linux-ubuntu16.04-x86_64
+   [+]  zaau4ki      ^suite-sparse@5.3.0%gcc@5.4.0~cuda~openmp+pic~tbb arch=linux-ubuntu16.04-x86_64
+   ==> Concretizing hdf5
+    -   zjgyn3w  hdf5@1.10.4%gcc@5.4.0~cxx~debug~fortran~hl+mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
+   [+]  p3f7p2r      ^mpich@3.2.1%gcc@5.4.0 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-ubuntu16.04-x86_64
+   [+]  d4iajxs          ^findutils@4.6.0%gcc@5.4.0 patches=84b916c0bf8c51b7e7b28417692f0ad3e7030d1f3c248ba77c42ede5c1c5d11e,bd9e4e5cc280f9753ae14956c4e4aa17fe7a210f55dd6c84aa60b12d106d47a2 arch=linux-ubuntu16.04-x86_64
+   [+]  3sx2gxe              ^autoconf@2.69%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  suf5jtc                  ^m4@1.4.18%gcc@5.4.0 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64
+   [+]  fypapcp                      ^libsigsegv@2.11%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  ic2kyoa                  ^perl@5.26.2%gcc@5.4.0+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-ubuntu16.04-x86_64
+   [+]  q4fpyuo                      ^gdbm@1.14.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  nxhwrg7                          ^readline@7.0%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  3o765ou                              ^ncurses@6.1%gcc@5.4.0~symlinks~termlib arch=linux-ubuntu16.04-x86_64
+   [+]  fovrh7a                                  ^pkgconf@1.4.2%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  rymw7im              ^automake@1.16.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  o2pfwjf              ^libtool@2.4.6%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  zs7a2pc              ^texinfo@6.5%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  5nus6kn      ^zlib@1.2.11%gcc@5.4.0+optimize+pic+shared arch=linux-ubuntu16.04-x86_64
+   ==> Concretizing gmp
+   [+]  qc4qcfz  gmp@6.1.2%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  3sx2gxe      ^autoconf@2.69%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  suf5jtc          ^m4@1.4.18%gcc@5.4.0 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64
+   [+]  fypapcp              ^libsigsegv@2.11%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  ic2kyoa          ^perl@5.26.2%gcc@5.4.0+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-ubuntu16.04-x86_64
+   [+]  q4fpyuo              ^gdbm@1.14.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  nxhwrg7                  ^readline@7.0%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  3o765ou                      ^ncurses@6.1%gcc@5.4.0~symlinks~termlib arch=linux-ubuntu16.04-x86_64
+   [+]  fovrh7a                          ^pkgconf@1.4.2%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  rymw7im      ^automake@1.16.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  o2pfwjf      ^libtool@2.4.6%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+
+Now, all the specs in the environemnt are concrete and ready to be
+installed wiht ``mpich`` as the MPI immplementation.
+
+Normally, we could just run ``spack config edit``, edit the environment
+configuration, ``spack add`` some specs, and ``install``.
+
+But, when we already have installed packages in the environment, we have
+to force everything in the environment to be re-concretized using ``spack
+concretize -f``.  *Then* we can re-run ``spack install``.
+
+
+-----------------------------------
+``spack.yaml`` and ``spack.lock``
+-----------------------------------
+
+So far we've shown you how to interact with environments from the command
+line, but they also have a file-based interface that can be used by
+developers and admins to manage workflows for projects.
+
+In this section we'll dive a little deeper to see how environments are
+implemented, and how you could use this in your day-to-day development.
+
+^^^^^^^^^^^^^^
+``spack.yaml``
+^^^^^^^^^^^^^^
+
+Earlier, we changed an environment's configuration using ``spack config
+edit``.  We were actually editing a special file called ``spack.yaml``.
+Let's take a look.
+
+We can get directly to the current environment's location using ``spack cd``:
+
+.. code-block:: console
+
+   $ spack cd -e myproject
+   $ pwd
+   ~/spack/var/spack/environments/myproject
+   $ ls
+   spack.lock  spack.yaml
+
+We notice two things here.  First, the environment is just a directory
+inside of ``var/spack/environments`` within the Spack installation.
+Second, it contains two important files: ``spack.yaml`` and
+``spack.lock``.
+
+``spack.yaml`` is the configuration file for environments that we've
+already seen, but it does not *have* to live inside Spack.  If you create
+an environment using ``spack env create``, it is *managed* by
+Spack in the ``var/spack/environments`` directory, and you can refer to
+it by name.
+
+You can actually put a ``spack.yaml`` file *anywhere*, and you can use it
+to bundle an environment, or a list of dependencies to install, with your
+project.  Let's make a simple project:
+
+.. code-block:: console
+
+   $ cd
+   $ mkdir code
+   $ cd code
+   $ spack env create -d .
+   ==> Created environment in ~/code
+
+Here, we made a new directory called *code*, and we used the ``-d``
+option to create an environment in it.
+
+What really happened?
+
+.. code-block:: console
+
+   $ ls
+   spack.yaml
+   $ cat spack.yaml
+   # This is a Spack Environment file.
+   #
+   # It describes a set of packages to be installed, along with
+   # configuration settings.
+   spack:
+     # add package specs to the `specs` list
+     specs: []
+
+Spack just created a ``spack.yaml`` file in the code directory, with an
+empty list of root specs.  Now we have a Spack environment, *in a
+directory*, that we can use to manage dependencies.  Suppose your project
+depends on ``boost``, ``trilinos``, and ``openmpi``.  You can add these
+to your spec list:
+
+.. code-block:: yaml
+
+   # This is a Spack Environment file.
+   #
+   # It describes a set of packages to be installed, along with
+   # configuration settings.
+   spack:
+     # add package specs to the `specs` list
+     specs:
+     - boost
+     - trilinos
+     - openmpi
+
+And now *anyone* who uses the *code* repository can use this format to
+install the project's dependencies.  They need only clone the repository,
+``cd`` into it, and type ``spack install``:
+
+.. code-block:: console
+
+   $ spack install
+   ==> Concretizing boost
+   [+]  zbgfxap  boost@1.68.0%gcc@5.4.0+atomic+chrono~clanglibcpp cxxstd=default +date_time~debug+exception+filesystem+graph~icu+iostreams+locale+log+math~mpi+multithreaded~numpy patches=2ab6c72d03dec6a4ae20220a9dfd5c8c572c5294252155b85c6874d97c323199 +program_options~python+random+regex+serialization+shared+signals~singlethreaded+system~taggedlayout+test+thread+timer~versionedlayout+wave arch=linux-ubuntu16.04-x86_64
+   [+]  ufczdvs      ^bzip2@1.0.6%gcc@5.4.0+shared arch=linux-ubuntu16.04-x86_64
+   [+]  2rhuivg          ^diffutils@3.6%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  5nus6kn      ^zlib@1.2.11%gcc@5.4.0+optimize+pic+shared arch=linux-ubuntu16.04-x86_64
+   ==> Concretizing trilinos
+   [+]  rlsruav  trilinos@12.12.1%gcc@5.4.0~alloptpkgs+amesos+amesos2+anasazi+aztec+belos+boost build_type=RelWithDebInfo ~cgns~complex~dtk+epetra+epetraext+exodus+explicit_template_instantiation~float+fortran~fortrilinos+gtest+hdf5+hypre+ifpack+ifpack2~intrepid~intrepid2~isorropia+kokkos+metis~minitensor+ml+muelu+mumps~nox~openmp~phalanx~piro~pnetcdf~python~rol~rythmos+sacado~shards+shared~stk+suite-sparse~superlu~superlu-dist~teko~tempus+teuchos+tpetra~x11~xsdkflags~zlib+zoltan+zoltan2 arch=linux-ubuntu16.04-x86_64
+   [+]  zbgfxap      ^boost@1.68.0%gcc@5.4.0+atomic+chrono~clanglibcpp cxxstd=default +date_time~debug+exception+filesystem+graph~icu+iostreams+locale+log+math~mpi+multithreaded~numpy patches=2ab6c72d03dec6a4ae20220a9dfd5c8c572c5294252155b85c6874d97c323199 +program_options~python+random+regex+serialization+shared+signals~singlethreaded+system~taggedlayout+test+thread+timer~versionedlayout+wave arch=linux-ubuntu16.04-x86_64
+   [+]  ufczdvs          ^bzip2@1.0.6%gcc@5.4.0+shared arch=linux-ubuntu16.04-x86_64
+   [+]  2rhuivg              ^diffutils@3.6%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  5nus6kn          ^zlib@1.2.11%gcc@5.4.0+optimize+pic+shared arch=linux-ubuntu16.04-x86_64
+   [+]  otafqzh      ^cmake@3.12.3%gcc@5.4.0~doc+ncurses+openssl+ownlibs patches=dd3a40d4d92f6b2158b87d6fb354c277947c776424aa03f6dc8096cf3135f5d0 ~qt arch=linux-ubuntu16.04-x86_64
+   [+]  3o765ou          ^ncurses@6.1%gcc@5.4.0~symlinks~termlib arch=linux-ubuntu16.04-x86_64
+   [+]  fovrh7a              ^pkgconf@1.4.2%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  b4y3w3b          ^openssl@1.0.2o%gcc@5.4.0+systemcerts arch=linux-ubuntu16.04-x86_64
+   [+]  ic2kyoa              ^perl@5.26.2%gcc@5.4.0+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-ubuntu16.04-x86_64
+   [+]  q4fpyuo                  ^gdbm@1.14.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  nxhwrg7                      ^readline@7.0%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  jnw622j      ^glm@0.9.7.1%gcc@5.4.0 build_type=RelWithDebInfo arch=linux-ubuntu16.04-x86_64
+   [+]  oqwnui7      ^hdf5@1.10.4%gcc@5.4.0~cxx~debug~fortran+hl+mpi+pic+shared~szip~threadsafe arch=linux-ubuntu16.04-x86_64
+   [+]  3njc4q5          ^openmpi@3.1.3%gcc@5.4.0~cuda+cxx_exceptions fabrics= ~java~legacylaunchers~memchecker~pmi schedulers= ~sqlite3~thread_multiple+vt arch=linux-ubuntu16.04-x86_64
+   [+]  43tkw5m              ^hwloc@1.11.9%gcc@5.4.0~cairo~cuda+libxml2+pci+shared arch=linux-ubuntu16.04-x86_64
+   [+]  5urc6tc                  ^libpciaccess@0.13.5%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  o2pfwjf                      ^libtool@2.4.6%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  suf5jtc                          ^m4@1.4.18%gcc@5.4.0 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64
+   [+]  fypapcp                              ^libsigsegv@2.11%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  milz7fm                      ^util-macros@1.19.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  wpexsph                  ^libxml2@2.9.8%gcc@5.4.0~python arch=linux-ubuntu16.04-x86_64
+   [+]  teneqii                      ^xz@5.2.4%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  ft463od                  ^numactl@2.0.11%gcc@5.4.0 patches=592f30f7f5f757dfc239ad0ffd39a9a048487ad803c26b419e0f96b8cda08c1a arch=linux-ubuntu16.04-x86_64
+   [+]  3sx2gxe                      ^autoconf@2.69%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  rymw7im                      ^automake@1.16.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  fshksdp      ^hypre@2.15.1%gcc@5.4.0~debug~int64~internal-superlu+mpi+shared arch=linux-ubuntu16.04-x86_64
+   [+]  cyeg2yi          ^openblas@0.3.3%gcc@5.4.0 cpu_target= ~ilp64 patches=47cfa7a952ac7b2e4632c73ae199d69fb54490627b66a62c681e21019c4ddc9d,714aea33692304a50bd0ccde42590c176c82ded4a8ac7f06e573dc8071929c33 +pic+shared threads=none ~virtual_machine arch=linux-ubuntu16.04-x86_64
+   [+]  lmzdgss      ^matio@1.5.9%gcc@5.4.0+hdf5+shared+zlib arch=linux-ubuntu16.04-x86_64
+   [+]  3wnvp4j      ^metis@5.1.0%gcc@5.4.0 build_type=Release ~gdb~int64 patches=4991da938c1d3a1d3dea78e49bbebecba00273f98df2a656e38b83d55b281da1 ~real64+shared arch=linux-ubuntu16.04-x86_64
+   [+]  acsg2dz      ^mumps@5.1.1%gcc@5.4.0+complex+double+float~int64~metis+mpi~parmetis~ptscotch~scotch+shared arch=linux-ubuntu16.04-x86_64
+   [+]  wotpfwf          ^netlib-scalapack@2.0.2%gcc@5.4.0 build_type=RelWithDebInfo ~pic+shared arch=linux-ubuntu16.04-x86_64
+   [+]  mhm4izp      ^netcdf@4.6.1%gcc@5.4.0~dap~hdf4 maxdims=1024 maxvars=8192 +mpi~parallel-netcdf+shared arch=linux-ubuntu16.04-x86_64
+   [+]  uv6h3sq      ^parmetis@4.0.3%gcc@5.4.0 build_type=RelWithDebInfo ~gdb patches=4f892531eb0a807eb1b82e683a416d3e35154a455274cf9b162fb02054d11a5b,50ed2081bc939269689789942067c58b3e522c269269a430d5d34c00edbc5870,704b84f7c7444d4372cb59cca6e1209df4ef3b033bc4ee3cf50f369bce972a9d +shared arch=linux-ubuntu16.04-x86_64
+   [+]  zaau4ki      ^suite-sparse@5.3.0%gcc@5.4.0~cuda~openmp+pic~tbb arch=linux-ubuntu16.04-x86_64
+   ==> Concretizing openmpi
+   [+]  3njc4q5  openmpi@3.1.3%gcc@5.4.0~cuda+cxx_exceptions fabrics= ~java~legacylaunchers~memchecker~pmi schedulers= ~sqlite3~thread_multiple+vt arch=linux-ubuntu16.04-x86_64
+   [+]  43tkw5m      ^hwloc@1.11.9%gcc@5.4.0~cairo~cuda+libxml2+pci+shared arch=linux-ubuntu16.04-x86_64
+   [+]  5urc6tc          ^libpciaccess@0.13.5%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  o2pfwjf              ^libtool@2.4.6%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  suf5jtc                  ^m4@1.4.18%gcc@5.4.0 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu16.04-x86_64
+   [+]  fypapcp                      ^libsigsegv@2.11%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  fovrh7a              ^pkgconf@1.4.2%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  milz7fm              ^util-macros@1.19.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  wpexsph          ^libxml2@2.9.8%gcc@5.4.0~python arch=linux-ubuntu16.04-x86_64
+   [+]  teneqii              ^xz@5.2.4%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  5nus6kn              ^zlib@1.2.11%gcc@5.4.0+optimize+pic+shared arch=linux-ubuntu16.04-x86_64
+   [+]  ft463od          ^numactl@2.0.11%gcc@5.4.0 patches=592f30f7f5f757dfc239ad0ffd39a9a048487ad803c26b419e0f96b8cda08c1a arch=linux-ubuntu16.04-x86_64
+   [+]  3sx2gxe              ^autoconf@2.69%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  ic2kyoa                  ^perl@5.26.2%gcc@5.4.0+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-ubuntu16.04-x86_64
+   [+]  q4fpyuo                      ^gdbm@1.14.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  nxhwrg7                          ^readline@7.0%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   [+]  3o765ou                              ^ncurses@6.1%gcc@5.4.0~symlinks~termlib arch=linux-ubuntu16.04-x86_64
+   [+]  rymw7im              ^automake@1.16.1%gcc@5.4.0 arch=linux-ubuntu16.04-x86_64
+   ==> Installing environment ~/code
+   ==> boost is already installed in ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/boost-1.68.0-zbgfxapchxa4awxdwpleubfuznblxzvt
+   ==> trilinos is already installed in ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/trilinos-12.12.1-rlsruavxqvwk2tgxzxboclbo6ykjf54r
+   ==> openmpi is already installed in ~/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.1.3-3njc4q5pqdpptq6jvqjrezkffwokv2sx
+
+
+Spack concretizes the specs in the ``spack.yaml`` file and installs them.
+
+What happened here?  If you ``cd`` into a directory tha has a
+``spack.yaml`` file in it, Spack considers this directory's environment
+to be activated.  The directory does not have to live within Spack; it
+can be anywhere.
+
+So, from ``~/code``, we can actually manipulate ``spack.yaml`` using
+``spack add`` and ``spack remove`` (just like managed environments):
+
+.. code-block:: console
+
+   $ spack add hdf5@5.5.1
+   ==> Adding hdf5 to environment ~/code
+   $ cat spack.yaml
+   # This is a Spack Environment file.
+   #
+   # It describes a set of packages to be installed, along with
+   # configuration settings.
+   spack:
+     # add package specs to the `specs` list
+     specs:
+     - boost
+     - trilinos
+     - openmpi
+     - hdf5@5.5.1
+
+   $ spack remove hdf5
+   ==> Removing hdf5 from environment ~/code
+   $ cat spack.yaml
+   # This is a Spack Environment file.
+   #
+   # It describes a set of packages to be installed, along with
+   # configuration settings.
+   spack:
+     # add package specs to the `specs` list
+     specs:
+     - boost
+     - trilinos
+     - openmpi
+
+
+^^^^^^^^^^^^^^
+``spack.lock``
+^^^^^^^^^^^^^^
+
+Ok, we've covered managed environments, environments in directories, and
+the last thing we'll cover is ``spack.lock``. You may remember that when
+we ran ``spack install``, Spack concretized all the specs in the
+``spack.yaml`` file and installed them.
+
+Whenever we concretize Specs in an environment, all concrete specs in the
+environment are written out to a ``spack.lock`` file *alongside*
+``spack.yaml``.  The ``spack.lock`` file is not really human-readable
+like the ``spack.yaml`` file.  It is a ``json`` format that contains all
+the information that we need to ``reproduce`` the build of an
+environment:
+
+.. code-block:: console
+
+   $ head spack.lock
+   {
+     "concrete_specs": {
+      "teneqii2xv5u6zl5r6qi3pwurc6pmypz": {
+       "xz": {
+         "version": "5.2.4",
+         "arch": {
+           "platform": "linux",
+           "platform_os": "ubuntu16.04",
+         "target": "x86_64"
+    },
+    ...
+
+``spack.yaml`` and ``spack.lock`` correspond to two fundamental concepts
+in Spack, but for environments:
+
+  * ``spack.yaml`` is the set of *abstract* specs and configuration that
+    you want to install.
+  * ``spack.lock`` is the set of all fully *concretized* specs generated
+    from concretizing ``spack.yaml``
+
+Using either of these, you can recreate an environment that someone else
+built.  ``spack env create`` takes an extra optional argument, which can
+be either a ``spack.yaml`` or a ``spack.lock`` file:
+
+.. code-block:: console
+
+   $ spack env create my-project spack.yaml
+
+   $ spack env create my-project spack.lock
+
+Both of these create a new environment called ``my-project``, but which
+one you choose to use depends on your needs:
+
+  1.  copying the yaml file allows someone else to build your *requirements*,
+      potentially a different way.
+
+  2. copying the lock file allows someone else to rebuild your
+     *installation* exactly as you built it.
+
+The first use case can *re-concretize* the same specs on new platforms in
+order to build, but it will preserve the abstract requirements.  The
+second use case (currently) requires you to be on the same machine, but
+it retains all decisions made during concretization and is faithful to a
+prior install.
diff --git a/lib/spack/docs/tutorial_modules.rst b/lib/spack/docs/tutorial_modules.rst
index 21e1e5e886..31fb1cd749 100644
--- a/lib/spack/docs/tutorial_modules.rst
+++ b/lib/spack/docs/tutorial_modules.rst
@@ -1,3 +1,8 @@
+.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 .. _modules-tutorial:
 
 ============
@@ -144,77 +149,16 @@ how Spack can help with similar situations, as they will happen on real HPC clus
 For instance, it's often preferable for Spack to use vendor-provided MPI
 implementations than to build one itself.
 
-The best way to follow along is to use a Docker image, which comes
-with Spack and all the software used in the following parts already
-pre-installed. If you want to proceed this way, read :ref:`module_file_tutorial_use_docker`.
-
-If you don't have Docker installed or for any other reason you
-prefer to work locally, follow instead :ref:`module_file_tutorial_work_locally`
-to know how to clone Spack and install the software.
-Be aware that the set-up will take longer and that the details of the snippets
-below assume the Docker image and may need changes to work in your particular
-environment.
+To keep the set of software we're dealing with manageable, we're going
+to uninstall everything from earlier in the tutorial.
 
-.. _module_file_tutorial_use_docker:
-
-^^^^^^^^^^^^^^^^^^
-Use a Docker image
-^^^^^^^^^^^^^^^^^^
+.. code-block: console
 
-The fastest way to set-up your environment is to :ref:`use a Docker image <workflow_create_docker_image>`:
+  $ spack uninstall -ay
 
-.. code-block:: console
-
-  $ docker pull alalazo/spack:module_tutorial
-  $ docker run --rm -h module-file-tutorial -it alalazo/spack:module_tutorial
-  root@module-file-tutorial:/#
-
-If you arrived at this point you should be ready to start, as all the software needed is
-pre-installed in the image:
-
-.. code-block:: console
-
-  root@module-file-tutorial:/# which spack
-  /usr/local/bin/spack
-  root@module-file-tutorial:/# spack find
-  ==> 46 installed packages.
-  -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
-  autoconf@2.69    gcc@7.2.0  git@2.9.4  isl@0.18         libtool@2.4.6  lua@5.3.4                lua-luaposix@33.4.0  mpc@1.0.3   ncurses@6.0  pkg-config@0.29.2  tcl@8.6.6
-  automake@1.15.1  gdbm@1.13  gmp@6.1.2  libsigsegv@2.11  lmod@7.7       lua-luafilesystem@1_6_3  m4@1.4.18            mpfr@3.1.5  perl@5.24.1  readline@7.0       zlib@1.2.11
-
-  -- linux-ubuntu16.04-x86_64 / gcc@7.2.0 -------------------------
-  bzip2@1.0.6  ncurses@6.0             netlib-scalapack@2.0.2  openblas@0.2.20  pkg-config@0.29.2  py-packaging@16.8   py-setuptools@35.0.2  readline@7.0
-  cmake@3.9.4  netlib-lapack@3.6.1     netlib-scalapack@2.0.2  openmpi@1.10.2   py-appdirs@1.4.3   py-pyparsing@2.2.0  py-six@1.10.0         sqlite@3.20.0
-  mpich@3.2    netlib-scalapack@2.0.2  netlib-scalapack@2.0.2  openssl@1.0.2k   py-numpy@1.13.1    py-scipy@0.19.1     python@2.7.14         zlib@1.2.11
-
-Go to :ref:`module_file_tutorial_non_hierarchical` to proceed with the tutorial.
-
-.. note::
-  Dockerfile for this image
-    Those of you that want to build a similar container themselves can find the
-    ``Dockerfile`` and the other resources in Spack's ``share/spack/docs/docker``
-    folder.
-
-.. _module_file_tutorial_work_locally:
-
-^^^^^^^^^^^^^^^^^^^^^^
-Work in a local folder
-^^^^^^^^^^^^^^^^^^^^^^
-
-If you don't feel like using a container, you can set-up your environment
-locally. Let's start by cloning the Spack repository and moving to the directory
-where it was checked out:
-
-.. code-block:: console
-
-  $ git clone https://github.com/spack/spack.git
-  $ cd spack
-
-From here we'll be building the required stack of software.
-
-"""""""""""""""""""
+^^^^^^^^^^^^^^^^^^^
 Build a module tool
-"""""""""""""""""""
+^^^^^^^^^^^^^^^^^^^
 
 The first thing that we need is the module tool. In this case we
 choose ``lmod`` as it can work with both hierarchical and non-hierarchical
@@ -233,7 +177,8 @@ to remember, we'll employ the command ``spack location`` to retrieve the
 
   $ . $(spack location -i lmod)/lmod/lmod/init/bash
 
-Now we can source the setup file and activate the :ref:`shell support <shell-support>`:
+Now we can re-source the setup file and Spack modules will be put in
+our module path.
 
 .. code-block:: console
 
@@ -246,26 +191,15 @@ Now we can source the setup file and activate the :ref:`shell support <shell-sup
   to the documentation :ref:`here <InstallEnvironmentModules>`.
 
 
-""""""""""""""""""
+^^^^^^^^^^^^^^^^^^
 Add a new compiler
-""""""""""""""""""
+^^^^^^^^^^^^^^^^^^
 
 The second step is to build a recent compiler. On first use, Spack
-scans the environment and automatically locates the
-compiler(s) already available on the system. This is what you'll see
-on Ubuntu 14.04:
-
-.. code-block:: console
-
-  $ uname -a
-  Linux nuvolari 4.4.0-45-generic #66~14.04.1-Ubuntu SMP Wed Oct 19 15:05:38 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
+scans the environment and automatically locates the compiler(s)
+already available on the system. For this tutorial, however, we want
+to use ``gcc@7.2.0``.
 
-  $ spack compilers
-  ==> Available compilers
-  -- gcc ----------------------------------------------------------
-  gcc@4.8
-
-Let's bootstrap a more recent compiler with the one that was automatically detected:
 
 .. code-block:: console
 
@@ -294,7 +228,7 @@ You can use this command to double check:
 
   $ module list
   Currently Loaded Modules:
-  1) lmod-7.7-gcc-4.8-okcwjgw 2) gcc-7.2.0-gcc-4.8-twd5nqg
+  1) gcc-7.2.0-gcc-5.4.0-b7smjjc
 
 Note that the 7-digit hash at the end of the generated module may vary depending
 on architecture or package version. Now that we have ``gcc@7.2.0`` in ``PATH`` we
@@ -303,38 +237,23 @@ can finally add it to the list of compilers known to Spack:
 .. code-block:: console
 
   $ spack compiler add
-  ==> Added 1 new compiler to ~/.spack/linux/compilers.yaml
+  ==> Added 1 new compiler to /home/spack1/.spack/linux/compilers.yaml
       gcc@7.2.0
+  ==> Compilers are defined in the following files:
+      /home/spack1/.spack/linux/compilers.yaml
 
-  $ spack compilers
+  $ spack compiler list
   ==> Available compilers
-  -- gcc ----------------------------------------------------------
-  gcc@7.2.0  gcc@4.8
-
-
-""""""""""""""""""""""""""""""""""""""""""""""""""""
-Build the software that will be used in the tutorial
-""""""""""""""""""""""""""""""""""""""""""""""""""""
-
-The last step is to install the software stack needed later on. To mimic
-an external installation of an MPI provider we'll install ``openmpi`` on
-the system we are working on. On Ubuntu 14.04 it boils down to:
-
-.. code-block:: console
+  -- clang ubuntu16.04-x86_64 -------------------------------------
+  clang@3.8.0-2ubuntu4  clang@3.7.1-2ubuntu2
 
-  $ sudo apt-get install openmpi-bin openmpi-common libopenmpi-dev
-  ...
-
-but the exact command varies according to your OS. Then we need to prepare
-a ``packages.yaml`` file that instructs Spack to use an externally provided MPI:
+  -- gcc ubuntu16.04-x86_64 ---------------------------------------
+  gcc@7.2.0  gcc@5.4.0  gcc@4.7
 
-.. code-block:: yaml
 
-  packages:
-    openmpi:
-      buildable: False
-      paths:
-        openmpi@1.6: /usr
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Build the software that will be used in the tutorial
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Finally, we should use Spack to install the packages used in the examples:
 
@@ -357,19 +276,36 @@ If you arrived to this point you should have an environment that looks similar t
 
 .. code-block:: console
 
-  root@module-file-tutorial:/# module avail
+  $ module avail
+
+  ----------------------------------------------- /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64 -----------------------------------------------
+     autoconf-2.69-gcc-5.4.0-3sx2gxe              libsigsegv-2.11-gcc-7.2.0-g67xpfd            openssl-1.0.2o-gcc-5.4.0-b4y3w3b
+     autoconf-2.69-gcc-7.2.0-yb2makb              libtool-2.4.6-gcc-5.4.0-o2pfwjf              openssl-1.0.2o-gcc-7.2.0-cvldq3v
+     automake-1.16.1-gcc-5.4.0-rymw7im            libtool-2.4.6-gcc-7.2.0-kt2udm6              pcre-8.42-gcc-5.4.0-gt5lgzi
+     automake-1.16.1-gcc-7.2.0-qoowd5q            libxml2-2.9.8-gcc-5.4.0-wpexsph              perl-5.26.2-gcc-5.4.0-ic2kyoa
+     bzip2-1.0.6-gcc-5.4.0-ufczdvs                libxml2-2.9.8-gcc-7.2.0-47gf5kk              perl-5.26.2-gcc-7.2.0-fdwz5yu
+     bzip2-1.0.6-gcc-7.2.0-mwamumj                lmod-7.8-gcc-5.4.0-kmhks3p                   pkgconf-1.4.2-gcc-5.4.0-fovrh7a
+     cmake-3.12.3-gcc-7.2.0-obqgn2v               lua-5.3.4-gcc-5.4.0-cpfeo2w                  pkgconf-1.4.2-gcc-7.2.0-yoxwmgb
+     curl-7.60.0-gcc-5.4.0-vzqreb2                lua-luafilesystem-1_6_3-gcc-5.4.0-alakjim    py-numpy-1.15.2-gcc-7.2.0-wbwtcxf
+     diffutils-3.6-gcc-5.4.0-2rhuivg              lua-luaposix-33.4.0-gcc-5.4.0-7wqhwoc        py-scipy-1.1.0-gcc-7.2.0-d5n3cph
+     diffutils-3.6-gcc-7.2.0-eauxwi7              m4-1.4.18-gcc-5.4.0-suf5jtc                  py-setuptools-40.4.3-gcc-7.2.0-5dbwfwn
+     expat-2.2.5-gcc-5.4.0-emyv67q                m4-1.4.18-gcc-7.2.0-wdzvagl                  python-2.7.15-gcc-7.2.0-ucmr2mn
+     findutils-4.6.0-gcc-7.2.0-ca4b7zq            mpc-1.1.0-gcc-5.4.0-iuf3gc3                  readline-7.0-gcc-5.4.0-nxhwrg7
+     gcc-7.2.0-gcc-5.4.0-b7smjjc           (L)    mpfr-3.1.6-gcc-5.4.0-jnt2nnp                 readline-7.0-gcc-7.2.0-ccruj2i
+     gdbm-1.14.1-gcc-5.4.0-q4fpyuo                mpich-3.2.1-gcc-7.2.0-vt5xcat                sqlite-3.23.1-gcc-7.2.0-5ltus3a
+     gdbm-1.14.1-gcc-7.2.0-zk5lhob                ncurses-6.1-gcc-5.4.0-3o765ou                tar-1.30-gcc-5.4.0-dk7lrpo
+     gettext-0.19.8.1-gcc-5.4.0-tawgous           ncurses-6.1-gcc-7.2.0-xcgzqdv                tcl-8.6.8-gcc-5.4.0-qhwyccy
+     git-2.19.1-gcc-5.4.0-p3gjnfa                 netlib-lapack-3.8.0-gcc-7.2.0-fj7nayd        texinfo-6.5-gcc-7.2.0-cuqnfgf
+     gmp-6.1.2-gcc-5.4.0-qc4qcfz                  netlib-scalapack-2.0.2-gcc-7.2.0-67nmj7g     unzip-6.0-gcc-5.4.0-ba23fbg
+     hwloc-1.11.9-gcc-7.2.0-gbyc65s               netlib-scalapack-2.0.2-gcc-7.2.0-6jgjbyg     util-macros-1.19.1-gcc-7.2.0-t62kozq
+     isl-0.18-gcc-5.4.0-vttqout                   netlib-scalapack-2.0.2-gcc-7.2.0-prgo67d     xz-5.2.4-gcc-5.4.0-teneqii
+     libbsd-0.8.6-gcc-5.4.0-f4qkkwm               netlib-scalapack-2.0.2-gcc-7.2.0-zxpt252     xz-5.2.4-gcc-7.2.0-rql5kog
+     libiconv-1.15-gcc-5.4.0-u2x3umv              numactl-2.0.11-gcc-7.2.0-rifwktk             zlib-1.2.11-gcc-5.4.0-5nus6kn
+     libpciaccess-0.13.5-gcc-7.2.0-riipwi2        openblas-0.3.3-gcc-7.2.0-xxoxfh4             zlib-1.2.11-gcc-7.2.0-ezuwp4p
+     libsigsegv-2.11-gcc-5.4.0-fypapcp            openmpi-3.1.3-gcc-7.2.0-do5xfer
 
-  ----------------------------------------------------------------------------- /usr/local/share/spack/modules/linux-ubuntu16.04-x86_64 -----------------------------------------------------------------------------
-     autoconf-2.69-gcc-5.4.0-bvabhji      libtool-2.4.6-gcc-5.4.0-o2pfwjf              ncurses-6.0-gcc-7.2.0-oh6pqty               pkg-config-0.29.2-gcc-5.4.0-ae2hwm7       readline-7.0-gcc-5.4.0-gizxpch
-     automake-1.15.1-gcc-5.4.0-kaiefe4    lmod-7.7-gcc-5.4.0-okcwjgw                   netlib-lapack-3.6.1-gcc-7.2.0-5sywztc       pkg-config-0.29.2-gcc-7.2.0-76z7ehw       readline-7.0-gcc-7.2.0-eqos6rz
-     bzip2-1.0.6-gcc-7.2.0-mwamumj        lua-5.3.4-gcc-5.4.0-ytxw2gq                  netlib-scalapack-2.0.2-gcc-7.2.0-5lb2j5p    py-appdirs-1.4.3-gcc-7.2.0-7ncu7zr        sqlite-3.20.0-gcc-7.2.0-hfmjilk
-     cmake-3.9.4-gcc-7.2.0-6bxdr6h        lua-luafilesystem-1_6_3-gcc-5.4.0-5dzzlt4    netlib-scalapack-2.0.2-gcc-7.2.0-ax6aza6    py-numpy-1.13.1-gcc-7.2.0-22n5oub         tcl-8.6.6-gcc-5.4.0-767ls4i
-     gcc-7.2.0-gcc-5.4.0-go3z4hb          lua-luaposix-33.4.0-gcc-5.4.0-w5jpnwm        netlib-scalapack-2.0.2-gcc-7.2.0-c4v5l7j    py-packaging-16.8-gcc-7.2.0-c37cjmq       zlib-1.2.11-gcc-5.4.0-swly52a
-     gdbm-1.13-gcc-5.4.0-vdhoris          m4-1.4.18-gcc-5.4.0-r5envx3                  netlib-scalapack-2.0.2-gcc-7.2.0-m7rzcmh    py-pyparsing-2.2.0-gcc-7.2.0-ahdh5cx      zlib-1.2.11-gcc-7.2.0-lv5fabl
-     git-2.9.4-gcc-5.4.0-atwjs4i          mpc-1.0.3-gcc-5.4.0-tumbpsh                  openblas-0.2.20-gcc-7.2.0-kvddide           py-scipy-0.19.1-gcc-7.2.0-7hi7r5j
-     gmp-6.1.2-gcc-5.4.0-qc4qcfz          mpfr-3.1.5-gcc-5.4.0-mdi6irz                 openmpi-1.10.2-gcc-7.2.0-ufw7pdi            py-setuptools-35.0.2-gcc-7.2.0-cvasi7i
-     isl-0.18-gcc-5.4.0-vttqout           mpich-3.2-gcc-7.2.0-7gxffhv                  openssl-1.0.2k-gcc-7.2.0-pxv3dh4            py-six-1.10.0-gcc-7.2.0-3xk5mod
-     libsigsegv-2.11-gcc-5.4.0-fypapcp    ncurses-6.0-gcc-5.4.0-ukq4tcc                perl-5.24.1-gcc-5.4.0-mfzwy6y               python-2.7.14-gcc-7.2.0-555u7ea
+    Where:
+     L:  Module is loaded
 
   Use "module spider" to find all possible modules.
   Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".
@@ -380,19 +316,24 @@ Taking a look at the ``gcc`` module you'll see, for example:
 
 .. code-block:: console
 
-  root@module-file-tutorial:/# module show gcc-7.2.0-gcc-5.4.0-go3z4hb
-  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
-     /usr/local/share/spack/modules/linux-ubuntu16.04-x86_64/gcc-7.2.0-gcc-5.4.0-go3z4hb:
-  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+  $ module show gcc-7.2.0-gcc-5.4.0-b7smjjc
+  -------------------------------------------------------------------------------------------------------------------------------------------------------------------
+     /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64/gcc-7.2.0-gcc-5.4.0-b7smjjc:
+  -------------------------------------------------------------------------------------------------------------------------------------------------------------------
   whatis("The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Ada, and Go, as well as libraries for these languages. ")
-  prepend_path("PATH","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/bin")
-  prepend_path("MANPATH","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/share/man")
-  prepend_path("LIBRARY_PATH","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/lib")
-  prepend_path("LD_LIBRARY_PATH","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/lib")
-  prepend_path("LIBRARY_PATH","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/lib64")
-  prepend_path("LD_LIBRARY_PATH","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/lib64")
-  prepend_path("CPATH","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/include")
-  prepend_path("CMAKE_PREFIX_PATH","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/")
+  prepend_path("PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin")
+  prepend_path("MANPATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/share/man")
+  prepend_path("LD_LIBRARY_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/lib")
+  prepend_path("LIBRARY_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/lib")
+  prepend_path("LD_LIBRARY_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/lib64")
+  prepend_path("LIBRARY_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/lib64")
+  prepend_path("CPATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/include")
+  prepend_path("CMAKE_PREFIX_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/")
+  setenv("CC","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gcc")
+  setenv("CXX","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/g++")
+  setenv("FC","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran")
+  setenv("F77","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran")
+  setenv("F90","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran")
   help([[The GNU Compiler Collection includes front ends for C, C++, Objective-C,
   Fortran, Ada, and Go, as well as libraries for these languages.
   ]])
@@ -422,19 +363,26 @@ Next you should regenerate all the module files:
 
 .. code-block:: console
 
-  root@module-file-tutorial:/# spack module refresh --module-type tcl
+  $ spack module tcl refresh
   ==> You are about to regenerate tcl module files for:
 
   -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
-  bvabhji autoconf@2.69    vdhoris gdbm@1.13  vttqout isl@0.18         okcwjgw lmod@7.7                 w5jpnwm lua-luaposix@33.4.0  mdi6irz mpfr@3.1.5   ae2hwm7 pkg-config@0.29.2  swly52a zlib@1.2.11
-  kaiefe4 automake@1.15.1  atwjs4i git@2.9.4  fypapcp libsigsegv@2.11  ytxw2gq lua@5.3.4                r5envx3 m4@1.4.18            ukq4tcc ncurses@6.0  gizxpch readline@7.0
-  go3z4hb gcc@7.2.0        qc4qcfz gmp@6.1.2  o2pfwjf libtool@2.4.6    5dzzlt4 lua-luafilesystem@1_6_3  tumbpsh mpc@1.0.3            mfzwy6y perl@5.24.1  767ls4i tcl@8.6.6
+  3sx2gxe autoconf@2.69    b7smjjc gcc@7.2.0         f4qkkwm libbsd@0.8.6     cpfeo2w lua@5.3.4                3o765ou ncurses@6.1     dk7lrpo tar@1.30
+  rymw7im automake@1.16.1  q4fpyuo gdbm@1.14.1       u2x3umv libiconv@1.15    alakjim lua-luafilesystem@1_6_3  b4y3w3b openssl@1.0.2o  qhwyccy tcl@8.6.8
+  ufczdvs bzip2@1.0.6      tawgous gettext@0.19.8.1  fypapcp libsigsegv@2.11  7wqhwoc lua-luaposix@33.4.0      gt5lgzi pcre@8.42       ba23fbg unzip@6.0
+  vzqreb2 curl@7.60.0      p3gjnfa git@2.19.1        o2pfwjf libtool@2.4.6    suf5jtc m4@1.4.18                ic2kyoa perl@5.26.2     teneqii xz@5.2.4
+  2rhuivg diffutils@3.6    qc4qcfz gmp@6.1.2         wpexsph libxml2@2.9.8    iuf3gc3 mpc@1.1.0                fovrh7a pkgconf@1.4.2   5nus6kn zlib@1.2.11
+  emyv67q expat@2.2.5      vttqout isl@0.18          kmhks3p lmod@7.8         jnt2nnp mpfr@3.1.6               nxhwrg7 readline@7.0
 
   -- linux-ubuntu16.04-x86_64 / gcc@7.2.0 -------------------------
-  mwamumj bzip2@1.0.6  5sywztc netlib-lapack@3.6.1     m7rzcmh netlib-scalapack@2.0.2  76z7ehw pkg-config@0.29.2  ahdh5cx py-pyparsing@2.2.0    555u7ea python@2.7.14
-  6bxdr6h cmake@3.9.4  ax6aza6 netlib-scalapack@2.0.2  kvddide openblas@0.2.20         7ncu7zr py-appdirs@1.4.3   7hi7r5j py-scipy@0.19.1       eqos6rz readline@7.0
-  7gxffhv mpich@3.2    c4v5l7j netlib-scalapack@2.0.2  ufw7pdi openmpi@1.10.2          22n5oub py-numpy@1.13.1    cvasi7i py-setuptools@35.0.2  hfmjilk sqlite@3.20.0
-  oh6pqty ncurses@6.0  5lb2j5p netlib-scalapack@2.0.2  pxv3dh4 openssl@1.0.2k          c37cjmq py-packaging@16.8  3xk5mod py-six@1.10.0         lv5fabl zlib@1.2.11
+  yb2makb autoconf@2.69    riipwi2 libpciaccess@0.13.5  6jgjbyg netlib-scalapack@2.0.2  fdwz5yu perl@5.26.2           cuqnfgf texinfo@6.5
+  qoowd5q automake@1.16.1  g67xpfd libsigsegv@2.11      zxpt252 netlib-scalapack@2.0.2  yoxwmgb pkgconf@1.4.2         t62kozq util-macros@1.19.1
+  mwamumj bzip2@1.0.6      kt2udm6 libtool@2.4.6        67nmj7g netlib-scalapack@2.0.2  wbwtcxf py-numpy@1.15.2       rql5kog xz@5.2.4
+  obqgn2v cmake@3.12.3     47gf5kk libxml2@2.9.8        prgo67d netlib-scalapack@2.0.2  d5n3cph py-scipy@1.1.0        ezuwp4p zlib@1.2.11
+  eauxwi7 diffutils@3.6    wdzvagl m4@1.4.18            rifwktk numactl@2.0.11          5dbwfwn py-setuptools@40.4.3
+  ca4b7zq findutils@4.6.0  vt5xcat mpich@3.2.1          xxoxfh4 openblas@0.3.3          ucmr2mn python@2.7.15
+  zk5lhob gdbm@1.14.1      xcgzqdv ncurses@6.1          do5xfer openmpi@3.1.3           ccruj2i readline@7.0
+  gbyc65s hwloc@1.11.9     fj7nayd netlib-lapack@3.8.0  cvldq3v openssl@1.0.2o          5ltus3a sqlite@3.23.1
 
   ==> Do you want to proceed? [y/n] y
   ==> Regenerating tcl module files
@@ -444,16 +392,21 @@ paths have disappeared:
 
 .. code-block:: console
 
-  root@module-file-tutorial:/# module show gcc-7.2.0-gcc-5.4.0-go3z4hb
-  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
-     /usr/local/share/spack/modules/linux-ubuntu16.04-x86_64/gcc-7.2.0-gcc-5.4.0-go3z4hb:
-  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+  $ module show gcc-7.2.0-gcc-5.4.0-b7smjjc
+  -------------------------------------------------------------------------------------------------------------------------------------------------------------------
+     /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64/gcc-7.2.0-gcc-5.4.0-b7smjjc:
+  -------------------------------------------------------------------------------------------------------------------------------------------------------------------
   whatis("The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Ada, and Go, as well as libraries for these languages. ")
-  prepend_path("PATH","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/bin")
-  prepend_path("MANPATH","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/share/man")
-  prepend_path("LD_LIBRARY_PATH","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/lib")
-  prepend_path("LD_LIBRARY_PATH","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/lib64")
-  prepend_path("CMAKE_PREFIX_PATH","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/")
+  prepend_path("PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin")
+  prepend_path("MANPATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/share/man")
+  prepend_path("LD_LIBRARY_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/lib")
+  prepend_path("LD_LIBRARY_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/lib64")
+  prepend_path("CMAKE_PREFIX_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/")
+  setenv("CC","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gcc")
+  setenv("CXX","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/g++")
+  setenv("FC","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran")
+  setenv("F77","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran")
+  setenv("F90","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran")
   help([[The GNU Compiler Collection includes front ends for C, C++, Objective-C,
   Fortran, Ada, and Go, as well as libraries for these languages.
   ]])
@@ -482,41 +435,55 @@ To do this you should add a ``blacklist`` keyword to ``~/.spack/modules.yaml``:
 
 and regenerate the module files:
 
+This time it is convenient to pass the option ``--delete-tree`` to the command that
+regenerates the module files to instruct it to delete the existing tree and regenerate
+a new one instead of overwriting the files in the existing directory.
+
 .. code-block:: console
 
-  root@module-file-tutorial:/# spack module refresh --module-type tcl --delete-tree
+  $ spack module tcl refresh --delete-tree
   ==> You are about to regenerate tcl module files for:
 
   -- linux-ubuntu16.04-x86_64 / gcc@5.4.0 -------------------------
-  bvabhji autoconf@2.69    vdhoris gdbm@1.13  vttqout isl@0.18         okcwjgw lmod@7.7                 w5jpnwm lua-luaposix@33.4.0  mdi6irz mpfr@3.1.5   ae2hwm7 pkg-config@0.29.2  swly52a zlib@1.2.11
-  kaiefe4 automake@1.15.1  atwjs4i git@2.9.4  fypapcp libsigsegv@2.11  ytxw2gq lua@5.3.4                r5envx3 m4@1.4.18            ukq4tcc ncurses@6.0  gizxpch readline@7.0
-  go3z4hb gcc@7.2.0        qc4qcfz gmp@6.1.2  o2pfwjf libtool@2.4.6    5dzzlt4 lua-luafilesystem@1_6_3  tumbpsh mpc@1.0.3            mfzwy6y perl@5.24.1  767ls4i tcl@8.6.6
+  3sx2gxe autoconf@2.69    b7smjjc gcc@7.2.0         f4qkkwm libbsd@0.8.6     cpfeo2w lua@5.3.4                3o765ou ncurses@6.1     dk7lrpo tar@1.30
+  rymw7im automake@1.16.1  q4fpyuo gdbm@1.14.1       u2x3umv libiconv@1.15    alakjim lua-luafilesystem@1_6_3  b4y3w3b openssl@1.0.2o  qhwyccy tcl@8.6.8
+  ufczdvs bzip2@1.0.6      tawgous gettext@0.19.8.1  fypapcp libsigsegv@2.11  7wqhwoc lua-luaposix@33.4.0      gt5lgzi pcre@8.42       ba23fbg unzip@6.0
+  vzqreb2 curl@7.60.0      p3gjnfa git@2.19.1        o2pfwjf libtool@2.4.6    suf5jtc m4@1.4.18                ic2kyoa perl@5.26.2     teneqii xz@5.2.4
+  2rhuivg diffutils@3.6    qc4qcfz gmp@6.1.2         wpexsph libxml2@2.9.8    iuf3gc3 mpc@1.1.0                fovrh7a pkgconf@1.4.2   5nus6kn zlib@1.2.11
+  emyv67q expat@2.2.5      vttqout isl@0.18          kmhks3p lmod@7.8         jnt2nnp mpfr@3.1.6               nxhwrg7 readline@7.0
 
   -- linux-ubuntu16.04-x86_64 / gcc@7.2.0 -------------------------
-  mwamumj bzip2@1.0.6  5sywztc netlib-lapack@3.6.1     m7rzcmh netlib-scalapack@2.0.2  76z7ehw pkg-config@0.29.2  ahdh5cx py-pyparsing@2.2.0    555u7ea python@2.7.14
-  6bxdr6h cmake@3.9.4  ax6aza6 netlib-scalapack@2.0.2  kvddide openblas@0.2.20         7ncu7zr py-appdirs@1.4.3   7hi7r5j py-scipy@0.19.1       eqos6rz readline@7.0
-  7gxffhv mpich@3.2    c4v5l7j netlib-scalapack@2.0.2  ufw7pdi openmpi@1.10.2          22n5oub py-numpy@1.13.1    cvasi7i py-setuptools@35.0.2  hfmjilk sqlite@3.20.0
-  oh6pqty ncurses@6.0  5lb2j5p netlib-scalapack@2.0.2  pxv3dh4 openssl@1.0.2k          c37cjmq py-packaging@16.8  3xk5mod py-six@1.10.0         lv5fabl zlib@1.2.11
+  yb2makb autoconf@2.69    riipwi2 libpciaccess@0.13.5  6jgjbyg netlib-scalapack@2.0.2  fdwz5yu perl@5.26.2           cuqnfgf texinfo@6.5
+  qoowd5q automake@1.16.1  g67xpfd libsigsegv@2.11      zxpt252 netlib-scalapack@2.0.2  yoxwmgb pkgconf@1.4.2         t62kozq util-macros@1.19.1
+  mwamumj bzip2@1.0.6      kt2udm6 libtool@2.4.6        67nmj7g netlib-scalapack@2.0.2  wbwtcxf py-numpy@1.15.2       rql5kog xz@5.2.4
+  obqgn2v cmake@3.12.3     47gf5kk libxml2@2.9.8        prgo67d netlib-scalapack@2.0.2  d5n3cph py-scipy@1.1.0        ezuwp4p zlib@1.2.11
+  eauxwi7 diffutils@3.6    wdzvagl m4@1.4.18            rifwktk numactl@2.0.11          5dbwfwn py-setuptools@40.4.3
+  ca4b7zq findutils@4.6.0  vt5xcat mpich@3.2.1          xxoxfh4 openblas@0.3.3          ucmr2mn python@2.7.15
+  zk5lhob gdbm@1.14.1      xcgzqdv ncurses@6.1          do5xfer openmpi@3.1.3           ccruj2i readline@7.0
+  gbyc65s hwloc@1.11.9     fj7nayd netlib-lapack@3.8.0  cvldq3v openssl@1.0.2o          5ltus3a sqlite@3.23.1
 
   ==> Do you want to proceed? [y/n] y
   ==> Regenerating tcl module files
 
-  root@module-file-tutorial:/# module avail
-
-  ----------------------------------------------------------------------------- /usr/local/share/spack/modules/linux-ubuntu16.04-x86_64 -----------------------------------------------------------------------------
-     bzip2-1.0.6-gcc-7.2.0-mwamumj            netlib-scalapack-2.0.2-gcc-7.2.0-5lb2j5p    openmpi-1.10.2-gcc-7.2.0-ufw7pdi       py-packaging-16.8-gcc-7.2.0-c37cjmq       python-2.7.14-gcc-7.2.0-555u7ea
-     cmake-3.9.4-gcc-7.2.0-6bxdr6h            netlib-scalapack-2.0.2-gcc-7.2.0-ax6aza6    openssl-1.0.2k-gcc-7.2.0-pxv3dh4       py-pyparsing-2.2.0-gcc-7.2.0-ahdh5cx      readline-7.0-gcc-7.2.0-eqos6rz
-     mpich-3.2-gcc-7.2.0-7gxffhv              netlib-scalapack-2.0.2-gcc-7.2.0-c4v5l7j    pkg-config-0.29.2-gcc-7.2.0-76z7ehw    py-scipy-0.19.1-gcc-7.2.0-7hi7r5j         sqlite-3.20.0-gcc-7.2.0-hfmjilk
-     ncurses-6.0-gcc-7.2.0-oh6pqty            netlib-scalapack-2.0.2-gcc-7.2.0-m7rzcmh    py-appdirs-1.4.3-gcc-7.2.0-7ncu7zr     py-setuptools-35.0.2-gcc-7.2.0-cvasi7i    zlib-1.2.11-gcc-7.2.0-lv5fabl
-     netlib-lapack-3.6.1-gcc-7.2.0-5sywztc    openblas-0.2.20-gcc-7.2.0-kvddide           py-numpy-1.13.1-gcc-7.2.0-22n5oub      py-six-1.10.0-gcc-7.2.0-3xk5mod
+  $ module avail
+
+  ----------------------------------------------- /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64 -----------------------------------------------
+     autoconf-2.69-gcc-7.2.0-yb2makb          m4-1.4.18-gcc-7.2.0-wdzvagl                 perl-5.26.2-gcc-7.2.0-fdwz5yu
+     automake-1.16.1-gcc-7.2.0-qoowd5q        mpich-3.2.1-gcc-7.2.0-vt5xcat               pkgconf-1.4.2-gcc-7.2.0-yoxwmgb
+     bzip2-1.0.6-gcc-7.2.0-mwamumj            ncurses-6.1-gcc-7.2.0-xcgzqdv               py-numpy-1.15.2-gcc-7.2.0-wbwtcxf
+     cmake-3.12.3-gcc-7.2.0-obqgn2v           netlib-lapack-3.8.0-gcc-7.2.0-fj7nayd       py-scipy-1.1.0-gcc-7.2.0-d5n3cph
+     diffutils-3.6-gcc-7.2.0-eauxwi7          netlib-scalapack-2.0.2-gcc-7.2.0-67nmj7g    py-setuptools-40.4.3-gcc-7.2.0-5dbwfwn
+     findutils-4.6.0-gcc-7.2.0-ca4b7zq        netlib-scalapack-2.0.2-gcc-7.2.0-6jgjbyg    python-2.7.15-gcc-7.2.0-ucmr2mn
+     gdbm-1.14.1-gcc-7.2.0-zk5lhob            netlib-scalapack-2.0.2-gcc-7.2.0-prgo67d    readline-7.0-gcc-7.2.0-ccruj2i
+     hwloc-1.11.9-gcc-7.2.0-gbyc65s           netlib-scalapack-2.0.2-gcc-7.2.0-zxpt252    sqlite-3.23.1-gcc-7.2.0-5ltus3a
+     libpciaccess-0.13.5-gcc-7.2.0-riipwi2    numactl-2.0.11-gcc-7.2.0-rifwktk            texinfo-6.5-gcc-7.2.0-cuqnfgf
+     libsigsegv-2.11-gcc-7.2.0-g67xpfd        openblas-0.3.3-gcc-7.2.0-xxoxfh4            util-macros-1.19.1-gcc-7.2.0-t62kozq
+     libtool-2.4.6-gcc-7.2.0-kt2udm6          openmpi-3.1.3-gcc-7.2.0-do5xfer             xz-5.2.4-gcc-7.2.0-rql5kog
+     libxml2-2.9.8-gcc-7.2.0-47gf5kk          openssl-1.0.2o-gcc-7.2.0-cvldq3v            zlib-1.2.11-gcc-7.2.0-ezuwp4p
 
   Use "module spider" to find all possible modules.
   Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".
 
-This time it is convenient to pass the option ``--delete-tree`` to the command that
-regenerates the module files to instruct it to delete the existing tree and regenerate
-a new one instead of overwriting the files in the existing directory.
-
 If you look closely you'll see though that we went too far in blacklisting modules:
 the module for ``gcc@7.2.0`` disappeared as it was bootstrapped with ``gcc@5.4.0``. To specify
 exceptions to the blacklist rules you can use ``whitelist``:
@@ -538,7 +505,7 @@ exceptions to the blacklist rules you can use ``whitelist``:
 
 .. code-block:: console
 
-  root@module-file-tutorial:/# spack module refresh --module-type tcl -y
+  $ spack module tcl refresh -y
   ==> Regenerating tcl module files
 
 
@@ -546,14 +513,33 @@ you'll see that now the module for ``gcc@7.2.0`` has reappeared:
 
 .. code-block:: console
 
-  root@module-file-tutorial:/# module avail gcc-7.2.0-gcc-5.4.0-go3z4hb
+  $ module avail gcc-7.2.0-gcc-5.4.0-b7smjjc
 
-  ----------------------------------------------------------------------------- /usr/local/share/spack/modules/linux-ubuntu16.04-x86_64 -----------------------------------------------------------------------------
-     gcc-7.2.0-gcc-5.4.0-go3z4hb
+  -------------------------------------------- /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64 ---------------------------------------------
+     gcc-7.2.0-gcc-5.4.0-b7smjjc
 
   Use "module spider" to find all possible modules.
   Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".
 
+An additional possibility that you can leverage to unclutter the environment
+is that of preventing the generation of module files for implicitly installed
+packages. In this case all one needs to do is to add the following line:
+
+.. code-block:: yaml
+  :emphasize-lines: 3
+
+  modules:
+    tcl:
+      blacklist_implicits: true
+      whitelist:
+        -  gcc
+      blacklist:
+        -  '%gcc@5.4.0'
+      all:
+        filter:
+          environment_blacklist: ['CPATH', 'LIBRARY_PATH']
+
+to ``modules.yaml`` and regenerate the module file tree as above.
 
 ^^^^^^^^^^^^^^^^^^^^^^^^^
 Change module file naming
@@ -564,8 +550,6 @@ improve their naming scheme.
 To reduce the length of the hash or remove it altogether you can
 use the ``hash_length`` keyword in the configuration file:
 
-.. TODO: give reasons to remove hashes if they are not evident enough?
-
 .. code-block:: yaml
   :emphasize-lines: 3
 
@@ -584,10 +568,10 @@ If you try to regenerate the module files now you will get an error:
 
 .. code-block:: console
 
-  root@module-file-tutorial:/# spack module refresh --module-type tcl --delete-tree -y
+  $ spack module tcl refresh --delete-tree -y
   ==> Error: Name clashes detected in module files:
 
-  file: /usr/local/share/spack/modules/linux-ubuntu16.04-x86_64/netlib-scalapack-2.0.2-gcc-7.2.0
+  file: /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64/netlib-scalapack-2.0.2-gcc-7.2.0
   spec: netlib-scalapack@2.0.2%gcc@7.2.0 build_type=RelWithDebInfo ~pic+shared arch=linux-ubuntu16.04-x86_64
   spec: netlib-scalapack@2.0.2%gcc@7.2.0 build_type=RelWithDebInfo ~pic+shared arch=linux-ubuntu16.04-x86_64
   spec: netlib-scalapack@2.0.2%gcc@7.2.0 build_type=RelWithDebInfo ~pic+shared arch=linux-ubuntu16.04-x86_64
@@ -631,17 +615,24 @@ Regenerating module files now we obtain:
 
 .. code-block:: console
 
-  root@module-file-tutorial:/# spack module refresh --module-type tcl --delete-tree -y
+  $ spack module tcl refresh --delete-tree -y
   ==> Regenerating tcl module files
-
-  root@module-file-tutorial:/# module avail
-
-  ----------------------------------------------------------------------------- /usr/local/share/spack/modules/linux-ubuntu16.04-x86_64 -----------------------------------------------------------------------------
-     bzip2-1.0.6-gcc-7.2.0    netlib-lapack-3.6.1-gcc-7.2.0                        openblas-0.2.20-gcc-7.2.0      py-numpy-1.13.1-gcc-7.2.0-openblas    py-six-1.10.0-gcc-7.2.0
-     cmake-3.9.4-gcc-7.2.0    netlib-scalapack-2.0.2-gcc-7.2.0-netlib-mpich        openmpi-1.10.2-gcc-7.2.0       py-packaging-16.8-gcc-7.2.0           python-2.7.14-gcc-7.2.0
-     gcc-7.2.0-gcc-5.4.0      netlib-scalapack-2.0.2-gcc-7.2.0-netlib-openmpi      openssl-1.0.2k-gcc-7.2.0       py-pyparsing-2.2.0-gcc-7.2.0          readline-7.0-gcc-7.2.0
-     mpich-3.2-gcc-7.2.0      netlib-scalapack-2.0.2-gcc-7.2.0-openblas-mpich      pkg-config-0.29.2-gcc-7.2.0    py-scipy-0.19.1-gcc-7.2.0-openblas    sqlite-3.20.0-gcc-7.2.0
-     ncurses-6.0-gcc-7.2.0    netlib-scalapack-2.0.2-gcc-7.2.0-openblas-openmpi    py-appdirs-1.4.3-gcc-7.2.0     py-setuptools-35.0.2-gcc-7.2.0        zlib-1.2.11-gcc-7.2.0
+  $ module avail
+
+  ----------------------------------------------- /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64 -----------------------------------------------
+     autoconf-2.69-gcc-7.2.0          m4-1.4.18-gcc-7.2.0                                  pkgconf-1.4.2-gcc-7.2.0
+     automake-1.16.1-gcc-7.2.0        mpich-3.2.1-gcc-7.2.0                                py-numpy-1.15.2-gcc-7.2.0-openblas
+     bzip2-1.0.6-gcc-7.2.0            ncurses-6.1-gcc-7.2.0                                py-scipy-1.1.0-gcc-7.2.0-openblas
+     cmake-3.12.3-gcc-7.2.0           netlib-lapack-3.8.0-gcc-7.2.0                        py-setuptools-40.4.3-gcc-7.2.0
+     diffutils-3.6-gcc-7.2.0          netlib-scalapack-2.0.2-gcc-7.2.0-netlib-mpich        python-2.7.15-gcc-7.2.0
+     findutils-4.6.0-gcc-7.2.0        netlib-scalapack-2.0.2-gcc-7.2.0-netlib-openmpi      readline-7.0-gcc-7.2.0
+     gcc-7.2.0-gcc-5.4.0              netlib-scalapack-2.0.2-gcc-7.2.0-openblas-mpich      sqlite-3.23.1-gcc-7.2.0
+     gdbm-1.14.1-gcc-7.2.0            netlib-scalapack-2.0.2-gcc-7.2.0-openblas-openmpi    texinfo-6.5-gcc-7.2.0
+     hwloc-1.11.9-gcc-7.2.0           numactl-2.0.11-gcc-7.2.0                             util-macros-1.19.1-gcc-7.2.0
+     libpciaccess-0.13.5-gcc-7.2.0    openblas-0.3.3-gcc-7.2.0                             xz-5.2.4-gcc-7.2.0
+     libsigsegv-2.11-gcc-7.2.0        openmpi-3.1.3-gcc-7.2.0                              zlib-1.2.11-gcc-7.2.0
+     libtool-2.4.6-gcc-7.2.0          openssl-1.0.2o-gcc-7.2.0
+     libxml2-2.9.8-gcc-7.2.0          perl-5.26.2-gcc-7.2.0
 
   Use "module spider" to find all possible modules.
   Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".
@@ -677,16 +668,24 @@ The final result should look like:
 
 .. code-block:: console
 
-  root@module-file-tutorial:/# spack module refresh --module-type tcl --delete-tree -y
+  $ spack module tcl refresh --delete-tree -y
   ==> Regenerating tcl module files
-  root@module-file-tutorial:/# module avail
-
-  ----------------------------------------------------------------------------- /usr/local/share/spack/modules/linux-ubuntu16.04-x86_64 -----------------------------------------------------------------------------
-     bzip2/1.0.6-gcc-7.2.0    netlib-lapack/3.6.1-gcc-7.2.0                            openblas/0.2.20-gcc-7.2.0      py-numpy/1.13.1-gcc-7.2.0-openblas    py-six/1.10.0-gcc-7.2.0
-     cmake/3.9.4-gcc-7.2.0    netlib-scalapack/2.0.2-gcc-7.2.0-netlib-mpich            openmpi/1.10.2-gcc-7.2.0       py-packaging/16.8-gcc-7.2.0           python/2.7.14-gcc-7.2.0
-     gcc/7.2.0-gcc-5.4.0      netlib-scalapack/2.0.2-gcc-7.2.0-netlib-openmpi          openssl/1.0.2k-gcc-7.2.0       py-pyparsing/2.2.0-gcc-7.2.0          readline/7.0-gcc-7.2.0
-     mpich/3.2-gcc-7.2.0      netlib-scalapack/2.0.2-gcc-7.2.0-openblas-mpich          pkg-config/0.29.2-gcc-7.2.0    py-scipy/0.19.1-gcc-7.2.0-openblas    sqlite/3.20.0-gcc-7.2.0
-     ncurses/6.0-gcc-7.2.0    netlib-scalapack/2.0.2-gcc-7.2.0-openblas-openmpi (D)    py-appdirs/1.4.3-gcc-7.2.0     py-setuptools/35.0.2-gcc-7.2.0        zlib/1.2.11-gcc-7.2.0
+  $ module avail
+
+  ----------------------------------------------- /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64 -----------------------------------------------
+     autoconf/2.69-gcc-7.2.0          m4/1.4.18-gcc-7.2.0                                      pkgconf/1.4.2-gcc-7.2.0
+     automake/1.16.1-gcc-7.2.0        mpich/3.2.1-gcc-7.2.0                                    py-numpy/1.15.2-gcc-7.2.0-openblas
+     bzip2/1.0.6-gcc-7.2.0            ncurses/6.1-gcc-7.2.0                                    py-scipy/1.1.0-gcc-7.2.0-openblas
+     cmake/3.12.3-gcc-7.2.0           netlib-lapack/3.8.0-gcc-7.2.0                            py-setuptools/40.4.3-gcc-7.2.0
+     diffutils/3.6-gcc-7.2.0          netlib-scalapack/2.0.2-gcc-7.2.0-netlib-mpich            python/2.7.15-gcc-7.2.0
+     findutils/4.6.0-gcc-7.2.0        netlib-scalapack/2.0.2-gcc-7.2.0-netlib-openmpi          readline/7.0-gcc-7.2.0
+     gcc/7.2.0-gcc-5.4.0              netlib-scalapack/2.0.2-gcc-7.2.0-openblas-mpich          sqlite/3.23.1-gcc-7.2.0
+     gdbm/1.14.1-gcc-7.2.0            netlib-scalapack/2.0.2-gcc-7.2.0-openblas-openmpi (D)    texinfo/6.5-gcc-7.2.0
+     hwloc/1.11.9-gcc-7.2.0           numactl/2.0.11-gcc-7.2.0                                 util-macros/1.19.1-gcc-7.2.0
+     libpciaccess/0.13.5-gcc-7.2.0    openblas/0.3.3-gcc-7.2.0                                 xz/5.2.4-gcc-7.2.0
+     libsigsegv/2.11-gcc-7.2.0        openmpi/3.1.3-gcc-7.2.0                                  zlib/1.2.11-gcc-7.2.0
+     libtool/2.4.6-gcc-7.2.0          openssl/1.0.2o-gcc-7.2.0
+     libxml2/2.9.8-gcc-7.2.0          perl/5.26.2-gcc-7.2.0
 
     Where:
      D:  Default Module
@@ -748,21 +747,26 @@ Regenerating the module files results in something like:
 .. code-block:: console
   :emphasize-lines: 15
 
-  root@module-file-tutorial:/# spack module refresh -y --module-type tcl
+  $ spack module tcl refresh -y
   ==> Regenerating tcl module files
 
-  root@module-file-tutorial:/# module show gcc
-  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
-     /usr/local/share/spack/modules/linux-ubuntu16.04-x86_64/gcc/7.2.0-gcc-5.4.0:
-  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+  $ module show gcc
+  -------------------------------------------------------------------------------------------------------------------------------------------------------------------
+     /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64/gcc/7.2.0-gcc-5.4.0:
+  -------------------------------------------------------------------------------------------------------------------------------------------------------------------
   whatis("The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Ada, and Go, as well as libraries for these languages. ")
   conflict("gcc")
-  prepend_path("PATH","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/bin")
-  prepend_path("MANPATH","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/share/man")
-  prepend_path("LD_LIBRARY_PATH","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/lib")
-  prepend_path("LD_LIBRARY_PATH","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/lib64")
-  prepend_path("CMAKE_PREFIX_PATH","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/")
-  setenv("GCC_ROOT","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd")
+  prepend_path("PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin")
+  prepend_path("MANPATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/share/man")
+  prepend_path("LD_LIBRARY_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/lib")
+  prepend_path("LD_LIBRARY_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/lib64")
+  prepend_path("CMAKE_PREFIX_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/")
+  setenv("CC","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gcc")
+  setenv("CXX","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/g++")
+  setenv("FC","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran")
+  setenv("F77","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran")
+  setenv("F90","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran")
+  setenv("GCC_ROOT","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs")
   help([[The GNU Compiler Collection includes front ends for C, C++, Objective-C,
   Fortran, Ada, and Go, as well as libraries for these languages.
   ]])
@@ -819,54 +823,60 @@ This time we will be more selective and regenerate only the ``gcc`` and
 
 .. code-block:: console
 
-  root@module-file-tutorial:/#  spack module refresh -y --module-type tcl gcc
+  $ spack module tcl refresh -y gcc
   ==> Regenerating tcl module files
 
-  root@module-file-tutorial:/# spack module refresh -y --module-type tcl openmpi
+  $ spack module tcl refresh -y openmpi
   ==> Regenerating tcl module files
 
-  root@module-file-tutorial:/# module show gcc
-  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
-     /usr/local/share/spack/modules/linux-ubuntu16.04-x86_64/gcc/7.2.0-gcc-5.4.0:
-  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+  $ module show gcc
+  -------------------------------------------------------------------------------------------------------------------------------------------------------------------
+     /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64/gcc/7.2.0-gcc-5.4.0:
+  -------------------------------------------------------------------------------------------------------------------------------------------------------------------
   whatis("The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Ada, and Go, as well as libraries for these languages. ")
   conflict("gcc")
-  prepend_path("PATH","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/bin")
-  prepend_path("MANPATH","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/share/man")
-  prepend_path("LD_LIBRARY_PATH","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/lib")
-  prepend_path("LD_LIBRARY_PATH","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/lib64")
-  prepend_path("CMAKE_PREFIX_PATH","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd/")
-  setenv("GCC_ROOT","/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-go3z4hbsa6wycoaedr3fforx5qnazdhd")
+  prepend_path("PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin")
+  prepend_path("MANPATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/share/man")
+  prepend_path("LD_LIBRARY_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/lib")
+  prepend_path("LD_LIBRARY_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/lib64")
+  prepend_path("CMAKE_PREFIX_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/")
+  setenv("CC","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gcc")
+  setenv("CXX","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/g++")
+  setenv("FC","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran")
+  setenv("F77","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran")
+  setenv("F90","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs/bin/gfortran")
+  setenv("GCC_ROOT","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/gcc-7.2.0-b7smjjcsmwe5u5fcsvjmonlhlzzctnfs")
   setenv("CC","gcc")
-  setenv("CXX","g++")
+  setenv("CXX","g++'")
   setenv("FC","gfortran")
-  setenv("F90","gfortran")
   setenv("F77","gfortran")
+  setenv("F90","gfortran")
   help([[The GNU Compiler Collection includes front ends for C, C++, Objective-C,
   Fortran, Ada, and Go, as well as libraries for these languages.
   ]])
 
-  root@module-file-tutorial:/# module show openmpi
-  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
-     /usr/local/share/spack/modules/linux-ubuntu16.04-x86_64/openmpi/1.10.2-gcc-7.2.0:
-  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
-  whatis("The Open MPI Project is an open source Message Passing Interface implementation that is developed and maintained by a consortium of academic, research, and industry partners. Open MPI is therefore able t
-  o combine the expertise, technologies, and resources from all across the High Performance Computing community in order to build the best MPI library available. Open MPI offers advantages for system and software
-  vendors, application developers and computer science researchers.  ")
+  $ module show openmpi
+  -------------------------------------------------------------------------------------------------------------------------------------------------------------------
+    /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64/openmpi/3.1.3-gcc-7.2.0:
+  -------------------------------------------------------------------------------------------------------------------------------------------------------------------
+  whatis("An open source Message Passing Interface implementation. ")
   conflict("openmpi")
-  prepend_path("MANPATH","/usr/share/man")
-  prepend_path("ACLOCAL_PATH","/usr/share/aclocal")
-  prepend_path("PKG_CONFIG_PATH","/usr/lib/pkgconfig")
-  setenv("OPENMPI_ROOT","/usr")
+  prepend_path("PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/openmpi-3.1.3-do5xfer2whhk7gc26atgs3ozr3ljbvs4/bin")
+  prepend_path("MANPATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/openmpi-3.1.3-do5xfer2whhk7gc26atgs3ozr3ljbvs4/share/man")
+  prepend_path("LD_LIBRARY_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/openmpi-3.1.3-do5xfer2whhk7gc26atgs3ozr3ljbvs4/lib")
+  prepend_path("PKG_CONFIG_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/openmpi-3.1.3-do5xfer2whhk7gc26atgs3ozr3ljbvs4/lib/pkgconfig")
+  prepend_path("CMAKE_PREFIX_PATH","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/openmpi-3.1.3-do5xfer2whhk7gc26atgs3ozr3ljbvs4/")
+  setenv("OPENMPI_ROOT","/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/openmpi-3.1.3-do5xfer2whhk7gc26atgs3ozr3ljbvs4")
   setenv("SLURM_MPI_TYPE","pmi2")
   setenv("OMPI_MCA_btl_openib_warn_default_gid_prefix","0")
-  help([[The Open MPI Project is an open source Message Passing Interface
-  implementation that is developed and maintained by a consortium of
-  academic, research, and industry partners. Open MPI is therefore able to
-  combine the expertise, technologies, and resources from all across the
-  High Performance Computing community in order to build the best MPI
-  library available. Open MPI offers advantages for system and software
-  vendors, application developers and computer science researchers.
+  help([[An open source Message Passing Interface implementation. The Open MPI
+  Project is an open source Message Passing Interface implementation that
+  is developed and maintained by a consortium of academic, research, and
+  industry partners. Open MPI is therefore able to combine the expertise,
+  technologies, and resources from all across the High Performance
+  Computing community in order to build the best MPI library available.
+  Open MPI offers advantages for system and software vendors, application
+  developers and computer science researchers.
   ]])
 
 
@@ -926,7 +936,7 @@ and regenerating the module files for every package that depends on ``python``:
 
 .. code-block:: console
 
-  root@module-file-tutorial:/# spack module refresh -y --module-type tcl ^python
+  root@module-file-tutorial:/# spack module tcl refresh -y ^python
   ==> Regenerating tcl module files
 
 Now the ``py-scipy`` module will be:
@@ -934,47 +944,47 @@ Now the ``py-scipy`` module will be:
 .. code-block:: tcl
 
   #%Module1.0
-  ## Module file created by spack (https://github.com/spack/spack) on 2017-10-07 15:02:14.974937
+  ## Module file created by spack (https://github.com/spack/spack) on 2018-11-11 22:10:48.834221
   ##
-  ## py-scipy@0.19.1%gcc@7.2.0 arch=linux-ubuntu16.04-x86_64 /7hi7r5j
+  ## py-scipy@1.1.0%gcc@7.2.0 arch=linux-ubuntu16.04-x86_64 /d5n3cph
   ##
 
 
   module-whatis "SciPy (pronounced 'Sigh Pie') is a Scientific Library for Python. It provides many user-friendly and efficient numerical routines such as routines for numerical integration and optimization."
 
   proc ModulesHelp { } {
-  puts stderr "SciPy (pronounced 'Sigh Pie') is a Scientific Library for Python. It"
+  puts stderr "SciPy (pronounced "Sigh Pie") is a Scientific Library for Python. It"
   puts stderr "provides many user-friendly and efficient numerical routines such as"
   puts stderr "routines for numerical integration and optimization."
   }
 
-  if ![ is-loaded python/2.7.14-gcc-7.2.0 ] {
-      puts stderr "Autoloading python/2.7.14-gcc-7.2.0"
-      module load python/2.7.14-gcc-7.2.0
+  if { [ module-info mode load ] && ![ is-loaded python/2.7.15-gcc-7.2.0 ] } {
+      puts stderr "Autoloading python/2.7.15-gcc-7.2.0"
+      module load python/2.7.15-gcc-7.2.0
   }
-  if ![ is-loaded openblas/0.2.20-gcc-7.2.0 ] {
-      puts stderr "Autoloading openblas/0.2.20-gcc-7.2.0"
-      module load openblas/0.2.20-gcc-7.2.0
+  if { [ module-info mode load ] && ![ is-loaded openblas/0.3.3-gcc-7.2.0 ] } {
+      puts stderr "Autoloading openblas/0.3.3-gcc-7.2.0"
+      module load openblas/0.3.3-gcc-7.2.0
   }
-  if ![ is-loaded py-numpy/1.13.1-gcc-7.2.0-openblas ] {
-      puts stderr "Autoloading py-numpy/1.13.1-gcc-7.2.0-openblas"
-      module load py-numpy/1.13.1-gcc-7.2.0-openblas
+  if { [ module-info mode load ] && ![ is-loaded py-numpy/1.15.2-gcc-7.2.0-openblas ] } {
+      puts stderr "Autoloading py-numpy/1.15.2-gcc-7.2.0-openblas"
+      module load py-numpy/1.15.2-gcc-7.2.0-openblas
   }
   conflict py-scipy
 
-  prepend-path LD_LIBRARY_PATH "/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/py-scipy-0.19.1-7hi7r5jri7bmohh4oontvfxo7rgj4hef/lib"
-  prepend-path CMAKE_PREFIX_PATH "/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/py-scipy-0.19.1-7hi7r5jri7bmohh4oontvfxo7rgj4hef/"
-  prepend-path PYTHONPATH "/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/py-scipy-0.19.1-7hi7r5jri7bmohh4oontvfxo7rgj4hef/lib/python2.7/site-packages"
-  setenv PY_SCIPY_ROOT "/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/py-scipy-0.19.1-7hi7r5jri7bmohh4oontvfxo7rgj4hef"
+  prepend-path LD_LIBRARY_PATH "/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/py-scipy-1.1.0-d5n3cphk2lx2v74ypwb6h7tna7vvgdyn/lib"
+  prepend-path CMAKE_PREFIX_PATH "/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/py-scipy-1.1.0-d5n3cphk2lx2v74ypwb6h7tna7vvgdyn/"
+  prepend-path PYTHONPATH "/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/py-scipy-1.1.0-d5n3cphk2lx2v74ypwb6h7tna7vvgdyn/lib/python2.7/site-packages"
+  setenv PY_SCIPY_ROOT "/home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/py-scipy-1.1.0-d5n3cphk2lx2v74ypwb6h7tna7vvgdyn"
 
 and will contain code to autoload all the dependencies:
 
 .. code-block:: console
 
-  root@module-file-tutorial:/# module load py-scipy
-  Autoloading python/2.7.14-gcc-7.2.0
-  Autoloading openblas/0.2.20-gcc-7.2.0
-  Autoloading py-numpy/1.13.1-gcc-7.2.0-openblas
+  $ module load py-scipy
+  Autoloading python/2.7.15-gcc-7.2.0
+  Autoloading openblas/0.3.3-gcc-7.2.0
+  Autoloading py-numpy/1.15.2-gcc-7.2.0-openblas
 
 In case messages are unwanted during the autoload procedure, it will be
 sufficient to omit the line setting ``verbose: True`` in the configuration file above.
@@ -990,16 +1000,25 @@ all the software is visible at the same time:
 
 .. code-block:: console
 
-  root@module-file-tutorial:/# module avail
-
-  ----------------------------------------------------------------------------- /usr/local/share/spack/modules/linux-ubuntu16.04-x86_64 -----------------------------------------------------------------------------
-     bzip2/1.0.6-gcc-7.2.0    netlib-lapack/3.6.1-gcc-7.2.0                            openblas/0.2.20-gcc-7.2.0      py-numpy/1.13.1-gcc-7.2.0-openblas    py-six/1.10.0-gcc-7.2.0
-     cmake/3.9.4-gcc-7.2.0    netlib-scalapack/2.0.2-gcc-7.2.0-netlib-mpich            openmpi/1.10.2-gcc-7.2.0       py-packaging/16.8-gcc-7.2.0           python/2.7.14-gcc-7.2.0
-     gcc/7.2.0-gcc-5.4.0      netlib-scalapack/2.0.2-gcc-7.2.0-netlib-openmpi          openssl/1.0.2k-gcc-7.2.0       py-pyparsing/2.2.0-gcc-7.2.0          readline/7.0-gcc-7.2.0
-     mpich/3.2-gcc-7.2.0      netlib-scalapack/2.0.2-gcc-7.2.0-openblas-mpich          pkg-config/0.29.2-gcc-7.2.0    py-scipy/0.19.1-gcc-7.2.0-openblas    sqlite/3.20.0-gcc-7.2.0
-     ncurses/6.0-gcc-7.2.0    netlib-scalapack/2.0.2-gcc-7.2.0-openblas-openmpi (D)    py-appdirs/1.4.3-gcc-7.2.0     py-setuptools/35.0.2-gcc-7.2.0        zlib/1.2.11-gcc-7.2.0
+  $ module avail
+
+  ----------------------------------------------- /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64 -----------------------------------------------
+     autoconf/2.69-gcc-7.2.0          m4/1.4.18-gcc-7.2.0                                      pkgconf/1.4.2-gcc-7.2.0
+     automake/1.16.1-gcc-7.2.0        mpich/3.2.1-gcc-7.2.0                                    py-numpy/1.15.2-gcc-7.2.0-openblas (L)
+     bzip2/1.0.6-gcc-7.2.0            ncurses/6.1-gcc-7.2.0                                    py-scipy/1.1.0-gcc-7.2.0-openblas  (L)
+     cmake/3.12.3-gcc-7.2.0           netlib-lapack/3.8.0-gcc-7.2.0                            py-setuptools/40.4.3-gcc-7.2.0
+     diffutils/3.6-gcc-7.2.0          netlib-scalapack/2.0.2-gcc-7.2.0-netlib-mpich           python/2.7.15-gcc-7.2.0            (L)
+     findutils/4.6.0-gcc-7.2.0        netlib-scalapack/2.0.2-gcc-7.2.0-netlib-openmpi         readline/7.0-gcc-7.2.0
+     gcc/7.2.0-gcc-5.4.0              netlib-scalapack/2.0.2-gcc-7.2.0-openblas-mpich          sqlite/3.23.1-gcc-7.2.0
+     gdbm/1.14.1-gcc-7.2.0            netlib-scalapack/2.0.2-gcc-7.2.0-openblas-openmpi (D)    texinfo/6.5-gcc-7.2.0
+     hwloc/1.11.9-gcc-7.2.0           numactl/2.0.11-gcc-7.2.0                                 util-macros/1.19.1-gcc-7.2.0
+     libpciaccess/0.13.5-gcc-7.2.0    openblas/0.3.3-gcc-7.2.0                          (L)    xz/5.2.4-gcc-7.2.0
+     libsigsegv/2.11-gcc-7.2.0        openmpi/3.1.3-gcc-7.2.0                                  zlib/1.2.11-gcc-7.2.0
+     libtool/2.4.6-gcc-7.2.0          openssl/1.0.2o-gcc-7.2.0
+     libxml2/2.9.8-gcc-7.2.0          perl/5.26.2-gcc-7.2.0
 
     Where:
+     L:  Module is loaded
      D:  Default Module
 
   Use "module spider" to find all possible modules.
@@ -1010,11 +1029,12 @@ that nothing prevents users from loading incompatible sets of modules:
 
 .. code-block:: console
 
-  root@module-file-tutorial:/# module load netlib-lapack/3.6.1-gcc-7.2.0 openblas/0.2.20-gcc-7.2.0
-  root@module-file-tutorial:/# module list
+  $ module purge
+  $ module load netlib-lapack/3.8.0-gcc-7.2.0 openblas/0.3.3-gcc-7.2.0
+  $ module list
 
   Currently Loaded Modules:
-    1) netlib-lapack/3.6.1-gcc-7.2.0   2) openblas/0.2.20-gcc-7.2.0
+    1) netlib-lapack/3.8.0-gcc-7.2.0   2) openblas/0.3.3-gcc-7.2.0
 
 Even if ``conflicts`` directives are carefully placed in module files, they:
 
@@ -1102,23 +1122,24 @@ If we now regenerate the module files:
 
 .. code-block:: console
 
-  root@module-file-tutorial:/# spack module refresh --module-type lmod --delete-tree -y
+  $ spack module lmod refresh --delete-tree -y
   ==> Regenerating lmod module files
 
 and update ``MODULEPATH`` to point to the ``Core``:
 
 .. code-block:: console
 
-  root@module-file-tutorial:/# module unuse /usr/local/share/spack/modules/linux-ubuntu16.04-x86_64
-  root@module-file-tutorial:/# module use /usr/local/share/spack/lmod/linux-ubuntu16.04-x86_64/Core
+  $ module purge
+  $ module unuse /home/spack1/spack/share/spack/modules/linux-ubuntu16.04-x86_64
+  $ module use /home/spack1/spack/share/spack/lmod/linux-ubuntu16.04-x86_64/Core
 
 asking for the available modules will return:
 
 .. code-block:: console
 
-  root@module-file-tutorial:/# module avail
+  $ module avail
 
-  ---------------------------------------------------------------------------- /usr/local/share/spack/lmod/linux-ubuntu16.04-x86_64/Core ----------------------------------------------------------------------------
+  ----------------------------------------------------------- share/spack/lmod/linux-ubuntu16.04-x86_64/Core ------------------------------------------------------------
      gcc/7.2.0
 
   Use "module spider" to find all possible modules.
@@ -1129,14 +1150,17 @@ the ``Compiler`` part of the hierarchy:
 
 .. code-block:: console
 
-  root@module-file-tutorial:/# module load gcc
-  root@module-file-tutorial:/# module avail
+  $ module load gcc
+  $ module avail
 
-  ------------------------------------------------------------------------- /usr/local/share/spack/lmod/linux-ubuntu16.04-x86_64/gcc/7.2.0 --------------------------------------------------------------------------
-     bzip2/1.0.6    mpich/3.2      netlib-lapack/3.6.1    openmpi/1.10.2    pkg-config/0.29.2    py-numpy/1.13.1-openblas    py-pyparsing/2.2.0          py-setuptools/35.0.2    python/2.7.14    sqlite/3.20.0
-     cmake/3.9.4    ncurses/6.0    openblas/0.2.20        openssl/1.0.2k    py-appdirs/1.4.3     py-packaging/16.8           py-scipy/0.19.1-openblas    py-six/1.10.0           readline/7.0     zlib/1.2.11
+  ------------------------------------------- /home/spack1/spack/share/spack/lmod/linux-ubuntu16.04-x86_64/gcc/7.2.0 --------------------------------------------
+     autoconf/2.69      findutils/4.6.0        libtool/2.4.6    netlib-lapack/3.8.0    perl/5.26.2                 python/2.7.15         xz/5.2.4
+     automake/1.16.1    gdbm/1.14.1            libxml2/2.9.8    numactl/2.0.11         pkgconf/1.4.2               readline/7.0          zlib/1.2.11
+     bzip2/1.0.6        hwloc/1.11.9           m4/1.4.18        openblas/0.3.3         py-numpy/1.15.2-openblas    sqlite/3.23.1
+     cmake/3.12.3       libpciaccess/0.13.5    mpich/3.2.1      openmpi/3.1.3          py-scipy/1.1.0-openblas     texinfo/6.5
+     diffutils/3.6      libsigsegv/2.11        ncurses/6.1      openssl/1.0.2o         py-setuptools/40.4.3        util-macros/1.19.1
 
-  ---------------------------------------------------------------------------- /usr/local/share/spack/lmod/linux-ubuntu16.04-x86_64/Core ----------------------------------------------------------------------------
+  ----------------------------------------------------------- share/spack/lmod/linux-ubuntu16.04-x86_64/Core ------------------------------------------------------------
      gcc/7.2.0 (L)
 
     Where:
@@ -1150,17 +1174,20 @@ either ``mpich`` or ``openmpi``. Let's start by loading ``mpich``:
 
 .. code-block:: console
 
-  root@module-file-tutorial:/# module load mpich
-  root@module-file-tutorial:/# module avail
+  $ module load mpich
+  $ module avail
 
-  ---------------------------------------------------------------- /usr/local/share/spack/lmod/linux-ubuntu16.04-x86_64/mpich/3.2-7gxffhv/gcc/7.2.0 -----------------------------------------------------------------
+  --------------------------------- /home/spack1/spack/share/spack/lmod/linux-ubuntu16.04-x86_64/mpich/3.2.1-vt5xcat/gcc/7.2.0 ----------------------------------
      netlib-scalapack/2.0.2-netlib    netlib-scalapack/2.0.2-openblas (D)
 
-  ------------------------------------------------------------------------- /usr/local/share/spack/lmod/linux-ubuntu16.04-x86_64/gcc/7.2.0 --------------------------------------------------------------------------
-     bzip2/1.0.6    mpich/3.2   (L)    netlib-lapack/3.6.1    openmpi/1.10.2    pkg-config/0.29.2    py-numpy/1.13.1-openblas    py-pyparsing/2.2.0          py-setuptools/35.0.2    python/2.7.14    sqlite/3.20.0
-     cmake/3.9.4    ncurses/6.0        openblas/0.2.20        openssl/1.0.2k    py-appdirs/1.4.3     py-packaging/16.8           py-scipy/0.19.1-openblas    py-six/1.10.0           readline/7.0     zlib/1.2.11
+  ------------------------------------------- /home/spack1/spack/share/spack/lmod/linux-ubuntu16.04-x86_64/gcc/7.2.0 --------------------------------------------
+     autoconf/2.69      findutils/4.6.0        libtool/2.4.6        netlib-lapack/3.8.0    perl/5.26.2                 python/2.7.15         xz/5.2.4
+     automake/1.16.1    gdbm/1.14.1            libxml2/2.9.8        numactl/2.0.11         pkgconf/1.4.2               readline/7.0          zlib/1.2.11
+     bzip2/1.0.6        hwloc/1.11.9           m4/1.4.18            openblas/0.3.3         py-numpy/1.15.2-openblas    sqlite/3.23.1
+     cmake/3.12.3       libpciaccess/0.13.5    mpich/3.2.1   (L)    openmpi/3.1.3          py-scipy/1.1.0-openblas     texinfo/6.5
+     diffutils/3.6      libsigsegv/2.11        ncurses/6.1          openssl/1.0.2o         py-setuptools/40.4.3        util-macros/1.19.1
 
-  ---------------------------------------------------------------------------- /usr/local/share/spack/lmod/linux-ubuntu16.04-x86_64/Core ----------------------------------------------------------------------------
+  ----------------------------------------------------------- share/spack/lmod/linux-ubuntu16.04-x86_64/Core ------------------------------------------------------------
      gcc/7.2.0 (L)
 
     Where:
@@ -1175,16 +1202,17 @@ either ``mpich`` or ``openmpi``. Let's start by loading ``mpich``:
   root@module-file-tutorial:/# module list
 
   Currently Loaded Modules:
-    1) gcc/7.2.0   2) mpich/3.2   3) openblas/0.2.20   4) netlib-scalapack/2.0.2-openblas
+    1) gcc/7.2.0   2) mpich/3.2.1   3) openblas/0.3.3   4) netlib-scalapack/2.0.2-openblas
 
 At this point we can showcase the improved consistency that a hierarchical layout provides
 over a non-hierarchical one:
 
 .. code-block:: console
 
-  root@module-file-tutorial:/# module load openmpi
+  $ module load openmpi
+
+  Lmod is automatically replacing "mpich/3.2.1" with "openmpi/3.1.3".
 
-  Lmod is automatically replacing "mpich/3.2" with "openmpi/1.10.2".
 
   Due to MODULEPATH changes, the following have been reloaded:
     1) netlib-scalapack/2.0.2-openblas
@@ -1213,10 +1241,9 @@ for ``LAPACK`` implementations:
   root@module-file-tutorial:/# module list
 
   Currently Loaded Modules:
-    1) gcc/7.2.0   2) openblas/0.2.20   3) openmpi/1.10.2   4) netlib-scalapack/2.0.2-openblas
+    1) gcc/7.2.0   2) openblas/0.3.3   3) openmpi/3.1.3   4) netlib-scalapack/2.0.2-openblas
 
   root@module-file-tutorial:/# module load netlib-scalapack/2.0.2-netlib
-  Autoloading netlib-lapack/3.6.1
 
   The following have been reloaded with a version change:
     1) netlib-scalapack/2.0.2-openblas => netlib-scalapack/2.0.2-netlib
@@ -1224,7 +1251,7 @@ for ``LAPACK`` implementations:
   root@module-file-tutorial:/# module list
 
   Currently Loaded Modules:
-    1) gcc/7.2.0   2) openblas/0.2.20   3) openmpi/1.10.2   4) netlib-lapack/3.6.1   5) netlib-scalapack/2.0.2-netlib
+    1) gcc/7.2.0   2) openblas/0.3.3   3) openmpi/3.1.3   4) netlib-scalapack/2.0.2-netlib
 
 Hierarchies that are deeper than ``Core``/``Compiler``/``MPI`` are
 probably still considered "unusual" or "impractical" at many sites, mainly because
@@ -1266,7 +1293,6 @@ Coming back to our example, let's add ``lapack`` to the hierarchy and remove any
         - gcc
       blacklist:
         - '%gcc@5.4.0'
-        - readline
       all:
         filter:
           environment_blacklist: ['CPATH', 'LIBRARY_PATH']
@@ -1293,25 +1319,28 @@ After module files have been regenerated as usual:
 
   root@module-file-tutorial:/# module purge
 
-  root@module-file-tutorial:/# spack module refresh --delete-tree -y -m lmod
+  root@module-file-tutorial:/# spack module lmod refresh --delete-tree -y
   ==> Regenerating lmod module files
 
 we can see that now we have additional components in the hierarchy:
 
 .. code-block:: console
 
-  root@module-file-tutorial:/# module load gcc
-  root@module-file-tutorial:/# module load openblas
-  root@module-file-tutorial:/# module avail
+  $ module load gcc
+  $ module load openblas
+  $ module avail
 
-  ------------------------------------------------------------- /usr/local/share/spack/lmod/linux-ubuntu16.04-x86_64/openblas/0.2.20-kvddide/gcc/7.2.0 --------------------------------------------------------------
-     py-numpy/1.13.1    py-scipy/0.19.1
+  -------------------------------- /home/spack1/spack/share/spack/lmod/linux-ubuntu16.04-x86_64/openblas/0.3.3-xxoxfh4/gcc/7.2.0 --------------------------------
+     py-numpy/1.15.2    py-scipy/1.1.0
 
-  ------------------------------------------------------------------------- /usr/local/share/spack/lmod/linux-ubuntu16.04-x86_64/gcc/7.2.0 --------------------------------------------------------------------------
-     bzip2/1.0.6    mpich/3.2      netlib-lapack/3.6.1        openmpi/1.10.2    pkg-config/0.29.2    py-packaging/16.8     py-setuptools/35.0.2    python/2.7.14    sqlite/3.20.0
-     cmake/3.9.4    ncurses/6.0    openblas/0.2.20     (L)    openssl/1.0.2k    py-appdirs/1.4.3     py-pyparsing/2.2.0    py-six/1.10.0           readline/7.0     zlib/1.2.11
+  ------------------------------------------- /home/spack1/spack/share/spack/lmod/linux-ubuntu16.04-x86_64/gcc/7.2.0 --------------------------------------------
+     autoconf/2.69      findutils/4.6.0        libtool/2.4.6    netlib-lapack/3.8.0        perl/5.26.2             sqlite/3.23.1
+     automake/1.16.1    gdbm/1.14.1            libxml2/2.9.8    numactl/2.0.11             pkgconf/1.4.2           texinfo/6.5
+     bzip2/1.0.6        hwloc/1.11.9           m4/1.4.18        openblas/0.3.3      (L)    py-setuptools/40.4.3    util-macros/1.19.1
+     cmake/3.12.3       libpciaccess/0.13.5    mpich/3.2.1      openmpi/3.1.3              python/2.7.15           xz/5.2.4
+     diffutils/3.6      libsigsegv/2.11        ncurses/6.1      openssl/1.0.2o             readline/7.0            zlib/1.2.11
 
-  ---------------------------------------------------------------------------- /usr/local/share/spack/lmod/linux-ubuntu16.04-x86_64/Core ----------------------------------------------------------------------------
+  ----------------------------------------------------------- share/spack/lmod/linux-ubuntu16.04-x86_64/Core ------------------------------------------------------------
      gcc/7.2.0 (L)
 
     Where:
@@ -1321,20 +1350,23 @@ we can see that now we have additional components in the hierarchy:
   Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".
 
 
-  root@module-file-tutorial:/# module load openmpi
-  root@module-file-tutorial:/# module avail
+  $ module load openmpi
+  $ module avail
 
-  -------------------------------------------------- /usr/local/share/spack/lmod/linux-ubuntu16.04-x86_64/openmpi/1.10.2-ufw7pdi/openblas/0.2.20-kvddide/gcc/7.2.0 --------------------------------------------------
+  --------------------- /home/spack1/spack/share/spack/lmod/linux-ubuntu16.04-x86_64/openmpi/3.1.3-do5xfer/openblas/0.3.3-xxoxfh4/gcc/7.2.0 ---------------------
      netlib-scalapack/2.0.2
 
-  ------------------------------------------------------------- /usr/local/share/spack/lmod/linux-ubuntu16.04-x86_64/openblas/0.2.20-kvddide/gcc/7.2.0 --------------------------------------------------------------
-     py-numpy/1.13.1    py-scipy/0.19.1
+  -------------------------------- /home/spack1/spack/share/spack/lmod/linux-ubuntu16.04-x86_64/openblas/0.3.3-xxoxfh4/gcc/7.2.0 --------------------------------
+     py-numpy/1.15.2    py-scipy/1.1.0
 
-  ------------------------------------------------------------------------- /usr/local/share/spack/lmod/linux-ubuntu16.04-x86_64/gcc/7.2.0 --------------------------------------------------------------------------
-     bzip2/1.0.6    mpich/3.2      netlib-lapack/3.6.1        openmpi/1.10.2 (L)    pkg-config/0.29.2    py-packaging/16.8     py-setuptools/35.0.2    python/2.7.14    sqlite/3.20.0
-     cmake/3.9.4    ncurses/6.0    openblas/0.2.20     (L)    openssl/1.0.2k        py-appdirs/1.4.3     py-pyparsing/2.2.0    py-six/1.10.0           readline/7.0     zlib/1.2.11
+  ------------------------------------------- /home/spack1/spack/share/spack/lmod/linux-ubuntu16.04-x86_64/gcc/7.2.0 --------------------------------------------
+     autoconf/2.69      findutils/4.6.0        libtool/2.4.6    netlib-lapack/3.8.0        perl/5.26.2             sqlite/3.23.1
+     automake/1.16.1    gdbm/1.14.1            libxml2/2.9.8    numactl/2.0.11             pkgconf/1.4.2           texinfo/6.5
+     bzip2/1.0.6        hwloc/1.11.9           m4/1.4.18        openblas/0.3.3      (L)    py-setuptools/40.4.3    util-macros/1.19.1
+     cmake/3.12.3       libpciaccess/0.13.5    mpich/3.2.1      openmpi/3.1.3       (L)    python/2.7.15           xz/5.2.4
+     diffutils/3.6      libsigsegv/2.11        ncurses/6.1      openssl/1.0.2o             readline/7.0            zlib/1.2.11
 
-  ---------------------------------------------------------------------------- /usr/local/share/spack/lmod/linux-ubuntu16.04-x86_64/Core ----------------------------------------------------------------------------
+  ---------------------------------------------- /home/spack1/spack/share/spack/lmod/linux-ubuntu16.04-x86_64/Core ----------------------------------------------
      gcc/7.2.0 (L)
 
     Where:
@@ -1347,18 +1379,18 @@ Both ``MPI`` and ``LAPACK`` providers will now benefit from the same safety feat
 
 .. code-block:: console
 
-  root@module-file-tutorial:/# module load py-numpy netlib-scalapack
-  root@module-file-tutorial:/# module load mpich
+  $ module load py-numpy netlib-scalapack
+  $ module load mpich
 
-  Lmod is automatically replacing "openmpi/1.10.2" with "mpich/3.2".
+  Lmod is automatically replacing "openmpi/3.1.3" with "mpich/3.2.1".
 
 
   Due to MODULEPATH changes, the following have been reloaded:
     1) netlib-scalapack/2.0.2
 
-  root@module-file-tutorial:/# module load netlib-lapack
+  $ module load netlib-lapack
 
-  Lmod is automatically replacing "openblas/0.2.20" with "netlib-lapack/3.6.1".
+  Lmod is automatically replacing "openblas/0.3.3" with "netlib-lapack/3.8.0".
 
 
   Inactive Modules:
@@ -1385,11 +1417,12 @@ Module file templates
 ^^^^^^^^^^^^^^^^^^^^^
 
 The templates that Spack uses to generate module files are stored in the
-``templates/module`` directory, and they all share the same common structure.
-Usually, they start with a header that identifies the type of
-module being generated. In the case of hierarchical module files it's:
+``share/spack/templates/module`` directory within the Spack prefix, and
+they all share the same common structure.  Usually, they start with a
+header that identifies the type of module being generated. In the case of
+hierarchical module files it's:
 
-.. literalinclude:: ../../../templates/modules/modulefile.lua
+.. literalinclude:: ../../../share/spack/templates/modules/modulefile.lua
   :language: jinja
   :lines: 1-6
 
@@ -1403,7 +1436,7 @@ that can be overridden or extended by users, if need be.
 , delimited by ``{% ... %}``,
 are also permitted in the template language:
 
-.. literalinclude:: ../../../templates/modules/modulefile.lua
+.. literalinclude:: ../../../share/spack/templates/modules/modulefile.lua
   :language: jinja
   :lines: 73-88
 
@@ -1522,7 +1555,7 @@ If we regenerate the module files one last time:
 
 .. code-block:: console
 
-  root@module-file-tutorial:/# spack  module refresh -y -m lmod netlib-scalapack
+  root@module-file-tutorial:/# spack module lmod refresh -y netlib-scalapack
   ==> Regenerating lmod module files
 
 we'll find the following at the end of each ``netlib-scalapack`` module file:
@@ -1530,7 +1563,7 @@ we'll find the following at the end of each ``netlib-scalapack`` module file:
 .. code-block:: lua
 
   -- Access is granted only to specific groups
-  if not isDir("/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/netlib-scalapack-2.0.2-ax6aza6vyepceyr3fihewp7rbr2vp7ym") then
+  if not isDir("/usr/local/opt/spack/linux-ubuntu16.04-x86_64/gcc-7.2.0/netlib-scalapack-2.0.2-d3lertflood3twaor44eam2kcr4l72ag") then
       LmodError (
           "You don't have the necessary rights to run \"netlib-scalapack\".\n\n",
           "\tPlease write an e-mail to 1234@foo.com if you need further information on how to get access to it.\n"
diff --git a/lib/spack/docs/tutorial_packaging.rst b/lib/spack/docs/tutorial_packaging.rst
index e85be7c637..328c36b61f 100644
--- a/lib/spack/docs/tutorial_packaging.rst
+++ b/lib/spack/docs/tutorial_packaging.rst
@@ -1,3 +1,8 @@
+.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 .. _packaging-tutorial:
 
 =========================
@@ -43,6 +48,16 @@ A few things before we get started:
 Creating the Package File
 -------------------------
 
+We will use a separate package repository for the tutorial. Package
+repositories allow you to separate sets of packages that take
+precedence over one another. We will use the tutorial repo that ships
+with Spack to avoid breaking the builtin Spack packages.
+
+.. code-block:: console
+
+  $ spack repo add $SPACK_ROOT/var/spack/repos/tutorial/
+  ==> Added repo with namespace 'tutorial'.
+
 Spack comes with a handy command to create a new package: ``spack create``.
 
 This command is given the location of a package's source code, downloads
@@ -55,9 +70,9 @@ we run ``spack create`` on it:
   $ spack create -t generic -f https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz
   ==> This looks like a URL for mpileaks
   ==> Found 1 version of mpileaks:
-    
+
     1.0  https://github.com/LLNL/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz
-  
+
   ==> How many would you like to checksum? (default is 1, q to abort) 1
   ==> Downloading...
   ==> Fetching https://github.com/LLNL/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz
@@ -65,7 +80,7 @@ we run ``spack create`` on it:
   ==> Checksummed 1 version of mpileaks
   ==> Using specified package template: 'generic'
   ==> Created template for mpileaks package
-  ==> Created package file: $SPACK_ROOT/var/spack/repos/builtin/packages/mpileaks/package.py
+  ==> Created package file: /home/spack1/spack/var/spack/repos/builtin/packages/mpileaks/package.py
 
 And Spack should spawn a text editor with this file:
 
@@ -73,7 +88,7 @@ And Spack should spawn a text editor with this file:
    :language: python
 
 Spack has created this file in
-``$SPACK_ROOT/var/spack/repos/builtin/packages/mpileaks/package.py``.  Take a
+``/home/spack1/spack/var/spack/repos/builtin/packages/mpileaks/package.py``.  Take a
 moment to look over the file.  There's a few placeholders that Spack has
 created, which we'll fill in as part of this tutorial:
 
@@ -88,26 +103,27 @@ to build this package:
 .. code-block:: console
 
   $ spack install mpileaks
-  ==> Installing mpileaks
-  ==> Using cached archive: /usr/workspace/wsa/legendre/spack/var/spack/cache/mpileaks/mpileaks-1.0.tar.gz
-  ==> Staging archive: /usr/workspace/wsa/legendre/spack/var/spack/stage/mpileaks-1.0-hufwhwpq5benv3sslie6ryflk5s6nm35/mpileaks-1.0.tar.gz
-  ==> Created stage in /usr/workspace/wsa/legendre/spack/var/spack/stage/mpileaks-1.0-hufwhwpq5benv3sslie6ryflk5s6nm35
-  ==> Ran patch() for mpileaks
-  ==> Building mpileaks [AutotoolsPackage]
-  ==> Executing phase : 'autoreconf'
-  ==> Executing phase : 'configure'
-  ==> Error: ProcessError: Command exited with status 1:
-      './configure' '--prefix=/usr/workspace/wsa/legendre/spack/opt/spack/linux-rhel7-x86_64/gcc-4.9.3/mpileaks-1.0-hufwhwpq5benv3sslie6ryflk5s6nm35'
-  /usr/workspace/wsa/legendre/spack/lib/spack/spack/build_systems/autotools.py:150, in configure:
-       145      def configure(self, spec, prefix):
-       146          """Runs configure with the arguments specified in `configure_args`
-       147          and an appropriately set prefix
-       148          """
-       149          options = ['--prefix={0}'.format(prefix)] + self.configure_args()
-    >> 150          inspect.getmodule(self).configure(*options)
+  ==> No binary for mpileaks found: installing from source
+  ==> Fetching file:///mirror/mpileaks/mpileaks-1.0.tar.gz
+  curl: (37) Couldn't open file /mirror/mpileaks/mpileaks-1.0.tar.gz
+  ==> Fetching from file:///mirror/mpileaks/mpileaks-1.0.tar.gz failed.
+  ==> Fetching https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz
+  ######################################################################## 100.0%
+  ==> Staging archive: /home/ubuntu/packaging/spack/var/spack/stage/mpileaks-1.0-sv75n3u5ev6mljwcezisz3slooozbbxu/mpileaks-1.0.tar.gz
+  ==> Created stage in /home/ubuntu/packaging/spack/var/spack/stage/mpileaks-1.0-sv75n3u5ev6mljwcezisz3slooozbbxu
+  ==> No patches needed for mpileaks
+  ==> Building mpileaks [Package]
+  ==> Executing phase: 'install'
+  ==> Error: ProcessError: Command exited with status 2:
+      'make' '-j16'
+
+  1 error found in build log:
+       1    ==> Executing phase: 'install'
+       2    ==> 'make' '-j16'
+    >> 3    make: *** No targets specified and no makefile found.  Stop.
 
   See build log for details:
-    /tmp/legendre/spack-stage/spack-stage-8HVzqu/mpileaks-1.0/spack-build.out
+    /home/ubuntu/packaging/spack/var/spack/stage/mpileaks-1.0-sv75n3u5ev6mljwcezisz3slooozbbxu/mpileaks-1.0/spack-build.out
 
 This obviously didn't work; we need to fill in the package-specific
 information.  Specifically, Spack didn't try to build any of mpileaks'
@@ -133,7 +149,7 @@ found in ``$SPACK_ROOT/lib/spack/docs/tutorial/examples/1.package.py``
 and are below.  Make these changes to your ``package.py``:
 
 .. literalinclude:: tutorial/examples/1.package.py
-   :lines: 25-
+   :lines: 6-
    :language: python
 
 We've filled in the comment that describes what this package does and
@@ -143,8 +159,19 @@ allow Spack to provide some documentation on this package to other users:
 .. code-block:: console
 
   $ spack info mpileaks
-  AutotoolsPackage:    mpileaks
-  Homepage:            https://github.com/hpc/mpileaks
+  Package:   mpileaks
+
+  Description:
+      Tool to detect and report MPI objects like MPI_Requests and
+      MPI_Datatypes.
+
+  Homepage: https://github.com/hpc/mpileaks
+
+  Tags:
+      None
+
+  Preferred version:
+      1.0    https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz
 
   Safe versions:
       1.0    https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz
@@ -153,7 +180,7 @@ allow Spack to provide some documentation on this package to other users:
       None
 
   Installation Phases:
-      autoreconf    configure    build    install
+      install
 
   Build Dependencies:
       None
@@ -167,10 +194,6 @@ allow Spack to provide some documentation on this package to other users:
   Virtual Packages:
       None
 
-  Description:
-      Tool to detect and report MPI objects like MPI_Requests and
-      MPI_Datatypes
-
 As we fill in more information about this package the ``spack info`` command
 will become more informative.  Now let's start making this package build.
 
@@ -184,7 +207,7 @@ The mpileaks packages depends on three other package: ``MPI``,
 ``$SPACK_ROOT/lib/spack/docs/tutorial/examples/2.package.py``):
 
 .. literalinclude:: tutorial/examples/2.package.py
-   :lines: 25-
+   :lines: 6-
    :language: python
 
 Now when we go to build mpileaks, Spack will fetch and build these
@@ -201,26 +224,40 @@ Now when we try to install this package a lot more happens:
 
   $ spack install mpileaks
   ...
-  ==> libdwarf is already installed in SPACK_ROOT/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libdwarf-20160507-er4jrjynul6uba7wiu5tasuj35roxw6m
-  ==> dyninst is already installed in SPACK_ROOT/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/dyninst-9.3.2-t7mau34jv3e76mpspdzhf2p2a6k7qubg
-  ==> callpath is already installed in SPACK_ROOT/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/callpath-1.0.4-ikbbkvfmsfmqzo624nvvrbooovf7egoc
+  ==> Successfully installed libdwarf from binary cache
+  [+] /home/ubuntu/packaging/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/libdwarf-20180129-p4jeflorwlnkoq2vpuyocwrbcht2ayak
+  ==> Installing callpath
+  ==> Searching for binary cache of callpath
+  ==> Installing callpath from binary cache
+  ==> Fetching file:///mirror/build_cache/linux-ubuntu16.04-x86_64/gcc-5.4.0/callpath-1.0.4/linux-ubuntu16.04-x86_64-gcc-5.4.0-callpath-1.0.4-empvyxdkc4j4pwg7gznwhbiumruey66x.spack
+  ######################################################################## 100.0%
+  gpg: Signature made Sat 10 Nov 2018 05:30:21 AM UTC using RSA key ID 3B7C69B2
+  gpg: Good signature from "sc-tutorial (GPG created for Spack) <becker33@llnl.gov>" [unknown]
+  gpg: WARNING: This key is not certified with a trusted signature!
+  gpg:          There is no indication that the signature belongs to the owner.
+  Primary key fingerprint: 95C7 1787 7AC0 0FFD AA8F  D6E9 9CFA 4A45 3B7C 69B2
+  ==> Successfully installed callpath from binary cache
+  [+] /home/ubuntu/packaging/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/callpath-1.0.4-empvyxdkc4j4pwg7gznwhbiumruey66x
   ==> Installing mpileaks
-  ==> Using cached archive: SPACK_ROOT/var/spack/cache/mpileaks/mpileaks-1.0.tar.gz
-  ==> Already staged mpileaks-1.0-lfgf53rns5mswq25rxckzgvmjc6ywam7 in SPACK_ROOT/var/spack/stage/mpileaks-1.0-lfgf53rns5mswq25rxckzgvmjc6ywam7
+  ==> Searching for binary cache of mpileaks
+  ==> No binary for mpileaks found: installing from source
+  ==> Using cached archive: /home/ubuntu/packaging/spack/var/spack/cache/mpileaks/mpileaks-1.0.tar.gz
+  ==> Staging archive: /home/ubuntu/packaging/spack/var/spack/stage/mpileaks-1.0-csoikctsalli4cdkkdk377gprkc472rb/mpileaks-1.0.tar.gz
+  ==> Created stage in /home/ubuntu/packaging/spack/var/spack/stage/mpileaks-1.0-csoikctsalli4cdkkdk377gprkc472rb
   ==> No patches needed for mpileaks
   ==> Building mpileaks [Package]
   ==> Executing phase: 'install'
   ==> Error: ProcessError: Command exited with status 2:
-      'make' '-j36'
-  
+      'make' '-j16'
+
   1 error found in build log:
-       1     ==> Executing phase: 'install'
-       2     ==> 'make' '-j36'
-    >> 3     make: *** No targets specified and no makefile found.  Stop.
-  
+       1    ==> Executing phase: 'install'
+       2    ==> 'make' '-j16'
+    >> 3    make: *** No targets specified and no makefile found.  Stop.
+
   See build log for details:
-    SPACK_ROOT/var/spack/stage/mpileaks-1.0-lfgf53rns5mswq25rxckzgvmjc6ywam7/mpileaks-1.0/spack-build.out
-  
+    /home/ubuntu/packaging/spack/var/spack/stage/mpileaks-1.0-csoikctsalli4cdkkdk377gprkc472rb/mpileaks-1.0/spack-build.out
+
 Note that this command may take a while to run and produce more output if
 you don't have an MPI already installed or configured in Spack.
 
@@ -239,35 +276,51 @@ call to ``configure()`` to the top of the install routine. The resulting
 package.py is in ``$SPACK_ROOT/lib/spack/docs/tutorial/examples/3.package.py``:
 
 .. literalinclude:: tutorial/examples/3.package.py
-  :lines: 25-
+  :lines: 6-
   :language: python
 
 If we re-run we still get errors:
 
 .. code-block:: console
 
+  $ spack install mpileask
+  ...
   ==> Installing mpileaks
-  ==> Using cached archive: SPACK_ROOT/var/spack/cache/mpileaks/mpileaks-1.0.tar.gz
-  ==> Already staged mpileaks-1.0-lfgf53rns5mswq25rxckzgvmjc6ywam7 in SPACK_ROOT/var/spack/stage/mpileaks-1.0-lfgf53rns5mswq25rxckzgvmjc6ywam7
+  ==> Searching for binary cache of mpileaks
+  ==> Finding buildcaches in /mirror/build_cache
+  ==> No binary for mpileaks found: installing from source
+  ==> Using cached archive: /home/ubuntu/packaging/spack/var/spack/cache/mpileaks/mpileaks-1.0.tar.gz
+  ==> Staging archive: /home/ubuntu/packaging/spack/var/spack/stage/mpileaks-1.0-csoikctsalli4cdkkdk377gprkc472rb/mpileaks-1.0.tar.gz
+  ==> Created stage in /home/ubuntu/packaging/spack/var/spack/stage/mpileaks-1.0-csoikctsalli4cdkkdk377gprkc472rb
   ==> No patches needed for mpileaks
   ==> Building mpileaks [Package]
   ==> Executing phase: 'install'
   ==> Error: ProcessError: Command exited with status 1:
       './configure'
-  
+
   1 error found in build log:
-       [ ... ]
-       21    checking whether SPACK_ROOT/lib/spack/env/gcc/gcc and cc understand -c and -o together... yes
-       22    checking whether we are using the GNU C++ compiler... yes
-       23    checking whether SPACK_ROOT/lib/spack/env/gcc/g++ accepts -g... yes
-       24    checking dependency style of SPACK_ROOT/lib/spack/env/gcc/g++... gcc3
-       25    checking for SPACK_ROOT/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc... SPACK_ROOT/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc
-       26    Checking whether SPACK_ROOT/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc responds to '-showme:compile'... yes
-    >> 27    configure: error: unable to locate adept-utils installation
-  
+       25    checking for /home/ubuntu/packaging/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-
+             5.4.0/openmpi-3.1.3-3njc4q5pqdpptq6jvqjrezkffwokv2sx/bin/mpicc... /home/ubuntu/pa
+             ckaging/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.1.3-3njc4q5p
+             qdpptq6jvqjrezkffwokv2sx/bin/mpicc
+       26    Checking whether /home/ubuntu/packaging/spack/opt/spack/linux-ubuntu16.04-x86_64/
+             gcc-5.4.0/openmpi-3.1.3-3njc4q5pqdpptq6jvqjrezkffwokv2sx/bin/mpicc responds to '-
+             showme:compile'... no
+       27    Checking whether /home/ubuntu/packaging/spack/opt/spack/linux-ubuntu16.04-x86_64/
+             gcc-5.4.0/openmpi-3.1.3-3njc4q5pqdpptq6jvqjrezkffwokv2sx/bin/mpicc responds to '-
+             showme'... no
+       28    Checking whether /home/ubuntu/packaging/spack/opt/spack/linux-ubuntu16.04-x86_64/
+             gcc-5.4.0/openmpi-3.1.3-3njc4q5pqdpptq6jvqjrezkffwokv2sx/bin/mpicc responds to '-
+             compile-info'... no
+       29    Checking whether /home/ubuntu/packaging/spack/opt/spack/linux-ubuntu16.04-x86_64/
+             gcc-5.4.0/openmpi-3.1.3-3njc4q5pqdpptq6jvqjrezkffwokv2sx/bin/mpicc responds to '-
+             show'... no
+       30    ./configure: line 4809: Echo: command not found
+    >> 31    configure: error: unable to locate adept-utils installation
+
   See build log for details:
-    SPACK_ROOT/var/spack/stage/mpileaks-1.0-lfgf53rns5mswq25rxckzgvmjc6ywam7/mpileaks-1.0/spack-build.out
-  
+    /home/ubuntu/packaging/spack/var/spack/stage/mpileaks-1.0-csoikctsalli4cdkkdk377gprkc472rb/mpileaks-1.0/spack-build.out
+
 Again, the problem may be obvious.  But let's pretend we're not
 all intelligent developers and use this opportunity spend some
 time debugging.  We have a few options that can tell us about
@@ -276,7 +329,7 @@ what's going wrong:
 As per the error message, Spack has given us a ``spack-build.out`` debug log:
 
 .. code-block:: console
-  
+
   ==> Executing phase: 'install'
   ==> './configure'
   checking metadata... no
@@ -286,23 +339,23 @@ As per the error message, Spack has given us a ``spack-build.out`` debug log:
   checking for a thread-safe mkdir -p... /bin/mkdir -p
   checking for gawk... gawk
   checking whether make sets $(MAKE)... yes
-  checking for gcc... SPACK_ROOT/lib/spack/env/gcc/gcc
+  checking for gcc... /home/spack1/spack/lib/spack/env/gcc/gcc
   checking for C compiler default output file name... a.out
   checking whether the C compiler works... yes
   checking whether we are cross compiling... no
-  checking for suffix of executables... 
+  checking for suffix of executables...
   checking for suffix of object files... o
   checking whether we are using the GNU C compiler... yes
-  checking whether SPACK_ROOT/lib/spack/env/gcc/gcc accepts -g... yes
-  checking for SPACK_ROOT/lib/spack/env/gcc/gcc option to accept ISO C89... none needed
+  checking whether /home/spack1/spack/lib/spack/env/gcc/gcc accepts -g... yes
+  checking for /home/spack1/spack/lib/spack/env/gcc/gcc option to accept ISO C89... none needed
   checking for style of include used by make... GNU
-  checking dependency style of SPACK_ROOT/lib/spack/env/gcc/gcc... gcc3
-  checking whether SPACK_ROOT/lib/spack/env/gcc/gcc and cc understand -c and -o together... yes
+  checking dependency style of /home/spack1/spack/lib/spack/env/gcc/gcc... gcc3
+  checking whether /home/spack1/spack/lib/spack/env/gcc/gcc and cc understand -c and -o together... yes
   checking whether we are using the GNU C++ compiler... yes
-  checking whether SPACK_ROOT/lib/spack/env/gcc/g++ accepts -g... yes
-  checking dependency style of SPACK_ROOT/lib/spack/env/gcc/g++... gcc3
-  checking for SPACK_ROOT/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc... SPACK_ROOT/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc
-  Checking whether SPACK_ROOT/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc responds to '-showme:compile'... yes
+  checking whether /home/spack1/spack/lib/spack/env/gcc/g++ accepts -g... yes
+  checking dependency style of /home/spack1/spack/lib/spack/env/gcc/g++... gcc3
+  checking for /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc... /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc
+  Checking whether /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc responds to '-showme:compile'... yes
   configure: error: unable to locate adept-utils installation
 
 This gives us the output from the build, and mpileaks isn't
@@ -317,7 +370,7 @@ We can also enter the build area and try to manually run the build:
 
 .. code-block:: console
 
-  $ spack env mpileaks bash
+  $ spack build-env mpileaks bash
   $ spack cd mpileaks
 
 The ``spack env`` command spawned a new shell that contains the same
@@ -336,23 +389,23 @@ From here we can manually re-run the build:
   checking for a thread-safe mkdir -p... /bin/mkdir -p
   checking for gawk... gawk
   checking whether make sets $(MAKE)... yes
-  checking for gcc... SPACK_ROOT/lib/spack/env/gcc/gcc
+  checking for gcc... /home/spack1/spack/lib/spack/env/gcc/gcc
   checking for C compiler default output file name... a.out
   checking whether the C compiler works... yes
   checking whether we are cross compiling... no
-  checking for suffix of executables... 
+  checking for suffix of executables...
   checking for suffix of object files... o
   checking whether we are using the GNU C compiler... yes
-  checking whether SPACK_ROOT/lib/spack/env/gcc/gcc accepts -g... yes
-  checking for SPACK_ROOT/lib/spack/env/gcc/gcc option to accept ISO C89... none needed
+  checking whether /home/spack1/spack/lib/spack/env/gcc/gcc accepts -g... yes
+  checking for /home/spack1/spack/lib/spack/env/gcc/gcc option to accept ISO C89... none needed
   checking for style of include used by make... GNU
-  checking dependency style of SPACK_ROOT/lib/spack/env/gcc/gcc... gcc3
-  checking whether SPACK_ROOT/lib/spack/env/gcc/gcc and cc understand -c and -o together... yes
+  checking dependency style of /home/spack1/spack/lib/spack/env/gcc/gcc... gcc3
+  checking whether /home/spack1/spack/lib/spack/env/gcc/gcc and cc understand -c and -o together... yes
   checking whether we are using the GNU C++ compiler... yes
-  checking whether SPACK_ROOT/lib/spack/env/gcc/g++ accepts -g... yes
-  checking dependency style of SPACK_ROOT/lib/spack/env/gcc/g++... gcc3
-  checking for SPACK_ROOT/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc... SPACK_ROOT/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc
-  Checking whether SPACK_ROOT/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc responds to '-showme:compile'... yes
+  checking whether /home/spack1/spack/lib/spack/env/gcc/g++ accepts -g... yes
+  checking dependency style of /home/spack1/spack/lib/spack/env/gcc/g++... gcc3
+  checking for /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc... /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc
+  Checking whether /home/spack1/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.0.0-yo5qkfvumpmgmvlbalqcadu46j5bd52f/bin/mpicc responds to '-showme:compile'... yes
   configure: error: unable to locate adept-utils installation
 
 We're seeing the same error, but now we're in a shell where we can run
@@ -372,7 +425,7 @@ version can be found in
 ``$SPACK_ROOT/lib/spack/docs/tutorial/examples/4.package.py``:
 
 .. literalinclude:: tutorial/examples/4.package.py
-   :lines: 25-
+   :lines: 6-
    :language: python
 
 This is all we need for working mpileaks!  If we install now we'll see:
@@ -382,16 +435,18 @@ This is all we need for working mpileaks!  If we install now we'll see:
   $ spack install mpileaks
   ...
   ==> Installing mpileaks
-  ==> Using cached archive: SPACK_ROOT/var/spack/cache/mpileaks/mpileaks-1.0.tar.gz
-  ==> Staging archive: SPACK_ROOT/var/spack/stage/mpileaks-1.0-lfgf53rns5mswq25rxckzgvmjc6ywam7/mpileaks-1.0.tar.gz
-  ==> Created stage in SPACK_ROOT/var/spack/stage/mpileaks-1.0-lfgf53rns5mswq25rxckzgvmjc6ywam7
+  ==> Searching for binary cache of mpileaks
+  ==> Finding buildcaches in /mirror/build_cache
+  ==> No binary for mpileaks found: installing from source
+  ==> Using cached archive: /home/ubuntu/packaging/spack/var/spack/cache/mpileaks/mpileaks-1.0.tar.gz
+  ==> Staging archive: /home/ubuntu/packaging/spack/var/spack/stage/mpileaks-1.0-csoikctsalli4cdkkdk377gprkc472rb/mpileaks-1.0.tar.gz
+  ==> Created stage in /home/ubuntu/packaging/spack/var/spack/stage/mpileaks-1.0-csoikctsalli4cdkkdk377gprkc472rb
   ==> No patches needed for mpileaks
   ==> Building mpileaks [Package]
   ==> Executing phase: 'install'
   ==> Successfully installed mpileaks
-  Fetch: 0.00s.  Build: 9.01s.  Total: 9.01s.
-  [+] SPACK_ROOT/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpileaks-1.0-lfgf53rns5mswq25rxckzgvmjc6ywam7
-
+    Fetch: 0.00s.  Build: 9.41s.  Total: 9.41s.
+  [+] /home/ubuntu/packaging/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpileaks-1.0-csoikctsalli4cdkkdk377gprkc472rb
 
 There are some special circumstances in package that are worth highlighting.
 Normally spack would have automatically detected that mpileaks was an
@@ -408,7 +463,7 @@ a full install routine we would have just written:
 Similarly, if this had been a CMake-based package we
 would have been filling in a ``cmake_args`` function instead of
 ``configure_args``.  There are similar default package types for
-many build environments.
+many build environments that will be discussed later in the tutorial.
 
 --------
 Variants
@@ -423,7 +478,7 @@ To do this, we'll add a variant to our package, as per the following (see
 ``$SPACK_ROOT/lib/spack/docs/tutorial/examples/5.package.py``):
 
 .. literalinclude:: tutorial/examples/5.package.py
-   :lines: 25-
+   :lines: 6-
    :language: python
 
 We've added the variant ``stackstart``, and given it a default value of
@@ -435,13 +490,16 @@ configure line (output truncated for length):
   $ spack install --verbose mpileaks stackstart=4
   ...
   ==> Installing mpileaks
-  ==> Using cached archive: SPACK_ROOT/var/spack/cache/mpileaks/mpileaks-1.0.tar.gz
-  ==> Staging archive: SPACK_ROOT/var/spack/stage/mpileaks-1.0-gxxi4fp57b4j6xalra5t65hyx5rj25t7/mpileaks-1.0.tar.gz
-  ==> Created stage in SPACK_ROOT/var/spack/stage/mpileaks-1.0-gxxi4fp57b4j6xalra5t65hyx5rj25t7
+  ==> Searching for binary cache of mpileaks
+  ==> Finding buildcaches in /mirror/build_cache
+  ==> No binary for mpileaks found: installing from source
+  ==> Using cached archive: /home/ubuntu/packaging/spack/var/spack/cache/mpileaks/mpileaks-1.0.tar.gz
+  ==> Staging archive: /home/ubuntu/packaging/spack/var/spack/stage/mpileaks-1.0-meufjojkxve3l7rci2mbud3faidgplto/mpileaks-1.0.tar.gz
+  ==> Created stage in /home/ubuntu/packaging/spack/var/spack/stage/mpileaks-1.0-meufjojkxve3l7rci2mbud3faidgplto
   ==> No patches needed for mpileaks
   ==> Building mpileaks [Package]
   ==> Executing phase: 'install'
-  ==> './configure' '--with-adept-utils=SPACK_ROOT/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/adept-utils-1.0.1-pm3gffhrnwsdtqthtvsfvs2tny4r65wb' '--with-callpath=SPACK_ROOT/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/callpath-1.0.4-ikbbkvfmsfmqzo624nvvrbooovf7egoc' '--prefix=SPACK_ROOT/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpileaks-1.0-gxxi4fp57b4j6xalra5t65hyx5rj25t7' '--with-stack-start-c=4' '--with-stack-start-fortran=4'
+  ==> './configure' '--with-adept-utils=/home/ubuntu/packaging/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/adept-utils-1.0.1-7tippnvo5g76wpijk7x5kwfpr3iqiaen' '--with-callpath=/home/ubuntu/packaging/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/callpath-1.0.4-empvyxdkc4j4pwg7gznwhbiumruey66x' '--prefix=/home/ubuntu/packaging/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/mpileaks-1.0-meufjojkxve3l7rci2mbud3faidgplto' '--with-stack-start-c=4' '--with-stack-start-fortran=4'
 
 ---------------
 The Spec Object
diff --git a/lib/spack/docs/workflows.rst b/lib/spack/docs/workflows.rst
index 4c674f92e4..b55c8bfd49 100644
--- a/lib/spack/docs/workflows.rst
+++ b/lib/spack/docs/workflows.rst
@@ -1,3 +1,8 @@
+.. Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+   Spack Project Developers. See the top-level COPYRIGHT file for details.
+
+   SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 =========
 Workflows
 =========
@@ -276,11 +281,11 @@ have some drawbacks:
 2. The ``spack spec`` and ``spack install`` commands use a
    sophisticated concretization algorithm that chooses the "best"
    among several options, taking into account ``packages.yaml`` file.
-   The ``spack load`` and ``spack module loads`` commands, on the
+   The ``spack load`` and ``spack module tcl loads`` commands, on the
    other hand, are not very smart: if the user-supplied spec matches
-   more than one installed package, then ``spack module loads`` will
+   more than one installed package, then ``spack module tcl loads`` will
    fail. This may change in the future.  For now, the workaround is to
-   be more specific on any ``spack module loads`` lines that fail.
+   be more specific on any ``spack module tcl loads`` lines that fail.
 
 
 """"""""""""""""""""""
@@ -290,7 +295,7 @@ Generated Load Scripts
 Another problem with using `spack load` is, it is slow; a typical user
 environment could take several seconds to load, and would not be
 appropriate to put into ``.bashrc`` directly.  It is preferable to use
-a series of ``spack module loads`` commands to pre-compute which
+a series of ``spack module tcl loads`` commands to pre-compute which
 modules to load.  These can be put in a script that is run whenever
 installed Spack packages change.  For example:
 
@@ -301,7 +306,7 @@ installed Spack packages change.  For example:
    # Generate module load commands in ~/env/spackenv
 
    cat <<EOF | /bin/sh >$HOME/env/spackenv
-   FIND='spack module loads --prefix linux-SuSE11-x86_64/'
+   FIND='spack module tcl loads --prefix linux-SuSE11-x86_64/'
 
    \$FIND modele-utils
    \$FIND emacs
@@ -346,14 +351,14 @@ Users may now put ``source ~/env/spackenv`` into ``.bashrc``.
    Some module systems put a prefix on the names of modules created
    by Spack.  For example, that prefix is ``linux-SuSE11-x86_64/`` in
    the above case.  If a prefix is not needed, you may omit the
-   ``--prefix`` flag from ``spack module loads``.
+   ``--prefix`` flag from ``spack module tcl loads``.
 
 
 """""""""""""""""""""""
 Transitive Dependencies
 """""""""""""""""""""""
 
-In the script above, each ``spack module loads`` command generates a
+In the script above, each ``spack module tcl loads`` command generates a
 *single* ``module load`` line.  Transitive dependencies do not usually
 need to be loaded, only modules the user needs in ``$PATH``.  This is
 because Spack builds binaries with RPATH.  Spack's RPATH policy has
@@ -394,38 +399,13 @@ Unfortunately, Spack's RPATH support does not work in all case.  For example:
 In cases where RPATH support doesn't make things "just work," it can
 be necessary to load a module's dependencies as well as the module
 itself.  This is done by adding the ``--dependencies`` flag to the
-``spack module loads`` command.  For example, the following line,
+``spack module tcl loads`` command.  For example, the following line,
 added to the script above, would be used to load SciPy, along with
 Numpy, core Python, BLAS/LAPACK and anything else needed:
 
 .. code-block:: sh
 
-   spack module loads --dependencies py-scipy
-
-^^^^^^^^^^^^^^^^^^
-Extension Packages
-^^^^^^^^^^^^^^^^^^
-
-:ref:`packaging_extensions` may be used as an alternative to loading
-Python (and similar systems) packages directly.  If extensions are
-activated, then ``spack load python`` will also load all the
-extensions activated for the given ``python``.  This reduces the need
-for users to load a large number of modules.
-
-However, Spack extensions have two potential drawbacks:
-
-#. Activated packages that involve compiled C extensions may still
-   need their dependencies to be loaded manually.  For example,
-   ``spack load openblas`` might be required to make ``py-numpy``
-   work.
-
-#. Extensions "break" a core feature of Spack, which is that multiple
-   versions of a package can co-exist side-by-side.  For example,
-   suppose you wish to run a Python package in two different
-   environments but the same basic Python --- one with
-   ``py-numpy@1.7`` and one with ``py-numpy@1.8``.  Spack extensions
-   will not support this potential debugging use case.
-
+   spack module tcl loads --dependencies py-scipy
 
 ^^^^^^^^^^^^^^
 Dummy Packages
@@ -447,6 +427,8 @@ it.  A disadvantage is the set of packages will be consistent; this
 means you cannot load up two applications this way if they are not
 consistent with each other.
 
+.. _filesystem-views:
+
 ^^^^^^^^^^^^^^^^
 Filesystem Views
 ^^^^^^^^^^^^^^^^
@@ -537,7 +519,7 @@ dependencies, but not ``appsy`` itself:
 
 .. code-block:: console
 
-   $ spack view symlink --dependencies yes --exclude appsy appsy
+   $ spack view --dependencies yes --exclude appsy symlink /path/to/MYVIEW/ appsy
 
 Alternately, you wish to create a view whose purpose is to provide
 binary executables to end users.  You only need to include
@@ -546,7 +528,7 @@ dependencies.  In this case, you might use:
 
 .. code-block:: console
 
-   $ spack view symlink --dependencies no cmake
+   $ spack view --dependencies no symlink /path/to/MYVIEW/ cmake
 
 
 """""""""""""""""""""""
@@ -587,6 +569,29 @@ symlinks.  At any time one can delete ``/path/to/MYVIEW`` or use
 ``spack view`` to manage it surgically.  None of this will affect the
 real Spack install area.
 
+^^^^^^^^^^^^^^^^^^
+Global Activations
+^^^^^^^^^^^^^^^^^^
+
+:ref:`cmd-spack-activate` may be used as an alternative to loading
+Python (and similar systems) packages directly or creating a view.
+If extensions are globally activated, then ``spack load python`` will
+also load all the extensions activated for the given ``python``.
+This reduces the need for users to load a large number of modules.
+
+However, Spack global activations have two potential drawbacks:
+
+#. Activated packages that involve compiled C extensions may still
+   need their dependencies to be loaded manually.  For example,
+   ``spack load openblas`` might be required to make ``py-numpy``
+   work.
+
+#. Global activations "break" a core feature of Spack, which is that
+   multiple versions of a package can co-exist side-by-side.  For example,
+   suppose you wish to run a Python package in two different
+   environments but the same basic Python --- one with
+   ``py-numpy@1.7`` and one with ``py-numpy@1.8``.  Spack extensions
+   will not support this potential debugging use case.
 
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 Discussion: Running Binaries
@@ -630,7 +635,7 @@ environments:
   and extension packages.
 
 * Views and activated extensions maintain state that is semantically
-  equivalent to the information in a ``spack module loads`` script.
+  equivalent to the information in a ``spack module tcl loads`` script.
   Administrators might find things easier to maintain without the
   added "heavyweight" state of a view.
 
@@ -787,7 +792,7 @@ for the ``mylib`` package (ellipses for brevity):
        depends_on('cmake', type='build')
        depends_on('doxygen', type='build')
 
-       def configure_args(self):
+       def cmake_args(self):
            spec = self.spec
            return [
                '-DUSE_EVERYTRACE=%s' % ('YES' if '+everytrace' in spec else 'NO'),
@@ -1254,6 +1259,28 @@ Just use the `docker bootstraping mechanism <http://singularity.lbl.gov/quicksta
    %runscript
    exec /bin/bash -l
 
+""""""""""""""""""""""
+Docker for Development
+""""""""""""""""""""""
+
+For examples of how we use docker in development, see
+:ref:`docker_for_developers`.
+
+"""""""""""""""""""""""""
+Docker on Windows and OSX
+"""""""""""""""""""""""""
+
+On Mac OS and Windows, docker runs on a hypervisor that is not allocated much
+memory by default, and some spack packages may fail to build due to lack of
+memory. To work around this issue, consider configuring your docker installation
+to use more of your host memory. In some cases, you can also ease the memory
+pressure on parallel builds by limiting the parallelism in your config.yaml.
+
+.. code-block:: yaml
+
+   config:
+     build_jobs: 2
+
 ------------------
 Upstream Bug Fixes
 ------------------
diff --git a/lib/spack/env/cc b/lib/spack/env/cc
index b06c6fd6fc..3b83291cc2 100755
--- a/lib/spack/env/cc
+++ b/lib/spack/env/cc
@@ -1,28 +1,10 @@
 #!/bin/bash
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 # Spack compiler wrapper script.
 #
@@ -52,6 +34,7 @@ parameters=(
     SPACK_F77_RPATH_ARG
     SPACK_FC_RPATH_ARG
     SPACK_SHORT_SPEC
+    SPACK_SYSTEM_DIRS
 )
 
 # The compiler input variables are checked for sanity later:
@@ -73,7 +56,31 @@ function die {
     exit 1
 }
 
-for param in ${parameters[@]}; do
+# read input parameters into proper bash arrays.
+# SYSTEM_DIRS is delimited by :
+IFS=':' read -ra SPACK_SYSTEM_DIRS <<< "${SPACK_SYSTEM_DIRS}"
+
+# SPACK_<LANG>FLAGS and SPACK_LDLIBS are split by ' '
+IFS=' ' read -ra SPACK_FFLAGS   <<< "$SPACK_FFLAGS"
+IFS=' ' read -ra SPACK_CPPFLAGS <<< "$SPACK_CPPFLAGS"
+IFS=' ' read -ra SPACK_CFLAGS   <<< "$SPACK_CFLAGS"
+IFS=' ' read -ra SPACK_CXXFLAGS <<< "$SPACK_CXXFLAGS"
+IFS=' ' read -ra SPACK_LDFLAGS  <<< "$SPACK_LDFLAGS"
+IFS=' ' read -ra SPACK_LDLIBS   <<< "$SPACK_LDLIBS"
+
+# test whether a path is a system directory
+function system_dir {
+    path="$1"
+    for sd in "${SPACK_SYSTEM_DIRS[@]}"; do
+        if [ "${path}" == "${sd}" ] || [ "${path}" == "${sd}/" ]; then
+            # success if path starts with a system prefix
+            return 0
+        fi
+    done
+    return 1  # fail if path starts no system prefix
+}
+
+for param in "${parameters[@]}"; do
     if [[ -z ${!param} ]]; then
         die "Spack compiler must be run from Spack! Input '$param' is missing."
     fi
@@ -117,7 +124,7 @@ case "$command" in
         comp="FC"
         lang_flags=F
         ;;
-    f77|gfortran|flang|ifort|pgfortran|xlf|xlf_r|nagfor|ftn)
+    f77|xlf|xlf_r|pgf77)
         command="$SPACK_F77"
         language="Fortran 77"
         comp="F77"
@@ -136,10 +143,12 @@ esac
 # libraries.
 if [[ -z $mode ]] || [[ $mode == ld ]]; then
     for arg in "$@"; do
-        if [[ $arg == -v || $arg == -V || $arg == --version || $arg == -dumpversion ]]; then
-            mode=vcheck
-            break
-        fi
+        case $arg in
+            -v|-V|--version|-dumpversion)
+                mode=vcheck
+                break
+                ;;
+        esac
     done
 fi
 
@@ -163,7 +172,7 @@ fi
 # Set up rpath variable according to language.
 eval rpath=\$SPACK_${comp}_RPATH_ARG
 
-# Dump the version and exit if we're in testing mode.
+# Dump the mode and exit if the command is dump-mode.
 if [[ $SPACK_TEST_COMMAND == dump-mode ]]; then
     echo "$mode"
     exit
@@ -176,50 +185,40 @@ if [[ -z $command ]]; then
 fi
 
 #
-# Set paths as defined in the 'environment' section of the compiler config
-#   names are stored in SPACK_ENV_TO_SET
-#   values are stored in SPACK_ENV_SET_<varname>
-#
-IFS=':' read -ra env_set_varnames <<< "$SPACK_ENV_TO_SET"
-for varname in "${env_set_varnames[@]}"; do
-    spack_varname="SPACK_ENV_SET_$varname"
-    export $varname=${!spack_varname}
-    unset $spack_varname
-done
-
-#
 # Filter '.' and Spack environment directories out of PATH so that
 # this script doesn't just call itself
 #
 IFS=':' read -ra env_path <<< "$PATH"
 IFS=':' read -ra spack_env_dirs <<< "$SPACK_ENV_PATH"
 spack_env_dirs+=("" ".")
-PATH=""
+export PATH=""
 for dir in "${env_path[@]}"; do
     addpath=true
     for env_dir in "${spack_env_dirs[@]}"; do
-        if [[ $dir == $env_dir ]]; then
+        if [[ "$dir" == "$env_dir" ]]; then
             addpath=false
             break
         fi
     done
     if $addpath; then
-        PATH="${PATH:+$PATH:}$dir"
+        export PATH="${PATH:+$PATH:}$dir"
     fi
 done
-export PATH
 
 if [[ $mode == vcheck ]]; then
-    exec ${command} "$@"
+    exec "${command}" "$@"
 fi
 
 # Darwin's linker has a -r argument that merges object files together.
 # It doesn't work with -rpath.
 # This variable controls whether they are added.
 add_rpaths=true
-if [[ ($mode == ld || $mode == ccld) && "$SPACK_SHORT_SPEC" =~ "darwin" ]]; then
+if [[ ($mode == ld || $mode == ccld) && "$SPACK_SHORT_SPEC" =~ "darwin" ]];
+then
     for arg in "$@"; do
-        if [[ ($arg == -r && $mode == ld) || ($arg == -r && $mode == ccld) || ($arg == -Wl,-r && $mode == ccld) ]]; then
+        if [[ ($arg == -r && $mode == ld) ||
+              ($arg == -r && $mode == ccld) ||
+              ($arg == -Wl,-r && $mode == ccld) ]]; then
             add_rpaths=false
             break
         fi
@@ -227,126 +226,285 @@ if [[ ($mode == ld || $mode == ccld) && "$SPACK_SHORT_SPEC" =~ "darwin" ]]; then
 fi
 
 # Save original command for debug logging
-input_command="$@"
-args=("$@")
+input_command="$*"
+
+#
+# Parse the command line arguments.
+#
+# We extract -L, -I, and -Wl,-rpath arguments from the command line and
+# recombine them with Spack arguments later.  We parse these out so that
+# we can make sure that system paths come last, that package arguments
+# come first, and that Spack arguments are injected properly.
+#
+# All other arguments, including -l arguments, are treated as
+# 'other_args' and left in their original order.  This ensures that
+# --start-group, --end-group, and other order-sensitive flags continue to
+# work as the caller expects.
+#
+# The libs variable is initialized here for completeness, and it is also
+# used later to inject flags supplied via `ldlibs` on the command
+# line. These come into the wrappers via SPACK_LDLIBS.
+#
+includes=()
+libdirs=()
+rpaths=()
+system_includes=()
+system_libdirs=()
+system_rpaths=()
+libs=()
+other_args=()
 
-# Prepend cppflags, cflags, cxxflags, fcflags, fflags, and ldflags
+while [ -n "$1" ]; do
+    # an RPATH to be added after the case statement.
+    rp=""
 
-# Add ldflags
+    case "$1" in
+        -I*)
+            arg="${1#-I}"
+            if [ -z "$arg" ]; then shift; arg="$1"; fi
+            if system_dir "$arg"; then
+                system_includes+=("$arg")
+            else
+                includes+=("$arg")
+            fi
+            ;;
+        -L*)
+            arg="${1#-L}"
+            if [ -z "$arg" ]; then shift; arg="$1"; fi
+            if system_dir "$arg"; then
+                system_libdirs+=("$arg")
+            else
+                libdirs+=("$arg")
+            fi
+            ;;
+        -l*)
+            arg="${1#-l}"
+            if [ -z "$arg" ]; then shift; arg="$1"; fi
+            other_args+=("-l$arg")
+            ;;
+        -Wl,*)
+            arg="${1#-Wl,}"
+            if [ -z "$arg" ]; then shift; arg="$1"; fi
+            if [[ "$arg" = -rpath=* ]]; then
+                rp="${arg#-rpath=}"
+            elif [[ "$arg" = -rpath,* ]]; then
+                rp="${arg#-rpath,}"
+            elif [[ "$arg" = -rpath ]]; then
+                shift; arg="$1"
+                if [[ "$arg" != -Wl,* ]]; then
+                    die "-Wl,-rpath was not followed by -Wl,*"
+                fi
+                rp="${arg#-Wl,}"
+            else
+                other_args+=("-Wl,$arg")
+            fi
+            ;;
+        -Xlinker,*)
+            arg="${1#-Xlinker,}"
+            if [ -z "$arg" ]; then shift; arg="$1"; fi
+            if [[ "$arg" = -rpath=* ]]; then
+                rp="${arg#-rpath=}"
+            elif [[ "$arg" = -rpath ]]; then
+                shift; arg="$1"
+                if [[ "$arg" != -Xlinker,* ]]; then
+                    die "-Xlinker,-rpath was not followed by -Xlinker,*"
+                fi
+                rp="${arg#-Xlinker,}"
+            else
+                other_args+=("-Xlinker,$arg")
+            fi
+            ;;
+        -Xlinker)
+            if [[ "$2" == "-rpath" ]]; then
+                if [[ "$3" != "-Xlinker" ]]; then
+                    die "-Xlinker,-rpath was not followed by -Xlinker,*"
+                fi
+                shift 3;
+                rp="$1"
+            else
+                other_args+=("$1")
+            fi
+            ;;
+        *)
+            other_args+=("$1")
+            ;;
+    esac
+
+    # test rpaths against system directories in one place.
+    if [ -n "$rp" ]; then
+        if system_dir "$rp"; then
+            system_rpaths+=("$rp")
+        else
+            rpaths+=("$rp")
+        fi
+    fi
+    shift
+done
+
+#
+# Add flags from Spack's cppflags, cflags, cxxflags, fcflags, fflags, and
+# ldflags. We stick to the order that gmake puts the flags in by default.
+#
+# See the gmake manual on implicit rules for details:
+# https://www.gnu.org/software/make/manual/html_node/Implicit-Variables.html
+#
+flags=()
+
+# Fortran flags come before CPPFLAGS
 case "$mode" in
-    ld|ccld)
-        args=(${SPACK_LDFLAGS[@]} "${args[@]}") ;;
+    cc|ccld)
+        case $lang_flags in
+            F)
+                flags=("${flags[@]}" "${SPACK_FFLAGS[@]}") ;;
+        esac
+        ;;
+esac
+
+# C preprocessor flags come before any C/CXX flags
+case "$mode" in
+    cpp|as|cc|ccld)
+        flags=("${flags[@]}" "${SPACK_CPPFLAGS[@]}") ;;
 esac
 
-# Add compiler flags.
+
+# Add C and C++ flags
 case "$mode" in
     cc|ccld)
-    # Add c, cxx, fc, and f flags
         case $lang_flags in
             C)
-                args=(${SPACK_CFLAGS[@]} "${args[@]}") ;;
+                flags=("${flags[@]}" "${SPACK_CFLAGS[@]}") ;;
             CXX)
-                args=(${SPACK_CXXFLAGS[@]} "${args[@]}") ;;
+                flags=("${flags[@]}" "${SPACK_CXXFLAGS[@]}") ;;
         esac
         ;;
 esac
 
-# Add cppflags
+# Linker flags
 case "$mode" in
-    cpp|as|cc|ccld)
-        args=(${SPACK_CPPFLAGS[@]} "${args[@]}") ;;
+    ld|ccld)
+        flags=("${flags[@]}" "${SPACK_LDFLAGS[@]}") ;;
 esac
 
-case "$mode" in cc|ccld)
-        # Add fortran flags
-        case $lang_flags in
-            F)
-                args=(${SPACK_FFLAGS[@]} "${args[@]}") ;;
-        esac
+
+# Include the package's prefix/lib[64] dirs in rpath. We don't know until
+# *after* installation which one's correct, so we include both lib and
+# lib64, assuming that only one will be present.
+case "$mode" in
+    ld|ccld)
+        $add_rpaths && rpaths+=("$SPACK_PREFIX/lib")
+        $add_rpaths && rpaths+=("$SPACK_PREFIX/lib64")
         ;;
 esac
 
-# Read spack dependencies from the path environment variable
+# Read spack dependencies from the environment. This is a list of prefixes.
 IFS=':' read -ra deps <<< "$SPACK_DEPENDENCIES"
 for dep in "${deps[@]}"; do
-    # Prepend include directories
-    if [[ -d $dep/include ]]; then
-        if [[ $mode == cpp || $mode == cc || $mode == as || $mode == ccld ]]; then
-            args=("-I$dep/include" "${args[@]}")
-        fi
-    fi
-
-    # Prepend lib and RPATH directories
-    if [[ -d $dep/lib ]]; then
-        if [[ $mode == ccld ]]; then
-            if [[ $SPACK_RPATH_DEPS == *$dep* ]]; then
-                $add_rpaths && args=("$rpath$dep/lib" "${args[@]}")
-            fi
-            if [[ $SPACK_LINK_DEPS == *$dep* ]]; then
-                args=("-L$dep/lib" "${args[@]}")
-            fi
-        elif [[ $mode == ld ]]; then
-            if [[ $SPACK_RPATH_DEPS == *$dep* ]]; then
-                $add_rpaths && args=("-rpath" "$dep/lib" "${args[@]}")
+    # Append include directories in any compilation mode
+    case "$mode" in
+        cpp|cc|as|ccld)
+            if [[ -d $dep/include ]]; then
+                includes=("${includes[@]}" "$dep/include")
             fi
-            if [[ $SPACK_LINK_DEPS == *$dep* ]]; then
-                args=("-L$dep/lib" "${args[@]}")
-            fi
-        fi
-    fi
+            ;;
+    esac
 
-    # Prepend lib64 and RPATH directories
-    if [[ -d $dep/lib64 ]]; then
-        if [[ $mode == ccld ]]; then
-            if [[ $SPACK_RPATH_DEPS == *$dep* ]]; then
-                $add_rpaths && args=("$rpath$dep/lib64" "${args[@]}")
+    # Append lib/lib64 and RPATH directories, but only if we're linking
+    case "$mode" in
+        ld|ccld)
+            if [[ -d $dep/lib ]]; then
+                if [[ $SPACK_RPATH_DEPS == *$dep* ]]; then
+                    $add_rpaths && rpaths=("${rpaths[@]}" "$dep/lib")
+                fi
+                if [[ $SPACK_LINK_DEPS == *$dep* ]]; then
+                    libdirs=("${libdirs[@]}" "$dep/lib")
+                fi
             fi
-            if [[ $SPACK_LINK_DEPS == *$dep* ]]; then
-                args=("-L$dep/lib64" "${args[@]}")
-            fi
-        elif [[ $mode == ld ]]; then
-            if [[ $SPACK_RPATH_DEPS == *$dep* ]]; then
-                $add_rpaths && args=("-rpath" "$dep/lib64" "${args[@]}")
-            fi
-            if [[ $SPACK_LINK_DEPS == *$dep* ]]; then
-                args=("-L$dep/lib64" "${args[@]}")
+
+            if [[ -d $dep/lib64 ]]; then
+                if [[ $SPACK_RPATH_DEPS == *$dep* ]]; then
+                    $add_rpaths && rpaths+=("$dep/lib64")
+                fi
+                if [[ $SPACK_LINK_DEPS == *$dep* ]]; then
+                    libdirs+=("$dep/lib64")
+                fi
             fi
-        fi
-    fi
+            ;;
+    esac
 done
 
-# Include all -L's and prefix/whatever dirs in rpath
-if [[ $mode == ccld ]]; then
-    $add_rpaths && args=("$rpath$SPACK_PREFIX/lib64" "${args[@]}")
-    $add_rpaths && args=("$rpath$SPACK_PREFIX/lib"   "${args[@]}")
-elif [[ $mode == ld ]]; then
-    $add_rpaths && args=("-rpath" "$SPACK_PREFIX/lib64" "${args[@]}")
-    $add_rpaths && args=("-rpath" "$SPACK_PREFIX/lib"   "${args[@]}")
-fi
+# add RPATHs if we're in in any linking mode
+case "$mode" in
+    ld|ccld)
+        # Set extra RPATHs
+        IFS=':' read -ra extra_rpaths <<< "$SPACK_COMPILER_EXTRA_RPATHS"
+        for extra_rpath in "${extra_rpaths[@]}"; do
+            $add_rpaths && rpaths+=("$extra_rpath")
+            libdirs+=("$extra_rpath")
+        done
 
-# Set extra RPATHs
-IFS=':' read -ra extra_rpaths <<< "$SPACK_COMPILER_EXTRA_RPATHS"
-for extra_rpath in "${extra_rpaths[@]}"; do
-    if [[ $mode == ccld ]]; then
-        $add_rpaths && args=("$rpath$extra_rpath" "${args[@]}")
-        args=("-L$extra_rpath" "${args[@]}")
-    elif [[ $mode == ld ]]; then
-        $add_rpaths && args=("-rpath" "$extra_rpath" "${args[@]}")
-        args=("-L$extra_rpath" "${args[@]}")
-    fi
-done
+        # Add SPACK_LDLIBS to args
+        for lib in "${SPACK_LDLIBS[@]}"; do
+            libs+=("${lib#-l}")
+        done
+        ;;
+esac
+
+#
+# Finally, reassemble the command line.
+#
+
+# Includes and system includes first
+args=()
+
+# flags assembled earlier
+args+=("${flags[@]}")
 
-# Add SPACK_LDLIBS to args
+# include directory search paths
+for dir in "${includes[@]}";         do args+=("-I$dir"); done
+for dir in "${system_includes[@]}";  do args+=("-I$dir"); done
+
+# Library search paths
+for dir in "${libdirs[@]}";          do args+=("-L$dir"); done
+for dir in "${system_libdirs[@]}";   do args+=("-L$dir"); done
+
+# RPATHs arguments
 case "$mode" in
-    ld|ccld)
-        args=("${args[@]}" ${SPACK_LDLIBS[@]}) ;;
+    ccld)
+        for dir in "${rpaths[@]}";        do args+=("$rpath$dir"); done
+        for dir in "${system_rpaths[@]}"; do args+=("$rpath$dir"); done
+        ;;
+    ld)
+        for dir in "${rpaths[@]}";        do args+=("-rpath" "$dir"); done
+        for dir in "${system_rpaths[@]}"; do args+=("-rpath" "$dir"); done
+        ;;
 esac
 
+# Other arguments from the input command
+args+=("${other_args[@]}")
+
+# Inject SPACK_LDLIBS, if supplied
+for lib in "${libs[@]}"; do
+    args+=("-l$lib");
+done
+
 full_command=("$command" "${args[@]}")
 
-# In test command mode, write out full command for Spack tests.
+# prepend the ccache binary if we're using ccache
+if [ -n "$SPACK_CCACHE_BINARY" ]; then
+    case "$lang_flags" in
+        C|CXX)  # ccache only supports C languages
+            full_command=("${SPACK_CCACHE_BINARY}" "${full_command[@]}")
+            # workaround for stage being a temp folder
+            # see #3761#issuecomment-294352232
+            export CCACHE_NOHASHDIR=yes
+            ;;
+    esac
+fi
+
+# dump the full command if the caller supplies SPACK_TEST_COMMAND=dump-args
 if [[ $SPACK_TEST_COMMAND == dump-args ]]; then
-    echo "${full_command[@]}"
+    IFS="
+" && echo "${full_command[*]}"
     exit
 elif [[ -n $SPACK_TEST_COMMAND ]]; then
     die "ERROR: Unknown test command"
@@ -359,7 +517,7 @@ if [[ $SPACK_DEBUG == TRUE ]]; then
     input_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_DEBUG_LOG_ID.in.log"
     output_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_DEBUG_LOG_ID.out.log"
     echo "[$mode] $command $input_command" >> "$input_log"
-    echo "[$mode] ${full_command[@]}" >> "$output_log"
+    echo "[$mode] ${full_command[*]}" >> "$output_log"
 fi
 
 exec "${full_command[@]}"
diff --git a/lib/spack/external/__init__.py b/lib/spack/external/__init__.py
index 1dfdf7f72d..320d3a6341 100644
--- a/lib/spack/external/__init__.py
+++ b/lib/spack/external/__init__.py
@@ -1,51 +1,120 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-"""
-This module contains external, potentially separately licensed,
-packages that are included in spack.
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+"""This module contains the following external, potentially separately
+licensed, packages that are included in Spack:
+
+argparse
+--------
+
+* Homepage: https://pypi.python.org/pypi/argparse
+* Usage: We include our own version to be Python 2.6 compatible.
+* Version: 1.4.0
+* Note: This package has been slightly modified to improve
+  error message formatting. See the following commit if the
+  vendored copy ever needs to be updated again:
+  https://github.com/spack/spack/pull/6786/commits/dfcef577b77249106ea4e4c69a6cd9e64fa6c418
+
+ctest_log_parser
+----------------
+
+* Homepage: https://github.com/Kitware/CMake/blob/master/Source/CTest/cmCTestBuildHandler.cxx
+* Usage: Functions to parse build logs and extract error messages.
+* Version: Unversioned
+* Note: This is a homemade port of Kitware's CTest build handler.
+
+distro
+------
+
+* Homepage: https://pypi.python.org/pypi/distro
+* Usage: Provides a more stable linux distribution detection.
+* Version: 1.0.4 (last version supporting Python 2.6)
+
+functools
+---------
+
+* Homepage: https://github.com/python/cpython/blob/2.7/Lib/functools.py
+* Usage: Used for implementation of total_ordering.
+* Version: Unversioned
+* Note: This is the functools.total_ordering implementation
+  from Python 2.7 backported so we can run on Python 2.6.
+
+jinja2
+------
+
+* Homepage: https://pypi.python.org/pypi/Jinja2
+* Usage: A modern and designer-friendly templating language for Python.
+* Version: 2.10
+
+jsonschema
+----------
+
+* Homepage: https://pypi.python.org/pypi/jsonschema
+* Usage: An implementation of JSON Schema for Python.
+* Version: 2.4.0 (last version before functools32 dependency was added)
+* Note: functools32 doesn't support Python 2.6 or 3.0, so jsonschema
+  cannot be upgraded any further
+
+markupsafe
+----------
+
+* Homepage: https://pypi.python.org/pypi/MarkupSafe
+* Usage: Implements a XML/HTML/XHTML Markup safe string for Python.
+* Version: 1.0
+
+orderddict
+----------
+
+* Homepage: https://pypi.org/project/ordereddict/
+* Usage: A drop-in substitute for Py2.7's new collections.OrderedDict
+  that works in Python 2.4-2.6.
+* Version: 1.1
 
-So far:
-    argparse:    We include our own version to be Python 2.6 compatible.
+py
+--
 
-    distro:      Provides a more stable linux distribution detection.
+* Homepage: https://pypi.python.org/pypi/py
+* Usage: Needed by pytest. Library with cross-python path,
+  ini-parsing, io, code, and log facilities.
+* Version: 1.4.34 (last version supporting Python 2.6)
 
-    functools:   Used for implementation of total_ordering.
+pyqver
+------
 
-    jinja2:      A modern and designer-friendly templating language for Python
+* Homepage: https://github.com/ghewgill/pyqver
+* Usage: External script to query required python version of
+  python source code. Used for ensuring 2.6 compatibility.
+* Version: Unversioned
 
-    jsonschema:  An implementation of JSON Schema for Python.
+pytest
+------
 
-    ordereddict: We include our own version to be Python 2.6 compatible.
+* Homepage: https://pypi.python.org/pypi/pytest
+* Usage: Testing framework used by Spack.
+* Version: 3.2.5 (last version supporting Python 2.6)
+* Note: This package has been slightly modified to improve
+  Python 2.6 compatibility. See the following commit if the
+  vendored copy ever needs to be updated again:
+  https://github.com/spack/spack/pull/6801/commits/ff513c39f2c67ff615de5cbc581dd69a8ec96526
 
-    py:          Needed by pytest.  Library with cross-python path,
-                 ini-parsing, io, code, and log facilities.
+ruamel.yaml
+------
 
-    pyqver2:     External script to query required python version of
-                 python source code. Used for ensuring 2.6 compatibility.
+* Homepage: https://yaml.readthedocs.io/
+* Usage: Used for config files. Ruamel is based on PyYAML but is more
+  actively maintained and has more features, including round-tripping
+  comments read from config files.
+* Version: 0.11.15 (last version supporting Python 2.6)
+* Note: This package has been slightly modified to improve Python 2.6
+  compatibility -- some ``{}`` format strings were replaced, and the
+  import for ``OrderedDict`` was tweaked.
 
-    pytest:      Testing framework used by Spack.
+six
+---
 
-    yaml:        Used for config files.
+* Homepage: https://pypi.python.org/pypi/six
+* Usage: Python 2 and 3 compatibility utilities.
+* Version: 1.11.0
 """
diff --git a/lib/spack/external/_pytest/AUTHORS b/lib/spack/external/_pytest/AUTHORS
deleted file mode 100644
index 8c7cb19cee..0000000000
--- a/lib/spack/external/_pytest/AUTHORS
+++ /dev/null
@@ -1,141 +0,0 @@
-Holger Krekel, holger at merlinux eu
-merlinux GmbH, Germany, office at merlinux eu
-
-Contributors include::
-
-Abdeali JK
-Abhijeet Kasurde
-Ahn Ki-Wook
-Alexei Kozlenok
-Anatoly Bubenkoff
-Andreas Zeidler
-Andrzej Ostrowski
-Andy Freeland
-Anthon van der Neut
-Antony Lee
-Armin Rigo
-Aron Curzon
-Aviv Palivoda
-Ben Webb
-Benjamin Peterson
-Bernard Pratz
-Bob Ippolito
-Brian Dorsey
-Brian Okken
-Brianna Laugher
-Bruno Oliveira
-Cal Leeming
-Carl Friedrich Bolz
-Charles Cloud
-Charnjit SiNGH (CCSJ)
-Chris Lamb
-Christian Boelsen
-Christian Theunert
-Christian Tismer
-Christopher Gilling
-Daniel Grana
-Daniel Hahler
-Daniel Nuri
-Daniel Wandschneider
-Danielle Jenkins
-Dave Hunt
-David Díaz-Barquero
-David Mohr
-David Vierra
-Diego Russo
-Dmitry Dygalo
-Duncan Betts
-Edison Gustavo Muenz
-Edoardo Batini
-Eduardo Schettino
-Elizaveta Shashkova
-Endre Galaczi
-Eric Hunsberger
-Eric Siegerman
-Erik M. Bray
-Feng Ma
-Florian Bruhin
-Floris Bruynooghe
-Gabriel Reis
-Georgy Dyuldin
-Graham Horler
-Greg Price
-Grig Gheorghiu
-Grigorii Eremeev (budulianin)
-Guido Wesdorp
-Harald Armin Massa
-Ian Bicking
-Jaap Broekhuizen
-Jan Balster
-Janne Vanhala
-Jason R. Coombs
-Javier Domingo Cansino
-Javier Romero
-John Towler
-Jon Sonesen
-Jordan Guymon
-Joshua Bronson
-Jurko Gospodnetić
-Justyna Janczyszyn
-Kale Kundert
-Katarzyna Jachim
-Kevin Cox
-Lee Kamentsky
-Lev Maximov
-Lukas Bednar
-Luke Murphy
-Maciek Fijalkowski
-Maho
-Marc Schlaich
-Marcin Bachry
-Mark Abramowitz
-Markus Unterwaditzer
-Martijn Faassen
-Martin K. Scherer
-Martin Prusse
-Mathieu Clabaut
-Matt Bachmann
-Matt Williams
-Matthias Hafner
-mbyt
-Michael Aquilina
-Michael Birtwell
-Michael Droettboom
-Michael Seifert
-Mike Lundy
-Ned Batchelder
-Neven Mundar
-Nicolas Delaby
-Oleg Pidsadnyi
-Oliver Bestwalter
-Omar Kohl
-Pieter Mulder
-Piotr Banaszkiewicz
-Punyashloka Biswal
-Quentin Pradet
-Ralf Schmitt
-Raphael Pierzina
-Raquel Alegre
-Roberto Polli
-Romain Dorgueil
-Roman Bolshakov
-Ronny Pfannschmidt
-Ross Lawley
-Russel Winder
-Ryan Wooden
-Samuele Pedroni
-Simon Gomizelj
-Stefan Farmbauer
-Stefan Zimmermann
-Stefano Taschini
-Steffen Allner
-Stephan Obermann
-Tareq Alayan
-Ted Xiao
-Thomas Grainger
-Tom Viner
-Trevor Bekolay
-Tyler Goodlet
-Vasily Kuznetsov
-Wouter van Ackooy
-Xuecong Liao
diff --git a/lib/spack/external/_pytest/LICENSE b/lib/spack/external/_pytest/LICENSE
index 9e27bd7841..629df45ac4 100644
--- a/lib/spack/external/_pytest/LICENSE
+++ b/lib/spack/external/_pytest/LICENSE
@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2004-2016 Holger Krekel and others
+Copyright (c) 2004-2017 Holger Krekel and others
 
 Permission is hereby granted, free of charge, to any person obtaining a copy of
 this software and associated documentation files (the "Software"), to deal in
diff --git a/lib/spack/external/_pytest/README.rst b/lib/spack/external/_pytest/README.rst
deleted file mode 100644
index d5650af655..0000000000
--- a/lib/spack/external/_pytest/README.rst
+++ /dev/null
@@ -1,102 +0,0 @@
-.. image:: http://docs.pytest.org/en/latest/_static/pytest1.png
-   :target: http://docs.pytest.org
-   :align: center
-   :alt: pytest
-
-------
-
-.. image:: https://img.shields.io/pypi/v/pytest.svg
-   :target: https://pypi.python.org/pypi/pytest
-.. image:: https://img.shields.io/pypi/pyversions/pytest.svg
-  :target: https://pypi.python.org/pypi/pytest
-.. image:: https://img.shields.io/coveralls/pytest-dev/pytest/master.svg
-   :target: https://coveralls.io/r/pytest-dev/pytest
-.. image:: https://travis-ci.org/pytest-dev/pytest.svg?branch=master
-    :target: https://travis-ci.org/pytest-dev/pytest
-.. image:: https://ci.appveyor.com/api/projects/status/mrgbjaua7t33pg6b?svg=true
-    :target: https://ci.appveyor.com/project/pytestbot/pytest
-
-The ``pytest`` framework makes it easy to write small tests, yet
-scales to support complex functional testing for applications and libraries.
-
-An example of a simple test:
-
-.. code-block:: python
-
-    # content of test_sample.py
-    def inc(x):
-        return x + 1
-
-    def test_answer():
-        assert inc(3) == 5
-
-
-To execute it::
-
-    $ pytest
-    ============================= test session starts =============================    
-    collected 1 items
-
-    test_sample.py F
-
-    ================================== FAILURES ===================================
-    _________________________________ test_answer _________________________________
-
-        def test_answer():
-    >       assert inc(3) == 5
-    E       assert 4 == 5
-    E        +  where 4 = inc(3)
-
-    test_sample.py:5: AssertionError
-    ========================== 1 failed in 0.04 seconds ===========================
-
-
-Due to ``pytest``'s detailed assertion introspection, only plain ``assert`` statements are used. See `getting-started <http://docs.pytest.org/en/latest/getting-started.html#our-first-test-run>`_ for more examples.
-
-
-Features
---------
-
-- Detailed info on failing `assert statements <http://docs.pytest.org/en/latest/assert.html>`_ (no need to remember ``self.assert*`` names);
-
-- `Auto-discovery
-  <http://docs.pytest.org/en/latest/goodpractices.html#python-test-discovery>`_
-  of test modules and functions;
-
-- `Modular fixtures <http://docs.pytest.org/en/latest/fixture.html>`_ for
-  managing small or parametrized long-lived test resources;
-
-- Can run `unittest <http://docs.pytest.org/en/latest/unittest.html>`_ (or trial),
-  `nose <http://docs.pytest.org/en/latest/nose.html>`_ test suites out of the box;
-
-- Python2.6+, Python3.3+, PyPy-2.3, Jython-2.5 (untested);
-
-- Rich plugin architecture, with over 150+ `external plugins <http://docs.pytest.org/en/latest/plugins.html#installing-external-plugins-searching>`_ and thriving community;
-
-
-Documentation
--------------
-
-For full documentation, including installation, tutorials and PDF documents, please see http://docs.pytest.org.
-
-
-Bugs/Requests
--------------
-
-Please use the `GitHub issue tracker <https://github.com/pytest-dev/pytest/issues>`_ to submit bugs or request features.
-
-
-Changelog
----------
-
-Consult the `Changelog <http://docs.pytest.org/en/latest/changelog.html>`__ page for fixes and enhancements of each version.
-
-
-License
--------
-
-Copyright Holger Krekel and others, 2004-2016.
-
-Distributed under the terms of the `MIT`_ license, pytest is free and open source software.
-
-.. _`MIT`: https://github.com/pytest-dev/pytest/blob/master/LICENSE
diff --git a/lib/spack/external/_pytest/__init__.py b/lib/spack/external/_pytest/__init__.py
index be20d3d41c..6e41f0504e 100644
--- a/lib/spack/external/_pytest/__init__.py
+++ b/lib/spack/external/_pytest/__init__.py
@@ -1,2 +1,8 @@
-#
-__version__ = '3.0.5'
+__all__ = ['__version__']
+
+try:
+    from ._version import version as __version__
+except ImportError:
+    # broken installation, we don't even try
+    # unknown only works because we do poor mans version compare
+    __version__ = 'unknown'
diff --git a/lib/spack/external/_pytest/_argcomplete.py b/lib/spack/external/_pytest/_argcomplete.py
index 3ab679d8be..965ec79513 100644
--- a/lib/spack/external/_pytest/_argcomplete.py
+++ b/lib/spack/external/_pytest/_argcomplete.py
@@ -57,26 +57,29 @@ If things do not work right away:
   which should throw a KeyError: 'COMPLINE' (which is properly set by the
   global argcomplete script).
 """
-
+from __future__ import absolute_import, division, print_function
 import sys
 import os
 from glob import glob
 
+
 class FastFilesCompleter:
     'Fast file completer class'
+
     def __init__(self, directories=True):
         self.directories = directories
 
     def __call__(self, prefix, **kwargs):
         """only called on non option completions"""
-        if os.path.sep in prefix[1:]: #
+        if os.path.sep in prefix[1:]:
             prefix_dir = len(os.path.dirname(prefix) + os.path.sep)
         else:
             prefix_dir = 0
         completion = []
         globbed = []
         if '*' not in prefix and '?' not in prefix:
-            if prefix[-1] == os.path.sep:  # we are on unix, otherwise no bash
+            # we are on unix, otherwise no bash
+            if not prefix or prefix[-1] == os.path.sep:
                 globbed.extend(glob(prefix + '.*'))
             prefix += '*'
         globbed.extend(glob(prefix))
@@ -96,7 +99,8 @@ if os.environ.get('_ARGCOMPLETE'):
     filescompleter = FastFilesCompleter()
 
     def try_argcomplete(parser):
-        argcomplete.autocomplete(parser)
+        argcomplete.autocomplete(parser, always_complete_options=False)
 else:
-    def try_argcomplete(parser): pass
+    def try_argcomplete(parser):
+        pass
     filescompleter = None
diff --git a/lib/spack/external/_pytest/_code/__init__.py b/lib/spack/external/_pytest/_code/__init__.py
index 3463c11eac..815c13b42c 100644
--- a/lib/spack/external/_pytest/_code/__init__.py
+++ b/lib/spack/external/_pytest/_code/__init__.py
@@ -1,4 +1,5 @@
 """ python inspection/code generation API """
+from __future__ import absolute_import, division, print_function
 from .code import Code  # noqa
 from .code import ExceptionInfo  # noqa
 from .code import Frame  # noqa
diff --git a/lib/spack/external/_pytest/_code/_py2traceback.py b/lib/spack/external/_pytest/_code/_py2traceback.py
index a830d9899a..5aacf0a428 100644
--- a/lib/spack/external/_pytest/_code/_py2traceback.py
+++ b/lib/spack/external/_pytest/_code/_py2traceback.py
@@ -2,8 +2,10 @@
 # CHANGES:
 # - some_str is replaced, trying to create unicode strings
 #
+from __future__ import absolute_import, division, print_function
 import types
 
+
 def format_exception_only(etype, value):
     """Format the exception part of a traceback.
 
@@ -29,7 +31,7 @@ def format_exception_only(etype, value):
     # would throw another exception and mask the original problem.
     if (isinstance(etype, BaseException) or
         isinstance(etype, types.InstanceType) or
-        etype is None or type(etype) is str):
+            etype is None or type(etype) is str):
         return [_format_final_exc_line(etype, value)]
 
     stype = etype.__name__
@@ -61,6 +63,7 @@ def format_exception_only(etype, value):
     lines.append(_format_final_exc_line(stype, value))
     return lines
 
+
 def _format_final_exc_line(etype, value):
     """Return a list of a single line -- normal case for format_exception_only"""
     valuestr = _some_str(value)
@@ -70,6 +73,7 @@ def _format_final_exc_line(etype, value):
         line = "%s: %s\n" % (etype, valuestr)
     return line
 
+
 def _some_str(value):
     try:
         return unicode(value)
diff --git a/lib/spack/external/_pytest/_code/code.py b/lib/spack/external/_pytest/_code/code.py
index 616d5c4313..f3b7eedfce 100644
--- a/lib/spack/external/_pytest/_code/code.py
+++ b/lib/spack/external/_pytest/_code/code.py
@@ -1,14 +1,16 @@
+from __future__ import absolute_import, division, print_function
 import sys
 from inspect import CO_VARARGS, CO_VARKEYWORDS
 import re
 from weakref import ref
+from _pytest.compat import _PY2, _PY3, PY35, safe_str
 
 import py
 builtin_repr = repr
 
 reprlib = py.builtin._tryimport('repr', 'reprlib')
 
-if sys.version_info[0] >= 3:
+if _PY3:
     from traceback import format_exception_only
 else:
     from ._py2traceback import format_exception_only
@@ -16,6 +18,7 @@ else:
 
 class Code(object):
     """ wrapper around Python code objects """
+
     def __init__(self, rawcode):
         if not hasattr(rawcode, "co_filename"):
             rawcode = getrawcode(rawcode)
@@ -24,7 +27,7 @@ class Code(object):
             self.firstlineno = rawcode.co_firstlineno - 1
             self.name = rawcode.co_name
         except AttributeError:
-            raise TypeError("not a code object: %r" %(rawcode,))
+            raise TypeError("not a code object: %r" % (rawcode,))
         self.raw = rawcode
 
     def __eq__(self, other):
@@ -80,6 +83,7 @@ class Code(object):
             argcount += raw.co_flags & CO_VARKEYWORDS
         return raw.co_varnames[:argcount]
 
+
 class Frame(object):
     """Wrapper around a Python frame holding f_locals and f_globals
     in which expressions can be evaluated."""
@@ -117,7 +121,7 @@ class Frame(object):
         """
         f_locals = self.f_locals.copy()
         f_locals.update(vars)
-        py.builtin.exec_(code, self.f_globals, f_locals )
+        py.builtin.exec_(code, self.f_globals, f_locals)
 
     def repr(self, object):
         """ return a 'safe' (non-recursive, one-line) string repr for 'object'
@@ -141,6 +145,7 @@ class Frame(object):
                 pass     # this can occur when using Psyco
         return retval
 
+
 class TracebackEntry(object):
     """ a single entry in a traceback """
 
@@ -166,7 +171,7 @@ class TracebackEntry(object):
         return self.lineno - self.frame.code.firstlineno
 
     def __repr__(self):
-        return "<TracebackEntry %s:%d>" %(self.frame.code.path, self.lineno+1)
+        return "<TracebackEntry %s:%d>" % (self.frame.code.path, self.lineno + 1)
 
     @property
     def statement(self):
@@ -245,19 +250,21 @@ class TracebackEntry(object):
             line = str(self.statement).lstrip()
         except KeyboardInterrupt:
             raise
-        except:
+        except:  # noqa
             line = "???"
-        return "  File %r:%d in %s\n  %s\n" %(fn, self.lineno+1, name, line)
+        return "  File %r:%d in %s\n  %s\n" % (fn, self.lineno + 1, name, line)
 
     def name(self):
         return self.frame.code.raw.co_name
     name = property(name, None, None, "co_name of underlaying code")
 
+
 class Traceback(list):
     """ Traceback objects encapsulate and offer higher level
         access to Traceback entries.
     """
     Entry = TracebackEntry
+
     def __init__(self, tb, excinfo=None):
         """ initialize from given python traceback object and ExceptionInfo """
         self._excinfo = excinfo
@@ -287,7 +294,7 @@ class Traceback(list):
                 (excludepath is None or not hasattr(codepath, 'relto') or
                  not codepath.relto(excludepath)) and
                 (lineno is None or x.lineno == lineno) and
-                (firstlineno is None or x.frame.code.firstlineno == firstlineno)):
+                    (firstlineno is None or x.frame.code.firstlineno == firstlineno)):
                 return Traceback(x._rawentry, self._excinfo)
         return self
 
@@ -313,7 +320,7 @@ class Traceback(list):
         """ return last non-hidden traceback entry that lead
         to the exception of a traceback.
         """
-        for i in range(-1, -len(self)-1, -1):
+        for i in range(-1, -len(self) - 1, -1):
             entry = self[i]
             if not entry.ishidden():
                 return entry
@@ -328,30 +335,33 @@ class Traceback(list):
             # id for the code.raw is needed to work around
             # the strange metaprogramming in the decorator lib from pypi
             # which generates code objects that have hash/value equality
-            #XXX needs a test
+            # XXX needs a test
             key = entry.frame.code.path, id(entry.frame.code.raw), entry.lineno
-            #print "checking for recursion at", key
-            l = cache.setdefault(key, [])
-            if l:
+            # print "checking for recursion at", key
+            values = cache.setdefault(key, [])
+            if values:
                 f = entry.frame
                 loc = f.f_locals
-                for otherloc in l:
+                for otherloc in values:
                     if f.is_true(f.eval(co_equal,
-                        __recursioncache_locals_1=loc,
-                        __recursioncache_locals_2=otherloc)):
+                                        __recursioncache_locals_1=loc,
+                                        __recursioncache_locals_2=otherloc)):
                         return i
-            l.append(entry.frame.f_locals)
+            values.append(entry.frame.f_locals)
         return None
 
 
 co_equal = compile('__recursioncache_locals_1 == __recursioncache_locals_2',
                    '?', 'eval')
 
+
 class ExceptionInfo(object):
     """ wraps sys.exc_info() objects and offers
         help for navigating the traceback.
     """
     _striptext = ''
+    _assert_start_repr = "AssertionError(u\'assert " if _PY2 else "AssertionError(\'assert "
+
     def __init__(self, tup=None, exprinfo=None):
         import _pytest._code
         if tup is None:
@@ -359,8 +369,8 @@ class ExceptionInfo(object):
             if exprinfo is None and isinstance(tup[1], AssertionError):
                 exprinfo = getattr(tup[1], 'msg', None)
                 if exprinfo is None:
-                    exprinfo = py._builtin._totext(tup[1])
-                if exprinfo and exprinfo.startswith('assert '):
+                    exprinfo = py.io.saferepr(tup[1])
+                if exprinfo and exprinfo.startswith(self._assert_start_repr):
                     self._striptext = 'AssertionError: '
         self._excinfo = tup
         #: the exception class
@@ -401,10 +411,10 @@ class ExceptionInfo(object):
         exconly = self.exconly(tryshort=True)
         entry = self.traceback.getcrashentry()
         path, lineno = entry.frame.code.raw.co_filename, entry.lineno
-        return ReprFileLocation(path, lineno+1, exconly)
+        return ReprFileLocation(path, lineno + 1, exconly)
 
     def getrepr(self, showlocals=False, style="long",
-            abspath=False, tbfilter=True, funcargs=False):
+                abspath=False, tbfilter=True, funcargs=False):
         """ return str()able representation of this exception info.
             showlocals: show locals per traceback entry
             style: long|short|no|native traceback style
@@ -421,7 +431,7 @@ class ExceptionInfo(object):
                 )), self._getreprcrash())
 
         fmt = FormattedExcinfo(showlocals=showlocals, style=style,
-            abspath=abspath, tbfilter=tbfilter, funcargs=funcargs)
+                               abspath=abspath, tbfilter=tbfilter, funcargs=funcargs)
         return fmt.repr_excinfo(self)
 
     def __str__(self):
@@ -465,15 +475,15 @@ class FormattedExcinfo(object):
     def _getindent(self, source):
         # figure out indent for given source
         try:
-            s = str(source.getstatement(len(source)-1))
+            s = str(source.getstatement(len(source) - 1))
         except KeyboardInterrupt:
             raise
-        except:
+        except:  # noqa
             try:
                 s = str(source[-1])
             except KeyboardInterrupt:
                 raise
-            except:
+            except:  # noqa
                 return 0
         return 4 + (len(s) - len(s.lstrip()))
 
@@ -509,7 +519,7 @@ class FormattedExcinfo(object):
             for line in source.lines[:line_index]:
                 lines.append(space_prefix + line)
             lines.append(self.flow_marker + "   " + source.lines[line_index])
-            for line in source.lines[line_index+1:]:
+            for line in source.lines[line_index + 1:]:
                 lines.append(space_prefix + line)
         if excinfo is not None:
             indent = 4 if short else self._getindent(source)
@@ -542,10 +552,10 @@ class FormattedExcinfo(object):
                     # _repr() function, which is only reprlib.Repr in
                     # disguise, so is very configurable.
                     str_repr = self._saferepr(value)
-                    #if len(str_repr) < 70 or not isinstance(value,
+                    # if len(str_repr) < 70 or not isinstance(value,
                     #                            (list, tuple, dict)):
-                    lines.append("%-10s = %s" %(name, str_repr))
-                    #else:
+                    lines.append("%-10s = %s" % (name, str_repr))
+                    # else:
                     #    self._line("%-10s =\\" % (name,))
                     #    # XXX
                     #    py.std.pprint.pprint(value, stream=self.excinfowriter)
@@ -571,14 +581,14 @@ class FormattedExcinfo(object):
             s = self.get_source(source, line_index, excinfo, short=short)
             lines.extend(s)
             if short:
-                message = "in %s" %(entry.name)
+                message = "in %s" % (entry.name)
             else:
                 message = excinfo and excinfo.typename or ""
             path = self._makepath(entry.path)
-            filelocrepr = ReprFileLocation(path, entry.lineno+1, message)
+            filelocrepr = ReprFileLocation(path, entry.lineno + 1, message)
             localsrepr = None
             if not short:
-                localsrepr =  self.repr_locals(entry.locals)
+                localsrepr = self.repr_locals(entry.locals)
             return ReprEntry(lines, reprargs, localsrepr, filelocrepr, style)
         if excinfo:
             lines.extend(self.get_exconly(excinfo, indent=4))
@@ -598,24 +608,54 @@ class FormattedExcinfo(object):
         traceback = excinfo.traceback
         if self.tbfilter:
             traceback = traceback.filter()
-        recursionindex = None
+
         if is_recursion_error(excinfo):
-            recursionindex = traceback.recursionindex()
+            traceback, extraline = self._truncate_recursive_traceback(traceback)
+        else:
+            extraline = None
+
         last = traceback[-1]
         entries = []
-        extraline = None
         for index, entry in enumerate(traceback):
             einfo = (last == entry) and excinfo or None
             reprentry = self.repr_traceback_entry(entry, einfo)
             entries.append(reprentry)
-            if index == recursionindex:
-                extraline = "!!! Recursion detected (same locals & position)"
-                break
         return ReprTraceback(entries, extraline, style=self.style)
 
+    def _truncate_recursive_traceback(self, traceback):
+        """
+        Truncate the given recursive traceback trying to find the starting point
+        of the recursion.
+
+        The detection is done by going through each traceback entry and finding the
+        point in which the locals of the frame are equal to the locals of a previous frame (see ``recursionindex()``.
+
+        Handle the situation where the recursion process might raise an exception (for example
+        comparing numpy arrays using equality raises a TypeError), in which case we do our best to
+        warn the user of the error and show a limited traceback.
+        """
+        try:
+            recursionindex = traceback.recursionindex()
+        except Exception as e:
+            max_frames = 10
+            extraline = (
+                '!!! Recursion error detected, but an error occurred locating the origin of recursion.\n'
+                '  The following exception happened when comparing locals in the stack frame:\n'
+                '    {exc_type}: {exc_msg}\n'
+                '  Displaying first and last {max_frames} stack frames out of {total}.'
+            ).format(exc_type=type(e).__name__, exc_msg=safe_str(e), max_frames=max_frames, total=len(traceback))
+            traceback = traceback[:max_frames] + traceback[-max_frames:]
+        else:
+            if recursionindex is not None:
+                extraline = "!!! Recursion detected (same locals & position)"
+                traceback = traceback[:recursionindex + 1]
+            else:
+                extraline = None
+
+        return traceback, extraline
 
     def repr_excinfo(self, excinfo):
-        if sys.version_info[0] < 3:
+        if _PY2:
             reprtraceback = self.repr_traceback(excinfo)
             reprcrash = excinfo._getreprcrash()
 
@@ -639,7 +679,7 @@ class FormattedExcinfo(object):
                     e = e.__cause__
                     excinfo = ExceptionInfo((type(e), e, e.__traceback__)) if e.__traceback__ else None
                     descr = 'The above exception was the direct cause of the following exception:'
-                elif e.__context__ is not None:
+                elif (e.__context__ is not None and not e.__suppress_context__):
                     e = e.__context__
                     excinfo = ExceptionInfo((type(e), e, e.__traceback__)) if e.__traceback__ else None
                     descr = 'During handling of the above exception, another exception occurred:'
@@ -652,7 +692,7 @@ class FormattedExcinfo(object):
 class TerminalRepr(object):
     def __str__(self):
         s = self.__unicode__()
-        if sys.version_info[0] < 3:
+        if _PY2:
             s = s.encode('utf-8')
         return s
 
@@ -665,7 +705,7 @@ class TerminalRepr(object):
         return io.getvalue().strip()
 
     def __repr__(self):
-        return "<%s instance at %0x>" %(self.__class__, id(self))
+        return "<%s instance at %0x>" % (self.__class__, id(self))
 
 
 class ExceptionRepr(TerminalRepr):
@@ -709,6 +749,7 @@ class ReprExceptionInfo(ExceptionRepr):
         self.reprtraceback.toterminal(tw)
         super(ReprExceptionInfo, self).toterminal(tw)
 
+
 class ReprTraceback(TerminalRepr):
     entrysep = "_ "
 
@@ -724,7 +765,7 @@ class ReprTraceback(TerminalRepr):
                 tw.line("")
             entry.toterminal(tw)
             if i < len(self.reprentries) - 1:
-                next_entry = self.reprentries[i+1]
+                next_entry = self.reprentries[i + 1]
                 if entry.style == "long" or \
                    entry.style == "short" and next_entry.style == "long":
                     tw.sep(self.entrysep)
@@ -732,12 +773,14 @@ class ReprTraceback(TerminalRepr):
         if self.extraline:
             tw.line(self.extraline)
 
+
 class ReprTracebackNative(ReprTraceback):
     def __init__(self, tblines):
         self.style = "native"
         self.reprentries = [ReprEntryNative(tblines)]
         self.extraline = None
 
+
 class ReprEntryNative(TerminalRepr):
     style = "native"
 
@@ -747,6 +790,7 @@ class ReprEntryNative(TerminalRepr):
     def toterminal(self, tw):
         tw.write("".join(self.lines))
 
+
 class ReprEntry(TerminalRepr):
     localssep = "_ "
 
@@ -763,7 +807,7 @@ class ReprEntry(TerminalRepr):
             for line in self.lines:
                 red = line.startswith("E   ")
                 tw.line(line, bold=True, red=red)
-            #tw.line("")
+            # tw.line("")
             return
         if self.reprfuncargs:
             self.reprfuncargs.toterminal(tw)
@@ -771,7 +815,7 @@ class ReprEntry(TerminalRepr):
             red = line.startswith("E   ")
             tw.line(line, bold=True, red=red)
         if self.reprlocals:
-            #tw.sep(self.localssep, "Locals")
+            # tw.sep(self.localssep, "Locals")
             tw.line("")
             self.reprlocals.toterminal(tw)
         if self.reprfileloc:
@@ -784,6 +828,7 @@ class ReprEntry(TerminalRepr):
                                self.reprlocals,
                                self.reprfileloc)
 
+
 class ReprFileLocation(TerminalRepr):
     def __init__(self, path, lineno, message):
         self.path = str(path)
@@ -800,6 +845,7 @@ class ReprFileLocation(TerminalRepr):
         tw.write(self.path, bold=True, red=True)
         tw.line(":%s: %s" % (self.lineno, msg))
 
+
 class ReprLocals(TerminalRepr):
     def __init__(self, lines):
         self.lines = lines
@@ -808,6 +854,7 @@ class ReprLocals(TerminalRepr):
         for line in self.lines:
             tw.line(line)
 
+
 class ReprFuncArgs(TerminalRepr):
     def __init__(self, args):
         self.args = args
@@ -816,11 +863,11 @@ class ReprFuncArgs(TerminalRepr):
         if self.args:
             linesofar = ""
             for name, value in self.args:
-                ns = "%s = %s" %(name, value)
+                ns = "%s = %s" % (safe_str(name), safe_str(value))
                 if len(ns) + len(linesofar) + 2 > tw.fullwidth:
                     if linesofar:
                         tw.line(linesofar)
-                    linesofar =  ns
+                    linesofar = ns
                 else:
                     if linesofar:
                         linesofar += ", " + ns
@@ -848,7 +895,7 @@ def getrawcode(obj, trycall=True):
         return obj
 
 
-if sys.version_info[:2] >= (3, 5):  # RecursionError introduced in 3.5
+if PY35:  # RecursionError introduced in 3.5
     def is_recursion_error(excinfo):
         return excinfo.errisinstance(RecursionError)  # noqa
 else:
diff --git a/lib/spack/external/_pytest/_code/source.py b/lib/spack/external/_pytest/_code/source.py
index fcec0f5ca7..fc41712649 100644
--- a/lib/spack/external/_pytest/_code/source.py
+++ b/lib/spack/external/_pytest/_code/source.py
@@ -1,8 +1,9 @@
-from __future__ import generators
+from __future__ import absolute_import, division, generators, print_function
 
 from bisect import bisect_right
 import sys
-import inspect, tokenize
+import inspect
+import tokenize
 import py
 cpy_compile = compile
 
@@ -19,6 +20,7 @@ class Source(object):
         possibly deindenting it.
     """
     _compilecounter = 0
+
     def __init__(self, *parts, **kwargs):
         self.lines = lines = []
         de = kwargs.get('deindent', True)
@@ -73,7 +75,7 @@ class Source(object):
         start, end = 0, len(self)
         while start < end and not self.lines[start].strip():
             start += 1
-        while end > start and not self.lines[end-1].strip():
+        while end > start and not self.lines[end - 1].strip():
             end -= 1
         source = Source()
         source.lines[:] = self.lines[start:end]
@@ -86,8 +88,8 @@ class Source(object):
         before = Source(before)
         after = Source(after)
         newsource = Source()
-        lines = [ (indent + line) for line in self.lines]
-        newsource.lines = before.lines + lines +  after.lines
+        lines = [(indent + line) for line in self.lines]
+        newsource.lines = before.lines + lines + after.lines
         return newsource
 
     def indent(self, indent=' ' * 4):
@@ -95,7 +97,7 @@ class Source(object):
             all lines indented by the given indent-string.
         """
         newsource = Source()
-        newsource.lines = [(indent+line) for line in self.lines]
+        newsource.lines = [(indent + line) for line in self.lines]
         return newsource
 
     def getstatement(self, lineno, assertion=False):
@@ -134,7 +136,8 @@ class Source(object):
         try:
             import parser
         except ImportError:
-            syntax_checker = lambda x: compile(x, 'asd', 'exec')
+            def syntax_checker(x):
+                return compile(x, 'asd', 'exec')
         else:
             syntax_checker = parser.suite
 
@@ -143,8 +146,8 @@ class Source(object):
         else:
             source = str(self)
         try:
-            #compile(source+'\n', "x", "exec")
-            syntax_checker(source+'\n')
+            # compile(source+'\n', "x", "exec")
+            syntax_checker(source + '\n')
         except KeyboardInterrupt:
             raise
         except Exception:
@@ -164,8 +167,8 @@ class Source(object):
         """
         if not filename or py.path.local(filename).check(file=0):
             if _genframe is None:
-                _genframe = sys._getframe(1) # the caller
-            fn,lineno = _genframe.f_code.co_filename, _genframe.f_lineno
+                _genframe = sys._getframe(1)  # the caller
+            fn, lineno = _genframe.f_code.co_filename, _genframe.f_lineno
             base = "<%d-codegen " % self._compilecounter
             self.__class__._compilecounter += 1
             if not filename:
@@ -180,7 +183,7 @@ class Source(object):
             # re-represent syntax errors from parsing python strings
             msglines = self.lines[:ex.lineno]
             if ex.offset:
-                msglines.append(" "*ex.offset + '^')
+                msglines.append(" " * ex.offset + '^')
             msglines.append("(code was compiled probably from here: %s)" % filename)
             newex = SyntaxError('\n'.join(msglines))
             newex.offset = ex.offset
@@ -198,8 +201,8 @@ class Source(object):
 # public API shortcut functions
 #
 
-def compile_(source, filename=None, mode='exec', flags=
-            generators.compiler_flag, dont_inherit=0):
+
+def compile_(source, filename=None, mode='exec', flags=generators.compiler_flag, dont_inherit=0):
     """ compile the given source to a raw code object,
         and maintain an internal cache which allows later
         retrieval of the source code for the code object
@@ -208,7 +211,7 @@ def compile_(source, filename=None, mode='exec', flags=
     if _ast is not None and isinstance(source, _ast.AST):
         # XXX should Source support having AST?
         return cpy_compile(source, filename, mode, flags, dont_inherit)
-    _genframe = sys._getframe(1) # the caller
+    _genframe = sys._getframe(1)  # the caller
     s = Source(source)
     co = s.compile(filename, mode, flags, _genframe=_genframe)
     return co
@@ -245,12 +248,13 @@ def getfslineno(obj):
 # helper functions
 #
 
+
 def findsource(obj):
     try:
         sourcelines, lineno = py.std.inspect.findsource(obj)
     except py.builtin._sysex:
         raise
-    except:
+    except:  # noqa
         return None, -1
     source = Source()
     source.lines = [line.rstrip() for line in sourcelines]
@@ -274,7 +278,7 @@ def deindent(lines, offset=None):
             line = line.expandtabs()
             s = line.lstrip()
             if s:
-                offset = len(line)-len(s)
+                offset = len(line) - len(s)
                 break
         else:
             offset = 0
@@ -293,11 +297,11 @@ def deindent(lines, offset=None):
     try:
         for _, _, (sline, _), (eline, _), _ in tokenize.generate_tokens(lambda: next(it)):
             if sline > len(lines):
-                break # End of input reached
+                break  # End of input reached
             if sline > len(newlines):
                 line = lines[sline - 1].expandtabs()
                 if line.lstrip() and line[:offset].isspace():
-                    line = line[offset:] # Deindent
+                    line = line[offset:]  # Deindent
                 newlines.append(line)
 
             for i in range(sline, eline):
@@ -315,29 +319,29 @@ def get_statement_startend2(lineno, node):
     import ast
     # flatten all statements and except handlers into one lineno-list
     # AST's line numbers start indexing at 1
-    l = []
+    values = []
     for x in ast.walk(node):
         if isinstance(x, _ast.stmt) or isinstance(x, _ast.ExceptHandler):
-            l.append(x.lineno - 1)
+            values.append(x.lineno - 1)
             for name in "finalbody", "orelse":
                 val = getattr(x, name, None)
                 if val:
                     # treat the finally/orelse part as its own statement
-                    l.append(val[0].lineno - 1 - 1)
-    l.sort()
-    insert_index = bisect_right(l, lineno)
-    start = l[insert_index - 1]
-    if insert_index >= len(l):
+                    values.append(val[0].lineno - 1 - 1)
+    values.sort()
+    insert_index = bisect_right(values, lineno)
+    start = values[insert_index - 1]
+    if insert_index >= len(values):
         end = None
     else:
-        end = l[insert_index]
+        end = values[insert_index]
     return start, end
 
 
 def getstatementrange_ast(lineno, source, assertion=False, astnode=None):
     if astnode is None:
         content = str(source)
-        if sys.version_info < (2,7):
+        if sys.version_info < (2, 7):
             content += "\n"
         try:
             astnode = compile(content, "source", "exec", 1024)  # 1024 for AST
@@ -393,7 +397,7 @@ def getstatementrange_old(lineno, source, assertion=False):
                 raise IndexError("likely a subclass")
             if "assert" not in line and "raise" not in line:
                 continue
-        trylines = source.lines[start:lineno+1]
+        trylines = source.lines[start:lineno + 1]
         # quick hack to prepare parsing an indented line with
         # compile_command() (which errors on "return" outside defs)
         trylines.insert(0, 'def xxx():')
@@ -405,10 +409,8 @@ def getstatementrange_old(lineno, source, assertion=False):
             continue
 
         # 2. find the end of the statement
-        for end in range(lineno+1, len(source)+1):
+        for end in range(lineno + 1, len(source) + 1):
             trysource = source[start:end]
             if trysource.isparseable():
                 return start, end
     raise SyntaxError("no valid source range around line %d " % (lineno,))
-
-
diff --git a/lib/spack/external/_pytest/_pluggy.py b/lib/spack/external/_pytest/_pluggy.py
index 87d32cf8dd..6cc1d3d54a 100644
--- a/lib/spack/external/_pytest/_pluggy.py
+++ b/lib/spack/external/_pytest/_pluggy.py
@@ -2,7 +2,7 @@
 imports symbols from vendored "pluggy" if available, otherwise
 falls back to importing "pluggy" from the default namespace.
 """
-
+from __future__ import absolute_import, division, print_function
 try:
     from _pytest.vendored_packages.pluggy import *  # noqa
     from _pytest.vendored_packages.pluggy import __version__  # noqa
diff --git a/lib/spack/external/_pytest/_version.py b/lib/spack/external/_pytest/_version.py
new file mode 100644
index 0000000000..3edb7da9ad
--- /dev/null
+++ b/lib/spack/external/_pytest/_version.py
@@ -0,0 +1,4 @@
+# coding: utf-8
+# file generated by setuptools_scm
+# don't change, don't track in version control
+version = '3.2.5'
diff --git a/lib/spack/external/_pytest/assertion/__init__.py b/lib/spack/external/_pytest/assertion/__init__.py
index 3f14a7ae76..b0ef667d56 100644
--- a/lib/spack/external/_pytest/assertion/__init__.py
+++ b/lib/spack/external/_pytest/assertion/__init__.py
@@ -1,12 +1,13 @@
 """
 support for presenting detailed information in failing assertions.
 """
+from __future__ import absolute_import, division, print_function
 import py
-import os
 import sys
 
 from _pytest.assertion import util
 from _pytest.assertion import rewrite
+from _pytest.assertion import truncate
 
 
 def pytest_addoption(parser):
@@ -24,10 +25,6 @@ def pytest_addoption(parser):
                             expression information.""")
 
 
-def pytest_namespace():
-    return {'register_assert_rewrite': register_assert_rewrite}
-
-
 def register_assert_rewrite(*names):
     """Register one or more module names to be rewritten on import.
 
@@ -100,12 +97,6 @@ def pytest_collection(session):
             assertstate.hook.set_session(session)
 
 
-def _running_on_ci():
-    """Check if we're currently running on a CI system."""
-    env_vars = ['CI', 'BUILD_NUMBER']
-    return any(var in os.environ for var in env_vars)
-
-
 def pytest_runtest_setup(item):
     """Setup the pytest_assertrepr_compare hook
 
@@ -119,8 +110,8 @@ def pytest_runtest_setup(item):
 
         This uses the first result from the hook and then ensures the
         following:
-        * Overly verbose explanations are dropped unless -vv was used or
-          running on a CI.
+        * Overly verbose explanations are truncated unless configured otherwise
+          (eg. if running in verbose mode).
         * Embedded newlines are escaped to help util.format_explanation()
           later.
         * If the rewrite mode is used embedded %-characters are replaced
@@ -133,14 +124,7 @@ def pytest_runtest_setup(item):
             config=item.config, op=op, left=left, right=right)
         for new_expl in hook_result:
             if new_expl:
-                if (sum(len(p) for p in new_expl[1:]) > 80*8 and
-                        item.config.option.verbose < 2 and
-                        not _running_on_ci()):
-                    show_max = 10
-                    truncated_lines = len(new_expl) - show_max
-                    new_expl[show_max:] = [py.builtin._totext(
-                        'Detailed information truncated (%d more lines)'
-                        ', use "-vv" to show' % truncated_lines)]
+                new_expl = truncate.truncate_if_required(new_expl, item)
                 new_expl = [line.replace("\n", "\\n") for line in new_expl]
                 res = py.builtin._totext("\n~").join(new_expl)
                 if item.config.getvalue("assertmode") == "rewrite":
diff --git a/lib/spack/external/_pytest/assertion/rewrite.py b/lib/spack/external/_pytest/assertion/rewrite.py
index abf5b491fe..d48b6648fb 100644
--- a/lib/spack/external/_pytest/assertion/rewrite.py
+++ b/lib/spack/external/_pytest/assertion/rewrite.py
@@ -1,5 +1,5 @@
 """Rewrite assertion AST to produce nice error messages"""
-
+from __future__ import absolute_import, division, print_function
 import ast
 import _ast
 import errno
@@ -11,7 +11,6 @@ import re
 import struct
 import sys
 import types
-from fnmatch import fnmatch
 
 import py
 from _pytest.assertion import util
@@ -37,10 +36,11 @@ PYC_TAIL = "." + PYTEST_TAG + PYC_EXT
 REWRITE_NEWLINES = sys.version_info[:2] != (2, 7) and sys.version_info < (3, 2)
 ASCII_IS_DEFAULT_ENCODING = sys.version_info[0] < 3
 
-if sys.version_info >= (3,5):
+if sys.version_info >= (3, 5):
     ast_Call = ast.Call
 else:
-    ast_Call = lambda a,b,c: ast.Call(a, b, c, None, None)
+    def ast_Call(a, b, c):
+        return ast.Call(a, b, c, None, None)
 
 
 class AssertionRewritingHook(object):
@@ -163,11 +163,7 @@ class AssertionRewritingHook(object):
         # modules not passed explicitly on the command line are only
         # rewritten if they match the naming convention for test files
         for pat in self.fnpats:
-            # use fnmatch instead of fn_pypath.fnmatch because the
-            # latter might trigger an import to fnmatch.fnmatch
-            # internally, which would cause this method to be
-            # called recursively
-            if fnmatch(fn_pypath.basename, pat):
+            if fn_pypath.fnmatch(pat):
                 state.trace("matched test file %r" % (fn,))
                 return True
 
@@ -214,13 +210,12 @@ class AssertionRewritingHook(object):
             mod.__cached__ = pyc
             mod.__loader__ = self
             py.builtin.exec_(co, mod.__dict__)
-        except:
-            del sys.modules[name]
+        except:  # noqa
+            if name in sys.modules:
+                del sys.modules[name]
             raise
         return sys.modules[name]
 
-
-
     def is_package(self, name):
         try:
             fd, fn, desc = imp.find_module(name)
@@ -265,7 +260,7 @@ def _write_pyc(state, co, source_stat, pyc):
         fp = open(pyc, "wb")
     except IOError:
         err = sys.exc_info()[1].errno
-        state.trace("error writing pyc file at %s: errno=%s" %(pyc, err))
+        state.trace("error writing pyc file at %s: errno=%s" % (pyc, err))
         # we ignore any failure to write the cache file
         # there are many reasons, permission-denied, __pycache__ being a
         # file etc.
@@ -287,6 +282,7 @@ N = "\n".encode("utf-8")
 cookie_re = re.compile(r"^[ \t\f]*#.*coding[:=][ \t]*[-\w.]+")
 BOM_UTF8 = '\xef\xbb\xbf'
 
+
 def _rewrite_test(config, fn):
     """Try to read and rewrite *fn* and return the code object."""
     state = config._assertstate
@@ -311,7 +307,7 @@ def _rewrite_test(config, fn):
         end2 = source.find("\n", end1 + 1)
         if (not source.startswith(BOM_UTF8) and
             cookie_re.match(source[0:end1]) is None and
-            cookie_re.match(source[end1 + 1:end2]) is None):
+                cookie_re.match(source[end1 + 1:end2]) is None):
             if hasattr(state, "_indecode"):
                 # encodings imported us again, so don't rewrite.
                 return None, None
@@ -336,7 +332,7 @@ def _rewrite_test(config, fn):
         return None, None
     rewrite_asserts(tree, fn, config)
     try:
-        co = compile(tree, fn.strpath, "exec")
+        co = compile(tree, fn.strpath, "exec", dont_inherit=True)
     except SyntaxError:
         # It's possible that this error is from some bug in the
         # assertion rewriting, but I don't know of a fast way to tell.
@@ -344,6 +340,7 @@ def _rewrite_test(config, fn):
         return None, None
     return stat, co
 
+
 def _make_rewritten_pyc(state, source_stat, pyc, co):
     """Try to dump rewritten code to *pyc*."""
     if sys.platform.startswith("win"):
@@ -357,6 +354,7 @@ def _make_rewritten_pyc(state, source_stat, pyc, co):
         if _write_pyc(state, co, source_stat, proc_pyc):
             os.rename(proc_pyc, pyc)
 
+
 def _read_pyc(source, pyc, trace=lambda x: None):
     """Possibly read a pytest pyc containing rewritten code.
 
@@ -414,7 +412,8 @@ def _saferepr(obj):
     return repr.replace(t("\n"), t("\\n"))
 
 
-from _pytest.assertion.util import format_explanation as _format_explanation # noqa
+from _pytest.assertion.util import format_explanation as _format_explanation  # noqa
+
 
 def _format_assertmsg(obj):
     """Format the custom assertion message given.
@@ -443,9 +442,11 @@ def _format_assertmsg(obj):
         s = s.replace(t("\\n"), t("\n~"))
     return s
 
+
 def _should_repr_global_name(obj):
     return not hasattr(obj, "__name__") and not py.builtin.callable(obj)
 
+
 def _format_boolop(explanations, is_or):
     explanation = "(" + (is_or and " or " or " and ").join(explanations) + ")"
     if py.builtin._istext(explanation):
@@ -454,6 +455,7 @@ def _format_boolop(explanations, is_or):
         t = py.builtin.bytes
     return explanation.replace(t('%'), t('%%'))
 
+
 def _call_reprcompare(ops, results, expls, each_obj):
     for i, res, expl in zip(range(len(ops)), results, expls):
         try:
@@ -487,7 +489,7 @@ binop_map = {
     ast.Mult: "*",
     ast.Div: "/",
     ast.FloorDiv: "//",
-    ast.Mod: "%%", # escaped for string formatting
+    ast.Mod: "%%",  # escaped for string formatting
     ast.Eq: "==",
     ast.NotEq: "!=",
     ast.Lt: "<",
@@ -593,23 +595,26 @@ class AssertionRewriter(ast.NodeVisitor):
         # docstrings and __future__ imports.
         aliases = [ast.alias(py.builtin.builtins.__name__, "@py_builtins"),
                    ast.alias("_pytest.assertion.rewrite", "@pytest_ar")]
-        expect_docstring = True
+        doc = getattr(mod, "docstring", None)
+        expect_docstring = doc is None
+        if doc is not None and self.is_rewrite_disabled(doc):
+            return
         pos = 0
-        lineno = 0
+        lineno = 1
         for item in mod.body:
             if (expect_docstring and isinstance(item, ast.Expr) and
                     isinstance(item.value, ast.Str)):
                 doc = item.value.s
-                if "PYTEST_DONT_REWRITE" in doc:
-                    # The module has disabled assertion rewriting.
+                if self.is_rewrite_disabled(doc):
                     return
-                lineno += len(doc) - 1
                 expect_docstring = False
             elif (not isinstance(item, ast.ImportFrom) or item.level > 0 or
                   item.module != "__future__"):
                 lineno = item.lineno
                 break
             pos += 1
+        else:
+            lineno = item.lineno
         imports = [ast.Import([alias], lineno=lineno, col_offset=0)
                    for alias in aliases]
         mod.body[pos:pos] = imports
@@ -635,6 +640,9 @@ class AssertionRewriter(ast.NodeVisitor):
                       not isinstance(field, ast.expr)):
                     nodes.append(field)
 
+    def is_rewrite_disabled(self, docstring):
+        return "PYTEST_DONT_REWRITE" in docstring
+
     def variable(self):
         """Get a new variable."""
         # Use a character invalid in python identifiers to avoid clashing.
@@ -727,7 +735,7 @@ class AssertionRewriter(ast.NodeVisitor):
         if isinstance(assert_.test, ast.Tuple) and self.config is not None:
             fslocation = (self.module_path, assert_.lineno)
             self.config.warn('R1', 'assertion is always true, perhaps '
-                              'remove parentheses?', fslocation=fslocation)
+                             'remove parentheses?', fslocation=fslocation)
         self.statements = []
         self.variables = []
         self.variable_counter = itertools.count()
@@ -791,7 +799,7 @@ class AssertionRewriter(ast.NodeVisitor):
             if i:
                 fail_inner = []
                 # cond is set in a prior loop iteration below
-                self.on_failure.append(ast.If(cond, fail_inner, [])) # noqa
+                self.on_failure.append(ast.If(cond, fail_inner, []))  # noqa
                 self.on_failure = fail_inner
             self.push_format_context()
             res, expl = self.visit(v)
@@ -843,7 +851,7 @@ class AssertionRewriter(ast.NodeVisitor):
             new_kwargs.append(ast.keyword(keyword.arg, res))
             if keyword.arg:
                 arg_expls.append(keyword.arg + "=" + expl)
-            else: ## **args have `arg` keywords with an .arg of None
+            else:  # **args have `arg` keywords with an .arg of None
                 arg_expls.append("**" + expl)
 
         expl = "%s(%s)" % (func_expl, ', '.join(arg_expls))
@@ -897,7 +905,6 @@ class AssertionRewriter(ast.NodeVisitor):
     else:
         visit_Call = visit_Call_legacy
 
-
     def visit_Attribute(self, attr):
         if not isinstance(attr.ctx, ast.Load):
             return self.generic_visit(attr)
diff --git a/lib/spack/external/_pytest/assertion/truncate.py b/lib/spack/external/_pytest/assertion/truncate.py
new file mode 100644
index 0000000000..1e13063569
--- /dev/null
+++ b/lib/spack/external/_pytest/assertion/truncate.py
@@ -0,0 +1,102 @@
+"""
+Utilities for truncating assertion output.
+
+Current default behaviour is to truncate assertion explanations at
+~8 terminal lines, unless running in "-vv" mode or running on CI.
+"""
+from __future__ import absolute_import, division, print_function
+import os
+
+import py
+
+
+DEFAULT_MAX_LINES = 8
+DEFAULT_MAX_CHARS = 8 * 80
+USAGE_MSG = "use '-vv' to show"
+
+
+def truncate_if_required(explanation, item, max_length=None):
+    """
+    Truncate this assertion explanation if the given test item is eligible.
+    """
+    if _should_truncate_item(item):
+        return _truncate_explanation(explanation)
+    return explanation
+
+
+def _should_truncate_item(item):
+    """
+    Whether or not this test item is eligible for truncation.
+    """
+    verbose = item.config.option.verbose
+    return verbose < 2 and not _running_on_ci()
+
+
+def _running_on_ci():
+    """Check if we're currently running on a CI system."""
+    env_vars = ['CI', 'BUILD_NUMBER']
+    return any(var in os.environ for var in env_vars)
+
+
+def _truncate_explanation(input_lines, max_lines=None, max_chars=None):
+    """
+    Truncate given list of strings that makes up the assertion explanation.
+
+    Truncates to either 8 lines, or 640 characters - whichever the input reaches
+    first. The remaining lines will be replaced by a usage message.
+    """
+
+    if max_lines is None:
+        max_lines = DEFAULT_MAX_LINES
+    if max_chars is None:
+        max_chars = DEFAULT_MAX_CHARS
+
+    # Check if truncation required
+    input_char_count = len("".join(input_lines))
+    if len(input_lines) <= max_lines and input_char_count <= max_chars:
+        return input_lines
+
+    # Truncate first to max_lines, and then truncate to max_chars if max_chars
+    # is exceeded.
+    truncated_explanation = input_lines[:max_lines]
+    truncated_explanation = _truncate_by_char_count(truncated_explanation, max_chars)
+
+    # Add ellipsis to final line
+    truncated_explanation[-1] = truncated_explanation[-1] + "..."
+
+    # Append useful message to explanation
+    truncated_line_count = len(input_lines) - len(truncated_explanation)
+    truncated_line_count += 1  # Account for the part-truncated final line
+    msg = '...Full output truncated'
+    if truncated_line_count == 1:
+        msg += ' ({0} line hidden)'.format(truncated_line_count)
+    else:
+        msg += ' ({0} lines hidden)'.format(truncated_line_count)
+    msg += ", {0}" .format(USAGE_MSG)
+    truncated_explanation.extend([
+        py.builtin._totext(""),
+        py.builtin._totext(msg),
+    ])
+    return truncated_explanation
+
+
+def _truncate_by_char_count(input_lines, max_chars):
+    # Check if truncation required
+    if len("".join(input_lines)) <= max_chars:
+        return input_lines
+
+    # Find point at which input length exceeds total allowed length
+    iterated_char_count = 0
+    for iterated_index, input_line in enumerate(input_lines):
+        if iterated_char_count + len(input_line) > max_chars:
+            break
+        iterated_char_count += len(input_line)
+
+    # Create truncated explanation with modified final line
+    truncated_result = input_lines[:iterated_index]
+    final_line = input_lines[iterated_index]
+    if final_line:
+        final_line_truncate_point = max_chars - iterated_char_count
+        final_line = final_line[:final_line_truncate_point]
+    truncated_result.append(final_line)
+    return truncated_result
diff --git a/lib/spack/external/_pytest/assertion/util.py b/lib/spack/external/_pytest/assertion/util.py
index 4a0a4e4310..9f00929073 100644
--- a/lib/spack/external/_pytest/assertion/util.py
+++ b/lib/spack/external/_pytest/assertion/util.py
@@ -1,4 +1,5 @@
 """Utilities for assertion debugging"""
+from __future__ import absolute_import, division, print_function
 import pprint
 
 import _pytest._code
@@ -8,7 +9,7 @@ try:
 except ImportError:
     Sequence = list
 
-BuiltinAssertionError = py.builtin.builtins.AssertionError
+
 u = py.builtin._totext
 
 # The _reprcompare attribute on the util module is used by the new assertion
@@ -52,11 +53,11 @@ def _split_explanation(explanation):
     """
     raw_lines = (explanation or u('')).split('\n')
     lines = [raw_lines[0]]
-    for l in raw_lines[1:]:
-        if l and l[0] in ['{', '}', '~', '>']:
-            lines.append(l)
+    for values in raw_lines[1:]:
+        if values and values[0] in ['{', '}', '~', '>']:
+            lines.append(values)
         else:
-            lines[-1] += '\\n' + l
+            lines[-1] += '\\n' + values
     return lines
 
 
@@ -81,7 +82,7 @@ def _format_lines(lines):
             stack.append(len(result))
             stackcnt[-1] += 1
             stackcnt.append(0)
-            result.append(u(' +') + u('  ')*(len(stack)-1) + s + line[1:])
+            result.append(u(' +') + u('  ') * (len(stack) - 1) + s + line[1:])
         elif line.startswith('}'):
             stack.pop()
             stackcnt.pop()
@@ -90,7 +91,7 @@ def _format_lines(lines):
             assert line[0] in ['~', '>']
             stack[-1] += 1
             indent = len(stack) if line.startswith('~') else len(stack) - 1
-            result.append(u('  ')*indent + line[1:])
+            result.append(u('  ') * indent + line[1:])
     assert len(stack) == 1
     return result
 
@@ -105,16 +106,22 @@ except NameError:
 def assertrepr_compare(config, op, left, right):
     """Return specialised explanations for some operators/operands"""
     width = 80 - 15 - len(op) - 2  # 15 chars indentation, 1 space around op
-    left_repr = py.io.saferepr(left, maxsize=int(width//2))
-    right_repr = py.io.saferepr(right, maxsize=width-len(left_repr))
+    left_repr = py.io.saferepr(left, maxsize=int(width // 2))
+    right_repr = py.io.saferepr(right, maxsize=width - len(left_repr))
 
     summary = u('%s %s %s') % (ecu(left_repr), op, ecu(right_repr))
 
-    issequence = lambda x: (isinstance(x, (list, tuple, Sequence)) and
-                            not isinstance(x, basestring))
-    istext = lambda x: isinstance(x, basestring)
-    isdict = lambda x: isinstance(x, dict)
-    isset = lambda x: isinstance(x, (set, frozenset))
+    def issequence(x):
+        return (isinstance(x, (list, tuple, Sequence)) and not isinstance(x, basestring))
+
+    def istext(x):
+        return isinstance(x, basestring)
+
+    def isdict(x):
+        return isinstance(x, dict)
+
+    def isset(x):
+        return isinstance(x, (set, frozenset))
 
     def isiterable(obj):
         try:
@@ -256,8 +263,8 @@ def _compare_eq_dict(left, right, verbose=False):
     explanation = []
     common = set(left).intersection(set(right))
     same = dict((k, left[k]) for k in common if left[k] == right[k])
-    if same and not verbose:
-        explanation += [u('Omitting %s identical items, use -v to show') %
+    if same and verbose < 2:
+        explanation += [u('Omitting %s identical items, use -vv to show') %
                         len(same)]
     elif same:
         explanation += [u('Common items:')]
@@ -284,7 +291,7 @@ def _compare_eq_dict(left, right, verbose=False):
 def _notin_text(term, text, verbose=False):
     index = text.find(term)
     head = text[:index]
-    tail = text[index+len(term):]
+    tail = text[index + len(term):]
     correct_text = head + tail
     diff = _diff_text(correct_text, text, verbose)
     newdiff = [u('%s is contained here:') % py.io.saferepr(term, maxsize=42)]
diff --git a/lib/spack/external/_pytest/cacheprovider.py b/lib/spack/external/_pytest/cacheprovider.py
index 0657001f2d..c537c14472 100644..100755
--- a/lib/spack/external/_pytest/cacheprovider.py
+++ b/lib/spack/external/_pytest/cacheprovider.py
@@ -1,20 +1,21 @@
 """
 merged implementation of the cache provider
 
-the name cache was not choosen to ensure pluggy automatically
+the name cache was not chosen to ensure pluggy automatically
 ignores the external pytest-cache
 """
-
+from __future__ import absolute_import, division, print_function
 import py
 import pytest
 import json
+import os
 from os.path import sep as _sep, altsep as _altsep
 
 
 class Cache(object):
     def __init__(self, config):
         self.config = config
-        self._cachedir = config.rootdir.join(".cache")
+        self._cachedir = Cache.cache_dir_from_config(config)
         self.trace = config.trace.root.get("cache")
         if config.getvalue("cacheclear"):
             self.trace("clearing cachedir")
@@ -22,6 +23,16 @@ class Cache(object):
                 self._cachedir.remove()
             self._cachedir.mkdir()
 
+    @staticmethod
+    def cache_dir_from_config(config):
+        cache_dir = config.getini("cache_dir")
+        cache_dir = os.path.expanduser(cache_dir)
+        cache_dir = os.path.expandvars(cache_dir)
+        if os.path.isabs(cache_dir):
+            return py.path.local(cache_dir)
+        else:
+            return config.rootdir.join(cache_dir)
+
     def makedir(self, name):
         """ return a directory path object with the given name.  If the
         directory does not yet exist, it will be created.  You can use it
@@ -89,31 +100,31 @@ class Cache(object):
 
 class LFPlugin:
     """ Plugin which implements the --lf (run last-failing) option """
+
     def __init__(self, config):
         self.config = config
         active_keys = 'lf', 'failedfirst'
         self.active = any(config.getvalue(key) for key in active_keys)
-        if self.active:
-            self.lastfailed = config.cache.get("cache/lastfailed", {})
-        else:
-            self.lastfailed = {}
+        self.lastfailed = config.cache.get("cache/lastfailed", {})
+        self._previously_failed_count = None
 
-    def pytest_report_header(self):
+    def pytest_report_collectionfinish(self):
         if self.active:
-            if not self.lastfailed:
+            if not self._previously_failed_count:
                 mode = "run all (no recorded failures)"
             else:
-                mode = "rerun last %d failures%s" % (
-                    len(self.lastfailed),
-                    " first" if self.config.getvalue("failedfirst") else "")
+                noun = 'failure' if self._previously_failed_count == 1 else 'failures'
+                suffix = " first" if self.config.getvalue("failedfirst") else ""
+                mode = "rerun previous {count} {noun}{suffix}".format(
+                    count=self._previously_failed_count, suffix=suffix, noun=noun
+                )
             return "run-last-failure: %s" % mode
 
     def pytest_runtest_logreport(self, report):
-        if report.failed and "xfail" not in report.keywords:
+        if (report.when == 'call' and report.passed) or report.skipped:
+            self.lastfailed.pop(report.nodeid, None)
+        elif report.failed:
             self.lastfailed[report.nodeid] = True
-        elif not report.failed:
-            if report.when == "call":
-                self.lastfailed.pop(report.nodeid, None)
 
     def pytest_collectreport(self, report):
         passed = report.outcome in ('passed', 'skipped')
@@ -135,22 +146,24 @@ class LFPlugin:
                     previously_failed.append(item)
                 else:
                     previously_passed.append(item)
-            if not previously_failed and previously_passed:
+            self._previously_failed_count = len(previously_failed)
+            if not previously_failed:
                 # running a subset of all tests with recorded failures outside
                 # of the set of tests currently executing
-                pass
-            elif self.config.getvalue("failedfirst"):
-                items[:] = previously_failed + previously_passed
-            else:
+                return
+            if self.config.getvalue("lf"):
                 items[:] = previously_failed
                 config.hook.pytest_deselected(items=previously_passed)
+            else:
+                items[:] = previously_failed + previously_passed
 
     def pytest_sessionfinish(self, session):
         config = self.config
         if config.getvalue("cacheshow") or hasattr(config, "slaveinput"):
             return
-        prev_failed = config.cache.get("cache/lastfailed", None) is not None
-        if (session.testscollected and prev_failed) or self.lastfailed:
+
+        saved_lastfailed = config.cache.get("cache/lastfailed", {})
+        if saved_lastfailed != self.lastfailed:
             config.cache.set("cache/lastfailed", self.lastfailed)
 
 
@@ -171,6 +184,9 @@ def pytest_addoption(parser):
     group.addoption(
         '--cache-clear', action='store_true', dest="cacheclear",
         help="remove all cache contents at start of test run.")
+    parser.addini(
+        "cache_dir", default='.cache',
+        help="cache directory path.")
 
 
 def pytest_cmdline_main(config):
@@ -179,7 +195,6 @@ def pytest_cmdline_main(config):
         return wrap_session(config, cacheshow)
 
 
-
 @pytest.hookimpl(tryfirst=True)
 def pytest_configure(config):
     config.cache = Cache(config)
@@ -219,12 +234,12 @@ def cacheshow(config, session):
     basedir = config.cache._cachedir
     vdir = basedir.join("v")
     tw.sep("-", "cache values")
-    for valpath in vdir.visit(lambda x: x.isfile()):
+    for valpath in sorted(vdir.visit(lambda x: x.isfile())):
         key = valpath.relto(vdir).replace(valpath.sep, "/")
         val = config.cache.get(key, dummy)
         if val is dummy:
             tw.line("%s contains unreadable content, "
-                  "will be ignored" % key)
+                    "will be ignored" % key)
         else:
             tw.line("%s contains:" % key)
             stream = py.io.TextIO()
@@ -235,8 +250,8 @@ def cacheshow(config, session):
     ddir = basedir.join("d")
     if ddir.isdir() and ddir.listdir():
         tw.sep("-", "cache directories")
-        for p in basedir.join("d").visit():
-            #if p.check(dir=1):
+        for p in sorted(basedir.join("d").visit()):
+            # if p.check(dir=1):
             #    print("%s/" % p.relto(basedir))
             if p.isfile():
                 key = p.relto(basedir)
diff --git a/lib/spack/external/_pytest/capture.py b/lib/spack/external/_pytest/capture.py
index eea81ca187..cb5af6fcb3 100644
--- a/lib/spack/external/_pytest/capture.py
+++ b/lib/spack/external/_pytest/capture.py
@@ -2,17 +2,19 @@
 per-test stdout/stderr capturing mechanism.
 
 """
-from __future__ import with_statement
+from __future__ import absolute_import, division, print_function
 
 import contextlib
 import sys
 import os
+import io
+from io import UnsupportedOperation
 from tempfile import TemporaryFile
 
 import py
 import pytest
+from _pytest.compat import CaptureIO
 
-from py.io import TextIO
 unicode = py.builtin.text
 
 patchsysdict = {0: 'stdin', 1: 'stdout', 2: 'stderr'}
@@ -32,8 +34,11 @@ def pytest_addoption(parser):
 
 @pytest.hookimpl(hookwrapper=True)
 def pytest_load_initial_conftests(early_config, parser, args):
-    _readline_workaround()
     ns = early_config.known_args_namespace
+    if ns.capture == "fd":
+        _py36_windowsconsoleio_workaround(sys.stdout)
+    _colorama_workaround()
+    _readline_workaround()
     pluginmanager = early_config.pluginmanager
     capman = CaptureManager(ns.capture)
     pluginmanager.register(capman, "capturemanager")
@@ -130,7 +135,7 @@ class CaptureManager:
         self.resumecapture()
         self.activate_funcargs(item)
         yield
-        #self.deactivate_funcargs() called from suspendcapture()
+        # self.deactivate_funcargs() called from suspendcapture()
         self.suspendcapture_item(item, "call")
 
     @pytest.hookimpl(hookwrapper=True)
@@ -167,6 +172,7 @@ def capsys(request):
     request.node._capfuncarg = c = CaptureFixture(SysCapture, request)
     return c
 
+
 @pytest.fixture
 def capfd(request):
     """Enable capturing of writes to file descriptors 1 and 2 and make
@@ -234,6 +240,7 @@ def safe_text_dupfile(f, mode, default_encoding="UTF8"):
 
 class EncodedFile(object):
     errors = "strict"  # possibly needed by py3 code (issue555)
+
     def __init__(self, buffer, encoding):
         self.buffer = buffer
         self.encoding = encoding
@@ -247,6 +254,11 @@ class EncodedFile(object):
         data = ''.join(linelist)
         self.write(data)
 
+    @property
+    def name(self):
+        """Ensure that file.name is a string."""
+        return repr(self.buffer)
+
     def __getattr__(self, name):
         return getattr(object.__getattribute__(self, "buffer"), name)
 
@@ -314,9 +326,11 @@ class MultiCapture(object):
         return (self.out.snap() if self.out is not None else "",
                 self.err.snap() if self.err is not None else "")
 
+
 class NoCapture:
     __init__ = start = done = suspend = resume = lambda *args: None
 
+
 class FDCapture:
     """ Capture IO to/from a given os-level filedescriptor. """
 
@@ -389,7 +403,7 @@ class FDCapture:
     def writeorg(self, data):
         """ write to original file descriptor. """
         if py.builtin._istext(data):
-            data = data.encode("utf8") # XXX use encoding of original stream
+            data = data.encode("utf8")  # XXX use encoding of original stream
         os.write(self.targetfd_save, data)
 
 
@@ -402,7 +416,7 @@ class SysCapture:
             if name == "stdin":
                 tmpfile = DontReadFromInput()
             else:
-                tmpfile = TextIO()
+                tmpfile = CaptureIO()
         self.tmpfile = tmpfile
 
     def start(self):
@@ -448,7 +462,8 @@ class DontReadFromInput:
     __iter__ = read
 
     def fileno(self):
-        raise ValueError("redirected Stdin is pseudofile, has no fileno()")
+        raise UnsupportedOperation("redirected stdin is pseudofile, "
+                                   "has no fileno()")
 
     def isatty(self):
         return False
@@ -458,12 +473,30 @@ class DontReadFromInput:
 
     @property
     def buffer(self):
-        if sys.version_info >= (3,0):
+        if sys.version_info >= (3, 0):
             return self
         else:
             raise AttributeError('redirected stdin has no attribute buffer')
 
 
+def _colorama_workaround():
+    """
+    Ensure colorama is imported so that it attaches to the correct stdio
+    handles on Windows.
+
+    colorama uses the terminal on import time. So if something does the
+    first import of colorama while I/O capture is active, colorama will
+    fail in various ways.
+    """
+
+    if not sys.platform.startswith('win32'):
+        return
+    try:
+        import colorama  # noqa
+    except ImportError:
+        pass
+
+
 def _readline_workaround():
     """
     Ensure readline is imported so that it attaches to the correct stdio
@@ -489,3 +522,56 @@ def _readline_workaround():
         import readline  # noqa
     except ImportError:
         pass
+
+
+def _py36_windowsconsoleio_workaround(stream):
+    """
+    Python 3.6 implemented unicode console handling for Windows. This works
+    by reading/writing to the raw console handle using
+    ``{Read,Write}ConsoleW``.
+
+    The problem is that we are going to ``dup2`` over the stdio file
+    descriptors when doing ``FDCapture`` and this will ``CloseHandle`` the
+    handles used by Python to write to the console. Though there is still some
+    weirdness and the console handle seems to only be closed randomly and not
+    on the first call to ``CloseHandle``, or maybe it gets reopened with the
+    same handle value when we suspend capturing.
+
+    The workaround in this case will reopen stdio with a different fd which
+    also means a different handle by replicating the logic in
+    "Py_lifecycle.c:initstdio/create_stdio".
+
+    :param stream: in practice ``sys.stdout`` or ``sys.stderr``, but given
+        here as parameter for unittesting purposes.
+
+    See https://github.com/pytest-dev/py/issues/103
+    """
+    if not sys.platform.startswith('win32') or sys.version_info[:2] < (3, 6):
+        return
+
+    # bail out if ``stream`` doesn't seem like a proper ``io`` stream (#2666)
+    if not hasattr(stream, 'buffer'):
+        return
+
+    buffered = hasattr(stream.buffer, 'raw')
+    raw_stdout = stream.buffer.raw if buffered else stream.buffer
+
+    if not isinstance(raw_stdout, io._WindowsConsoleIO):
+        return
+
+    def _reopen_stdio(f, mode):
+        if not buffered and mode[0] == 'w':
+            buffering = 0
+        else:
+            buffering = -1
+
+        return io.TextIOWrapper(
+            open(os.dup(f.fileno()), mode, buffering),
+            f.encoding,
+            f.errors,
+            f.newlines,
+            f.line_buffering)
+
+    sys.__stdin__ = sys.stdin = _reopen_stdio(sys.stdin, 'rb')
+    sys.__stdout__ = sys.stdout = _reopen_stdio(sys.stdout, 'wb')
+    sys.__stderr__ = sys.stderr = _reopen_stdio(sys.stderr, 'wb')
diff --git a/lib/spack/external/_pytest/compat.py b/lib/spack/external/_pytest/compat.py
index 51fc3bc5c1..255f69ce0d 100644
--- a/lib/spack/external/_pytest/compat.py
+++ b/lib/spack/external/_pytest/compat.py
@@ -1,6 +1,7 @@
 """
 python version compatibility code
 """
+from __future__ import absolute_import, division, print_function
 import sys
 import inspect
 import types
@@ -9,8 +10,8 @@ import functools
 
 import py
 
-import  _pytest
-
+import _pytest
+from _pytest.outcomes import TEST_OUTCOME
 
 
 try:
@@ -19,6 +20,7 @@ except ImportError:  # pragma: no cover
     # Only available in Python 3.4+ or as a backport
     enum = None
 
+
 _PY3 = sys.version_info > (3, 0)
 _PY2 = not _PY3
 
@@ -26,6 +28,10 @@ _PY2 = not _PY3
 NoneType = type(None)
 NOTSET = object()
 
+PY35 = sys.version_info[:2] >= (3, 5)
+PY36 = sys.version_info[:2] >= (3, 6)
+MODULE_NOT_FOUND_ERROR = 'ModuleNotFoundError' if PY36 else 'ImportError'
+
 if hasattr(inspect, 'signature'):
     def _format_args(func):
         return str(inspect.signature(func))
@@ -42,11 +48,18 @@ REGEX_TYPE = type(re.compile(''))
 
 
 def is_generator(func):
-    try:
-        return _pytest._code.getrawcode(func).co_flags & 32 # generator function
-    except AttributeError: # builtin functions have no bytecode
-        # assume them to not be generators
-        return False
+    genfunc = inspect.isgeneratorfunction(func)
+    return genfunc and not iscoroutinefunction(func)
+
+
+def iscoroutinefunction(func):
+    """Return True if func is a decorated coroutine function.
+
+    Note: copied and modified from Python 3.5's builtin couroutines.py to avoid import asyncio directly,
+    which in turns also initializes the "logging" module as side-effect (see issue #8).
+    """
+    return (getattr(func, '_is_coroutine', False) or
+            (hasattr(inspect, 'iscoroutinefunction') and inspect.iscoroutinefunction(func)))
 
 
 def getlocation(function, curdir):
@@ -55,7 +68,7 @@ def getlocation(function, curdir):
     lineno = py.builtin._getcode(function).co_firstlineno
     if fn.relto(curdir):
         fn = fn.relto(curdir)
-    return "%s:%d" %(fn, lineno+1)
+    return "%s:%d" % (fn, lineno + 1)
 
 
 def num_mock_patch_args(function):
@@ -66,13 +79,21 @@ def num_mock_patch_args(function):
     mock = sys.modules.get("mock", sys.modules.get("unittest.mock", None))
     if mock is not None:
         return len([p for p in patchings
-                        if not p.attribute_name and p.new is mock.DEFAULT])
+                    if not p.attribute_name and p.new is mock.DEFAULT])
     return len(patchings)
 
 
-def getfuncargnames(function, startindex=None):
+def getfuncargnames(function, startindex=None, cls=None):
+    """
+    @RonnyPfannschmidt: This function should be refactored when we revisit fixtures. The
+    fixture mechanism should ask the node for the fixture names, and not try to obtain
+    directly from the function object well after collection has occurred.
+    """
+    if startindex is None and cls is not None:
+        is_staticmethod = isinstance(cls.__dict__.get(function.__name__, None), staticmethod)
+        startindex = 0 if is_staticmethod else 1
     # XXX merge with main.py's varnames
-    #assert not isclass(function)
+    # assert not isclass(function)
     realfunction = function
     while hasattr(realfunction, "__wrapped__"):
         realfunction = realfunction.__wrapped__
@@ -98,8 +119,7 @@ def getfuncargnames(function, startindex=None):
     return tuple(argnames[startindex:])
 
 
-
-if  sys.version_info[:2] == (2, 6):
+if sys.version_info[:2] == (2, 6):
     def isclass(object):
         """ Return true if the object is a class. Overrides inspect.isclass for
         python 2.6 because it will return True for objects which always return
@@ -111,10 +131,12 @@ if  sys.version_info[:2] == (2, 6):
 
 if _PY3:
     import codecs
-
+    imap = map
+    izip = zip
     STRING_TYPES = bytes, str
+    UNICODE_TYPES = str,
 
-    def _escape_strings(val):
+    def _ascii_escaped(val):
         """If val is pure ascii, returns it as a str().  Otherwise, escapes
         bytes objects into a sequence of escaped bytes:
 
@@ -144,8 +166,11 @@ if _PY3:
             return val.encode('unicode_escape').decode('ascii')
 else:
     STRING_TYPES = bytes, str, unicode
+    UNICODE_TYPES = unicode,
 
-    def _escape_strings(val):
+    from itertools import imap, izip  # NOQA
+
+    def _ascii_escaped(val):
         """In py2 bytes and str are the same type, so return if it's a bytes
         object, return it unchanged if it is a full ascii string,
         otherwise escape it into its binary form.
@@ -167,8 +192,18 @@ def get_real_func(obj):
     """ gets the real function object of the (possibly) wrapped object by
     functools.wraps or functools.partial.
     """
-    while hasattr(obj, "__wrapped__"):
-        obj = obj.__wrapped__
+    start_obj = obj
+    for i in range(100):
+        new_obj = getattr(obj, '__wrapped__', None)
+        if new_obj is None:
+            break
+        obj = new_obj
+    else:
+        raise ValueError(
+            ("could not find real function of {start}"
+             "\nstopped at {current}").format(
+                start=py.io.saferepr(start_obj),
+                current=py.io.saferepr(obj)))
     if isinstance(obj, functools.partial):
         obj = obj.func
     return obj
@@ -195,14 +230,16 @@ def getimfunc(func):
 
 
 def safe_getattr(object, name, default):
-    """ Like getattr but return default upon any Exception.
+    """ Like getattr but return default upon any Exception or any OutcomeException.
 
     Attribute access can potentially fail for 'evil' Python objects.
-    See issue214
+    See issue #214.
+    It catches OutcomeException because of #2490 (issue #580), new outcomes are derived from BaseException
+    instead of Exception (for more details check #2707)
     """
     try:
         return getattr(object, name, default)
-    except Exception:
+    except TEST_OUTCOME:
         return default
 
 
@@ -226,5 +263,64 @@ else:
         try:
             return str(v)
         except UnicodeError:
+            if not isinstance(v, unicode):
+                v = unicode(v)
             errors = 'replace'
-            return v.encode('ascii', errors)
+            return v.encode('utf-8', errors)
+
+
+COLLECT_FAKEMODULE_ATTRIBUTES = (
+    'Collector',
+    'Module',
+    'Generator',
+    'Function',
+    'Instance',
+    'Session',
+    'Item',
+    'Class',
+    'File',
+    '_fillfuncargs',
+)
+
+
+def _setup_collect_fakemodule():
+    from types import ModuleType
+    import pytest
+    pytest.collect = ModuleType('pytest.collect')
+    pytest.collect.__all__ = []  # used for setns
+    for attr in COLLECT_FAKEMODULE_ATTRIBUTES:
+        setattr(pytest.collect, attr, getattr(pytest, attr))
+
+
+if _PY2:
+    # Without this the test_dupfile_on_textio will fail, otherwise CaptureIO could directly inherit from StringIO.
+    from py.io import TextIO
+
+    class CaptureIO(TextIO):
+
+        @property
+        def encoding(self):
+            return getattr(self, '_encoding', 'UTF-8')
+
+else:
+    import io
+
+    class CaptureIO(io.TextIOWrapper):
+        def __init__(self):
+            super(CaptureIO, self).__init__(
+                io.BytesIO(),
+                encoding='UTF-8', newline='', write_through=True,
+            )
+
+        def getvalue(self):
+            return self.buffer.getvalue().decode('UTF-8')
+
+
+class FuncargnamesCompatAttr(object):
+    """ helper class so that Metafunc, Function and FixtureRequest
+    don't need to each define the "funcargnames" compatibility attribute.
+    """
+    @property
+    def funcargnames(self):
+        """ alias attribute for ``fixturenames`` for pre-2.3 compatibility"""
+        return self.fixturenames
diff --git a/lib/spack/external/_pytest/config.py b/lib/spack/external/_pytest/config.py
index fe386ed0b1..19835d2c39 100644
--- a/lib/spack/external/_pytest/config.py
+++ b/lib/spack/external/_pytest/config.py
@@ -1,4 +1,5 @@
 """ command line options, ini-file and conftest.py processing. """
+from __future__ import absolute_import, division, print_function
 import argparse
 import shlex
 import traceback
@@ -7,7 +8,8 @@ import warnings
 
 import py
 # DON't import pytest here because it causes import cycle troubles
-import sys, os
+import sys
+import os
 import _pytest._code
 import _pytest.hookspec  # the extension point definitions
 import _pytest.assertion
@@ -53,15 +55,15 @@ def main(args=None, plugins=None):
             return 4
         else:
             try:
-                config.pluginmanager.check_pending()
                 return config.hook.pytest_cmdline_main(config=config)
             finally:
                 config._ensure_unconfigure()
     except UsageError as e:
         for msg in e.args:
-            sys.stderr.write("ERROR: %s\n" %(msg,))
+            sys.stderr.write("ERROR: %s\n" % (msg,))
         return 4
 
+
 class cmdline:  # compatibility namespace
     main = staticmethod(main)
 
@@ -70,6 +72,12 @@ class UsageError(Exception):
     """ error in pytest usage or invocation"""
 
 
+class PrintHelp(Exception):
+    """Raised when pytest should print it's help to skip the rest of the
+    argument parsing and validation."""
+    pass
+
+
 def filename_arg(path, optname):
     """ Argparse type validator for filename arguments.
 
@@ -95,10 +103,11 @@ def directory_arg(path, optname):
 _preinit = []
 
 default_plugins = (
-     "mark main terminal runner python fixtures debugging unittest capture skipping "
-     "tmpdir monkeypatch recwarn pastebin helpconfig nose assertion "
-     "junitxml resultlog doctest cacheprovider freeze_support "
-     "setuponly setupplan").split()
+    "mark main terminal runner python fixtures debugging unittest capture skipping "
+    "tmpdir monkeypatch recwarn pastebin helpconfig nose assertion "
+    "junitxml resultlog doctest cacheprovider freeze_support "
+    "setuponly setupplan warnings").split()
+
 
 builtin_plugins = set(default_plugins)
 builtin_plugins.add("pytester")
@@ -108,6 +117,7 @@ def _preloadplugins():
     assert not _preinit
     _preinit.append(get_config())
 
+
 def get_config():
     if _preinit:
         return _preinit.pop(0)
@@ -118,6 +128,7 @@ def get_config():
         pluginmanager.import_plugin(spec)
     return config
 
+
 def get_plugin_manager():
     """
     Obtain a new instance of the
@@ -129,6 +140,7 @@ def get_plugin_manager():
     """
     return get_config().pluginmanager
 
+
 def _prepareconfig(args=None, plugins=None):
     warning = None
     if args is None:
@@ -153,7 +165,7 @@ def _prepareconfig(args=None, plugins=None):
         if warning:
             config.warn('C1', warning)
         return pluginmanager.hook.pytest_cmdline_parse(
-                pluginmanager=pluginmanager, args=args)
+            pluginmanager=pluginmanager, args=args)
     except BaseException:
         config._ensure_unconfigure()
         raise
@@ -161,13 +173,14 @@ def _prepareconfig(args=None, plugins=None):
 
 class PytestPluginManager(PluginManager):
     """
-    Overwrites :py:class:`pluggy.PluginManager` to add pytest-specific
+    Overwrites :py:class:`pluggy.PluginManager <_pytest.vendored_packages.pluggy.PluginManager>` to add pytest-specific
     functionality:
 
     * loading plugins from the command line, ``PYTEST_PLUGIN`` env variable and
       ``pytest_plugins`` global variables found in plugins being loaded;
     * ``conftest.py`` loading during start-up;
     """
+
     def __init__(self):
         super(PytestPluginManager, self).__init__("pytest", implprefix="pytest_")
         self._conftest_plugins = set()
@@ -198,7 +211,8 @@ class PytestPluginManager(PluginManager):
         """
         .. deprecated:: 2.8
 
-        Use :py:meth:`pluggy.PluginManager.add_hookspecs` instead.
+        Use :py:meth:`pluggy.PluginManager.add_hookspecs <_pytest.vendored_packages.pluggy.PluginManager.add_hookspecs>`
+        instead.
         """
         warning = dict(code="I2",
                        fslocation=_pytest._code.getfslineno(sys._getframe(1)),
@@ -227,7 +241,7 @@ class PytestPluginManager(PluginManager):
 
     def parse_hookspec_opts(self, module_or_class, name):
         opts = super(PytestPluginManager, self).parse_hookspec_opts(
-                                                module_or_class, name)
+            module_or_class, name)
         if opts is None:
             method = getattr(module_or_class, name)
             if name.startswith("pytest_"):
@@ -250,7 +264,10 @@ class PytestPluginManager(PluginManager):
         ret = super(PytestPluginManager, self).register(plugin, name)
         if ret:
             self.hook.pytest_plugin_registered.call_historic(
-                      kwargs=dict(plugin=plugin, manager=self))
+                kwargs=dict(plugin=plugin, manager=self))
+
+            if isinstance(plugin, types.ModuleType):
+                self.consider_module(plugin)
         return ret
 
     def getplugin(self, name):
@@ -265,11 +282,11 @@ class PytestPluginManager(PluginManager):
         # XXX now that the pluginmanager exposes hookimpl(tryfirst...)
         # we should remove tryfirst/trylast as markers
         config.addinivalue_line("markers",
-            "tryfirst: mark a hook implementation function such that the "
-            "plugin machinery will try to call it first/as early as possible.")
+                                "tryfirst: mark a hook implementation function such that the "
+                                "plugin machinery will try to call it first/as early as possible.")
         config.addinivalue_line("markers",
-            "trylast: mark a hook implementation function such that the "
-            "plugin machinery will try to call it last/as late as possible.")
+                                "trylast: mark a hook implementation function such that the "
+                                "plugin machinery will try to call it last/as late as possible.")
 
     def _warn(self, message):
         kwargs = message if isinstance(message, dict) else {
@@ -293,7 +310,7 @@ class PytestPluginManager(PluginManager):
         """
         current = py.path.local()
         self._confcutdir = current.join(namespace.confcutdir, abs=True) \
-                                if namespace.confcutdir else None
+            if namespace.confcutdir else None
         self._noconftest = namespace.noconftest
         testpaths = namespace.file_or_dir
         foundanchor = False
@@ -304,7 +321,7 @@ class PytestPluginManager(PluginManager):
             if i != -1:
                 path = path[:i]
             anchor = current.join(path, abs=1)
-            if exists(anchor): # we found some file object
+            if exists(anchor):  # we found some file object
                 self._try_load_conftest(anchor)
                 foundanchor = True
         if not foundanchor:
@@ -371,7 +388,7 @@ class PytestPluginManager(PluginManager):
                     if path and path.relto(dirpath) or path == dirpath:
                         assert mod not in mods
                         mods.append(mod)
-            self.trace("loaded conftestmodule %r" %(mod))
+            self.trace("loaded conftestmodule %r" % (mod))
             self.consider_conftest(mod)
             return mod
 
@@ -381,7 +398,7 @@ class PytestPluginManager(PluginManager):
     #
 
     def consider_preparse(self, args):
-        for opt1,opt2 in zip(args, args[1:]):
+        for opt1, opt2 in zip(args, args[1:]):
             if opt1 == "-p":
                 self.consider_pluginarg(opt2)
 
@@ -395,38 +412,33 @@ class PytestPluginManager(PluginManager):
             self.import_plugin(arg)
 
     def consider_conftest(self, conftestmodule):
-        if self.register(conftestmodule, name=conftestmodule.__file__):
-            self.consider_module(conftestmodule)
+        self.register(conftestmodule, name=conftestmodule.__file__)
 
     def consider_env(self):
         self._import_plugin_specs(os.environ.get("PYTEST_PLUGINS"))
 
     def consider_module(self, mod):
-        plugins = getattr(mod, 'pytest_plugins', [])
-        if isinstance(plugins, str):
-            plugins = [plugins]
-        self.rewrite_hook.mark_rewrite(*plugins)
-        self._import_plugin_specs(plugins)
+        self._import_plugin_specs(getattr(mod, 'pytest_plugins', []))
 
     def _import_plugin_specs(self, spec):
-        if spec:
-            if isinstance(spec, str):
-                spec = spec.split(",")
-            for import_spec in spec:
-                self.import_plugin(import_spec)
+        plugins = _get_plugin_specs_as_list(spec)
+        for import_spec in plugins:
+            self.import_plugin(import_spec)
 
     def import_plugin(self, modname):
         # most often modname refers to builtin modules, e.g. "pytester",
         # "terminal" or "capture".  Those plugins are registered under their
         # basename for historic purposes but must be imported with the
         # _pytest prefix.
-        assert isinstance(modname, str)
+        assert isinstance(modname, (py.builtin.text, str)), "module name as text required, got %r" % modname
+        modname = str(modname)
         if self.get_plugin(modname) is not None:
             return
         if modname in builtin_plugins:
             importspec = "_pytest." + modname
         else:
             importspec = modname
+        self.rewrite_hook.mark_rewrite(importspec)
         try:
             __import__(importspec)
         except ImportError as e:
@@ -440,11 +452,28 @@ class PytestPluginManager(PluginManager):
             import pytest
             if not hasattr(pytest, 'skip') or not isinstance(e, pytest.skip.Exception):
                 raise
-            self._warn("skipped plugin %r: %s" %((modname, e.msg)))
+            self._warn("skipped plugin %r: %s" % ((modname, e.msg)))
         else:
             mod = sys.modules[importspec]
             self.register(mod, modname)
-            self.consider_module(mod)
+
+
+def _get_plugin_specs_as_list(specs):
+    """
+    Parses a list of "plugin specs" and returns a list of plugin names.
+
+    Plugin specs can be given as a list of strings separated by "," or already as a list/tuple in
+    which case it is returned as a list. Specs can also be `None` in which case an
+    empty list is returned.
+    """
+    if specs is not None:
+        if isinstance(specs, str):
+            specs = specs.split(',') if specs else []
+        if not isinstance(specs, (list, tuple)):
+            raise UsageError("Plugin specs must be a ','-separated string or a "
+                             "list/tuple of strings for plugin names. Given: %r" % specs)
+        return list(specs)
+    return []
 
 
 class Parser:
@@ -488,7 +517,7 @@ class Parser:
         for i, grp in enumerate(self._groups):
             if grp.name == after:
                 break
-        self._groups.insert(i+1, group)
+        self._groups.insert(i + 1, group)
         return group
 
     def addoption(self, *opts, **attrs):
@@ -526,7 +555,7 @@ class Parser:
                     a = option.attrs()
                     arggroup.add_argument(*n, **a)
         # bash like autocompletion for dirs (appending '/')
-        optparser.add_argument(FILE_OR_DIR, nargs='*').completer=filescompleter
+        optparser.add_argument(FILE_OR_DIR, nargs='*').completer = filescompleter
         return optparser
 
     def parse_setoption(self, args, option, namespace=None):
@@ -670,7 +699,7 @@ class Argument:
         if self._attrs.get('help'):
             a = self._attrs['help']
             a = a.replace('%default', '%(default)s')
-            #a = a.replace('%prog', '%(prog)s')
+            # a = a.replace('%prog', '%(prog)s')
             self._attrs['help'] = a
         return self._attrs
 
@@ -754,7 +783,7 @@ class MyOptionParser(argparse.ArgumentParser):
             extra_info = {}
         self._parser = parser
         argparse.ArgumentParser.__init__(self, usage=parser._usage,
-            add_help=False, formatter_class=DropShorterLongHelpFormatter)
+                                         add_help=False, formatter_class=DropShorterLongHelpFormatter)
         # extra_info is a dict of (param -> value) to display if there's
         # an usage error to provide more contextual information to the user
         self.extra_info = extra_info
@@ -782,9 +811,10 @@ class DropShorterLongHelpFormatter(argparse.HelpFormatter):
     - shortcut if there are only two options and one of them is a short one
     - cache result on action object as this is called at least 2 times
     """
+
     def _format_action_invocation(self, action):
         orgstr = argparse.HelpFormatter._format_action_invocation(self, action)
-        if orgstr and orgstr[0] != '-': # only optional arguments
+        if orgstr and orgstr[0] != '-':  # only optional arguments
             return orgstr
         res = getattr(action, '_formatted_action_invocation', None)
         if res:
@@ -795,7 +825,7 @@ class DropShorterLongHelpFormatter(argparse.HelpFormatter):
             action._formatted_action_invocation = orgstr
             return orgstr
         return_list = []
-        option_map =  getattr(action, 'map_long_option', {})
+        option_map = getattr(action, 'map_long_option', {})
         if option_map is None:
             option_map = {}
         short_long = {}
@@ -813,7 +843,7 @@ class DropShorterLongHelpFormatter(argparse.HelpFormatter):
                     short_long[shortened] = xxoption
         # now short_long has been filled out to the longest with dashes
         # **and** we keep the right option ordering from add_argument
-        for option in options: #
+        for option in options:
             if len(option) == 2 or option[2] == ' ':
                 return_list.append(option)
             if option[2:] == short_long.get(option.replace('-', '')):
@@ -822,22 +852,26 @@ class DropShorterLongHelpFormatter(argparse.HelpFormatter):
         return action._formatted_action_invocation
 
 
-
 def _ensure_removed_sysmodule(modname):
     try:
         del sys.modules[modname]
     except KeyError:
         pass
 
+
 class CmdOptions(object):
     """ holds cmdline options as attributes."""
+
     def __init__(self, values=()):
         self.__dict__.update(values)
+
     def __repr__(self):
-        return "<CmdOptions %r>" %(self.__dict__,)
+        return "<CmdOptions %r>" % (self.__dict__,)
+
     def copy(self):
         return CmdOptions(self.__dict__)
 
+
 class Notset:
     def __repr__(self):
         return "<NOTSET>"
@@ -847,6 +881,18 @@ notset = Notset()
 FILE_OR_DIR = 'file_or_dir'
 
 
+def _iter_rewritable_modules(package_files):
+    for fn in package_files:
+        is_simple_module = '/' not in fn and fn.endswith('.py')
+        is_package = fn.count('/') == 1 and fn.endswith('__init__.py')
+        if is_simple_module:
+            module_name, _ = os.path.splitext(fn)
+            yield module_name
+        elif is_package:
+            package_name = os.path.dirname(fn)
+            yield package_name
+
+
 class Config(object):
     """ access to configuration values, pluginmanager and plugin hooks.  """
 
@@ -864,6 +910,7 @@ class Config(object):
         self.trace = self.pluginmanager.trace.root.get("config")
         self.hook = self.pluginmanager.hook
         self._inicache = {}
+        self._override_ini = ()
         self._opt2dest = {}
         self._cleanup = []
         self._warn = self.pluginmanager._warn
@@ -896,11 +943,11 @@ class Config(object):
             fin = self._cleanup.pop()
             fin()
 
-    def warn(self, code, message, fslocation=None):
+    def warn(self, code, message, fslocation=None, nodeid=None):
         """ generate a warning for this test session. """
         self.hook.pytest_logwarning.call_historic(kwargs=dict(
             code=code, message=message,
-            fslocation=fslocation, nodeid=None))
+            fslocation=fslocation, nodeid=nodeid))
 
     def get_terminal_writer(self):
         return self.pluginmanager.get_plugin("terminalreporter")._tw
@@ -916,14 +963,14 @@ class Config(object):
         else:
             style = "native"
         excrepr = excinfo.getrepr(funcargs=True,
-            showlocals=getattr(option, 'showlocals', False),
-            style=style,
-        )
+                                  showlocals=getattr(option, 'showlocals', False),
+                                  style=style,
+                                  )
         res = self.hook.pytest_internalerror(excrepr=excrepr,
                                              excinfo=excinfo)
         if not py.builtin.any(res):
             for line in str(excrepr).split("\n"):
-                sys.stderr.write("INTERNALERROR> %s\n" %line)
+                sys.stderr.write("INTERNALERROR> %s\n" % line)
                 sys.stderr.flush()
 
     def cwd_relative_nodeid(self, nodeid):
@@ -964,8 +1011,9 @@ class Config(object):
         self.invocation_dir = py.path.local()
         self._parser.addini('addopts', 'extra command line options', 'args')
         self._parser.addini('minversion', 'minimally required pytest version')
+        self._override_ini = ns.override_ini or ()
 
-    def _consider_importhook(self, args, entrypoint_name):
+    def _consider_importhook(self, args):
         """Install the PEP 302 import hook if using assertion re-writing.
 
         Needs to parse the --assert=<mode> option from the commandline
@@ -980,26 +1028,34 @@ class Config(object):
             except SystemError:
                 mode = 'plain'
             else:
-                import pkg_resources
-                self.pluginmanager.rewrite_hook = hook
-                for entrypoint in pkg_resources.iter_entry_points('pytest11'):
-                    # 'RECORD' available for plugins installed normally (pip install)
-                    # 'SOURCES.txt' available for plugins installed in dev mode (pip install -e)
-                    # for installed plugins 'SOURCES.txt' returns an empty list, and vice-versa
-                    # so it shouldn't be an issue
-                    for metadata in ('RECORD', 'SOURCES.txt'):
-                        for entry in entrypoint.dist._get_metadata(metadata):
-                            fn = entry.split(',')[0]
-                            is_simple_module = os.sep not in fn and fn.endswith('.py')
-                            is_package = fn.count(os.sep) == 1 and fn.endswith('__init__.py')
-                            if is_simple_module:
-                                module_name, ext = os.path.splitext(fn)
-                                hook.mark_rewrite(module_name)
-                            elif is_package:
-                                package_name = os.path.dirname(fn)
-                                hook.mark_rewrite(package_name)
+                self._mark_plugins_for_rewrite(hook)
         self._warn_about_missing_assertion(mode)
 
+    def _mark_plugins_for_rewrite(self, hook):
+        """
+        Given an importhook, mark for rewrite any top-level
+        modules or packages in the distribution package for
+        all pytest plugins.
+        """
+        import pkg_resources
+        self.pluginmanager.rewrite_hook = hook
+
+        # 'RECORD' available for plugins installed normally (pip install)
+        # 'SOURCES.txt' available for plugins installed in dev mode (pip install -e)
+        # for installed plugins 'SOURCES.txt' returns an empty list, and vice-versa
+        # so it shouldn't be an issue
+        metadata_files = 'RECORD', 'SOURCES.txt'
+
+        package_files = (
+            entry.split(',')[0]
+            for entrypoint in pkg_resources.iter_entry_points('pytest11')
+            for metadata in metadata_files
+            for entry in entrypoint.dist._get_metadata(metadata)
+        )
+
+        for name in _iter_rewritable_modules(package_files):
+            hook.mark_rewrite(name)
+
     def _warn_about_missing_assertion(self, mode):
         try:
             assert False
@@ -1023,19 +1079,17 @@ class Config(object):
             args[:] = shlex.split(os.environ.get('PYTEST_ADDOPTS', '')) + args
             args[:] = self.getini("addopts") + args
         self._checkversion()
-        entrypoint_name = 'pytest11'
-        self._consider_importhook(args, entrypoint_name)
+        self._consider_importhook(args)
         self.pluginmanager.consider_preparse(args)
-        self.pluginmanager.load_setuptools_entrypoints(entrypoint_name)
+        self.pluginmanager.load_setuptools_entrypoints('pytest11')
         self.pluginmanager.consider_env()
         self.known_args_namespace = ns = self._parser.parse_known_args(args, namespace=self.option.copy())
-        confcutdir = self.known_args_namespace.confcutdir
         if self.known_args_namespace.confcutdir is None and self.inifile:
             confcutdir = py.path.local(self.inifile).dirname
             self.known_args_namespace.confcutdir = confcutdir
         try:
             self.hook.pytest_load_initial_conftests(early_config=self,
-                    args=args, parser=self._parser)
+                                                    args=args, parser=self._parser)
         except ConftestImportFailure:
             e = sys.exc_info()[1]
             if ns.help or ns.version:
@@ -1053,28 +1107,32 @@ class Config(object):
             myver = pytest.__version__.split(".")
             if myver < ver:
                 raise pytest.UsageError(
-                    "%s:%d: requires pytest-%s, actual pytest-%s'" %(
-                    self.inicfg.config.path, self.inicfg.lineof('minversion'),
-                    minver, pytest.__version__))
+                    "%s:%d: requires pytest-%s, actual pytest-%s'" % (
+                        self.inicfg.config.path, self.inicfg.lineof('minversion'),
+                        minver, pytest.__version__))
 
     def parse(self, args, addopts=True):
         # parse given cmdline arguments into this config object.
         assert not hasattr(self, 'args'), (
-                "can only parse cmdline args at most once per Config object")
+            "can only parse cmdline args at most once per Config object")
         self._origargs = args
         self.hook.pytest_addhooks.call_historic(
-                                  kwargs=dict(pluginmanager=self.pluginmanager))
+            kwargs=dict(pluginmanager=self.pluginmanager))
         self._preparse(args, addopts=addopts)
         # XXX deprecated hook:
         self.hook.pytest_cmdline_preparse(config=self, args=args)
-        args = self._parser.parse_setoption(args, self.option, namespace=self.option)
-        if not args:
-            cwd = os.getcwd()
-            if cwd == self.rootdir:
-                args = self.getini('testpaths')
+        self._parser.after_preparse = True
+        try:
+            args = self._parser.parse_setoption(args, self.option, namespace=self.option)
             if not args:
-                args = [cwd]
-        self.args = args
+                cwd = os.getcwd()
+                if cwd == self.rootdir:
+                    args = self.getini('testpaths')
+                if not args:
+                    args = [cwd]
+            self.args = args
+        except PrintHelp:
+            pass
 
     def addinivalue_line(self, name, line):
         """ add a line to an ini-file option. The option must have been
@@ -1082,12 +1140,12 @@ class Config(object):
         the first line in its value. """
         x = self.getini(name)
         assert isinstance(x, list)
-        x.append(line) # modifies the cached list inline
+        x.append(line)  # modifies the cached list inline
 
     def getini(self, name):
         """ return configuration value from an :ref:`ini file <inifiles>`. If the
         specified name hasn't been registered through a prior
-        :py:func:`parser.addini <pytest.config.Parser.addini>`
+        :py:func:`parser.addini <_pytest.config.Parser.addini>`
         call (usually from a plugin), a ValueError is raised. """
         try:
             return self._inicache[name]
@@ -1099,7 +1157,7 @@ class Config(object):
         try:
             description, type, default = self._parser._inidict[name]
         except KeyError:
-            raise ValueError("unknown configuration value: %r" %(name,))
+            raise ValueError("unknown configuration value: %r" % (name,))
         value = self._get_override_ini_value(name)
         if value is None:
             try:
@@ -1112,10 +1170,10 @@ class Config(object):
                 return []
         if type == "pathlist":
             dp = py.path.local(self.inicfg.config.path).dirpath()
-            l = []
+            values = []
             for relpath in shlex.split(value):
-                l.append(dp.join(relpath, abs=True))
-            return l
+                values.append(dp.join(relpath, abs=True))
+            return values
         elif type == "args":
             return shlex.split(value)
         elif type == "linelist":
@@ -1132,13 +1190,13 @@ class Config(object):
         except KeyError:
             return None
         modpath = py.path.local(mod.__file__).dirpath()
-        l = []
+        values = []
         for relroot in relroots:
             if not isinstance(relroot, py.path.local):
                 relroot = relroot.replace("/", py.path.local.sep)
                 relroot = modpath.join(relroot, abs=True)
-            l.append(relroot)
-        return l
+            values.append(relroot)
+        return values
 
     def _get_override_ini_value(self, name):
         value = None
@@ -1146,15 +1204,14 @@ class Config(object):
         # and -o foo1=bar1 -o foo2=bar2 options
         # always use the last item if multiple value set for same ini-name,
         # e.g. -o foo=bar1 -o foo=bar2 will set foo to bar2
-        if self.getoption("override_ini", None):
-            for ini_config_list in self.option.override_ini:
-                for ini_config in ini_config_list:
-                    try:
-                        (key, user_ini_value) = ini_config.split("=", 1)
-                    except ValueError:
-                        raise UsageError("-o/--override-ini expects option=value style.")
-                    if key == name:
-                        value = user_ini_value
+        for ini_config_list in self._override_ini:
+            for ini_config in ini_config_list:
+                try:
+                    (key, user_ini_value) = ini_config.split("=", 1)
+                except ValueError:
+                    raise UsageError("-o/--override-ini expects option=value style.")
+                if key == name:
+                    value = user_ini_value
         return value
 
     def getoption(self, name, default=notset, skip=False):
@@ -1177,7 +1234,7 @@ class Config(object):
                 return default
             if skip:
                 import pytest
-                pytest.skip("no %r option found" %(name,))
+                pytest.skip("no %r option found" % (name,))
             raise ValueError("no option named %r" % (name,))
 
     def getvalue(self, name, path=None):
@@ -1188,12 +1245,14 @@ class Config(object):
         """ (deprecated, use getoption(skip=True)) """
         return self.getoption(name, skip=True)
 
+
 def exists(path, ignore=EnvironmentError):
     try:
         return path.check()
     except ignore:
         return False
 
+
 def getcfg(args, warnfunc=None):
     """
     Search the list of arguments for a valid ini-file for pytest,
@@ -1228,25 +1287,20 @@ def getcfg(args, warnfunc=None):
     return None, None, None
 
 
-def get_common_ancestor(args):
-    # args are what we get after early command line parsing (usually
-    # strings, but can be py.path.local objects as well)
+def get_common_ancestor(paths):
     common_ancestor = None
-    for arg in args:
-        if str(arg)[0] == "-":
-            continue
-        p = py.path.local(arg)
-        if not p.exists():
+    for path in paths:
+        if not path.exists():
             continue
         if common_ancestor is None:
-            common_ancestor = p
+            common_ancestor = path
         else:
-            if p.relto(common_ancestor) or p == common_ancestor:
+            if path.relto(common_ancestor) or path == common_ancestor:
                 continue
-            elif common_ancestor.relto(p):
-                common_ancestor = p
+            elif common_ancestor.relto(path):
+                common_ancestor = path
             else:
-                shared = p.common(common_ancestor)
+                shared = path.common(common_ancestor)
                 if shared is not None:
                     common_ancestor = shared
     if common_ancestor is None:
@@ -1257,9 +1311,29 @@ def get_common_ancestor(args):
 
 
 def get_dirs_from_args(args):
-    return [d for d in (py.path.local(x) for x in args
-                        if not str(x).startswith("-"))
-            if d.exists()]
+    def is_option(x):
+        return str(x).startswith('-')
+
+    def get_file_part_from_node_id(x):
+        return str(x).split('::')[0]
+
+    def get_dir_from_path(path):
+        if path.isdir():
+            return path
+        return py.path.local(path.dirname)
+
+    # These look like paths but may not exist
+    possible_paths = (
+        py.path.local(get_file_part_from_node_id(arg))
+        for arg in args
+        if not is_option(arg)
+    )
+
+    return [
+        get_dir_from_path(path)
+        for path in possible_paths
+        if path.exists()
+    ]
 
 
 def determine_setup(inifile, args, warnfunc=None):
@@ -1282,7 +1356,7 @@ def determine_setup(inifile, args, warnfunc=None):
                 rootdir, inifile, inicfg = getcfg(dirs, warnfunc=warnfunc)
                 if rootdir is None:
                     rootdir = get_common_ancestor([py.path.local(), ancestor])
-                    is_fs_root = os.path.splitdrive(str(rootdir))[1] == os.sep
+                    is_fs_root = os.path.splitdrive(str(rootdir))[1] == '/'
                     if is_fs_root:
                         rootdir = ancestor
     return rootdir, inifile, inicfg or {}
@@ -1304,7 +1378,7 @@ def setns(obj, dic):
         else:
             setattr(obj, name, value)
             obj.__all__.append(name)
-            #if obj != pytest:
+            # if obj != pytest:
             #    pytest.__all__.append(name)
             setattr(pytest, name, value)
 
diff --git a/lib/spack/external/_pytest/debugging.py b/lib/spack/external/_pytest/debugging.py
index d96170bd8b..aa9c9a3863 100644
--- a/lib/spack/external/_pytest/debugging.py
+++ b/lib/spack/external/_pytest/debugging.py
@@ -1,10 +1,8 @@
 """ interactive debugging with PDB, the Python Debugger. """
-from __future__ import absolute_import
+from __future__ import absolute_import, division, print_function
 import pdb
 import sys
 
-import pytest
-
 
 def pytest_addoption(parser):
     group = parser.getgroup("general")
@@ -16,19 +14,17 @@ def pytest_addoption(parser):
         help="start a custom interactive Python debugger on errors. "
              "For example: --pdbcls=IPython.terminal.debugger:TerminalPdb")
 
-def pytest_namespace():
-    return {'set_trace': pytestPDB().set_trace}
 
 def pytest_configure(config):
-    if config.getvalue("usepdb") or config.getvalue("usepdb_cls"):
+    if config.getvalue("usepdb_cls"):
+        modname, classname = config.getvalue("usepdb_cls").split(":")
+        __import__(modname)
+        pdb_cls = getattr(sys.modules[modname], classname)
+    else:
+        pdb_cls = pdb.Pdb
+
+    if config.getvalue("usepdb"):
         config.pluginmanager.register(PdbInvoke(), 'pdbinvoke')
-        if config.getvalue("usepdb_cls"):
-            modname, classname = config.getvalue("usepdb_cls").split(":")
-            __import__(modname)
-            pdb_cls = getattr(sys.modules[modname], classname)
-        else:
-            pdb_cls = pdb.Pdb
-        pytestPDB._pdb_cls = pdb_cls
 
     old = (pdb.set_trace, pytestPDB._pluginmanager)
 
@@ -37,30 +33,33 @@ def pytest_configure(config):
         pytestPDB._config = None
         pytestPDB._pdb_cls = pdb.Pdb
 
-    pdb.set_trace = pytest.set_trace
+    pdb.set_trace = pytestPDB.set_trace
     pytestPDB._pluginmanager = config.pluginmanager
     pytestPDB._config = config
+    pytestPDB._pdb_cls = pdb_cls
     config._cleanup.append(fin)
 
+
 class pytestPDB:
     """ Pseudo PDB that defers to the real pdb. """
     _pluginmanager = None
     _config = None
     _pdb_cls = pdb.Pdb
 
-    def set_trace(self):
+    @classmethod
+    def set_trace(cls):
         """ invoke PDB set_trace debugging, dropping any IO capturing. """
         import _pytest.config
         frame = sys._getframe().f_back
-        if self._pluginmanager is not None:
-            capman = self._pluginmanager.getplugin("capturemanager")
+        if cls._pluginmanager is not None:
+            capman = cls._pluginmanager.getplugin("capturemanager")
             if capman:
                 capman.suspendcapture(in_=True)
-            tw = _pytest.config.create_terminal_writer(self._config)
+            tw = _pytest.config.create_terminal_writer(cls._config)
             tw.line()
             tw.sep(">", "PDB set_trace (IO-capturing turned off)")
-            self._pluginmanager.hook.pytest_enter_pdb(config=self._config)
-        self._pdb_cls().set_trace(frame)
+            cls._pluginmanager.hook.pytest_enter_pdb(config=cls._config)
+        cls._pdb_cls().set_trace(frame)
 
 
 class PdbInvoke:
@@ -74,7 +73,7 @@ class PdbInvoke:
 
     def pytest_internalerror(self, excrepr, excinfo):
         for line in str(excrepr).split("\n"):
-            sys.stderr.write("INTERNALERROR> %s\n" %line)
+            sys.stderr.write("INTERNALERROR> %s\n" % line)
             sys.stderr.flush()
         tb = _postmortem_traceback(excinfo)
         post_mortem(tb)
diff --git a/lib/spack/external/_pytest/deprecated.py b/lib/spack/external/_pytest/deprecated.py
index 6edc475f6e..38e9496778 100644
--- a/lib/spack/external/_pytest/deprecated.py
+++ b/lib/spack/external/_pytest/deprecated.py
@@ -5,10 +5,15 @@ that is planned to be removed in the next pytest release.
 Keeping it in a central location makes it easy to track what is deprecated and should
 be removed when the time comes.
 """
+from __future__ import absolute_import, division, print_function
+
+
+class RemovedInPytest4Warning(DeprecationWarning):
+    """warning class for features removed in pytest 4.0"""
 
 
 MAIN_STR_ARGS = 'passing a string to pytest.main() is deprecated, ' \
-                      'pass a list of arguments instead.'
+    'pass a list of arguments instead.'
 
 YIELD_TESTS = 'yield tests are deprecated, and scheduled to be removed in pytest 4.0'
 
@@ -21,4 +26,17 @@ SETUP_CFG_PYTEST = '[pytest] section in setup.cfg files is deprecated, use [tool
 
 GETFUNCARGVALUE = "use of getfuncargvalue is deprecated, use getfixturevalue"
 
-RESULT_LOG = '--result-log is deprecated and scheduled for removal in pytest 4.0'
+RESULT_LOG = (
+    '--result-log is deprecated and scheduled for removal in pytest 4.0.\n'
+    'See https://docs.pytest.org/en/latest/usage.html#creating-resultlog-format-files for more information.'
+)
+
+MARK_INFO_ATTRIBUTE = RemovedInPytest4Warning(
+    "MarkInfo objects are deprecated as they contain the merged marks"
+)
+
+MARK_PARAMETERSET_UNPACKING = RemovedInPytest4Warning(
+    "Applying marks directly to parameters is deprecated,"
+    " please use pytest.param(..., marks=...) instead.\n"
+    "For more details, see: https://docs.pytest.org/en/latest/parametrize.html"
+)
diff --git a/lib/spack/external/_pytest/doctest.py b/lib/spack/external/_pytest/doctest.py
index f4782dded5..4c05acddf7 100644
--- a/lib/spack/external/_pytest/doctest.py
+++ b/lib/spack/external/_pytest/doctest.py
@@ -1,5 +1,5 @@
 """ discover and run doctests in modules and test files."""
-from __future__ import absolute_import
+from __future__ import absolute_import, division, print_function
 
 import traceback
 
@@ -22,27 +22,29 @@ DOCTEST_REPORT_CHOICES = (
     DOCTEST_REPORT_CHOICE_ONLY_FIRST_FAILURE,
 )
 
+
 def pytest_addoption(parser):
     parser.addini('doctest_optionflags', 'option flags for doctests',
-        type="args", default=["ELLIPSIS"])
+                  type="args", default=["ELLIPSIS"])
+    parser.addini("doctest_encoding", 'encoding used for doctest files', default="utf-8")
     group = parser.getgroup("collect")
     group.addoption("--doctest-modules",
-        action="store_true", default=False,
-        help="run doctests in all .py modules",
-        dest="doctestmodules")
+                    action="store_true", default=False,
+                    help="run doctests in all .py modules",
+                    dest="doctestmodules")
     group.addoption("--doctest-report",
-        type=str.lower, default="udiff",
-        help="choose another output format for diffs on doctest failure",
-        choices=DOCTEST_REPORT_CHOICES,
-        dest="doctestreport")
+                    type=str.lower, default="udiff",
+                    help="choose another output format for diffs on doctest failure",
+                    choices=DOCTEST_REPORT_CHOICES,
+                    dest="doctestreport")
     group.addoption("--doctest-glob",
-        action="append", default=[], metavar="pat",
-        help="doctests file matching pattern, default: test*.txt",
-        dest="doctestglob")
+                    action="append", default=[], metavar="pat",
+                    help="doctests file matching pattern, default: test*.txt",
+                    dest="doctestglob")
     group.addoption("--doctest-ignore-import-errors",
-        action="store_true", default=False,
-        help="ignore doctest ImportErrors",
-        dest="doctest_ignore_import_errors")
+                    action="store_true", default=False,
+                    help="ignore doctest ImportErrors",
+                    dest="doctest_ignore_import_errors")
 
 
 def pytest_collect_file(path, parent):
@@ -118,7 +120,7 @@ class DoctestItem(pytest.Item):
                 lines = ["%03d %s" % (i + test.lineno + 1, x)
                          for (i, x) in enumerate(lines)]
                 # trim docstring error lines to 10
-                lines = lines[example.lineno - 9:example.lineno + 1]
+                lines = lines[max(example.lineno - 9, 0):example.lineno + 1]
             else:
                 lines = ['EXAMPLE LOCATION UNKNOWN, not showing all tests of that example']
                 indent = '>>>'
@@ -127,18 +129,18 @@ class DoctestItem(pytest.Item):
                     indent = '...'
             if excinfo.errisinstance(doctest.DocTestFailure):
                 lines += checker.output_difference(example,
-                        doctestfailure.got, report_choice).split("\n")
+                                                   doctestfailure.got, report_choice).split("\n")
             else:
                 inner_excinfo = ExceptionInfo(excinfo.value.exc_info)
                 lines += ["UNEXPECTED EXCEPTION: %s" %
-                            repr(inner_excinfo.value)]
+                          repr(inner_excinfo.value)]
                 lines += traceback.format_exception(*excinfo.value.exc_info)
             return ReprFailDoctest(reprlocation, lines)
         else:
             return super(DoctestItem, self).repr_failure(excinfo)
 
     def reportinfo(self):
-        return self.fspath, None, "[doctest] %s" % self.name
+        return self.fspath, self.dtest.lineno, "[doctest] %s" % self.name
 
 
 def _get_flag_lookup():
@@ -171,15 +173,16 @@ class DoctestTextfile(pytest.Module):
 
         # inspired by doctest.testfile; ideally we would use it directly,
         # but it doesn't support passing a custom checker
-        text = self.fspath.read()
+        encoding = self.config.getini("doctest_encoding")
+        text = self.fspath.read_text(encoding)
         filename = str(self.fspath)
         name = self.fspath.basename
         globs = {'__name__': '__main__'}
 
-
         optionflags = get_optionflags(self)
         runner = doctest.DebugRunner(verbose=0, optionflags=optionflags,
                                      checker=_get_checker())
+        _fix_spoof_python2(runner, encoding)
 
         parser = doctest.DocTestParser()
         test = parser.get_doctest(text, globs, name, filename, 0)
@@ -215,6 +218,7 @@ class DoctestModule(pytest.Module):
         optionflags = get_optionflags(self)
         runner = doctest.DebugRunner(verbose=0, optionflags=optionflags,
                                      checker=_get_checker())
+
         for test in finder.find(module, module.__name__):
             if test.examples:  # skip empty doctests
                 yield DoctestItem(test.name, self, runner, test)
@@ -323,6 +327,33 @@ def _get_report_choice(key):
         DOCTEST_REPORT_CHOICE_NONE: 0,
     }[key]
 
+
+def _fix_spoof_python2(runner, encoding):
+    """
+    Installs a "SpoofOut" into the given DebugRunner so it properly deals with unicode output. This
+    should patch only doctests for text files because they don't have a way to declare their
+    encoding. Doctests in docstrings from Python modules don't have the same problem given that
+    Python already decoded the strings.
+
+    This fixes the problem related in issue #2434.
+    """
+    from _pytest.compat import _PY2
+    if not _PY2:
+        return
+
+    from doctest import _SpoofOut
+
+    class UnicodeSpoof(_SpoofOut):
+
+        def getvalue(self):
+            result = _SpoofOut.getvalue(self)
+            if encoding:
+                result = result.decode(encoding)
+            return result
+
+    runner._fakeout = UnicodeSpoof()
+
+
 @pytest.fixture(scope='session')
 def doctest_namespace():
     """
diff --git a/lib/spack/external/_pytest/fixtures.py b/lib/spack/external/_pytest/fixtures.py
index 28bcd4d8d7..98317a4889 100644
--- a/lib/spack/external/_pytest/fixtures.py
+++ b/lib/spack/external/_pytest/fixtures.py
@@ -1,22 +1,36 @@
-import sys
+from __future__ import absolute_import, division, print_function
 
-from py._code.code import FormattedExcinfo
+import inspect
+import sys
+import warnings
 
 import py
-import pytest
-import warnings
+from py._code.code import FormattedExcinfo
 
-import inspect
 import _pytest
+from _pytest import nodes
 from _pytest._code.code import TerminalRepr
 from _pytest.compat import (
     NOTSET, exc_clear, _format_args,
     getfslineno, get_real_func,
     is_generator, isclass, getimfunc,
     getlocation, getfuncargnames,
+    safe_getattr,
+    FuncargnamesCompatAttr,
 )
+from _pytest.outcomes import fail, TEST_OUTCOME
+
+
+from ordereddict_backport import OrderedDict
+
 
 def pytest_sessionstart(session):
+    import _pytest.python
+    scopename2class.update({
+        'class': _pytest.python.Class,
+        'module': _pytest.python.Module,
+        'function': _pytest.main.Item,
+    })
     session._fixturemanager = FixtureManager(session)
 
 
@@ -29,6 +43,7 @@ scope2props["class"] = scope2props["module"] + ("cls",)
 scope2props["instance"] = scope2props["class"] + ("instance", )
 scope2props["function"] = scope2props["instance"] + ("function", "keywords")
 
+
 def scopeproperty(name=None, doc=None):
     def decoratescope(func):
         scopename = name or func.__name__
@@ -43,19 +58,6 @@ def scopeproperty(name=None, doc=None):
     return decoratescope
 
 
-def pytest_namespace():
-    scopename2class.update({
-        'class': pytest.Class,
-        'module': pytest.Module,
-        'function': pytest.Item,
-    })
-    return {
-        'fixture': fixture,
-        'yield_fixture': yield_fixture,
-        'collect': {'_fillfuncargs': fillfixtures}
-    }
-
-
 def get_scope_node(node, scope):
     cls = scopename2class.get(scope)
     if cls is None:
@@ -73,7 +75,7 @@ def add_funcarg_pseudo_fixture_def(collector, metafunc, fixturemanager):
     # XXX we can probably avoid this algorithm  if we modify CallSpec2
     # to directly care for creating the fixturedefs within its methods.
     if not metafunc._calls[0].funcargs:
-        return # this function call does not have direct parametrization
+        return  # this function call does not have direct parametrization
     # collect funcargs of all callspecs into a list of values
     arg2params = {}
     arg2scope = {}
@@ -103,36 +105,32 @@ def add_funcarg_pseudo_fixture_def(collector, metafunc, fixturemanager):
         if scope != "function":
             node = get_scope_node(collector, scope)
             if node is None:
-                assert scope == "class" and isinstance(collector, pytest.Module)
+                assert scope == "class" and isinstance(collector, _pytest.python.Module)
                 # use module-level collector for class-scope (for now)
                 node = collector
         if node and argname in node._name2pseudofixturedef:
             arg2fixturedefs[argname] = [node._name2pseudofixturedef[argname]]
         else:
-            fixturedef =  FixtureDef(fixturemanager, '', argname,
-                           get_direct_param_fixture_func,
-                           arg2scope[argname],
-                           valuelist, False, False)
+            fixturedef = FixtureDef(fixturemanager, '', argname,
+                                    get_direct_param_fixture_func,
+                                    arg2scope[argname],
+                                    valuelist, False, False)
             arg2fixturedefs[argname] = [fixturedef]
             if node is not None:
                 node._name2pseudofixturedef[argname] = fixturedef
 
 
-
 def getfixturemarker(obj):
     """ return fixturemarker or None if it doesn't exist or raised
     exceptions."""
     try:
         return getattr(obj, "_pytestfixturefunction", None)
-    except KeyboardInterrupt:
-        raise
-    except Exception:
+    except TEST_OUTCOME:
         # some objects raise errors like request (from flask import request)
         # we don't expect them to be fixture functions
         return None
 
 
-
 def get_parametrized_fixture_keys(item, scopenum):
     """ return list of keys for all parametrized arguments which match
     the specified scope. """
@@ -142,10 +140,10 @@ def get_parametrized_fixture_keys(item, scopenum):
     except AttributeError:
         pass
     else:
-        # cs.indictes.items() is random order of argnames but
-        # then again different functions (items) can change order of
-        # arguments so it doesn't matter much probably
-        for argname, param_index in cs.indices.items():
+        # cs.indices.items() is random order of argnames.  Need to
+        # sort this so that different calls to
+        # get_parametrized_fixture_keys will be deterministic.
+        for argname, param_index in sorted(cs.indices.items()):
             if cs._arg2scopenum[argname] != scopenum:
                 continue
             if scopenum == 0:    # session
@@ -167,20 +165,21 @@ def reorder_items(items):
     for scopenum in range(0, scopenum_function):
         argkeys_cache[scopenum] = d = {}
         for item in items:
-            keys = set(get_parametrized_fixture_keys(item, scopenum))
+            keys = OrderedDict.fromkeys(get_parametrized_fixture_keys(item, scopenum))
             if keys:
                 d[item] = keys
     return reorder_items_atscope(items, set(), argkeys_cache, 0)
 
+
 def reorder_items_atscope(items, ignore, argkeys_cache, scopenum):
     if scopenum >= scopenum_function or len(items) < 3:
         return items
     items_done = []
     while 1:
         items_before, items_same, items_other, newignore = \
-                slice_items(items, ignore, argkeys_cache[scopenum])
+            slice_items(items, ignore, argkeys_cache[scopenum])
         items_before = reorder_items_atscope(
-                            items_before, ignore, argkeys_cache,scopenum+1)
+            items_before, ignore, argkeys_cache, scopenum + 1)
         if items_same is None:
             # nothing to reorder in this scope
             assert items_other is None
@@ -201,9 +200,9 @@ def slice_items(items, ignore, scoped_argkeys_cache):
         for i, item in enumerate(it):
             argkeys = scoped_argkeys_cache.get(item)
             if argkeys is not None:
-                argkeys = argkeys.difference(ignore)
-                if argkeys:  # found a slicing key
-                    slicing_argkey = argkeys.pop()
+                newargkeys = OrderedDict.fromkeys(k for k in argkeys if k not in ignore)
+                if newargkeys:  # found a slicing key
+                    slicing_argkey, _ = newargkeys.popitem()
                     items_before = items[:i]
                     items_same = [item]
                     items_other = []
@@ -211,7 +210,7 @@ def slice_items(items, ignore, scoped_argkeys_cache):
                     for item in it:
                         argkeys = scoped_argkeys_cache.get(item)
                         if argkeys and slicing_argkey in argkeys and \
-                            slicing_argkey not in ignore:
+                                slicing_argkey not in ignore:
                             items_same.append(item)
                         else:
                             items_other.append(item)
@@ -221,17 +220,6 @@ def slice_items(items, ignore, scoped_argkeys_cache):
     return items, None, None, None
 
 
-
-class FuncargnamesCompatAttr:
-    """ helper class so that Metafunc, Function and FixtureRequest
-    don't need to each define the "funcargnames" compatibility attribute.
-    """
-    @property
-    def funcargnames(self):
-        """ alias attribute for ``fixturenames`` for pre-2.3 compatibility"""
-        return self.fixturenames
-
-
 def fillfixtures(function):
     """ fill missing funcargs for a test function. """
     try:
@@ -254,10 +242,10 @@ def fillfixtures(function):
         request._fillfixtures()
 
 
-
 def get_direct_param_fixture_func(request):
     return request.param
 
+
 class FuncFixtureInfo:
     def __init__(self, argnames, names_closure, name2fixturedefs):
         self.argnames = argnames
@@ -296,7 +284,6 @@ class FixtureRequest(FuncargnamesCompatAttr):
         """ underlying collection node (depends on current request scope)"""
         return self._getscopeitem(self.scope)
 
-
     def _getnextfixturedef(self, argname):
         fixturedefs = self._arg2fixturedefs.get(argname, None)
         if fixturedefs is None:
@@ -318,7 +305,6 @@ class FixtureRequest(FuncargnamesCompatAttr):
         """ the pytest config object associated with this request. """
         return self._pyfuncitem.config
 
-
     @scopeproperty()
     def function(self):
         """ test function object if the request has a per-function scope. """
@@ -327,7 +313,7 @@ class FixtureRequest(FuncargnamesCompatAttr):
     @scopeproperty("class")
     def cls(self):
         """ class (can be None) where the test function was collected. """
-        clscol = self._pyfuncitem.getparent(pytest.Class)
+        clscol = self._pyfuncitem.getparent(_pytest.python.Class)
         if clscol:
             return clscol.obj
 
@@ -345,7 +331,7 @@ class FixtureRequest(FuncargnamesCompatAttr):
     @scopeproperty()
     def module(self):
         """ python module object where the test function was collected. """
-        return self._pyfuncitem.getparent(pytest.Module).obj
+        return self._pyfuncitem.getparent(_pytest.python.Module).obj
 
     @scopeproperty()
     def fspath(self):
@@ -414,7 +400,7 @@ class FixtureRequest(FuncargnamesCompatAttr):
         :arg extrakey: added to internal caching key of (funcargname, scope).
         """
         if not hasattr(self.config, '_setupcache'):
-            self.config._setupcache = {} # XXX weakref?
+            self.config._setupcache = {}  # XXX weakref?
         cachekey = (self.fixturename, self._getscopeitem(scope), extrakey)
         cache = self.config._setupcache
         try:
@@ -445,7 +431,8 @@ class FixtureRequest(FuncargnamesCompatAttr):
         from _pytest import deprecated
         warnings.warn(
             deprecated.GETFUNCARGVALUE,
-            DeprecationWarning)
+            DeprecationWarning,
+            stacklevel=2)
         return self.getfixturevalue(argname)
 
     def _get_active_fixturedef(self, argname):
@@ -470,13 +457,13 @@ class FixtureRequest(FuncargnamesCompatAttr):
 
     def _get_fixturestack(self):
         current = self
-        l = []
+        values = []
         while 1:
             fixturedef = getattr(current, "_fixturedef", None)
             if fixturedef is None:
-                l.reverse()
-                return l
-            l.append(fixturedef)
+                values.reverse()
+                return values
+            values.append(fixturedef)
             current = current._parent_request
 
     def _getfixturevalue(self, fixturedef):
@@ -508,7 +495,7 @@ class FixtureRequest(FuncargnamesCompatAttr):
                         source_lineno,
                     )
                 )
-                pytest.fail(msg)
+                fail(msg)
         else:
             # indices might not be set if old-style metafunc.addcall() was used
             param_index = funcitem.callspec.indices.get(argname, 0)
@@ -541,11 +528,11 @@ class FixtureRequest(FuncargnamesCompatAttr):
         if scopemismatch(invoking_scope, requested_scope):
             # try to report something helpful
             lines = self._factorytraceback()
-            pytest.fail("ScopeMismatch: You tried to access the %r scoped "
-                "fixture %r with a %r scoped request object, "
-                "involved factories\n%s" %(
-                (requested_scope, argname, invoking_scope, "\n".join(lines))),
-                pytrace=False)
+            fail("ScopeMismatch: You tried to access the %r scoped "
+                 "fixture %r with a %r scoped request object, "
+                 "involved factories\n%s" % (
+                     (requested_scope, argname, invoking_scope, "\n".join(lines))),
+                 pytrace=False)
 
     def _factorytraceback(self):
         lines = []
@@ -554,7 +541,7 @@ class FixtureRequest(FuncargnamesCompatAttr):
             fs, lineno = getfslineno(factory)
             p = self._pyfuncitem.session.fspath.bestrelpath(fs)
             args = _format_args(factory)
-            lines.append("%s:%d:  def %s%s" %(
+            lines.append("%s:%d:  def %s%s" % (
                 p, lineno, factory.__name__, args))
         return lines
 
@@ -570,12 +557,13 @@ class FixtureRequest(FuncargnamesCompatAttr):
         return node
 
     def __repr__(self):
-        return "<FixtureRequest for %r>" %(self.node)
+        return "<FixtureRequest for %r>" % (self.node)
 
 
 class SubRequest(FixtureRequest):
     """ a sub request for handling getting a fixture from a
     test function/fixture. """
+
     def __init__(self, request, scope, param, param_index, fixturedef):
         self._parent_request = request
         self.fixturename = fixturedef.argname
@@ -584,9 +572,8 @@ class SubRequest(FixtureRequest):
         self.param_index = param_index
         self.scope = scope
         self._fixturedef = fixturedef
-        self.addfinalizer = fixturedef.addfinalizer
         self._pyfuncitem = request._pyfuncitem
-        self._fixture_values  = request._fixture_values
+        self._fixture_values = request._fixture_values
         self._fixture_defs = request._fixture_defs
         self._arg2fixturedefs = request._arg2fixturedefs
         self._arg2index = request._arg2index
@@ -595,6 +582,9 @@ class SubRequest(FixtureRequest):
     def __repr__(self):
         return "<SubRequest %r for %r>" % (self.fixturename, self._pyfuncitem)
 
+    def addfinalizer(self, finalizer):
+        self._fixturedef.addfinalizer(finalizer)
+
 
 class ScopeMismatchError(Exception):
     """ A fixture function tries to use a different fixture function which
@@ -626,6 +616,7 @@ def scope2index(scope, descr, where=None):
 
 class FixtureLookupError(LookupError):
     """ could not return a requested Fixture (missing or invalid). """
+
     def __init__(self, argname, request, msg=None):
         self.argname = argname
         self.request = request
@@ -648,9 +639,9 @@ class FixtureLookupError(LookupError):
                 lines, _ = inspect.getsourcelines(get_real_func(function))
             except (IOError, IndexError, TypeError):
                 error_msg = "file %s, line %s: source code not available"
-                addline(error_msg % (fspath, lineno+1))
+                addline(error_msg % (fspath, lineno + 1))
             else:
-                addline("file %s, line %s" % (fspath, lineno+1))
+                addline("file %s, line %s" % (fspath, lineno + 1))
                 for i, line in enumerate(lines):
                     line = line.rstrip()
                     addline("  " + line)
@@ -666,7 +657,7 @@ class FixtureLookupError(LookupError):
                 if faclist and name not in available:
                     available.append(name)
             msg = "fixture %r not found" % (self.argname,)
-            msg += "\n available fixtures: %s" %(", ".join(sorted(available)),)
+            msg += "\n available fixtures: %s" % (", ".join(sorted(available)),)
             msg += "\n use 'pytest --fixtures [testpath]' for help on them."
 
         return FixtureLookupErrorRepr(fspath, lineno, tblines, msg, self.argname)
@@ -692,15 +683,16 @@ class FixtureLookupErrorRepr(TerminalRepr):
                 tw.line('{0}       {1}'.format(FormattedExcinfo.flow_marker,
                                                line.strip()), red=True)
         tw.line()
-        tw.line("%s:%d" % (self.filename, self.firstlineno+1))
+        tw.line("%s:%d" % (self.filename, self.firstlineno + 1))
 
 
 def fail_fixturefunc(fixturefunc, msg):
     fs, lineno = getfslineno(fixturefunc)
-    location = "%s:%s" % (fs, lineno+1)
+    location = "%s:%s" % (fs, lineno + 1)
     source = _pytest._code.Source(fixturefunc)
-    pytest.fail(msg + ":\n\n" + str(source.indent()) + "\n" + location,
-                pytrace=False)
+    fail(msg + ":\n\n" + str(source.indent()) + "\n" + location,
+         pytrace=False)
+
 
 def call_fixture_func(fixturefunc, request, kwargs):
     yieldctx = is_generator(fixturefunc)
@@ -715,7 +707,7 @@ def call_fixture_func(fixturefunc, request, kwargs):
                 pass
             else:
                 fail_fixturefunc(fixturefunc,
-                    "yield_fixture function has more than one 'yield'")
+                                 "yield_fixture function has more than one 'yield'")
 
         request.addfinalizer(teardown)
     else:
@@ -725,6 +717,7 @@ def call_fixture_func(fixturefunc, request, kwargs):
 
 class FixtureDef:
     """ A container for a factory definition. """
+
     def __init__(self, fixturemanager, baseid, argname, func, scope, params,
                  unittest=False, ids=None):
         self._fixturemanager = fixturemanager
@@ -749,10 +742,19 @@ class FixtureDef:
         self._finalizer.append(finalizer)
 
     def finish(self):
+        exceptions = []
         try:
             while self._finalizer:
-                func = self._finalizer.pop()
-                func()
+                try:
+                    func = self._finalizer.pop()
+                    func()
+                except:  # noqa
+                    exceptions.append(sys.exc_info())
+            if exceptions:
+                e = exceptions[0]
+                del exceptions  # ensure we don't keep all frames alive because of the traceback
+                py.builtin._reraise(*e)
+
         finally:
             ihook = self._fixturemanager.session.ihook
             ihook.pytest_fixture_post_finalizer(fixturedef=self)
@@ -790,6 +792,7 @@ class FixtureDef:
         return ("<FixtureDef name=%r scope=%r baseid=%r >" %
                 (self.argname, self.scope, self.baseid))
 
+
 def pytest_fixture_setup(fixturedef, request):
     """ Execution of fixture setup. """
     kwargs = {}
@@ -815,7 +818,7 @@ def pytest_fixture_setup(fixturedef, request):
     my_cache_key = request.param_index
     try:
         result = call_fixture_func(fixturefunc, request, kwargs)
-    except Exception:
+    except TEST_OUTCOME:
         fixturedef.cached_result = (None, my_cache_key, sys.exc_info())
         raise
     fixturedef.cached_result = (result, my_cache_key, None)
@@ -833,17 +836,16 @@ class FixtureFunctionMarker:
     def __call__(self, function):
         if isclass(function):
             raise ValueError(
-                    "class fixtures not supported (may be in the future)")
+                "class fixtures not supported (may be in the future)")
         function._pytestfixturefunction = self
         return function
 
 
-
 def fixture(scope="function", params=None, autouse=False, ids=None, name=None):
     """ (return a) decorator to mark a fixture factory function.
 
-    This decorator can be used (with or or without parameters) to define
-    a fixture function.  The name of the fixture function can later be
+    This decorator can be used (with or without parameters) to define a
+    fixture function.  The name of the fixture function can later be
     referenced to cause its invocation ahead of running tests: test
     modules or classes can use the pytest.mark.usefixtures(fixturename)
     marker.  Test functions can directly use fixture names as input
@@ -862,25 +864,25 @@ def fixture(scope="function", params=None, autouse=False, ids=None, name=None):
                 reference is needed to activate the fixture.
 
     :arg ids: list of string ids each corresponding to the params
-       so that they are part of the test id. If no ids are provided
-       they will be generated automatically from the params.
+                so that they are part of the test id. If no ids are provided
+                they will be generated automatically from the params.
 
     :arg name: the name of the fixture. This defaults to the name of the
-               decorated function. If a fixture is used in the same module in
-               which it is defined, the function name of the fixture will be
-               shadowed by the function arg that requests the fixture; one way
-               to resolve this is to name the decorated function
-               ``fixture_<fixturename>`` and then use
-               ``@pytest.fixture(name='<fixturename>')``.
+                decorated function. If a fixture is used in the same module in
+                which it is defined, the function name of the fixture will be
+                shadowed by the function arg that requests the fixture; one way
+                to resolve this is to name the decorated function
+                ``fixture_<fixturename>`` and then use
+                ``@pytest.fixture(name='<fixturename>')``.
 
     Fixtures can optionally provide their values to test functions using a ``yield`` statement,
     instead of ``return``. In this case, the code block after the ``yield`` statement is executed
     as teardown code regardless of the test outcome. A fixture function must yield exactly once.
     """
-    if callable(scope) and params is None and autouse == False:
+    if callable(scope) and params is None and autouse is False:
         # direct decoration
         return FixtureFunctionMarker(
-                "function", params, autouse, name=name)(scope)
+            "function", params, autouse, name=name)(scope)
     if params is not None and not isinstance(params, (list, tuple)):
         params = list(params)
     return FixtureFunctionMarker(scope, params, autouse, ids=ids, name=name)
@@ -895,7 +897,7 @@ def yield_fixture(scope="function", params=None, autouse=False, ids=None, name=N
     if callable(scope) and params is None and not autouse:
         # direct decoration
         return FixtureFunctionMarker(
-                "function", params, autouse, ids=ids, name=name)(scope)
+            "function", params, autouse, ids=ids, name=name)(scope)
     else:
         return FixtureFunctionMarker(scope, params, autouse, ids=ids, name=name)
 
@@ -954,14 +956,9 @@ class FixtureManager:
         self._nodeid_and_autousenames = [("", self.config.getini("usefixtures"))]
         session.config.pluginmanager.register(self, "funcmanage")
 
-
     def getfixtureinfo(self, node, func, cls, funcargs=True):
         if funcargs and not hasattr(node, "nofuncargs"):
-            if cls is not None:
-                startindex = 1
-            else:
-                startindex = None
-            argnames = getfuncargnames(func, startindex)
+            argnames = getfuncargnames(func, cls=cls)
         else:
             argnames = ()
         usefixtures = getattr(func, "usefixtures", None)
@@ -985,8 +982,8 @@ class FixtureManager:
             # by their test id)
             if p.basename.startswith("conftest.py"):
                 nodeid = p.dirpath().relto(self.config.rootdir)
-                if p.sep != "/":
-                    nodeid = nodeid.replace(p.sep, "/")
+                if p.sep != nodes.SEP:
+                    nodeid = nodeid.replace(p.sep, nodes.SEP)
         self.parsefactories(plugin, nodeid)
 
     def _getautousenames(self, nodeid):
@@ -996,7 +993,7 @@ class FixtureManager:
             if nodeid.startswith(baseid):
                 if baseid:
                     i = len(baseid)
-                    nextchar = nodeid[i:i+1]
+                    nextchar = nodeid[i:i + 1]
                     if nextchar and nextchar not in ":/":
                         continue
                 autousenames.extend(basenames)
@@ -1041,9 +1038,14 @@ class FixtureManager:
             if faclist:
                 fixturedef = faclist[-1]
                 if fixturedef.params is not None:
-                    func_params = getattr(getattr(metafunc.function, 'parametrize', None), 'args', [[None]])
+                    parametrize_func = getattr(metafunc.function, 'parametrize', None)
+                    func_params = getattr(parametrize_func, 'args', [[None]])
+                    func_kwargs = getattr(parametrize_func, 'kwargs', {})
                     # skip directly parametrized arguments
-                    argnames = func_params[0]
+                    if "argnames" in func_kwargs:
+                        argnames = parametrize_func.kwargs["argnames"]
+                    else:
+                        argnames = func_params[0]
                     if not isinstance(argnames, (tuple, list)):
                         argnames = [x.strip() for x in argnames.split(",") if x.strip()]
                     if argname not in func_params and argname not in argnames:
@@ -1068,7 +1070,9 @@ class FixtureManager:
         self._holderobjseen.add(holderobj)
         autousenames = []
         for name in dir(holderobj):
-            obj = getattr(holderobj, name, None)
+            # The attribute can be an arbitrary descriptor, so the attribute
+            # access below can raise. safe_getatt() ignores such exceptions.
+            obj = safe_getattr(holderobj, name, None)
             # fixture functions have a pytest_funcarg__ prefix (pre-2.3 style)
             # or are "@pytest.fixture" marked
             marker = getfixturemarker(obj)
@@ -1079,7 +1083,7 @@ class FixtureManager:
                     continue
                 marker = defaultfuncargprefixmarker
                 from _pytest import deprecated
-                self.config.warn('C1', deprecated.FUNCARG_PREFIX.format(name=name))
+                self.config.warn('C1', deprecated.FUNCARG_PREFIX.format(name=name), nodeid=nodeid)
                 name = name[len(self._argprefix):]
             elif not isinstance(marker, FixtureFunctionMarker):
                 # magic globals  with __getattr__ might have got us a wrong
@@ -1129,6 +1133,5 @@ class FixtureManager:
 
     def _matchfactories(self, fixturedefs, nodeid):
         for fixturedef in fixturedefs:
-            if nodeid.startswith(fixturedef.baseid):
+            if nodes.ischildnode(fixturedef.baseid, nodeid):
                 yield fixturedef
-
diff --git a/lib/spack/external/_pytest/freeze_support.py b/lib/spack/external/_pytest/freeze_support.py
index b27f59d74a..97147a8825 100644
--- a/lib/spack/external/_pytest/freeze_support.py
+++ b/lib/spack/external/_pytest/freeze_support.py
@@ -2,9 +2,7 @@
 Provides a function to report all internal modules for using freezing tools
 pytest
 """
-
-def pytest_namespace():
-    return {'freeze_includes': freeze_includes}
+from __future__ import absolute_import, division, print_function
 
 
 def freeze_includes():
diff --git a/lib/spack/external/_pytest/helpconfig.py b/lib/spack/external/_pytest/helpconfig.py
index 6e66b11c48..e744637f86 100644
--- a/lib/spack/external/_pytest/helpconfig.py
+++ b/lib/spack/external/_pytest/helpconfig.py
@@ -1,25 +1,61 @@
 """ version info, help messages, tracing configuration.  """
+from __future__ import absolute_import, division, print_function
+
 import py
 import pytest
-import os, sys
+from _pytest.config import PrintHelp
+import os
+import sys
+from argparse import Action
+
+
+class HelpAction(Action):
+    """This is an argparse Action that will raise an exception in
+    order to skip the rest of the argument parsing when --help is passed.
+    This prevents argparse from quitting due to missing required arguments
+    when any are defined, for example by ``pytest_addoption``.
+    This is similar to the way that the builtin argparse --help option is
+    implemented by raising SystemExit.
+    """
+
+    def __init__(self,
+                 option_strings,
+                 dest=None,
+                 default=False,
+                 help=None):
+        super(HelpAction, self).__init__(
+            option_strings=option_strings,
+            dest=dest,
+            const=True,
+            default=default,
+            nargs=0,
+            help=help)
+
+    def __call__(self, parser, namespace, values, option_string=None):
+        setattr(namespace, self.dest, self.const)
+
+        # We should only skip the rest of the parsing after preparse is done
+        if getattr(parser._parser, 'after_preparse', False):
+            raise PrintHelp
+
 
 def pytest_addoption(parser):
     group = parser.getgroup('debugconfig')
     group.addoption('--version', action="store_true",
-            help="display pytest lib version and import information.")
-    group._addoption("-h", "--help", action="store_true", dest="help",
-            help="show help message and configuration info")
-    group._addoption('-p', action="append", dest="plugins", default = [],
-               metavar="name",
-               help="early-load given plugin (multi-allowed). "
-                    "To avoid loading of plugins, use the `no:` prefix, e.g. "
-                    "`no:doctest`.")
+                    help="display pytest lib version and import information.")
+    group._addoption("-h", "--help", action=HelpAction, dest="help",
+                     help="show help message and configuration info")
+    group._addoption('-p', action="append", dest="plugins", default=[],
+                     metavar="name",
+                     help="early-load given plugin (multi-allowed). "
+                     "To avoid loading of plugins, use the `no:` prefix, e.g. "
+                     "`no:doctest`.")
     group.addoption('--traceconfig', '--trace-config',
-               action="store_true", default=False,
-               help="trace considerations of conftest.py files."),
+                    action="store_true", default=False,
+                    help="trace considerations of conftest.py files."),
     group.addoption('--debug',
-               action="store_true", dest="debug", default=False,
-               help="store internal tracing debug information in 'pytestdebug.log'.")
+                    action="store_true", dest="debug", default=False,
+                    help="store internal tracing debug information in 'pytestdebug.log'.")
     group._addoption(
         '-o', '--override-ini', nargs='*', dest="override_ini",
         action="append",
@@ -34,10 +70,10 @@ def pytest_cmdline_parse():
         path = os.path.abspath("pytestdebug.log")
         debugfile = open(path, 'w')
         debugfile.write("versions pytest-%s, py-%s, "
-                "python-%s\ncwd=%s\nargs=%s\n\n" %(
-            pytest.__version__, py.__version__,
-            ".".join(map(str, sys.version_info)),
-            os.getcwd(), config._origargs))
+                        "python-%s\ncwd=%s\nargs=%s\n\n" % (
+                            pytest.__version__, py.__version__,
+                            ".".join(map(str, sys.version_info)),
+                            os.getcwd(), config._origargs))
         config.trace.root.setwriter(debugfile.write)
         undo_tracing = config.pluginmanager.enable_tracing()
         sys.stderr.write("writing pytestdebug information to %s\n" % path)
@@ -51,11 +87,12 @@ def pytest_cmdline_parse():
 
         config.add_cleanup(unset_tracing)
 
+
 def pytest_cmdline_main(config):
     if config.option.version:
         p = py.path.local(pytest.__file__)
         sys.stderr.write("This is pytest version %s, imported from %s\n" %
-            (pytest.__version__, p))
+                         (pytest.__version__, p))
         plugininfo = getpluginversioninfo(config)
         if plugininfo:
             for line in plugininfo:
@@ -67,6 +104,7 @@ def pytest_cmdline_main(config):
         config._ensure_unconfigure()
         return 0
 
+
 def showhelp(config):
     reporter = config.pluginmanager.get_plugin('terminalreporter')
     tw = reporter._tw
@@ -82,7 +120,7 @@ def showhelp(config):
         if type is None:
             type = "string"
         spec = "%s (%s)" % (name, type)
-        line = "  %-24s %s" %(spec, help)
+        line = "  %-24s %s" % (spec, help)
         tw.line(line[:tw.fullwidth])
 
     tw.line()
@@ -111,6 +149,7 @@ conftest_options = [
     ('pytest_plugins', 'list of plugin names to load'),
 ]
 
+
 def getpluginversioninfo(config):
     lines = []
     plugininfo = config.pluginmanager.list_plugin_distinfo()
@@ -122,11 +161,12 @@ def getpluginversioninfo(config):
             lines.append("  " + content)
     return lines
 
+
 def pytest_report_header(config):
     lines = []
     if config.option.debug or config.option.traceconfig:
         lines.append("using: pytest-%s pylib-%s" %
-            (pytest.__version__,py.__version__))
+                     (pytest.__version__, py.__version__))
 
         verinfo = getpluginversioninfo(config)
         if verinfo:
@@ -140,5 +180,5 @@ def pytest_report_header(config):
                 r = plugin.__file__
             else:
                 r = repr(plugin)
-            lines.append("    %-20s: %s" %(name, r))
+            lines.append("    %-20s: %s" % (name, r))
     return lines
diff --git a/lib/spack/external/_pytest/hookspec.py b/lib/spack/external/_pytest/hookspec.py
index b5f51eccf5..e5c966e58b 100644
--- a/lib/spack/external/_pytest/hookspec.py
+++ b/lib/spack/external/_pytest/hookspec.py
@@ -8,6 +8,7 @@ hookspec = HookspecMarker("pytest")
 # Initialization hooks called for every plugin
 # -------------------------------------------------------------------------
 
+
 @hookspec(historic=True)
 def pytest_addhooks(pluginmanager):
     """called at plugin registration time to allow adding new hooks via a call to
@@ -16,11 +17,14 @@ def pytest_addhooks(pluginmanager):
 
 @hookspec(historic=True)
 def pytest_namespace():
-    """return dict of name->object to be made globally available in
+    """
+    DEPRECATED: this hook causes direct monkeypatching on pytest, its use is strongly discouraged
+    return dict of name->object to be made globally available in
     the pytest namespace.  This hook is called at plugin registration
     time.
     """
 
+
 @hookspec(historic=True)
 def pytest_plugin_registered(plugin, manager):
     """ a new pytest plugin got registered. """
@@ -56,11 +60,20 @@ def pytest_addoption(parser):
     via (deprecated) ``pytest.config``.
     """
 
+
 @hookspec(historic=True)
 def pytest_configure(config):
-    """ called after command line options have been parsed
-    and all plugins and initial conftest files been loaded.
-    This hook is called for every plugin.
+    """
+    Allows plugins and conftest files to perform initial configuration.
+
+    This hook is called for every plugin and initial conftest file
+    after command line options have been parsed.
+
+    After that, the hook is called for other conftest files as they are
+    imported.
+
+    :arg config: pytest config object
+    :type config: _pytest.config.Config
     """
 
 # -------------------------------------------------------------------------
@@ -69,17 +82,25 @@ def pytest_configure(config):
 # discoverable conftest.py local plugins.
 # -------------------------------------------------------------------------
 
+
 @hookspec(firstresult=True)
 def pytest_cmdline_parse(pluginmanager, args):
-    """return initialized config object, parsing the specified args. """
+    """return initialized config object, parsing the specified args.
+
+    Stops at first non-None result, see :ref:`firstresult` """
+
 
 def pytest_cmdline_preparse(config, args):
     """(deprecated) modify command line arguments before option parsing. """
 
+
 @hookspec(firstresult=True)
 def pytest_cmdline_main(config):
     """ called for performing the main command line action. The default
-    implementation will invoke the configure hooks and runtest_mainloop. """
+    implementation will invoke the configure hooks and runtest_mainloop.
+
+    Stops at first non-None result, see :ref:`firstresult` """
+
 
 def pytest_load_initial_conftests(early_config, parser, args):
     """ implements the loading of initial conftest files ahead
@@ -92,88 +113,124 @@ def pytest_load_initial_conftests(early_config, parser, args):
 
 @hookspec(firstresult=True)
 def pytest_collection(session):
-    """ perform the collection protocol for the given session. """
+    """ perform the collection protocol for the given session.
+
+    Stops at first non-None result, see :ref:`firstresult` """
+
 
 def pytest_collection_modifyitems(session, config, items):
     """ called after collection has been performed, may filter or re-order
     the items in-place."""
 
+
 def pytest_collection_finish(session):
     """ called after collection has been performed and modified. """
 
+
 @hookspec(firstresult=True)
 def pytest_ignore_collect(path, config):
     """ return True to prevent considering this path for collection.
     This hook is consulted for all files and directories prior to calling
     more specific hooks.
+
+    Stops at first non-None result, see :ref:`firstresult`
     """
 
+
 @hookspec(firstresult=True)
 def pytest_collect_directory(path, parent):
-    """ called before traversing a directory for collection files. """
+    """ called before traversing a directory for collection files.
+
+    Stops at first non-None result, see :ref:`firstresult` """
+
 
 def pytest_collect_file(path, parent):
     """ return collection Node or None for the given path. Any new node
     needs to have the specified ``parent`` as a parent."""
 
 # logging hooks for collection
+
+
 def pytest_collectstart(collector):
     """ collector starts collecting. """
 
+
 def pytest_itemcollected(item):
     """ we just collected a test item. """
 
+
 def pytest_collectreport(report):
     """ collector finished collecting. """
 
+
 def pytest_deselected(items):
     """ called for test items deselected by keyword. """
 
+
 @hookspec(firstresult=True)
 def pytest_make_collect_report(collector):
-    """ perform ``collector.collect()`` and return a CollectReport. """
+    """ perform ``collector.collect()`` and return a CollectReport.
+
+    Stops at first non-None result, see :ref:`firstresult` """
 
 # -------------------------------------------------------------------------
 # Python test function related hooks
 # -------------------------------------------------------------------------
 
+
 @hookspec(firstresult=True)
 def pytest_pycollect_makemodule(path, parent):
     """ return a Module collector or None for the given path.
     This hook will be called for each matching test module path.
     The pytest_collect_file hook needs to be used if you want to
     create test modules for files that do not match as a test module.
-    """
+
+    Stops at first non-None result, see :ref:`firstresult` """
+
 
 @hookspec(firstresult=True)
 def pytest_pycollect_makeitem(collector, name, obj):
-    """ return custom item/collector for a python object in a module, or None.  """
+    """ return custom item/collector for a python object in a module, or None.
+
+    Stops at first non-None result, see :ref:`firstresult` """
+
 
 @hookspec(firstresult=True)
 def pytest_pyfunc_call(pyfuncitem):
-    """ call underlying test function. """
+    """ call underlying test function.
+
+    Stops at first non-None result, see :ref:`firstresult` """
+
 
 def pytest_generate_tests(metafunc):
     """ generate (multiple) parametrized calls to a test function."""
 
+
 @hookspec(firstresult=True)
-def pytest_make_parametrize_id(config, val):
+def pytest_make_parametrize_id(config, val, argname):
     """Return a user-friendly string representation of the given ``val`` that will be used
     by @pytest.mark.parametrize calls. Return None if the hook doesn't know about ``val``.
-    """
+    The parameter name is available as ``argname``, if required.
+
+    Stops at first non-None result, see :ref:`firstresult` """
 
 # -------------------------------------------------------------------------
 # generic runtest related hooks
 # -------------------------------------------------------------------------
 
+
 @hookspec(firstresult=True)
 def pytest_runtestloop(session):
     """ called for performing the main runtest loop
-    (after collection finished). """
+    (after collection finished).
+
+    Stops at first non-None result, see :ref:`firstresult` """
+
 
 def pytest_itemstart(item, node):
     """ (deprecated, use pytest_runtest_logstart). """
 
+
 @hookspec(firstresult=True)
 def pytest_runtest_protocol(item, nextitem):
     """ implements the runtest_setup/call/teardown protocol for
@@ -187,17 +244,23 @@ def pytest_runtest_protocol(item, nextitem):
                    :py:func:`pytest_runtest_teardown`.
 
     :return boolean: True if no further hook implementations should be invoked.
-    """
+
+
+    Stops at first non-None result, see :ref:`firstresult` """
+
 
 def pytest_runtest_logstart(nodeid, location):
     """ signal the start of running a single test item. """
 
+
 def pytest_runtest_setup(item):
     """ called before ``pytest_runtest_call(item)``. """
 
+
 def pytest_runtest_call(item):
     """ called to execute the test ``item``. """
 
+
 def pytest_runtest_teardown(item, nextitem):
     """ called after ``pytest_runtest_call``.
 
@@ -207,12 +270,15 @@ def pytest_runtest_teardown(item, nextitem):
                    so that nextitem only needs to call setup-functions.
     """
 
+
 @hookspec(firstresult=True)
 def pytest_runtest_makereport(item, call):
     """ return a :py:class:`_pytest.runner.TestReport` object
-    for the given :py:class:`pytest.Item` and
+    for the given :py:class:`pytest.Item <_pytest.main.Item>` and
     :py:class:`_pytest.runner.CallInfo`.
-    """
+
+    Stops at first non-None result, see :ref:`firstresult` """
+
 
 def pytest_runtest_logreport(report):
     """ process a test setup/call/teardown report relating to
@@ -222,9 +288,13 @@ def pytest_runtest_logreport(report):
 # Fixture related hooks
 # -------------------------------------------------------------------------
 
+
 @hookspec(firstresult=True)
 def pytest_fixture_setup(fixturedef, request):
-    """ performs fixture setup execution. """
+    """ performs fixture setup execution.
+
+    Stops at first non-None result, see :ref:`firstresult` """
+
 
 def pytest_fixture_post_finalizer(fixturedef):
     """ called after fixture teardown, but before the cache is cleared so
@@ -235,18 +305,21 @@ def pytest_fixture_post_finalizer(fixturedef):
 # test session related hooks
 # -------------------------------------------------------------------------
 
+
 def pytest_sessionstart(session):
     """ before session.main() is called. """
 
+
 def pytest_sessionfinish(session, exitstatus):
     """ whole test run finishes. """
 
+
 def pytest_unconfigure(config):
     """ called before test process is exited.  """
 
 
 # -------------------------------------------------------------------------
-# hooks for customising the assert methods
+# hooks for customizing the assert methods
 # -------------------------------------------------------------------------
 
 def pytest_assertrepr_compare(config, op, left, right):
@@ -255,19 +328,48 @@ def pytest_assertrepr_compare(config, op, left, right):
     Return None for no custom explanation, otherwise return a list
     of strings.  The strings will be joined by newlines but any newlines
     *in* a string will be escaped.  Note that all but the first line will
-    be indented sligthly, the intention is for the first line to be a summary.
+    be indented slightly, the intention is for the first line to be a summary.
     """
 
 # -------------------------------------------------------------------------
 # hooks for influencing reporting (invoked from _pytest_terminal)
 # -------------------------------------------------------------------------
 
+
 def pytest_report_header(config, startdir):
-    """ return a string to be displayed as header info for terminal reporting."""
+    """ return a string or list of strings to be displayed as header info for terminal reporting.
+
+    :param config: the pytest config object.
+    :param startdir: py.path object with the starting dir
+
+    .. note::
+
+        This function should be implemented only in plugins or ``conftest.py``
+        files situated at the tests root directory due to how pytest
+        :ref:`discovers plugins during startup <pluginorder>`.
+    """
+
+
+def pytest_report_collectionfinish(config, startdir, items):
+    """
+    .. versionadded:: 3.2
+
+    return a string or list of strings to be displayed after collection has finished successfully.
+
+    This strings will be displayed after the standard "collected X items" message.
+
+    :param config: the pytest config object.
+    :param startdir: py.path object with the starting dir
+    :param items: list of pytest items that are going to be executed; this list should not be modified.
+    """
+
 
 @hookspec(firstresult=True)
 def pytest_report_teststatus(report):
-    """ return result-category, shortletter and verbose word for reporting."""
+    """ return result-category, shortletter and verbose word for reporting.
+
+    Stops at first non-None result, see :ref:`firstresult` """
+
 
 def pytest_terminal_summary(terminalreporter, exitstatus):
     """ add additional section in terminal summary reporting.  """
@@ -283,20 +385,26 @@ def pytest_logwarning(message, code, nodeid, fslocation):
 # doctest hooks
 # -------------------------------------------------------------------------
 
+
 @hookspec(firstresult=True)
 def pytest_doctest_prepare_content(content):
-    """ return processed content for a given doctest"""
+    """ return processed content for a given doctest
+
+    Stops at first non-None result, see :ref:`firstresult` """
 
 # -------------------------------------------------------------------------
 # error handling and internal debugging hooks
 # -------------------------------------------------------------------------
 
+
 def pytest_internalerror(excrepr, excinfo):
     """ called for internal errors. """
 
+
 def pytest_keyboard_interrupt(excinfo):
     """ called for keyboard interrupt. """
 
+
 def pytest_exception_interact(node, call, report):
     """called when an exception was raised which can potentially be
     interactively handled.
@@ -305,6 +413,7 @@ def pytest_exception_interact(node, call, report):
     that is not an internal exception like ``skip.Exception``.
     """
 
+
 def pytest_enter_pdb(config):
     """ called upon pdb.set_trace(), can be used by plugins to take special
     action just before the python debugger enters in interactive mode.
diff --git a/lib/spack/external/_pytest/junitxml.py b/lib/spack/external/_pytest/junitxml.py
index 317382e637..7fb40dc354 100644
--- a/lib/spack/external/_pytest/junitxml.py
+++ b/lib/spack/external/_pytest/junitxml.py
@@ -4,9 +4,11 @@
 
 
 Based on initial code from Ross Lawley.
+
+Output conforms to https://github.com/jenkinsci/xunit-plugin/blob/master/
+src/main/resources/org/jenkinsci/plugins/xunit/types/model/xsd/junit-10.xsd
 """
-# Output conforms to https://github.com/jenkinsci/xunit-plugin/blob/master/
-# src/main/resources/org/jenkinsci/plugins/xunit/types/model/xsd/junit-10.xsd
+from __future__ import absolute_import, division, print_function
 
 import functools
 import py
@@ -15,6 +17,7 @@ import re
 import sys
 import time
 import pytest
+from _pytest import nodes
 from _pytest.config import filename_arg
 
 # Python 2.X and 3.X compatibility
@@ -105,6 +108,8 @@ class _NodeReporter(object):
         }
         if testreport.location[1] is not None:
             attrs["line"] = testreport.location[1]
+        if hasattr(testreport, "url"):
+            attrs["url"] = testreport.url
         self.attrs = attrs
 
     def to_xml(self):
@@ -119,7 +124,7 @@ class _NodeReporter(object):
         node = kind(data, message=message)
         self.append(node)
 
-    def _write_captured_output(self, report):
+    def write_captured_output(self, report):
         for capname in ('out', 'err'):
             content = getattr(report, 'capstd' + capname)
             if content:
@@ -128,7 +133,6 @@ class _NodeReporter(object):
 
     def append_pass(self, report):
         self.add_stats('passed')
-        self._write_captured_output(report)
 
     def append_failure(self, report):
         # msg = str(report.longrepr.reprtraceback.extraline)
@@ -147,7 +151,6 @@ class _NodeReporter(object):
             fail = Junit.failure(message=message)
             fail.append(bin_xml_escape(report.longrepr))
             self.append(fail)
-        self._write_captured_output(report)
 
     def append_collect_error(self, report):
         # msg = str(report.longrepr.reprtraceback.extraline)
@@ -165,7 +168,6 @@ class _NodeReporter(object):
             msg = "test setup failure"
         self._add_simple(
             Junit.error, msg, report.longrepr)
-        self._write_captured_output(report)
 
     def append_skipped(self, report):
         if hasattr(report, "wasxfail"):
@@ -180,7 +182,7 @@ class _NodeReporter(object):
                 Junit.skipped("%s:%s: %s" % (filename, lineno, skipreason),
                               type="pytest.skip",
                               message=skipreason))
-        self._write_captured_output(report)
+        self.write_captured_output(report)
 
     def finalize(self):
         data = self.to_xml().unicode(indent=0)
@@ -225,13 +227,14 @@ def pytest_addoption(parser):
         metavar="str",
         default=None,
         help="prepend prefix to classnames in junit-xml output")
+    parser.addini("junit_suite_name", "Test suite name for JUnit report", default="pytest")
 
 
 def pytest_configure(config):
     xmlpath = config.option.xmlpath
     # prevent opening xmllog on slave nodes (xdist)
     if xmlpath and not hasattr(config, 'slaveinput'):
-        config._xml = LogXML(xmlpath, config.option.junitprefix)
+        config._xml = LogXML(xmlpath, config.option.junitprefix, config.getini("junit_suite_name"))
         config.pluginmanager.register(config._xml)
 
 
@@ -250,7 +253,7 @@ def mangle_test_address(address):
     except ValueError:
         pass
     # convert file path to dotted path
-    names[0] = names[0].replace("/", '.')
+    names[0] = names[0].replace(nodes.SEP, '.')
     names[0] = _py_ext_re.sub("", names[0])
     # put any params back
     names[-1] += possible_open_bracket + params
@@ -258,10 +261,11 @@ def mangle_test_address(address):
 
 
 class LogXML(object):
-    def __init__(self, logfile, prefix):
+    def __init__(self, logfile, prefix, suite_name="pytest"):
         logfile = os.path.expanduser(os.path.expandvars(logfile))
         self.logfile = os.path.normpath(os.path.abspath(logfile))
         self.prefix = prefix
+        self.suite_name = suite_name
         self.stats = dict.fromkeys([
             'error',
             'passed',
@@ -271,6 +275,9 @@ class LogXML(object):
         self.node_reporters = {}  # nodeid -> _NodeReporter
         self.node_reporters_ordered = []
         self.global_properties = []
+        # List of reports that failed on call but teardown is pending.
+        self.open_reports = []
+        self.cnt_double_fail_tests = 0
 
     def finalize(self, report):
         nodeid = getattr(report, 'nodeid', report)
@@ -330,14 +337,33 @@ class LogXML(object):
             -> teardown node2
             -> teardown node1
         """
+        close_report = None
         if report.passed:
             if report.when == "call":  # ignore setup/teardown
                 reporter = self._opentestcase(report)
                 reporter.append_pass(report)
         elif report.failed:
+            if report.when == "teardown":
+                # The following vars are needed when xdist plugin is used
+                report_wid = getattr(report, "worker_id", None)
+                report_ii = getattr(report, "item_index", None)
+                close_report = next(
+                    (rep for rep in self.open_reports
+                     if (rep.nodeid == report.nodeid and
+                         getattr(rep, "item_index", None) == report_ii and
+                         getattr(rep, "worker_id", None) == report_wid
+                         )
+                     ), None)
+                if close_report:
+                    # We need to open new testcase in case we have failure in
+                    # call and error in teardown in order to follow junit
+                    # schema
+                    self.finalize(close_report)
+                    self.cnt_double_fail_tests += 1
             reporter = self._opentestcase(report)
             if report.when == "call":
                 reporter.append_failure(report)
+                self.open_reports.append(report)
             else:
                 reporter.append_error(report)
         elif report.skipped:
@@ -345,7 +371,20 @@ class LogXML(object):
             reporter.append_skipped(report)
         self.update_testcase_duration(report)
         if report.when == "teardown":
+            reporter = self._opentestcase(report)
+            reporter.write_captured_output(report)
             self.finalize(report)
+            report_wid = getattr(report, "worker_id", None)
+            report_ii = getattr(report, "item_index", None)
+            close_report = next(
+                (rep for rep in self.open_reports
+                 if (rep.nodeid == report.nodeid and
+                     getattr(rep, "item_index", None) == report_ii and
+                     getattr(rep, "worker_id", None) == report_wid
+                     )
+                 ), None)
+            if close_report:
+                self.open_reports.remove(close_report)
 
     def update_testcase_duration(self, report):
         """accumulates total duration for nodeid from given report and updates
@@ -378,14 +417,15 @@ class LogXML(object):
         suite_stop_time = time.time()
         suite_time_delta = suite_stop_time - self.suite_start_time
 
-        numtests = self.stats['passed'] + self.stats['failure'] + self.stats['skipped'] + self.stats['error']
-
+        numtests = (self.stats['passed'] + self.stats['failure'] +
+                    self.stats['skipped'] + self.stats['error'] -
+                    self.cnt_double_fail_tests)
         logfile.write('<?xml version="1.0" encoding="utf-8"?>')
 
         logfile.write(Junit.testsuite(
             self._get_global_properties_node(),
             [x.to_xml() for x in self.node_reporters_ordered],
-            name="pytest",
+            name=self.suite_name,
             errors=self.stats['error'],
             failures=self.stats['failure'],
             skips=self.stats['skipped'],
@@ -405,9 +445,9 @@ class LogXML(object):
         """
         if self.global_properties:
             return Junit.properties(
-                    [
-                        Junit.property(name=name, value=value)
-                        for name, value in self.global_properties
-                    ]
+                [
+                    Junit.property(name=name, value=value)
+                    for name, value in self.global_properties
+                ]
             )
         return ''
diff --git a/lib/spack/external/_pytest/main.py b/lib/spack/external/_pytest/main.py
index 52876c12a4..eacae8dab1 100644
--- a/lib/spack/external/_pytest/main.py
+++ b/lib/spack/external/_pytest/main.py
@@ -1,18 +1,21 @@
 """ core implementation of testing process: init, session, runtest loop. """
+from __future__ import absolute_import, division, print_function
+
 import functools
 import os
 import sys
 
 import _pytest
+from _pytest import nodes
 import _pytest._code
 import py
-import pytest
 try:
     from collections import MutableMapping as MappingMixin
 except ImportError:
     from UserDict import DictMixin as MappingMixin
 
-from _pytest.config import directory_arg
+from _pytest.config import directory_arg, UsageError, hookimpl
+from _pytest.outcomes import exit
 from _pytest.runner import collect_one_node
 
 tracebackcutdir = py.path.local(_pytest.__file__).dirpath()
@@ -25,63 +28,73 @@ EXIT_INTERNALERROR = 3
 EXIT_USAGEERROR = 4
 EXIT_NOTESTSCOLLECTED = 5
 
+
 def pytest_addoption(parser):
     parser.addini("norecursedirs", "directory patterns to avoid for recursion",
-        type="args", default=['.*', 'build', 'dist', 'CVS', '_darcs', '{arch}', '*.egg'])
-    parser.addini("testpaths", "directories to search for tests when no files or directories are given in the command line.",
-        type="args", default=[])
-    #parser.addini("dirpatterns",
+                  type="args", default=['.*', 'build', 'dist', 'CVS', '_darcs', '{arch}', '*.egg', 'venv'])
+    parser.addini("testpaths", "directories to search for tests when no files or directories are given in the "
+                               "command line.",
+                  type="args", default=[])
+    # parser.addini("dirpatterns",
     #    "patterns specifying possible locations of test files",
     #    type="linelist", default=["**/test_*.txt",
     #            "**/test_*.py", "**/*_test.py"]
-    #)
+    # )
     group = parser.getgroup("general", "running and selection options")
     group._addoption('-x', '--exitfirst', action="store_const",
-               dest="maxfail", const=1,
-               help="exit instantly on first error or failed test."),
+                     dest="maxfail", const=1,
+                     help="exit instantly on first error or failed test."),
     group._addoption('--maxfail', metavar="num",
-               action="store", type=int, dest="maxfail", default=0,
-               help="exit after first num failures or errors.")
+                     action="store", type=int, dest="maxfail", default=0,
+                     help="exit after first num failures or errors.")
     group._addoption('--strict', action="store_true",
-               help="run pytest in strict mode, warnings become errors.")
+                     help="marks not registered in configuration file raise errors.")
     group._addoption("-c", metavar="file", type=str, dest="inifilename",
-               help="load configuration from `file` instead of trying to locate one of the implicit configuration files.")
+                     help="load configuration from `file` instead of trying to locate one of the implicit "
+                          "configuration files.")
     group._addoption("--continue-on-collection-errors", action="store_true",
-               default=False, dest="continue_on_collection_errors",
-               help="Force test execution even if collection errors occur.")
+                     default=False, dest="continue_on_collection_errors",
+                     help="Force test execution even if collection errors occur.")
 
     group = parser.getgroup("collect", "collection")
     group.addoption('--collectonly', '--collect-only', action="store_true",
-        help="only collect tests, don't execute them."),
+                    help="only collect tests, don't execute them."),
     group.addoption('--pyargs', action="store_true",
-        help="try to interpret all arguments as python packages.")
+                    help="try to interpret all arguments as python packages.")
     group.addoption("--ignore", action="append", metavar="path",
-        help="ignore path during collection (multi-allowed).")
+                    help="ignore path during collection (multi-allowed).")
     # when changing this to --conf-cut-dir, config.py Conftest.setinitial
     # needs upgrading as well
     group.addoption('--confcutdir', dest="confcutdir", default=None,
-        metavar="dir", type=functools.partial(directory_arg, optname="--confcutdir"),
-        help="only load conftest.py's relative to specified dir.")
+                    metavar="dir", type=functools.partial(directory_arg, optname="--confcutdir"),
+                    help="only load conftest.py's relative to specified dir.")
     group.addoption('--noconftest', action="store_true",
-        dest="noconftest", default=False,
-        help="Don't load any conftest.py files.")
+                    dest="noconftest", default=False,
+                    help="Don't load any conftest.py files.")
     group.addoption('--keepduplicates', '--keep-duplicates', action="store_true",
-        dest="keepduplicates", default=False,
-        help="Keep duplicate tests.")
+                    dest="keepduplicates", default=False,
+                    help="Keep duplicate tests.")
+    group.addoption('--collect-in-virtualenv', action='store_true',
+                    dest='collect_in_virtualenv', default=False,
+                    help="Don't ignore tests in a local virtualenv directory")
 
     group = parser.getgroup("debugconfig",
-        "test session debugging and configuration")
+                            "test session debugging and configuration")
     group.addoption('--basetemp', dest="basetemp", default=None, metavar="dir",
-               help="base temporary directory for this test run.")
+                    help="base temporary directory for this test run.")
 
 
 def pytest_namespace():
-    collect = dict(Item=Item, Collector=Collector, File=File, Session=Session)
-    return dict(collect=collect)
+    """keeping this one works around a deeper startup issue in pytest
+
+    i tried to find it for a while but the amount of time turned unsustainable,
+    so i put a hack in to revisit later
+    """
+    return {}
 
 
 def pytest_configure(config):
-    pytest.config = config # compatibiltiy
+    __import__('pytest').config = config  # compatibiltiy
 
 
 def wrap_session(config, doit):
@@ -96,17 +109,16 @@ def wrap_session(config, doit):
             config.hook.pytest_sessionstart(session=session)
             initstate = 2
             session.exitstatus = doit(config, session) or 0
-        except pytest.UsageError:
+        except UsageError:
             raise
         except KeyboardInterrupt:
             excinfo = _pytest._code.ExceptionInfo()
-            if initstate < 2 and isinstance(
-                    excinfo.value, pytest.exit.Exception):
+            if initstate < 2 and isinstance(excinfo.value, exit.Exception):
                 sys.stderr.write('{0}: {1}\n'.format(
                     excinfo.typename, excinfo.value.msg))
             config.hook.pytest_keyboard_interrupt(excinfo=excinfo)
             session.exitstatus = EXIT_INTERRUPTED
-        except:
+        except:  # noqa
             excinfo = _pytest._code.ExceptionInfo()
             config.notify_exception(excinfo, config.option)
             session.exitstatus = EXIT_INTERNALERROR
@@ -123,9 +135,11 @@ def wrap_session(config, doit):
         config._ensure_unconfigure()
     return session.exitstatus
 
+
 def pytest_cmdline_main(config):
     return wrap_session(config, _main)
 
+
 def _main(config, session):
     """ default command line protocol for initialization, session,
     running tests and reporting. """
@@ -137,9 +151,11 @@ def _main(config, session):
     elif session.testscollected == 0:
         return EXIT_NOTESTSCOLLECTED
 
+
 def pytest_collection(session):
     return session.perform_collect()
 
+
 def pytest_runtestloop(session):
     if (session.testsfailed and
             not session.config.option.continue_on_collection_errors):
@@ -150,21 +166,36 @@ def pytest_runtestloop(session):
         return True
 
     for i, item in enumerate(session.items):
-        nextitem = session.items[i+1] if i+1 < len(session.items) else None
+        nextitem = session.items[i + 1] if i + 1 < len(session.items) else None
         item.config.hook.pytest_runtest_protocol(item=item, nextitem=nextitem)
         if session.shouldstop:
             raise session.Interrupted(session.shouldstop)
     return True
 
+
+def _in_venv(path):
+    """Attempts to detect if ``path`` is the root of a Virtual Environment by
+    checking for the existence of the appropriate activate script"""
+    bindir = path.join('Scripts' if sys.platform.startswith('win') else 'bin')
+    if not bindir.exists():
+        return False
+    activates = ('activate', 'activate.csh', 'activate.fish',
+                 'Activate', 'Activate.bat', 'Activate.ps1')
+    return any([fname.basename in activates for fname in bindir.listdir()])
+
+
 def pytest_ignore_collect(path, config):
-    p = path.dirpath()
-    ignore_paths = config._getconftest_pathlist("collect_ignore", path=p)
+    ignore_paths = config._getconftest_pathlist("collect_ignore", path=path.dirpath())
     ignore_paths = ignore_paths or []
     excludeopt = config.getoption("ignore")
     if excludeopt:
         ignore_paths.extend([py.path.local(x) for x in excludeopt])
 
-    if path in ignore_paths:
+    if py.path.local(path) in ignore_paths:
+        return True
+
+    allow_in_venv = config.getoption("collect_in_virtualenv")
+    if _in_venv(path) and not allow_in_venv:
         return True
 
     # Skip duplicate paths.
@@ -190,14 +221,22 @@ class FSHookProxy:
         self.__dict__[name] = x
         return x
 
-def compatproperty(name):
-    def fget(self):
-        import warnings
-        warnings.warn("This usage is deprecated, please use pytest.{0} instead".format(name),
-                      PendingDeprecationWarning, stacklevel=2)
-        return getattr(pytest, name)
 
-    return property(fget)
+class _CompatProperty(object):
+    def __init__(self, name):
+        self.name = name
+
+    def __get__(self, obj, owner):
+        if obj is None:
+            return self
+
+        # TODO: reenable in the features branch
+        # warnings.warn(
+        #     "usage of {owner!r}.{name} is deprecated, please use pytest.{name} instead".format(
+        #         name=self.name, owner=type(owner).__name__),
+        #     PendingDeprecationWarning, stacklevel=2)
+        return getattr(__import__('pytest'), self.name)
+
 
 class NodeKeywords(MappingMixin):
     def __init__(self, node):
@@ -269,24 +308,28 @@ class Node(object):
         """ fspath sensitive hook proxy used to call pytest hooks"""
         return self.session.gethookproxy(self.fspath)
 
-    Module = compatproperty("Module")
-    Class = compatproperty("Class")
-    Instance = compatproperty("Instance")
-    Function = compatproperty("Function")
-    File = compatproperty("File")
-    Item = compatproperty("Item")
+    Module = _CompatProperty("Module")
+    Class = _CompatProperty("Class")
+    Instance = _CompatProperty("Instance")
+    Function = _CompatProperty("Function")
+    File = _CompatProperty("File")
+    Item = _CompatProperty("Item")
 
     def _getcustomclass(self, name):
-        cls = getattr(self, name)
-        if cls != getattr(pytest, name):
-            py.log._apiwarn("2.0", "use of node.%s is deprecated, "
-                "use pytest_pycollect_makeitem(...) to create custom "
-                "collection nodes" % name)
+        maybe_compatprop = getattr(type(self), name)
+        if isinstance(maybe_compatprop, _CompatProperty):
+            return getattr(__import__('pytest'), name)
+        else:
+            cls = getattr(self, name)
+            # TODO: reenable in the features branch
+            # warnings.warn("use of node.%s is deprecated, "
+            #    "use pytest_pycollect_makeitem(...) to create custom "
+            #    "collection nodes" % name, category=DeprecationWarning)
         return cls
 
     def __repr__(self):
-        return "<%s %r>" %(self.__class__.__name__,
-                           getattr(self, 'name', None))
+        return "<%s %r>" % (self.__class__.__name__,
+                            getattr(self, 'name', None))
 
     def warn(self, code, message):
         """ generate a warning with the given code and message for this
@@ -295,9 +338,6 @@ class Node(object):
         fslocation = getattr(self, "location", None)
         if fslocation is None:
             fslocation = getattr(self, "fspath", None)
-        else:
-            fslocation = "%s:%s" % (fslocation[0], fslocation[1] + 1)
-
         self.ihook.pytest_logwarning.call_historic(kwargs=dict(
             code=code, message=message,
             nodeid=self.nodeid, fslocation=fslocation))
@@ -335,7 +375,7 @@ class Node(object):
             res = function()
         except py.builtin._sysex:
             raise
-        except:
+        except:  # noqa
             failure = sys.exc_info()
             setattr(self, exattrname, failure)
             raise
@@ -358,9 +398,9 @@ class Node(object):
 
         ``marker`` can be a string or pytest.mark.* instance.
         """
-        from _pytest.mark import MarkDecorator
+        from _pytest.mark import MarkDecorator, MARK_GEN
         if isinstance(marker, py.builtin._basestring):
-            marker = MarkDecorator(marker)
+            marker = getattr(MARK_GEN, marker)
         elif not isinstance(marker, MarkDecorator):
             raise ValueError("is not a string or pytest.mark.* Marker")
         self.keywords[marker.name] = marker
@@ -410,7 +450,7 @@ class Node(object):
             return excinfo.value.formatrepr()
         tbfilter = True
         if self.config.option.fulltrace:
-            style="long"
+            style = "long"
         else:
             tb = _pytest._code.Traceback([excinfo.traceback[-1]])
             self._prunetraceback(excinfo)
@@ -438,6 +478,7 @@ class Node(object):
 
     repr_failure = _repr_failure_py
 
+
 class Collector(Node):
     """ Collector instances create children through collect()
         and thus iteratively build a tree.
@@ -459,10 +500,6 @@ class Collector(Node):
             return str(exc.args[0])
         return self._repr_failure_py(excinfo, style="short")
 
-    def _memocollect(self):
-        """ internal helper method to cache results of calling collect(). """
-        return self._memoizedcall('_collected', lambda: list(self.collect()))
-
     def _prunetraceback(self, excinfo):
         if hasattr(self, 'fspath'):
             traceback = excinfo.traceback
@@ -471,27 +508,38 @@ class Collector(Node):
                 ntraceback = ntraceback.cut(excludepath=tracebackcutdir)
             excinfo.traceback = ntraceback.filter()
 
+
 class FSCollector(Collector):
     def __init__(self, fspath, parent=None, config=None, session=None):
-        fspath = py.path.local(fspath) # xxx only for test_resultlog.py?
+        fspath = py.path.local(fspath)  # xxx only for test_resultlog.py?
         name = fspath.basename
         if parent is not None:
             rel = fspath.relto(parent.fspath)
             if rel:
                 name = rel
-            name = name.replace(os.sep, "/")
+            name = name.replace(os.sep, nodes.SEP)
         super(FSCollector, self).__init__(name, parent, config, session)
         self.fspath = fspath
 
+    def _check_initialpaths_for_relpath(self):
+        for initialpath in self.session._initialpaths:
+            if self.fspath.common(initialpath) == initialpath:
+                return self.fspath.relto(initialpath.dirname)
+
     def _makeid(self):
         relpath = self.fspath.relto(self.config.rootdir)
-        if os.sep != "/":
-            relpath = relpath.replace(os.sep, "/")
+
+        if not relpath:
+            relpath = self._check_initialpaths_for_relpath()
+        if os.sep != nodes.SEP:
+            relpath = relpath.replace(os.sep, nodes.SEP)
         return relpath
 
+
 class File(FSCollector):
     """ base class for collecting tests from a file. """
 
+
 class Item(Node):
     """ a basic test invocation item. Note that for a single function
     there might be multiple test invocation items.
@@ -503,6 +551,21 @@ class Item(Node):
         self._report_sections = []
 
     def add_report_section(self, when, key, content):
+        """
+        Adds a new report section, similar to what's done internally to add stdout and
+        stderr captured output::
+
+            item.add_report_section("call", "stdout", "report section contents")
+
+        :param str when:
+            One of the possible capture states, ``"setup"``, ``"call"``, ``"teardown"``.
+        :param str key:
+            Name of the section, can be customized at will. Pytest uses ``"stdout"`` and
+            ``"stderr"`` internally.
+
+        :param str content:
+            The full contents as a string.
+        """
         if content:
             self._report_sections.append((when, key, content))
 
@@ -526,12 +589,15 @@ class Item(Node):
             self._location = location
             return location
 
+
 class NoMatch(Exception):
     """ raised if matching cannot locate a matching names. """
 
+
 class Interrupted(KeyboardInterrupt):
     """ signals an interrupted test run. """
-    __module__ = 'builtins' # for py3
+    __module__ = 'builtins'  # for py3
+
 
 class Session(FSCollector):
     Interrupted = Interrupted
@@ -550,12 +616,12 @@ class Session(FSCollector):
     def _makeid(self):
         return ""
 
-    @pytest.hookimpl(tryfirst=True)
+    @hookimpl(tryfirst=True)
     def pytest_collectstart(self):
         if self.shouldstop:
             raise self.Interrupted(self.shouldstop)
 
-    @pytest.hookimpl(tryfirst=True)
+    @hookimpl(tryfirst=True)
     def pytest_runtest_logreport(self, report):
         if report.failed and not hasattr(report, 'wasxfail'):
             self.testsfailed += 1
@@ -586,8 +652,9 @@ class Session(FSCollector):
         hook = self.config.hook
         try:
             items = self._perform_collect(args, genitems)
+            self.config.pluginmanager.check_pending()
             hook.pytest_collection_modifyitems(session=self,
-                config=self.config, items=items)
+                                               config=self.config, items=items)
         finally:
             hook.pytest_collection_finish(session=self)
         self.testscollected = len(items)
@@ -614,8 +681,8 @@ class Session(FSCollector):
             for arg, exc in self._notfound:
                 line = "(no name %r in any of %r)" % (arg, exc.args[0])
                 errors.append("not found: %s\n%s" % (arg, line))
-                #XXX: test this
-            raise pytest.UsageError(*errors)
+                # XXX: test this
+            raise UsageError(*errors)
         if not genitems:
             return rep.result
         else:
@@ -643,7 +710,7 @@ class Session(FSCollector):
         names = self._parsearg(arg)
         path = names.pop(0)
         if path.check(dir=1):
-            assert not names, "invalid arg %r" %(arg,)
+            assert not names, "invalid arg %r" % (arg,)
             for path in path.visit(fil=lambda x: x.check(file=1),
                                    rec=self._recurse, bf=True, sort=True):
                 for x in self._collectfile(path):
@@ -702,9 +769,11 @@ class Session(FSCollector):
         path = self.config.invocation_dir.join(relpath, abs=True)
         if not path.check():
             if self.config.option.pyargs:
-                raise pytest.UsageError("file or package not found: " + arg + " (missing __init__.py?)")
+                raise UsageError(
+                    "file or package not found: " + arg +
+                    " (missing __init__.py?)")
             else:
-                raise pytest.UsageError("file not found: " + arg)
+                raise UsageError("file not found: " + arg)
         parts[0] = path
         return parts
 
@@ -727,11 +796,11 @@ class Session(FSCollector):
         nextnames = names[1:]
         resultnodes = []
         for node in matching:
-            if isinstance(node, pytest.Item):
+            if isinstance(node, Item):
                 if not names:
                     resultnodes.append(node)
                 continue
-            assert isinstance(node, pytest.Collector)
+            assert isinstance(node, Collector)
             rep = collect_one_node(node)
             if rep.passed:
                 has_matched = False
@@ -744,16 +813,20 @@ class Session(FSCollector):
                 if not has_matched and len(rep.result) == 1 and x.name == "()":
                     nextnames.insert(0, name)
                     resultnodes.extend(self.matchnodes([x], nextnames))
-            node.ihook.pytest_collectreport(report=rep)
+            else:
+                # report collection failures here to avoid failing to run some test
+                # specified in the command line because the module could not be
+                # imported (#134)
+                node.ihook.pytest_collectreport(report=rep)
         return resultnodes
 
     def genitems(self, node):
         self.trace("genitems", node)
-        if isinstance(node, pytest.Item):
+        if isinstance(node, Item):
             node.ihook.pytest_itemcollected(item=node)
             yield node
         else:
-            assert isinstance(node, pytest.Collector)
+            assert isinstance(node, Collector)
             rep = collect_one_node(node)
             if rep.passed:
                 for subnode in rep.result:
diff --git a/lib/spack/external/_pytest/mark.py b/lib/spack/external/_pytest/mark.py
index 357a60492e..454722ca2c 100644
--- a/lib/spack/external/_pytest/mark.py
+++ b/lib/spack/external/_pytest/mark.py
@@ -1,5 +1,75 @@
 """ generic mechanism for marking and selecting python functions. """
+from __future__ import absolute_import, division, print_function
+
 import inspect
+import warnings
+from collections import namedtuple
+from operator import attrgetter
+from .compat import imap
+from .deprecated import MARK_PARAMETERSET_UNPACKING
+
+
+def alias(name, warning=None):
+    getter = attrgetter(name)
+
+    def warned(self):
+        warnings.warn(warning, stacklevel=2)
+        return getter(self)
+
+    return property(getter if warning is None else warned, doc='alias for ' + name)
+
+
+class ParameterSet(namedtuple('ParameterSet', 'values, marks, id')):
+    @classmethod
+    def param(cls, *values, **kw):
+        marks = kw.pop('marks', ())
+        if isinstance(marks, MarkDecorator):
+            marks = marks,
+        else:
+            assert isinstance(marks, (tuple, list, set))
+
+        def param_extract_id(id=None):
+            return id
+
+        id = param_extract_id(**kw)
+        return cls(values, marks, id)
+
+    @classmethod
+    def extract_from(cls, parameterset, legacy_force_tuple=False):
+        """
+        :param parameterset:
+            a legacy style parameterset that may or may not be a tuple,
+            and may or may not be wrapped into a mess of mark objects
+
+        :param legacy_force_tuple:
+            enforce tuple wrapping so single argument tuple values
+            don't get decomposed and break tests
+
+        """
+
+        if isinstance(parameterset, cls):
+            return parameterset
+        if not isinstance(parameterset, MarkDecorator) and legacy_force_tuple:
+            return cls.param(parameterset)
+
+        newmarks = []
+        argval = parameterset
+        while isinstance(argval, MarkDecorator):
+            newmarks.append(MarkDecorator(Mark(
+                argval.markname, argval.args[:-1], argval.kwargs)))
+            argval = argval.args[-1]
+        assert not isinstance(argval, ParameterSet)
+        if legacy_force_tuple:
+            argval = argval,
+
+        if newmarks:
+            warnings.warn(MARK_PARAMETERSET_UNPACKING)
+
+        return cls(argval, marks=newmarks, id=None)
+
+    @property
+    def deprecated_arg_dict(self):
+        return dict((mark.name, mark) for mark in self.marks)
 
 
 class MarkerError(Exception):
@@ -7,8 +77,8 @@ class MarkerError(Exception):
     """Error in use of a pytest marker/attribute."""
 
 
-def pytest_namespace():
-    return {'mark': MarkGenerator()}
+def param(*values, **kw):
+    return ParameterSet.param(*values, **kw)
 
 
 def pytest_addoption(parser):
@@ -21,7 +91,8 @@ def pytest_addoption(parser):
              "where all names are substring-matched against test names "
              "and their parent classes. Example: -k 'test_method or test_"
              "other' matches all test functions and classes whose name "
-             "contains 'test_method' or 'test_other'. "
+             "contains 'test_method' or 'test_other', while -k 'not test_method' "
+             "matches those that don't contain 'test_method' in their names. "
              "Additionally keywords are matched to classes and functions "
              "containing extra names in their 'extra_keyword_matches' set, "
              "as well as functions which have names assigned directly to them."
@@ -66,7 +137,7 @@ def pytest_collection_modifyitems(items, config):
         return
     # pytest used to allow "-" for negating
     # but today we just allow "-" at the beginning, use "not" instead
-    # we probably remove "-" alltogether soon
+    # we probably remove "-" altogether soon
     if keywordexpr.startswith("-"):
         keywordexpr = "not " + keywordexpr[1:]
     selectuntil = False
@@ -96,6 +167,7 @@ def pytest_collection_modifyitems(items, config):
 class MarkMapping:
     """Provides a local mapping for markers where item access
     resolves to True if the marker is present. """
+
     def __init__(self, keywords):
         mymarks = set()
         for key, value in keywords.items():
@@ -111,6 +183,7 @@ class KeywordMapping:
     """Provides a local mapping for keywords.
     Given a list of names, map any substring of one of these names to True.
     """
+
     def __init__(self, names):
         self._names = names
 
@@ -162,9 +235,13 @@ def matchkeyword(colitem, keywordexpr):
 
 
 def pytest_configure(config):
-    import pytest
+    config._old_mark_config = MARK_GEN._config
     if config.option.strict:
-        pytest.mark._config = config
+        MARK_GEN._config = config
+
+
+def pytest_unconfigure(config):
+    MARK_GEN._config = getattr(config, '_old_mark_config', None)
 
 
 class MarkGenerator:
@@ -178,13 +255,14 @@ class MarkGenerator:
 
     will set a 'slowtest' :class:`MarkInfo` object
     on the ``test_function`` object. """
+    _config = None
 
     def __getattr__(self, name):
         if name[0] == "_":
             raise AttributeError("Marker name must NOT start with underscore")
-        if hasattr(self, '_config'):
+        if self._config is not None:
             self._check(name)
-        return MarkDecorator(name)
+        return MarkDecorator(Mark(name, (), {}))
 
     def _check(self, name):
         try:
@@ -192,18 +270,21 @@ class MarkGenerator:
                 return
         except AttributeError:
             pass
-        self._markers = l = set()
+        self._markers = values = set()
         for line in self._config.getini("markers"):
-            beginning = line.split(":", 1)
-            x = beginning[0].split("(", 1)[0]
-            l.add(x)
+            marker, _ = line.split(":", 1)
+            marker = marker.rstrip()
+            x = marker.split("(", 1)[0]
+            values.add(x)
         if name not in self._markers:
             raise AttributeError("%r not a registered marker" % (name,))
 
+
 def istestfunc(func):
     return hasattr(func, "__call__") and \
         getattr(func, "__name__", "<lambda>") != "<lambda>"
 
+
 class MarkDecorator:
     """ A decorator for test functions and test classes.  When applied
     it will create :class:`MarkInfo` objects which may be
@@ -237,19 +318,35 @@ class MarkDecorator:
     additional keyword or positional arguments.
 
     """
-    def __init__(self, name, args=None, kwargs=None):
-        self.name = name
-        self.args = args or ()
-        self.kwargs = kwargs or {}
+
+    def __init__(self, mark):
+        assert isinstance(mark, Mark), repr(mark)
+        self.mark = mark
+
+    name = alias('mark.name')
+    args = alias('mark.args')
+    kwargs = alias('mark.kwargs')
 
     @property
     def markname(self):
-        return self.name # for backward-compat (2.4.1 had this attr)
+        return self.name  # for backward-compat (2.4.1 had this attr)
+
+    def __eq__(self, other):
+        return self.mark == other.mark if isinstance(other, MarkDecorator) else False
 
     def __repr__(self):
-        d = self.__dict__.copy()
-        name = d.pop('name')
-        return "<MarkDecorator %r %r>" % (name, d)
+        return "<MarkDecorator %r>" % (self.mark,)
+
+    def with_args(self, *args, **kwargs):
+        """ return a MarkDecorator with extra arguments added
+
+        unlike call this can be used even if the sole argument is a callable/class
+
+        :return: MarkDecorator
+        """
+
+        mark = Mark(self.name, args, kwargs)
+        return self.__class__(self.mark.combined_with(mark))
 
     def __call__(self, *args, **kwargs):
         """ if passed a single callable argument: decorate it with mark info.
@@ -259,70 +356,110 @@ class MarkDecorator:
             is_class = inspect.isclass(func)
             if len(args) == 1 and (istestfunc(func) or is_class):
                 if is_class:
-                    if hasattr(func, 'pytestmark'):
-                        mark_list = func.pytestmark
-                        if not isinstance(mark_list, list):
-                            mark_list = [mark_list]
-                        # always work on a copy to avoid updating pytestmark
-                        # from a superclass by accident
-                        mark_list = mark_list + [self]
-                        func.pytestmark = mark_list
-                    else:
-                        func.pytestmark = [self]
+                    store_mark(func, self.mark)
                 else:
-                    holder = getattr(func, self.name, None)
-                    if holder is None:
-                        holder = MarkInfo(
-                            self.name, self.args, self.kwargs
-                        )
-                        setattr(func, self.name, holder)
-                    else:
-                        holder.add(self.args, self.kwargs)
+                    store_legacy_markinfo(func, self.mark)
+                    store_mark(func, self.mark)
                 return func
-        kw = self.kwargs.copy()
-        kw.update(kwargs)
-        args = self.args + args
-        return self.__class__(self.name, args=args, kwargs=kw)
-
-
-def extract_argvalue(maybe_marked_args):
-    # TODO: incorrect mark data, the old code wanst able to collect lists
-    # individual parametrized argument sets can be wrapped in a series
-    # of markers in which case we unwrap the values and apply the mark
-    # at Function init
-    newmarks = {}
-    argval = maybe_marked_args
-    while isinstance(argval, MarkDecorator):
-        newmark = MarkDecorator(argval.markname,
-                                argval.args[:-1], argval.kwargs)
-        newmarks[newmark.markname] = newmark
-        argval = argval.args[-1]
-    return argval, newmarks
-
-
-class MarkInfo:
+        return self.with_args(*args, **kwargs)
+
+
+def get_unpacked_marks(obj):
+    """
+    obtain the unpacked marks that are stored on a object
+    """
+    mark_list = getattr(obj, 'pytestmark', [])
+
+    if not isinstance(mark_list, list):
+        mark_list = [mark_list]
+    return [
+        getattr(mark, 'mark', mark)  # unpack MarkDecorator
+        for mark in mark_list
+    ]
+
+
+def store_mark(obj, mark):
+    """store a Mark on a object
+    this is used to implement the Mark declarations/decorators correctly
+    """
+    assert isinstance(mark, Mark), mark
+    # always reassign name to avoid updating pytestmark
+    # in a reference that was only borrowed
+    obj.pytestmark = get_unpacked_marks(obj) + [mark]
+
+
+def store_legacy_markinfo(func, mark):
+    """create the legacy MarkInfo objects and put them onto the function
+    """
+    if not isinstance(mark, Mark):
+        raise TypeError("got {mark!r} instead of a Mark".format(mark=mark))
+    holder = getattr(func, mark.name, None)
+    if holder is None:
+        holder = MarkInfo(mark)
+        setattr(func, mark.name, holder)
+    else:
+        holder.add_mark(mark)
+
+
+class Mark(namedtuple('Mark', 'name, args, kwargs')):
+
+    def combined_with(self, other):
+        assert self.name == other.name
+        return Mark(
+            self.name, self.args + other.args,
+            dict(self.kwargs, **other.kwargs))
+
+
+class MarkInfo(object):
     """ Marking object created by :class:`MarkDecorator` instances. """
-    def __init__(self, name, args, kwargs):
-        #: name of attribute
-        self.name = name
-        #: positional argument list, empty if none specified
-        self.args = args
-        #: keyword argument dictionary, empty if nothing specified
-        self.kwargs = kwargs.copy()
-        self._arglist = [(args, kwargs.copy())]
+
+    def __init__(self, mark):
+        assert isinstance(mark, Mark), repr(mark)
+        self.combined = mark
+        self._marks = [mark]
+
+    name = alias('combined.name')
+    args = alias('combined.args')
+    kwargs = alias('combined.kwargs')
 
     def __repr__(self):
-        return "<MarkInfo %r args=%r kwargs=%r>" % (
-            self.name, self.args, self.kwargs
-        )
+        return "<MarkInfo {0!r}>".format(self.combined)
 
-    def add(self, args, kwargs):
+    def add_mark(self, mark):
         """ add a MarkInfo with the given args and kwargs. """
-        self._arglist.append((args, kwargs))
-        self.args += args
-        self.kwargs.update(kwargs)
+        self._marks.append(mark)
+        self.combined = self.combined.combined_with(mark)
 
     def __iter__(self):
         """ yield MarkInfo objects each relating to a marking-call. """
-        for args, kwargs in self._arglist:
-            yield MarkInfo(self.name, args, kwargs)
+        return imap(MarkInfo, self._marks)
+
+
+MARK_GEN = MarkGenerator()
+
+
+def _marked(func, mark):
+    """ Returns True if :func: is already marked with :mark:, False otherwise.
+    This can happen if marker is applied to class and the test file is
+    invoked more than once.
+    """
+    try:
+        func_mark = getattr(func, mark.name)
+    except AttributeError:
+        return False
+    return mark.args == func_mark.args and mark.kwargs == func_mark.kwargs
+
+
+def transfer_markers(funcobj, cls, mod):
+    """
+    this function transfers class level markers and module level markers
+    into function level markinfo objects
+
+    this is the main reason why marks are so broken
+    the resolution will involve phasing out function level MarkInfo objects
+
+    """
+    for obj in (cls, mod):
+        for mark in get_unpacked_marks(obj):
+            if not _marked(funcobj, mark):
+                store_legacy_markinfo(funcobj, mark)
diff --git a/lib/spack/external/_pytest/monkeypatch.py b/lib/spack/external/_pytest/monkeypatch.py
index 852e72beda..39ac770135 100644
--- a/lib/spack/external/_pytest/monkeypatch.py
+++ b/lib/spack/external/_pytest/monkeypatch.py
@@ -1,17 +1,18 @@
 """ monkeypatching and mocking functionality.  """
+from __future__ import absolute_import, division, print_function
 
-import os, sys
+import os
+import sys
 import re
 
 from py.builtin import _basestring
-
-import pytest
+from _pytest.fixtures import fixture
 
 RE_IMPORT_ERROR_NAME = re.compile("^No module named (.*)$")
 
 
-@pytest.fixture
-def monkeypatch(request):
+@fixture
+def monkeypatch():
     """The returned ``monkeypatch`` fixture provides these
     helper methods to modify objects, dictionaries or os.environ::
 
@@ -30,8 +31,8 @@ def monkeypatch(request):
     will be raised if the set/deletion operation has no target.
     """
     mpatch = MonkeyPatch()
-    request.addfinalizer(mpatch.undo)
-    return mpatch
+    yield mpatch
+    mpatch.undo()
 
 
 def resolve(name):
@@ -70,9 +71,9 @@ def annotated_getattr(obj, name, ann):
         obj = getattr(obj, name)
     except AttributeError:
         raise AttributeError(
-                '%r object at %s has no attribute %r' % (
-                    type(obj).__name__, ann, name
-                )
+            '%r object at %s has no attribute %r' % (
+                type(obj).__name__, ann, name
+            )
         )
     return obj
 
diff --git a/lib/spack/external/_pytest/nodes.py b/lib/spack/external/_pytest/nodes.py
new file mode 100644
index 0000000000..ad3af2ce67
--- /dev/null
+++ b/lib/spack/external/_pytest/nodes.py
@@ -0,0 +1,37 @@
+SEP = "/"
+
+
+def _splitnode(nodeid):
+    """Split a nodeid into constituent 'parts'.
+
+    Node IDs are strings, and can be things like:
+        ''
+        'testing/code'
+        'testing/code/test_excinfo.py'
+        'testing/code/test_excinfo.py::TestFormattedExcinfo::()'
+
+    Return values are lists e.g.
+        []
+        ['testing', 'code']
+        ['testing', 'code', 'test_excinfo.py']
+        ['testing', 'code', 'test_excinfo.py', 'TestFormattedExcinfo', '()']
+    """
+    if nodeid == '':
+        # If there is no root node at all, return an empty list so the caller's logic can remain sane
+        return []
+    parts = nodeid.split(SEP)
+    # Replace single last element 'test_foo.py::Bar::()' with multiple elements 'test_foo.py', 'Bar', '()'
+    parts[-1:] = parts[-1].split("::")
+    return parts
+
+
+def ischildnode(baseid, nodeid):
+    """Return True if the nodeid is a child node of the baseid.
+
+    E.g. 'foo/bar::Baz::()' is a child of 'foo', 'foo/bar' and 'foo/bar::Baz', but not of 'foo/blorp'
+    """
+    base_parts = _splitnode(baseid)
+    node_parts = _splitnode(nodeid)
+    if len(node_parts) < len(base_parts):
+        return False
+    return node_parts[:len(base_parts)] == base_parts
diff --git a/lib/spack/external/_pytest/nose.py b/lib/spack/external/_pytest/nose.py
index 0387468686..d246c5603d 100644
--- a/lib/spack/external/_pytest/nose.py
+++ b/lib/spack/external/_pytest/nose.py
@@ -1,10 +1,11 @@
 """ run test suites written for nose. """
+from __future__ import absolute_import, division, print_function
 
 import sys
 
 import py
-import pytest
-from _pytest import unittest
+from _pytest import unittest, runner, python
+from _pytest.config import hookimpl
 
 
 def get_skip_exceptions():
@@ -19,45 +20,46 @@ def get_skip_exceptions():
 def pytest_runtest_makereport(item, call):
     if call.excinfo and call.excinfo.errisinstance(get_skip_exceptions()):
         # let's substitute the excinfo with a pytest.skip one
-        call2 = call.__class__(lambda:
-                    pytest.skip(str(call.excinfo.value)), call.when)
+        call2 = call.__class__(
+            lambda: runner.skip(str(call.excinfo.value)), call.when)
         call.excinfo = call2.excinfo
 
 
-@pytest.hookimpl(trylast=True)
+@hookimpl(trylast=True)
 def pytest_runtest_setup(item):
     if is_potential_nosetest(item):
-        if isinstance(item.parent, pytest.Generator):
+        if isinstance(item.parent, python.Generator):
             gen = item.parent
             if not hasattr(gen, '_nosegensetup'):
                 call_optional(gen.obj, 'setup')
-                if isinstance(gen.parent, pytest.Instance):
+                if isinstance(gen.parent, python.Instance):
                     call_optional(gen.parent.obj, 'setup')
                 gen._nosegensetup = True
         if not call_optional(item.obj, 'setup'):
             # call module level setup if there is no object level one
             call_optional(item.parent.obj, 'setup')
-        #XXX this implies we only call teardown when setup worked
+        # XXX this implies we only call teardown when setup worked
         item.session._setupstate.addfinalizer((lambda: teardown_nose(item)), item)
 
+
 def teardown_nose(item):
     if is_potential_nosetest(item):
         if not call_optional(item.obj, 'teardown'):
             call_optional(item.parent.obj, 'teardown')
-        #if hasattr(item.parent, '_nosegensetup'):
+        # if hasattr(item.parent, '_nosegensetup'):
         #    #call_optional(item._nosegensetup, 'teardown')
         #    del item.parent._nosegensetup
 
 
 def pytest_make_collect_report(collector):
-    if isinstance(collector, pytest.Generator):
+    if isinstance(collector, python.Generator):
         call_optional(collector.obj, 'setup')
 
 
 def is_potential_nosetest(item):
     # extra check needed since we do not do nose style setup/teardown
     # on direct unittest style classes
-    return isinstance(item, pytest.Function) and \
+    return isinstance(item, python.Function) and \
         not isinstance(item, unittest.TestCaseFunction)
 
 
diff --git a/lib/spack/external/_pytest/outcomes.py b/lib/spack/external/_pytest/outcomes.py
new file mode 100644
index 0000000000..ff5ef756d9
--- /dev/null
+++ b/lib/spack/external/_pytest/outcomes.py
@@ -0,0 +1,140 @@
+"""
+exception classes and constants handling test outcomes
+as well as functions creating them
+"""
+from __future__ import absolute_import, division, print_function
+import py
+import sys
+
+
+class OutcomeException(BaseException):
+    """ OutcomeException and its subclass instances indicate and
+        contain info about test and collection outcomes.
+    """
+    def __init__(self, msg=None, pytrace=True):
+        BaseException.__init__(self, msg)
+        self.msg = msg
+        self.pytrace = pytrace
+
+    def __repr__(self):
+        if self.msg:
+            val = self.msg
+            if isinstance(val, bytes):
+                val = py._builtin._totext(val, errors='replace')
+            return val
+        return "<%s instance>" % (self.__class__.__name__,)
+    __str__ = __repr__
+
+
+TEST_OUTCOME = (OutcomeException, Exception)
+
+
+class Skipped(OutcomeException):
+    # XXX hackish: on 3k we fake to live in the builtins
+    # in order to have Skipped exception printing shorter/nicer
+    __module__ = 'builtins'
+
+    def __init__(self, msg=None, pytrace=True, allow_module_level=False):
+        OutcomeException.__init__(self, msg=msg, pytrace=pytrace)
+        self.allow_module_level = allow_module_level
+
+
+class Failed(OutcomeException):
+    """ raised from an explicit call to pytest.fail() """
+    __module__ = 'builtins'
+
+
+class Exit(KeyboardInterrupt):
+    """ raised for immediate program exits (no tracebacks/summaries)"""
+    def __init__(self, msg="unknown reason"):
+        self.msg = msg
+        KeyboardInterrupt.__init__(self, msg)
+
+# exposed helper methods
+
+
+def exit(msg):
+    """ exit testing process as if KeyboardInterrupt was triggered. """
+    __tracebackhide__ = True
+    raise Exit(msg)
+
+
+exit.Exception = Exit
+
+
+def skip(msg=""):
+    """ skip an executing test with the given message.  Note: it's usually
+    better to use the pytest.mark.skipif marker to declare a test to be
+    skipped under certain conditions like mismatching platforms or
+    dependencies.  See the pytest_skipping plugin for details.
+    """
+    __tracebackhide__ = True
+    raise Skipped(msg=msg)
+
+
+skip.Exception = Skipped
+
+
+def fail(msg="", pytrace=True):
+    """ explicitly fail an currently-executing test with the given Message.
+
+    :arg pytrace: if false the msg represents the full failure information
+                  and no python traceback will be reported.
+    """
+    __tracebackhide__ = True
+    raise Failed(msg=msg, pytrace=pytrace)
+
+
+fail.Exception = Failed
+
+
+class XFailed(fail.Exception):
+    """ raised from an explicit call to pytest.xfail() """
+
+
+def xfail(reason=""):
+    """ xfail an executing test or setup functions with the given reason."""
+    __tracebackhide__ = True
+    raise XFailed(reason)
+
+
+xfail.Exception = XFailed
+
+
+def importorskip(modname, minversion=None):
+    """ return imported module if it has at least "minversion" as its
+    __version__ attribute.  If no minversion is specified the a skip
+    is only triggered if the module can not be imported.
+    """
+    import warnings
+    __tracebackhide__ = True
+    compile(modname, '', 'eval')  # to catch syntaxerrors
+    should_skip = False
+
+    with warnings.catch_warnings():
+        # make sure to ignore ImportWarnings that might happen because
+        # of existing directories with the same name we're trying to
+        # import but without a __init__.py file
+        warnings.simplefilter('ignore')
+        try:
+            __import__(modname)
+        except ImportError:
+            # Do not raise chained exception here(#1485)
+            should_skip = True
+    if should_skip:
+        raise Skipped("could not import %r" % (modname,), allow_module_level=True)
+    mod = sys.modules[modname]
+    if minversion is None:
+        return mod
+    verattr = getattr(mod, '__version__', None)
+    if minversion is not None:
+        try:
+            from pkg_resources import parse_version as pv
+        except ImportError:
+            raise Skipped("we have a required version for %r but can not import "
+                          "pkg_resources to parse version strings." % (modname,),
+                          allow_module_level=True)
+        if verattr is None or pv(verattr) < pv(minversion):
+            raise Skipped("module %r has __version__ %r, required is: %r" % (
+                          modname, verattr, minversion), allow_module_level=True)
+    return mod
diff --git a/lib/spack/external/_pytest/pastebin.py b/lib/spack/external/_pytest/pastebin.py
index 9f1cf90637..9d689819f0 100644
--- a/lib/spack/external/_pytest/pastebin.py
+++ b/lib/spack/external/_pytest/pastebin.py
@@ -1,4 +1,6 @@
 """ submit failure or test session information to a pastebin service. """
+from __future__ import absolute_import, division, print_function
+
 import pytest
 import sys
 import tempfile
@@ -7,9 +9,9 @@ import tempfile
 def pytest_addoption(parser):
     group = parser.getgroup("terminal reporting")
     group._addoption('--pastebin', metavar="mode",
-        action='store', dest="pastebin", default=None,
-        choices=['failed', 'all'],
-        help="send failed|all info to bpaste.net pastebin service.")
+                     action='store', dest="pastebin", default=None,
+                     choices=['failed', 'all'],
+                     help="send failed|all info to bpaste.net pastebin service.")
 
 
 @pytest.hookimpl(trylast=True)
@@ -95,4 +97,4 @@ def pytest_terminal_summary(terminalreporter):
             s = tw.stringio.getvalue()
             assert len(s)
             pastebinurl = create_new_paste(s)
-            tr.write_line("%s --> %s" %(msg, pastebinurl))
+            tr.write_line("%s --> %s" % (msg, pastebinurl))
diff --git a/lib/spack/external/_pytest/pytester.py b/lib/spack/external/_pytest/pytester.py
index d87c0a762a..2db85dff22 100644
--- a/lib/spack/external/_pytest/pytester.py
+++ b/lib/spack/external/_pytest/pytester.py
@@ -1,4 +1,6 @@
 """ (disabled by default) support for testing pytest and pytest plugins. """
+from __future__ import absolute_import, division, print_function
+
 import codecs
 import gc
 import os
@@ -10,8 +12,9 @@ import time
 import traceback
 from fnmatch import fnmatch
 
-from py.builtin import print_
+from weakref import WeakKeyDictionary
 
+from _pytest.capture import MultiCapture, SysCapture
 from _pytest._code import Source
 import py
 import pytest
@@ -22,13 +25,13 @@ from _pytest.assertion.rewrite import AssertionRewritingHook
 def pytest_addoption(parser):
     # group = parser.getgroup("pytester", "pytester (self-tests) options")
     parser.addoption('--lsof',
-           action="store_true", dest="lsof", default=False,
-           help=("run FD checks if lsof is available"))
+                     action="store_true", dest="lsof", default=False,
+                     help=("run FD checks if lsof is available"))
 
     parser.addoption('--runpytest', default="inprocess", dest="runpytest",
-           choices=("inprocess", "subprocess", ),
-           help=("run pytest sub runs in tests using an 'inprocess' "
-                 "or 'subprocess' (python -m main) method"))
+                     choices=("inprocess", "subprocess", ),
+                     help=("run pytest sub runs in tests using an 'inprocess' "
+                           "or 'subprocess' (python -m main) method"))
 
 
 def pytest_configure(config):
@@ -59,7 +62,7 @@ class LsofFdLeakChecker(object):
     def _parse_lsof_output(self, out):
         def isopen(line):
             return line.startswith('f') and ("deleted" not in line and
-                'mem' not in line and "txt" not in line and 'cwd' not in line)
+                                             'mem' not in line and "txt" not in line and 'cwd' not in line)
 
         open_files = []
 
@@ -85,7 +88,7 @@ class LsofFdLeakChecker(object):
             return True
 
     @pytest.hookimpl(hookwrapper=True, tryfirst=True)
-    def pytest_runtest_item(self, item):
+    def pytest_runtest_protocol(self, item):
         lines1 = self.get_open_files()
         yield
         if hasattr(sys, "pypy_version_info"):
@@ -104,7 +107,8 @@ class LsofFdLeakChecker(object):
             error.extend([str(f) for f in lines2])
             error.append(error[0])
             error.append("*** function %s:%s: %s " % item.location)
-            pytest.fail("\n".join(error), pytrace=False)
+            error.append("See issue #2366")
+            item.warn('', "\n".join(error))
 
 
 # XXX copied from execnet's conftest.py - needs to be merged
@@ -118,6 +122,7 @@ winpymap = {
     'python3.5': r'C:\Python35\python.exe',
 }
 
+
 def getexecutable(name, cache={}):
     try:
         return cache[name]
@@ -126,19 +131,20 @@ def getexecutable(name, cache={}):
         if executable:
             import subprocess
             popen = subprocess.Popen([str(executable), "--version"],
-                universal_newlines=True, stderr=subprocess.PIPE)
+                                     universal_newlines=True, stderr=subprocess.PIPE)
             out, err = popen.communicate()
             if name == "jython":
                 if not err or "2.5" not in err:
                     executable = None
                 if "2.5.2" in err:
-                    executable = None # http://bugs.jython.org/issue1790
+                    executable = None  # http://bugs.jython.org/issue1790
             elif popen.returncode != 0:
                 # Handle pyenv's 127.
                 executable = None
         cache[name] = executable
         return executable
 
+
 @pytest.fixture(params=['python2.6', 'python2.7', 'python3.3', "python3.4",
                         'pypy', 'pypy3'])
 def anypython(request):
@@ -155,6 +161,8 @@ def anypython(request):
     return executable
 
 # used at least by pytest-xdist plugin
+
+
 @pytest.fixture
 def _pytest(request):
     """ Return a helper which offers a gethookrecorder(hook)
@@ -163,6 +171,7 @@ def _pytest(request):
     """
     return PytestArg(request)
 
+
 class PytestArg:
     def __init__(self, request):
         self.request = request
@@ -173,9 +182,9 @@ class PytestArg:
         return hookrecorder
 
 
-def get_public_names(l):
-    """Only return names from iterator l without a leading underscore."""
-    return [x for x in l if x[0] != "_"]
+def get_public_names(values):
+    """Only return names from iterator values without a leading underscore."""
+    return [x for x in values if x[0] != "_"]
 
 
 class ParsedCall:
@@ -186,7 +195,7 @@ class ParsedCall:
     def __repr__(self):
         d = self.__dict__.copy()
         del d['_name']
-        return "<ParsedCall %r(**%r)>" %(self._name, d)
+        return "<ParsedCall %r(**%r)>" % (self._name, d)
 
 
 class HookRecorder:
@@ -226,15 +235,15 @@ class HookRecorder:
             name, check = entries.pop(0)
             for ind, call in enumerate(self.calls[i:]):
                 if call._name == name:
-                    print_("NAMEMATCH", name, call)
+                    print("NAMEMATCH", name, call)
                     if eval(check, backlocals, call.__dict__):
-                        print_("CHECKERMATCH", repr(check), "->", call)
+                        print("CHECKERMATCH", repr(check), "->", call)
                     else:
-                        print_("NOCHECKERMATCH", repr(check), "-", call)
+                        print("NOCHECKERMATCH", repr(check), "-", call)
                         continue
                     i += ind + 1
                     break
-                print_("NONAMEMATCH", name, "with", call)
+                print("NONAMEMATCH", name, "with", call)
             else:
                 pytest.fail("could not find %r check %r" % (name, check))
 
@@ -249,9 +258,9 @@ class HookRecorder:
         pytest.fail("\n".join(lines))
 
     def getcall(self, name):
-        l = self.getcalls(name)
-        assert len(l) == 1, (name, l)
-        return l[0]
+        values = self.getcalls(name)
+        assert len(values) == 1, (name, values)
+        return values[0]
 
     # functionality for test reports
 
@@ -260,9 +269,9 @@ class HookRecorder:
         return [x.report for x in self.getcalls(names)]
 
     def matchreport(self, inamepart="",
-        names="pytest_runtest_logreport pytest_collectreport", when=None):
+                    names="pytest_runtest_logreport pytest_collectreport", when=None):
         """ return a testreport whose dotted import path matches """
-        l = []
+        values = []
         for rep in self.getreports(names=names):
             try:
                 if not when and rep.when != "call" and rep.passed:
@@ -273,14 +282,14 @@ class HookRecorder:
             if when and getattr(rep, 'when', None) != when:
                 continue
             if not inamepart or inamepart in rep.nodeid.split("::"):
-                l.append(rep)
-        if not l:
+                values.append(rep)
+        if not values:
             raise ValueError("could not find test report matching %r: "
                              "no test reports at all!" % (inamepart,))
-        if len(l) > 1:
+        if len(values) > 1:
             raise ValueError(
-                "found 2 or more testreports matching %r: %s" %(inamepart, l))
-        return l[0]
+                "found 2 or more testreports matching %r: %s" % (inamepart, values))
+        return values[0]
 
     def getfailures(self,
                     names='pytest_runtest_logreport pytest_collectreport'):
@@ -294,7 +303,7 @@ class HookRecorder:
         skipped = []
         failed = []
         for rep in self.getreports(
-            "pytest_collectreport pytest_runtest_logreport"):
+                "pytest_collectreport pytest_runtest_logreport"):
             if rep.passed:
                 if getattr(rep, "when", None) == "call":
                     passed.append(rep)
@@ -332,7 +341,9 @@ def testdir(request, tmpdir_factory):
     return Testdir(request, tmpdir_factory)
 
 
-rex_outcome = re.compile("(\d+) ([\w-]+)")
+rex_outcome = re.compile(r"(\d+) ([\w-]+)")
+
+
 class RunResult:
     """The result of running a command.
 
@@ -348,6 +359,7 @@ class RunResult:
     :duration: Duration in seconds.
 
     """
+
     def __init__(self, ret, outlines, errlines, duration):
         self.ret = ret
         self.outlines = outlines
@@ -367,15 +379,19 @@ class RunResult:
                     for num, cat in outcomes:
                         d[cat] = int(num)
                     return d
+        raise ValueError("Pytest terminal report not found")
 
-    def assert_outcomes(self, passed=0, skipped=0, failed=0):
+    def assert_outcomes(self, passed=0, skipped=0, failed=0, error=0):
         """ assert that the specified outcomes appear with the respective
         numbers (0 means it didn't occur) in the text output from a test run."""
         d = self.parseoutcomes()
-        assert passed == d.get("passed", 0)
-        assert skipped == d.get("skipped", 0)
-        assert failed == d.get("failed", 0)
-
+        obtained = {
+            'passed': d.get('passed', 0),
+            'skipped': d.get('skipped', 0),
+            'failed': d.get('failed', 0),
+            'error': d.get('error', 0),
+        }
+        assert obtained == dict(passed=passed, skipped=skipped, failed=failed, error=error)
 
 
 class Testdir:
@@ -401,6 +417,7 @@ class Testdir:
 
     def __init__(self, request, tmpdir_factory):
         self.request = request
+        self._mod_collections = WeakKeyDictionary()
         # XXX remove duplication with tmpdir plugin
         basetmp = tmpdir_factory.ensuretemp("testdir")
         name = request.function.__name__
@@ -414,7 +431,7 @@ class Testdir:
         self.plugins = []
         self._savesyspath = (list(sys.path), list(sys.meta_path))
         self._savemodulekeys = set(sys.modules)
-        self.chdir() # always chdir
+        self.chdir()  # always chdir
         self.request.addfinalizer(self.finalize)
         method = self.request.config.getoption("--runpytest")
         if method == "inprocess":
@@ -446,9 +463,10 @@ class Testdir:
         the module is re-imported.
         """
         for name in set(sys.modules).difference(self._savemodulekeys):
-            # it seems zope.interfaces is keeping some state
-            # (used by twisted related tests)
-            if name != "zope.interface":
+            # some zope modules used by twisted-related tests keeps internal
+            # state and can't be deleted; we had some trouble in the past
+            # with zope.interface for example
+            if not name.startswith("zope"):
                 del sys.modules[name]
 
     def make_hook_recorder(self, pluginmanager):
@@ -468,7 +486,7 @@ class Testdir:
         if not hasattr(self, '_olddir'):
             self._olddir = old
 
-    def _makefile(self, ext, args, kwargs):
+    def _makefile(self, ext, args, kwargs, encoding="utf-8"):
         items = list(kwargs.items())
         if args:
             source = py.builtin._totext("\n").join(
@@ -488,8 +506,8 @@ class Testdir:
 
             source_unicode = "\n".join([my_totext(line) for line in source.lines])
             source = py.builtin._totext(source_unicode)
-            content = source.strip().encode("utf-8") # + "\n"
-            #content = content.rstrip() + "\n"
+            content = source.strip().encode(encoding)  # + "\n"
+            # content = content.rstrip() + "\n"
             p.write(content, "wb")
             if ret is None:
                 ret = p
@@ -565,7 +583,7 @@ class Testdir:
     def mkpydir(self, name):
         """Create a new python package.
 
-        This creates a (sub)direcotry with an empty ``__init__.py``
+        This creates a (sub)directory with an empty ``__init__.py``
         file so that is recognised as a python package.
 
         """
@@ -574,6 +592,7 @@ class Testdir:
         return p
 
     Session = Session
+
     def getnode(self, config, arg):
         """Return the collection node of a file.
 
@@ -654,13 +673,13 @@ class Testdir:
 
         """
         p = self.makepyfile(source)
-        l = list(cmdlineargs) + [p]
-        return self.inline_run(*l)
+        values = list(cmdlineargs) + [p]
+        return self.inline_run(*values)
 
     def inline_genitems(self, *args):
         """Run ``pytest.main(['--collectonly'])`` in-process.
 
-        Retuns a tuple of the collected items and a
+        Returns a tuple of the collected items and a
         :py:class:`HookRecorder` instance.
 
         This runs the :py:func:`pytest.main` function to run all of
@@ -733,7 +752,8 @@ class Testdir:
         if kwargs.get("syspathinsert"):
             self.syspathinsert()
         now = time.time()
-        capture = py.io.StdCapture()
+        capture = MultiCapture(Capture=SysCapture)
+        capture.start_capturing()
         try:
             try:
                 reprec = self.inline_run(*args, **kwargs)
@@ -748,13 +768,14 @@ class Testdir:
                 class reprec:
                     ret = 3
         finally:
-            out, err = capture.reset()
+            out, err = capture.readouterr()
+            capture.stop_capturing()
             sys.stdout.write(out)
             sys.stderr.write(err)
 
         res = RunResult(reprec.ret,
                         out.split("\n"), err.split("\n"),
-                        time.time()-now)
+                        time.time() - now)
         res.reprec = reprec
         return res
 
@@ -770,11 +791,11 @@ class Testdir:
         args = [str(x) for x in args]
         for x in args:
             if str(x).startswith('--basetemp'):
-                #print ("basedtemp exists: %s" %(args,))
+                # print("basedtemp exists: %s" %(args,))
                 break
         else:
             args.append("--basetemp=%s" % self.tmpdir.dirpath('basetemp'))
-            #print ("added basetemp: %s" %(args,))
+            # print("added basetemp: %s" %(args,))
         return args
 
     def parseconfig(self, *args):
@@ -812,7 +833,7 @@ class Testdir:
         self.request.addfinalizer(config._ensure_unconfigure)
         return config
 
-    def getitem(self,  source, funcname="test_func"):
+    def getitem(self, source, funcname="test_func"):
         """Return the test item for a test function.
 
         This writes the source to a python file and runs pytest's
@@ -829,10 +850,10 @@ class Testdir:
         for item in items:
             if item.name == funcname:
                 return item
-        assert 0, "%r item not found in module:\n%s\nitems: %s" %(
+        assert 0, "%r item not found in module:\n%s\nitems: %s" % (
                   funcname, source, items)
 
-    def getitems(self,  source):
+    def getitems(self, source):
         """Return all test items collected from the module.
 
         This writes the source to a python file and runs pytest's
@@ -843,7 +864,7 @@ class Testdir:
         modcol = self.getmodulecol(source)
         return self.genitems([modcol])
 
-    def getmodulecol(self,  source, configargs=(), withinit=False):
+    def getmodulecol(self, source, configargs=(), withinit=False):
         """Return the module collection node for ``source``.
 
         This writes ``source`` to a file using :py:meth:`makepyfile`
@@ -856,15 +877,16 @@ class Testdir:
            :py:meth:`parseconfigure`.
 
         :param withinit: Whether to also write a ``__init__.py`` file
-           to the temporarly directory to ensure it is a package.
+           to the temporary directory to ensure it is a package.
 
         """
         kw = {self.request.function.__name__: Source(source).strip()}
         path = self.makepyfile(**kw)
         if withinit:
-            self.makepyfile(__init__ = "#")
+            self.makepyfile(__init__="#")
         self.config = config = self.parseconfigure(path, *configargs)
         node = self.getnode(config, path)
+
         return node
 
     def collect_by_name(self, modcol, name):
@@ -879,7 +901,9 @@ class Testdir:
         :param name: The name of the node to return.
 
         """
-        for colitem in modcol._memocollect():
+        if modcol not in self._mod_collections:
+            self._mod_collections[modcol] = list(modcol.collect())
+        for colitem in self._mod_collections[modcol]:
             if colitem.name == name:
                 return colitem
 
@@ -896,8 +920,11 @@ class Testdir:
         env['PYTHONPATH'] = os.pathsep.join(filter(None, [
             str(os.getcwd()), env.get('PYTHONPATH', '')]))
         kw['env'] = env
-        return subprocess.Popen(cmdargs,
-                                stdout=stdout, stderr=stderr, **kw)
+
+        popen = subprocess.Popen(cmdargs, stdin=subprocess.PIPE, stdout=stdout, stderr=stderr, **kw)
+        popen.stdin.close()
+
+        return popen
 
     def run(self, *cmdargs):
         """Run a command with arguments.
@@ -914,14 +941,14 @@ class Testdir:
         cmdargs = [str(x) for x in cmdargs]
         p1 = self.tmpdir.join("stdout")
         p2 = self.tmpdir.join("stderr")
-        print_("running:", ' '.join(cmdargs))
-        print_("     in:", str(py.path.local()))
+        print("running:", ' '.join(cmdargs))
+        print("     in:", str(py.path.local()))
         f1 = codecs.open(str(p1), "w", encoding="utf8")
         f2 = codecs.open(str(p2), "w", encoding="utf8")
         try:
             now = time.time()
             popen = self.popen(cmdargs, stdout=f1, stderr=f2,
-                close_fds=(sys.platform != "win32"))
+                               close_fds=(sys.platform != "win32"))
             ret = popen.wait()
         finally:
             f1.close()
@@ -936,19 +963,19 @@ class Testdir:
             f2.close()
         self._dump_lines(out, sys.stdout)
         self._dump_lines(err, sys.stderr)
-        return RunResult(ret, out, err, time.time()-now)
+        return RunResult(ret, out, err, time.time() - now)
 
     def _dump_lines(self, lines, fp):
         try:
             for line in lines:
-                py.builtin.print_(line, file=fp)
+                print(line, file=fp)
         except UnicodeEncodeError:
             print("couldn't print to %s because of encoding" % (fp,))
 
     def _getpytestargs(self):
         # we cannot use "(sys.executable,script)"
         # because on windows the script is e.g. a pytest.exe
-        return (sys.executable, _pytest_fullpath,) # noqa
+        return (sys.executable, _pytest_fullpath,)  # noqa
 
     def runpython(self, script):
         """Run a python script using sys.executable as interpreter.
@@ -975,12 +1002,12 @@ class Testdir:
 
         """
         p = py.path.local.make_numbered_dir(prefix="runpytest-",
-            keep=None, rootdir=self.tmpdir)
+                                            keep=None, rootdir=self.tmpdir)
         args = ('--basetemp=%s' % p, ) + args
-        #for x in args:
+        # for x in args:
         #    if '--confcutdir' in str(x):
         #        break
-        #else:
+        # else:
         #    pass
         #    args = ('--confcutdir=.',) + args
         plugins = [x for x in self.plugins if isinstance(x, str)]
@@ -998,7 +1025,7 @@ class Testdir:
         The pexpect child is returned.
 
         """
-        basetemp = self.tmpdir.mkdir("pexpect")
+        basetemp = self.tmpdir.mkdir("temp-pexpect")
         invoke = " ".join(map(str, self._getpytestargs()))
         cmd = "%s --basetemp=%s %s" % (invoke, basetemp, string)
         return self.spawn(cmd, expect_timeout=expect_timeout)
@@ -1019,12 +1046,13 @@ class Testdir:
         child.timeout = expect_timeout
         return child
 
+
 def getdecoded(out):
-        try:
-            return out.decode("utf-8")
-        except UnicodeDecodeError:
-            return "INTERNAL not-utf8-decodeable, truncated string:\n%s" % (
-                    py.io.saferepr(out),)
+    try:
+        return out.decode("utf-8")
+    except UnicodeDecodeError:
+        return "INTERNAL not-utf8-decodeable, truncated string:\n%s" % (
+            py.io.saferepr(out),)
 
 
 class LineComp:
@@ -1054,7 +1082,7 @@ class LineMatcher:
 
     """
 
-    def __init__(self,  lines):
+    def __init__(self, lines):
         self.lines = lines
         self._log_output = []
 
@@ -1093,7 +1121,7 @@ class LineMatcher:
         """
         for i, line in enumerate(self.lines):
             if fnline == line or fnmatch(line, fnline):
-                return self.lines[i+1:]
+                return self.lines[i + 1:]
         raise ValueError("line %r not found in output" % fnline)
 
     def _log(self, *args):
diff --git a/lib/spack/external/_pytest/python.py b/lib/spack/external/_pytest/python.py
index 53815da2f0..41fd2bdb7f 100644
--- a/lib/spack/external/_pytest/python.py
+++ b/lib/spack/external/_pytest/python.py
@@ -1,26 +1,30 @@
 """ Python test discovery, setup and run of test functions. """
+from __future__ import absolute_import, division, print_function
 
 import fnmatch
 import inspect
 import sys
+import os
 import collections
-import math
+from textwrap import dedent
 from itertools import count
 
 import py
-import pytest
 from _pytest.mark import MarkerError
-
+from _pytest.config import hookimpl
 
 import _pytest
 import _pytest._pluggy as pluggy
 from _pytest import fixtures
+from _pytest import main
 from _pytest.compat import (
-    isclass, isfunction, is_generator, _escape_strings,
+    isclass, isfunction, is_generator, _ascii_escaped,
     REGEX_TYPE, STRING_TYPES, NoneType, NOTSET,
     get_real_func, getfslineno, safe_getattr,
-    getlocation, enum,
+    safe_str, getlocation, enum,
 )
+from _pytest.outcomes import fail
+from _pytest.mark import transfer_markers
 
 cutdir1 = py.path.local(pluggy.__file__.rstrip("oc"))
 cutdir2 = py.path.local(_pytest.__file__).dirpath()
@@ -45,10 +49,9 @@ def filter_traceback(entry):
     return p != cutdir1 and not p.relto(cutdir2) and not p.relto(cutdir3)
 
 
-
 def pyobj_property(name):
     def get(self):
-        node = self.getparent(getattr(pytest, name))
+        node = self.getparent(getattr(__import__('pytest'), name))
         if node is not None:
             return node.obj
     doc = "python %s object this node was collected from (can be None)." % (
@@ -59,8 +62,8 @@ def pyobj_property(name):
 def pytest_addoption(parser):
     group = parser.getgroup("general")
     group.addoption('--fixtures', '--funcargs',
-               action="store_true", dest="showfixtures", default=False,
-               help="show available fixtures, sorted by plugin appearance")
+                    action="store_true", dest="showfixtures", default=False,
+                    help="show available fixtures, sorted by plugin appearance")
     group.addoption(
         '--fixtures-per-test',
         action="store_true",
@@ -69,20 +72,20 @@ def pytest_addoption(parser):
         help="show fixtures per test",
     )
     parser.addini("usefixtures", type="args", default=[],
-        help="list of default fixtures to be used with this project")
+                  help="list of default fixtures to be used with this project")
     parser.addini("python_files", type="args",
-        default=['test_*.py', '*_test.py'],
-        help="glob-style file patterns for Python test module discovery")
-    parser.addini("python_classes", type="args", default=["Test",],
-        help="prefixes or glob names for Python test class discovery")
-    parser.addini("python_functions", type="args", default=["test",],
-        help="prefixes or glob names for Python test function and "
-             "method discovery")
+                  default=['test_*.py', '*_test.py'],
+                  help="glob-style file patterns for Python test module discovery")
+    parser.addini("python_classes", type="args", default=["Test", ],
+                  help="prefixes or glob names for Python test class discovery")
+    parser.addini("python_functions", type="args", default=["test", ],
+                  help="prefixes or glob names for Python test function and "
+                  "method discovery")
 
     group.addoption("--import-mode", default="prepend",
-        choices=["prepend", "append"], dest="importmode",
-        help="prepend/append to sys.path when importing test modules, "
-             "default is to prepend.")
+                    choices=["prepend", "append"], dest="importmode",
+                    help="prepend/append to sys.path when importing test modules, "
+                    "default is to prepend.")
 
 
 def pytest_cmdline_main(config):
@@ -109,39 +112,25 @@ def pytest_generate_tests(metafunc):
     for marker in markers:
         metafunc.parametrize(*marker.args, **marker.kwargs)
 
+
 def pytest_configure(config):
     config.addinivalue_line("markers",
-        "parametrize(argnames, argvalues): call a test function multiple "
-        "times passing in different arguments in turn. argvalues generally "
-        "needs to be a list of values if argnames specifies only one name "
-        "or a list of tuples of values if argnames specifies multiple names. "
-        "Example: @parametrize('arg1', [1,2]) would lead to two calls of the "
-        "decorated test function, one with arg1=1 and another with arg1=2."
-        "see http://pytest.org/latest/parametrize.html for more info and "
-        "examples."
-    )
+                            "parametrize(argnames, argvalues): call a test function multiple "
+                            "times passing in different arguments in turn. argvalues generally "
+                            "needs to be a list of values if argnames specifies only one name "
+                            "or a list of tuples of values if argnames specifies multiple names. "
+                            "Example: @parametrize('arg1', [1,2]) would lead to two calls of the "
+                            "decorated test function, one with arg1=1 and another with arg1=2."
+                            "see http://pytest.org/latest/parametrize.html for more info and "
+                            "examples."
+                            )
     config.addinivalue_line("markers",
-        "usefixtures(fixturename1, fixturename2, ...): mark tests as needing "
-        "all of the specified fixtures. see http://pytest.org/latest/fixture.html#usefixtures "
-    )
+                            "usefixtures(fixturename1, fixturename2, ...): mark tests as needing "
+                            "all of the specified fixtures. see http://pytest.org/latest/fixture.html#usefixtures "
+                            )
+
 
-@pytest.hookimpl(trylast=True)
-def pytest_namespace():
-    raises.Exception = pytest.fail.Exception
-    return {
-        'raises': raises,
-        'approx': approx,
-        'collect': {
-            'Module': Module,
-            'Class': Class,
-            'Instance': Instance,
-            'Function': Function,
-            'Generator': Generator,
-        }
-    }
-
-
-@pytest.hookimpl(trylast=True)
+@hookimpl(trylast=True)
 def pytest_pyfunc_call(pyfuncitem):
     testfunction = pyfuncitem.obj
     if pyfuncitem._isyieldedfunction():
@@ -154,6 +143,7 @@ def pytest_pyfunc_call(pyfuncitem):
         testfunction(**testargs)
     return True
 
+
 def pytest_collect_file(path, parent):
     ext = path.ext
     if ext == ".py":
@@ -162,19 +152,21 @@ def pytest_collect_file(path, parent):
                 if path.fnmatch(pat):
                     break
             else:
-               return
+                return
         ihook = parent.session.gethookproxy(path)
         return ihook.pytest_pycollect_makemodule(path=path, parent=parent)
 
+
 def pytest_pycollect_makemodule(path, parent):
     return Module(path, parent)
 
-@pytest.hookimpl(hookwrapper=True)
+
+@hookimpl(hookwrapper=True)
 def pytest_pycollect_makeitem(collector, name, obj):
     outcome = yield
     res = outcome.get_result()
     if res is not None:
-        raise StopIteration
+        return
     # nothing was collected elsewhere, let's do it here
     if isclass(obj):
         if collector.istestclass(obj, name):
@@ -187,9 +179,8 @@ def pytest_pycollect_makeitem(collector, name, obj):
         # or a funtools.wrapped.
         # We musn't if it's been wrapped with mock.patch (python 2 only)
         if not (isfunction(obj) or isfunction(get_real_func(obj))):
-            collector.warn(code="C2", message=
-                "cannot collect %r because it is not a function."
-                % name, )
+            collector.warn(code="C2", message="cannot collect %r because it is not a function."
+                           % name, )
         elif getattr(obj, "__test__", True):
             if is_generator(obj):
                 res = Generator(name, parent=collector)
@@ -197,9 +188,9 @@ def pytest_pycollect_makeitem(collector, name, obj):
                 res = list(collector._genfunctions(name, obj))
             outcome.force_result(res)
 
-def pytest_make_parametrize_id(config, val):
-    return None
 
+def pytest_make_parametrize_id(config, val, argname=None):
+    return None
 
 
 class PyobjContext(object):
@@ -207,6 +198,7 @@ class PyobjContext(object):
     cls = pyobj_property("Class")
     instance = pyobj_property("Instance")
 
+
 class PyobjMixin(PyobjContext):
     def obj():
         def fget(self):
@@ -235,8 +227,7 @@ class PyobjMixin(PyobjContext):
                 continue
             name = node.name
             if isinstance(node, Module):
-                assert name.endswith(".py")
-                name = name[:-3]
+                name = os.path.splitext(name)[0]
                 if stopatmodule:
                     if includemodule:
                         parts.append(name)
@@ -265,7 +256,8 @@ class PyobjMixin(PyobjContext):
         assert isinstance(lineno, int)
         return fspath, lineno, modpath
 
-class PyCollector(PyobjMixin, pytest.Collector):
+
+class PyCollector(PyobjMixin, main.Collector):
 
     def funcnamefilter(self, name):
         return self._matches_prefix_or_glob_option('python_functions', name)
@@ -283,10 +275,22 @@ class PyCollector(PyobjMixin, pytest.Collector):
         return self._matches_prefix_or_glob_option('python_classes', name)
 
     def istestfunction(self, obj, name):
-        return (
-            (self.funcnamefilter(name) or self.isnosetest(obj)) and
-            safe_getattr(obj, "__call__", False) and fixtures.getfixturemarker(obj) is None
-        )
+        if self.funcnamefilter(name) or self.isnosetest(obj):
+            if isinstance(obj, staticmethod):
+                # static methods need to be unwrapped
+                obj = safe_getattr(obj, '__func__', False)
+                if obj is False:
+                    # Python 2.6 wraps in a different way that we won't try to handle
+                    msg = "cannot collect static method %r because " \
+                          "it is not a function (always the case in Python 2.6)"
+                    self.warn(
+                        code="C2", message=msg % name)
+                    return False
+            return (
+                safe_getattr(obj, "__call__", False) and fixtures.getfixturemarker(obj) is None
+            )
+        else:
+            return False
 
     def istestclass(self, obj, name):
         return self.classnamefilter(name) or self.isnosetest(obj)
@@ -317,7 +321,7 @@ class PyCollector(PyobjMixin, pytest.Collector):
         for basecls in inspect.getmro(self.obj.__class__):
             dicts.append(basecls.__dict__)
         seen = {}
-        l = []
+        values = []
         for dic in dicts:
             for name, obj in list(dic.items()):
                 if name in seen:
@@ -328,12 +332,12 @@ class PyCollector(PyobjMixin, pytest.Collector):
                     continue
                 if not isinstance(res, list):
                     res = [res]
-                l.extend(res)
-        l.sort(key=lambda item: item.reportinfo()[:2])
-        return l
+                values.extend(res)
+        values.sort(key=lambda item: item.reportinfo()[:2])
+        return values
 
     def makeitem(self, name, obj):
-        #assert self.ihook.fspath == self.fspath, self
+        # assert self.ihook.fspath == self.fspath, self
         return self.ihook.pytest_pycollect_makeitem(
             collector=self, name=name, obj=obj)
 
@@ -369,43 +373,16 @@ class PyCollector(PyobjMixin, pytest.Collector):
                 yield Function(name=subname, parent=self,
                                callspec=callspec, callobj=funcobj,
                                fixtureinfo=fixtureinfo,
-                               keywords={callspec.id:True},
+                               keywords={callspec.id: True},
                                originalname=name,
                                )
 
 
-def _marked(func, mark):
-    """ Returns True if :func: is already marked with :mark:, False otherwise.
-    This can happen if marker is applied to class and the test file is
-    invoked more than once.
-    """
-    try:
-        func_mark = getattr(func, mark.name)
-    except AttributeError:
-        return False
-    return mark.args == func_mark.args and mark.kwargs == func_mark.kwargs
-
-
-def transfer_markers(funcobj, cls, mod):
-    # XXX this should rather be code in the mark plugin or the mark
-    # plugin should merge with the python plugin.
-    for holder in (cls, mod):
-        try:
-            pytestmark = holder.pytestmark
-        except AttributeError:
-            continue
-        if isinstance(pytestmark, list):
-            for mark in pytestmark:
-                if not _marked(funcobj, mark):
-                    mark(funcobj)
-        else:
-            if not _marked(funcobj, pytestmark):
-                pytestmark(funcobj)
-
-class Module(pytest.File, PyCollector):
+class Module(main.File, PyCollector):
     """ Collector for test classes and functions. """
+
     def _getobj(self):
-        return self._memoizedcall('_obj', self._importtestmodule)
+        return self._importtestmodule()
 
     def collect(self):
         self.session._fixturemanager.parsefactories(self)
@@ -429,7 +406,7 @@ class Module(pytest.File, PyCollector):
                 "  %s\n"
                 "HINT: remove __pycache__ / .pyc files and/or use a "
                 "unique basename for your test file modules"
-                 % e.args
+                % e.args
             )
         except ImportError:
             from _pytest._code.code import ExceptionInfo
@@ -437,7 +414,7 @@ class Module(pytest.File, PyCollector):
             if self.config.getoption('verbose') < 2:
                 exc_info.traceback = exc_info.traceback.filter(filter_traceback)
             exc_repr = exc_info.getrepr(style='short') if exc_info.traceback else exc_info.exconly()
-            formatted_tb = py._builtin._totext(exc_repr)
+            formatted_tb = safe_str(exc_repr)
             raise self.CollectError(
                 "ImportError while importing test module '{fspath}'.\n"
                 "Hint: make sure your test modules/packages have valid Python names.\n"
@@ -448,9 +425,10 @@ class Module(pytest.File, PyCollector):
             if e.allow_module_level:
                 raise
             raise self.CollectError(
-                "Using pytest.skip outside of a test is not allowed. If you are "
-                "trying to decorate a test function, use the @pytest.mark.skip "
-                "or @pytest.mark.skipif decorators instead."
+                "Using pytest.skip outside of a test is not allowed. "
+                "To decorate a test function, use the @pytest.mark.skip "
+                "or @pytest.mark.skipif decorators instead, and to skip a "
+                "module use `pytestmark = pytest.mark.{skip,skipif}."
             )
         self.config.pluginmanager.consider_module(mod)
         return mod
@@ -501,10 +479,13 @@ def _get_xunit_func(obj, name):
 
 class Class(PyCollector):
     """ Collector for test methods. """
+
     def collect(self):
+        if not safe_getattr(self.obj, "__test__", True):
+            return []
         if hasinit(self.obj):
             self.warn("C1", "cannot collect test class %r because it has a "
-                "__init__ constructor" % self.obj.__name__)
+                      "__init__ constructor" % self.obj.__name__)
             return []
         elif hasnew(self.obj):
             self.warn("C1", "cannot collect test class %r because it has a "
@@ -525,6 +506,7 @@ class Class(PyCollector):
             fin_class = getattr(fin_class, '__func__', fin_class)
             self.addfinalizer(lambda: fin_class(self.obj))
 
+
 class Instance(PyCollector):
     def _getobj(self):
         return self.parent.obj()
@@ -537,6 +519,7 @@ class Instance(PyCollector):
         self.obj = self._getobj()
         return self.obj
 
+
 class FunctionMixin(PyobjMixin):
     """ mixin for the code common to Function and Generator.
     """
@@ -572,7 +555,7 @@ class FunctionMixin(PyobjMixin):
             if ntraceback == traceback:
                 ntraceback = ntraceback.cut(path=path)
                 if ntraceback == traceback:
-                    #ntraceback = ntraceback.cut(excludepath=cutdir2)
+                    # ntraceback = ntraceback.cut(excludepath=cutdir2)
                     ntraceback = ntraceback.filter(filter_traceback)
                     if not ntraceback:
                         ntraceback = traceback
@@ -586,11 +569,11 @@ class FunctionMixin(PyobjMixin):
                         entry.set_repr_style('short')
 
     def _repr_failure_py(self, excinfo, style="long"):
-        if excinfo.errisinstance(pytest.fail.Exception):
+        if excinfo.errisinstance(fail.Exception):
             if not excinfo.value.pytrace:
                 return py._builtin._totext(excinfo.value)
         return super(FunctionMixin, self)._repr_failure_py(excinfo,
-            style=style)
+                                                           style=style)
 
     def repr_failure(self, excinfo, outerr=None):
         assert outerr is None, "XXX outerr usage is deprecated"
@@ -609,27 +592,27 @@ class Generator(FunctionMixin, PyCollector):
         self.session._setupstate.prepare(self)
         # see FunctionMixin.setup and test_setupstate_is_preserved_134
         self._preservedparent = self.parent.obj
-        l = []
+        values = []
         seen = {}
         for i, x in enumerate(self.obj()):
             name, call, args = self.getcallargs(x)
             if not callable(call):
-                raise TypeError("%r yielded non callable test %r" %(self.obj, call,))
+                raise TypeError("%r yielded non callable test %r" % (self.obj, call,))
             if name is None:
                 name = "[%d]" % i
             else:
                 name = "['%s']" % name
             if name in seen:
-                raise ValueError("%r generated tests with non-unique name %r" %(self, name))
+                raise ValueError("%r generated tests with non-unique name %r" % (self, name))
             seen[name] = True
-            l.append(self.Function(name, self, args=args, callobj=call))
-            self.config.warn('C1', deprecated.YIELD_TESTS, fslocation=self.fspath)
-        return l
+            values.append(self.Function(name, self, args=args, callobj=call))
+        self.warn('C1', deprecated.YIELD_TESTS)
+        return values
 
     def getcallargs(self, obj):
         if not isinstance(obj, (tuple, list)):
             obj = (obj,)
-        # explict naming
+        # explicit naming
         if isinstance(obj[0], py.builtin._basestring):
             name = obj[0]
             obj = obj[1:]
@@ -679,7 +662,7 @@ class CallSpec2(object):
 
     def _checkargnotcontained(self, arg):
         if arg in self.params or arg in self.funcargs:
-            raise ValueError("duplicate %r" %(arg,))
+            raise ValueError("duplicate %r" % (arg,))
 
     def getparam(self, name):
         try:
@@ -695,7 +678,7 @@ class CallSpec2(object):
 
     def setmulti(self, valtypes, argnames, valset, id, keywords, scopenum,
                  param_index):
-        for arg,val in zip(argnames, valset):
+        for arg, val in zip(argnames, valset):
             self._checkargnotcontained(arg)
             valtype_for_arg = valtypes[arg]
             getattr(self, valtype_for_arg)[arg] = val
@@ -724,6 +707,7 @@ class Metafunc(fixtures.FuncargnamesCompatAttr):
     test configuration or values specified in the class or module where a
     test function is defined.
     """
+
     def __init__(self, function, fixtureinfo, config, cls=None, module=None):
         #: access to the :class:`_pytest.config.Config` object for the test session
         self.config = config
@@ -745,7 +729,7 @@ class Metafunc(fixtures.FuncargnamesCompatAttr):
         self._arg2fixturedefs = fixtureinfo.name2fixturedefs
 
     def parametrize(self, argnames, argvalues, indirect=False, ids=None,
-        scope=None):
+                    scope=None):
         """ Add new invocations to the underlying test function using the list
         of argvalues for the given argnames.  Parametrization is performed
         during the collection phase.  If you need to setup expensive resources
@@ -784,36 +768,34 @@ class Metafunc(fixtures.FuncargnamesCompatAttr):
             to set a dynamic scope using test context or configuration.
         """
         from _pytest.fixtures import scope2index
-        from _pytest.mark import extract_argvalue
+        from _pytest.mark import MARK_GEN, ParameterSet
         from py.io import saferepr
 
-        unwrapped_argvalues = []
-        newkeywords = []
-        for maybe_marked_args in argvalues:
-            argval, newmarks = extract_argvalue(maybe_marked_args)
-            unwrapped_argvalues.append(argval)
-            newkeywords.append(newmarks)
-        argvalues = unwrapped_argvalues
-
         if not isinstance(argnames, (tuple, list)):
             argnames = [x.strip() for x in argnames.split(",") if x.strip()]
-            if len(argnames) == 1:
-                argvalues = [(val,) for val in argvalues]
-        if not argvalues:
-            argvalues = [(NOTSET,) * len(argnames)]
-            # we passed a empty list to parameterize, skip that test
-            #
+            force_tuple = len(argnames) == 1
+        else:
+            force_tuple = False
+        parameters = [
+            ParameterSet.extract_from(x, legacy_force_tuple=force_tuple)
+            for x in argvalues]
+        del argvalues
+
+        if not parameters:
             fs, lineno = getfslineno(self.function)
-            newmark = pytest.mark.skip(
-                reason="got empty parameter set %r, function %s at %s:%d" % (
-                    argnames, self.function.__name__, fs, lineno))
-            newkeywords = [{newmark.markname: newmark}]
+            reason = "got empty parameter set %r, function %s at %s:%d" % (
+                argnames, self.function.__name__, fs, lineno)
+            mark = MARK_GEN.skip(reason=reason)
+            parameters.append(ParameterSet(
+                values=(NOTSET,) * len(argnames),
+                marks=[mark],
+                id=None,
+            ))
 
         if scope is None:
             scope = _find_parametrized_scope(argnames, self._arg2fixturedefs, indirect)
 
-        scopenum = scope2index(
-            scope, descr='call to {0}'.format(self.parametrize))
+        scopenum = scope2index(scope, descr='call to {0}'.format(self.parametrize))
         valtypes = {}
         for arg in argnames:
             if arg not in self.fixturenames:
@@ -823,7 +805,7 @@ class Metafunc(fixtures.FuncargnamesCompatAttr):
                     name = 'fixture' if indirect else 'argument'
                 raise ValueError(
                     "%r uses no %s %r" % (
-                            self.function, name, arg))
+                        self.function, name, arg))
 
         if indirect is True:
             valtypes = dict.fromkeys(argnames, "params")
@@ -841,22 +823,26 @@ class Metafunc(fixtures.FuncargnamesCompatAttr):
             idfn = ids
             ids = None
         if ids:
-            if len(ids) != len(argvalues):
-                raise ValueError('%d tests specified with %d ids' %(
-                                 len(argvalues), len(ids)))
+            if len(ids) != len(parameters):
+                raise ValueError('%d tests specified with %d ids' % (
+                                 len(parameters), len(ids)))
             for id_value in ids:
                 if id_value is not None and not isinstance(id_value, py.builtin._basestring):
                     msg = 'ids must be list of strings, found: %s (type: %s)'
                     raise ValueError(msg % (saferepr(id_value), type(id_value).__name__))
-        ids = idmaker(argnames, argvalues, idfn, ids, self.config)
+        ids = idmaker(argnames, parameters, idfn, ids, self.config)
         newcalls = []
         for callspec in self._calls or [CallSpec2(self)]:
-            elements = zip(ids, argvalues, newkeywords, count())
-            for a_id, valset, keywords, param_index in elements:
-                assert len(valset) == len(argnames)
+            elements = zip(ids, parameters, count())
+            for a_id, param, param_index in elements:
+                if len(param.values) != len(argnames):
+                    raise ValueError(
+                        'In "parametrize" the number of values ({0}) must be '
+                        'equal to the number of names ({1})'.format(
+                            param.values, argnames))
                 newcallspec = callspec.copy(self)
-                newcallspec.setmulti(valtypes, argnames, valset, a_id,
-                                     keywords, scopenum, param_index)
+                newcallspec.setmulti(valtypes, argnames, param.values, a_id,
+                                     param.deprecated_arg_dict, scopenum, param_index)
                 newcalls.append(newcallspec)
         self._calls = newcalls
 
@@ -880,7 +866,7 @@ class Metafunc(fixtures.FuncargnamesCompatAttr):
         if funcargs is not None:
             for name in funcargs:
                 if name not in self.fixturenames:
-                    pytest.fail("funcarg %r not used in this function." % name)
+                    fail("funcarg %r not used in this function." % name)
         else:
             funcargs = {}
         if id is None:
@@ -910,7 +896,7 @@ def _find_parametrized_scope(argnames, arg2fixturedefs, indirect):
     from _pytest.fixtures import scopes
     indirect_as_list = isinstance(indirect, (list, tuple))
     all_arguments_are_fixtures = indirect is True or \
-                                 indirect_as_list and len(indirect) == argnames
+        indirect_as_list and len(indirect) == argnames
     if all_arguments_are_fixtures:
         fixturedefs = arg2fixturedefs or {}
         used_scopes = [fixturedef[0].scope for name, fixturedef in fixturedefs.items()]
@@ -925,41 +911,51 @@ def _find_parametrized_scope(argnames, arg2fixturedefs, indirect):
 
 def _idval(val, argname, idx, idfn, config=None):
     if idfn:
+        s = None
         try:
             s = idfn(val)
-            if s:
-                return _escape_strings(s)
         except Exception:
-            pass
+            # See issue https://github.com/pytest-dev/pytest/issues/2169
+            import warnings
+            msg = "Raised while trying to determine id of parameter %s at position %d." % (argname, idx)
+            msg += '\nUpdate your code as this will raise an error in pytest-4.0.'
+            warnings.warn(msg, DeprecationWarning)
+        if s:
+            return _ascii_escaped(s)
 
     if config:
-        hook_id = config.hook.pytest_make_parametrize_id(config=config, val=val)
+        hook_id = config.hook.pytest_make_parametrize_id(
+            config=config, val=val, argname=argname)
         if hook_id:
             return hook_id
 
     if isinstance(val, STRING_TYPES):
-        return _escape_strings(val)
+        return _ascii_escaped(val)
     elif isinstance(val, (float, int, bool, NoneType)):
         return str(val)
     elif isinstance(val, REGEX_TYPE):
-        return _escape_strings(val.pattern)
+        return _ascii_escaped(val.pattern)
     elif enum is not None and isinstance(val, enum.Enum):
         return str(val)
     elif isclass(val) and hasattr(val, '__name__'):
         return val.__name__
-    return str(argname)+str(idx)
+    return str(argname) + str(idx)
 
-def _idvalset(idx, valset, argnames, idfn, ids, config=None):
+
+def _idvalset(idx, parameterset, argnames, idfn, ids, config=None):
+    if parameterset.id is not None:
+        return parameterset.id
     if ids is None or (idx >= len(ids) or ids[idx] is None):
         this_id = [_idval(val, argname, idx, idfn, config)
-                   for val, argname in zip(valset, argnames)]
+                   for val, argname in zip(parameterset.values, argnames)]
         return "-".join(this_id)
     else:
-        return _escape_strings(ids[idx])
+        return _ascii_escaped(ids[idx])
+
 
-def idmaker(argnames, argvalues, idfn=None, ids=None, config=None):
-    ids = [_idvalset(valindex, valset, argnames, idfn, ids, config)
-           for valindex, valset in enumerate(argvalues)]
+def idmaker(argnames, parametersets, idfn=None, ids=None, config=None):
+    ids = [_idvalset(valindex, parameterset, argnames, idfn, ids, config)
+           for valindex, parameterset in enumerate(parametersets)]
     if len(set(ids)) != len(ids):
         # The ids are not unique
         duplicates = [testid for testid in ids if ids.count(testid) > 1]
@@ -983,58 +979,55 @@ def _show_fixtures_per_test(config, session):
     tw = _pytest.config.create_terminal_writer(config)
     verbose = config.getvalue("verbose")
 
-    def get_best_rel(func):
+    def get_best_relpath(func):
         loc = getlocation(func, curdir)
         return curdir.bestrelpath(loc)
 
     def write_fixture(fixture_def):
         argname = fixture_def.argname
-
         if verbose <= 0 and argname.startswith("_"):
             return
         if verbose > 0:
-            bestrel = get_best_rel(fixture_def.func)
+            bestrel = get_best_relpath(fixture_def.func)
             funcargspec = "{0} -- {1}".format(argname, bestrel)
         else:
             funcargspec = argname
         tw.line(funcargspec, green=True)
-
-        INDENT = '    {0}'
         fixture_doc = fixture_def.func.__doc__
-
         if fixture_doc:
-            for line in fixture_doc.strip().split('\n'):
-                tw.line(INDENT.format(line.strip()))
+            write_docstring(tw, fixture_doc)
         else:
-            tw.line(INDENT.format('no docstring available'), red=True)
+            tw.line('    no docstring available', red=True)
 
     def write_item(item):
-        name2fixturedefs = item._fixtureinfo.name2fixturedefs
-
-        if not name2fixturedefs:
-            # The given test item does not use any fixtures
+        try:
+            info = item._fixtureinfo
+        except AttributeError:
+            # doctests items have no _fixtureinfo attribute
+            return
+        if not info.name2fixturedefs:
+            # this test item does not use any fixtures
             return
-        bestrel = get_best_rel(item.function)
-
         tw.line()
         tw.sep('-', 'fixtures used by {0}'.format(item.name))
-        tw.sep('-', '({0})'.format(bestrel))
-        for argname, fixture_defs in sorted(name2fixturedefs.items()):
-            assert fixture_defs is not None
-            if not fixture_defs:
+        tw.sep('-', '({0})'.format(get_best_relpath(item.function)))
+        # dict key not used in loop but needed for sorting
+        for _, fixturedefs in sorted(info.name2fixturedefs.items()):
+            assert fixturedefs is not None
+            if not fixturedefs:
                 continue
-            # The last fixture def item in the list is expected
-            # to be the one used by the test item
-            write_fixture(fixture_defs[-1])
+            # last item is expected to be the one used by the test item
+            write_fixture(fixturedefs[-1])
 
-    for item in session.items:
-        write_item(item)
+    for session_item in session.items:
+        write_item(session_item)
 
 
 def showfixtures(config):
     from _pytest.main import wrap_session
     return wrap_session(config, _showfixtures_main)
 
+
 def _showfixtures_main(config, session):
     import _pytest.config
     session.perform_collect()
@@ -1067,444 +1060,46 @@ def _showfixtures_main(config, session):
         if currentmodule != module:
             if not module.startswith("_pytest."):
                 tw.line()
-                tw.sep("-", "fixtures defined from %s" %(module,))
+                tw.sep("-", "fixtures defined from %s" % (module,))
                 currentmodule = module
         if verbose <= 0 and argname[0] == "_":
             continue
         if verbose > 0:
-            funcargspec = "%s -- %s" %(argname, bestrel,)
+            funcargspec = "%s -- %s" % (argname, bestrel,)
         else:
             funcargspec = argname
         tw.line(funcargspec, green=True)
         loc = getlocation(fixturedef.func, curdir)
         doc = fixturedef.func.__doc__ or ""
         if doc:
-            for line in doc.strip().split("\n"):
-                tw.line("    " + line.strip())
+            write_docstring(tw, doc)
         else:
-            tw.line("    %s: no docstring available" %(loc,),
-                red=True)
-
-
-# builtin pytest.raises helper
-
-def raises(expected_exception, *args, **kwargs):
-    """
-    Assert that a code block/function call raises ``expected_exception``
-    and raise a failure exception otherwise.
-
-    This helper produces a ``ExceptionInfo()`` object (see below).
-
-    If using Python 2.5 or above, you may use this function as a
-    context manager::
-
-        >>> with raises(ZeroDivisionError):
-        ...    1/0
-
-    .. versionchanged:: 2.10
+            tw.line("    %s: no docstring available" % (loc,),
+                    red=True)
 
-    In the context manager form you may use the keyword argument
-    ``message`` to specify a custom failure message::
 
-        >>> with raises(ZeroDivisionError, message="Expecting ZeroDivisionError"):
-        ...    pass
-        Traceback (most recent call last):
-          ...
-        Failed: Expecting ZeroDivisionError
-
-
-    .. note::
-
-       When using ``pytest.raises`` as a context manager, it's worthwhile to
-       note that normal context manager rules apply and that the exception
-       raised *must* be the final line in the scope of the context manager.
-       Lines of code after that, within the scope of the context manager will
-       not be executed. For example::
-
-           >>> value = 15
-           >>> with raises(ValueError) as exc_info:
-           ...     if value > 10:
-           ...         raise ValueError("value must be <= 10")
-           ...     assert str(exc_info.value) == "value must be <= 10"  # this will not execute
-
-       Instead, the following approach must be taken (note the difference in
-       scope)::
-
-           >>> with raises(ValueError) as exc_info:
-           ...     if value > 10:
-           ...         raise ValueError("value must be <= 10")
-           ...
-           >>> assert str(exc_info.value) == "value must be <= 10"
-
-
-    Or you can specify a callable by passing a to-be-called lambda::
-
-        >>> raises(ZeroDivisionError, lambda: 1/0)
-        <ExceptionInfo ...>
-
-    or you can specify an arbitrary callable with arguments::
-
-        >>> def f(x): return 1/x
-        ...
-        >>> raises(ZeroDivisionError, f, 0)
-        <ExceptionInfo ...>
-        >>> raises(ZeroDivisionError, f, x=0)
-        <ExceptionInfo ...>
-
-    A third possibility is to use a string to be executed::
-
-        >>> raises(ZeroDivisionError, "f(0)")
-        <ExceptionInfo ...>
-
-    .. autoclass:: _pytest._code.ExceptionInfo
-        :members:
-
-    .. note::
-        Similar to caught exception objects in Python, explicitly clearing
-        local references to returned ``ExceptionInfo`` objects can
-        help the Python interpreter speed up its garbage collection.
-
-        Clearing those references breaks a reference cycle
-        (``ExceptionInfo`` --> caught exception --> frame stack raising
-        the exception --> current frame stack --> local variables -->
-        ``ExceptionInfo``) which makes Python keep all objects referenced
-        from that cycle (including all local variables in the current
-        frame) alive until the next cyclic garbage collection run. See the
-        official Python ``try`` statement documentation for more detailed
-        information.
-
-    """
-    __tracebackhide__ = True
-    if expected_exception is AssertionError:
-        # we want to catch a AssertionError
-        # replace our subclass with the builtin one
-        # see https://github.com/pytest-dev/pytest/issues/176
-        from _pytest.assertion.util import BuiltinAssertionError \
-            as expected_exception
-    msg = ("exceptions must be old-style classes or"
-           " derived from BaseException, not %s")
-    if isinstance(expected_exception, tuple):
-        for exc in expected_exception:
-            if not isclass(exc):
-                raise TypeError(msg % type(exc))
-    elif not isclass(expected_exception):
-        raise TypeError(msg % type(expected_exception))
-
-    message = "DID NOT RAISE {0}".format(expected_exception)
-
-    if not args:
-        if "message" in kwargs:
-            message = kwargs.pop("message")
-        return RaisesContext(expected_exception, message)
-    elif isinstance(args[0], str):
-        code, = args
-        assert isinstance(code, str)
-        frame = sys._getframe(1)
-        loc = frame.f_locals.copy()
-        loc.update(kwargs)
-        #print "raises frame scope: %r" % frame.f_locals
-        try:
-            code = _pytest._code.Source(code).compile()
-            py.builtin.exec_(code, frame.f_globals, loc)
-            # XXX didn'T mean f_globals == f_locals something special?
-            #     this is destroyed here ...
-        except expected_exception:
-            return _pytest._code.ExceptionInfo()
+def write_docstring(tw, doc):
+    INDENT = "    "
+    doc = doc.rstrip()
+    if "\n" in doc:
+        firstline, rest = doc.split("\n", 1)
     else:
-        func = args[0]
-        try:
-            func(*args[1:], **kwargs)
-        except expected_exception:
-            return _pytest._code.ExceptionInfo()
-    pytest.fail(message)
-
-class RaisesContext(object):
-    def __init__(self, expected_exception, message):
-        self.expected_exception = expected_exception
-        self.message = message
-        self.excinfo = None
-
-    def __enter__(self):
-        self.excinfo = object.__new__(_pytest._code.ExceptionInfo)
-        return self.excinfo
-
-    def __exit__(self, *tp):
-        __tracebackhide__ = True
-        if tp[0] is None:
-            pytest.fail(self.message)
-        if sys.version_info < (2, 7):
-            # py26: on __exit__() exc_value often does not contain the
-            # exception value.
-            # http://bugs.python.org/issue7853
-            if not isinstance(tp[1], BaseException):
-                exc_type, value, traceback = tp
-                tp = exc_type, exc_type(value), traceback
-        self.excinfo.__init__(tp)
-        suppress_exception = issubclass(self.excinfo.type, self.expected_exception)
-        if sys.version_info[0] == 2 and suppress_exception:
-            sys.exc_clear()
-        return suppress_exception
-
-
-# builtin pytest.approx helper
-
-class approx(object):
-    """
-    Assert that two numbers (or two sets of numbers) are equal to each other
-    within some tolerance.
-
-    Due to the `intricacies of floating-point arithmetic`__, numbers that we
-    would intuitively expect to be equal are not always so::
-
-        >>> 0.1 + 0.2 == 0.3
-        False
-
-    __ https://docs.python.org/3/tutorial/floatingpoint.html
-
-    This problem is commonly encountered when writing tests, e.g. when making
-    sure that floating-point values are what you expect them to be.  One way to
-    deal with this problem is to assert that two floating-point numbers are
-    equal to within some appropriate tolerance::
-
-        >>> abs((0.1 + 0.2) - 0.3) < 1e-6
-        True
-
-    However, comparisons like this are tedious to write and difficult to
-    understand.  Furthermore, absolute comparisons like the one above are
-    usually discouraged because there's no tolerance that works well for all
-    situations.  ``1e-6`` is good for numbers around ``1``, but too small for
-    very big numbers and too big for very small ones.  It's better to express
-    the tolerance as a fraction of the expected value, but relative comparisons
-    like that are even more difficult to write correctly and concisely.
-
-    The ``approx`` class performs floating-point comparisons using a syntax
-    that's as intuitive as possible::
-
-        >>> from pytest import approx
-        >>> 0.1 + 0.2 == approx(0.3)
-        True
-
-    The same syntax also works on sequences of numbers::
-
-        >>> (0.1 + 0.2, 0.2 + 0.4) == approx((0.3, 0.6))
-        True
-
-    By default, ``approx`` considers numbers within a relative tolerance of
-    ``1e-6`` (i.e. one part in a million) of its expected value to be equal.
-    This treatment would lead to surprising results if the expected value was
-    ``0.0``, because nothing but ``0.0`` itself is relatively close to ``0.0``.
-    To handle this case less surprisingly, ``approx`` also considers numbers
-    within an absolute tolerance of ``1e-12`` of its expected value to be
-    equal.  Infinite numbers are another special case.  They are only
-    considered equal to themselves, regardless of the relative tolerance.  Both
-    the relative and absolute tolerances can be changed by passing arguments to
-    the ``approx`` constructor::
-
-        >>> 1.0001 == approx(1)
-        False
-        >>> 1.0001 == approx(1, rel=1e-3)
-        True
-        >>> 1.0001 == approx(1, abs=1e-3)
-        True
-
-    If you specify ``abs`` but not ``rel``, the comparison will not consider
-    the relative tolerance at all.  In other words, two numbers that are within
-    the default relative tolerance of ``1e-6`` will still be considered unequal
-    if they exceed the specified absolute tolerance.  If you specify both
-    ``abs`` and ``rel``, the numbers will be considered equal if either
-    tolerance is met::
-
-        >>> 1 + 1e-8 == approx(1)
-        True
-        >>> 1 + 1e-8 == approx(1, abs=1e-12)
-        False
-        >>> 1 + 1e-8 == approx(1, rel=1e-6, abs=1e-12)
-        True
-
-    If you're thinking about using ``approx``, then you might want to know how
-    it compares to other good ways of comparing floating-point numbers.  All of
-    these algorithms are based on relative and absolute tolerances and should
-    agree for the most part, but they do have meaningful differences:
-
-    - ``math.isclose(a, b, rel_tol=1e-9, abs_tol=0.0)``:  True if the relative
-      tolerance is met w.r.t. either ``a`` or ``b`` or if the absolute
-      tolerance is met.  Because the relative tolerance is calculated w.r.t.
-      both ``a`` and ``b``, this test is symmetric (i.e.  neither ``a`` nor
-      ``b`` is a "reference value").  You have to specify an absolute tolerance
-      if you want to compare to ``0.0`` because there is no tolerance by
-      default.  Only available in python>=3.5.  `More information...`__
-
-      __ https://docs.python.org/3/library/math.html#math.isclose
-
-    - ``numpy.isclose(a, b, rtol=1e-5, atol=1e-8)``: True if the difference
-      between ``a`` and ``b`` is less that the sum of the relative tolerance
-      w.r.t. ``b`` and the absolute tolerance.  Because the relative tolerance
-      is only calculated w.r.t. ``b``, this test is asymmetric and you can
-      think of ``b`` as the reference value.  Support for comparing sequences
-      is provided by ``numpy.allclose``.  `More information...`__
-
-      __ http://docs.scipy.org/doc/numpy-1.10.0/reference/generated/numpy.isclose.html
-
-    - ``unittest.TestCase.assertAlmostEqual(a, b)``: True if ``a`` and ``b``
-      are within an absolute tolerance of ``1e-7``.  No relative tolerance is
-      considered and the absolute tolerance cannot be changed, so this function
-      is not appropriate for very large or very small numbers.  Also, it's only
-      available in subclasses of ``unittest.TestCase`` and it's ugly because it
-      doesn't follow PEP8.  `More information...`__
-
-      __ https://docs.python.org/3/library/unittest.html#unittest.TestCase.assertAlmostEqual
-
-    - ``a == pytest.approx(b, rel=1e-6, abs=1e-12)``: True if the relative
-      tolerance is met w.r.t. ``b`` or if the absolute tolerance is met.
-      Because the relative tolerance is only calculated w.r.t. ``b``, this test
-      is asymmetric and you can think of ``b`` as the reference value.  In the
-      special case that you explicitly specify an absolute tolerance but not a
-      relative tolerance, only the absolute tolerance is considered.
-    """
-
-    def __init__(self, expected, rel=None, abs=None):
-        self.expected = expected
-        self.abs = abs
-        self.rel = rel
+        firstline, rest = doc, ""
 
-    def __repr__(self):
-        return ', '.join(repr(x) for x in self.expected)
-
-    def __eq__(self, actual):
-        from collections import Iterable
-        if not isinstance(actual, Iterable):
-            actual = [actual]
-        if len(actual) != len(self.expected):
-            return False
-        return all(a == x for a, x in zip(actual, self.expected))
+    if firstline.strip():
+        tw.line(INDENT + firstline.strip())
 
-    __hash__ = None
+    if rest:
+        for line in dedent(rest).split("\n"):
+            tw.write(INDENT + line + "\n")
 
-    def __ne__(self, actual):
-        return not (actual == self)
-
-    @property
-    def expected(self):
-        # Regardless of whether the user-specified expected value is a number
-        # or a sequence of numbers, return a list of ApproxNotIterable objects
-        # that can be compared against.
-        from collections import Iterable
-        approx_non_iter = lambda x: ApproxNonIterable(x, self.rel, self.abs)
-        if isinstance(self._expected, Iterable):
-            return [approx_non_iter(x) for x in self._expected]
-        else:
-            return [approx_non_iter(self._expected)]
 
-    @expected.setter
-    def expected(self, expected):
-        self._expected = expected
-
-
-class ApproxNonIterable(object):
-    """
-    Perform approximate comparisons for single numbers only.
-
-    In other words, the ``expected`` attribute for objects of this class must
-    be some sort of number.  This is in contrast to the ``approx`` class, where
-    the ``expected`` attribute can either be a number of a sequence of numbers.
-    This class is responsible for making comparisons, while ``approx`` is
-    responsible for abstracting the difference between numbers and sequences of
-    numbers.  Although this class can stand on its own, it's only meant to be
-    used within ``approx``.
-    """
-
-    def __init__(self, expected, rel=None, abs=None):
-        self.expected = expected
-        self.abs = abs
-        self.rel = rel
-
-    def __repr__(self):
-        if isinstance(self.expected, complex):
-            return str(self.expected)
-
-        # Infinities aren't compared using tolerances, so don't show a
-        # tolerance.
-        if math.isinf(self.expected):
-            return str(self.expected)
-
-        # If a sensible tolerance can't be calculated, self.tolerance will
-        # raise a ValueError.  In this case, display '???'.
-        try:
-            vetted_tolerance = '{:.1e}'.format(self.tolerance)
-        except ValueError:
-            vetted_tolerance = '???'
-
-        if sys.version_info[0] == 2:
-            return '{0} +- {1}'.format(self.expected, vetted_tolerance)
-        else:
-            return u'{0} \u00b1 {1}'.format(self.expected, vetted_tolerance)
-
-    def __eq__(self, actual):
-        # Short-circuit exact equality.
-        if actual == self.expected:
-            return True
-
-        # Infinity shouldn't be approximately equal to anything but itself, but
-        # if there's a relative tolerance, it will be infinite and infinity
-        # will seem approximately equal to everything.  The equal-to-itself
-        # case would have been short circuited above, so here we can just
-        # return false if the expected value is infinite.  The abs() call is
-        # for compatibility with complex numbers.
-        if math.isinf(abs(self.expected)):
-            return False
-
-        # Return true if the two numbers are within the tolerance.
-        return abs(self.expected - actual) <= self.tolerance
-
-    __hash__ = None
-
-    def __ne__(self, actual):
-        return not (actual == self)
-
-    @property
-    def tolerance(self):
-        set_default = lambda x, default: x if x is not None else default
-
-        # Figure out what the absolute tolerance should be.  ``self.abs`` is
-        # either None or a value specified by the user.
-        absolute_tolerance = set_default(self.abs, 1e-12)
-
-        if absolute_tolerance < 0:
-            raise ValueError("absolute tolerance can't be negative: {0}".format(absolute_tolerance))
-        if math.isnan(absolute_tolerance):
-            raise ValueError("absolute tolerance can't be NaN.")
-
-        # If the user specified an absolute tolerance but not a relative one,
-        # just return the absolute tolerance.
-        if self.rel is None:
-            if self.abs is not None:
-                return absolute_tolerance
-
-        # Figure out what the relative tolerance should be.  ``self.rel`` is
-        # either None or a value specified by the user.  This is done after
-        # we've made sure the user didn't ask for an absolute tolerance only,
-        # because we don't want to raise errors about the relative tolerance if
-        # we aren't even going to use it.
-        relative_tolerance = set_default(self.rel, 1e-6) * abs(self.expected)
-
-        if relative_tolerance < 0:
-            raise ValueError("relative tolerance can't be negative: {0}".format(absolute_tolerance))
-        if math.isnan(relative_tolerance):
-            raise ValueError("relative tolerance can't be NaN.")
-
-        # Return the larger of the relative and absolute tolerances.
-        return max(relative_tolerance, absolute_tolerance)
-
-
-#
-#  the basic pytest Function item
-#
-
-class Function(FunctionMixin, pytest.Item, fixtures.FuncargnamesCompatAttr):
+class Function(FunctionMixin, main.Item, fixtures.FuncargnamesCompatAttr):
     """ a Function Item is responsible for setting up and executing a
     Python test function.
     """
     _genid = None
+
     def __init__(self, name, parent, args=None, config=None,
                  callspec=None, callobj=NOTSET, keywords=None, session=None,
                  fixtureinfo=None, originalname=None):
@@ -1556,7 +1151,7 @@ class Function(FunctionMixin, pytest.Item, fixtures.FuncargnamesCompatAttr):
 
     def _getobj(self):
         name = self.name
-        i = name.find("[") # parametrization
+        i = name.find("[")  # parametrization
         if i != -1:
             name = name[:i]
         return getattr(self.parent.obj, name)
diff --git a/lib/spack/external/_pytest/python_api.py b/lib/spack/external/_pytest/python_api.py
new file mode 100644
index 0000000000..cfc01193b0
--- /dev/null
+++ b/lib/spack/external/_pytest/python_api.py
@@ -0,0 +1,626 @@
+import math
+import sys
+
+import py
+
+from _pytest.compat import isclass, izip
+from _pytest.outcomes import fail
+import _pytest._code
+
+
+def _cmp_raises_type_error(self, other):
+    """__cmp__ implementation which raises TypeError. Used
+    by Approx base classes to implement only == and != and raise a
+    TypeError for other comparisons.
+
+    Needed in Python 2 only, Python 3 all it takes is not implementing the
+    other operators at all.
+    """
+    __tracebackhide__ = True
+    raise TypeError('Comparison operators other than == and != not supported by approx objects')
+
+
+# builtin pytest.approx helper
+
+
+class ApproxBase(object):
+    """
+    Provide shared utilities for making approximate comparisons between numbers
+    or sequences of numbers.
+    """
+
+    def __init__(self, expected, rel=None, abs=None, nan_ok=False):
+        self.expected = expected
+        self.abs = abs
+        self.rel = rel
+        self.nan_ok = nan_ok
+
+    def __repr__(self):
+        raise NotImplementedError
+
+    def __eq__(self, actual):
+        return all(
+            a == self._approx_scalar(x)
+            for a, x in self._yield_comparisons(actual))
+
+    __hash__ = None
+
+    def __ne__(self, actual):
+        return not (actual == self)
+
+    if sys.version_info[0] == 2:
+        __cmp__ = _cmp_raises_type_error
+
+    def _approx_scalar(self, x):
+        return ApproxScalar(x, rel=self.rel, abs=self.abs, nan_ok=self.nan_ok)
+
+    def _yield_comparisons(self, actual):
+        """
+        Yield all the pairs of numbers to be compared.  This is used to
+        implement the `__eq__` method.
+        """
+        raise NotImplementedError
+
+
+class ApproxNumpy(ApproxBase):
+    """
+    Perform approximate comparisons for numpy arrays.
+    """
+
+    # Tell numpy to use our `__eq__` operator instead of its.
+    __array_priority__ = 100
+
+    def __repr__(self):
+        # It might be nice to rewrite this function to account for the
+        # shape of the array...
+        return "approx({0!r})".format(list(
+            self._approx_scalar(x) for x in self.expected))
+
+    if sys.version_info[0] == 2:
+        __cmp__ = _cmp_raises_type_error
+
+    def __eq__(self, actual):
+        import numpy as np
+
+        try:
+            actual = np.asarray(actual)
+        except:  # noqa
+            raise TypeError("cannot compare '{0}' to numpy.ndarray".format(actual))
+
+        if actual.shape != self.expected.shape:
+            return False
+
+        return ApproxBase.__eq__(self, actual)
+
+    def _yield_comparisons(self, actual):
+        import numpy as np
+
+        # We can be sure that `actual` is a numpy array, because it's
+        # casted in `__eq__` before being passed to `ApproxBase.__eq__`,
+        # which is the only method that calls this one.
+        for i in np.ndindex(self.expected.shape):
+            yield actual[i], self.expected[i]
+
+
+class ApproxMapping(ApproxBase):
+    """
+    Perform approximate comparisons for mappings where the values are numbers
+    (the keys can be anything).
+    """
+
+    def __repr__(self):
+        return "approx({0!r})".format(dict(
+            (k, self._approx_scalar(v))
+            for k, v in self.expected.items()))
+
+    def __eq__(self, actual):
+        if set(actual.keys()) != set(self.expected.keys()):
+            return False
+
+        return ApproxBase.__eq__(self, actual)
+
+    def _yield_comparisons(self, actual):
+        for k in self.expected.keys():
+            yield actual[k], self.expected[k]
+
+
+class ApproxSequence(ApproxBase):
+    """
+    Perform approximate comparisons for sequences of numbers.
+    """
+
+    # Tell numpy to use our `__eq__` operator instead of its.
+    __array_priority__ = 100
+
+    def __repr__(self):
+        seq_type = type(self.expected)
+        if seq_type not in (tuple, list, set):
+            seq_type = list
+        return "approx({0!r})".format(seq_type(
+            self._approx_scalar(x) for x in self.expected))
+
+    def __eq__(self, actual):
+        if len(actual) != len(self.expected):
+            return False
+        return ApproxBase.__eq__(self, actual)
+
+    def _yield_comparisons(self, actual):
+        return izip(actual, self.expected)
+
+
+class ApproxScalar(ApproxBase):
+    """
+    Perform approximate comparisons for single numbers only.
+    """
+
+    def __repr__(self):
+        """
+        Return a string communicating both the expected value and the tolerance
+        for the comparison being made, e.g. '1.0 +- 1e-6'.  Use the unicode
+        plus/minus symbol if this is python3 (it's too hard to get right for
+        python2).
+        """
+        if isinstance(self.expected, complex):
+            return str(self.expected)
+
+        # Infinities aren't compared using tolerances, so don't show a
+        # tolerance.
+        if math.isinf(self.expected):
+            return str(self.expected)
+
+        # If a sensible tolerance can't be calculated, self.tolerance will
+        # raise a ValueError.  In this case, display '???'.
+        try:
+            vetted_tolerance = '{:.1e}'.format(self.tolerance)
+        except ValueError:
+            vetted_tolerance = '???'
+
+        if sys.version_info[0] == 2:
+            return '{0} +- {1}'.format(self.expected, vetted_tolerance)
+        else:
+            return u'{0} \u00b1 {1}'.format(self.expected, vetted_tolerance)
+
+    def __eq__(self, actual):
+        """
+        Return true if the given value is equal to the expected value within
+        the pre-specified tolerance.
+        """
+
+        # Short-circuit exact equality.
+        if actual == self.expected:
+            return True
+
+        # Allow the user to control whether NaNs are considered equal to each
+        # other or not.  The abs() calls are for compatibility with complex
+        # numbers.
+        if math.isnan(abs(self.expected)):
+            return self.nan_ok and math.isnan(abs(actual))
+
+        # Infinity shouldn't be approximately equal to anything but itself, but
+        # if there's a relative tolerance, it will be infinite and infinity
+        # will seem approximately equal to everything.  The equal-to-itself
+        # case would have been short circuited above, so here we can just
+        # return false if the expected value is infinite.  The abs() call is
+        # for compatibility with complex numbers.
+        if math.isinf(abs(self.expected)):
+            return False
+
+        # Return true if the two numbers are within the tolerance.
+        return abs(self.expected - actual) <= self.tolerance
+
+    __hash__ = None
+
+    @property
+    def tolerance(self):
+        """
+        Return the tolerance for the comparison.  This could be either an
+        absolute tolerance or a relative tolerance, depending on what the user
+        specified or which would be larger.
+        """
+        def set_default(x, default):
+            return x if x is not None else default
+
+        # Figure out what the absolute tolerance should be.  ``self.abs`` is
+        # either None or a value specified by the user.
+        absolute_tolerance = set_default(self.abs, 1e-12)
+
+        if absolute_tolerance < 0:
+            raise ValueError("absolute tolerance can't be negative: {0}".format(absolute_tolerance))
+        if math.isnan(absolute_tolerance):
+            raise ValueError("absolute tolerance can't be NaN.")
+
+        # If the user specified an absolute tolerance but not a relative one,
+        # just return the absolute tolerance.
+        if self.rel is None:
+            if self.abs is not None:
+                return absolute_tolerance
+
+        # Figure out what the relative tolerance should be.  ``self.rel`` is
+        # either None or a value specified by the user.  This is done after
+        # we've made sure the user didn't ask for an absolute tolerance only,
+        # because we don't want to raise errors about the relative tolerance if
+        # we aren't even going to use it.
+        relative_tolerance = set_default(self.rel, 1e-6) * abs(self.expected)
+
+        if relative_tolerance < 0:
+            raise ValueError("relative tolerance can't be negative: {0}".format(absolute_tolerance))
+        if math.isnan(relative_tolerance):
+            raise ValueError("relative tolerance can't be NaN.")
+
+        # Return the larger of the relative and absolute tolerances.
+        return max(relative_tolerance, absolute_tolerance)
+
+
+def approx(expected, rel=None, abs=None, nan_ok=False):
+    """
+    Assert that two numbers (or two sets of numbers) are equal to each other
+    within some tolerance.
+
+    Due to the `intricacies of floating-point arithmetic`__, numbers that we
+    would intuitively expect to be equal are not always so::
+
+        >>> 0.1 + 0.2 == 0.3
+        False
+
+    __ https://docs.python.org/3/tutorial/floatingpoint.html
+
+    This problem is commonly encountered when writing tests, e.g. when making
+    sure that floating-point values are what you expect them to be.  One way to
+    deal with this problem is to assert that two floating-point numbers are
+    equal to within some appropriate tolerance::
+
+        >>> abs((0.1 + 0.2) - 0.3) < 1e-6
+        True
+
+    However, comparisons like this are tedious to write and difficult to
+    understand.  Furthermore, absolute comparisons like the one above are
+    usually discouraged because there's no tolerance that works well for all
+    situations.  ``1e-6`` is good for numbers around ``1``, but too small for
+    very big numbers and too big for very small ones.  It's better to express
+    the tolerance as a fraction of the expected value, but relative comparisons
+    like that are even more difficult to write correctly and concisely.
+
+    The ``approx`` class performs floating-point comparisons using a syntax
+    that's as intuitive as possible::
+
+        >>> from pytest import approx
+        >>> 0.1 + 0.2 == approx(0.3)
+        True
+
+    The same syntax also works for sequences of numbers::
+
+        >>> (0.1 + 0.2, 0.2 + 0.4) == approx((0.3, 0.6))
+        True
+
+    Dictionary *values*::
+
+        >>> {'a': 0.1 + 0.2, 'b': 0.2 + 0.4} == approx({'a': 0.3, 'b': 0.6})
+        True
+
+    And ``numpy`` arrays::
+
+        >>> import numpy as np                                                          # doctest: +SKIP
+        >>> np.array([0.1, 0.2]) + np.array([0.2, 0.4]) == approx(np.array([0.3, 0.6])) # doctest: +SKIP
+        True
+
+    By default, ``approx`` considers numbers within a relative tolerance of
+    ``1e-6`` (i.e. one part in a million) of its expected value to be equal.
+    This treatment would lead to surprising results if the expected value was
+    ``0.0``, because nothing but ``0.0`` itself is relatively close to ``0.0``.
+    To handle this case less surprisingly, ``approx`` also considers numbers
+    within an absolute tolerance of ``1e-12`` of its expected value to be
+    equal.  Infinity and NaN are special cases.  Infinity is only considered
+    equal to itself, regardless of the relative tolerance.  NaN is not
+    considered equal to anything by default, but you can make it be equal to
+    itself by setting the ``nan_ok`` argument to True.  (This is meant to
+    facilitate comparing arrays that use NaN to mean "no data".)
+
+    Both the relative and absolute tolerances can be changed by passing
+    arguments to the ``approx`` constructor::
+
+        >>> 1.0001 == approx(1)
+        False
+        >>> 1.0001 == approx(1, rel=1e-3)
+        True
+        >>> 1.0001 == approx(1, abs=1e-3)
+        True
+
+    If you specify ``abs`` but not ``rel``, the comparison will not consider
+    the relative tolerance at all.  In other words, two numbers that are within
+    the default relative tolerance of ``1e-6`` will still be considered unequal
+    if they exceed the specified absolute tolerance.  If you specify both
+    ``abs`` and ``rel``, the numbers will be considered equal if either
+    tolerance is met::
+
+        >>> 1 + 1e-8 == approx(1)
+        True
+        >>> 1 + 1e-8 == approx(1, abs=1e-12)
+        False
+        >>> 1 + 1e-8 == approx(1, rel=1e-6, abs=1e-12)
+        True
+
+    If you're thinking about using ``approx``, then you might want to know how
+    it compares to other good ways of comparing floating-point numbers.  All of
+    these algorithms are based on relative and absolute tolerances and should
+    agree for the most part, but they do have meaningful differences:
+
+    - ``math.isclose(a, b, rel_tol=1e-9, abs_tol=0.0)``:  True if the relative
+      tolerance is met w.r.t. either ``a`` or ``b`` or if the absolute
+      tolerance is met.  Because the relative tolerance is calculated w.r.t.
+      both ``a`` and ``b``, this test is symmetric (i.e.  neither ``a`` nor
+      ``b`` is a "reference value").  You have to specify an absolute tolerance
+      if you want to compare to ``0.0`` because there is no tolerance by
+      default.  Only available in python>=3.5.  `More information...`__
+
+      __ https://docs.python.org/3/library/math.html#math.isclose
+
+    - ``numpy.isclose(a, b, rtol=1e-5, atol=1e-8)``: True if the difference
+      between ``a`` and ``b`` is less that the sum of the relative tolerance
+      w.r.t. ``b`` and the absolute tolerance.  Because the relative tolerance
+      is only calculated w.r.t. ``b``, this test is asymmetric and you can
+      think of ``b`` as the reference value.  Support for comparing sequences
+      is provided by ``numpy.allclose``.  `More information...`__
+
+      __ http://docs.scipy.org/doc/numpy-1.10.0/reference/generated/numpy.isclose.html
+
+    - ``unittest.TestCase.assertAlmostEqual(a, b)``: True if ``a`` and ``b``
+      are within an absolute tolerance of ``1e-7``.  No relative tolerance is
+      considered and the absolute tolerance cannot be changed, so this function
+      is not appropriate for very large or very small numbers.  Also, it's only
+      available in subclasses of ``unittest.TestCase`` and it's ugly because it
+      doesn't follow PEP8.  `More information...`__
+
+      __ https://docs.python.org/3/library/unittest.html#unittest.TestCase.assertAlmostEqual
+
+    - ``a == pytest.approx(b, rel=1e-6, abs=1e-12)``: True if the relative
+      tolerance is met w.r.t. ``b`` or if the absolute tolerance is met.
+      Because the relative tolerance is only calculated w.r.t. ``b``, this test
+      is asymmetric and you can think of ``b`` as the reference value.  In the
+      special case that you explicitly specify an absolute tolerance but not a
+      relative tolerance, only the absolute tolerance is considered.
+
+    .. warning::
+
+       .. versionchanged:: 3.2
+
+       In order to avoid inconsistent behavior, ``TypeError`` is
+       raised for ``>``, ``>=``, ``<`` and ``<=`` comparisons.
+       The example below illustrates the problem::
+
+           assert approx(0.1) > 0.1 + 1e-10  # calls approx(0.1).__gt__(0.1 + 1e-10)
+           assert 0.1 + 1e-10 > approx(0.1)  # calls approx(0.1).__lt__(0.1 + 1e-10)
+
+       In the second example one expects ``approx(0.1).__le__(0.1 + 1e-10)``
+       to be called. But instead, ``approx(0.1).__lt__(0.1 + 1e-10)`` is used to
+       comparison. This is because the call hierarchy of rich comparisons
+       follows a fixed behavior. `More information...`__
+
+       __ https://docs.python.org/3/reference/datamodel.html#object.__ge__
+    """
+
+    from collections import Mapping, Sequence
+    from _pytest.compat import STRING_TYPES as String
+
+    # Delegate the comparison to a class that knows how to deal with the type
+    # of the expected value (e.g. int, float, list, dict, numpy.array, etc).
+    #
+    # This architecture is really driven by the need to support numpy arrays.
+    # The only way to override `==` for arrays without requiring that approx be
+    # the left operand is to inherit the approx object from `numpy.ndarray`.
+    # But that can't be a general solution, because it requires (1) numpy to be
+    # installed and (2) the expected value to be a numpy array.  So the general
+    # solution is to delegate each type of expected value to a different class.
+    #
+    # This has the advantage that it made it easy to support mapping types
+    # (i.e. dict).  The old code accepted mapping types, but would only compare
+    # their keys, which is probably not what most people would expect.
+
+    if _is_numpy_array(expected):
+        cls = ApproxNumpy
+    elif isinstance(expected, Mapping):
+        cls = ApproxMapping
+    elif isinstance(expected, Sequence) and not isinstance(expected, String):
+        cls = ApproxSequence
+    else:
+        cls = ApproxScalar
+
+    return cls(expected, rel, abs, nan_ok)
+
+
+def _is_numpy_array(obj):
+    """
+    Return true if the given object is a numpy array.  Make a special effort to
+    avoid importing numpy unless it's really necessary.
+    """
+    import inspect
+
+    for cls in inspect.getmro(type(obj)):
+        if cls.__module__ == 'numpy':
+            try:
+                import numpy as np
+                return isinstance(obj, np.ndarray)
+            except ImportError:
+                pass
+
+    return False
+
+
+# builtin pytest.raises helper
+
+def raises(expected_exception, *args, **kwargs):
+    """
+    Assert that a code block/function call raises ``expected_exception``
+    and raise a failure exception otherwise.
+
+    This helper produces a ``ExceptionInfo()`` object (see below).
+
+    If using Python 2.5 or above, you may use this function as a
+    context manager::
+
+        >>> with raises(ZeroDivisionError):
+        ...    1/0
+
+    .. versionchanged:: 2.10
+
+    In the context manager form you may use the keyword argument
+    ``message`` to specify a custom failure message::
+
+        >>> with raises(ZeroDivisionError, message="Expecting ZeroDivisionError"):
+        ...    pass
+        Traceback (most recent call last):
+          ...
+        Failed: Expecting ZeroDivisionError
+
+    .. note::
+
+       When using ``pytest.raises`` as a context manager, it's worthwhile to
+       note that normal context manager rules apply and that the exception
+       raised *must* be the final line in the scope of the context manager.
+       Lines of code after that, within the scope of the context manager will
+       not be executed. For example::
+
+           >>> value = 15
+           >>> with raises(ValueError) as exc_info:
+           ...     if value > 10:
+           ...         raise ValueError("value must be <= 10")
+           ...     assert exc_info.type == ValueError  # this will not execute
+
+       Instead, the following approach must be taken (note the difference in
+       scope)::
+
+           >>> with raises(ValueError) as exc_info:
+           ...     if value > 10:
+           ...         raise ValueError("value must be <= 10")
+           ...
+           >>> assert exc_info.type == ValueError
+
+
+    Since version ``3.1`` you can use the keyword argument ``match`` to assert that the
+    exception matches a text or regex::
+
+        >>> with raises(ValueError, match='must be 0 or None'):
+        ...     raise ValueError("value must be 0 or None")
+
+        >>> with raises(ValueError, match=r'must be \d+$'):
+        ...     raise ValueError("value must be 42")
+
+    **Legacy forms**
+
+    The forms below are fully supported but are discouraged for new code because the
+    context manager form is regarded as more readable and less error-prone.
+
+    It is possible to specify a callable by passing a to-be-called lambda::
+
+        >>> raises(ZeroDivisionError, lambda: 1/0)
+        <ExceptionInfo ...>
+
+    or you can specify an arbitrary callable with arguments::
+
+        >>> def f(x): return 1/x
+        ...
+        >>> raises(ZeroDivisionError, f, 0)
+        <ExceptionInfo ...>
+        >>> raises(ZeroDivisionError, f, x=0)
+        <ExceptionInfo ...>
+
+    It is also possible to pass a string to be evaluated at runtime::
+
+        >>> raises(ZeroDivisionError, "f(0)")
+        <ExceptionInfo ...>
+
+    The string will be evaluated using the same ``locals()`` and ``globals()``
+    at the moment of the ``raises`` call.
+
+    .. autoclass:: _pytest._code.ExceptionInfo
+        :members:
+
+    .. note::
+        Similar to caught exception objects in Python, explicitly clearing
+        local references to returned ``ExceptionInfo`` objects can
+        help the Python interpreter speed up its garbage collection.
+
+        Clearing those references breaks a reference cycle
+        (``ExceptionInfo`` --> caught exception --> frame stack raising
+        the exception --> current frame stack --> local variables -->
+        ``ExceptionInfo``) which makes Python keep all objects referenced
+        from that cycle (including all local variables in the current
+        frame) alive until the next cyclic garbage collection run. See the
+        official Python ``try`` statement documentation for more detailed
+        information.
+
+    """
+    __tracebackhide__ = True
+    msg = ("exceptions must be old-style classes or"
+           " derived from BaseException, not %s")
+    if isinstance(expected_exception, tuple):
+        for exc in expected_exception:
+            if not isclass(exc):
+                raise TypeError(msg % type(exc))
+    elif not isclass(expected_exception):
+        raise TypeError(msg % type(expected_exception))
+
+    message = "DID NOT RAISE {0}".format(expected_exception)
+    match_expr = None
+
+    if not args:
+        if "message" in kwargs:
+            message = kwargs.pop("message")
+        if "match" in kwargs:
+            match_expr = kwargs.pop("match")
+            message += " matching '{0}'".format(match_expr)
+        return RaisesContext(expected_exception, message, match_expr)
+    elif isinstance(args[0], str):
+        code, = args
+        assert isinstance(code, str)
+        frame = sys._getframe(1)
+        loc = frame.f_locals.copy()
+        loc.update(kwargs)
+        # print "raises frame scope: %r" % frame.f_locals
+        try:
+            code = _pytest._code.Source(code).compile()
+            py.builtin.exec_(code, frame.f_globals, loc)
+            # XXX didn'T mean f_globals == f_locals something special?
+            #     this is destroyed here ...
+        except expected_exception:
+            return _pytest._code.ExceptionInfo()
+    else:
+        func = args[0]
+        try:
+            func(*args[1:], **kwargs)
+        except expected_exception:
+            return _pytest._code.ExceptionInfo()
+    fail(message)
+
+
+raises.Exception = fail.Exception
+
+
+class RaisesContext(object):
+    def __init__(self, expected_exception, message, match_expr):
+        self.expected_exception = expected_exception
+        self.message = message
+        self.match_expr = match_expr
+        self.excinfo = None
+
+    def __enter__(self):
+        self.excinfo = object.__new__(_pytest._code.ExceptionInfo)
+        return self.excinfo
+
+    def __exit__(self, *tp):
+        __tracebackhide__ = True
+        if tp[0] is None:
+            fail(self.message)
+        if sys.version_info < (2, 7):
+            # py26: on __exit__() exc_value often does not contain the
+            # exception value.
+            # http://bugs.python.org/issue7853
+            if not isinstance(tp[1], BaseException):
+                exc_type, value, traceback = tp
+                tp = exc_type, exc_type(value), traceback
+        self.excinfo.__init__(tp)
+        suppress_exception = issubclass(self.excinfo.type, self.expected_exception)
+        if sys.version_info[0] == 2 and suppress_exception:
+            sys.exc_clear()
+        if self.match_expr:
+            self.excinfo.match(self.match_expr)
+        return suppress_exception
diff --git a/lib/spack/external/_pytest/recwarn.py b/lib/spack/external/_pytest/recwarn.py
index 87823bfbc6..c9fa872c07 100644
--- a/lib/spack/external/_pytest/recwarn.py
+++ b/lib/spack/external/_pytest/recwarn.py
@@ -1,4 +1,5 @@
 """ recording warnings during test function execution. """
+from __future__ import absolute_import, division, print_function
 
 import inspect
 
@@ -6,11 +7,13 @@ import _pytest._code
 import py
 import sys
 import warnings
-import pytest
 
+from _pytest.fixtures import yield_fixture
+from _pytest.outcomes import fail
 
-@pytest.yield_fixture
-def recwarn(request):
+
+@yield_fixture
+def recwarn():
     """Return a WarningsRecorder instance that provides these methods:
 
     * ``pop(category=None)``: return last warning matching the category.
@@ -25,16 +28,9 @@ def recwarn(request):
         yield wrec
 
 
-def pytest_namespace():
-    return {'deprecated_call': deprecated_call,
-            'warns': warns}
-
-
 def deprecated_call(func=None, *args, **kwargs):
-    """ assert that calling ``func(*args, **kwargs)`` triggers a
-    ``DeprecationWarning`` or ``PendingDeprecationWarning``.
-
-    This function can be used as a context manager::
+    """context manager that can be used to ensure a block of code triggers a
+    ``DeprecationWarning`` or ``PendingDeprecationWarning``::
 
         >>> import warnings
         >>> def api_call_v2():
@@ -44,40 +40,47 @@ def deprecated_call(func=None, *args, **kwargs):
         >>> with deprecated_call():
         ...    assert api_call_v2() == 200
 
-    Note: we cannot use WarningsRecorder here because it is still subject
-    to the mechanism that prevents warnings of the same type from being
-    triggered twice for the same module. See #1190.
+    ``deprecated_call`` can also be used by passing a function and ``*args`` and ``*kwargs``,
+    in which case it will ensure calling ``func(*args, **kwargs)`` produces one of the warnings
+    types above.
     """
     if not func:
-        return WarningsChecker(expected_warning=DeprecationWarning)
+        return _DeprecatedCallContext()
+    else:
+        __tracebackhide__ = True
+        with _DeprecatedCallContext():
+            return func(*args, **kwargs)
+
 
-    categories = []
+class _DeprecatedCallContext(object):
+    """Implements the logic to capture deprecation warnings as a context manager."""
 
-    def warn_explicit(message, category, *args, **kwargs):
-        categories.append(category)
-        old_warn_explicit(message, category, *args, **kwargs)
+    def __enter__(self):
+        self._captured_categories = []
+        self._old_warn = warnings.warn
+        self._old_warn_explicit = warnings.warn_explicit
+        warnings.warn_explicit = self._warn_explicit
+        warnings.warn = self._warn
 
-    def warn(message, category=None, *args, **kwargs):
+    def _warn_explicit(self, message, category, *args, **kwargs):
+        self._captured_categories.append(category)
+
+    def _warn(self, message, category=None, *args, **kwargs):
         if isinstance(message, Warning):
-            categories.append(message.__class__)
+            self._captured_categories.append(message.__class__)
         else:
-            categories.append(category)
-        old_warn(message, category, *args, **kwargs)
-
-    old_warn = warnings.warn
-    old_warn_explicit = warnings.warn_explicit
-    warnings.warn_explicit = warn_explicit
-    warnings.warn = warn
-    try:
-        ret = func(*args, **kwargs)
-    finally:
-        warnings.warn_explicit = old_warn_explicit
-        warnings.warn = old_warn
-    deprecation_categories = (DeprecationWarning, PendingDeprecationWarning)
-    if not any(issubclass(c, deprecation_categories) for c in categories):
-        __tracebackhide__ = True
-        raise AssertionError("%r did not produce DeprecationWarning" % (func,))
-    return ret
+            self._captured_categories.append(category)
+
+    def __exit__(self, exc_type, exc_val, exc_tb):
+        warnings.warn_explicit = self._old_warn_explicit
+        warnings.warn = self._old_warn
+
+        if exc_type is None:
+            deprecation_categories = (DeprecationWarning, PendingDeprecationWarning)
+            if not any(issubclass(c, deprecation_categories) for c in self._captured_categories):
+                __tracebackhide__ = True
+                msg = "Did not produce DeprecationWarning or PendingDeprecationWarning"
+                raise AssertionError(msg)
 
 
 def warns(expected_warning, *args, **kwargs):
@@ -115,24 +118,14 @@ def warns(expected_warning, *args, **kwargs):
             return func(*args[1:], **kwargs)
 
 
-class RecordedWarning(object):
-    def __init__(self, message, category, filename, lineno, file, line):
-        self.message = message
-        self.category = category
-        self.filename = filename
-        self.lineno = lineno
-        self.file = file
-        self.line = line
-
-
-class WarningsRecorder(object):
+class WarningsRecorder(warnings.catch_warnings):
     """A context manager to record raised warnings.
 
     Adapted from `warnings.catch_warnings`.
     """
 
-    def __init__(self, module=None):
-        self._module = sys.modules['warnings'] if module is None else module
+    def __init__(self):
+        super(WarningsRecorder, self).__init__(record=True)
         self._entered = False
         self._list = []
 
@@ -169,38 +162,20 @@ class WarningsRecorder(object):
         if self._entered:
             __tracebackhide__ = True
             raise RuntimeError("Cannot enter %r twice" % self)
-        self._entered = True
-        self._filters = self._module.filters
-        self._module.filters = self._filters[:]
-        self._showwarning = self._module.showwarning
-
-        def showwarning(message, category, filename, lineno,
-                        file=None, line=None):
-            self._list.append(RecordedWarning(
-                message, category, filename, lineno, file, line))
-
-            # still perform old showwarning functionality
-            self._showwarning(
-                message, category, filename, lineno, file=file, line=line)
-
-        self._module.showwarning = showwarning
-
-        # allow the same warning to be raised more than once
-
-        self._module.simplefilter('always')
+        self._list = super(WarningsRecorder, self).__enter__()
+        warnings.simplefilter('always')
         return self
 
     def __exit__(self, *exc_info):
         if not self._entered:
             __tracebackhide__ = True
             raise RuntimeError("Cannot exit %r without entering first" % self)
-        self._module.filters = self._filters
-        self._module.showwarning = self._showwarning
+        super(WarningsRecorder, self).__exit__(*exc_info)
 
 
 class WarningsChecker(WarningsRecorder):
-    def __init__(self, expected_warning=None, module=None):
-        super(WarningsChecker, self).__init__(module=module)
+    def __init__(self, expected_warning=None):
+        super(WarningsChecker, self).__init__()
 
         msg = ("exceptions must be old-style classes or "
                "derived from Warning, not %s")
@@ -221,6 +196,10 @@ class WarningsChecker(WarningsRecorder):
         # only check if we're not currently handling an exception
         if all(a is None for a in exc_info):
             if self.expected_warning is not None:
-                if not any(r.category in self.expected_warning for r in self):
+                if not any(issubclass(r.category, self.expected_warning)
+                           for r in self):
                     __tracebackhide__ = True
-                    pytest.fail("DID NOT WARN")
+                    fail("DID NOT WARN. No warnings of type {0} was emitted. "
+                         "The list of emitted warnings is: {1}.".format(
+                             self.expected_warning,
+                             [each.message for each in self]))
diff --git a/lib/spack/external/_pytest/resultlog.py b/lib/spack/external/_pytest/resultlog.py
index fc00259834..9f9c2d1f65 100644
--- a/lib/spack/external/_pytest/resultlog.py
+++ b/lib/spack/external/_pytest/resultlog.py
@@ -1,15 +1,18 @@
 """ log machine-parseable test session result information in a plain
 text file.
 """
+from __future__ import absolute_import, division, print_function
 
 import py
 import os
 
+
 def pytest_addoption(parser):
     group = parser.getgroup("terminal reporting", "resultlog plugin options")
     group.addoption('--resultlog', '--result-log', action="store",
-        metavar="path", default=None,
-        help="DEPRECATED path for machine-readable result log.")
+                    metavar="path", default=None,
+                    help="DEPRECATED path for machine-readable result log.")
+
 
 def pytest_configure(config):
     resultlog = config.option.resultlog
@@ -18,13 +21,14 @@ def pytest_configure(config):
         dirname = os.path.dirname(os.path.abspath(resultlog))
         if not os.path.isdir(dirname):
             os.makedirs(dirname)
-        logfile = open(resultlog, 'w', 1) # line buffered
+        logfile = open(resultlog, 'w', 1)  # line buffered
         config._resultlog = ResultLog(config, logfile)
         config.pluginmanager.register(config._resultlog)
 
         from _pytest.deprecated import RESULT_LOG
         config.warn('C1', RESULT_LOG)
 
+
 def pytest_unconfigure(config):
     resultlog = getattr(config, '_resultlog', None)
     if resultlog:
@@ -32,6 +36,7 @@ def pytest_unconfigure(config):
         del config._resultlog
         config.pluginmanager.unregister(resultlog)
 
+
 def generic_path(item):
     chain = item.listchain()
     gpath = [chain[0].name]
@@ -55,15 +60,16 @@ def generic_path(item):
         fspath = newfspath
     return ''.join(gpath)
 
+
 class ResultLog(object):
     def __init__(self, config, logfile):
         self.config = config
-        self.logfile = logfile # preferably line buffered
+        self.logfile = logfile  # preferably line buffered
 
     def write_log_entry(self, testpath, lettercode, longrepr):
-        py.builtin.print_("%s %s" % (lettercode, testpath), file=self.logfile)
+        print("%s %s" % (lettercode, testpath), file=self.logfile)
         for line in longrepr.splitlines():
-            py.builtin.print_(" %s" % line, file=self.logfile)
+            print(" %s" % line, file=self.logfile)
 
     def log_outcome(self, report, lettercode, longrepr):
         testpath = getattr(report, 'nodeid', None)
diff --git a/lib/spack/external/_pytest/runner.py b/lib/spack/external/_pytest/runner.py
index eb29e7370c..b643fa3c91 100644
--- a/lib/spack/external/_pytest/runner.py
+++ b/lib/spack/external/_pytest/runner.py
@@ -1,29 +1,26 @@
 """ basic collect and runtest protocol implementations """
+from __future__ import absolute_import, division, print_function
+
 import bdb
+import os
 import sys
 from time import time
 
 import py
-import pytest
+from _pytest.compat import _PY2
 from _pytest._code.code import TerminalRepr, ExceptionInfo
-
-
-def pytest_namespace():
-    return {
-        'fail'         : fail,
-        'skip'         : skip,
-        'importorskip' : importorskip,
-        'exit'         : exit,
-    }
+from _pytest.outcomes import skip, Skipped, TEST_OUTCOME
 
 #
 # pytest plugin hooks
 
+
 def pytest_addoption(parser):
     group = parser.getgroup("terminal reporting", "reporting", after="general")
     group.addoption('--durations',
-         action="store", type=int, default=None, metavar="N",
-         help="show N slowest setup/test durations (N=0 for all)."),
+                    action="store", type=int, default=None, metavar="N",
+                    help="show N slowest setup/test durations (N=0 for all)."),
+
 
 def pytest_terminal_summary(terminalreporter):
     durations = terminalreporter.config.option.durations
@@ -48,16 +45,16 @@ def pytest_terminal_summary(terminalreporter):
     for rep in dlist:
         nodeid = rep.nodeid.replace("::()::", "::")
         tr.write_line("%02.2fs %-8s %s" %
-            (rep.duration, rep.when, nodeid))
+                      (rep.duration, rep.when, nodeid))
+
 
 def pytest_sessionstart(session):
     session._setupstate = SetupState()
+
+
 def pytest_sessionfinish(session):
     session._setupstate.teardown_all()
 
-class NodeInfo:
-    def __init__(self, location):
-        self.location = location
 
 def pytest_runtest_protocol(item, nextitem):
     item.ihook.pytest_runtest_logstart(
@@ -66,6 +63,7 @@ def pytest_runtest_protocol(item, nextitem):
     runtestprotocol(item, nextitem=nextitem)
     return True
 
+
 def runtestprotocol(item, log=True, nextitem=None):
     hasrequest = hasattr(item, "_request")
     if hasrequest and not item._request:
@@ -78,7 +76,7 @@ def runtestprotocol(item, log=True, nextitem=None):
         if not item.config.option.setuponly:
             reports.append(call_and_report(item, "call", log))
     reports.append(call_and_report(item, "teardown", log,
-        nextitem=nextitem))
+                                   nextitem=nextitem))
     # after all teardown hooks have been called
     # want funcargs and request info to go away
     if hasrequest:
@@ -86,6 +84,7 @@ def runtestprotocol(item, log=True, nextitem=None):
         item.funcargs = None
     return reports
 
+
 def show_test_item(item):
     """Show test function, parameters and the fixtures of the test item."""
     tw = item.config.get_terminal_writer()
@@ -96,10 +95,14 @@ def show_test_item(item):
     if used_fixtures:
         tw.write(' (fixtures used: {0})'.format(', '.join(used_fixtures)))
 
+
 def pytest_runtest_setup(item):
+    _update_current_test_var(item, 'setup')
     item.session._setupstate.prepare(item)
 
+
 def pytest_runtest_call(item):
+    _update_current_test_var(item, 'call')
     try:
         item.runtest()
     except Exception:
@@ -112,8 +115,29 @@ def pytest_runtest_call(item):
         del tb  # Get rid of it in this namespace
         raise
 
+
 def pytest_runtest_teardown(item, nextitem):
+    _update_current_test_var(item, 'teardown')
     item.session._setupstate.teardown_exact(item, nextitem)
+    _update_current_test_var(item, None)
+
+
+def _update_current_test_var(item, when):
+    """
+    Update PYTEST_CURRENT_TEST to reflect the current item and stage.
+
+    If ``when`` is None, delete PYTEST_CURRENT_TEST from the environment.
+    """
+    var_name = 'PYTEST_CURRENT_TEST'
+    if when:
+        value = '{0} ({1})'.format(item.nodeid, when)
+        if _PY2:
+            # python 2 doesn't like null bytes on environment variables (see #2644)
+            value = value.replace('\x00', '(null)')
+        os.environ[var_name] = value
+    else:
+        os.environ.pop(var_name)
+
 
 def pytest_report_teststatus(report):
     if report.when in ("setup", "teardown"):
@@ -139,21 +163,25 @@ def call_and_report(item, when, log=True, **kwds):
         hook.pytest_exception_interact(node=item, call=call, report=report)
     return report
 
+
 def check_interactive_exception(call, report):
     return call.excinfo and not (
-                hasattr(report, "wasxfail") or
-                call.excinfo.errisinstance(skip.Exception) or
-                call.excinfo.errisinstance(bdb.BdbQuit))
+        hasattr(report, "wasxfail") or
+        call.excinfo.errisinstance(skip.Exception) or
+        call.excinfo.errisinstance(bdb.BdbQuit))
+
 
 def call_runtest_hook(item, when, **kwds):
     hookname = "pytest_runtest_" + when
     ihook = getattr(item.ihook, hookname)
     return CallInfo(lambda: ihook(item=item, **kwds), when=when)
 
+
 class CallInfo:
     """ Result/Exception info a function invocation. """
     #: None or ExceptionInfo object.
     excinfo = None
+
     def __init__(self, func, when):
         #: context of invocation: one of "setup", "call",
         #: "teardown", "memocollect"
@@ -164,7 +192,7 @@ class CallInfo:
         except KeyboardInterrupt:
             self.stop = time()
             raise
-        except:
+        except:  # noqa
             self.excinfo = ExceptionInfo()
         self.stop = time()
 
@@ -175,6 +203,7 @@ class CallInfo:
             status = "result: %r" % (self.result,)
         return "<CallInfo when=%r %s>" % (self.when, status)
 
+
 def getslaveinfoline(node):
     try:
         return node._slaveinfocache
@@ -185,6 +214,7 @@ def getslaveinfoline(node):
             d['id'], d['sysplatform'], ver, d['executable'])
         return s
 
+
 class BaseReport(object):
 
     def __init__(self, **kw):
@@ -249,10 +279,11 @@ class BaseReport(object):
     def fspath(self):
         return self.nodeid.split("::")[0]
 
+
 def pytest_runtest_makereport(item, call):
     when = call.when
-    duration = call.stop-call.start
-    keywords = dict([(x,1) for x in item.keywords])
+    duration = call.stop - call.start
+    keywords = dict([(x, 1) for x in item.keywords])
     excinfo = call.excinfo
     sections = []
     if not call.excinfo:
@@ -262,7 +293,7 @@ def pytest_runtest_makereport(item, call):
         if not isinstance(excinfo, ExceptionInfo):
             outcome = "failed"
             longrepr = excinfo
-        elif excinfo.errisinstance(pytest.skip.Exception):
+        elif excinfo.errisinstance(skip.Exception):
             outcome = "skipped"
             r = excinfo._getreprcrash()
             longrepr = (str(r.path), r.lineno, r.message)
@@ -270,19 +301,21 @@ def pytest_runtest_makereport(item, call):
             outcome = "failed"
             if call.when == "call":
                 longrepr = item.repr_failure(excinfo)
-            else: # exception in setup or teardown
+            else:  # exception in setup or teardown
                 longrepr = item._repr_failure_py(excinfo,
-                                            style=item.config.option.tbstyle)
+                                                 style=item.config.option.tbstyle)
     for rwhen, key, content in item._report_sections:
-        sections.append(("Captured %s %s" %(key, rwhen), content))
+        sections.append(("Captured %s %s" % (key, rwhen), content))
     return TestReport(item.nodeid, item.location,
                       keywords, outcome, longrepr, when,
                       sections, duration)
 
+
 class TestReport(BaseReport):
     """ Basic test report object (also used for setup and teardown calls if
     they fail).
     """
+
     def __init__(self, nodeid, location, keywords, outcome,
                  longrepr, when, sections=(), duration=0, **extra):
         #: normalized collection node id
@@ -321,16 +354,21 @@ class TestReport(BaseReport):
         return "<TestReport %r when=%r outcome=%r>" % (
             self.nodeid, self.when, self.outcome)
 
+
 class TeardownErrorReport(BaseReport):
     outcome = "failed"
     when = "teardown"
+
     def __init__(self, longrepr, **extra):
         self.longrepr = longrepr
         self.sections = []
         self.__dict__.update(extra)
 
+
 def pytest_make_collect_report(collector):
-    call = CallInfo(collector._memocollect, "memocollect")
+    call = CallInfo(
+        lambda: list(collector.collect()),
+        'collect')
     longrepr = None
     if not call.excinfo:
         outcome = "passed"
@@ -348,7 +386,7 @@ def pytest_make_collect_report(collector):
                 errorinfo = CollectErrorRepr(errorinfo)
             longrepr = errorinfo
     rep = CollectReport(collector.nodeid, outcome, longrepr,
-        getattr(call, 'result', None))
+                        getattr(call, 'result', None))
     rep.call = call  # see collect_one_node
     return rep
 
@@ -369,16 +407,20 @@ class CollectReport(BaseReport):
 
     def __repr__(self):
         return "<CollectReport %r lenresult=%s outcome=%r>" % (
-                self.nodeid, len(self.result), self.outcome)
+            self.nodeid, len(self.result), self.outcome)
+
 
 class CollectErrorRepr(TerminalRepr):
     def __init__(self, msg):
         self.longrepr = msg
+
     def toterminal(self, out):
         out.line(self.longrepr, red=True)
 
+
 class SetupState(object):
     """ shared state for setting up/tearing down test items or collectors. """
+
     def __init__(self):
         self.stack = []
         self._finalizers = {}
@@ -390,7 +432,7 @@ class SetupState(object):
         """
         assert colitem and not isinstance(colitem, tuple)
         assert py.builtin.callable(finalizer)
-        #assert colitem in self.stack  # some unit tests don't setup stack :/
+        # assert colitem in self.stack  # some unit tests don't setup stack :/
         self._finalizers.setdefault(colitem, []).append(finalizer)
 
     def _pop_and_teardown(self):
@@ -404,7 +446,7 @@ class SetupState(object):
             fin = finalizers.pop()
             try:
                 fin()
-            except Exception:
+            except TEST_OUTCOME:
                 # XXX Only first exception will be seen by user,
                 #     ideally all should be reported.
                 if exc is None:
@@ -418,7 +460,7 @@ class SetupState(object):
             colitem.teardown()
         for colitem in self._finalizers:
             assert colitem is None or colitem in self.stack \
-             or isinstance(colitem, tuple)
+                or isinstance(colitem, tuple)
 
     def teardown_all(self):
         while self.stack:
@@ -451,10 +493,11 @@ class SetupState(object):
             self.stack.append(col)
             try:
                 col.setup()
-            except Exception:
+            except TEST_OUTCOME:
                 col._prepare_exc = sys.exc_info()
                 raise
 
+
 def collect_one_node(collector):
     ihook = collector.ihook
     ihook.pytest_collectstart(collector=collector)
@@ -463,116 +506,3 @@ def collect_one_node(collector):
     if call and check_interactive_exception(call, rep):
         ihook.pytest_exception_interact(node=collector, call=call, report=rep)
     return rep
-
-
-# =============================================================
-# Test OutcomeExceptions and helpers for creating them.
-
-
-class OutcomeException(Exception):
-    """ OutcomeException and its subclass instances indicate and
-        contain info about test and collection outcomes.
-    """
-    def __init__(self, msg=None, pytrace=True):
-        Exception.__init__(self, msg)
-        self.msg = msg
-        self.pytrace = pytrace
-
-    def __repr__(self):
-        if self.msg:
-            val = self.msg
-            if isinstance(val, bytes):
-                val = py._builtin._totext(val, errors='replace')
-            return val
-        return "<%s instance>" %(self.__class__.__name__,)
-    __str__ = __repr__
-
-class Skipped(OutcomeException):
-    # XXX hackish: on 3k we fake to live in the builtins
-    # in order to have Skipped exception printing shorter/nicer
-    __module__ = 'builtins'
-
-    def __init__(self, msg=None, pytrace=True, allow_module_level=False):
-        OutcomeException.__init__(self, msg=msg, pytrace=pytrace)
-        self.allow_module_level = allow_module_level
-
-
-class Failed(OutcomeException):
-    """ raised from an explicit call to pytest.fail() """
-    __module__ = 'builtins'
-
-
-class Exit(KeyboardInterrupt):
-    """ raised for immediate program exits (no tracebacks/summaries)"""
-    def __init__(self, msg="unknown reason"):
-        self.msg = msg
-        KeyboardInterrupt.__init__(self, msg)
-
-# exposed helper methods
-
-def exit(msg):
-    """ exit testing process as if KeyboardInterrupt was triggered. """
-    __tracebackhide__ = True
-    raise Exit(msg)
-
-
-exit.Exception = Exit
-
-
-def skip(msg=""):
-    """ skip an executing test with the given message.  Note: it's usually
-    better to use the pytest.mark.skipif marker to declare a test to be
-    skipped under certain conditions like mismatching platforms or
-    dependencies.  See the pytest_skipping plugin for details.
-    """
-    __tracebackhide__ = True
-    raise Skipped(msg=msg)
-
-
-skip.Exception = Skipped
-
-
-def fail(msg="", pytrace=True):
-    """ explicitly fail an currently-executing test with the given Message.
-
-    :arg pytrace: if false the msg represents the full failure information
-                  and no python traceback will be reported.
-    """
-    __tracebackhide__ = True
-    raise Failed(msg=msg, pytrace=pytrace)
-
-
-fail.Exception = Failed
-
-
-def importorskip(modname, minversion=None):
-    """ return imported module if it has at least "minversion" as its
-    __version__ attribute.  If no minversion is specified the a skip
-    is only triggered if the module can not be imported.
-    """
-    __tracebackhide__ = True
-    compile(modname, '', 'eval') # to catch syntaxerrors
-    should_skip = False
-    try:
-        __import__(modname)
-    except ImportError:
-        # Do not raise chained exception here(#1485)
-        should_skip = True
-    if should_skip:
-        raise Skipped("could not import %r" %(modname,), allow_module_level=True)
-    mod = sys.modules[modname]
-    if minversion is None:
-        return mod
-    verattr = getattr(mod, '__version__', None)
-    if minversion is not None:
-        try:
-            from pkg_resources import parse_version as pv
-        except ImportError:
-            raise Skipped("we have a required version for %r but can not import "
-                          "pkg_resources to parse version strings." % (modname,),
-                          allow_module_level=True)
-        if verattr is None or pv(verattr) < pv(minversion):
-            raise Skipped("module %r has __version__ %r, required is: %r" %(
-                          modname, verattr, minversion), allow_module_level=True)
-    return mod
-
diff --git a/lib/spack/external/_pytest/setuponly.py b/lib/spack/external/_pytest/setuponly.py
index 1752c575f5..15e195ad5a 100644
--- a/lib/spack/external/_pytest/setuponly.py
+++ b/lib/spack/external/_pytest/setuponly.py
@@ -1,3 +1,5 @@
+from __future__ import absolute_import, division, print_function
+
 import pytest
 import sys
 
diff --git a/lib/spack/external/_pytest/setupplan.py b/lib/spack/external/_pytest/setupplan.py
index f0853dee54..e11bd40698 100644
--- a/lib/spack/external/_pytest/setupplan.py
+++ b/lib/spack/external/_pytest/setupplan.py
@@ -1,3 +1,5 @@
+from __future__ import absolute_import, division, print_function
+
 import pytest
 
 
diff --git a/lib/spack/external/_pytest/skipping.py b/lib/spack/external/_pytest/skipping.py
index a8eaea98aa..b92800d10b 100644
--- a/lib/spack/external/_pytest/skipping.py
+++ b/lib/spack/external/_pytest/skipping.py
@@ -1,18 +1,21 @@
 """ support for skip/xfail functions and markers. """
+from __future__ import absolute_import, division, print_function
+
 import os
 import sys
 import traceback
 
 import py
-import pytest
+from _pytest.config import hookimpl
 from _pytest.mark import MarkInfo, MarkDecorator
+from _pytest.outcomes import fail, skip, xfail, TEST_OUTCOME
 
 
 def pytest_addoption(parser):
     group = parser.getgroup("general")
     group.addoption('--runxfail',
-           action="store_true", dest="runxfail", default=False,
-           help="run tests even if they are marked xfail")
+                    action="store_true", dest="runxfail", default=False,
+                    help="run tests even if they are marked xfail")
 
     parser.addini("xfail_strict", "default for the strict parameter of xfail "
                                   "markers when not given explicitly (default: "
@@ -23,53 +26,38 @@ def pytest_addoption(parser):
 
 def pytest_configure(config):
     if config.option.runxfail:
+        # yay a hack
+        import pytest
         old = pytest.xfail
         config._cleanup.append(lambda: setattr(pytest, "xfail", old))
 
         def nop(*args, **kwargs):
             pass
 
-        nop.Exception = XFailed
+        nop.Exception = xfail.Exception
         setattr(pytest, "xfail", nop)
 
     config.addinivalue_line("markers",
-        "skip(reason=None): skip the given test function with an optional reason. "
-        "Example: skip(reason=\"no way of currently testing this\") skips the "
-        "test."
-    )
+                            "skip(reason=None): skip the given test function with an optional reason. "
+                            "Example: skip(reason=\"no way of currently testing this\") skips the "
+                            "test."
+                            )
     config.addinivalue_line("markers",
-        "skipif(condition): skip the given test function if eval(condition) "
-        "results in a True value.  Evaluation happens within the "
-        "module global context. Example: skipif('sys.platform == \"win32\"') "
-        "skips the test if we are on the win32 platform. see "
-        "http://pytest.org/latest/skipping.html"
-    )
+                            "skipif(condition): skip the given test function if eval(condition) "
+                            "results in a True value.  Evaluation happens within the "
+                            "module global context. Example: skipif('sys.platform == \"win32\"') "
+                            "skips the test if we are on the win32 platform. see "
+                            "http://pytest.org/latest/skipping.html"
+                            )
     config.addinivalue_line("markers",
-        "xfail(condition, reason=None, run=True, raises=None, strict=False): "
-        "mark the the test function as an expected failure if eval(condition) "
-        "has a True value. Optionally specify a reason for better reporting "
-        "and run=False if you don't even want to execute the test function. "
-        "If only specific exception(s) are expected, you can list them in "
-        "raises, and if the test fails in other ways, it will be reported as "
-        "a true failure. See http://pytest.org/latest/skipping.html"
-    )
-
-
-def pytest_namespace():
-    return dict(xfail=xfail)
-
-
-class XFailed(pytest.fail.Exception):
-    """ raised from an explicit call to pytest.xfail() """
-
-
-def xfail(reason=""):
-    """ xfail an executing test or setup functions with the given reason."""
-    __tracebackhide__ = True
-    raise XFailed(reason)
-
-
-xfail.Exception = XFailed
+                            "xfail(condition, reason=None, run=True, raises=None, strict=False): "
+                            "mark the test function as an expected failure if eval(condition) "
+                            "has a True value. Optionally specify a reason for better reporting "
+                            "and run=False if you don't even want to execute the test function. "
+                            "If only specific exception(s) are expected, you can list them in "
+                            "raises, and if the test fails in other ways, it will be reported as "
+                            "a true failure. See http://pytest.org/latest/skipping.html"
+                            )
 
 
 class MarkEvaluator:
@@ -97,51 +85,50 @@ class MarkEvaluator:
     def istrue(self):
         try:
             return self._istrue()
-        except Exception:
+        except TEST_OUTCOME:
             self.exc = sys.exc_info()
             if isinstance(self.exc[1], SyntaxError):
-                msg = [" " * (self.exc[1].offset + 4) + "^",]
+                msg = [" " * (self.exc[1].offset + 4) + "^", ]
                 msg.append("SyntaxError: invalid syntax")
             else:
                 msg = traceback.format_exception_only(*self.exc[:2])
-            pytest.fail("Error evaluating %r expression\n"
-                        "    %s\n"
-                        "%s"
-                        %(self.name, self.expr, "\n".join(msg)),
-                        pytrace=False)
+            fail("Error evaluating %r expression\n"
+                 "    %s\n"
+                 "%s"
+                 % (self.name, self.expr, "\n".join(msg)),
+                 pytrace=False)
 
     def _getglobals(self):
         d = {'os': os, 'sys': sys, 'config': self.item.config}
-        d.update(self.item.obj.__globals__)
+        if hasattr(self.item, 'obj'):
+            d.update(self.item.obj.__globals__)
         return d
 
     def _istrue(self):
         if hasattr(self, 'result'):
             return self.result
         if self.holder:
-            d = self._getglobals()
             if self.holder.args or 'condition' in self.holder.kwargs:
                 self.result = False
                 # "holder" might be a MarkInfo or a MarkDecorator; only
                 # MarkInfo keeps track of all parameters it received in an
                 # _arglist attribute
-                if hasattr(self.holder, '_arglist'):
-                    arglist = self.holder._arglist
-                else:
-                    arglist = [(self.holder.args, self.holder.kwargs)]
-                for args, kwargs in arglist:
+                marks = getattr(self.holder, '_marks', None) \
+                    or [self.holder.mark]
+                for _, args, kwargs in marks:
                     if 'condition' in kwargs:
                         args = (kwargs['condition'],)
                     for expr in args:
                         self.expr = expr
                         if isinstance(expr, py.builtin._basestring):
+                            d = self._getglobals()
                             result = cached_eval(self.item.config, expr, d)
                         else:
                             if "reason" not in kwargs:
                                 # XXX better be checked at collection time
                                 msg = "you need to specify reason=STRING " \
                                       "when using booleans as conditions."
-                                pytest.fail(msg)
+                                fail(msg)
                             result = bool(expr)
                         if result:
                             self.result = True
@@ -165,7 +152,7 @@ class MarkEvaluator:
         return expl
 
 
-@pytest.hookimpl(tryfirst=True)
+@hookimpl(tryfirst=True)
 def pytest_runtest_setup(item):
     # Check if skip or skipif are specified as pytest marks
 
@@ -174,23 +161,23 @@ def pytest_runtest_setup(item):
         eval_skipif = MarkEvaluator(item, 'skipif')
         if eval_skipif.istrue():
             item._evalskip = eval_skipif
-            pytest.skip(eval_skipif.getexplanation())
+            skip(eval_skipif.getexplanation())
 
     skip_info = item.keywords.get('skip')
     if isinstance(skip_info, (MarkInfo, MarkDecorator)):
         item._evalskip = True
         if 'reason' in skip_info.kwargs:
-            pytest.skip(skip_info.kwargs['reason'])
+            skip(skip_info.kwargs['reason'])
         elif skip_info.args:
-            pytest.skip(skip_info.args[0])
+            skip(skip_info.args[0])
         else:
-            pytest.skip("unconditional skip")
+            skip("unconditional skip")
 
     item._evalxfail = MarkEvaluator(item, 'xfail')
     check_xfail_no_run(item)
 
 
-@pytest.mark.hookwrapper
+@hookimpl(hookwrapper=True)
 def pytest_pyfunc_call(pyfuncitem):
     check_xfail_no_run(pyfuncitem)
     outcome = yield
@@ -205,7 +192,7 @@ def check_xfail_no_run(item):
         evalxfail = item._evalxfail
         if evalxfail.istrue():
             if not evalxfail.get('run', True):
-                pytest.xfail("[NOTRUN] " + evalxfail.getexplanation())
+                xfail("[NOTRUN] " + evalxfail.getexplanation())
 
 
 def check_strict_xfail(pyfuncitem):
@@ -217,10 +204,10 @@ def check_strict_xfail(pyfuncitem):
         if is_strict_xfail:
             del pyfuncitem._evalxfail
             explanation = evalxfail.getexplanation()
-            pytest.fail('[XPASS(strict)] ' + explanation, pytrace=False)
+            fail('[XPASS(strict)] ' + explanation, pytrace=False)
 
 
-@pytest.hookimpl(hookwrapper=True)
+@hookimpl(hookwrapper=True)
 def pytest_runtest_makereport(item, call):
     outcome = yield
     rep = outcome.get_result()
@@ -240,11 +227,11 @@ def pytest_runtest_makereport(item, call):
             rep.wasxfail = rep.longrepr
     elif item.config.option.runxfail:
         pass   # don't interefere
-    elif call.excinfo and call.excinfo.errisinstance(pytest.xfail.Exception):
+    elif call.excinfo and call.excinfo.errisinstance(xfail.Exception):
         rep.wasxfail = "reason: " + call.excinfo.value.msg
         rep.outcome = "skipped"
     elif evalxfail and not rep.skipped and evalxfail.wasvalid() and \
-        evalxfail.istrue():
+            evalxfail.istrue():
         if call.excinfo:
             if evalxfail.invalidraise(call.excinfo.value):
                 rep.outcome = "failed"
@@ -270,6 +257,8 @@ def pytest_runtest_makereport(item, call):
         rep.longrepr = filename, line, reason
 
 # called by terminalreporter progress reporting
+
+
 def pytest_report_teststatus(report):
     if hasattr(report, "wasxfail"):
         if report.skipped:
@@ -278,10 +267,12 @@ def pytest_report_teststatus(report):
             return "xpassed", "X", ("XPASS", {'yellow': True})
 
 # called by the terminalreporter instance/plugin
+
+
 def pytest_terminal_summary(terminalreporter):
     tr = terminalreporter
     if not tr.reportchars:
-        #for name in "xfailed skipped failed xpassed":
+        # for name in "xfailed skipped failed xpassed":
         #    if not tr.stats.get(name, 0):
         #        tr.write_line("HINT: use '-r' option to see extra "
         #              "summary info about tests")
@@ -308,12 +299,14 @@ def pytest_terminal_summary(terminalreporter):
         for line in lines:
             tr._tw.line(line)
 
+
 def show_simple(terminalreporter, lines, stat, format):
     failed = terminalreporter.stats.get(stat)
     if failed:
         for rep in failed:
             pos = terminalreporter.config.cwd_relative_nodeid(rep.nodeid)
-            lines.append(format %(pos,))
+            lines.append(format % (pos,))
+
 
 def show_xfailed(terminalreporter, lines):
     xfailed = terminalreporter.stats.get("xfailed")
@@ -325,13 +318,15 @@ def show_xfailed(terminalreporter, lines):
             if reason:
                 lines.append("  " + str(reason))
 
+
 def show_xpassed(terminalreporter, lines):
     xpassed = terminalreporter.stats.get("xpassed")
     if xpassed:
         for rep in xpassed:
             pos = terminalreporter.config.cwd_relative_nodeid(rep.nodeid)
             reason = rep.wasxfail
-            lines.append("XPASS %s %s" %(pos, reason))
+            lines.append("XPASS %s %s" % (pos, reason))
+
 
 def cached_eval(config, expr, d):
     if not hasattr(config, '_evalcache'):
@@ -351,25 +346,27 @@ def folded_skips(skipped):
         key = event.longrepr
         assert len(key) == 3, (event, key)
         d.setdefault(key, []).append(event)
-    l = []
+    values = []
     for key, events in d.items():
-        l.append((len(events),) + key)
-    return l
+        values.append((len(events),) + key)
+    return values
+
 
 def show_skipped(terminalreporter, lines):
     tr = terminalreporter
     skipped = tr.stats.get('skipped', [])
     if skipped:
-        #if not tr.hasopt('skipped'):
+        # if not tr.hasopt('skipped'):
         #    tr.write_line(
         #        "%d skipped tests, specify -rs for more info" %
         #        len(skipped))
         #    return
         fskips = folded_skips(skipped)
         if fskips:
-            #tr.write_sep("_", "skipped test summary")
+            # tr.write_sep("_", "skipped test summary")
             for num, fspath, lineno, reason in fskips:
                 if reason.startswith("Skipped: "):
                     reason = reason[9:]
-                lines.append("SKIP [%d] %s:%d: %s" %
-                    (num, fspath, lineno, reason))
+                lines.append(
+                    "SKIP [%d] %s:%d: %s" %
+                    (num, fspath, lineno + 1, reason))
diff --git a/lib/spack/external/_pytest/terminal.py b/lib/spack/external/_pytest/terminal.py
index 16bf757338..9da94d0c91 100644
--- a/lib/spack/external/_pytest/terminal.py
+++ b/lib/spack/external/_pytest/terminal.py
@@ -2,6 +2,9 @@
 
 This is a good source for looking at the various reporting hooks.
 """
+from __future__ import absolute_import, division, print_function
+
+import itertools
 from _pytest.main import EXIT_OK, EXIT_TESTSFAILED, EXIT_INTERRUPTED, \
     EXIT_USAGEERROR, EXIT_NOTESTSCOLLECTED
 import pytest
@@ -10,39 +13,41 @@ import sys
 import time
 import platform
 
+from _pytest import nodes
 import _pytest._pluggy as pluggy
 
 
 def pytest_addoption(parser):
     group = parser.getgroup("terminal reporting", "reporting", after="general")
     group._addoption('-v', '--verbose', action="count",
-               dest="verbose", default=0, help="increase verbosity."),
+                     dest="verbose", default=0, help="increase verbosity."),
     group._addoption('-q', '--quiet', action="count",
-               dest="quiet", default=0, help="decrease verbosity."),
+                     dest="quiet", default=0, help="decrease verbosity."),
     group._addoption('-r',
-         action="store", dest="reportchars", default='', metavar="chars",
-         help="show extra test summary info as specified by chars (f)ailed, "
-              "(E)error, (s)skipped, (x)failed, (X)passed, "
-              "(p)passed, (P)passed with output, (a)all except pP. "
-              "The pytest warnings are displayed at all times except when "
-              "--disable-pytest-warnings is set")
-    group._addoption('--disable-pytest-warnings', default=False,
-                     dest='disablepytestwarnings', action='store_true',
-                     help='disable warnings summary, overrides -r w flag')
+                     action="store", dest="reportchars", default='', metavar="chars",
+                     help="show extra test summary info as specified by chars (f)ailed, "
+                     "(E)error, (s)skipped, (x)failed, (X)passed, "
+                     "(p)passed, (P)passed with output, (a)all except pP. "
+                     "Warnings are displayed at all times except when "
+                     "--disable-warnings is set")
+    group._addoption('--disable-warnings', '--disable-pytest-warnings', default=False,
+                     dest='disable_warnings', action='store_true',
+                     help='disable warnings summary')
     group._addoption('-l', '--showlocals',
-         action="store_true", dest="showlocals", default=False,
-         help="show locals in tracebacks (disabled by default).")
+                     action="store_true", dest="showlocals", default=False,
+                     help="show locals in tracebacks (disabled by default).")
     group._addoption('--tb', metavar="style",
-               action="store", dest="tbstyle", default='auto',
-               choices=['auto', 'long', 'short', 'no', 'line', 'native'],
-               help="traceback print mode (auto/long/short/line/native/no).")
+                     action="store", dest="tbstyle", default='auto',
+                     choices=['auto', 'long', 'short', 'no', 'line', 'native'],
+                     help="traceback print mode (auto/long/short/line/native/no).")
     group._addoption('--fulltrace', '--full-trace',
-               action="store_true", default=False,
-               help="don't cut any tracebacks (default is to cut).")
+                     action="store_true", default=False,
+                     help="don't cut any tracebacks (default is to cut).")
     group._addoption('--color', metavar="color",
-               action="store", dest="color", default='auto',
-               choices=['yes', 'no', 'auto'],
-               help="color terminal output (yes/no/auto).")
+                     action="store", dest="color", default='auto',
+                     choices=['yes', 'no', 'auto'],
+                     help="color terminal output (yes/no/auto).")
+
 
 def pytest_configure(config):
     config.option.verbose -= config.option.quiet
@@ -54,12 +59,13 @@ def pytest_configure(config):
             reporter.write_line("[traceconfig] " + msg)
         config.trace.root.setprocessor("pytest:config", mywriter)
 
+
 def getreportopt(config):
     reportopts = ""
     reportchars = config.option.reportchars
-    if not config.option.disablepytestwarnings and 'w' not in reportchars:
+    if not config.option.disable_warnings and 'w' not in reportchars:
         reportchars += 'w'
-    elif config.option.disablepytestwarnings and 'w' in reportchars:
+    elif config.option.disable_warnings and 'w' in reportchars:
         reportchars = reportchars.replace('w', '')
     if reportchars:
         for char in reportchars:
@@ -69,6 +75,7 @@ def getreportopt(config):
                 reportopts = 'fEsxXw'
     return reportopts
 
+
 def pytest_report_teststatus(report):
     if report.passed:
         letter = "."
@@ -80,13 +87,41 @@ def pytest_report_teststatus(report):
             letter = "f"
     return report.outcome, letter, report.outcome.upper()
 
+
 class WarningReport:
+    """
+    Simple structure to hold warnings information captured by ``pytest_logwarning``.
+    """
+
     def __init__(self, code, message, nodeid=None, fslocation=None):
+        """
+        :param code: unused
+        :param str message: user friendly message about the warning
+        :param str|None nodeid: node id that generated the warning (see ``get_location``).
+        :param tuple|py.path.local fslocation:
+            file system location of the source of the warning (see ``get_location``).
+        """
         self.code = code
         self.message = message
         self.nodeid = nodeid
         self.fslocation = fslocation
 
+    def get_location(self, config):
+        """
+        Returns the more user-friendly information about the location
+        of a warning, or None.
+        """
+        if self.nodeid:
+            return self.nodeid
+        if self.fslocation:
+            if isinstance(self.fslocation, tuple) and len(self.fslocation) >= 2:
+                filename, linenum = self.fslocation[:2]
+                relpath = py.path.local(filename).relto(config.invocation_dir)
+                return '%s:%s' % (relpath, linenum)
+            else:
+                return str(self.fslocation)
+        return None
+
 
 class TerminalReporter:
     def __init__(self, config, file=None):
@@ -146,8 +181,22 @@ class TerminalReporter:
         self._tw.line(line, **markup)
 
     def rewrite(self, line, **markup):
+        """
+        Rewinds the terminal cursor to the beginning and writes the given line.
+
+        :kwarg erase: if True, will also add spaces until the full terminal width to ensure
+            previous lines are properly erased.
+
+        The rest of the keyword arguments are markup instructions.
+        """
+        erase = markup.pop('erase', False)
+        if erase:
+            fill_count = self._tw.fullwidth - len(line)
+            fill = ' ' * fill_count
+        else:
+            fill = ''
         line = str(line)
-        self._tw.write("\r" + line, **markup)
+        self._tw.write("\r" + line + fill, **markup)
 
     def write_sep(self, sep, title=None, **markup):
         self.ensure_newline()
@@ -166,8 +215,6 @@ class TerminalReporter:
 
     def pytest_logwarning(self, code, fslocation, message, nodeid):
         warnings = self.stats.setdefault("warnings", [])
-        if isinstance(fslocation, tuple):
-            fslocation = "%s:%d" % fslocation
         warning = WarningReport(code=code, fslocation=fslocation,
                                 message=message, nodeid=nodeid)
         warnings.append(warning)
@@ -212,15 +259,15 @@ class TerminalReporter:
                 word, markup = word
             else:
                 if rep.passed:
-                    markup = {'green':True}
+                    markup = {'green': True}
                 elif rep.failed:
-                    markup = {'red':True}
+                    markup = {'red': True}
                 elif rep.skipped:
-                    markup = {'yellow':True}
+                    markup = {'yellow': True}
             line = self._locationline(rep.nodeid, *rep.location)
             if not hasattr(rep, 'node'):
                 self.write_ensure_prefix(line, word, **markup)
-                #self._tw.write(word, **markup)
+                # self._tw.write(word, **markup)
             else:
                 self.ensure_newline()
                 if hasattr(rep, 'node'):
@@ -241,7 +288,7 @@ class TerminalReporter:
         items = [x for x in report.result if isinstance(x, pytest.Item)]
         self._numcollected += len(items)
         if self.isatty:
-            #self.write_fspath_result(report.nodeid, 'E')
+            # self.write_fspath_result(report.nodeid, 'E')
             self.report_collect()
 
     def report_collect(self, final=False):
@@ -254,15 +301,15 @@ class TerminalReporter:
             line = "collected "
         else:
             line = "collecting "
-        line += str(self._numcollected) + " items"
+        line += str(self._numcollected) + " item" + ('' if self._numcollected == 1 else 's')
         if errors:
             line += " / %d errors" % errors
         if skipped:
             line += " / %d skipped" % skipped
         if self.isatty:
+            self.rewrite(line, bold=True, erase=True)
             if final:
-                line += " \n"
-            self.rewrite(line, bold=True)
+                self.write('\n')
         else:
             self.write_line(line)
 
@@ -288,6 +335,9 @@ class TerminalReporter:
         self.write_line(msg)
         lines = self.config.hook.pytest_report_header(
             config=self.config, startdir=self.startdir)
+        self._write_report_lines_from_hooks(lines)
+
+    def _write_report_lines_from_hooks(self, lines):
         lines.reverse()
         for line in flatten(lines):
             self.write_line(line)
@@ -295,8 +345,8 @@ class TerminalReporter:
     def pytest_report_header(self, config):
         inifile = ""
         if config.inifile:
-            inifile = config.rootdir.bestrelpath(config.inifile)
-        lines = ["rootdir: %s, inifile: %s" %(config.rootdir, inifile)]
+            inifile = " " + config.rootdir.bestrelpath(config.inifile)
+        lines = ["rootdir: %s, inifile:%s" % (config.rootdir, inifile)]
 
         plugininfo = config.pluginmanager.list_plugin_distinfo()
         if plugininfo:
@@ -314,10 +364,9 @@ class TerminalReporter:
                     rep.toterminal(self._tw)
                 return 1
             return 0
-        if not self.showheader:
-            return
-        #for i, testarg in enumerate(self.config.args):
-        #    self.write_line("test path %d: %s" %(i+1, testarg))
+        lines = self.config.hook.pytest_report_collectionfinish(
+            config=self.config, startdir=self.startdir, items=session.items)
+        self._write_report_lines_from_hooks(lines)
 
     def _printcollecteditems(self, items):
         # to print out items and their parent collectors
@@ -340,14 +389,14 @@ class TerminalReporter:
         stack = []
         indent = ""
         for item in items:
-            needed_collectors = item.listchain()[1:] # strip root node
+            needed_collectors = item.listchain()[1:]  # strip root node
             while stack:
                 if stack == needed_collectors[:len(stack)]:
                     break
                 stack.pop()
             for col in needed_collectors[len(stack):]:
                 stack.append(col)
-                #if col.name == "()":
+                # if col.name == "()":
                 #    continue
                 indent = (len(stack) - 1) * "  "
                 self._tw.line("%s%s" % (indent, col))
@@ -396,15 +445,15 @@ class TerminalReporter:
             line = self.config.cwd_relative_nodeid(nodeid)
             if domain and line.endswith(domain):
                 line = line[:-len(domain)]
-                l = domain.split("[")
-                l[0] = l[0].replace('.', '::')  # don't replace '.' in params
-                line += "[".join(l)
+                values = domain.split("[")
+                values[0] = values[0].replace('.', '::')  # don't replace '.' in params
+                line += "[".join(values)
             return line
         # collect_fspath comes from testid which has a "/"-normalized path
 
         if fspath:
             res = mkrel(nodeid).replace("::()", "")  # parens-normalization
-            if nodeid.split("::")[0] != fspath.replace("\\", "/"):
+            if nodeid.split("::")[0] != fspath.replace("\\", nodes.SEP):
                 res += " <- " + self.startdir.bestrelpath(fspath)
         else:
             res = "[location]"
@@ -415,7 +464,7 @@ class TerminalReporter:
             fspath, lineno, domain = rep.location
             return domain
         else:
-            return "test session" # XXX?
+            return "test session"  # XXX?
 
     def _getcrashline(self, rep):
         try:
@@ -430,21 +479,29 @@ class TerminalReporter:
     # summaries for sessionfinish
     #
     def getreports(self, name):
-        l = []
+        values = []
         for x in self.stats.get(name, []):
             if not hasattr(x, '_pdbshown'):
-                l.append(x)
-        return l
+                values.append(x)
+        return values
 
     def summary_warnings(self):
         if self.hasopt("w"):
-            warnings = self.stats.get("warnings")
-            if not warnings:
+            all_warnings = self.stats.get("warnings")
+            if not all_warnings:
                 return
-            self.write_sep("=", "pytest-warning summary")
-            for w in warnings:
-                self._tw.line("W%s %s %s" % (w.code,
-                              w.fslocation, w.message))
+
+            grouped = itertools.groupby(all_warnings, key=lambda wr: wr.get_location(self.config))
+
+            self.write_sep("=", "warnings summary", yellow=True, bold=False)
+            for location, warnings in grouped:
+                self._tw.line(str(location) or '<undetermined location>')
+                for w in warnings:
+                    lines = w.message.splitlines()
+                    indented = '\n'.join('  ' + x for x in lines)
+                    self._tw.line(indented)
+                self._tw.line()
+            self._tw.line('-- Docs: http://doc.pytest.org/en/latest/warnings.html')
 
     def summary_passes(self):
         if self.config.option.tbstyle != "no":
@@ -466,7 +523,6 @@ class TerminalReporter:
                     content = content[:-1]
                 self._tw.line(content)
 
-
     def summary_failures(self):
         if self.config.option.tbstyle != "no":
             reports = self.getreports('failed')
@@ -528,6 +584,7 @@ class TerminalReporter:
             self.write_sep("=", "%d tests deselected" % (
                 len(self.stats['deselected'])), bold=True)
 
+
 def repr_pythonversion(v=None):
     if v is None:
         v = sys.version_info
@@ -536,30 +593,30 @@ def repr_pythonversion(v=None):
     except (TypeError, ValueError):
         return str(v)
 
-def flatten(l):
-    for x in l:
+
+def flatten(values):
+    for x in values:
         if isinstance(x, (list, tuple)):
             for y in flatten(x):
                 yield y
         else:
             yield x
 
+
 def build_summary_stats_line(stats):
     keys = ("failed passed skipped deselected "
-           "xfailed xpassed warnings error").split()
-    key_translation = {'warnings': 'pytest-warnings'}
+            "xfailed xpassed warnings error").split()
     unknown_key_seen = False
     for key in stats.keys():
         if key not in keys:
-            if key: # setup/teardown reports have an empty key, ignore them
+            if key:  # setup/teardown reports have an empty key, ignore them
                 keys.append(key)
                 unknown_key_seen = True
     parts = []
     for key in keys:
         val = stats.get(key, None)
         if val:
-            key_name = key_translation.get(key, key)
-            parts.append("%d %s" % (len(val), key_name))
+            parts.append("%d %s" % (len(val), key))
 
     if parts:
         line = ", ".join(parts)
@@ -579,7 +636,7 @@ def build_summary_stats_line(stats):
 
 
 def _plugin_nameversions(plugininfo):
-    l = []
+    values = []
     for plugin, dist in plugininfo:
         # gets us name and version!
         name = '{dist.project_name}-{dist.version}'.format(dist=dist)
@@ -588,6 +645,6 @@ def _plugin_nameversions(plugininfo):
             name = name[7:]
         # we decided to print python package names
         # they can have more than one plugin
-        if name not in l:
-            l.append(name)
-    return l
+        if name not in values:
+            values.append(name)
+    return values
diff --git a/lib/spack/external/_pytest/tmpdir.py b/lib/spack/external/_pytest/tmpdir.py
index 28a6b06366..da1b032237 100644
--- a/lib/spack/external/_pytest/tmpdir.py
+++ b/lib/spack/external/_pytest/tmpdir.py
@@ -1,4 +1,6 @@
 """ support for providing temporary directories to test functions.  """
+from __future__ import absolute_import, division, print_function
+
 import re
 
 import pytest
@@ -23,7 +25,7 @@ class TempdirFactory:
             provides an empty unique-per-test-invocation directory
             and is guaranteed to be empty.
         """
-        #py.log._apiwarn(">1.1", "use tmpdir function argument")
+        # py.log._apiwarn(">1.1", "use tmpdir function argument")
         return self.getbasetemp().ensure(string, dir=dir)
 
     def mktemp(self, basename, numbered=True):
@@ -36,7 +38,7 @@ class TempdirFactory:
             p = basetemp.mkdir(basename)
         else:
             p = py.path.local.make_numbered_dir(prefix=basename,
-                keep=0, rootdir=basetemp, lock_timeout=None)
+                                                keep=0, rootdir=basetemp, lock_timeout=None)
         self.trace("mktemp", p)
         return p
 
@@ -116,7 +118,7 @@ def tmpdir(request, tmpdir_factory):
     path object.
     """
     name = request.node.name
-    name = re.sub("[\W]", "_", name)
+    name = re.sub(r"[\W]", "_", name)
     MAXVAL = 30
     if len(name) > MAXVAL:
         name = name[:MAXVAL]
diff --git a/lib/spack/external/_pytest/unittest.py b/lib/spack/external/_pytest/unittest.py
index 73224010b2..52c9813e8b 100644
--- a/lib/spack/external/_pytest/unittest.py
+++ b/lib/spack/external/_pytest/unittest.py
@@ -1,13 +1,14 @@
 """ discovery and running of std-library "unittest" style tests. """
-from __future__ import absolute_import
+from __future__ import absolute_import, division, print_function
 
 import sys
 import traceback
 
-import pytest
-# for transfering markers
+# for transferring markers
 import _pytest._code
-from _pytest.python import transfer_markers
+from _pytest.config import hookimpl
+from _pytest.outcomes import fail, skip, xfail
+from _pytest.python import transfer_markers, Class, Module, Function
 from _pytest.skipping import MarkEvaluator
 
 
@@ -22,11 +23,11 @@ def pytest_pycollect_makeitem(collector, name, obj):
     return UnitTestCase(name, parent=collector)
 
 
-class UnitTestCase(pytest.Class):
+class UnitTestCase(Class):
     # marker for fixturemanger.getfixtureinfo()
     # to declare that our children do not support funcargs
     nofuncargs = True
-                                              
+
     def setup(self):
         cls = self.obj
         if getattr(cls, '__unittest_skip__', False):
@@ -46,7 +47,7 @@ class UnitTestCase(pytest.Class):
             return
         self.session._fixturemanager.parsefactories(self, unittest=True)
         loader = TestLoader()
-        module = self.getparent(pytest.Module).obj
+        module = self.getparent(Module).obj
         foundsomething = False
         for name in loader.getTestCaseNames(self.obj):
             x = getattr(self.obj, name)
@@ -65,8 +66,7 @@ class UnitTestCase(pytest.Class):
                     yield TestCaseFunction('runTest', parent=self)
 
 
-
-class TestCaseFunction(pytest.Function):
+class TestCaseFunction(Function):
     _excinfo = None
 
     def setup(self):
@@ -109,38 +109,39 @@ class TestCaseFunction(pytest.Function):
         except TypeError:
             try:
                 try:
-                    l = traceback.format_exception(*rawexcinfo)
-                    l.insert(0, "NOTE: Incompatible Exception Representation, "
-                        "displaying natively:\n\n")
-                    pytest.fail("".join(l), pytrace=False)
-                except (pytest.fail.Exception, KeyboardInterrupt):
+                    values = traceback.format_exception(*rawexcinfo)
+                    values.insert(0, "NOTE: Incompatible Exception Representation, "
+                                  "displaying natively:\n\n")
+                    fail("".join(values), pytrace=False)
+                except (fail.Exception, KeyboardInterrupt):
                     raise
-                except:
-                    pytest.fail("ERROR: Unknown Incompatible Exception "
-                        "representation:\n%r" %(rawexcinfo,), pytrace=False)
+                except:  # noqa
+                    fail("ERROR: Unknown Incompatible Exception "
+                         "representation:\n%r" % (rawexcinfo,), pytrace=False)
             except KeyboardInterrupt:
                 raise
-            except pytest.fail.Exception:
+            except fail.Exception:
                 excinfo = _pytest._code.ExceptionInfo()
         self.__dict__.setdefault('_excinfo', []).append(excinfo)
 
     def addError(self, testcase, rawexcinfo):
         self._addexcinfo(rawexcinfo)
+
     def addFailure(self, testcase, rawexcinfo):
         self._addexcinfo(rawexcinfo)
 
     def addSkip(self, testcase, reason):
         try:
-            pytest.skip(reason)
-        except pytest.skip.Exception:
+            skip(reason)
+        except skip.Exception:
             self._evalskip = MarkEvaluator(self, 'SkipTest')
             self._evalskip.result = True
             self._addexcinfo(sys.exc_info())
 
     def addExpectedFailure(self, testcase, rawexcinfo, reason=""):
         try:
-            pytest.xfail(str(reason))
-        except pytest.xfail.Exception:
+            xfail(str(reason))
+        except xfail.Exception:
             self._addexcinfo(sys.exc_info())
 
     def addUnexpectedSuccess(self, testcase, reason=""):
@@ -152,22 +153,42 @@ class TestCaseFunction(pytest.Function):
     def stopTest(self, testcase):
         pass
 
+    def _handle_skip(self):
+        # implements the skipping machinery (see #2137)
+        # analog to pythons Lib/unittest/case.py:run
+        testMethod = getattr(self._testcase, self._testcase._testMethodName)
+        if (getattr(self._testcase.__class__, "__unittest_skip__", False) or
+                getattr(testMethod, "__unittest_skip__", False)):
+            # If the class or method was skipped.
+            skip_why = (getattr(self._testcase.__class__, '__unittest_skip_why__', '') or
+                        getattr(testMethod, '__unittest_skip_why__', ''))
+            try:  # PY3, unittest2 on PY2
+                self._testcase._addSkip(self, self._testcase, skip_why)
+            except TypeError:  # PY2
+                if sys.version_info[0] != 2:
+                    raise
+                self._testcase._addSkip(self, skip_why)
+            return True
+        return False
+
     def runtest(self):
         if self.config.pluginmanager.get_plugin("pdbinvoke") is None:
             self._testcase(result=self)
         else:
             # disables tearDown and cleanups for post mortem debugging (see #1890)
+            if self._handle_skip():
+                return
             self._testcase.debug()
 
-
     def _prunetraceback(self, excinfo):
-        pytest.Function._prunetraceback(self, excinfo)
+        Function._prunetraceback(self, excinfo)
         traceback = excinfo.traceback.filter(
-            lambda x:not x.frame.f_globals.get('__unittest'))
+            lambda x: not x.frame.f_globals.get('__unittest'))
         if traceback:
             excinfo.traceback = traceback
 
-@pytest.hookimpl(tryfirst=True)
+
+@hookimpl(tryfirst=True)
 def pytest_runtest_makereport(item, call):
     if isinstance(item, TestCaseFunction):
         if item._excinfo:
@@ -179,7 +200,8 @@ def pytest_runtest_makereport(item, call):
 
 # twisted trial support
 
-@pytest.hookimpl(hookwrapper=True)
+
+@hookimpl(hookwrapper=True)
 def pytest_runtest_protocol(item):
     if isinstance(item, TestCaseFunction) and \
        'twisted.trial.unittest' in sys.modules:
@@ -188,7 +210,7 @@ def pytest_runtest_protocol(item):
         check_testcase_implements_trial_reporter()
 
         def excstore(self, exc_value=None, exc_type=None, exc_tb=None,
-            captureVars=None):
+                     captureVars=None):
             if exc_value is None:
                 self._rawexcinfo = sys.exc_info()
             else:
@@ -197,7 +219,7 @@ def pytest_runtest_protocol(item):
                 self._rawexcinfo = (exc_type, exc_value, exc_tb)
             try:
                 Failure__init__(self, exc_value, exc_type, exc_tb,
-                    captureVars=captureVars)
+                                captureVars=captureVars)
             except TypeError:
                 Failure__init__(self, exc_value, exc_type, exc_tb)
 
diff --git a/lib/spack/external/_pytest/vendored_packages/pluggy.py b/lib/spack/external/_pytest/vendored_packages/pluggy.py
index 9c13932b36..aebddad01d 100644
--- a/lib/spack/external/_pytest/vendored_packages/pluggy.py
+++ b/lib/spack/external/_pytest/vendored_packages/pluggy.py
@@ -540,7 +540,7 @@ class PluginManager(object):
         of HookImpl instances and the keyword arguments for the hook call.
 
         ``after(outcome, hook_name, hook_impls, kwargs)`` receives the
-        same arguments as ``before`` but also a :py:class:`_CallOutcome`` object
+        same arguments as ``before`` but also a :py:class:`_CallOutcome <_pytest.vendored_packages.pluggy._CallOutcome>` object
         which represents the result of the overall hook call.
         """
         return _TracedHookExecution(self, before, after).undo
diff --git a/lib/spack/external/_pytest/warnings.py b/lib/spack/external/_pytest/warnings.py
new file mode 100644
index 0000000000..926b1f5811
--- /dev/null
+++ b/lib/spack/external/_pytest/warnings.py
@@ -0,0 +1,94 @@
+from __future__ import absolute_import, division, print_function
+
+import warnings
+from contextlib import contextmanager
+
+import pytest
+
+from _pytest import compat
+
+
+def _setoption(wmod, arg):
+    """
+    Copy of the warning._setoption function but does not escape arguments.
+    """
+    parts = arg.split(':')
+    if len(parts) > 5:
+        raise wmod._OptionError("too many fields (max 5): %r" % (arg,))
+    while len(parts) < 5:
+        parts.append('')
+    action, message, category, module, lineno = [s.strip()
+                                                 for s in parts]
+    action = wmod._getaction(action)
+    category = wmod._getcategory(category)
+    if lineno:
+        try:
+            lineno = int(lineno)
+            if lineno < 0:
+                raise ValueError
+        except (ValueError, OverflowError):
+            raise wmod._OptionError("invalid lineno %r" % (lineno,))
+    else:
+        lineno = 0
+    wmod.filterwarnings(action, message, category, module, lineno)
+
+
+def pytest_addoption(parser):
+    group = parser.getgroup("pytest-warnings")
+    group.addoption(
+        '-W', '--pythonwarnings', action='append',
+        help="set which warnings to report, see -W option of python itself.")
+    parser.addini("filterwarnings", type="linelist",
+                  help="Each line specifies a pattern for "
+                  "warnings.filterwarnings. "
+                  "Processed after -W and --pythonwarnings.")
+
+
+@contextmanager
+def catch_warnings_for_item(item):
+    """
+    catches the warnings generated during setup/call/teardown execution
+    of the given item and after it is done posts them as warnings to this
+    item.
+    """
+    args = item.config.getoption('pythonwarnings') or []
+    inifilters = item.config.getini("filterwarnings")
+    with warnings.catch_warnings(record=True) as log:
+        for arg in args:
+            warnings._setoption(arg)
+
+        for arg in inifilters:
+            _setoption(warnings, arg)
+
+        mark = item.get_marker('filterwarnings')
+        if mark:
+            for arg in mark.args:
+                warnings._setoption(arg)
+
+        yield
+
+        for warning in log:
+            warn_msg = warning.message
+            unicode_warning = False
+
+            if compat._PY2 and any(isinstance(m, compat.UNICODE_TYPES) for m in warn_msg.args):
+                new_args = [compat.safe_str(m) for m in warn_msg.args]
+                unicode_warning = warn_msg.args != new_args
+                warn_msg.args = new_args
+
+            msg = warnings.formatwarning(
+                warn_msg, warning.category,
+                warning.filename, warning.lineno, warning.line)
+            item.warn("unused", msg)
+
+            if unicode_warning:
+                warnings.warn(
+                    "Warning is using unicode non convertible to ascii, "
+                    "converting to a safe representation:\n  %s" % msg,
+                    UnicodeWarning)
+
+
+@pytest.hookimpl(hookwrapper=True)
+def pytest_runtest_protocol(item):
+    with catch_warnings_for_item(item):
+        yield
diff --git a/lib/spack/external/argparse.py b/lib/spack/external/argparse.py
index ec9a9ee738..d2d232d51e 100644
--- a/lib/spack/external/argparse.py
+++ b/lib/spack/external/argparse.py
@@ -1,25 +1,6 @@
-# argparse is (c) 2006-2009 Steven J. Bethard <steven.bethard@gmail.com>.
-#
-# The argparse module was contributed to Python as of Python 2.7 and thus
-# was licensed under the Python license. Same license applies to all files in
-# the argparse package project.
-#
-# For details about the Python License, please see doc/Python-License.txt.
-#
-# History
-# -------
-#
-# Before (and including) argparse 1.1, the argparse package was licensed under
-# Apache License v2.0.
-#
-# After argparse 1.1, all project files from the argparse project were deleted
-# due to license compatibility issues between Apache License 2.0 and GNU GPL v2.
-#
-# The project repository then had a clean start with some files taken from
-# Python 2.7.1, so definitely all files are under Python License now.
-#
 # Author: Steven J. Bethard <steven.bethard@gmail.com>.
-#
+# Maintainer: Thomas Waldmann <tw@waldmann-edv.de>
+
 """Command-line parsing library
 
 This module is an optparse-inspired command-line parsing library that:
@@ -81,7 +62,12 @@ considered public as object names -- the API of the formatter objects is
 still considered an implementation detail.)
 """
 
-__version__ = '1.2.1'
+__version__ = '1.4.0'  # we use our own version number independant of the
+                       # one in stdlib and we release this on pypi.
+
+__external_lib__ = True  # to make sure the tests really test THIS lib,
+                         # not the builtin one in Python stdlib
+
 __all__ = [
     'ArgumentParser',
     'ArgumentError',
@@ -370,8 +356,6 @@ class HelpFormatter(object):
                 pos_usage = format(positionals, groups)
                 opt_parts = _re.findall(part_regexp, opt_usage)
                 pos_parts = _re.findall(part_regexp, pos_usage)
-                assert ' '.join(opt_parts) == opt_usage
-                assert ' '.join(pos_parts) == pos_usage
 
                 # helper for wrapping lines
                 def get_lines(parts, indent, prefix=None):
@@ -1073,7 +1057,7 @@ class _SubParsersAction(Action):
                 metavar += ' (%s)' % ', '.join(aliases)
             sup = super(_SubParsersAction._ChoicesPseudoAction, self)
             sup.__init__(option_strings=[], dest=dest, help=help,
-                         metavar=metavar)
+                        metavar=metavar)
 
     def __init__(self,
                  option_strings,
@@ -1134,9 +1118,8 @@ class _SubParsersAction(Action):
         try:
             parser = self._name_parser_map[parser_name]
         except KeyError:
-            args = {'parser_name': parser_name,
-                    'choices': ', '.join(self._name_parser_map)}
-            msg = _('unknown parser %(parser_name)r (choices: %(choices)s)') % args
+            tup = parser_name, ', '.join(self._name_parser_map)
+            msg = _('unknown parser %r (choices: %s)' % tup)
             raise ArgumentError(self, msg)
 
         # parse all the remaining options into the namespace
@@ -1180,11 +1163,16 @@ class FileType(object):
                 msg = _('argument "-" with mode %r' % self._mode)
                 raise ValueError(msg)
 
-        # all other arguments are used as file names
-        if self._bufsize:
-            return open(string, self._mode, self._bufsize)
-        else:
-            return open(string, self._mode)
+        try:
+            # all other arguments are used as file names
+            if self._bufsize:
+                return open(string, self._mode, self._bufsize)
+            else:
+                return open(string, self._mode)
+        except IOError:
+            err = _sys.exc_info()[1]
+            message = _("can't open '%s': %s")
+            raise ArgumentTypeError(message % (string, err))
 
     def __repr__(self):
         args = [self._mode, self._bufsize]
@@ -1720,21 +1708,6 @@ class ArgumentParser(_AttributeHolder, _ActionsContainer):
             self._positionals._add_action(action)
         return action
 
-
-    def get_subparser(self, name):
-        """Gets a subparser added with the supplied name.
-           This is an extension to the standard argparse API.
-        """
-        subpasrsers_actions = [
-            action for action in self._actions
-            if isinstance(action, _SubParsersAction)]
-        for action in subpasrsers_actions:
-            for choice, subparser in action.choices.items():
-                if choice == name:
-                    return subparser
-        return None
-
-
     def _get_optional_actions(self):
         return [action
                 for action in self._actions
@@ -1769,10 +1742,7 @@ class ArgumentParser(_AttributeHolder, _ActionsContainer):
             if action.dest is not SUPPRESS:
                 if not hasattr(namespace, action.dest):
                     if action.default is not SUPPRESS:
-                        default = action.default
-                        if isinstance(action.default, basestring):
-                            default = self._get_value(action, default)
-                        setattr(namespace, action.dest, default)
+                        setattr(namespace, action.dest, action.default)
 
         # add any parser defaults that aren't present
         for dest in self._defaults:
@@ -2000,12 +1970,23 @@ class ArgumentParser(_AttributeHolder, _ActionsContainer):
         if positionals:
             self.error(_('too few arguments'))
 
-        # make sure all required actions were present
+        # make sure all required actions were present, and convert defaults.
         for action in self._actions:
-            if action.required:
-                if action not in seen_actions:
+            if action not in seen_actions:
+                if action.required:
                     name = _get_action_name(action)
                     self.error(_('argument %s is required') % name)
+                else:
+                    # Convert action default now instead of doing it before
+                    # parsing arguments to avoid calling convert functions
+                    # twice (which may fail) if the argument was given, but
+                    # only if it was defined already in the namespace
+                    if (action.default is not None and
+                            isinstance(action.default, basestring) and
+                            hasattr(namespace, action.dest) and
+                            action.default is getattr(namespace, action.dest)):
+                        setattr(namespace, action.dest,
+                                self._get_value(action, action.default))
 
         # make sure all required groups had one option present
         for group in self._mutually_exclusive_groups:
diff --git a/lib/spack/external/ctest_log_parser.py b/lib/spack/external/ctest_log_parser.py
index 6ef9642d85..0437b6e524 100644
--- a/lib/spack/external/ctest_log_parser.py
+++ b/lib/spack/external/ctest_log_parser.py
@@ -65,30 +65,72 @@ algorithms that duplicate the way CTest scrapes log files.  To keep this
 up to date with CTest, just make sure the ``*_matches`` and
 ``*_exceptions`` lists are kept up to date with CTest's build handler.
 """
+from __future__ import print_function
+from __future__ import division
+
 import re
+import math
+import multiprocessing
+import time
+from contextlib import contextmanager
+
 from six import StringIO
 from six import string_types
 
+class prefilter(object):
+    """Make regular expressions faster with a simple prefiltering predicate.
+
+    Some regular expressions seem to be much more costly than others.  In
+    most cases, we can evaluate a simple precondition, e.g.::
+
+        lambda x: "error" in x
+
+    to avoid evaluating expensive regexes on all lines in a file. This
+    can reduce parse time for large files by orders of magnitude when
+    evaluating lots of expressions.
+
+    A ``prefilter`` object is designed to act like a regex,, but
+    ``search`` and ``match`` check the precondition before bothering to
+    evaluate the regular expression.
 
-error_matches = [
+    Note that ``match`` and ``search`` just return ``True`` and ``False``
+    at the moment. Make them return a ``MatchObject`` or ``None`` if it
+    becomes necessary.
+    """
+    def __init__(self, precondition, *patterns):
+        self.patterns = [re.compile(p) for p in patterns]
+        self.pre = precondition
+        self.pattern = "\n                            ".join(
+            ('MERGED:',) + patterns)
+
+    def search(self, text):
+        return self.pre(text) and any(p.search(text) for p in self.patterns)
+
+    def match(self, text):
+        return self.pre(text) and any(p.match(text) for p in self.patterns)
+
+
+_error_matches = [
+    prefilter(
+        lambda x: any(s in x for s in (
+            'Error:', 'error', 'undefined reference', 'multiply defined')),
+        "([^:]+): error[ \\t]*[0-9]+[ \\t]*:",
+        "([^:]+): (Error:|error|undefined reference|multiply defined)",
+        "([^ :]+) ?: (error|fatal error|catastrophic error)",
+        "([^:]+)\\(([^\\)]+)\\) ?: (error|fatal error|catastrophic error)"),
     "^[Bb]us [Ee]rror",
     "^[Ss]egmentation [Vv]iolation",
     "^[Ss]egmentation [Ff]ault",
     ":.*[Pp]ermission [Dd]enied",
-    "([^ :]+):([0-9]+): ([^ \\t])",
-    "([^:]+): error[ \\t]*[0-9]+[ \\t]*:",
     "^Error ([0-9]+):",
     "^Fatal",
-    "^Error: ",
+    "^[Ee]rror: ",
     "^Error ",
     "[0-9] ERROR: ",
     "^\"[^\"]+\", line [0-9]+: [^Ww]",
     "^cc[^C]*CC: ERROR File = ([^,]+), Line = ([0-9]+)",
     "^ld([^:])*:([ \\t])*ERROR([^:])*:",
     "^ild:([ \\t])*\\(undefined symbol\\)",
-    "([^ :]+) : (error|fatal error|catastrophic error)",
-    "([^:]+): (Error:|error|undefined reference|multiply defined)",
-    "([^:]+)\\(([^\\)]+)\\) ?: (error|fatal error|catastrophic error)",
     "^fatal error C[0-9]+:",
     ": syntax error ",
     "^collect2: ld returned 1 exit status",
@@ -128,7 +170,7 @@ error_matches = [
     "^Command .* failed with exit code",
 ]
 
-error_exceptions = [
+_error_exceptions = [
     "instantiated from ",
     "candidates are:",
     ": warning",
@@ -143,32 +185,38 @@ error_exceptions = [
 ]
 
 #: Regexes to match file/line numbers in error/warning messages
-warning_matches = [
-    "([^ :]+):([0-9]+): warning:",
-    "([^ :]+):([0-9]+): note:",
+_warning_matches = [
+    prefilter(
+        lambda x: 'warning' in x,
+        "([^ :]+):([0-9]+): warning:",
+        "([^:]+): warning ([0-9]+):",
+        "([^:]+): warning[ \\t]*[0-9]+[ \\t]*:",
+        "([^ :]+) : warning",
+        "([^:]+): warning"),
+    prefilter(
+        lambda x: 'note:' in x,
+        "^([^ :]+):([0-9]+): note:"),
+    prefilter(
+        lambda x: any(s in x for s in ('Warning', 'Warnung')),
+        "^(Warning|Warnung) ([0-9]+):",
+        "^(Warning|Warnung)[ :]",
+        "^cxx: Warning:",
+        "([^ :]+):([0-9]+): (Warning|Warnung)",
+        "^CMake Warning.*:"),
+    "file: .* has no symbols",
     "^cc[^C]*CC: WARNING File = ([^,]+), Line = ([0-9]+)",
     "^ld([^:])*:([ \\t])*WARNING([^:])*:",
-    "([^:]+): warning ([0-9]+):",
     "^\"[^\"]+\", line [0-9]+: [Ww](arning|arnung)",
-    "([^:]+): warning[ \\t]*[0-9]+[ \\t]*:",
-    "^(Warning|Warnung) ([0-9]+):",
-    "^(Warning|Warnung)[ :]",
     "WARNING: ",
-    "([^ :]+) : warning",
-    "([^:]+): warning",
     "\", line [0-9]+\\.[0-9]+: [0-9]+-[0-9]+ \\([WI]\\)",
-    "^cxx: Warning:",
-    ".*file: .* has no symbols",
-    "([^ :]+):([0-9]+): (Warning|Warnung)",
     "\\([0-9]*\\): remark #[0-9]*",
     "\".*\", line [0-9]+: remark\\([0-9]*\\):",
     "cc-[0-9]* CC: REMARK File = .*, Line = [0-9]*",
-    "^CMake Warning.*:",
     "^\\[WARNING\\]",
 ]
 
 #: Regexes to match file/line numbers in error/warning messages
-warning_exceptions = [
+_warning_exceptions = [
     "/usr/.*/X11/Xlib\\.h:[0-9]+: war.*: ANSI C\\+\\+ forbids declaration",
     "/usr/.*/X11/Xutil\\.h:[0-9]+: war.*: ANSI C\\+\\+ forbids declaration",
     "/usr/.*/X11/XResource\\.h:[0-9]+: war.*: ANSI C\\+\\+ forbids declaration",
@@ -188,7 +236,7 @@ warning_exceptions = [
 ]
 
 #: Regexes to match file/line numbers in error/warning messages
-file_line_matches = [
+_file_line_matches = [
     "^Warning W[0-9]+ ([a-zA-Z.\\:/0-9_+ ~-]+) ([0-9]+):",
     "^([a-zA-Z./0-9_+ ~-]+):([0-9]+):",
     "^([a-zA-Z.\\:/0-9_+ ~-]+)\\(([0-9]+)\\)",
@@ -250,25 +298,120 @@ class BuildWarning(LogEvent):
     """LogEvent subclass for build warnings."""
 
 
+def chunks(l, n):
+    """Divide l into n approximately-even chunks."""
+    chunksize = int(math.ceil(len(l) / n))
+    return [l[i:i + chunksize] for i in range(0, len(l), chunksize)]
+
+
+@contextmanager
+def _time(times, i):
+    start = time.time()
+    yield
+    end = time.time()
+    times[i] += end - start
+
+
 def _match(matches, exceptions, line):
     """True if line matches a regex in matches and none in exceptions."""
     return (any(m.search(line) for m in matches) and
             not any(e.search(line) for e in exceptions))
 
 
-class CTestLogParser(object):
-    """Log file parser that extracts errors and warnings."""
-    def __init__(self):
-        def compile(regex_array):
-            return [re.compile(regex) for regex in regex_array]
+def _profile_match(matches, exceptions, line, match_times, exc_times):
+    """Profiled version of match().
+
+    Timing is expensive so we have two whole functions.  This is much
+    longer because we have to break up the ``any()`` calls.
+
+    """
+    for i, m in enumerate(matches):
+        with _time(match_times, i):
+            if m.search(line):
+                break
+    else:
+        return False
+
+    for i, m in enumerate(exceptions):
+        with _time(exc_times, i):
+            if m.search(line):
+                return False
+    else:
+        return True
+
+
+def _parse(lines, offset, profile):
+    def compile(regex_array):
+        return [regex if isinstance(regex, prefilter) else re.compile(regex)
+                for regex in regex_array]
+
+    error_matches      = compile(_error_matches)
+    error_exceptions   = compile(_error_exceptions)
+    warning_matches    = compile(_warning_matches)
+    warning_exceptions = compile(_warning_exceptions)
+    file_line_matches  = compile(_file_line_matches)
+
+    matcher, args = _match, []
+    timings = []
+    if profile:
+        matcher = _profile_match
+        timings = [
+            [0.0] * len(error_matches), [0.0] * len(error_exceptions),
+            [0.0] * len(warning_matches), [0.0] * len(warning_exceptions)]
+
+    errors = []
+    warnings = []
+    for i, line in enumerate(lines):
+        # use CTest's regular expressions to scrape the log for events
+        if matcher(error_matches, error_exceptions, line, *timings[:2]):
+            event = BuildError(line.strip(), offset + i + 1)
+            errors.append(event)
+        elif matcher(warning_matches, warning_exceptions, line, *timings[2:]):
+            event = BuildWarning(line.strip(), offset + i + 1)
+            warnings.append(event)
+        else:
+            continue
+
+        # get file/line number for each event, if possible
+        for flm in file_line_matches:
+            match = flm.search(line)
+            if match:
+                event.source_file, event.source_line_no = match.groups()
+
+    return errors, warnings, timings
+
+
+def _parse_unpack(args):
+    return _parse(*args)
 
-        self.error_matches      = compile(error_matches)
-        self.error_exceptions   = compile(error_exceptions)
-        self.warning_matches    = compile(warning_matches)
-        self.warning_exceptions = compile(warning_exceptions)
-        self.file_line_matches  = compile(file_line_matches)
 
-    def parse(self, stream, context=6):
+class CTestLogParser(object):
+    """Log file parser that extracts errors and warnings."""
+    def __init__(self, profile=False):
+        # whether to record timing information
+        self.timings = []
+        self.profile = profile
+
+    def print_timings(self):
+        """Print out profile of time spent in different regular expressions."""
+        def stringify(elt):
+            return elt if isinstance(elt, str) else elt.pattern
+
+        index = 0
+        for name, arr in [('error_matches', _error_matches),
+                          ('error_exceptions', _error_exceptions),
+                          ('warning_matches', _warning_matches),
+                          ('warning_exceptions', _warning_exceptions)]:
+
+            print()
+            print(name)
+            for i, elt in enumerate(arr):
+                print("%16.2f        %s" % (
+                    self.timings[index][i] * 1e6, stringify(elt)))
+            index += 1
+
+
+    def parse(self, stream, context=6, jobs=None):
         """Parse a log file by searching each line for errors and warnings.
 
         Args:
@@ -276,35 +419,50 @@ class CTestLogParser(object):
             context (int): lines of context to extract around each log event
 
         Returns:
-            (tuple): two lists containig ``BuildError`` and
+            (tuple): two lists containing ``BuildError`` and
                 ``BuildWarning`` objects.
         """
         if isinstance(stream, string_types):
             with open(stream) as f:
-                return self.parse(f)
+                return self.parse(f, context, jobs)
 
         lines = [line for line in stream]
 
-        errors = []
-        warnings = []
-        for i, line in enumerate(lines):
-            # use CTest's regular expressions to scrape the log for events
-            if _match(self.error_matches, self.error_exceptions, line):
-                event = BuildError(line.strip(), i + 1)
-                errors.append(event)
-            elif _match(self.warning_matches, self.warning_exceptions, line):
-                event = BuildWarning(line.strip(), i + 1)
-                warnings.append(event)
-            else:
-                continue
-
-            # get file/line number for each event, if possible
-            for flm in self.file_line_matches:
-                match = flm.search(line)
-                if match:
-                    event.source_file, source_line_no = match.groups()
-
-            # add log context, as well
+        if jobs is None:
+            jobs = multiprocessing.cpu_count()
+
+        # single-thread small logs
+        if len(lines) < 10 * jobs:
+            errors, warnings, self.timings = _parse(lines, 0, self.profile)
+
+        else:
+            # Build arguments for parallel jobs
+            args = []
+            offset = 0
+            for chunk in chunks(lines, jobs):
+                args.append((chunk, offset, self.profile))
+                offset += len(chunk)
+
+            # create a pool and farm out the matching job
+            pool = multiprocessing.Pool(jobs)
+            try:
+                # this is a workaround for a Python bug in Pool with ctrl-C
+                results = pool.map_async(_parse_unpack, args, 1).get(9999999)
+                errors, warnings, timings = zip(*results)
+            finally:
+                pool.terminate()
+
+            # merge results
+            errors = sum(errors, [])
+            warnings = sum(warnings, [])
+
+            if self.profile:
+                self.timings = [
+                    [sum(i) for i in zip(*t)] for t in zip(*timings)]
+
+        # add log context to all events
+        for event in (errors + warnings):
+            i = event.line_no - 1
             event.pre_context = [
                 l.rstrip() for l in lines[i - context:i]]
             event.post_context = [
diff --git a/lib/spack/external/distro.py b/lib/spack/external/distro.py
index c4905c25a5..b63451640a 100644
--- a/lib/spack/external/distro.py
+++ b/lib/spack/external/distro.py
@@ -41,7 +41,7 @@ import subprocess
 if not sys.platform.startswith('linux'):
     raise ImportError('Unsupported platform: {0}'.format(sys.platform))
 
-_UNIXCONFDIR = '/etc'
+_UNIXCONFDIR = os.environ.get('UNIXCONFDIR', '/etc')
 _OS_RELEASE_BASENAME = 'os-release'
 
 #: Translation table for normalizing the "ID" attribute defined in os-release
@@ -983,28 +983,41 @@ class LinuxDistribution(object):
                 distro_info['id'] = match.group(1)
             return distro_info
         else:
-            basenames = os.listdir(_UNIXCONFDIR)
-            # We sort for repeatability in cases where there are multiple
-            # distro specific files; e.g. CentOS, Oracle, Enterprise all
-            # containing `redhat-release` on top of their own.
-            basenames.sort()
+            try:
+                basenames = os.listdir(_UNIXCONFDIR)
+                # We sort for repeatability in cases where there are multiple
+                # distro specific files; e.g. CentOS, Oracle, Enterprise all
+                # containing `redhat-release` on top of their own.
+                basenames.sort()
+            except OSError:
+                # This may occur when /etc is not readable but we can't be
+                # sure about the *-release files. Check common entries of
+                # /etc for information. If they turn out to not be there the
+                # error is handled in `_parse_distro_release_file()`.
+                basenames = ['SuSE-release',
+                             'arch-release',
+                             'base-release',
+                             'centos-release',
+                             'fedora-release',
+                             'gentoo-release',
+                             'mageia-release',
+                             'manjaro-release',
+                             'oracle-release',
+                             'redhat-release',
+                             'sl-release',
+                             'slackware-version']
             for basename in basenames:
                 if basename in _DISTRO_RELEASE_IGNORE_BASENAMES:
                     continue
                 match = _DISTRO_RELEASE_BASENAME_PATTERN.match(basename)
                 if match:
-                    try:
-                        filepath = os.path.join(_UNIXCONFDIR, basename)
-                        distro_info = self._parse_distro_release_file(filepath)
-                        if 'name' in distro_info:
-                            # The name is always present if the pattern matches
-                            self.distro_release_file = filepath
-                            distro_info['id'] = match.group(1)
-                            return distro_info
-                    except IOError:
-                        # We found a file we do not have permission to read
-                        # Continue checking candidate files for distro file.
-                        continue
+                    filepath = os.path.join(_UNIXCONFDIR, basename)
+                    distro_info = self._parse_distro_release_file(filepath)
+                    if 'name' in distro_info:
+                        # The name is always present if the pattern matches
+                        self.distro_release_file = filepath
+                        distro_info['id'] = match.group(1)
+                        return distro_info
             return {}
 
     def _parse_distro_release_file(self, filepath):
@@ -1018,12 +1031,16 @@ class LinuxDistribution(object):
         Returns:
             A dictionary containing all information items.
         """
-        if os.path.isfile(filepath):
+        try:
             with open(filepath) as fp:
                 # Only parse the first line. For instance, on SLES there
                 # are multiple lines. We don't want them...
                 return self._parse_distro_release_content(fp.readline())
-        return {}
+        except (OSError, IOError):
+            # Ignore not being able to read a specific, seemingly version
+            # related file.
+            # See https://github.com/nir0s/distro/issues/162
+            return {}
 
     @staticmethod
     def _parse_distro_release_content(line):
@@ -1075,11 +1092,9 @@ def main():
     else:
         logger.info('Name: %s', name(pretty=True))
         distribution_version = version(pretty=True)
-        if distribution_version:
-            logger.info('Version: %s', distribution_version)
+        logger.info('Version: %s', distribution_version)
         distribution_codename = codename()
-        if distribution_codename:
-            logger.info('Codename: %s', distribution_codename)
+        logger.info('Codename: %s', distribution_codename)
 
 
 if __name__ == '__main__':
diff --git a/lib/spack/external/jinja2/AUTHORS b/lib/spack/external/jinja2/AUTHORS
deleted file mode 100644
index 943f625f87..0000000000
--- a/lib/spack/external/jinja2/AUTHORS
+++ /dev/null
@@ -1,33 +0,0 @@
-Jinja is written and maintained by the Jinja Team and various
-contributors:
-
-Lead Developer:
-
-- Armin Ronacher <armin.ronacher@active-4.com>
-
-Developers:
-
-- Christoph Hack
-- Georg Brandl
-
-Contributors:
-
-- Bryan McLemore
-- Mickaël Guérin <kael@crocobox.org>
-- Cameron Knight
-- Lawrence Journal-World.
-- David Cramer
-
-Patches and suggestions:
-
-- Ronny Pfannschmidt
-- Axel Böhm
-- Alexey Melchakov
-- Bryan McLemore
-- Clovis Fabricio (nosklo)
-- Cameron Knight
-- Peter van Dijk (Habbie)
-- Stefan Ebner
-- Rene Leonhardt
-- Thomas Waldmann
-- Cory Benfield (Lukasa)
diff --git a/lib/spack/external/jinja2/LICENSE b/lib/spack/external/jinja2/LICENSE
deleted file mode 100644
index 10145a2643..0000000000
--- a/lib/spack/external/jinja2/LICENSE
+++ /dev/null
@@ -1,31 +0,0 @@
-Copyright (c) 2009 by the Jinja Team, see AUTHORS for more details.

-

-Some rights reserved.

-

-Redistribution and use in source and binary forms, with or without

-modification, are permitted provided that the following conditions are

-met:

-

-    * Redistributions of source code must retain the above copyright

-      notice, this list of conditions and the following disclaimer.

-

-    * Redistributions in binary form must reproduce the above

-      copyright notice, this list of conditions and the following

-      disclaimer in the documentation and/or other materials provided

-      with the distribution.

-

-    * The names of the contributors may not be used to endorse or

-      promote products derived from this software without specific

-      prior written permission.

-

-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS

-"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT

-LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR

-A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT

-OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,

-SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT

-LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,

-DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY

-THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT

-(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE

-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

diff --git a/lib/spack/external/jinja2/README.rst b/lib/spack/external/jinja2/README.rst
deleted file mode 100644
index c36b9426d6..0000000000
--- a/lib/spack/external/jinja2/README.rst
+++ /dev/null
@@ -1,51 +0,0 @@
-Jinja2
-~~~~~~
-
-Jinja2 is a template engine written in pure Python.  It provides a
-`Django`_ inspired non-XML syntax but supports inline expressions and
-an optional `sandboxed`_ environment.
-
-Nutshell
---------
-
-Here a small example of a Jinja template:
-
-.. code-block:: jinja
-
-    {% extends 'base.html' %}
-    {% block title %}Memberlist{% endblock %}
-    {% block content %}
-      <ul>
-      {% for user in users %}
-        <li><a href="{{ user.url }}">{{ user.username }}</a></li>
-      {% endfor %}
-      </ul>
-    {% endblock %}
-
-Philosophy
-----------
-
-Application logic is for the controller, but don't make the template designer's
-life difficult by restricting functionality too much.
-
-For more information visit the new `Jinja2 webpage`_ and `documentation`_.
-
-The `Jinja2 tip`_ is installable via ``pip`` with ``pip install
-https://github.com/pallets/jinja/zipball/master``.
-
-.. _sandboxed: http://en.wikipedia.org/wiki/Sandbox_(computer_security)
-.. _Django: http://www.djangoproject.com/
-.. _Jinja2 webpage: http://jinja.pocoo.org/
-.. _documentation: http://jinja.pocoo.org/docs/
-.. _Jinja2 tip: http://jinja.pocoo.org/docs/intro/#as-a-python-egg-via-easy-install
-
-Builds
-------
-
-+---------------------+------------------------------------------------------------------------------+
-| ``master``          | .. image:: https://travis-ci.org/pallets/jinja.svg?branch=master             |
-|                     |     :target: https://travis-ci.org/pallets/jinja                             |
-+---------------------+------------------------------------------------------------------------------+
-| ``2.9-maintenance`` | .. image:: https://travis-ci.org/pallets/jinja.svg?branch=2.9-maintenance    |
-|                     |     :target: https://travis-ci.org/pallets/jinja                             |
-+---------------------+------------------------------------------------------------------------------+
diff --git a/lib/spack/external/jinja2/__init__.py b/lib/spack/external/jinja2/__init__.py
index 4b0b7a8d7f..42aa763d57 100644
--- a/lib/spack/external/jinja2/__init__.py
+++ b/lib/spack/external/jinja2/__init__.py
@@ -27,7 +27,7 @@
     :license: BSD, see LICENSE for more details.
 """
 __docformat__ = 'restructuredtext en'
-__version__ = '2.9.6'
+__version__ = '2.10'
 
 # high level interface
 from jinja2.environment import Environment, Template
@@ -48,7 +48,7 @@ from jinja2.runtime import Undefined, DebugUndefined, StrictUndefined, \
 # exceptions
 from jinja2.exceptions import TemplateError, UndefinedError, \
      TemplateNotFound, TemplatesNotFound, TemplateSyntaxError, \
-     TemplateAssertionError
+     TemplateAssertionError, TemplateRuntimeError
 
 # decorators and public utilities
 from jinja2.filters import environmentfilter, contextfilter, \
@@ -64,6 +64,7 @@ __all__ = [
     'MemcachedBytecodeCache', 'Undefined', 'DebugUndefined',
     'StrictUndefined', 'TemplateError', 'UndefinedError', 'TemplateNotFound',
     'TemplatesNotFound', 'TemplateSyntaxError', 'TemplateAssertionError',
+    'TemplateRuntimeError',
     'ModuleLoader', 'environmentfilter', 'contextfilter', 'Markup', 'escape',
     'environmentfunction', 'contextfunction', 'clear_caches', 'is_undefined',
     'evalcontextfilter', 'evalcontextfunction', 'make_logging_undefined',
diff --git a/lib/spack/external/jinja2/_identifier.py b/lib/spack/external/jinja2/_identifier.py
new file mode 100644
index 0000000000..2eac35d5c3
--- /dev/null
+++ b/lib/spack/external/jinja2/_identifier.py
@@ -0,0 +1,2 @@
+# generated by scripts/generate_identifier_pattern.py
+pattern = '·̀-ͯ·҃-֑҇-ׇֽֿׁׂׅׄؐ-ًؚ-ٰٟۖ-ۜ۟-۪ۤۧۨ-ܑۭܰ-݊ަ-ް߫-߳ࠖ-࠙ࠛ-ࠣࠥ-ࠧࠩ-࡙࠭-࡛ࣔ-ࣣ࣡-ःऺ-़ा-ॏ॑-ॗॢॣঁ-ঃ়া-ৄেৈো-্ৗৢৣਁ-ਃ਼ਾ-ੂੇੈੋ-੍ੑੰੱੵઁ-ઃ઼ા-ૅે-ૉો-્ૢૣଁ-ଃ଼ା-ୄେୈୋ-୍ୖୗୢୣஂா-ூெ-ைொ-்ௗఀ-ఃా-ౄె-ైొ-్ౕౖౢౣಁ-ಃ಼ಾ-ೄೆ-ೈೊ-್ೕೖೢೣഁ-ഃാ-ൄെ-ൈൊ-്ൗൢൣංඃ්ා-ුූෘ-ෟෲෳัิ-ฺ็-๎ັິ-ູົຼ່-ໍ༹༘༙༵༷༾༿ཱ-྄྆྇ྍ-ྗྙ-ྼ࿆ါ-ှၖ-ၙၞ-ၠၢ-ၤၧ-ၭၱ-ၴႂ-ႍႏႚ-ႝ፝-፟ᜒ-᜔ᜲ-᜴ᝒᝓᝲᝳ឴-៓៝᠋-᠍ᢅᢆᢩᤠ-ᤫᤰ-᤻ᨗ-ᨛᩕ-ᩞ᩠-᩿᩼᪰-᪽ᬀ-ᬄ᬴-᭄᭫-᭳ᮀ-ᮂᮡ-ᮭ᯦-᯳ᰤ-᰷᳐-᳔᳒-᳨᳭ᳲ-᳴᳸᳹᷀-᷵᷻-᷿‿⁀⁔⃐-⃥⃜⃡-⃰℘℮⳯-⵿⳱ⷠ-〪ⷿ-゙゚〯꙯ꙴ-꙽ꚞꚟ꛰꛱ꠂ꠆ꠋꠣ-ꠧꢀꢁꢴ-ꣅ꣠-꣱ꤦ-꤭ꥇ-꥓ꦀ-ꦃ꦳-꧀ꧥꨩ-ꨶꩃꩌꩍꩻ-ꩽꪰꪲ-ꪴꪷꪸꪾ꪿꫁ꫫ-ꫯꫵ꫶ꯣ-ꯪ꯬꯭ﬞ︀-️︠-︯︳︴﹍-﹏＿𐇽𐋠𐍶-𐍺𐨁-𐨃𐨅𐨆𐨌-𐨏𐨸-𐨿𐨺𐫦𐫥𑀀-𑀂𑀸-𑁆𑁿-𑂂𑂰-𑂺𑄀-𑄂𑄧-𑅳𑄴𑆀-𑆂𑆳-𑇊𑇀-𑇌𑈬-𑈷𑈾𑋟-𑋪𑌀-𑌃𑌼𑌾-𑍄𑍇𑍈𑍋-𑍍𑍗𑍢𑍣𑍦-𑍬𑍰-𑍴𑐵-𑑆𑒰-𑓃𑖯-𑖵𑖸-𑗀𑗜𑗝𑘰-𑙀𑚫-𑚷𑜝-𑜫𑰯-𑰶𑰸-𑰿𑲒-𑲧𑲩-𑲶𖫰-𖫴𖬰-𖬶𖽑-𖽾𖾏-𖾒𛲝𛲞𝅥-𝅩𝅭-𝅲𝅻-𝆂𝆅-𝆋𝆪-𝆭𝉂-𝉄𝨀-𝨶𝨻-𝩬𝩵𝪄𝪛-𝪟𝪡-𝪯𞀀-𞀆𞀈-𞀘𞀛-𞀡𞀣𞀤𞀦-𞣐𞀪-𞣖𞥄-𞥊󠄀-󠇯'
diff --git a/lib/spack/external/jinja2/_stringdefs.py b/lib/spack/external/jinja2/_stringdefs.py
deleted file mode 100644
index a5689f6695..0000000000
--- a/lib/spack/external/jinja2/_stringdefs.py
+++ /dev/null
@@ -1,71 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-    jinja2._stringdefs
-    ~~~~~~~~~~~~~~~~~~
-
-    Strings of all Unicode characters of a certain category.
-    Used for matching in Unicode-aware languages. Run to regenerate.
-
-    Inspired by chartypes_create.py from the MoinMoin project, original
-    implementation from Pygments.
-
-    :copyright: Copyright 2006-2017 by the Jinja team, see AUTHORS.
-    :license: BSD, see LICENSE for details.
-"""
-
-# Generated code start
-
-xid_start = 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-xid_continue = 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\ufa56\ufa57\ufa58\ufa59\ufa5a\ufa5b\ufa5c\ufa5d\ufa5e\ufa5f\ufa60\ufa61\ufa62\ufa63\ufa64\ufa65\ufa66\ufa67\ufa68\ufa69\ufa6a\ufa6b\ufa6d\ufa70\ufa71\ufa72\ufa73\ufa74\ufa75\ufa76\ufa77\ufa78\ufa79\ufa7a\ufa7b\ufa7c\ufa7d\ufa7e\ufa7f\ufa80\ufa81\ufa82\ufa83\ufa84\ufa85\ufa86\ufa87\ufa88\ufa89\ufa8a\ufa8b\ufa8c\ufa8d\ufa8e\ufa8f\ufa90\ufa91\ufa92\ufa93\ufa94\ufa95\ufa96\ufa97\ufa98\ufa99\ufa9a\ufa9b\ufa9c\ufa9d\ufa9e\ufa9f\ufaa0\ufaa1\ufaa2\ufaa3\ufaa4\ufaa5\ufaa6\ufaa7\ufaa8\ufaa9\ufaaa\ufaab\ufaac\ufaad\ufaae\ufaaf\ufab0\ufab1\ufab2\ufab3\ufab4\ufab5\ufab6\ufab7\ufab8\ufab9\ufaba\ufabb\ufabc\ufabd\ufabe\ufabf\ufac0\ufac1\ufac2\ufac3\ufac4\ufac5\ufac6\ufac7\ufac8\ufac9\ufaca\ufacb\ufacc\ufacd\uface\ufad2\ufad3\ufad4\ufad8\ufad9\ufb1e\ufb20\ufb21\ufb22\ufb23\ufb24\ufb25\ufb26\ufb27\ufb28\ufb50\ufb51\ufb52\ufb53\ufb54\ufb55\ufb56\ufb57\ufb58\ufb59\ufb5a\ufb5b\ufb5c\ufb5d\ufb5e\ufb5f\ufb60\ufb61\ufb62\ufb63\ufb64\ufb65\ufb66\ufb67\ufb68\ufb69\ufb6a\ufb6b\ufb6c\ufb6d\ufb6e\ufb6f\ufb70\ufb71\ufb72\ufb73\ufb74\ufb75\ufb76\ufb77\ufb78\ufb79\ufb7a\ufb7b\ufb7c\ufb7d\ufb7e\ufb7f\ufb80\ufb81\ufb82\ufb83\ufb84\ufb85\ufb86\ufb87\ufb88\ufb89\ufb8a\ufb8b\ufb8c\ufb8d\ufb8e\ufb8f\ufb90\ufb91\ufb92\ufb93\ufb94\ufb95\ufb96\ufb97\ufb98\ufb99\ufb9a\ufb9b\ufb9c\ufb9d\ufb9e\ufb9f\ufba0\ufba1\ufba2\ufba3\ufba4\ufba5\ufba6\ufba7\ufba8\ufba9\ufbaa\ufbab\ufbac\ufbad\ufbae\ufbaf\ufbb0\ufbb1\ufbd3\ufbd4\ufbd5\ufbd6\ufbd7\ufbd8\ufbd9\ufbda\ufbdb\ufbdc\ufbde\ufbdf\ufbe0\ufbe1\ufbe2\ufbe3\ufbe4\ufbe5\ufbe6\ufbe7\ufbe8\ufbe9\ufbfc\ufbfd\ufbfe\ufbff\ufe00\ufe01\ufe02\ufe03\ufe04\ufe05\ufe06\ufe07\ufe08\ufe09\ufe0a\ufe0b\ufe0c\ufe0d\ufe0e\ufe0f\ufe20\ufe21\ufe22\ufe23\ufe24\ufe25\ufe26\ufe27\ufe28\ufe29\ufe2a\ufe2b\ufe2c\ufe2d\ufe2e\ufe2f\ufe33\ufe34\ufe4d\ufe4e\ufe4f\ufe73\ufe80\ufe81\ufe82\ufe83\ufe84\ufe85\ufe86\ufe87\ufe88\ufe89\ufe8a\ufe8b\ufe8c\ufe8d\ufe8e\ufe8f\ufe90\ufe91\ufe92\ufe93\ufe94\ufe95\ufe96\ufe97\ufe98\ufe99\ufe9a\ufe9b\ufe9c\ufe9d\ufe9e\ufe9f\ufea0\ufea1\ufea2\ufea3\ufea4\ufea5\ufea6\ufea7\ufea8\ufea9\ufeaa\ufeab\ufeac\ufead\ufeae\ufeaf\ufeb0\ufeb1\ufeb2\ufeb3\ufeb4\ufeb5\ufeb6\ufeb7\ufeb8\ufeb9\ufeba\ufebb\ufebc\ufebd\ufebe\ufebf\ufec0\ufec1\ufec2\ufec3\ufec4\ufec5\ufec6\ufec7\ufec8\ufec9\ufeca\ufecb\ufecc\ufecd\ufece\ufecf\ufed0\ufed1\ufed2\ufed3\ufed4\ufed5\ufed6\ufed7\ufed8\ufed9\ufeda\ufedb\ufedc\ufedd\ufede\ufedf\ufee0\ufee1\ufee2\ufee3\ufee4\ufee5\ufee6\ufee7\ufee8\ufee9\ufeea\ufeeb\ufeec\ufeed\ufeee\ufeef\ufef0\ufef1\ufef2\ufef3\ufef4\uff10\uff11\uff12\uff13\uff14\uff15\uff16\uff17\uff18\uff19\uff21\uff22\uff23\uff24\uff25\uff26\uff27\uff28\uff29\uff2a\uff2b\uff2c\uff2d\uff2e\uff2f\uff30\uff31\uff32\uff33\uff34\uff35\uff36\uff37\uff38\uff39\uff3a\uff3f\uff41\uff42\uff43\uff44\uff45\uff46\uff47\uff48\uff49\uff4a\uff4b\uff4c\uff4d\uff4e\uff4f\uff50\uff51\uff52\uff53\uff54\uff55\uff56\uff57\uff58\uff59\uff5a\uff66\uff67\uff68\uff69\uff6a\uff6b\uff6c\uff6d\uff6e\uff6f\uff70\uff71\uff72\uff73\uff74\uff75\uff76\uff77\uff78\uff79\uff7a\uff7b\uff7c\uff7d\uff7e\uff7f\uff80\uff81\uff82\uff83\uff84\uff85\uff86\uff87\uff88\uff89\uff8a\uff8b\uff8c\uff8d\uff8e\uff8f\uff90\uff91\uff92\uff93\uff94\uff95\uff96\uff97\uff98\uff99\uff9a\uff9b\uff9c\uff9d\uff9e\uff9f\uffa0\uffa1\uffa2\uffa3\uffa4\uffa5\uffa6\uffa7\uffa8\uffa9\uffaa\uffab\uffac\uffad\uffae\uffaf\uffb0\uffb1\uffb2\uffb3\uffb4\uffb5\uffb6\uffb7\uffb8\uffb9\uffba\uffbb\uffbc\uffbd\uffbe\uffc2\uffc3\uffc4\uffc5\uffc6\uffc7\uffca\uffcb\uffcc\uffcd\uffce\uffcf\uffd2\uffd3\uffd4\uffd5\uffd6\uffd7\uffda\uffdb\uffdc'
-# Generated code end
-
-if __name__ == '__main__':
-    import sys
-    import unicodedata
-
-    if sys.version_info[0] < 3:
-        raise RuntimeError('This needs to run on python 3')
-
-    categories = {}
-
-    f = open(__file__.rstrip('co'))
-    try:
-        content = f.read()
-    finally:
-        f.close()
-
-    start = '# Generated code start\n'
-    header = content[:content.find(start) + len(start)] + '\n'
-    footer = content[content.find("# Generated code end\n"):]
-
-    for code in range(65535):
-        c = chr(code)
-        cat = unicodedata.category(c)
-        categories.setdefault(cat, []).append(c)
-
-    # from 8.0.0 PropList (Other_ID_Start) + underscore
-    id_start = set(u'_\u2118\u212E\u309B\u309C')
-    for cat in 'Lu', 'Ll', 'Lt', 'Lm', 'Lo', 'Nl':
-        id_start.update(categories[cat])
-
-    # from 8.0.0 PropList (Other_ID_Continue)
-    id_continue = set(id_start)
-    id_continue.update(u'\u00B7\u0387\u1369\u1370\u1371\u19DA')
-    for cat in 'Mn', 'Mc', 'Nd', 'Pc':
-        id_continue.update(categories[cat])
-
-    xid_start = u''.join(sorted(c for c in id_continue if
-                                unicodedata.normalize('NFKC', c)
-                                in id_start))
-    xid_continue = u''.join(sorted(c for c in id_continue if
-                                   unicodedata.normalize('NFKC', c) in
-                                   id_continue))
-
-    f = open(__file__, 'w')
-    f.write(header)
-
-    f.write('xid_start = %s\nxid_continue = %s\n' % (ascii(xid_start),
-                                                     ascii(xid_continue)))
-
-    f.write(footer)
-    f.close()
diff --git a/lib/spack/external/jinja2/asyncsupport.py b/lib/spack/external/jinja2/asyncsupport.py
index f4f264ad8c..b1e7b5ce9a 100644
--- a/lib/spack/external/jinja2/asyncsupport.py
+++ b/lib/spack/external/jinja2/asyncsupport.py
@@ -189,9 +189,9 @@ async def auto_aiter(iterable):
 
 class AsyncLoopContext(LoopContextBase):
 
-    def __init__(self, async_iterator, after, length, recurse=None,
+    def __init__(self, async_iterator, undefined, after, length, recurse=None,
                  depth0=0):
-        LoopContextBase.__init__(self, recurse, depth0)
+        LoopContextBase.__init__(self, undefined, recurse, depth0)
         self._async_iterator = async_iterator
         self._after = after
         self._length = length
@@ -221,15 +221,16 @@ class AsyncLoopContextIterator(object):
         ctx.index0 += 1
         if ctx._after is _last_iteration:
             raise StopAsyncIteration()
-        next_elem = ctx._after
+        ctx._before = ctx._current
+        ctx._current = ctx._after
         try:
             ctx._after = await ctx._async_iterator.__anext__()
         except StopAsyncIteration:
             ctx._after = _last_iteration
-        return next_elem, ctx
+        return ctx._current, ctx
 
 
-async def make_async_loop_context(iterable, recurse=None, depth0=0):
+async def make_async_loop_context(iterable, undefined, recurse=None, depth0=0):
     # Length is more complicated and less efficient in async mode.  The
     # reason for this is that we cannot know if length will be used
     # upfront but because length is a property we cannot lazily execute it
@@ -251,4 +252,5 @@ async def make_async_loop_context(iterable, recurse=None, depth0=0):
         after = await async_iterator.__anext__()
     except StopAsyncIteration:
         after = _last_iteration
-    return AsyncLoopContext(async_iterator, after, length, recurse, depth0)
+    return AsyncLoopContext(async_iterator, undefined, after, length, recurse,
+                            depth0)
diff --git a/lib/spack/external/jinja2/bccache.py b/lib/spack/external/jinja2/bccache.py
index d687d036fb..080e527cab 100644
--- a/lib/spack/external/jinja2/bccache.py
+++ b/lib/spack/external/jinja2/bccache.py
@@ -297,7 +297,7 @@ class MemcachedBytecodeCache(BytecodeCache):
     Libraries compatible with this class:
 
     -   `werkzeug <http://werkzeug.pocoo.org/>`_.contrib.cache
-    -   `python-memcached <http://www.tummy.com/Community/software/python-memcached/>`_
+    -   `python-memcached <https://www.tummy.com/Community/software/python-memcached/>`_
     -   `cmemcache <http://gijsbert.org/cmemcache/>`_
 
     (Unfortunately the django cache interface is not compatible because it
diff --git a/lib/spack/external/jinja2/compiler.py b/lib/spack/external/jinja2/compiler.py
index b2ab6fe6a8..d534a82739 100644
--- a/lib/spack/external/jinja2/compiler.py
+++ b/lib/spack/external/jinja2/compiler.py
@@ -130,9 +130,10 @@ class MacroRef(object):
 class Frame(object):
     """Holds compile time information for us."""
 
-    def __init__(self, eval_ctx, parent=None):
+    def __init__(self, eval_ctx, parent=None, level=None):
         self.eval_ctx = eval_ctx
-        self.symbols = Symbols(parent and parent.symbols or None)
+        self.symbols = Symbols(parent and parent.symbols or None,
+                               level=level)
 
         # a toplevel frame is the root + soft frames such as if conditions.
         self.toplevel = False
@@ -168,8 +169,10 @@ class Frame(object):
         rv.symbols = self.symbols.copy()
         return rv
 
-    def inner(self):
+    def inner(self, isolated=False):
         """Return an inner frame."""
+        if isolated:
+            return Frame(self.eval_ctx, level=self.symbols.level + 1)
         return Frame(self.eval_ctx, self)
 
     def soft(self):
@@ -302,6 +305,9 @@ class CodeGenerator(NodeVisitor):
         # Tracks parameter definition blocks
         self._param_def_block = []
 
+        # Tracks the current context.
+        self._context_reference_stack = ['context']
+
     # -- Various compilation helpers
 
     def fail(self, msg, lineno):
@@ -472,8 +478,8 @@ class CodeGenerator(NodeVisitor):
             if action == VAR_LOAD_PARAMETER:
                 pass
             elif action == VAR_LOAD_RESOLVE:
-                self.writeline('%s = resolve(%r)' %
-                               (target, param))
+                self.writeline('%s = %s(%r)' %
+                               (target, self.get_resolve_func(), param))
             elif action == VAR_LOAD_ALIAS:
                 self.writeline('%s = %s' % (target, param))
             elif action == VAR_LOAD_UNDEFINED:
@@ -625,6 +631,27 @@ class CodeGenerator(NodeVisitor):
         if self._param_def_block:
             self._param_def_block[-1].discard(target)
 
+    def push_context_reference(self, target):
+        self._context_reference_stack.append(target)
+
+    def pop_context_reference(self):
+        self._context_reference_stack.pop()
+
+    def get_context_ref(self):
+        return self._context_reference_stack[-1]
+
+    def get_resolve_func(self):
+        target = self._context_reference_stack[-1]
+        if target == 'context':
+            return 'resolve'
+        return '%s.resolve' % target
+
+    def derive_context(self, frame):
+        return '%s.derived(%s)' % (
+            self.get_context_ref(),
+            self.dump_local_context(frame),
+        )
+
     def parameter_is_undeclared(self, target):
         """Checks if a given target is an undeclared parameter."""
         if not self._param_def_block:
@@ -793,8 +820,11 @@ class CodeGenerator(NodeVisitor):
                 self.writeline('if parent_template is None:')
                 self.indent()
                 level += 1
-        context = node.scoped and (
-            'context.derived(%s)' % self.dump_local_context(frame)) or 'context'
+
+        if node.scoped:
+            context = self.derive_context(frame)
+        else:
+            context = self.get_context_ref()
 
         if supports_yield_from and not self.environment.is_async and \
            frame.buffer is None:
@@ -1082,9 +1112,9 @@ class CodeGenerator(NodeVisitor):
             self.write(')')
 
         if node.recursive:
-            self.write(', loop_render_func, depth):')
+            self.write(', undefined, loop_render_func, depth):')
         else:
-            self.write(extended_loop and '):' or ':')
+            self.write(extended_loop and ', undefined):' or ':')
 
         self.indent()
         self.enter_frame(loop_frame)
@@ -1129,6 +1159,13 @@ class CodeGenerator(NodeVisitor):
         self.indent()
         self.blockvisit(node.body, if_frame)
         self.outdent()
+        for elif_ in node.elif_:
+            self.writeline('elif ', elif_)
+            self.visit(elif_.test, if_frame)
+            self.write(':')
+            self.indent()
+            self.blockvisit(elif_.body, if_frame)
+            self.outdent()
         if node.else_:
             self.writeline('else:')
             self.indent()
@@ -1348,7 +1385,12 @@ class CodeGenerator(NodeVisitor):
         self.newline(node)
         self.visit(node.target, frame)
         self.write(' = (Markup if context.eval_ctx.autoescape '
-                   'else identity)(concat(%s))' % block_frame.buffer)
+                   'else identity)(')
+        if node.filter is not None:
+            self.visit_Filter(node.filter, block_frame)
+        else:
+            self.write('concat(%s)' % block_frame.buffer)
+        self.write(')')
         self.pop_assign_tracking(frame)
         self.leave_frame(block_frame)
 
@@ -1373,6 +1415,18 @@ class CodeGenerator(NodeVisitor):
 
         self.write(ref)
 
+    def visit_NSRef(self, node, frame):
+        # NSRefs can only be used to store values; since they use the normal
+        # `foo.bar` notation they will be parsed as a normal attribute access
+        # when used anywhere but in a `set` context
+        ref = frame.symbols.ref(node.name)
+        self.writeline('if not isinstance(%s, Namespace):' % ref)
+        self.indent()
+        self.writeline('raise TemplateRuntimeError(%r)' %
+                       'cannot assign attribute on non-namespace object')
+        self.outdent()
+        self.writeline('%s[%r]' % (ref, node.attr))
+
     def visit_Const(self, node, frame):
         val = node.as_const(frame.eval_ctx)
         if isinstance(val, float):
@@ -1631,6 +1685,20 @@ class CodeGenerator(NodeVisitor):
         self.blockvisit(node.body, scope_frame)
         self.leave_frame(scope_frame)
 
+    def visit_OverlayScope(self, node, frame):
+        ctx = self.temporary_identifier()
+        self.writeline('%s = %s' % (ctx, self.derive_context(frame)))
+        self.writeline('%s.vars = ' % ctx)
+        self.visit(node.context, frame)
+        self.push_context_reference(ctx)
+
+        scope_frame = frame.inner(isolated=True)
+        scope_frame.symbols.analyze_node(node)
+        self.enter_frame(scope_frame)
+        self.blockvisit(node.body, scope_frame)
+        self.leave_frame(scope_frame)
+        self.pop_context_reference()
+
     def visit_EvalContextModifier(self, node, frame):
         for keyword in node.options:
             self.writeline('context.eval_ctx.%s = ' % keyword.key)
diff --git a/lib/spack/external/jinja2/debug.py b/lib/spack/external/jinja2/debug.py
index 07c21f1a8b..b61139f0cd 100644
--- a/lib/spack/external/jinja2/debug.py
+++ b/lib/spack/external/jinja2/debug.py
@@ -198,7 +198,7 @@ def translate_exception(exc_info, initial_skip=0):
 def get_jinja_locals(real_locals):
     ctx = real_locals.get('context')
     if ctx:
-        locals = ctx.get_all()
+        locals = ctx.get_all().copy()
     else:
         locals = {}
 
diff --git a/lib/spack/external/jinja2/defaults.py b/lib/spack/external/jinja2/defaults.py
index 35903883cd..7c93dec0ae 100644
--- a/lib/spack/external/jinja2/defaults.py
+++ b/lib/spack/external/jinja2/defaults.py
@@ -9,7 +9,7 @@
     :license: BSD, see LICENSE for more details.
 """
 from jinja2._compat import range_type
-from jinja2.utils import generate_lorem_ipsum, Cycler, Joiner
+from jinja2.utils import generate_lorem_ipsum, Cycler, Joiner, Namespace
 
 
 # defaults for the parser / lexer
@@ -35,7 +35,8 @@ DEFAULT_NAMESPACE = {
     'dict':         dict,
     'lipsum':       generate_lorem_ipsum,
     'cycler':       Cycler,
-    'joiner':       Joiner
+    'joiner':       Joiner,
+    'namespace':    Namespace
 }
 
 
@@ -47,6 +48,7 @@ DEFAULT_POLICIES = {
     'truncate.leeway':      5,
     'json.dumps_function':  None,
     'json.dumps_kwargs':    {'sort_keys': True},
+    'ext.i18n.trimmed':     False,
 }
 
 
diff --git a/lib/spack/external/jinja2/environment.py b/lib/spack/external/jinja2/environment.py
index 2a4d3d7da9..549d9afab4 100644
--- a/lib/spack/external/jinja2/environment.py
+++ b/lib/spack/external/jinja2/environment.py
@@ -809,7 +809,7 @@ class Environment(object):
     @internalcode
     def get_template(self, name, parent=None, globals=None):
         """Load a template from the loader.  If a loader is configured this
-        method ask the loader for the template and returns a :class:`Template`.
+        method asks the loader for the template and returns a :class:`Template`.
         If the `parent` parameter is not `None`, :meth:`join_path` is called
         to get the real template name before loading.
 
diff --git a/lib/spack/external/jinja2/ext.py b/lib/spack/external/jinja2/ext.py
index 75e1f3b625..0734a84f73 100644
--- a/lib/spack/external/jinja2/ext.py
+++ b/lib/spack/external/jinja2/ext.py
@@ -10,6 +10,8 @@
     :copyright: (c) 2017 by the Jinja Team.
     :license: BSD.
 """
+import re
+
 from jinja2 import nodes
 from jinja2.defaults import BLOCK_START_STRING, \
      BLOCK_END_STRING, VARIABLE_START_STRING, VARIABLE_END_STRING, \
@@ -223,6 +225,7 @@ class InternationalizationExtension(Extension):
         plural_expr = None
         plural_expr_assignment = None
         variables = {}
+        trimmed = None
         while parser.stream.current.type != 'block_end':
             if variables:
                 parser.stream.expect('comma')
@@ -241,6 +244,9 @@ class InternationalizationExtension(Extension):
             if parser.stream.current.type == 'assign':
                 next(parser.stream)
                 variables[name.value] = var = parser.parse_expression()
+            elif trimmed is None and name.value in ('trimmed', 'notrimmed'):
+                trimmed = name.value == 'trimmed'
+                continue
             else:
                 variables[name.value] = var = nodes.Name(name.value, 'load')
 
@@ -256,7 +262,7 @@ class InternationalizationExtension(Extension):
 
         parser.stream.expect('block_end')
 
-        plural = plural_names = None
+        plural = None
         have_plural = False
         referenced = set()
 
@@ -297,6 +303,13 @@ class InternationalizationExtension(Extension):
         elif plural_expr is None:
             parser.fail('pluralize without variables', lineno)
 
+        if trimmed is None:
+            trimmed = self.environment.policies['ext.i18n.trimmed']
+        if trimmed:
+            singular = self._trim_whitespace(singular)
+            if plural:
+                plural = self._trim_whitespace(plural)
+
         node = self._make_node(singular, plural, variables, plural_expr,
                                bool(referenced),
                                num_called_num and have_plural)
@@ -306,6 +319,9 @@ class InternationalizationExtension(Extension):
         else:
             return node
 
+    def _trim_whitespace(self, string, _ws_re=re.compile(r'\s*\n\s*')):
+        return _ws_re.sub(' ', string.strip())
+
     def _parse_block(self, parser, allow_pluralize):
         """Parse until the next block tag with a given name."""
         referenced = []
@@ -583,6 +599,8 @@ def babel_extract(fileobj, keywords, comment_tags, options):
         auto_reload=False
     )
 
+    if getbool(options, 'trimmed'):
+        environment.policies['ext.i18n.trimmed'] = True
     if getbool(options, 'newstyle_gettext'):
         environment.newstyle_gettext = True
 
diff --git a/lib/spack/external/jinja2/filters.py b/lib/spack/external/jinja2/filters.py
index 76e04db665..267ddddaa0 100644
--- a/lib/spack/external/jinja2/filters.py
+++ b/lib/spack/external/jinja2/filters.py
@@ -10,9 +10,10 @@
 """
 import re
 import math
+import random
+import warnings
 
-from random import choice
-from itertools import groupby
+from itertools import groupby, chain
 from collections import namedtuple
 from jinja2.utils import Markup, escape, pformat, urlize, soft_unicode, \
      unicode_urlencode, htmlsafe_json_dumps
@@ -52,22 +53,34 @@ def environmentfilter(f):
     return f
 
 
-def make_attrgetter(environment, attribute):
+def ignore_case(value):
+    """For use as a postprocessor for :func:`make_attrgetter`. Converts strings
+    to lowercase and returns other types as-is."""
+    return value.lower() if isinstance(value, string_types) else value
+
+
+def make_attrgetter(environment, attribute, postprocess=None):
     """Returns a callable that looks up the given attribute from a
     passed object with the rules of the environment.  Dots are allowed
     to access attributes of attributes.  Integer parts in paths are
     looked up as integers.
     """
-    if not isinstance(attribute, string_types) \
-       or ('.' not in attribute and not attribute.isdigit()):
-        return lambda x: environment.getitem(x, attribute)
-    attribute = attribute.split('.')
+    if attribute is None:
+        attribute = []
+    elif isinstance(attribute, string_types):
+        attribute = [int(x) if x.isdigit() else x for x in attribute.split('.')]
+    else:
+        attribute = [attribute]
+
     def attrgetter(item):
         for part in attribute:
-            if part.isdigit():
-                part = int(part)
             item = environment.getitem(item, part)
+
+        if postprocess is not None:
+            item = postprocess(item)
+
         return item
+
     return attrgetter
 
 
@@ -190,7 +203,7 @@ def do_title(s):
          if item])
 
 
-def do_dictsort(value, case_sensitive=False, by='key'):
+def do_dictsort(value, case_sensitive=False, by='key', reverse=False):
     """Sort a dict and yield (key, value) pairs. Because python dicts are
     unsorted you may want to use this function to order them by either
     key or value:
@@ -200,6 +213,9 @@ def do_dictsort(value, case_sensitive=False, by='key'):
         {% for item in mydict|dictsort %}
             sort the dict by key, case insensitive
 
+        {% for item in mydict|dictsort(reverse=true) %}
+            sort the dict by key, case insensitive, reverse order
+
         {% for item in mydict|dictsort(true) %}
             sort the dict by key, case sensitive
 
@@ -211,20 +227,25 @@ def do_dictsort(value, case_sensitive=False, by='key'):
     elif by == 'value':
         pos = 1
     else:
-        raise FilterArgumentError('You can only sort by either '
-                                  '"key" or "value"')
+        raise FilterArgumentError(
+            'You can only sort by either "key" or "value"'
+        )
+
     def sort_func(item):
         value = item[pos]
-        if isinstance(value, string_types) and not case_sensitive:
-            value = value.lower()
+
+        if not case_sensitive:
+            value = ignore_case(value)
+
         return value
 
-    return sorted(value.items(), key=sort_func)
+    return sorted(value.items(), key=sort_func, reverse=reverse)
 
 
 @environmentfilter
-def do_sort(environment, value, reverse=False, case_sensitive=False,
-            attribute=None):
+def do_sort(
+    environment, value, reverse=False, case_sensitive=False, attribute=None
+):
     """Sort an iterable.  Per default it sorts ascending, if you pass it
     true as first argument it will reverse the sorting.
 
@@ -250,18 +271,85 @@ def do_sort(environment, value, reverse=False, case_sensitive=False,
     .. versionchanged:: 2.6
        The `attribute` parameter was added.
     """
-    if not case_sensitive:
-        def sort_func(item):
-            if isinstance(item, string_types):
-                item = item.lower()
-            return item
-    else:
-        sort_func = None
-    if attribute is not None:
-        getter = make_attrgetter(environment, attribute)
-        def sort_func(item, processor=sort_func or (lambda x: x)):
-            return processor(getter(item))
-    return sorted(value, key=sort_func, reverse=reverse)
+    key_func = make_attrgetter(
+        environment, attribute,
+        postprocess=ignore_case if not case_sensitive else None
+    )
+    return sorted(value, key=key_func, reverse=reverse)
+
+
+@environmentfilter
+def do_unique(environment, value, case_sensitive=False, attribute=None):
+    """Returns a list of unique items from the the given iterable.
+
+    .. sourcecode:: jinja
+
+        {{ ['foo', 'bar', 'foobar', 'FooBar']|unique }}
+            -> ['foo', 'bar', 'foobar']
+
+    The unique items are yielded in the same order as their first occurrence in
+    the iterable passed to the filter.
+
+    :param case_sensitive: Treat upper and lower case strings as distinct.
+    :param attribute: Filter objects with unique values for this attribute.
+    """
+    getter = make_attrgetter(
+        environment, attribute,
+        postprocess=ignore_case if not case_sensitive else None
+    )
+    seen = set()
+
+    for item in value:
+        key = getter(item)
+
+        if key not in seen:
+            seen.add(key)
+            yield item
+
+
+def _min_or_max(environment, value, func, case_sensitive, attribute):
+    it = iter(value)
+
+    try:
+        first = next(it)
+    except StopIteration:
+        return environment.undefined('No aggregated item, sequence was empty.')
+
+    key_func = make_attrgetter(
+        environment, attribute,
+        ignore_case if not case_sensitive else None
+    )
+    return func(chain([first], it), key=key_func)
+
+
+@environmentfilter
+def do_min(environment, value, case_sensitive=False, attribute=None):
+    """Return the smallest item from the sequence.
+
+    .. sourcecode:: jinja
+
+        {{ [1, 2, 3]|min }}
+            -> 1
+
+    :param case_sensitive: Treat upper and lower case strings as distinct.
+    :param attribute: Get the object with the max value of this attribute.
+    """
+    return _min_or_max(environment, value, min, case_sensitive, attribute)
+
+
+@environmentfilter
+def do_max(environment, value, case_sensitive=False, attribute=None):
+    """Return the largest item from the sequence.
+
+    .. sourcecode:: jinja
+
+        {{ [1, 2, 3]|max }}
+            -> 3
+
+    :param case_sensitive: Treat upper and lower case strings as distinct.
+    :param attribute: Get the object with the max value of this attribute.
+    """
+    return _min_or_max(environment, value, max, case_sensitive, attribute)
 
 
 def do_default(value, default_value=u'', boolean=False):
@@ -359,13 +447,13 @@ def do_last(environment, seq):
         return environment.undefined('No last item, sequence was empty.')
 
 
-@environmentfilter
-def do_random(environment, seq):
+@contextfilter
+def do_random(context, seq):
     """Return a random item from the sequence."""
     try:
-        return choice(seq)
+        return random.choice(seq)
     except IndexError:
-        return environment.undefined('No random item, sequence was empty.')
+        return context.environment.undefined('No random item, sequence was empty.')
 
 
 def do_filesizeformat(value, binary=False):
@@ -445,21 +533,44 @@ def do_urlize(eval_ctx, value, trim_url_limit=None, nofollow=False,
     return rv
 
 
-def do_indent(s, width=4, indentfirst=False):
-    """Return a copy of the passed string, each line indented by
-    4 spaces. The first line is not indented. If you want to
-    change the number of spaces or indent the first line too
-    you can pass additional parameters to the filter:
+def do_indent(
+    s, width=4, first=False, blank=False, indentfirst=None
+):
+    """Return a copy of the string with each line indented by 4 spaces. The
+    first line and blank lines are not indented by default.
 
-    .. sourcecode:: jinja
+    :param width: Number of spaces to indent by.
+    :param first: Don't skip indenting the first line.
+    :param blank: Don't skip indenting empty lines.
 
-        {{ mytext|indent(2, true) }}
-            indent by two spaces and indent the first line too.
+    .. versionchanged:: 2.10
+        Blank lines are not indented by default.
+
+        Rename the ``indentfirst`` argument to ``first``.
     """
+    if indentfirst is not None:
+        warnings.warn(DeprecationWarning(
+            'The "indentfirst" argument is renamed to "first".'
+        ), stacklevel=2)
+        first = indentfirst
+
+    s += u'\n'  # this quirk is necessary for splitlines method
     indention = u' ' * width
-    rv = (u'\n' + indention).join(s.splitlines())
-    if indentfirst:
+
+    if blank:
+        rv = (u'\n' + indention).join(s.splitlines())
+    else:
+        lines = s.splitlines()
+        rv = lines.pop(0)
+
+        if lines:
+            rv += u'\n' + u'\n'.join(
+                indention + line if line else line for line in lines
+            )
+
+    if first:
         rv = indention + rv
+
     return rv
 
 
@@ -865,6 +976,9 @@ def do_select(*args, **kwargs):
 
         {{ numbers|select("odd") }}
         {{ numbers|select("odd") }}
+        {{ numbers|select("divisibleby", 3) }}
+        {{ numbers|select("lessthan", 42) }}
+        {{ strings|select("equalto", "mystring") }}
 
     .. versionadded:: 2.7
     """
@@ -1045,6 +1159,8 @@ FILTERS = {
     'list':                 do_list,
     'lower':                do_lower,
     'map':                  do_map,
+    'min':                  do_min,
+    'max':                  do_max,
     'pprint':               do_pprint,
     'random':               do_random,
     'reject':               do_reject,
@@ -1063,6 +1179,7 @@ FILTERS = {
     'title':                do_title,
     'trim':                 do_trim,
     'truncate':             do_truncate,
+    'unique':               do_unique,
     'upper':                do_upper,
     'urlencode':            do_urlencode,
     'urlize':               do_urlize,
diff --git a/lib/spack/external/jinja2/idtracking.py b/lib/spack/external/jinja2/idtracking.py
index 8479b72c23..491bfe0836 100644
--- a/lib/spack/external/jinja2/idtracking.py
+++ b/lib/spack/external/jinja2/idtracking.py
@@ -24,11 +24,13 @@ def symbols_for_node(node, parent_symbols=None):
 
 class Symbols(object):
 
-    def __init__(self, parent=None):
-        if parent is None:
-            self.level = 0
-        else:
-            self.level = parent.level + 1
+    def __init__(self, parent=None, level=None):
+        if level is None:
+            if parent is None:
+                level = 0
+            else:
+                level = parent.level + 1
+        self.level = level
         self.parent = parent
         self.refs = {}
         self.loads = {}
@@ -167,6 +169,10 @@ class RootVisitor(NodeVisitor):
         for child in node.iter_child_nodes(exclude=('call',)):
             self.sym_visitor.visit(child)
 
+    def visit_OverlayScope(self, node, **kwargs):
+        for child in node.body:
+            self.sym_visitor.visit(child)
+
     def visit_For(self, node, for_branch='body', **kwargs):
         if for_branch == 'body':
             self.sym_visitor.visit(node.target, store_as_param=True)
@@ -209,6 +215,9 @@ class FrameSymbolVisitor(NodeVisitor):
         elif node.ctx == 'load':
             self.symbols.load(node.name)
 
+    def visit_NSRef(self, node, **kwargs):
+        self.symbols.load(node.name)
+
     def visit_If(self, node, **kwargs):
         self.visit(node.test, **kwargs)
 
@@ -222,9 +231,10 @@ class FrameSymbolVisitor(NodeVisitor):
             return rv
 
         body_symbols = inner_visit(node.body)
+        elif_symbols = inner_visit(node.elif_)
         else_symbols = inner_visit(node.else_ or ())
 
-        self.symbols.branch_update([body_symbols, else_symbols])
+        self.symbols.branch_update([body_symbols, elif_symbols, else_symbols])
 
     def visit_Macro(self, node, **kwargs):
         self.symbols.store(node.name)
@@ -271,3 +281,6 @@ class FrameSymbolVisitor(NodeVisitor):
 
     def visit_Block(self, node, **kwargs):
         """Stop visiting at blocks."""
+
+    def visit_OverlayScope(self, node, **kwargs):
+        """Do not visit into overlay scopes."""
diff --git a/lib/spack/external/jinja2/lexer.py b/lib/spack/external/jinja2/lexer.py
index 30e82fb019..6fd135dd5b 100644
--- a/lib/spack/external/jinja2/lexer.py
+++ b/lib/spack/external/jinja2/lexer.py
@@ -15,14 +15,12 @@
     :license: BSD, see LICENSE for more details.
 """
 import re
-import sys
-
-from operator import itemgetter
 from collections import deque
+from operator import itemgetter
+
+from jinja2._compat import implements_iterator, intern, iteritems, text_type
 from jinja2.exceptions import TemplateSyntaxError
 from jinja2.utils import LRUCache
-from jinja2._compat import iteritems, implements_iterator, text_type, intern
-
 
 # cache for the lexers. Exists in order to be able to have multiple
 # environments with the same lexer
@@ -34,28 +32,25 @@ string_re = re.compile(r"('([^'\\]*(?:\\.[^'\\]*)*)'"
                        r'|"([^"\\]*(?:\\.[^"\\]*)*)")', re.S)
 integer_re = re.compile(r'\d+')
 
-def _make_name_re():
-    try:
-        compile('föö', '<unknown>', 'eval')
-    except SyntaxError:
-        return re.compile(r'\b[a-zA-Z_][a-zA-Z0-9_]*\b')
-
+try:
+    # check if this Python supports Unicode identifiers
+    compile('föö', '<unknown>', 'eval')
+except SyntaxError:
+    # no Unicode support, use ASCII identifiers
+    name_re = re.compile(r'[a-zA-Z_][a-zA-Z0-9_]*')
+    check_ident = False
+else:
+    # Unicode support, build a pattern to match valid characters, and set flag
+    # to use str.isidentifier to validate during lexing
+    from jinja2 import _identifier
+    name_re = re.compile(r'[\w{0}]+'.format(_identifier.pattern))
+    check_ident = True
+    # remove the pattern from memory after building the regex
+    import sys
+    del sys.modules['jinja2._identifier']
     import jinja2
-    from jinja2 import _stringdefs
-    name_re = re.compile(r'[%s][%s]*' % (_stringdefs.xid_start,
-                                         _stringdefs.xid_continue))
-
-    # Save some memory here
-    sys.modules.pop('jinja2._stringdefs')
-    del _stringdefs
-    del jinja2._stringdefs
-
-    return name_re
-
-# we use the unicode identifier rule if this python version is able
-# to handle unicode identifiers, otherwise the standard ASCII one.
-name_re = _make_name_re()
-del _make_name_re
+    del jinja2._identifier
+    del _identifier
 
 float_re = re.compile(r'(?<!\.)\d+\.\d+')
 newline_re = re.compile(r'(\r\n|\r|\n)')
@@ -352,7 +347,10 @@ class TokenStream(object):
         return self.next_if(expr) is not None
 
     def __next__(self):
-        """Go one token ahead and return the old one"""
+        """Go one token ahead and return the old one.
+
+        Use the built-in :func:`next` instead of calling this directly.
+        """
         rv = self.current
         if self._pushed:
             self.current = self._pushed.popleft()
@@ -577,6 +575,10 @@ class Lexer(object):
                 token = value
             elif token == 'name':
                 value = str(value)
+                if check_ident and not value.isidentifier():
+                    raise TemplateSyntaxError(
+                        'Invalid character in identifier',
+                        lineno, name, filename)
             elif token == 'string':
                 # try to unescape string
                 try:
diff --git a/lib/spack/external/jinja2/nativetypes.py b/lib/spack/external/jinja2/nativetypes.py
new file mode 100644
index 0000000000..fe17e4138d
--- /dev/null
+++ b/lib/spack/external/jinja2/nativetypes.py
@@ -0,0 +1,220 @@
+import sys
+from ast import literal_eval
+from itertools import islice, chain
+from jinja2 import nodes
+from jinja2._compat import text_type
+from jinja2.compiler import CodeGenerator, has_safe_repr
+from jinja2.environment import Environment, Template
+from jinja2.utils import concat, escape
+
+
+def native_concat(nodes):
+    """Return a native Python type from the list of compiled nodes. If the
+    result is a single node, its value is returned. Otherwise, the nodes are
+    concatenated as strings. If the result can be parsed with
+    :func:`ast.literal_eval`, the parsed value is returned. Otherwise, the
+    string is returned.
+    """
+    head = list(islice(nodes, 2))
+
+    if not head:
+        return None
+
+    if len(head) == 1:
+        out = head[0]
+    else:
+        out = u''.join([text_type(v) for v in chain(head, nodes)])
+
+    try:
+        return literal_eval(out)
+    except (ValueError, SyntaxError, MemoryError):
+        return out
+
+
+class NativeCodeGenerator(CodeGenerator):
+    """A code generator which avoids injecting ``to_string()`` calls around the
+    internal code Jinja uses to render templates.
+    """
+
+    def visit_Output(self, node, frame):
+        """Same as :meth:`CodeGenerator.visit_Output`, but do not call
+        ``to_string`` on output nodes in generated code.
+        """
+        if self.has_known_extends and frame.require_output_check:
+            return
+
+        finalize = self.environment.finalize
+        finalize_context = getattr(finalize, 'contextfunction', False)
+        finalize_eval = getattr(finalize, 'evalcontextfunction', False)
+        finalize_env = getattr(finalize, 'environmentfunction', False)
+
+        if finalize is not None:
+            if finalize_context or finalize_eval:
+                const_finalize = None
+            elif finalize_env:
+                def const_finalize(x):
+                    return finalize(self.environment, x)
+            else:
+                const_finalize = finalize
+        else:
+            def const_finalize(x):
+                return x
+
+        # If we are inside a frame that requires output checking, we do so.
+        outdent_later = False
+
+        if frame.require_output_check:
+            self.writeline('if parent_template is None:')
+            self.indent()
+            outdent_later = True
+
+        # Try to evaluate as many chunks as possible into a static string at
+        # compile time.
+        body = []
+
+        for child in node.nodes:
+            try:
+                if const_finalize is None:
+                    raise nodes.Impossible()
+
+                const = child.as_const(frame.eval_ctx)
+                if not has_safe_repr(const):
+                    raise nodes.Impossible()
+            except nodes.Impossible:
+                body.append(child)
+                continue
+
+            # the frame can't be volatile here, because otherwise the as_const
+            # function would raise an Impossible exception at that point
+            try:
+                if frame.eval_ctx.autoescape:
+                    if hasattr(const, '__html__'):
+                        const = const.__html__()
+                    else:
+                        const = escape(const)
+
+                const = const_finalize(const)
+            except Exception:
+                # if something goes wrong here we evaluate the node at runtime
+                # for easier debugging
+                body.append(child)
+                continue
+
+            if body and isinstance(body[-1], list):
+                body[-1].append(const)
+            else:
+                body.append([const])
+
+        # if we have less than 3 nodes or a buffer we yield or extend/append
+        if len(body) < 3 or frame.buffer is not None:
+            if frame.buffer is not None:
+                # for one item we append, for more we extend
+                if len(body) == 1:
+                    self.writeline('%s.append(' % frame.buffer)
+                else:
+                    self.writeline('%s.extend((' % frame.buffer)
+
+                self.indent()
+
+            for item in body:
+                if isinstance(item, list):
+                    val = repr(native_concat(item))
+
+                    if frame.buffer is None:
+                        self.writeline('yield ' + val)
+                    else:
+                        self.writeline(val + ',')
+                else:
+                    if frame.buffer is None:
+                        self.writeline('yield ', item)
+                    else:
+                        self.newline(item)
+
+                    close = 0
+
+                    if finalize is not None:
+                        self.write('environment.finalize(')
+
+                        if finalize_context:
+                            self.write('context, ')
+
+                        close += 1
+
+                    self.visit(item, frame)
+
+                    if close > 0:
+                        self.write(')' * close)
+
+                    if frame.buffer is not None:
+                        self.write(',')
+
+            if frame.buffer is not None:
+                # close the open parentheses
+                self.outdent()
+                self.writeline(len(body) == 1 and ')' or '))')
+
+        # otherwise we create a format string as this is faster in that case
+        else:
+            format = []
+            arguments = []
+
+            for item in body:
+                if isinstance(item, list):
+                    format.append(native_concat(item).replace('%', '%%'))
+                else:
+                    format.append('%s')
+                    arguments.append(item)
+
+            self.writeline('yield ')
+            self.write(repr(concat(format)) + ' % (')
+            self.indent()
+
+            for argument in arguments:
+                self.newline(argument)
+                close = 0
+
+                if finalize is not None:
+                    self.write('environment.finalize(')
+
+                    if finalize_context:
+                        self.write('context, ')
+                    elif finalize_eval:
+                        self.write('context.eval_ctx, ')
+                    elif finalize_env:
+                        self.write('environment, ')
+
+                    close += 1
+
+                self.visit(argument, frame)
+                self.write(')' * close + ', ')
+
+            self.outdent()
+            self.writeline(')')
+
+        if outdent_later:
+            self.outdent()
+
+
+class NativeTemplate(Template):
+    def render(self, *args, **kwargs):
+        """Render the template to produce a native Python type. If the result
+        is a single node, its value is returned. Otherwise, the nodes are
+        concatenated as strings. If the result can be parsed with
+        :func:`ast.literal_eval`, the parsed value is returned. Otherwise, the
+        string is returned.
+        """
+        vars = dict(*args, **kwargs)
+
+        try:
+            return native_concat(self.root_render_func(self.new_context(vars)))
+        except Exception:
+            exc_info = sys.exc_info()
+
+        return self.environment.handle_exception(exc_info, True)
+
+
+class NativeEnvironment(Environment):
+    """An environment that renders templates to native Python types."""
+
+    code_generator_class = NativeCodeGenerator
+    template_class = NativeTemplate
diff --git a/lib/spack/external/jinja2/nodes.py b/lib/spack/external/jinja2/nodes.py
index aa4df72380..4d9a01ad8b 100644
--- a/lib/spack/external/jinja2/nodes.py
+++ b/lib/spack/external/jinja2/nodes.py
@@ -314,7 +314,7 @@ class For(Stmt):
 
 class If(Stmt):
     """If `test` is true, `body` is rendered, else `else_`."""
-    fields = ('test', 'body', 'else_')
+    fields = ('test', 'body', 'elif_', 'else_')
 
 
 class Macro(Stmt):
@@ -387,7 +387,7 @@ class Assign(Stmt):
 
 class AssignBlock(Stmt):
     """Assigns a block to a target."""
-    fields = ('target', 'body')
+    fields = ('target', 'filter', 'body')
 
 
 class Expr(Node):
@@ -465,6 +465,18 @@ class Name(Expr):
                                  'True', 'False', 'None')
 
 
+class NSRef(Expr):
+    """Reference to a namespace value assignment"""
+    fields = ('name', 'attr')
+
+    def can_assign(self):
+        # We don't need any special checks here; NSRef assignments have a
+        # runtime check to ensure the target is a namespace object which will
+        # have been checked already as it is created using a normal assignment
+        # which goes through a `Name` node.
+        return True
+
+
 class Literal(Expr):
     """Baseclass for literals."""
     abstract = True
@@ -587,6 +599,25 @@ class CondExpr(Expr):
         return self.expr2.as_const(eval_ctx)
 
 
+def args_as_const(node, eval_ctx):
+    args = [x.as_const(eval_ctx) for x in node.args]
+    kwargs = dict(x.as_const(eval_ctx) for x in node.kwargs)
+
+    if node.dyn_args is not None:
+        try:
+            args.extend(node.dyn_args.as_const(eval_ctx))
+        except Exception:
+            raise Impossible()
+
+    if node.dyn_kwargs is not None:
+        try:
+            kwargs.update(node.dyn_kwargs.as_const(eval_ctx))
+        except Exception:
+            raise Impossible()
+
+    return args, kwargs
+
+
 class Filter(Expr):
     """This node applies a filter on an expression.  `name` is the name of
     the filter, the rest of the fields are the same as for :class:`Call`.
@@ -594,44 +625,41 @@ class Filter(Expr):
     If the `node` of a filter is `None` the contents of the last buffer are
     filtered.  Buffers are created by macros and filter blocks.
     """
+
     fields = ('node', 'name', 'args', 'kwargs', 'dyn_args', 'dyn_kwargs')
 
     def as_const(self, eval_ctx=None):
         eval_ctx = get_eval_context(self, eval_ctx)
+
         if eval_ctx.volatile or self.node is None:
             raise Impossible()
+
         # we have to be careful here because we call filter_ below.
         # if this variable would be called filter, 2to3 would wrap the
         # call in a list beause it is assuming we are talking about the
         # builtin filter function here which no longer returns a list in
         # python 3.  because of that, do not rename filter_ to filter!
         filter_ = self.environment.filters.get(self.name)
+
         if filter_ is None or getattr(filter_, 'contextfilter', False):
             raise Impossible()
 
         # We cannot constant handle async filters, so we need to make sure
         # to not go down this path.
-        if eval_ctx.environment.is_async and \
-           getattr(filter_, 'asyncfiltervariant', False):
+        if (
+            eval_ctx.environment.is_async
+            and getattr(filter_, 'asyncfiltervariant', False)
+        ):
             raise Impossible()
 
-        obj = self.node.as_const(eval_ctx)
-        args = [obj] + [x.as_const(eval_ctx) for x in self.args]
+        args, kwargs = args_as_const(self, eval_ctx)
+        args.insert(0, self.node.as_const(eval_ctx))
+
         if getattr(filter_, 'evalcontextfilter', False):
             args.insert(0, eval_ctx)
         elif getattr(filter_, 'environmentfilter', False):
             args.insert(0, self.environment)
-        kwargs = dict(x.as_const(eval_ctx) for x in self.kwargs)
-        if self.dyn_args is not None:
-            try:
-                args.extend(self.dyn_args.as_const(eval_ctx))
-            except Exception:
-                raise Impossible()
-        if self.dyn_kwargs is not None:
-            try:
-                kwargs.update(self.dyn_kwargs.as_const(eval_ctx))
-            except Exception:
-                raise Impossible()
+
         try:
             return filter_(*args, **kwargs)
         except Exception:
@@ -642,8 +670,24 @@ class Test(Expr):
     """Applies a test on an expression.  `name` is the name of the test, the
     rest of the fields are the same as for :class:`Call`.
     """
+
     fields = ('node', 'name', 'args', 'kwargs', 'dyn_args', 'dyn_kwargs')
 
+    def as_const(self, eval_ctx=None):
+        test = self.environment.tests.get(self.name)
+
+        if test is None:
+            raise Impossible()
+
+        eval_ctx = get_eval_context(self, eval_ctx)
+        args, kwargs = args_as_const(self, eval_ctx)
+        args.insert(0, self.node.as_const(eval_ctx))
+
+        try:
+            return test(*args, **kwargs)
+        except Exception:
+            raise Impossible()
+
 
 class Call(Expr):
     """Calls an expression.  `args` is a list of arguments, `kwargs` a list
@@ -914,6 +958,22 @@ class Scope(Stmt):
     fields = ('body',)
 
 
+class OverlayScope(Stmt):
+    """An overlay scope for extensions.  This is a largely unoptimized scope
+    that however can be used to introduce completely arbitrary variables into
+    a sub scope from a dictionary or dictionary like object.  The `context`
+    field has to evaluate to a dictionary object.
+
+    Example usage::
+
+        OverlayScope(context=self.call_method('get_context'),
+                     body=[...])
+
+    .. versionadded:: 2.10
+    """
+    fields = ('context', 'body')
+
+
 class EvalContextModifier(Stmt):
     """Modifies the eval context.  For each option that should be modified,
     a :class:`Keyword` has to be added to the :attr:`options` list.
diff --git a/lib/spack/external/jinja2/parser.py b/lib/spack/external/jinja2/parser.py
index 0bf74c9459..ed00d9708e 100644
--- a/lib/spack/external/jinja2/parser.py
+++ b/lib/spack/external/jinja2/parser.py
@@ -176,13 +176,14 @@ class Parser(object):
     def parse_set(self):
         """Parse an assign statement."""
         lineno = next(self.stream).lineno
-        target = self.parse_assign_target()
+        target = self.parse_assign_target(with_namespace=True)
         if self.stream.skip_if('assign'):
             expr = self.parse_tuple()
             return nodes.Assign(target, expr, lineno=lineno)
+        filter_node = self.parse_filter(None)
         body = self.parse_statements(('name:endset',),
                                      drop_needle=True)
-        return nodes.AssignBlock(target, body, lineno=lineno)
+        return nodes.AssignBlock(target, filter_node, body, lineno=lineno)
 
     def parse_for(self):
         """Parse a for loop."""
@@ -210,17 +211,16 @@ class Parser(object):
             node.test = self.parse_tuple(with_condexpr=False)
             node.body = self.parse_statements(('name:elif', 'name:else',
                                                'name:endif'))
+            node.elif_ = []
+            node.else_ = []
             token = next(self.stream)
             if token.test('name:elif'):
-                new_node = nodes.If(lineno=self.stream.current.lineno)
-                node.else_ = [new_node]
-                node = new_node
+                node = nodes.If(lineno=self.stream.current.lineno)
+                result.elif_.append(node)
                 continue
             elif token.test('name:else'):
-                node.else_ = self.parse_statements(('name:endif',),
-                                                   drop_needle=True)
-            else:
-                node.else_ = []
+                result.else_ = self.parse_statements(('name:endif',),
+                                                     drop_needle=True)
             break
         return result
 
@@ -334,10 +334,9 @@ class Parser(object):
                 if parse_context() or self.stream.current.type != 'comma':
                     break
             else:
-                break
+                self.stream.expect('name')
         if not hasattr(node, 'with_context'):
             node.with_context = False
-            self.stream.skip_if('comma')
         return node
 
     def parse_signature(self, node):
@@ -395,15 +394,21 @@ class Parser(object):
         return node
 
     def parse_assign_target(self, with_tuple=True, name_only=False,
-                            extra_end_rules=None):
+                            extra_end_rules=None, with_namespace=False):
         """Parse an assignment target.  As Jinja2 allows assignments to
         tuples, this function can parse all allowed assignment targets.  Per
         default assignments to tuples are parsed, that can be disable however
         by setting `with_tuple` to `False`.  If only assignments to names are
         wanted `name_only` can be set to `True`.  The `extra_end_rules`
-        parameter is forwarded to the tuple parsing function.
+        parameter is forwarded to the tuple parsing function.  If
+        `with_namespace` is enabled, a namespace assignment may be parsed.
         """
-        if name_only:
+        if with_namespace and self.stream.look().type == 'dot':
+            token = self.stream.expect('name')
+            next(self.stream)  # dot
+            attr = self.stream.expect('name')
+            target = nodes.NSRef(token.value, attr.value, lineno=token.lineno)
+        elif name_only:
             token = self.stream.expect('name')
             target = nodes.Name(token.value, 'store', lineno=token.lineno)
         else:
diff --git a/lib/spack/external/jinja2/runtime.py b/lib/spack/external/jinja2/runtime.py
index 00d5f03ca6..f9d7a6806c 100644
--- a/lib/spack/external/jinja2/runtime.py
+++ b/lib/spack/external/jinja2/runtime.py
@@ -15,7 +15,7 @@ from types import MethodType
 
 from jinja2.nodes import EvalContext, _context_function_types
 from jinja2.utils import Markup, soft_unicode, escape, missing, concat, \
-     internalcode, object_type_repr, evalcontextfunction
+     internalcode, object_type_repr, evalcontextfunction, Namespace
 from jinja2.exceptions import UndefinedError, TemplateRuntimeError, \
      TemplateNotFound
 from jinja2._compat import imap, text_type, iteritems, \
@@ -27,7 +27,7 @@ from jinja2._compat import imap, text_type, iteritems, \
 __all__ = ['LoopContext', 'TemplateReference', 'Macro', 'Markup',
            'TemplateRuntimeError', 'missing', 'concat', 'escape',
            'markup_join', 'unicode_join', 'to_string', 'identity',
-           'TemplateNotFound']
+           'TemplateNotFound', 'Namespace']
 
 #: the name of the function that is used to convert something into
 #: a string.  We can just use the text type here.
@@ -36,6 +36,7 @@ to_string = text_type
 #: the identity function.  Useful for certain things in the environment
 identity = lambda x: x
 
+_first_iteration = object()
 _last_iteration = object()
 
 
@@ -241,13 +242,14 @@ class Context(with_metaclass(ContextMeta)):
             __traceback_hide__ = True  # noqa
 
         # Allow callable classes to take a context
-        fn = __obj.__call__
-        for fn_type in ('contextfunction',
-                        'evalcontextfunction',
-                        'environmentfunction'):
-            if hasattr(fn, fn_type):
-                __obj = fn
-                break
+        if hasattr(__obj, '__call__'):
+            fn = __obj.__call__
+            for fn_type in ('contextfunction',
+                            'evalcontextfunction',
+                            'environmentfunction'):
+                if hasattr(fn, fn_type):
+                    __obj = fn
+                    break
 
         if isinstance(__obj, _context_function_types):
             if getattr(__obj, 'contextfunction', 0):
@@ -349,13 +351,17 @@ class BlockReference(object):
 class LoopContextBase(object):
     """A loop context for dynamic iteration."""
 
+    _before = _first_iteration
+    _current = _first_iteration
     _after = _last_iteration
     _length = None
 
-    def __init__(self, recurse=None, depth0=0):
+    def __init__(self, undefined, recurse=None, depth0=0):
+        self._undefined = undefined
         self._recurse = recurse
         self.index0 = -1
         self.depth0 = depth0
+        self._last_checked_value = missing
 
     def cycle(self, *args):
         """Cycles among the arguments with the current loop index."""
@@ -363,6 +369,13 @@ class LoopContextBase(object):
             raise TypeError('no items for cycling given')
         return args[self.index0 % len(args)]
 
+    def changed(self, *value):
+        """Checks whether the value has changed since the last call."""
+        if self._last_checked_value != value:
+            self._last_checked_value = value
+            return True
+        return False
+
     first = property(lambda x: x.index0 == 0)
     last = property(lambda x: x._after is _last_iteration)
     index = property(lambda x: x.index0 + 1)
@@ -370,6 +383,18 @@ class LoopContextBase(object):
     revindex0 = property(lambda x: x.length - x.index)
     depth = property(lambda x: x.depth0 + 1)
 
+    @property
+    def previtem(self):
+        if self._before is _first_iteration:
+            return self._undefined('there is no previous item')
+        return self._before
+
+    @property
+    def nextitem(self):
+        if self._after is _last_iteration:
+            return self._undefined('there is no next item')
+        return self._after
+
     def __len__(self):
         return self.length
 
@@ -395,8 +420,8 @@ class LoopContextBase(object):
 
 class LoopContext(LoopContextBase):
 
-    def __init__(self, iterable, recurse=None, depth0=0):
-        LoopContextBase.__init__(self, recurse, depth0)
+    def __init__(self, iterable, undefined, recurse=None, depth0=0):
+        LoopContextBase.__init__(self, undefined, recurse, depth0)
         self._iterator = iter(iterable)
 
         # try to get the length of the iterable early.  This must be done
@@ -448,9 +473,10 @@ class LoopContextIterator(object):
         ctx.index0 += 1
         if ctx._after is _last_iteration:
             raise StopIteration()
-        next_elem = ctx._after
+        ctx._before = ctx._current
+        ctx._current = ctx._after
         ctx._after = ctx._safe_next()
-        return next_elem, ctx
+        return ctx._current, ctx
 
 
 class Macro(object):
diff --git a/lib/spack/external/jinja2/sandbox.py b/lib/spack/external/jinja2/sandbox.py
index 32e2435010..93fb9d45f3 100644
--- a/lib/spack/external/jinja2/sandbox.py
+++ b/lib/spack/external/jinja2/sandbox.py
@@ -107,7 +107,7 @@ class _MagicFormatMapping(Mapping):
     """This class implements a dummy wrapper to fix a bug in the Python
     standard library for string formatting.
 
-    See http://bugs.python.org/issue13598 for information about why
+    See https://bugs.python.org/issue13598 for information about why
     this is necessary.
     """
 
diff --git a/lib/spack/external/jinja2/tests.py b/lib/spack/external/jinja2/tests.py
index bd843b77bc..0adc3d4dbc 100644
--- a/lib/spack/external/jinja2/tests.py
+++ b/lib/spack/external/jinja2/tests.py
@@ -8,6 +8,7 @@
     :copyright: (c) 2017 by the Jinja Team.
     :license: BSD, see LICENSE for more details.
 """
+import operator
 import re
 from collections import Mapping
 from jinja2.runtime import Undefined
@@ -103,28 +104,6 @@ def test_sequence(value):
     return True
 
 
-def test_equalto(value, other):
-    """Check if an object has the same value as another object:
-
-    .. sourcecode:: jinja
-
-        {% if foo.expression is equalto 42 %}
-            the foo attribute evaluates to the constant 42
-        {% endif %}
-
-    This appears to be a useless test as it does exactly the same as the
-    ``==`` operator, but it can be useful when used together with the
-    `selectattr` function:
-
-    .. sourcecode:: jinja
-
-        {{ users|selectattr("email", "equalto", "foo@bar.invalid") }}
-
-    .. versionadded:: 2.8
-    """
-    return value == other
-
-
 def test_sameas(value, other):
     """Check if an object points to the same memory address than another
     object:
@@ -152,14 +131,12 @@ def test_escaped(value):
     return hasattr(value, '__html__')
 
 
-def test_greaterthan(value, other):
-    """Check if value is greater than other."""
-    return value > other
-
+def test_in(value, seq):
+    """Check if value is in seq.
 
-def test_lessthan(value, other):
-    """Check if value is less than other."""
-    return value < other
+    .. versionadded:: 2.10
+    """
+    return value in seq
 
 
 TESTS = {
@@ -178,8 +155,21 @@ TESTS = {
     'iterable':         test_iterable,
     'callable':         test_callable,
     'sameas':           test_sameas,
-    'equalto':          test_equalto,
     'escaped':          test_escaped,
-    'greaterthan':      test_greaterthan,
-    'lessthan':         test_lessthan
+    'in':               test_in,
+    '==':               operator.eq,
+    'eq':               operator.eq,
+    'equalto':          operator.eq,
+    '!=':               operator.ne,
+    'ne':               operator.ne,
+    '>':                operator.gt,
+    'gt':               operator.gt,
+    'greaterthan':      operator.gt,
+    'ge':               operator.ge,
+    '>=':               operator.ge,
+    '<':                operator.lt,
+    'lt':               operator.lt,
+    'lessthan':         operator.lt,
+    '<=':               operator.le,
+    'le':               operator.le,
 }
diff --git a/lib/spack/external/jinja2/utils.py b/lib/spack/external/jinja2/utils.py
index b96d309546..502a311c08 100644
--- a/lib/spack/external/jinja2/utils.py
+++ b/lib/spack/external/jinja2/utils.py
@@ -567,7 +567,7 @@ def htmlsafe_json_dumps(obj, dumper=None, **kwargs):
         .replace(u'>', u'\\u003e') \
         .replace(u'&', u'\\u0026') \
         .replace(u"'", u'\\u0027')
-    return rv
+    return Markup(rv)
 
 
 @implements_iterator
@@ -612,6 +612,29 @@ class Joiner(object):
         return self.sep
 
 
+class Namespace(object):
+    """A namespace object that can hold arbitrary attributes.  It may be
+    initialized from a dictionary or with keyword argments."""
+
+    def __init__(*args, **kwargs):
+        self, args = args[0], args[1:]
+        self.__attrs = dict(*args, **kwargs)
+
+    def __getattribute__(self, name):
+        if name == '_Namespace__attrs':
+            return object.__getattribute__(self, name)
+        try:
+            return self.__attrs[name]
+        except KeyError:
+            raise AttributeError(name)
+
+    def __setitem__(self, name, value):
+        self.__attrs[name] = value
+
+    def __repr__(self):
+        return '<Namespace %r>' % self.__attrs
+
+
 # does this python version support async for in and async generators?
 try:
     exec('async def _():\n async for _ in ():\n  yield _')
diff --git a/lib/spack/external/ordereddict_backport.py b/lib/spack/external/ordereddict_backport.py
index 154e5d1872..9bb788f093 100644
--- a/lib/spack/external/ordereddict_backport.py
+++ b/lib/spack/external/ordereddict_backport.py
@@ -1,268 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# Backport of OrderedDict() class that runs on Python 2.4, 2.5, 2.6, 2.7 and pypy.
-# Passes Python2.7's test suite and incorporates all the latest updates.
-#
-# From http://code.activestate.com/recipes/576693-ordered-dictionary-for-py24/
-# This file is in the public domain, and has no particular license.
-#
-try:
-    from thread import get_ident as _get_ident
-except ImportError:
-    try:
-        from dummy_thread import get_ident as _get_ident
-    except ImportError:
-        try:
-            from _dummy_thread import get_ident as _get_ident
-        except ImportError:
-            from threading import get_ident as _get_ident  # nopyqver
-
-try:
-    from _abcoll import KeysView, ValuesView, ItemsView
-except ImportError:
-    pass
-
-
-class OrderedDict(dict):
-    'Dictionary that remembers insertion order'
-    # An inherited dict maps keys to values.
-    # The inherited dict provides __getitem__, __len__, __contains__, and get.
-    # The remaining methods are order-aware.
-    # Big-O running times for all methods are the same as for regular dictionaries.
-
-    # The internal self.__map dictionary maps keys to links in a doubly linked list.
-    # The circular doubly linked list starts and ends with a sentinel element.
-    # The sentinel element never gets deleted (this simplifies the algorithm).
-    # Each link is stored as a list of length three:  [PREV, NEXT, KEY].
-
-    def __init__(self, *args, **kwds):
-        '''Initialize an ordered dictionary.  Signature is the same as for
-        regular dictionaries, but keyword arguments are not recommended
-        because their insertion order is arbitrary.
-
-        '''
-        if len(args) > 1:
-            raise TypeError('expected at most 1 arguments, got %d' % len(args))
-        try:
-            self.__root
-        except AttributeError:
-            self.__root = root = []                     # sentinel node
-            root[:] = [root, root, None]
-            self.__map = {}
-        self.__update(*args, **kwds)
-
-    def __setitem__(self, key, value, dict_setitem=dict.__setitem__):
-        'od.__setitem__(i, y) <==> od[i]=y'
-        # Setting a new item creates a new link which goes at the end of the linked
-        # list, and the inherited dictionary is updated with the new key/value pair.
-        if key not in self:
-            root = self.__root
-            last = root[0]
-            last[1] = root[0] = self.__map[key] = [last, root, key]
-        dict_setitem(self, key, value)
-
-    def __delitem__(self, key, dict_delitem=dict.__delitem__):
-        'od.__delitem__(y) <==> del od[y]'
-        # Deleting an existing item uses self.__map to find the link which is
-        # then removed by updating the links in the predecessor and successor nodes.
-        dict_delitem(self, key)
-        link_prev, link_next, key = self.__map.pop(key)
-        link_prev[1] = link_next
-        link_next[0] = link_prev
-
-    def __iter__(self):
-        'od.__iter__() <==> iter(od)'
-        root = self.__root
-        curr = root[1]
-        while curr is not root:
-            yield curr[2]
-            curr = curr[1]
-
-    def __reversed__(self):
-        'od.__reversed__() <==> reversed(od)'
-        root = self.__root
-        curr = root[0]
-        while curr is not root:
-            yield curr[2]
-            curr = curr[0]
-
-    def clear(self):
-        'od.clear() -> None.  Remove all items from od.'
-        try:
-            for node in self.__map.itervalues():
-                del node[:]
-            root = self.__root
-            root[:] = [root, root, None]
-            self.__map.clear()
-        except AttributeError:
-            pass
-        dict.clear(self)
-
-    def popitem(self, last=True):
-        '''od.popitem() -> (k, v), return and remove a (key, value) pair.
-        Pairs are returned in LIFO order if last is true or FIFO order if false.
-
-        '''
-        if not self:
-            raise KeyError('dictionary is empty')
-        root = self.__root
-        if last:
-            link = root[0]
-            link_prev = link[0]
-            link_prev[1] = root
-            root[0] = link_prev
-        else:
-            link = root[1]
-            link_next = link[1]
-            root[1] = link_next
-            link_next[0] = root
-        key = link[2]
-        del self.__map[key]
-        value = dict.pop(self, key)
-        return key, value
-
-    # -- the following methods do not depend on the internal structure --
-
-    def keys(self):
-        'od.keys() -> list of keys in od'
-        return list(self)
-
-    def values(self):
-        'od.values() -> list of values in od'
-        return [self[key] for key in self]
-
-    def items(self):
-        'od.items() -> list of (key, value) pairs in od'
-        return [(key, self[key]) for key in self]
-
-    def iterkeys(self):
-        'od.iterkeys() -> an iterator over the keys in od'
-        return iter(self)
-
-    def itervalues(self):
-        'od.itervalues -> an iterator over the values in od'
-        for k in self:
-            yield self[k]
-
-    def iteritems(self):
-        'od.iteritems -> an iterator over the (key, value) items in od'
-        for k in self:
-            yield (k, self[k])
-
-    def update(*args, **kwds):
-        '''od.update(E, **F) -> None.  Update od from dict/iterable E and F.
-
-        If E is a dict instance, does:           for k in E: od[k] = E[k]
-        If E has a .keys() method, does:         for k in E.keys(): od[k] = E[k]
-        Or if E is an iterable of items, does:   for k, v in E: od[k] = v
-        In either case, this is followed by:     for k, v in F.items(): od[k] = v
-
-        '''
-        if len(args) > 2:
-            raise TypeError('update() takes at most 2 positional '
-                            'arguments (%d given)' % (len(args),))
-        elif not args:
-            raise TypeError('update() takes at least 1 argument (0 given)')
-        self = args[0]
-        # Make progressively weaker assumptions about "other"
-        other = ()
-        if len(args) == 2:
-            other = args[1]
-        if isinstance(other, dict):
-            for key in other:
-                self[key] = other[key]
-        elif hasattr(other, 'keys'):
-            for key in other.keys():
-                self[key] = other[key]
-        else:
-            for key, value in other:
-                self[key] = value
-        for key, value in kwds.items():
-            self[key] = value
-
-    __update = update  # let subclasses override update without breaking __init__
-
-    __marker = object()
-
-    def pop(self, key, default=__marker):
-        '''od.pop(k[,d]) -> v, remove specified key and return the corresponding value.
-        If key is not found, d is returned if given, otherwise KeyError is raised.
-
-        '''
-        if key in self:
-            result = self[key]
-            del self[key]
-            return result
-        if default is self.__marker:
-            raise KeyError(key)
-        return default
-
-    def setdefault(self, key, default=None):
-        'od.setdefault(k[,d]) -> od.get(k,d), also set od[k]=d if k not in od'
-        if key in self:
-            return self[key]
-        self[key] = default
-        return default
-
-    def __repr__(self, _repr_running={}):
-        'od.__repr__() <==> repr(od)'
-        call_key = id(self), _get_ident()
-        if call_key in _repr_running:
-            return '...'
-        _repr_running[call_key] = 1
-        try:
-            if not self:
-                return '%s()' % (self.__class__.__name__,)
-            return '%s(%r)' % (self.__class__.__name__, self.items())
-        finally:
-            del _repr_running[call_key]
-
-    def __reduce__(self):
-        'Return state information for pickling'
-        items = [[k, self[k]] for k in self]
-        inst_dict = vars(self).copy()
-        for k in vars(OrderedDict()):
-            inst_dict.pop(k, None)
-        if inst_dict:
-            return (self.__class__, (items,), inst_dict)
-        return self.__class__, (items,)
-
-    def copy(self):
-        'od.copy() -> a shallow copy of od'
-        return self.__class__(self)
-
-    @classmethod
-    def fromkeys(cls, iterable, value=None):
-        '''OD.fromkeys(S[, v]) -> New ordered dictionary with keys from S
-        and values equal to v (which defaults to None).
-
-        '''
-        d = cls()
-        for key in iterable:
-            d[key] = value
-        return d
-
-    def __eq__(self, other):
-        '''od.__eq__(y) <==> od==y.  Comparison to another OD is order-sensitive
-        while comparison to a regular mapping is order-insensitive.
-
-        '''
-        if isinstance(other, OrderedDict):
-            return len(self)==len(other) and self.items() == other.items()
-        return dict.__eq__(self, other)
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-    def __ne__(self, other):
-        return not self == other
+"""This file dispatches to the correct implementation of OrderedDict."""
 
-    # -- the following methods are only used in Python 2.7 --
+# TODO: this file, along with py26/ordereddict.py, can be removed when
+# TODO: support for python 2.6 will be dropped
 
-    def viewkeys(self):
-        "od.viewkeys() -> a set-like object providing a view on od's keys"
-        return KeysView(self)
+# Removing this import will make python 2.6
+# fail on import of ordereddict
+from __future__ import absolute_import
 
-    def viewvalues(self):
-        "od.viewvalues() -> an object providing a view on od's values"
-        return ValuesView(self)
+import sys
 
-    def viewitems(self):
-        "od.viewitems() -> a set-like object providing a view on od's items"
-        return ItemsView(self)
+if sys.version_info[:2] == (2, 6):
+    import ordereddict
+    OrderedDict = ordereddict.OrderedDict
+else:
+    import collections
+    OrderedDict = collections.OrderedDict
diff --git a/lib/spack/external/py/AUTHORS b/lib/spack/external/py/AUTHORS
deleted file mode 100644
index 8c0cf9b71b..0000000000
--- a/lib/spack/external/py/AUTHORS
+++ /dev/null
@@ -1,24 +0,0 @@
-Holger Krekel, holger at merlinux eu
-Benjamin Peterson, benjamin at python org
-Ronny Pfannschmidt, Ronny.Pfannschmidt at gmx de
-Guido Wesdorp, johnny at johnnydebris net 
-Samuele Pedroni, pedronis at openend se 
-Carl Friedrich Bolz, cfbolz at gmx de
-Armin Rigo, arigo at tunes org 
-Maciek Fijalkowski, fijal at genesilico pl
-Brian Dorsey, briandorsey at gmail com 
-Floris Bruynooghe, flub at devork be
-merlinux GmbH, Germany, office at merlinux eu
-
-Contributors include:: 
-
-Ross Lawley
-Ralf Schmitt
-Chris Lamb 
-Harald Armin Massa
-Martijn Faassen
-Ian Bicking 
-Jan Balster
-Grig Gheorghiu
-Bob Ippolito
-Christian Tismer
diff --git a/lib/spack/external/py/LICENSE b/lib/spack/external/py/LICENSE
deleted file mode 100644
index 31ecdfb1db..0000000000
--- a/lib/spack/external/py/LICENSE
+++ /dev/null
@@ -1,19 +0,0 @@
-
-  Permission is hereby granted, free of charge, to any person obtaining a copy
-  of this software and associated documentation files (the "Software"), to deal
-  in the Software without restriction, including without limitation the rights
-  to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-  copies of the Software, and to permit persons to whom the Software is
-  furnished to do so, subject to the following conditions:
-     
-  The above copyright notice and this permission notice shall be included in all
-  copies or substantial portions of the Software.
- 
-  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-  SOFTWARE.
-
diff --git a/lib/spack/external/py/README.rst b/lib/spack/external/py/README.rst
deleted file mode 100644
index e836b7b50a..0000000000
--- a/lib/spack/external/py/README.rst
+++ /dev/null
@@ -1,21 +0,0 @@
-.. image:: https://img.shields.io/pypi/pyversions/pytest.svg
-  :target: https://pypi.org/project/py
-.. image:: https://img.shields.io/travis/pytest-dev/py.svg
-   :target: https://travis-ci.org/pytest-dev/py
-
-The py lib is a Python development support library featuring
-the following tools and modules:
-
-* ``py.path``:  uniform local and svn path objects
-* ``py.apipkg``:  explicit API control and lazy-importing
-* ``py.iniconfig``:  easy parsing of .ini files
-* ``py.code``: dynamic code generation and introspection
-
-NOTE: prior to the 1.4 release this distribution used to
-contain py.test which is now its own package, see http://pytest.org
-
-For questions and more information please visit http://pylib.readthedocs.org
-
-Bugs and issues: https://github.com/pytest-dev/py
-
-Authors: Holger Krekel and others, 2004-2016
diff --git a/lib/spack/external/py/__init__.py b/lib/spack/external/py/__init__.py
index c2273a2e64..85af650f5c 100644
--- a/lib/spack/external/py/__init__.py
+++ b/lib/spack/external/py/__init__.py
@@ -1,5 +1,5 @@
 """
-py.test and pylib: rapid testing and development utils
+pylib: rapid testing and development utils
 
 this module uses apipkg.py for lazy-loading sub modules
 and classes.  The initpkg-dictionary  below specifies
@@ -8,13 +8,15 @@ dictionary or an import path.
 
 (c) Holger Krekel and others, 2004-2014
 """
-__version__ = '1.4.32'
+__version__ = '1.4.34'
 
 from py import _apipkg
 
 # so that py.error.* instances are picklable
 import sys
 sys.modules['py.error'] = _apipkg.AliasModule("py.error", "py._error", 'error')
+import py.error  # "Dereference" it now just to be safe (issue110)
+
 
 _apipkg.initpkg(__name__, attr={'_apipkg': _apipkg}, exportdefs={
     # access to all standard lib modules
diff --git a/lib/spack/external/py/_code/code.py b/lib/spack/external/py/_code/code.py
index f14c562a29..20fd965c97 100644
--- a/lib/spack/external/py/_code/code.py
+++ b/lib/spack/external/py/_code/code.py
@@ -419,7 +419,7 @@ class ExceptionInfo(object):
     def __unicode__(self):
         entry = self.traceback[-1]
         loc = ReprFileLocation(entry.path, entry.lineno + 1, self.exconly())
-        return unicode(loc)
+        return loc.__unicode__()
 
 
 class FormattedExcinfo(object):
diff --git a/lib/spack/external/py/_path/common.py b/lib/spack/external/py/_path/common.py
index bf42ed5092..5512e51efe 100644
--- a/lib/spack/external/py/_path/common.py
+++ b/lib/spack/external/py/_path/common.py
@@ -1,6 +1,7 @@
 """
 """
 import os, sys, posixpath
+import fnmatch
 import py
 
 # Moved from local.py.
@@ -169,11 +170,16 @@ class PathBase(object):
     def readlines(self, cr=1):
         """ read and return a list of lines from the path. if cr is False, the
 newline will be removed from the end of each line. """
+        if sys.version_info < (3, ):
+            mode = 'rU'
+        else:  # python 3 deprecates mode "U" in favor of "newline" option
+            mode = 'r'
+
         if not cr:
-            content = self.read('rU')
+            content = self.read(mode)
             return content.split('\n')
         else:
-            f = self.open('rU')
+            f = self.open(mode)
             try:
                 return f.readlines()
             finally:
@@ -378,7 +384,7 @@ newline will be removed from the end of each line. """
         return self.strpath == str(other)
 
     def __fspath__(self):
-        return str(self)
+        return self.strpath
 
 class Visitor:
     def __init__(self, fil, rec, ignore, bf, sort):
@@ -436,4 +442,4 @@ class FNMatcher:
             name = str(path) # path.strpath # XXX svn?
             if not os.path.isabs(pattern):
                 pattern = '*' + path.sep + pattern
-        return py.std.fnmatch.fnmatch(name, pattern)
+        return fnmatch.fnmatch(name, pattern)
diff --git a/lib/spack/external/py/_path/local.py b/lib/spack/external/py/_path/local.py
index 0d4e4c93d1..2ffdaddf06 100644
--- a/lib/spack/external/py/_path/local.py
+++ b/lib/spack/external/py/_path/local.py
@@ -10,7 +10,7 @@ from py._path import common
 from py._path.common import iswin32, fspath
 from stat import S_ISLNK, S_ISDIR, S_ISREG
 
-from os.path import abspath, normpath, isabs, exists, isdir, isfile, islink, dirname
+from os.path import abspath, normcase, normpath, isabs, exists, isdir, isfile, islink, dirname
 
 if sys.version_info > (3,0):
     def map_as_list(func, iter):
@@ -205,14 +205,14 @@ class LocalPath(FSBase):
             if rec:
                 # force remove of readonly files on windows
                 if iswin32:
-                    self.chmod(448, rec=1) # octcal 0700
+                    self.chmod(0o700, rec=1)
                 py.error.checked_call(py.std.shutil.rmtree, self.strpath,
                     ignore_errors=ignore_errors)
             else:
                 py.error.checked_call(os.rmdir, self.strpath)
         else:
             if iswin32:
-                self.chmod(448) # octcal 0700
+                self.chmod(0o700)
             py.error.checked_call(os.remove, self.strpath)
 
     def computehash(self, hashtype="md5", chunksize=524288):
@@ -801,12 +801,13 @@ class LocalPath(FSBase):
         if rootdir is None:
             rootdir = cls.get_temproot()
 
+        nprefix = normcase(prefix)
         def parse_num(path):
             """ parse the number out of a path (if it matches the prefix) """
-            bn = path.basename
-            if bn.startswith(prefix):
+            nbasename = normcase(path.basename)
+            if nbasename.startswith(nprefix):
                 try:
-                    return int(bn[len(prefix):])
+                    return int(nbasename[len(nprefix):])
                 except ValueError:
                     pass
 
@@ -898,6 +899,7 @@ class LocalPath(FSBase):
         return udir
     make_numbered_dir = classmethod(make_numbered_dir)
 
+
 def copymode(src, dest):
     """ copy permission from src to dst. """
     py.std.shutil.copymode(src, dest)
diff --git a/lib/spack/external/py/_path/svnurl.py b/lib/spack/external/py/_path/svnurl.py
index 78d71317ac..6589a71d09 100644
--- a/lib/spack/external/py/_path/svnurl.py
+++ b/lib/spack/external/py/_path/svnurl.py
@@ -315,7 +315,7 @@ class InfoSvnCommand:
     # locked, see 'svn help ls'
     lspattern = re.compile(
         r'^ *(?P<rev>\d+) +(?P<author>.+?) +(0? *(?P<size>\d+))? '
-            '*(?P<date>\w+ +\d{2} +[\d:]+) +(?P<file>.*)$')
+            r'*(?P<date>\w+ +\d{2} +[\d:]+) +(?P<file>.*)$')
     def __init__(self, line):
         # this is a typical line from 'svn ls http://...'
         #_    1127      jum        0 Jul 13 15:28 branch/
diff --git a/lib/spack/external/py/_path/svnwc.py b/lib/spack/external/py/_path/svnwc.py
index 00d3b4bbaf..992223c04a 100644
--- a/lib/spack/external/py/_path/svnwc.py
+++ b/lib/spack/external/py/_path/svnwc.py
@@ -327,7 +327,7 @@ def fixlocale():
     return ''
 
 # some nasty chunk of code to solve path and url conversion and quoting issues
-ILLEGAL_CHARS = '* | \ / : < > ? \t \n \x0b \x0c \r'.split(' ')
+ILLEGAL_CHARS = '* | \\ / : < > ? \t \n \x0b \x0c \r'.split(' ')
 if os.sep in ILLEGAL_CHARS:
     ILLEGAL_CHARS.remove(os.sep)
 ISWINDOWS = sys.platform == 'win32'
diff --git a/lib/spack/external/py26/ordereddict.py b/lib/spack/external/py26/ordereddict.py
new file mode 100644
index 0000000000..7242b5060d
--- /dev/null
+++ b/lib/spack/external/py26/ordereddict.py
@@ -0,0 +1,127 @@
+# Copyright (c) 2009 Raymond Hettinger
+#
+# Permission is hereby granted, free of charge, to any person
+# obtaining a copy of this software and associated documentation files
+# (the "Software"), to deal in the Software without restriction,
+# including without limitation the rights to use, copy, modify, merge,
+# publish, distribute, sublicense, and/or sell copies of the Software,
+# and to permit persons to whom the Software is furnished to do so,
+# subject to the following conditions:
+#
+#     The above copyright notice and this permission notice shall be
+#     included in all copies or substantial portions of the Software.
+#
+#     THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+#     EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+#     OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+#     NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+#     HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+#     WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+#     FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+#     OTHER DEALINGS IN THE SOFTWARE.
+
+from UserDict import DictMixin
+
+class OrderedDict(dict, DictMixin):
+
+    def __init__(self, *args, **kwds):
+        if len(args) > 1:
+            raise TypeError('expected at most 1 arguments, got %d' % len(args))
+        try:
+            self.__end
+        except AttributeError:
+            self.clear()
+        self.update(*args, **kwds)
+
+    def clear(self):
+        self.__end = end = []
+        end += [None, end, end]         # sentinel node for doubly linked list
+        self.__map = {}                 # key --> [key, prev, next]
+        dict.clear(self)
+
+    def __setitem__(self, key, value):
+        if key not in self:
+            end = self.__end
+            curr = end[1]
+            curr[2] = end[1] = self.__map[key] = [key, curr, end]
+        dict.__setitem__(self, key, value)
+
+    def __delitem__(self, key):
+        dict.__delitem__(self, key)
+        key, prev, next = self.__map.pop(key)
+        prev[2] = next
+        next[1] = prev
+
+    def __iter__(self):
+        end = self.__end
+        curr = end[2]
+        while curr is not end:
+            yield curr[0]
+            curr = curr[2]
+
+    def __reversed__(self):
+        end = self.__end
+        curr = end[1]
+        while curr is not end:
+            yield curr[0]
+            curr = curr[1]
+
+    def popitem(self, last=True):
+        if not self:
+            raise KeyError('dictionary is empty')
+        if last:
+            key = reversed(self).next()
+        else:
+            key = iter(self).next()
+        value = self.pop(key)
+        return key, value
+
+    def __reduce__(self):
+        items = [[k, self[k]] for k in self]
+        tmp = self.__map, self.__end
+        del self.__map, self.__end
+        inst_dict = vars(self).copy()
+        self.__map, self.__end = tmp
+        if inst_dict:
+            return (self.__class__, (items,), inst_dict)
+        return self.__class__, (items,)
+
+    def keys(self):
+        return list(self)
+
+    setdefault = DictMixin.setdefault
+    update = DictMixin.update
+    pop = DictMixin.pop
+    values = DictMixin.values
+    items = DictMixin.items
+    iterkeys = DictMixin.iterkeys
+    itervalues = DictMixin.itervalues
+    iteritems = DictMixin.iteritems
+
+    def __repr__(self):
+        if not self:
+            return '%s()' % (self.__class__.__name__,)
+        return '%s(%r)' % (self.__class__.__name__, self.items())
+
+    def copy(self):
+        return self.__class__(self)
+
+    @classmethod
+    def fromkeys(cls, iterable, value=None):
+        d = cls()
+        for key in iterable:
+            d[key] = value
+        return d
+
+    def __eq__(self, other):
+        if isinstance(other, OrderedDict):
+            if len(self) != len(other):
+                return False
+            for p, q in  zip(self.items(), other.items()):
+                if p != q:
+                    return False
+            return True
+        return dict.__eq__(self, other)
+
+    def __ne__(self, other):
+        return not self == other
diff --git a/lib/spack/external/pytest.py b/lib/spack/external/pytest.py
index e376e417e8..6e124db418 100644
--- a/lib/spack/external/pytest.py
+++ b/lib/spack/external/pytest.py
@@ -1,7 +1,55 @@
+# The MIT License (MIT)
+#
+# Copyright (c) 2004-2017 Holger Krekel and others
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy of
+# this software and associated documentation files (the "Software"), to deal in
+# the Software without restriction, including without limitation the rights to
+# use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
+# of the Software, and to permit persons to whom the Software is furnished to do
+# so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
 # PYTHON_ARGCOMPLETE_OK
 """
 pytest: unit and functional testing with Python.
 """
+
+
+# else we are imported
+
+from _pytest.config import (
+    main, UsageError, _preloadplugins, cmdline,
+    hookspec, hookimpl
+)
+from _pytest.fixtures import fixture, yield_fixture
+from _pytest.assertion import register_assert_rewrite
+from _pytest.freeze_support import freeze_includes
+from _pytest import __version__
+from _pytest.debugging import pytestPDB as __pytestPDB
+from _pytest.recwarn import warns, deprecated_call
+from _pytest.outcomes import fail, skip, importorskip, exit, xfail
+from _pytest.mark import MARK_GEN as mark, param
+from _pytest.main import Item, Collector, File, Session
+from _pytest.fixtures import fillfixtures as _fillfuncargs
+from _pytest.python import (
+    Module, Class, Instance, Function, Generator,
+)
+
+from _pytest.python_api import approx, raises
+
+set_trace = __pytestPDB.set_trace
+
 __all__ = [
     'main',
     'UsageError',
@@ -9,20 +57,44 @@ __all__ = [
     'hookspec',
     'hookimpl',
     '__version__',
+    'register_assert_rewrite',
+    'freeze_includes',
+    'set_trace',
+    'warns',
+    'deprecated_call',
+    'fixture',
+    'yield_fixture',
+    'fail',
+    'skip',
+    'xfail',
+    'importorskip',
+    'exit',
+    'mark',
+    'param',
+    'approx',
+    '_fillfuncargs',
+
+    'Item',
+    'File',
+    'Collector',
+    'Session',
+    'Module',
+    'Class',
+    'Instance',
+    'Function',
+    'Generator',
+    'raises',
+
+
 ]
 
-if __name__ == '__main__': # if run as a script or by 'python -m pytest'
+if __name__ == '__main__':
+    # if run as a script or by 'python -m pytest'
     # we trigger the below "else" condition by the following import
     import pytest
     raise SystemExit(pytest.main())
+else:
 
-# else we are imported
-
-from _pytest.config import (
-    main, UsageError, _preloadplugins, cmdline,
-    hookspec, hookimpl
-)
-from _pytest import __version__
-
-_preloadplugins() # to populate pytest.* namespace so help(pytest) works
-
+    from _pytest.compat import _setup_collect_fakemodule
+    _preloadplugins()  # to populate pytest.* namespace so help(pytest) works
+    _setup_collect_fakemodule()
diff --git a/lib/spack/external/ruamel/__init__.py b/lib/spack/external/ruamel/__init__.py
new file mode 100644
index 0000000000..e69de29bb2
--- /dev/null
+++ b/lib/spack/external/ruamel/__init__.py
diff --git a/lib/spack/external/ruamel/yaml/.ruamel/__init__.py b/lib/spack/external/ruamel/yaml/.ruamel/__init__.py
new file mode 100644
index 0000000000..ece379ce2f
--- /dev/null
+++ b/lib/spack/external/ruamel/yaml/.ruamel/__init__.py
@@ -0,0 +1,2 @@
+import pkg_resources
+pkg_resources.declare_namespace(__name__)
diff --git a/lib/spack/external/ruamel/yaml/LICENSE b/lib/spack/external/ruamel/yaml/LICENSE
new file mode 100644
index 0000000000..f6f753a366
--- /dev/null
+++ b/lib/spack/external/ruamel/yaml/LICENSE
@@ -0,0 +1,21 @@
+ 
+ The MIT License (MIT)
+
+ Permission is hereby granted, free of charge, to any person obtaining a copy
+ of this software and associated documentation files (the "Software"), to deal
+ in the Software without restriction, including without limitation the rights
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ copies of the Software, and to permit persons to whom the Software is
+ furnished to do so, subject to the following conditions:
+     
+ The above copyright notice and this permission notice shall be included in
+ all copies or substantial portions of the Software.
+ 
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN 
+ THE SOFTWARE.
+
diff --git a/lib/spack/external/ruamel/yaml/README.rst b/lib/spack/external/ruamel/yaml/README.rst
new file mode 100644
index 0000000000..993cf35542
--- /dev/null
+++ b/lib/spack/external/ruamel/yaml/README.rst
@@ -0,0 +1,38 @@
+
+ruamel.yaml
+===========
+
+``ruamel.yaml`` is a YAML 1.2 loader/dumper package for Python.
+
+* `Overview <http://yaml.readthedocs.org/en/latest/overview.html>`_
+* `Installing <http://yaml.readthedocs.org/en/latest/install.html>`_
+* `Details <http://yaml.readthedocs.org/en/latest/detail.html>`_
+* `Examples <http://yaml.readthedocs.org/en/latest/example.html>`_
+* `Differences with PyYAML <http://yaml.readthedocs.org/en/latest/pyyaml.html>`_
+
+.. image:: https://readthedocs.org/projects/yaml/badge/?version=stable
+   :target: https://yaml.readthedocs.org/en/stable
+
+ChangeLog
+=========
+
+::
+
+  0.11.15 (2016-XX-XX):
+    - Change to prevent FutureWarning in NumPy, as reported by tgehring
+    ("comparison to None will result in an elementwise object comparison in the future")
+
+  0.11.14 (2016-07-06):
+    - fix preserve_quotes missing on original Loaders (as reported
+      by Leynos, bitbucket issue 38)
+
+  0.11.13 (2016-07-06):
+    - documentation only, automated linux wheels
+
+  0.11.12 (2016-07-06):
+    - added support for roundtrip of single/double quoted scalars using:
+      ruamel.yaml.round_trip_load(stream, preserve_quotes=True)
+
+  0.11.0 (2016-02-18):
+    - RoundTripLoader loads 1.2 by default (no sexagesimals, 012 octals nor
+      yes/no/on/off booleans
diff --git a/lib/spack/external/ruamel/yaml/__init__.py b/lib/spack/external/ruamel/yaml/__init__.py
new file mode 100644
index 0000000000..b77032fc83
--- /dev/null
+++ b/lib/spack/external/ruamel/yaml/__init__.py
@@ -0,0 +1,85 @@
+# coding: utf-8
+
+from __future__ import print_function
+from __future__ import absolute_import
+
+# install_requires of ruamel.base is not really required but the old
+# ruamel.base installed __init__.py, and thus a new version should
+# be installed at some point
+
+_package_data = dict(
+    full_package_name="ruamel.yaml",
+    version_info=(0, 11, 15),
+    author="Anthon van der Neut",
+    author_email="a.van.der.neut@ruamel.eu",
+    description="ruamel.yaml is a YAML parser/emitter that supports roundtrip preservation of comments, seq/map flow style, and map key order",  # NOQA
+    entry_points=None,
+    install_requires=dict(
+        any=[],
+        py26=["ruamel.ordereddict"],
+        py27=["ruamel.ordereddict"]
+    ),
+    ext_modules=[dict(
+        name="_ruamel_yaml",
+        src=["ext/_ruamel_yaml.c", "ext/api.c", "ext/writer.c", "ext/dumper.c",
+                "ext/loader.c", "ext/reader.c", "ext/scanner.c", "ext/parser.c",
+                "ext/emitter.c"],
+        lib=[],
+        # test='#include "ext/yaml.h"\n\nint main(int argc, char* argv[])\n{\nyaml_parser_t parser;\nparser = parser;  /* prevent warning */\nreturn 0;\n}\n'  # NOQA
+        )
+    ],
+    classifiers=[
+        "Programming Language :: Python :: 2.6",
+        "Programming Language :: Python :: 2.7",
+        "Programming Language :: Python :: 3.3",
+        "Programming Language :: Python :: 3.4",
+        "Programming Language :: Python :: 3.5",
+        "Programming Language :: Python :: Implementation :: CPython",
+        "Programming Language :: Python :: Implementation :: PyPy",
+        "Programming Language :: Python :: Implementation :: Jython",
+        "Topic :: Software Development :: Libraries :: Python Modules",
+        "Topic :: Text Processing :: Markup"
+    ],
+    windows_wheels=True,
+    read_the_docs='yaml',
+    many_linux='libyaml-devel',
+)
+
+
+# < from ruamel.util.new import _convert_version
+def _convert_version(tup):
+    """create a PEP 386 pseudo-format conformant string from tuple tup"""
+    ret_val = str(tup[0])  # first is always digit
+    next_sep = "."  # separator for next extension, can be "" or "."
+    for x in tup[1:]:
+        if isinstance(x, int):
+            ret_val += next_sep + str(x)
+            next_sep = '.'
+            continue
+        first_letter = x[0].lower()
+        next_sep = ''
+        if first_letter in 'abcr':
+            ret_val += 'rc' if first_letter == 'r' else first_letter
+        elif first_letter in 'pd':
+            ret_val += '.post' if first_letter == 'p' else '.dev'
+    return ret_val
+
+
+# <
+version_info = _package_data['version_info']
+__version__ = _convert_version(version_info)
+
+del _convert_version
+
+try:
+    from .cyaml import *                               # NOQA
+    __with_libyaml__ = True
+except (ImportError, ValueError):  # for Jython
+    __with_libyaml__ = False
+
+
+# body extracted to main.py
+try:
+    from .main import *                               # NOQA
+except ImportError:
+    from ruamel.yaml.main import *                               # NOQA
diff --git a/lib/spack/external/ruamel/yaml/comments.py b/lib/spack/external/ruamel/yaml/comments.py
new file mode 100644
index 0000000000..b8a5010ad8
--- /dev/null
+++ b/lib/spack/external/ruamel/yaml/comments.py
@@ -0,0 +1,481 @@
+# coding: utf-8
+
+from __future__ import absolute_import
+from __future__ import print_function
+
+"""
+stuff to deal with comments and formatting on dict/list/ordereddict/set
+these are not really related, formatting could be factored out as
+a separate base
+"""
+
+from collections import MutableSet
+
+__all__ = ["CommentedSeq", "CommentedMap", "CommentedOrderedMap",
+           "CommentedSet", 'comment_attrib', 'merge_attrib']
+
+
+try:
+    from .compat import ordereddict
+except ImportError:
+    from ruamel.yaml.compat import ordereddict
+
+comment_attrib = '_yaml_comment'
+format_attrib = '_yaml_format'
+line_col_attrib = '_yaml_line_col'
+anchor_attrib = '_yaml_anchor'
+merge_attrib = '_yaml_merge'
+tag_attrib = '_yaml_tag'
+
+
+class Comment(object):
+    # sys.getsize tested the Comment objects, __slots__ make them bigger
+    # and adding self.end did not matter
+    attrib = comment_attrib
+
+    def __init__(self):
+        self.comment = None  # [post, [pre]]
+        # map key (mapping/omap/dict) or index (sequence/list) to a  list of
+        # dict: post_key, pre_key, post_value, pre_value
+        # list: pre item, post item
+        self._items = {}
+        # self._start = [] # should not put these on first item
+        self._end = []  # end of document comments
+
+    def __str__(self):
+        if self._end:
+            end = ',\n  end=' + str(self._end)
+        else:
+            end = ''
+        return "Comment(comment={0},\n  items={1}{2})".format(
+            self.comment, self._items, end)
+
+    @property
+    def items(self):
+        return self._items
+
+    @property
+    def end(self):
+        return self._end
+
+    @end.setter
+    def end(self, value):
+        self._end = value
+
+    @property
+    def start(self):
+        return self._start
+
+    @start.setter
+    def start(self, value):
+        self._start = value
+
+
+# to distinguish key from None
+def NoComment():
+    pass
+
+
+class Format(object):
+    attrib = format_attrib
+
+    def __init__(self):
+        self._flow_style = None
+
+    def set_flow_style(self):
+        self._flow_style = True
+
+    def set_block_style(self):
+        self._flow_style = False
+
+    def flow_style(self, default=None):
+        """if default (the flow_style) is None, the flow style tacked on to
+        the object explicitly will be taken. If that is None as well the
+        default flow style rules the format down the line, or the type
+        of the constituent values (simple -> flow, map/list -> block)"""
+        if self._flow_style is None:
+            return default
+        return self._flow_style
+
+
+class LineCol(object):
+    attrib = line_col_attrib
+
+    def __init__(self):
+        self.line = None
+        self.col = None
+        self.data = None
+
+    def add_kv_line_col(self, key, data):
+        if self.data is None:
+            self.data = {}
+        self.data[key] = data
+
+    def key(self, k):
+        return self._kv(k, 0, 1)
+
+    def value(self, k):
+        return self._kv(k, 2, 3)
+
+    def _kv(self, k, x0, x1):
+        if self.data is None:
+            return None
+        data = self.data[k]
+        return data[x0], data[x1]
+
+    def item(self, idx):
+        if self.data is None:
+            return None
+        return self.data[idx][0], self.data[idx][1]
+
+    def add_idx_line_col(self, key, data):
+        if self.data is None:
+            self.data = {}
+        self.data[key] = data
+
+
+class Anchor(object):
+    attrib = anchor_attrib
+
+    def __init__(self):
+        self.value = None
+        self.always_dump = False
+
+
+class Tag(object):
+    """store tag information for roundtripping"""
+    attrib = tag_attrib
+
+    def __init__(self):
+        self.value = None
+
+
+class CommentedBase(object):
+    @property
+    def ca(self):
+        if not hasattr(self, Comment.attrib):
+            setattr(self, Comment.attrib, Comment())
+        return getattr(self, Comment.attrib)
+
+    def yaml_end_comment_extend(self, comment, clear=False):
+        if clear:
+            self.ca.end = []
+        self.ca.end.extend(comment)
+
+    def yaml_key_comment_extend(self, key, comment, clear=False):
+        l = self.ca._items.setdefault(key, [None, None, None, None])
+        if clear or l[1] is None:
+            if comment[1] is not None:
+                assert isinstance(comment[1], list)
+            l[1] = comment[1]
+        else:
+            l[1].extend(comment[0])
+        l[0] = comment[0]
+
+    def yaml_value_comment_extend(self, key, comment, clear=False):
+        l = self.ca._items.setdefault(key, [None, None, None, None])
+        if clear or l[3] is None:
+            if comment[1] is not None:
+                assert isinstance(comment[1], list)
+            l[3] = comment[1]
+        else:
+            l[3].extend(comment[0])
+        l[2] = comment[0]
+
+    def yaml_set_start_comment(self, comment, indent=0):
+        """overwrites any preceding comment lines on an object
+        expects comment to be without `#` and possible have mutlple lines
+        """
+        from .error import Mark
+        from .tokens import CommentToken
+        pre_comments = self._yaml_get_pre_comment()
+        if comment[-1] == '\n':
+            comment = comment[:-1]  # strip final newline if there
+        start_mark = Mark(None, None, None, indent, None, None)
+        for com in comment.split('\n'):
+            pre_comments.append(CommentToken('# ' + com + '\n', start_mark, None))
+
+    @property
+    def fa(self):
+        """format attribute
+
+        set_flow_style()/set_block_style()"""
+        if not hasattr(self, Format.attrib):
+            setattr(self, Format.attrib, Format())
+        return getattr(self, Format.attrib)
+
+    def yaml_add_eol_comment(self, comment, key=NoComment, column=None):
+        """
+        there is a problem as eol comments should start with ' #'
+        (but at the beginning of the line the space doesn't have to be before
+        the #. The column index is for the # mark
+        """
+        from .tokens import CommentToken
+        from .error import Mark
+        if column is None:
+            column = self._yaml_get_column(key)
+        if comment[0] != '#':
+            comment = '# ' + comment
+        if column is None:
+            if comment[0] == '#':
+                comment = ' ' + comment
+                column = 0
+        start_mark = Mark(None, None, None, column, None, None)
+        ct = [CommentToken(comment, start_mark, None), None]
+        self._yaml_add_eol_comment(ct, key=key)
+
+    @property
+    def lc(self):
+        if not hasattr(self, LineCol.attrib):
+            setattr(self, LineCol.attrib, LineCol())
+        return getattr(self, LineCol.attrib)
+
+    def _yaml_set_line_col(self, line, col):
+        self.lc.line = line
+        self.lc.col = col
+
+    def _yaml_set_kv_line_col(self, key, data):
+        self.lc.add_kv_line_col(key, data)
+
+    def _yaml_set_idx_line_col(self, key, data):
+        self.lc.add_idx_line_col(key, data)
+
+    @property
+    def anchor(self):
+        if not hasattr(self, Anchor.attrib):
+            setattr(self, Anchor.attrib, Anchor())
+        return getattr(self, Anchor.attrib)
+
+    def yaml_anchor(self):
+        if not hasattr(self, Anchor.attrib):
+            return None
+        return self.anchor
+
+    def yaml_set_anchor(self, value, always_dump=False):
+        self.anchor.value = value
+        self.anchor.always_dump = always_dump
+
+    @property
+    def tag(self):
+        if not hasattr(self, Tag.attrib):
+            setattr(self, Tag.attrib, Tag())
+        return getattr(self, Tag.attrib)
+
+    def yaml_set_tag(self, value):
+        self.tag.value = value
+
+
+class CommentedSeq(list, CommentedBase):
+    __slots__ = [Comment.attrib, ]
+
+    def _yaml_add_comment(self, comment, key=NoComment):
+        if key is not NoComment:
+            self.yaml_key_comment_extend(key, comment)
+        else:
+            self.ca.comment = comment
+
+    def _yaml_add_eol_comment(self, comment, key):
+        self._yaml_add_comment(comment, key=key)
+
+    def _yaml_get_columnX(self, key):
+        return self.ca.items[key][0].start_mark.column
+
+    def insert(self, idx, val):
+        """the comments after the insertion have to move forward"""
+        list.insert(self, idx, val)
+        for list_index in sorted(self.ca.items, reverse=True):
+            if list_index < idx:
+                break
+            self.ca.items[list_index+1] = self.ca.items.pop(list_index)
+
+    def pop(self, idx):
+        res = list.pop(self, idx)
+        self.ca.items.pop(idx, None)  # might not be there -> default value
+        for list_index in sorted(self.ca.items):
+            if list_index < idx:
+                continue
+            self.ca.items[list_index-1] = self.ca.items.pop(list_index)
+        return res
+
+    def _yaml_get_column(self, key):
+        column = None
+        sel_idx = None
+        pre, post = key-1, key+1
+        if pre in self.ca.items:
+            sel_idx = pre
+        elif post in self.ca.items:
+            sel_idx = post
+        else:
+            # self.ca.items is not ordered
+            for row_idx, k1 in enumerate(self):
+                if row_idx >= key:
+                    break
+                if row_idx not in self.ca.items:
+                    continue
+                sel_idx = row_idx
+        if sel_idx is not None:
+            column = self._yaml_get_columnX(sel_idx)
+        return column
+
+    def _yaml_get_pre_comment(self):
+        if self.ca.comment is None:
+            pre_comments = []
+            self.ca.comment = [None, pre_comments]
+        else:
+            pre_comments = self.ca.comment[1] = []
+        return pre_comments
+
+
+class CommentedMap(ordereddict, CommentedBase):
+    __slots__ = [Comment.attrib, ]
+
+    def _yaml_add_comment(self, comment, key=NoComment, value=NoComment):
+        """values is set to key to indicate a value attachment of comment"""
+        if key is not NoComment:
+            self.yaml_key_comment_extend(key, comment)
+            return
+        if value is not NoComment:
+            self.yaml_value_comment_extend(value, comment)
+        else:
+            self.ca.comment = comment
+
+    def _yaml_add_eol_comment(self, comment, key):
+        """add on the value line, with value specified by the key"""
+        self._yaml_add_comment(comment, value=key)
+
+    def _yaml_get_columnX(self, key):
+        return self.ca.items[key][2].start_mark.column
+
+    def _yaml_get_column(self, key):
+        column = None
+        sel_idx = None
+        pre, post, last = None, None, None
+        for x in self:
+            if pre is not None and x != key:
+                post = x
+                break
+            if x == key:
+                pre = last
+            last = x
+        if pre in self.ca.items:
+            sel_idx = pre
+        elif post in self.ca.items:
+            sel_idx = post
+        else:
+            # self.ca.items is not ordered
+            for row_idx, k1 in enumerate(self):
+                if k1 >= key:
+                    break
+                if k1 not in self.ca.items:
+                    continue
+                sel_idx = k1
+        if sel_idx is not None:
+            column = self._yaml_get_columnX(sel_idx)
+        return column
+
+    def _yaml_get_pre_comment(self):
+        if self.ca.comment is None:
+            pre_comments = []
+            self.ca.comment = [None, pre_comments]
+        else:
+            pre_comments = self.ca.comment[1] = []
+        return pre_comments
+
+    def update(self, *vals, **kwds):
+        try:
+            ordereddict.update(self, *vals, **kwds)
+        except TypeError:
+            # probably a dict that is used
+            for x in vals:
+                self[x] = vals[x]
+
+    def insert(self, pos, key, value, comment=None):
+        """insert key value into given position
+        attach comment if provided
+        """
+        ordereddict.insert(self, pos, key, value)
+        if comment is not None:
+            self.yaml_add_eol_comment(comment, key=key)
+
+    def mlget(self, key, default=None, list_ok=False):
+        """multi-level get that expects dicts within dicts"""
+        if not isinstance(key, list):
+            return self.get(key, default)
+        # assume that the key is a list of recursively accessible dicts
+
+        def get_one_level(key_list, level, d):
+            if not list_ok:
+                assert isinstance(d, dict)
+            if level >= len(key_list):
+                if level > len(key_list):
+                    raise IndexError
+                return d[key_list[level-1]]
+            return get_one_level(key_list, level+1, d[key_list[level-1]])
+
+        try:
+            return get_one_level(key, 1, self)
+        except KeyError:
+            return default
+        except (TypeError, IndexError):
+            if not list_ok:
+                raise
+            return default
+
+    def __getitem__(self, key):
+        try:
+            return ordereddict.__getitem__(self, key)
+        except KeyError:
+            for merged in getattr(self, merge_attrib, []):
+                if key in merged[1]:
+                    return merged[1][key]
+            raise
+
+    def get(self, key, default=None):
+        try:
+            return self.__getitem__(key)
+        except:
+            return default
+
+    @property
+    def merge(self):
+        if not hasattr(self, merge_attrib):
+            setattr(self, merge_attrib, [])
+        return getattr(self, merge_attrib)
+
+    def add_yaml_merge(self, value):
+        self.merge.extend(value)
+
+
+class CommentedOrderedMap(CommentedMap):
+    __slots__ = [Comment.attrib, ]
+
+
+class CommentedSet(MutableSet, CommentedMap):
+    __slots__ = [Comment.attrib, 'odict']
+
+    def __init__(self, values=None):
+        self.odict = ordereddict()
+        MutableSet.__init__(self)
+        if values is not None:
+            self |= values
+
+    def add(self, value):
+        """Add an element."""
+        self.odict[value] = None
+
+    def discard(self, value):
+        """Remove an element.  Do not raise an exception if absent."""
+        del self.odict[value]
+
+    def __contains__(self, x):
+        return x in self.odict
+
+    def __iter__(self):
+        for x in self.odict:
+            yield x
+
+    def __len__(self):
+        return len(self.odict)
+
+    def __repr__(self):
+        return 'set({0!r})'.format(self.odict.keys())
diff --git a/lib/spack/external/ruamel/yaml/compat.py b/lib/spack/external/ruamel/yaml/compat.py
new file mode 100644
index 0000000000..6eee151c51
--- /dev/null
+++ b/lib/spack/external/ruamel/yaml/compat.py
@@ -0,0 +1,120 @@
+# coding: utf-8
+
+from __future__ import print_function
+
+# partially from package six by Benjamin Peterson
+
+import sys
+import os
+import types
+
+try:
+    from ruamel.ordereddict import ordereddict
+except:
+    try:
+        from collections import OrderedDict  # nopyqver
+    except ImportError:
+        from ordereddict import OrderedDict
+    # to get the right name import ... as ordereddict doesn't do that
+
+    class ordereddict(OrderedDict):
+        if not hasattr(OrderedDict, 'insert'):
+            def insert(self, pos, key, value):
+                if pos >= len(self):
+                    self[key] = value
+                    return
+                od = ordereddict()
+                od.update(self)
+                for k in od:
+                    del self[k]
+                for index, old_key in enumerate(od):
+                    if pos == index:
+                        self[key] = value
+                    self[old_key] = od[old_key]
+
+
+PY2 = sys.version_info[0] == 2
+PY3 = sys.version_info[0] == 3
+
+if PY3:
+    def utf8(s):
+        return s
+
+    def to_str(s):
+        return s
+
+    def to_unicode(s):
+        return s
+
+else:
+    def utf8(s):
+        return s.encode('utf-8')
+
+    def to_str(s):
+        return str(s)
+
+    def to_unicode(s):
+        return unicode(s)
+
+if PY3:
+    string_types = str,
+    integer_types = int,
+    class_types = type,
+    text_type = str
+    binary_type = bytes
+
+    MAXSIZE = sys.maxsize
+    unichr = chr
+    import io
+    StringIO = io.StringIO
+    BytesIO = io.BytesIO
+
+else:
+    string_types = basestring,
+    integer_types = (int, long)
+    class_types = (type, types.ClassType)
+    text_type = unicode
+    binary_type = str
+
+    unichr = unichr  # to allow importing
+    import StringIO
+    StringIO = StringIO.StringIO
+    import cStringIO
+    BytesIO = cStringIO.StringIO
+
+if PY3:
+    builtins_module = 'builtins'
+else:
+    builtins_module = '__builtin__'
+
+
+def with_metaclass(meta, *bases):
+    """Create a base class with a metaclass."""
+    return meta("NewBase", bases, {})
+
+DBG_TOKEN = 1
+DBG_EVENT = 2
+DBG_NODE = 4
+
+
+_debug = None
+
+
+# used from yaml util when testing
+def dbg(val=None):
+    global _debug
+    if _debug is None:
+        # set to true or false
+        _debug = os.environ.get('YAMLDEBUG')
+        if _debug is None:
+            _debug = 0
+        else:
+            _debug = int(_debug)
+    if val is None:
+        return _debug
+    return _debug & val
+
+
+def nprint(*args, **kw):
+    if dbg:
+        print(*args, **kw)
diff --git a/lib/spack/external/yaml/lib/yaml/composer.py b/lib/spack/external/ruamel/yaml/composer.py
index 06e5ac782f..fb0a55c759 100644
--- a/lib/spack/external/yaml/lib/yaml/composer.py
+++ b/lib/spack/external/ruamel/yaml/composer.py
@@ -1,15 +1,32 @@
+# coding: utf-8
+
+from __future__ import absolute_import
+from __future__ import print_function
+
+
+try:
+    from .error import MarkedYAMLError
+    from .compat import utf8
+except (ImportError, ValueError):  # for Jython
+    from ruamel.yaml.error import MarkedYAMLError
+    from ruamel.yaml.compat import utf8
+
+from ruamel.yaml.events import (
+    StreamStartEvent, StreamEndEvent, MappingStartEvent, MappingEndEvent,
+    SequenceStartEvent, SequenceEndEvent, AliasEvent, ScalarEvent,
+)
+from ruamel.yaml.nodes import (
+    MappingNode, ScalarNode, SequenceNode,
+)
 
 __all__ = ['Composer', 'ComposerError']
 
-from error import MarkedYAMLError
-from events import *
-from nodes import *
 
 class ComposerError(MarkedYAMLError):
     pass
 
-class Composer(object):
 
+class Composer(object):
     def __init__(self):
         self.anchors = {}
 
@@ -38,9 +55,10 @@ class Composer(object):
         # Ensure that the stream contains no more documents.
         if not self.check_event(StreamEndEvent):
             event = self.get_event()
-            raise ComposerError("expected a single document in the stream",
-                    document.start_mark, "but found another document",
-                    event.start_mark)
+            raise ComposerError(
+                "expected a single document in the stream",
+                document.start_mark, "but found another document",
+                event.start_mark)
 
         # Drop the STREAM-END event.
         self.get_event()
@@ -63,18 +81,20 @@ class Composer(object):
     def compose_node(self, parent, index):
         if self.check_event(AliasEvent):
             event = self.get_event()
-            anchor = event.anchor
-            if anchor not in self.anchors:
-                raise ComposerError(None, None, "found undefined alias %r"
-                        % anchor.encode('utf-8'), event.start_mark)
-            return self.anchors[anchor]
+            alias = event.anchor
+            if alias not in self.anchors:
+                raise ComposerError(
+                    None, None, "found undefined alias %r"
+                    % utf8(alias), event.start_mark)
+            return self.anchors[alias]
         event = self.peek_event()
         anchor = event.anchor
-        if anchor is not None:
+        if anchor is not None:  # have an anchor
             if anchor in self.anchors:
-                raise ComposerError("found duplicate anchor %r; first occurence"
-                        % anchor.encode('utf-8'), self.anchors[anchor].start_mark,
-                        "second occurence", event.start_mark)
+                raise ComposerError(
+                    "found duplicate anchor %r; first occurence"
+                    % utf8(anchor), self.anchors[anchor].start_mark,
+                    "second occurence", event.start_mark)
         self.descend_resolver(parent, index)
         if self.check_event(ScalarEvent):
             node = self.compose_scalar_node(anchor)
@@ -91,7 +111,8 @@ class Composer(object):
         if tag is None or tag == u'!':
             tag = self.resolve(ScalarNode, event.value, event.implicit)
         node = ScalarNode(tag, event.value,
-                event.start_mark, event.end_mark, style=event.style)
+                          event.start_mark, event.end_mark, style=event.style,
+                          comment=event.comment)
         if anchor is not None:
             self.anchors[anchor] = node
         return node
@@ -102,8 +123,9 @@ class Composer(object):
         if tag is None or tag == u'!':
             tag = self.resolve(SequenceNode, None, start_event.implicit)
         node = SequenceNode(tag, [],
-                start_event.start_mark, None,
-                flow_style=start_event.flow_style)
+                            start_event.start_mark, None,
+                            flow_style=start_event.flow_style,
+                            comment=start_event.comment, anchor=anchor)
         if anchor is not None:
             self.anchors[anchor] = node
         index = 0
@@ -111,7 +133,13 @@ class Composer(object):
             node.value.append(self.compose_node(node, index))
             index += 1
         end_event = self.get_event()
+        if node.flow_style is True and end_event.comment is not None:
+            if node.comment is not None:
+                print('Warning: unexpected end_event commment in sequence '
+                      'node {0}'.format(node.flow_style))
+            node.comment = end_event.comment
         node.end_mark = end_event.end_mark
+        self.check_end_doc_comment(end_event, node)
         return node
 
     def compose_mapping_node(self, anchor):
@@ -120,20 +148,35 @@ class Composer(object):
         if tag is None or tag == u'!':
             tag = self.resolve(MappingNode, None, start_event.implicit)
         node = MappingNode(tag, [],
-                start_event.start_mark, None,
-                flow_style=start_event.flow_style)
+                           start_event.start_mark, None,
+                           flow_style=start_event.flow_style,
+                           comment=start_event.comment, anchor=anchor)
         if anchor is not None:
             self.anchors[anchor] = node
         while not self.check_event(MappingEndEvent):
-            #key_event = self.peek_event()
+            # key_event = self.peek_event()
             item_key = self.compose_node(node, None)
-            #if item_key in node.value:
-            #    raise ComposerError("while composing a mapping", start_event.start_mark,
-            #            "found duplicate key", key_event.start_mark)
+            # if item_key in node.value:
+            #     raise ComposerError("while composing a mapping",
+            #             start_event.start_mark,
+            #             "found duplicate key", key_event.start_mark)
             item_value = self.compose_node(node, item_key)
-            #node.value[item_key] = item_value
+            # node.value[item_key] = item_value
             node.value.append((item_key, item_value))
         end_event = self.get_event()
+        if node.flow_style is True and end_event.comment is not None:
+            node.comment = end_event.comment
         node.end_mark = end_event.end_mark
+        self.check_end_doc_comment(end_event, node)
         return node
 
+    def check_end_doc_comment(self, end_event, node):
+        if end_event.comment and end_event.comment[1]:
+            # pre comments on an end_event, no following to move to
+            if node.comment is None:
+                node.comment = [None, None]
+            assert not isinstance(node, ScalarEvent)
+            # this is a post comment on a mapping node, add as third element
+            # in the list
+            node.comment.append(end_event.comment[1])
+            end_event.comment[1] = None
diff --git a/lib/spack/external/ruamel/yaml/configobjwalker.py b/lib/spack/external/ruamel/yaml/configobjwalker.py
new file mode 100644
index 0000000000..bab910cb11
--- /dev/null
+++ b/lib/spack/external/ruamel/yaml/configobjwalker.py
@@ -0,0 +1,9 @@
+# coding: utf-8
+
+import warnings
+from ruamel.yaml.util import configobj_walker as new_configobj_walker
+
+
+def configobj_walker(cfg):
+    warnings.warn("configobj_walker has move to ruamel.yaml.util, please update your code")
+    return new_configobj_walker(cfg)
diff --git a/lib/spack/external/ruamel/yaml/constructor.py b/lib/spack/external/ruamel/yaml/constructor.py
new file mode 100644
index 0000000000..f809df4bf9
--- /dev/null
+++ b/lib/spack/external/ruamel/yaml/constructor.py
@@ -0,0 +1,1167 @@
+# coding: utf-8
+
+from __future__ import absolute_import
+from __future__ import print_function
+
+import collections
+import datetime
+import base64
+import binascii
+import re
+import sys
+import types
+
+try:
+    from .error import *                               # NOQA
+    from .nodes import *                               # NOQA
+    from .compat import utf8, builtins_module, to_str, PY2, PY3, ordereddict, text_type
+    from .comments import *                               # NOQA
+    from .scalarstring import *                           # NOQA
+except (ImportError, ValueError):  # for Jython
+    from ruamel.yaml.error import *                               # NOQA
+    from ruamel.yaml.nodes import *                               # NOQA
+    from ruamel.yaml.compat import (utf8, builtins_module, to_str, PY2, PY3,
+                                    ordereddict, text_type)
+    from ruamel.yaml.comments import *                               # NOQA
+    from ruamel.yaml.scalarstring import *                           # NOQA
+
+
+__all__ = ['BaseConstructor', 'SafeConstructor', 'Constructor',
+           'ConstructorError', 'RoundTripConstructor']
+
+
+class ConstructorError(MarkedYAMLError):
+    pass
+
+
+class BaseConstructor(object):
+
+    yaml_constructors = {}
+    yaml_multi_constructors = {}
+
+    def __init__(self, preserve_quotes=None):
+        self.constructed_objects = {}
+        self.recursive_objects = {}
+        self.state_generators = []
+        self.deep_construct = False
+        self._preserve_quotes = preserve_quotes
+
+    def check_data(self):
+        # If there are more documents available?
+        return self.check_node()
+
+    def get_data(self):
+        # Construct and return the next document.
+        if self.check_node():
+            return self.construct_document(self.get_node())
+
+    def get_single_data(self):
+        # Ensure that the stream contains a single document and construct it.
+        node = self.get_single_node()
+        if node is not None:
+            return self.construct_document(node)
+        return None
+
+    def construct_document(self, node):
+        data = self.construct_object(node)
+        while self.state_generators:
+            state_generators = self.state_generators
+            self.state_generators = []
+            for generator in state_generators:
+                for dummy in generator:
+                    pass
+        self.constructed_objects = {}
+        self.recursive_objects = {}
+        self.deep_construct = False
+        return data
+
+    def construct_object(self, node, deep=False):
+        """deep is True when creating an object/mapping recursively,
+        in that case want the underlying elements available during construction
+        """
+        if node in self.constructed_objects:
+            return self.constructed_objects[node]
+        if deep:
+            old_deep = self.deep_construct
+            self.deep_construct = True
+        if node in self.recursive_objects:
+            raise ConstructorError(
+                None, None,
+                "found unconstructable recursive node", node.start_mark)
+        self.recursive_objects[node] = None
+        constructor = None
+        tag_suffix = None
+        if node.tag in self.yaml_constructors:
+            constructor = self.yaml_constructors[node.tag]
+        else:
+            for tag_prefix in self.yaml_multi_constructors:
+                if node.tag.startswith(tag_prefix):
+                    tag_suffix = node.tag[len(tag_prefix):]
+                    constructor = self.yaml_multi_constructors[tag_prefix]
+                    break
+            else:
+                if None in self.yaml_multi_constructors:
+                    tag_suffix = node.tag
+                    constructor = self.yaml_multi_constructors[None]
+                elif None in self.yaml_constructors:
+                    constructor = self.yaml_constructors[None]
+                elif isinstance(node, ScalarNode):
+                    constructor = self.__class__.construct_scalar
+                elif isinstance(node, SequenceNode):
+                    constructor = self.__class__.construct_sequence
+                elif isinstance(node, MappingNode):
+                    constructor = self.__class__.construct_mapping
+        if tag_suffix is None:
+            data = constructor(self, node)
+        else:
+            data = constructor(self, tag_suffix, node)
+        if isinstance(data, types.GeneratorType):
+            generator = data
+            data = next(generator)
+            if self.deep_construct:
+                for dummy in generator:
+                    pass
+            else:
+                self.state_generators.append(generator)
+        self.constructed_objects[node] = data
+        del self.recursive_objects[node]
+        if deep:
+            self.deep_construct = old_deep
+        return data
+
+    def construct_scalar(self, node):
+        if not isinstance(node, ScalarNode):
+            raise ConstructorError(
+                None, None,
+                "expected a scalar node, but found %s" % node.id,
+                node.start_mark)
+        return node.value
+
+    def construct_sequence(self, node, deep=False):
+        """deep is True when creating an object/mapping recursively,
+        in that case want the underlying elements available during construction
+        """
+        if not isinstance(node, SequenceNode):
+            raise ConstructorError(
+                None, None,
+                "expected a sequence node, but found %s" % node.id,
+                node.start_mark)
+        return [self.construct_object(child, deep=deep)
+                for child in node.value]
+
+    def construct_mapping(self, node, deep=False):
+        """deep is True when creating an object/mapping recursively,
+        in that case want the underlying elements available during construction
+        """
+        if not isinstance(node, MappingNode):
+            raise ConstructorError(
+                None, None,
+                "expected a mapping node, but found %s" % node.id,
+                node.start_mark)
+        mapping = {}
+        for key_node, value_node in node.value:
+            # keys can be list -> deep
+            key = self.construct_object(key_node, deep=True)
+            # lists are not hashable, but tuples are
+            if not isinstance(key, collections.Hashable):
+                if isinstance(key, list):
+                    key = tuple(key)
+            if PY2:
+                try:
+                    hash(key)
+                except TypeError as exc:
+                    raise ConstructorError(
+                        "while constructing a mapping", node.start_mark,
+                        "found unacceptable key (%s)" %
+                        exc, key_node.start_mark)
+            else:
+                if not isinstance(key, collections.Hashable):
+                    raise ConstructorError(
+                        "while constructing a mapping", node.start_mark,
+                        "found unhashable key", key_node.start_mark)
+
+            value = self.construct_object(value_node, deep=deep)
+            mapping[key] = value
+        return mapping
+
+    def construct_pairs(self, node, deep=False):
+        if not isinstance(node, MappingNode):
+            raise ConstructorError(
+                None, None,
+                "expected a mapping node, but found %s" % node.id,
+                node.start_mark)
+        pairs = []
+        for key_node, value_node in node.value:
+            key = self.construct_object(key_node, deep=deep)
+            value = self.construct_object(value_node, deep=deep)
+            pairs.append((key, value))
+        return pairs
+
+    @classmethod
+    def add_constructor(cls, tag, constructor):
+        if 'yaml_constructors' not in cls.__dict__:
+            cls.yaml_constructors = cls.yaml_constructors.copy()
+        cls.yaml_constructors[tag] = constructor
+
+    @classmethod
+    def add_multi_constructor(cls, tag_prefix, multi_constructor):
+        if 'yaml_multi_constructors' not in cls.__dict__:
+            cls.yaml_multi_constructors = cls.yaml_multi_constructors.copy()
+        cls.yaml_multi_constructors[tag_prefix] = multi_constructor
+
+
+class SafeConstructor(BaseConstructor):
+    def construct_scalar(self, node):
+        if isinstance(node, MappingNode):
+            for key_node, value_node in node.value:
+                if key_node.tag == u'tag:yaml.org,2002:value':
+                    return self.construct_scalar(value_node)
+        return BaseConstructor.construct_scalar(self, node)
+
+    def flatten_mapping(self, node):
+        """
+        This implements the merge key feature http://yaml.org/type/merge.html
+        by inserting keys from the merge dict/list of dicts if not yet
+        available in this node
+        """
+        merge = []
+        index = 0
+        while index < len(node.value):
+            key_node, value_node = node.value[index]
+            if key_node.tag == u'tag:yaml.org,2002:merge':
+                del node.value[index]
+                if isinstance(value_node, MappingNode):
+                    self.flatten_mapping(value_node)
+                    merge.extend(value_node.value)
+                elif isinstance(value_node, SequenceNode):
+                    submerge = []
+                    for subnode in value_node.value:
+                        if not isinstance(subnode, MappingNode):
+                            raise ConstructorError(
+                                "while constructing a mapping",
+                                node.start_mark,
+                                "expected a mapping for merging, but found %s"
+                                % subnode.id, subnode.start_mark)
+                        self.flatten_mapping(subnode)
+                        submerge.append(subnode.value)
+                    submerge.reverse()
+                    for value in submerge:
+                        merge.extend(value)
+                else:
+                    raise ConstructorError(
+                        "while constructing a mapping", node.start_mark,
+                        "expected a mapping or list of mappings for merging, "
+                        "but found %s"
+                        % value_node.id, value_node.start_mark)
+            elif key_node.tag == u'tag:yaml.org,2002:value':
+                key_node.tag = u'tag:yaml.org,2002:str'
+                index += 1
+            else:
+                index += 1
+        if merge:
+            node.value = merge + node.value
+
+    def construct_mapping(self, node, deep=False):
+        """deep is True when creating an object/mapping recursively,
+        in that case want the underlying elements available during construction
+        """
+        if isinstance(node, MappingNode):
+            self.flatten_mapping(node)
+        return BaseConstructor.construct_mapping(self, node, deep=deep)
+
+    def construct_yaml_null(self, node):
+        self.construct_scalar(node)
+        return None
+
+    # YAML 1.2 spec doesn't mention yes/no etc any more, 1.1 does
+    bool_values = {
+        u'yes':     True,
+        u'no':      False,
+        u'true':    True,
+        u'false':   False,
+        u'on':      True,
+        u'off':     False,
+    }
+
+    def construct_yaml_bool(self, node):
+        value = self.construct_scalar(node)
+        return self.bool_values[value.lower()]
+
+    def construct_yaml_int(self, node):
+        value = to_str(self.construct_scalar(node))
+        value = value.replace('_', '')
+        sign = +1
+        if value[0] == '-':
+            sign = -1
+        if value[0] in '+-':
+            value = value[1:]
+        if value == '0':
+            return 0
+        elif value.startswith('0b'):
+            return sign*int(value[2:], 2)
+        elif value.startswith('0x'):
+            return sign*int(value[2:], 16)
+        elif value.startswith('0o'):
+            return sign*int(value[2:], 8)
+        elif self.processing_version != (1, 2) and value[0] == '0':
+            return sign*int(value, 8)
+        elif self.processing_version != (1, 2) and ':' in value:
+            digits = [int(part) for part in value.split(':')]
+            digits.reverse()
+            base = 1
+            value = 0
+            for digit in digits:
+                value += digit*base
+                base *= 60
+            return sign*value
+        else:
+            return sign*int(value)
+
+    inf_value = 1e300
+    while inf_value != inf_value*inf_value:
+        inf_value *= inf_value
+    nan_value = -inf_value/inf_value   # Trying to make a quiet NaN (like C99).
+
+    def construct_yaml_float(self, node):
+        value = to_str(self.construct_scalar(node))
+        value = value.replace('_', '').lower()
+        sign = +1
+        if value[0] == '-':
+            sign = -1
+        if value[0] in '+-':
+            value = value[1:]
+        if value == '.inf':
+            return sign*self.inf_value
+        elif value == '.nan':
+            return self.nan_value
+        elif ':' in value:
+            digits = [float(part) for part in value.split(':')]
+            digits.reverse()
+            base = 1
+            value = 0.0
+            for digit in digits:
+                value += digit*base
+                base *= 60
+            return sign*value
+        else:
+            return sign*float(value)
+
+    if PY3:
+        def construct_yaml_binary(self, node):
+            try:
+                value = self.construct_scalar(node).encode('ascii')
+            except UnicodeEncodeError as exc:
+                raise ConstructorError(
+                    None, None,
+                    "failed to convert base64 data into ascii: %s" % exc,
+                    node.start_mark)
+            try:
+                if hasattr(base64, 'decodebytes'):
+                    return base64.decodebytes(value)
+                else:
+                    return base64.decodestring(value)
+            except binascii.Error as exc:
+                raise ConstructorError(
+                    None, None,
+                    "failed to decode base64 data: %s" % exc, node.start_mark)
+    else:
+        def construct_yaml_binary(self, node):
+            value = self.construct_scalar(node)
+            try:
+                return to_str(value).decode('base64')
+            except (binascii.Error, UnicodeEncodeError) as exc:
+                raise ConstructorError(
+                    None, None,
+                    "failed to decode base64 data: %s" % exc, node.start_mark)
+
+    timestamp_regexp = re.compile(
+        u'''^(?P<year>[0-9][0-9][0-9][0-9])
+          -(?P<month>[0-9][0-9]?)
+          -(?P<day>[0-9][0-9]?)
+          (?:(?:[Tt]|[ \\t]+)
+          (?P<hour>[0-9][0-9]?)
+          :(?P<minute>[0-9][0-9])
+          :(?P<second>[0-9][0-9])
+          (?:\\.(?P<fraction>[0-9]*))?
+          (?:[ \\t]*(?P<tz>Z|(?P<tz_sign>[-+])(?P<tz_hour>[0-9][0-9]?)
+          (?::(?P<tz_minute>[0-9][0-9]))?))?)?$''', re.X)
+
+    def construct_yaml_timestamp(self, node):
+        value = self.construct_scalar(node)  # NOQA
+        match = self.timestamp_regexp.match(node.value)
+        values = match.groupdict()
+        year = int(values['year'])
+        month = int(values['month'])
+        day = int(values['day'])
+        if not values['hour']:
+            return datetime.date(year, month, day)
+        hour = int(values['hour'])
+        minute = int(values['minute'])
+        second = int(values['second'])
+        fraction = 0
+        if values['fraction']:
+            fraction = values['fraction'][:6]
+            while len(fraction) < 6:
+                fraction += '0'
+            fraction = int(fraction)
+        delta = None
+        if values['tz_sign']:
+            tz_hour = int(values['tz_hour'])
+            tz_minute = int(values['tz_minute'] or 0)
+            delta = datetime.timedelta(hours=tz_hour, minutes=tz_minute)
+            if values['tz_sign'] == '-':
+                delta = -delta
+        data = datetime.datetime(year, month, day, hour, minute, second,
+                                 fraction)
+        if delta:
+            data -= delta
+        return data
+
+    def construct_yaml_omap(self, node):
+        # Note: we do now check for duplicate keys
+        omap = ordereddict()
+        yield omap
+        if not isinstance(node, SequenceNode):
+            raise ConstructorError(
+                "while constructing an ordered map", node.start_mark,
+                "expected a sequence, but found %s" % node.id, node.start_mark)
+        for subnode in node.value:
+            if not isinstance(subnode, MappingNode):
+                raise ConstructorError(
+                    "while constructing an ordered map", node.start_mark,
+                    "expected a mapping of length 1, but found %s" %
+                    subnode.id,
+                    subnode.start_mark)
+            if len(subnode.value) != 1:
+                raise ConstructorError(
+                    "while constructing an ordered map", node.start_mark,
+                    "expected a single mapping item, but found %d items" %
+                    len(subnode.value),
+                    subnode.start_mark)
+            key_node, value_node = subnode.value[0]
+            key = self.construct_object(key_node)
+            assert key not in omap
+            value = self.construct_object(value_node)
+            omap[key] = value
+
+    def construct_yaml_pairs(self, node):
+        # Note: the same code as `construct_yaml_omap`.
+        pairs = []
+        yield pairs
+        if not isinstance(node, SequenceNode):
+            raise ConstructorError(
+                "while constructing pairs", node.start_mark,
+                "expected a sequence, but found %s" % node.id, node.start_mark)
+        for subnode in node.value:
+            if not isinstance(subnode, MappingNode):
+                raise ConstructorError(
+                    "while constructing pairs", node.start_mark,
+                    "expected a mapping of length 1, but found %s" %
+                    subnode.id,
+                    subnode.start_mark)
+            if len(subnode.value) != 1:
+                raise ConstructorError(
+                    "while constructing pairs", node.start_mark,
+                    "expected a single mapping item, but found %d items" %
+                    len(subnode.value),
+                    subnode.start_mark)
+            key_node, value_node = subnode.value[0]
+            key = self.construct_object(key_node)
+            value = self.construct_object(value_node)
+            pairs.append((key, value))
+
+    def construct_yaml_set(self, node):
+        data = set()
+        yield data
+        value = self.construct_mapping(node)
+        data.update(value)
+
+    def construct_yaml_str(self, node):
+        value = self.construct_scalar(node)
+        if PY3:
+            return value
+        try:
+            return value.encode('ascii')
+        except UnicodeEncodeError:
+            return value
+
+    def construct_yaml_seq(self, node):
+        data = []
+        yield data
+        data.extend(self.construct_sequence(node))
+
+    def construct_yaml_map(self, node):
+        data = {}
+        yield data
+        value = self.construct_mapping(node)
+        data.update(value)
+
+    def construct_yaml_object(self, node, cls):
+        data = cls.__new__(cls)
+        yield data
+        if hasattr(data, '__setstate__'):
+            state = self.construct_mapping(node, deep=True)
+            data.__setstate__(state)
+        else:
+            state = self.construct_mapping(node)
+            data.__dict__.update(state)
+
+    def construct_undefined(self, node):
+        raise ConstructorError(
+            None, None,
+            "could not determine a constructor for the tag %r" %
+            utf8(node.tag),
+            node.start_mark)
+
+SafeConstructor.add_constructor(
+    u'tag:yaml.org,2002:null',
+    SafeConstructor.construct_yaml_null)
+
+SafeConstructor.add_constructor(
+    u'tag:yaml.org,2002:bool',
+    SafeConstructor.construct_yaml_bool)
+
+SafeConstructor.add_constructor(
+    u'tag:yaml.org,2002:int',
+    SafeConstructor.construct_yaml_int)
+
+SafeConstructor.add_constructor(
+    u'tag:yaml.org,2002:float',
+    SafeConstructor.construct_yaml_float)
+
+SafeConstructor.add_constructor(
+    u'tag:yaml.org,2002:binary',
+    SafeConstructor.construct_yaml_binary)
+
+SafeConstructor.add_constructor(
+    u'tag:yaml.org,2002:timestamp',
+    SafeConstructor.construct_yaml_timestamp)
+
+SafeConstructor.add_constructor(
+    u'tag:yaml.org,2002:omap',
+    SafeConstructor.construct_yaml_omap)
+
+SafeConstructor.add_constructor(
+    u'tag:yaml.org,2002:pairs',
+    SafeConstructor.construct_yaml_pairs)
+
+SafeConstructor.add_constructor(
+    u'tag:yaml.org,2002:set',
+    SafeConstructor.construct_yaml_set)
+
+SafeConstructor.add_constructor(
+    u'tag:yaml.org,2002:str',
+    SafeConstructor.construct_yaml_str)
+
+SafeConstructor.add_constructor(
+    u'tag:yaml.org,2002:seq',
+    SafeConstructor.construct_yaml_seq)
+
+SafeConstructor.add_constructor(
+    u'tag:yaml.org,2002:map',
+    SafeConstructor.construct_yaml_map)
+
+SafeConstructor.add_constructor(
+    None, SafeConstructor.construct_undefined)
+
+
+class Constructor(SafeConstructor):
+
+    def construct_python_str(self, node):
+        return utf8(self.construct_scalar(node))
+
+    def construct_python_unicode(self, node):
+        return self.construct_scalar(node)
+
+    if PY3:
+        def construct_python_bytes(self, node):
+            try:
+                value = self.construct_scalar(node).encode('ascii')
+            except UnicodeEncodeError as exc:
+                raise ConstructorError(
+                    None, None,
+                    "failed to convert base64 data into ascii: %s" % exc,
+                    node.start_mark)
+            try:
+                if hasattr(base64, 'decodebytes'):
+                    return base64.decodebytes(value)
+                else:
+                    return base64.decodestring(value)
+            except binascii.Error as exc:
+                raise ConstructorError(
+                    None, None,
+                    "failed to decode base64 data: %s" % exc, node.start_mark)
+
+    def construct_python_long(self, node):
+        val = self.construct_yaml_int(node)
+        if PY3:
+            return val
+        return int(val)
+
+    def construct_python_complex(self, node):
+        return complex(self.construct_scalar(node))
+
+    def construct_python_tuple(self, node):
+        return tuple(self.construct_sequence(node))
+
+    def find_python_module(self, name, mark):
+        if not name:
+            raise ConstructorError(
+                "while constructing a Python module", mark,
+                "expected non-empty name appended to the tag", mark)
+        try:
+            __import__(name)
+        except ImportError as exc:
+            raise ConstructorError(
+                "while constructing a Python module", mark,
+                "cannot find module %r (%s)" % (utf8(name), exc), mark)
+        return sys.modules[name]
+
+    def find_python_name(self, name, mark):
+        if not name:
+            raise ConstructorError(
+                "while constructing a Python object", mark,
+                "expected non-empty name appended to the tag", mark)
+        if u'.' in name:
+            module_name, object_name = name.rsplit('.', 1)
+        else:
+            module_name = builtins_module
+            object_name = name
+        try:
+            __import__(module_name)
+        except ImportError as exc:
+            raise ConstructorError(
+                "while constructing a Python object", mark,
+                "cannot find module %r (%s)" % (utf8(module_name), exc), mark)
+        module = sys.modules[module_name]
+        if not hasattr(module, object_name):
+            raise ConstructorError(
+                "while constructing a Python object", mark,
+                "cannot find %r in the module %r" % (utf8(object_name),
+                                                     module.__name__), mark)
+        return getattr(module, object_name)
+
+    def construct_python_name(self, suffix, node):
+        value = self.construct_scalar(node)
+        if value:
+            raise ConstructorError(
+                "while constructing a Python name", node.start_mark,
+                "expected the empty value, but found %r" % utf8(value),
+                node.start_mark)
+        return self.find_python_name(suffix, node.start_mark)
+
+    def construct_python_module(self, suffix, node):
+        value = self.construct_scalar(node)
+        if value:
+            raise ConstructorError(
+                "while constructing a Python module", node.start_mark,
+                "expected the empty value, but found %r" % utf8(value),
+                node.start_mark)
+        return self.find_python_module(suffix, node.start_mark)
+
+    if PY2:
+        class classobj:
+            pass
+
+    def make_python_instance(self, suffix, node,
+                             args=None, kwds=None, newobj=False):
+        if not args:
+            args = []
+        if not kwds:
+            kwds = {}
+        cls = self.find_python_name(suffix, node.start_mark)
+        if PY3:
+            if newobj and isinstance(cls, type):
+                return cls.__new__(cls, *args, **kwds)
+            else:
+                return cls(*args, **kwds)
+        else:
+            if newobj and isinstance(cls, type(self.classobj))  \
+                    and not args and not kwds:
+                instance = self.classobj()
+                instance.__class__ = cls
+                return instance
+            elif newobj and isinstance(cls, type):
+                return cls.__new__(cls, *args, **kwds)
+            else:
+                return cls(*args, **kwds)
+
+    def set_python_instance_state(self, instance, state):
+        if hasattr(instance, '__setstate__'):
+            instance.__setstate__(state)
+        else:
+            slotstate = {}
+            if isinstance(state, tuple) and len(state) == 2:
+                state, slotstate = state
+            if hasattr(instance, '__dict__'):
+                instance.__dict__.update(state)
+            elif state:
+                slotstate.update(state)
+            for key, value in slotstate.items():
+                setattr(object, key, value)
+
+    def construct_python_object(self, suffix, node):
+        # Format:
+        #   !!python/object:module.name { ... state ... }
+        instance = self.make_python_instance(suffix, node, newobj=True)
+        yield instance
+        deep = hasattr(instance, '__setstate__')
+        state = self.construct_mapping(node, deep=deep)
+        self.set_python_instance_state(instance, state)
+
+    def construct_python_object_apply(self, suffix, node, newobj=False):
+        # Format:
+        #   !!python/object/apply       # (or !!python/object/new)
+        #   args: [ ... arguments ... ]
+        #   kwds: { ... keywords ... }
+        #   state: ... state ...
+        #   listitems: [ ... listitems ... ]
+        #   dictitems: { ... dictitems ... }
+        # or short format:
+        #   !!python/object/apply [ ... arguments ... ]
+        # The difference between !!python/object/apply and !!python/object/new
+        # is how an object is created, check make_python_instance for details.
+        if isinstance(node, SequenceNode):
+            args = self.construct_sequence(node, deep=True)
+            kwds = {}
+            state = {}
+            listitems = []
+            dictitems = {}
+        else:
+            value = self.construct_mapping(node, deep=True)
+            args = value.get('args', [])
+            kwds = value.get('kwds', {})
+            state = value.get('state', {})
+            listitems = value.get('listitems', [])
+            dictitems = value.get('dictitems', {})
+        instance = self.make_python_instance(suffix, node, args, kwds, newobj)
+        if state:
+            self.set_python_instance_state(instance, state)
+        if listitems:
+            instance.extend(listitems)
+        if dictitems:
+            for key in dictitems:
+                instance[key] = dictitems[key]
+        return instance
+
+    def construct_python_object_new(self, suffix, node):
+        return self.construct_python_object_apply(suffix, node, newobj=True)
+
+Constructor.add_constructor(
+    u'tag:yaml.org,2002:python/none',
+    Constructor.construct_yaml_null)
+
+Constructor.add_constructor(
+    u'tag:yaml.org,2002:python/bool',
+    Constructor.construct_yaml_bool)
+
+Constructor.add_constructor(
+    u'tag:yaml.org,2002:python/str',
+    Constructor.construct_python_str)
+
+Constructor.add_constructor(
+    u'tag:yaml.org,2002:python/unicode',
+    Constructor.construct_python_unicode)
+
+if PY3:
+    Constructor.add_constructor(
+        u'tag:yaml.org,2002:python/bytes',
+        Constructor.construct_python_bytes)
+
+Constructor.add_constructor(
+    u'tag:yaml.org,2002:python/int',
+    Constructor.construct_yaml_int)
+
+Constructor.add_constructor(
+    u'tag:yaml.org,2002:python/long',
+    Constructor.construct_python_long)
+
+Constructor.add_constructor(
+    u'tag:yaml.org,2002:python/float',
+    Constructor.construct_yaml_float)
+
+Constructor.add_constructor(
+    u'tag:yaml.org,2002:python/complex',
+    Constructor.construct_python_complex)
+
+Constructor.add_constructor(
+    u'tag:yaml.org,2002:python/list',
+    Constructor.construct_yaml_seq)
+
+Constructor.add_constructor(
+    u'tag:yaml.org,2002:python/tuple',
+    Constructor.construct_python_tuple)
+
+Constructor.add_constructor(
+    u'tag:yaml.org,2002:python/dict',
+    Constructor.construct_yaml_map)
+
+Constructor.add_multi_constructor(
+    u'tag:yaml.org,2002:python/name:',
+    Constructor.construct_python_name)
+
+Constructor.add_multi_constructor(
+    u'tag:yaml.org,2002:python/module:',
+    Constructor.construct_python_module)
+
+Constructor.add_multi_constructor(
+    u'tag:yaml.org,2002:python/object:',
+    Constructor.construct_python_object)
+
+Constructor.add_multi_constructor(
+    u'tag:yaml.org,2002:python/object/apply:',
+    Constructor.construct_python_object_apply)
+
+Constructor.add_multi_constructor(
+    u'tag:yaml.org,2002:python/object/new:',
+    Constructor.construct_python_object_new)
+
+
+class RoundTripConstructor(SafeConstructor):
+    """need to store the comments on the node itself,
+    as well as on the items
+    """
+
+    def construct_scalar(self, node):
+        if not isinstance(node, ScalarNode):
+            raise ConstructorError(
+                None, None,
+                "expected a scalar node, but found %s" % node.id,
+                node.start_mark)
+
+        if node.style == '|' and isinstance(node.value, text_type):
+            return PreservedScalarString(node.value)
+        elif self._preserve_quotes and isinstance(node.value, text_type):
+            if node.style == "'":
+                return SingleQuotedScalarString(node.value)
+            if node.style == '"':
+                return DoubleQuotedScalarString(node.value)
+        return node.value
+
+    def construct_yaml_str(self, node):
+        value = self.construct_scalar(node)
+        if isinstance(value, ScalarString):
+            return value
+        if PY3:
+            return value
+        try:
+            return value.encode('ascii')
+        except AttributeError:
+            # in case you replace the node dynamically e.g. with a dict
+            return value
+        except UnicodeEncodeError:
+            return value
+
+    def construct_sequence(self, node, seqtyp, deep=False):
+        if not isinstance(node, SequenceNode):
+            raise ConstructorError(
+                None, None,
+                "expected a sequence node, but found %s" % node.id,
+                node.start_mark)
+        ret_val = []
+        if node.comment:
+            seqtyp._yaml_add_comment(node.comment[:2])
+            if len(node.comment) > 2:
+                seqtyp.yaml_end_comment_extend(node.comment[2], clear=True)
+        if node.anchor:
+            from ruamel.yaml.serializer import templated_id
+            if not templated_id(node.anchor):
+                seqtyp.yaml_set_anchor(node.anchor)
+        for idx, child in enumerate(node.value):
+            ret_val.append(self.construct_object(child, deep=deep))
+            if child.comment:
+                seqtyp._yaml_add_comment(child.comment, key=idx)
+            seqtyp._yaml_set_idx_line_col(
+                idx, [child.start_mark.line, child.start_mark.column])
+        return ret_val
+
+    def flatten_mapping(self, node):
+        """
+        This implements the merge key feature http://yaml.org/type/merge.html
+        by inserting keys from the merge dict/list of dicts if not yet
+        available in this node
+        """
+
+        def constructed(value_node):
+            # If the contents of a merge are defined within the
+            # merge marker, then they won't have been constructed
+            # yet. But if they were already constructed, we need to use
+            # the existing object.
+            if value_node in self.constructed_objects:
+                value = self.constructed_objects[value_node]
+            else:
+                value = self.construct_object(value_node, deep=False)
+            return value
+
+        # merge = []
+        merge_map_list = []
+        index = 0
+        while index < len(node.value):
+            key_node, value_node = node.value[index]
+            if key_node.tag == u'tag:yaml.org,2002:merge':
+                del node.value[index]
+                if isinstance(value_node, MappingNode):
+                    merge_map_list.append(
+                        (index, constructed(value_node)))
+                    # self.flatten_mapping(value_node)
+                    # merge.extend(value_node.value)
+                elif isinstance(value_node, SequenceNode):
+                    # submerge = []
+                    for subnode in value_node.value:
+                        if not isinstance(subnode, MappingNode):
+                            raise ConstructorError(
+                                "while constructing a mapping",
+                                node.start_mark,
+                                "expected a mapping for merging, but found %s"
+                                % subnode.id, subnode.start_mark)
+                        merge_map_list.append(
+                            (index, constructed(subnode)))
+                    #     self.flatten_mapping(subnode)
+                    #     submerge.append(subnode.value)
+                    # submerge.reverse()
+                    # for value in submerge:
+                    #     merge.extend(value)
+                else:
+                    raise ConstructorError(
+                        "while constructing a mapping", node.start_mark,
+                        "expected a mapping or list of mappings for merging, "
+                        "but found %s"
+                        % value_node.id, value_node.start_mark)
+            elif key_node.tag == u'tag:yaml.org,2002:value':
+                key_node.tag = u'tag:yaml.org,2002:str'
+                index += 1
+            else:
+                index += 1
+        # print ('merge_map_list', merge_map_list)
+        return merge_map_list
+        # if merge:
+        #     node.value = merge + node.value
+
+    def construct_mapping(self, node, maptyp, deep=False):
+        if not isinstance(node, MappingNode):
+            raise ConstructorError(
+                None, None,
+                "expected a mapping node, but found %s" % node.id,
+                node.start_mark)
+        merge_map = self.flatten_mapping(node)
+        if merge_map:
+            maptyp.add_yaml_merge(merge_map)
+        # mapping = {}
+        if node.comment:
+            maptyp._yaml_add_comment(node.comment[:2])
+            if len(node.comment) > 2:
+                maptyp.yaml_end_comment_extend(node.comment[2], clear=True)
+        if node.anchor:
+            from ruamel.yaml.serializer import templated_id
+            if not templated_id(node.anchor):
+                maptyp.yaml_set_anchor(node.anchor)
+        for key_node, value_node in node.value:
+            # keys can be list -> deep
+            key = self.construct_object(key_node, deep=True)
+            # lists are not hashable, but tuples are
+            if not isinstance(key, collections.Hashable):
+                if isinstance(key, list):
+                    key = tuple(key)
+            if PY2:
+                try:
+                    hash(key)
+                except TypeError as exc:
+                    raise ConstructorError(
+                        "while constructing a mapping", node.start_mark,
+                        "found unacceptable key (%s)" %
+                        exc, key_node.start_mark)
+            else:
+                if not isinstance(key, collections.Hashable):
+                    raise ConstructorError(
+                        "while constructing a mapping", node.start_mark,
+                        "found unhashable key", key_node.start_mark)
+            value = self.construct_object(value_node, deep=deep)
+            if key_node.comment:
+                maptyp._yaml_add_comment(key_node.comment, key=key)
+            if value_node.comment:
+                maptyp._yaml_add_comment(value_node.comment, value=key)
+            maptyp._yaml_set_kv_line_col(
+                key, [key_node.start_mark.line, key_node.start_mark.column,
+                      value_node.start_mark.line, value_node.start_mark.column])
+            maptyp[key] = value
+
+    def construct_setting(self, node, typ, deep=False):
+        if not isinstance(node, MappingNode):
+            raise ConstructorError(
+                None, None,
+                "expected a mapping node, but found %s" % node.id,
+                node.start_mark)
+        if node.comment:
+            typ._yaml_add_comment(node.comment[:2])
+            if len(node.comment) > 2:
+                typ.yaml_end_comment_extend(node.comment[2], clear=True)
+        if node.anchor:
+            from ruamel.yaml.serializer import templated_id
+            if not templated_id(node.anchor):
+                typ.yaml_set_anchor(node.anchor)
+        for key_node, value_node in node.value:
+            # keys can be list -> deep
+            key = self.construct_object(key_node, deep=True)
+            # lists are not hashable, but tuples are
+            if not isinstance(key, collections.Hashable):
+                if isinstance(key, list):
+                    key = tuple(key)
+            if PY2:
+                try:
+                    hash(key)
+                except TypeError as exc:
+                    raise ConstructorError(
+                        "while constructing a mapping", node.start_mark,
+                        "found unacceptable key (%s)" %
+                        exc, key_node.start_mark)
+            else:
+                if not isinstance(key, collections.Hashable):
+                    raise ConstructorError(
+                        "while constructing a mapping", node.start_mark,
+                        "found unhashable key", key_node.start_mark)
+            value = self.construct_object(value_node, deep=deep)  # NOQA
+            if key_node.comment:
+                typ._yaml_add_comment(key_node.comment, key=key)
+            if value_node.comment:
+                typ._yaml_add_comment(value_node.comment, value=key)
+            typ.add(key)
+
+    def construct_yaml_seq(self, node):
+        data = CommentedSeq()
+        data._yaml_set_line_col(node.start_mark.line, node.start_mark.column)
+        if node.flow_style is True:
+            data.fa.set_flow_style()
+        elif node.flow_style is False:
+            data.fa.set_block_style()
+        if node.comment:
+            data._yaml_add_comment(node.comment)
+        yield data
+        data.extend(self.construct_sequence(node, data))
+
+    def construct_yaml_map(self, node):
+        data = CommentedMap()
+        data._yaml_set_line_col(node.start_mark.line, node.start_mark.column)
+        if node.flow_style is True:
+            data.fa.set_flow_style()
+        elif node.flow_style is False:
+            data.fa.set_block_style()
+        yield data
+        self.construct_mapping(node, data)
+
+    def construct_yaml_omap(self, node):
+        # Note: we do now check for duplicate keys
+        omap = CommentedOrderedMap()
+        omap._yaml_set_line_col(node.start_mark.line, node.start_mark.column)
+        if node.flow_style is True:
+            omap.fa.set_flow_style()
+        elif node.flow_style is False:
+            omap.fa.set_block_style()
+        yield omap
+        if node.comment:
+            omap._yaml_add_comment(node.comment[:2])
+            if len(node.comment) > 2:
+                omap.yaml_end_comment_extend(node.comment[2], clear=True)
+        if not isinstance(node, SequenceNode):
+            raise ConstructorError(
+                "while constructing an ordered map", node.start_mark,
+                "expected a sequence, but found %s" % node.id, node.start_mark)
+        for subnode in node.value:
+            if not isinstance(subnode, MappingNode):
+                raise ConstructorError(
+                    "while constructing an ordered map", node.start_mark,
+                    "expected a mapping of length 1, but found %s" %
+                    subnode.id,
+                    subnode.start_mark)
+            if len(subnode.value) != 1:
+                raise ConstructorError(
+                    "while constructing an ordered map", node.start_mark,
+                    "expected a single mapping item, but found %d items" %
+                    len(subnode.value),
+                    subnode.start_mark)
+            key_node, value_node = subnode.value[0]
+            key = self.construct_object(key_node)
+            assert key not in omap
+            value = self.construct_object(value_node)
+            if key_node.comment:
+                omap._yaml_add_comment(key_node.comment, key=key)
+            if subnode.comment:
+                omap._yaml_add_comment(subnode.comment, key=key)
+            if value_node.comment:
+                omap._yaml_add_comment(value_node.comment, value=key)
+            omap[key] = value
+
+    def construct_yaml_set(self, node):
+        data = CommentedSet()
+        data._yaml_set_line_col(node.start_mark.line, node.start_mark.column)
+        yield data
+        self.construct_setting(node, data)
+
+    def construct_undefined(self, node):
+        try:
+            data = CommentedMap()
+            data._yaml_set_line_col(node.start_mark.line, node.start_mark.column)
+            if node.flow_style is True:
+                data.fa.set_flow_style()
+            elif node.flow_style is False:
+                data.fa.set_block_style()
+            data.yaml_set_tag(node.tag)
+            yield data
+            self.construct_mapping(node, data)
+        except:
+            raise ConstructorError(
+                None, None,
+                "could not determine a constructor for the tag %r" %
+                utf8(node.tag),
+                node.start_mark)
+
+
+RoundTripConstructor.add_constructor(
+    u'tag:yaml.org,2002:null',
+    RoundTripConstructor.construct_yaml_null)
+
+RoundTripConstructor.add_constructor(
+    u'tag:yaml.org,2002:bool',
+    RoundTripConstructor.construct_yaml_bool)
+
+RoundTripConstructor.add_constructor(
+    u'tag:yaml.org,2002:int',
+    RoundTripConstructor.construct_yaml_int)
+
+RoundTripConstructor.add_constructor(
+    u'tag:yaml.org,2002:float',
+    RoundTripConstructor.construct_yaml_float)
+
+RoundTripConstructor.add_constructor(
+    u'tag:yaml.org,2002:binary',
+    RoundTripConstructor.construct_yaml_binary)
+
+RoundTripConstructor.add_constructor(
+    u'tag:yaml.org,2002:timestamp',
+    RoundTripConstructor.construct_yaml_timestamp)
+
+RoundTripConstructor.add_constructor(
+    u'tag:yaml.org,2002:omap',
+    RoundTripConstructor.construct_yaml_omap)
+
+RoundTripConstructor.add_constructor(
+    u'tag:yaml.org,2002:pairs',
+    RoundTripConstructor.construct_yaml_pairs)
+
+RoundTripConstructor.add_constructor(
+    u'tag:yaml.org,2002:set',
+    RoundTripConstructor.construct_yaml_set)
+
+RoundTripConstructor.add_constructor(
+    u'tag:yaml.org,2002:str',
+    RoundTripConstructor.construct_yaml_str)
+
+RoundTripConstructor.add_constructor(
+    u'tag:yaml.org,2002:seq',
+    RoundTripConstructor.construct_yaml_seq)
+
+RoundTripConstructor.add_constructor(
+    u'tag:yaml.org,2002:map',
+    RoundTripConstructor.construct_yaml_map)
+
+RoundTripConstructor.add_constructor(
+    None, RoundTripConstructor.construct_undefined)
diff --git a/lib/spack/external/ruamel/yaml/dumper.py b/lib/spack/external/ruamel/yaml/dumper.py
new file mode 100644
index 0000000000..90e2ca9d1b
--- /dev/null
+++ b/lib/spack/external/ruamel/yaml/dumper.py
@@ -0,0 +1,102 @@
+# coding: utf-8
+
+from __future__ import absolute_import
+
+__all__ = ['BaseDumper', 'SafeDumper', 'Dumper', 'RoundTripDumper']
+
+try:
+    from .emitter import *                               # NOQA
+    from .serializer import *                               # NOQA
+    from .representer import *                               # NOQA
+    from .resolver import *                               # NOQA
+except (ImportError, ValueError):  # for Jython
+    from ruamel.yaml.emitter import *                               # NOQA
+    from ruamel.yaml.serializer import *                               # NOQA
+    from ruamel.yaml.representer import *                               # NOQA
+    from ruamel.yaml.resolver import *                               # NOQA
+
+
+class BaseDumper(Emitter, Serializer, BaseRepresenter, BaseResolver):
+    def __init__(self, stream,
+                 default_style=None, default_flow_style=None,
+                 canonical=None, indent=None, width=None,
+                 allow_unicode=None, line_break=None,
+                 encoding=None, explicit_start=None, explicit_end=None,
+                 version=None, tags=None, block_seq_indent=None,
+                 top_level_colon_align=None, prefix_colon=None):
+        Emitter.__init__(self, stream, canonical=canonical,
+                         indent=indent, width=width,
+                         allow_unicode=allow_unicode, line_break=line_break,
+                         block_seq_indent=block_seq_indent)
+        Serializer.__init__(self, encoding=encoding,
+                            explicit_start=explicit_start,
+                            explicit_end=explicit_end,
+                            version=version, tags=tags)
+        Representer.__init__(self, default_style=default_style,
+                             default_flow_style=default_flow_style)
+        Resolver.__init__(self)
+
+
+class SafeDumper(Emitter, Serializer, SafeRepresenter, Resolver):
+    def __init__(self, stream,
+                 default_style=None, default_flow_style=None,
+                 canonical=None, indent=None, width=None,
+                 allow_unicode=None, line_break=None,
+                 encoding=None, explicit_start=None, explicit_end=None,
+                 version=None, tags=None, block_seq_indent=None,
+                 top_level_colon_align=None, prefix_colon=None):
+        Emitter.__init__(self, stream, canonical=canonical,
+                         indent=indent, width=width,
+                         allow_unicode=allow_unicode, line_break=line_break,
+                         block_seq_indent=block_seq_indent)
+        Serializer.__init__(self, encoding=encoding,
+                            explicit_start=explicit_start,
+                            explicit_end=explicit_end,
+                            version=version, tags=tags)
+        SafeRepresenter.__init__(self, default_style=default_style,
+                                 default_flow_style=default_flow_style)
+        Resolver.__init__(self)
+
+
+class Dumper(Emitter, Serializer, Representer, Resolver):
+    def __init__(self, stream,
+                 default_style=None, default_flow_style=None,
+                 canonical=None, indent=None, width=None,
+                 allow_unicode=None, line_break=None,
+                 encoding=None, explicit_start=None, explicit_end=None,
+                 version=None, tags=None, block_seq_indent=None,
+                 top_level_colon_align=None, prefix_colon=None):
+        Emitter.__init__(self, stream, canonical=canonical,
+                         indent=indent, width=width,
+                         allow_unicode=allow_unicode, line_break=line_break,
+                         block_seq_indent=block_seq_indent)
+        Serializer.__init__(self, encoding=encoding,
+                            explicit_start=explicit_start,
+                            explicit_end=explicit_end,
+                            version=version, tags=tags)
+        Representer.__init__(self, default_style=default_style,
+                             default_flow_style=default_flow_style)
+        Resolver.__init__(self)
+
+
+class RoundTripDumper(Emitter, Serializer, RoundTripRepresenter, VersionedResolver):
+    def __init__(self, stream,
+                 default_style=None, default_flow_style=None,
+                 canonical=None, indent=None, width=None,
+                 allow_unicode=None, line_break=None,
+                 encoding=None, explicit_start=None, explicit_end=None,
+                 version=None, tags=None, block_seq_indent=None,
+                 top_level_colon_align=None, prefix_colon=None):
+        Emitter.__init__(self, stream, canonical=canonical,
+                         indent=indent, width=width,
+                         allow_unicode=allow_unicode, line_break=line_break,
+                         block_seq_indent=block_seq_indent,
+                         top_level_colon_align=top_level_colon_align,
+                         prefix_colon=prefix_colon)
+        Serializer.__init__(self, encoding=encoding,
+                            explicit_start=explicit_start,
+                            explicit_end=explicit_end,
+                            version=version, tags=tags)
+        RoundTripRepresenter.__init__(self, default_style=default_style,
+                                      default_flow_style=default_flow_style)
+        VersionedResolver.__init__(self)
diff --git a/lib/spack/external/yaml/lib/yaml/emitter.py b/lib/spack/external/ruamel/yaml/emitter.py
index e5bcdcccbb..b754bc04e1 100644
--- a/lib/spack/external/yaml/lib/yaml/emitter.py
+++ b/lib/spack/external/ruamel/yaml/emitter.py
@@ -1,3 +1,7 @@
+# coding: utf-8
+
+from __future__ import absolute_import
+from __future__ import print_function
 
 # Emitter expects events obeying the following grammar:
 # stream ::= STREAM-START document* STREAM-END
@@ -8,17 +12,25 @@
 
 __all__ = ['Emitter', 'EmitterError']
 
-from error import YAMLError
-from events import *
+try:
+    from .error import YAMLError
+    from .events import *                                                # NOQA
+    from .compat import utf8, text_type, PY2, nprint, dbg, DBG_EVENT
+except (ImportError, ValueError):  # for Jython
+    from ruamel.yaml.error import YAMLError
+    from ruamel.yaml.events import *                                     # NOQA
+    from ruamel.yaml.compat import utf8, text_type, PY2, nprint, dbg, DBG_EVENT
+
 
 class EmitterError(YAMLError):
     pass
 
+
 class ScalarAnalysis(object):
     def __init__(self, scalar, empty, multiline,
-            allow_flow_plain, allow_block_plain,
-            allow_single_quoted, allow_double_quoted,
-            allow_block):
+                 allow_flow_plain, allow_block_plain,
+                 allow_single_quoted, allow_double_quoted,
+                 allow_block):
         self.scalar = scalar
         self.empty = empty
         self.multiline = multiline
@@ -28,15 +40,18 @@ class ScalarAnalysis(object):
         self.allow_double_quoted = allow_double_quoted
         self.allow_block = allow_block
 
-class Emitter(object):
 
+class Emitter(object):
     DEFAULT_TAG_PREFIXES = {
-        u'!' : u'!',
-        u'tag:yaml.org,2002:' : u'!!',
+        u'!': u'!',
+        u'tag:yaml.org,2002:': u'!!',
     }
 
+    MAX_SIMPLE_KEY_LENGTH = 128
+
     def __init__(self, stream, canonical=None, indent=None, width=None,
-            allow_unicode=None, line_break=None):
+                 allow_unicode=None, line_break=None, block_seq_indent=None,
+                 top_level_colon_align=None, prefix_colon=None):
 
         # The stream should have the methods `write` and possibly `flush`.
         self.stream = stream
@@ -75,16 +90,25 @@ class Emitter(object):
         self.column = 0
         self.whitespace = True
         self.indention = True
+        self.no_newline = None  # set if directly after `- `
 
         # Whether the document requires an explicit document indicator
         self.open_ended = False
 
+        # colon handling
+        self.colon = u':'
+        self.prefixed_colon = self.colon if prefix_colon is None else prefix_colon + self.colon
+
         # Formatting details.
         self.canonical = canonical
         self.allow_unicode = allow_unicode
+        self.block_seq_indent = block_seq_indent if block_seq_indent else 0
+        self.top_level_colon_align = top_level_colon_align
         self.best_indent = 2
         if indent and 1 < indent < 10:
             self.best_indent = indent
+        # if self.best_indent < self.block_seq_indent + 1:
+        #     self.best_indent = self.block_seq_indent + 1
         self.best_width = 80
         if width and width > self.best_indent*2:
             self.best_width = width
@@ -109,6 +133,8 @@ class Emitter(object):
         self.state = None
 
     def emit(self, event):
+        if dbg(DBG_EVENT):
+            nprint(event)
         self.events.append(event)
         while not self.need_more_events():
             self.event = self.events.pop(0)
@@ -143,7 +169,7 @@ class Emitter(object):
                 return False
         return (len(self.events) < count+1)
 
-    def increase_indent(self, flow=False, indentless=False):
+    def increase_indent(self, flow=False, sequence=None, indentless=False):
         self.indents.append(self.indent)
         if self.indent is None:
             if flow:
@@ -152,6 +178,8 @@ class Emitter(object):
                 self.indent = 0
         elif not indentless:
             self.indent += self.best_indent
+            # if self.sequence_context and (self.block_seq_indent + 2) > self.best_indent:
+            #    self.indent = self.block_seq_indent + 2
 
     # States.
 
@@ -159,13 +187,19 @@ class Emitter(object):
 
     def expect_stream_start(self):
         if isinstance(self.event, StreamStartEvent):
-            if self.event.encoding and not getattr(self.stream, 'encoding', None):
-                self.encoding = self.event.encoding
+            if PY2:
+                if self.event.encoding \
+                   and not getattr(self.stream, 'encoding', None):
+                    self.encoding = self.event.encoding
+            else:
+                if self.event.encoding \
+                   and not hasattr(self.stream, 'encoding'):
+                    self.encoding = self.event.encoding
             self.write_stream_start()
             self.state = self.expect_first_document_start
         else:
-            raise EmitterError("expected StreamStartEvent, but got %s"
-                    % self.event)
+            raise EmitterError("expected StreamStartEvent, but got %s" %
+                               self.event)
 
     def expect_nothing(self):
         raise EmitterError("expected nothing, but got %s" % self.event)
@@ -185,17 +219,19 @@ class Emitter(object):
                 self.write_version_directive(version_text)
             self.tag_prefixes = self.DEFAULT_TAG_PREFIXES.copy()
             if self.event.tags:
-                handles = self.event.tags.keys()
-                handles.sort()
+                handles = sorted(self.event.tags.keys())
                 for handle in handles:
                     prefix = self.event.tags[handle]
                     self.tag_prefixes[prefix] = handle
                     handle_text = self.prepare_tag_handle(handle)
                     prefix_text = self.prepare_tag_prefix(prefix)
                     self.write_tag_directive(handle_text, prefix_text)
-            implicit = (first and not self.event.explicit and not self.canonical
-                    and not self.event.version and not self.event.tags
-                    and not self.check_empty_document())
+            implicit = (first and
+                        not self.event.explicit and
+                        not self.canonical and
+                        not self.event.version and
+                        not self.event.tags and
+                        not self.check_empty_document())
             if not implicit:
                 self.write_indent()
                 self.write_indicator(u'---', True)
@@ -209,8 +245,8 @@ class Emitter(object):
             self.write_stream_end()
             self.state = self.expect_nothing
         else:
-            raise EmitterError("expected DocumentStartEvent, but got %s"
-                    % self.event)
+            raise EmitterError("expected DocumentStartEvent, but got %s" %
+                               self.event)
 
     def expect_document_end(self):
         if isinstance(self.event, DocumentEndEvent):
@@ -221,8 +257,8 @@ class Emitter(object):
             self.flush_stream()
             self.state = self.expect_document_start
         else:
-            raise EmitterError("expected DocumentEndEvent, but got %s"
-                    % self.event)
+            raise EmitterError("expected DocumentEndEvent, but got %s" %
+                               self.event)
 
     def expect_document_root(self):
         self.states.append(self.expect_document_end)
@@ -231,9 +267,9 @@ class Emitter(object):
     # Node handlers.
 
     def expect_node(self, root=False, sequence=False, mapping=False,
-            simple_key=False):
+                    simple_key=False):
         self.root_context = root
-        self.sequence_context = sequence
+        self.sequence_context = sequence   # not used in PyYAML
         self.mapping_context = mapping
         self.simple_key_context = simple_key
         if isinstance(self.event, AliasEvent):
@@ -244,13 +280,22 @@ class Emitter(object):
             if isinstance(self.event, ScalarEvent):
                 self.expect_scalar()
             elif isinstance(self.event, SequenceStartEvent):
-                if self.flow_level or self.canonical or self.event.flow_style   \
-                        or self.check_empty_sequence():
+                if self.event.comment:
+                    self.write_pre_comment(self.event)
+                    if self.event.flow_style is False and self.event.comment:
+                        self.write_post_comment(self.event)
+                # print('seq event', self.event)
+                if self.flow_level or self.canonical or self.event.flow_style or \
+                        self.check_empty_sequence():
                     self.expect_flow_sequence()
                 else:
                     self.expect_block_sequence()
             elif isinstance(self.event, MappingStartEvent):
-                if self.flow_level or self.canonical or self.event.flow_style   \
+                if self.event.flow_style is False and self.event.comment:
+                    self.write_post_comment(self.event)
+                if self.event.comment and self.event.comment[1]:
+                    self.write_pre_comment(self.event)
+                if self.flow_level or self.canonical or self.event.flow_style \
                         or self.check_empty_mapping():
                     self.expect_flow_mapping()
                 else:
@@ -275,7 +320,7 @@ class Emitter(object):
     def expect_flow_sequence(self):
         self.write_indicator(u'[', True, whitespace=True)
         self.flow_level += 1
-        self.increase_indent(flow=True)
+        self.increase_indent(flow=True, sequence=True)
         self.state = self.expect_first_flow_sequence_item
 
     def expect_first_flow_sequence_item(self):
@@ -298,6 +343,9 @@ class Emitter(object):
                 self.write_indicator(u',', False)
                 self.write_indent()
             self.write_indicator(u']', False)
+            if self.event.comment and self.event.comment[0]:
+                # eol comment on flow sequence
+                self.write_post_comment(self.event)
             self.state = self.states.pop()
         else:
             self.write_indicator(u',', False)
@@ -311,7 +359,7 @@ class Emitter(object):
     def expect_flow_mapping(self):
         self.write_indicator(u'{', True, whitespace=True)
         self.flow_level += 1
-        self.increase_indent(flow=True)
+        self.increase_indent(flow=True, sequence=False)
         self.state = self.expect_first_flow_mapping_key
 
     def expect_first_flow_mapping_key(self):
@@ -319,6 +367,9 @@ class Emitter(object):
             self.indent = self.indents.pop()
             self.flow_level -= 1
             self.write_indicator(u'}', False)
+            # if self.event.comment and self.event.comment[0]:
+            #     # eol comment on flow sequence
+            #     self.write_post_comment(self.event)
             self.state = self.states.pop()
         else:
             if self.canonical or self.column > self.best_width:
@@ -333,12 +384,17 @@ class Emitter(object):
 
     def expect_flow_mapping_key(self):
         if isinstance(self.event, MappingEndEvent):
+            # if self.event.comment and self.event.comment[1]:
+            #     self.write_pre_comment(self.event)
             self.indent = self.indents.pop()
             self.flow_level -= 1
             if self.canonical:
                 self.write_indicator(u',', False)
                 self.write_indent()
             self.write_indicator(u'}', False)
+            if self.event.comment and self.event.comment[0]:
+                # eol comment on flow mapping
+                self.write_post_comment(self.event)
             self.state = self.states.pop()
         else:
             self.write_indicator(u',', False)
@@ -353,14 +409,14 @@ class Emitter(object):
                 self.expect_node(mapping=True)
 
     def expect_flow_mapping_simple_value(self):
-        self.write_indicator(u':', False)
+        self.write_indicator(self.prefixed_colon, False)
         self.states.append(self.expect_flow_mapping_key)
         self.expect_node(mapping=True)
 
     def expect_flow_mapping_value(self):
         if self.canonical or self.column > self.best_width:
             self.write_indent()
-        self.write_indicator(u':', True)
+        self.write_indicator(self.prefixed_colon, True)
         self.states.append(self.expect_flow_mapping_key)
         self.expect_node(mapping=True)
 
@@ -368,7 +424,7 @@ class Emitter(object):
 
     def expect_block_sequence(self):
         indentless = (self.mapping_context and not self.indention)
-        self.increase_indent(flow=False, indentless=indentless)
+        self.increase_indent(flow=False, sequence=True, indentless=indentless)
         self.state = self.expect_first_block_sequence_item
 
     def expect_first_block_sequence_item(self):
@@ -376,18 +432,26 @@ class Emitter(object):
 
     def expect_block_sequence_item(self, first=False):
         if not first and isinstance(self.event, SequenceEndEvent):
+            if self.event.comment and self.event.comment[1]:
+                # final comments from a doc
+                self.write_pre_comment(self.event)
             self.indent = self.indents.pop()
             self.state = self.states.pop()
         else:
             self.write_indent()
-            self.write_indicator(u'-', True, indention=True)
+            if self.event.comment and self.event.comment[1]:
+                self.write_pre_comment(self.event)
+            self.write_indent()
+            self.write_indicator((u' ' * self.block_seq_indent) + u'-', True, indention=True)
+            if self.block_seq_indent + 2 > self.best_indent:
+                self.no_newline = True
             self.states.append(self.expect_block_sequence_item)
             self.expect_node(sequence=True)
 
     # Block mapping handlers.
 
     def expect_block_mapping(self):
-        self.increase_indent(flow=False)
+        self.increase_indent(flow=False, sequence=False)
         self.state = self.expect_first_block_mapping_key
 
     def expect_first_block_mapping_key(self):
@@ -395,11 +459,19 @@ class Emitter(object):
 
     def expect_block_mapping_key(self, first=False):
         if not first and isinstance(self.event, MappingEndEvent):
+            if self.event.comment and self.event.comment[1]:
+                # final comments from a doc
+                self.write_pre_comment(self.event)
             self.indent = self.indents.pop()
             self.state = self.states.pop()
         else:
+            if self.event.comment and self.event.comment[1]:
+                # final comments from a doc
+                self.write_pre_comment(self.event)
             self.write_indent()
             if self.check_simple_key():
+                if self.event.style == '?':
+                    self.write_indicator(u'?', True, indention=True)
                 self.states.append(self.expect_block_mapping_simple_value)
                 self.expect_node(mapping=True, simple_key=True)
             else:
@@ -408,32 +480,39 @@ class Emitter(object):
                 self.expect_node(mapping=True)
 
     def expect_block_mapping_simple_value(self):
-        self.write_indicator(u':', False)
+        if getattr(self.event, 'style', None) != '?':
+            # prefix = u''
+            if self.indent == 0 and self.top_level_colon_align is not None:
+                # write non-prefixed colon
+                c = u' ' * (self.top_level_colon_align - self.column) + self.colon
+            else:
+                c = self.prefixed_colon
+            self.write_indicator(c, False)
         self.states.append(self.expect_block_mapping_key)
         self.expect_node(mapping=True)
 
     def expect_block_mapping_value(self):
         self.write_indent()
-        self.write_indicator(u':', True, indention=True)
+        self.write_indicator(self.prefixed_colon, True, indention=True)
         self.states.append(self.expect_block_mapping_key)
         self.expect_node(mapping=True)
 
     # Checkers.
 
     def check_empty_sequence(self):
-        return (isinstance(self.event, SequenceStartEvent) and self.events
-                and isinstance(self.events[0], SequenceEndEvent))
+        return (isinstance(self.event, SequenceStartEvent) and self.events and
+                isinstance(self.events[0], SequenceEndEvent))
 
     def check_empty_mapping(self):
-        return (isinstance(self.event, MappingStartEvent) and self.events
-                and isinstance(self.events[0], MappingEndEvent))
+        return (isinstance(self.event, MappingStartEvent) and self.events and
+                isinstance(self.events[0], MappingEndEvent))
 
     def check_empty_document(self):
         if not isinstance(self.event, DocumentStartEvent) or not self.events:
             return False
         event = self.events[0]
-        return (isinstance(event, ScalarEvent) and event.anchor is None
-                and event.tag is None and event.implicit and event.value == u'')
+        return (isinstance(event, ScalarEvent) and event.anchor is None and
+                event.tag is None and event.implicit and event.value == u'')
 
     def check_simple_key(self):
         length = 0
@@ -450,10 +529,11 @@ class Emitter(object):
             if self.analysis is None:
                 self.analysis = self.analyze_scalar(self.event.value)
             length += len(self.analysis.scalar)
-        return (length < 128 and (isinstance(self.event, AliasEvent)
-            or (isinstance(self.event, ScalarEvent)
-                    and not self.analysis.empty and not self.analysis.multiline)
-            or self.check_empty_sequence() or self.check_empty_mapping()))
+        return (length < self.MAX_SIMPLE_KEY_LENGTH and (
+            isinstance(self.event, AliasEvent) or
+            (isinstance(self.event, ScalarEvent) and
+             not self.analysis.empty and not self.analysis.multiline) or
+            self.check_empty_sequence() or self.check_empty_mapping()))
 
     # Anchor, Tag, and Scalar processors.
 
@@ -473,8 +553,8 @@ class Emitter(object):
             if self.style is None:
                 self.style = self.choose_scalar_style()
             if ((not self.canonical or tag is None) and
-                ((self.style == '' and self.event.implicit[0])
-                        or (self.style != '' and self.event.implicit[1]))):
+                ((self.style == '' and self.event.implicit[0]) or
+                 (self.style != '' and self.event.implicit[1]))):
                 self.prepared_tag = None
                 return
             if self.event.implicit[0] and tag is None:
@@ -497,15 +577,16 @@ class Emitter(object):
             self.analysis = self.analyze_scalar(self.event.value)
         if self.event.style == '"' or self.canonical:
             return '"'
-        if not self.event.style and self.event.implicit[0]:
+        if (not self.event.style or self.event.style == '?') and \
+           self.event.implicit[0]:
             if (not (self.simple_key_context and
-                    (self.analysis.empty or self.analysis.multiline))
-                and (self.flow_level and self.analysis.allow_flow_plain
-                    or (not self.flow_level and self.analysis.allow_block_plain))):
+                     (self.analysis.empty or self.analysis.multiline)) and
+                (self.flow_level and self.analysis.allow_flow_plain or
+                    (not self.flow_level and self.analysis.allow_block_plain))):
                 return ''
         if self.event.style and self.event.style in '|>':
-            if (not self.flow_level and not self.simple_key_context
-                    and self.analysis.allow_block):
+            if (not self.flow_level and not self.simple_key_context and
+                    self.analysis.allow_block):
                 return self.event.style
         if not self.event.style or self.event.style == '\'':
             if (self.analysis.allow_single_quoted and
@@ -519,9 +600,11 @@ class Emitter(object):
         if self.style is None:
             self.style = self.choose_scalar_style()
         split = (not self.simple_key_context)
-        #if self.analysis.multiline and split    \
-        #        and (not self.style or self.style in '\'\"'):
-        #    self.write_indent()
+        # if self.analysis.multiline and split    \
+        #         and (not self.style or self.style in '\'\"'):
+        #     self.write_indent()
+        if self.sequence_context and not self.flow_level:
+            self.write_indent()
         if self.style == '"':
             self.write_double_quoted(self.analysis.scalar, split)
         elif self.style == '\'':
@@ -534,13 +617,16 @@ class Emitter(object):
             self.write_plain(self.analysis.scalar, split)
         self.analysis = None
         self.style = None
+        if self.event.comment:
+            self.write_post_comment(self.event)
 
     # Analyzers.
 
     def prepare_version(self, version):
         major, minor = version
         if major != 1:
-            raise EmitterError("unsupported YAML version: %d.%d" % (major, minor))
+            raise EmitterError("unsupported YAML version: %d.%d" %
+                               (major, minor))
         return u'%d.%d' % (major, minor)
 
     def prepare_tag_handle(self, handle):
@@ -548,12 +634,12 @@ class Emitter(object):
             raise EmitterError("tag handle must not be empty")
         if handle[0] != u'!' or handle[-1] != u'!':
             raise EmitterError("tag handle must start and end with '!': %r"
-                    % (handle.encode('utf-8')))
+                               % (utf8(handle)))
         for ch in handle[1:-1]:
-            if not (u'0' <= ch <= u'9' or u'A' <= ch <= u'Z' or u'a' <= ch <= u'z'  \
-                    or ch in u'-_'):
+            if not (u'0' <= ch <= u'9' or u'A' <= ch <= u'Z' or
+                    u'a' <= ch <= u'z' or ch in u'-_'):
                 raise EmitterError("invalid character %r in the tag handle: %r"
-                        % (ch.encode('utf-8'), handle.encode('utf-8')))
+                                   % (utf8(ch), utf8(handle)))
         return handle
 
     def prepare_tag_prefix(self, prefix):
@@ -572,7 +658,7 @@ class Emitter(object):
                 if start < end:
                     chunks.append(prefix[start:end])
                 start = end = end+1
-                data = ch.encode('utf-8')
+                data = utf8(ch)
                 for ch in data:
                     chunks.append(u'%%%02X' % ord(ch))
         if start < end:
@@ -586,8 +672,7 @@ class Emitter(object):
             return tag
         handle = None
         suffix = tag
-        prefixes = self.tag_prefixes.keys()
-        prefixes.sort()
+        prefixes = sorted(self.tag_prefixes.keys())
         for prefix in prefixes:
             if tag.startswith(prefix)   \
                     and (prefix == u'!' or len(prefix) < len(tag)):
@@ -605,7 +690,7 @@ class Emitter(object):
                 if start < end:
                     chunks.append(suffix[start:end])
                 start = end = end+1
-                data = ch.encode('utf-8')
+                data = utf8(ch)
                 for ch in data:
                     chunks.append(u'%%%02X' % ord(ch))
         if start < end:
@@ -620,20 +705,21 @@ class Emitter(object):
         if not anchor:
             raise EmitterError("anchor must not be empty")
         for ch in anchor:
-            if not (u'0' <= ch <= u'9' or u'A' <= ch <= u'Z' or u'a' <= ch <= u'z'  \
-                    or ch in u'-_'):
+            if not (u'0' <= ch <= u'9' or u'A' <= ch <= u'Z' or
+                    u'a' <= ch <= u'z' or ch in u'-_'):
                 raise EmitterError("invalid character %r in the anchor: %r"
-                        % (ch.encode('utf-8'), anchor.encode('utf-8')))
+                                   % (utf8(ch), utf8(anchor)))
         return anchor
 
     def analyze_scalar(self, scalar):
 
         # Empty scalar is a special case.
         if not scalar:
-            return ScalarAnalysis(scalar=scalar, empty=True, multiline=False,
-                    allow_flow_plain=False, allow_block_plain=True,
-                    allow_single_quoted=True, allow_double_quoted=True,
-                    allow_block=False)
+            return ScalarAnalysis(
+                scalar=scalar, empty=True, multiline=False,
+                allow_flow_plain=False, allow_block_plain=True,
+                allow_single_quoted=True, allow_double_quoted=True,
+                allow_block=False)
 
         # Indicators and special characters.
         block_indicators = False
@@ -659,7 +745,7 @@ class Emitter(object):
 
         # Last character or followed by a whitespace.
         followed_by_whitespace = (len(scalar) == 1 or
-                scalar[1] in u'\0 \t\r\n\x85\u2028\u2029')
+                                  scalar[1] in u'\0 \t\r\n\x85\u2028\u2029')
 
         # The previous character is a space.
         previous_space = False
@@ -674,7 +760,7 @@ class Emitter(object):
             # Check for indicators.
             if index == 0:
                 # Leading indicators are special characters.
-                if ch in u'#,[]{}&*!|>\'\"%@`': 
+                if ch in u'#,[]{}&*!|>\'\"%@`':
                     flow_indicators = True
                     block_indicators = True
                 if ch in u'?:':
@@ -700,9 +786,9 @@ class Emitter(object):
             if ch in u'\n\x85\u2028\u2029':
                 line_breaks = True
             if not (ch == u'\n' or u'\x20' <= ch <= u'\x7E'):
-                if (ch == u'\x85' or u'\xA0' <= ch <= u'\uD7FF'
-                        or u'\uE000' <= ch <= u'\uFFFD') and ch != u'\uFEFF':
-                    unicode_characters = True
+                if (ch == u'\x85' or u'\xA0' <= ch <= u'\uD7FF' or
+                        u'\uE000' <= ch <= u'\uFFFD') and ch != u'\uFEFF':
+                    # unicode_characters = True
                     if not self.allow_unicode:
                         special_characters = True
                 else:
@@ -734,8 +820,9 @@ class Emitter(object):
             # Prepare for the next character.
             index += 1
             preceeded_by_whitespace = (ch in u'\0 \t\r\n\x85\u2028\u2029')
-            followed_by_whitespace = (index+1 >= len(scalar) or
-                    scalar[index+1] in u'\0 \t\r\n\x85\u2028\u2029')
+            followed_by_whitespace = (
+                index+1 >= len(scalar) or
+                scalar[index+1] in u'\0 \t\r\n\x85\u2028\u2029')
 
         # Let's decide what styles are allowed.
         allow_flow_plain = True
@@ -745,8 +832,7 @@ class Emitter(object):
         allow_block = True
 
         # Leading and trailing whitespaces are bad for plain scalars.
-        if (leading_space or leading_break
-                or trailing_space or trailing_break):
+        if (leading_space or leading_break or trailing_space or trailing_break):
             allow_flow_plain = allow_block_plain = False
 
         # We do not permit trailing spaces for block scalars.
@@ -761,8 +847,8 @@ class Emitter(object):
         # Spaces followed by breaks, as well as special character are only
         # allowed for double quoted scalars.
         if space_break or special_characters:
-            allow_flow_plain = allow_block_plain =  \
-            allow_single_quoted = allow_block = False
+            allow_flow_plain = allow_block_plain = \
+                allow_single_quoted = allow_block = False
 
         # Although the plain scalar writer supports breaks, we never emit
         # multiline plain scalars.
@@ -778,12 +864,12 @@ class Emitter(object):
             allow_block_plain = False
 
         return ScalarAnalysis(scalar=scalar,
-                empty=False, multiline=line_breaks,
-                allow_flow_plain=allow_flow_plain,
-                allow_block_plain=allow_block_plain,
-                allow_single_quoted=allow_single_quoted,
-                allow_double_quoted=allow_double_quoted,
-                allow_block=allow_block)
+                              empty=False, multiline=line_breaks,
+                              allow_flow_plain=allow_flow_plain,
+                              allow_block_plain=allow_block_plain,
+                              allow_single_quoted=allow_single_quoted,
+                              allow_double_quoted=allow_double_quoted,
+                              allow_block=allow_block)
 
     # Writers.
 
@@ -800,7 +886,7 @@ class Emitter(object):
         self.flush_stream()
 
     def write_indicator(self, indicator, need_whitespace,
-            whitespace=False, indention=False):
+                        whitespace=False, indention=False):
         if self.whitespace or not need_whitespace:
             data = indicator
         else:
@@ -817,7 +903,10 @@ class Emitter(object):
         indent = self.indent or 0
         if not self.indention or self.column > indent   \
                 or (self.column == indent and not self.whitespace):
-            self.write_line_break()
+            if self.no_newline:
+                self.no_newline = False
+            else:
+                self.write_line_break()
         if self.column < indent:
             self.whitespace = True
             data = u' '*(indent-self.column)
@@ -933,10 +1022,9 @@ class Emitter(object):
             if end < len(text):
                 ch = text[end]
             if ch is None or ch in u'"\\\x85\u2028\u2029\uFEFF' \
-                    or not (u'\x20' <= ch <= u'\x7E'
-                        or (self.allow_unicode
-                            and (u'\xA0' <= ch <= u'\uD7FF'
-                                or u'\uE000' <= ch <= u'\uFFFD'))):
+               or not (u'\x20' <= ch <= u'\x7E' or
+                       (self.allow_unicode and
+                        (u'\xA0' <= ch <= u'\uD7FF' or u'\uE000' <= ch <= u'\uFFFD'))):
                 if start < end:
                     data = text[start:end]
                     self.column += len(data)
@@ -983,7 +1071,7 @@ class Emitter(object):
         hints = u''
         if text:
             if text[0] in u' \n\x85\u2028\u2029':
-                hints += unicode(self.best_indent)
+                hints += text_type(self.best_indent)
             if text[-1] not in u'\n\x85\u2028\u2029':
                 hints += u'-'
             elif len(text) == 1 or text[-2] in u'\n\x85\u2028\u2029':
@@ -1101,7 +1189,8 @@ class Emitter(object):
                 ch = text[end]
             if spaces:
                 if ch != u' ':
-                    if start+1 == end and self.column > self.best_width and split:
+                    if start+1 == end and self.column > self.best_width \
+                       and split:
                         self.write_indent()
                         self.whitespace = False
                         self.indention = False
@@ -1138,3 +1227,56 @@ class Emitter(object):
                 breaks = (ch in u'\n\x85\u2028\u2029')
             end += 1
 
+    def write_comment(self, comment):
+        value = comment.value
+        # print('{:02d} {:02d} {}'.format(self.column, comment.start_mark.column, value))
+        if value[-1] == '\n':
+            value = value[:-1]
+        try:
+            # get original column position
+            col = comment.start_mark.column
+            if col < self.column + 1:
+                ValueError
+        except ValueError:
+            col = self.column + 1
+        # print('post_comment', self.line, self.column, value)
+        try:
+            # at least one space if the current column >= the start column of the comment
+            # but not at the start of a line
+            nr_spaces = col - self.column
+            if self.column and value.strip() and nr_spaces < 1:
+                nr_spaces = 1
+            value = ' ' * nr_spaces + value
+            try:
+                if self.encoding:
+                    value = value.encode(self.encoding)
+            except UnicodeDecodeError:
+                pass
+            self.stream.write(value)
+        except TypeError:
+            raise
+        self.write_line_break()
+
+    def write_pre_comment(self, event):
+        comments = event.comment[1]
+        if comments is None:
+            return
+        try:
+            for comment in comments:
+                if isinstance(event, MappingStartEvent) and \
+                   getattr(comment, 'pre_done', None):
+                    continue
+                if self.column != 0:
+                        self.write_line_break()
+                self.write_comment(comment)
+                if isinstance(event, MappingStartEvent):
+                    comment.pre_done = True
+        except TypeError:
+            print ('eventtt', type(event), event)
+            raise
+
+    def write_post_comment(self, event):
+        if self.event.comment[0] is None:
+            return
+        comment = event.comment[0]
+        self.write_comment(comment)
diff --git a/lib/spack/external/yaml/lib/yaml/error.py b/lib/spack/external/ruamel/yaml/error.py
index 577686db5f..1ec77e60ec 100644
--- a/lib/spack/external/yaml/lib/yaml/error.py
+++ b/lib/spack/external/ruamel/yaml/error.py
@@ -1,8 +1,16 @@
+# coding: utf-8
+
+from __future__ import absolute_import
 
 __all__ = ['Mark', 'YAMLError', 'MarkedYAMLError']
 
-class Mark(object):
+try:
+    from .compat import utf8
+except (ImportError, ValueError):  # for Jython
+    from ruamel.yaml.compat import utf8
 
+
+class Mark(object):
     def __init__(self, name, index, line, column, buffer, pointer):
         self.name = name
         self.index = index
@@ -16,7 +24,8 @@ class Mark(object):
             return None
         head = ''
         start = self.pointer
-        while start > 0 and self.buffer[start-1] not in u'\0\r\n\x85\u2028\u2029':
+        while (start > 0 and
+               self.buffer[start-1] not in u'\0\r\n\x85\u2028\u2029'):
             start -= 1
             if self.pointer-start > max_length/2-1:
                 head = ' ... '
@@ -24,15 +33,16 @@ class Mark(object):
                 break
         tail = ''
         end = self.pointer
-        while end < len(self.buffer) and self.buffer[end] not in u'\0\r\n\x85\u2028\u2029':
+        while (end < len(self.buffer) and
+               self.buffer[end] not in u'\0\r\n\x85\u2028\u2029'):
             end += 1
             if end-self.pointer > max_length/2-1:
                 tail = ' ... '
                 end -= 5
                 break
-        snippet = self.buffer[start:end].encode('utf-8')
-        return ' '*indent + head + snippet + tail + '\n'  \
-                + ' '*(indent+self.pointer-start+len(head)) + '^'
+        snippet = utf8(self.buffer[start:end])
+        return ' '*indent + head + snippet + tail + '\n' \
+               + ' '*(indent+self.pointer-start+len(head)) + '^'
 
     def __str__(self):
         snippet = self.get_snippet()
@@ -42,13 +52,14 @@ class Mark(object):
             where += ":\n"+snippet
         return where
 
+
 class YAMLError(Exception):
     pass
 
-class MarkedYAMLError(YAMLError):
 
+class MarkedYAMLError(YAMLError):
     def __init__(self, context=None, context_mark=None,
-            problem=None, problem_mark=None, note=None):
+                 problem=None, problem_mark=None, note=None):
         self.context = context
         self.context_mark = context_mark
         self.problem = problem
@@ -60,10 +71,10 @@ class MarkedYAMLError(YAMLError):
         if self.context is not None:
             lines.append(self.context)
         if self.context_mark is not None  \
-            and (self.problem is None or self.problem_mark is None
-                    or self.context_mark.name != self.problem_mark.name
-                    or self.context_mark.line != self.problem_mark.line
-                    or self.context_mark.column != self.problem_mark.column):
+           and (self.problem is None or self.problem_mark is None or
+                self.context_mark.name != self.problem_mark.name or
+                self.context_mark.line != self.problem_mark.line or
+                self.context_mark.column != self.problem_mark.column):
             lines.append(str(self.context_mark))
         if self.problem is not None:
             lines.append(self.problem)
@@ -72,4 +83,3 @@ class MarkedYAMLError(YAMLError):
         if self.note is not None:
             lines.append(self.note)
         return '\n'.join(lines)
-
diff --git a/lib/spack/external/yaml/lib3/yaml/events.py b/lib/spack/external/ruamel/yaml/events.py
index f79ad389cb..7667c016be 100644
--- a/lib/spack/external/yaml/lib3/yaml/events.py
+++ b/lib/spack/external/ruamel/yaml/events.py
@@ -1,86 +1,106 @@
+# coding: utf-8
 
 # Abstract classes.
 
+
+def CommentCheck():
+    pass
+
+
 class Event(object):
-    def __init__(self, start_mark=None, end_mark=None):
+    def __init__(self, start_mark=None, end_mark=None, comment=CommentCheck):
         self.start_mark = start_mark
         self.end_mark = end_mark
+        # assert comment is not CommentCheck
+        if comment is CommentCheck:
+            comment = None
+        self.comment = comment
+
     def __repr__(self):
-        attributes = [key for key in ['anchor', 'tag', 'implicit', 'value']
-                if hasattr(self, key)]
+        attributes = [key for key in ['anchor', 'tag', 'implicit', 'value',
+                                      'flow_style', 'style']
+                      if hasattr(self, key)]
         arguments = ', '.join(['%s=%r' % (key, getattr(self, key))
-                for key in attributes])
+                               for key in attributes])
+        if self.comment not in [None, CommentCheck]:
+            arguments += ', comment={!r}'.format(self.comment)
         return '%s(%s)' % (self.__class__.__name__, arguments)
 
+
 class NodeEvent(Event):
-    def __init__(self, anchor, start_mark=None, end_mark=None):
+    def __init__(self, anchor, start_mark=None, end_mark=None, comment=None):
+        Event.__init__(self, start_mark, end_mark, comment)
         self.anchor = anchor
-        self.start_mark = start_mark
-        self.end_mark = end_mark
+
 
 class CollectionStartEvent(NodeEvent):
     def __init__(self, anchor, tag, implicit, start_mark=None, end_mark=None,
-            flow_style=None):
+                 flow_style=None, comment=None):
+        Event.__init__(self, start_mark, end_mark, comment)
         self.anchor = anchor
         self.tag = tag
         self.implicit = implicit
-        self.start_mark = start_mark
-        self.end_mark = end_mark
         self.flow_style = flow_style
 
+
 class CollectionEndEvent(Event):
     pass
 
 # Implementations.
 
+
 class StreamStartEvent(Event):
-    def __init__(self, start_mark=None, end_mark=None, encoding=None):
-        self.start_mark = start_mark
-        self.end_mark = end_mark
+    def __init__(self, start_mark=None, end_mark=None, encoding=None,
+                 comment=None):
+        Event.__init__(self, start_mark, end_mark, comment)
         self.encoding = encoding
 
+
 class StreamEndEvent(Event):
     pass
 
+
 class DocumentStartEvent(Event):
     def __init__(self, start_mark=None, end_mark=None,
-            explicit=None, version=None, tags=None):
-        self.start_mark = start_mark
-        self.end_mark = end_mark
+                 explicit=None, version=None, tags=None, comment=None):
+        Event.__init__(self, start_mark, end_mark, comment)
         self.explicit = explicit
         self.version = version
         self.tags = tags
 
+
 class DocumentEndEvent(Event):
     def __init__(self, start_mark=None, end_mark=None,
-            explicit=None):
-        self.start_mark = start_mark
-        self.end_mark = end_mark
+                 explicit=None, comment=None):
+        Event.__init__(self, start_mark, end_mark, comment)
         self.explicit = explicit
 
+
 class AliasEvent(NodeEvent):
     pass
 
+
 class ScalarEvent(NodeEvent):
     def __init__(self, anchor, tag, implicit, value,
-            start_mark=None, end_mark=None, style=None):
-        self.anchor = anchor
+                 start_mark=None, end_mark=None, style=None, comment=None):
+        NodeEvent.__init__(self, anchor, start_mark, end_mark, comment)
         self.tag = tag
         self.implicit = implicit
         self.value = value
-        self.start_mark = start_mark
-        self.end_mark = end_mark
         self.style = style
 
+
 class SequenceStartEvent(CollectionStartEvent):
     pass
 
+
 class SequenceEndEvent(CollectionEndEvent):
     pass
 
+
 class MappingStartEvent(CollectionStartEvent):
     pass
 
+
 class MappingEndEvent(CollectionEndEvent):
     pass
-
diff --git a/lib/spack/external/ruamel/yaml/loader.py b/lib/spack/external/ruamel/yaml/loader.py
new file mode 100644
index 0000000000..b5ba20a0a1
--- /dev/null
+++ b/lib/spack/external/ruamel/yaml/loader.py
@@ -0,0 +1,61 @@
+# coding: utf-8
+
+from __future__ import absolute_import
+
+__all__ = ['BaseLoader', 'SafeLoader', 'Loader', 'RoundTripLoader']
+
+try:
+    from .reader import *                                # NOQA
+    from .scanner import *                               # NOQA
+    from .parser import *                                # NOQA
+    from .composer import *                              # NOQA
+    from .constructor import *                           # NOQA
+    from .resolver import *                              # NOQA
+except (ImportError, ValueError):  # for Jython
+    from ruamel.yaml.reader import *                                # NOQA
+    from ruamel.yaml.scanner import *                               # NOQA
+    from ruamel.yaml.parser import *                                # NOQA
+    from ruamel.yaml.composer import *                              # NOQA
+    from ruamel.yaml.constructor import *                           # NOQA
+    from ruamel.yaml.resolver import *                              # NOQA
+
+
+class BaseLoader(Reader, Scanner, Parser, Composer, BaseConstructor, BaseResolver):
+    def __init__(self, stream, version=None, preserve_quotes=None):
+        Reader.__init__(self, stream)
+        Scanner.__init__(self)
+        Parser.__init__(self)
+        Composer.__init__(self)
+        BaseConstructor.__init__(self)
+        BaseResolver.__init__(self)
+
+
+class SafeLoader(Reader, Scanner, Parser, Composer, SafeConstructor, Resolver):
+    def __init__(self, stream, version=None, preserve_quotes=None):
+        Reader.__init__(self, stream)
+        Scanner.__init__(self)
+        Parser.__init__(self)
+        Composer.__init__(self)
+        SafeConstructor.__init__(self)
+        Resolver.__init__(self)
+
+
+class Loader(Reader, Scanner, Parser, Composer, Constructor, Resolver):
+    def __init__(self, stream, version=None, preserve_quotes=None):
+        Reader.__init__(self, stream)
+        Scanner.__init__(self)
+        Parser.__init__(self)
+        Composer.__init__(self)
+        Constructor.__init__(self)
+        Resolver.__init__(self)
+
+
+class RoundTripLoader(Reader, RoundTripScanner, RoundTripParser, Composer,
+                      RoundTripConstructor, VersionedResolver):
+    def __init__(self, stream, version=None, preserve_quotes=None):
+        Reader.__init__(self, stream)
+        RoundTripScanner.__init__(self)
+        RoundTripParser.__init__(self)
+        Composer.__init__(self)
+        RoundTripConstructor.__init__(self, preserve_quotes=preserve_quotes)
+        VersionedResolver.__init__(self, version)
diff --git a/lib/spack/external/yaml/lib3/yaml/__init__.py b/lib/spack/external/ruamel/yaml/main.py
index d7d27fe63b..797bdcde65 100644
--- a/lib/spack/external/yaml/lib3/yaml/__init__.py
+++ b/lib/spack/external/ruamel/yaml/main.py
@@ -1,21 +1,20 @@
+# coding: utf-8
 
-from .error import *
+from __future__ import absolute_import
 
-from .tokens import *
-from .events import *
-from .nodes import *
 
-from .loader import *
-from .dumper import *
+from ruamel.yaml.error import *                                # NOQA
 
-__version__ = '3.12'
-try:
-    from .cyaml import *
-    __with_libyaml__ = True
-except ImportError:
-    __with_libyaml__ = False
+from ruamel.yaml.tokens import *                               # NOQA
+from ruamel.yaml.events import *                               # NOQA
+from ruamel.yaml.nodes import *                                # NOQA
+
+from ruamel.yaml.loader import *                               # NOQA
+from ruamel.yaml.dumper import *                               # NOQA
+from ruamel.yaml.compat import StringIO, BytesIO, with_metaclass, PY3
+
+# import io
 
-import io
 
 def scan(stream, Loader=Loader):
     """
@@ -28,6 +27,7 @@ def scan(stream, Loader=Loader):
     finally:
         loader.dispose()
 
+
 def parse(stream, Loader=Loader):
     """
     Parse a YAML stream and produce parsing events.
@@ -39,6 +39,7 @@ def parse(stream, Loader=Loader):
     finally:
         loader.dispose()
 
+
 def compose(stream, Loader=Loader):
     """
     Parse the first YAML document in a stream
@@ -50,6 +51,7 @@ def compose(stream, Loader=Loader):
     finally:
         loader.dispose()
 
+
 def compose_all(stream, Loader=Loader):
     """
     Parse all YAML documents in a stream
@@ -62,58 +64,81 @@ def compose_all(stream, Loader=Loader):
     finally:
         loader.dispose()
 
-def load(stream, Loader=Loader):
+
+def load(stream, Loader=Loader, version=None, preserve_quotes=None):
     """
     Parse the first YAML document in a stream
     and produce the corresponding Python object.
     """
-    loader = Loader(stream)
+    loader = Loader(stream, version, preserve_quotes=preserve_quotes)
     try:
         return loader.get_single_data()
     finally:
         loader.dispose()
 
-def load_all(stream, Loader=Loader):
+
+def load_all(stream, Loader=Loader, version=None):
     """
     Parse all YAML documents in a stream
     and produce corresponding Python objects.
     """
-    loader = Loader(stream)
+    loader = Loader(stream, version)
     try:
         while loader.check_data():
             yield loader.get_data()
     finally:
         loader.dispose()
 
-def safe_load(stream):
+
+def safe_load(stream, version=None):
     """
     Parse the first YAML document in a stream
     and produce the corresponding Python object.
     Resolve only basic YAML tags.
     """
-    return load(stream, SafeLoader)
+    return load(stream, SafeLoader, version)
+
 
-def safe_load_all(stream):
+def safe_load_all(stream, version=None):
     """
     Parse all YAML documents in a stream
     and produce corresponding Python objects.
     Resolve only basic YAML tags.
     """
-    return load_all(stream, SafeLoader)
+    return load_all(stream, SafeLoader, version)
+
+
+def round_trip_load(stream, version=None, preserve_quotes=None):
+    """
+    Parse the first YAML document in a stream
+    and produce the corresponding Python object.
+    Resolve only basic YAML tags.
+    """
+    return load(stream, RoundTripLoader, version, preserve_quotes=preserve_quotes)
+
+
+def round_trip_load_all(stream, version=None, preserve_quotes=None):
+    """
+    Parse all YAML documents in a stream
+    and produce corresponding Python objects.
+    Resolve only basic YAML tags.
+    """
+    return load_all(stream, RoundTripLoader, version, preserve_quotes=preserve_quotes)
+
 
 def emit(events, stream=None, Dumper=Dumper,
-        canonical=None, indent=None, width=None,
-        allow_unicode=None, line_break=None):
+         canonical=None, indent=None, width=None,
+         allow_unicode=None, line_break=None):
     """
     Emit YAML parsing events into a stream.
     If stream is None, return the produced string instead.
     """
     getvalue = None
     if stream is None:
-        stream = io.StringIO()
+        stream = StringIO()
         getvalue = stream.getvalue
     dumper = Dumper(stream, canonical=canonical, indent=indent, width=width,
-            allow_unicode=allow_unicode, line_break=line_break)
+                    allow_unicode=allow_unicode, line_break=line_break)
     try:
         for event in events:
             dumper.emit(event)
@@ -122,11 +147,14 @@ def emit(events, stream=None, Dumper=Dumper,
     if getvalue:
         return getvalue()
 
+enc = None if PY3 else 'utf-8'
+
+
 def serialize_all(nodes, stream=None, Dumper=Dumper,
-        canonical=None, indent=None, width=None,
-        allow_unicode=None, line_break=None,
-        encoding=None, explicit_start=None, explicit_end=None,
-        version=None, tags=None):
+                  canonical=None, indent=None, width=None,
+                  allow_unicode=None, line_break=None,
+                  encoding=enc, explicit_start=None, explicit_end=None,
+                  version=None, tags=None):
     """
     Serialize a sequence of representation trees into a YAML stream.
     If stream is None, return the produced string instead.
@@ -134,14 +162,14 @@ def serialize_all(nodes, stream=None, Dumper=Dumper,
     getvalue = None
     if stream is None:
         if encoding is None:
-            stream = io.StringIO()
+            stream = StringIO()
         else:
-            stream = io.BytesIO()
+            stream = BytesIO()
         getvalue = stream.getvalue
     dumper = Dumper(stream, canonical=canonical, indent=indent, width=width,
-            allow_unicode=allow_unicode, line_break=line_break,
-            encoding=encoding, version=version, tags=tags,
-            explicit_start=explicit_start, explicit_end=explicit_end)
+                    allow_unicode=allow_unicode, line_break=line_break,
+                    encoding=encoding, version=version, tags=tags,
+                    explicit_start=explicit_start, explicit_end=explicit_end)
     try:
         dumper.open()
         for node in nodes:
@@ -152,6 +180,7 @@ def serialize_all(nodes, stream=None, Dumper=Dumper,
     if getvalue:
         return getvalue()
 
+
 def serialize(node, stream=None, Dumper=Dumper, **kwds):
     """
     Serialize a representation tree into a YAML stream.
@@ -159,29 +188,36 @@ def serialize(node, stream=None, Dumper=Dumper, **kwds):
     """
     return serialize_all([node], stream, Dumper=Dumper, **kwds)
 
+
 def dump_all(documents, stream=None, Dumper=Dumper,
-        default_style=None, default_flow_style=None,
-        canonical=None, indent=None, width=None,
-        allow_unicode=None, line_break=None,
-        encoding=None, explicit_start=None, explicit_end=None,
-        version=None, tags=None):
+             default_style=None, default_flow_style=None,
+             canonical=None, indent=None, width=None,
+             allow_unicode=None, line_break=None,
+             encoding=enc, explicit_start=None, explicit_end=None,
+             version=None, tags=None, block_seq_indent=None,
+             top_level_colon_align=None, prefix_colon=None):
     """
     Serialize a sequence of Python objects into a YAML stream.
     If stream is None, return the produced string instead.
     """
     getvalue = None
+    if top_level_colon_align is True:
+        top_level_colon_align = max([len(str(x)) for x in documents[0]])
     if stream is None:
         if encoding is None:
-            stream = io.StringIO()
+            stream = StringIO()
         else:
-            stream = io.BytesIO()
+            stream = BytesIO()
         getvalue = stream.getvalue
     dumper = Dumper(stream, default_style=default_style,
-            default_flow_style=default_flow_style,
-            canonical=canonical, indent=indent, width=width,
-            allow_unicode=allow_unicode, line_break=line_break,
-            encoding=encoding, version=version, tags=tags,
-            explicit_start=explicit_start, explicit_end=explicit_end)
+                    default_flow_style=default_flow_style,
+                    canonical=canonical, indent=indent, width=width,
+                    allow_unicode=allow_unicode, line_break=line_break,
+                    encoding=encoding, explicit_start=explicit_start,
+                    explicit_end=explicit_end, version=version,
+                    tags=tags, block_seq_indent=block_seq_indent,
+                    top_level_colon_align=top_level_colon_align, prefix_colon=prefix_colon,
+                    )
     try:
         dumper.open()
         for data in documents:
@@ -192,12 +228,31 @@ def dump_all(documents, stream=None, Dumper=Dumper,
     if getvalue:
         return getvalue()
 
-def dump(data, stream=None, Dumper=Dumper, **kwds):
+
+def dump(data, stream=None, Dumper=Dumper,
+         default_style=None, default_flow_style=None,
+         canonical=None, indent=None, width=None,
+         allow_unicode=None, line_break=None,
+         encoding=enc, explicit_start=None, explicit_end=None,
+         version=None, tags=None, block_seq_indent=None):
     """
     Serialize a Python object into a YAML stream.
     If stream is None, return the produced string instead.
+
+    default_style ∈ None, '', '"', "'", '|', '>'
+
     """
-    return dump_all([data], stream, Dumper=Dumper, **kwds)
+    return dump_all([data], stream, Dumper=Dumper,
+                    default_style=default_style,
+                    default_flow_style=default_flow_style,
+                    canonical=canonical,
+                    indent=indent, width=width,
+                    allow_unicode=allow_unicode,
+                    line_break=line_break,
+                    encoding=encoding, explicit_start=explicit_start,
+                    explicit_end=explicit_end,
+                    version=version, tags=tags, block_seq_indent=block_seq_indent)
+
 
 def safe_dump_all(documents, stream=None, **kwds):
     """
@@ -207,6 +262,7 @@ def safe_dump_all(documents, stream=None, **kwds):
     """
     return dump_all(documents, stream, Dumper=SafeDumper, **kwds)
 
+
 def safe_dump(data, stream=None, **kwds):
     """
     Serialize a Python object into a YAML stream.
@@ -215,8 +271,30 @@ def safe_dump(data, stream=None, **kwds):
     """
     return dump_all([data], stream, Dumper=SafeDumper, **kwds)
 
+
+def round_trip_dump(data, stream=None, Dumper=RoundTripDumper,
+                    default_style=None, default_flow_style=None,
+                    canonical=None, indent=None, width=None,
+                    allow_unicode=None, line_break=None,
+                    encoding=enc, explicit_start=None, explicit_end=None,
+                    version=None, tags=None, block_seq_indent=None,
+                    top_level_colon_align=None, prefix_colon=None):
+    allow_unicode = True if allow_unicode is None else allow_unicode
+    return dump_all([data], stream, Dumper=Dumper,
+                    default_style=default_style,
+                    default_flow_style=default_flow_style,
+                    canonical=canonical,
+                    indent=indent, width=width,
+                    allow_unicode=allow_unicode,
+                    line_break=line_break,
+                    encoding=encoding, explicit_start=explicit_start,
+                    explicit_end=explicit_end,
+                    version=version, tags=tags, block_seq_indent=block_seq_indent,
+                    top_level_colon_align=top_level_colon_align, prefix_colon=prefix_colon)
+
+
 def add_implicit_resolver(tag, regexp, first=None,
-        Loader=Loader, Dumper=Dumper):
+                          Loader=Loader, Dumper=Dumper):
     """
     Add an implicit scalar detector.
     If an implicit scalar value matches the given regexp,
@@ -226,6 +304,7 @@ def add_implicit_resolver(tag, regexp, first=None,
     Loader.add_implicit_resolver(tag, regexp, first)
     Dumper.add_implicit_resolver(tag, regexp, first)
 
+
 def add_path_resolver(tag, path, kind=None, Loader=Loader, Dumper=Dumper):
     """
     Add a path based resolver for the given tag.
@@ -236,6 +315,7 @@ def add_path_resolver(tag, path, kind=None, Loader=Loader, Dumper=Dumper):
     Loader.add_path_resolver(tag, path, kind)
     Dumper.add_path_resolver(tag, path, kind)
 
+
 def add_constructor(tag, constructor, Loader=Loader):
     """
     Add a constructor for the given tag.
@@ -244,6 +324,7 @@ def add_constructor(tag, constructor, Loader=Loader):
     """
     Loader.add_constructor(tag, constructor)
 
+
 def add_multi_constructor(tag_prefix, multi_constructor, Loader=Loader):
     """
     Add a multi-constructor for the given tag prefix.
@@ -253,6 +334,7 @@ def add_multi_constructor(tag_prefix, multi_constructor, Loader=Loader):
     """
     Loader.add_multi_constructor(tag_prefix, multi_constructor)
 
+
 def add_representer(data_type, representer, Dumper=Dumper):
     """
     Add a representer for the given type.
@@ -262,6 +344,7 @@ def add_representer(data_type, representer, Dumper=Dumper):
     """
     Dumper.add_representer(data_type, representer)
 
+
 def add_multi_representer(data_type, multi_representer, Dumper=Dumper):
     """
     Add a representer for the given type.
@@ -271,6 +354,7 @@ def add_multi_representer(data_type, multi_representer, Dumper=Dumper):
     """
     Dumper.add_multi_representer(data_type, multi_representer)
 
+
 class YAMLObjectMetaclass(type):
     """
     The metaclass for YAMLObject.
@@ -281,12 +365,12 @@ class YAMLObjectMetaclass(type):
             cls.yaml_loader.add_constructor(cls.yaml_tag, cls.from_yaml)
             cls.yaml_dumper.add_representer(cls, cls.to_yaml)
 
-class YAMLObject(metaclass=YAMLObjectMetaclass):
+
+class YAMLObject(with_metaclass(YAMLObjectMetaclass)):
     """
     An object that can dump itself to a YAML stream
     and load itself from a YAML stream.
     """
-
     __slots__ = ()  # no direct instantiation, so allow immutable subclasses
 
     yaml_loader = Loader
@@ -308,5 +392,4 @@ class YAMLObject(metaclass=YAMLObjectMetaclass):
         Convert a Python object to a representation node.
         """
         return dumper.represent_yaml_object(cls.yaml_tag, data, cls,
-                flow_style=cls.yaml_flow_style)
-
+                                            flow_style=cls.yaml_flow_style)
diff --git a/lib/spack/external/ruamel/yaml/nodes.py b/lib/spack/external/ruamel/yaml/nodes.py
new file mode 100644
index 0000000000..26c6d77ae6
--- /dev/null
+++ b/lib/spack/external/ruamel/yaml/nodes.py
@@ -0,0 +1,86 @@
+# coding: utf-8
+
+from __future__ import print_function
+
+
+class Node(object):
+    def __init__(self, tag, value, start_mark, end_mark, comment=None):
+        self.tag = tag
+        self.value = value
+        self.start_mark = start_mark
+        self.end_mark = end_mark
+        self.comment = comment
+        self.anchor = None
+
+    def __repr__(self):
+        value = self.value
+        # if isinstance(value, list):
+        #     if len(value) == 0:
+        #         value = '<empty>'
+        #     elif len(value) == 1:
+        #         value = '<1 item>'
+        #     else:
+        #         value = '<%d items>' % len(value)
+        # else:
+        #     if len(value) > 75:
+        #         value = repr(value[:70]+u' ... ')
+        #     else:
+        #         value = repr(value)
+        value = repr(value)
+        return '%s(tag=%r, value=%s)' % (self.__class__.__name__,
+                                         self.tag, value)
+
+    def dump(self, indent=0):
+        if isinstance(self.value, basestring):
+            print('{0}{1}(tag={!r}, value={!r})'.format(
+                '  ' * indent, self.__class__.__name__, self.tag, self.value))
+            if self.comment:
+                print('    {0}comment: {1})'.format(
+                    '  ' * indent, self.comment))
+            return
+        print('{0}{1}(tag={!r})'.format(
+            '  ' * indent, self.__class__.__name__, self.tag))
+        if self.comment:
+            print('    {0}comment: {1})'.format(
+                '  ' * indent, self.comment))
+        for v in self.value:
+            if isinstance(v, tuple):
+                for v1 in v:
+                    v1.dump(indent+1)
+            elif isinstance(v, Node):
+                v.dump(indent+1)
+            else:
+                print('Node value type?', type(v))
+
+
+class ScalarNode(Node):
+    """
+    styles:
+      ? -> set() ? key, no value
+      " -> double quoted
+      ' -> single quoted
+      | -> literal style
+      > ->
+    """
+    id = 'scalar'
+
+    def __init__(self, tag, value, start_mark=None, end_mark=None, style=None,
+                 comment=None):
+        Node.__init__(self, tag, value, start_mark, end_mark, comment=comment)
+        self.style = style
+
+
+class CollectionNode(Node):
+    def __init__(self, tag, value, start_mark=None, end_mark=None,
+                 flow_style=None, comment=None, anchor=None):
+        Node.__init__(self, tag, value, start_mark, end_mark, comment=comment)
+        self.flow_style = flow_style
+        self.anchor = anchor
+
+
+class SequenceNode(CollectionNode):
+    id = 'sequence'
+
+
+class MappingNode(CollectionNode):
+    id = 'mapping'
diff --git a/lib/spack/external/yaml/lib/yaml/parser.py b/lib/spack/external/ruamel/yaml/parser.py
index f9e3057f33..543cca9b43 100644
--- a/lib/spack/external/yaml/lib/yaml/parser.py
+++ b/lib/spack/external/ruamel/yaml/parser.py
@@ -1,13 +1,18 @@
+# coding: utf-8
+
+from __future__ import absolute_import
 
 # The following YAML grammar is LL(1) and is parsed by a recursive descent
 # parser.
 #
-# stream            ::= STREAM-START implicit_document? explicit_document* STREAM-END
+# stream            ::= STREAM-START implicit_document? explicit_document*
+#                                                                   STREAM-END
 # implicit_document ::= block_node DOCUMENT-END*
 # explicit_document ::= DIRECTIVE* DOCUMENT-START block_node? DOCUMENT-END*
 # block_node_or_indentless_sequence ::=
 #                       ALIAS
-#                       | properties (block_content | indentless_block_sequence)?
+#                       | properties (block_content |
+#                                                   indentless_block_sequence)?
 #                       | block_content
 #                       | indentless_block_sequence
 # block_node        ::= ALIAS
@@ -21,7 +26,8 @@
 # flow_content      ::= flow_collection | SCALAR
 # block_collection  ::= block_sequence | block_mapping
 # flow_collection   ::= flow_sequence | flow_mapping
-# block_sequence    ::= BLOCK-SEQUENCE-START (BLOCK-ENTRY block_node?)* BLOCK-END
+# block_sequence    ::= BLOCK-SEQUENCE-START (BLOCK-ENTRY block_node?)*
+#                                                                   BLOCK-END
 # indentless_sequence   ::= (BLOCK-ENTRY block_node?)+
 # block_mapping     ::= BLOCK-MAPPING_START
 #                       ((KEY block_node_or_indentless_sequence?)?
@@ -43,32 +49,44 @@
 # stream: { STREAM-START }
 # explicit_document: { DIRECTIVE DOCUMENT-START }
 # implicit_document: FIRST(block_node)
-# block_node: { ALIAS TAG ANCHOR SCALAR BLOCK-SEQUENCE-START BLOCK-MAPPING-START FLOW-SEQUENCE-START FLOW-MAPPING-START }
+# block_node: { ALIAS TAG ANCHOR SCALAR BLOCK-SEQUENCE-START
+#                  BLOCK-MAPPING-START FLOW-SEQUENCE-START FLOW-MAPPING-START }
 # flow_node: { ALIAS ANCHOR TAG SCALAR FLOW-SEQUENCE-START FLOW-MAPPING-START }
-# block_content: { BLOCK-SEQUENCE-START BLOCK-MAPPING-START FLOW-SEQUENCE-START FLOW-MAPPING-START SCALAR }
+# block_content: { BLOCK-SEQUENCE-START BLOCK-MAPPING-START
+#                               FLOW-SEQUENCE-START FLOW-MAPPING-START SCALAR }
 # flow_content: { FLOW-SEQUENCE-START FLOW-MAPPING-START SCALAR }
 # block_collection: { BLOCK-SEQUENCE-START BLOCK-MAPPING-START }
 # flow_collection: { FLOW-SEQUENCE-START FLOW-MAPPING-START }
 # block_sequence: { BLOCK-SEQUENCE-START }
 # block_mapping: { BLOCK-MAPPING-START }
-# block_node_or_indentless_sequence: { ALIAS ANCHOR TAG SCALAR BLOCK-SEQUENCE-START BLOCK-MAPPING-START FLOW-SEQUENCE-START FLOW-MAPPING-START BLOCK-ENTRY }
+# block_node_or_indentless_sequence: { ALIAS ANCHOR TAG SCALAR
+#               BLOCK-SEQUENCE-START BLOCK-MAPPING-START FLOW-SEQUENCE-START
+#               FLOW-MAPPING-START BLOCK-ENTRY }
 # indentless_sequence: { ENTRY }
 # flow_collection: { FLOW-SEQUENCE-START FLOW-MAPPING-START }
 # flow_sequence: { FLOW-SEQUENCE-START }
 # flow_mapping: { FLOW-MAPPING-START }
-# flow_sequence_entry: { ALIAS ANCHOR TAG SCALAR FLOW-SEQUENCE-START FLOW-MAPPING-START KEY }
-# flow_mapping_entry: { ALIAS ANCHOR TAG SCALAR FLOW-SEQUENCE-START FLOW-MAPPING-START KEY }
+# flow_sequence_entry: { ALIAS ANCHOR TAG SCALAR FLOW-SEQUENCE-START
+#                                                    FLOW-MAPPING-START KEY }
+# flow_mapping_entry: { ALIAS ANCHOR TAG SCALAR FLOW-SEQUENCE-START
+#                                                    FLOW-MAPPING-START KEY }
+
+__all__ = ['Parser', 'RoundTripParser', 'ParserError']
 
-__all__ = ['Parser', 'ParserError']
+# need to have full path, as pkg_resources tries to load parser.py in __init__.py
+# only to not do anything with the package afterwards
+# and for Jython too
+from ruamel.yaml.error import MarkedYAMLError                  # NOQA
+from ruamel.yaml.tokens import *                               # NOQA
+from ruamel.yaml.events import *                               # NOQA
+from ruamel.yaml.scanner import *                              # NOQA
+from ruamel.yaml.compat import utf8                            # NOQA
 
-from error import MarkedYAMLError
-from tokens import *
-from events import *
-from scanner import *
 
 class ParserError(MarkedYAMLError):
     pass
 
+
 class Parser(object):
     # Since writing a recursive-descendant parser is a straightforward task, we
     # do not give many comments here.
@@ -120,7 +138,8 @@ class Parser(object):
         self.current_event = None
         return value
 
-    # stream    ::= STREAM-START implicit_document? explicit_document* STREAM-END
+    # stream    ::= STREAM-START implicit_document? explicit_document*
+    #                                                               STREAM-END
     # implicit_document ::= block_node DOCUMENT-END*
     # explicit_document ::= DIRECTIVE* DOCUMENT-START block_node? DOCUMENT-END*
 
@@ -128,8 +147,9 @@ class Parser(object):
 
         # Parse the stream start.
         token = self.get_token()
+        token.move_comment(self.peek_token())
         event = StreamStartEvent(token.start_mark, token.end_mark,
-                encoding=token.encoding)
+                                 encoding=token.encoding)
 
         # Prepare the next state.
         self.state = self.parse_implicit_document_start
@@ -140,12 +160,12 @@ class Parser(object):
 
         # Parse an implicit document.
         if not self.check_token(DirectiveToken, DocumentStartToken,
-                StreamEndToken):
+                                StreamEndToken):
             self.tag_handles = self.DEFAULT_TAGS
             token = self.peek_token()
             start_mark = end_mark = token.start_mark
             event = DocumentStartEvent(start_mark, end_mark,
-                    explicit=False)
+                                       explicit=False)
 
             # Prepare the next state.
             self.states.append(self.parse_document_end)
@@ -169,19 +189,21 @@ class Parser(object):
             version, tags = self.process_directives()
             if not self.check_token(DocumentStartToken):
                 raise ParserError(None, None,
-                        "expected '<document start>', but found %r"
-                        % self.peek_token().id,
-                        self.peek_token().start_mark)
+                                  "expected '<document start>', but found %r"
+                                  % self.peek_token().id,
+                                  self.peek_token().start_mark)
             token = self.get_token()
             end_mark = token.end_mark
-            event = DocumentStartEvent(start_mark, end_mark,
-                    explicit=True, version=version, tags=tags)
+            event = DocumentStartEvent(
+                start_mark, end_mark,
+                explicit=True, version=version, tags=tags)
             self.states.append(self.parse_document_end)
             self.state = self.parse_document_content
         else:
             # Parse the end of the stream.
             token = self.get_token()
-            event = StreamEndEvent(token.start_mark, token.end_mark)
+            event = StreamEndEvent(token.start_mark, token.end_mark,
+                                   comment=token.comment)
             assert not self.states
             assert not self.marks
             self.state = None
@@ -197,8 +219,7 @@ class Parser(object):
             token = self.get_token()
             end_mark = token.end_mark
             explicit = True
-        event = DocumentEndEvent(start_mark, end_mark,
-                explicit=explicit)
+        event = DocumentEndEvent(start_mark, end_mark, explicit=explicit)
 
         # Prepare the next state.
         self.state = self.parse_document_start
@@ -206,8 +227,9 @@ class Parser(object):
         return event
 
     def parse_document_content(self):
-        if self.check_token(DirectiveToken,
-                DocumentStartToken, DocumentEndToken, StreamEndToken):
+        if self.check_token(
+           DirectiveToken,
+           DocumentStartToken, DocumentEndToken, StreamEndToken):
             event = self.process_empty_scalar(self.peek_token().start_mark)
             self.state = self.states.pop()
             return event
@@ -221,20 +243,23 @@ class Parser(object):
             token = self.get_token()
             if token.name == u'YAML':
                 if self.yaml_version is not None:
-                    raise ParserError(None, None,
-                            "found duplicate YAML directive", token.start_mark)
+                    raise ParserError(
+                        None, None,
+                        "found duplicate YAML directive", token.start_mark)
                 major, minor = token.value
                 if major != 1:
-                    raise ParserError(None, None,
-                            "found incompatible YAML document (version 1.* is required)",
-                            token.start_mark)
+                    raise ParserError(
+                        None, None,
+                        "found incompatible YAML document (version 1.* is "
+                        "required)",
+                        token.start_mark)
                 self.yaml_version = token.value
             elif token.name == u'TAG':
                 handle, prefix = token.value
                 if handle in self.tag_handles:
                     raise ParserError(None, None,
-                            "duplicate tag handle %r" % handle.encode('utf-8'),
-                            token.start_mark)
+                                      "duplicate tag handle %r" % utf8(handle),
+                                      token.start_mark)
                 self.tag_handles[handle] = prefix
         if self.tag_handles:
             value = self.yaml_version, self.tag_handles.copy()
@@ -270,6 +295,9 @@ class Parser(object):
     def parse_block_node_or_indentless_sequence(self):
         return self.parse_node(block=True, indentless_sequence=True)
 
+    def transform_tag(self, handle, suffix):
+        return self.tag_handles[handle] + suffix
+
     def parse_node(self, block=False, indentless_sequence=False):
         if self.check_token(AliasToken):
             token = self.get_token()
@@ -302,16 +330,18 @@ class Parser(object):
                 handle, suffix = tag
                 if handle is not None:
                     if handle not in self.tag_handles:
-                        raise ParserError("while parsing a node", start_mark,
-                                "found undefined tag handle %r" % handle.encode('utf-8'),
-                                tag_mark)
-                    tag = self.tag_handles[handle]+suffix
+                        raise ParserError(
+                            "while parsing a node", start_mark,
+                            "found undefined tag handle %r" % utf8(handle),
+                            tag_mark)
+                    tag = self.transform_tag(handle, suffix)
                 else:
                     tag = suffix
-            #if tag == u'!':
-            #    raise ParserError("while parsing a node", start_mark,
-            #            "found non-specific tag '!'", tag_mark,
-            #            "Please check 'http://pyyaml.org/wiki/YAMLNonSpecificTag' and share your opinion.")
+            # if tag == u'!':
+            #     raise ParserError("while parsing a node", start_mark,
+            #             "found non-specific tag '!'", tag_mark,
+            #      "Please check 'http://pyyaml.org/wiki/YAMLNonSpecificTag'
+            #     and share your opinion.")
             if start_mark is None:
                 start_mark = end_mark = self.peek_token().start_mark
             event = None
@@ -319,7 +349,7 @@ class Parser(object):
             if indentless_sequence and self.check_token(BlockEntryToken):
                 end_mark = self.peek_token().end_mark
                 event = SequenceStartEvent(anchor, tag, implicit,
-                        start_mark, end_mark)
+                                           start_mark, end_mark)
                 self.state = self.parse_indentless_sequence_entry
             else:
                 if self.check_token(ScalarToken):
@@ -331,34 +361,52 @@ class Parser(object):
                         implicit = (False, True)
                     else:
                         implicit = (False, False)
-                    event = ScalarEvent(anchor, tag, implicit, token.value,
-                            start_mark, end_mark, style=token.style)
+                    event = ScalarEvent(
+                        anchor, tag, implicit, token.value,
+                        start_mark, end_mark, style=token.style,
+                        comment=token.comment
+                    )
                     self.state = self.states.pop()
                 elif self.check_token(FlowSequenceStartToken):
                     end_mark = self.peek_token().end_mark
-                    event = SequenceStartEvent(anchor, tag, implicit,
-                            start_mark, end_mark, flow_style=True)
+                    event = SequenceStartEvent(
+                        anchor, tag, implicit,
+                        start_mark, end_mark, flow_style=True)
                     self.state = self.parse_flow_sequence_first_entry
                 elif self.check_token(FlowMappingStartToken):
                     end_mark = self.peek_token().end_mark
-                    event = MappingStartEvent(anchor, tag, implicit,
-                            start_mark, end_mark, flow_style=True)
+                    event = MappingStartEvent(
+                        anchor, tag, implicit,
+                        start_mark, end_mark, flow_style=True)
                     self.state = self.parse_flow_mapping_first_key
                 elif block and self.check_token(BlockSequenceStartToken):
                     end_mark = self.peek_token().start_mark
-                    event = SequenceStartEvent(anchor, tag, implicit,
-                            start_mark, end_mark, flow_style=False)
+                    # should inserting the comment be dependent on the
+                    # indentation?
+                    pt = self.peek_token()
+                    comment = pt.comment
+                    # print('pt0', type(pt))
+                    if comment is None or comment[1] is None:
+                        comment = pt.split_comment()
+                    # print('pt1', comment)
+                    event = SequenceStartEvent(
+                        anchor, tag, implicit, start_mark, end_mark,
+                        flow_style=False,
+                        comment=comment,
+                    )
                     self.state = self.parse_block_sequence_first_entry
                 elif block and self.check_token(BlockMappingStartToken):
                     end_mark = self.peek_token().start_mark
-                    event = MappingStartEvent(anchor, tag, implicit,
-                            start_mark, end_mark, flow_style=False)
+                    comment = self.peek_token().comment
+                    event = MappingStartEvent(
+                        anchor, tag, implicit, start_mark, end_mark,
+                        flow_style=False, comment=comment)
                     self.state = self.parse_block_mapping_first_key
                 elif anchor is not None or tag is not None:
                     # Empty scalars are allowed even if a tag or an anchor is
                     # specified.
                     event = ScalarEvent(anchor, tag, (implicit, False), u'',
-                            start_mark, end_mark)
+                                        start_mark, end_mark)
                     self.state = self.states.pop()
                 else:
                     if block:
@@ -366,21 +414,26 @@ class Parser(object):
                     else:
                         node = 'flow'
                     token = self.peek_token()
-                    raise ParserError("while parsing a %s node" % node, start_mark,
-                            "expected the node content, but found %r" % token.id,
-                            token.start_mark)
+                    raise ParserError(
+                        "while parsing a %s node" % node, start_mark,
+                        "expected the node content, but found %r" % token.id,
+                        token.start_mark)
         return event
 
-    # block_sequence ::= BLOCK-SEQUENCE-START (BLOCK-ENTRY block_node?)* BLOCK-END
+    # block_sequence ::= BLOCK-SEQUENCE-START (BLOCK-ENTRY block_node?)*
+    #                                                               BLOCK-END
 
     def parse_block_sequence_first_entry(self):
         token = self.get_token()
+        # move any comment from start token
+        # token.move_comment(self.peek_token())
         self.marks.append(token.start_mark)
         return self.parse_block_sequence_entry()
 
     def parse_block_sequence_entry(self):
         if self.check_token(BlockEntryToken):
             token = self.get_token()
+            token.move_comment(self.peek_token())
             if not self.check_token(BlockEntryToken, BlockEndToken):
                 self.states.append(self.parse_block_sequence_entry)
                 return self.parse_block_node()
@@ -389,28 +442,38 @@ class Parser(object):
                 return self.process_empty_scalar(token.end_mark)
         if not self.check_token(BlockEndToken):
             token = self.peek_token()
-            raise ParserError("while parsing a block collection", self.marks[-1],
-                    "expected <block end>, but found %r" % token.id, token.start_mark)
-        token = self.get_token()
-        event = SequenceEndEvent(token.start_mark, token.end_mark)
+            raise ParserError(
+                "while parsing a block collection", self.marks[-1],
+                "expected <block end>, but found %r" %
+                token.id, token.start_mark)
+        token = self.get_token()  # BlockEndToken
+        event = SequenceEndEvent(token.start_mark, token.end_mark,
+                                 comment=token.comment)
         self.state = self.states.pop()
         self.marks.pop()
         return event
 
     # indentless_sequence ::= (BLOCK-ENTRY block_node?)+
 
+    # indentless_sequence?
+    # sequence:
+    # - entry
+    #  - nested
+
     def parse_indentless_sequence_entry(self):
         if self.check_token(BlockEntryToken):
             token = self.get_token()
+            token.move_comment(self.peek_token())
             if not self.check_token(BlockEntryToken,
-                    KeyToken, ValueToken, BlockEndToken):
+                                    KeyToken, ValueToken, BlockEndToken):
                 self.states.append(self.parse_indentless_sequence_entry)
                 return self.parse_block_node()
             else:
                 self.state = self.parse_indentless_sequence_entry
                 return self.process_empty_scalar(token.end_mark)
         token = self.peek_token()
-        event = SequenceEndEvent(token.start_mark, token.start_mark)
+        event = SequenceEndEvent(token.start_mark, token.start_mark,
+                                 comment=token.comment)
         self.state = self.states.pop()
         return event
 
@@ -427,6 +490,7 @@ class Parser(object):
     def parse_block_mapping_key(self):
         if self.check_token(KeyToken):
             token = self.get_token()
+            token.move_comment(self.peek_token())
             if not self.check_token(KeyToken, ValueToken, BlockEndToken):
                 self.states.append(self.parse_block_mapping_value)
                 return self.parse_block_node_or_indentless_sequence()
@@ -435,10 +499,14 @@ class Parser(object):
                 return self.process_empty_scalar(token.end_mark)
         if not self.check_token(BlockEndToken):
             token = self.peek_token()
-            raise ParserError("while parsing a block mapping", self.marks[-1],
-                    "expected <block end>, but found %r" % token.id, token.start_mark)
+            raise ParserError(
+                "while parsing a block mapping", self.marks[-1],
+                "expected <block end>, but found %r" % token.id,
+                token.start_mark)
         token = self.get_token()
-        event = MappingEndEvent(token.start_mark, token.end_mark)
+        token.move_comment(self.peek_token())
+        event = MappingEndEvent(token.start_mark, token.end_mark,
+                                comment=token.comment)
         self.state = self.states.pop()
         self.marks.pop()
         return event
@@ -446,6 +514,8 @@ class Parser(object):
     def parse_block_mapping_value(self):
         if self.check_token(ValueToken):
             token = self.get_token()
+            # value token might have post comment move it to e.g. block
+            token.move_comment(self.peek_token())
             if not self.check_token(KeyToken, ValueToken, BlockEndToken):
                 self.states.append(self.parse_block_mapping_key)
                 return self.parse_block_node_or_indentless_sequence()
@@ -480,21 +550,24 @@ class Parser(object):
                     self.get_token()
                 else:
                     token = self.peek_token()
-                    raise ParserError("while parsing a flow sequence", self.marks[-1],
-                            "expected ',' or ']', but got %r" % token.id, token.start_mark)
-            
+                    raise ParserError(
+                        "while parsing a flow sequence", self.marks[-1],
+                        "expected ',' or ']', but got %r" % token.id,
+                        token.start_mark)
+
             if self.check_token(KeyToken):
                 token = self.peek_token()
                 event = MappingStartEvent(None, None, True,
-                        token.start_mark, token.end_mark,
-                        flow_style=True)
+                                          token.start_mark, token.end_mark,
+                                          flow_style=True)
                 self.state = self.parse_flow_sequence_entry_mapping_key
                 return event
             elif not self.check_token(FlowSequenceEndToken):
                 self.states.append(self.parse_flow_sequence_entry)
                 return self.parse_flow_node()
         token = self.get_token()
-        event = SequenceEndEvent(token.start_mark, token.end_mark)
+        event = SequenceEndEvent(token.start_mark, token.end_mark,
+                                 comment=token.comment)
         self.state = self.states.pop()
         self.marks.pop()
         return event
@@ -502,7 +575,7 @@ class Parser(object):
     def parse_flow_sequence_entry_mapping_key(self):
         token = self.get_token()
         if not self.check_token(ValueToken,
-                FlowEntryToken, FlowSequenceEndToken):
+                                FlowEntryToken, FlowSequenceEndToken):
             self.states.append(self.parse_flow_sequence_entry_mapping_value)
             return self.parse_flow_node()
         else:
@@ -546,12 +619,14 @@ class Parser(object):
                     self.get_token()
                 else:
                     token = self.peek_token()
-                    raise ParserError("while parsing a flow mapping", self.marks[-1],
-                            "expected ',' or '}', but got %r" % token.id, token.start_mark)
+                    raise ParserError(
+                        "while parsing a flow mapping", self.marks[-1],
+                        "expected ',' or '}', but got %r" % token.id,
+                        token.start_mark)
             if self.check_token(KeyToken):
                 token = self.get_token()
                 if not self.check_token(ValueToken,
-                        FlowEntryToken, FlowMappingEndToken):
+                                        FlowEntryToken, FlowMappingEndToken):
                     self.states.append(self.parse_flow_mapping_value)
                     return self.parse_flow_node()
                 else:
@@ -561,7 +636,8 @@ class Parser(object):
                 self.states.append(self.parse_flow_mapping_empty_value)
                 return self.parse_flow_node()
         token = self.get_token()
-        event = MappingEndEvent(token.start_mark, token.end_mark)
+        event = MappingEndEvent(token.start_mark, token.end_mark,
+                                comment=token.comment)
         self.state = self.states.pop()
         self.marks.pop()
         return event
@@ -587,3 +663,13 @@ class Parser(object):
     def process_empty_scalar(self, mark):
         return ScalarEvent(None, None, (True, False), u'', mark, mark)
 
+
+class RoundTripParser(Parser):
+    """roundtrip is a safe loader, that wants to see the unmangled tag"""
+    def transform_tag(self, handle, suffix):
+        # return self.tag_handles[handle]+suffix
+        if handle == '!!' and suffix in (u'null', u'bool', u'int', u'float', u'binary',
+                                         u'timestamp', u'omap', u'pairs', u'set', u'str',
+                                         u'seq', u'map'):
+            return Parser.transform_tag(self, handle, suffix)
+        return handle+suffix
diff --git a/lib/spack/external/yaml/lib3/yaml/reader.py b/lib/spack/external/ruamel/yaml/reader.py
index f70e920f44..376c6de8c6 100644
--- a/lib/spack/external/yaml/lib3/yaml/reader.py
+++ b/lib/spack/external/ruamel/yaml/reader.py
@@ -1,3 +1,6 @@
+# coding: utf-8
+
+from __future__ import absolute_import
 # This module contains abstractions for the input stream. You don't have to
 # looks further, there are no pretty code.
 #
@@ -11,15 +14,24 @@
 # Reader determines the encoding of `data` and converts it to unicode.
 # Reader provides the following methods and attributes:
 #   reader.peek(length=1) - return the next `length` characters
-#   reader.forward(length=1) - move the current position to `length` characters.
+#   reader.forward(length=1) - move the current position to `length`
+#      characters.
 #   reader.index - the number of the current character.
-#   reader.line, stream.column - the line and the column of the current character.
+#   reader.line, stream.column - the line and the column of the current
+#      character.
 
-__all__ = ['Reader', 'ReaderError']
+import codecs
+import re
 
-from .error import YAMLError, Mark
+try:
+    from .error import YAMLError, Mark
+    from .compat import text_type, binary_type, PY3
+except (ImportError, ValueError):  # for Jython
+    from ruamel.yaml.error import YAMLError, Mark
+    from ruamel.yaml.compat import text_type, binary_type, PY3
+
+__all__ = ['Reader', 'ReaderError']
 
-import codecs, re
 
 class ReaderError(YAMLError):
 
@@ -31,16 +43,17 @@ class ReaderError(YAMLError):
         self.reason = reason
 
     def __str__(self):
-        if isinstance(self.character, bytes):
+        if isinstance(self.character, binary_type):
             return "'%s' codec can't decode byte #x%02x: %s\n"  \
-                    "  in \"%s\", position %d"    \
-                    % (self.encoding, ord(self.character), self.reason,
-                            self.name, self.position)
+                   "  in \"%s\", position %d"    \
+                   % (self.encoding, ord(self.character), self.reason,
+                      self.name, self.position)
         else:
             return "unacceptable character #x%04x: %s\n"    \
-                    "  in \"%s\", position %d"    \
-                    % (self.character, self.reason,
-                            self.name, self.position)
+                   "  in \"%s\", position %d"    \
+                   % (self.character, self.reason,
+                      self.name, self.position)
+
 
 class Reader(object):
     # Reader:
@@ -49,8 +62,8 @@ class Reader(object):
     # - adds '\0' to the end.
 
     # Reader accepts
-    #  - a `bytes` object,
-    #  - a `str` object,
+    #  - a `str` object (PY2) / a `bytes` object (PY3),
+    #  - a `unicode` object (PY2) / a `str` object (PY3),
     #  - a file-like object with its `read` method returning `str`,
     #  - a file-like object with its `read` method returning `unicode`.
 
@@ -61,7 +74,7 @@ class Reader(object):
         self.stream = None
         self.stream_pointer = 0
         self.eof = True
-        self.buffer = ''
+        self.buffer = u''
         self.pointer = 0
         self.raw_buffer = None
         self.raw_decode = None
@@ -69,11 +82,11 @@ class Reader(object):
         self.index = 0
         self.line = 0
         self.column = 0
-        if isinstance(stream, str):
+        if isinstance(stream, text_type):
             self.name = "<unicode string>"
             self.check_printable(stream)
-            self.buffer = stream+'\0'
-        elif isinstance(stream, bytes):
+            self.buffer = stream+u'\0'
+        elif isinstance(stream, binary_type):
             self.name = "<byte string>"
             self.raw_buffer = stream
             self.determine_encoding()
@@ -103,26 +116,27 @@ class Reader(object):
             ch = self.buffer[self.pointer]
             self.pointer += 1
             self.index += 1
-            if ch in '\n\x85\u2028\u2029'  \
-                    or (ch == '\r' and self.buffer[self.pointer] != '\n'):
+            if ch in u'\n\x85\u2028\u2029'  \
+                    or (ch == u'\r' and self.buffer[self.pointer] != u'\n'):
                 self.line += 1
                 self.column = 0
-            elif ch != '\uFEFF':
+            elif ch != u'\uFEFF':
                 self.column += 1
             length -= 1
 
     def get_mark(self):
         if self.stream is None:
             return Mark(self.name, self.index, self.line, self.column,
-                    self.buffer, self.pointer)
+                        self.buffer, self.pointer)
         else:
             return Mark(self.name, self.index, self.line, self.column,
-                    None, None)
+                        None, None)
 
     def determine_encoding(self):
-        while not self.eof and (self.raw_buffer is None or len(self.raw_buffer) < 2):
+        while not self.eof and (self.raw_buffer is None or
+                                len(self.raw_buffer) < 2):
             self.update_raw()
-        if isinstance(self.raw_buffer, bytes):
+        if isinstance(self.raw_buffer, binary_type):
             if self.raw_buffer.startswith(codecs.BOM_UTF16_LE):
                 self.raw_decode = codecs.utf_16_le_decode
                 self.encoding = 'utf-16-le'
@@ -134,14 +148,16 @@ class Reader(object):
                 self.encoding = 'utf-8'
         self.update(1)
 
-    NON_PRINTABLE = re.compile('[^\x09\x0A\x0D\x20-\x7E\x85\xA0-\uD7FF\uE000-\uFFFD]')
+    NON_PRINTABLE = re.compile(
+        u'[^\x09\x0A\x0D\x20-\x7E\x85\xA0-\uD7FF\uE000-\uFFFD]')
+
     def check_printable(self, data):
         match = self.NON_PRINTABLE.search(data)
         if match:
             character = match.group()
             position = self.index+(len(self.buffer)-self.pointer)+match.start()
             raise ReaderError(self.name, position, ord(character),
-                    'unicode', "special characters are not allowed")
+                              'unicode', "special characters are not allowed")
 
     def update(self, length):
         if self.raw_buffer is None:
@@ -154,15 +170,19 @@ class Reader(object):
             if self.raw_decode is not None:
                 try:
                     data, converted = self.raw_decode(self.raw_buffer,
-                            'strict', self.eof)
+                                                      'strict', self.eof)
                 except UnicodeDecodeError as exc:
-                    character = self.raw_buffer[exc.start]
+                    if PY3:
+                        character = self.raw_buffer[exc.start]
+                    else:
+                        character = exc.object[exc.start]
                     if self.stream is not None:
-                        position = self.stream_pointer-len(self.raw_buffer)+exc.start
+                        position = self.stream_pointer - \
+                            len(self.raw_buffer) + exc.start
                     else:
                         position = exc.start
                     raise ReaderError(self.name, position, character,
-                            exc.encoding, exc.reason)
+                                      exc.encoding, exc.reason)
             else:
                 data = self.raw_buffer
                 converted = len(data)
@@ -170,11 +190,13 @@ class Reader(object):
             self.buffer += data
             self.raw_buffer = self.raw_buffer[converted:]
             if self.eof:
-                self.buffer += '\0'
+                self.buffer += u'\0'
                 self.raw_buffer = None
                 break
 
-    def update_raw(self, size=4096):
+    def update_raw(self, size=None):
+        if size is None:
+            size = 4096 if PY3 else 1024
         data = self.stream.read(size)
         if self.raw_buffer is None:
             self.raw_buffer = data
@@ -184,9 +206,8 @@ class Reader(object):
         if not data:
             self.eof = True
 
-#try:
-#    import psyco
-#    psyco.bind(Reader)
-#except ImportError:
-#    pass
-
+# try:
+#     import psyco
+#     psyco.bind(Reader)
+# except ImportError:
+#     pass
diff --git a/lib/spack/external/ruamel/yaml/representer.py b/lib/spack/external/ruamel/yaml/representer.py
new file mode 100644
index 0000000000..b4625bfae9
--- /dev/null
+++ b/lib/spack/external/ruamel/yaml/representer.py
@@ -0,0 +1,888 @@
+# coding: utf-8
+
+from __future__ import absolute_import
+from __future__ import print_function
+
+try:
+    from .error import *                                  # NOQA
+    from .nodes import *                                  # NOQA
+    from .compat import text_type, binary_type, to_unicode, PY2, PY3, ordereddict
+    from .scalarstring import *                           # NOQA
+except (ImportError, ValueError):  # for Jython
+    from ruamel.yaml.error import *                       # NOQA
+    from ruamel.yaml.nodes import *                       # NOQA
+    from ruamel.yaml.compat import text_type, binary_type, to_unicode, PY2, PY3, ordereddict
+    from ruamel.yaml.scalarstring import *                # NOQA
+
+
+import datetime
+import sys
+import types
+if PY3:
+    import copyreg
+    import base64
+else:
+    import copy_reg as copyreg
+
+
+__all__ = ['BaseRepresenter', 'SafeRepresenter', 'Representer',
+           'RepresenterError', 'RoundTripRepresenter']
+
+
+class RepresenterError(YAMLError):
+    pass
+
+
+class BaseRepresenter(object):
+
+    yaml_representers = {}
+    yaml_multi_representers = {}
+
+    def __init__(self, default_style=None, default_flow_style=None):
+        self.default_style = default_style
+        self.default_flow_style = default_flow_style
+        self.represented_objects = {}
+        self.object_keeper = []
+        self.alias_key = None
+
+    def represent(self, data):
+        node = self.represent_data(data)
+        self.serialize(node)
+        self.represented_objects = {}
+        self.object_keeper = []
+        self.alias_key = None
+
+    if PY2:
+        def get_classobj_bases(self, cls):
+            bases = [cls]
+            for base in cls.__bases__:
+                bases.extend(self.get_classobj_bases(base))
+            return bases
+
+    def represent_data(self, data):
+        if self.ignore_aliases(data):
+            self.alias_key = None
+        else:
+            self.alias_key = id(data)
+        if self.alias_key is not None:
+            if self.alias_key in self.represented_objects:
+                node = self.represented_objects[self.alias_key]
+                # if node is None:
+                #     raise RepresenterError(
+                #          "recursive objects are not allowed: %r" % data)
+                return node
+            # self.represented_objects[alias_key] = None
+            self.object_keeper.append(data)
+        data_types = type(data).__mro__
+        if PY2:
+            # if type(data) is types.InstanceType:
+            if isinstance(data, types.InstanceType):
+                data_types = self.get_classobj_bases(data.__class__) + \
+                    list(data_types)
+        if data_types[0] in self.yaml_representers:
+            node = self.yaml_representers[data_types[0]](self, data)
+        else:
+            for data_type in data_types:
+                if data_type in self.yaml_multi_representers:
+                    node = self.yaml_multi_representers[data_type](self, data)
+                    break
+            else:
+                if None in self.yaml_multi_representers:
+                    node = self.yaml_multi_representers[None](self, data)
+                elif None in self.yaml_representers:
+                    node = self.yaml_representers[None](self, data)
+                else:
+                    node = ScalarNode(None, text_type(data))
+        # if alias_key is not None:
+        #     self.represented_objects[alias_key] = node
+        return node
+
+    def represent_key(self, data):
+        """
+        David Fraser: Extract a method to represent keys in mappings, so that
+        a subclass can choose not to quote them (for example)
+        used in repesent_mapping
+        https://bitbucket.org/davidfraser/pyyaml/commits/d81df6eb95f20cac4a79eed95ae553b5c6f77b8c
+        """
+        return self.represent_data(data)
+
+    @classmethod
+    def add_representer(cls, data_type, representer):
+        if 'yaml_representers' not in cls.__dict__:
+            cls.yaml_representers = cls.yaml_representers.copy()
+        cls.yaml_representers[data_type] = representer
+
+    @classmethod
+    def add_multi_representer(cls, data_type, representer):
+        if 'yaml_multi_representers' not in cls.__dict__:
+            cls.yaml_multi_representers = cls.yaml_multi_representers.copy()
+        cls.yaml_multi_representers[data_type] = representer
+
+    def represent_scalar(self, tag, value, style=None):
+        if style is None:
+            style = self.default_style
+        node = ScalarNode(tag, value, style=style)
+        if self.alias_key is not None:
+            self.represented_objects[self.alias_key] = node
+        return node
+
+    def represent_sequence(self, tag, sequence, flow_style=None):
+        value = []
+        node = SequenceNode(tag, value, flow_style=flow_style)
+        if self.alias_key is not None:
+            self.represented_objects[self.alias_key] = node
+        best_style = True
+        for item in sequence:
+            node_item = self.represent_data(item)
+            if not (isinstance(node_item, ScalarNode) and not node_item.style):
+                best_style = False
+            value.append(node_item)
+        if flow_style is None:
+            if self.default_flow_style is not None:
+                node.flow_style = self.default_flow_style
+            else:
+                node.flow_style = best_style
+        return node
+
+    def represent_omap(self, tag, omap, flow_style=None):
+        value = []
+        node = SequenceNode(tag, value, flow_style=flow_style)
+        if self.alias_key is not None:
+            self.represented_objects[self.alias_key] = node
+        best_style = True
+        for item_key in omap:
+            item_val = omap[item_key]
+            node_item = self.represent_data({item_key: item_val})
+            # if not (isinstance(node_item, ScalarNode) \
+            #    and not node_item.style):
+            #     best_style = False
+            value.append(node_item)
+        if flow_style is None:
+            if self.default_flow_style is not None:
+                node.flow_style = self.default_flow_style
+            else:
+                node.flow_style = best_style
+        return node
+
+    def represent_mapping(self, tag, mapping, flow_style=None):
+        value = []
+        node = MappingNode(tag, value, flow_style=flow_style)
+        if self.alias_key is not None:
+            self.represented_objects[self.alias_key] = node
+        best_style = True
+        if hasattr(mapping, 'items'):
+            mapping = list(mapping.items())
+            try:
+                mapping = sorted(mapping)
+            except TypeError:
+                pass
+        for item_key, item_value in mapping:
+            node_key = self.represent_key(item_key)
+            node_value = self.represent_data(item_value)
+            if not (isinstance(node_key, ScalarNode) and not node_key.style):
+                best_style = False
+            if not (isinstance(node_value, ScalarNode) and not
+                    node_value.style):
+                best_style = False
+            value.append((node_key, node_value))
+        if flow_style is None:
+            if self.default_flow_style is not None:
+                node.flow_style = self.default_flow_style
+            else:
+                node.flow_style = best_style
+        return node
+
+    def ignore_aliases(self, data):
+        return False
+
+
+class SafeRepresenter(BaseRepresenter):
+
+    def ignore_aliases(self, data):
+        # https://docs.python.org/3/reference/expressions.html#parenthesized-forms :
+        # "i.e. two occurrences of the empty tuple may or may not yield the same object"
+        # so "data is ()" should not be used
+        if data is None or data == ():
+            return True
+        if isinstance(data, (binary_type, text_type, bool, int, float)):
+            return True
+
+    def represent_none(self, data):
+        return self.represent_scalar(u'tag:yaml.org,2002:null',
+                                     u'null')
+
+    if PY3:
+        def represent_str(self, data):
+            return self.represent_scalar(u'tag:yaml.org,2002:str', data)
+
+        def represent_binary(self, data):
+            if hasattr(base64, 'encodebytes'):
+                data = base64.encodebytes(data).decode('ascii')
+            else:
+                data = base64.encodestring(data).decode('ascii')
+            return self.represent_scalar(u'tag:yaml.org,2002:binary', data,
+                                         style='|')
+    else:
+        def represent_str(self, data):
+            tag = None
+            style = None
+            try:
+                data = unicode(data, 'ascii')
+                tag = u'tag:yaml.org,2002:str'
+            except UnicodeDecodeError:
+                try:
+                    data = unicode(data, 'utf-8')
+                    tag = u'tag:yaml.org,2002:str'
+                except UnicodeDecodeError:
+                    data = data.encode('base64')
+                    tag = u'tag:yaml.org,2002:binary'
+                    style = '|'
+            return self.represent_scalar(tag, data, style=style)
+
+        def represent_unicode(self, data):
+            return self.represent_scalar(u'tag:yaml.org,2002:str', data)
+
+    def represent_bool(self, data):
+        if data:
+            value = u'true'
+        else:
+            value = u'false'
+        return self.represent_scalar(u'tag:yaml.org,2002:bool', value)
+
+    def represent_int(self, data):
+        return self.represent_scalar(u'tag:yaml.org,2002:int', text_type(data))
+
+    if PY2:
+        def represent_long(self, data):
+            return self.represent_scalar(u'tag:yaml.org,2002:int',
+                                         text_type(data))
+
+    inf_value = 1e300
+    while repr(inf_value) != repr(inf_value*inf_value):
+        inf_value *= inf_value
+
+    def represent_float(self, data):
+        if data != data or (data == 0.0 and data == 1.0):
+            value = u'.nan'
+        elif data == self.inf_value:
+            value = u'.inf'
+        elif data == -self.inf_value:
+            value = u'-.inf'
+        else:
+            value = to_unicode(repr(data)).lower()
+            # Note that in some cases `repr(data)` represents a float number
+            # without the decimal parts.  For instance:
+            #   >>> repr(1e17)
+            #   '1e17'
+            # Unfortunately, this is not a valid float representation according
+            # to the definition of the `!!float` tag.  We fix this by adding
+            # '.0' before the 'e' symbol.
+            if u'.' not in value and u'e' in value:
+                value = value.replace(u'e', u'.0e', 1)
+        return self.represent_scalar(u'tag:yaml.org,2002:float', value)
+
+    def represent_list(self, data):
+        # pairs = (len(data) > 0 and isinstance(data, list))
+        # if pairs:
+        #     for item in data:
+        #         if not isinstance(item, tuple) or len(item) != 2:
+        #             pairs = False
+        #             break
+        # if not pairs:
+            return self.represent_sequence(u'tag:yaml.org,2002:seq', data)
+        # value = []
+        # for item_key, item_value in data:
+        #     value.append(self.represent_mapping(u'tag:yaml.org,2002:map',
+        #         [(item_key, item_value)]))
+        # return SequenceNode(u'tag:yaml.org,2002:pairs', value)
+
+    def represent_dict(self, data):
+        return self.represent_mapping(u'tag:yaml.org,2002:map', data)
+
+    def represent_ordereddict(self, data):
+        return self.represent_omap(u'tag:yaml.org,2002:omap', data)
+
+    def represent_set(self, data):
+        value = {}
+        for key in data:
+            value[key] = None
+        return self.represent_mapping(u'tag:yaml.org,2002:set', value)
+
+    def represent_date(self, data):
+        value = to_unicode(data.isoformat())
+        return self.represent_scalar(u'tag:yaml.org,2002:timestamp', value)
+
+    def represent_datetime(self, data):
+        value = to_unicode(data.isoformat(' '))
+        return self.represent_scalar(u'tag:yaml.org,2002:timestamp', value)
+
+    def represent_yaml_object(self, tag, data, cls, flow_style=None):
+        if hasattr(data, '__getstate__'):
+            state = data.__getstate__()
+        else:
+            state = data.__dict__.copy()
+        return self.represent_mapping(tag, state, flow_style=flow_style)
+
+    def represent_undefined(self, data):
+        raise RepresenterError("cannot represent an object: %s" % data)
+
+SafeRepresenter.add_representer(type(None),
+                                SafeRepresenter.represent_none)
+
+SafeRepresenter.add_representer(str,
+                                SafeRepresenter.represent_str)
+
+if PY2:
+    SafeRepresenter.add_representer(unicode,
+                                    SafeRepresenter.represent_unicode)
+else:
+    SafeRepresenter.add_representer(bytes,
+                                    SafeRepresenter.represent_binary)
+
+SafeRepresenter.add_representer(bool,
+                                SafeRepresenter.represent_bool)
+
+SafeRepresenter.add_representer(int,
+                                SafeRepresenter.represent_int)
+
+if PY2:
+    SafeRepresenter.add_representer(long,
+                                    SafeRepresenter.represent_long)
+
+SafeRepresenter.add_representer(float,
+                                SafeRepresenter.represent_float)
+
+SafeRepresenter.add_representer(list,
+                                SafeRepresenter.represent_list)
+
+SafeRepresenter.add_representer(tuple,
+                                SafeRepresenter.represent_list)
+
+SafeRepresenter.add_representer(dict,
+                                SafeRepresenter.represent_dict)
+
+SafeRepresenter.add_representer(set,
+                                SafeRepresenter.represent_set)
+
+SafeRepresenter.add_representer(ordereddict,
+                                SafeRepresenter.represent_ordereddict)
+
+SafeRepresenter.add_representer(datetime.date,
+                                SafeRepresenter.represent_date)
+
+SafeRepresenter.add_representer(datetime.datetime,
+                                SafeRepresenter.represent_datetime)
+
+SafeRepresenter.add_representer(None,
+                                SafeRepresenter.represent_undefined)
+
+
+class Representer(SafeRepresenter):
+    if PY2:
+        def represent_str(self, data):
+            tag = None
+            style = None
+            try:
+                data = unicode(data, 'ascii')
+                tag = u'tag:yaml.org,2002:str'
+            except UnicodeDecodeError:
+                try:
+                    data = unicode(data, 'utf-8')
+                    tag = u'tag:yaml.org,2002:python/str'
+                except UnicodeDecodeError:
+                    data = data.encode('base64')
+                    tag = u'tag:yaml.org,2002:binary'
+                    style = '|'
+            return self.represent_scalar(tag, data, style=style)
+
+        def represent_unicode(self, data):
+            tag = None
+            try:
+                data.encode('ascii')
+                tag = u'tag:yaml.org,2002:python/unicode'
+            except UnicodeEncodeError:
+                tag = u'tag:yaml.org,2002:str'
+            return self.represent_scalar(tag, data)
+
+        def represent_long(self, data):
+            tag = u'tag:yaml.org,2002:int'
+            if int(data) is not data:
+                tag = u'tag:yaml.org,2002:python/long'
+            return self.represent_scalar(tag, to_unicode(data))
+
+    def represent_complex(self, data):
+        if data.imag == 0.0:
+            data = u'%r' % data.real
+        elif data.real == 0.0:
+            data = u'%rj' % data.imag
+        elif data.imag > 0:
+            data = u'%r+%rj' % (data.real, data.imag)
+        else:
+            data = u'%r%rj' % (data.real, data.imag)
+        return self.represent_scalar(u'tag:yaml.org,2002:python/complex', data)
+
+    def represent_tuple(self, data):
+        return self.represent_sequence(u'tag:yaml.org,2002:python/tuple', data)
+
+    def represent_name(self, data):
+        name = u'%s.%s' % (data.__module__, data.__name__)
+        return self.represent_scalar(u'tag:yaml.org,2002:python/name:' +
+                                     name, u'')
+
+    def represent_module(self, data):
+        return self.represent_scalar(
+            u'tag:yaml.org,2002:python/module:'+data.__name__, u'')
+
+    if PY2:
+        def represent_instance(self, data):
+            # For instances of classic classes, we use __getinitargs__ and
+            # __getstate__ to serialize the data.
+
+            # If data.__getinitargs__ exists, the object must be reconstructed
+            # by calling cls(**args), where args is a tuple returned by
+            # __getinitargs__. Otherwise, the cls.__init__ method should never
+            # be called and the class instance is created by instantiating a
+            # trivial class and assigning to the instance's __class__ variable.
+
+            # If data.__getstate__ exists, it returns the state of the object.
+            # Otherwise, the state of the object is data.__dict__.
+
+            # We produce either a !!python/object or !!python/object/new node.
+            # If data.__getinitargs__ does not exist and state is a dictionary,
+            # we produce a !!python/object node . Otherwise we produce a
+            # !!python/object/new node.
+
+            cls = data.__class__
+            class_name = u'%s.%s' % (cls.__module__, cls.__name__)
+            args = None
+            state = None
+            if hasattr(data, '__getinitargs__'):
+                args = list(data.__getinitargs__())
+            if hasattr(data, '__getstate__'):
+                state = data.__getstate__()
+            else:
+                state = data.__dict__
+            if args is None and isinstance(state, dict):
+                return self.represent_mapping(
+                    u'tag:yaml.org,2002:python/object:'+class_name, state)
+            if isinstance(state, dict) and not state:
+                return self.represent_sequence(
+                    u'tag:yaml.org,2002:python/object/new:' +
+                    class_name, args)
+            value = {}
+            if args:
+                value['args'] = args
+            value['state'] = state
+            return self.represent_mapping(
+                u'tag:yaml.org,2002:python/object/new:'+class_name, value)
+
+    def represent_object(self, data):
+        # We use __reduce__ API to save the data. data.__reduce__ returns
+        # a tuple of length 2-5:
+        #   (function, args, state, listitems, dictitems)
+
+        # For reconstructing, we calls function(*args), then set its state,
+        # listitems, and dictitems if they are not None.
+
+        # A special case is when function.__name__ == '__newobj__'. In this
+        # case we create the object with args[0].__new__(*args).
+
+        # Another special case is when __reduce__ returns a string - we don't
+        # support it.
+
+        # We produce a !!python/object, !!python/object/new or
+        # !!python/object/apply node.
+
+        cls = type(data)
+        if cls in copyreg.dispatch_table:
+            reduce = copyreg.dispatch_table[cls](data)
+        elif hasattr(data, '__reduce_ex__'):
+            reduce = data.__reduce_ex__(2)
+        elif hasattr(data, '__reduce__'):
+            reduce = data.__reduce__()
+        else:
+            raise RepresenterError("cannot represent object: %r" % data)
+        reduce = (list(reduce)+[None]*5)[:5]
+        function, args, state, listitems, dictitems = reduce
+        args = list(args)
+        if state is None:
+            state = {}
+        if listitems is not None:
+            listitems = list(listitems)
+        if dictitems is not None:
+            dictitems = dict(dictitems)
+        if function.__name__ == '__newobj__':
+            function = args[0]
+            args = args[1:]
+            tag = u'tag:yaml.org,2002:python/object/new:'
+            newobj = True
+        else:
+            tag = u'tag:yaml.org,2002:python/object/apply:'
+            newobj = False
+        function_name = u'%s.%s' % (function.__module__, function.__name__)
+        if not args and not listitems and not dictitems \
+                and isinstance(state, dict) and newobj:
+            return self.represent_mapping(
+                u'tag:yaml.org,2002:python/object:'+function_name, state)
+        if not listitems and not dictitems  \
+                and isinstance(state, dict) and not state:
+            return self.represent_sequence(tag+function_name, args)
+        value = {}
+        if args:
+            value['args'] = args
+        if state or not isinstance(state, dict):
+            value['state'] = state
+        if listitems:
+            value['listitems'] = listitems
+        if dictitems:
+            value['dictitems'] = dictitems
+        return self.represent_mapping(tag+function_name, value)
+
+if PY2:
+    Representer.add_representer(str,
+                                Representer.represent_str)
+
+    Representer.add_representer(unicode,
+                                Representer.represent_unicode)
+
+    Representer.add_representer(long,
+                                Representer.represent_long)
+
+Representer.add_representer(complex,
+                            Representer.represent_complex)
+
+Representer.add_representer(tuple,
+                            Representer.represent_tuple)
+
+Representer.add_representer(type,
+                            Representer.represent_name)
+
+if PY2:
+    Representer.add_representer(types.ClassType,
+                                Representer.represent_name)
+
+Representer.add_representer(types.FunctionType,
+                            Representer.represent_name)
+
+Representer.add_representer(types.BuiltinFunctionType,
+                            Representer.represent_name)
+
+Representer.add_representer(types.ModuleType,
+                            Representer.represent_module)
+
+if PY2:
+    Representer.add_multi_representer(types.InstanceType,
+                                      Representer.represent_instance)
+
+Representer.add_multi_representer(object,
+                                  Representer.represent_object)
+
+
+try:
+    from .comments import CommentedMap, CommentedOrderedMap, CommentedSeq, \
+        CommentedSet, comment_attrib, merge_attrib
+except ImportError:  # for Jython
+    from ruamel.yaml.comments import CommentedMap, CommentedOrderedMap, \
+        CommentedSeq, CommentedSet, comment_attrib, merge_attrib
+
+
+class RoundTripRepresenter(SafeRepresenter):
+    # need to add type here and write out the .comment
+    # in serializer and emitter
+
+    def __init__(self, default_style=None, default_flow_style=None):
+        if default_flow_style is None:
+            default_flow_style = False
+        SafeRepresenter.__init__(self, default_style=default_style,
+                                 default_flow_style=default_flow_style)
+
+    def represent_none(self, data):
+        return self.represent_scalar(u'tag:yaml.org,2002:null',
+                                     u'')
+
+    def represent_preserved_scalarstring(self, data):
+        tag = None
+        style = '|'
+        if PY2 and not isinstance(data, unicode):
+            data = unicode(data, 'ascii')
+        tag = u'tag:yaml.org,2002:str'
+        return self.represent_scalar(tag, data, style=style)
+
+    def represent_single_quoted_scalarstring(self, data):
+        tag = None
+        style = "'"
+        if PY2 and not isinstance(data, unicode):
+            data = unicode(data, 'ascii')
+        tag = u'tag:yaml.org,2002:str'
+        return self.represent_scalar(tag, data, style=style)
+
+    def represent_double_quoted_scalarstring(self, data):
+        tag = None
+        style = '"'
+        if PY2 and not isinstance(data, unicode):
+            data = unicode(data, 'ascii')
+        tag = u'tag:yaml.org,2002:str'
+        return self.represent_scalar(tag, data, style=style)
+
+    def represent_sequence(self, tag, sequence, flow_style=None):
+        value = []
+        # if the flow_style is None, the flow style tacked on to the object
+        # explicitly will be taken. If that is None as well the default flow
+        # style rules
+        try:
+            flow_style = sequence.fa.flow_style(flow_style)
+        except AttributeError:
+            flow_style = flow_style
+        try:
+            anchor = sequence.yaml_anchor()
+        except AttributeError:
+            anchor = None
+        node = SequenceNode(tag, value, flow_style=flow_style, anchor=anchor)
+        if self.alias_key is not None:
+            self.represented_objects[self.alias_key] = node
+        best_style = True
+        try:
+            comment = getattr(sequence, comment_attrib)
+            item_comments = comment.items
+            node.comment = comment.comment
+            try:
+                node.comment.append(comment.end)
+            except AttributeError:
+                pass
+        except AttributeError:
+            item_comments = {}
+        for idx, item in enumerate(sequence):
+            node_item = self.represent_data(item)
+            node_item.comment = item_comments.get(idx)
+            if not (isinstance(node_item, ScalarNode) and not node_item.style):
+                best_style = False
+            value.append(node_item)
+        if flow_style is None:
+            if self.default_flow_style is not None:
+                node.flow_style = self.default_flow_style
+            else:
+                node.flow_style = best_style
+        return node
+
+    def represent_mapping(self, tag, mapping, flow_style=None):
+        value = []
+        try:
+            flow_style = mapping.fa.flow_style(flow_style)
+        except AttributeError:
+            flow_style = flow_style
+        try:
+            anchor = mapping.yaml_anchor()
+        except AttributeError:
+            anchor = None
+        node = MappingNode(tag, value, flow_style=flow_style, anchor=anchor)
+        if self.alias_key is not None:
+            self.represented_objects[self.alias_key] = node
+        best_style = True
+        # no sorting! !!
+        try:
+            comment = getattr(mapping, comment_attrib)
+            node.comment = comment.comment
+            if node.comment and node.comment[1]:
+                for ct in node.comment[1]:
+                    ct.reset()
+            item_comments = comment.items
+            for v in item_comments.values():
+                if v and v[1]:
+                    for ct in v[1]:
+                        ct.reset()
+            try:
+                node.comment.append(comment.end)
+            except AttributeError:
+                pass
+        except AttributeError:
+            item_comments = {}
+        for item_key, item_value in mapping.items():
+            node_key = self.represent_key(item_key)
+            node_value = self.represent_data(item_value)
+            item_comment = item_comments.get(item_key)
+            if item_comment:
+                assert getattr(node_key, 'comment', None) is None
+                node_key.comment = item_comment[:2]
+                nvc = getattr(node_value, 'comment', None)
+                if nvc is not None:  # end comment already there
+                    nvc[0] = item_comment[2]
+                    nvc[1] = item_comment[3]
+                else:
+                    node_value.comment = item_comment[2:]
+            if not (isinstance(node_key, ScalarNode) and not node_key.style):
+                best_style = False
+            if not (isinstance(node_value, ScalarNode) and not
+                    node_value.style):
+                best_style = False
+            value.append((node_key, node_value))
+        if flow_style is None:
+            if self.default_flow_style is not None:
+                node.flow_style = self.default_flow_style
+            else:
+                node.flow_style = best_style
+        merge_list = [m[1] for m in getattr(mapping, merge_attrib, [])]
+        if merge_list:
+            # because of the call to represent_data here, the anchors
+            # are marked as being used and thereby created
+            if len(merge_list) == 1:
+                arg = self.represent_data(merge_list[0])
+            else:
+                arg = self.represent_data(merge_list)
+                arg.flow_style = True
+            value.insert(0,
+                         (ScalarNode(u'tag:yaml.org,2002:merge', '<<'), arg))
+        return node
+
+    def represent_omap(self, tag, omap, flow_style=None):
+        value = []
+        try:
+            flow_style = omap.fa.flow_style(flow_style)
+        except AttributeError:
+            flow_style = flow_style
+        try:
+            anchor = omap.yaml_anchor()
+        except AttributeError:
+            anchor = None
+        node = SequenceNode(tag, value, flow_style=flow_style, anchor=anchor)
+        if self.alias_key is not None:
+            self.represented_objects[self.alias_key] = node
+        best_style = True
+        try:
+            comment = getattr(omap, comment_attrib)
+            node.comment = comment.comment
+            if node.comment and node.comment[1]:
+                for ct in node.comment[1]:
+                    ct.reset()
+            item_comments = comment.items
+            for v in item_comments.values():
+                if v and v[1]:
+                    for ct in v[1]:
+                        ct.reset()
+            try:
+                node.comment.append(comment.end)
+            except AttributeError:
+                pass
+        except AttributeError:
+            item_comments = {}
+        for item_key in omap:
+            item_val = omap[item_key]
+            node_item = self.represent_data({item_key: item_val})
+            # node item has two scalars in value: node_key and node_value
+            item_comment = item_comments.get(item_key)
+            if item_comment:
+                if item_comment[1]:
+                    node_item.comment = [None, item_comment[1]]
+                assert getattr(node_item.value[0][0], 'comment', None) is None
+                node_item.value[0][0].comment = [item_comment[0], None]
+                nvc = getattr(node_item.value[0][1], 'comment', None)
+                if nvc is not None:  # end comment already there
+                    nvc[0] = item_comment[2]
+                    nvc[1] = item_comment[3]
+                else:
+                    node_item.value[0][1].comment = item_comment[2:]
+            # if not (isinstance(node_item, ScalarNode) \
+            #    and not node_item.style):
+            #     best_style = False
+            value.append(node_item)
+        if flow_style is None:
+            if self.default_flow_style is not None:
+                node.flow_style = self.default_flow_style
+            else:
+                node.flow_style = best_style
+        return node
+
+    def represent_set(self, setting):
+        flow_style = False
+        tag = u'tag:yaml.org,2002:set'
+        # return self.represent_mapping(tag, value)
+        value = []
+        flow_style = setting.fa.flow_style(flow_style)
+        try:
+            anchor = setting.yaml_anchor()
+        except AttributeError:
+            anchor = None
+        node = MappingNode(tag, value, flow_style=flow_style, anchor=anchor)
+        if self.alias_key is not None:
+            self.represented_objects[self.alias_key] = node
+        best_style = True
+        # no sorting! !!
+        try:
+            comment = getattr(setting, comment_attrib)
+            node.comment = comment.comment
+            if node.comment and node.comment[1]:
+                for ct in node.comment[1]:
+                    ct.reset()
+            item_comments = comment.items
+            for v in item_comments.values():
+                if v and v[1]:
+                    for ct in v[1]:
+                        ct.reset()
+            try:
+                node.comment.append(comment.end)
+            except AttributeError:
+                pass
+        except AttributeError:
+            item_comments = {}
+        for item_key in setting.odict:
+            node_key = self.represent_key(item_key)
+            node_value = self.represent_data(None)
+            item_comment = item_comments.get(item_key)
+            if item_comment:
+                assert getattr(node_key, 'comment', None) is None
+                node_key.comment = item_comment[:2]
+            node_key.style = node_value.style = "?"
+            if not (isinstance(node_key, ScalarNode) and not node_key.style):
+                best_style = False
+            if not (isinstance(node_value, ScalarNode) and not
+                    node_value.style):
+                best_style = False
+            value.append((node_key, node_value))
+        best_style = best_style
+        return node
+
+    def represent_dict(self, data):
+        """write out tag if saved on loading"""
+        try:
+            t = data.tag.value
+        except AttributeError:
+            t = None
+        if t:
+            while t and t[0] == '!':
+                t = t[1:]
+            tag = 'tag:yaml.org,2002:' + t
+        else:
+            tag = u'tag:yaml.org,2002:map'
+        return self.represent_mapping(tag, data)
+
+
+RoundTripRepresenter.add_representer(type(None),
+                                     RoundTripRepresenter.represent_none)
+
+RoundTripRepresenter.add_representer(
+    PreservedScalarString,
+    RoundTripRepresenter.represent_preserved_scalarstring)
+
+RoundTripRepresenter.add_representer(
+    SingleQuotedScalarString,
+    RoundTripRepresenter.represent_single_quoted_scalarstring)
+
+RoundTripRepresenter.add_representer(
+    DoubleQuotedScalarString,
+    RoundTripRepresenter.represent_double_quoted_scalarstring)
+
+RoundTripRepresenter.add_representer(CommentedSeq,
+                                     RoundTripRepresenter.represent_list)
+
+RoundTripRepresenter.add_representer(CommentedMap,
+                                     RoundTripRepresenter.represent_dict)
+
+RoundTripRepresenter.add_representer(CommentedOrderedMap,
+                                     RoundTripRepresenter.represent_ordereddict)
+
+if sys.version_info >= (2, 7):
+    import collections
+    RoundTripRepresenter.add_representer(collections.OrderedDict,
+                                         RoundTripRepresenter.represent_ordereddict)
+
+RoundTripRepresenter.add_representer(CommentedSet,
+                                     RoundTripRepresenter.represent_set)
diff --git a/lib/spack/external/ruamel/yaml/resolver.py b/lib/spack/external/ruamel/yaml/resolver.py
new file mode 100644
index 0000000000..84227072e0
--- /dev/null
+++ b/lib/spack/external/ruamel/yaml/resolver.py
@@ -0,0 +1,397 @@
+# coding: utf-8
+
+from __future__ import absolute_import
+
+import re
+
+try:
+    from .error import *                               # NOQA
+    from .nodes import *                               # NOQA
+    from .compat import string_types
+except (ImportError, ValueError):  # for Jython
+    from ruamel.yaml.error import *                               # NOQA
+    from ruamel.yaml.nodes import *                               # NOQA
+    from ruamel.yaml.compat import string_types
+
+__all__ = ['BaseResolver', 'Resolver', 'VersionedResolver']
+
+
+_DEFAULT_VERSION = (1, 2)
+
+
+class ResolverError(YAMLError):
+    pass
+
+
+class BaseResolver(object):
+
+    DEFAULT_SCALAR_TAG = u'tag:yaml.org,2002:str'
+    DEFAULT_SEQUENCE_TAG = u'tag:yaml.org,2002:seq'
+    DEFAULT_MAPPING_TAG = u'tag:yaml.org,2002:map'
+
+    yaml_implicit_resolvers = {}
+    yaml_path_resolvers = {}
+
+    def __init__(self):
+        self._loader_version = None
+        self.resolver_exact_paths = []
+        self.resolver_prefix_paths = []
+
+    @classmethod
+    def add_implicit_resolver(cls, tag, regexp, first):
+        if 'yaml_implicit_resolvers' not in cls.__dict__:
+            cls.yaml_implicit_resolvers = cls.yaml_implicit_resolvers.copy()
+        if first is None:
+            first = [None]
+        for ch in first:
+            cls.yaml_implicit_resolvers.setdefault(ch, []).append(
+                (tag, regexp))
+
+    @classmethod
+    def add_path_resolver(cls, tag, path, kind=None):
+        # Note: `add_path_resolver` is experimental.  The API could be changed.
+        # `new_path` is a pattern that is matched against the path from the
+        # root to the node that is being considered.  `node_path` elements are
+        # tuples `(node_check, index_check)`.  `node_check` is a node class:
+        # `ScalarNode`, `SequenceNode`, `MappingNode` or `None`.  `None`
+        # matches any kind of a node.  `index_check` could be `None`, a boolean
+        # value, a string value, or a number.  `None` and `False` match against
+        # any _value_ of sequence and mapping nodes.  `True` matches against
+        # any _key_ of a mapping node.  A string `index_check` matches against
+        # a mapping value that corresponds to a scalar key which content is
+        # equal to the `index_check` value.  An integer `index_check` matches
+        # against a sequence value with the index equal to `index_check`.
+        if 'yaml_path_resolvers' not in cls.__dict__:
+            cls.yaml_path_resolvers = cls.yaml_path_resolvers.copy()
+        new_path = []
+        for element in path:
+            if isinstance(element, (list, tuple)):
+                if len(element) == 2:
+                    node_check, index_check = element
+                elif len(element) == 1:
+                    node_check = element[0]
+                    index_check = True
+                else:
+                    raise ResolverError("Invalid path element: %s" % element)
+            else:
+                node_check = None
+                index_check = element
+            if node_check is str:
+                node_check = ScalarNode
+            elif node_check is list:
+                node_check = SequenceNode
+            elif node_check is dict:
+                node_check = MappingNode
+            elif node_check not in [ScalarNode, SequenceNode, MappingNode]  \
+                    and not isinstance(node_check, string_types)  \
+                    and node_check is not None:
+                raise ResolverError("Invalid node checker: %s" % node_check)
+            if not isinstance(index_check, (string_types, int))   \
+                    and index_check is not None:
+                raise ResolverError("Invalid index checker: %s" % index_check)
+            new_path.append((node_check, index_check))
+        if kind is str:
+            kind = ScalarNode
+        elif kind is list:
+            kind = SequenceNode
+        elif kind is dict:
+            kind = MappingNode
+        elif kind not in [ScalarNode, SequenceNode, MappingNode]    \
+                and kind is not None:
+            raise ResolverError("Invalid node kind: %s" % kind)
+        cls.yaml_path_resolvers[tuple(new_path), kind] = tag
+
+    def descend_resolver(self, current_node, current_index):
+        if not self.yaml_path_resolvers:
+            return
+        exact_paths = {}
+        prefix_paths = []
+        if current_node:
+            depth = len(self.resolver_prefix_paths)
+            for path, kind in self.resolver_prefix_paths[-1]:
+                if self.check_resolver_prefix(depth, path, kind,
+                                              current_node, current_index):
+                    if len(path) > depth:
+                        prefix_paths.append((path, kind))
+                    else:
+                        exact_paths[kind] = self.yaml_path_resolvers[path,
+                                                                     kind]
+        else:
+            for path, kind in self.yaml_path_resolvers:
+                if not path:
+                    exact_paths[kind] = self.yaml_path_resolvers[path, kind]
+                else:
+                    prefix_paths.append((path, kind))
+        self.resolver_exact_paths.append(exact_paths)
+        self.resolver_prefix_paths.append(prefix_paths)
+
+    def ascend_resolver(self):
+        if not self.yaml_path_resolvers:
+            return
+        self.resolver_exact_paths.pop()
+        self.resolver_prefix_paths.pop()
+
+    def check_resolver_prefix(self, depth, path, kind,
+                              current_node, current_index):
+        node_check, index_check = path[depth-1]
+        if isinstance(node_check, string_types):
+            if current_node.tag != node_check:
+                return
+        elif node_check is not None:
+            if not isinstance(current_node, node_check):
+                return
+        if index_check is True and current_index is not None:
+            return
+        if (index_check is False or index_check is None)    \
+                and current_index is None:
+            return
+        if isinstance(index_check, string_types):
+            if not (isinstance(current_index, ScalarNode) and
+                    index_check == current_index.value):
+                return
+        elif isinstance(index_check, int) and not isinstance(index_check,
+                                                             bool):
+            if index_check != current_index:
+                return
+        return True
+
+    def resolve(self, kind, value, implicit):
+        if kind is ScalarNode and implicit[0]:
+            if value == u'':
+                resolvers = self.yaml_implicit_resolvers.get(u'', [])
+            else:
+                resolvers = self.yaml_implicit_resolvers.get(value[0], [])
+            resolvers += self.yaml_implicit_resolvers.get(None, [])
+            for tag, regexp in resolvers:
+                if regexp.match(value):
+                    return tag
+            implicit = implicit[1]
+        if self.yaml_path_resolvers:
+            exact_paths = self.resolver_exact_paths[-1]
+            if kind in exact_paths:
+                return exact_paths[kind]
+            if None in exact_paths:
+                return exact_paths[None]
+        if kind is ScalarNode:
+            return self.DEFAULT_SCALAR_TAG
+        elif kind is SequenceNode:
+            return self.DEFAULT_SEQUENCE_TAG
+        elif kind is MappingNode:
+            return self.DEFAULT_MAPPING_TAG
+
+    @property
+    def processing_version(self):
+        return None
+
+
+class Resolver(BaseResolver):
+    pass
+
+Resolver.add_implicit_resolver(
+    u'tag:yaml.org,2002:bool',
+    re.compile(u'''^(?:yes|Yes|YES|no|No|NO
+    |true|True|TRUE|false|False|FALSE
+    |on|On|ON|off|Off|OFF)$''', re.X),
+    list(u'yYnNtTfFoO'))
+
+Resolver.add_implicit_resolver(
+    u'tag:yaml.org,2002:float',
+    re.compile(u'''^(?:
+     [-+]?(?:[0-9][0-9_]*)\\.[0-9_]*(?:[eE][-+]?[0-9]+)?
+    |[-+]?(?:[0-9][0-9_]*)(?:[eE][-+]?[0-9]+)
+    |\\.[0-9_]+(?:[eE][-+][0-9]+)?
+    |[-+]?[0-9][0-9_]*(?::[0-5]?[0-9])+\\.[0-9_]*
+    |[-+]?\\.(?:inf|Inf|INF)
+    |\\.(?:nan|NaN|NAN))$''', re.X),
+    list(u'-+0123456789.'))
+
+Resolver.add_implicit_resolver(
+    u'tag:yaml.org,2002:int',
+    re.compile(u'''^(?:[-+]?0b[0-1_]+
+    |[-+]?0o?[0-7_]+
+    |[-+]?(?:0|[1-9][0-9_]*)
+    |[-+]?0x[0-9a-fA-F_]+
+    |[-+]?[1-9][0-9_]*(?::[0-5]?[0-9])+)$''', re.X),
+    list(u'-+0123456789'))
+
+Resolver.add_implicit_resolver(
+    u'tag:yaml.org,2002:merge',
+    re.compile(u'^(?:<<)$'),
+    [u'<'])
+
+Resolver.add_implicit_resolver(
+    u'tag:yaml.org,2002:null',
+    re.compile(u'''^(?: ~
+    |null|Null|NULL
+    | )$''', re.X),
+    [u'~', u'n', u'N', u''])
+
+Resolver.add_implicit_resolver(
+    u'tag:yaml.org,2002:timestamp',
+    re.compile(u'''^(?:[0-9][0-9][0-9][0-9]-[0-9][0-9]-[0-9][0-9]
+    |[0-9][0-9][0-9][0-9] -[0-9][0-9]? -[0-9][0-9]?
+    (?:[Tt]|[ \\t]+)[0-9][0-9]?
+    :[0-9][0-9] :[0-9][0-9] (?:\\.[0-9]*)?
+    (?:[ \\t]*(?:Z|[-+][0-9][0-9]?(?::[0-9][0-9])?))?)$''', re.X),
+    list(u'0123456789'))
+
+Resolver.add_implicit_resolver(
+    u'tag:yaml.org,2002:value',
+    re.compile(u'^(?:=)$'),
+    [u'='])
+
+# The following resolver is only for documentation purposes. It cannot work
+# because plain scalars cannot start with '!', '&', or '*'.
+Resolver.add_implicit_resolver(
+    u'tag:yaml.org,2002:yaml',
+    re.compile(u'^(?:!|&|\\*)$'),
+    list(u'!&*'))
+
+# resolvers consist of
+# - a list of applicable version
+# - a tag
+# - a regexp
+# - a list of first characters to match
+implicit_resolvers = [
+    ([(1, 2)],
+        u'tag:yaml.org,2002:bool',
+        re.compile(u'''^(?:true|True|TRUE|false|False|FALSE)$''', re.X),
+        list(u'tTfF')),
+    ([(1, 1)],
+        u'tag:yaml.org,2002:bool',
+        re.compile(u'''^(?:yes|Yes|YES|no|No|NO
+        |true|True|TRUE|false|False|FALSE
+        |on|On|ON|off|Off|OFF)$''', re.X),
+        list(u'yYnNtTfFoO')),
+    ([(1, 2), (1, 1)],
+        u'tag:yaml.org,2002:float',
+        re.compile(u'''^(?:
+         [-+]?(?:[0-9][0-9_]*)\\.[0-9_]*(?:[eE][-+]?[0-9]+)?
+        |[-+]?(?:[0-9][0-9_]*)(?:[eE][-+]?[0-9]+)
+        |\\.[0-9_]+(?:[eE][-+][0-9]+)?
+        |[-+]?[0-9][0-9_]*(?::[0-5]?[0-9])+\\.[0-9_]*
+        |[-+]?\\.(?:inf|Inf|INF)
+        |\\.(?:nan|NaN|NAN))$''', re.X),
+        list(u'-+0123456789.')),
+    ([(1, 2)],
+        u'tag:yaml.org,2002:int',
+        re.compile(u'''^(?:[-+]?0b[0-1_]+
+        |[-+]?0o?[0-7_]+
+        |[-+]?(?:0|[1-9][0-9_]*)
+        |[-+]?0x[0-9a-fA-F_]+)$''', re.X),
+        list(u'-+0123456789')),
+    ([(1, 1)],
+        u'tag:yaml.org,2002:int',
+        re.compile(u'''^(?:[-+]?0b[0-1_]+
+        |[-+]?0o?[0-7_]+
+        |[-+]?(?:0|[1-9][0-9_]*)
+        |[-+]?0x[0-9a-fA-F_]+
+        |[-+]?[1-9][0-9_]*(?::[0-5]?[0-9])+)$''', re.X),
+        list(u'-+0123456789')),
+    ([(1, 2), (1, 1)],
+        u'tag:yaml.org,2002:merge',
+        re.compile(u'^(?:<<)$'),
+        [u'<']),
+    ([(1, 2), (1, 1)],
+        u'tag:yaml.org,2002:null',
+        re.compile(u'''^(?: ~
+        |null|Null|NULL
+        | )$''', re.X),
+        [u'~', u'n', u'N', u'']),
+    ([(1, 2), (1, 1)],
+        u'tag:yaml.org,2002:timestamp',
+        re.compile(u'''^(?:[0-9][0-9][0-9][0-9]-[0-9][0-9]-[0-9][0-9]
+        |[0-9][0-9][0-9][0-9] -[0-9][0-9]? -[0-9][0-9]?
+        (?:[Tt]|[ \\t]+)[0-9][0-9]?
+        :[0-9][0-9] :[0-9][0-9] (?:\\.[0-9]*)?
+        (?:[ \\t]*(?:Z|[-+][0-9][0-9]?(?::[0-9][0-9])?))?)$''', re.X),
+        list(u'0123456789')),
+    ([(1, 2), (1, 1)],
+        u'tag:yaml.org,2002:value',
+        re.compile(u'^(?:=)$'),
+        [u'=']),
+    # The following resolver is only for documentation purposes. It cannot work
+    # because plain scalars cannot start with '!', '&', or '*'.
+    ([(1, 2), (1, 1)],
+        u'tag:yaml.org,2002:yaml',
+        re.compile(u'^(?:!|&|\\*)$'),
+        list(u'!&*')),
+]
+
+
+class VersionedResolver(BaseResolver):
+    """
+    contrary to the "normal" resolver, the smart resolver delays loading
+    the pattern matching rules. That way it can decide to load 1.1 rules
+    or the (default) 1.2 that no longer support octal without 0o, sexagesimals
+    and Yes/No/On/Off booleans.
+    """
+
+    def __init__(self, version=None):
+        BaseResolver.__init__(self)
+        self._loader_version = self.get_loader_version(version)
+        self._version_implicit_resolver = {}
+
+    def add_version_implicit_resolver(self, version, tag, regexp, first):
+        if first is None:
+            first = [None]
+        impl_resolver = self._version_implicit_resolver.setdefault(version, {})
+        for ch in first:
+            impl_resolver.setdefault(ch, []).append((tag, regexp))
+
+    def get_loader_version(self, version):
+        if version is None or isinstance(version, tuple):
+            return version
+        if isinstance(version, list):
+            return tuple(version)
+        # assume string
+        return tuple(map(int, version.split(u'.')))
+
+    @property
+    def resolver(self):
+        """
+        select the resolver based on the version we are parsing
+        """
+        version = self.processing_version
+        if version not in self._version_implicit_resolver:
+            for x in implicit_resolvers:
+                if version in x[0]:
+                    self.add_version_implicit_resolver(version, x[1], x[2], x[3])
+        return self._version_implicit_resolver[version]
+
+    def resolve(self, kind, value, implicit):
+        if kind is ScalarNode and implicit[0]:
+            if value == u'':
+                resolvers = self.resolver.get(u'', [])
+            else:
+                resolvers = self.resolver.get(value[0], [])
+            resolvers += self.resolver.get(None, [])
+            for tag, regexp in resolvers:
+                if regexp.match(value):
+                    return tag
+            implicit = implicit[1]
+        if self.yaml_path_resolvers:
+            exact_paths = self.resolver_exact_paths[-1]
+            if kind in exact_paths:
+                return exact_paths[kind]
+            if None in exact_paths:
+                return exact_paths[None]
+        if kind is ScalarNode:
+            return self.DEFAULT_SCALAR_TAG
+        elif kind is SequenceNode:
+            return self.DEFAULT_SEQUENCE_TAG
+        elif kind is MappingNode:
+            return self.DEFAULT_MAPPING_TAG
+
+    @property
+    def processing_version(self):
+        try:
+            version = self.yaml_version
+        except AttributeError:
+            # dumping
+            version = self.use_version
+        if version is None:
+            version = self._loader_version
+            if version is None:
+                version = _DEFAULT_VERSION
+        return version
diff --git a/lib/spack/external/ruamel/yaml/scalarstring.py b/lib/spack/external/ruamel/yaml/scalarstring.py
new file mode 100644
index 0000000000..d3abaff4db
--- /dev/null
+++ b/lib/spack/external/ruamel/yaml/scalarstring.py
@@ -0,0 +1,60 @@
+# coding: utf-8
+
+from __future__ import absolute_import
+from __future__ import print_function
+
+__all__ = ["ScalarString", "PreservedScalarString", "SingleQuotedScalarString",
+           "DoubleQuotedScalarString"]
+
+try:
+    from .compat import text_type
+except (ImportError, ValueError):  # for Jython
+    from ruamel.yaml.compat import text_type
+
+
+class ScalarString(text_type):
+    def __new__(cls, *args, **kw):
+        return text_type.__new__(cls, *args, **kw)
+
+
+class PreservedScalarString(ScalarString):
+    def __new__(cls, value):
+        return ScalarString.__new__(cls, value)
+
+
+class SingleQuotedScalarString(ScalarString):
+    def __new__(cls, value):
+        return ScalarString.__new__(cls, value)
+
+
+class DoubleQuotedScalarString(ScalarString):
+    def __new__(cls, value):
+        return ScalarString.__new__(cls, value)
+
+
+def preserve_literal(s):
+    return PreservedScalarString(s.replace('\r\n', '\n').replace('\r', '\n'))
+
+
+def walk_tree(base):
+    """
+    the routine here walks over a simple yaml tree (recursing in
+    dict values and list items) and converts strings that
+    have multiple lines to literal scalars
+    """
+    from ruamel.yaml.compat import string_types
+
+    if isinstance(base, dict):
+        for k in base:
+            v = base[k]
+            if isinstance(v, string_types) and '\n' in v:
+                base[k] = preserve_literal(v)
+            else:
+                walk_tree(v)
+    elif isinstance(base, list):
+        for idx, elem in enumerate(base):
+            if isinstance(elem, string_types) and '\n' in elem:
+                print(elem)
+                base[idx] = preserve_literal(elem)
+            else:
+                walk_tree(elem)
diff --git a/lib/spack/external/yaml/lib/yaml/scanner.py b/lib/spack/external/ruamel/yaml/scanner.py
index 834f662a4c..61feb34043 100644
--- a/lib/spack/external/yaml/lib/yaml/scanner.py
+++ b/lib/spack/external/ruamel/yaml/scanner.py
@@ -1,3 +1,7 @@
+# coding: utf-8
+
+from __future__ import absolute_import
+from __future__ import print_function
 
 # Scanner produces tokens of the following types:
 # STREAM-START
@@ -21,17 +25,28 @@
 # TAG(value)
 # SCALAR(value, plain, style)
 #
+# RoundTripScanner
+# COMMENT(value)
+#
 # Read comments in the Scanner code for more details.
 #
 
-__all__ = ['Scanner', 'ScannerError']
+__all__ = ['Scanner', 'RoundTripScanner', 'ScannerError']
+
+try:
+    from .error import MarkedYAMLError
+    from .tokens import *                           # NOQA
+    from .compat import utf8, unichr, PY3
+except (ImportError, ValueError):  # for Jython
+    from ruamel.yaml.error import MarkedYAMLError
+    from ruamel.yaml.tokens import *                # NOQA
+    from ruamel.yaml.compat import utf8, unichr, PY3
 
-from error import MarkedYAMLError
-from tokens import *
 
 class ScannerError(MarkedYAMLError):
     pass
 
+
 class SimpleKey(object):
     # See below simple keys treatment.
 
@@ -43,6 +58,7 @@ class SimpleKey(object):
         self.column = column
         self.mark = mark
 
+
 class Scanner(object):
 
     def __init__(self):
@@ -52,9 +68,9 @@ class Scanner(object):
         # input data to Unicode. It also adds NUL to the end.
         #
         # Reader supports the following methods
-        #   self.peek(i=0)       # peek the next i-th character
-        #   self.prefix(l=1)     # peek the next l characters
-        #   self.forward(l=1)    # read the next l characters and move the pointer.
+        #   self.peek(i=0)    # peek the next i-th character
+        #   self.prefix(l=1)  # peek the next l characters
+        #   self.forward(l=1) # read the next l characters and move the pointer
 
         # Had we reached the end of the stream?
         self.done = False
@@ -153,7 +169,10 @@ class Scanner(object):
     def fetch_more_tokens(self):
 
         # Eat whitespaces and comments until we reach the next token.
-        self.scan_to_next_token()
+        comment = self.scan_to_next_token()
+
+        if comment is not None:  # never happens for base scanner
+            return self.fetch_comment(comment)
 
         # Remove obsolete possible simple keys.
         self.stale_possible_simple_keys()
@@ -182,8 +201,8 @@ class Scanner(object):
             return self.fetch_document_end()
 
         # TODO: support for BOM within a stream.
-        #if ch == u'\uFEFF':
-        #    return self.fetch_bom()    <-- issue BOMToken
+        # if ch == u'\uFEFF':
+        #     return self.fetch_bom()    <-- issue BOMToken
 
         # Note: the order of the following checks is NOT significant.
 
@@ -253,8 +272,8 @@ class Scanner(object):
 
         # No? It's an error. Let's produce a nice error message.
         raise ScannerError("while scanning for the next token", None,
-                "found character %r that cannot start any token"
-                % ch.encode('utf-8'), self.get_mark())
+                           "found character %r that cannot start any token"
+                           % utf8(ch), self.get_mark())
 
     # Simple keys treatment.
 
@@ -280,13 +299,14 @@ class Scanner(object):
         # - should be no longer than 1024 characters.
         # Disabling this procedure will allow simple keys of any length and
         # height (may cause problems if indentation is broken though).
-        for level in self.possible_simple_keys.keys():
+        for level in list(self.possible_simple_keys):
             key = self.possible_simple_keys[level]
             if key.line != self.line  \
                     or self.index-key.index > 1024:
                 if key.required:
-                    raise ScannerError("while scanning a simple key", key.mark,
-                            "could not find expected ':'", self.get_mark())
+                    raise ScannerError(
+                        "while scanning a simple key", key.mark,
+                        "could not find expected ':'", self.get_mark())
                 del self.possible_simple_keys[level]
 
     def save_possible_simple_key(self):
@@ -302,18 +322,20 @@ class Scanner(object):
         if self.allow_simple_key:
             self.remove_possible_simple_key()
             token_number = self.tokens_taken+len(self.tokens)
-            key = SimpleKey(token_number, required,
-                    self.index, self.line, self.column, self.get_mark())
+            key = SimpleKey(
+                token_number, required,
+                self.index, self.line, self.column, self.get_mark())
             self.possible_simple_keys[self.flow_level] = key
 
     def remove_possible_simple_key(self):
         # Remove the saved possible key position at the current flow level.
         if self.flow_level in self.possible_simple_keys:
             key = self.possible_simple_keys[self.flow_level]
-            
+
             if key.required:
-                raise ScannerError("while scanning a simple key", key.mark,
-                        "could not find expected ':'", self.get_mark())
+                raise ScannerError(
+                    "while scanning a simple key", key.mark,
+                    "could not find expected ':'", self.get_mark())
 
             del self.possible_simple_keys[self.flow_level]
 
@@ -321,16 +343,17 @@ class Scanner(object):
 
     def unwind_indent(self, column):
 
-        ## In flow context, tokens should respect indentation.
-        ## Actually the condition should be `self.indent >= column` according to
-        ## the spec. But this condition will prohibit intuitively correct
-        ## constructions such as
-        ## key : {
-        ## }
-        #if self.flow_level and self.indent > column:
-        #    raise ScannerError(None, None,
-        #            "invalid intendation or unclosed '[' or '{'",
-        #            self.get_mark())
+        # In flow context, tokens should respect indentation.
+        # Actually the condition should be `self.indent >= column` according to
+        # the spec. But this condition will prohibit intuitively correct
+        # constructions such as
+        # key : {
+        # }
+        # ####
+        # if self.flow_level and self.indent > column:
+        #     raise ScannerError(None, None,
+        #             "invalid intendation or unclosed '[' or '{'",
+        #             self.get_mark())
 
         # In the flow context, indentation is ignored. We make the scanner less
         # restrictive then specification requires.
@@ -359,11 +382,10 @@ class Scanner(object):
 
         # Read the token.
         mark = self.get_mark()
-        
+
         # Add STREAM-START.
         self.tokens.append(StreamStartToken(mark, mark,
-            encoding=self.encoding))
-        
+                                            encoding=self.encoding))
 
     def fetch_stream_end(self):
 
@@ -377,7 +399,7 @@ class Scanner(object):
 
         # Read the token.
         mark = self.get_mark()
-        
+
         # Add STREAM-END.
         self.tokens.append(StreamEndToken(mark, mark))
 
@@ -385,7 +407,7 @@ class Scanner(object):
         self.done = True
 
     def fetch_directive(self):
-        
+
         # Set the current intendation to -1.
         self.unwind_indent(-1)
 
@@ -486,8 +508,8 @@ class Scanner(object):
             # Are we allowed to start a new entry?
             if not self.allow_simple_key:
                 raise ScannerError(None, None,
-                        "sequence entries are not allowed here",
-                        self.get_mark())
+                                   "sequence entries are not allowed here",
+                                   self.get_mark())
 
             # We may need to add BLOCK-SEQUENCE-START.
             if self.add_indent(self.column):
@@ -512,15 +534,15 @@ class Scanner(object):
         self.tokens.append(BlockEntryToken(start_mark, end_mark))
 
     def fetch_key(self):
-        
+
         # Block context needs additional checks.
         if not self.flow_level:
 
             # Are we allowed to start a key (not nessesary a simple)?
             if not self.allow_simple_key:
                 raise ScannerError(None, None,
-                        "mapping keys are not allowed here",
-                        self.get_mark())
+                                   "mapping keys are not allowed here",
+                                   self.get_mark())
 
             # We may need to add BLOCK-MAPPING-START.
             if self.add_indent(self.column):
@@ -543,26 +565,26 @@ class Scanner(object):
 
         # Do we determine a simple key?
         if self.flow_level in self.possible_simple_keys:
-
             # Add KEY.
             key = self.possible_simple_keys[self.flow_level]
             del self.possible_simple_keys[self.flow_level]
             self.tokens.insert(key.token_number-self.tokens_taken,
-                    KeyToken(key.mark, key.mark))
+                               KeyToken(key.mark, key.mark))
 
             # If this key starts a new block mapping, we need to add
             # BLOCK-MAPPING-START.
             if not self.flow_level:
                 if self.add_indent(key.column):
-                    self.tokens.insert(key.token_number-self.tokens_taken,
-                            BlockMappingStartToken(key.mark, key.mark))
+                    self.tokens.insert(
+                        key.token_number-self.tokens_taken,
+                        BlockMappingStartToken(key.mark, key.mark))
 
             # There cannot be two simple keys one after another.
             self.allow_simple_key = False
 
         # It must be a part of a complex key.
         else:
-            
+
             # Block context needs additional checks.
             # (Do we really need them? They will be catched by the parser
             # anyway.)
@@ -572,8 +594,8 @@ class Scanner(object):
                 # we can start a simple key.
                 if not self.allow_simple_key:
                     raise ScannerError(None, None,
-                            "mapping values are not allowed here",
-                            self.get_mark())
+                                       "mapping values are not allowed here",
+                                       self.get_mark())
 
             # If this value starts a new block mapping, we need to add
             # BLOCK-MAPPING-START.  It will be detected as an error later by
@@ -726,7 +748,6 @@ class Scanner(object):
             return self.peek(1) in u'\0 \t\r\n\x85\u2028\u2029'
 
     def check_plain(self):
-
         # A plain scalar may start with any non-space character except:
         #   '-', '?', ':', ',', '[', ']', '{', '}',
         #   '#', '&', '*', '!', '|', '>', '\'', '\"',
@@ -740,9 +761,9 @@ class Scanner(object):
         # '-' character) because we want the flow context to be space
         # independent.
         ch = self.peek()
-        return ch not in u'\0 \t\r\n\x85\u2028\u2029-?:,[]{}#&*!|>\'\"%@`'  \
-                or (self.peek(1) not in u'\0 \t\r\n\x85\u2028\u2029'
-                        and (ch == u'-' or (not self.flow_level and ch in u'?:')))
+        return ch not in u'\0 \t\r\n\x85\u2028\u2029-?:,[]{}#&*!|>\'\"%@`' or \
+            (self.peek(1) not in u'\0 \t\r\n\x85\u2028\u2029' and
+             (ch == u'-' or (not self.flow_level and ch in u'?:')))
 
     # Scanners.
 
@@ -804,21 +825,23 @@ class Scanner(object):
         # See the specification for details.
         length = 0
         ch = self.peek(length)
-        while u'0' <= ch <= u'9' or u'A' <= ch <= u'Z' or u'a' <= ch <= u'z'    \
-                or ch in u'-_':
+        while u'0' <= ch <= u'9' or u'A' <= ch <= u'Z' or u'a' <= ch <= u'z' \
+                or ch in u'-_:.':
             length += 1
             ch = self.peek(length)
         if not length:
-            raise ScannerError("while scanning a directive", start_mark,
-                    "expected alphabetic or numeric character, but found %r"
-                    % ch.encode('utf-8'), self.get_mark())
+            raise ScannerError(
+                "while scanning a directive", start_mark,
+                "expected alphabetic or numeric character, but found %r"
+                % utf8(ch), self.get_mark())
         value = self.prefix(length)
         self.forward(length)
         ch = self.peek()
         if ch not in u'\0 \r\n\x85\u2028\u2029':
-            raise ScannerError("while scanning a directive", start_mark,
-                    "expected alphabetic or numeric character, but found %r"
-                    % ch.encode('utf-8'), self.get_mark())
+            raise ScannerError(
+                "while scanning a directive", start_mark,
+                "expected alphabetic or numeric character, but found %r"
+                % utf8(ch), self.get_mark())
         return value
 
     def scan_yaml_directive_value(self, start_mark):
@@ -827,26 +850,29 @@ class Scanner(object):
             self.forward()
         major = self.scan_yaml_directive_number(start_mark)
         if self.peek() != '.':
-            raise ScannerError("while scanning a directive", start_mark,
-                    "expected a digit or '.', but found %r"
-                    % self.peek().encode('utf-8'),
-                    self.get_mark())
+            raise ScannerError(
+                "while scanning a directive", start_mark,
+                "expected a digit or '.', but found %r"
+                % utf8(self.peek()),
+                self.get_mark())
         self.forward()
         minor = self.scan_yaml_directive_number(start_mark)
         if self.peek() not in u'\0 \r\n\x85\u2028\u2029':
-            raise ScannerError("while scanning a directive", start_mark,
-                    "expected a digit or ' ', but found %r"
-                    % self.peek().encode('utf-8'),
-                    self.get_mark())
+            raise ScannerError(
+                "while scanning a directive", start_mark,
+                "expected a digit or ' ', but found %r"
+                % utf8(self.peek()),
+                self.get_mark())
         return (major, minor)
 
     def scan_yaml_directive_number(self, start_mark):
         # See the specification for details.
         ch = self.peek()
         if not (u'0' <= ch <= u'9'):
-            raise ScannerError("while scanning a directive", start_mark,
-                    "expected a digit, but found %r" % ch.encode('utf-8'),
-                    self.get_mark())
+            raise ScannerError(
+                "while scanning a directive", start_mark,
+                "expected a digit, but found %r" % utf8(ch),
+                self.get_mark())
         length = 0
         while u'0' <= self.peek(length) <= u'9':
             length += 1
@@ -870,8 +896,8 @@ class Scanner(object):
         ch = self.peek()
         if ch != u' ':
             raise ScannerError("while scanning a directive", start_mark,
-                    "expected ' ', but found %r" % ch.encode('utf-8'),
-                    self.get_mark())
+                               "expected ' ', but found %r" % utf8(ch),
+                               self.get_mark())
         return value
 
     def scan_tag_directive_prefix(self, start_mark):
@@ -880,8 +906,8 @@ class Scanner(object):
         ch = self.peek()
         if ch not in u'\0 \r\n\x85\u2028\u2029':
             raise ScannerError("while scanning a directive", start_mark,
-                    "expected ' ', but found %r" % ch.encode('utf-8'),
-                    self.get_mark())
+                               "expected ' ', but found %r" % utf8(ch),
+                               self.get_mark())
         return value
 
     def scan_directive_ignored_line(self, start_mark):
@@ -893,9 +919,10 @@ class Scanner(object):
                 self.forward()
         ch = self.peek()
         if ch not in u'\0\r\n\x85\u2028\u2029':
-            raise ScannerError("while scanning a directive", start_mark,
-                    "expected a comment or a line break, but found %r"
-                        % ch.encode('utf-8'), self.get_mark())
+            raise ScannerError(
+                "while scanning a directive", start_mark,
+                "expected a comment or a line break, but found %r"
+                % utf8(ch), self.get_mark())
         self.scan_line_break()
 
     def scan_anchor(self, TokenClass):
@@ -916,21 +943,23 @@ class Scanner(object):
         self.forward()
         length = 0
         ch = self.peek(length)
-        while u'0' <= ch <= u'9' or u'A' <= ch <= u'Z' or u'a' <= ch <= u'z'    \
+        while u'0' <= ch <= u'9' or u'A' <= ch <= u'Z' or u'a' <= ch <= u'z' \
                 or ch in u'-_':
             length += 1
             ch = self.peek(length)
         if not length:
-            raise ScannerError("while scanning an %s" % name, start_mark,
-                    "expected alphabetic or numeric character, but found %r"
-                    % ch.encode('utf-8'), self.get_mark())
+            raise ScannerError(
+                "while scanning an %s" % name, start_mark,
+                "expected alphabetic or numeric character, but found %r"
+                % utf8(ch), self.get_mark())
         value = self.prefix(length)
         self.forward(length)
         ch = self.peek()
         if ch not in u'\0 \t\r\n\x85\u2028\u2029?:,]}%@`':
-            raise ScannerError("while scanning an %s" % name, start_mark,
-                    "expected alphabetic or numeric character, but found %r"
-                    % ch.encode('utf-8'), self.get_mark())
+            raise ScannerError(
+                "while scanning an %s" % name, start_mark,
+                "expected alphabetic or numeric character, but found %r"
+                % utf8(ch), self.get_mark())
         end_mark = self.get_mark()
         return TokenClass(value, start_mark, end_mark)
 
@@ -943,9 +972,10 @@ class Scanner(object):
             self.forward(2)
             suffix = self.scan_tag_uri('tag', start_mark)
             if self.peek() != u'>':
-                raise ScannerError("while parsing a tag", start_mark,
-                        "expected '>', but found %r" % self.peek().encode('utf-8'),
-                        self.get_mark())
+                raise ScannerError(
+                    "while parsing a tag", start_mark,
+                    "expected '>', but found %r" % utf8(self.peek()),
+                    self.get_mark())
             self.forward()
         elif ch in u'\0 \t\r\n\x85\u2028\u2029':
             handle = None
@@ -970,8 +1000,8 @@ class Scanner(object):
         ch = self.peek()
         if ch not in u'\0 \r\n\x85\u2028\u2029':
             raise ScannerError("while scanning a tag", start_mark,
-                    "expected ' ', but found %r" % ch.encode('utf-8'),
-                    self.get_mark())
+                               "expected ' ', but found %r" % utf8(ch),
+                               self.get_mark())
         value = (handle, suffix)
         end_mark = self.get_mark()
         return TagToken(value, start_mark, end_mark)
@@ -1020,37 +1050,49 @@ class Scanner(object):
                 # Unfortunately, folding rules are ambiguous.
                 #
                 # This is the folding according to the specification:
-                
+
                 if folded and line_break == u'\n'   \
                         and leading_non_space and self.peek() not in u' \t':
                     if not breaks:
                         chunks.append(u' ')
                 else:
                     chunks.append(line_break)
-                
+
                 # This is Clark Evans's interpretation (also in the spec
                 # examples):
                 #
-                #if folded and line_break == u'\n':
-                #    if not breaks:
-                #        if self.peek() not in ' \t':
-                #            chunks.append(u' ')
-                #        else:
-                #            chunks.append(line_break)
-                #else:
-                #    chunks.append(line_break)
+                # if folded and line_break == u'\n':
+                #     if not breaks:
+                #         if self.peek() not in ' \t':
+                #             chunks.append(u' ')
+                #         else:
+                #             chunks.append(line_break)
+                # else:
+                #     chunks.append(line_break)
             else:
                 break
 
-        # Chomp the tail.
-        if chomping is not False:
+        # Process trailing line breaks. The 'chomping' setting determines
+        # whether they are included in the value.
+        comment = []
+        if chomping in [None, True]:
             chunks.append(line_break)
         if chomping is True:
             chunks.extend(breaks)
+        elif chomping in [None, False]:
+            comment.extend(breaks)
 
         # We are done.
-        return ScalarToken(u''.join(chunks), False, start_mark, end_mark,
-                style)
+        token = ScalarToken(u''.join(chunks), False, start_mark, end_mark,
+                            style)
+        if len(comment) > 0:
+            # Keep track of the trailing whitespace as a comment token, if
+            # isn't all included in the actual value.
+            comment_end_mark = self.get_mark()
+            comment = CommentToken(''.join(comment), end_mark,
+                                   comment_end_mark)
+            token.add_post_comment(comment)
+        return token
 
     def scan_block_scalar_indicators(self, start_mark):
         # See the specification for details.
@@ -1067,16 +1109,19 @@ class Scanner(object):
             if ch in u'0123456789':
                 increment = int(ch)
                 if increment == 0:
-                    raise ScannerError("while scanning a block scalar", start_mark,
-                            "expected indentation indicator in the range 1-9, but found 0",
-                            self.get_mark())
+                    raise ScannerError(
+                        "while scanning a block scalar", start_mark,
+                        "expected indentation indicator in the range 1-9, "
+                        "but found 0", self.get_mark())
                 self.forward()
         elif ch in u'0123456789':
             increment = int(ch)
             if increment == 0:
-                raise ScannerError("while scanning a block scalar", start_mark,
-                        "expected indentation indicator in the range 1-9, but found 0",
-                        self.get_mark())
+                raise ScannerError(
+                    "while scanning a block scalar", start_mark,
+                    "expected indentation indicator in the range 1-9, "
+                    "but found 0",
+                    self.get_mark())
             self.forward()
             ch = self.peek()
             if ch in u'+-':
@@ -1087,9 +1132,10 @@ class Scanner(object):
                 self.forward()
         ch = self.peek()
         if ch not in u'\0 \r\n\x85\u2028\u2029':
-            raise ScannerError("while scanning a block scalar", start_mark,
-                    "expected chomping or indentation indicators, but found %r"
-                        % ch.encode('utf-8'), self.get_mark())
+            raise ScannerError(
+                "while scanning a block scalar", start_mark,
+                "expected chomping or indentation indicators, but found %r"
+                % utf8(ch), self.get_mark())
         return chomping, increment
 
     def scan_block_scalar_ignored_line(self, start_mark):
@@ -1101,9 +1147,10 @@ class Scanner(object):
                 self.forward()
         ch = self.peek()
         if ch not in u'\0\r\n\x85\u2028\u2029':
-            raise ScannerError("while scanning a block scalar", start_mark,
-                    "expected a comment or a line break, but found %r"
-                        % ch.encode('utf-8'), self.get_mark())
+            raise ScannerError(
+                "while scanning a block scalar", start_mark,
+                "expected a comment or a line break, but found %r"
+                % utf8(ch), self.get_mark())
         self.scan_line_break()
 
     def scan_block_scalar_indentation(self):
@@ -1156,7 +1203,7 @@ class Scanner(object):
         self.forward()
         end_mark = self.get_mark()
         return ScalarToken(u''.join(chunks), False, start_mark, end_mark,
-                style)
+                           style)
 
     ESCAPE_REPLACEMENTS = {
         u'0':   u'\0',
@@ -1171,6 +1218,7 @@ class Scanner(object):
         u'e':   u'\x1B',
         u' ':   u'\x20',
         u'\"':  u'\"',
+        u'/':   u'/',  # as per http://www.json.org/
         u'\\':  u'\\',
         u'N':   u'\x85',
         u'_':   u'\xA0',
@@ -1212,18 +1260,24 @@ class Scanner(object):
                     self.forward()
                     for k in range(length):
                         if self.peek(k) not in u'0123456789ABCDEFabcdef':
-                            raise ScannerError("while scanning a double-quoted scalar", start_mark,
-                                    "expected escape sequence of %d hexdecimal numbers, but found %r" %
-                                        (length, self.peek(k).encode('utf-8')), self.get_mark())
+                            raise ScannerError(
+                                "while scanning a double-quoted scalar",
+                                start_mark,
+                                "expected escape sequence of %d hexdecimal "
+                                "numbers, but found %r" %
+                                (length, utf8(self.peek(k))), self.get_mark())
                     code = int(self.prefix(length), 16)
                     chunks.append(unichr(code))
                     self.forward(length)
                 elif ch in u'\r\n\x85\u2028\u2029':
                     self.scan_line_break()
-                    chunks.extend(self.scan_flow_scalar_breaks(double, start_mark))
+                    chunks.extend(self.scan_flow_scalar_breaks(
+                        double, start_mark))
                 else:
-                    raise ScannerError("while scanning a double-quoted scalar", start_mark,
-                            "found unknown escape character %r" % ch.encode('utf-8'), self.get_mark())
+                    raise ScannerError(
+                        "while scanning a double-quoted scalar", start_mark,
+                        "found unknown escape character %r" % utf8(ch),
+                        self.get_mark())
             else:
                 return chunks
 
@@ -1237,8 +1291,9 @@ class Scanner(object):
         self.forward(length)
         ch = self.peek()
         if ch == u'\0':
-            raise ScannerError("while scanning a quoted scalar", start_mark,
-                    "found unexpected end of stream", self.get_mark())
+            raise ScannerError(
+                "while scanning a quoted scalar", start_mark,
+                "found unexpected end of stream", self.get_mark())
         elif ch in u'\r\n\x85\u2028\u2029':
             line_break = self.scan_line_break()
             breaks = self.scan_flow_scalar_breaks(double, start_mark)
@@ -1260,8 +1315,10 @@ class Scanner(object):
             prefix = self.prefix(3)
             if (prefix == u'---' or prefix == u'...')   \
                     and self.peek(3) in u'\0 \t\r\n\x85\u2028\u2029':
-                raise ScannerError("while scanning a quoted scalar", start_mark,
-                        "found unexpected document separator", self.get_mark())
+                raise ScannerError("while scanning a quoted scalar",
+                                   start_mark,
+                                   "found unexpected document separator",
+                                   self.get_mark())
             while self.peek() in u' \t':
                 self.forward()
             if self.peek() in u'\r\n\x85\u2028\u2029':
@@ -1281,8 +1338,8 @@ class Scanner(object):
         indent = self.indent+1
         # We allow zero indentation for scalars, but then we need to check for
         # document separators at the beginning of the line.
-        #if indent == 0:
-        #    indent = 1
+        # if indent == 0:
+        #     indent = 1
         spaces = []
         while True:
             length = 0
@@ -1290,19 +1347,22 @@ class Scanner(object):
                 break
             while True:
                 ch = self.peek(length)
-                if ch in u'\0 \t\r\n\x85\u2028\u2029'   \
-                        or (not self.flow_level and ch == u':' and
-                                self.peek(length+1) in u'\0 \t\r\n\x85\u2028\u2029') \
-                        or (self.flow_level and ch in u',:?[]{}'):
+                if ch in u'\0 \t\r\n\x85\u2028\u2029' \
+                   or (not self.flow_level and ch == u':' and
+                       self.peek(length+1) in u'\0 \t\r\n\x85\u2028\u2029') \
+                   or (self.flow_level and ch in u',:?[]{}'):
                     break
                 length += 1
             # It's not clear what we should do with ':' in the flow context.
-            if (self.flow_level and ch == u':'
-                    and self.peek(length+1) not in u'\0 \t\r\n\x85\u2028\u2029,[]{}'):
+            if (self.flow_level and ch == u':' and
+               self.peek(length+1) not in u'\0 \t\r\n\x85\u2028\u2029,[]{}'):
                 self.forward(length)
-                raise ScannerError("while scanning a plain scalar", start_mark,
+                raise ScannerError(
+                    "while scanning a plain scalar", start_mark,
                     "found unexpected ':'", self.get_mark(),
-                    "Please check http://pyyaml.org/wiki/YAMLColonInFlowContext for details.")
+                    "Please check "
+                    "http://pyyaml.org/wiki/YAMLColonInFlowContext "
+                    "for details.")
             if length == 0:
                 break
             self.allow_simple_key = False
@@ -1314,7 +1374,13 @@ class Scanner(object):
             if not spaces or self.peek() == u'#' \
                     or (not self.flow_level and self.column < indent):
                 break
-        return ScalarToken(u''.join(chunks), True, start_mark, end_mark)
+
+        token = ScalarToken(u''.join(chunks), True, start_mark, end_mark)
+        if spaces and spaces[0] == '\n':
+            # Create a comment token to preserve the trailing line breaks.
+            comment = CommentToken(''.join(spaces) + '\n', start_mark, end_mark)
+            token.add_post_comment(comment)
+        return token
 
     def scan_plain_spaces(self, indent, start_mark):
         # See the specification for details.
@@ -1342,7 +1408,7 @@ class Scanner(object):
                     breaks.append(self.scan_line_break())
                     prefix = self.prefix(3)
                     if (prefix == u'---' or prefix == u'...')   \
-                            and self.peek(3) in u'\0 \t\r\n\x85\u2028\u2029':
+                       and self.peek(3) in u'\0 \t\r\n\x85\u2028\u2029':
                         return
             if line_break != u'\n':
                 chunks.append(line_break)
@@ -1360,20 +1426,21 @@ class Scanner(object):
         ch = self.peek()
         if ch != u'!':
             raise ScannerError("while scanning a %s" % name, start_mark,
-                    "expected '!', but found %r" % ch.encode('utf-8'),
-                    self.get_mark())
+                               "expected '!', but found %r" % utf8(ch),
+                               self.get_mark())
         length = 1
         ch = self.peek(length)
         if ch != u' ':
-            while u'0' <= ch <= u'9' or u'A' <= ch <= u'Z' or u'a' <= ch <= u'z'    \
-                    or ch in u'-_':
+            while u'0' <= ch <= u'9' or u'A' <= ch <= u'Z' \
+                  or u'a' <= ch <= u'z' \
+                  or ch in u'-_':
                 length += 1
                 ch = self.peek(length)
             if ch != u'!':
                 self.forward(length)
                 raise ScannerError("while scanning a %s" % name, start_mark,
-                        "expected '!', but found %r" % ch.encode('utf-8'),
-                        self.get_mark())
+                                   "expected '!', but found %r" % utf8(ch),
+                                   self.get_mark())
             length += 1
         value = self.prefix(length)
         self.forward(length)
@@ -1401,27 +1468,36 @@ class Scanner(object):
             length = 0
         if not chunks:
             raise ScannerError("while parsing a %s" % name, start_mark,
-                    "expected URI, but found %r" % ch.encode('utf-8'),
-                    self.get_mark())
+                               "expected URI, but found %r" % utf8(ch),
+                               self.get_mark())
         return u''.join(chunks)
 
     def scan_uri_escapes(self, name, start_mark):
         # See the specification for details.
-        bytes = []
+        code_bytes = []
         mark = self.get_mark()
         while self.peek() == u'%':
             self.forward()
             for k in range(2):
                 if self.peek(k) not in u'0123456789ABCDEFabcdef':
-                    raise ScannerError("while scanning a %s" % name, start_mark,
-                            "expected URI escape sequence of 2 hexdecimal numbers, but found %r" %
-                                (self.peek(k).encode('utf-8')), self.get_mark())
-            bytes.append(chr(int(self.prefix(2), 16)))
+                    raise ScannerError(
+                        "while scanning a %s" % name, start_mark,
+                        "expected URI escape sequence of 2 hexdecimal numbers,"
+                        " but found %r"
+                        % utf8(self.peek(k)), self.get_mark())
+            if PY3:
+                code_bytes.append(int(self.prefix(2), 16))
+            else:
+                code_bytes.append(chr(int(self.prefix(2), 16)))
             self.forward(2)
         try:
-            value = unicode(''.join(bytes), 'utf-8')
-        except UnicodeDecodeError, exc:
-            raise ScannerError("while scanning a %s" % name, start_mark, str(exc), mark)
+            if PY3:
+                value = bytes(code_bytes).decode('utf-8')
+            else:
+                value = unicode(''.join(code_bytes), 'utf-8')
+        except UnicodeDecodeError as exc:
+            raise ScannerError("while scanning a %s" % name, start_mark,
+                               str(exc), mark)
         return value
 
     def scan_line_break(self):
@@ -1445,9 +1521,141 @@ class Scanner(object):
             return ch
         return u''
 
-#try:
-#    import psyco
-#    psyco.bind(Scanner)
-#except ImportError:
-#    pass
 
+class RoundTripScanner(Scanner):
+    def check_token(self, *choices):
+        # Check if the next token is one of the given types.
+        while self.need_more_tokens():
+            self.fetch_more_tokens()
+        self._gather_comments()
+        if self.tokens:
+            if not choices:
+                return True
+            for choice in choices:
+                if isinstance(self.tokens[0], choice):
+                    return True
+        return False
+
+    def peek_token(self):
+        # Return the next token, but do not delete if from the queue.
+        while self.need_more_tokens():
+            self.fetch_more_tokens()
+        self._gather_comments()
+        if self.tokens:
+            return self.tokens[0]
+
+    def _gather_comments(self):
+        """combine multiple comment lines"""
+        comments = []
+        if not self.tokens:
+            return comments
+        if isinstance(self.tokens[0], CommentToken):
+            comment = self.tokens.pop(0)
+            self.tokens_taken += 1
+            # print('################ dropping', comment)
+            comments.append(comment)
+        while self.need_more_tokens():
+            self.fetch_more_tokens()
+            if not self.tokens:
+                return comments
+            if isinstance(self.tokens[0], CommentToken):
+                self.tokens_taken += 1
+                comment = self.tokens.pop(0)
+                # print 'dropping2', comment
+                comments.append(comment)
+        if len(comments) >= 1:
+            # print('  len', len(comments), comments)
+            # print('  com', comments[0], comments[0].start_mark.line)
+            # print('  tok', self.tokens[0].end_mark.line)
+            self.tokens[0].add_pre_comments(comments)
+        # pull in post comment on e.g. ':'
+        if not self.done and len(self.tokens) < 2:
+            self.fetch_more_tokens()
+
+    def get_token(self):
+        # Return the next token.
+        while self.need_more_tokens():
+            self.fetch_more_tokens()
+        self._gather_comments()
+        if self.tokens:
+            # only add post comment to single line tokens:
+            # scalar, value token. FlowXEndToken, otherwise
+            # hidden streamtokens could get them (leave them and they will be
+            # pre comments for the next map/seq
+            if len(self.tokens) > 1 and \
+               isinstance(self.tokens[0], (
+                   ScalarToken,
+                   ValueToken,
+                   FlowSequenceEndToken,
+                   FlowMappingEndToken,
+                   )) and \
+               isinstance(self.tokens[1], CommentToken) and \
+               self.tokens[0].end_mark.line == self.tokens[1].start_mark.line:
+                self.tokens_taken += 1
+                self.tokens[0].add_post_comment(self.tokens.pop(1))
+            self.tokens_taken += 1
+            return self.tokens.pop(0)
+
+    def fetch_comment(self, comment):  # XXXX
+        value, start_mark, end_mark = comment
+        self.tokens.append(CommentToken(value, start_mark, end_mark))
+
+    # scanner
+
+    def scan_to_next_token(self):
+        # We ignore spaces, line breaks and comments.
+        # If we find a line break in the block context, we set the flag
+        # `allow_simple_key` on.
+        # The byte order mark is stripped if it's the first character in the
+        # stream. We do not yet support BOM inside the stream as the
+        # specification requires. Any such mark will be considered as a part
+        # of the document.
+        #
+        # TODO: We need to make tab handling rules more sane. A good rule is
+        #   Tabs cannot precede tokens
+        #   BLOCK-SEQUENCE-START, BLOCK-MAPPING-START, BLOCK-END,
+        #   KEY(block), VALUE(block), BLOCK-ENTRY
+        # So the checking code is
+        #   if <TAB>:
+        #       self.allow_simple_keys = False
+        # We also need to add the check for `allow_simple_keys == True` to
+        # `unwind_indent` before issuing BLOCK-END.
+        # Scanners for block, flow, and plain scalars need to be modified.
+
+        if self.index == 0 and self.peek() == u'\uFEFF':
+            self.forward()
+        found = False
+        while not found:
+            while self.peek() == u' ':
+                self.forward()
+            ch = self.peek()
+            if ch == u'#':
+                start_mark = self.get_mark()
+                comment = ch
+                self.forward()
+                while ch not in u'\0\r\n\x85\u2028\u2029':
+                    ch = self.peek()
+                    if ch == u'\0':  # don't gobble the end-of-stream character
+                        break
+                    comment += ch
+                    self.forward()
+                # gather any blank lines following the comment too
+                ch = self.scan_line_break()
+                while len(ch) > 0:
+                    comment += ch
+                    ch = self.scan_line_break()
+                end_mark = self.get_mark()
+                if not self.flow_level:
+                    self.allow_simple_key = True
+                return comment, start_mark, end_mark
+            if self.scan_line_break():
+                if not self.flow_level:
+                    self.allow_simple_key = True
+            else:
+                found = True
+
+# try:
+#     import psyco
+#     psyco.bind(Scanner)
+# except ImportError:
+#     pass
diff --git a/lib/spack/external/ruamel/yaml/serializer.py b/lib/spack/external/ruamel/yaml/serializer.py
new file mode 100644
index 0000000000..60dd5170ca
--- /dev/null
+++ b/lib/spack/external/ruamel/yaml/serializer.py
@@ -0,0 +1,178 @@
+# coding: utf-8
+
+from __future__ import absolute_import
+
+import re
+
+try:
+    from .error import YAMLError
+    from .compat import nprint, DBG_NODE, dbg, string_types
+except (ImportError, ValueError):  # for Jython
+    from ruamel.yaml.error import YAMLError
+    from ruamel.yaml.compat import nprint, DBG_NODE, dbg, string_types
+
+from ruamel.yaml.events import (
+    StreamStartEvent, StreamEndEvent, MappingStartEvent, MappingEndEvent,
+    SequenceStartEvent, SequenceEndEvent, AliasEvent, ScalarEvent,
+    DocumentStartEvent, DocumentEndEvent,
+)
+from ruamel.yaml.nodes import (
+    MappingNode, ScalarNode, SequenceNode,
+)
+
+__all__ = ['Serializer', 'SerializerError']
+
+
+class SerializerError(YAMLError):
+    pass
+
+
+class Serializer(object):
+
+    # 'id' and 3+ numbers, but not 000
+    ANCHOR_TEMPLATE = u'id%03d'
+    ANCHOR_RE = re.compile(u'id(?!000$)\\d{3,}')
+
+    def __init__(self, encoding=None, explicit_start=None, explicit_end=None,
+                 version=None, tags=None):
+        self.use_encoding = encoding
+        self.use_explicit_start = explicit_start
+        self.use_explicit_end = explicit_end
+        if isinstance(version, string_types):
+            self.use_version = tuple(map(int, version.split('.')))
+        else:
+            self.use_version = version
+        self.use_tags = tags
+        self.serialized_nodes = {}
+        self.anchors = {}
+        self.last_anchor_id = 0
+        self.closed = None
+        self._templated_id = None
+
+    def open(self):
+        if self.closed is None:
+            self.emit(StreamStartEvent(encoding=self.use_encoding))
+            self.closed = False
+        elif self.closed:
+            raise SerializerError("serializer is closed")
+        else:
+            raise SerializerError("serializer is already opened")
+
+    def close(self):
+        if self.closed is None:
+            raise SerializerError("serializer is not opened")
+        elif not self.closed:
+            self.emit(StreamEndEvent())
+            self.closed = True
+
+    # def __del__(self):
+    #     self.close()
+
+    def serialize(self, node):
+        if dbg(DBG_NODE):
+            nprint('Serializing nodes')
+            node.dump()
+        if self.closed is None:
+            raise SerializerError("serializer is not opened")
+        elif self.closed:
+            raise SerializerError("serializer is closed")
+        self.emit(DocumentStartEvent(explicit=self.use_explicit_start,
+                                     version=self.use_version,
+                                     tags=self.use_tags))
+        self.anchor_node(node)
+        self.serialize_node(node, None, None)
+        self.emit(DocumentEndEvent(explicit=self.use_explicit_end))
+        self.serialized_nodes = {}
+        self.anchors = {}
+        self.last_anchor_id = 0
+
+    def anchor_node(self, node):
+        if node in self.anchors:
+            if self.anchors[node] is None:
+                self.anchors[node] = self.generate_anchor(node)
+        else:
+            anchor = None
+            try:
+                if node.anchor.always_dump:
+                    anchor = node.anchor.value
+            except:
+                pass
+            self.anchors[node] = anchor
+            if isinstance(node, SequenceNode):
+                for item in node.value:
+                    self.anchor_node(item)
+            elif isinstance(node, MappingNode):
+                for key, value in node.value:
+                    self.anchor_node(key)
+                    self.anchor_node(value)
+
+    def generate_anchor(self, node):
+        try:
+            anchor = node.anchor.value
+        except:
+            anchor = None
+        if anchor is None:
+            self.last_anchor_id += 1
+            return self.ANCHOR_TEMPLATE % self.last_anchor_id
+        return anchor
+
+    def serialize_node(self, node, parent, index):
+        alias = self.anchors[node]
+        if node in self.serialized_nodes:
+            self.emit(AliasEvent(alias))
+        else:
+            self.serialized_nodes[node] = True
+            self.descend_resolver(parent, index)
+            if isinstance(node, ScalarNode):
+                # here check if the node.tag equals the one that would result from parsing
+                # if not equal quoting is necessary for strings
+                detected_tag = self.resolve(ScalarNode, node.value, (True, False))
+                default_tag = self.resolve(ScalarNode, node.value, (False, True))
+                implicit = (node.tag == detected_tag), (node.tag == default_tag)
+                self.emit(ScalarEvent(alias, node.tag, implicit, node.value,
+                                      style=node.style, comment=node.comment))
+            elif isinstance(node, SequenceNode):
+                implicit = (node.tag == self.resolve(SequenceNode, node.value, True))
+                comment = node.comment
+                # print('comment >>>>>>>>>>>>>.', comment, node.flow_style)
+                end_comment = None
+                seq_comment = None
+                if node.flow_style is True:
+                    if comment:  # eol comment on flow style sequence
+                        seq_comment = comment[0]
+                        # comment[0] = None
+                if comment and len(comment) > 2:
+                    end_comment = comment[2]
+                else:
+                    end_comment = None
+                self.emit(SequenceStartEvent(alias, node.tag, implicit,
+                                             flow_style=node.flow_style,
+                                             comment=node.comment))
+                index = 0
+                for item in node.value:
+                    self.serialize_node(item, node, index)
+                    index += 1
+                self.emit(SequenceEndEvent(comment=[seq_comment, end_comment]))
+            elif isinstance(node, MappingNode):
+                implicit = (node.tag == self.resolve(MappingNode, node.value, True))
+                comment = node.comment
+                end_comment = None
+                map_comment = None
+                if node.flow_style is True:
+                    if comment:  # eol comment on flow style sequence
+                        map_comment = comment[0]
+                        # comment[0] = None
+                if comment and len(comment) > 2:
+                    end_comment = comment[2]
+                self.emit(MappingStartEvent(alias, node.tag, implicit,
+                                            flow_style=node.flow_style,
+                                            comment=node.comment))
+                for key, value in node.value:
+                    self.serialize_node(key, node, None)
+                    self.serialize_node(value, node, key)
+                self.emit(MappingEndEvent(comment=[map_comment, end_comment]))
+            self.ascend_resolver()
+
+
+def templated_id(s):
+    return Serializer.ANCHOR_RE.match(s)
diff --git a/lib/spack/external/ruamel/yaml/setup.cfg b/lib/spack/external/ruamel/yaml/setup.cfg
new file mode 100644
index 0000000000..861a9f5542
--- /dev/null
+++ b/lib/spack/external/ruamel/yaml/setup.cfg
@@ -0,0 +1,5 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+tag_svn_revision = 0
+
diff --git a/lib/spack/external/ruamel/yaml/tokens.py b/lib/spack/external/ruamel/yaml/tokens.py
new file mode 100644
index 0000000000..bd97785b82
--- /dev/null
+++ b/lib/spack/external/ruamel/yaml/tokens.py
@@ -0,0 +1,195 @@
+# # header
+# coding: utf-8
+
+
+class Token(object):
+    def __init__(self, start_mark, end_mark):
+        self.start_mark = start_mark
+        self.end_mark = end_mark
+
+    def __repr__(self):
+        attributes = [key for key in self.__dict__
+                      if not key.endswith('_mark')]
+        attributes.sort()
+        arguments = ', '.join(['%s=%r' % (key, getattr(self, key))
+                               for key in attributes])
+        return '%s(%s)' % (self.__class__.__name__, arguments)
+
+    def add_post_comment(self, comment):
+        if not hasattr(self, '_comment'):
+            self._comment = [None, None]
+        self._comment[0] = comment
+
+    def add_pre_comments(self, comments):
+        if not hasattr(self, '_comment'):
+            self._comment = [None, None]
+        assert self._comment[1] is None
+        self._comment[1] = comments
+
+    def get_comment(self):
+        return getattr(self, '_comment', None)
+
+    @property
+    def comment(self):
+        return getattr(self, '_comment', None)
+
+    def move_comment(self, target):
+        """move a comment from this token to target (normally next token)
+        used to combine e.g. comments before a BlockEntryToken to the
+        ScalarToken that follows it
+        """
+        c = self.comment
+        if c is None:
+            return
+        # don't push beyond last element
+        if isinstance(target, StreamEndToken):
+            return
+        delattr(self, '_comment')
+        tc = target.comment
+        if not tc:  # target comment, just insert
+            target._comment = c
+            return self
+        if c[0] and tc[0] or c[1] and tc[1]:
+            raise NotImplementedError('overlap in comment %r %r' % c, tc)
+        if c[0]:
+            tc[0] = c[0]
+        if c[1]:
+            tc[1] = c[1]
+        return self
+
+    def split_comment(self):
+        """ split the post part of a comment, and return it
+        as comment to be added. Delete second part if [None, None]
+         abc:  # this goes to sequence
+           # this goes to first element
+           - first element
+        """
+        comment = self.comment
+        if comment is None or comment[0] is None:
+            return None  # nothing to do
+        ret_val = [comment[0], None]
+        if comment[1] is None:
+            delattr(self, '_comment')
+        return ret_val
+
+
+# class BOMToken(Token):
+#     id = '<byte order mark>'
+
+class DirectiveToken(Token):
+    id = '<directive>'
+
+    def __init__(self, name, value, start_mark, end_mark):
+        Token.__init__(self, start_mark, end_mark)
+        self.name = name
+        self.value = value
+
+
+class DocumentStartToken(Token):
+    id = '<document start>'
+
+
+class DocumentEndToken(Token):
+    id = '<document end>'
+
+
+class StreamStartToken(Token):
+    id = '<stream start>'
+
+    def __init__(self, start_mark=None, end_mark=None, encoding=None):
+        Token.__init__(self, start_mark, end_mark)
+        self.encoding = encoding
+
+
+class StreamEndToken(Token):
+    id = '<stream end>'
+
+
+class BlockSequenceStartToken(Token):
+    id = '<block sequence start>'
+
+
+class BlockMappingStartToken(Token):
+    id = '<block mapping start>'
+
+
+class BlockEndToken(Token):
+    id = '<block end>'
+
+
+class FlowSequenceStartToken(Token):
+    id = '['
+
+
+class FlowMappingStartToken(Token):
+    id = '{'
+
+
+class FlowSequenceEndToken(Token):
+    id = ']'
+
+
+class FlowMappingEndToken(Token):
+    id = '}'
+
+
+class KeyToken(Token):
+    id = '?'
+
+
+class ValueToken(Token):
+    id = ':'
+
+
+class BlockEntryToken(Token):
+    id = '-'
+
+
+class FlowEntryToken(Token):
+    id = ','
+
+
+class AliasToken(Token):
+    id = '<alias>'
+
+    def __init__(self, value, start_mark, end_mark):
+        Token.__init__(self, start_mark, end_mark)
+        self.value = value
+
+
+class AnchorToken(Token):
+    id = '<anchor>'
+
+    def __init__(self, value, start_mark, end_mark):
+        Token.__init__(self, start_mark, end_mark)
+        self.value = value
+
+
+class TagToken(Token):
+    id = '<tag>'
+
+    def __init__(self, value, start_mark, end_mark):
+        Token.__init__(self, start_mark, end_mark)
+        self.value = value
+
+
+class ScalarToken(Token):
+    id = '<scalar>'
+
+    def __init__(self, value, plain, start_mark, end_mark, style=None):
+        Token.__init__(self, start_mark, end_mark)
+        self.value = value
+        self.plain = plain
+        self.style = style
+
+
+class CommentToken(Token):
+    id = '<comment>'
+
+    def __init__(self, value, start_mark, end_mark):
+        Token.__init__(self, start_mark, end_mark)
+        self.value = value
+
+    def reset(self):
+        if hasattr(self, 'pre_done'):
+            delattr(self, 'pre_done')
diff --git a/lib/spack/external/ruamel/yaml/util.py b/lib/spack/external/ruamel/yaml/util.py
new file mode 100644
index 0000000000..afc46fb12a
--- /dev/null
+++ b/lib/spack/external/ruamel/yaml/util.py
@@ -0,0 +1,139 @@
+# coding: utf-8
+
+"""
+some helper functions that might be generally useful
+"""
+
+from __future__ import print_function
+from __future__ import absolute_import
+
+from .compat import text_type, binary_type
+from .main import round_trip_load
+
+
+# originally as comment
+# https://github.com/pre-commit/pre-commit/pull/211#issuecomment-186466605
+# if you use this in your code, I suggest adding a test in your test suite
+# that check this routines output against a known piece of your YAML
+# before upgrades to this code break your round-tripped YAML
+def load_yaml_guess_indent(stream, **kw):
+    """guess the indent and block sequence indent of yaml stream/string
+
+    returns round_trip_loaded stream, indent level, block sequence indent
+    - block sequence indent is the number of spaces before a dash relative to previous indent
+    - if there are no block sequences, indent is taken from nested mappings, block sequence
+      indent is unset (None) in that case
+    """
+    # load a yaml file guess the indentation, if you use TABs ...
+    def leading_spaces(l):
+        idx = 0
+        while idx < len(l) and l[idx] == ' ':
+            idx += 1
+        return idx
+
+    if isinstance(stream, text_type):
+        yaml_str = stream
+    elif isinstance(stream, binary_type):
+        yaml_str = stream.decode('utf-8')  # most likely, but the Reader checks BOM for this
+    else:
+        yaml_str = stream.read()
+    map_indent = None
+    indent = None  # default if not found for some reason
+    block_seq_indent = None
+    prev_line_key_only = None
+    key_indent = 0
+    for line in yaml_str.splitlines():
+        rline = line.rstrip()
+        lline = rline.lstrip()
+        if lline.startswith('- '):
+            l_s = leading_spaces(line)
+            block_seq_indent = l_s - key_indent
+            idx = l_s + 1
+            while line[idx] == ' ':  # this will end as we rstripped
+                idx += 1
+            if line[idx] == '#':     # comment after -
+                continue
+            indent = idx - key_indent
+            break
+        if map_indent is None and prev_line_key_only is not None and rline:
+            idx = 0
+            while line[idx] in ' -':
+                idx += 1
+            if idx > prev_line_key_only:
+                map_indent = idx - prev_line_key_only
+        if rline.endswith(':'):
+            key_indent = leading_spaces(line)
+            idx = 0
+            while line[idx] == ' ':  # this will end on ':'
+                idx += 1
+            prev_line_key_only = idx
+            continue
+        prev_line_key_only = None
+    if indent is None and map_indent is not None:
+        indent = map_indent
+    return round_trip_load(yaml_str, **kw), indent, block_seq_indent
+
+
+def configobj_walker(cfg):
+    """
+    walks over a ConfigObj (INI file with comments) generating
+    corresponding YAML output (including comments
+    """
+    from configobj import ConfigObj
+    assert isinstance(cfg, ConfigObj)
+    for c in cfg.initial_comment:
+        if c.strip():
+            yield c
+    for s in _walk_section(cfg):
+        if s.strip():
+            yield s
+    for c in cfg.final_comment:
+        if c.strip():
+            yield c
+
+
+def _walk_section(s, level=0):
+    from configobj import Section
+    assert isinstance(s, Section)
+    indent = u'  ' * level
+    for name in s.scalars:
+        for c in s.comments[name]:
+            yield indent + c.strip()
+        x = s[name]
+        if u'\n' in x:
+            i = indent + u'  '
+            x = u'|\n' + i + x.strip().replace(u'\n', u'\n' + i)
+        elif ':' in x:
+            x = u"'" + x.replace(u"'", u"''") + u"'"
+        line = u'{0}{1}: {2}'.format(indent, name, x)
+        c = s.inline_comments[name]
+        if c:
+            line += u' ' + c
+        yield line
+    for name in s.sections:
+        for c in s.comments[name]:
+            yield indent + c.strip()
+        line = u'{0}{1}:'.format(indent, name)
+        c = s.inline_comments[name]
+        if c:
+            line += u' ' + c
+        yield line
+        for val in _walk_section(s[name], level=level+1):
+            yield val
+
+# def config_obj_2_rt_yaml(cfg):
+#     from .comments import CommentedMap, CommentedSeq
+#     from configobj import ConfigObj
+#     assert isinstance(cfg, ConfigObj)
+#     #for c in cfg.initial_comment:
+#     #    if c.strip():
+#     #        pass
+#     cm = CommentedMap()
+#     for name in s.sections:
+#         cm[name] = d = CommentedMap()
+#
+#
+#     #for c in cfg.final_comment:
+#     #    if c.strip():
+#     #        yield c
+#     return cm
diff --git a/lib/spack/external/six.py b/lib/spack/external/six.py
index 5293325821..6bf4fd3810 100644
--- a/lib/spack/external/six.py
+++ b/lib/spack/external/six.py
@@ -29,7 +29,7 @@ import sys
 import types
 
 __author__ = "Benjamin Peterson <benjamin@python.org>"
-__version__ = "1.10.0"
+__version__ = "1.11.0"
 
 
 # Useful for very coarse version differentiation.
@@ -241,7 +241,6 @@ _moved_attributes = [
     MovedAttribute("map", "itertools", "builtins", "imap", "map"),
     MovedAttribute("getcwd", "os", "os", "getcwdu", "getcwd"),
     MovedAttribute("getcwdb", "os", "os", "getcwd", "getcwdb"),
-    MovedAttribute("getstatusoutput", "commands", "subprocess"),
     MovedAttribute("getoutput", "commands", "subprocess"),
     MovedAttribute("range", "__builtin__", "builtins", "xrange", "range"),
     MovedAttribute("reload_module", "__builtin__", "importlib" if PY34 else "imp", "reload"),
@@ -421,6 +420,8 @@ _urllib_request_moved_attributes = [
     MovedAttribute("URLopener", "urllib", "urllib.request"),
     MovedAttribute("FancyURLopener", "urllib", "urllib.request"),
     MovedAttribute("proxy_bypass", "urllib", "urllib.request"),
+    MovedAttribute("parse_http_list", "urllib2", "urllib.request"),
+    MovedAttribute("parse_keqv_list", "urllib2", "urllib.request"),
 ]
 for attr in _urllib_request_moved_attributes:
     setattr(Module_six_moves_urllib_request, attr.name, attr)
@@ -820,10 +821,14 @@ def with_metaclass(meta, *bases):
     # This requires a bit of explanation: the basic idea is to make a dummy
     # metaclass for one level of class instantiation that replaces itself with
     # the actual metaclass.
-    class metaclass(meta):
+    class metaclass(type):
 
         def __new__(cls, name, this_bases, d):
             return meta(name, bases, d)
+
+        @classmethod
+        def __prepare__(cls, name, this_bases):
+            return meta.__prepare__(name, bases)
     return type.__new__(metaclass, 'temporary_class', (), {})
 
 
diff --git a/lib/spack/external/yaml/LICENSE b/lib/spack/external/yaml/LICENSE
deleted file mode 100644
index 050ced23f6..0000000000
--- a/lib/spack/external/yaml/LICENSE
+++ /dev/null
@@ -1,19 +0,0 @@
-Copyright (c) 2006 Kirill Simonov
-
-Permission is hereby granted, free of charge, to any person obtaining a copy of
-this software and associated documentation files (the "Software"), to deal in
-the Software without restriction, including without limitation the rights to
-use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
-of the Software, and to permit persons to whom the Software is furnished to do
-so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
diff --git a/lib/spack/external/yaml/README b/lib/spack/external/yaml/README
deleted file mode 100644
index d186328eeb..0000000000
--- a/lib/spack/external/yaml/README
+++ /dev/null
@@ -1,35 +0,0 @@
-PyYAML - The next generation YAML parser and emitter for Python.
-
-To install, type 'python setup.py install'.
-
-By default, the setup.py script checks whether LibYAML is installed
-and if so, builds and installs LibYAML bindings.  To skip the check
-and force installation of LibYAML bindings, use the option '--with-libyaml':
-'python setup.py --with-libyaml install'.  To disable the check and
-skip building and installing LibYAML bindings, use '--without-libyaml':
-'python setup.py --without-libyaml install'.
-
-When LibYAML bindings are installed, you may use fast LibYAML-based
-parser and emitter as follows:
-
-    >>> yaml.load(stream, Loader=yaml.CLoader)
-    >>> yaml.dump(data, Dumper=yaml.CDumper)
-
-PyYAML includes a comprehensive test suite.  To run the tests,
-type 'python setup.py test'.
-
-For more information, check the PyYAML homepage:
-'http://pyyaml.org/wiki/PyYAML'.
-
-For PyYAML tutorial and reference, see:
-'http://pyyaml.org/wiki/PyYAMLDocumentation'.
-
-Post your questions and opinions to the YAML-Core mailing list:
-'http://lists.sourceforge.net/lists/listinfo/yaml-core'.
-
-Submit bug reports and feature requests to the PyYAML bug tracker:
-'https://bitbucket.org/xi/pyyaml/issues/new'.
-
-PyYAML is written by Kirill Simonov <xi@resolvent.net>.  It is released
-under the MIT license. See the file LICENSE for more details.
-
diff --git a/lib/spack/external/yaml/lib/yaml/__init__.py b/lib/spack/external/yaml/lib/yaml/__init__.py
deleted file mode 100644
index 87c15d38aa..0000000000
--- a/lib/spack/external/yaml/lib/yaml/__init__.py
+++ /dev/null
@@ -1,315 +0,0 @@
-
-from error import *
-
-from tokens import *
-from events import *
-from nodes import *
-
-from loader import *
-from dumper import *
-
-__version__ = '3.12'
-
-try:
-    from cyaml import *
-    __with_libyaml__ = True
-except ImportError:
-    __with_libyaml__ = False
-
-def scan(stream, Loader=Loader):
-    """
-    Scan a YAML stream and produce scanning tokens.
-    """
-    loader = Loader(stream)
-    try:
-        while loader.check_token():
-            yield loader.get_token()
-    finally:
-        loader.dispose()
-
-def parse(stream, Loader=Loader):
-    """
-    Parse a YAML stream and produce parsing events.
-    """
-    loader = Loader(stream)
-    try:
-        while loader.check_event():
-            yield loader.get_event()
-    finally:
-        loader.dispose()
-
-def compose(stream, Loader=Loader):
-    """
-    Parse the first YAML document in a stream
-    and produce the corresponding representation tree.
-    """
-    loader = Loader(stream)
-    try:
-        return loader.get_single_node()
-    finally:
-        loader.dispose()
-
-def compose_all(stream, Loader=Loader):
-    """
-    Parse all YAML documents in a stream
-    and produce corresponding representation trees.
-    """
-    loader = Loader(stream)
-    try:
-        while loader.check_node():
-            yield loader.get_node()
-    finally:
-        loader.dispose()
-
-def load(stream, Loader=Loader):
-    """
-    Parse the first YAML document in a stream
-    and produce the corresponding Python object.
-    """
-    loader = Loader(stream)
-    try:
-        return loader.get_single_data()
-    finally:
-        loader.dispose()
-
-def load_all(stream, Loader=Loader):
-    """
-    Parse all YAML documents in a stream
-    and produce corresponding Python objects.
-    """
-    loader = Loader(stream)
-    try:
-        while loader.check_data():
-            yield loader.get_data()
-    finally:
-        loader.dispose()
-
-def safe_load(stream):
-    """
-    Parse the first YAML document in a stream
-    and produce the corresponding Python object.
-    Resolve only basic YAML tags.
-    """
-    return load(stream, SafeLoader)
-
-def safe_load_all(stream):
-    """
-    Parse all YAML documents in a stream
-    and produce corresponding Python objects.
-    Resolve only basic YAML tags.
-    """
-    return load_all(stream, SafeLoader)
-
-def emit(events, stream=None, Dumper=Dumper,
-        canonical=None, indent=None, width=None,
-        allow_unicode=None, line_break=None):
-    """
-    Emit YAML parsing events into a stream.
-    If stream is None, return the produced string instead.
-    """
-    getvalue = None
-    if stream is None:
-        from StringIO import StringIO
-        stream = StringIO()
-        getvalue = stream.getvalue
-    dumper = Dumper(stream, canonical=canonical, indent=indent, width=width,
-            allow_unicode=allow_unicode, line_break=line_break)
-    try:
-        for event in events:
-            dumper.emit(event)
-    finally:
-        dumper.dispose()
-    if getvalue:
-        return getvalue()
-
-def serialize_all(nodes, stream=None, Dumper=Dumper,
-        canonical=None, indent=None, width=None,
-        allow_unicode=None, line_break=None,
-        encoding='utf-8', explicit_start=None, explicit_end=None,
-        version=None, tags=None):
-    """
-    Serialize a sequence of representation trees into a YAML stream.
-    If stream is None, return the produced string instead.
-    """
-    getvalue = None
-    if stream is None:
-        if encoding is None:
-            from StringIO import StringIO
-        else:
-            from cStringIO import StringIO
-        stream = StringIO()
-        getvalue = stream.getvalue
-    dumper = Dumper(stream, canonical=canonical, indent=indent, width=width,
-            allow_unicode=allow_unicode, line_break=line_break,
-            encoding=encoding, version=version, tags=tags,
-            explicit_start=explicit_start, explicit_end=explicit_end)
-    try:
-        dumper.open()
-        for node in nodes:
-            dumper.serialize(node)
-        dumper.close()
-    finally:
-        dumper.dispose()
-    if getvalue:
-        return getvalue()
-
-def serialize(node, stream=None, Dumper=Dumper, **kwds):
-    """
-    Serialize a representation tree into a YAML stream.
-    If stream is None, return the produced string instead.
-    """
-    return serialize_all([node], stream, Dumper=Dumper, **kwds)
-
-def dump_all(documents, stream=None, Dumper=Dumper,
-        default_style=None, default_flow_style=None,
-        canonical=None, indent=None, width=None,
-        allow_unicode=None, line_break=None,
-        encoding='utf-8', explicit_start=None, explicit_end=None,
-        version=None, tags=None):
-    """
-    Serialize a sequence of Python objects into a YAML stream.
-    If stream is None, return the produced string instead.
-    """
-    getvalue = None
-    if stream is None:
-        if encoding is None:
-            from StringIO import StringIO
-        else:
-            from cStringIO import StringIO
-        stream = StringIO()
-        getvalue = stream.getvalue
-    dumper = Dumper(stream, default_style=default_style,
-            default_flow_style=default_flow_style,
-            canonical=canonical, indent=indent, width=width,
-            allow_unicode=allow_unicode, line_break=line_break,
-            encoding=encoding, version=version, tags=tags,
-            explicit_start=explicit_start, explicit_end=explicit_end)
-    try:
-        dumper.open()
-        for data in documents:
-            dumper.represent(data)
-        dumper.close()
-    finally:
-        dumper.dispose()
-    if getvalue:
-        return getvalue()
-
-def dump(data, stream=None, Dumper=Dumper, **kwds):
-    """
-    Serialize a Python object into a YAML stream.
-    If stream is None, return the produced string instead.
-    """
-    return dump_all([data], stream, Dumper=Dumper, **kwds)
-
-def safe_dump_all(documents, stream=None, **kwds):
-    """
-    Serialize a sequence of Python objects into a YAML stream.
-    Produce only basic YAML tags.
-    If stream is None, return the produced string instead.
-    """
-    return dump_all(documents, stream, Dumper=SafeDumper, **kwds)
-
-def safe_dump(data, stream=None, **kwds):
-    """
-    Serialize a Python object into a YAML stream.
-    Produce only basic YAML tags.
-    If stream is None, return the produced string instead.
-    """
-    return dump_all([data], stream, Dumper=SafeDumper, **kwds)
-
-def add_implicit_resolver(tag, regexp, first=None,
-        Loader=Loader, Dumper=Dumper):
-    """
-    Add an implicit scalar detector.
-    If an implicit scalar value matches the given regexp,
-    the corresponding tag is assigned to the scalar.
-    first is a sequence of possible initial characters or None.
-    """
-    Loader.add_implicit_resolver(tag, regexp, first)
-    Dumper.add_implicit_resolver(tag, regexp, first)
-
-def add_path_resolver(tag, path, kind=None, Loader=Loader, Dumper=Dumper):
-    """
-    Add a path based resolver for the given tag.
-    A path is a list of keys that forms a path
-    to a node in the representation tree.
-    Keys can be string values, integers, or None.
-    """
-    Loader.add_path_resolver(tag, path, kind)
-    Dumper.add_path_resolver(tag, path, kind)
-
-def add_constructor(tag, constructor, Loader=Loader):
-    """
-    Add a constructor for the given tag.
-    Constructor is a function that accepts a Loader instance
-    and a node object and produces the corresponding Python object.
-    """
-    Loader.add_constructor(tag, constructor)
-
-def add_multi_constructor(tag_prefix, multi_constructor, Loader=Loader):
-    """
-    Add a multi-constructor for the given tag prefix.
-    Multi-constructor is called for a node if its tag starts with tag_prefix.
-    Multi-constructor accepts a Loader instance, a tag suffix,
-    and a node object and produces the corresponding Python object.
-    """
-    Loader.add_multi_constructor(tag_prefix, multi_constructor)
-
-def add_representer(data_type, representer, Dumper=Dumper):
-    """
-    Add a representer for the given type.
-    Representer is a function accepting a Dumper instance
-    and an instance of the given data type
-    and producing the corresponding representation node.
-    """
-    Dumper.add_representer(data_type, representer)
-
-def add_multi_representer(data_type, multi_representer, Dumper=Dumper):
-    """
-    Add a representer for the given type.
-    Multi-representer is a function accepting a Dumper instance
-    and an instance of the given data type or subtype
-    and producing the corresponding representation node.
-    """
-    Dumper.add_multi_representer(data_type, multi_representer)
-
-class YAMLObjectMetaclass(type):
-    """
-    The metaclass for YAMLObject.
-    """
-    def __init__(cls, name, bases, kwds):
-        super(YAMLObjectMetaclass, cls).__init__(name, bases, kwds)
-        if 'yaml_tag' in kwds and kwds['yaml_tag'] is not None:
-            cls.yaml_loader.add_constructor(cls.yaml_tag, cls.from_yaml)
-            cls.yaml_dumper.add_representer(cls, cls.to_yaml)
-
-class YAMLObject(object):
-    """
-    An object that can dump itself to a YAML stream
-    and load itself from a YAML stream.
-    """
-
-    __metaclass__ = YAMLObjectMetaclass
-    __slots__ = ()  # no direct instantiation, so allow immutable subclasses
-
-    yaml_loader = Loader
-    yaml_dumper = Dumper
-
-    yaml_tag = None
-    yaml_flow_style = None
-
-    def from_yaml(cls, loader, node):
-        """
-        Convert a representation node to a Python object.
-        """
-        return loader.construct_yaml_object(node, cls)
-    from_yaml = classmethod(from_yaml)
-
-    def to_yaml(cls, dumper, data):
-        """
-        Convert a Python object to a representation node.
-        """
-        return dumper.represent_yaml_object(cls.yaml_tag, data, cls,
-                flow_style=cls.yaml_flow_style)
-    to_yaml = classmethod(to_yaml)
-
diff --git a/lib/spack/external/yaml/lib/yaml/constructor.py b/lib/spack/external/yaml/lib/yaml/constructor.py
deleted file mode 100644
index 635faac3e6..0000000000
--- a/lib/spack/external/yaml/lib/yaml/constructor.py
+++ /dev/null
@@ -1,675 +0,0 @@
-
-__all__ = ['BaseConstructor', 'SafeConstructor', 'Constructor',
-    'ConstructorError']
-
-from error import *
-from nodes import *
-
-import datetime
-
-import binascii, re, sys, types
-
-class ConstructorError(MarkedYAMLError):
-    pass
-
-class BaseConstructor(object):
-
-    yaml_constructors = {}
-    yaml_multi_constructors = {}
-
-    def __init__(self):
-        self.constructed_objects = {}
-        self.recursive_objects = {}
-        self.state_generators = []
-        self.deep_construct = False
-
-    def check_data(self):
-        # If there are more documents available?
-        return self.check_node()
-
-    def get_data(self):
-        # Construct and return the next document.
-        if self.check_node():
-            return self.construct_document(self.get_node())
-
-    def get_single_data(self):
-        # Ensure that the stream contains a single document and construct it.
-        node = self.get_single_node()
-        if node is not None:
-            return self.construct_document(node)
-        return None
-
-    def construct_document(self, node):
-        data = self.construct_object(node)
-        while self.state_generators:
-            state_generators = self.state_generators
-            self.state_generators = []
-            for generator in state_generators:
-                for dummy in generator:
-                    pass
-        self.constructed_objects = {}
-        self.recursive_objects = {}
-        self.deep_construct = False
-        return data
-
-    def construct_object(self, node, deep=False):
-        if node in self.constructed_objects:
-            return self.constructed_objects[node]
-        if deep:
-            old_deep = self.deep_construct
-            self.deep_construct = True
-        if node in self.recursive_objects:
-            raise ConstructorError(None, None,
-                    "found unconstructable recursive node", node.start_mark)
-        self.recursive_objects[node] = None
-        constructor = None
-        tag_suffix = None
-        if node.tag in self.yaml_constructors:
-            constructor = self.yaml_constructors[node.tag]
-        else:
-            for tag_prefix in self.yaml_multi_constructors:
-                if node.tag.startswith(tag_prefix):
-                    tag_suffix = node.tag[len(tag_prefix):]
-                    constructor = self.yaml_multi_constructors[tag_prefix]
-                    break
-            else:
-                if None in self.yaml_multi_constructors:
-                    tag_suffix = node.tag
-                    constructor = self.yaml_multi_constructors[None]
-                elif None in self.yaml_constructors:
-                    constructor = self.yaml_constructors[None]
-                elif isinstance(node, ScalarNode):
-                    constructor = self.__class__.construct_scalar
-                elif isinstance(node, SequenceNode):
-                    constructor = self.__class__.construct_sequence
-                elif isinstance(node, MappingNode):
-                    constructor = self.__class__.construct_mapping
-        if tag_suffix is None:
-            data = constructor(self, node)
-        else:
-            data = constructor(self, tag_suffix, node)
-        if isinstance(data, types.GeneratorType):
-            generator = data
-            data = generator.next()
-            if self.deep_construct:
-                for dummy in generator:
-                    pass
-            else:
-                self.state_generators.append(generator)
-        self.constructed_objects[node] = data
-        del self.recursive_objects[node]
-        if deep:
-            self.deep_construct = old_deep
-        return data
-
-    def construct_scalar(self, node):
-        if not isinstance(node, ScalarNode):
-            raise ConstructorError(None, None,
-                    "expected a scalar node, but found %s" % node.id,
-                    node.start_mark)
-        return node.value
-
-    def construct_sequence(self, node, deep=False):
-        if not isinstance(node, SequenceNode):
-            raise ConstructorError(None, None,
-                    "expected a sequence node, but found %s" % node.id,
-                    node.start_mark)
-        return [self.construct_object(child, deep=deep)
-                for child in node.value]
-
-    def construct_mapping(self, node, deep=False):
-        if not isinstance(node, MappingNode):
-            raise ConstructorError(None, None,
-                    "expected a mapping node, but found %s" % node.id,
-                    node.start_mark)
-        mapping = {}
-        for key_node, value_node in node.value:
-            key = self.construct_object(key_node, deep=deep)
-            try:
-                hash(key)
-            except TypeError, exc:
-                raise ConstructorError("while constructing a mapping", node.start_mark,
-                        "found unacceptable key (%s)" % exc, key_node.start_mark)
-            value = self.construct_object(value_node, deep=deep)
-            mapping[key] = value
-        return mapping
-
-    def construct_pairs(self, node, deep=False):
-        if not isinstance(node, MappingNode):
-            raise ConstructorError(None, None,
-                    "expected a mapping node, but found %s" % node.id,
-                    node.start_mark)
-        pairs = []
-        for key_node, value_node in node.value:
-            key = self.construct_object(key_node, deep=deep)
-            value = self.construct_object(value_node, deep=deep)
-            pairs.append((key, value))
-        return pairs
-
-    def add_constructor(cls, tag, constructor):
-        if not 'yaml_constructors' in cls.__dict__:
-            cls.yaml_constructors = cls.yaml_constructors.copy()
-        cls.yaml_constructors[tag] = constructor
-    add_constructor = classmethod(add_constructor)
-
-    def add_multi_constructor(cls, tag_prefix, multi_constructor):
-        if not 'yaml_multi_constructors' in cls.__dict__:
-            cls.yaml_multi_constructors = cls.yaml_multi_constructors.copy()
-        cls.yaml_multi_constructors[tag_prefix] = multi_constructor
-    add_multi_constructor = classmethod(add_multi_constructor)
-
-class SafeConstructor(BaseConstructor):
-
-    def construct_scalar(self, node):
-        if isinstance(node, MappingNode):
-            for key_node, value_node in node.value:
-                if key_node.tag == u'tag:yaml.org,2002:value':
-                    return self.construct_scalar(value_node)
-        return BaseConstructor.construct_scalar(self, node)
-
-    def flatten_mapping(self, node):
-        merge = []
-        index = 0
-        while index < len(node.value):
-            key_node, value_node = node.value[index]
-            if key_node.tag == u'tag:yaml.org,2002:merge':
-                del node.value[index]
-                if isinstance(value_node, MappingNode):
-                    self.flatten_mapping(value_node)
-                    merge.extend(value_node.value)
-                elif isinstance(value_node, SequenceNode):
-                    submerge = []
-                    for subnode in value_node.value:
-                        if not isinstance(subnode, MappingNode):
-                            raise ConstructorError("while constructing a mapping",
-                                    node.start_mark,
-                                    "expected a mapping for merging, but found %s"
-                                    % subnode.id, subnode.start_mark)
-                        self.flatten_mapping(subnode)
-                        submerge.append(subnode.value)
-                    submerge.reverse()
-                    for value in submerge:
-                        merge.extend(value)
-                else:
-                    raise ConstructorError("while constructing a mapping", node.start_mark,
-                            "expected a mapping or list of mappings for merging, but found %s"
-                            % value_node.id, value_node.start_mark)
-            elif key_node.tag == u'tag:yaml.org,2002:value':
-                key_node.tag = u'tag:yaml.org,2002:str'
-                index += 1
-            else:
-                index += 1
-        if merge:
-            node.value = merge + node.value
-
-    def construct_mapping(self, node, deep=False):
-        if isinstance(node, MappingNode):
-            self.flatten_mapping(node)
-        return BaseConstructor.construct_mapping(self, node, deep=deep)
-
-    def construct_yaml_null(self, node):
-        self.construct_scalar(node)
-        return None
-
-    bool_values = {
-        u'yes':     True,
-        u'no':      False,
-        u'true':    True,
-        u'false':   False,
-        u'on':      True,
-        u'off':     False,
-    }
-
-    def construct_yaml_bool(self, node):
-        value = self.construct_scalar(node)
-        return self.bool_values[value.lower()]
-
-    def construct_yaml_int(self, node):
-        value = str(self.construct_scalar(node))
-        value = value.replace('_', '')
-        sign = +1
-        if value[0] == '-':
-            sign = -1
-        if value[0] in '+-':
-            value = value[1:]
-        if value == '0':
-            return 0
-        elif value.startswith('0b'):
-            return sign*int(value[2:], 2)
-        elif value.startswith('0x'):
-            return sign*int(value[2:], 16)
-        elif value[0] == '0':
-            return sign*int(value, 8)
-        elif ':' in value:
-            digits = [int(part) for part in value.split(':')]
-            digits.reverse()
-            base = 1
-            value = 0
-            for digit in digits:
-                value += digit*base
-                base *= 60
-            return sign*value
-        else:
-            return sign*int(value)
-
-    inf_value = 1e300
-    while inf_value != inf_value*inf_value:
-        inf_value *= inf_value
-    nan_value = -inf_value/inf_value   # Trying to make a quiet NaN (like C99).
-
-    def construct_yaml_float(self, node):
-        value = str(self.construct_scalar(node))
-        value = value.replace('_', '').lower()
-        sign = +1
-        if value[0] == '-':
-            sign = -1
-        if value[0] in '+-':
-            value = value[1:]
-        if value == '.inf':
-            return sign*self.inf_value
-        elif value == '.nan':
-            return self.nan_value
-        elif ':' in value:
-            digits = [float(part) for part in value.split(':')]
-            digits.reverse()
-            base = 1
-            value = 0.0
-            for digit in digits:
-                value += digit*base
-                base *= 60
-            return sign*value
-        else:
-            return sign*float(value)
-
-    def construct_yaml_binary(self, node):
-        value = self.construct_scalar(node)
-        try:
-            return str(value).decode('base64')
-        except (binascii.Error, UnicodeEncodeError), exc:
-            raise ConstructorError(None, None,
-                    "failed to decode base64 data: %s" % exc, node.start_mark) 
-
-    timestamp_regexp = re.compile(
-            ur'''^(?P<year>[0-9][0-9][0-9][0-9])
-                -(?P<month>[0-9][0-9]?)
-                -(?P<day>[0-9][0-9]?)
-                (?:(?:[Tt]|[ \t]+)
-                (?P<hour>[0-9][0-9]?)
-                :(?P<minute>[0-9][0-9])
-                :(?P<second>[0-9][0-9])
-                (?:\.(?P<fraction>[0-9]*))?
-                (?:[ \t]*(?P<tz>Z|(?P<tz_sign>[-+])(?P<tz_hour>[0-9][0-9]?)
-                (?::(?P<tz_minute>[0-9][0-9]))?))?)?$''', re.X)
-
-    def construct_yaml_timestamp(self, node):
-        value = self.construct_scalar(node)
-        match = self.timestamp_regexp.match(node.value)
-        values = match.groupdict()
-        year = int(values['year'])
-        month = int(values['month'])
-        day = int(values['day'])
-        if not values['hour']:
-            return datetime.date(year, month, day)
-        hour = int(values['hour'])
-        minute = int(values['minute'])
-        second = int(values['second'])
-        fraction = 0
-        if values['fraction']:
-            fraction = values['fraction'][:6]
-            while len(fraction) < 6:
-                fraction += '0'
-            fraction = int(fraction)
-        delta = None
-        if values['tz_sign']:
-            tz_hour = int(values['tz_hour'])
-            tz_minute = int(values['tz_minute'] or 0)
-            delta = datetime.timedelta(hours=tz_hour, minutes=tz_minute)
-            if values['tz_sign'] == '-':
-                delta = -delta
-        data = datetime.datetime(year, month, day, hour, minute, second, fraction)
-        if delta:
-            data -= delta
-        return data
-
-    def construct_yaml_omap(self, node):
-        # Note: we do not check for duplicate keys, because it's too
-        # CPU-expensive.
-        omap = []
-        yield omap
-        if not isinstance(node, SequenceNode):
-            raise ConstructorError("while constructing an ordered map", node.start_mark,
-                    "expected a sequence, but found %s" % node.id, node.start_mark)
-        for subnode in node.value:
-            if not isinstance(subnode, MappingNode):
-                raise ConstructorError("while constructing an ordered map", node.start_mark,
-                        "expected a mapping of length 1, but found %s" % subnode.id,
-                        subnode.start_mark)
-            if len(subnode.value) != 1:
-                raise ConstructorError("while constructing an ordered map", node.start_mark,
-                        "expected a single mapping item, but found %d items" % len(subnode.value),
-                        subnode.start_mark)
-            key_node, value_node = subnode.value[0]
-            key = self.construct_object(key_node)
-            value = self.construct_object(value_node)
-            omap.append((key, value))
-
-    def construct_yaml_pairs(self, node):
-        # Note: the same code as `construct_yaml_omap`.
-        pairs = []
-        yield pairs
-        if not isinstance(node, SequenceNode):
-            raise ConstructorError("while constructing pairs", node.start_mark,
-                    "expected a sequence, but found %s" % node.id, node.start_mark)
-        for subnode in node.value:
-            if not isinstance(subnode, MappingNode):
-                raise ConstructorError("while constructing pairs", node.start_mark,
-                        "expected a mapping of length 1, but found %s" % subnode.id,
-                        subnode.start_mark)
-            if len(subnode.value) != 1:
-                raise ConstructorError("while constructing pairs", node.start_mark,
-                        "expected a single mapping item, but found %d items" % len(subnode.value),
-                        subnode.start_mark)
-            key_node, value_node = subnode.value[0]
-            key = self.construct_object(key_node)
-            value = self.construct_object(value_node)
-            pairs.append((key, value))
-
-    def construct_yaml_set(self, node):
-        data = set()
-        yield data
-        value = self.construct_mapping(node)
-        data.update(value)
-
-    def construct_yaml_str(self, node):
-        value = self.construct_scalar(node)
-        try:
-            return value.encode('ascii')
-        except UnicodeEncodeError:
-            return value
-
-    def construct_yaml_seq(self, node):
-        data = []
-        yield data
-        data.extend(self.construct_sequence(node))
-
-    def construct_yaml_map(self, node):
-        data = {}
-        yield data
-        value = self.construct_mapping(node)
-        data.update(value)
-
-    def construct_yaml_object(self, node, cls):
-        data = cls.__new__(cls)
-        yield data
-        if hasattr(data, '__setstate__'):
-            state = self.construct_mapping(node, deep=True)
-            data.__setstate__(state)
-        else:
-            state = self.construct_mapping(node)
-            data.__dict__.update(state)
-
-    def construct_undefined(self, node):
-        raise ConstructorError(None, None,
-                "could not determine a constructor for the tag %r" % node.tag.encode('utf-8'),
-                node.start_mark)
-
-SafeConstructor.add_constructor(
-        u'tag:yaml.org,2002:null',
-        SafeConstructor.construct_yaml_null)
-
-SafeConstructor.add_constructor(
-        u'tag:yaml.org,2002:bool',
-        SafeConstructor.construct_yaml_bool)
-
-SafeConstructor.add_constructor(
-        u'tag:yaml.org,2002:int',
-        SafeConstructor.construct_yaml_int)
-
-SafeConstructor.add_constructor(
-        u'tag:yaml.org,2002:float',
-        SafeConstructor.construct_yaml_float)
-
-SafeConstructor.add_constructor(
-        u'tag:yaml.org,2002:binary',
-        SafeConstructor.construct_yaml_binary)
-
-SafeConstructor.add_constructor(
-        u'tag:yaml.org,2002:timestamp',
-        SafeConstructor.construct_yaml_timestamp)
-
-SafeConstructor.add_constructor(
-        u'tag:yaml.org,2002:omap',
-        SafeConstructor.construct_yaml_omap)
-
-SafeConstructor.add_constructor(
-        u'tag:yaml.org,2002:pairs',
-        SafeConstructor.construct_yaml_pairs)
-
-SafeConstructor.add_constructor(
-        u'tag:yaml.org,2002:set',
-        SafeConstructor.construct_yaml_set)
-
-SafeConstructor.add_constructor(
-        u'tag:yaml.org,2002:str',
-        SafeConstructor.construct_yaml_str)
-
-SafeConstructor.add_constructor(
-        u'tag:yaml.org,2002:seq',
-        SafeConstructor.construct_yaml_seq)
-
-SafeConstructor.add_constructor(
-        u'tag:yaml.org,2002:map',
-        SafeConstructor.construct_yaml_map)
-
-SafeConstructor.add_constructor(None,
-        SafeConstructor.construct_undefined)
-
-class Constructor(SafeConstructor):
-
-    def construct_python_str(self, node):
-        return self.construct_scalar(node).encode('utf-8')
-
-    def construct_python_unicode(self, node):
-        return self.construct_scalar(node)
-
-    def construct_python_long(self, node):
-        return long(self.construct_yaml_int(node))
-
-    def construct_python_complex(self, node):
-       return complex(self.construct_scalar(node))
-
-    def construct_python_tuple(self, node):
-        return tuple(self.construct_sequence(node))
-
-    def find_python_module(self, name, mark):
-        if not name:
-            raise ConstructorError("while constructing a Python module", mark,
-                    "expected non-empty name appended to the tag", mark)
-        try:
-            __import__(name)
-        except ImportError, exc:
-            raise ConstructorError("while constructing a Python module", mark,
-                    "cannot find module %r (%s)" % (name.encode('utf-8'), exc), mark)
-        return sys.modules[name]
-
-    def find_python_name(self, name, mark):
-        if not name:
-            raise ConstructorError("while constructing a Python object", mark,
-                    "expected non-empty name appended to the tag", mark)
-        if u'.' in name:
-            module_name, object_name = name.rsplit('.', 1)
-        else:
-            module_name = '__builtin__'
-            object_name = name
-        try:
-            __import__(module_name)
-        except ImportError, exc:
-            raise ConstructorError("while constructing a Python object", mark,
-                    "cannot find module %r (%s)" % (module_name.encode('utf-8'), exc), mark)
-        module = sys.modules[module_name]
-        if not hasattr(module, object_name):
-            raise ConstructorError("while constructing a Python object", mark,
-                    "cannot find %r in the module %r" % (object_name.encode('utf-8'),
-                        module.__name__), mark)
-        return getattr(module, object_name)
-
-    def construct_python_name(self, suffix, node):
-        value = self.construct_scalar(node)
-        if value:
-            raise ConstructorError("while constructing a Python name", node.start_mark,
-                    "expected the empty value, but found %r" % value.encode('utf-8'),
-                    node.start_mark)
-        return self.find_python_name(suffix, node.start_mark)
-
-    def construct_python_module(self, suffix, node):
-        value = self.construct_scalar(node)
-        if value:
-            raise ConstructorError("while constructing a Python module", node.start_mark,
-                    "expected the empty value, but found %r" % value.encode('utf-8'),
-                    node.start_mark)
-        return self.find_python_module(suffix, node.start_mark)
-
-    class classobj: pass
-
-    def make_python_instance(self, suffix, node,
-            args=None, kwds=None, newobj=False):
-        if not args:
-            args = []
-        if not kwds:
-            kwds = {}
-        cls = self.find_python_name(suffix, node.start_mark)
-        if newobj and isinstance(cls, type(self.classobj))  \
-                and not args and not kwds:
-            instance = self.classobj()
-            instance.__class__ = cls
-            return instance
-        elif newobj and isinstance(cls, type):
-            return cls.__new__(cls, *args, **kwds)
-        else:
-            return cls(*args, **kwds)
-
-    def set_python_instance_state(self, instance, state):
-        if hasattr(instance, '__setstate__'):
-            instance.__setstate__(state)
-        else:
-            slotstate = {}
-            if isinstance(state, tuple) and len(state) == 2:
-                state, slotstate = state
-            if hasattr(instance, '__dict__'):
-                instance.__dict__.update(state)
-            elif state:
-                slotstate.update(state)
-            for key, value in slotstate.items():
-                setattr(object, key, value)
-
-    def construct_python_object(self, suffix, node):
-        # Format:
-        #   !!python/object:module.name { ... state ... }
-        instance = self.make_python_instance(suffix, node, newobj=True)
-        yield instance
-        deep = hasattr(instance, '__setstate__')
-        state = self.construct_mapping(node, deep=deep)
-        self.set_python_instance_state(instance, state)
-
-    def construct_python_object_apply(self, suffix, node, newobj=False):
-        # Format:
-        #   !!python/object/apply       # (or !!python/object/new)
-        #   args: [ ... arguments ... ]
-        #   kwds: { ... keywords ... }
-        #   state: ... state ...
-        #   listitems: [ ... listitems ... ]
-        #   dictitems: { ... dictitems ... }
-        # or short format:
-        #   !!python/object/apply [ ... arguments ... ]
-        # The difference between !!python/object/apply and !!python/object/new
-        # is how an object is created, check make_python_instance for details.
-        if isinstance(node, SequenceNode):
-            args = self.construct_sequence(node, deep=True)
-            kwds = {}
-            state = {}
-            listitems = []
-            dictitems = {}
-        else:
-            value = self.construct_mapping(node, deep=True)
-            args = value.get('args', [])
-            kwds = value.get('kwds', {})
-            state = value.get('state', {})
-            listitems = value.get('listitems', [])
-            dictitems = value.get('dictitems', {})
-        instance = self.make_python_instance(suffix, node, args, kwds, newobj)
-        if state:
-            self.set_python_instance_state(instance, state)
-        if listitems:
-            instance.extend(listitems)
-        if dictitems:
-            for key in dictitems:
-                instance[key] = dictitems[key]
-        return instance
-
-    def construct_python_object_new(self, suffix, node):
-        return self.construct_python_object_apply(suffix, node, newobj=True)
-
-Constructor.add_constructor(
-    u'tag:yaml.org,2002:python/none',
-    Constructor.construct_yaml_null)
-
-Constructor.add_constructor(
-    u'tag:yaml.org,2002:python/bool',
-    Constructor.construct_yaml_bool)
-
-Constructor.add_constructor(
-    u'tag:yaml.org,2002:python/str',
-    Constructor.construct_python_str)
-
-Constructor.add_constructor(
-    u'tag:yaml.org,2002:python/unicode',
-    Constructor.construct_python_unicode)
-
-Constructor.add_constructor(
-    u'tag:yaml.org,2002:python/int',
-    Constructor.construct_yaml_int)
-
-Constructor.add_constructor(
-    u'tag:yaml.org,2002:python/long',
-    Constructor.construct_python_long)
-
-Constructor.add_constructor(
-    u'tag:yaml.org,2002:python/float',
-    Constructor.construct_yaml_float)
-
-Constructor.add_constructor(
-    u'tag:yaml.org,2002:python/complex',
-    Constructor.construct_python_complex)
-
-Constructor.add_constructor(
-    u'tag:yaml.org,2002:python/list',
-    Constructor.construct_yaml_seq)
-
-Constructor.add_constructor(
-    u'tag:yaml.org,2002:python/tuple',
-    Constructor.construct_python_tuple)
-
-Constructor.add_constructor(
-    u'tag:yaml.org,2002:python/dict',
-    Constructor.construct_yaml_map)
-
-Constructor.add_multi_constructor(
-    u'tag:yaml.org,2002:python/name:',
-    Constructor.construct_python_name)
-
-Constructor.add_multi_constructor(
-    u'tag:yaml.org,2002:python/module:',
-    Constructor.construct_python_module)
-
-Constructor.add_multi_constructor(
-    u'tag:yaml.org,2002:python/object:',
-    Constructor.construct_python_object)
-
-Constructor.add_multi_constructor(
-    u'tag:yaml.org,2002:python/object/apply:',
-    Constructor.construct_python_object_apply)
-
-Constructor.add_multi_constructor(
-    u'tag:yaml.org,2002:python/object/new:',
-    Constructor.construct_python_object_new)
-
diff --git a/lib/spack/external/yaml/lib/yaml/cyaml.py b/lib/spack/external/yaml/lib/yaml/cyaml.py
deleted file mode 100644
index 68dcd75192..0000000000
--- a/lib/spack/external/yaml/lib/yaml/cyaml.py
+++ /dev/null
@@ -1,85 +0,0 @@
-
-__all__ = ['CBaseLoader', 'CSafeLoader', 'CLoader',
-        'CBaseDumper', 'CSafeDumper', 'CDumper']
-
-from _yaml import CParser, CEmitter
-
-from constructor import *
-
-from serializer import *
-from representer import *
-
-from resolver import *
-
-class CBaseLoader(CParser, BaseConstructor, BaseResolver):
-
-    def __init__(self, stream):
-        CParser.__init__(self, stream)
-        BaseConstructor.__init__(self)
-        BaseResolver.__init__(self)
-
-class CSafeLoader(CParser, SafeConstructor, Resolver):
-
-    def __init__(self, stream):
-        CParser.__init__(self, stream)
-        SafeConstructor.__init__(self)
-        Resolver.__init__(self)
-
-class CLoader(CParser, Constructor, Resolver):
-
-    def __init__(self, stream):
-        CParser.__init__(self, stream)
-        Constructor.__init__(self)
-        Resolver.__init__(self)
-
-class CBaseDumper(CEmitter, BaseRepresenter, BaseResolver):
-
-    def __init__(self, stream,
-            default_style=None, default_flow_style=None,
-            canonical=None, indent=None, width=None,
-            allow_unicode=None, line_break=None,
-            encoding=None, explicit_start=None, explicit_end=None,
-            version=None, tags=None):
-        CEmitter.__init__(self, stream, canonical=canonical,
-                indent=indent, width=width, encoding=encoding,
-                allow_unicode=allow_unicode, line_break=line_break,
-                explicit_start=explicit_start, explicit_end=explicit_end,
-                version=version, tags=tags)
-        Representer.__init__(self, default_style=default_style,
-                default_flow_style=default_flow_style)
-        Resolver.__init__(self)
-
-class CSafeDumper(CEmitter, SafeRepresenter, Resolver):
-
-    def __init__(self, stream,
-            default_style=None, default_flow_style=None,
-            canonical=None, indent=None, width=None,
-            allow_unicode=None, line_break=None,
-            encoding=None, explicit_start=None, explicit_end=None,
-            version=None, tags=None):
-        CEmitter.__init__(self, stream, canonical=canonical,
-                indent=indent, width=width, encoding=encoding,
-                allow_unicode=allow_unicode, line_break=line_break,
-                explicit_start=explicit_start, explicit_end=explicit_end,
-                version=version, tags=tags)
-        SafeRepresenter.__init__(self, default_style=default_style,
-                default_flow_style=default_flow_style)
-        Resolver.__init__(self)
-
-class CDumper(CEmitter, Serializer, Representer, Resolver):
-
-    def __init__(self, stream,
-            default_style=None, default_flow_style=None,
-            canonical=None, indent=None, width=None,
-            allow_unicode=None, line_break=None,
-            encoding=None, explicit_start=None, explicit_end=None,
-            version=None, tags=None):
-        CEmitter.__init__(self, stream, canonical=canonical,
-                indent=indent, width=width, encoding=encoding,
-                allow_unicode=allow_unicode, line_break=line_break,
-                explicit_start=explicit_start, explicit_end=explicit_end,
-                version=version, tags=tags)
-        Representer.__init__(self, default_style=default_style,
-                default_flow_style=default_flow_style)
-        Resolver.__init__(self)
-
diff --git a/lib/spack/external/yaml/lib/yaml/dumper.py b/lib/spack/external/yaml/lib/yaml/dumper.py
deleted file mode 100644
index f811d2c919..0000000000
--- a/lib/spack/external/yaml/lib/yaml/dumper.py
+++ /dev/null
@@ -1,62 +0,0 @@
-
-__all__ = ['BaseDumper', 'SafeDumper', 'Dumper']
-
-from emitter import *
-from serializer import *
-from representer import *
-from resolver import *
-
-class BaseDumper(Emitter, Serializer, BaseRepresenter, BaseResolver):
-
-    def __init__(self, stream,
-            default_style=None, default_flow_style=None,
-            canonical=None, indent=None, width=None,
-            allow_unicode=None, line_break=None,
-            encoding=None, explicit_start=None, explicit_end=None,
-            version=None, tags=None):
-        Emitter.__init__(self, stream, canonical=canonical,
-                indent=indent, width=width,
-                allow_unicode=allow_unicode, line_break=line_break)
-        Serializer.__init__(self, encoding=encoding,
-                explicit_start=explicit_start, explicit_end=explicit_end,
-                version=version, tags=tags)
-        Representer.__init__(self, default_style=default_style,
-                default_flow_style=default_flow_style)
-        Resolver.__init__(self)
-
-class SafeDumper(Emitter, Serializer, SafeRepresenter, Resolver):
-
-    def __init__(self, stream,
-            default_style=None, default_flow_style=None,
-            canonical=None, indent=None, width=None,
-            allow_unicode=None, line_break=None,
-            encoding=None, explicit_start=None, explicit_end=None,
-            version=None, tags=None):
-        Emitter.__init__(self, stream, canonical=canonical,
-                indent=indent, width=width,
-                allow_unicode=allow_unicode, line_break=line_break)
-        Serializer.__init__(self, encoding=encoding,
-                explicit_start=explicit_start, explicit_end=explicit_end,
-                version=version, tags=tags)
-        SafeRepresenter.__init__(self, default_style=default_style,
-                default_flow_style=default_flow_style)
-        Resolver.__init__(self)
-
-class Dumper(Emitter, Serializer, Representer, Resolver):
-
-    def __init__(self, stream,
-            default_style=None, default_flow_style=None,
-            canonical=None, indent=None, width=None,
-            allow_unicode=None, line_break=None,
-            encoding=None, explicit_start=None, explicit_end=None,
-            version=None, tags=None):
-        Emitter.__init__(self, stream, canonical=canonical,
-                indent=indent, width=width,
-                allow_unicode=allow_unicode, line_break=line_break)
-        Serializer.__init__(self, encoding=encoding,
-                explicit_start=explicit_start, explicit_end=explicit_end,
-                version=version, tags=tags)
-        Representer.__init__(self, default_style=default_style,
-                default_flow_style=default_flow_style)
-        Resolver.__init__(self)
-
diff --git a/lib/spack/external/yaml/lib/yaml/events.py b/lib/spack/external/yaml/lib/yaml/events.py
deleted file mode 100644
index f79ad389cb..0000000000
--- a/lib/spack/external/yaml/lib/yaml/events.py
+++ /dev/null
@@ -1,86 +0,0 @@
-
-# Abstract classes.
-
-class Event(object):
-    def __init__(self, start_mark=None, end_mark=None):
-        self.start_mark = start_mark
-        self.end_mark = end_mark
-    def __repr__(self):
-        attributes = [key for key in ['anchor', 'tag', 'implicit', 'value']
-                if hasattr(self, key)]
-        arguments = ', '.join(['%s=%r' % (key, getattr(self, key))
-                for key in attributes])
-        return '%s(%s)' % (self.__class__.__name__, arguments)
-
-class NodeEvent(Event):
-    def __init__(self, anchor, start_mark=None, end_mark=None):
-        self.anchor = anchor
-        self.start_mark = start_mark
-        self.end_mark = end_mark
-
-class CollectionStartEvent(NodeEvent):
-    def __init__(self, anchor, tag, implicit, start_mark=None, end_mark=None,
-            flow_style=None):
-        self.anchor = anchor
-        self.tag = tag
-        self.implicit = implicit
-        self.start_mark = start_mark
-        self.end_mark = end_mark
-        self.flow_style = flow_style
-
-class CollectionEndEvent(Event):
-    pass
-
-# Implementations.
-
-class StreamStartEvent(Event):
-    def __init__(self, start_mark=None, end_mark=None, encoding=None):
-        self.start_mark = start_mark
-        self.end_mark = end_mark
-        self.encoding = encoding
-
-class StreamEndEvent(Event):
-    pass
-
-class DocumentStartEvent(Event):
-    def __init__(self, start_mark=None, end_mark=None,
-            explicit=None, version=None, tags=None):
-        self.start_mark = start_mark
-        self.end_mark = end_mark
-        self.explicit = explicit
-        self.version = version
-        self.tags = tags
-
-class DocumentEndEvent(Event):
-    def __init__(self, start_mark=None, end_mark=None,
-            explicit=None):
-        self.start_mark = start_mark
-        self.end_mark = end_mark
-        self.explicit = explicit
-
-class AliasEvent(NodeEvent):
-    pass
-
-class ScalarEvent(NodeEvent):
-    def __init__(self, anchor, tag, implicit, value,
-            start_mark=None, end_mark=None, style=None):
-        self.anchor = anchor
-        self.tag = tag
-        self.implicit = implicit
-        self.value = value
-        self.start_mark = start_mark
-        self.end_mark = end_mark
-        self.style = style
-
-class SequenceStartEvent(CollectionStartEvent):
-    pass
-
-class SequenceEndEvent(CollectionEndEvent):
-    pass
-
-class MappingStartEvent(CollectionStartEvent):
-    pass
-
-class MappingEndEvent(CollectionEndEvent):
-    pass
-
diff --git a/lib/spack/external/yaml/lib/yaml/loader.py b/lib/spack/external/yaml/lib/yaml/loader.py
deleted file mode 100644
index 293ff467b1..0000000000
--- a/lib/spack/external/yaml/lib/yaml/loader.py
+++ /dev/null
@@ -1,40 +0,0 @@
-
-__all__ = ['BaseLoader', 'SafeLoader', 'Loader']
-
-from reader import *
-from scanner import *
-from parser import *
-from composer import *
-from constructor import *
-from resolver import *
-
-class BaseLoader(Reader, Scanner, Parser, Composer, BaseConstructor, BaseResolver):
-
-    def __init__(self, stream):
-        Reader.__init__(self, stream)
-        Scanner.__init__(self)
-        Parser.__init__(self)
-        Composer.__init__(self)
-        BaseConstructor.__init__(self)
-        BaseResolver.__init__(self)
-
-class SafeLoader(Reader, Scanner, Parser, Composer, SafeConstructor, Resolver):
-
-    def __init__(self, stream):
-        Reader.__init__(self, stream)
-        Scanner.__init__(self)
-        Parser.__init__(self)
-        Composer.__init__(self)
-        SafeConstructor.__init__(self)
-        Resolver.__init__(self)
-
-class Loader(Reader, Scanner, Parser, Composer, Constructor, Resolver):
-
-    def __init__(self, stream):
-        Reader.__init__(self, stream)
-        Scanner.__init__(self)
-        Parser.__init__(self)
-        Composer.__init__(self)
-        Constructor.__init__(self)
-        Resolver.__init__(self)
-
diff --git a/lib/spack/external/yaml/lib/yaml/nodes.py b/lib/spack/external/yaml/lib/yaml/nodes.py
deleted file mode 100644
index c4f070c41e..0000000000
--- a/lib/spack/external/yaml/lib/yaml/nodes.py
+++ /dev/null
@@ -1,49 +0,0 @@
-
-class Node(object):
-    def __init__(self, tag, value, start_mark, end_mark):
-        self.tag = tag
-        self.value = value
-        self.start_mark = start_mark
-        self.end_mark = end_mark
-    def __repr__(self):
-        value = self.value
-        #if isinstance(value, list):
-        #    if len(value) == 0:
-        #        value = '<empty>'
-        #    elif len(value) == 1:
-        #        value = '<1 item>'
-        #    else:
-        #        value = '<%d items>' % len(value)
-        #else:
-        #    if len(value) > 75:
-        #        value = repr(value[:70]+u' ... ')
-        #    else:
-        #        value = repr(value)
-        value = repr(value)
-        return '%s(tag=%r, value=%s)' % (self.__class__.__name__, self.tag, value)
-
-class ScalarNode(Node):
-    id = 'scalar'
-    def __init__(self, tag, value,
-            start_mark=None, end_mark=None, style=None):
-        self.tag = tag
-        self.value = value
-        self.start_mark = start_mark
-        self.end_mark = end_mark
-        self.style = style
-
-class CollectionNode(Node):
-    def __init__(self, tag, value,
-            start_mark=None, end_mark=None, flow_style=None):
-        self.tag = tag
-        self.value = value
-        self.start_mark = start_mark
-        self.end_mark = end_mark
-        self.flow_style = flow_style
-
-class SequenceNode(CollectionNode):
-    id = 'sequence'
-
-class MappingNode(CollectionNode):
-    id = 'mapping'
-
diff --git a/lib/spack/external/yaml/lib/yaml/reader.py b/lib/spack/external/yaml/lib/yaml/reader.py
deleted file mode 100644
index 3249e6b9f5..0000000000
--- a/lib/spack/external/yaml/lib/yaml/reader.py
+++ /dev/null
@@ -1,190 +0,0 @@
-# This module contains abstractions for the input stream. You don't have to
-# looks further, there are no pretty code.
-#
-# We define two classes here.
-#
-#   Mark(source, line, column)
-# It's just a record and its only use is producing nice error messages.
-# Parser does not use it for any other purposes.
-#
-#   Reader(source, data)
-# Reader determines the encoding of `data` and converts it to unicode.
-# Reader provides the following methods and attributes:
-#   reader.peek(length=1) - return the next `length` characters
-#   reader.forward(length=1) - move the current position to `length` characters.
-#   reader.index - the number of the current character.
-#   reader.line, stream.column - the line and the column of the current character.
-
-__all__ = ['Reader', 'ReaderError']
-
-from error import YAMLError, Mark
-
-import codecs, re
-
-class ReaderError(YAMLError):
-
-    def __init__(self, name, position, character, encoding, reason):
-        self.name = name
-        self.character = character
-        self.position = position
-        self.encoding = encoding
-        self.reason = reason
-
-    def __str__(self):
-        if isinstance(self.character, str):
-            return "'%s' codec can't decode byte #x%02x: %s\n"  \
-                    "  in \"%s\", position %d"    \
-                    % (self.encoding, ord(self.character), self.reason,
-                            self.name, self.position)
-        else:
-            return "unacceptable character #x%04x: %s\n"    \
-                    "  in \"%s\", position %d"    \
-                    % (self.character, self.reason,
-                            self.name, self.position)
-
-class Reader(object):
-    # Reader:
-    # - determines the data encoding and converts it to unicode,
-    # - checks if characters are in allowed range,
-    # - adds '\0' to the end.
-
-    # Reader accepts
-    #  - a `str` object,
-    #  - a `unicode` object,
-    #  - a file-like object with its `read` method returning `str`,
-    #  - a file-like object with its `read` method returning `unicode`.
-
-    # Yeah, it's ugly and slow.
-
-    def __init__(self, stream):
-        self.name = None
-        self.stream = None
-        self.stream_pointer = 0
-        self.eof = True
-        self.buffer = u''
-        self.pointer = 0
-        self.raw_buffer = None
-        self.raw_decode = None
-        self.encoding = None
-        self.index = 0
-        self.line = 0
-        self.column = 0
-        if isinstance(stream, unicode):
-            self.name = "<unicode string>"
-            self.check_printable(stream)
-            self.buffer = stream+u'\0'
-        elif isinstance(stream, str):
-            self.name = "<string>"
-            self.raw_buffer = stream
-            self.determine_encoding()
-        else:
-            self.stream = stream
-            self.name = getattr(stream, 'name', "<file>")
-            self.eof = False
-            self.raw_buffer = ''
-            self.determine_encoding()
-
-    def peek(self, index=0):
-        try:
-            return self.buffer[self.pointer+index]
-        except IndexError:
-            self.update(index+1)
-            return self.buffer[self.pointer+index]
-
-    def prefix(self, length=1):
-        if self.pointer+length >= len(self.buffer):
-            self.update(length)
-        return self.buffer[self.pointer:self.pointer+length]
-
-    def forward(self, length=1):
-        if self.pointer+length+1 >= len(self.buffer):
-            self.update(length+1)
-        while length:
-            ch = self.buffer[self.pointer]
-            self.pointer += 1
-            self.index += 1
-            if ch in u'\n\x85\u2028\u2029'  \
-                    or (ch == u'\r' and self.buffer[self.pointer] != u'\n'):
-                self.line += 1
-                self.column = 0
-            elif ch != u'\uFEFF':
-                self.column += 1
-            length -= 1
-
-    def get_mark(self):
-        if self.stream is None:
-            return Mark(self.name, self.index, self.line, self.column,
-                    self.buffer, self.pointer)
-        else:
-            return Mark(self.name, self.index, self.line, self.column,
-                    None, None)
-
-    def determine_encoding(self):
-        while not self.eof and len(self.raw_buffer) < 2:
-            self.update_raw()
-        if not isinstance(self.raw_buffer, unicode):
-            if self.raw_buffer.startswith(codecs.BOM_UTF16_LE):
-                self.raw_decode = codecs.utf_16_le_decode
-                self.encoding = 'utf-16-le'
-            elif self.raw_buffer.startswith(codecs.BOM_UTF16_BE):
-                self.raw_decode = codecs.utf_16_be_decode
-                self.encoding = 'utf-16-be'
-            else:
-                self.raw_decode = codecs.utf_8_decode
-                self.encoding = 'utf-8'
-        self.update(1)
-
-    NON_PRINTABLE = re.compile(u'[^\x09\x0A\x0D\x20-\x7E\x85\xA0-\uD7FF\uE000-\uFFFD]')
-    def check_printable(self, data):
-        match = self.NON_PRINTABLE.search(data)
-        if match:
-            character = match.group()
-            position = self.index+(len(self.buffer)-self.pointer)+match.start()
-            raise ReaderError(self.name, position, ord(character),
-                    'unicode', "special characters are not allowed")
-
-    def update(self, length):
-        if self.raw_buffer is None:
-            return
-        self.buffer = self.buffer[self.pointer:]
-        self.pointer = 0
-        while len(self.buffer) < length:
-            if not self.eof:
-                self.update_raw()
-            if self.raw_decode is not None:
-                try:
-                    data, converted = self.raw_decode(self.raw_buffer,
-                            'strict', self.eof)
-                except UnicodeDecodeError, exc:
-                    character = exc.object[exc.start]
-                    if self.stream is not None:
-                        position = self.stream_pointer-len(self.raw_buffer)+exc.start
-                    else:
-                        position = exc.start
-                    raise ReaderError(self.name, position, character,
-                            exc.encoding, exc.reason)
-            else:
-                data = self.raw_buffer
-                converted = len(data)
-            self.check_printable(data)
-            self.buffer += data
-            self.raw_buffer = self.raw_buffer[converted:]
-            if self.eof:
-                self.buffer += u'\0'
-                self.raw_buffer = None
-                break
-
-    def update_raw(self, size=1024):
-        data = self.stream.read(size)
-        if data:
-            self.raw_buffer += data
-            self.stream_pointer += len(data)
-        else:
-            self.eof = True
-
-#try:
-#    import psyco
-#    psyco.bind(Reader)
-#except ImportError:
-#    pass
-
diff --git a/lib/spack/external/yaml/lib/yaml/representer.py b/lib/spack/external/yaml/lib/yaml/representer.py
deleted file mode 100644
index 4ea8cb1fe1..0000000000
--- a/lib/spack/external/yaml/lib/yaml/representer.py
+++ /dev/null
@@ -1,486 +0,0 @@
-
-__all__ = ['BaseRepresenter', 'SafeRepresenter', 'Representer',
-    'RepresenterError']
-
-from error import *
-from nodes import *
-
-import datetime
-
-import sys, copy_reg, types
-
-class RepresenterError(YAMLError):
-    pass
-
-class BaseRepresenter(object):
-
-    yaml_representers = {}
-    yaml_multi_representers = {}
-
-    def __init__(self, default_style=None, default_flow_style=None):
-        self.default_style = default_style
-        self.default_flow_style = default_flow_style
-        self.represented_objects = {}
-        self.object_keeper = []
-        self.alias_key = None
-
-    def represent(self, data):
-        node = self.represent_data(data)
-        self.serialize(node)
-        self.represented_objects = {}
-        self.object_keeper = []
-        self.alias_key = None
-
-    def get_classobj_bases(self, cls):
-        bases = [cls]
-        for base in cls.__bases__:
-            bases.extend(self.get_classobj_bases(base))
-        return bases
-
-    def represent_data(self, data):
-        if self.ignore_aliases(data):
-            self.alias_key = None
-        else:
-            self.alias_key = id(data)
-        if self.alias_key is not None:
-            if self.alias_key in self.represented_objects:
-                node = self.represented_objects[self.alias_key]
-                #if node is None:
-                #    raise RepresenterError("recursive objects are not allowed: %r" % data)
-                return node
-            #self.represented_objects[alias_key] = None
-            self.object_keeper.append(data)
-        data_types = type(data).__mro__
-        if type(data) is types.InstanceType:
-            data_types = self.get_classobj_bases(data.__class__)+list(data_types)
-        if data_types[0] in self.yaml_representers:
-            node = self.yaml_representers[data_types[0]](self, data)
-        else:
-            for data_type in data_types:
-                if data_type in self.yaml_multi_representers:
-                    node = self.yaml_multi_representers[data_type](self, data)
-                    break
-            else:
-                if None in self.yaml_multi_representers:
-                    node = self.yaml_multi_representers[None](self, data)
-                elif None in self.yaml_representers:
-                    node = self.yaml_representers[None](self, data)
-                else:
-                    node = ScalarNode(None, unicode(data))
-        #if alias_key is not None:
-        #    self.represented_objects[alias_key] = node
-        return node
-
-    def add_representer(cls, data_type, representer):
-        if not 'yaml_representers' in cls.__dict__:
-            cls.yaml_representers = cls.yaml_representers.copy()
-        cls.yaml_representers[data_type] = representer
-    add_representer = classmethod(add_representer)
-
-    def add_multi_representer(cls, data_type, representer):
-        if not 'yaml_multi_representers' in cls.__dict__:
-            cls.yaml_multi_representers = cls.yaml_multi_representers.copy()
-        cls.yaml_multi_representers[data_type] = representer
-    add_multi_representer = classmethod(add_multi_representer)
-
-    def represent_scalar(self, tag, value, style=None):
-        if style is None:
-            style = self.default_style
-        node = ScalarNode(tag, value, style=style)
-        if self.alias_key is not None:
-            self.represented_objects[self.alias_key] = node
-        return node
-
-    def represent_sequence(self, tag, sequence, flow_style=None):
-        value = []
-        node = SequenceNode(tag, value, flow_style=flow_style)
-        if self.alias_key is not None:
-            self.represented_objects[self.alias_key] = node
-        best_style = True
-        for item in sequence:
-            node_item = self.represent_data(item)
-            if not (isinstance(node_item, ScalarNode) and not node_item.style):
-                best_style = False
-            value.append(node_item)
-        if flow_style is None:
-            if self.default_flow_style is not None:
-                node.flow_style = self.default_flow_style
-            else:
-                node.flow_style = best_style
-        return node
-
-    def represent_mapping(self, tag, mapping, flow_style=None):
-        value = []
-        node = MappingNode(tag, value, flow_style=flow_style)
-        if self.alias_key is not None:
-            self.represented_objects[self.alias_key] = node
-        best_style = True
-        if hasattr(mapping, 'items'):
-            mapping = mapping.items()
-            mapping.sort()
-        for item_key, item_value in mapping:
-            node_key = self.represent_data(item_key)
-            node_value = self.represent_data(item_value)
-            if not (isinstance(node_key, ScalarNode) and not node_key.style):
-                best_style = False
-            if not (isinstance(node_value, ScalarNode) and not node_value.style):
-                best_style = False
-            value.append((node_key, node_value))
-        if flow_style is None:
-            if self.default_flow_style is not None:
-                node.flow_style = self.default_flow_style
-            else:
-                node.flow_style = best_style
-        return node
-
-    def ignore_aliases(self, data):
-        return False
-
-class SafeRepresenter(BaseRepresenter):
-
-    def ignore_aliases(self, data):
-        if data is None:
-            return True
-        if isinstance(data, tuple) and data == ():
-            return True
-        if isinstance(data, (str, unicode, bool, int, float)):
-            return True
-
-    def represent_none(self, data):
-        return self.represent_scalar(u'tag:yaml.org,2002:null',
-                u'null')
-
-    def represent_str(self, data):
-        tag = None
-        style = None
-        try:
-            data = unicode(data, 'ascii')
-            tag = u'tag:yaml.org,2002:str'
-        except UnicodeDecodeError:
-            try:
-                data = unicode(data, 'utf-8')
-                tag = u'tag:yaml.org,2002:str'
-            except UnicodeDecodeError:
-                data = data.encode('base64')
-                tag = u'tag:yaml.org,2002:binary'
-                style = '|'
-        return self.represent_scalar(tag, data, style=style)
-
-    def represent_unicode(self, data):
-        return self.represent_scalar(u'tag:yaml.org,2002:str', data)
-
-    def represent_bool(self, data):
-        if data:
-            value = u'true'
-        else:
-            value = u'false'
-        return self.represent_scalar(u'tag:yaml.org,2002:bool', value)
-
-    def represent_int(self, data):
-        return self.represent_scalar(u'tag:yaml.org,2002:int', unicode(data))
-
-    def represent_long(self, data):
-        return self.represent_scalar(u'tag:yaml.org,2002:int', unicode(data))
-
-    inf_value = 1e300
-    while repr(inf_value) != repr(inf_value*inf_value):
-        inf_value *= inf_value
-
-    def represent_float(self, data):
-        if data != data or (data == 0.0 and data == 1.0):
-            value = u'.nan'
-        elif data == self.inf_value:
-            value = u'.inf'
-        elif data == -self.inf_value:
-            value = u'-.inf'
-        else:
-            value = unicode(repr(data)).lower()
-            # Note that in some cases `repr(data)` represents a float number
-            # without the decimal parts.  For instance:
-            #   >>> repr(1e17)
-            #   '1e17'
-            # Unfortunately, this is not a valid float representation according
-            # to the definition of the `!!float` tag.  We fix this by adding
-            # '.0' before the 'e' symbol.
-            if u'.' not in value and u'e' in value:
-                value = value.replace(u'e', u'.0e', 1)
-        return self.represent_scalar(u'tag:yaml.org,2002:float', value)
-
-    def represent_list(self, data):
-        #pairs = (len(data) > 0 and isinstance(data, list))
-        #if pairs:
-        #    for item in data:
-        #        if not isinstance(item, tuple) or len(item) != 2:
-        #            pairs = False
-        #            break
-        #if not pairs:
-            return self.represent_sequence(u'tag:yaml.org,2002:seq', data)
-        #value = []
-        #for item_key, item_value in data:
-        #    value.append(self.represent_mapping(u'tag:yaml.org,2002:map',
-        #        [(item_key, item_value)]))
-        #return SequenceNode(u'tag:yaml.org,2002:pairs', value)
-
-    def represent_dict(self, data):
-        return self.represent_mapping(u'tag:yaml.org,2002:map', data)
-
-    def represent_set(self, data):
-        value = {}
-        for key in data:
-            value[key] = None
-        return self.represent_mapping(u'tag:yaml.org,2002:set', value)
-
-    def represent_date(self, data):
-        value = unicode(data.isoformat())
-        return self.represent_scalar(u'tag:yaml.org,2002:timestamp', value)
-
-    def represent_datetime(self, data):
-        value = unicode(data.isoformat(' '))
-        return self.represent_scalar(u'tag:yaml.org,2002:timestamp', value)
-
-    def represent_yaml_object(self, tag, data, cls, flow_style=None):
-        if hasattr(data, '__getstate__'):
-            state = data.__getstate__()
-        else:
-            state = data.__dict__.copy()
-        return self.represent_mapping(tag, state, flow_style=flow_style)
-
-    def represent_undefined(self, data):
-        raise RepresenterError("cannot represent an object: %s" % data)
-
-SafeRepresenter.add_representer(type(None),
-        SafeRepresenter.represent_none)
-
-SafeRepresenter.add_representer(str,
-        SafeRepresenter.represent_str)
-
-SafeRepresenter.add_representer(unicode,
-        SafeRepresenter.represent_unicode)
-
-SafeRepresenter.add_representer(bool,
-        SafeRepresenter.represent_bool)
-
-SafeRepresenter.add_representer(int,
-        SafeRepresenter.represent_int)
-
-SafeRepresenter.add_representer(long,
-        SafeRepresenter.represent_long)
-
-SafeRepresenter.add_representer(float,
-        SafeRepresenter.represent_float)
-
-SafeRepresenter.add_representer(list,
-        SafeRepresenter.represent_list)
-
-SafeRepresenter.add_representer(tuple,
-        SafeRepresenter.represent_list)
-
-SafeRepresenter.add_representer(dict,
-        SafeRepresenter.represent_dict)
-
-SafeRepresenter.add_representer(set,
-        SafeRepresenter.represent_set)
-
-SafeRepresenter.add_representer(datetime.date,
-        SafeRepresenter.represent_date)
-
-SafeRepresenter.add_representer(datetime.datetime,
-        SafeRepresenter.represent_datetime)
-
-SafeRepresenter.add_representer(None,
-        SafeRepresenter.represent_undefined)
-
-class Representer(SafeRepresenter):
-
-    def represent_str(self, data):
-        tag = None
-        style = None
-        try:
-            data = unicode(data, 'ascii')
-            tag = u'tag:yaml.org,2002:str'
-        except UnicodeDecodeError:
-            try:
-                data = unicode(data, 'utf-8')
-                tag = u'tag:yaml.org,2002:python/str'
-            except UnicodeDecodeError:
-                data = data.encode('base64')
-                tag = u'tag:yaml.org,2002:binary'
-                style = '|'
-        return self.represent_scalar(tag, data, style=style)
-
-    def represent_unicode(self, data):
-        tag = None
-        try:
-            data.encode('ascii')
-            tag = u'tag:yaml.org,2002:python/unicode'
-        except UnicodeEncodeError:
-            tag = u'tag:yaml.org,2002:str'
-        return self.represent_scalar(tag, data)
-
-    def represent_long(self, data):
-        tag = u'tag:yaml.org,2002:int'
-        if int(data) is not data:
-            tag = u'tag:yaml.org,2002:python/long'
-        return self.represent_scalar(tag, unicode(data))
-
-    def represent_complex(self, data):
-        if data.imag == 0.0:
-            data = u'%r' % data.real
-        elif data.real == 0.0:
-            data = u'%rj' % data.imag
-        elif data.imag > 0:
-            data = u'%r+%rj' % (data.real, data.imag)
-        else:
-            data = u'%r%rj' % (data.real, data.imag)
-        return self.represent_scalar(u'tag:yaml.org,2002:python/complex', data)
-
-    def represent_tuple(self, data):
-        return self.represent_sequence(u'tag:yaml.org,2002:python/tuple', data)
-
-    def represent_name(self, data):
-        name = u'%s.%s' % (data.__module__, data.__name__)
-        return self.represent_scalar(u'tag:yaml.org,2002:python/name:'+name, u'')
-
-    def represent_module(self, data):
-        return self.represent_scalar(
-                u'tag:yaml.org,2002:python/module:'+data.__name__, u'')
-
-    def represent_instance(self, data):
-        # For instances of classic classes, we use __getinitargs__ and
-        # __getstate__ to serialize the data.
-
-        # If data.__getinitargs__ exists, the object must be reconstructed by
-        # calling cls(**args), where args is a tuple returned by
-        # __getinitargs__. Otherwise, the cls.__init__ method should never be
-        # called and the class instance is created by instantiating a trivial
-        # class and assigning to the instance's __class__ variable.
-
-        # If data.__getstate__ exists, it returns the state of the object.
-        # Otherwise, the state of the object is data.__dict__.
-
-        # We produce either a !!python/object or !!python/object/new node.
-        # If data.__getinitargs__ does not exist and state is a dictionary, we
-        # produce a !!python/object node . Otherwise we produce a
-        # !!python/object/new node.
-
-        cls = data.__class__
-        class_name = u'%s.%s' % (cls.__module__, cls.__name__)
-        args = None
-        state = None
-        if hasattr(data, '__getinitargs__'):
-            args = list(data.__getinitargs__())
-        if hasattr(data, '__getstate__'):
-            state = data.__getstate__()
-        else:
-            state = data.__dict__
-        if args is None and isinstance(state, dict):
-            return self.represent_mapping(
-                    u'tag:yaml.org,2002:python/object:'+class_name, state)
-        if isinstance(state, dict) and not state:
-            return self.represent_sequence(
-                    u'tag:yaml.org,2002:python/object/new:'+class_name, args)
-        value = {}
-        if args:
-            value['args'] = args
-        value['state'] = state
-        return self.represent_mapping(
-                u'tag:yaml.org,2002:python/object/new:'+class_name, value)
-
-    def represent_object(self, data):
-        # We use __reduce__ API to save the data. data.__reduce__ returns
-        # a tuple of length 2-5:
-        #   (function, args, state, listitems, dictitems)
-
-        # For reconstructing, we calls function(*args), then set its state,
-        # listitems, and dictitems if they are not None.
-
-        # A special case is when function.__name__ == '__newobj__'. In this
-        # case we create the object with args[0].__new__(*args).
-
-        # Another special case is when __reduce__ returns a string - we don't
-        # support it.
-
-        # We produce a !!python/object, !!python/object/new or
-        # !!python/object/apply node.
-
-        cls = type(data)
-        if cls in copy_reg.dispatch_table:
-            reduce = copy_reg.dispatch_table[cls](data)
-        elif hasattr(data, '__reduce_ex__'):
-            reduce = data.__reduce_ex__(2)
-        elif hasattr(data, '__reduce__'):
-            reduce = data.__reduce__()
-        else:
-            raise RepresenterError("cannot represent object: %r" % data)
-        reduce = (list(reduce)+[None]*5)[:5]
-        function, args, state, listitems, dictitems = reduce
-        args = list(args)
-        if state is None:
-            state = {}
-        if listitems is not None:
-            listitems = list(listitems)
-        if dictitems is not None:
-            dictitems = dict(dictitems)
-        if function.__name__ == '__newobj__':
-            function = args[0]
-            args = args[1:]
-            tag = u'tag:yaml.org,2002:python/object/new:'
-            newobj = True
-        else:
-            tag = u'tag:yaml.org,2002:python/object/apply:'
-            newobj = False
-        function_name = u'%s.%s' % (function.__module__, function.__name__)
-        if not args and not listitems and not dictitems \
-                and isinstance(state, dict) and newobj:
-            return self.represent_mapping(
-                    u'tag:yaml.org,2002:python/object:'+function_name, state)
-        if not listitems and not dictitems  \
-                and isinstance(state, dict) and not state:
-            return self.represent_sequence(tag+function_name, args)
-        value = {}
-        if args:
-            value['args'] = args
-        if state or not isinstance(state, dict):
-            value['state'] = state
-        if listitems:
-            value['listitems'] = listitems
-        if dictitems:
-            value['dictitems'] = dictitems
-        return self.represent_mapping(tag+function_name, value)
-
-Representer.add_representer(str,
-        Representer.represent_str)
-
-Representer.add_representer(unicode,
-        Representer.represent_unicode)
-
-Representer.add_representer(long,
-        Representer.represent_long)
-
-Representer.add_representer(complex,
-        Representer.represent_complex)
-
-Representer.add_representer(tuple,
-        Representer.represent_tuple)
-
-Representer.add_representer(type,
-        Representer.represent_name)
-
-Representer.add_representer(types.ClassType,
-        Representer.represent_name)
-
-Representer.add_representer(types.FunctionType,
-        Representer.represent_name)
-
-Representer.add_representer(types.BuiltinFunctionType,
-        Representer.represent_name)
-
-Representer.add_representer(types.ModuleType,
-        Representer.represent_module)
-
-Representer.add_multi_representer(types.InstanceType,
-        Representer.represent_instance)
-
-Representer.add_multi_representer(object,
-        Representer.represent_object)
-
diff --git a/lib/spack/external/yaml/lib/yaml/resolver.py b/lib/spack/external/yaml/lib/yaml/resolver.py
deleted file mode 100644
index 528fbc0ead..0000000000
--- a/lib/spack/external/yaml/lib/yaml/resolver.py
+++ /dev/null
@@ -1,227 +0,0 @@
-
-__all__ = ['BaseResolver', 'Resolver']
-
-from error import *
-from nodes import *
-
-import re
-
-class ResolverError(YAMLError):
-    pass
-
-class BaseResolver(object):
-
-    DEFAULT_SCALAR_TAG = u'tag:yaml.org,2002:str'
-    DEFAULT_SEQUENCE_TAG = u'tag:yaml.org,2002:seq'
-    DEFAULT_MAPPING_TAG = u'tag:yaml.org,2002:map'
-
-    yaml_implicit_resolvers = {}
-    yaml_path_resolvers = {}
-
-    def __init__(self):
-        self.resolver_exact_paths = []
-        self.resolver_prefix_paths = []
-
-    def add_implicit_resolver(cls, tag, regexp, first):
-        if not 'yaml_implicit_resolvers' in cls.__dict__:
-            implicit_resolvers = {}
-            for key in cls.yaml_implicit_resolvers:
-                implicit_resolvers[key] = cls.yaml_implicit_resolvers[key][:]
-            cls.yaml_implicit_resolvers = implicit_resolvers
-        if first is None:
-            first = [None]
-        for ch in first:
-            cls.yaml_implicit_resolvers.setdefault(ch, []).append((tag, regexp))
-    add_implicit_resolver = classmethod(add_implicit_resolver)
-
-    def add_path_resolver(cls, tag, path, kind=None):
-        # Note: `add_path_resolver` is experimental.  The API could be changed.
-        # `new_path` is a pattern that is matched against the path from the
-        # root to the node that is being considered.  `node_path` elements are
-        # tuples `(node_check, index_check)`.  `node_check` is a node class:
-        # `ScalarNode`, `SequenceNode`, `MappingNode` or `None`.  `None`
-        # matches any kind of a node.  `index_check` could be `None`, a boolean
-        # value, a string value, or a number.  `None` and `False` match against
-        # any _value_ of sequence and mapping nodes.  `True` matches against
-        # any _key_ of a mapping node.  A string `index_check` matches against
-        # a mapping value that corresponds to a scalar key which content is
-        # equal to the `index_check` value.  An integer `index_check` matches
-        # against a sequence value with the index equal to `index_check`.
-        if not 'yaml_path_resolvers' in cls.__dict__:
-            cls.yaml_path_resolvers = cls.yaml_path_resolvers.copy()
-        new_path = []
-        for element in path:
-            if isinstance(element, (list, tuple)):
-                if len(element) == 2:
-                    node_check, index_check = element
-                elif len(element) == 1:
-                    node_check = element[0]
-                    index_check = True
-                else:
-                    raise ResolverError("Invalid path element: %s" % element)
-            else:
-                node_check = None
-                index_check = element
-            if node_check is str:
-                node_check = ScalarNode
-            elif node_check is list:
-                node_check = SequenceNode
-            elif node_check is dict:
-                node_check = MappingNode
-            elif node_check not in [ScalarNode, SequenceNode, MappingNode]  \
-                    and not isinstance(node_check, basestring)  \
-                    and node_check is not None:
-                raise ResolverError("Invalid node checker: %s" % node_check)
-            if not isinstance(index_check, (basestring, int))   \
-                    and index_check is not None:
-                raise ResolverError("Invalid index checker: %s" % index_check)
-            new_path.append((node_check, index_check))
-        if kind is str:
-            kind = ScalarNode
-        elif kind is list:
-            kind = SequenceNode
-        elif kind is dict:
-            kind = MappingNode
-        elif kind not in [ScalarNode, SequenceNode, MappingNode]    \
-                and kind is not None:
-            raise ResolverError("Invalid node kind: %s" % kind)
-        cls.yaml_path_resolvers[tuple(new_path), kind] = tag
-    add_path_resolver = classmethod(add_path_resolver)
-
-    def descend_resolver(self, current_node, current_index):
-        if not self.yaml_path_resolvers:
-            return
-        exact_paths = {}
-        prefix_paths = []
-        if current_node:
-            depth = len(self.resolver_prefix_paths)
-            for path, kind in self.resolver_prefix_paths[-1]:
-                if self.check_resolver_prefix(depth, path, kind,
-                        current_node, current_index):
-                    if len(path) > depth:
-                        prefix_paths.append((path, kind))
-                    else:
-                        exact_paths[kind] = self.yaml_path_resolvers[path, kind]
-        else:
-            for path, kind in self.yaml_path_resolvers:
-                if not path:
-                    exact_paths[kind] = self.yaml_path_resolvers[path, kind]
-                else:
-                    prefix_paths.append((path, kind))
-        self.resolver_exact_paths.append(exact_paths)
-        self.resolver_prefix_paths.append(prefix_paths)
-
-    def ascend_resolver(self):
-        if not self.yaml_path_resolvers:
-            return
-        self.resolver_exact_paths.pop()
-        self.resolver_prefix_paths.pop()
-
-    def check_resolver_prefix(self, depth, path, kind,
-            current_node, current_index):
-        node_check, index_check = path[depth-1]
-        if isinstance(node_check, basestring):
-            if current_node.tag != node_check:
-                return
-        elif node_check is not None:
-            if not isinstance(current_node, node_check):
-                return
-        if index_check is True and current_index is not None:
-            return
-        if (index_check is False or index_check is None)    \
-                and current_index is None:
-            return
-        if isinstance(index_check, basestring):
-            if not (isinstance(current_index, ScalarNode)
-                    and index_check == current_index.value):
-                return
-        elif isinstance(index_check, int) and not isinstance(index_check, bool):
-            if index_check != current_index:
-                return
-        return True
-
-    def resolve(self, kind, value, implicit):
-        if kind is ScalarNode and implicit[0]:
-            if value == u'':
-                resolvers = self.yaml_implicit_resolvers.get(u'', [])
-            else:
-                resolvers = self.yaml_implicit_resolvers.get(value[0], [])
-            resolvers += self.yaml_implicit_resolvers.get(None, [])
-            for tag, regexp in resolvers:
-                if regexp.match(value):
-                    return tag
-            implicit = implicit[1]
-        if self.yaml_path_resolvers:
-            exact_paths = self.resolver_exact_paths[-1]
-            if kind in exact_paths:
-                return exact_paths[kind]
-            if None in exact_paths:
-                return exact_paths[None]
-        if kind is ScalarNode:
-            return self.DEFAULT_SCALAR_TAG
-        elif kind is SequenceNode:
-            return self.DEFAULT_SEQUENCE_TAG
-        elif kind is MappingNode:
-            return self.DEFAULT_MAPPING_TAG
-
-class Resolver(BaseResolver):
-    pass
-
-Resolver.add_implicit_resolver(
-        u'tag:yaml.org,2002:bool',
-        re.compile(ur'''^(?:yes|Yes|YES|no|No|NO
-                    |true|True|TRUE|false|False|FALSE
-                    |on|On|ON|off|Off|OFF)$''', re.X),
-        list(u'yYnNtTfFoO'))
-
-Resolver.add_implicit_resolver(
-        u'tag:yaml.org,2002:float',
-        re.compile(ur'''^(?:[-+]?(?:[0-9][0-9_]*)\.[0-9_]*(?:[eE][-+][0-9]+)?
-                    |\.[0-9_]+(?:[eE][-+][0-9]+)?
-                    |[-+]?[0-9][0-9_]*(?::[0-5]?[0-9])+\.[0-9_]*
-                    |[-+]?\.(?:inf|Inf|INF)
-                    |\.(?:nan|NaN|NAN))$''', re.X),
-        list(u'-+0123456789.'))
-
-Resolver.add_implicit_resolver(
-        u'tag:yaml.org,2002:int',
-        re.compile(ur'''^(?:[-+]?0b[0-1_]+
-                    |[-+]?0[0-7_]+
-                    |[-+]?(?:0|[1-9][0-9_]*)
-                    |[-+]?0x[0-9a-fA-F_]+
-                    |[-+]?[1-9][0-9_]*(?::[0-5]?[0-9])+)$''', re.X),
-        list(u'-+0123456789'))
-
-Resolver.add_implicit_resolver(
-        u'tag:yaml.org,2002:merge',
-        re.compile(ur'^(?:<<)$'),
-        [u'<'])
-
-Resolver.add_implicit_resolver(
-        u'tag:yaml.org,2002:null',
-        re.compile(ur'''^(?: ~
-                    |null|Null|NULL
-                    | )$''', re.X),
-        [u'~', u'n', u'N', u''])
-
-Resolver.add_implicit_resolver(
-        u'tag:yaml.org,2002:timestamp',
-        re.compile(ur'''^(?:[0-9][0-9][0-9][0-9]-[0-9][0-9]-[0-9][0-9]
-                    |[0-9][0-9][0-9][0-9] -[0-9][0-9]? -[0-9][0-9]?
-                     (?:[Tt]|[ \t]+)[0-9][0-9]?
-                     :[0-9][0-9] :[0-9][0-9] (?:\.[0-9]*)?
-                     (?:[ \t]*(?:Z|[-+][0-9][0-9]?(?::[0-9][0-9])?))?)$''', re.X),
-        list(u'0123456789'))
-
-Resolver.add_implicit_resolver(
-        u'tag:yaml.org,2002:value',
-        re.compile(ur'^(?:=)$'),
-        [u'='])
-
-# The following resolver is only for documentation purposes. It cannot work
-# because plain scalars cannot start with '!', '&', or '*'.
-Resolver.add_implicit_resolver(
-        u'tag:yaml.org,2002:yaml',
-        re.compile(ur'^(?:!|&|\*)$'),
-        list(u'!&*'))
-
diff --git a/lib/spack/external/yaml/lib/yaml/serializer.py b/lib/spack/external/yaml/lib/yaml/serializer.py
deleted file mode 100644
index 0bf1e96dc1..0000000000
--- a/lib/spack/external/yaml/lib/yaml/serializer.py
+++ /dev/null
@@ -1,111 +0,0 @@
-
-__all__ = ['Serializer', 'SerializerError']
-
-from error import YAMLError
-from events import *
-from nodes import *
-
-class SerializerError(YAMLError):
-    pass
-
-class Serializer(object):
-
-    ANCHOR_TEMPLATE = u'id%03d'
-
-    def __init__(self, encoding=None,
-            explicit_start=None, explicit_end=None, version=None, tags=None):
-        self.use_encoding = encoding
-        self.use_explicit_start = explicit_start
-        self.use_explicit_end = explicit_end
-        self.use_version = version
-        self.use_tags = tags
-        self.serialized_nodes = {}
-        self.anchors = {}
-        self.last_anchor_id = 0
-        self.closed = None
-
-    def open(self):
-        if self.closed is None:
-            self.emit(StreamStartEvent(encoding=self.use_encoding))
-            self.closed = False
-        elif self.closed:
-            raise SerializerError("serializer is closed")
-        else:
-            raise SerializerError("serializer is already opened")
-
-    def close(self):
-        if self.closed is None:
-            raise SerializerError("serializer is not opened")
-        elif not self.closed:
-            self.emit(StreamEndEvent())
-            self.closed = True
-
-    #def __del__(self):
-    #    self.close()
-
-    def serialize(self, node):
-        if self.closed is None:
-            raise SerializerError("serializer is not opened")
-        elif self.closed:
-            raise SerializerError("serializer is closed")
-        self.emit(DocumentStartEvent(explicit=self.use_explicit_start,
-            version=self.use_version, tags=self.use_tags))
-        self.anchor_node(node)
-        self.serialize_node(node, None, None)
-        self.emit(DocumentEndEvent(explicit=self.use_explicit_end))
-        self.serialized_nodes = {}
-        self.anchors = {}
-        self.last_anchor_id = 0
-
-    def anchor_node(self, node):
-        if node in self.anchors:
-            if self.anchors[node] is None:
-                self.anchors[node] = self.generate_anchor(node)
-        else:
-            self.anchors[node] = None
-            if isinstance(node, SequenceNode):
-                for item in node.value:
-                    self.anchor_node(item)
-            elif isinstance(node, MappingNode):
-                for key, value in node.value:
-                    self.anchor_node(key)
-                    self.anchor_node(value)
-
-    def generate_anchor(self, node):
-        self.last_anchor_id += 1
-        return self.ANCHOR_TEMPLATE % self.last_anchor_id
-
-    def serialize_node(self, node, parent, index):
-        alias = self.anchors[node]
-        if node in self.serialized_nodes:
-            self.emit(AliasEvent(alias))
-        else:
-            self.serialized_nodes[node] = True
-            self.descend_resolver(parent, index)
-            if isinstance(node, ScalarNode):
-                detected_tag = self.resolve(ScalarNode, node.value, (True, False))
-                default_tag = self.resolve(ScalarNode, node.value, (False, True))
-                implicit = (node.tag == detected_tag), (node.tag == default_tag)
-                self.emit(ScalarEvent(alias, node.tag, implicit, node.value,
-                    style=node.style))
-            elif isinstance(node, SequenceNode):
-                implicit = (node.tag
-                            == self.resolve(SequenceNode, node.value, True))
-                self.emit(SequenceStartEvent(alias, node.tag, implicit,
-                    flow_style=node.flow_style))
-                index = 0
-                for item in node.value:
-                    self.serialize_node(item, node, index)
-                    index += 1
-                self.emit(SequenceEndEvent())
-            elif isinstance(node, MappingNode):
-                implicit = (node.tag
-                            == self.resolve(MappingNode, node.value, True))
-                self.emit(MappingStartEvent(alias, node.tag, implicit,
-                    flow_style=node.flow_style))
-                for key, value in node.value:
-                    self.serialize_node(key, node, None)
-                    self.serialize_node(value, node, key)
-                self.emit(MappingEndEvent())
-            self.ascend_resolver()
-
diff --git a/lib/spack/external/yaml/lib/yaml/tokens.py b/lib/spack/external/yaml/lib/yaml/tokens.py
deleted file mode 100644
index 4d0b48a394..0000000000
--- a/lib/spack/external/yaml/lib/yaml/tokens.py
+++ /dev/null
@@ -1,104 +0,0 @@
-
-class Token(object):
-    def __init__(self, start_mark, end_mark):
-        self.start_mark = start_mark
-        self.end_mark = end_mark
-    def __repr__(self):
-        attributes = [key for key in self.__dict__
-                if not key.endswith('_mark')]
-        attributes.sort()
-        arguments = ', '.join(['%s=%r' % (key, getattr(self, key))
-                for key in attributes])
-        return '%s(%s)' % (self.__class__.__name__, arguments)
-
-#class BOMToken(Token):
-#    id = '<byte order mark>'
-
-class DirectiveToken(Token):
-    id = '<directive>'
-    def __init__(self, name, value, start_mark, end_mark):
-        self.name = name
-        self.value = value
-        self.start_mark = start_mark
-        self.end_mark = end_mark
-
-class DocumentStartToken(Token):
-    id = '<document start>'
-
-class DocumentEndToken(Token):
-    id = '<document end>'
-
-class StreamStartToken(Token):
-    id = '<stream start>'
-    def __init__(self, start_mark=None, end_mark=None,
-            encoding=None):
-        self.start_mark = start_mark
-        self.end_mark = end_mark
-        self.encoding = encoding
-
-class StreamEndToken(Token):
-    id = '<stream end>'
-
-class BlockSequenceStartToken(Token):
-    id = '<block sequence start>'
-
-class BlockMappingStartToken(Token):
-    id = '<block mapping start>'
-
-class BlockEndToken(Token):
-    id = '<block end>'
-
-class FlowSequenceStartToken(Token):
-    id = '['
-
-class FlowMappingStartToken(Token):
-    id = '{'
-
-class FlowSequenceEndToken(Token):
-    id = ']'
-
-class FlowMappingEndToken(Token):
-    id = '}'
-
-class KeyToken(Token):
-    id = '?'
-
-class ValueToken(Token):
-    id = ':'
-
-class BlockEntryToken(Token):
-    id = '-'
-
-class FlowEntryToken(Token):
-    id = ','
-
-class AliasToken(Token):
-    id = '<alias>'
-    def __init__(self, value, start_mark, end_mark):
-        self.value = value
-        self.start_mark = start_mark
-        self.end_mark = end_mark
-
-class AnchorToken(Token):
-    id = '<anchor>'
-    def __init__(self, value, start_mark, end_mark):
-        self.value = value
-        self.start_mark = start_mark
-        self.end_mark = end_mark
-
-class TagToken(Token):
-    id = '<tag>'
-    def __init__(self, value, start_mark, end_mark):
-        self.value = value
-        self.start_mark = start_mark
-        self.end_mark = end_mark
-
-class ScalarToken(Token):
-    id = '<scalar>'
-    def __init__(self, value, plain, start_mark, end_mark, style=None):
-        self.value = value
-        self.plain = plain
-        self.start_mark = start_mark
-        self.end_mark = end_mark
-        self.style = style
-
diff --git a/lib/spack/external/yaml/lib3/yaml/composer.py b/lib/spack/external/yaml/lib3/yaml/composer.py
deleted file mode 100644
index d5c6a7acd9..0000000000
--- a/lib/spack/external/yaml/lib3/yaml/composer.py
+++ /dev/null
@@ -1,139 +0,0 @@
-
-__all__ = ['Composer', 'ComposerError']
-
-from .error import MarkedYAMLError
-from .events import *
-from .nodes import *
-
-class ComposerError(MarkedYAMLError):
-    pass
-
-class Composer:
-
-    def __init__(self):
-        self.anchors = {}
-
-    def check_node(self):
-        # Drop the STREAM-START event.
-        if self.check_event(StreamStartEvent):
-            self.get_event()
-
-        # If there are more documents available?
-        return not self.check_event(StreamEndEvent)
-
-    def get_node(self):
-        # Get the root node of the next document.
-        if not self.check_event(StreamEndEvent):
-            return self.compose_document()
-
-    def get_single_node(self):
-        # Drop the STREAM-START event.
-        self.get_event()
-
-        # Compose a document if the stream is not empty.
-        document = None
-        if not self.check_event(StreamEndEvent):
-            document = self.compose_document()
-
-        # Ensure that the stream contains no more documents.
-        if not self.check_event(StreamEndEvent):
-            event = self.get_event()
-            raise ComposerError("expected a single document in the stream",
-                    document.start_mark, "but found another document",
-                    event.start_mark)
-
-        # Drop the STREAM-END event.
-        self.get_event()
-
-        return document
-
-    def compose_document(self):
-        # Drop the DOCUMENT-START event.
-        self.get_event()
-
-        # Compose the root node.
-        node = self.compose_node(None, None)
-
-        # Drop the DOCUMENT-END event.
-        self.get_event()
-
-        self.anchors = {}
-        return node
-
-    def compose_node(self, parent, index):
-        if self.check_event(AliasEvent):
-            event = self.get_event()
-            anchor = event.anchor
-            if anchor not in self.anchors:
-                raise ComposerError(None, None, "found undefined alias %r"
-                        % anchor, event.start_mark)
-            return self.anchors[anchor]
-        event = self.peek_event()
-        anchor = event.anchor
-        if anchor is not None:
-            if anchor in self.anchors:
-                raise ComposerError("found duplicate anchor %r; first occurence"
-                        % anchor, self.anchors[anchor].start_mark,
-                        "second occurence", event.start_mark)
-        self.descend_resolver(parent, index)
-        if self.check_event(ScalarEvent):
-            node = self.compose_scalar_node(anchor)
-        elif self.check_event(SequenceStartEvent):
-            node = self.compose_sequence_node(anchor)
-        elif self.check_event(MappingStartEvent):
-            node = self.compose_mapping_node(anchor)
-        self.ascend_resolver()
-        return node
-
-    def compose_scalar_node(self, anchor):
-        event = self.get_event()
-        tag = event.tag
-        if tag is None or tag == '!':
-            tag = self.resolve(ScalarNode, event.value, event.implicit)
-        node = ScalarNode(tag, event.value,
-                event.start_mark, event.end_mark, style=event.style)
-        if anchor is not None:
-            self.anchors[anchor] = node
-        return node
-
-    def compose_sequence_node(self, anchor):
-        start_event = self.get_event()
-        tag = start_event.tag
-        if tag is None or tag == '!':
-            tag = self.resolve(SequenceNode, None, start_event.implicit)
-        node = SequenceNode(tag, [],
-                start_event.start_mark, None,
-                flow_style=start_event.flow_style)
-        if anchor is not None:
-            self.anchors[anchor] = node
-        index = 0
-        while not self.check_event(SequenceEndEvent):
-            node.value.append(self.compose_node(node, index))
-            index += 1
-        end_event = self.get_event()
-        node.end_mark = end_event.end_mark
-        return node
-
-    def compose_mapping_node(self, anchor):
-        start_event = self.get_event()
-        tag = start_event.tag
-        if tag is None or tag == '!':
-            tag = self.resolve(MappingNode, None, start_event.implicit)
-        node = MappingNode(tag, [],
-                start_event.start_mark, None,
-                flow_style=start_event.flow_style)
-        if anchor is not None:
-            self.anchors[anchor] = node
-        while not self.check_event(MappingEndEvent):
-            #key_event = self.peek_event()
-            item_key = self.compose_node(node, None)
-            #if item_key in node.value:
-            #    raise ComposerError("while composing a mapping", start_event.start_mark,
-            #            "found duplicate key", key_event.start_mark)
-            item_value = self.compose_node(node, item_key)
-            #node.value[item_key] = item_value
-            node.value.append((item_key, item_value))
-        end_event = self.get_event()
-        node.end_mark = end_event.end_mark
-        return node
-
diff --git a/lib/spack/external/yaml/lib3/yaml/constructor.py b/lib/spack/external/yaml/lib3/yaml/constructor.py
deleted file mode 100644
index 981543aebb..0000000000
--- a/lib/spack/external/yaml/lib3/yaml/constructor.py
+++ /dev/null
@@ -1,686 +0,0 @@
-
-__all__ = ['BaseConstructor', 'SafeConstructor', 'Constructor',
-    'ConstructorError']
-
-from .error import *
-from .nodes import *
-
-import collections, datetime, base64, binascii, re, sys, types
-
-class ConstructorError(MarkedYAMLError):
-    pass
-
-class BaseConstructor:
-
-    yaml_constructors = {}
-    yaml_multi_constructors = {}
-
-    def __init__(self):
-        self.constructed_objects = {}
-        self.recursive_objects = {}
-        self.state_generators = []
-        self.deep_construct = False
-
-    def check_data(self):
-        # If there are more documents available?
-        return self.check_node()
-
-    def get_data(self):
-        # Construct and return the next document.
-        if self.check_node():
-            return self.construct_document(self.get_node())
-
-    def get_single_data(self):
-        # Ensure that the stream contains a single document and construct it.
-        node = self.get_single_node()
-        if node is not None:
-            return self.construct_document(node)
-        return None
-
-    def construct_document(self, node):
-        data = self.construct_object(node)
-        while self.state_generators:
-            state_generators = self.state_generators
-            self.state_generators = []
-            for generator in state_generators:
-                for dummy in generator:
-                    pass
-        self.constructed_objects = {}
-        self.recursive_objects = {}
-        self.deep_construct = False
-        return data
-
-    def construct_object(self, node, deep=False):
-        if node in self.constructed_objects:
-            return self.constructed_objects[node]
-        if deep:
-            old_deep = self.deep_construct
-            self.deep_construct = True
-        if node in self.recursive_objects:
-            raise ConstructorError(None, None,
-                    "found unconstructable recursive node", node.start_mark)
-        self.recursive_objects[node] = None
-        constructor = None
-        tag_suffix = None
-        if node.tag in self.yaml_constructors:
-            constructor = self.yaml_constructors[node.tag]
-        else:
-            for tag_prefix in self.yaml_multi_constructors:
-                if node.tag.startswith(tag_prefix):
-                    tag_suffix = node.tag[len(tag_prefix):]
-                    constructor = self.yaml_multi_constructors[tag_prefix]
-                    break
-            else:
-                if None in self.yaml_multi_constructors:
-                    tag_suffix = node.tag
-                    constructor = self.yaml_multi_constructors[None]
-                elif None in self.yaml_constructors:
-                    constructor = self.yaml_constructors[None]
-                elif isinstance(node, ScalarNode):
-                    constructor = self.__class__.construct_scalar
-                elif isinstance(node, SequenceNode):
-                    constructor = self.__class__.construct_sequence
-                elif isinstance(node, MappingNode):
-                    constructor = self.__class__.construct_mapping
-        if tag_suffix is None:
-            data = constructor(self, node)
-        else:
-            data = constructor(self, tag_suffix, node)
-        if isinstance(data, types.GeneratorType):
-            generator = data
-            data = next(generator)
-            if self.deep_construct:
-                for dummy in generator:
-                    pass
-            else:
-                self.state_generators.append(generator)
-        self.constructed_objects[node] = data
-        del self.recursive_objects[node]
-        if deep:
-            self.deep_construct = old_deep
-        return data
-
-    def construct_scalar(self, node):
-        if not isinstance(node, ScalarNode):
-            raise ConstructorError(None, None,
-                    "expected a scalar node, but found %s" % node.id,
-                    node.start_mark)
-        return node.value
-
-    def construct_sequence(self, node, deep=False):
-        if not isinstance(node, SequenceNode):
-            raise ConstructorError(None, None,
-                    "expected a sequence node, but found %s" % node.id,
-                    node.start_mark)
-        return [self.construct_object(child, deep=deep)
-                for child in node.value]
-
-    def construct_mapping(self, node, deep=False):
-        if not isinstance(node, MappingNode):
-            raise ConstructorError(None, None,
-                    "expected a mapping node, but found %s" % node.id,
-                    node.start_mark)
-        mapping = {}
-        for key_node, value_node in node.value:
-            key = self.construct_object(key_node, deep=deep)
-            if not isinstance(key, collections.Hashable):
-                raise ConstructorError("while constructing a mapping", node.start_mark,
-                        "found unhashable key", key_node.start_mark)
-            value = self.construct_object(value_node, deep=deep)
-            mapping[key] = value
-        return mapping
-
-    def construct_pairs(self, node, deep=False):
-        if not isinstance(node, MappingNode):
-            raise ConstructorError(None, None,
-                    "expected a mapping node, but found %s" % node.id,
-                    node.start_mark)
-        pairs = []
-        for key_node, value_node in node.value:
-            key = self.construct_object(key_node, deep=deep)
-            value = self.construct_object(value_node, deep=deep)
-            pairs.append((key, value))
-        return pairs
-
-    @classmethod
-    def add_constructor(cls, tag, constructor):
-        if not 'yaml_constructors' in cls.__dict__:
-            cls.yaml_constructors = cls.yaml_constructors.copy()
-        cls.yaml_constructors[tag] = constructor
-
-    @classmethod
-    def add_multi_constructor(cls, tag_prefix, multi_constructor):
-        if not 'yaml_multi_constructors' in cls.__dict__:
-            cls.yaml_multi_constructors = cls.yaml_multi_constructors.copy()
-        cls.yaml_multi_constructors[tag_prefix] = multi_constructor
-
-class SafeConstructor(BaseConstructor):
-
-    def construct_scalar(self, node):
-        if isinstance(node, MappingNode):
-            for key_node, value_node in node.value:
-                if key_node.tag == 'tag:yaml.org,2002:value':
-                    return self.construct_scalar(value_node)
-        return super().construct_scalar(node)
-
-    def flatten_mapping(self, node):
-        merge = []
-        index = 0
-        while index < len(node.value):
-            key_node, value_node = node.value[index]
-            if key_node.tag == 'tag:yaml.org,2002:merge':
-                del node.value[index]
-                if isinstance(value_node, MappingNode):
-                    self.flatten_mapping(value_node)
-                    merge.extend(value_node.value)
-                elif isinstance(value_node, SequenceNode):
-                    submerge = []
-                    for subnode in value_node.value:
-                        if not isinstance(subnode, MappingNode):
-                            raise ConstructorError("while constructing a mapping",
-                                    node.start_mark,
-                                    "expected a mapping for merging, but found %s"
-                                    % subnode.id, subnode.start_mark)
-                        self.flatten_mapping(subnode)
-                        submerge.append(subnode.value)
-                    submerge.reverse()
-                    for value in submerge:
-                        merge.extend(value)
-                else:
-                    raise ConstructorError("while constructing a mapping", node.start_mark,
-                            "expected a mapping or list of mappings for merging, but found %s"
-                            % value_node.id, value_node.start_mark)
-            elif key_node.tag == 'tag:yaml.org,2002:value':
-                key_node.tag = 'tag:yaml.org,2002:str'
-                index += 1
-            else:
-                index += 1
-        if merge:
-            node.value = merge + node.value
-
-    def construct_mapping(self, node, deep=False):
-        if isinstance(node, MappingNode):
-            self.flatten_mapping(node)
-        return super().construct_mapping(node, deep=deep)
-
-    def construct_yaml_null(self, node):
-        self.construct_scalar(node)
-        return None
-
-    bool_values = {
-        'yes':      True,
-        'no':       False,
-        'true':     True,
-        'false':    False,
-        'on':       True,
-        'off':      False,
-    }
-
-    def construct_yaml_bool(self, node):
-        value = self.construct_scalar(node)
-        return self.bool_values[value.lower()]
-
-    def construct_yaml_int(self, node):
-        value = self.construct_scalar(node)
-        value = value.replace('_', '')
-        sign = +1
-        if value[0] == '-':
-            sign = -1
-        if value[0] in '+-':
-            value = value[1:]
-        if value == '0':
-            return 0
-        elif value.startswith('0b'):
-            return sign*int(value[2:], 2)
-        elif value.startswith('0x'):
-            return sign*int(value[2:], 16)
-        elif value[0] == '0':
-            return sign*int(value, 8)
-        elif ':' in value:
-            digits = [int(part) for part in value.split(':')]
-            digits.reverse()
-            base = 1
-            value = 0
-            for digit in digits:
-                value += digit*base
-                base *= 60
-            return sign*value
-        else:
-            return sign*int(value)
-
-    inf_value = 1e300
-    while inf_value != inf_value*inf_value:
-        inf_value *= inf_value
-    nan_value = -inf_value/inf_value   # Trying to make a quiet NaN (like C99).
-
-    def construct_yaml_float(self, node):
-        value = self.construct_scalar(node)
-        value = value.replace('_', '').lower()
-        sign = +1
-        if value[0] == '-':
-            sign = -1
-        if value[0] in '+-':
-            value = value[1:]
-        if value == '.inf':
-            return sign*self.inf_value
-        elif value == '.nan':
-            return self.nan_value
-        elif ':' in value:
-            digits = [float(part) for part in value.split(':')]
-            digits.reverse()
-            base = 1
-            value = 0.0
-            for digit in digits:
-                value += digit*base
-                base *= 60
-            return sign*value
-        else:
-            return sign*float(value)
-
-    def construct_yaml_binary(self, node):
-        try:
-            value = self.construct_scalar(node).encode('ascii')
-        except UnicodeEncodeError as exc:
-            raise ConstructorError(None, None,
-                    "failed to convert base64 data into ascii: %s" % exc,
-                    node.start_mark)
-        try:
-            if hasattr(base64, 'decodebytes'):
-                return base64.decodebytes(value)
-            else:
-                return base64.decodestring(value)
-        except binascii.Error as exc:
-            raise ConstructorError(None, None,
-                    "failed to decode base64 data: %s" % exc, node.start_mark)
-
-    timestamp_regexp = re.compile(
-            r'''^(?P<year>[0-9][0-9][0-9][0-9])
-                -(?P<month>[0-9][0-9]?)
-                -(?P<day>[0-9][0-9]?)
-                (?:(?:[Tt]|[ \t]+)
-                (?P<hour>[0-9][0-9]?)
-                :(?P<minute>[0-9][0-9])
-                :(?P<second>[0-9][0-9])
-                (?:\.(?P<fraction>[0-9]*))?
-                (?:[ \t]*(?P<tz>Z|(?P<tz_sign>[-+])(?P<tz_hour>[0-9][0-9]?)
-                (?::(?P<tz_minute>[0-9][0-9]))?))?)?$''', re.X)
-
-    def construct_yaml_timestamp(self, node):
-        value = self.construct_scalar(node)
-        match = self.timestamp_regexp.match(node.value)
-        values = match.groupdict()
-        year = int(values['year'])
-        month = int(values['month'])
-        day = int(values['day'])
-        if not values['hour']:
-            return datetime.date(year, month, day)
-        hour = int(values['hour'])
-        minute = int(values['minute'])
-        second = int(values['second'])
-        fraction = 0
-        if values['fraction']:
-            fraction = values['fraction'][:6]
-            while len(fraction) < 6:
-                fraction += '0'
-            fraction = int(fraction)
-        delta = None
-        if values['tz_sign']:
-            tz_hour = int(values['tz_hour'])
-            tz_minute = int(values['tz_minute'] or 0)
-            delta = datetime.timedelta(hours=tz_hour, minutes=tz_minute)
-            if values['tz_sign'] == '-':
-                delta = -delta
-        data = datetime.datetime(year, month, day, hour, minute, second, fraction)
-        if delta:
-            data -= delta
-        return data
-
-    def construct_yaml_omap(self, node):
-        # Note: we do not check for duplicate keys, because it's too
-        # CPU-expensive.
-        omap = []
-        yield omap
-        if not isinstance(node, SequenceNode):
-            raise ConstructorError("while constructing an ordered map", node.start_mark,
-                    "expected a sequence, but found %s" % node.id, node.start_mark)
-        for subnode in node.value:
-            if not isinstance(subnode, MappingNode):
-                raise ConstructorError("while constructing an ordered map", node.start_mark,
-                        "expected a mapping of length 1, but found %s" % subnode.id,
-                        subnode.start_mark)
-            if len(subnode.value) != 1:
-                raise ConstructorError("while constructing an ordered map", node.start_mark,
-                        "expected a single mapping item, but found %d items" % len(subnode.value),
-                        subnode.start_mark)
-            key_node, value_node = subnode.value[0]
-            key = self.construct_object(key_node)
-            value = self.construct_object(value_node)
-            omap.append((key, value))
-
-    def construct_yaml_pairs(self, node):
-        # Note: the same code as `construct_yaml_omap`.
-        pairs = []
-        yield pairs
-        if not isinstance(node, SequenceNode):
-            raise ConstructorError("while constructing pairs", node.start_mark,
-                    "expected a sequence, but found %s" % node.id, node.start_mark)
-        for subnode in node.value:
-            if not isinstance(subnode, MappingNode):
-                raise ConstructorError("while constructing pairs", node.start_mark,
-                        "expected a mapping of length 1, but found %s" % subnode.id,
-                        subnode.start_mark)
-            if len(subnode.value) != 1:
-                raise ConstructorError("while constructing pairs", node.start_mark,
-                        "expected a single mapping item, but found %d items" % len(subnode.value),
-                        subnode.start_mark)
-            key_node, value_node = subnode.value[0]
-            key = self.construct_object(key_node)
-            value = self.construct_object(value_node)
-            pairs.append((key, value))
-
-    def construct_yaml_set(self, node):
-        data = set()
-        yield data
-        value = self.construct_mapping(node)
-        data.update(value)
-
-    def construct_yaml_str(self, node):
-        return self.construct_scalar(node)
-
-    def construct_yaml_seq(self, node):
-        data = []
-        yield data
-        data.extend(self.construct_sequence(node))
-
-    def construct_yaml_map(self, node):
-        data = {}
-        yield data
-        value = self.construct_mapping(node)
-        data.update(value)
-
-    def construct_yaml_object(self, node, cls):
-        data = cls.__new__(cls)
-        yield data
-        if hasattr(data, '__setstate__'):
-            state = self.construct_mapping(node, deep=True)
-            data.__setstate__(state)
-        else:
-            state = self.construct_mapping(node)
-            data.__dict__.update(state)
-
-    def construct_undefined(self, node):
-        raise ConstructorError(None, None,
-                "could not determine a constructor for the tag %r" % node.tag,
-                node.start_mark)
-
-SafeConstructor.add_constructor(
-        'tag:yaml.org,2002:null',
-        SafeConstructor.construct_yaml_null)
-
-SafeConstructor.add_constructor(
-        'tag:yaml.org,2002:bool',
-        SafeConstructor.construct_yaml_bool)
-
-SafeConstructor.add_constructor(
-        'tag:yaml.org,2002:int',
-        SafeConstructor.construct_yaml_int)
-
-SafeConstructor.add_constructor(
-        'tag:yaml.org,2002:float',
-        SafeConstructor.construct_yaml_float)
-
-SafeConstructor.add_constructor(
-        'tag:yaml.org,2002:binary',
-        SafeConstructor.construct_yaml_binary)
-
-SafeConstructor.add_constructor(
-        'tag:yaml.org,2002:timestamp',
-        SafeConstructor.construct_yaml_timestamp)
-
-SafeConstructor.add_constructor(
-        'tag:yaml.org,2002:omap',
-        SafeConstructor.construct_yaml_omap)
-
-SafeConstructor.add_constructor(
-        'tag:yaml.org,2002:pairs',
-        SafeConstructor.construct_yaml_pairs)
-
-SafeConstructor.add_constructor(
-        'tag:yaml.org,2002:set',
-        SafeConstructor.construct_yaml_set)
-
-SafeConstructor.add_constructor(
-        'tag:yaml.org,2002:str',
-        SafeConstructor.construct_yaml_str)
-
-SafeConstructor.add_constructor(
-        'tag:yaml.org,2002:seq',
-        SafeConstructor.construct_yaml_seq)
-
-SafeConstructor.add_constructor(
-        'tag:yaml.org,2002:map',
-        SafeConstructor.construct_yaml_map)
-
-SafeConstructor.add_constructor(None,
-        SafeConstructor.construct_undefined)
-
-class Constructor(SafeConstructor):
-
-    def construct_python_str(self, node):
-        return self.construct_scalar(node)
-
-    def construct_python_unicode(self, node):
-        return self.construct_scalar(node)
-
-    def construct_python_bytes(self, node):
-        try:
-            value = self.construct_scalar(node).encode('ascii')
-        except UnicodeEncodeError as exc:
-            raise ConstructorError(None, None,
-                    "failed to convert base64 data into ascii: %s" % exc,
-                    node.start_mark)
-        try:
-            if hasattr(base64, 'decodebytes'):
-                return base64.decodebytes(value)
-            else:
-                return base64.decodestring(value)
-        except binascii.Error as exc:
-            raise ConstructorError(None, None,
-                    "failed to decode base64 data: %s" % exc, node.start_mark)
-
-    def construct_python_long(self, node):
-        return self.construct_yaml_int(node)
-
-    def construct_python_complex(self, node):
-       return complex(self.construct_scalar(node))
-
-    def construct_python_tuple(self, node):
-        return tuple(self.construct_sequence(node))
-
-    def find_python_module(self, name, mark):
-        if not name:
-            raise ConstructorError("while constructing a Python module", mark,
-                    "expected non-empty name appended to the tag", mark)
-        try:
-            __import__(name)
-        except ImportError as exc:
-            raise ConstructorError("while constructing a Python module", mark,
-                    "cannot find module %r (%s)" % (name, exc), mark)
-        return sys.modules[name]
-
-    def find_python_name(self, name, mark):
-        if not name:
-            raise ConstructorError("while constructing a Python object", mark,
-                    "expected non-empty name appended to the tag", mark)
-        if '.' in name:
-            module_name, object_name = name.rsplit('.', 1)
-        else:
-            module_name = 'builtins'
-            object_name = name
-        try:
-            __import__(module_name)
-        except ImportError as exc:
-            raise ConstructorError("while constructing a Python object", mark,
-                    "cannot find module %r (%s)" % (module_name, exc), mark)
-        module = sys.modules[module_name]
-        if not hasattr(module, object_name):
-            raise ConstructorError("while constructing a Python object", mark,
-                    "cannot find %r in the module %r"
-                    % (object_name, module.__name__), mark)
-        return getattr(module, object_name)
-
-    def construct_python_name(self, suffix, node):
-        value = self.construct_scalar(node)
-        if value:
-            raise ConstructorError("while constructing a Python name", node.start_mark,
-                    "expected the empty value, but found %r" % value, node.start_mark)
-        return self.find_python_name(suffix, node.start_mark)
-
-    def construct_python_module(self, suffix, node):
-        value = self.construct_scalar(node)
-        if value:
-            raise ConstructorError("while constructing a Python module", node.start_mark,
-                    "expected the empty value, but found %r" % value, node.start_mark)
-        return self.find_python_module(suffix, node.start_mark)
-
-    def make_python_instance(self, suffix, node,
-            args=None, kwds=None, newobj=False):
-        if not args:
-            args = []
-        if not kwds:
-            kwds = {}
-        cls = self.find_python_name(suffix, node.start_mark)
-        if newobj and isinstance(cls, type):
-            return cls.__new__(cls, *args, **kwds)
-        else:
-            return cls(*args, **kwds)
-
-    def set_python_instance_state(self, instance, state):
-        if hasattr(instance, '__setstate__'):
-            instance.__setstate__(state)
-        else:
-            slotstate = {}
-            if isinstance(state, tuple) and len(state) == 2:
-                state, slotstate = state
-            if hasattr(instance, '__dict__'):
-                instance.__dict__.update(state)
-            elif state:
-                slotstate.update(state)
-            for key, value in slotstate.items():
-                setattr(object, key, value)
-
-    def construct_python_object(self, suffix, node):
-        # Format:
-        #   !!python/object:module.name { ... state ... }
-        instance = self.make_python_instance(suffix, node, newobj=True)
-        yield instance
-        deep = hasattr(instance, '__setstate__')
-        state = self.construct_mapping(node, deep=deep)
-        self.set_python_instance_state(instance, state)
-
-    def construct_python_object_apply(self, suffix, node, newobj=False):
-        # Format:
-        #   !!python/object/apply       # (or !!python/object/new)
-        #   args: [ ... arguments ... ]
-        #   kwds: { ... keywords ... }
-        #   state: ... state ...
-        #   listitems: [ ... listitems ... ]
-        #   dictitems: { ... dictitems ... }
-        # or short format:
-        #   !!python/object/apply [ ... arguments ... ]
-        # The difference between !!python/object/apply and !!python/object/new
-        # is how an object is created, check make_python_instance for details.
-        if isinstance(node, SequenceNode):
-            args = self.construct_sequence(node, deep=True)
-            kwds = {}
-            state = {}
-            listitems = []
-            dictitems = {}
-        else:
-            value = self.construct_mapping(node, deep=True)
-            args = value.get('args', [])
-            kwds = value.get('kwds', {})
-            state = value.get('state', {})
-            listitems = value.get('listitems', [])
-            dictitems = value.get('dictitems', {})
-        instance = self.make_python_instance(suffix, node, args, kwds, newobj)
-        if state:
-            self.set_python_instance_state(instance, state)
-        if listitems:
-            instance.extend(listitems)
-        if dictitems:
-            for key in dictitems:
-                instance[key] = dictitems[key]
-        return instance
-
-    def construct_python_object_new(self, suffix, node):
-        return self.construct_python_object_apply(suffix, node, newobj=True)
-
-Constructor.add_constructor(
-    'tag:yaml.org,2002:python/none',
-    Constructor.construct_yaml_null)
-
-Constructor.add_constructor(
-    'tag:yaml.org,2002:python/bool',
-    Constructor.construct_yaml_bool)
-
-Constructor.add_constructor(
-    'tag:yaml.org,2002:python/str',
-    Constructor.construct_python_str)
-
-Constructor.add_constructor(
-    'tag:yaml.org,2002:python/unicode',
-    Constructor.construct_python_unicode)
-
-Constructor.add_constructor(
-    'tag:yaml.org,2002:python/bytes',
-    Constructor.construct_python_bytes)
-
-Constructor.add_constructor(
-    'tag:yaml.org,2002:python/int',
-    Constructor.construct_yaml_int)
-
-Constructor.add_constructor(
-    'tag:yaml.org,2002:python/long',
-    Constructor.construct_python_long)
-
-Constructor.add_constructor(
-    'tag:yaml.org,2002:python/float',
-    Constructor.construct_yaml_float)
-
-Constructor.add_constructor(
-    'tag:yaml.org,2002:python/complex',
-    Constructor.construct_python_complex)
-
-Constructor.add_constructor(
-    'tag:yaml.org,2002:python/list',
-    Constructor.construct_yaml_seq)
-
-Constructor.add_constructor(
-    'tag:yaml.org,2002:python/tuple',
-    Constructor.construct_python_tuple)
-
-Constructor.add_constructor(
-    'tag:yaml.org,2002:python/dict',
-    Constructor.construct_yaml_map)
-
-Constructor.add_multi_constructor(
-    'tag:yaml.org,2002:python/name:',
-    Constructor.construct_python_name)
-
-Constructor.add_multi_constructor(
-    'tag:yaml.org,2002:python/module:',
-    Constructor.construct_python_module)
-
-Constructor.add_multi_constructor(
-    'tag:yaml.org,2002:python/object:',
-    Constructor.construct_python_object)
-
-Constructor.add_multi_constructor(
-    'tag:yaml.org,2002:python/object/apply:',
-    Constructor.construct_python_object_apply)
-
-Constructor.add_multi_constructor(
-    'tag:yaml.org,2002:python/object/new:',
-    Constructor.construct_python_object_new)
-
diff --git a/lib/spack/external/yaml/lib3/yaml/cyaml.py b/lib/spack/external/yaml/lib3/yaml/cyaml.py
deleted file mode 100644
index d5cb87e994..0000000000
--- a/lib/spack/external/yaml/lib3/yaml/cyaml.py
+++ /dev/null
@@ -1,85 +0,0 @@
-
-__all__ = ['CBaseLoader', 'CSafeLoader', 'CLoader',
-        'CBaseDumper', 'CSafeDumper', 'CDumper']
-
-from _yaml import CParser, CEmitter
-
-from .constructor import *
-
-from .serializer import *
-from .representer import *
-
-from .resolver import *
-
-class CBaseLoader(CParser, BaseConstructor, BaseResolver):
-
-    def __init__(self, stream):
-        CParser.__init__(self, stream)
-        BaseConstructor.__init__(self)
-        BaseResolver.__init__(self)
-
-class CSafeLoader(CParser, SafeConstructor, Resolver):
-
-    def __init__(self, stream):
-        CParser.__init__(self, stream)
-        SafeConstructor.__init__(self)
-        Resolver.__init__(self)
-
-class CLoader(CParser, Constructor, Resolver):
-
-    def __init__(self, stream):
-        CParser.__init__(self, stream)
-        Constructor.__init__(self)
-        Resolver.__init__(self)
-
-class CBaseDumper(CEmitter, BaseRepresenter, BaseResolver):
-
-    def __init__(self, stream,
-            default_style=None, default_flow_style=None,
-            canonical=None, indent=None, width=None,
-            allow_unicode=None, line_break=None,
-            encoding=None, explicit_start=None, explicit_end=None,
-            version=None, tags=None):
-        CEmitter.__init__(self, stream, canonical=canonical,
-                indent=indent, width=width, encoding=encoding,
-                allow_unicode=allow_unicode, line_break=line_break,
-                explicit_start=explicit_start, explicit_end=explicit_end,
-                version=version, tags=tags)
-        Representer.__init__(self, default_style=default_style,
-                default_flow_style=default_flow_style)
-        Resolver.__init__(self)
-
-class CSafeDumper(CEmitter, SafeRepresenter, Resolver):
-
-    def __init__(self, stream,
-            default_style=None, default_flow_style=None,
-            canonical=None, indent=None, width=None,
-            allow_unicode=None, line_break=None,
-            encoding=None, explicit_start=None, explicit_end=None,
-            version=None, tags=None):
-        CEmitter.__init__(self, stream, canonical=canonical,
-                indent=indent, width=width, encoding=encoding,
-                allow_unicode=allow_unicode, line_break=line_break,
-                explicit_start=explicit_start, explicit_end=explicit_end,
-                version=version, tags=tags)
-        SafeRepresenter.__init__(self, default_style=default_style,
-                default_flow_style=default_flow_style)
-        Resolver.__init__(self)
-
-class CDumper(CEmitter, Serializer, Representer, Resolver):
-
-    def __init__(self, stream,
-            default_style=None, default_flow_style=None,
-            canonical=None, indent=None, width=None,
-            allow_unicode=None, line_break=None,
-            encoding=None, explicit_start=None, explicit_end=None,
-            version=None, tags=None):
-        CEmitter.__init__(self, stream, canonical=canonical,
-                indent=indent, width=width, encoding=encoding,
-                allow_unicode=allow_unicode, line_break=line_break,
-                explicit_start=explicit_start, explicit_end=explicit_end,
-                version=version, tags=tags)
-        Representer.__init__(self, default_style=default_style,
-                default_flow_style=default_flow_style)
-        Resolver.__init__(self)
-
diff --git a/lib/spack/external/yaml/lib3/yaml/dumper.py b/lib/spack/external/yaml/lib3/yaml/dumper.py
deleted file mode 100644
index 0b69128771..0000000000
--- a/lib/spack/external/yaml/lib3/yaml/dumper.py
+++ /dev/null
@@ -1,62 +0,0 @@
-
-__all__ = ['BaseDumper', 'SafeDumper', 'Dumper']
-
-from .emitter import *
-from .serializer import *
-from .representer import *
-from .resolver import *
-
-class BaseDumper(Emitter, Serializer, BaseRepresenter, BaseResolver):
-
-    def __init__(self, stream,
-            default_style=None, default_flow_style=None,
-            canonical=None, indent=None, width=None,
-            allow_unicode=None, line_break=None,
-            encoding=None, explicit_start=None, explicit_end=None,
-            version=None, tags=None):
-        Emitter.__init__(self, stream, canonical=canonical,
-                indent=indent, width=width,
-                allow_unicode=allow_unicode, line_break=line_break)
-        Serializer.__init__(self, encoding=encoding,
-                explicit_start=explicit_start, explicit_end=explicit_end,
-                version=version, tags=tags)
-        Representer.__init__(self, default_style=default_style,
-                default_flow_style=default_flow_style)
-        Resolver.__init__(self)
-
-class SafeDumper(Emitter, Serializer, SafeRepresenter, Resolver):
-
-    def __init__(self, stream,
-            default_style=None, default_flow_style=None,
-            canonical=None, indent=None, width=None,
-            allow_unicode=None, line_break=None,
-            encoding=None, explicit_start=None, explicit_end=None,
-            version=None, tags=None):
-        Emitter.__init__(self, stream, canonical=canonical,
-                indent=indent, width=width,
-                allow_unicode=allow_unicode, line_break=line_break)
-        Serializer.__init__(self, encoding=encoding,
-                explicit_start=explicit_start, explicit_end=explicit_end,
-                version=version, tags=tags)
-        SafeRepresenter.__init__(self, default_style=default_style,
-                default_flow_style=default_flow_style)
-        Resolver.__init__(self)
-
-class Dumper(Emitter, Serializer, Representer, Resolver):
-
-    def __init__(self, stream,
-            default_style=None, default_flow_style=None,
-            canonical=None, indent=None, width=None,
-            allow_unicode=None, line_break=None,
-            encoding=None, explicit_start=None, explicit_end=None,
-            version=None, tags=None):
-        Emitter.__init__(self, stream, canonical=canonical,
-                indent=indent, width=width,
-                allow_unicode=allow_unicode, line_break=line_break)
-        Serializer.__init__(self, encoding=encoding,
-                explicit_start=explicit_start, explicit_end=explicit_end,
-                version=version, tags=tags)
-        Representer.__init__(self, default_style=default_style,
-                default_flow_style=default_flow_style)
-        Resolver.__init__(self)
-
diff --git a/lib/spack/external/yaml/lib3/yaml/emitter.py b/lib/spack/external/yaml/lib3/yaml/emitter.py
deleted file mode 100644
index 34cb145a5f..0000000000
--- a/lib/spack/external/yaml/lib3/yaml/emitter.py
+++ /dev/null
@@ -1,1137 +0,0 @@
-
-# Emitter expects events obeying the following grammar:
-# stream ::= STREAM-START document* STREAM-END
-# document ::= DOCUMENT-START node DOCUMENT-END
-# node ::= SCALAR | sequence | mapping
-# sequence ::= SEQUENCE-START node* SEQUENCE-END
-# mapping ::= MAPPING-START (node node)* MAPPING-END
-
-__all__ = ['Emitter', 'EmitterError']
-
-from .error import YAMLError
-from .events import *
-
-class EmitterError(YAMLError):
-    pass
-
-class ScalarAnalysis:
-    def __init__(self, scalar, empty, multiline,
-            allow_flow_plain, allow_block_plain,
-            allow_single_quoted, allow_double_quoted,
-            allow_block):
-        self.scalar = scalar
-        self.empty = empty
-        self.multiline = multiline
-        self.allow_flow_plain = allow_flow_plain
-        self.allow_block_plain = allow_block_plain
-        self.allow_single_quoted = allow_single_quoted
-        self.allow_double_quoted = allow_double_quoted
-        self.allow_block = allow_block
-
-class Emitter:
-
-    DEFAULT_TAG_PREFIXES = {
-        '!' : '!',
-        'tag:yaml.org,2002:' : '!!',
-    }
-
-    def __init__(self, stream, canonical=None, indent=None, width=None,
-            allow_unicode=None, line_break=None):
-
-        # The stream should have the methods `write` and possibly `flush`.
-        self.stream = stream
-
-        # Encoding can be overriden by STREAM-START.
-        self.encoding = None
-
-        # Emitter is a state machine with a stack of states to handle nested
-        # structures.
-        self.states = []
-        self.state = self.expect_stream_start
-
-        # Current event and the event queue.
-        self.events = []
-        self.event = None
-
-        # The current indentation level and the stack of previous indents.
-        self.indents = []
-        self.indent = None
-
-        # Flow level.
-        self.flow_level = 0
-
-        # Contexts.
-        self.root_context = False
-        self.sequence_context = False
-        self.mapping_context = False
-        self.simple_key_context = False
-
-        # Characteristics of the last emitted character:
-        #  - current position.
-        #  - is it a whitespace?
-        #  - is it an indention character
-        #    (indentation space, '-', '?', or ':')?
-        self.line = 0
-        self.column = 0
-        self.whitespace = True
-        self.indention = True
-
-        # Whether the document requires an explicit document indicator
-        self.open_ended = False
-
-        # Formatting details.
-        self.canonical = canonical
-        self.allow_unicode = allow_unicode
-        self.best_indent = 2
-        if indent and 1 < indent < 10:
-            self.best_indent = indent
-        self.best_width = 80
-        if width and width > self.best_indent*2:
-            self.best_width = width
-        self.best_line_break = '\n'
-        if line_break in ['\r', '\n', '\r\n']:
-            self.best_line_break = line_break
-
-        # Tag prefixes.
-        self.tag_prefixes = None
-
-        # Prepared anchor and tag.
-        self.prepared_anchor = None
-        self.prepared_tag = None
-
-        # Scalar analysis and style.
-        self.analysis = None
-        self.style = None
-
-    def dispose(self):
-        # Reset the state attributes (to clear self-references)
-        self.states = []
-        self.state = None
-
-    def emit(self, event):
-        self.events.append(event)
-        while not self.need_more_events():
-            self.event = self.events.pop(0)
-            self.state()
-            self.event = None
-
-    # In some cases, we wait for a few next events before emitting.
-
-    def need_more_events(self):
-        if not self.events:
-            return True
-        event = self.events[0]
-        if isinstance(event, DocumentStartEvent):
-            return self.need_events(1)
-        elif isinstance(event, SequenceStartEvent):
-            return self.need_events(2)
-        elif isinstance(event, MappingStartEvent):
-            return self.need_events(3)
-        else:
-            return False
-
-    def need_events(self, count):
-        level = 0
-        for event in self.events[1:]:
-            if isinstance(event, (DocumentStartEvent, CollectionStartEvent)):
-                level += 1
-            elif isinstance(event, (DocumentEndEvent, CollectionEndEvent)):
-                level -= 1
-            elif isinstance(event, StreamEndEvent):
-                level = -1
-            if level < 0:
-                return False
-        return (len(self.events) < count+1)
-
-    def increase_indent(self, flow=False, indentless=False):
-        self.indents.append(self.indent)
-        if self.indent is None:
-            if flow:
-                self.indent = self.best_indent
-            else:
-                self.indent = 0
-        elif not indentless:
-            self.indent += self.best_indent
-
-    # States.
-
-    # Stream handlers.
-
-    def expect_stream_start(self):
-        if isinstance(self.event, StreamStartEvent):
-            if self.event.encoding and not hasattr(self.stream, 'encoding'):
-                self.encoding = self.event.encoding
-            self.write_stream_start()
-            self.state = self.expect_first_document_start
-        else:
-            raise EmitterError("expected StreamStartEvent, but got %s"
-                    % self.event)
-
-    def expect_nothing(self):
-        raise EmitterError("expected nothing, but got %s" % self.event)
-
-    # Document handlers.
-
-    def expect_first_document_start(self):
-        return self.expect_document_start(first=True)
-
-    def expect_document_start(self, first=False):
-        if isinstance(self.event, DocumentStartEvent):
-            if (self.event.version or self.event.tags) and self.open_ended:
-                self.write_indicator('...', True)
-                self.write_indent()
-            if self.event.version:
-                version_text = self.prepare_version(self.event.version)
-                self.write_version_directive(version_text)
-            self.tag_prefixes = self.DEFAULT_TAG_PREFIXES.copy()
-            if self.event.tags:
-                handles = sorted(self.event.tags.keys())
-                for handle in handles:
-                    prefix = self.event.tags[handle]
-                    self.tag_prefixes[prefix] = handle
-                    handle_text = self.prepare_tag_handle(handle)
-                    prefix_text = self.prepare_tag_prefix(prefix)
-                    self.write_tag_directive(handle_text, prefix_text)
-            implicit = (first and not self.event.explicit and not self.canonical
-                    and not self.event.version and not self.event.tags
-                    and not self.check_empty_document())
-            if not implicit:
-                self.write_indent()
-                self.write_indicator('---', True)
-                if self.canonical:
-                    self.write_indent()
-            self.state = self.expect_document_root
-        elif isinstance(self.event, StreamEndEvent):
-            if self.open_ended:
-                self.write_indicator('...', True)
-                self.write_indent()
-            self.write_stream_end()
-            self.state = self.expect_nothing
-        else:
-            raise EmitterError("expected DocumentStartEvent, but got %s"
-                    % self.event)
-
-    def expect_document_end(self):
-        if isinstance(self.event, DocumentEndEvent):
-            self.write_indent()
-            if self.event.explicit:
-                self.write_indicator('...', True)
-                self.write_indent()
-            self.flush_stream()
-            self.state = self.expect_document_start
-        else:
-            raise EmitterError("expected DocumentEndEvent, but got %s"
-                    % self.event)
-
-    def expect_document_root(self):
-        self.states.append(self.expect_document_end)
-        self.expect_node(root=True)
-
-    # Node handlers.
-
-    def expect_node(self, root=False, sequence=False, mapping=False,
-            simple_key=False):
-        self.root_context = root
-        self.sequence_context = sequence
-        self.mapping_context = mapping
-        self.simple_key_context = simple_key
-        if isinstance(self.event, AliasEvent):
-            self.expect_alias()
-        elif isinstance(self.event, (ScalarEvent, CollectionStartEvent)):
-            self.process_anchor('&')
-            self.process_tag()
-            if isinstance(self.event, ScalarEvent):
-                self.expect_scalar()
-            elif isinstance(self.event, SequenceStartEvent):
-                if self.flow_level or self.canonical or self.event.flow_style   \
-                        or self.check_empty_sequence():
-                    self.expect_flow_sequence()
-                else:
-                    self.expect_block_sequence()
-            elif isinstance(self.event, MappingStartEvent):
-                if self.flow_level or self.canonical or self.event.flow_style   \
-                        or self.check_empty_mapping():
-                    self.expect_flow_mapping()
-                else:
-                    self.expect_block_mapping()
-        else:
-            raise EmitterError("expected NodeEvent, but got %s" % self.event)
-
-    def expect_alias(self):
-        if self.event.anchor is None:
-            raise EmitterError("anchor is not specified for alias")
-        self.process_anchor('*')
-        self.state = self.states.pop()
-
-    def expect_scalar(self):
-        self.increase_indent(flow=True)
-        self.process_scalar()
-        self.indent = self.indents.pop()
-        self.state = self.states.pop()
-
-    # Flow sequence handlers.
-
-    def expect_flow_sequence(self):
-        self.write_indicator('[', True, whitespace=True)
-        self.flow_level += 1
-        self.increase_indent(flow=True)
-        self.state = self.expect_first_flow_sequence_item
-
-    def expect_first_flow_sequence_item(self):
-        if isinstance(self.event, SequenceEndEvent):
-            self.indent = self.indents.pop()
-            self.flow_level -= 1
-            self.write_indicator(']', False)
-            self.state = self.states.pop()
-        else:
-            if self.canonical or self.column > self.best_width:
-                self.write_indent()
-            self.states.append(self.expect_flow_sequence_item)
-            self.expect_node(sequence=True)
-
-    def expect_flow_sequence_item(self):
-        if isinstance(self.event, SequenceEndEvent):
-            self.indent = self.indents.pop()
-            self.flow_level -= 1
-            if self.canonical:
-                self.write_indicator(',', False)
-                self.write_indent()
-            self.write_indicator(']', False)
-            self.state = self.states.pop()
-        else:
-            self.write_indicator(',', False)
-            if self.canonical or self.column > self.best_width:
-                self.write_indent()
-            self.states.append(self.expect_flow_sequence_item)
-            self.expect_node(sequence=True)
-
-    # Flow mapping handlers.
-
-    def expect_flow_mapping(self):
-        self.write_indicator('{', True, whitespace=True)
-        self.flow_level += 1
-        self.increase_indent(flow=True)
-        self.state = self.expect_first_flow_mapping_key
-
-    def expect_first_flow_mapping_key(self):
-        if isinstance(self.event, MappingEndEvent):
-            self.indent = self.indents.pop()
-            self.flow_level -= 1
-            self.write_indicator('}', False)
-            self.state = self.states.pop()
-        else:
-            if self.canonical or self.column > self.best_width:
-                self.write_indent()
-            if not self.canonical and self.check_simple_key():
-                self.states.append(self.expect_flow_mapping_simple_value)
-                self.expect_node(mapping=True, simple_key=True)
-            else:
-                self.write_indicator('?', True)
-                self.states.append(self.expect_flow_mapping_value)
-                self.expect_node(mapping=True)
-
-    def expect_flow_mapping_key(self):
-        if isinstance(self.event, MappingEndEvent):
-            self.indent = self.indents.pop()
-            self.flow_level -= 1
-            if self.canonical:
-                self.write_indicator(',', False)
-                self.write_indent()
-            self.write_indicator('}', False)
-            self.state = self.states.pop()
-        else:
-            self.write_indicator(',', False)
-            if self.canonical or self.column > self.best_width:
-                self.write_indent()
-            if not self.canonical and self.check_simple_key():
-                self.states.append(self.expect_flow_mapping_simple_value)
-                self.expect_node(mapping=True, simple_key=True)
-            else:
-                self.write_indicator('?', True)
-                self.states.append(self.expect_flow_mapping_value)
-                self.expect_node(mapping=True)
-
-    def expect_flow_mapping_simple_value(self):
-        self.write_indicator(':', False)
-        self.states.append(self.expect_flow_mapping_key)
-        self.expect_node(mapping=True)
-
-    def expect_flow_mapping_value(self):
-        if self.canonical or self.column > self.best_width:
-            self.write_indent()
-        self.write_indicator(':', True)
-        self.states.append(self.expect_flow_mapping_key)
-        self.expect_node(mapping=True)
-
-    # Block sequence handlers.
-
-    def expect_block_sequence(self):
-        indentless = (self.mapping_context and not self.indention)
-        self.increase_indent(flow=False, indentless=indentless)
-        self.state = self.expect_first_block_sequence_item
-
-    def expect_first_block_sequence_item(self):
-        return self.expect_block_sequence_item(first=True)
-
-    def expect_block_sequence_item(self, first=False):
-        if not first and isinstance(self.event, SequenceEndEvent):
-            self.indent = self.indents.pop()
-            self.state = self.states.pop()
-        else:
-            self.write_indent()
-            self.write_indicator('-', True, indention=True)
-            self.states.append(self.expect_block_sequence_item)
-            self.expect_node(sequence=True)
-
-    # Block mapping handlers.
-
-    def expect_block_mapping(self):
-        self.increase_indent(flow=False)
-        self.state = self.expect_first_block_mapping_key
-
-    def expect_first_block_mapping_key(self):
-        return self.expect_block_mapping_key(first=True)
-
-    def expect_block_mapping_key(self, first=False):
-        if not first and isinstance(self.event, MappingEndEvent):
-            self.indent = self.indents.pop()
-            self.state = self.states.pop()
-        else:
-            self.write_indent()
-            if self.check_simple_key():
-                self.states.append(self.expect_block_mapping_simple_value)
-                self.expect_node(mapping=True, simple_key=True)
-            else:
-                self.write_indicator('?', True, indention=True)
-                self.states.append(self.expect_block_mapping_value)
-                self.expect_node(mapping=True)
-
-    def expect_block_mapping_simple_value(self):
-        self.write_indicator(':', False)
-        self.states.append(self.expect_block_mapping_key)
-        self.expect_node(mapping=True)
-
-    def expect_block_mapping_value(self):
-        self.write_indent()
-        self.write_indicator(':', True, indention=True)
-        self.states.append(self.expect_block_mapping_key)
-        self.expect_node(mapping=True)
-
-    # Checkers.
-
-    def check_empty_sequence(self):
-        return (isinstance(self.event, SequenceStartEvent) and self.events
-                and isinstance(self.events[0], SequenceEndEvent))
-
-    def check_empty_mapping(self):
-        return (isinstance(self.event, MappingStartEvent) and self.events
-                and isinstance(self.events[0], MappingEndEvent))
-
-    def check_empty_document(self):
-        if not isinstance(self.event, DocumentStartEvent) or not self.events:
-            return False
-        event = self.events[0]
-        return (isinstance(event, ScalarEvent) and event.anchor is None
-                and event.tag is None and event.implicit and event.value == '')
-
-    def check_simple_key(self):
-        length = 0
-        if isinstance(self.event, NodeEvent) and self.event.anchor is not None:
-            if self.prepared_anchor is None:
-                self.prepared_anchor = self.prepare_anchor(self.event.anchor)
-            length += len(self.prepared_anchor)
-        if isinstance(self.event, (ScalarEvent, CollectionStartEvent))  \
-                and self.event.tag is not None:
-            if self.prepared_tag is None:
-                self.prepared_tag = self.prepare_tag(self.event.tag)
-            length += len(self.prepared_tag)
-        if isinstance(self.event, ScalarEvent):
-            if self.analysis is None:
-                self.analysis = self.analyze_scalar(self.event.value)
-            length += len(self.analysis.scalar)
-        return (length < 128 and (isinstance(self.event, AliasEvent)
-            or (isinstance(self.event, ScalarEvent)
-                    and not self.analysis.empty and not self.analysis.multiline)
-            or self.check_empty_sequence() or self.check_empty_mapping()))
-
-    # Anchor, Tag, and Scalar processors.
-
-    def process_anchor(self, indicator):
-        if self.event.anchor is None:
-            self.prepared_anchor = None
-            return
-        if self.prepared_anchor is None:
-            self.prepared_anchor = self.prepare_anchor(self.event.anchor)
-        if self.prepared_anchor:
-            self.write_indicator(indicator+self.prepared_anchor, True)
-        self.prepared_anchor = None
-
-    def process_tag(self):
-        tag = self.event.tag
-        if isinstance(self.event, ScalarEvent):
-            if self.style is None:
-                self.style = self.choose_scalar_style()
-            if ((not self.canonical or tag is None) and
-                ((self.style == '' and self.event.implicit[0])
-                        or (self.style != '' and self.event.implicit[1]))):
-                self.prepared_tag = None
-                return
-            if self.event.implicit[0] and tag is None:
-                tag = '!'
-                self.prepared_tag = None
-        else:
-            if (not self.canonical or tag is None) and self.event.implicit:
-                self.prepared_tag = None
-                return
-        if tag is None:
-            raise EmitterError("tag is not specified")
-        if self.prepared_tag is None:
-            self.prepared_tag = self.prepare_tag(tag)
-        if self.prepared_tag:
-            self.write_indicator(self.prepared_tag, True)
-        self.prepared_tag = None
-
-    def choose_scalar_style(self):
-        if self.analysis is None:
-            self.analysis = self.analyze_scalar(self.event.value)
-        if self.event.style == '"' or self.canonical:
-            return '"'
-        if not self.event.style and self.event.implicit[0]:
-            if (not (self.simple_key_context and
-                    (self.analysis.empty or self.analysis.multiline))
-                and (self.flow_level and self.analysis.allow_flow_plain
-                    or (not self.flow_level and self.analysis.allow_block_plain))):
-                return ''
-        if self.event.style and self.event.style in '|>':
-            if (not self.flow_level and not self.simple_key_context
-                    and self.analysis.allow_block):
-                return self.event.style
-        if not self.event.style or self.event.style == '\'':
-            if (self.analysis.allow_single_quoted and
-                    not (self.simple_key_context and self.analysis.multiline)):
-                return '\''
-        return '"'
-
-    def process_scalar(self):
-        if self.analysis is None:
-            self.analysis = self.analyze_scalar(self.event.value)
-        if self.style is None:
-            self.style = self.choose_scalar_style()
-        split = (not self.simple_key_context)
-        #if self.analysis.multiline and split    \
-        #        and (not self.style or self.style in '\'\"'):
-        #    self.write_indent()
-        if self.style == '"':
-            self.write_double_quoted(self.analysis.scalar, split)
-        elif self.style == '\'':
-            self.write_single_quoted(self.analysis.scalar, split)
-        elif self.style == '>':
-            self.write_folded(self.analysis.scalar)
-        elif self.style == '|':
-            self.write_literal(self.analysis.scalar)
-        else:
-            self.write_plain(self.analysis.scalar, split)
-        self.analysis = None
-        self.style = None
-
-    # Analyzers.
-
-    def prepare_version(self, version):
-        major, minor = version
-        if major != 1:
-            raise EmitterError("unsupported YAML version: %d.%d" % (major, minor))
-        return '%d.%d' % (major, minor)
-
-    def prepare_tag_handle(self, handle):
-        if not handle:
-            raise EmitterError("tag handle must not be empty")
-        if handle[0] != '!' or handle[-1] != '!':
-            raise EmitterError("tag handle must start and end with '!': %r" % handle)
-        for ch in handle[1:-1]:
-            if not ('0' <= ch <= '9' or 'A' <= ch <= 'Z' or 'a' <= ch <= 'z'    \
-                    or ch in '-_'):
-                raise EmitterError("invalid character %r in the tag handle: %r"
-                        % (ch, handle))
-        return handle
-
-    def prepare_tag_prefix(self, prefix):
-        if not prefix:
-            raise EmitterError("tag prefix must not be empty")
-        chunks = []
-        start = end = 0
-        if prefix[0] == '!':
-            end = 1
-        while end < len(prefix):
-            ch = prefix[end]
-            if '0' <= ch <= '9' or 'A' <= ch <= 'Z' or 'a' <= ch <= 'z' \
-                    or ch in '-;/?!:@&=+$,_.~*\'()[]':
-                end += 1
-            else:
-                if start < end:
-                    chunks.append(prefix[start:end])
-                start = end = end+1
-                data = ch.encode('utf-8')
-                for ch in data:
-                    chunks.append('%%%02X' % ord(ch))
-        if start < end:
-            chunks.append(prefix[start:end])
-        return ''.join(chunks)
-
-    def prepare_tag(self, tag):
-        if not tag:
-            raise EmitterError("tag must not be empty")
-        if tag == '!':
-            return tag
-        handle = None
-        suffix = tag
-        prefixes = sorted(self.tag_prefixes.keys())
-        for prefix in prefixes:
-            if tag.startswith(prefix)   \
-                    and (prefix == '!' or len(prefix) < len(tag)):
-                handle = self.tag_prefixes[prefix]
-                suffix = tag[len(prefix):]
-        chunks = []
-        start = end = 0
-        while end < len(suffix):
-            ch = suffix[end]
-            if '0' <= ch <= '9' or 'A' <= ch <= 'Z' or 'a' <= ch <= 'z' \
-                    or ch in '-;/?:@&=+$,_.~*\'()[]'   \
-                    or (ch == '!' and handle != '!'):
-                end += 1
-            else:
-                if start < end:
-                    chunks.append(suffix[start:end])
-                start = end = end+1
-                data = ch.encode('utf-8')
-                for ch in data:
-                    chunks.append('%%%02X' % ord(ch))
-        if start < end:
-            chunks.append(suffix[start:end])
-        suffix_text = ''.join(chunks)
-        if handle:
-            return '%s%s' % (handle, suffix_text)
-        else:
-            return '!<%s>' % suffix_text
-
-    def prepare_anchor(self, anchor):
-        if not anchor:
-            raise EmitterError("anchor must not be empty")
-        for ch in anchor:
-            if not ('0' <= ch <= '9' or 'A' <= ch <= 'Z' or 'a' <= ch <= 'z'    \
-                    or ch in '-_'):
-                raise EmitterError("invalid character %r in the anchor: %r"
-                        % (ch, anchor))
-        return anchor
-
-    def analyze_scalar(self, scalar):
-
-        # Empty scalar is a special case.
-        if not scalar:
-            return ScalarAnalysis(scalar=scalar, empty=True, multiline=False,
-                    allow_flow_plain=False, allow_block_plain=True,
-                    allow_single_quoted=True, allow_double_quoted=True,
-                    allow_block=False)
-
-        # Indicators and special characters.
-        block_indicators = False
-        flow_indicators = False
-        line_breaks = False
-        special_characters = False
-
-        # Important whitespace combinations.
-        leading_space = False
-        leading_break = False
-        trailing_space = False
-        trailing_break = False
-        break_space = False
-        space_break = False
-
-        # Check document indicators.
-        if scalar.startswith('---') or scalar.startswith('...'):
-            block_indicators = True
-            flow_indicators = True
-
-        # First character or preceded by a whitespace.
-        preceeded_by_whitespace = True
-
-        # Last character or followed by a whitespace.
-        followed_by_whitespace = (len(scalar) == 1 or
-                scalar[1] in '\0 \t\r\n\x85\u2028\u2029')
-
-        # The previous character is a space.
-        previous_space = False
-
-        # The previous character is a break.
-        previous_break = False
-
-        index = 0
-        while index < len(scalar):
-            ch = scalar[index]
-
-            # Check for indicators.
-            if index == 0:
-                # Leading indicators are special characters.
-                if ch in '#,[]{}&*!|>\'\"%@`': 
-                    flow_indicators = True
-                    block_indicators = True
-                if ch in '?:':
-                    flow_indicators = True
-                    if followed_by_whitespace:
-                        block_indicators = True
-                if ch == '-' and followed_by_whitespace:
-                    flow_indicators = True
-                    block_indicators = True
-            else:
-                # Some indicators cannot appear within a scalar as well.
-                if ch in ',?[]{}':
-                    flow_indicators = True
-                if ch == ':':
-                    flow_indicators = True
-                    if followed_by_whitespace:
-                        block_indicators = True
-                if ch == '#' and preceeded_by_whitespace:
-                    flow_indicators = True
-                    block_indicators = True
-
-            # Check for line breaks, special, and unicode characters.
-            if ch in '\n\x85\u2028\u2029':
-                line_breaks = True
-            if not (ch == '\n' or '\x20' <= ch <= '\x7E'):
-                if (ch == '\x85' or '\xA0' <= ch <= '\uD7FF'
-                        or '\uE000' <= ch <= '\uFFFD') and ch != '\uFEFF':
-                    unicode_characters = True
-                    if not self.allow_unicode:
-                        special_characters = True
-                else:
-                    special_characters = True
-
-            # Detect important whitespace combinations.
-            if ch == ' ':
-                if index == 0:
-                    leading_space = True
-                if index == len(scalar)-1:
-                    trailing_space = True
-                if previous_break:
-                    break_space = True
-                previous_space = True
-                previous_break = False
-            elif ch in '\n\x85\u2028\u2029':
-                if index == 0:
-                    leading_break = True
-                if index == len(scalar)-1:
-                    trailing_break = True
-                if previous_space:
-                    space_break = True
-                previous_space = False
-                previous_break = True
-            else:
-                previous_space = False
-                previous_break = False
-
-            # Prepare for the next character.
-            index += 1
-            preceeded_by_whitespace = (ch in '\0 \t\r\n\x85\u2028\u2029')
-            followed_by_whitespace = (index+1 >= len(scalar) or
-                    scalar[index+1] in '\0 \t\r\n\x85\u2028\u2029')
-
-        # Let's decide what styles are allowed.
-        allow_flow_plain = True
-        allow_block_plain = True
-        allow_single_quoted = True
-        allow_double_quoted = True
-        allow_block = True
-
-        # Leading and trailing whitespaces are bad for plain scalars.
-        if (leading_space or leading_break
-                or trailing_space or trailing_break):
-            allow_flow_plain = allow_block_plain = False
-
-        # We do not permit trailing spaces for block scalars.
-        if trailing_space:
-            allow_block = False
-
-        # Spaces at the beginning of a new line are only acceptable for block
-        # scalars.
-        if break_space:
-            allow_flow_plain = allow_block_plain = allow_single_quoted = False
-
-        # Spaces followed by breaks, as well as special character are only
-        # allowed for double quoted scalars.
-        if space_break or special_characters:
-            allow_flow_plain = allow_block_plain =  \
-            allow_single_quoted = allow_block = False
-
-        # Although the plain scalar writer supports breaks, we never emit
-        # multiline plain scalars.
-        if line_breaks:
-            allow_flow_plain = allow_block_plain = False
-
-        # Flow indicators are forbidden for flow plain scalars.
-        if flow_indicators:
-            allow_flow_plain = False
-
-        # Block indicators are forbidden for block plain scalars.
-        if block_indicators:
-            allow_block_plain = False
-
-        return ScalarAnalysis(scalar=scalar,
-                empty=False, multiline=line_breaks,
-                allow_flow_plain=allow_flow_plain,
-                allow_block_plain=allow_block_plain,
-                allow_single_quoted=allow_single_quoted,
-                allow_double_quoted=allow_double_quoted,
-                allow_block=allow_block)
-
-    # Writers.
-
-    def flush_stream(self):
-        if hasattr(self.stream, 'flush'):
-            self.stream.flush()
-
-    def write_stream_start(self):
-        # Write BOM if needed.
-        if self.encoding and self.encoding.startswith('utf-16'):
-            self.stream.write('\uFEFF'.encode(self.encoding))
-
-    def write_stream_end(self):
-        self.flush_stream()
-
-    def write_indicator(self, indicator, need_whitespace,
-            whitespace=False, indention=False):
-        if self.whitespace or not need_whitespace:
-            data = indicator
-        else:
-            data = ' '+indicator
-        self.whitespace = whitespace
-        self.indention = self.indention and indention
-        self.column += len(data)
-        self.open_ended = False
-        if self.encoding:
-            data = data.encode(self.encoding)
-        self.stream.write(data)
-
-    def write_indent(self):
-        indent = self.indent or 0
-        if not self.indention or self.column > indent   \
-                or (self.column == indent and not self.whitespace):
-            self.write_line_break()
-        if self.column < indent:
-            self.whitespace = True
-            data = ' '*(indent-self.column)
-            self.column = indent
-            if self.encoding:
-                data = data.encode(self.encoding)
-            self.stream.write(data)
-
-    def write_line_break(self, data=None):
-        if data is None:
-            data = self.best_line_break
-        self.whitespace = True
-        self.indention = True
-        self.line += 1
-        self.column = 0
-        if self.encoding:
-            data = data.encode(self.encoding)
-        self.stream.write(data)
-
-    def write_version_directive(self, version_text):
-        data = '%%YAML %s' % version_text
-        if self.encoding:
-            data = data.encode(self.encoding)
-        self.stream.write(data)
-        self.write_line_break()
-
-    def write_tag_directive(self, handle_text, prefix_text):
-        data = '%%TAG %s %s' % (handle_text, prefix_text)
-        if self.encoding:
-            data = data.encode(self.encoding)
-        self.stream.write(data)
-        self.write_line_break()
-
-    # Scalar streams.
-
-    def write_single_quoted(self, text, split=True):
-        self.write_indicator('\'', True)
-        spaces = False
-        breaks = False
-        start = end = 0
-        while end <= len(text):
-            ch = None
-            if end < len(text):
-                ch = text[end]
-            if spaces:
-                if ch is None or ch != ' ':
-                    if start+1 == end and self.column > self.best_width and split   \
-                            and start != 0 and end != len(text):
-                        self.write_indent()
-                    else:
-                        data = text[start:end]
-                        self.column += len(data)
-                        if self.encoding:
-                            data = data.encode(self.encoding)
-                        self.stream.write(data)
-                    start = end
-            elif breaks:
-                if ch is None or ch not in '\n\x85\u2028\u2029':
-                    if text[start] == '\n':
-                        self.write_line_break()
-                    for br in text[start:end]:
-                        if br == '\n':
-                            self.write_line_break()
-                        else:
-                            self.write_line_break(br)
-                    self.write_indent()
-                    start = end
-            else:
-                if ch is None or ch in ' \n\x85\u2028\u2029' or ch == '\'':
-                    if start < end:
-                        data = text[start:end]
-                        self.column += len(data)
-                        if self.encoding:
-                            data = data.encode(self.encoding)
-                        self.stream.write(data)
-                        start = end
-            if ch == '\'':
-                data = '\'\''
-                self.column += 2
-                if self.encoding:
-                    data = data.encode(self.encoding)
-                self.stream.write(data)
-                start = end + 1
-            if ch is not None:
-                spaces = (ch == ' ')
-                breaks = (ch in '\n\x85\u2028\u2029')
-            end += 1
-        self.write_indicator('\'', False)
-
-    ESCAPE_REPLACEMENTS = {
-        '\0':       '0',
-        '\x07':     'a',
-        '\x08':     'b',
-        '\x09':     't',
-        '\x0A':     'n',
-        '\x0B':     'v',
-        '\x0C':     'f',
-        '\x0D':     'r',
-        '\x1B':     'e',
-        '\"':       '\"',
-        '\\':       '\\',
-        '\x85':     'N',
-        '\xA0':     '_',
-        '\u2028':   'L',
-        '\u2029':   'P',
-    }
-
-    def write_double_quoted(self, text, split=True):
-        self.write_indicator('"', True)
-        start = end = 0
-        while end <= len(text):
-            ch = None
-            if end < len(text):
-                ch = text[end]
-            if ch is None or ch in '"\\\x85\u2028\u2029\uFEFF' \
-                    or not ('\x20' <= ch <= '\x7E'
-                        or (self.allow_unicode
-                            and ('\xA0' <= ch <= '\uD7FF'
-                                or '\uE000' <= ch <= '\uFFFD'))):
-                if start < end:
-                    data = text[start:end]
-                    self.column += len(data)
-                    if self.encoding:
-                        data = data.encode(self.encoding)
-                    self.stream.write(data)
-                    start = end
-                if ch is not None:
-                    if ch in self.ESCAPE_REPLACEMENTS:
-                        data = '\\'+self.ESCAPE_REPLACEMENTS[ch]
-                    elif ch <= '\xFF':
-                        data = '\\x%02X' % ord(ch)
-                    elif ch <= '\uFFFF':
-                        data = '\\u%04X' % ord(ch)
-                    else:
-                        data = '\\U%08X' % ord(ch)
-                    self.column += len(data)
-                    if self.encoding:
-                        data = data.encode(self.encoding)
-                    self.stream.write(data)
-                    start = end+1
-            if 0 < end < len(text)-1 and (ch == ' ' or start >= end)    \
-                    and self.column+(end-start) > self.best_width and split:
-                data = text[start:end]+'\\'
-                if start < end:
-                    start = end
-                self.column += len(data)
-                if self.encoding:
-                    data = data.encode(self.encoding)
-                self.stream.write(data)
-                self.write_indent()
-                self.whitespace = False
-                self.indention = False
-                if text[start] == ' ':
-                    data = '\\'
-                    self.column += len(data)
-                    if self.encoding:
-                        data = data.encode(self.encoding)
-                    self.stream.write(data)
-            end += 1
-        self.write_indicator('"', False)
-
-    def determine_block_hints(self, text):
-        hints = ''
-        if text:
-            if text[0] in ' \n\x85\u2028\u2029':
-                hints += str(self.best_indent)
-            if text[-1] not in '\n\x85\u2028\u2029':
-                hints += '-'
-            elif len(text) == 1 or text[-2] in '\n\x85\u2028\u2029':
-                hints += '+'
-        return hints
-
-    def write_folded(self, text):
-        hints = self.determine_block_hints(text)
-        self.write_indicator('>'+hints, True)
-        if hints[-1:] == '+':
-            self.open_ended = True
-        self.write_line_break()
-        leading_space = True
-        spaces = False
-        breaks = True
-        start = end = 0
-        while end <= len(text):
-            ch = None
-            if end < len(text):
-                ch = text[end]
-            if breaks:
-                if ch is None or ch not in '\n\x85\u2028\u2029':
-                    if not leading_space and ch is not None and ch != ' '   \
-                            and text[start] == '\n':
-                        self.write_line_break()
-                    leading_space = (ch == ' ')
-                    for br in text[start:end]:
-                        if br == '\n':
-                            self.write_line_break()
-                        else:
-                            self.write_line_break(br)
-                    if ch is not None:
-                        self.write_indent()
-                    start = end
-            elif spaces:
-                if ch != ' ':
-                    if start+1 == end and self.column > self.best_width:
-                        self.write_indent()
-                    else:
-                        data = text[start:end]
-                        self.column += len(data)
-                        if self.encoding:
-                            data = data.encode(self.encoding)
-                        self.stream.write(data)
-                    start = end
-            else:
-                if ch is None or ch in ' \n\x85\u2028\u2029':
-                    data = text[start:end]
-                    self.column += len(data)
-                    if self.encoding:
-                        data = data.encode(self.encoding)
-                    self.stream.write(data)
-                    if ch is None:
-                        self.write_line_break()
-                    start = end
-            if ch is not None:
-                breaks = (ch in '\n\x85\u2028\u2029')
-                spaces = (ch == ' ')
-            end += 1
-
-    def write_literal(self, text):
-        hints = self.determine_block_hints(text)
-        self.write_indicator('|'+hints, True)
-        if hints[-1:] == '+':
-            self.open_ended = True
-        self.write_line_break()
-        breaks = True
-        start = end = 0
-        while end <= len(text):
-            ch = None
-            if end < len(text):
-                ch = text[end]
-            if breaks:
-                if ch is None or ch not in '\n\x85\u2028\u2029':
-                    for br in text[start:end]:
-                        if br == '\n':
-                            self.write_line_break()
-                        else:
-                            self.write_line_break(br)
-                    if ch is not None:
-                        self.write_indent()
-                    start = end
-            else:
-                if ch is None or ch in '\n\x85\u2028\u2029':
-                    data = text[start:end]
-                    if self.encoding:
-                        data = data.encode(self.encoding)
-                    self.stream.write(data)
-                    if ch is None:
-                        self.write_line_break()
-                    start = end
-            if ch is not None:
-                breaks = (ch in '\n\x85\u2028\u2029')
-            end += 1
-
-    def write_plain(self, text, split=True):
-        if self.root_context:
-            self.open_ended = True
-        if not text:
-            return
-        if not self.whitespace:
-            data = ' '
-            self.column += len(data)
-            if self.encoding:
-                data = data.encode(self.encoding)
-            self.stream.write(data)
-        self.whitespace = False
-        self.indention = False
-        spaces = False
-        breaks = False
-        start = end = 0
-        while end <= len(text):
-            ch = None
-            if end < len(text):
-                ch = text[end]
-            if spaces:
-                if ch != ' ':
-                    if start+1 == end and self.column > self.best_width and split:
-                        self.write_indent()
-                        self.whitespace = False
-                        self.indention = False
-                    else:
-                        data = text[start:end]
-                        self.column += len(data)
-                        if self.encoding:
-                            data = data.encode(self.encoding)
-                        self.stream.write(data)
-                    start = end
-            elif breaks:
-                if ch not in '\n\x85\u2028\u2029':
-                    if text[start] == '\n':
-                        self.write_line_break()
-                    for br in text[start:end]:
-                        if br == '\n':
-                            self.write_line_break()
-                        else:
-                            self.write_line_break(br)
-                    self.write_indent()
-                    self.whitespace = False
-                    self.indention = False
-                    start = end
-            else:
-                if ch is None or ch in ' \n\x85\u2028\u2029':
-                    data = text[start:end]
-                    self.column += len(data)
-                    if self.encoding:
-                        data = data.encode(self.encoding)
-                    self.stream.write(data)
-                    start = end
-            if ch is not None:
-                spaces = (ch == ' ')
-                breaks = (ch in '\n\x85\u2028\u2029')
-            end += 1
-
diff --git a/lib/spack/external/yaml/lib3/yaml/error.py b/lib/spack/external/yaml/lib3/yaml/error.py
deleted file mode 100644
index b796b4dc51..0000000000
--- a/lib/spack/external/yaml/lib3/yaml/error.py
+++ /dev/null
@@ -1,75 +0,0 @@
-
-__all__ = ['Mark', 'YAMLError', 'MarkedYAMLError']
-
-class Mark:
-
-    def __init__(self, name, index, line, column, buffer, pointer):
-        self.name = name
-        self.index = index
-        self.line = line
-        self.column = column
-        self.buffer = buffer
-        self.pointer = pointer
-
-    def get_snippet(self, indent=4, max_length=75):
-        if self.buffer is None:
-            return None
-        head = ''
-        start = self.pointer
-        while start > 0 and self.buffer[start-1] not in '\0\r\n\x85\u2028\u2029':
-            start -= 1
-            if self.pointer-start > max_length/2-1:
-                head = ' ... '
-                start += 5
-                break
-        tail = ''
-        end = self.pointer
-        while end < len(self.buffer) and self.buffer[end] not in '\0\r\n\x85\u2028\u2029':
-            end += 1
-            if end-self.pointer > max_length/2-1:
-                tail = ' ... '
-                end -= 5
-                break
-        snippet = self.buffer[start:end]
-        return ' '*indent + head + snippet + tail + '\n'  \
-                + ' '*(indent+self.pointer-start+len(head)) + '^'
-
-    def __str__(self):
-        snippet = self.get_snippet()
-        where = "  in \"%s\", line %d, column %d"   \
-                % (self.name, self.line+1, self.column+1)
-        if snippet is not None:
-            where += ":\n"+snippet
-        return where
-
-class YAMLError(Exception):
-    pass
-
-class MarkedYAMLError(YAMLError):
-
-    def __init__(self, context=None, context_mark=None,
-            problem=None, problem_mark=None, note=None):
-        self.context = context
-        self.context_mark = context_mark
-        self.problem = problem
-        self.problem_mark = problem_mark
-        self.note = note
-
-    def __str__(self):
-        lines = []
-        if self.context is not None:
-            lines.append(self.context)
-        if self.context_mark is not None  \
-            and (self.problem is None or self.problem_mark is None
-                    or self.context_mark.name != self.problem_mark.name
-                    or self.context_mark.line != self.problem_mark.line
-                    or self.context_mark.column != self.problem_mark.column):
-            lines.append(str(self.context_mark))
-        if self.problem is not None:
-            lines.append(self.problem)
-        if self.problem_mark is not None:
-            lines.append(str(self.problem_mark))
-        if self.note is not None:
-            lines.append(self.note)
-        return '\n'.join(lines)
-
diff --git a/lib/spack/external/yaml/lib3/yaml/loader.py b/lib/spack/external/yaml/lib3/yaml/loader.py
deleted file mode 100644
index 08c8f01b34..0000000000
--- a/lib/spack/external/yaml/lib3/yaml/loader.py
+++ /dev/null
@@ -1,40 +0,0 @@
-
-__all__ = ['BaseLoader', 'SafeLoader', 'Loader']
-
-from .reader import *
-from .scanner import *
-from .parser import *
-from .composer import *
-from .constructor import *
-from .resolver import *
-
-class BaseLoader(Reader, Scanner, Parser, Composer, BaseConstructor, BaseResolver):
-
-    def __init__(self, stream):
-        Reader.__init__(self, stream)
-        Scanner.__init__(self)
-        Parser.__init__(self)
-        Composer.__init__(self)
-        BaseConstructor.__init__(self)
-        BaseResolver.__init__(self)
-
-class SafeLoader(Reader, Scanner, Parser, Composer, SafeConstructor, Resolver):
-
-    def __init__(self, stream):
-        Reader.__init__(self, stream)
-        Scanner.__init__(self)
-        Parser.__init__(self)
-        Composer.__init__(self)
-        SafeConstructor.__init__(self)
-        Resolver.__init__(self)
-
-class Loader(Reader, Scanner, Parser, Composer, Constructor, Resolver):
-
-    def __init__(self, stream):
-        Reader.__init__(self, stream)
-        Scanner.__init__(self)
-        Parser.__init__(self)
-        Composer.__init__(self)
-        Constructor.__init__(self)
-        Resolver.__init__(self)
-
diff --git a/lib/spack/external/yaml/lib3/yaml/nodes.py b/lib/spack/external/yaml/lib3/yaml/nodes.py
deleted file mode 100644
index c4f070c41e..0000000000
--- a/lib/spack/external/yaml/lib3/yaml/nodes.py
+++ /dev/null
@@ -1,49 +0,0 @@
-
-class Node(object):
-    def __init__(self, tag, value, start_mark, end_mark):
-        self.tag = tag
-        self.value = value
-        self.start_mark = start_mark
-        self.end_mark = end_mark
-    def __repr__(self):
-        value = self.value
-        #if isinstance(value, list):
-        #    if len(value) == 0:
-        #        value = '<empty>'
-        #    elif len(value) == 1:
-        #        value = '<1 item>'
-        #    else:
-        #        value = '<%d items>' % len(value)
-        #else:
-        #    if len(value) > 75:
-        #        value = repr(value[:70]+u' ... ')
-        #    else:
-        #        value = repr(value)
-        value = repr(value)
-        return '%s(tag=%r, value=%s)' % (self.__class__.__name__, self.tag, value)
-
-class ScalarNode(Node):
-    id = 'scalar'
-    def __init__(self, tag, value,
-            start_mark=None, end_mark=None, style=None):
-        self.tag = tag
-        self.value = value
-        self.start_mark = start_mark
-        self.end_mark = end_mark
-        self.style = style
-
-class CollectionNode(Node):
-    def __init__(self, tag, value,
-            start_mark=None, end_mark=None, flow_style=None):
-        self.tag = tag
-        self.value = value
-        self.start_mark = start_mark
-        self.end_mark = end_mark
-        self.flow_style = flow_style
-
-class SequenceNode(CollectionNode):
-    id = 'sequence'
-
-class MappingNode(CollectionNode):
-    id = 'mapping'
-
diff --git a/lib/spack/external/yaml/lib3/yaml/parser.py b/lib/spack/external/yaml/lib3/yaml/parser.py
deleted file mode 100644
index 13a5995d29..0000000000
--- a/lib/spack/external/yaml/lib3/yaml/parser.py
+++ /dev/null
@@ -1,589 +0,0 @@
-
-# The following YAML grammar is LL(1) and is parsed by a recursive descent
-# parser.
-#
-# stream            ::= STREAM-START implicit_document? explicit_document* STREAM-END
-# implicit_document ::= block_node DOCUMENT-END*
-# explicit_document ::= DIRECTIVE* DOCUMENT-START block_node? DOCUMENT-END*
-# block_node_or_indentless_sequence ::=
-#                       ALIAS
-#                       | properties (block_content | indentless_block_sequence)?
-#                       | block_content
-#                       | indentless_block_sequence
-# block_node        ::= ALIAS
-#                       | properties block_content?
-#                       | block_content
-# flow_node         ::= ALIAS
-#                       | properties flow_content?
-#                       | flow_content
-# properties        ::= TAG ANCHOR? | ANCHOR TAG?
-# block_content     ::= block_collection | flow_collection | SCALAR
-# flow_content      ::= flow_collection | SCALAR
-# block_collection  ::= block_sequence | block_mapping
-# flow_collection   ::= flow_sequence | flow_mapping
-# block_sequence    ::= BLOCK-SEQUENCE-START (BLOCK-ENTRY block_node?)* BLOCK-END
-# indentless_sequence   ::= (BLOCK-ENTRY block_node?)+
-# block_mapping     ::= BLOCK-MAPPING_START
-#                       ((KEY block_node_or_indentless_sequence?)?
-#                       (VALUE block_node_or_indentless_sequence?)?)*
-#                       BLOCK-END
-# flow_sequence     ::= FLOW-SEQUENCE-START
-#                       (flow_sequence_entry FLOW-ENTRY)*
-#                       flow_sequence_entry?
-#                       FLOW-SEQUENCE-END
-# flow_sequence_entry   ::= flow_node | KEY flow_node? (VALUE flow_node?)?
-# flow_mapping      ::= FLOW-MAPPING-START
-#                       (flow_mapping_entry FLOW-ENTRY)*
-#                       flow_mapping_entry?
-#                       FLOW-MAPPING-END
-# flow_mapping_entry    ::= flow_node | KEY flow_node? (VALUE flow_node?)?
-#
-# FIRST sets:
-#
-# stream: { STREAM-START }
-# explicit_document: { DIRECTIVE DOCUMENT-START }
-# implicit_document: FIRST(block_node)
-# block_node: { ALIAS TAG ANCHOR SCALAR BLOCK-SEQUENCE-START BLOCK-MAPPING-START FLOW-SEQUENCE-START FLOW-MAPPING-START }
-# flow_node: { ALIAS ANCHOR TAG SCALAR FLOW-SEQUENCE-START FLOW-MAPPING-START }
-# block_content: { BLOCK-SEQUENCE-START BLOCK-MAPPING-START FLOW-SEQUENCE-START FLOW-MAPPING-START SCALAR }
-# flow_content: { FLOW-SEQUENCE-START FLOW-MAPPING-START SCALAR }
-# block_collection: { BLOCK-SEQUENCE-START BLOCK-MAPPING-START }
-# flow_collection: { FLOW-SEQUENCE-START FLOW-MAPPING-START }
-# block_sequence: { BLOCK-SEQUENCE-START }
-# block_mapping: { BLOCK-MAPPING-START }
-# block_node_or_indentless_sequence: { ALIAS ANCHOR TAG SCALAR BLOCK-SEQUENCE-START BLOCK-MAPPING-START FLOW-SEQUENCE-START FLOW-MAPPING-START BLOCK-ENTRY }
-# indentless_sequence: { ENTRY }
-# flow_collection: { FLOW-SEQUENCE-START FLOW-MAPPING-START }
-# flow_sequence: { FLOW-SEQUENCE-START }
-# flow_mapping: { FLOW-MAPPING-START }
-# flow_sequence_entry: { ALIAS ANCHOR TAG SCALAR FLOW-SEQUENCE-START FLOW-MAPPING-START KEY }
-# flow_mapping_entry: { ALIAS ANCHOR TAG SCALAR FLOW-SEQUENCE-START FLOW-MAPPING-START KEY }
-
-__all__ = ['Parser', 'ParserError']
-
-from .error import MarkedYAMLError
-from .tokens import *
-from .events import *
-from .scanner import *
-
-class ParserError(MarkedYAMLError):
-    pass
-
-class Parser:
-    # Since writing a recursive-descendant parser is a straightforward task, we
-    # do not give many comments here.
-
-    DEFAULT_TAGS = {
-        '!':   '!',
-        '!!':  'tag:yaml.org,2002:',
-    }
-
-    def __init__(self):
-        self.current_event = None
-        self.yaml_version = None
-        self.tag_handles = {}
-        self.states = []
-        self.marks = []
-        self.state = self.parse_stream_start
-
-    def dispose(self):
-        # Reset the state attributes (to clear self-references)
-        self.states = []
-        self.state = None
-
-    def check_event(self, *choices):
-        # Check the type of the next event.
-        if self.current_event is None:
-            if self.state:
-                self.current_event = self.state()
-        if self.current_event is not None:
-            if not choices:
-                return True
-            for choice in choices:
-                if isinstance(self.current_event, choice):
-                    return True
-        return False
-
-    def peek_event(self):
-        # Get the next event.
-        if self.current_event is None:
-            if self.state:
-                self.current_event = self.state()
-        return self.current_event
-
-    def get_event(self):
-        # Get the next event and proceed further.
-        if self.current_event is None:
-            if self.state:
-                self.current_event = self.state()
-        value = self.current_event
-        self.current_event = None
-        return value
-
-    # stream    ::= STREAM-START implicit_document? explicit_document* STREAM-END
-    # implicit_document ::= block_node DOCUMENT-END*
-    # explicit_document ::= DIRECTIVE* DOCUMENT-START block_node? DOCUMENT-END*
-
-    def parse_stream_start(self):
-
-        # Parse the stream start.
-        token = self.get_token()
-        event = StreamStartEvent(token.start_mark, token.end_mark,
-                encoding=token.encoding)
-
-        # Prepare the next state.
-        self.state = self.parse_implicit_document_start
-
-        return event
-
-    def parse_implicit_document_start(self):
-
-        # Parse an implicit document.
-        if not self.check_token(DirectiveToken, DocumentStartToken,
-                StreamEndToken):
-            self.tag_handles = self.DEFAULT_TAGS
-            token = self.peek_token()
-            start_mark = end_mark = token.start_mark
-            event = DocumentStartEvent(start_mark, end_mark,
-                    explicit=False)
-
-            # Prepare the next state.
-            self.states.append(self.parse_document_end)
-            self.state = self.parse_block_node
-
-            return event
-
-        else:
-            return self.parse_document_start()
-
-    def parse_document_start(self):
-
-        # Parse any extra document end indicators.
-        while self.check_token(DocumentEndToken):
-            self.get_token()
-
-        # Parse an explicit document.
-        if not self.check_token(StreamEndToken):
-            token = self.peek_token()
-            start_mark = token.start_mark
-            version, tags = self.process_directives()
-            if not self.check_token(DocumentStartToken):
-                raise ParserError(None, None,
-                        "expected '<document start>', but found %r"
-                        % self.peek_token().id,
-                        self.peek_token().start_mark)
-            token = self.get_token()
-            end_mark = token.end_mark
-            event = DocumentStartEvent(start_mark, end_mark,
-                    explicit=True, version=version, tags=tags)
-            self.states.append(self.parse_document_end)
-            self.state = self.parse_document_content
-        else:
-            # Parse the end of the stream.
-            token = self.get_token()
-            event = StreamEndEvent(token.start_mark, token.end_mark)
-            assert not self.states
-            assert not self.marks
-            self.state = None
-        return event
-
-    def parse_document_end(self):
-
-        # Parse the document end.
-        token = self.peek_token()
-        start_mark = end_mark = token.start_mark
-        explicit = False
-        if self.check_token(DocumentEndToken):
-            token = self.get_token()
-            end_mark = token.end_mark
-            explicit = True
-        event = DocumentEndEvent(start_mark, end_mark,
-                explicit=explicit)
-
-        # Prepare the next state.
-        self.state = self.parse_document_start
-
-        return event
-
-    def parse_document_content(self):
-        if self.check_token(DirectiveToken,
-                DocumentStartToken, DocumentEndToken, StreamEndToken):
-            event = self.process_empty_scalar(self.peek_token().start_mark)
-            self.state = self.states.pop()
-            return event
-        else:
-            return self.parse_block_node()
-
-    def process_directives(self):
-        self.yaml_version = None
-        self.tag_handles = {}
-        while self.check_token(DirectiveToken):
-            token = self.get_token()
-            if token.name == 'YAML':
-                if self.yaml_version is not None:
-                    raise ParserError(None, None,
-                            "found duplicate YAML directive", token.start_mark)
-                major, minor = token.value
-                if major != 1:
-                    raise ParserError(None, None,
-                            "found incompatible YAML document (version 1.* is required)",
-                            token.start_mark)
-                self.yaml_version = token.value
-            elif token.name == 'TAG':
-                handle, prefix = token.value
-                if handle in self.tag_handles:
-                    raise ParserError(None, None,
-                            "duplicate tag handle %r" % handle,
-                            token.start_mark)
-                self.tag_handles[handle] = prefix
-        if self.tag_handles:
-            value = self.yaml_version, self.tag_handles.copy()
-        else:
-            value = self.yaml_version, None
-        for key in self.DEFAULT_TAGS:
-            if key not in self.tag_handles:
-                self.tag_handles[key] = self.DEFAULT_TAGS[key]
-        return value
-
-    # block_node_or_indentless_sequence ::= ALIAS
-    #               | properties (block_content | indentless_block_sequence)?
-    #               | block_content
-    #               | indentless_block_sequence
-    # block_node    ::= ALIAS
-    #                   | properties block_content?
-    #                   | block_content
-    # flow_node     ::= ALIAS
-    #                   | properties flow_content?
-    #                   | flow_content
-    # properties    ::= TAG ANCHOR? | ANCHOR TAG?
-    # block_content     ::= block_collection | flow_collection | SCALAR
-    # flow_content      ::= flow_collection | SCALAR
-    # block_collection  ::= block_sequence | block_mapping
-    # flow_collection   ::= flow_sequence | flow_mapping
-
-    def parse_block_node(self):
-        return self.parse_node(block=True)
-
-    def parse_flow_node(self):
-        return self.parse_node()
-
-    def parse_block_node_or_indentless_sequence(self):
-        return self.parse_node(block=True, indentless_sequence=True)
-
-    def parse_node(self, block=False, indentless_sequence=False):
-        if self.check_token(AliasToken):
-            token = self.get_token()
-            event = AliasEvent(token.value, token.start_mark, token.end_mark)
-            self.state = self.states.pop()
-        else:
-            anchor = None
-            tag = None
-            start_mark = end_mark = tag_mark = None
-            if self.check_token(AnchorToken):
-                token = self.get_token()
-                start_mark = token.start_mark
-                end_mark = token.end_mark
-                anchor = token.value
-                if self.check_token(TagToken):
-                    token = self.get_token()
-                    tag_mark = token.start_mark
-                    end_mark = token.end_mark
-                    tag = token.value
-            elif self.check_token(TagToken):
-                token = self.get_token()
-                start_mark = tag_mark = token.start_mark
-                end_mark = token.end_mark
-                tag = token.value
-                if self.check_token(AnchorToken):
-                    token = self.get_token()
-                    end_mark = token.end_mark
-                    anchor = token.value
-            if tag is not None:
-                handle, suffix = tag
-                if handle is not None:
-                    if handle not in self.tag_handles:
-                        raise ParserError("while parsing a node", start_mark,
-                                "found undefined tag handle %r" % handle,
-                                tag_mark)
-                    tag = self.tag_handles[handle]+suffix
-                else:
-                    tag = suffix
-            #if tag == '!':
-            #    raise ParserError("while parsing a node", start_mark,
-            #            "found non-specific tag '!'", tag_mark,
-            #            "Please check 'http://pyyaml.org/wiki/YAMLNonSpecificTag' and share your opinion.")
-            if start_mark is None:
-                start_mark = end_mark = self.peek_token().start_mark
-            event = None
-            implicit = (tag is None or tag == '!')
-            if indentless_sequence and self.check_token(BlockEntryToken):
-                end_mark = self.peek_token().end_mark
-                event = SequenceStartEvent(anchor, tag, implicit,
-                        start_mark, end_mark)
-                self.state = self.parse_indentless_sequence_entry
-            else:
-                if self.check_token(ScalarToken):
-                    token = self.get_token()
-                    end_mark = token.end_mark
-                    if (token.plain and tag is None) or tag == '!':
-                        implicit = (True, False)
-                    elif tag is None:
-                        implicit = (False, True)
-                    else:
-                        implicit = (False, False)
-                    event = ScalarEvent(anchor, tag, implicit, token.value,
-                            start_mark, end_mark, style=token.style)
-                    self.state = self.states.pop()
-                elif self.check_token(FlowSequenceStartToken):
-                    end_mark = self.peek_token().end_mark
-                    event = SequenceStartEvent(anchor, tag, implicit,
-                            start_mark, end_mark, flow_style=True)
-                    self.state = self.parse_flow_sequence_first_entry
-                elif self.check_token(FlowMappingStartToken):
-                    end_mark = self.peek_token().end_mark
-                    event = MappingStartEvent(anchor, tag, implicit,
-                            start_mark, end_mark, flow_style=True)
-                    self.state = self.parse_flow_mapping_first_key
-                elif block and self.check_token(BlockSequenceStartToken):
-                    end_mark = self.peek_token().start_mark
-                    event = SequenceStartEvent(anchor, tag, implicit,
-                            start_mark, end_mark, flow_style=False)
-                    self.state = self.parse_block_sequence_first_entry
-                elif block and self.check_token(BlockMappingStartToken):
-                    end_mark = self.peek_token().start_mark
-                    event = MappingStartEvent(anchor, tag, implicit,
-                            start_mark, end_mark, flow_style=False)
-                    self.state = self.parse_block_mapping_first_key
-                elif anchor is not None or tag is not None:
-                    # Empty scalars are allowed even if a tag or an anchor is
-                    # specified.
-                    event = ScalarEvent(anchor, tag, (implicit, False), '',
-                            start_mark, end_mark)
-                    self.state = self.states.pop()
-                else:
-                    if block:
-                        node = 'block'
-                    else:
-                        node = 'flow'
-                    token = self.peek_token()
-                    raise ParserError("while parsing a %s node" % node, start_mark,
-                            "expected the node content, but found %r" % token.id,
-                            token.start_mark)
-        return event
-
-    # block_sequence ::= BLOCK-SEQUENCE-START (BLOCK-ENTRY block_node?)* BLOCK-END
-
-    def parse_block_sequence_first_entry(self):
-        token = self.get_token()
-        self.marks.append(token.start_mark)
-        return self.parse_block_sequence_entry()
-
-    def parse_block_sequence_entry(self):
-        if self.check_token(BlockEntryToken):
-            token = self.get_token()
-            if not self.check_token(BlockEntryToken, BlockEndToken):
-                self.states.append(self.parse_block_sequence_entry)
-                return self.parse_block_node()
-            else:
-                self.state = self.parse_block_sequence_entry
-                return self.process_empty_scalar(token.end_mark)
-        if not self.check_token(BlockEndToken):
-            token = self.peek_token()
-            raise ParserError("while parsing a block collection", self.marks[-1],
-                    "expected <block end>, but found %r" % token.id, token.start_mark)
-        token = self.get_token()
-        event = SequenceEndEvent(token.start_mark, token.end_mark)
-        self.state = self.states.pop()
-        self.marks.pop()
-        return event
-
-    # indentless_sequence ::= (BLOCK-ENTRY block_node?)+
-
-    def parse_indentless_sequence_entry(self):
-        if self.check_token(BlockEntryToken):
-            token = self.get_token()
-            if not self.check_token(BlockEntryToken,
-                    KeyToken, ValueToken, BlockEndToken):
-                self.states.append(self.parse_indentless_sequence_entry)
-                return self.parse_block_node()
-            else:
-                self.state = self.parse_indentless_sequence_entry
-                return self.process_empty_scalar(token.end_mark)
-        token = self.peek_token()
-        event = SequenceEndEvent(token.start_mark, token.start_mark)
-        self.state = self.states.pop()
-        return event
-
-    # block_mapping     ::= BLOCK-MAPPING_START
-    #                       ((KEY block_node_or_indentless_sequence?)?
-    #                       (VALUE block_node_or_indentless_sequence?)?)*
-    #                       BLOCK-END
-
-    def parse_block_mapping_first_key(self):
-        token = self.get_token()
-        self.marks.append(token.start_mark)
-        return self.parse_block_mapping_key()
-
-    def parse_block_mapping_key(self):
-        if self.check_token(KeyToken):
-            token = self.get_token()
-            if not self.check_token(KeyToken, ValueToken, BlockEndToken):
-                self.states.append(self.parse_block_mapping_value)
-                return self.parse_block_node_or_indentless_sequence()
-            else:
-                self.state = self.parse_block_mapping_value
-                return self.process_empty_scalar(token.end_mark)
-        if not self.check_token(BlockEndToken):
-            token = self.peek_token()
-            raise ParserError("while parsing a block mapping", self.marks[-1],
-                    "expected <block end>, but found %r" % token.id, token.start_mark)
-        token = self.get_token()
-        event = MappingEndEvent(token.start_mark, token.end_mark)
-        self.state = self.states.pop()
-        self.marks.pop()
-        return event
-
-    def parse_block_mapping_value(self):
-        if self.check_token(ValueToken):
-            token = self.get_token()
-            if not self.check_token(KeyToken, ValueToken, BlockEndToken):
-                self.states.append(self.parse_block_mapping_key)
-                return self.parse_block_node_or_indentless_sequence()
-            else:
-                self.state = self.parse_block_mapping_key
-                return self.process_empty_scalar(token.end_mark)
-        else:
-            self.state = self.parse_block_mapping_key
-            token = self.peek_token()
-            return self.process_empty_scalar(token.start_mark)
-
-    # flow_sequence     ::= FLOW-SEQUENCE-START
-    #                       (flow_sequence_entry FLOW-ENTRY)*
-    #                       flow_sequence_entry?
-    #                       FLOW-SEQUENCE-END
-    # flow_sequence_entry   ::= flow_node | KEY flow_node? (VALUE flow_node?)?
-    #
-    # Note that while production rules for both flow_sequence_entry and
-    # flow_mapping_entry are equal, their interpretations are different.
-    # For `flow_sequence_entry`, the part `KEY flow_node? (VALUE flow_node?)?`
-    # generate an inline mapping (set syntax).
-
-    def parse_flow_sequence_first_entry(self):
-        token = self.get_token()
-        self.marks.append(token.start_mark)
-        return self.parse_flow_sequence_entry(first=True)
-
-    def parse_flow_sequence_entry(self, first=False):
-        if not self.check_token(FlowSequenceEndToken):
-            if not first:
-                if self.check_token(FlowEntryToken):
-                    self.get_token()
-                else:
-                    token = self.peek_token()
-                    raise ParserError("while parsing a flow sequence", self.marks[-1],
-                            "expected ',' or ']', but got %r" % token.id, token.start_mark)
-            
-            if self.check_token(KeyToken):
-                token = self.peek_token()
-                event = MappingStartEvent(None, None, True,
-                        token.start_mark, token.end_mark,
-                        flow_style=True)
-                self.state = self.parse_flow_sequence_entry_mapping_key
-                return event
-            elif not self.check_token(FlowSequenceEndToken):
-                self.states.append(self.parse_flow_sequence_entry)
-                return self.parse_flow_node()
-        token = self.get_token()
-        event = SequenceEndEvent(token.start_mark, token.end_mark)
-        self.state = self.states.pop()
-        self.marks.pop()
-        return event
-
-    def parse_flow_sequence_entry_mapping_key(self):
-        token = self.get_token()
-        if not self.check_token(ValueToken,
-                FlowEntryToken, FlowSequenceEndToken):
-            self.states.append(self.parse_flow_sequence_entry_mapping_value)
-            return self.parse_flow_node()
-        else:
-            self.state = self.parse_flow_sequence_entry_mapping_value
-            return self.process_empty_scalar(token.end_mark)
-
-    def parse_flow_sequence_entry_mapping_value(self):
-        if self.check_token(ValueToken):
-            token = self.get_token()
-            if not self.check_token(FlowEntryToken, FlowSequenceEndToken):
-                self.states.append(self.parse_flow_sequence_entry_mapping_end)
-                return self.parse_flow_node()
-            else:
-                self.state = self.parse_flow_sequence_entry_mapping_end
-                return self.process_empty_scalar(token.end_mark)
-        else:
-            self.state = self.parse_flow_sequence_entry_mapping_end
-            token = self.peek_token()
-            return self.process_empty_scalar(token.start_mark)
-
-    def parse_flow_sequence_entry_mapping_end(self):
-        self.state = self.parse_flow_sequence_entry
-        token = self.peek_token()
-        return MappingEndEvent(token.start_mark, token.start_mark)
-
-    # flow_mapping  ::= FLOW-MAPPING-START
-    #                   (flow_mapping_entry FLOW-ENTRY)*
-    #                   flow_mapping_entry?
-    #                   FLOW-MAPPING-END
-    # flow_mapping_entry    ::= flow_node | KEY flow_node? (VALUE flow_node?)?
-
-    def parse_flow_mapping_first_key(self):
-        token = self.get_token()
-        self.marks.append(token.start_mark)
-        return self.parse_flow_mapping_key(first=True)
-
-    def parse_flow_mapping_key(self, first=False):
-        if not self.check_token(FlowMappingEndToken):
-            if not first:
-                if self.check_token(FlowEntryToken):
-                    self.get_token()
-                else:
-                    token = self.peek_token()
-                    raise ParserError("while parsing a flow mapping", self.marks[-1],
-                            "expected ',' or '}', but got %r" % token.id, token.start_mark)
-            if self.check_token(KeyToken):
-                token = self.get_token()
-                if not self.check_token(ValueToken,
-                        FlowEntryToken, FlowMappingEndToken):
-                    self.states.append(self.parse_flow_mapping_value)
-                    return self.parse_flow_node()
-                else:
-                    self.state = self.parse_flow_mapping_value
-                    return self.process_empty_scalar(token.end_mark)
-            elif not self.check_token(FlowMappingEndToken):
-                self.states.append(self.parse_flow_mapping_empty_value)
-                return self.parse_flow_node()
-        token = self.get_token()
-        event = MappingEndEvent(token.start_mark, token.end_mark)
-        self.state = self.states.pop()
-        self.marks.pop()
-        return event
-
-    def parse_flow_mapping_value(self):
-        if self.check_token(ValueToken):
-            token = self.get_token()
-            if not self.check_token(FlowEntryToken, FlowMappingEndToken):
-                self.states.append(self.parse_flow_mapping_key)
-                return self.parse_flow_node()
-            else:
-                self.state = self.parse_flow_mapping_key
-                return self.process_empty_scalar(token.end_mark)
-        else:
-            self.state = self.parse_flow_mapping_key
-            token = self.peek_token()
-            return self.process_empty_scalar(token.start_mark)
-
-    def parse_flow_mapping_empty_value(self):
-        self.state = self.parse_flow_mapping_key
-        return self.process_empty_scalar(self.peek_token().start_mark)
-
-    def process_empty_scalar(self, mark):
-        return ScalarEvent(None, None, (True, False), '', mark, mark)
-
diff --git a/lib/spack/external/yaml/lib3/yaml/representer.py b/lib/spack/external/yaml/lib3/yaml/representer.py
deleted file mode 100644
index b9e65c5109..0000000000
--- a/lib/spack/external/yaml/lib3/yaml/representer.py
+++ /dev/null
@@ -1,387 +0,0 @@
-
-__all__ = ['BaseRepresenter', 'SafeRepresenter', 'Representer',
-    'RepresenterError']
-
-from .error import *
-from .nodes import *
-
-import datetime, sys, copyreg, types, base64, collections
-
-class RepresenterError(YAMLError):
-    pass
-
-class BaseRepresenter:
-
-    yaml_representers = {}
-    yaml_multi_representers = {}
-
-    def __init__(self, default_style=None, default_flow_style=None):
-        self.default_style = default_style
-        self.default_flow_style = default_flow_style
-        self.represented_objects = {}
-        self.object_keeper = []
-        self.alias_key = None
-
-    def represent(self, data):
-        node = self.represent_data(data)
-        self.serialize(node)
-        self.represented_objects = {}
-        self.object_keeper = []
-        self.alias_key = None
-
-    def represent_data(self, data):
-        if self.ignore_aliases(data):
-            self.alias_key = None
-        else:
-            self.alias_key = id(data)
-        if self.alias_key is not None:
-            if self.alias_key in self.represented_objects:
-                node = self.represented_objects[self.alias_key]
-                #if node is None:
-                #    raise RepresenterError("recursive objects are not allowed: %r" % data)
-                return node
-            #self.represented_objects[alias_key] = None
-            self.object_keeper.append(data)
-        data_types = type(data).__mro__
-        if data_types[0] in self.yaml_representers:
-            node = self.yaml_representers[data_types[0]](self, data)
-        else:
-            for data_type in data_types:
-                if data_type in self.yaml_multi_representers:
-                    node = self.yaml_multi_representers[data_type](self, data)
-                    break
-            else:
-                if None in self.yaml_multi_representers:
-                    node = self.yaml_multi_representers[None](self, data)
-                elif None in self.yaml_representers:
-                    node = self.yaml_representers[None](self, data)
-                else:
-                    node = ScalarNode(None, str(data))
-        #if alias_key is not None:
-        #    self.represented_objects[alias_key] = node
-        return node
-
-    @classmethod
-    def add_representer(cls, data_type, representer):
-        if not 'yaml_representers' in cls.__dict__:
-            cls.yaml_representers = cls.yaml_representers.copy()
-        cls.yaml_representers[data_type] = representer
-
-    @classmethod
-    def add_multi_representer(cls, data_type, representer):
-        if not 'yaml_multi_representers' in cls.__dict__:
-            cls.yaml_multi_representers = cls.yaml_multi_representers.copy()
-        cls.yaml_multi_representers[data_type] = representer
-
-    def represent_scalar(self, tag, value, style=None):
-        if style is None:
-            style = self.default_style
-        node = ScalarNode(tag, value, style=style)
-        if self.alias_key is not None:
-            self.represented_objects[self.alias_key] = node
-        return node
-
-    def represent_sequence(self, tag, sequence, flow_style=None):
-        value = []
-        node = SequenceNode(tag, value, flow_style=flow_style)
-        if self.alias_key is not None:
-            self.represented_objects[self.alias_key] = node
-        best_style = True
-        for item in sequence:
-            node_item = self.represent_data(item)
-            if not (isinstance(node_item, ScalarNode) and not node_item.style):
-                best_style = False
-            value.append(node_item)
-        if flow_style is None:
-            if self.default_flow_style is not None:
-                node.flow_style = self.default_flow_style
-            else:
-                node.flow_style = best_style
-        return node
-
-    def represent_mapping(self, tag, mapping, flow_style=None):
-        value = []
-        node = MappingNode(tag, value, flow_style=flow_style)
-        if self.alias_key is not None:
-            self.represented_objects[self.alias_key] = node
-        best_style = True
-        if hasattr(mapping, 'items'):
-            mapping = list(mapping.items())
-            try:
-                mapping = sorted(mapping)
-            except TypeError:
-                pass
-        for item_key, item_value in mapping:
-            node_key = self.represent_data(item_key)
-            node_value = self.represent_data(item_value)
-            if not (isinstance(node_key, ScalarNode) and not node_key.style):
-                best_style = False
-            if not (isinstance(node_value, ScalarNode) and not node_value.style):
-                best_style = False
-            value.append((node_key, node_value))
-        if flow_style is None:
-            if self.default_flow_style is not None:
-                node.flow_style = self.default_flow_style
-            else:
-                node.flow_style = best_style
-        return node
-
-    def ignore_aliases(self, data):
-        return False
-
-class SafeRepresenter(BaseRepresenter):
-
-    def ignore_aliases(self, data):
-        if data is None:
-            return True
-        if isinstance(data, tuple) and data == ():
-            return True
-        if isinstance(data, (str, bytes, bool, int, float)):
-            return True
-
-    def represent_none(self, data):
-        return self.represent_scalar('tag:yaml.org,2002:null', 'null')
-
-    def represent_str(self, data):
-        return self.represent_scalar('tag:yaml.org,2002:str', data)
-
-    def represent_binary(self, data):
-        if hasattr(base64, 'encodebytes'):
-            data = base64.encodebytes(data).decode('ascii')
-        else:
-            data = base64.encodestring(data).decode('ascii')
-        return self.represent_scalar('tag:yaml.org,2002:binary', data, style='|')
-
-    def represent_bool(self, data):
-        if data:
-            value = 'true'
-        else:
-            value = 'false'
-        return self.represent_scalar('tag:yaml.org,2002:bool', value)
-
-    def represent_int(self, data):
-        return self.represent_scalar('tag:yaml.org,2002:int', str(data))
-
-    inf_value = 1e300
-    while repr(inf_value) != repr(inf_value*inf_value):
-        inf_value *= inf_value
-
-    def represent_float(self, data):
-        if data != data or (data == 0.0 and data == 1.0):
-            value = '.nan'
-        elif data == self.inf_value:
-            value = '.inf'
-        elif data == -self.inf_value:
-            value = '-.inf'
-        else:
-            value = repr(data).lower()
-            # Note that in some cases `repr(data)` represents a float number
-            # without the decimal parts.  For instance:
-            #   >>> repr(1e17)
-            #   '1e17'
-            # Unfortunately, this is not a valid float representation according
-            # to the definition of the `!!float` tag.  We fix this by adding
-            # '.0' before the 'e' symbol.
-            if '.' not in value and 'e' in value:
-                value = value.replace('e', '.0e', 1)
-        return self.represent_scalar('tag:yaml.org,2002:float', value)
-
-    def represent_list(self, data):
-        #pairs = (len(data) > 0 and isinstance(data, list))
-        #if pairs:
-        #    for item in data:
-        #        if not isinstance(item, tuple) or len(item) != 2:
-        #            pairs = False
-        #            break
-        #if not pairs:
-            return self.represent_sequence('tag:yaml.org,2002:seq', data)
-        #value = []
-        #for item_key, item_value in data:
-        #    value.append(self.represent_mapping(u'tag:yaml.org,2002:map',
-        #        [(item_key, item_value)]))
-        #return SequenceNode(u'tag:yaml.org,2002:pairs', value)
-
-    def represent_dict(self, data):
-        return self.represent_mapping('tag:yaml.org,2002:map', data)
-
-    def represent_set(self, data):
-        value = {}
-        for key in data:
-            value[key] = None
-        return self.represent_mapping('tag:yaml.org,2002:set', value)
-
-    def represent_date(self, data):
-        value = data.isoformat()
-        return self.represent_scalar('tag:yaml.org,2002:timestamp', value)
-
-    def represent_datetime(self, data):
-        value = data.isoformat(' ')
-        return self.represent_scalar('tag:yaml.org,2002:timestamp', value)
-
-    def represent_yaml_object(self, tag, data, cls, flow_style=None):
-        if hasattr(data, '__getstate__'):
-            state = data.__getstate__()
-        else:
-            state = data.__dict__.copy()
-        return self.represent_mapping(tag, state, flow_style=flow_style)
-
-    def represent_undefined(self, data):
-        raise RepresenterError("cannot represent an object: %s" % data)
-
-SafeRepresenter.add_representer(type(None),
-        SafeRepresenter.represent_none)
-
-SafeRepresenter.add_representer(str,
-        SafeRepresenter.represent_str)
-
-SafeRepresenter.add_representer(bytes,
-        SafeRepresenter.represent_binary)
-
-SafeRepresenter.add_representer(bool,
-        SafeRepresenter.represent_bool)
-
-SafeRepresenter.add_representer(int,
-        SafeRepresenter.represent_int)
-
-SafeRepresenter.add_representer(float,
-        SafeRepresenter.represent_float)
-
-SafeRepresenter.add_representer(list,
-        SafeRepresenter.represent_list)
-
-SafeRepresenter.add_representer(tuple,
-        SafeRepresenter.represent_list)
-
-SafeRepresenter.add_representer(dict,
-        SafeRepresenter.represent_dict)
-
-SafeRepresenter.add_representer(set,
-        SafeRepresenter.represent_set)
-
-SafeRepresenter.add_representer(datetime.date,
-        SafeRepresenter.represent_date)
-
-SafeRepresenter.add_representer(datetime.datetime,
-        SafeRepresenter.represent_datetime)
-
-SafeRepresenter.add_representer(None,
-        SafeRepresenter.represent_undefined)
-
-class Representer(SafeRepresenter):
-
-    def represent_complex(self, data):
-        if data.imag == 0.0:
-            data = '%r' % data.real
-        elif data.real == 0.0:
-            data = '%rj' % data.imag
-        elif data.imag > 0:
-            data = '%r+%rj' % (data.real, data.imag)
-        else:
-            data = '%r%rj' % (data.real, data.imag)
-        return self.represent_scalar('tag:yaml.org,2002:python/complex', data)
-
-    def represent_tuple(self, data):
-        return self.represent_sequence('tag:yaml.org,2002:python/tuple', data)
-
-    def represent_name(self, data):
-        name = '%s.%s' % (data.__module__, data.__name__)
-        return self.represent_scalar('tag:yaml.org,2002:python/name:'+name, '')
-
-    def represent_module(self, data):
-        return self.represent_scalar(
-                'tag:yaml.org,2002:python/module:'+data.__name__, '')
-
-    def represent_object(self, data):
-        # We use __reduce__ API to save the data. data.__reduce__ returns
-        # a tuple of length 2-5:
-        #   (function, args, state, listitems, dictitems)
-
-        # For reconstructing, we calls function(*args), then set its state,
-        # listitems, and dictitems if they are not None.
-
-        # A special case is when function.__name__ == '__newobj__'. In this
-        # case we create the object with args[0].__new__(*args).
-
-        # Another special case is when __reduce__ returns a string - we don't
-        # support it.
-
-        # We produce a !!python/object, !!python/object/new or
-        # !!python/object/apply node.
-
-        cls = type(data)
-        if cls in copyreg.dispatch_table:
-            reduce = copyreg.dispatch_table[cls](data)
-        elif hasattr(data, '__reduce_ex__'):
-            reduce = data.__reduce_ex__(2)
-        elif hasattr(data, '__reduce__'):
-            reduce = data.__reduce__()
-        else:
-            raise RepresenterError("cannot represent object: %r" % data)
-        reduce = (list(reduce)+[None]*5)[:5]
-        function, args, state, listitems, dictitems = reduce
-        args = list(args)
-        if state is None:
-            state = {}
-        if listitems is not None:
-            listitems = list(listitems)
-        if dictitems is not None:
-            dictitems = dict(dictitems)
-        if function.__name__ == '__newobj__':
-            function = args[0]
-            args = args[1:]
-            tag = 'tag:yaml.org,2002:python/object/new:'
-            newobj = True
-        else:
-            tag = 'tag:yaml.org,2002:python/object/apply:'
-            newobj = False
-        function_name = '%s.%s' % (function.__module__, function.__name__)
-        if not args and not listitems and not dictitems \
-                and isinstance(state, dict) and newobj:
-            return self.represent_mapping(
-                    'tag:yaml.org,2002:python/object:'+function_name, state)
-        if not listitems and not dictitems  \
-                and isinstance(state, dict) and not state:
-            return self.represent_sequence(tag+function_name, args)
-        value = {}
-        if args:
-            value['args'] = args
-        if state or not isinstance(state, dict):
-            value['state'] = state
-        if listitems:
-            value['listitems'] = listitems
-        if dictitems:
-            value['dictitems'] = dictitems
-        return self.represent_mapping(tag+function_name, value)
-
-    def represent_ordered_dict(self, data):
-        # Provide uniform representation across different Python versions.
-        data_type = type(data)
-        tag = 'tag:yaml.org,2002:python/object/apply:%s.%s' \
-                % (data_type.__module__, data_type.__name__)
-        items = [[key, value] for key, value in data.items()]
-        return self.represent_sequence(tag, [items])
-
-Representer.add_representer(complex,
-        Representer.represent_complex)
-
-Representer.add_representer(tuple,
-        Representer.represent_tuple)
-
-Representer.add_representer(type,
-        Representer.represent_name)
-
-Representer.add_representer(collections.OrderedDict,
-        Representer.represent_ordered_dict)
-
-Representer.add_representer(types.FunctionType,
-        Representer.represent_name)
-
-Representer.add_representer(types.BuiltinFunctionType,
-        Representer.represent_name)
-
-Representer.add_representer(types.ModuleType,
-        Representer.represent_module)
-
-Representer.add_multi_representer(object,
-        Representer.represent_object)
-
diff --git a/lib/spack/external/yaml/lib3/yaml/resolver.py b/lib/spack/external/yaml/lib3/yaml/resolver.py
deleted file mode 100644
index 02b82e73ee..0000000000
--- a/lib/spack/external/yaml/lib3/yaml/resolver.py
+++ /dev/null
@@ -1,227 +0,0 @@
-
-__all__ = ['BaseResolver', 'Resolver']
-
-from .error import *
-from .nodes import *
-
-import re
-
-class ResolverError(YAMLError):
-    pass
-
-class BaseResolver:
-
-    DEFAULT_SCALAR_TAG = 'tag:yaml.org,2002:str'
-    DEFAULT_SEQUENCE_TAG = 'tag:yaml.org,2002:seq'
-    DEFAULT_MAPPING_TAG = 'tag:yaml.org,2002:map'
-
-    yaml_implicit_resolvers = {}
-    yaml_path_resolvers = {}
-
-    def __init__(self):
-        self.resolver_exact_paths = []
-        self.resolver_prefix_paths = []
-
-    @classmethod
-    def add_implicit_resolver(cls, tag, regexp, first):
-        if not 'yaml_implicit_resolvers' in cls.__dict__:
-            implicit_resolvers = {}
-            for key in cls.yaml_implicit_resolvers:
-                implicit_resolvers[key] = cls.yaml_implicit_resolvers[key][:]
-            cls.yaml_implicit_resolvers = implicit_resolvers
-        if first is None:
-            first = [None]
-        for ch in first:
-            cls.yaml_implicit_resolvers.setdefault(ch, []).append((tag, regexp))
-
-    @classmethod
-    def add_path_resolver(cls, tag, path, kind=None):
-        # Note: `add_path_resolver` is experimental.  The API could be changed.
-        # `new_path` is a pattern that is matched against the path from the
-        # root to the node that is being considered.  `node_path` elements are
-        # tuples `(node_check, index_check)`.  `node_check` is a node class:
-        # `ScalarNode`, `SequenceNode`, `MappingNode` or `None`.  `None`
-        # matches any kind of a node.  `index_check` could be `None`, a boolean
-        # value, a string value, or a number.  `None` and `False` match against
-        # any _value_ of sequence and mapping nodes.  `True` matches against
-        # any _key_ of a mapping node.  A string `index_check` matches against
-        # a mapping value that corresponds to a scalar key which content is
-        # equal to the `index_check` value.  An integer `index_check` matches
-        # against a sequence value with the index equal to `index_check`.
-        if not 'yaml_path_resolvers' in cls.__dict__:
-            cls.yaml_path_resolvers = cls.yaml_path_resolvers.copy()
-        new_path = []
-        for element in path:
-            if isinstance(element, (list, tuple)):
-                if len(element) == 2:
-                    node_check, index_check = element
-                elif len(element) == 1:
-                    node_check = element[0]
-                    index_check = True
-                else:
-                    raise ResolverError("Invalid path element: %s" % element)
-            else:
-                node_check = None
-                index_check = element
-            if node_check is str:
-                node_check = ScalarNode
-            elif node_check is list:
-                node_check = SequenceNode
-            elif node_check is dict:
-                node_check = MappingNode
-            elif node_check not in [ScalarNode, SequenceNode, MappingNode]  \
-                    and not isinstance(node_check, str) \
-                    and node_check is not None:
-                raise ResolverError("Invalid node checker: %s" % node_check)
-            if not isinstance(index_check, (str, int))  \
-                    and index_check is not None:
-                raise ResolverError("Invalid index checker: %s" % index_check)
-            new_path.append((node_check, index_check))
-        if kind is str:
-            kind = ScalarNode
-        elif kind is list:
-            kind = SequenceNode
-        elif kind is dict:
-            kind = MappingNode
-        elif kind not in [ScalarNode, SequenceNode, MappingNode]    \
-                and kind is not None:
-            raise ResolverError("Invalid node kind: %s" % kind)
-        cls.yaml_path_resolvers[tuple(new_path), kind] = tag
-
-    def descend_resolver(self, current_node, current_index):
-        if not self.yaml_path_resolvers:
-            return
-        exact_paths = {}
-        prefix_paths = []
-        if current_node:
-            depth = len(self.resolver_prefix_paths)
-            for path, kind in self.resolver_prefix_paths[-1]:
-                if self.check_resolver_prefix(depth, path, kind,
-                        current_node, current_index):
-                    if len(path) > depth:
-                        prefix_paths.append((path, kind))
-                    else:
-                        exact_paths[kind] = self.yaml_path_resolvers[path, kind]
-        else:
-            for path, kind in self.yaml_path_resolvers:
-                if not path:
-                    exact_paths[kind] = self.yaml_path_resolvers[path, kind]
-                else:
-                    prefix_paths.append((path, kind))
-        self.resolver_exact_paths.append(exact_paths)
-        self.resolver_prefix_paths.append(prefix_paths)
-
-    def ascend_resolver(self):
-        if not self.yaml_path_resolvers:
-            return
-        self.resolver_exact_paths.pop()
-        self.resolver_prefix_paths.pop()
-
-    def check_resolver_prefix(self, depth, path, kind,
-            current_node, current_index):
-        node_check, index_check = path[depth-1]
-        if isinstance(node_check, str):
-            if current_node.tag != node_check:
-                return
-        elif node_check is not None:
-            if not isinstance(current_node, node_check):
-                return
-        if index_check is True and current_index is not None:
-            return
-        if (index_check is False or index_check is None)    \
-                and current_index is None:
-            return
-        if isinstance(index_check, str):
-            if not (isinstance(current_index, ScalarNode)
-                    and index_check == current_index.value):
-                return
-        elif isinstance(index_check, int) and not isinstance(index_check, bool):
-            if index_check != current_index:
-                return
-        return True
-
-    def resolve(self, kind, value, implicit):
-        if kind is ScalarNode and implicit[0]:
-            if value == '':
-                resolvers = self.yaml_implicit_resolvers.get('', [])
-            else:
-                resolvers = self.yaml_implicit_resolvers.get(value[0], [])
-            resolvers += self.yaml_implicit_resolvers.get(None, [])
-            for tag, regexp in resolvers:
-                if regexp.match(value):
-                    return tag
-            implicit = implicit[1]
-        if self.yaml_path_resolvers:
-            exact_paths = self.resolver_exact_paths[-1]
-            if kind in exact_paths:
-                return exact_paths[kind]
-            if None in exact_paths:
-                return exact_paths[None]
-        if kind is ScalarNode:
-            return self.DEFAULT_SCALAR_TAG
-        elif kind is SequenceNode:
-            return self.DEFAULT_SEQUENCE_TAG
-        elif kind is MappingNode:
-            return self.DEFAULT_MAPPING_TAG
-
-class Resolver(BaseResolver):
-    pass
-
-Resolver.add_implicit_resolver(
-        'tag:yaml.org,2002:bool',
-        re.compile(r'''^(?:yes|Yes|YES|no|No|NO
-                    |true|True|TRUE|false|False|FALSE
-                    |on|On|ON|off|Off|OFF)$''', re.X),
-        list('yYnNtTfFoO'))
-
-Resolver.add_implicit_resolver(
-        'tag:yaml.org,2002:float',
-        re.compile(r'''^(?:[-+]?(?:[0-9][0-9_]*)\.[0-9_]*(?:[eE][-+][0-9]+)?
-                    |\.[0-9_]+(?:[eE][-+][0-9]+)?
-                    |[-+]?[0-9][0-9_]*(?::[0-5]?[0-9])+\.[0-9_]*
-                    |[-+]?\.(?:inf|Inf|INF)
-                    |\.(?:nan|NaN|NAN))$''', re.X),
-        list('-+0123456789.'))
-
-Resolver.add_implicit_resolver(
-        'tag:yaml.org,2002:int',
-        re.compile(r'''^(?:[-+]?0b[0-1_]+
-                    |[-+]?0[0-7_]+
-                    |[-+]?(?:0|[1-9][0-9_]*)
-                    |[-+]?0x[0-9a-fA-F_]+
-                    |[-+]?[1-9][0-9_]*(?::[0-5]?[0-9])+)$''', re.X),
-        list('-+0123456789'))
-
-Resolver.add_implicit_resolver(
-        'tag:yaml.org,2002:merge',
-        re.compile(r'^(?:<<)$'),
-        ['<'])
-
-Resolver.add_implicit_resolver(
-        'tag:yaml.org,2002:null',
-        re.compile(r'''^(?: ~
-                    |null|Null|NULL
-                    | )$''', re.X),
-        ['~', 'n', 'N', ''])
-
-Resolver.add_implicit_resolver(
-        'tag:yaml.org,2002:timestamp',
-        re.compile(r'''^(?:[0-9][0-9][0-9][0-9]-[0-9][0-9]-[0-9][0-9]
-                    |[0-9][0-9][0-9][0-9] -[0-9][0-9]? -[0-9][0-9]?
-                     (?:[Tt]|[ \t]+)[0-9][0-9]?
-                     :[0-9][0-9] :[0-9][0-9] (?:\.[0-9]*)?
-                     (?:[ \t]*(?:Z|[-+][0-9][0-9]?(?::[0-9][0-9])?))?)$''', re.X),
-        list('0123456789'))
-
-Resolver.add_implicit_resolver(
-        'tag:yaml.org,2002:value',
-        re.compile(r'^(?:=)$'),
-        ['='])
-
-# The following resolver is only for documentation purposes. It cannot work
-# because plain scalars cannot start with '!', '&', or '*'.
-Resolver.add_implicit_resolver(
-        'tag:yaml.org,2002:yaml',
-        re.compile(r'^(?:!|&|\*)$'),
-        list('!&*'))
-
diff --git a/lib/spack/external/yaml/lib3/yaml/scanner.py b/lib/spack/external/yaml/lib3/yaml/scanner.py
deleted file mode 100644
index c8d127b8ec..0000000000
--- a/lib/spack/external/yaml/lib3/yaml/scanner.py
+++ /dev/null
@@ -1,1444 +0,0 @@
-
-# Scanner produces tokens of the following types:
-# STREAM-START
-# STREAM-END
-# DIRECTIVE(name, value)
-# DOCUMENT-START
-# DOCUMENT-END
-# BLOCK-SEQUENCE-START
-# BLOCK-MAPPING-START
-# BLOCK-END
-# FLOW-SEQUENCE-START
-# FLOW-MAPPING-START
-# FLOW-SEQUENCE-END
-# FLOW-MAPPING-END
-# BLOCK-ENTRY
-# FLOW-ENTRY
-# KEY
-# VALUE
-# ALIAS(value)
-# ANCHOR(value)
-# TAG(value)
-# SCALAR(value, plain, style)
-#
-# Read comments in the Scanner code for more details.
-#
-
-__all__ = ['Scanner', 'ScannerError']
-
-from .error import MarkedYAMLError
-from .tokens import *
-
-class ScannerError(MarkedYAMLError):
-    pass
-
-class SimpleKey:
-    # See below simple keys treatment.
-
-    def __init__(self, token_number, required, index, line, column, mark):
-        self.token_number = token_number
-        self.required = required
-        self.index = index
-        self.line = line
-        self.column = column
-        self.mark = mark
-
-class Scanner:
-
-    def __init__(self):
-        """Initialize the scanner."""
-        # It is assumed that Scanner and Reader will have a common descendant.
-        # Reader do the dirty work of checking for BOM and converting the
-        # input data to Unicode. It also adds NUL to the end.
-        #
-        # Reader supports the following methods
-        #   self.peek(i=0)       # peek the next i-th character
-        #   self.prefix(l=1)     # peek the next l characters
-        #   self.forward(l=1)    # read the next l characters and move the pointer.
-
-        # Had we reached the end of the stream?
-        self.done = False
-
-        # The number of unclosed '{' and '['. `flow_level == 0` means block
-        # context.
-        self.flow_level = 0
-
-        # List of processed tokens that are not yet emitted.
-        self.tokens = []
-
-        # Add the STREAM-START token.
-        self.fetch_stream_start()
-
-        # Number of tokens that were emitted through the `get_token` method.
-        self.tokens_taken = 0
-
-        # The current indentation level.
-        self.indent = -1
-
-        # Past indentation levels.
-        self.indents = []
-
-        # Variables related to simple keys treatment.
-
-        # A simple key is a key that is not denoted by the '?' indicator.
-        # Example of simple keys:
-        #   ---
-        #   block simple key: value
-        #   ? not a simple key:
-        #   : { flow simple key: value }
-        # We emit the KEY token before all keys, so when we find a potential
-        # simple key, we try to locate the corresponding ':' indicator.
-        # Simple keys should be limited to a single line and 1024 characters.
-
-        # Can a simple key start at the current position? A simple key may
-        # start:
-        # - at the beginning of the line, not counting indentation spaces
-        #       (in block context),
-        # - after '{', '[', ',' (in the flow context),
-        # - after '?', ':', '-' (in the block context).
-        # In the block context, this flag also signifies if a block collection
-        # may start at the current position.
-        self.allow_simple_key = True
-
-        # Keep track of possible simple keys. This is a dictionary. The key
-        # is `flow_level`; there can be no more that one possible simple key
-        # for each level. The value is a SimpleKey record:
-        #   (token_number, required, index, line, column, mark)
-        # A simple key may start with ALIAS, ANCHOR, TAG, SCALAR(flow),
-        # '[', or '{' tokens.
-        self.possible_simple_keys = {}
-
-    # Public methods.
-
-    def check_token(self, *choices):
-        # Check if the next token is one of the given types.
-        while self.need_more_tokens():
-            self.fetch_more_tokens()
-        if self.tokens:
-            if not choices:
-                return True
-            for choice in choices:
-                if isinstance(self.tokens[0], choice):
-                    return True
-        return False
-
-    def peek_token(self):
-        # Return the next token, but do not delete if from the queue.
-        while self.need_more_tokens():
-            self.fetch_more_tokens()
-        if self.tokens:
-            return self.tokens[0]
-
-    def get_token(self):
-        # Return the next token.
-        while self.need_more_tokens():
-            self.fetch_more_tokens()
-        if self.tokens:
-            self.tokens_taken += 1
-            return self.tokens.pop(0)
-
-    # Private methods.
-
-    def need_more_tokens(self):
-        if self.done:
-            return False
-        if not self.tokens:
-            return True
-        # The current token may be a potential simple key, so we
-        # need to look further.
-        self.stale_possible_simple_keys()
-        if self.next_possible_simple_key() == self.tokens_taken:
-            return True
-
-    def fetch_more_tokens(self):
-
-        # Eat whitespaces and comments until we reach the next token.
-        self.scan_to_next_token()
-
-        # Remove obsolete possible simple keys.
-        self.stale_possible_simple_keys()
-
-        # Compare the current indentation and column. It may add some tokens
-        # and decrease the current indentation level.
-        self.unwind_indent(self.column)
-
-        # Peek the next character.
-        ch = self.peek()
-
-        # Is it the end of stream?
-        if ch == '\0':
-            return self.fetch_stream_end()
-
-        # Is it a directive?
-        if ch == '%' and self.check_directive():
-            return self.fetch_directive()
-
-        # Is it the document start?
-        if ch == '-' and self.check_document_start():
-            return self.fetch_document_start()
-
-        # Is it the document end?
-        if ch == '.' and self.check_document_end():
-            return self.fetch_document_end()
-
-        # TODO: support for BOM within a stream.
-        #if ch == '\uFEFF':
-        #    return self.fetch_bom()    <-- issue BOMToken
-
-        # Note: the order of the following checks is NOT significant.
-
-        # Is it the flow sequence start indicator?
-        if ch == '[':
-            return self.fetch_flow_sequence_start()
-
-        # Is it the flow mapping start indicator?
-        if ch == '{':
-            return self.fetch_flow_mapping_start()
-
-        # Is it the flow sequence end indicator?
-        if ch == ']':
-            return self.fetch_flow_sequence_end()
-
-        # Is it the flow mapping end indicator?
-        if ch == '}':
-            return self.fetch_flow_mapping_end()
-
-        # Is it the flow entry indicator?
-        if ch == ',':
-            return self.fetch_flow_entry()
-
-        # Is it the block entry indicator?
-        if ch == '-' and self.check_block_entry():
-            return self.fetch_block_entry()
-
-        # Is it the key indicator?
-        if ch == '?' and self.check_key():
-            return self.fetch_key()
-
-        # Is it the value indicator?
-        if ch == ':' and self.check_value():
-            return self.fetch_value()
-
-        # Is it an alias?
-        if ch == '*':
-            return self.fetch_alias()
-
-        # Is it an anchor?
-        if ch == '&':
-            return self.fetch_anchor()
-
-        # Is it a tag?
-        if ch == '!':
-            return self.fetch_tag()
-
-        # Is it a literal scalar?
-        if ch == '|' and not self.flow_level:
-            return self.fetch_literal()
-
-        # Is it a folded scalar?
-        if ch == '>' and not self.flow_level:
-            return self.fetch_folded()
-
-        # Is it a single quoted scalar?
-        if ch == '\'':
-            return self.fetch_single()
-
-        # Is it a double quoted scalar?
-        if ch == '\"':
-            return self.fetch_double()
-
-        # It must be a plain scalar then.
-        if self.check_plain():
-            return self.fetch_plain()
-
-        # No? It's an error. Let's produce a nice error message.
-        raise ScannerError("while scanning for the next token", None,
-                "found character %r that cannot start any token" % ch,
-                self.get_mark())
-
-    # Simple keys treatment.
-
-    def next_possible_simple_key(self):
-        # Return the number of the nearest possible simple key. Actually we
-        # don't need to loop through the whole dictionary. We may replace it
-        # with the following code:
-        #   if not self.possible_simple_keys:
-        #       return None
-        #   return self.possible_simple_keys[
-        #           min(self.possible_simple_keys.keys())].token_number
-        min_token_number = None
-        for level in self.possible_simple_keys:
-            key = self.possible_simple_keys[level]
-            if min_token_number is None or key.token_number < min_token_number:
-                min_token_number = key.token_number
-        return min_token_number
-
-    def stale_possible_simple_keys(self):
-        # Remove entries that are no longer possible simple keys. According to
-        # the YAML specification, simple keys
-        # - should be limited to a single line,
-        # - should be no longer than 1024 characters.
-        # Disabling this procedure will allow simple keys of any length and
-        # height (may cause problems if indentation is broken though).
-        for level in list(self.possible_simple_keys):
-            key = self.possible_simple_keys[level]
-            if key.line != self.line  \
-                    or self.index-key.index > 1024:
-                if key.required:
-                    raise ScannerError("while scanning a simple key", key.mark,
-                            "could not find expected ':'", self.get_mark())
-                del self.possible_simple_keys[level]
-
-    def save_possible_simple_key(self):
-        # The next token may start a simple key. We check if it's possible
-        # and save its position. This function is called for
-        #   ALIAS, ANCHOR, TAG, SCALAR(flow), '[', and '{'.
-
-        # Check if a simple key is required at the current position.
-        required = not self.flow_level and self.indent == self.column
-
-        # The next token might be a simple key. Let's save it's number and
-        # position.
-        if self.allow_simple_key:
-            self.remove_possible_simple_key()
-            token_number = self.tokens_taken+len(self.tokens)
-            key = SimpleKey(token_number, required,
-                    self.index, self.line, self.column, self.get_mark())
-            self.possible_simple_keys[self.flow_level] = key
-
-    def remove_possible_simple_key(self):
-        # Remove the saved possible key position at the current flow level.
-        if self.flow_level in self.possible_simple_keys:
-            key = self.possible_simple_keys[self.flow_level]
-            
-            if key.required:
-                raise ScannerError("while scanning a simple key", key.mark,
-                        "could not find expected ':'", self.get_mark())
-
-            del self.possible_simple_keys[self.flow_level]
-
-    # Indentation functions.
-
-    def unwind_indent(self, column):
-
-        ## In flow context, tokens should respect indentation.
-        ## Actually the condition should be `self.indent >= column` according to
-        ## the spec. But this condition will prohibit intuitively correct
-        ## constructions such as
-        ## key : {
-        ## }
-        #if self.flow_level and self.indent > column:
-        #    raise ScannerError(None, None,
-        #            "invalid intendation or unclosed '[' or '{'",
-        #            self.get_mark())
-
-        # In the flow context, indentation is ignored. We make the scanner less
-        # restrictive then specification requires.
-        if self.flow_level:
-            return
-
-        # In block context, we may need to issue the BLOCK-END tokens.
-        while self.indent > column:
-            mark = self.get_mark()
-            self.indent = self.indents.pop()
-            self.tokens.append(BlockEndToken(mark, mark))
-
-    def add_indent(self, column):
-        # Check if we need to increase indentation.
-        if self.indent < column:
-            self.indents.append(self.indent)
-            self.indent = column
-            return True
-        return False
-
-    # Fetchers.
-
-    def fetch_stream_start(self):
-        # We always add STREAM-START as the first token and STREAM-END as the
-        # last token.
-
-        # Read the token.
-        mark = self.get_mark()
-        
-        # Add STREAM-START.
-        self.tokens.append(StreamStartToken(mark, mark,
-            encoding=self.encoding))
-        
-
-    def fetch_stream_end(self):
-
-        # Set the current intendation to -1.
-        self.unwind_indent(-1)
-
-        # Reset simple keys.
-        self.remove_possible_simple_key()
-        self.allow_simple_key = False
-        self.possible_simple_keys = {}
-
-        # Read the token.
-        mark = self.get_mark()
-        
-        # Add STREAM-END.
-        self.tokens.append(StreamEndToken(mark, mark))
-
-        # The steam is finished.
-        self.done = True
-
-    def fetch_directive(self):
-        
-        # Set the current intendation to -1.
-        self.unwind_indent(-1)
-
-        # Reset simple keys.
-        self.remove_possible_simple_key()
-        self.allow_simple_key = False
-
-        # Scan and add DIRECTIVE.
-        self.tokens.append(self.scan_directive())
-
-    def fetch_document_start(self):
-        self.fetch_document_indicator(DocumentStartToken)
-
-    def fetch_document_end(self):
-        self.fetch_document_indicator(DocumentEndToken)
-
-    def fetch_document_indicator(self, TokenClass):
-
-        # Set the current intendation to -1.
-        self.unwind_indent(-1)
-
-        # Reset simple keys. Note that there could not be a block collection
-        # after '---'.
-        self.remove_possible_simple_key()
-        self.allow_simple_key = False
-
-        # Add DOCUMENT-START or DOCUMENT-END.
-        start_mark = self.get_mark()
-        self.forward(3)
-        end_mark = self.get_mark()
-        self.tokens.append(TokenClass(start_mark, end_mark))
-
-    def fetch_flow_sequence_start(self):
-        self.fetch_flow_collection_start(FlowSequenceStartToken)
-
-    def fetch_flow_mapping_start(self):
-        self.fetch_flow_collection_start(FlowMappingStartToken)
-
-    def fetch_flow_collection_start(self, TokenClass):
-
-        # '[' and '{' may start a simple key.
-        self.save_possible_simple_key()
-
-        # Increase the flow level.
-        self.flow_level += 1
-
-        # Simple keys are allowed after '[' and '{'.
-        self.allow_simple_key = True
-
-        # Add FLOW-SEQUENCE-START or FLOW-MAPPING-START.
-        start_mark = self.get_mark()
-        self.forward()
-        end_mark = self.get_mark()
-        self.tokens.append(TokenClass(start_mark, end_mark))
-
-    def fetch_flow_sequence_end(self):
-        self.fetch_flow_collection_end(FlowSequenceEndToken)
-
-    def fetch_flow_mapping_end(self):
-        self.fetch_flow_collection_end(FlowMappingEndToken)
-
-    def fetch_flow_collection_end(self, TokenClass):
-
-        # Reset possible simple key on the current level.
-        self.remove_possible_simple_key()
-
-        # Decrease the flow level.
-        self.flow_level -= 1
-
-        # No simple keys after ']' or '}'.
-        self.allow_simple_key = False
-
-        # Add FLOW-SEQUENCE-END or FLOW-MAPPING-END.
-        start_mark = self.get_mark()
-        self.forward()
-        end_mark = self.get_mark()
-        self.tokens.append(TokenClass(start_mark, end_mark))
-
-    def fetch_flow_entry(self):
-
-        # Simple keys are allowed after ','.
-        self.allow_simple_key = True
-
-        # Reset possible simple key on the current level.
-        self.remove_possible_simple_key()
-
-        # Add FLOW-ENTRY.
-        start_mark = self.get_mark()
-        self.forward()
-        end_mark = self.get_mark()
-        self.tokens.append(FlowEntryToken(start_mark, end_mark))
-
-    def fetch_block_entry(self):
-
-        # Block context needs additional checks.
-        if not self.flow_level:
-
-            # Are we allowed to start a new entry?
-            if not self.allow_simple_key:
-                raise ScannerError(None, None,
-                        "sequence entries are not allowed here",
-                        self.get_mark())
-
-            # We may need to add BLOCK-SEQUENCE-START.
-            if self.add_indent(self.column):
-                mark = self.get_mark()
-                self.tokens.append(BlockSequenceStartToken(mark, mark))
-
-        # It's an error for the block entry to occur in the flow context,
-        # but we let the parser detect this.
-        else:
-            pass
-
-        # Simple keys are allowed after '-'.
-        self.allow_simple_key = True
-
-        # Reset possible simple key on the current level.
-        self.remove_possible_simple_key()
-
-        # Add BLOCK-ENTRY.
-        start_mark = self.get_mark()
-        self.forward()
-        end_mark = self.get_mark()
-        self.tokens.append(BlockEntryToken(start_mark, end_mark))
-
-    def fetch_key(self):
-        
-        # Block context needs additional checks.
-        if not self.flow_level:
-
-            # Are we allowed to start a key (not nessesary a simple)?
-            if not self.allow_simple_key:
-                raise ScannerError(None, None,
-                        "mapping keys are not allowed here",
-                        self.get_mark())
-
-            # We may need to add BLOCK-MAPPING-START.
-            if self.add_indent(self.column):
-                mark = self.get_mark()
-                self.tokens.append(BlockMappingStartToken(mark, mark))
-
-        # Simple keys are allowed after '?' in the block context.
-        self.allow_simple_key = not self.flow_level
-
-        # Reset possible simple key on the current level.
-        self.remove_possible_simple_key()
-
-        # Add KEY.
-        start_mark = self.get_mark()
-        self.forward()
-        end_mark = self.get_mark()
-        self.tokens.append(KeyToken(start_mark, end_mark))
-
-    def fetch_value(self):
-
-        # Do we determine a simple key?
-        if self.flow_level in self.possible_simple_keys:
-
-            # Add KEY.
-            key = self.possible_simple_keys[self.flow_level]
-            del self.possible_simple_keys[self.flow_level]
-            self.tokens.insert(key.token_number-self.tokens_taken,
-                    KeyToken(key.mark, key.mark))
-
-            # If this key starts a new block mapping, we need to add
-            # BLOCK-MAPPING-START.
-            if not self.flow_level:
-                if self.add_indent(key.column):
-                    self.tokens.insert(key.token_number-self.tokens_taken,
-                            BlockMappingStartToken(key.mark, key.mark))
-
-            # There cannot be two simple keys one after another.
-            self.allow_simple_key = False
-
-        # It must be a part of a complex key.
-        else:
-            
-            # Block context needs additional checks.
-            # (Do we really need them? They will be catched by the parser
-            # anyway.)
-            if not self.flow_level:
-
-                # We are allowed to start a complex value if and only if
-                # we can start a simple key.
-                if not self.allow_simple_key:
-                    raise ScannerError(None, None,
-                            "mapping values are not allowed here",
-                            self.get_mark())
-
-            # If this value starts a new block mapping, we need to add
-            # BLOCK-MAPPING-START.  It will be detected as an error later by
-            # the parser.
-            if not self.flow_level:
-                if self.add_indent(self.column):
-                    mark = self.get_mark()
-                    self.tokens.append(BlockMappingStartToken(mark, mark))
-
-            # Simple keys are allowed after ':' in the block context.
-            self.allow_simple_key = not self.flow_level
-
-            # Reset possible simple key on the current level.
-            self.remove_possible_simple_key()
-
-        # Add VALUE.
-        start_mark = self.get_mark()
-        self.forward()
-        end_mark = self.get_mark()
-        self.tokens.append(ValueToken(start_mark, end_mark))
-
-    def fetch_alias(self):
-
-        # ALIAS could be a simple key.
-        self.save_possible_simple_key()
-
-        # No simple keys after ALIAS.
-        self.allow_simple_key = False
-
-        # Scan and add ALIAS.
-        self.tokens.append(self.scan_anchor(AliasToken))
-
-    def fetch_anchor(self):
-
-        # ANCHOR could start a simple key.
-        self.save_possible_simple_key()
-
-        # No simple keys after ANCHOR.
-        self.allow_simple_key = False
-
-        # Scan and add ANCHOR.
-        self.tokens.append(self.scan_anchor(AnchorToken))
-
-    def fetch_tag(self):
-
-        # TAG could start a simple key.
-        self.save_possible_simple_key()
-
-        # No simple keys after TAG.
-        self.allow_simple_key = False
-
-        # Scan and add TAG.
-        self.tokens.append(self.scan_tag())
-
-    def fetch_literal(self):
-        self.fetch_block_scalar(style='|')
-
-    def fetch_folded(self):
-        self.fetch_block_scalar(style='>')
-
-    def fetch_block_scalar(self, style):
-
-        # A simple key may follow a block scalar.
-        self.allow_simple_key = True
-
-        # Reset possible simple key on the current level.
-        self.remove_possible_simple_key()
-
-        # Scan and add SCALAR.
-        self.tokens.append(self.scan_block_scalar(style))
-
-    def fetch_single(self):
-        self.fetch_flow_scalar(style='\'')
-
-    def fetch_double(self):
-        self.fetch_flow_scalar(style='"')
-
-    def fetch_flow_scalar(self, style):
-
-        # A flow scalar could be a simple key.
-        self.save_possible_simple_key()
-
-        # No simple keys after flow scalars.
-        self.allow_simple_key = False
-
-        # Scan and add SCALAR.
-        self.tokens.append(self.scan_flow_scalar(style))
-
-    def fetch_plain(self):
-
-        # A plain scalar could be a simple key.
-        self.save_possible_simple_key()
-
-        # No simple keys after plain scalars. But note that `scan_plain` will
-        # change this flag if the scan is finished at the beginning of the
-        # line.
-        self.allow_simple_key = False
-
-        # Scan and add SCALAR. May change `allow_simple_key`.
-        self.tokens.append(self.scan_plain())
-
-    # Checkers.
-
-    def check_directive(self):
-
-        # DIRECTIVE:        ^ '%' ...
-        # The '%' indicator is already checked.
-        if self.column == 0:
-            return True
-
-    def check_document_start(self):
-
-        # DOCUMENT-START:   ^ '---' (' '|'\n')
-        if self.column == 0:
-            if self.prefix(3) == '---'  \
-                    and self.peek(3) in '\0 \t\r\n\x85\u2028\u2029':
-                return True
-
-    def check_document_end(self):
-
-        # DOCUMENT-END:     ^ '...' (' '|'\n')
-        if self.column == 0:
-            if self.prefix(3) == '...'  \
-                    and self.peek(3) in '\0 \t\r\n\x85\u2028\u2029':
-                return True
-
-    def check_block_entry(self):
-
-        # BLOCK-ENTRY:      '-' (' '|'\n')
-        return self.peek(1) in '\0 \t\r\n\x85\u2028\u2029'
-
-    def check_key(self):
-
-        # KEY(flow context):    '?'
-        if self.flow_level:
-            return True
-
-        # KEY(block context):   '?' (' '|'\n')
-        else:
-            return self.peek(1) in '\0 \t\r\n\x85\u2028\u2029'
-
-    def check_value(self):
-
-        # VALUE(flow context):  ':'
-        if self.flow_level:
-            return True
-
-        # VALUE(block context): ':' (' '|'\n')
-        else:
-            return self.peek(1) in '\0 \t\r\n\x85\u2028\u2029'
-
-    def check_plain(self):
-
-        # A plain scalar may start with any non-space character except:
-        #   '-', '?', ':', ',', '[', ']', '{', '}',
-        #   '#', '&', '*', '!', '|', '>', '\'', '\"',
-        #   '%', '@', '`'.
-        #
-        # It may also start with
-        #   '-', '?', ':'
-        # if it is followed by a non-space character.
-        #
-        # Note that we limit the last rule to the block context (except the
-        # '-' character) because we want the flow context to be space
-        # independent.
-        ch = self.peek()
-        return ch not in '\0 \t\r\n\x85\u2028\u2029-?:,[]{}#&*!|>\'\"%@`'  \
-                or (self.peek(1) not in '\0 \t\r\n\x85\u2028\u2029'
-                        and (ch == '-' or (not self.flow_level and ch in '?:')))
-
-    # Scanners.
-
-    def scan_to_next_token(self):
-        # We ignore spaces, line breaks and comments.
-        # If we find a line break in the block context, we set the flag
-        # `allow_simple_key` on.
-        # The byte order mark is stripped if it's the first character in the
-        # stream. We do not yet support BOM inside the stream as the
-        # specification requires. Any such mark will be considered as a part
-        # of the document.
-        #
-        # TODO: We need to make tab handling rules more sane. A good rule is
-        #   Tabs cannot precede tokens
-        #   BLOCK-SEQUENCE-START, BLOCK-MAPPING-START, BLOCK-END,
-        #   KEY(block), VALUE(block), BLOCK-ENTRY
-        # So the checking code is
-        #   if <TAB>:
-        #       self.allow_simple_keys = False
-        # We also need to add the check for `allow_simple_keys == True` to
-        # `unwind_indent` before issuing BLOCK-END.
-        # Scanners for block, flow, and plain scalars need to be modified.
-
-        if self.index == 0 and self.peek() == '\uFEFF':
-            self.forward()
-        found = False
-        while not found:
-            while self.peek() == ' ':
-                self.forward()
-            if self.peek() == '#':
-                while self.peek() not in '\0\r\n\x85\u2028\u2029':
-                    self.forward()
-            if self.scan_line_break():
-                if not self.flow_level:
-                    self.allow_simple_key = True
-            else:
-                found = True
-
-    def scan_directive(self):
-        # See the specification for details.
-        start_mark = self.get_mark()
-        self.forward()
-        name = self.scan_directive_name(start_mark)
-        value = None
-        if name == 'YAML':
-            value = self.scan_yaml_directive_value(start_mark)
-            end_mark = self.get_mark()
-        elif name == 'TAG':
-            value = self.scan_tag_directive_value(start_mark)
-            end_mark = self.get_mark()
-        else:
-            end_mark = self.get_mark()
-            while self.peek() not in '\0\r\n\x85\u2028\u2029':
-                self.forward()
-        self.scan_directive_ignored_line(start_mark)
-        return DirectiveToken(name, value, start_mark, end_mark)
-
-    def scan_directive_name(self, start_mark):
-        # See the specification for details.
-        length = 0
-        ch = self.peek(length)
-        while '0' <= ch <= '9' or 'A' <= ch <= 'Z' or 'a' <= ch <= 'z'  \
-                or ch in '-_':
-            length += 1
-            ch = self.peek(length)
-        if not length:
-            raise ScannerError("while scanning a directive", start_mark,
-                    "expected alphabetic or numeric character, but found %r"
-                    % ch, self.get_mark())
-        value = self.prefix(length)
-        self.forward(length)
-        ch = self.peek()
-        if ch not in '\0 \r\n\x85\u2028\u2029':
-            raise ScannerError("while scanning a directive", start_mark,
-                    "expected alphabetic or numeric character, but found %r"
-                    % ch, self.get_mark())
-        return value
-
-    def scan_yaml_directive_value(self, start_mark):
-        # See the specification for details.
-        while self.peek() == ' ':
-            self.forward()
-        major = self.scan_yaml_directive_number(start_mark)
-        if self.peek() != '.':
-            raise ScannerError("while scanning a directive", start_mark,
-                    "expected a digit or '.', but found %r" % self.peek(),
-                    self.get_mark())
-        self.forward()
-        minor = self.scan_yaml_directive_number(start_mark)
-        if self.peek() not in '\0 \r\n\x85\u2028\u2029':
-            raise ScannerError("while scanning a directive", start_mark,
-                    "expected a digit or ' ', but found %r" % self.peek(),
-                    self.get_mark())
-        return (major, minor)
-
-    def scan_yaml_directive_number(self, start_mark):
-        # See the specification for details.
-        ch = self.peek()
-        if not ('0' <= ch <= '9'):
-            raise ScannerError("while scanning a directive", start_mark,
-                    "expected a digit, but found %r" % ch, self.get_mark())
-        length = 0
-        while '0' <= self.peek(length) <= '9':
-            length += 1
-        value = int(self.prefix(length))
-        self.forward(length)
-        return value
-
-    def scan_tag_directive_value(self, start_mark):
-        # See the specification for details.
-        while self.peek() == ' ':
-            self.forward()
-        handle = self.scan_tag_directive_handle(start_mark)
-        while self.peek() == ' ':
-            self.forward()
-        prefix = self.scan_tag_directive_prefix(start_mark)
-        return (handle, prefix)
-
-    def scan_tag_directive_handle(self, start_mark):
-        # See the specification for details.
-        value = self.scan_tag_handle('directive', start_mark)
-        ch = self.peek()
-        if ch != ' ':
-            raise ScannerError("while scanning a directive", start_mark,
-                    "expected ' ', but found %r" % ch, self.get_mark())
-        return value
-
-    def scan_tag_directive_prefix(self, start_mark):
-        # See the specification for details.
-        value = self.scan_tag_uri('directive', start_mark)
-        ch = self.peek()
-        if ch not in '\0 \r\n\x85\u2028\u2029':
-            raise ScannerError("while scanning a directive", start_mark,
-                    "expected ' ', but found %r" % ch, self.get_mark())
-        return value
-
-    def scan_directive_ignored_line(self, start_mark):
-        # See the specification for details.
-        while self.peek() == ' ':
-            self.forward()
-        if self.peek() == '#':
-            while self.peek() not in '\0\r\n\x85\u2028\u2029':
-                self.forward()
-        ch = self.peek()
-        if ch not in '\0\r\n\x85\u2028\u2029':
-            raise ScannerError("while scanning a directive", start_mark,
-                    "expected a comment or a line break, but found %r"
-                        % ch, self.get_mark())
-        self.scan_line_break()
-
-    def scan_anchor(self, TokenClass):
-        # The specification does not restrict characters for anchors and
-        # aliases. This may lead to problems, for instance, the document:
-        #   [ *alias, value ]
-        # can be interpteted in two ways, as
-        #   [ "value" ]
-        # and
-        #   [ *alias , "value" ]
-        # Therefore we restrict aliases to numbers and ASCII letters.
-        start_mark = self.get_mark()
-        indicator = self.peek()
-        if indicator == '*':
-            name = 'alias'
-        else:
-            name = 'anchor'
-        self.forward()
-        length = 0
-        ch = self.peek(length)
-        while '0' <= ch <= '9' or 'A' <= ch <= 'Z' or 'a' <= ch <= 'z'  \
-                or ch in '-_':
-            length += 1
-            ch = self.peek(length)
-        if not length:
-            raise ScannerError("while scanning an %s" % name, start_mark,
-                    "expected alphabetic or numeric character, but found %r"
-                    % ch, self.get_mark())
-        value = self.prefix(length)
-        self.forward(length)
-        ch = self.peek()
-        if ch not in '\0 \t\r\n\x85\u2028\u2029?:,]}%@`':
-            raise ScannerError("while scanning an %s" % name, start_mark,
-                    "expected alphabetic or numeric character, but found %r"
-                    % ch, self.get_mark())
-        end_mark = self.get_mark()
-        return TokenClass(value, start_mark, end_mark)
-
-    def scan_tag(self):
-        # See the specification for details.
-        start_mark = self.get_mark()
-        ch = self.peek(1)
-        if ch == '<':
-            handle = None
-            self.forward(2)
-            suffix = self.scan_tag_uri('tag', start_mark)
-            if self.peek() != '>':
-                raise ScannerError("while parsing a tag", start_mark,
-                        "expected '>', but found %r" % self.peek(),
-                        self.get_mark())
-            self.forward()
-        elif ch in '\0 \t\r\n\x85\u2028\u2029':
-            handle = None
-            suffix = '!'
-            self.forward()
-        else:
-            length = 1
-            use_handle = False
-            while ch not in '\0 \r\n\x85\u2028\u2029':
-                if ch == '!':
-                    use_handle = True
-                    break
-                length += 1
-                ch = self.peek(length)
-            handle = '!'
-            if use_handle:
-                handle = self.scan_tag_handle('tag', start_mark)
-            else:
-                handle = '!'
-                self.forward()
-            suffix = self.scan_tag_uri('tag', start_mark)
-        ch = self.peek()
-        if ch not in '\0 \r\n\x85\u2028\u2029':
-            raise ScannerError("while scanning a tag", start_mark,
-                    "expected ' ', but found %r" % ch, self.get_mark())
-        value = (handle, suffix)
-        end_mark = self.get_mark()
-        return TagToken(value, start_mark, end_mark)
-
-    def scan_block_scalar(self, style):
-        # See the specification for details.
-
-        if style == '>':
-            folded = True
-        else:
-            folded = False
-
-        chunks = []
-        start_mark = self.get_mark()
-
-        # Scan the header.
-        self.forward()
-        chomping, increment = self.scan_block_scalar_indicators(start_mark)
-        self.scan_block_scalar_ignored_line(start_mark)
-
-        # Determine the indentation level and go to the first non-empty line.
-        min_indent = self.indent+1
-        if min_indent < 1:
-            min_indent = 1
-        if increment is None:
-            breaks, max_indent, end_mark = self.scan_block_scalar_indentation()
-            indent = max(min_indent, max_indent)
-        else:
-            indent = min_indent+increment-1
-            breaks, end_mark = self.scan_block_scalar_breaks(indent)
-        line_break = ''
-
-        # Scan the inner part of the block scalar.
-        while self.column == indent and self.peek() != '\0':
-            chunks.extend(breaks)
-            leading_non_space = self.peek() not in ' \t'
-            length = 0
-            while self.peek(length) not in '\0\r\n\x85\u2028\u2029':
-                length += 1
-            chunks.append(self.prefix(length))
-            self.forward(length)
-            line_break = self.scan_line_break()
-            breaks, end_mark = self.scan_block_scalar_breaks(indent)
-            if self.column == indent and self.peek() != '\0':
-
-                # Unfortunately, folding rules are ambiguous.
-                #
-                # This is the folding according to the specification:
-                
-                if folded and line_break == '\n'    \
-                        and leading_non_space and self.peek() not in ' \t':
-                    if not breaks:
-                        chunks.append(' ')
-                else:
-                    chunks.append(line_break)
-                
-                # This is Clark Evans's interpretation (also in the spec
-                # examples):
-                #
-                #if folded and line_break == '\n':
-                #    if not breaks:
-                #        if self.peek() not in ' \t':
-                #            chunks.append(' ')
-                #        else:
-                #            chunks.append(line_break)
-                #else:
-                #    chunks.append(line_break)
-            else:
-                break
-
-        # Chomp the tail.
-        if chomping is not False:
-            chunks.append(line_break)
-        if chomping is True:
-            chunks.extend(breaks)
-
-        # We are done.
-        return ScalarToken(''.join(chunks), False, start_mark, end_mark,
-                style)
-
-    def scan_block_scalar_indicators(self, start_mark):
-        # See the specification for details.
-        chomping = None
-        increment = None
-        ch = self.peek()
-        if ch in '+-':
-            if ch == '+':
-                chomping = True
-            else:
-                chomping = False
-            self.forward()
-            ch = self.peek()
-            if ch in '0123456789':
-                increment = int(ch)
-                if increment == 0:
-                    raise ScannerError("while scanning a block scalar", start_mark,
-                            "expected indentation indicator in the range 1-9, but found 0",
-                            self.get_mark())
-                self.forward()
-        elif ch in '0123456789':
-            increment = int(ch)
-            if increment == 0:
-                raise ScannerError("while scanning a block scalar", start_mark,
-                        "expected indentation indicator in the range 1-9, but found 0",
-                        self.get_mark())
-            self.forward()
-            ch = self.peek()
-            if ch in '+-':
-                if ch == '+':
-                    chomping = True
-                else:
-                    chomping = False
-                self.forward()
-        ch = self.peek()
-        if ch not in '\0 \r\n\x85\u2028\u2029':
-            raise ScannerError("while scanning a block scalar", start_mark,
-                    "expected chomping or indentation indicators, but found %r"
-                    % ch, self.get_mark())
-        return chomping, increment
-
-    def scan_block_scalar_ignored_line(self, start_mark):
-        # See the specification for details.
-        while self.peek() == ' ':
-            self.forward()
-        if self.peek() == '#':
-            while self.peek() not in '\0\r\n\x85\u2028\u2029':
-                self.forward()
-        ch = self.peek()
-        if ch not in '\0\r\n\x85\u2028\u2029':
-            raise ScannerError("while scanning a block scalar", start_mark,
-                    "expected a comment or a line break, but found %r" % ch,
-                    self.get_mark())
-        self.scan_line_break()
-
-    def scan_block_scalar_indentation(self):
-        # See the specification for details.
-        chunks = []
-        max_indent = 0
-        end_mark = self.get_mark()
-        while self.peek() in ' \r\n\x85\u2028\u2029':
-            if self.peek() != ' ':
-                chunks.append(self.scan_line_break())
-                end_mark = self.get_mark()
-            else:
-                self.forward()
-                if self.column > max_indent:
-                    max_indent = self.column
-        return chunks, max_indent, end_mark
-
-    def scan_block_scalar_breaks(self, indent):
-        # See the specification for details.
-        chunks = []
-        end_mark = self.get_mark()
-        while self.column < indent and self.peek() == ' ':
-            self.forward()
-        while self.peek() in '\r\n\x85\u2028\u2029':
-            chunks.append(self.scan_line_break())
-            end_mark = self.get_mark()
-            while self.column < indent and self.peek() == ' ':
-                self.forward()
-        return chunks, end_mark
-
-    def scan_flow_scalar(self, style):
-        # See the specification for details.
-        # Note that we loose indentation rules for quoted scalars. Quoted
-        # scalars don't need to adhere indentation because " and ' clearly
-        # mark the beginning and the end of them. Therefore we are less
-        # restrictive then the specification requires. We only need to check
-        # that document separators are not included in scalars.
-        if style == '"':
-            double = True
-        else:
-            double = False
-        chunks = []
-        start_mark = self.get_mark()
-        quote = self.peek()
-        self.forward()
-        chunks.extend(self.scan_flow_scalar_non_spaces(double, start_mark))
-        while self.peek() != quote:
-            chunks.extend(self.scan_flow_scalar_spaces(double, start_mark))
-            chunks.extend(self.scan_flow_scalar_non_spaces(double, start_mark))
-        self.forward()
-        end_mark = self.get_mark()
-        return ScalarToken(''.join(chunks), False, start_mark, end_mark,
-                style)
-
-    ESCAPE_REPLACEMENTS = {
-        '0':    '\0',
-        'a':    '\x07',
-        'b':    '\x08',
-        't':    '\x09',
-        '\t':   '\x09',
-        'n':    '\x0A',
-        'v':    '\x0B',
-        'f':    '\x0C',
-        'r':    '\x0D',
-        'e':    '\x1B',
-        ' ':    '\x20',
-        '\"':   '\"',
-        '\\':   '\\',
-        'N':    '\x85',
-        '_':    '\xA0',
-        'L':    '\u2028',
-        'P':    '\u2029',
-    }
-
-    ESCAPE_CODES = {
-        'x':    2,
-        'u':    4,
-        'U':    8,
-    }
-
-    def scan_flow_scalar_non_spaces(self, double, start_mark):
-        # See the specification for details.
-        chunks = []
-        while True:
-            length = 0
-            while self.peek(length) not in '\'\"\\\0 \t\r\n\x85\u2028\u2029':
-                length += 1
-            if length:
-                chunks.append(self.prefix(length))
-                self.forward(length)
-            ch = self.peek()
-            if not double and ch == '\'' and self.peek(1) == '\'':
-                chunks.append('\'')
-                self.forward(2)
-            elif (double and ch == '\'') or (not double and ch in '\"\\'):
-                chunks.append(ch)
-                self.forward()
-            elif double and ch == '\\':
-                self.forward()
-                ch = self.peek()
-                if ch in self.ESCAPE_REPLACEMENTS:
-                    chunks.append(self.ESCAPE_REPLACEMENTS[ch])
-                    self.forward()
-                elif ch in self.ESCAPE_CODES:
-                    length = self.ESCAPE_CODES[ch]
-                    self.forward()
-                    for k in range(length):
-                        if self.peek(k) not in '0123456789ABCDEFabcdef':
-                            raise ScannerError("while scanning a double-quoted scalar", start_mark,
-                                    "expected escape sequence of %d hexdecimal numbers, but found %r" %
-                                        (length, self.peek(k)), self.get_mark())
-                    code = int(self.prefix(length), 16)
-                    chunks.append(chr(code))
-                    self.forward(length)
-                elif ch in '\r\n\x85\u2028\u2029':
-                    self.scan_line_break()
-                    chunks.extend(self.scan_flow_scalar_breaks(double, start_mark))
-                else:
-                    raise ScannerError("while scanning a double-quoted scalar", start_mark,
-                            "found unknown escape character %r" % ch, self.get_mark())
-            else:
-                return chunks
-
-    def scan_flow_scalar_spaces(self, double, start_mark):
-        # See the specification for details.
-        chunks = []
-        length = 0
-        while self.peek(length) in ' \t':
-            length += 1
-        whitespaces = self.prefix(length)
-        self.forward(length)
-        ch = self.peek()
-        if ch == '\0':
-            raise ScannerError("while scanning a quoted scalar", start_mark,
-                    "found unexpected end of stream", self.get_mark())
-        elif ch in '\r\n\x85\u2028\u2029':
-            line_break = self.scan_line_break()
-            breaks = self.scan_flow_scalar_breaks(double, start_mark)
-            if line_break != '\n':
-                chunks.append(line_break)
-            elif not breaks:
-                chunks.append(' ')
-            chunks.extend(breaks)
-        else:
-            chunks.append(whitespaces)
-        return chunks
-
-    def scan_flow_scalar_breaks(self, double, start_mark):
-        # See the specification for details.
-        chunks = []
-        while True:
-            # Instead of checking indentation, we check for document
-            # separators.
-            prefix = self.prefix(3)
-            if (prefix == '---' or prefix == '...')   \
-                    and self.peek(3) in '\0 \t\r\n\x85\u2028\u2029':
-                raise ScannerError("while scanning a quoted scalar", start_mark,
-                        "found unexpected document separator", self.get_mark())
-            while self.peek() in ' \t':
-                self.forward()
-            if self.peek() in '\r\n\x85\u2028\u2029':
-                chunks.append(self.scan_line_break())
-            else:
-                return chunks
-
-    def scan_plain(self):
-        # See the specification for details.
-        # We add an additional restriction for the flow context:
-        #   plain scalars in the flow context cannot contain ',', ':' and '?'.
-        # We also keep track of the `allow_simple_key` flag here.
-        # Indentation rules are loosed for the flow context.
-        chunks = []
-        start_mark = self.get_mark()
-        end_mark = start_mark
-        indent = self.indent+1
-        # We allow zero indentation for scalars, but then we need to check for
-        # document separators at the beginning of the line.
-        #if indent == 0:
-        #    indent = 1
-        spaces = []
-        while True:
-            length = 0
-            if self.peek() == '#':
-                break
-            while True:
-                ch = self.peek(length)
-                if ch in '\0 \t\r\n\x85\u2028\u2029'    \
-                        or (not self.flow_level and ch == ':' and
-                                self.peek(length+1) in '\0 \t\r\n\x85\u2028\u2029') \
-                        or (self.flow_level and ch in ',:?[]{}'):
-                    break
-                length += 1
-            # It's not clear what we should do with ':' in the flow context.
-            if (self.flow_level and ch == ':'
-                    and self.peek(length+1) not in '\0 \t\r\n\x85\u2028\u2029,[]{}'):
-                self.forward(length)
-                raise ScannerError("while scanning a plain scalar", start_mark,
-                    "found unexpected ':'", self.get_mark(),
-                    "Please check http://pyyaml.org/wiki/YAMLColonInFlowContext for details.")
-            if length == 0:
-                break
-            self.allow_simple_key = False
-            chunks.extend(spaces)
-            chunks.append(self.prefix(length))
-            self.forward(length)
-            end_mark = self.get_mark()
-            spaces = self.scan_plain_spaces(indent, start_mark)
-            if not spaces or self.peek() == '#' \
-                    or (not self.flow_level and self.column < indent):
-                break
-        return ScalarToken(''.join(chunks), True, start_mark, end_mark)
-
-    def scan_plain_spaces(self, indent, start_mark):
-        # See the specification for details.
-        # The specification is really confusing about tabs in plain scalars.
-        # We just forbid them completely. Do not use tabs in YAML!
-        chunks = []
-        length = 0
-        while self.peek(length) in ' ':
-            length += 1
-        whitespaces = self.prefix(length)
-        self.forward(length)
-        ch = self.peek()
-        if ch in '\r\n\x85\u2028\u2029':
-            line_break = self.scan_line_break()
-            self.allow_simple_key = True
-            prefix = self.prefix(3)
-            if (prefix == '---' or prefix == '...')   \
-                    and self.peek(3) in '\0 \t\r\n\x85\u2028\u2029':
-                return
-            breaks = []
-            while self.peek() in ' \r\n\x85\u2028\u2029':
-                if self.peek() == ' ':
-                    self.forward()
-                else:
-                    breaks.append(self.scan_line_break())
-                    prefix = self.prefix(3)
-                    if (prefix == '---' or prefix == '...')   \
-                            and self.peek(3) in '\0 \t\r\n\x85\u2028\u2029':
-                        return
-            if line_break != '\n':
-                chunks.append(line_break)
-            elif not breaks:
-                chunks.append(' ')
-            chunks.extend(breaks)
-        elif whitespaces:
-            chunks.append(whitespaces)
-        return chunks
-
-    def scan_tag_handle(self, name, start_mark):
-        # See the specification for details.
-        # For some strange reasons, the specification does not allow '_' in
-        # tag handles. I have allowed it anyway.
-        ch = self.peek()
-        if ch != '!':
-            raise ScannerError("while scanning a %s" % name, start_mark,
-                    "expected '!', but found %r" % ch, self.get_mark())
-        length = 1
-        ch = self.peek(length)
-        if ch != ' ':
-            while '0' <= ch <= '9' or 'A' <= ch <= 'Z' or 'a' <= ch <= 'z'  \
-                    or ch in '-_':
-                length += 1
-                ch = self.peek(length)
-            if ch != '!':
-                self.forward(length)
-                raise ScannerError("while scanning a %s" % name, start_mark,
-                        "expected '!', but found %r" % ch, self.get_mark())
-            length += 1
-        value = self.prefix(length)
-        self.forward(length)
-        return value
-
-    def scan_tag_uri(self, name, start_mark):
-        # See the specification for details.
-        # Note: we do not check if URI is well-formed.
-        chunks = []
-        length = 0
-        ch = self.peek(length)
-        while '0' <= ch <= '9' or 'A' <= ch <= 'Z' or 'a' <= ch <= 'z'  \
-                or ch in '-;/?:@&=+$,_.!~*\'()[]%':
-            if ch == '%':
-                chunks.append(self.prefix(length))
-                self.forward(length)
-                length = 0
-                chunks.append(self.scan_uri_escapes(name, start_mark))
-            else:
-                length += 1
-            ch = self.peek(length)
-        if length:
-            chunks.append(self.prefix(length))
-            self.forward(length)
-            length = 0
-        if not chunks:
-            raise ScannerError("while parsing a %s" % name, start_mark,
-                    "expected URI, but found %r" % ch, self.get_mark())
-        return ''.join(chunks)
-
-    def scan_uri_escapes(self, name, start_mark):
-        # See the specification for details.
-        codes = []
-        mark = self.get_mark()
-        while self.peek() == '%':
-            self.forward()
-            for k in range(2):
-                if self.peek(k) not in '0123456789ABCDEFabcdef':
-                    raise ScannerError("while scanning a %s" % name, start_mark,
-                            "expected URI escape sequence of 2 hexdecimal numbers, but found %r"
-                            % self.peek(k), self.get_mark())
-            codes.append(int(self.prefix(2), 16))
-            self.forward(2)
-        try:
-            value = bytes(codes).decode('utf-8')
-        except UnicodeDecodeError as exc:
-            raise ScannerError("while scanning a %s" % name, start_mark, str(exc), mark)
-        return value
-
-    def scan_line_break(self):
-        # Transforms:
-        #   '\r\n'      :   '\n'
-        #   '\r'        :   '\n'
-        #   '\n'        :   '\n'
-        #   '\x85'      :   '\n'
-        #   '\u2028'    :   '\u2028'
-        #   '\u2029     :   '\u2029'
-        #   default     :   ''
-        ch = self.peek()
-        if ch in '\r\n\x85':
-            if self.prefix(2) == '\r\n':
-                self.forward(2)
-            else:
-                self.forward()
-            return '\n'
-        elif ch in '\u2028\u2029':
-            self.forward()
-            return ch
-        return ''
-
-#try:
-#    import psyco
-#    psyco.bind(Scanner)
-#except ImportError:
-#    pass
-
diff --git a/lib/spack/external/yaml/lib3/yaml/serializer.py b/lib/spack/external/yaml/lib3/yaml/serializer.py
deleted file mode 100644
index fe911e67ae..0000000000
--- a/lib/spack/external/yaml/lib3/yaml/serializer.py
+++ /dev/null
@@ -1,111 +0,0 @@
-
-__all__ = ['Serializer', 'SerializerError']
-
-from .error import YAMLError
-from .events import *
-from .nodes import *
-
-class SerializerError(YAMLError):
-    pass
-
-class Serializer:
-
-    ANCHOR_TEMPLATE = 'id%03d'
-
-    def __init__(self, encoding=None,
-            explicit_start=None, explicit_end=None, version=None, tags=None):
-        self.use_encoding = encoding
-        self.use_explicit_start = explicit_start
-        self.use_explicit_end = explicit_end
-        self.use_version = version
-        self.use_tags = tags
-        self.serialized_nodes = {}
-        self.anchors = {}
-        self.last_anchor_id = 0
-        self.closed = None
-
-    def open(self):
-        if self.closed is None:
-            self.emit(StreamStartEvent(encoding=self.use_encoding))
-            self.closed = False
-        elif self.closed:
-            raise SerializerError("serializer is closed")
-        else:
-            raise SerializerError("serializer is already opened")
-
-    def close(self):
-        if self.closed is None:
-            raise SerializerError("serializer is not opened")
-        elif not self.closed:
-            self.emit(StreamEndEvent())
-            self.closed = True
-
-    #def __del__(self):
-    #    self.close()
-
-    def serialize(self, node):
-        if self.closed is None:
-            raise SerializerError("serializer is not opened")
-        elif self.closed:
-            raise SerializerError("serializer is closed")
-        self.emit(DocumentStartEvent(explicit=self.use_explicit_start,
-            version=self.use_version, tags=self.use_tags))
-        self.anchor_node(node)
-        self.serialize_node(node, None, None)
-        self.emit(DocumentEndEvent(explicit=self.use_explicit_end))
-        self.serialized_nodes = {}
-        self.anchors = {}
-        self.last_anchor_id = 0
-
-    def anchor_node(self, node):
-        if node in self.anchors:
-            if self.anchors[node] is None:
-                self.anchors[node] = self.generate_anchor(node)
-        else:
-            self.anchors[node] = None
-            if isinstance(node, SequenceNode):
-                for item in node.value:
-                    self.anchor_node(item)
-            elif isinstance(node, MappingNode):
-                for key, value in node.value:
-                    self.anchor_node(key)
-                    self.anchor_node(value)
-
-    def generate_anchor(self, node):
-        self.last_anchor_id += 1
-        return self.ANCHOR_TEMPLATE % self.last_anchor_id
-
-    def serialize_node(self, node, parent, index):
-        alias = self.anchors[node]
-        if node in self.serialized_nodes:
-            self.emit(AliasEvent(alias))
-        else:
-            self.serialized_nodes[node] = True
-            self.descend_resolver(parent, index)
-            if isinstance(node, ScalarNode):
-                detected_tag = self.resolve(ScalarNode, node.value, (True, False))
-                default_tag = self.resolve(ScalarNode, node.value, (False, True))
-                implicit = (node.tag == detected_tag), (node.tag == default_tag)
-                self.emit(ScalarEvent(alias, node.tag, implicit, node.value,
-                    style=node.style))
-            elif isinstance(node, SequenceNode):
-                implicit = (node.tag
-                            == self.resolve(SequenceNode, node.value, True))
-                self.emit(SequenceStartEvent(alias, node.tag, implicit,
-                    flow_style=node.flow_style))
-                index = 0
-                for item in node.value:
-                    self.serialize_node(item, node, index)
-                    index += 1
-                self.emit(SequenceEndEvent())
-            elif isinstance(node, MappingNode):
-                implicit = (node.tag
-                            == self.resolve(MappingNode, node.value, True))
-                self.emit(MappingStartEvent(alias, node.tag, implicit,
-                    flow_style=node.flow_style))
-                for key, value in node.value:
-                    self.serialize_node(key, node, None)
-                    self.serialize_node(value, node, key)
-                self.emit(MappingEndEvent())
-            self.ascend_resolver()
-
diff --git a/lib/spack/external/yaml/lib3/yaml/tokens.py b/lib/spack/external/yaml/lib3/yaml/tokens.py
deleted file mode 100644
index 4d0b48a394..0000000000
--- a/lib/spack/external/yaml/lib3/yaml/tokens.py
+++ /dev/null
@@ -1,104 +0,0 @@
-
-class Token(object):
-    def __init__(self, start_mark, end_mark):
-        self.start_mark = start_mark
-        self.end_mark = end_mark
-    def __repr__(self):
-        attributes = [key for key in self.__dict__
-                if not key.endswith('_mark')]
-        attributes.sort()
-        arguments = ', '.join(['%s=%r' % (key, getattr(self, key))
-                for key in attributes])
-        return '%s(%s)' % (self.__class__.__name__, arguments)
-
-#class BOMToken(Token):
-#    id = '<byte order mark>'
-
-class DirectiveToken(Token):
-    id = '<directive>'
-    def __init__(self, name, value, start_mark, end_mark):
-        self.name = name
-        self.value = value
-        self.start_mark = start_mark
-        self.end_mark = end_mark
-
-class DocumentStartToken(Token):
-    id = '<document start>'
-
-class DocumentEndToken(Token):
-    id = '<document end>'
-
-class StreamStartToken(Token):
-    id = '<stream start>'
-    def __init__(self, start_mark=None, end_mark=None,
-            encoding=None):
-        self.start_mark = start_mark
-        self.end_mark = end_mark
-        self.encoding = encoding
-
-class StreamEndToken(Token):
-    id = '<stream end>'
-
-class BlockSequenceStartToken(Token):
-    id = '<block sequence start>'
-
-class BlockMappingStartToken(Token):
-    id = '<block mapping start>'
-
-class BlockEndToken(Token):
-    id = '<block end>'
-
-class FlowSequenceStartToken(Token):
-    id = '['
-
-class FlowMappingStartToken(Token):
-    id = '{'
-
-class FlowSequenceEndToken(Token):
-    id = ']'
-
-class FlowMappingEndToken(Token):
-    id = '}'
-
-class KeyToken(Token):
-    id = '?'
-
-class ValueToken(Token):
-    id = ':'
-
-class BlockEntryToken(Token):
-    id = '-'
-
-class FlowEntryToken(Token):
-    id = ','
-
-class AliasToken(Token):
-    id = '<alias>'
-    def __init__(self, value, start_mark, end_mark):
-        self.value = value
-        self.start_mark = start_mark
-        self.end_mark = end_mark
-
-class AnchorToken(Token):
-    id = '<anchor>'
-    def __init__(self, value, start_mark, end_mark):
-        self.value = value
-        self.start_mark = start_mark
-        self.end_mark = end_mark
-
-class TagToken(Token):
-    id = '<tag>'
-    def __init__(self, value, start_mark, end_mark):
-        self.value = value
-        self.start_mark = start_mark
-        self.end_mark = end_mark
-
-class ScalarToken(Token):
-    id = '<scalar>'
-    def __init__(self, value, plain, start_mark, end_mark, style=None):
-        self.value = value
-        self.plain = plain
-        self.start_mark = start_mark
-        self.end_mark = end_mark
-        self.style = style
-
diff --git a/lib/spack/llnl/__init__.py b/lib/spack/llnl/__init__.py
index 8922701e9f..4f442db458 100644
--- a/lib/spack/llnl/__init__.py
+++ b/lib/spack/llnl/__init__.py
@@ -1,24 +1,4 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
diff --git a/lib/spack/llnl/util/__init__.py b/lib/spack/llnl/util/__init__.py
index 8922701e9f..4f442db458 100644
--- a/lib/spack/llnl/util/__init__.py
+++ b/lib/spack/llnl/util/__init__.py
@@ -1,24 +1,4 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
diff --git a/lib/spack/llnl/util/argparsewriter.py b/lib/spack/llnl/util/argparsewriter.py
new file mode 100644
index 0000000000..7ae89b81a8
--- /dev/null
+++ b/lib/spack/llnl/util/argparsewriter.py
@@ -0,0 +1,203 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from __future__ import print_function
+import re
+import argparse
+import errno
+import sys
+
+
+class ArgparseWriter(object):
+    """Analyzes an argparse ArgumentParser for easy generation of help."""
+    def __init__(self):
+        self.level = 0
+
+    def _write(self, parser, root=True, level=0):
+        self.parser = parser
+        self.level = level
+        actions = parser._actions
+
+        # allow root level to be flattened with rest of commands
+        if type(root) == int:
+            self.level = root
+            root = True
+
+        # go through actions and split them into optionals, positionals,
+        # and subcommands
+        optionals = []
+        positionals = []
+        subcommands = []
+        for action in actions:
+            if action.option_strings:
+                optionals.append(action)
+            elif isinstance(action, argparse._SubParsersAction):
+                for subaction in action._choices_actions:
+                    subparser = action._name_parser_map[subaction.dest]
+                    subcommands.append(subparser)
+            else:
+                positionals.append(action)
+
+        groups = parser._mutually_exclusive_groups
+        fmt = parser._get_formatter()
+        description = parser.description
+
+        def action_group(function, actions):
+            for action in actions:
+                arg = fmt._format_action_invocation(action)
+                help = action.help if action.help else ''
+                function(arg, re.sub('\n', ' ', help))
+
+        if root:
+            self.begin_command(parser.prog)
+
+            if description:
+                self.description(parser.description)
+
+            usage = fmt._format_usage(None, actions, groups, '').strip()
+            self.usage(usage)
+
+            if positionals:
+                self.begin_positionals()
+                action_group(self.positional, positionals)
+                self.end_positionals()
+
+            if optionals:
+                self.begin_optionals()
+                action_group(self.optional, optionals)
+                self.end_optionals()
+
+        if subcommands:
+            self.begin_subcommands(subcommands)
+            for subparser in subcommands:
+                self._write(subparser, root=True, level=level + 1)
+            self.end_subcommands(subcommands)
+
+        if root:
+            self.end_command(parser.prog)
+
+    def write(self, parser, root=True):
+        """Write out details about an ArgumentParser.
+
+        Args:
+            parser (ArgumentParser): an ``argparse`` parser
+            root (bool or int): if bool, whether to include the root parser;
+                or ``1`` to flatten the root parser with first-level
+                subcommands
+        """
+        try:
+            self._write(parser, root, level=0)
+        except IOError as e:
+            # swallow pipe errors
+            if e.errno != errno.EPIPE:
+                raise
+
+    def begin_command(self, prog):
+        pass
+
+    def end_command(self, prog):
+        pass
+
+    def description(self, description):
+        pass
+
+    def usage(self, usage):
+        pass
+
+    def begin_positionals(self):
+        pass
+
+    def positional(self, name, help):
+        pass
+
+    def end_positionals(self):
+        pass
+
+    def begin_optionals(self):
+        pass
+
+    def optional(self, option, help):
+        pass
+
+    def end_optionals(self):
+        pass
+
+    def begin_subcommands(self, subcommands):
+        pass
+
+    def end_subcommands(self, subcommands):
+        pass
+
+
+_rst_levels = ['=', '-', '^', '~', ':', '`']
+
+
+class ArgparseRstWriter(ArgparseWriter):
+    """Write argparse output as rst sections."""
+
+    def __init__(self, out=sys.stdout, rst_levels=_rst_levels,
+                 strip_root_prog=True):
+        """Create a new ArgparseRstWriter.
+
+        Args:
+            out (file object): file to write to
+            rst_levels (list of str): list of characters
+                for rst section headings
+            strip_root_prog (bool): if ``True``, strip the base command name
+                from subcommands in output
+        """
+        super(ArgparseWriter, self).__init__()
+        self.out = out
+        self.rst_levels = rst_levels
+        self.strip_root_prog = strip_root_prog
+
+    def line(self, string=''):
+        self.out.write('%s\n' % string)
+
+    def begin_command(self, prog):
+        self.line()
+        self.line('----')
+        self.line()
+        self.line('.. _%s:\n' % prog.replace(' ', '-'))
+        self.line('%s' % prog)
+        self.line(self.rst_levels[self.level] * len(prog) + '\n')
+
+    def description(self, description):
+        self.line('%s\n' % description)
+
+    def usage(self, usage):
+        self.line('.. code-block:: console\n')
+        self.line('    %s\n' % usage)
+
+    def begin_positionals(self):
+        self.line()
+        self.line('**Positional arguments**\n')
+
+    def positional(self, name, help):
+        self.line(name)
+        self.line('  %s\n' % help)
+
+    def begin_optionals(self):
+        self.line()
+        self.line('**Optional arguments**\n')
+
+    def optional(self, opts, help):
+        self.line('``%s``' % opts)
+        self.line('  %s\n' % help)
+
+    def begin_subcommands(self, subcommands):
+        self.line()
+        self.line('**Subcommands**\n')
+        self.line('.. hlist::')
+        self.line('   :columns: 4\n')
+
+        for cmd in subcommands:
+            prog = cmd.prog
+            if self.strip_root_prog:
+                prog = re.sub(r'^[^ ]* ', '', prog)
+
+            self.line('   * :ref:`%s <%s>`'
+                      % (prog, cmd.prog.replace(' ', '-')))
+        self.line()
diff --git a/lib/spack/llnl/util/filesystem.py b/lib/spack/llnl/util/filesystem.py
index 36be87580c..bb74eea9e7 100644
--- a/lib/spack/llnl/util/filesystem.py
+++ b/lib/spack/llnl/util/filesystem.py
@@ -1,39 +1,20 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import collections
 import errno
 import hashlib
 import fileinput
-import fnmatch
 import glob
+import grp
 import numbers
 import os
+import pwd
 import re
 import shutil
 import stat
-import subprocess
 import sys
 import tempfile
 from contextlib import contextmanager
@@ -41,6 +22,7 @@ from contextlib import contextmanager
 import six
 from llnl.util import tty
 from llnl.util.lang import dedupe
+from spack.util.executable import Executable
 
 __all__ = [
     'FileFilter',
@@ -59,8 +41,9 @@ __all__ = [
     'fix_darwin_install_name',
     'force_remove',
     'force_symlink',
-    'hide_files',
+    'copy',
     'install',
+    'copy_tree',
     'install_tree',
     'is_exe',
     'join_path',
@@ -78,6 +61,18 @@ __all__ = [
 ]
 
 
+def path_contains_subdirectory(path, root):
+    norm_root = os.path.abspath(root).rstrip(os.path.sep) + os.path.sep
+    norm_path = os.path.abspath(path).rstrip(os.path.sep) + os.path.sep
+    return norm_path.startswith(norm_root)
+
+
+def same_path(path1, path2):
+    norm1 = os.path.abspath(path1).rstrip(os.path.sep)
+    norm2 = os.path.abspath(path2).rstrip(os.path.sep)
+    return norm1 == norm2
+
+
 def filter_file(regex, repl, *filenames, **kwargs):
     r"""Like sed, but uses python regular expressions.
 
@@ -119,9 +114,15 @@ def filter_file(regex, repl, *filenames, **kwargs):
         regex = re.escape(regex)
 
     for filename in filenames:
+
+        msg = 'FILTER FILE: {0} [replacing "{1}"]'
+        tty.debug(msg.format(filename, regex))
+
         backup_filename = filename + "~"
 
         if ignore_absent and not os.path.exists(filename):
+            msg = 'FILTER FILE: file "{0}" not found. Skipping to next file.'
+            tty.debug(msg.format(filename))
             continue
 
         # Create backup file. Don't overwrite an existing backup
@@ -196,9 +197,9 @@ def change_sed_delimiter(old_delim, new_delim, *filenames):
 
 def set_install_permissions(path):
     """Set appropriate permissions on the installed file."""
-# If this points to a file maintained in a Spack prefix, it is assumed that
-# this function will be invoked on the target. If the file is outside a
-# Spack-maintained prefix, the permissions should not be modified.
+    # If this points to a file maintained in a Spack prefix, it is assumed that
+    # this function will be invoked on the target. If the file is outside a
+    # Spack-maintained prefix, the permissions should not be modified.
     if os.path.islink(path):
         return
     if os.path.isdir(path):
@@ -207,6 +208,40 @@ def set_install_permissions(path):
         os.chmod(path, 0o644)
 
 
+def group_ids(uid=None):
+    """Get group ids that a uid is a member of.
+
+    Arguments:
+        uid (int): id of user, or None for current user
+
+    Returns:
+        (list of int): gids of groups the user is a member of
+    """
+    if uid is None:
+        uid = os.getuid()
+    user = pwd.getpwuid(uid).pw_name
+    return [g.gr_gid for g in grp.getgrall() if user in g.gr_mem]
+
+
+def chgrp(path, group):
+    """Implement the bash chgrp function on a single path"""
+    gid = grp.getgrnam(group).gr_gid
+    os.chown(path, -1, gid)
+
+
+def chmod_x(entry, perms):
+    """Implements chmod, treating all executable bits as set using the chmod
+    utility's `+X` option.
+    """
+    mode = os.stat(entry).st_mode
+    if os.path.isfile(entry):
+        if not mode & (stat.S_IXUSR | stat.S_IXGRP | stat.S_IXOTH):
+            perms &= ~stat.S_IXUSR
+            perms &= ~stat.S_IXGRP
+            perms &= ~stat.S_IXOTH
+    os.chmod(entry, perms)
+
+
 def copy_mode(src, dest):
     """Set the mode of dest to that of src unless it is a link.
     """
@@ -231,27 +266,135 @@ def unset_executable_mode(path):
     os.chmod(path, mode)
 
 
-def install(src, dest):
-    """Manually install a file to a particular location."""
-    tty.debug("Installing %s to %s" % (src, dest))
+def copy(src, dest, _permissions=False):
+    """Copies the file *src* to the file or directory *dest*.
+
+    If *dest* specifies a directory, the file will be copied into *dest*
+    using the base filename from *src*.
+
+    Parameters:
+        src (str): the file to copy
+        dest (str): the destination file or directory
+        _permissions (bool): for internal use only
+    """
+    if _permissions:
+        tty.debug('Installing {0} to {1}'.format(src, dest))
+    else:
+        tty.debug('Copying {0} to {1}'.format(src, dest))
 
     # Expand dest to its eventual full path if it is a directory.
     if os.path.isdir(dest):
         dest = join_path(dest, os.path.basename(src))
 
     shutil.copy(src, dest)
-    set_install_permissions(dest)
-    copy_mode(src, dest)
 
+    if _permissions:
+        set_install_permissions(dest)
+        copy_mode(src, dest)
+
+
+def install(src, dest):
+    """Installs the file *src* to the file or directory *dest*.
+
+    Same as :py:func:`copy` with the addition of setting proper
+    permissions on the installed file.
+
+    Parameters:
+        src (str): the file to install
+        dest (str): the destination file or directory
+    """
+    copy(src, dest, _permissions=True)
+
+
+def resolve_link_target_relative_to_the_link(l):
+    """
+    os.path.isdir uses os.path.exists, which for links will check
+    the existence of the link target. If the link target is relative to
+    the link, we need to construct a pathname that is valid from
+    our cwd (which may not be the same as the link's directory)
+    """
+    target = os.readlink(l)
+    if os.path.isabs(target):
+        return target
+    link_dir = os.path.dirname(os.path.abspath(l))
+    return os.path.join(link_dir, target)
+
+
+def copy_tree(src, dest, symlinks=True, ignore=None, _permissions=False):
+    """Recursively copy an entire directory tree rooted at *src*.
 
-def install_tree(src, dest, **kwargs):
-    """Manually install a directory tree to a particular location."""
-    tty.debug("Installing %s to %s" % (src, dest))
-    shutil.copytree(src, dest, **kwargs)
+    If the destination directory *dest* does not already exist, it will
+    be created as well as missing parent directories.
 
-    for s, d in traverse_tree(src, dest, follow_nonexisting=False):
-        set_install_permissions(d)
-        copy_mode(s, d)
+    If *symlinks* is true, symbolic links in the source tree are represented
+    as symbolic links in the new tree and the metadata of the original links
+    will be copied as far as the platform allows; if false, the contents and
+    metadata of the linked files are copied to the new tree.
+
+    If *ignore* is set, then each path relative to *src* will be passed to
+    this function; the function returns whether that path should be skipped.
+
+    Parameters:
+        src (str): the directory to copy
+        dest (str): the destination directory
+        symlinks (bool): whether or not to preserve symlinks
+        ignore (function): function indicating which files to ignore
+        _permissions (bool): for internal use only
+    """
+    if _permissions:
+        tty.debug('Installing {0} to {1}'.format(src, dest))
+    else:
+        tty.debug('Copying {0} to {1}'.format(src, dest))
+
+    mkdirp(dest)
+
+    src = os.path.abspath(src)
+    dest = os.path.abspath(dest)
+
+    for s, d in traverse_tree(src, dest, order='pre',
+                              follow_symlinks=not symlinks,
+                              ignore=ignore,
+                              follow_nonexisting=True):
+        if os.path.islink(s):
+            link_target = resolve_link_target_relative_to_the_link(s)
+            if symlinks:
+                target = os.readlink(s)
+                if os.path.isabs(target):
+                    new_target = re.sub(src, dest, target)
+                    if new_target != target:
+                        tty.debug("Redirecting link {0} to {1}"
+                                  .format(target, new_target))
+                        target = new_target
+
+                os.symlink(target, d)
+            elif os.path.isdir(link_target):
+                mkdirp(d)
+            else:
+                shutil.copyfile(s, d)
+        else:
+            if os.path.isdir(s):
+                mkdirp(d)
+            else:
+                shutil.copyfile(s, d)
+
+        if _permissions:
+            set_install_permissions(d)
+            copy_mode(s, d)
+
+
+def install_tree(src, dest, symlinks=True, ignore=None):
+    """Recursively install an entire directory tree rooted at *src*.
+
+    Same as :py:func:`copy_tree` with the addition of setting proper
+    permissions on the installed files and directories.
+
+    Parameters:
+        src (str): the directory to install
+        dest (str): the destination directory
+        symlinks (bool): whether or not to preserve symlinks
+        ignore (function): function indicating which files to ignore
+    """
+    copy_tree(src, dest, symlinks=symlinks, ignore=ignore, _permissions=True)
 
 
 def is_exe(path):
@@ -259,12 +402,34 @@ def is_exe(path):
     return os.path.isfile(path) and os.access(path, os.X_OK)
 
 
-def mkdirp(*paths):
-    """Creates a directory, as well as parent directories if needed."""
+def get_filetype(path_name):
+    """
+    Return the output of file path_name as a string to identify file type.
+    """
+    file = Executable('file')
+    file.add_default_env('LC_ALL', 'C')
+    output = file('-b', '-h', '%s' % path_name,
+                  output=str, error=str)
+    return output.strip()
+
+
+def mkdirp(*paths, **kwargs):
+    """Creates a directory, as well as parent directories if needed.
+
+    Arguments:
+        paths (str): paths to create with mkdirp
+
+    Keyword Aguments:
+        mode (permission bits or None, optional): optional permissions to
+            set on the created directory -- use OS default if not provided
+    """
+    mode = kwargs.get('mode', None)
     for path in paths:
         if not os.path.exists(path):
             try:
                 os.makedirs(path)
+                if mode is not None:
+                    os.chmod(path, mode)
             except OSError as e:
                 if e.errno != errno.EEXIST or not os.path.isdir(path):
                     raise e
@@ -347,18 +512,6 @@ def replace_directory_transaction(directory_name, tmp_root=None):
         tty.debug('TEMPORARY DIRECTORY DELETED [{0}]'.format(tmp_dir))
 
 
-@contextmanager
-def hide_files(*file_list):
-    try:
-        baks = ['%s.bak' % f for f in file_list]
-        for f, bak in zip(file_list, baks):
-            shutil.move(f, bak)
-        yield
-    finally:
-        for f, bak in zip(file_list, baks):
-            shutil.move(bak, f)
-
-
 def hash_directory(directory):
     """Hashes recursively the content of a directory.
 
@@ -385,6 +538,30 @@ def hash_directory(directory):
     return md5_hash.hexdigest()
 
 
+@contextmanager
+def write_tmp_and_move(filename):
+    """Write to a temporary file, then move into place."""
+    dirname = os.path.dirname(filename)
+    basename = os.path.basename(filename)
+    tmp = os.path.join(dirname, '.%s.tmp' % basename)
+    with open(tmp, 'w') as f:
+        yield f
+    shutil.move(tmp, filename)
+
+
+@contextmanager
+def open_if_filename(str_or_file, mode='r'):
+    """Takes either a path or a file object, and opens it if it is a path.
+
+    If it's a file object, just yields the file object.
+    """
+    if isinstance(str_or_file, six.string_types):
+        with open(str_or_file, mode) as f:
+            yield f
+    else:
+        yield str_or_file
+
+
 def touch(path):
     """Creates an empty file at the specified path."""
     perms = (os.O_WRONLY | os.O_CREAT | os.O_NONBLOCK | os.O_NOCTTY)
@@ -459,7 +636,7 @@ def traverse_tree(source_root, dest_root, rel_path='', **kwargs):
     Keyword Arguments:
         order (str): Whether to do pre- or post-order traversal. Accepted
             values are 'pre' and 'post'
-        ignore (str): Predicate indicating which files to ignore
+        ignore (function): function indicating which files to ignore
         follow_nonexisting (bool): Whether to descend into directories in
             ``src`` that do not exit in ``dest``. Default is True
         follow_links (bool): Whether to descend into symlinks in ``src``
@@ -473,7 +650,7 @@ def traverse_tree(source_root, dest_root, rel_path='', **kwargs):
         raise ValueError("Order must be 'pre' or 'post'.")
 
     # List of relative paths to ignore under the src root.
-    ignore = kwargs.get('ignore', lambda filename: False)
+    ignore = kwargs.get('ignore', None) or (lambda filename: False)
 
     # Don't descend into ignored directories
     if ignore(rel_path):
@@ -492,6 +669,9 @@ def traverse_tree(source_root, dest_root, rel_path='', **kwargs):
         rel_child = os.path.join(rel_path, f)
 
         # Treat as a directory
+        # TODO: for symlinks, os.path.isdir looks for the link target. If the
+        # target is relative to the link, then that may not resolve properly
+        # relative to our cwd - see resolve_link_target_relative_to_the_link
         if os.path.isdir(source_child) and (
                 follow_links or not os.path.islink(source_child)):
 
@@ -578,12 +758,10 @@ def fix_darwin_install_name(path):
     libs = glob.glob(join_path(path, "*.dylib"))
     for lib in libs:
         # fix install name first:
-        subprocess.Popen(
-            ["install_name_tool", "-id", lib, lib],
-            stdout=subprocess.PIPE).communicate()[0]
-        long_deps = subprocess.Popen(
-            ["otool", "-L", lib],
-            stdout=subprocess.PIPE).communicate()[0].split('\n')
+        install_name_tool = Executable('install_name_tool')
+        install_name_tool('-id', lib, lib)
+        otool = Executable('otool')
+        long_deps = otool('-L', lib, output=str).split('\n')
         deps = [dep.partition(' ')[0][1::] for dep in long_deps[2:-1]]
         # fix all dependencies:
         for dep in deps:
@@ -594,13 +772,11 @@ def fix_darwin_install_name(path):
                 # but we don't know builddir (nor how symbolic links look
                 # in builddir). We thus only compare the basenames.
                 if os.path.basename(dep) == os.path.basename(loc):
-                    subprocess.Popen(
-                        ["install_name_tool", "-change", dep, loc, lib],
-                        stdout=subprocess.PIPE).communicate()[0]
+                    install_name_tool('-change', dep, loc, lib)
                     break
 
 
-def find(root, files, recurse=True):
+def find(root, files, recursive=True):
     """Search for ``files`` starting from the ``root`` directory.
 
     Like GNU/BSD find but written entirely in Python.
@@ -621,7 +797,7 @@ def find(root, files, recurse=True):
 
     is equivalent to:
 
-    >>> find('/usr/local/bin', 'python', recurse=False)
+    >>> find('/usr/local/bin', 'python', recursive=False)
 
     Accepts any glob characters accepted by fnmatch:
 
@@ -646,7 +822,7 @@ def find(root, files, recurse=True):
     if isinstance(files, six.string_types):
         files = [files]
 
-    if recurse:
+    if recursive:
         return _find_recursive(root, files)
     else:
         return _find_non_recursive(root, files)
@@ -660,11 +836,14 @@ def _find_recursive(root, search_files):
     # found in a key, and reconstructing the stable order later.
     found_files = collections.defaultdict(list)
 
+    # Make the path absolute to have os.walk also return an absolute path
+    root = os.path.abspath(root)
+
     for path, _, list_files in os.walk(root):
         for search_file in search_files:
-            for list_file in list_files:
-                if fnmatch.fnmatch(list_file, search_file):
-                    found_files[search_file].append(join_path(path, list_file))
+            matches = glob.glob(os.path.join(path, search_file))
+            matches = [os.path.join(path, x) for x in matches]
+            found_files[search_file].extend(matches)
 
     answer = []
     for search_file in search_files:
@@ -678,10 +857,13 @@ def _find_non_recursive(root, search_files):
     # can return files in any order (does not preserve stability)
     found_files = collections.defaultdict(list)
 
-    for list_file in os.listdir(root):
-        for search_file in search_files:
-            if fnmatch.fnmatch(list_file, search_file):
-                found_files[search_file].append(join_path(root, list_file))
+    # Make the path absolute to have absolute path returned
+    root = os.path.abspath(root)
+
+    for search_file in search_files:
+        matches = glob.glob(os.path.join(root, search_file))
+        matches = [os.path.join(root, x) for x in matches]
+        found_files[search_file].extend(matches)
 
     answer = []
     for search_file in search_files:
@@ -872,7 +1054,7 @@ class HeaderList(FileList):
         self._macro_definitions.append(macro)
 
 
-def find_headers(headers, root, recurse=False):
+def find_headers(headers, root, recursive=False):
     """Returns an iterable object containing a list of full paths to
     headers if found.
 
@@ -890,7 +1072,7 @@ def find_headers(headers, root, recurse=False):
     Parameters:
         headers (str or list of str): Header name(s) to search for
         root (str): The root directory to start searching from
-        recurses (bool, optional): if False search only root folder,
+        recursive (bool, optional): if False search only root folder,
             if True descends top-down from the root. Defaults to False.
 
     Returns:
@@ -910,7 +1092,7 @@ def find_headers(headers, root, recurse=False):
     # List of headers we are searching with suffixes
     headers = ['{0}.{1}'.format(header, suffix) for header in headers]
 
-    return HeaderList(find(root, headers, recurse))
+    return HeaderList(find(root, headers, recursive))
 
 
 class LibraryList(FileList):
@@ -1051,7 +1233,7 @@ def find_system_libraries(libraries, shared=True):
 
     for library in libraries:
         for root in search_locations:
-            result = find_libraries(library, root, shared, recurse=True)
+            result = find_libraries(library, root, shared, recursive=True)
             if result:
                 libraries_found += result
                 break
@@ -1059,7 +1241,7 @@ def find_system_libraries(libraries, shared=True):
     return libraries_found
 
 
-def find_libraries(libraries, root, shared=True, recurse=False):
+def find_libraries(libraries, root, shared=True, recursive=False):
     """Returns an iterable of full paths to libraries found in a root dir.
 
     Accepts any glob characters accepted by fnmatch:
@@ -1078,7 +1260,7 @@ def find_libraries(libraries, root, shared=True, recurse=False):
         root (str): The root directory to start searching from
         shared (bool, optional): if True searches for shared libraries,
             otherwise for static. Defaults to True.
-        recurse (bool, optional): if False search only root folder,
+        recursive (bool, optional): if False search only root folder,
             if True descends top-down from the root. Defaults to False.
 
     Returns:
@@ -1100,4 +1282,4 @@ def find_libraries(libraries, root, shared=True, recurse=False):
     # List of libraries we are searching with suffixes
     libraries = ['{0}.{1}'.format(lib, suffix) for lib in libraries]
 
-    return LibraryList(find(root, libraries, recurse))
+    return LibraryList(find(root, libraries, recursive))
diff --git a/lib/spack/llnl/util/lang.py b/lib/spack/llnl/util/lang.py
index 7189b6c0f3..0a86896f5b 100644
--- a/lib/spack/llnl/util/lang.py
+++ b/lib/spack/llnl/util/lang.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from __future__ import division
 
 import os
@@ -29,7 +10,7 @@ import re
 import functools
 import collections
 import inspect
-from datetime import datetime
+from datetime import datetime, timedelta
 from six import string_types
 
 # Ignore emacs backups when listing modules
@@ -165,6 +146,26 @@ def has_method(cls, name):
     return False
 
 
+def union_dicts(*dicts):
+    """Use update() to combine all dicts into one.
+
+    This builds a new dictionary, into which we ``update()`` each element
+    of ``dicts`` in order.  Items from later dictionaries will override
+    items from earlier dictionaries.
+
+    Args:
+        dicts (list): list of dictionaries
+
+    Return: (dict): a merged dictionary containing combined keys and
+        values from ``dicts``.
+
+    """
+    result = {}
+    for d in dicts:
+        result.update(d)
+    return result
+
+
 class memoized(object):
     """Decorator that caches the results of a function, storing them
        in an attribute of that function."""
@@ -282,8 +283,8 @@ class HashableMap(collections.MutableMapping):
     def copy(self):
         """Type-agnostic clone method.  Preserves subclass type."""
         # Construct a new dict of my type
-        T = type(self)
-        clone = T()
+        self_type = type(self)
+        clone = self_type()
 
         # Copy everything from this dict into it.
         for key in self:
@@ -442,6 +443,65 @@ def pretty_date(time, now=None):
         return str(diff) + " years ago"
 
 
+def pretty_string_to_date(date_str, now=None):
+    """Parses a string representing a date and returns a datetime object.
+
+    Args:
+        date_str (str): string representing a date. This string might be
+            in different format (like ``YYYY``, ``YYYY-MM``, ``YYYY-MM-DD``)
+            or be a *pretty date* (like ``yesterday`` or ``two months ago``)
+
+    Returns:
+        (datetime): datetime object corresponding to ``date_str``
+    """
+
+    pattern = {}
+
+    now = now or datetime.now()
+
+    # datetime formats
+    pattern[re.compile(r'^\d{4}$')] = lambda x: datetime.strptime(x, '%Y')
+    pattern[re.compile(r'^\d{4}-\d{2}$')] = lambda x: datetime.strptime(
+        x, '%Y-%m'
+    )
+    pattern[re.compile(r'^\d{4}-\d{2}-\d{2}$')] = lambda x: datetime.strptime(
+        x, '%Y-%m-%d'
+    )
+
+    pretty_regex = re.compile(
+        r'(a|\d+)\s*(year|month|week|day|hour|minute|second)s?\s*ago')
+
+    def _n_xxx_ago(x):
+        how_many, time_period = pretty_regex.search(x).groups()
+
+        how_many = 1 if how_many == 'a' else int(how_many)
+
+        # timedelta natively supports time periods up to 'weeks'.
+        # To apply month or year we convert to 30 and 365 days
+        if time_period == 'month':
+            how_many *= 30
+            time_period = 'day'
+        elif time_period == 'year':
+            how_many *= 365
+            time_period = 'day'
+
+        kwargs = {(time_period + 's'): how_many}
+        return now - timedelta(**kwargs)
+
+    pattern[pretty_regex] = _n_xxx_ago
+
+    # yesterday
+    callback = lambda x: now - timedelta(days=1)
+    pattern[re.compile('^yesterday$')] = callback
+
+    for regexp, parser in pattern.items():
+        if bool(regexp.match(date_str)):
+            return parser(date_str)
+
+    msg = 'date "{0}" does not match any valid format'.format(date_str)
+    raise ValueError(msg)
+
+
 class RequiredAttributeError(ValueError):
 
     def __init__(self, message):
@@ -458,5 +518,74 @@ class ObjectWrapper(object):
     def __init__(self, wrapped_object):
         wrapped_cls = type(wrapped_object)
         wrapped_name = wrapped_cls.__name__
-        self.__class__ = type(wrapped_name, (type(self), wrapped_cls), {})
+
+        # If the wrapped object is already an ObjectWrapper, or a derived class
+        # of it, adding type(self) in front of type(wrapped_object)
+        # results in an inconsistent MRO.
+        #
+        # TODO: the implementation below doesn't account for the case where we
+        # TODO: have different base classes of ObjectWrapper, say A and B, and
+        # TODO: we want to wrap an instance of A with B.
+        if type(self) not in wrapped_cls.__mro__:
+            self.__class__ = type(wrapped_name, (type(self), wrapped_cls), {})
+        else:
+            self.__class__ = type(wrapped_name, (wrapped_cls,), {})
+
         self.__dict__ = wrapped_object.__dict__
+
+
+class Singleton(object):
+    """Simple wrapper for lazily initialized singleton objects."""
+
+    def __init__(self, factory):
+        """Create a new singleton to be inited with the factory function.
+
+        Args:
+            factory (function): function taking no arguments that
+                creates the singleton instance.
+        """
+        self.factory = factory
+        self._instance = None
+
+    @property
+    def instance(self):
+        if self._instance is None:
+            self._instance = self.factory()
+        return self._instance
+
+    def __getattr__(self, name):
+        return getattr(self.instance, name)
+
+    def __getitem__(self, name):
+        return self.instance[name]
+
+    def __contains__(self, element):
+        return element in self.instance
+
+    def __iter__(self):
+        return iter(self.instance)
+
+    def __str__(self):
+        return str(self.instance)
+
+    def __repr__(self):
+        return repr(self.instance)
+
+
+class LazyReference(object):
+    """Lazily evaluated reference to part of a singleton."""
+
+    def __init__(self, ref_function):
+        self.ref_function = ref_function
+
+    def __getattr__(self, name):
+        return getattr(self.ref_function(), name)
+
+    def __getitem__(self, name):
+        return self.ref_function()[name]
+
+    def __str__(self):
+        return str(self.ref_function())
+
+    def __repr__(self):
+        return repr(self.ref_function())
diff --git a/lib/spack/llnl/util/link_tree.py b/lib/spack/llnl/util/link_tree.py
index 60ab5cb2b0..e675523015 100644
--- a/lib/spack/llnl/util/link_tree.py
+++ b/lib/spack/llnl/util/link_tree.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """LinkTree class for setting up trees of symbolic links."""
 
 import os
@@ -29,6 +10,7 @@ import shutil
 import filecmp
 
 from llnl.util.filesystem import traverse_tree, mkdirp, touch
+import llnl.util.tty as tty
 
 __all__ = ['LinkTree']
 
@@ -44,37 +26,49 @@ class LinkTree(object):
     Trees comprise symlinks only to files; directries are never
     symlinked to, to prevent the source directory from ever being
     modified.
-
     """
-
     def __init__(self, source_root):
         if not os.path.exists(source_root):
             raise IOError("No such file or directory: '%s'", source_root)
 
         self._root = source_root
 
-    def find_conflict(self, dest_root, **kwargs):
+    def find_conflict(self, dest_root, ignore=None,
+                      ignore_file_conflicts=False):
         """Returns the first file in dest that conflicts with src"""
-        kwargs['follow_nonexisting'] = False
+        ignore = ignore or (lambda x: False)
+        conflicts = self.find_dir_conflicts(dest_root, ignore)
+
+        if not ignore_file_conflicts:
+            conflicts.extend(
+                dst for src, dst
+                in self.get_file_map(dest_root, ignore).items()
+                if os.path.exists(dst))
+
+        if conflicts:
+            return conflicts[0]
+
+    def find_dir_conflicts(self, dest_root, ignore):
+        conflicts = []
+        kwargs = {'follow_nonexisting': False, 'ignore': ignore}
         for src, dest in traverse_tree(self._root, dest_root, **kwargs):
             if os.path.isdir(src):
                 if os.path.exists(dest) and not os.path.isdir(dest):
-                    return dest
-            elif os.path.exists(dest):
-                return dest
-        return None
-
-    def merge(self, dest_root, link=os.symlink, **kwargs):
-        """Link all files in src into dest, creating directories
-           if necessary.
-           If ignore_conflicts is True, do not break when the target exists but
-           rather return a list of files that could not be linked.
-           Note that files blocking directories will still cause an error.
-        """
-        kwargs['order'] = 'pre'
-        ignore_conflicts = kwargs.get("ignore_conflicts", False)
-        existing = []
+                    conflicts.append("File blocks directory: %s" % dest)
+            elif os.path.exists(dest) and os.path.isdir(dest):
+                conflicts.append("Directory blocks directory: %s" % dest)
+        return conflicts
+
+    def get_file_map(self, dest_root, ignore):
+        merge_map = {}
+        kwargs = {'follow_nonexisting': True, 'ignore': ignore}
         for src, dest in traverse_tree(self._root, dest_root, **kwargs):
+            if not os.path.isdir(src):
+                merge_map[src] = dest
+        return merge_map
+
+    def merge_directories(self, dest_root, ignore):
+        for src, dest in traverse_tree(self._root, dest_root, ignore=ignore):
             if os.path.isdir(src):
                 if not os.path.exists(dest):
                     mkdirp(dest)
@@ -88,31 +82,13 @@ class LinkTree(object):
                     marker = os.path.join(dest, empty_file_name)
                     touch(marker)
 
-            else:
-                if os.path.exists(dest):
-                    if ignore_conflicts:
-                        existing.append(src)
-                    else:
-                        raise AssertionError("File already exists: %s" % dest)
-                else:
-                    link(src, dest)
-        if ignore_conflicts:
-            return existing
-
-    def unmerge(self, dest_root, **kwargs):
-        """Unlink all files in dest that exist in src.
-
-        Unlinks directories in dest if they are empty.
-
-        """
-        kwargs['order'] = 'post'
-        for src, dest in traverse_tree(self._root, dest_root, **kwargs):
+    def unmerge_directories(self, dest_root, ignore):
+        for src, dest in traverse_tree(
+                self._root, dest_root, ignore=ignore, order='post'):
             if os.path.isdir(src):
-                # Skip non-existing links.
                 if not os.path.exists(dest):
                     continue
-
-                if not os.path.isdir(dest):
+                elif not os.path.isdir(dest):
                     raise ValueError("File blocks directory: %s" % dest)
 
                 # remove directory if it is empty.
@@ -124,11 +100,61 @@ class LinkTree(object):
                 if os.path.exists(marker):
                     os.remove(marker)
 
-            elif os.path.exists(dest):
-                if not os.path.islink(dest):
-                    raise ValueError("%s is not a link tree!" % dest)
-                # remove if dest is a hardlink/symlink to src; this will only
-                # be false if two packages are merged into a prefix and have a
-                # conflicting file
-                if filecmp.cmp(src, dest, shallow=True):
-                    os.remove(dest)
+    def merge(self, dest_root, **kwargs):
+        """Link all files in src into dest, creating directories
+           if necessary.
+           If ignore_conflicts is True, do not break when the target exists but
+           rather return a list of files that could not be linked.
+           Note that files blocking directories will still cause an error.
+        """
+        ignore_conflicts = kwargs.get("ignore_conflicts", False)
+
+        ignore = kwargs.get('ignore', lambda x: False)
+        conflict = self.find_conflict(
+            dest_root, ignore=ignore, ignore_file_conflicts=ignore_conflicts)
+        if conflict:
+            raise MergeConflictError(conflict)
+
+        self.merge_directories(dest_root, ignore)
+        existing = []
+        merge_file = kwargs.get('merge_file', merge_link)
+        for src, dst in self.get_file_map(dest_root, ignore).items():
+            if os.path.exists(dst):
+                existing.append(dst)
+            else:
+                merge_file(src, dst)
+
+        for c in existing:
+            tty.warn("Could not merge: %s" % c)
+
+    def unmerge(self, dest_root, **kwargs):
+        """Unlink all files in dest that exist in src.
+
+        Unlinks directories in dest if they are empty.
+        """
+        remove_file = kwargs.get('remove_file', remove_link)
+        ignore = kwargs.get('ignore', lambda x: False)
+        for src, dst in self.get_file_map(dest_root, ignore).items():
+            remove_file(src, dst)
+        self.unmerge_directories(dest_root, ignore)
+
+
+def merge_link(src, dest):
+    os.symlink(src, dest)
+
+
+def remove_link(src, dest):
+    if not os.path.islink(dest):
+        raise ValueError("%s is not a link tree!" % dest)
+    # remove if dest is a hardlink/symlink to src; this will only
+    # be false if two packages are merged into a prefix and have a
+    # conflicting file
+    if filecmp.cmp(src, dest, shallow=True):
+        os.remove(dest)
+
+
+class MergeConflictError(Exception):
+
+    def __init__(self, path):
+        super(MergeConflictError, self).__init__(
+            "Package merge blocked by file: %s" % path)
diff --git a/lib/spack/llnl/util/lock.py b/lib/spack/llnl/util/lock.py
index 5467838744..3beb219bd9 100644
--- a/lib/spack/llnl/util/lock.py
+++ b/lib/spack/llnl/util/lock.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 import fcntl
 import errno
@@ -32,14 +13,8 @@ import llnl.util.tty as tty
 
 
 __all__ = ['Lock', 'LockTransaction', 'WriteTransaction', 'ReadTransaction',
-           'LockError']
-
-
-# Default timeout in seconds, after which locks will raise exceptions.
-_default_timeout = 60
-
-# Sleep time per iteration in spin loop (in seconds)
-_sleep_time = 1e-5
+           'LockError', 'LockTimeoutError',
+           'LockPermissionError', 'LockROFileError', 'CantCreateLockError']
 
 
 class Lock(object):
@@ -49,9 +24,15 @@ class Lock(object):
     any filesystem implementation that supports locking through the fcntl
     calls.  This includes distributed filesystems like Lustre (when flock
     is enabled) and recent NFS versions.
+
+    Note that this is for managing contention over resources *between*
+    processes and not for managing contention between threads in a process: the
+    functions of this object are not thread-safe. A process also must not
+    maintain multiple locks on the same file.
     """
 
-    def __init__(self, path, start=0, length=0):
+    def __init__(self, path, start=0, length=0, debug=False,
+                 default_timeout=None):
         """Construct a new lock on the file at ``path``.
 
         By default, the lock applies to the whole file.  Optionally,
@@ -72,12 +53,44 @@ class Lock(object):
         self._start = start
         self._length = length
 
-        # PID and host of lock holder
+        # enable debug mode
+        self.debug = debug
+
+        # If the user doesn't set a default timeout, or if they choose
+        # None, 0, etc. then lock attempts will not time out (unless the
+        # user sets a timeout for each attempt)
+        self.default_timeout = default_timeout or None
+
+        # PID and host of lock holder (only used in debug mode)
         self.pid = self.old_pid = None
         self.host = self.old_host = None
 
-    def _lock(self, op, timeout=_default_timeout):
-        """This takes a lock using POSIX locks (``fnctl.lockf``).
+    @staticmethod
+    def _poll_interval_generator(_wait_times=None):
+        """This implements a backoff scheme for polling a contended resource
+        by suggesting a succession of wait times between polls.
+
+        It suggests a poll interval of .1s until 2 seconds have passed,
+        then a poll interval of .2s until 10 seconds have passed, and finally
+        (for all requests after 10s) suggests a poll interval of .5s.
+
+        This doesn't actually track elapsed time, it estimates the waiting
+        time as though the caller always waits for the full length of time
+        suggested by this function.
+        """
+        num_requests = 0
+        stage1, stage2, stage3 = _wait_times or (1e-1, 2e-1, 5e-1)
+        wait_time = stage1
+        while True:
+            if num_requests >= 60:  # 40 * .2 = 8
+                wait_time = stage3
+            elif num_requests >= 20:  # 20 * .1 = 2
+                wait_time = stage2
+            num_requests += 1
+            yield wait_time
+
+    def _lock(self, op, timeout=None):
+        """This takes a lock using POSIX locks (``fcntl.lockf``).
 
         The lock is implemented as a spin lock using a nonblocking call
         to ``lockf()``.
@@ -86,77 +99,113 @@ class Lock(object):
         pid and host to the lock file, in case the holding process needs
         to be killed later.
 
-        If the lock times out, it raises a ``LockError``.
+        If the lock times out, it raises a ``LockError``. If the lock is
+        successfully acquired, the total wait time and the number of attempts
+        is returned.
         """
-        start_time = time.time()
-        while (time.time() - start_time) < timeout:
-            try:
-                # If we could write the file, we'd have opened it 'r+'.
-                # Raise an error when we attempt to upgrade to a write lock.
-                if op == fcntl.LOCK_EX:
-                    if self._file and self._file.mode == 'r':
-                        raise LockError(
-                            "Can't take exclusive lock on read-only file: %s"
-                            % self.path)
-
-                # Create file and parent directories if they don't exist.
-                if self._file is None:
-                    self._ensure_parent_directory()
-
-                    # Prefer to open 'r+' to allow upgrading to write
-                    # lock later if possible.  Open read-only if we can't
-                    # write the lock file at all.
-                    os_mode, fd_mode = (os.O_RDWR | os.O_CREAT), 'r+'
-                    if os.path.exists(self.path) and not os.access(
-                            self.path, os.W_OK):
+        assert op in (fcntl.LOCK_SH, fcntl.LOCK_EX)
+
+        timeout = timeout or self.default_timeout
+
+        # Create file and parent directories if they don't exist.
+        if self._file is None:
+            parent = self._ensure_parent_directory()
+
+            # Open writable files as 'r+' so we can upgrade to write later
+            os_mode, fd_mode = (os.O_RDWR | os.O_CREAT), 'r+'
+            if os.path.exists(self.path):
+                if not os.access(self.path, os.W_OK):
+                    if op == fcntl.LOCK_SH:
+                        # can still lock read-only files if we open 'r'
                         os_mode, fd_mode = os.O_RDONLY, 'r'
+                    else:
+                        raise LockROFileError(self.path)
+
+            elif not os.access(parent, os.W_OK):
+                raise CantCreateLockError(self.path)
+
+            fd = os.open(self.path, os_mode)
+            self._file = os.fdopen(fd, fd_mode)
 
-                    fd = os.open(self.path, os_mode)
-                    self._file = os.fdopen(fd, fd_mode)
+        elif op == fcntl.LOCK_EX and self._file.mode == 'r':
+            # Attempt to upgrade to write lock w/a read-only file.
+            # If the file were writable, we'd have opened it 'r+'
+            raise LockROFileError(self.path)
 
-                # Try to get the lock (will raise if not available.)
-                fcntl.lockf(self._file, op | fcntl.LOCK_NB,
-                            self._length, self._start, os.SEEK_SET)
+        poll_intervals = iter(Lock._poll_interval_generator())
+        start_time = time.time()
+        num_attempts = 0
+        while (not timeout) or (time.time() - start_time) < timeout:
+            num_attempts += 1
+            if self._poll_lock(op):
+                total_wait_time = time.time() - start_time
+                return total_wait_time, num_attempts
+
+            time.sleep(next(poll_intervals))
+
+        num_attempts += 1
+        if self._poll_lock(op):
+            total_wait_time = time.time() - start_time
+            return total_wait_time, num_attempts
+
+        raise LockTimeoutError("Timed out waiting for lock.")
+
+    def _poll_lock(self, op):
+        """Attempt to acquire the lock in a non-blocking manner. Return whether
+        the locking attempt succeeds
+        """
+        try:
+            # Try to get the lock (will raise if not available.)
+            fcntl.lockf(self._file, op | fcntl.LOCK_NB,
+                        self._length, self._start, os.SEEK_SET)
 
+            # help for debugging distributed locking
+            if self.debug:
                 # All locks read the owner PID and host
-                self._read_lock_data()
+                self._read_debug_data()
 
                 # Exclusive locks write their PID/host
                 if op == fcntl.LOCK_EX:
-                    self._write_lock_data()
+                    self._write_debug_data()
 
-                return
-
-            except IOError as e:
-                if e.errno in (errno.EAGAIN, errno.EACCES):
-                    # EAGAIN and EACCES == locked by another process
-                    pass
-                else:
-                    raise
-            time.sleep(_sleep_time)
+            return True
 
-        raise LockError("Timed out waiting for lock.")
+        except IOError as e:
+            if e.errno in (errno.EAGAIN, errno.EACCES):
+                # EAGAIN and EACCES == locked by another process
+                pass
+            else:
+                raise
 
     def _ensure_parent_directory(self):
         parent = os.path.dirname(self.path)
+
+        # relative paths to lockfiles in the current directory have no parent
+        if not parent:
+            return '.'
+
         try:
             os.makedirs(parent)
-            return True
         except OSError as e:
             # makedirs can fail when diretory already exists.
             if not (e.errno == errno.EEXIST and os.path.isdir(parent) or
                     e.errno == errno.EISDIR):
                 raise
+        return parent
 
-    def _read_lock_data(self):
+    def _read_debug_data(self):
         """Read PID and host data out of the file if it is there."""
+        self.old_pid = self.pid
+        self.old_host = self.host
+
         line = self._file.read()
         if line:
             pid, host = line.strip().split(',')
             _, _, self.pid = pid.rpartition('=')
             _, _, self.host = host.rpartition('=')
+            self.pid = int(self.pid)
 
-    def _write_lock_data(self):
+    def _write_debug_data(self):
         """Write PID and host data to the file, recording old values."""
         self.old_pid = self.pid
         self.old_host = self.host
@@ -183,7 +232,7 @@ class Lock(object):
         self._file.close()
         self._file = None
 
-    def acquire_read(self, timeout=_default_timeout):
+    def acquire_read(self, timeout=None):
         """Acquires a recursive, shared lock for reading.
 
         Read and write locks can be acquired and released in arbitrary
@@ -194,19 +243,22 @@ class Lock(object):
         the POSIX lock, False if it is a nested transaction.
 
         """
+        timeout = timeout or self.default_timeout
+
         if self._reads == 0 and self._writes == 0:
-            tty.debug('READ LOCK: {0.path}[{0._start}:{0._length}] [Acquiring]'
-                      .format(self))
-            self._lock(fcntl.LOCK_SH, timeout=timeout)   # can raise LockError.
-            tty.debug('READ LOCK: {0.path}[{0._start}:{0._length}] [Acquired]'
-                      .format(self))
+            self._debug(
+                'READ LOCK: {0.path}[{0._start}:{0._length}] [Acquiring]'
+                .format(self))
+            # can raise LockError.
+            wait_time, nattempts = self._lock(fcntl.LOCK_SH, timeout=timeout)
+            self._acquired_debug('READ LOCK', wait_time, nattempts)
             self._reads += 1
             return True
         else:
             self._reads += 1
             return False
 
-    def acquire_write(self, timeout=_default_timeout):
+    def acquire_write(self, timeout=None):
         """Acquires a recursive, exclusive lock for writing.
 
         Read and write locks can be acquired and released in arbitrary
@@ -217,13 +269,15 @@ class Lock(object):
         the POSIX lock, False if it is a nested transaction.
 
         """
+        timeout = timeout or self.default_timeout
+
         if self._writes == 0:
-            tty.debug(
+            self._debug(
                 'WRITE LOCK: {0.path}[{0._start}:{0._length}] [Acquiring]'
                 .format(self))
-            self._lock(fcntl.LOCK_EX, timeout=timeout)   # can raise LockError.
-            tty.debug('WRITE LOCK: {0.path}[{0._start}:{0._length}] [Acquired]'
-                      .format(self))
+            # can raise LockError.
+            wait_time, nattempts = self._lock(fcntl.LOCK_EX, timeout=timeout)
+            self._acquired_debug('WRITE LOCK', wait_time, nattempts)
             self._writes += 1
             return True
         else:
@@ -243,8 +297,9 @@ class Lock(object):
         assert self._reads > 0
 
         if self._reads == 1 and self._writes == 0:
-            tty.debug('READ LOCK: {0.path}[{0._start}:{0._length}] [Released]'
-                      .format(self))
+            self._debug(
+                'READ LOCK: {0.path}[{0._start}:{0._length}] [Released]'
+                .format(self))
             self._unlock()      # can raise LockError.
             self._reads -= 1
             return True
@@ -265,8 +320,9 @@ class Lock(object):
         assert self._writes > 0
 
         if self._writes == 1 and self._reads == 0:
-            tty.debug('WRITE LOCK: {0.path}[{0._start}:{0._length}] [Released]'
-                      .format(self))
+            self._debug(
+                'WRITE LOCK: {0.path}[{0._start}:{0._length}] [Released]'
+                .format(self))
             self._unlock()      # can raise LockError.
             self._writes -= 1
             return True
@@ -274,6 +330,21 @@ class Lock(object):
             self._writes -= 1
             return False
 
+    def _debug(self, *args):
+        tty.debug(*args)
+
+    def _acquired_debug(self, lock_type, wait_time, nattempts):
+        attempts_format = 'attempt' if nattempts == 1 else 'attempt'
+        if nattempts > 1:
+            acquired_attempts_format = ' after {0:0.2f}s and {1:d} {2}'.format(
+                wait_time, nattempts, attempts_format)
+        else:
+            # Dont print anything if we succeeded immediately
+            acquired_attempts_format = ''
+        self._debug(
+            '{0}: {1.path}[{1._start}:{1._length}] [Acquired{2}]'
+            .format(lock_type, self, acquired_attempts_format))
+
 
 class LockTransaction(object):
     """Simple nested transaction context manager that uses a file lock.
@@ -295,7 +366,7 @@ class LockTransaction(object):
     """
 
     def __init__(self, lock, acquire_fn=None, release_fn=None,
-                 timeout=_default_timeout):
+                 timeout=None):
         self._lock = lock
         self._timeout = timeout
         self._acquire_fn = acquire_fn
@@ -323,7 +394,7 @@ class LockTransaction(object):
 
 
 class ReadTransaction(LockTransaction):
-
+    """LockTransaction context manager that does a read and releases it."""
     def _enter(self):
         return self._lock.acquire_read(self._timeout)
 
@@ -332,7 +403,7 @@ class ReadTransaction(LockTransaction):
 
 
 class WriteTransaction(LockTransaction):
-
+    """LockTransaction context manager that does a write and releases it."""
     def _enter(self):
         return self._lock.acquire_write(self._timeout)
 
@@ -341,4 +412,27 @@ class WriteTransaction(LockTransaction):
 
 
 class LockError(Exception):
+    """Raised for any errors related to locks."""
+
+
+class LockTimeoutError(LockError):
     """Raised when an attempt to acquire a lock times out."""
+
+
+class LockPermissionError(LockError):
+    """Raised when there are permission issues with a lock."""
+
+
+class LockROFileError(LockPermissionError):
+    """Tried to take an exclusive lock on a read-only file."""
+    def __init__(self, path):
+        msg = "Can't take write lock on read-only file: %s" % path
+        super(LockROFileError, self).__init__(msg)
+
+
+class CantCreateLockError(LockPermissionError):
+    """Attempt to create a lock in an unwritable location."""
+    def __init__(self, path):
+        msg = "cannot create lock '%s': " % path
+        msg += "file does not exist and location is not writable"
+        super(LockError, self).__init__(msg)
diff --git a/lib/spack/spack/util/multiproc.py b/lib/spack/llnl/util/multiproc.py
index 3cbbac4566..9c555112ec 100644
--- a/lib/spack/spack/util/multiproc.py
+++ b/lib/spack/llnl/util/multiproc.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """
 This implements a parallel map operation but it can accept more values
 than multiprocessing.Pool.apply() can.  For example, apply() will fail
@@ -39,10 +20,10 @@ def spawn(f):
     return fun
 
 
-def parmap(f, X):
-    pipe = [Pipe() for x in X]
+def parmap(f, elements):
+    pipe = [Pipe() for x in elements]
     proc = [Process(target=spawn(f), args=(c, x))
-            for x, (p, c) in zip(X, pipe)]
+            for x, (p, c) in zip(elements, pipe)]
     [p.start() for p in proc]
     [p.join() for p in proc]
     return [p.recv() for (p, c) in pipe]
diff --git a/lib/spack/llnl/util/tty/__init__.py b/lib/spack/llnl/util/tty/__init__.py
index 1d04787372..49a2187ad3 100644
--- a/lib/spack/llnl/util/tty/__init__.py
+++ b/lib/spack/llnl/util/tty/__init__.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import fcntl
 import os
 import struct
@@ -246,18 +227,18 @@ def hline(label=None, **kwargs):
 
 def terminal_size():
     """Gets the dimensions of the console: (rows, cols)."""
-    def ioctl_GWINSZ(fd):
+    def ioctl_gwinsz(fd):
         try:
             rc = struct.unpack('hh', fcntl.ioctl(
                 fd, termios.TIOCGWINSZ, '1234'))
         except BaseException:
             return
         return rc
-    rc = ioctl_GWINSZ(0) or ioctl_GWINSZ(1) or ioctl_GWINSZ(2)
+    rc = ioctl_gwinsz(0) or ioctl_gwinsz(1) or ioctl_gwinsz(2)
     if not rc:
         try:
             fd = os.open(os.ctermid(), os.O_RDONLY)
-            rc = ioctl_GWINSZ(fd)
+            rc = ioctl_gwinsz(fd)
             os.close(fd)
         except BaseException:
             pass
diff --git a/lib/spack/llnl/util/tty/colify.py b/lib/spack/llnl/util/tty/colify.py
index eebb102fb1..b6cf15a574 100644
--- a/lib/spack/llnl/util/tty/colify.py
+++ b/lib/spack/llnl/util/tty/colify.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """
 Routines for printing columnar output.  See ``colify()`` for more information.
 """
@@ -29,7 +10,7 @@ from __future__ import division
 
 import os
 import sys
-from six import StringIO
+from six import StringIO, text_type
 
 from llnl.util.tty import terminal_size
 from llnl.util.tty.color import clen, cextra
@@ -156,7 +137,7 @@ def colify(elts, **options):
             % next(options.iterkeys()))
 
     # elts needs to be an array of strings so we can count the elements
-    elts = [str(elt) for elt in elts]
+    elts = [text_type(elt) for elt in elts]
     if not elts:
         return (0, ())
 
diff --git a/lib/spack/llnl/util/tty/color.py b/lib/spack/llnl/util/tty/color.py
index c1365a93a0..53a1150ada 100644
--- a/lib/spack/llnl/util/tty/color.py
+++ b/lib/spack/llnl/util/tty/color.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """
 This file implements an expression syntax, similar to ``printf``, for adding
 ANSI colors to text.
@@ -190,7 +171,7 @@ class match_to_ansi(object):
         string = styles[style]
         if color:
             if color not in colors:
-                raise ColorParseError("invalid color specifier: '%s' in '%s'"
+                raise ColorParseError("Invalid color specifier: '%s' in '%s'"
                                       % (color, match.string))
             string += ';' + str(colors[color])
 
@@ -215,7 +196,9 @@ def colorize(string, **kwargs):
             codes, for output to non-console devices.
     """
     color = _color_when_value(kwargs.get('color', get_color_when()))
-    return re.sub(color_re, match_to_ansi(color), string)
+    string = re.sub(color_re, match_to_ansi(color), string)
+    string = string.replace('}}', '}')
+    return string
 
 
 def clen(string):
@@ -224,14 +207,14 @@ def clen(string):
 
 
 def cextra(string):
-    """"Length of extra color characters in a string"""
+    """Length of extra color characters in a string"""
     return len(''.join(re.findall(r'\033[^m]*m', string)))
 
 
 def cwrite(string, stream=sys.stdout, color=None):
     """Replace all color expressions in string with ANSI control
        codes and write the result to the stream.  If color is
-       False, this will write plain text with o color.  If True,
+       False, this will write plain text with no color.  If True,
        then it will always write colored output.  If not supplied,
        then it will be set based on stream.isatty().
     """
@@ -246,8 +229,25 @@ def cprint(string, stream=sys.stdout, color=None):
 
 
 def cescape(string):
-    """Replace all @ with @@ in the string provided."""
-    return str(string).replace('@', '@@')
+    """Escapes special characters needed for color codes.
+
+    Replaces the following symbols with their equivalent literal forms:
+
+    =====  ======
+    ``@``  ``@@``
+    ``}``  ``}}``
+    =====  ======
+
+    Parameters:
+        string (str): the string to escape
+
+    Returns:
+        (str): the string with color codes escaped
+    """
+    string = str(string)
+    string = string.replace('@', '@@')
+    string = string.replace('}', '}}')
+    return string
 
 
 class ColorStream(object):
diff --git a/lib/spack/llnl/util/tty/log.py b/lib/spack/llnl/util/tty/log.py
index 40edca972e..df2d56cab2 100644
--- a/lib/spack/llnl/util/tty/log.py
+++ b/lib/spack/llnl/util/tty/log.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """Utility classes for logging the output of blocks of code.
 """
 import multiprocessing
@@ -446,10 +427,9 @@ class log_output(object):
         try:
             with keyboard_input(stdin):
                 while True:
-                    # Without the last parameter (timeout) select will
-                    # wait until at least one of the two streams are
-                    # ready. This may cause the function to hang.
-                    rlist, _, xlist = select.select(istreams, [], [], 0)
+                    # No need to set any timeout for select.select
+                    # Wait until a key press or an event on in_pipe.
+                    rlist, _, _ = select.select(istreams, [], [])
 
                     # Allow user to toggle echo with 'v' key.
                     # Currently ignores other chars.
diff --git a/lib/spack/spack/__init__.py b/lib/spack/spack/__init__.py
index a355b45f96..848dc4f670 100644
--- a/lib/spack/spack/__init__.py
+++ b/lib/spack/spack/__init__.py
@@ -1,266 +1,13 @@
-# flake8: noqa
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-import multiprocessing
-import os
-import sys
-import tempfile
-import getpass
-from llnl.util.filesystem import *
-import llnl.util.tty as tty
-
-#-----------------------------------------------------------------------------
-# Variables describing how Spack is laid out in its prefix.
-#-----------------------------------------------------------------------------
-# This file lives in $prefix/lib/spack/spack/__file__
-spack_root = ancestor(__file__, 4)
-
-# The spack script itself
-spack_file = join_path(spack_root, "bin", "spack")
-
-# spack directory hierarchy
-lib_path       = join_path(spack_root, "lib", "spack")
-external_path  = join_path(lib_path, "external")
-build_env_path = join_path(lib_path, "env")
-module_path    = join_path(lib_path, "spack")
-platform_path  = join_path(module_path, 'platforms')
-compilers_path = join_path(module_path, "compilers")
-build_systems_path = join_path(module_path, 'build_systems')
-operating_system_path = join_path(module_path, 'operating_systems')
-test_path      = join_path(module_path, "test")
-hooks_path     = join_path(module_path, "hooks")
-var_path       = join_path(spack_root, "var", "spack")
-stage_path     = join_path(var_path, "stage")
-repos_path     = join_path(var_path, "repos")
-share_path     = join_path(spack_root, "share", "spack")
-
-# Paths to built-in Spack repositories.
-packages_path      = join_path(repos_path, "builtin")
-mock_packages_path = join_path(repos_path, "builtin.mock")
-
-# User configuration location
-user_config_path = os.path.expanduser('~/.spack')
-
-prefix = spack_root
-opt_path        = join_path(prefix, "opt")
-etc_path        = join_path(prefix, "etc")
-system_etc_path = '/etc'
-
-# GPG paths.
-gpg_keys_path      = join_path(var_path, "gpg")
-mock_gpg_data_path = join_path(var_path, "gpg.mock", "data")
-mock_gpg_keys_path = join_path(var_path, "gpg.mock", "keys")
-gpg_path           = join_path(opt_path, "spack", "gpg")
-
-
-#-----------------------------------------------------------------------------
-# Initial imports (only for use in this file -- see __all__ below.)
-#-----------------------------------------------------------------------------
-# These imports depend on the paths above, or on each other
-# Group them here so it's easy to understand the order.
-# TODO: refactor this stuff to be more init order agnostic.
-import spack.repository
-import spack.error
-import spack.config
-import spack.fetch_strategy
-from spack.file_cache import FileCache
-from spack.abi import ABI
-from spack.concretize import DefaultConcretizer
-from spack.version import Version
-from spack.util.path import canonicalize_path
-from spack.package_prefs import PackageTesting
-
-#-----------------------------------------------------------------------------
-# Initialize various data structures & objects at the core of Spack.
-#-----------------------------------------------------------------------------
-# Version information
-spack_version = Version("0.11.1")
-
-
-# Set up the default packages database.
-try:
-    repo = spack.repository.RepoPath()
-    sys.meta_path.append(repo)
-except spack.error.SpackError as e:
-    tty.die('while initializing Spack RepoPath:', e.message)
-
-
-# Tests ABI compatibility between packages
-abi = ABI()
-
-
-# This controls how things are concretized in spack.
-# Replace it with a subclass if you want different
-# policies.
-concretizer = DefaultConcretizer()
-
-#-----------------------------------------------------------------------------
-# config.yaml options
-#-----------------------------------------------------------------------------
-_config = spack.config.get_config('config')
-
-
-# Path where downloaded source code is cached
-cache_path = canonicalize_path(
-    _config.get('source_cache', join_path(var_path, "cache")))
-fetch_cache = spack.fetch_strategy.FsCache(cache_path)
-
-
-# cache for miscellaneous stuff.
-misc_cache_path = canonicalize_path(
-    _config.get('misc_cache', join_path(user_config_path, 'cache')))
-misc_cache = FileCache(misc_cache_path)
-
-
-binary_cache_retrieved_specs = set()
-
-
-#: Directories where to search for templates
-template_dirs = spack.config.get_config('config')['template_dirs']
-template_dirs = [canonicalize_path(x) for x in template_dirs]
-
-# If this is enabled, tools that use SSL should not verify
-# certifiates. e.g., curl should use the -k option.
-insecure = not _config.get('verify_ssl', True)
-
-
-# Whether spack should allow installation of unsafe versions of software.
-# "Unsafe" versions are ones it doesn't have a checksum for.
-do_checksum = _config.get('checksum', True)
-
-
-# If this is True, spack will not clean the environment to remove
-# potentially harmful variables before builds.
-dirty = _config.get('dirty', False)
-
-
-# The number of jobs to use when building in parallel.
-# By default, use all cores on the machine.
-build_jobs = _config.get('build_jobs', multiprocessing.cpu_count())
-
-
-# Needed for test dependencies
-package_testing = PackageTesting()
-
-
-#-----------------------------------------------------------------------------
-# When packages call 'from spack import *', this extra stuff is brought in.
-#
-# Spack internal code should call 'import spack' and accesses other
-# variables (spack.repo, paths, etc.) directly.
-#
-# TODO: maybe this should be separated out to build_environment.py?
-# TODO: it's not clear where all the stuff that needs to be included in
-#       packages should live.  This file is overloaded for spack core vs.
-#       for packages.
-#
-#-----------------------------------------------------------------------------
-__all__ = []
-
-from spack.package import Package, run_before, run_after, on_package_attributes
-from spack.build_systems.makefile import MakefilePackage
-from spack.build_systems.aspell_dict import AspellDictPackage
-from spack.build_systems.autotools import AutotoolsPackage
-from spack.build_systems.cmake import CMakePackage
-from spack.build_systems.qmake import QMakePackage
-from spack.build_systems.scons import SConsPackage
-from spack.build_systems.waf import WafPackage
-from spack.build_systems.python import PythonPackage
-from spack.build_systems.r import RPackage
-from spack.build_systems.perl import PerlPackage
-from spack.build_systems.intel import IntelPackage
-
-__all__ += [
-    'run_before',
-    'run_after',
-    'on_package_attributes',
-    'Package',
-    'MakefilePackage',
-    'AspellDictPackage',
-    'AutotoolsPackage',
-    'CMakePackage',
-    'QMakePackage',
-    'SConsPackage',
-    'WafPackage',
-    'PythonPackage',
-    'RPackage',
-    'PerlPackage',
-    'IntelPackage',
-]
-
-from spack.version import Version, ver
-__all__ += ['Version', 'ver']
-
-from spack.spec import Spec
-__all__ += ['Spec']
-
-from spack.dependency import all_deptypes
-__all__ += ['all_deptypes']
-
-from spack.multimethod import when
-__all__ += ['when']
-
-import llnl.util.filesystem
-from llnl.util.filesystem import *
-__all__ += llnl.util.filesystem.__all__
-
-import spack.directives
-from spack.directives import *
-__all__ += spack.directives.__all__
-
-import spack.util.executable
-from spack.util.executable import *
-__all__ += spack.util.executable.__all__
-
-
-# Set up the user's editor
-# $EDITOR environment variable has the highest precedence
-editor = os.environ.get('EDITOR')
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-# if editor is not set, use some sensible defaults
-if editor is not None:
-    editor = Executable(editor)
-else:
-    editor = which('vim', 'vi', 'emacs', 'nano')
 
-# If there is no editor, only raise an error if we actually try to use it.
-if not editor:
-    def editor_not_found(*args, **kwargs):
-        raise EnvironmentError(
-            'No text editor found! Please set the EDITOR environment variable '
-            'to your preferred text editor.')
-    editor = editor_not_found
+#: major, minor, patch version for Spack, in a tuple
+spack_version_info = (0, 12, 0)
 
-from spack.package import \
-    install_dependency_symlinks, flatten_dependencies, \
-    DependencyConflictError, InstallError, ExternalPackageError
-__all__ += [
-    'install_dependency_symlinks', 'flatten_dependencies',
-    'DependencyConflictError', 'InstallError', 'ExternalPackageError']
+#: String containing Spack version joined with .'s
+spack_version = '.'.join(str(v) for v in spack_version_info)
 
-# Add default values for attributes that would otherwise be modified from
-# Spack main script
-debug = False
-spack_working_dir = None
+__all__ = ['spack_version_info', 'spack_version']
diff --git a/lib/spack/spack/abi.py b/lib/spack/spack/abi.py
index ad46e88e61..490c688911 100644
--- a/lib/spack/spack/abi.py
+++ b/lib/spack/spack/abi.py
@@ -1,36 +1,17 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 import os
-import spack
+
+from llnl.util.lang import memoized
+
 import spack.spec
 from spack.build_environment import dso_suffix
 from spack.spec import CompilerSpec
 from spack.util.executable import Executable, ProcessError
 from spack.compilers.clang import Clang
-from llnl.util.lang import memoized
 
 
 class ABI(object):
@@ -74,7 +55,7 @@ class ABI(object):
             return None
         if not output:
             return None
-        libpath = os.readlink(output.strip())
+        libpath = os.path.realpath(output.strip())
         if not libpath:
             return None
         return os.path.basename(libpath)
diff --git a/lib/spack/spack/architecture.py b/lib/spack/spack/architecture.py
index 62e2619d7f..1b7b602121 100644
--- a/lib/spack/spack/architecture.py
+++ b/lib/spack/spack/architecture.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """
 This module contains all the elements that are required to create an
 architecture object. These include, the target processor, the operating system,
@@ -79,16 +60,15 @@ import os
 import inspect
 import platform as py_platform
 
-from llnl.util.lang import memoized, list_modules, key_ordering
-from llnl.util.filesystem import join_path
+import llnl.util.multiproc as mp
 import llnl.util.tty as tty
+from llnl.util.lang import memoized, list_modules, key_ordering
 
-import spack
+import spack.paths
+import spack.error as serr
 from spack.util.naming import mod_to_class
 from spack.util.environment import get_path
-from spack.util.multiproc import parmap
 from spack.util.spack_yaml import syaml_dict
-import spack.error as serr
 
 
 class NoPlatformError(serr.SpackError):
@@ -194,14 +174,13 @@ class Platform(object):
         return self.operating_sys.get(name, None)
 
     @classmethod
-    def setup_platform_environment(self, pkg, env):
+    def setup_platform_environment(cls, pkg, env):
         """ Subclass can override this method if it requires any
             platform-specific build environment modifications.
         """
-        pass
 
     @classmethod
-    def detect(self):
+    def detect(cls):
         """ Subclass is responsible for implementing this method.
             Returns True if the Platform class detects that
             it is the current platform
@@ -240,8 +219,8 @@ class OperatingSystem(object):
     """
 
     def __init__(self, name, version):
-        self.name = name
-        self.version = version
+        self.name = name.replace('-', '_')
+        self.version = str(version).replace('-', '_')
 
     def __str__(self):
         return "%s%s" % (self.name, self.version)
@@ -271,7 +250,7 @@ class OperatingSystem(object):
             filtered_path.append(p)
 
             # Check for a bin directory, add it if it exists
-            bin = join_path(p, 'bin')
+            bin = os.path.join(p, 'bin')
             if os.path.isdir(bin):
                 filtered_path.append(os.path.realpath(bin))
 
@@ -281,9 +260,9 @@ class OperatingSystem(object):
         # NOTE: we import spack.compilers here to avoid init order cycles
         import spack.compilers
         types = spack.compilers.all_compiler_types()
-        compiler_lists = parmap(lambda cmp_cls:
-                                self.find_compiler(cmp_cls, *filtered_path),
-                                types)
+        compiler_lists = mp.parmap(
+            lambda cmp_cls: self.find_compiler(cmp_cls, *filtered_path),
+            types)
 
         # ensure all the version calls we made are cached in the parent
         # process, as well.  This speeds up Spack a lot.
@@ -301,7 +280,7 @@ class OperatingSystem(object):
            prefixes, suffixes, and versions.  e.g., gcc-mp-4.7 would
            be grouped with g++-mp-4.7 and gfortran-mp-4.7.
         """
-        dicts = parmap(
+        dicts = mp.parmap(
             lambda t: cmp_cls._find_matches_in_path(*t),
             [(cmp_cls.cc_names,  cmp_cls.cc_version)  + tuple(path),
              (cmp_cls.cxx_names, cmp_cls.cxx_version) + tuple(path),
@@ -463,7 +442,7 @@ def arch_for_spec(arch_spec):
 @memoized
 def all_platforms():
     classes = []
-    mod_path = spack.platform_path
+    mod_path = spack.paths.platform_path
     parent_module = "spack.platforms"
 
     for name in list_modules(mod_path):
diff --git a/lib/spack/spack/binary_distribution.py b/lib/spack/spack/binary_distribution.py
index 5a2db06424..ced7447db6 100644
--- a/lib/spack/spack/binary_distribution.py
+++ b/lib/spack/spack/binary_distribution.py
@@ -1,71 +1,84 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 import os
 import re
 import tarfile
-import yaml
 import shutil
 import platform
+import tempfile
+import hashlib
+from contextlib import closing
+
+import ruamel.yaml as yaml
 
 import llnl.util.tty as tty
-from spack.util.gpg import Gpg
-from llnl.util.filesystem import mkdirp, join_path, install_tree
-from spack.util.web import spider
+from llnl.util.filesystem import mkdirp, install_tree, get_filetype
+
 import spack.cmd
-import spack
-from spack.stage import Stage
 import spack.fetch_strategy as fs
-from contextlib import closing
 import spack.util.gpg as gpg_util
-import hashlib
-from spack.util.executable import ProcessError
 import spack.relocate as relocate
+from spack.stage import Stage
+from spack.util.gpg import Gpg
+from spack.util.web import spider
+from spack.util.executable import ProcessError
 
 
 class NoOverwriteException(Exception):
-    pass
+    """
+    Raised when a file exists and must be overwritten.
+    """
+    def __init__(self, file_path):
+        err_msg = "\n%s\nexists\n" % file_path
+        err_msg += "Use -f option to overwrite."
+        super(NoOverwriteException, self).__init__(err_msg)
 
 
-class NoGpgException(Exception):
+class NoGpgException(spack.error.SpackError):
+    """
+    Raised when gpg2 is not in PATH
+    """
     pass
 
 
-class PickKeyException(Exception):
+class NoKeyException(spack.error.SpackError):
+    """
+    Raised when gpg has no default key added.
+    """
     pass
 
 
-class NoKeyException(Exception):
+class PickKeyException(spack.error.SpackError):
+    """
+    Raised when multiple keys can be used to sign.
+    """
+    def __init__(self, keys):
+        err_msg = "Multi keys available for signing\n%s\n" % keys
+        err_msg += "Use spack buildcache create -k <key hash> to pick a key."
+        super(PickKeyException, self).__init__(err_msg)
+
+
+class NoVerifyException(spack.error.SpackError):
+    """
+    Raised if file fails signature verification.
+    """
     pass
 
 
-class NoVerifyException(Exception):
+class NoChecksumException(spack.error.SpackError):
+    """
+    Raised if file fails checksum verification.
+    """
     pass
 
 
-class NoChecksumException(Exception):
+class NewLayoutException(spack.error.SpackError):
+    """
+    Raised if directory layout is different from buildcache.
+    """
     pass
 
 
@@ -111,18 +124,25 @@ def write_buildinfo_file(prefix, workdir, rel=False):
         dirs[:] = [d for d in dirs if d not in blacklist]
         for filename in files:
             path_name = os.path.join(root, filename)
-            filetype = relocate.get_filetype(path_name)
-            if relocate.needs_binary_relocation(filetype, os_id):
-                rel_path_name = os.path.relpath(path_name, prefix)
-                binary_to_relocate.append(rel_path_name)
-            elif relocate.needs_text_relocation(filetype):
-                rel_path_name = os.path.relpath(path_name, prefix)
-                text_to_relocate.append(rel_path_name)
+            #  Check if the file contains a string with the installroot.
+            #  This cuts down on the number of files added to the list
+            #  of files potentially needing relocation
+            if relocate.strings_contains_installroot(
+                    path_name, spack.store.layout.root):
+                filetype = get_filetype(path_name)
+                if relocate.needs_binary_relocation(filetype, os_id):
+                    rel_path_name = os.path.relpath(path_name, prefix)
+                    binary_to_relocate.append(rel_path_name)
+                elif relocate.needs_text_relocation(filetype):
+                    rel_path_name = os.path.relpath(path_name, prefix)
+                    text_to_relocate.append(rel_path_name)
 
     # Create buildinfo data and write it to disk
     buildinfo = {}
     buildinfo['relative_rpaths'] = rel
     buildinfo['buildpath'] = spack.store.layout.root
+    buildinfo['relative_prefix'] = os.path.relpath(
+        prefix, spack.store.layout.root)
     buildinfo['relocate_textfiles'] = text_to_relocate
     buildinfo['relocate_binaries'] = binary_to_relocate
     filename = buildinfo_file_name(workdir)
@@ -164,29 +184,34 @@ def tarball_path_name(spec, ext):
 
 def checksum_tarball(file):
     # calculate sha256 hash of tar file
-    BLOCKSIZE = 65536
+    block_size = 65536
     hasher = hashlib.sha256()
     with open(file, 'rb') as tfile:
-        buf = tfile.read(BLOCKSIZE)
+        buf = tfile.read(block_size)
         while len(buf) > 0:
             hasher.update(buf)
-            buf = tfile.read(BLOCKSIZE)
+            buf = tfile.read(block_size)
     return hasher.hexdigest()
 
 
-def sign_tarball(yes_to_all, key, force, specfile_path):
+def sign_tarball(key, force, specfile_path):
     # Sign the packages if keys available
     if not has_gnupg2():
-        raise NoGpgException()
+        raise NoGpgException(
+            "gpg2 is not available in $PATH .\n"
+            "Use spack install gnupg and spack load gnupg.")
     else:
         if key is None:
             keys = Gpg.signing_keys()
             if len(keys) == 1:
                 key = keys[0]
             if len(keys) > 1:
-                raise PickKeyException()
+                raise PickKeyException(str(keys))
             if len(keys) == 0:
-                raise NoKeyException()
+                msg = "No default key available for signing.\n"
+                msg += "Use spack gpg init and spack gpg create"
+                msg += " to create a default key."
+                raise NoKeyException(msg)
     if os.path.exists('%s.asc' % specfile_path):
         if force:
             os.remove('%s.asc' % specfile_path)
@@ -210,17 +235,17 @@ def generate_index(outdir, indexfile_path):
     f.close()
 
 
-def build_tarball(spec, outdir, force=False, rel=False, yes_to_all=False,
-                  key=None):
+def build_tarball(spec, outdir, force=False, rel=False, unsigned=False,
+                  allow_root=False, key=None):
     """
     Build a tarball from given spec and put it into the directory structure
     used at the mirror (following <tarball_directory_name>).
     """
     # set up some paths
     tarfile_name = tarball_name(spec, '.tar.gz')
-    tarfile_dir = join_path(outdir, "build_cache",
-                            tarball_directory_name(spec))
-    tarfile_path = join_path(tarfile_dir, tarfile_name)
+    tarfile_dir = os.path.join(outdir, "build_cache",
+                               tarball_directory_name(spec))
+    tarfile_path = os.path.join(tarfile_dir, tarfile_name)
     mkdirp(tarfile_dir)
     spackfile_path = os.path.join(
         outdir, "build_cache", tarball_path_name(spec, '.spack'))
@@ -232,20 +257,18 @@ def build_tarball(spec, outdir, force=False, rel=False, yes_to_all=False,
     # need to copy the spec file so the build cache can be downloaded
     # without concretizing with the current spack packages
     # and preferences
-    spec_file = join_path(spec.prefix, ".spack", "spec.yaml")
+    spec_file = os.path.join(spec.prefix, ".spack", "spec.yaml")
     specfile_name = tarball_name(spec, '.spec.yaml')
     specfile_path = os.path.realpath(
-        join_path(outdir, "build_cache", specfile_name))
-    indexfile_path = join_path(outdir, "build_cache", "index.html")
+        os.path.join(outdir, "build_cache", specfile_name))
+    indexfile_path = os.path.join(outdir, "build_cache", "index.html")
     if os.path.exists(specfile_path):
         if force:
             os.remove(specfile_path)
         else:
             raise NoOverwriteException(str(specfile_path))
     # make a copy of the install directory to work with
-    workdir = join_path(outdir, os.path.basename(spec.prefix))
-    if os.path.exists(workdir):
-        shutil.rmtree(workdir)
+    workdir = os.path.join(tempfile.mkdtemp(), os.path.basename(spec.prefix))
     install_tree(spec.prefix, workdir, symlinks=True)
 
     # create info for later relocation and create tar
@@ -254,11 +277,23 @@ def build_tarball(spec, outdir, force=False, rel=False, yes_to_all=False,
     # optinally make the paths in the binaries relative to each other
     # in the spack install tree before creating tarball
     if rel:
-        make_package_relative(workdir, spec.prefix)
+        try:
+            make_package_relative(workdir, spec.prefix, allow_root)
+        except Exception as e:
+            shutil.rmtree(workdir)
+            shutil.rmtree(tarfile_dir)
+            tty.die(str(e))
+    else:
+        try:
+            make_package_placeholder(workdir, allow_root)
+        except Exception as e:
+            shutil.rmtree(workdir)
+            shutil.rmtree(tarfile_dir)
+            tty.die(str(e))
     # create compressed tarball of the install prefix
     with closing(tarfile.open(tarfile_path, 'w:gz')) as tar:
         tar.add(name='%s' % workdir,
-                arcname='%s' % os.path.basename(workdir))
+                arcname='%s' % os.path.basename(spec.prefix))
     # remove copy of install directory
     shutil.rmtree(workdir)
 
@@ -274,31 +309,28 @@ def build_tarball(spec, outdir, force=False, rel=False, yes_to_all=False,
     bchecksum['hash_algorithm'] = 'sha256'
     bchecksum['hash'] = checksum
     spec_dict['binary_cache_checksum'] = bchecksum
+    # Add original install prefix relative to layout root to spec.yaml.
+    # This will be used to determine is the directory layout has changed.
+    buildinfo = {}
+    buildinfo['relative_prefix'] = os.path.relpath(
+        spec.prefix, spack.store.layout.root)
+    spec_dict['buildinfo'] = buildinfo
     with open(specfile_path, 'w') as outfile:
         outfile.write(yaml.dump(spec_dict))
-    signed = False
-    if not yes_to_all:
-        # sign the tarball and spec file with gpg
-        try:
-            sign_tarball(yes_to_all, key, force, specfile_path)
-            signed = True
-        except NoGpgException:
-            raise NoGpgException()
-        except PickKeyException:
-            raise PickKeyException()
-        except NoKeyException():
-            raise NoKeyException()
+    # sign the tarball and spec file with gpg
+    if not unsigned:
+        sign_tarball(key, force, specfile_path)
     # put tarball, spec and signature files in .spack archive
     with closing(tarfile.open(spackfile_path, 'w')) as tar:
         tar.add(name='%s' % tarfile_path, arcname='%s' % tarfile_name)
         tar.add(name='%s' % specfile_path, arcname='%s' % specfile_name)
-        if signed:
+        if not unsigned:
             tar.add(name='%s.asc' % specfile_path,
                     arcname='%s.asc' % specfile_name)
 
     # cleanup file moved to archive
     os.remove(tarfile_path)
-    if signed:
+    if not unsigned:
         os.remove('%s.asc' % specfile_path)
 
     # create an index.html for the build_cache directory so specs can be found
@@ -313,7 +345,7 @@ def download_tarball(spec):
     Download binary tarball for given package into stage area
     Return True if successful
     """
-    mirrors = spack.config.get_config('mirrors')
+    mirrors = spack.config.get('mirrors')
     if len(mirrors) == 0:
         tty.die("Please add a spack mirror to allow " +
                 "download of pre-compiled packages.")
@@ -330,7 +362,7 @@ def download_tarball(spec):
     return None
 
 
-def make_package_relative(workdir, prefix):
+def make_package_relative(workdir, prefix, allow_root):
     """
     Change paths in binaries to relative paths
     """
@@ -341,26 +373,35 @@ def make_package_relative(workdir, prefix):
     for filename in buildinfo['relocate_binaries']:
         orig_path_names.append(os.path.join(prefix, filename))
         cur_path_names.append(os.path.join(workdir, filename))
-        relocate.make_binary_relative(cur_path_names, orig_path_names,
-                                      old_path)
+    relocate.make_binary_relative(cur_path_names, orig_path_names,
+                                  old_path, allow_root)
+
+
+def make_package_placeholder(workdir, allow_root):
+    """
+    Change paths in binaries to placeholder paths
+    """
+    buildinfo = read_buildinfo_file(workdir)
+    cur_path_names = list()
+    for filename in buildinfo['relocate_binaries']:
+        cur_path_names.append(os.path.join(workdir, filename))
+    relocate.make_binary_placeholder(cur_path_names, allow_root)
 
 
-def relocate_package(prefix):
+def relocate_package(workdir, allow_root):
     """
     Relocate the given package
     """
-    buildinfo = read_buildinfo_file(prefix)
+    buildinfo = read_buildinfo_file(workdir)
     new_path = spack.store.layout.root
     old_path = buildinfo['buildpath']
     rel = buildinfo.get('relative_rpaths', False)
-    if new_path == old_path and not rel:
-        return
 
     tty.msg("Relocating package from",
             "%s to %s." % (old_path, new_path))
     path_names = set()
     for filename in buildinfo['relocate_textfiles']:
-        path_name = os.path.join(prefix, filename)
+        path_name = os.path.join(workdir, filename)
         # Don't add backup files generated by filter_file during install step.
         if not path_name.endswith('~'):
             path_names.add(path_name)
@@ -370,39 +411,47 @@ def relocate_package(prefix):
     if not rel:
         path_names = set()
         for filename in buildinfo['relocate_binaries']:
-            path_name = os.path.join(prefix, filename)
+            path_name = os.path.join(workdir, filename)
             path_names.add(path_name)
-        relocate.relocate_binary(path_names, old_path, new_path)
+        relocate.relocate_binary(path_names, old_path, new_path,
+                                 allow_root)
 
 
-def extract_tarball(spec, filename, yes_to_all=False, force=False):
+def extract_tarball(spec, filename, allow_root=False, unsigned=False,
+                    force=False):
     """
     extract binary tarball for given package into install area
     """
-    installpath = spec.prefix
-    if os.path.exists(installpath):
+    if os.path.exists(spec.prefix):
         if force:
-            shutil.rmtree(installpath)
+            shutil.rmtree(spec.prefix)
         else:
-            raise NoOverwriteException(str(installpath))
+            raise NoOverwriteException(str(spec.prefix))
+
+    tmpdir = tempfile.mkdtemp()
     stagepath = os.path.dirname(filename)
     spackfile_name = tarball_name(spec, '.spack')
     spackfile_path = os.path.join(stagepath, spackfile_name)
     tarfile_name = tarball_name(spec, '.tar.gz')
-    tarfile_path = os.path.join(stagepath, tarfile_name)
+    tarfile_path = os.path.join(tmpdir, tarfile_name)
     specfile_name = tarball_name(spec, '.spec.yaml')
-    specfile_path = os.path.join(stagepath, specfile_name)
+    specfile_path = os.path.join(tmpdir, specfile_name)
 
     with closing(tarfile.open(spackfile_path, 'r')) as tar:
-        tar.extractall(stagepath)
-
-    if not yes_to_all:
+        tar.extractall(tmpdir)
+    if not unsigned:
         if os.path.exists('%s.asc' % specfile_path):
-            Gpg.verify('%s.asc' % specfile_path, specfile_path)
-            os.remove(specfile_path + '.asc')
+            try:
+                Gpg.verify('%s.asc' % specfile_path, specfile_path)
+            except Exception as e:
+                shutil.rmtree(tmpdir)
+                tty.die(str(e))
         else:
-            raise NoVerifyException()
-
+            shutil.rmtree(tmpdir)
+            raise NoVerifyException(
+                "Package spec file failed signature verification.\n"
+                "Use spack buildcache keys to download "
+                "and install a key for verification from the mirror.")
     # get the sha256 checksum of the tarball
     checksum = checksum_tarball(tarfile_path)
 
@@ -415,28 +464,65 @@ def extract_tarball(spec, filename, yes_to_all=False, force=False):
 
     # if the checksums don't match don't install
     if bchecksum['hash'] != checksum:
-        raise NoChecksumException()
-
-    # delay creating installpath until verification is complete
-    mkdirp(installpath)
+        shutil.rmtree(tmpdir)
+        raise NoChecksumException(
+            "Package tarball failed checksum verification.\n"
+            "It cannot be installed.")
+
+    new_relative_prefix = str(os.path.relpath(spec.prefix,
+                                              spack.store.layout.root))
+    # if the original relative prefix is in the spec file use it
+    buildinfo = spec_dict.get('buildinfo', {})
+    old_relative_prefix = buildinfo.get('relative_prefix', new_relative_prefix)
+    # if the original relative prefix and new relative prefix differ the
+    # directory layout has changed and the  buildcache cannot be installed
+    if old_relative_prefix != new_relative_prefix:
+        shutil.rmtree(tmpdir)
+        msg = "Package tarball was created from an install "
+        msg += "prefix with a different directory layout.\n"
+        msg += "It cannot be relocated."
+        raise NewLayoutException(msg)
+
+    # extract the tarball in a temp directory
     with closing(tarfile.open(tarfile_path, 'r')) as tar:
-        tar.extractall(path=join_path(installpath, '..'))
+        tar.extractall(path=tmpdir)
+    # the base of the install prefix is used when creating the tarball
+    # so the pathname should be the same now that the directory layout
+    # is confirmed
+    workdir = os.path.join(tmpdir, os.path.basename(spec.prefix))
 
+    # cleanup
     os.remove(tarfile_path)
     os.remove(specfile_path)
-    relocate_package(installpath)
+
+    try:
+        relocate_package(workdir, allow_root)
+    except Exception as e:
+        shutil.rmtree(workdir)
+        tty.die(str(e))
+    # Delay creating spec.prefix until verification is complete
+    # and any relocation has been done.
+    else:
+        install_tree(workdir, spec.prefix, symlinks=True)
+    finally:
+        shutil.rmtree(tmpdir)
+
+
+#: Internal cache for get_specs
+_cached_specs = None
 
 
 def get_specs(force=False):
     """
     Get spec.yaml's for build caches available on mirror
     """
-    if spack.binary_cache_retrieved_specs:
+    global _cached_specs
+
+    if _cached_specs:
         tty.debug("Using previously-retrieved specs")
-        previously_retrieved = spack.binary_cache_retrieved_specs
-        return previously_retrieved
+        return _cached_specs
 
-    mirrors = spack.config.get_config('mirrors')
+    mirrors = spack.config.get('mirrors')
     if len(mirrors) == 0:
         tty.warn("No Spack mirrors are currently configured")
         return {}
@@ -448,11 +534,12 @@ def get_specs(force=False):
         if url.startswith('file'):
             mirror = url.replace('file://', '') + '/build_cache'
             tty.msg("Finding buildcaches in %s" % mirror)
-            files = os.listdir(mirror)
-            for file in files:
-                if re.search('spec.yaml', file):
-                    link = 'file://' + mirror + '/' + file
-                    urls.add(link)
+            if os.path.exists(mirror):
+                files = os.listdir(mirror)
+                for file in files:
+                    if re.search('spec.yaml', file):
+                        link = 'file://' + mirror + '/' + file
+                        urls.add(link)
         else:
             tty.msg("Finding buildcaches on %s" % url)
             p, links = spider(url + "/build_cache")
@@ -460,7 +547,7 @@ def get_specs(force=False):
                 if re.search("spec.yaml", link) and re.search(path, link):
                     urls.add(link)
 
-    specs = set()
+    _cached_specs = set()
     for link in urls:
         with Stage(link, name="build_cache", keep=True) as stage:
             if force and os.path.exists(stage.save_filename):
@@ -476,17 +563,16 @@ def get_specs(force=False):
                 # we need to mark this spec concrete on read-in.
                 spec = spack.spec.Spec.from_yaml(f)
                 spec._mark_concrete()
-                specs.add(spec)
+                _cached_specs.add(spec)
 
-    spack.binary_cache_retrieved_specs = specs
-    return specs
+    return _cached_specs
 
 
-def get_keys(install=False, yes_to_all=False, force=False):
+def get_keys(install=False, trust=False, force=False):
     """
     Get pgp public keys available on mirror
     """
-    mirrors = spack.config.get_config('mirrors')
+    mirrors = spack.config.get('mirrors')
     if len(mirrors) == 0:
         tty.die("Please add a spack mirror to allow " +
                 "download of build caches.")
@@ -519,9 +605,9 @@ def get_keys(install=False, yes_to_all=False, force=False):
                         continue
             tty.msg('Found key %s' % link)
             if install:
-                if yes_to_all:
+                if trust:
                     Gpg.trust(stage.save_filename)
                     tty.msg('Added this key to trusted keys.')
                 else:
                     tty.msg('Will not add this key to trusted keys.'
-                            'Use -y to override')
+                            'Use -t to install all downloaded keys')
diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index dfadabb10c..9ef64a6f7e 100644
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """
 This module contains all routines related to setting up the package
 build environment.  All of this is set up by package.py just before
@@ -62,13 +43,20 @@ from six import iteritems
 from six import StringIO
 
 import llnl.util.tty as tty
-from llnl.util.tty.color import colorize
-from llnl.util.filesystem import join_path, mkdirp, install, install_tree
-
-import spack
+from llnl.util.tty.color import cescape, colorize
+from llnl.util.filesystem import mkdirp, install, install_tree
+
+import spack.build_systems.cmake
+import spack.build_systems.meson
+import spack.config
+import spack.main
+import spack.paths
 import spack.store
-from spack.environment import EnvironmentModifications, validate
+from spack.util.string import plural
+from spack.util.environment import EnvironmentModifications, validate
+from spack.util.environment import preserve_environment
 from spack.util.environment import env_flag, filter_system_paths, get_path
+from spack.util.environment import system_dirs
 from spack.util.executable import Executable
 from spack.util.module_cmd import load_module, get_path_from_module
 from spack.util.log_parse import parse_log_events, make_log_context
@@ -94,6 +82,8 @@ SPACK_DEBUG = 'SPACK_DEBUG'
 SPACK_SHORT_SPEC = 'SPACK_SHORT_SPEC'
 SPACK_DEBUG_LOG_ID = 'SPACK_DEBUG_LOG_ID'
 SPACK_DEBUG_LOG_DIR = 'SPACK_DEBUG_LOG_DIR'
+SPACK_CCACHE_BINARY = 'SPACK_CCACHE_BINARY'
+SPACK_SYSTEM_DIRS = 'SPACK_SYSTEM_DIRS'
 
 
 # Platform-specific library suffix.
@@ -101,11 +91,14 @@ dso_suffix = 'dylib' if sys.platform == 'darwin' else 'so'
 
 
 class MakeExecutable(Executable):
-    """Special callable executable object for make so the user can
-       specify parallel or not on a per-invocation basis.  Using
-       'parallel' as a kwarg will override whatever the package's
-       global setting is, so you can either default to true or false
-       and override particular calls.
+    """Special callable executable object for make so the user can specify
+       parallelism options on a per-invocation basis.  Specifying
+       'parallel' to the call will override whatever the package's
+       global setting is, so you can either default to true or false and
+       override particular calls. Specifying 'jobs_env' to a particular
+       call will name an environment variable which will be set to the
+       parallelism level (without affecting the normal invocation with
+       -j).
 
        Note that if the SPACK_NO_PARALLEL_MAKE env var is set it overrides
        everything.
@@ -116,18 +109,60 @@ class MakeExecutable(Executable):
         self.jobs = jobs
 
     def __call__(self, *args, **kwargs):
+        """parallel, and jobs_env from kwargs are swallowed and used here;
+        remaining arguments are passed through to the superclass.
+        """
+
         disable = env_flag(SPACK_NO_PARALLEL_MAKE)
-        parallel = not disable and kwargs.get('parallel', self.jobs > 1)
+        parallel = (not disable) and kwargs.pop('parallel', self.jobs > 1)
 
         if parallel:
-            jobs = "-j%d" % self.jobs
-            args = (jobs,) + args
+            args = ('-j{0}'.format(self.jobs),) + args
+            jobs_env = kwargs.pop('jobs_env', None)
+            if jobs_env:
+                # Caller wants us to set an environment variable to
+                # control the parallelism.
+                kwargs['extra_env'] = {jobs_env: str(self.jobs)}
 
         return super(MakeExecutable, self).__call__(*args, **kwargs)
 
 
+def clean_environment():
+    # Stuff in here sanitizes the build environment to eliminate
+    # anything the user has set that may interfere. We apply it immediately
+    # unlike the other functions so it doesn't overwrite what the modules load.
+    env = EnvironmentModifications()
+
+    # Remove these vars from the environment during build because they
+    # can affect how some packages find libraries.  We want to make
+    # sure that builds never pull in unintended external dependencies.
+    env.unset('LD_LIBRARY_PATH')
+    env.unset('LIBRARY_PATH')
+    env.unset('CPATH')
+    env.unset('LD_RUN_PATH')
+    env.unset('DYLD_LIBRARY_PATH')
+
+    build_lang = spack.config.get('config:build_language')
+    if build_lang:
+        # Override language-related variables. This can be used to force
+        # English compiler messages etc., which allows parse_log_events to
+        # show useful matches.
+        env.set('LC_ALL', build_lang)
+
+    # Remove any macports installs from the PATH.  The macports ld can
+    # cause conflicts with the built-in linker on el capitan.  Solves
+    # assembler issues, e.g.:
+    #    suffix or operands invalid for `movq'"
+    path = get_path('PATH')
+    for p in path:
+        if '/macports/' in p:
+            env.remove_path('PATH', p)
+
+    env.apply_modifications()
+
+
 def set_compiler_environment_variables(pkg, env):
-    assert(pkg.spec.concrete)
+    assert pkg.spec.concrete
     compiler = pkg.compiler
 
     # Set compiler variables used by CMake and autotools
@@ -138,21 +173,21 @@ def set_compiler_environment_variables(pkg, env):
     # and return it
     # TODO : add additional kwargs for better diagnostics, like requestor,
     # ttyout, ttyerr, etc.
-    link_dir = spack.build_env_path
+    link_dir = spack.paths.build_env_path
 
     # Set SPACK compiler variables so that our wrapper knows what to call
     if compiler.cc:
         env.set('SPACK_CC', compiler.cc)
-        env.set('CC', join_path(link_dir, compiler.link_paths['cc']))
+        env.set('CC', os.path.join(link_dir, compiler.link_paths['cc']))
     if compiler.cxx:
         env.set('SPACK_CXX', compiler.cxx)
-        env.set('CXX', join_path(link_dir, compiler.link_paths['cxx']))
+        env.set('CXX', os.path.join(link_dir, compiler.link_paths['cxx']))
     if compiler.f77:
         env.set('SPACK_F77', compiler.f77)
-        env.set('F77', join_path(link_dir, compiler.link_paths['f77']))
+        env.set('F77', os.path.join(link_dir, compiler.link_paths['f77']))
     if compiler.fc:
         env.set('SPACK_FC',  compiler.fc)
-        env.set('FC', join_path(link_dir, compiler.link_paths['fc']))
+        env.set('FC', os.path.join(link_dir, compiler.link_paths['fc']))
 
     # Set SPACK compiler rpath flags so that our wrapper knows what to use
     env.set('SPACK_CC_RPATH_ARG',  compiler.cc_rpath_arg)
@@ -197,6 +232,8 @@ def set_compiler_environment_variables(pkg, env):
 
     env.set('SPACK_COMPILER_SPEC', str(pkg.spec.compiler))
 
+    env.set('SPACK_SYSTEM_DIRS', ':'.join(system_dirs))
+
     compiler.setup_custom_environment(pkg, env)
 
     return env
@@ -256,39 +293,24 @@ def set_build_environment_variables(pkg, env, dirty):
     # Install root prefix
     env.set(SPACK_INSTALL, spack.store.root)
 
-    # Stuff in here sanitizes the build environment to eliminate
-    # anything the user has set that may interfere.
-    if not dirty:
-        # Remove these vars from the environment during build because they
-        # can affect how some packages find libraries.  We want to make
-        # sure that builds never pull in unintended external dependencies.
-        env.unset('LD_LIBRARY_PATH')
-        env.unset('LIBRARY_PATH')
-        env.unset('CPATH')
-        env.unset('LD_RUN_PATH')
-        env.unset('DYLD_LIBRARY_PATH')
-
-        # Remove any macports installs from the PATH.  The macports ld can
-        # cause conflicts with the built-in linker on el capitan.  Solves
-        # assembler issues, e.g.:
-        #    suffix or operands invalid for `movq'"
-        path = get_path('PATH')
-        for p in path:
-            if '/macports/' in p:
-                env.remove_path('PATH', p)
-
     # Set environment variables if specified for
     # the given compiler
     compiler = pkg.compiler
     environment = compiler.environment
-    if 'set' in environment:
-        env_to_set = environment['set']
-        for key, value in iteritems(env_to_set):
-            env.set('SPACK_ENV_SET_%s' % key, value)
-            env.set('%s' % key, value)
-        # Let shell know which variables to set
-        env_variables = ":".join(env_to_set.keys())
-        env.set('SPACK_ENV_TO_SET', env_variables)
+
+    for command, variable in iteritems(environment):
+        if command == 'set':
+            for name, value in iteritems(variable):
+                env.set(name, value)
+        elif command == 'unset':
+            for name, _ in iteritems(variable):
+                env.unset(name)
+        elif command == 'prepend-path':
+            for name, value in iteritems(variable):
+                env.prepend_path(name, value)
+        elif command == 'append-path':
+            for name, value in iteritems(variable):
+                env.append_path(name, value)
 
     if compiler.extra_rpaths:
         extra_rpaths = ':'.join(compiler.extra_rpaths)
@@ -302,20 +324,21 @@ def set_build_environment_variables(pkg, env, dirty):
                 env.prepend_path('PATH', bin_dir)
 
     # Add spack build environment path with compiler wrappers first in
-    # the path. We add both spack.env_path, which includes default
+    # the path. We add the compiler wrapper path, which includes default
     # wrappers (cc, c++, f77, f90), AND a subdirectory containing
     # compiler-specific symlinks.  The latter ensures that builds that
-    # are sensitive to the *name* of the compiler see the right name
-    # when we're building with the wrappers.
+    # are sensitive to the *name* of the compiler see the right name when
+    # we're building with the wrappers.
     #
     # Conflicts on case-insensitive systems (like "CC" and "cc") are
     # handled by putting one in the <build_env_path>/case-insensitive
     # directory.  Add that to the path too.
     env_paths = []
-    compiler_specific = join_path(spack.build_env_path, pkg.compiler.name)
-    for item in [spack.build_env_path, compiler_specific]:
+    compiler_specific = os.path.join(
+        spack.paths.build_env_path, pkg.compiler.name)
+    for item in [spack.paths.build_env_path, compiler_specific]:
         env_paths.append(item)
-        ci = join_path(item, 'case-insensitive')
+        ci = os.path.join(item, 'case-insensitive')
         if os.path.isdir(ci):
             env_paths.append(ci)
 
@@ -324,16 +347,23 @@ def set_build_environment_variables(pkg, env, dirty):
     env.set_path(SPACK_ENV_PATH, env_paths)
 
     # Working directory for the spack command itself, for debug logs.
-    if spack.debug:
+    if spack.config.get('config:debug'):
         env.set(SPACK_DEBUG, 'TRUE')
     env.set(SPACK_SHORT_SPEC, pkg.spec.short_spec)
     env.set(SPACK_DEBUG_LOG_ID, pkg.spec.format('${PACKAGE}-${HASH:7}'))
-    env.set(SPACK_DEBUG_LOG_DIR, spack.spack_working_dir)
+    env.set(SPACK_DEBUG_LOG_DIR, spack.main.spack_working_dir)
+
+    # Find ccache binary and hand it to build environment
+    if spack.config.get('config:ccache'):
+        ccache = Executable('ccache')
+        if not ccache:
+            raise RuntimeError("No ccache binary found in PATH")
+        env.set(SPACK_CCACHE_BINARY, ccache)
 
     # Add any pkgconfig directories to PKG_CONFIG_PATH
     for prefix in build_link_prefixes:
         for directory in ('lib', 'lib64', 'share'):
-            pcdir = join_path(prefix, directory, 'pkgconfig')
+            pcdir = os.path.join(prefix, directory, 'pkgconfig')
             if os.path.isdir(pcdir):
                 env.prepend_path('PKG_CONFIG_PATH', pcdir)
 
@@ -345,7 +375,7 @@ def set_module_variables_for_package(pkg, module):
        This makes things easier for package writers.
     """
     # number of jobs spack will build with.
-    jobs = spack.build_jobs
+    jobs = spack.config.get('config:build_jobs') or multiprocessing.cpu_count()
     if not pkg.parallel:
         jobs = 1
     elif pkg.make_jobs:
@@ -367,18 +397,20 @@ def set_module_variables_for_package(pkg, module):
     # Don't use which for this; we want to find it in the current dir.
     m.configure = Executable('./configure')
 
+    m.meson = Executable('meson')
     m.cmake = Executable('cmake')
-    m.ctest = Executable('ctest')
+    m.ctest = MakeExecutable('ctest', jobs)
 
     # Standard CMake arguments
-    m.std_cmake_args = spack.CMakePackage._std_args(pkg)
+    m.std_cmake_args = spack.build_systems.cmake.CMakePackage._std_args(pkg)
+    m.std_meson_args = spack.build_systems.meson.MesonPackage._std_args(pkg)
 
     # Put spack compiler paths in module scope.
-    link_dir = spack.build_env_path
-    m.spack_cc = join_path(link_dir, pkg.compiler.link_paths['cc'])
-    m.spack_cxx = join_path(link_dir, pkg.compiler.link_paths['cxx'])
-    m.spack_f77 = join_path(link_dir, pkg.compiler.link_paths['f77'])
-    m.spack_fc = join_path(link_dir, pkg.compiler.link_paths['fc'])
+    link_dir = spack.paths.build_env_path
+    m.spack_cc = os.path.join(link_dir, pkg.compiler.link_paths['cc'])
+    m.spack_cxx = os.path.join(link_dir, pkg.compiler.link_paths['cxx'])
+    m.spack_f77 = os.path.join(link_dir, pkg.compiler.link_paths['f77'])
+    m.spack_fc = os.path.join(link_dir, pkg.compiler.link_paths['fc'])
 
     # Emulate some shell commands for convenience
     m.pwd = os.getcwd
@@ -465,16 +497,16 @@ def _static_to_shared_library(arch, compiler, static_lib, shared_lib=None,
 
         compiler_args = [
             '-dynamiclib',
-            '-install_name {0}'.format(install_name),
+            '-install_name', '{0}'.format(install_name),
             '-Wl,-force_load,{0}'.format(static_lib)
         ]
 
         if compat_version:
-            compiler_args.append('-compatibility_version {0}'.format(
-                compat_version))
+            compiler_args.extend(['-compatibility_version', '{0}'.format(
+                compat_version)])
 
         if version:
-            compiler_args.append('-current_version {0}'.format(version))
+            compiler_args.extend(['-current_version', '{0}'.format(version)])
 
     if len(arguments) > 0:
         compiler_args.extend(arguments)
@@ -537,15 +569,31 @@ def get_std_cmake_args(pkg):
     Returns:
         list of str: arguments for cmake
     """
-    return spack.CMakePackage._std_args(pkg)
+    return spack.build_systems.cmake.CMakePackage._std_args(pkg)
+
+
+def get_std_meson_args(pkg):
+    """List of standard arguments used if a package is a MesonPackage.
+
+    Returns:
+        list of str: standard arguments that would be used if this
+        package were a MesonPackage instance.
+
+    Args:
+        pkg (PackageBase): package under consideration
+
+    Returns:
+        list of str: arguments for meson
+    """
+    return spack.build_systems.meson.MesonPackage._std_args(pkg)
 
 
 def parent_class_modules(cls):
     """
-    Get list of super class modules that are all descend from spack.Package
+    Get list of superclass modules that descend from spack.package.PackageBase
     """
-    if (not issubclass(cls, spack.package.Package) or
-        issubclass(spack.package.Package, cls)):
+    if (not issubclass(cls, spack.package.PackageBase) or
+        issubclass(spack.package.PackageBase, cls)):
         return []
     result = []
     module = sys.modules.get(cls.__module__)
@@ -575,18 +623,8 @@ def setup_package(pkg, dirty):
     spack_env = EnvironmentModifications()
     run_env = EnvironmentModifications()
 
-    # Before proceeding, ensure that specs and packages are consistent
-    #
-    # This is a confusing behavior due to how packages are
-    # constructed.  `setup_dependent_package` may set attributes on
-    # specs in the DAG for use by other packages' install
-    # method. However, spec.package will look up a package via
-    # spack.repo, which defensively copies specs into packages.  This
-    # code ensures that all packages in the DAG have pieces of the
-    # same spec object at build time.
-    #
-    for s in pkg.spec.traverse():
-        assert s.package.spec is s
+    if not dirty:
+        clean_environment()
 
     set_compiler_environment_variables(pkg, spack_env)
     set_build_environment_variables(pkg, spack_env, dirty)
@@ -594,10 +632,11 @@ def setup_package(pkg, dirty):
 
     # traverse in postorder so package can use vars from its dependencies
     spec = pkg.spec
-    for dspec in pkg.spec.traverse(order='post', root=False, deptype='build'):
+    for dspec in pkg.spec.traverse(order='post', root=False,
+                                   deptype=('build', 'test')):
         # If a user makes their own package repo, e.g.
-        # spack.repos.mystuff.libelf.Libelf, and they inherit from
-        # an existing class like spack.repos.original.libelf.Libelf,
+        # spack.pkg.mystuff.libelf.Libelf, and they inherit from
+        # an existing class like spack.pkg.original.libelf.Libelf,
         # then set the module variables for both classes so the
         # parent class can still use them if it gets called.
         spkg = dspec.package
@@ -614,25 +653,33 @@ def setup_package(pkg, dirty):
     set_module_variables_for_package(pkg, pkg.module)
     pkg.setup_environment(spack_env, run_env)
 
+    # Loading modules, in particular if they are meant to be used outside
+    # of Spack, can change environment variables that are relevant to the
+    # build of packages. To avoid a polluted environment, preserve the
+    # value of a few, selected, environment variables
+    # With the current ordering of environment modifications, this is strictly
+    # unnecessary. Modules affecting these variables will be overwritten anyway
+    with preserve_environment('CC', 'CXX', 'FC', 'F77'):
+        # All module loads that otherwise would belong in previous
+        # functions have to occur after the spack_env object has its
+        # modifications applied. Otherwise the environment modifications
+        # could undo module changes, such as unsetting LD_LIBRARY_PATH
+        # after a module changes it.
+        for mod in pkg.compiler.modules:
+            # Fixes issue https://github.com/spack/spack/issues/3153
+            if os.environ.get("CRAY_CPU_TARGET") == "mic-knl":
+                load_module("cce")
+            load_module(mod)
+
+        if pkg.architecture.target.module_name:
+            load_module(pkg.architecture.target.module_name)
+
+        load_external_modules(pkg)
+
     # Make sure nothing's strange about the Spack environment.
     validate(spack_env, tty.warn)
     spack_env.apply_modifications()
 
-    # All module loads that otherwise would belong in previous functions
-    # have to occur after the spack_env object has its modifications applied.
-    # Otherwise the environment modifications could undo module changes, such
-    # as unsetting LD_LIBRARY_PATH after a module changes it.
-    for mod in pkg.compiler.modules:
-        # Fixes issue https://github.com/spack/spack/issues/3153
-        if os.environ.get("CRAY_CPU_TARGET") == "mic-knl":
-            load_module("cce")
-        load_module(mod)
-
-    if pkg.architecture.target.module_name:
-        load_module(pkg.architecture.target.module_name)
-
-    load_external_modules(pkg)
-
 
 def fork(pkg, function, dirty, fake):
     """Fork a child process to do part of a spack build.
@@ -680,7 +727,7 @@ def fork(pkg, function, dirty, fake):
         except StopIteration as e:
             # StopIteration is used to stop installations
             # before the final stage, mainly for debug purposes
-            tty.msg(e.message)
+            tty.msg(e)
             child_pipe.send(None)
 
         except BaseException:
@@ -783,25 +830,33 @@ def get_package_context(traceback, context=3):
             if isinstance(obj, spack.package.PackageBase):
                 break
 
-    # we found obj, the Package implementation we care about.
-    # point out the location in the install method where we failed.
-    lines = []
-    lines.append("%s:%d, in %s:" % (
-        inspect.getfile(frame.f_code), frame.f_lineno, frame.f_code.co_name
-    ))
+    # We found obj, the Package implementation we care about.
+    # Point out the location in the install method where we failed.
+    lines = [
+        '{0}:{1:d}, in {2}:'.format(
+            inspect.getfile(frame.f_code),
+            frame.f_lineno - 1,  # subtract 1 because f_lineno is 0-indexed
+            frame.f_code.co_name
+        )
+    ]
 
     # Build a message showing context in the install method.
     sourcelines, start = inspect.getsourcelines(frame)
 
-    fl = frame.f_lineno - start
-    start_ctx = max(0, fl - context)
-    sourcelines = sourcelines[start_ctx:fl + context + 1]
+    # Calculate lineno of the error relative to the start of the function.
+    # Subtract 1 because f_lineno is 0-indexed.
+    fun_lineno = frame.f_lineno - start - 1
+    start_ctx = max(0, fun_lineno - context)
+    sourcelines = sourcelines[start_ctx:fun_lineno + context + 1]
+
     for i, line in enumerate(sourcelines):
-        is_error = start_ctx + i == fl
-        mark = ">> " if is_error else "   "
-        marked = "  %s%-6d%s" % (mark, start_ctx + i, line.rstrip())
+        is_error = start_ctx + i == fun_lineno
+        mark = '>> ' if is_error else '   '
+        # Add start to get lineno relative to start of file, not function.
+        marked = '  {0}{1:-6d}{2}'.format(
+            mark, start + start_ctx + i, line.rstrip())
         if is_error:
-            marked = colorize('@R{%s}' % marked)
+            marked = colorize('@R{%s}' % cescape(marked))
         lines.append(marked)
 
     return lines
@@ -869,29 +924,34 @@ class ChildError(InstallError):
 
         if (self.module, self.name) in ChildError.build_errors:
             # The error happened in some external executed process. Show
-            # the build log with errors highlighted.
-            if self.build_log:
+            # the build log with errors or warnings highlighted.
+            if self.build_log and os.path.exists(self.build_log):
                 errors, warnings = parse_log_events(self.build_log)
                 nerr = len(errors)
+                nwar = len(warnings)
                 if nerr > 0:
-                    if nerr == 1:
-                        out.write("\n1 error found in build log:\n")
-                    else:
-                        out.write("\n%d errors found in build log:\n" % nerr)
+                    # If errors are found, only display errors
+                    out.write(
+                        "\n%s found in build log:\n" % plural(nerr, 'error'))
                     out.write(make_log_context(errors))
+                elif nwar > 0:
+                    # If no errors are found but warnings are, display warnings
+                    out.write(
+                        "\n%s found in build log:\n" % plural(nwar, 'warning'))
+                    out.write(make_log_context(warnings))
 
         else:
             # The error happened in in the Python code, so try to show
             # some context from the Package itself.
-            out.write('%s: %s\n\n' % (self.name, self.message))
             if self.context:
+                out.write('\n')
                 out.write('\n'.join(self.context))
                 out.write('\n')
 
         if out.getvalue():
             out.write('\n')
 
-        if self.build_log:
+        if self.build_log and os.path.exists(self.build_log):
             out.write('See build log for details:\n')
             out.write('  %s' % self.build_log)
 
diff --git a/lib/spack/spack/build_systems/README-intel.rst b/lib/spack/spack/build_systems/README-intel.rst
new file mode 100644
index 0000000000..6efbd09dd4
--- /dev/null
+++ b/lib/spack/spack/build_systems/README-intel.rst
@@ -0,0 +1,660 @@
+====================================
+Development Notes on Intel Packages
+====================================
+
+These are notes for concepts and development of
+lib/spack/spack/build_systems/intel.py .
+
+For documentation on how to *use* ``IntelPackage``, see
+lib/spack/docs/build_systems/intelpackage.rst .
+
+-------------------------------------------------------------------------------
+Installation and path handling as implemented in ./intel.py
+-------------------------------------------------------------------------------
+
+
+***************************************************************************
+Prefix differences between Spack-external and Spack-internal installations
+***************************************************************************
+
+
+Problem summary
+~~~~~~~~~~~~~~~~
+
+For Intel packages that were installed external to Spack, ``self.prefix`` will
+be a *component-specific* path (e.g. to an MKL-specific dir hierarchy), whereas
+for a package installed by Spack itself, ``self.prefix`` will be a
+*vendor-level* path that holds one or more components (or parts thereof), and
+must be further qualified down to a particular desired component.
+
+It is possible that a similar conceptual difference is inherent to other
+package families that use a common vendor-style installer.
+
+
+Description
+~~~~~~~~~~~~
+
+Spack makes packages available through two routes, let's call them A and B:
+
+A. Packages pre-installed external to Spack and configured *for* Spack
+B. Packages built and installed *by* Spack.
+
+For a user who is interested in building end-user applications, it should not
+matter through which route any of its dependent packages has been installed.
+Most packages natively support a ``prefix`` concept which unifies the two
+routes just fine.
+
+Intel packages, however, are more complicated because they consist of a number
+of components that are released as a suite of varying extent, like "Intel
+Parallel Studio *Foo* Edition", or subsetted into products like "MKL" or "MPI",
+each of which also contain libraries from other components like the compiler
+runtime and multithreading libraries. For this reason, an Intel package is
+"anchored" during installation at a directory level higher than just the
+user-facing directory that has the conventional hierarchy of ``bin``, ``lib``,
+and others relevant for the end-product.
+
+As a result, internal to Spack, there is a conceptual difference in what
+``self.prefix`` represents for the two routes.
+
+For route A, consider MKL installed outside of Spack. It will likely be one
+product component among other products, at one particular release among others
+that are installed in sibling or cousin directories on the local system.
+Therefore, the path given to Spack in ``packages.yaml`` should be a
+*product-specific and fully version-specific* directory.  E.g., for an
+``intel-mkl`` package, ``self.prefix`` should look like::
+
+  /opt/intel/compilers_and_libraries_2018.1.163/linux/mkl
+
+In this route, the interaction point with the user is encapsulated in an
+environment variable which will be (in pseudo-code)::
+
+    MKLROOT := {self.prefix}
+
+For route B, a Spack-based installation of MKL will be placed in the directory
+given to the ``./install.sh`` script of Intel's package distribution.  This
+directory is taken to be the *vendor*-specific anchor directory, playing the
+same role as the default ``/opt/intel``. In this case, ``self.prefix`` will
+be::
+
+  $SPACK_ROOT/opt/spack/linux-centos6-x86_64/gcc-4.9.3/intel-mkl-2018.1.163-<HASH>
+
+However, now the environment variable will have to be constructed as *several
+directory levels down*::
+
+    MKLROOT := {self.prefix}/compilers_and_libraries_2018.1.163/linux/mkl
+
+A recent post on the Spack mailing list illustrates the confusion when route A
+was taken while route B was the only one that was coded in Spack:
+https://groups.google.com/d/msg/spack/x28qlmqPAys/Ewx6220uAgAJ
+
+
+Solution
+~~~~~~~~~
+
+Introduce a series of functions which will return the appropriate
+directories, regardless of whether the Intel package has been installed
+external or internal to Spack:
+
+==========================  ==================================================
+Function                    Example return values
+--------------------------  --------------------------------------------------
+normalize_suite_dir()       Spack-external installation:
+                                /opt/intel/compilers_and_libraries_2018.1.163
+                            Spack-internal installation:
+                                $SPACK_ROOT/...<HASH>/compilers_and_libraries_2018.1.163
+--------------------------  --------------------------------------------------
+normalize_path('mkl')       <suite_dir>/linux/mkl
+component_bin_dir()         <suite_dir>/linux/mkl/bin
+component_lib_dir()         <suite_dir>/linux/mkl/lib/intel64
+--------------------------  --------------------------------------------------
+normalize_path('mpi')       <suite_dir>/linux/mpi
+component_bin_dir('mpi')    <suite_dir>/linux/mpi/intel64/bin
+component_lib_dir('mpi')    <suite_dir>/linux/mpi/intel64/lib
+==========================  ==================================================
+
+
+*********************************
+Analysis of directory layouts
+*********************************
+
+Let's look at some sample directory layouts, using ``ls -lF``,
+but focusing on names and symlinks only.
+
+Spack-born installation of ``intel-mkl@2018.1.163``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+::
+
+  $ ls -l <prefix>
+
+  bin/
+      - compilervars.*sh (symlinked) ONLY
+
+  compilers_and_libraries -> compilers_and_libraries_2018
+      - generically-named entry point, stable across versions (one hopes)
+
+  compilers_and_libraries_2018/
+      - vaguely-versioned dirname, holding a stub hierarchy --ignorable
+
+      $ ls -l compilers_and_libraries_2018/linux/
+      bin         - actual compilervars.*sh (reg. files) ONLY
+      documentation -> ../../documentation_2018/
+      lib -> ../../compilers_and_libraries_2018.1.163/linux/compiler/lib/
+      mkl -> ../../compilers_and_libraries_2018.1.163/linux/mkl/
+      pkg_bin -> ../../compilers_and_libraries_2018.1.163/linux/bin/
+      samples -> ../../samples_2018/
+      tbb -> ../../compilers_and_libraries_2018.1.163/linux/tbb/
+
+  compilers_and_libraries_2018.1.163/
+      - Main "product" + a minimal set of libs from related products
+
+      $ ls -l compilers_and_libraries_2018.1.163/linux/
+      bin/        - compilervars.*sh, link_install*sh  ONLY
+      mkl/        - Main Product ==> to be assigned to MKLROOT
+      compiler/   - lib/intel64_lin/libiomp5*  ONLY
+      tbb/        - tbb/lib/intel64_lin/gcc4.[147]/libtbb*.so* ONLY
+
+  parallel_studio_xe_2018 -> parallel_studio_xe_2018.1.038/
+  parallel_studio_xe_2018.1.038/
+      - Alternate product packaging - ignorable
+
+      $ ls -l parallel_studio_xe_2018.1.038/
+      bin/               - actual psxevars.*sh (reg. files)
+      compilers_and_libraries_2018 -> <full_path>/comp...aries_2018.1.163
+      documentation_2018 -> <full_path_prefix>/documentation_2018
+      samples_2018 -> <full_path_prefix>/samples_2018
+      ...
+
+  documentation_2018/
+  samples_2018/
+  lib -> compilers_and_libraries/linux/lib/
+  mkl -> compilers_and_libraries/linux/mkl/
+  tbb -> compilers_and_libraries/linux/tbb/
+                  - auxiliaries and convenience links
+
+Spack-external installation of Intel-MPI 2018
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+For MPI, the layout is slightly different than MKL. The prefix will have to
+include an architecture directory (typically ``intel64``), which then contains
+bin/, lib/, ..., all without further architecture branching.  The environment
+variable ``I_MPI_ROOT`` from the API documentation, however, must be the
+package's top directory, not including the architecture.
+
+FIXME: For MANPATH, need the parent dir.
+
+::
+
+  $ ls -lF /opt/intel/compilers_and_libraries_2018.1.163/linux/mpi/
+  bin64 -> intel64/bin/
+  etc64 -> intel64/etc/
+  include64 -> intel64/include/
+  lib64 -> intel64/lib/
+
+  benchmarks/
+  binding/
+  intel64/
+  man/
+  test/
+
+The package contains an MPI-2019 preview; Curiously, its release notes contain
+the tag: "File structure clean-up." I could not find further documentation on
+this, however, so it is unclear what, if any, changes will make it to release.
+
+https://software.intel.com/en-us/articles/restoring-legacy-path-structure-on-intel-mpi-library-2019
+
+::
+
+  $ ls -lF /opt/intel/compilers_and_libraries_2018.1.163/linux/mpi_2019/
+  binding/
+  doc/
+  imb/
+  intel64/
+  man/
+  test/
+
+Spack-external installation of Intel Parallel Studio 2018
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+This is the main product bundle that I actually downloaded and installed on my
+system.  Its nominal installation directory mostly holds merely symlinks
+to components installed in sibling dirs::
+
+  $ ls -lF /opt/intel/parallel_studio_xe_2018.1.038/
+  advisor_2018		 -> /opt/intel/advisor_2018/
+  clck_2018		 -> /opt/intel/clck/2018.1/
+  compilers_and_libraries_2018 -> /opt/intel/comp....aries_2018.1.163/
+  documentation_2018	 -> /opt/intel/documentation_2018/
+  ide_support_2018	 -> /opt/intel/ide_support_2018/
+  inspector_2018		 -> /opt/intel/inspector_2018/
+  itac_2018		 -> /opt/intel/itac/2018.1.017/
+  man		         -> /opt/intel/man/
+  samples_2018		 -> /opt/intel/samples_2018/
+  vtune_amplifier_2018	 -> /opt/intel/vtune_amplifier_2018/
+
+  psxevars.csh		 -> ./bin/psxevars.csh*
+  psxevars.sh		 -> ./bin/psxevars.sh*
+  bin/            - *vars.*sh scripts + sshconnectivity.exp ONLY
+
+  licensing/
+  uninstall*
+
+The only relevant regular files are ``*vars.*sh``, but those also just churn
+through the subordinate vars files of the components.
+
+Installation model
+~~~~~~~~~~~~~~~~~~~~
+
+Intel packages come with an ``install.sh`` script that is normally run
+interactively (in either text or GUI mode) but can run unattended with a
+``--silent <file>`` option, which is of course what Spack uses.
+
+Format of configuration file
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The configuration file is conventionally called ``silent.cfg`` and has a simple
+``token=value`` syntax.  Before using the configuration file, the installer
+calls ``<staging_dir>/pset/check.awk`` to validate it. Example paths to the
+validator are::
+
+      .../l_mkl_2018.1.163/pset/check.awk .
+      .../parallel_studio_xe_2018_update1_cluster_edition/pset/check.awk
+
+The tokens that are accepted in the configuration file vary between packages.
+Tokens not supported for a given package **will cause the installer to stop
+and fail.** This is particularly relevant for license-related tokens, which are
+accepted only for packages that actually require a license.
+
+Reference: [Intel's documentation](https://software.intel.com/en-us/articles/configuration-file-format)
+
+See also:  https://software.intel.com/en-us/articles/silent-installation-guide-for-intel-parallel-studio-xe-composer-edition-for-os-x
+
+The following is from ``.../parallel_studio_xe_2018_update1_cluster_edition/pset/check.awk``:
+
+* Tokens valid for all packages encountered::
+
+    ACCEPT_EULA                                  {accept, decline}
+    CONTINUE_WITH_OPTIONAL_ERROR                 {yes, no}
+    PSET_INSTALL_DIR                             {/opt/intel, , filepat}
+    CONTINUE_WITH_INSTALLDIR_OVERWRITE           {yes, no}
+    COMPONENTS                                   {ALL, DEFAULTS, , anythingpat}
+    PSET_MODE                                    {install, repair, uninstall}
+    NONRPM_DB_DIR                                {, filepat}
+
+    SIGNING_ENABLED                              {yes, no}
+    ARCH_SELECTED                                {IA32, INTEL64, ALL}
+
+* Mentioned but unexplained in ``check.awk``::
+
+    NO_VALIDATE   (?!)
+
+* Only for licensed packages::
+
+    ACTIVATION_SERIAL_NUMBER                     {, snpat}
+    ACTIVATION_LICENSE_FILE                      {, lspat, filepat}
+    ACTIVATION_TYPE                              {exist_lic, license_server,
+                                                 license_file, trial_lic,
+
+    PHONEHOME_SEND_USAGE_DATA                    {yes, no}
+                                                 serial_number}
+
+* Only for Amplifier (obviously)::
+
+    AMPLIFIER_SAMPLING_DRIVER_INSTALL_TYPE       {build, kit}
+    AMPLIFIER_DRIVER_ACCESS_GROUP                {, anythingpat, vtune}
+    AMPLIFIER_DRIVER_PERMISSIONS                 {, anythingpat, 666}
+    AMPLIFIER_LOAD_DRIVER                        {yes, no}
+    AMPLIFIER_C_COMPILER                         {, filepat, auto, none}
+    AMPLIFIER_KERNEL_SRC_DIR                     {, filepat, auto, none}
+    AMPLIFIER_MAKE_COMMAND                       {, filepat, auto, none}
+    AMPLIFIER_INSTALL_BOOT_SCRIPT                {yes, no}
+    AMPLIFIER_DRIVER_PER_USER_MODE               {yes, no}
+
+* Only for MKL and Studio::
+
+    CLUSTER_INSTALL_REMOTE                       {yes, no}
+    CLUSTER_INSTALL_TEMP                         {, filepat}
+    CLUSTER_INSTALL_MACHINES_FILE                {, filepat}
+
+* "backward compatibility" (?)::
+
+    INSTALL_MODE                                 {RPM, NONRPM}
+    download_only                                {yes}
+    download_dir                                 {, filepat}
+
+
+Details for licensing tokens
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Quoted from
+https://software.intel.com/en-us/articles/configuration-file-format,
+for reference:
+
+[ed. note: As of 2018-05, the page incorrectly references ``ACTIVATION``, which
+was used only until about 2012; this is corrected to ``ACTIVATION_TYPE`` here.]
+
+    ...
+
+    ``ACTIVATION_TYPE=exist_lic``
+       This directive tells the install program to look for an existing
+       license during the install process.  This is the preferred method for
+       silent installs.  Take the time to register your serial number and get
+       a license file (see below).  Having a license file on the system
+       simplifies the process.  In addition, as an administrator it is good
+       practice to know WHERE your licenses are saved on your system.
+       License files are plain text files with a .lic extension.  By default
+       these are saved in /opt/intel/licenses which is searched by default.
+       If you save your license elsewhere, perhaps under an NFS folder, set
+       environment variable **INTEL_LICENSE_FILE** to the full path to your
+       license file prior to starting the installation or use the
+       configuration file directive ``ACTIVATION_LICENSE_FILE`` to specify the
+       full pathname to the license file.
+    
+       Options for ``ACTIVATION_TYPE`` are ``{ exist_lic, license_file, server_lic,
+       serial_number, trial_lic }``
+    
+    ``exist_lic``
+       directs the installer to search for a valid license on the server.
+       Searches will utilize the environment variable **INTEL_LICENSE_FILE**,
+       search the default license directory /opt/intel/licenses, or use the
+       ``ACTIVATION_LICENSE_FILE`` directive to find a valid license file.
+    
+    ``license_file``
+       is similar to exist_lic but directs the installer to use
+       ``ACTIVATION_LICENSE_FILE`` to find the license file.
+    
+    ``server_lic``
+       is similar to exist_lic and exist_lic but directs the installer that
+       this is a client installation and a floating license server will be
+       contacted to active the product.  This option will contact your
+       floating license server on your network to retrieve the license
+       information.  BEFORE using this option make sure your client is
+       correctly set up for your network including all networking, routing,
+       name service, and firewall configuration.  Insure that your client has
+       direct access to your floating license server and that firewalls are
+       set up to allow TCP/IP access for the 2 license server ports.
+       server_lic will use **INTEL_LICENSE_FILE** containing a port@host format
+       OR a client license file.  The formats for these are described here
+       https://software.intel.com/en-us/articles/licensing-setting-up-the-client-floating-license
+    
+    ``serial_number``
+       directs the installer to use directive ``ACTIVATION_SERIAL_NUMBER`` for
+       activation.  This method will require the installer to contact an
+       external Intel activation server over the Internet to confirm your
+       serial number.  Due to user and company firewalls, this method is more
+       complex and hence error prone of the available activation methods.  We
+       highly recommend using a license file or license server for activation
+       instead.
+    
+    ``trial_lic``
+       is used only if you do not have an existing license and intend to
+       temporarily evaluate the compiler.  This method creates a temporary
+       trial license in Trusted Storage on your system.
+    
+    ...
+
+*******************
+vars files
+*******************
+
+Intel's product packages contain a number of shell initialization files let's call them vars files.
+
+There are three kinds:
+
+#. Component-specific vars files, such as `mklvars` or `tbbvars`.
+#. Toplevel vars files such as "psxevars". They will scan for all
+   component-specific vars files associated with the product, and source them
+   if found.
+#. Symbolic links to either of them. Links may appear under a different name
+   for backward compatibility.
+
+At present, IntelPackage class is only concerned with the toplevel vars files,
+generally found in the product's toplevel bin/ directory.
+
+For reference, here is an overview of the names and locations of the vars files
+in the 2018 product releases, as seen for Spack-native installation. NB: May be
+incomplete as some components may have been omitted during installation.
+
+Names of vars files seen::
+
+    $ cd opt/spack/linux-centos6-x86_64
+    $ find intel* -name \*vars.sh -printf '%f\n' | sort -u | nl
+     1	advixe-vars.sh
+     2	amplxe-vars.sh
+     3	apsvars.sh
+     4	compilervars.sh
+     5	daalvars.sh
+     6	debuggervars.sh
+     7	iccvars.sh
+     8	ifortvars.sh
+     9	inspxe-vars.sh
+    10	ippvars.sh
+    11	mklvars.sh
+    12	mpivars.sh
+    13	pstlvars.sh
+    14	psxevars.sh
+    15	sep_vars.sh
+    16	tbbvars.sh
+
+Names and locations of vars files, sorted by Spack package name::
+
+    $ cd opt/spack/linux-centos6-x86_64
+    $ find intel* -name \*vars.sh -printf '%y\t%-15f\t%h\n' \
+        | cut -d/ -f1,4- \
+        | sed '/iccvars\|ifortvars/d; s,/,\t\t,; s,\.sh,,; s,  */\(intel[/-]\),\1,' \
+        | sort -k3,3 -k2,2 \
+        | nl \
+        | awk '{printf "%6i %-2s %-16s %-24s %s\n", $1, $2, $3, $4, $5}'
+
+    --------------------------------------------------------------------------------------------------------
+    item no.
+       file or link
+          name of vars file
+                           Spack package name
+                                                    dir relative to Spack install dir
+    --------------------------------------------------------------------------------------------------------
+
+     1 f  mpivars          intel                    compilers_and_libraries_2018.1.163/linux/mpi/intel64/bin
+     2 f  mpivars          intel                    compilers_and_libraries_2018.1.163/linux/mpirt/bin/ia32_lin
+     3 f  tbbvars          intel                    compilers_and_libraries_2018.1.163/linux/tbb/bin
+     4 f  pstlvars         intel                    compilers_and_libraries_2018.1.163/linux/pstl/bin
+     5 f  compilervars     intel                    compilers_and_libraries_2018.1.163/linux/bin
+     6 f  compilervars     intel                    compilers_and_libraries_2018/linux/bin
+     7 l  compilervars     intel                    bin
+     8 f  daalvars         intel-daal               compilers_and_libraries_2018.2.199/linux/daal/bin
+     9 f  psxevars         intel-daal               parallel_studio_xe_2018.2.046/bin
+    10 l  psxevars         intel-daal               parallel_studio_xe_2018.2.046
+    11 f  compilervars     intel-daal               compilers_and_libraries_2018.2.199/linux/bin
+    12 f  compilervars     intel-daal               compilers_and_libraries_2018/linux/bin
+    13 l  compilervars     intel-daal               bin
+    14 f  ippvars          intel-ipp                compilers_and_libraries_2018.2.199/linux/ipp/bin
+    15 f  psxevars         intel-ipp                parallel_studio_xe_2018.2.046/bin
+    16 l  psxevars         intel-ipp                parallel_studio_xe_2018.2.046
+    17 f  compilervars     intel-ipp                compilers_and_libraries_2018.2.199/linux/bin
+    18 f  compilervars     intel-ipp                compilers_and_libraries_2018/linux/bin
+    19 l  compilervars     intel-ipp                bin
+    20 f  mklvars          intel-mkl                compilers_and_libraries_2018.2.199/linux/mkl/bin
+    21 f  psxevars         intel-mkl                parallel_studio_xe_2018.2.046/bin
+    22 l  psxevars         intel-mkl                parallel_studio_xe_2018.2.046
+    23 f  compilervars     intel-mkl                compilers_and_libraries_2018.2.199/linux/bin
+    24 f  compilervars     intel-mkl                compilers_and_libraries_2018/linux/bin
+    25 l  compilervars     intel-mkl                bin
+    26 f  mpivars          intel-mpi                compilers_and_libraries_2018.2.199/linux/mpi_2019/intel64/bin
+    27 f  mpivars          intel-mpi                compilers_and_libraries_2018.2.199/linux/mpi/intel64/bin
+    28 f  psxevars         intel-mpi                parallel_studio_xe_2018.2.046/bin
+    29 l  psxevars         intel-mpi                parallel_studio_xe_2018.2.046
+    30 f  compilervars     intel-mpi                compilers_and_libraries_2018.2.199/linux/bin
+    31 f  compilervars     intel-mpi                compilers_and_libraries_2018/linux/bin
+    32 l  compilervars     intel-mpi                bin
+    33 f  apsvars          intel-parallel-studio    vtune_amplifier_2018.1.0.535340
+    34 l  apsvars          intel-parallel-studio    performance_snapshots_2018.1.0.535340
+    35 f  ippvars          intel-parallel-studio    compilers_and_libraries_2018.1.163/linux/ipp/bin
+    36 f  ippvars          intel-parallel-studio    composer_xe_2015.6.233/ipp/bin
+    37 f  mklvars          intel-parallel-studio    compilers_and_libraries_2018.1.163/linux/mkl/bin
+    38 f  mklvars          intel-parallel-studio    composer_xe_2015.6.233/mkl/bin
+    39 f  mpivars          intel-parallel-studio    compilers_and_libraries_2018.1.163/linux/mpi/intel64/bin
+    40 f  mpivars          intel-parallel-studio    compilers_and_libraries_2018.1.163/linux/mpirt/bin/ia32_lin
+    41 f  tbbvars          intel-parallel-studio    compilers_and_libraries_2018.1.163/linux/tbb/bin
+    42 f  tbbvars          intel-parallel-studio    composer_xe_2015.6.233/tbb/bin
+    43 f  daalvars         intel-parallel-studio    compilers_and_libraries_2018.1.163/linux/daal/bin
+    44 f  pstlvars         intel-parallel-studio    compilers_and_libraries_2018.1.163/linux/pstl/bin
+    45 f  psxevars         intel-parallel-studio    parallel_studio_xe_2018.1.038/bin
+    46 l  psxevars         intel-parallel-studio    parallel_studio_xe_2018.1.038
+    47 f  sep_vars         intel-parallel-studio    vtune_amplifier_2018.1.0.535340
+    48 f  sep_vars         intel-parallel-studio    vtune_amplifier_2018.1.0.535340/target/android_v4.1_x86_64
+    49 f  advixe-vars      intel-parallel-studio    advisor_2018.1.1.535164
+    50 f  amplxe-vars      intel-parallel-studio    vtune_amplifier_2018.1.0.535340
+    51 f  inspxe-vars      intel-parallel-studio    inspector_2018.1.1.535159
+    52 f  compilervars     intel-parallel-studio    compilers_and_libraries_2018.1.163/linux/bin
+    53 f  compilervars     intel-parallel-studio    compilers_and_libraries_2018/linux/bin
+    54 l  compilervars     intel-parallel-studio    bin
+    55 f  debuggervars     intel-parallel-studio    debugger_2018/bin
+
+
+********************
+MPI linkage
+********************
+
+
+Library selection
+~~~~~~~~~~~~~~~~~~~~~
+
+In the Spack code so far, the library selections for MPI are:
+
+::
+
+        libnames = ['libmpifort', 'libmpi']
+        if 'cxx' in self.spec.last_query.extra_parameters:
+            libnames = ['libmpicxx'] + libnames
+        return find_libraries(libnames,
+                              root=self.component_lib_dir('mpi'),
+                              shared=True, recursive=False)
+
+The problem is that there are multiple library versions under ``component_lib_dir``::
+
+    $ cd $I_MPI_ROOT 
+    $ find . -name libmpi.so | sort
+    ./intel64/lib/debug/libmpi.so
+    ./intel64/lib/debug_mt/libmpi.so
+    ./intel64/lib/libmpi.so
+    ./intel64/lib/release/libmpi.so
+    ./intel64/lib/release_mt/libmpi.so
+
+"mt" refers to multi-threading, not in the explicit sense but in the sense of being thread-safe::
+
+    $ mpiifort -help | grep mt
+       -mt_mpi         link the thread safe version of the Intel(R) MPI Library
+
+Well, why should we not inspect what the canonical script does?  The wrapper
+has its own hardcoded "prefix=..." and can thus tell us what it will do, from a
+*wiped environment* no less!::
+
+    $ env - intel64/bin/mpiicc -show hello.c | ld-unwrap-args 
+    icc 'hello.c' \
+        -I/opt/intel/compilers_and_libraries_2018.1.163/linux/mpi/intel64/include \
+        -L/opt/intel/compilers_and_libraries_2018.1.163/linux/mpi/intel64/lib/release_mt \
+        -L/opt/intel/compilers_and_libraries_2018.1.163/linux/mpi/intel64/lib \
+        -Xlinker --enable-new-dtags \
+        -Xlinker -rpath=/opt/intel/compilers_and_libraries_2018.1.163/linux/mpi/intel64/lib/release_mt \
+        -Xlinker -rpath=/opt/intel/compilers_and_libraries_2018.1.163/linux/mpi/intel64/lib \
+        -Xlinker -rpath=/opt/intel/mpi-rt/2017.0.0/intel64/lib/release_mt \
+        -Xlinker -rpath=/opt/intel/mpi-rt/2017.0.0/intel64/lib \
+        -lmpifort \
+        -lmpi \
+        -lmpigi \
+        -ldl \
+        -lrt \
+        -lpthread
+
+
+MPI Wrapper options
+~~~~~~~~~~~~~~~~~~~~~
+
+For reference, here's the wrapper's builtin help output::
+
+    $ mpiifort -help
+    Simple script to compile and/or link MPI programs.
+    Usage: mpiifort [options] <files>
+    ----------------------------------------------------------------------------
+    The following options are supported:
+       -fc=<name> | -f90=<name>
+                       specify a FORTRAN compiler name: i.e. -fc=ifort
+       -echo           print the scripts during their execution
+       -show           show command lines without real calling
+       -config=<name>  specify a configuration file: i.e. -config=ifort for mpif90-ifort.conf file
+       -v              print version info of mpiifort and its native compiler
+       -profile=<name> specify a profile configuration file (an MPI profiling
+                       library): i.e. -profile=myprofile for the myprofile.cfg file.
+                       As a special case, lib<name>.so or lib<name>.a may be used
+                       if the library is found
+       -check_mpi      link against the Intel(R) Trace Collector (-profile=vtmc).
+       -static_mpi     link the Intel(R) MPI Library statically
+       -mt_mpi         link the thread safe version of the Intel(R) MPI Library
+       -ilp64          link the ILP64 support of the Intel(R) MPI Library
+       -no_ilp64       disable ILP64 support explicitly
+       -fast           the same as -static_mpi + pass -fast option to a compiler.
+       -t or -trace
+                       link against the Intel(R) Trace Collector
+       -trace-imbalance
+                       link against the Intel(R) Trace Collector imbalance library
+                       (-profile=vtim)
+       -dynamic_log    link against the Intel(R) Trace Collector dynamically
+       -static         use static linkage method
+       -nostrip        turn off the debug information stripping during static linking
+       -O              enable optimization
+       -link_mpi=<name>
+                       link against the specified version of the Intel(R) MPI Library
+    All other options will be passed to the compiler without changing.
+    ----------------------------------------------------------------------------
+    The following environment variables are used:
+       I_MPI_ROOT      the Intel(R) MPI Library installation directory path
+       I_MPI_F90 or MPICH_F90
+                       the path/name of the underlying compiler to be used
+       I_MPI_FC_PROFILE or I_MPI_F90_PROFILE or MPIF90_PROFILE
+                       the name of profile file (without extension)
+       I_MPI_COMPILER_CONFIG_DIR
+                       the folder which contains configuration files *.conf
+       I_MPI_TRACE_PROFILE
+                       specify a default profile for the -trace option
+       I_MPI_CHECK_PROFILE
+                       specify a default profile for the -check_mpi option
+       I_MPI_CHECK_COMPILER
+                       enable compiler setup checks
+       I_MPI_LINK      specify the version of the Intel(R) MPI Library
+       I_MPI_DEBUG_INFO_STRIP
+                       turn on/off the debug information stripping during static linking
+       I_MPI_FCFLAGS
+                       special flags needed for compilation
+       I_MPI_LDFLAGS 
+                       special flags needed for linking
+    ----------------------------------------------------------------------------
+
+
+Side Note: MPI version divergence in 2015 release
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The package `intel-parallel-studio@cluster.2015.6` contains both a full MPI
+development version in `$prefix/impi` and an MPI Runtime under the
+`composer_xe*` suite directory. Curiously, these have *different versions*,
+with a release date nearly 1 year apart::
+
+    $ $SPACK_ROOT/...uaxaw7/impi/5.0.3.049/intel64/bin/mpiexec --version
+    Intel(R) MPI Library for Linux* OS, Version 5.0 Update 3 Build 20150804 (build id: 12452)
+    Copyright (C) 2003-2015, Intel Corporation. All rights reserved.
+
+    $ $SPACK_ROOT/...uaxaw7/composer_xe_2015.6.233/mpirt/bin/intel64/mpiexec --version
+    Intel(R) MPI Library for Linux* OS, Version 5.0 Update 1 Build 20140709
+    Copyright (C) 2003-2014, Intel Corporation. All rights reserved.
+
+I'm not sure what to make of it.
+
+
+**************
+macOS support
+**************
+
+- On macOS, the Spack methods here only include support to integrate an
+  externally installed MKL.
+
+- URLs in child packages will be Linux-specific; macOS download packages
+  are located in differently numbered dirs and are named m_*.dmg.
diff --git a/lib/spack/spack/build_systems/__init__.py b/lib/spack/spack/build_systems/__init__.py
index 8922701e9f..4f442db458 100644
--- a/lib/spack/spack/build_systems/__init__.py
+++ b/lib/spack/spack/build_systems/__init__.py
@@ -1,24 +1,4 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
diff --git a/lib/spack/spack/build_systems/aspell_dict.py b/lib/spack/spack/build_systems/aspell_dict.py
index edf9bdb5da..437983e8a7 100644
--- a/lib/spack/spack/build_systems/aspell_dict.py
+++ b/lib/spack/spack/build_systems/aspell_dict.py
@@ -1,32 +1,14 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 # Why doesn't this work for me?
 # from spack import *
 from llnl.util.filesystem import filter_file
 from spack.build_systems.autotools import AutotoolsPackage
 from spack.directives import extends
+from spack.package import ExtensionError
 from spack.util.executable import which
 
 
@@ -38,10 +20,21 @@ from spack.util.executable import which
 # They aren't really an Autotools package, but it's close enough
 # that this works if we override configure().
 class AspellDictPackage(AutotoolsPackage):
-    """Specialized class for builing aspell dictionairies."""
+    """Specialized class for building aspell dictionairies."""
 
     extends('aspell')
 
+    def view_destination(self, view):
+        aspell_spec = self.spec['aspell']
+        if view.root != aspell_spec.prefix:
+            raise ExtensionError(
+                'aspell does not support non-global extensions')
+        aspell = aspell_spec.command
+        return aspell('dump', 'config', 'dict-dir', output=str).strip()
+
+    def view_source(self):
+        return self.prefix.lib
+
     def patch(self):
         filter_file(r'^dictdir=.*$', 'dictdir=/lib', 'configure')
         filter_file(r'^datadir=.*$', 'datadir=/lib', 'configure')
diff --git a/lib/spack/spack/build_systems/autotools.py b/lib/spack/spack/build_systems/autotools.py
index 01a59feeba..a26c7f56bb 100644
--- a/lib/spack/spack/build_systems/autotools.py
+++ b/lib/spack/spack/build_systems/autotools.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 import inspect
 import os
@@ -32,7 +13,7 @@ from subprocess import PIPE
 from subprocess import check_call
 
 import llnl.util.tty as tty
-from llnl.util.filesystem import working_dir, join_path, force_remove
+from llnl.util.filesystem import working_dir, force_remove
 from spack.package import PackageBase, run_after, run_before
 from spack.util.executable import Executable
 
@@ -94,15 +75,20 @@ class AutotoolsPackage(PackageBase):
     #: Options to be passed to autoreconf when using the default implementation
     autoreconf_extra_args = []
 
+    @property
+    def archive_files(self):
+        """Files to archive for packages based on autotools"""
+        return [os.path.join(self.build_directory, 'config.log')]
+
     @run_after('autoreconf')
     def _do_patch_config_guess(self):
         """Some packages ship with an older config.guess and need to have
         this updated when installed on a newer architecture. In particular,
         config.guess fails for PPC64LE for version prior to a 2013-06-10
-        build date (automake 1.13.4)."""
+        build date (automake 1.13.4) and for ARM (aarch64)."""
 
-        if not self.patch_config_guess or not self.spec.satisfies(
-                'target=ppc64le'
+        if not self.patch_config_guess or (not self.spec.satisfies(
+                'target=ppc64le') and not self.spec.satisfies('target=aarch64')
         ):
             return
         my_config_guess = None
@@ -172,7 +158,7 @@ class AutotoolsPackage(PackageBase):
     @property
     def configure_abs_path(self):
         # Absolute path to configure
-        configure_abs_path = join_path(
+        configure_abs_path = os.path.join(
             os.path.abspath(self.configure_directory), 'configure'
         )
         return configure_abs_path
@@ -212,10 +198,10 @@ class AutotoolsPackage(PackageBase):
             # This line is what is needed most of the time
             # --install, --verbose, --force
             autoreconf_args = ['-ivf']
-            if 'pkg-config' in spec:
+            if 'pkgconfig' in spec:
                 autoreconf_args += [
                     '-I',
-                    join_path(spec['pkg-config'].prefix, 'share', 'aclocal'),
+                    os.path.join(spec['pkgconfig'].prefix, 'share', 'aclocal'),
                 ]
             autoreconf_args += self.autoreconf_extra_args
             m.autoreconf(*autoreconf_args)
diff --git a/lib/spack/spack/build_systems/cmake.py b/lib/spack/spack/build_systems/cmake.py
index 13c752eb2e..6f46643f83 100644
--- a/lib/spack/spack/build_systems/cmake.py
+++ b/lib/spack/spack/build_systems/cmake.py
@@ -1,34 +1,15 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 import inspect
 import os
 import platform
 
 import spack.build_environment
-from llnl.util.filesystem import working_dir, join_path
+from llnl.util.filesystem import working_dir
 from spack.util.environment import filter_system_paths
 from spack.directives import depends_on, variant
 from spack.package import PackageBase, InstallError, run_after
@@ -91,6 +72,11 @@ class CMakePackage(PackageBase):
     depends_on('cmake', type='build')
 
     @property
+    def archive_files(self):
+        """Files to archive for packages based on CMake"""
+        return [os.path.join(self.build_directory, 'CMakeCache.txt')]
+
+    @property
     def root_cmakelists_dir(self):
         """The relative path to the directory containing CMakeLists.txt
 
@@ -142,11 +128,14 @@ class CMakePackage(PackageBase):
         ]
 
         if platform.mac_ver()[0]:
-            args.append('-DCMAKE_FIND_FRAMEWORK:STRING=LAST')
+            args.extend([
+                '-DCMAKE_FIND_FRAMEWORK:STRING=LAST',
+                '-DCMAKE_FIND_APPBUNDLE:STRING=LAST'
+            ])
 
         # Set up CMake rpath
         args.append('-DCMAKE_INSTALL_RPATH_USE_LINK_PATH:BOOL=FALSE')
-        rpaths = ':'.join(spack.build_environment.get_rpaths(pkg))
+        rpaths = ';'.join(spack.build_environment.get_rpaths(pkg))
         args.append('-DCMAKE_INSTALL_RPATH:STRING={0}'.format(rpaths))
         # CMake's find_package() looks in CMAKE_PREFIX_PATH first, help CMake
         # to find immediate link dependencies in right places:
@@ -200,7 +189,7 @@ class CMakePackage(PackageBase):
 
         :return: directory where to build the package
         """
-        return join_path(self.stage.source_path, 'spack-build')
+        return os.path.join(self.stage.source_path, 'spack-build')
 
     def cmake_args(self):
         """Produces a list containing all the arguments that must be passed to
@@ -247,9 +236,13 @@ class CMakePackage(PackageBase):
         """
         with working_dir(self.build_directory):
             if self.generator == 'Unix Makefiles':
-                self._if_make_target_execute('test')
+                self._if_make_target_execute('test',
+                                             jobs_env='CTEST_PARALLEL_LEVEL')
+                self._if_make_target_execute('check')
             elif self.generator == 'Ninja':
-                self._if_ninja_target_execute('test')
+                self._if_ninja_target_execute('test',
+                                              jobs_env='CTEST_PARALLEL_LEVEL')
+                self._if_ninja_target_execute('check')
 
     # Check that self.prefix is there after installation
     run_after('install')(PackageBase.sanity_check_prefix)
diff --git a/lib/spack/spack/build_systems/cuda.py b/lib/spack/spack/build_systems/cuda.py
new file mode 100644
index 0000000000..2e395fe9dd
--- /dev/null
+++ b/lib/spack/spack/build_systems/cuda.py
@@ -0,0 +1,72 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import PackageBase
+from spack.directives import depends_on, variant, conflicts
+import platform
+
+
+class CudaPackage(PackageBase):
+    """Auxiliary class which contains CUDA variant, dependencies and conflicts
+    and is meant to unify and facilitate its usage.
+    """
+
+    # FIXME: keep cuda and cuda_arch separate to make usage easier untill
+    # Spack has depends_on(cuda, when='cuda_arch!=None') or alike
+    variant('cuda', default=False,
+            description='Build with CUDA')
+    # see http://docs.nvidia.com/cuda/cuda-compiler-driver-nvcc/index.html#gpu-feature-list
+    # https://developer.nvidia.com/cuda-gpus
+    variant('cuda_arch', default=None,
+            description='CUDA architecture',
+            values=('20', '30', '32', '35', '50', '52', '53', '60', '61',
+                    '62', '70'),
+            multi=True)
+
+    # see http://docs.nvidia.com/cuda/cuda-compiler-driver-nvcc/index.html#nvcc-examples
+    # and http://llvm.org/docs/CompileCudaWithLLVM.html#compiling-cuda-code
+    @staticmethod
+    def cuda_flags(arch_list):
+        return [('--generate-code arch=compute_{0},code=sm_{0} '
+                 '--generate-code arch=compute_{0},code=compute_{0}').format(s)
+                for s in arch_list]
+
+    depends_on("cuda@7:", when='+cuda')
+
+    # CUDA version vs Architecture
+    depends_on("cuda@8:", when='cuda_arch=60')
+    depends_on("cuda@8:", when='cuda_arch=61')
+    depends_on("cuda@8:", when='cuda_arch=62')
+    depends_on("cuda@9:", when='cuda_arch=70')
+
+    depends_on('cuda@:8', when='cuda_arch=20')
+
+    # Compiler conflicts:
+    # https://gist.github.com/ax3l/9489132
+    conflicts('%gcc@5:', when='+cuda ^cuda@:7.5')
+    conflicts('%gcc@6:', when='+cuda ^cuda@:8')
+    conflicts('%gcc@7:', when='+cuda ^cuda@:9.1')
+    conflicts('%gcc@8:', when='+cuda ^cuda@:9.99')
+    if (platform.system() != "Darwin"):
+        conflicts('%clang@:3.4,3.7:', when='+cuda ^cuda@7.5')
+        conflicts('%clang@:3.7,4:', when='+cuda ^cuda@8:9.0')
+        conflicts('%clang@:3.7,5:', when='+cuda ^cuda@9.1')
+        conflicts('%clang@:3.7,6:', when='+cuda ^cuda@9.2')
+    conflicts('%intel@:14,16:', when='+cuda ^cuda@7.5')
+    conflicts('%intel@:14,17:', when='+cuda ^cuda@8.0.44')
+    conflicts('%intel@:14,18:', when='+cuda ^cuda@8.0.61:9')
+
+    # Make sure cuda_arch can not be used without +cuda
+    conflicts('~cuda', when='cuda_arch=20')
+    conflicts('~cuda', when='cuda_arch=30')
+    conflicts('~cuda', when='cuda_arch=32')
+    conflicts('~cuda', when='cuda_arch=35')
+    conflicts('~cuda', when='cuda_arch=50')
+    conflicts('~cuda', when='cuda_arch=52')
+    conflicts('~cuda', when='cuda_arch=53')
+    conflicts('~cuda', when='cuda_arch=60')
+    conflicts('~cuda', when='cuda_arch=61')
+    conflicts('~cuda', when='cuda_arch=62')
+    conflicts('~cuda', when='cuda_arch=70')
diff --git a/lib/spack/spack/build_systems/intel.py b/lib/spack/spack/build_systems/intel.py
index d9ad0da2fa..fcab73e0a1 100644
--- a/lib/spack/spack/build_systems/intel.py
+++ b/lib/spack/spack/build_systems/intel.py
@@ -1,45 +1,83 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 import os
+import sys
+import glob
+import tempfile
+import re
+import inspect
 import xml.etree.ElementTree as ET
+import llnl.util.tty as tty
+
+from llnl.util.filesystem import \
+    install, ancestor, filter_file, \
+    HeaderList, find_headers, \
+    LibraryList, find_libraries, find_system_libraries
 
-from llnl.util.filesystem import install, join_path
-from spack.package import PackageBase, run_after
+from spack.version import Version, ver
+from spack.package import PackageBase, run_after, InstallError
+from spack.util.environment import EnvironmentModifications
 from spack.util.executable import Executable
+from spack.util.prefix import Prefix
+from spack.build_environment import dso_suffix
+
+
+# A couple of utility functions that might be useful in general. If so, they
+# should really be defined elsewhere, unless deemed heretical.
+# (Or na"ive on my part).
+
+def debug_print(msg, *args):
+    '''Prints a message (usu. a variable) and the callers' names for a couple
+    of stack frames.
+    '''
+    # https://docs.python.org/2/library/inspect.html#the-interpreter-stack
+    stack = inspect.stack()
+    _func_name = 3
+    tty.debug("%s.%s:\t%s" % (stack[2][_func_name], stack[1][_func_name], msg),
+              *args)
+
+
+def raise_lib_error(*args):
+    '''Bails out with an error message. Shows args after the first as one per
+    line, tab-indented, useful for long paths to line up and stand out.
+    '''
+    raise InstallError("\n\t".join(str(i) for i in args))
+
+
+def _expand_fields(s):
+    '''[Experimental] Expand arch-related fields in a string, typically a
+    filename.
 
+    Supported fields and their typical expansions are::
 
-def _valid_components():
-    """A generator that yields valid components."""
+        {platform}  linux, mac
+        {arch}      intel64 (including on Mac)
+        {libarch}   intel64, empty on Mac
+        {bits}      64
 
-    tree = ET.parse('pset/mediaconfig.xml')
-    root = tree.getroot()
+    '''
+    # Python-native string formatting requires arg list counts to match the
+    # replacement field count; optional fields are far easier with regexes.
 
-    components = root.findall('.//Abbr')
-    for component in components:
-        yield component.text
+    _bits = '64'
+    _arch = 'intel64'   # TBD: ia32
+
+    if 'linux' in sys.platform:         # NB: linux2 vs. linux
+        s = re.sub('{platform}', 'linux', s)
+        s = re.sub('{libarch}', _arch, s)
+    elif 'darwin' in sys.platform:
+        s = re.sub('{platform}', 'mac', s)
+        s = re.sub('{libarch}', '', s)  # no arch dirs are used (as of 2018)
+    # elif 'win' in sys.platform:            # TBD
+    #     s = re.sub('{platform}', 'windows', s)
+
+    s = re.sub('{arch}', _arch, s)
+    s = re.sub('{bits}', _bits, s)
+    return s
 
 
 class IntelPackage(PackageBase):
@@ -51,7 +89,7 @@ class IntelPackage(PackageBase):
     2. :py:meth:`~.IntelPackage.install`
 
     They both have sensible defaults and for many packages the
-    only thing necessary will be to override ``setup_environment``
+    only thing necessary will be to override setup_environment
     to set the appropriate environment variables.
     """
     #: Phases of an Intel package
@@ -61,15 +99,31 @@ class IntelPackage(PackageBase):
     #: system base class
     build_system_class = 'IntelPackage'
 
-    #: By default, we assume that all Intel software requires a license.
-    #: This can be overridden for packages that do not require a license.
-    license_required = True
+    #: A dict that maps Spack version specs to release years, needed to infer
+    #: the installation directory layout for pre-2016 versions in the family of
+    #: Intel packages.
+    #
+    # Like any property, it can be overridden in client packages, should older
+    # versions ever be added there.  The initial dict here contains the
+    # packages defined in Spack as of 2018-04.  Keys could conceivably overlap
+    # but preferably should not - only the first key in hash traversal order
+    # that satisfies self.spec will be used.
+    version_years = {
+        # intel-daal is versioned 2016 and later, no divining is needed
+        'intel-ipp@9.0:9.99':         2016,
+        'intel-mkl@11.3.0:11.3.999':  2016,
+        'intel-mpi@5.1:5.99':         2016,
+    }
 
-    #: Comment symbol used in the ``license.lic`` file
-    license_comment = '#'
+    @property
+    def license_required(self):
+        # The Intel libraries are provided without requiring a license as of
+        # version 2017.2. Trying to specify one anyway will fail. See:
+        # https://software.intel.com/en-us/articles/free-ipsxe-tools-and-libraries
+        return self._has_compilers or self.version < ver('2017.2')
 
-    #: Location where Intel searches for a license file
-    license_files = ['Licenses/license.lic']
+    #: Comment symbol used in the license.lic file
+    license_comment = '#'
 
     #: Environment variables that Intel searches for a license file
     license_vars = ['INTEL_LICENSE_FILE']
@@ -77,116 +131,1115 @@ class IntelPackage(PackageBase):
     #: URL providing information on how to acquire a license key
     license_url = 'https://software.intel.com/en-us/articles/intel-license-manager-faq'
 
-    #: Components of the package to install.
-    #: By default, install 'ALL' components.
-    components = ['ALL']
+    #: Location where Intel searches for a license file
+    @property
+    def license_files(self):
+        dirs = ['Licenses']
+
+        if self._has_compilers:
+            dirs.append(self.component_bin_dir('compiler'))
+
+            for variant, component_suite_dir in {
+                '+advisor':    'advisor',
+                '+inspector':  'inspector',
+                '+itac':       'itac',
+                '+vtune':      'vtune_amplifier',
+            }.items():
+                if variant in self.spec:
+                    dirs.append(self.normalize_path(
+                        'licenses', component_suite_dir, relative=True))
 
+        files = [os.path.join(d, 'license.lic') for d in dirs]
+        return files
+
+    #: Components to install (list of name patterns from pset/mediaconfig.xml)
+    # NB: Renamed from plain components() for coding and maintainability.
     @property
-    def _filtered_components(self):
-        """Returns a list or set of valid components that match
-        the requested components from ``components``."""
+    def pset_components(self):
+        # Do not detail single-purpose client packages.
+        if not self._has_compilers:
+            return ['ALL']
+
+        # tty.warn('DEBUG: installing ALL components')
+        # return ['ALL']
 
-        # Don't filter 'ALL'
-        if self.components == ['ALL']:
-            return self.components
+        # Always include compilers and closely related components.
+        # Pre-2016 compiler components have different names - throw in all.
+        # Later releases have overlapping minor parts that differ by "edition".
+        # NB: The spack package 'intel' is a subset of
+        # 'intel-parallel-studio@composer' without the lib variants.
+        c = ' intel-icc          intel-ifort' \
+            ' intel-ccomp        intel-fcomp        intel-comp-' \
+            ' intel-compilerproc intel-compilerprof intel-compilerpro-' \
+            ' intel-psxe intel-openmp'
+
+        additions_for = {
+            'cluster':      ' intel-icsxe',
+            'professional': ' intel-ips-',
+            'composer':     ' intel-compxe',
+        }
+        if self._edition in additions_for:
+            c += additions_for[self._edition]
+
+        for variant, components_to_add in {
+            '+daal':      ' intel-daal',   # Data Analytics Acceleration Lib
+            '+gdb':       ' intel-gdb',    # Integrated Performance Primitives
+            '+ipp':       ' intel-ipp intel-crypto-ipp',
+            '+mkl':       ' intel-mkl',    # Math Kernel Library
+            '+mpi':       ' intel-mpi intel-imb',  # MPI runtime, SDK, benchm.
+            '+tbb':       ' intel-tbb',    # Threading Building Blocks
+            '+advisor':   ' intel-advisor',
+            '+clck':      ' intel_clck',   # Cluster Checker
+            '+inspector': ' intel-inspector',
+            '+itac':      ' intel-itac intel-ta intel-tc'
+                          ' intel-trace-analyzer intel-trace-collector',
+                          # Trace Analyzer and Collector
+            '+vtune':     ' intel-vtune-amplifier',    # VTune
+        }.items():
+            if variant in self.spec:
+                c += components_to_add
+
+        debug_print(c)
+        return c.split()
+
+    # ---------------------------------------------------------------------
+    # Utilities
+    # ---------------------------------------------------------------------
+    @property
+    def _filtered_components(self):
+        '''Expands the list of desired component patterns to the exact names
+        present in the given download.
+        '''
+        c = self.pset_components
+        if 'ALL' in c or 'DEFAULTS' in c:    # No filter needed
+            return c
 
         # mediaconfig.xml is known to contain duplicate components.
         # If more than one copy of the same component is used, you
         # will get an error message about invalid components.
-        # Use a set to store components to prevent duplicates.
-        matches = set()
+        # Use sets to prevent duplicates and for efficient traversal.
+        requested = set(c)
+        confirmed = set()
+
+        # NB: To get a reasonable overview in pretty much the documented way:
+        #
+        #   grep -E '<Product|<Abbr|<Name>..[a-z]'  pset/mediaconfig.xml
+        #
+        # https://software.intel.com/en-us/articles/configuration-file-format
+        #
+        xmltree = ET.parse('pset/mediaconfig.xml')
+        for entry in xmltree.getroot().findall('.//Abbr'):  # XPath expression
+            name_present = entry.text
+            for name_requested in requested:
+                if name_present.startswith(name_requested):
+                    confirmed.add(name_present)
+
+        return list(confirmed)
+
+    @property
+    def intel64_int_suffix(self):
+        '''Provide the suffix for Intel library names to match a client
+        application's desired int size, conveyed by the active spec variant.
+        The possible suffixes and their meanings are:
+
+          ``ilp64``  all of int, long, and pointer are 64 bit,
+          `` lp64``  only long and pointer are 64 bit; int will be 32bit.
+        '''
+        if '+ilp64' in self.spec:
+            return 'ilp64'
+        else:
+            return 'lp64'
+
+    @property
+    def _has_compilers(self):
+        return self.name in ['intel', 'intel-parallel-studio']
+
+    @property
+    def _edition(self):
+        if self.name == 'intel-parallel-studio':
+            return self.version[0]      # clearer than .up_to(1), I think.
+        elif self.name == 'intel':
+            return 'composer'
+        else:
+            return ''
+
+    @property
+    def version_yearlike(self):
+        '''Return the version in a unified style, suitable for Version class
+        conditionals.
+        '''
+        # Input data for this routine:  self.version
+        # Returns:                      YYYY.Nupdate[.Buildseq]
+        #
+        # Specifics by package:
+        #
+        #   Package                     Format of self.version
+        #   ------------------------------------------------------------
+        #   'intel-parallel-studio'     <edition>.YYYY.Nupdate
+        #   'intel'                     YY.0.Nupdate (some assigned ad-hoc)
+        #   Recent lib packages         YYYY.Nupdate.Buildseq
+        #   Early lib packages          Major.Minor.Patch.Buildseq
+        #   ------------------------------------------------------------
+        #
+        #   Package                     Output
+        #   ------------------------------------------------------------
+        #   'intel-parallel-studio'     YYYY.Nupdate
+        #   'intel'                     YYYY.Nupdate
+        #   Recent lib packages         YYYY.Nupdate.Buildseq
+        #   Known early lib packages    YYYY.Minor.Patch.Buildseq (*)
+        #   Unknown early lib packages  (2000 + Major).Minor.Patch.Buildseq
+        #   ----------------------------------------------------------------
+        #
+        #   (*) YYYY is taken from @property "version_years" (a dict of specs)
+        #
+        try:
+            if self.name == 'intel':
+                # Has a "Minor" version element, but it is always set as 0. To
+                # be useful for comparisons, drop it and get YYYY.Nupdate.
+                v_tail = self.version[2:]   # coerced just fine via __getitem__
+            else:
+                v_tail = self.version[1:]
+        except IndexError:
+            # Hmm - this happens on "spack install intel-mkl@11".
+            # I thought concretization picks an actual version??
+            return self.version     # give up
+
+        if self.name == 'intel-parallel-studio':
+            return v_tail
+
+        v_year = self.version[0]
+        if v_year < 2000:
+            # Shoehorn Major into release year until we know better.
+            v_year += 2000
+            for spec, year in self.version_years.items():
+                if self.spec.satisfies(spec):
+                    v_year = year
+                    break
+
+        return ver('%s.%s' % (v_year, v_tail))
+
+    # ---------------------------------------------------------------------
+    # Directory handling common to all Intel components
+    # ---------------------------------------------------------------------
+    # For reference: classes using IntelPackage, as of Spack-0.11:
+    #
+    #  intel/               intel-ipp/          intel-mpi/
+    #  intel-daal/          intel-mkl/          intel-parallel-studio/
+    #
+    # Not using class IntelPackage:
+    #  intel-gpu-tools/        intel-mkl-dnn/          intel-tbb/
+    #
+    def normalize_suite_dir(self, suite_dir_name, version_globs=['*.*.*']):
+        '''Returns the version-specific and absolute path to the directory of
+        an Intel product or a suite of product components.
+
+        Parameters:
+
+            suite_dir_name (str):
+                Name of the product directory, without numeric version.
+
+                - Examples::
+
+                    composer_xe, parallel_studio_xe, compilers_and_libraries
+
+                The following will work as well, even though they are not
+                directly targets for Spack installation::
+
+                    advisor_xe, inspector_xe, vtune_amplifier_xe,
+                    performance_snapshots (new name for vtune as of 2018)
+
+                These are single-component products without subordinate
+                components and are normally made available to users by a
+                toplevel psxevars.sh or equivalent file to source (and thus by
+                the modulefiles that Spack produces).
+
+            version_globs (list of str): Suffix glob patterns (most specific
+                first) expected to qualify suite_dir_name to its fully
+                version-specific install directory (as opposed to a
+                compatibility directory or symlink).
+        '''
+        # See ./README-intel.rst for background and analysis of dir layouts.
+
+        d = self.prefix
+
+        # Distinguish between product installations that were done external to
+        # Spack (integrated via packages.yaml) and Spack-internal ones. The
+        # resulting prefixes may differ in directory depth and specificity.
+        unversioned_dirname = ''
+        if suite_dir_name and suite_dir_name in d:
+            # If e.g. MKL was installed outside of Spack, it is likely just one
+            # product or product component among possibly many other Intel
+            # products and their releases that were installed in sibling or
+            # cousin directories.  In such cases, the prefix given to Spack
+            # will inevitably be a highly product-specific and preferably fully
+            # version-specific directory.  This is what we want and need, and
+            # nothing more specific than that, i.e., if needed, convert, e.g.:
+            #   .../compilers_and_libraries*/* -> .../compilers_and_libraries*
+            d = re.sub('(%s%s.*?)%s.*' %
+                       (os.sep, re.escape(suite_dir_name), os.sep), r'\1', d)
+
+            # The Intel installer scripts try hard to place compatibility links
+            # named like this in the install dir to convey upgrade benefits to
+            # traditional client apps. But such a generic name can be trouble
+            # when given to Spack: the link target is bound to change outside
+            # of Spack's purview and when it does, the outcome of subsequent
+            # builds of dependent packages may be affected. (Though Intel has
+            # been remarkably good at backward compatibility.)
+            # I'm not sure if Spack's package hashing includes link targets.
+            if d.endswith(suite_dir_name):
+                # NB: This could get tiresome without a seen++ test.
+                # tty.warn('Intel product found in a version-neutral directory'
+                #          ' - future builds may not be reproducible.')
+                #
+                # Simply doing realpath() would not be enough, because:
+                #   compilers_and_libraries -> compilers_and_libraries_2018
+                # which is mostly a staging directory for symlinks (see next).
+                unversioned_dirname = d
+        else:
+            # By contrast, a Spack-internal MKL installation will inherit its
+            # prefix from install.sh of Intel's package distribution, where it
+            # means the high-level installation directory that is specific to
+            # the *vendor* (think of the default "/opt/intel"). We must now
+            # step down into the *product* directory to get the usual
+            # hierarchy. But let's not do that in haste ...
+            #
+            # For a Spack-born install, the fully-qualified release directory
+            # desired above may seem less important since product upgrades
+            # won't land in the same parent. However, only the fully qualified
+            # directory contains the regular files for the compiler commands:
+            #
+            # $ ls -lF <HASH>/compilers_and_libraries*/linux/bin/intel64/icc
+            #
+            # <HASH>/compilers_and_libraries_2018.1.163/linux/bin/intel64/icc*
+            #   A regular file in the actual release directory. Bingo!
+            #
+            # <HASH>/compilers_and_libraries_2018/linux/bin/intel64/icc -> ...
+            #   A symlink - no good. Note that "compilers_and_libraries_2018/"
+            #   is itself a directory (not symlink) but it merely holds a
+            #   compatibility dir hierarchy with lots of symlinks into the
+            #   release dir.
+            #
+            # <HASH>/compilers_and_libraries/linux/bin/intel64/icc -> ...
+            #   Ditto.
+            #
+            #  Now, the Spack packages for MKL and MPI packges use version
+            #  triplets, but the one for intel-parallel-studio does not.
+            #  So, we can't have it quite as easy as:
+            # d = Prefix(d.append('compilers_and_libraries_' + self.version))
+            #  Alright, let's see what we can find instead:
+            unversioned_dirname = os.path.join(d, suite_dir_name)
+
+        if unversioned_dirname:
+            for g in version_globs:
+                try_glob = unversioned_dirname + g
+                debug_print('trying %s' % try_glob)
+
+                matching_dirs = sorted(glob.glob(try_glob))
+                # NB: Python glob() returns results in arbitrary order - ugh!
+                # NB2: sorted() is a shortcut that is NOT number-aware.
+
+                if matching_dirs:
+                    debug_print('found %d:' % len(matching_dirs),
+                                matching_dirs)
+                    # Take the highest and thus presumably newest match, which
+                    # better be the sole one anyway.
+                    d = matching_dirs[-1]
+                    break
+
+            if not matching_dirs:
+                # No match -- this *will* happen during pre-build call to
+                # setup_environment() when the destination dir is still empty.
+                # Return a sensible value anyway.
+                d = unversioned_dirname
+
+        debug_print(d)
+        return Prefix(d)
+
+    def normalize_path(self, component_path, component_suite_dir=None,
+                       relative=False):
+        '''Returns the absolute or relative path to a component or file under a
+        component suite directory.
+
+        Intel's product names, scope, and directory layout changed over the
+        years.  This function provides a unified interface to their directory
+        names.
+
+        Parameters:
+
+            component_path (str): a component name like 'mkl', or 'mpi', or a
+                deeper relative path.
+
+            component_suite_dir (str): _Unversioned_ name of the expected
+                parent directory of component_path.  When absent or `None`, an
+                appropriate default will be used.  A present but empty string
+                `""` requests that `component_path` refer to `self.prefix`
+                directly.
+
+                Typical values: `compilers_and_libraries`, `composer_xe`,
+                `parallel_studio_xe`.
+
+                Also supported: `advisor`, `inspector`, `vtune`. The actual
+                directory name for these suites varies by release year. The
+                name will be corrected as needed for use in the return value.
+
+            relative (bool): When True, return path relative to self.prefix,
+                otherwise, return an absolute path (the default).
+        '''
+        # Design note: Choosing the default for `component_suite_dir` was a bit
+        # tricky since there better be a sensible means to specify direct
+        # parentage under self.prefix (even though you normally shouldn't need
+        # a function for that).  I chose "" to allow that case be represented,
+        # and 'None' or the absence of the kwarg to represent the most relevant
+        # case for the time of writing.
+        #
+        # In the 2015 releases (the earliest in Spack as of 2018), there were
+        # nominally two separate products that provided the compilers:
+        # "Composer" as lower tier, and "Parallel Studio" as upper tier. In
+        # Spack, we justifiably retcon both as "intel-parallel-studio@composer"
+        # and "...@cluster", respectively.  Both of these use the older
+        # "composer_xe" dir layout, as do their virtual package personas.
+        #
+        # All other "intel-foo" packages in Spack as of 2018-04 use the
+        # "compilers_and_libraries" layout, including the 2016 releases that
+        # are not natively versioned by year.
+
+        cs = component_suite_dir
+        if cs is None and component_path.startswith('ism'):
+            cs = 'parallel_studio_xe'
+
+        v = self.version_yearlike
+
+        # Glob variants to complete component_suite_dir.
+        # Helper var for older MPI versions - those are reparented, with each
+        # version in their own version-named dir.
+        standalone_glob = '[1-9]*.*.*'
+
+        # Most other components; try most specific glob first.
+        # flake8 is far too opinionated about lists - ugh.
+        normalize_kwargs = {
+            'version_globs': [
+                '_%s' % self.version,
+                '_%s.*' % v.up_to(2),   # should be: YYYY.Nupdate
+                '_*.*.*',               # last resort
+            ]
+        }
+        for rename_rule in [
+            # cs given as arg, in years, dir actually used, [version_globs]
+            [None,              ':2015', 'composer_xe'],
+            [None,              '2016:', 'compilers_and_libraries'],
+            ['advisor',         ':2016', 'advisor_xe'],
+            ['inspector',       ':2016', 'inspector_xe'],
+            ['vtune_amplifier', ':2017', 'vtune_amplifier_xe'],
+            ['vtune',           ':2017', 'vtune_amplifier_xe'],  # alt.
+            ['itac',            ':',     'itac',  [os.sep + standalone_glob]],
+        ]:
+            if cs == rename_rule[0] and v.satisfies(ver(rename_rule[1])):
+                cs = rename_rule[2]
+                if len(rename_rule) > 3:
+                    normalize_kwargs = {'version_globs': rename_rule[3]}
+                break
+
+        d = self.normalize_suite_dir(cs, **normalize_kwargs)
+
+        # Help find components not located directly under d.
+        # NB: ancestor() not well suited if version_globs may contain os.sep .
+        parent_dir = re.sub(os.sep + re.escape(cs) + '.*', '', d)
+
+        reparent_as = {}
+        if cs == 'compilers_and_libraries':     # must qualify further
+            d = os.path.join(d, _expand_fields('{platform}'))
+        elif cs == 'composer_xe':
+            reparent_as = {'mpi': 'impi'}
+            # ignore 'imb' (MPI Benchmarks)
+
+        for nominal_p, actual_p in reparent_as.items():
+            if component_path.startswith(nominal_p):
+                dirs = glob.glob(
+                    os.path.join(parent_dir, actual_p, standalone_glob))
+                debug_print('reparent dirs: %s' % dirs)
+                # Brazenly assume last match is the most recent version;
+                # convert back to relative of parent_dir, and re-assemble.
+                rel_dir = dirs[-1].split(parent_dir + os.sep, 1)[-1]
+                component_path = component_path.replace(nominal_p, rel_dir, 1)
+                d = parent_dir
+
+        d = os.path.join(d, component_path)
+
+        if relative:
+            d = os.path.relpath(os.path.realpath(d), parent_dir)
+
+        debug_print(d)
+        return d
+
+    def component_bin_dir(self, component, **kwargs):
+        d = self.normalize_path(component, **kwargs)
+
+        if component == 'compiler':     # bin dir is always under PARENT
+            d = os.path.join(ancestor(d), 'bin', _expand_fields('{libarch}'))
+            d = d.rstrip(os.sep)        # cosmetics, when {libarch} is empty
+            # NB: Works fine even with relative=True, e.g.:
+            #   composer_xe/compiler -> composer_xe/bin/intel64
+        elif component == 'mpi':
+            d = os.path.join(d, _expand_fields('{libarch}'), 'bin')
+        else:
+            d = os.path.join(d, 'bin')
+        debug_print(d)
+        return d
+
+    def component_lib_dir(self, component, **kwargs):
+        '''Provide directory suitable for find_libraries() and
+        SPACK_COMPILER_EXTRA_RPATHS.
+        '''
+        d = self.normalize_path(component, **kwargs)
+
+        if component == 'mpi':
+            d = os.path.join(d, _expand_fields('{libarch}'), 'lib')
+        else:
+            d = os.path.join(d, 'lib', _expand_fields('{libarch}'))
+            d = d.rstrip(os.sep)        # cosmetics, when {libarch} is empty
+
+        if component == 'tbb':      # must qualify further for abi
+            d = os.path.join(d, self._tbb_abi)
+
+        debug_print(d)
+        return d
+
+    def component_include_dir(self, component, **kwargs):
+        d = self.normalize_path(component, **kwargs)
+
+        if component == 'mpi':
+            d = os.path.join(d, _expand_fields('{libarch}'), 'include')
+        else:
+            d = os.path.join(d, 'include')
+
+        debug_print(d)
+        return d
 
-        for valid in _valid_components():
-            for requested in self.components:
-                if valid.startswith(requested):
-                    matches.add(valid)
+    @property
+    def file_to_source(self):
+        '''Full path of file to source for initializing an Intel package.
+        A client package could override as follows:
+        `    @property`
+        `    def file_to_source(self):`
+        `        return self.normalize_path("apsvars.sh", "vtune_amplifier")`
+        '''
+        vars_file_info_for = {
+            # key (usu. spack package name) -> [rel_path, component_suite_dir]
+            # Extension note: handle additions by Spack name or ad-hoc keys.
+            '@early_compiler':       ['bin/compilervars',           None],
+            'intel-parallel-studio': ['bin/psxevars', 'parallel_studio_xe'],
+            'intel':                 ['bin/compilervars',           None],
+            'intel-daal':            ['daal/bin/daalvars',          None],
+            'intel-ipp':             ['ipp/bin/ippvars',            None],
+            'intel-mkl':             ['mkl/bin/mklvars',            None],
+            'intel-mpi':             ['mpi/{libarch}/bin/mpivars',  None],
+        }
+        key = self.name
+        if self.version_yearlike.satisfies(ver(':2015')):
+            # Same file as 'intel' but 'None' for component_suite_dir will
+            # resolve differently. Listed as a separate entry to serve as
+            # example and to avoid pitfalls upon possible refactoring.
+            key = '@early_compiler'
+
+        f, component_suite_dir = vars_file_info_for[key]
+        f = _expand_fields(f) + '.sh'
+        # TODO?? win32 would have to handle os.sep, '.bat' (unless POSIX??)
+
+        f = self.normalize_path(f, component_suite_dir)
+        return f
+
+    # ---------------------------------------------------------------------
+    # Threading, including (WIP) support for virtual 'tbb'
+    # ---------------------------------------------------------------------
+    @property
+    def openmp_libs(self):
+        '''Supply LibraryList for linking OpenMP'''
+
+        if '%intel' in self.spec:
+            # NB: Hunting down explicit library files may be the Spack way of
+            # doing things, but be aware that "{icc|ifort} --help openmp"
+            # steers us towards options instead: -qopenmp-link={dynamic,static}
+
+            omp_libnames = ['libiomp5']
+            omp_libs = find_libraries(
+                omp_libnames,
+                root=self.component_lib_dir('compiler'),
+                shared=('+shared' in self.spec))
+            # Note about search root here: For MKL, the directory
+            # "$MKLROOT/../compiler" will be present even for an MKL-only
+            # product installation (as opposed to one being ghosted via
+            # packages.yaml), specificially to provide the 'iomp5' libs.
+
+        elif '%gcc' in self.spec:
+            gcc = Executable(self.compiler.cc)
+            omp_lib_path = gcc(
+                '--print-file-name', 'libgomp.%s' % dso_suffix, output=str)
+            omp_libs = LibraryList(omp_lib_path)
+
+        if len(omp_libs) < 1:
+            raise_lib_error('Cannot locate OpenMP libraries:', omp_libnames)
+
+        debug_print(omp_libs)
+        return omp_libs
+
+    @property
+    def tbb_libs(self):
+        '''Supply LibraryList for linking TBB'''
+
+        # TODO: When is 'libtbbmalloc' needed?
+        tbb_lib = find_libraries(
+            ['libtbb'], root=self.component_lib_dir('tbb'))
+        # NB: Like icc with -qopenmp, so does icpc steer us towards using an
+        # option: "icpc -tbb"
+
+        # TODO: clang(?)
+        gcc = Executable('gcc')     # must be gcc, not self.compiler.cc
+        cxx_lib_path = gcc(
+            '--print-file-name', 'libstdc++.%s' % dso_suffix, output=str)
+
+        libs = tbb_lib + LibraryList(cxx_lib_path)
+        debug_print(libs)
+        return libs
+
+    @property
+    def _tbb_abi(self):
+        '''Select the ABI needed for linking TBB'''
+        # Match the available gcc, as it's done in tbbvars.sh.
+        gcc = Executable('gcc')
+        matches = re.search(r'(gcc|LLVM).* ([0-9]+\.[0-9]+\.[0-9]+).*',
+                            gcc('--version', output=str), re.I | re.M)
+        abi = ''
+        if sys.platform == 'darwin':
+            pass
+        elif matches:
+            # TODO: Confirm that this covers clang (needed on Linux only)
+            gcc_version = Version(matches.groups()[1])
+            if gcc_version >= ver('4.7'):
+                abi = 'gcc4.7'
+            elif gcc_version >= ver('4.4'):
+                abi = 'gcc4.4'
+            else:
+                abi = 'gcc4.1'     # unlikely, one hopes.
+
+        # Alrighty then ...
+        debug_print(abi)
+        return abi
+
+    # ---------------------------------------------------------------------
+    # Support for virtual 'blas/lapack/scalapack'
+    # ---------------------------------------------------------------------
+    @property
+    def blas_libs(self):
+        # Main magic here.
+        # For reference, see The Intel Math Kernel Library Link Line Advisor:
+        # https://software.intel.com/en-us/articles/intel-mkl-link-line-advisor/
+
+        mkl_integer = 'libmkl_intel_' + self.intel64_int_suffix
+
+        if self.spec.satisfies('threads=openmp'):
+            if '%intel' in self.spec:
+                mkl_threading = 'libmkl_intel_thread'
+            elif '%gcc' in self.spec:
+                mkl_threading = 'libmkl_gnu_thread'
+            threading_engine_libs = self.openmp_libs()
+        elif self.spec.satisfies('threads=tbb'):
+            mkl_threading = 'libmkl_tbb_thread'
+            threading_engine_libs = self.tbb_libs()
+        elif self.spec.satisfies('threads=none'):
+            mkl_threading = 'libmkl_sequential'
+            threading_engine_libs = LibraryList([])
+        else:
+            raise_lib_error('Cannot determine MKL threading libraries.')
+
+        mkl_libnames = [mkl_integer, mkl_threading, 'libmkl_core']
+        mkl_libs = find_libraries(
+            mkl_libnames,
+            root=self.component_lib_dir('mkl'),
+            shared=('+shared' in self.spec))
+        debug_print(mkl_libs)
+
+        if len(mkl_libs) < 3:
+            raise_lib_error('Cannot locate core MKL libraries:', mkl_libnames)
+
+        # The Intel MKL link line advisor recommends these system libraries
+        system_libs = find_system_libraries(
+            'libpthread libm libdl'.split(),
+            shared=('+shared' in self.spec))
+        debug_print(system_libs)
 
-        return matches
+        return mkl_libs + threading_engine_libs + system_libs
 
     @property
+    def lapack_libs(self):
+        return self.blas_libs
+
+    @property
+    def scalapack_libs(self):
+        # Intel MKL does not directly depend on MPI but the BLACS library
+        # which underlies ScaLapack does. It comes in several personalities;
+        # we must supply a personality matching the MPI implementation that
+        # is active for the root package that asked for ScaLapack.
+        spec_root = self.spec.root
+        if sys.platform == 'darwin' and '^mpich' in spec_root:
+            # The only supported choice for MKL 2018 on Mac.
+            blacs_lib = 'libmkl_blacs_mpich'
+        elif '^openmpi' in spec_root:
+            blacs_lib = 'libmkl_blacs_openmpi'
+        elif '^mpich@1' in spec_root:
+            # Was supported only up to 2015.
+            blacs_lib = 'libmkl_blacs'
+        elif ('^mpich@2:' in spec_root or
+              '^mvapich2' in spec_root or
+              '^intel-mpi' in spec_root):
+            blacs_lib = 'libmkl_blacs_intelmpi'
+        elif '^mpt' in spec_root:
+            blacs_lib = 'libmkl_blacs_sgimpt'
+        else:
+            raise_lib_error('Cannot find a BLACS library for the given MPI.')
+
+        int_suff = '_' + self.intel64_int_suffix
+        scalapack_libnames = [
+            'libmkl_scalapack' + int_suff,
+            blacs_lib + int_suff,
+        ]
+        sca_libs = find_libraries(
+            scalapack_libnames,
+            root=self.component_lib_dir('mkl'),
+            shared=('+shared' in self.spec))
+        debug_print(sca_libs)
+
+        if len(sca_libs) < 2:
+            raise_lib_error(
+                'Cannot locate ScaLapack/BLACS libraries:', scalapack_libnames)
+        # NB: ScaLapack is installed as "cluster" components within MKL or
+        # MKL-encompassing products.  But those were *optional* for the ca.
+        # 2015/2016 product releases, which was easy to overlook, and I have
+        # been bitten by that.  Thus, complain early because it'd be a sore
+        # disappointment to have missing ScaLapack libs show up as a link error
+        # near the end phase of a client package's build phase.
+
+        return sca_libs
+
+    # ---------------------------------------------------------------------
+    # Support for virtual 'mpi'
+    # ---------------------------------------------------------------------
+    @property
+    def mpi_compiler_wrappers(self):
+        '''Return paths to compiler wrappers as a dict of env-like names
+        '''
+        # Intel comes with 2 different flavors of MPI wrappers:
+        #
+        # * mpiicc, mpiicpc, and mpiifort are hardcoded to wrap around
+        #   the Intel compilers.
+        # * mpicc, mpicxx, mpif90, and mpif77 allow you to set which
+        #   compilers to wrap using I_MPI_CC and friends. By default,
+        #   wraps around the GCC compilers.
+        #
+        # In theory, these should be equivalent as long as I_MPI_CC
+        # and friends are set to point to the Intel compilers, but in
+        # practice, mpicc fails to compile some applications while
+        # mpiicc works.
+        bindir = self.component_bin_dir('mpi')
+        if self.compiler.name == 'intel':
+            wrapper_vars = {
+                # eschew Prefix objects -- emphasize the command strings.
+                'MPICC':  os.path.join(bindir, 'mpiicc'),
+                'MPICXX': os.path.join(bindir, 'mpiicpc'),
+                'MPIF77': os.path.join(bindir, 'mpiifort'),
+                'MPIF90': os.path.join(bindir, 'mpiifort'),
+                'MPIFC':  os.path.join(bindir, 'mpiifort'),
+            }
+        else:
+            wrapper_vars = {
+                'MPICC':  os.path.join(bindir, 'mpicc'),
+                'MPICXX': os.path.join(bindir, 'mpicxx'),
+                'MPIF77': os.path.join(bindir, 'mpif77'),
+                'MPIF90': os.path.join(bindir, 'mpif90'),
+                'MPIFC':  os.path.join(bindir, 'mpif90'),
+            }
+        # debug_print("wrapper_vars =", wrapper_vars)
+        return wrapper_vars
+
+    def mpi_setup_dependent_environment(
+            self, spack_env, run_env, dependent_spec, compilers_of_client={}):
+        '''Unified back-end for setup_dependent_environment() of Intel packages
+        that provide 'mpi'.
+
+        Parameters:
+
+            spack_env, run_env, dependent_spec: same as in
+                setup_dependent_environment().
+
+            compilers_of_client (dict): Conveys spack_cc, spack_cxx, etc.,
+                from the scope of dependent packages; constructed in caller.
+        '''
+        # See also: setup_dependent_package()
+        wrapper_vars = {
+            'I_MPI_CC':   compilers_of_client['CC'],
+            'I_MPI_CXX':  compilers_of_client['CXX'],
+            'I_MPI_F77':  compilers_of_client['F77'],
+            'I_MPI_F90':  compilers_of_client['F90'],
+            'I_MPI_FC':   compilers_of_client['FC'],
+            # NB: Normally set by the modulefile, but that is not active here:
+            'I_MPI_ROOT': self.normalize_path('mpi'),
+        }
+
+        # CAUTION - SIMILAR code in:
+        #   var/spack/repos/builtin/packages/mpich/package.py
+        #   var/spack/repos/builtin/packages/openmpi/package.py
+        #   var/spack/repos/builtin/packages/mvapich2/package.py
+        #
+        # On Cray, the regular compiler wrappers *are* the MPI wrappers.
+        if 'platform=cray' in self.spec:
+            # TODO: Confirm
+            wrapper_vars.update({
+                'MPICC':  compilers_of_client['CC'],
+                'MPICXX': compilers_of_client['CXX'],
+                'MPIF77': compilers_of_client['F77'],
+                'MPIF90': compilers_of_client['F90'],
+            })
+        else:
+            compiler_wrapper_commands = self.mpi_compiler_wrappers
+            wrapper_vars.update({
+                'MPICC':  compiler_wrapper_commands['MPICC'],
+                'MPICXX': compiler_wrapper_commands['MPICXX'],
+                'MPIF77': compiler_wrapper_commands['MPIF77'],
+                'MPIF90': compiler_wrapper_commands['MPIF90'],
+            })
+
+        for key, value in wrapper_vars.items():
+            spack_env.set(key, value)
+
+        debug_print("adding to spack_env:", wrapper_vars)
+
+    # ---------------------------------------------------------------------
+    # General support for child packages
+    # ---------------------------------------------------------------------
+    @property
+    def headers(self):
+        result = HeaderList([])
+        if '+mpi' in self.spec or self.provides('mpi'):
+            result += find_headers(
+                ['mpi'],
+                root=self.component_include_dir('mpi'),
+                recursive=False)
+        if '+mkl' in self.spec or self.provides('mkl'):
+            result += find_headers(
+                ['mkl_cblas', 'mkl_lapacke'],
+                root=self.component_include_dir('mkl'),
+                recursive=False)
+        debug_print(result)
+        return result
+
+    @property
+    def libs(self):
+        result = LibraryList([])
+        if '+mpi' in self.spec or self.provides('mpi'):
+            # If prefix is too general, recursive searches may get files from
+            # supported but inappropriate sub-architectures like 'mic'.
+            libnames = ['libmpifort', 'libmpi']
+            if 'cxx' in self.spec.last_query.extra_parameters:
+                libnames = ['libmpicxx'] + libnames
+            result += find_libraries(
+                libnames,
+                root=self.component_lib_dir('mpi'),
+                shared=True, recursive=True)
+
+        # NB: MKL uses domain-specifics: blas_libs/lapack_libs/scalapack_libs
+
+        debug_print(result)
+        return result
+
+    def setup_environment(self, spack_env, run_env):
+        """Adds environment variables to the generated module file.
+
+        These environment variables come from running:
+
+        .. code-block:: console
+
+           $ source parallel_studio_xe_2017/bin/psxevars.sh intel64
+           [and likewise for MKL, MPI, and other components]
+        """
+        # https://spack.readthedocs.io/en/latest/spack.html#spack.package.PackageBase.setup_environment
+        #
+        #   spack_env   -> Applied when dependent is built within Spack.
+        #                  Not used here.
+        #   run_env     -> Applied to the modulefile of dependent.
+        #
+        # NOTE: Spack runs setup_environment twice, once pre-build to set up
+        # the build environment, and once post-installation to determine
+        # the environment variables needed at run-time to add to the module
+        # file. The script we need to source is only present post-installation,
+        # so check for its existence before sourcing.
+        # TODO: At some point we should split setup_environment into
+        # setup_build_environment and setup_run_environment to get around
+        # this problem.
+        f = self.file_to_source
+        if not f or not os.path.isfile(f):
+            return
+
+        tty.debug("sourcing " + f)
+
+        # All Intel packages expect at least the architecture as argument.
+        # Some accept more args, but those are not (yet?) handled here.
+        args = (_expand_fields('{arch}'),)
+
+        # On Mac, the platform is *also required*, at least as of 2018.
+        # I am not sure about earlier versions.
+        # if sys.platform == 'darwin':
+        #     args = ()
+
+        run_env.extend(EnvironmentModifications.from_sourcing_file(f, *args))
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        # https://spack.readthedocs.io/en/latest/spack.html#spack.package.PackageBase.setup_dependent_environment
+        #
+        #   spack_env   -> Applied when dependent is built within Spack.
+        #   run_env     -> Applied to the modulefile of dependent.
+        #                  Not used here.
+        #
+        # NB: This function is overwritten by 'mpi' provider packages:
+        #
+        # var/spack/repos/builtin/packages/intel-mpi/package.py
+        # var/spack/repos/builtin/packages/intel-parallel-studio/package.py
+        #
+        # They call _setup_dependent_env_callback() as well, but with the
+        # dictionary kwarg compilers_of_client{} present and populated.
+
+        # Handle everything in a callback version.
+        self._setup_dependent_env_callback(spack_env, run_env, dependent_spec)
+
+    def _setup_dependent_env_callback(
+            self, spack_env, run_env, dependent_spec, compilers_of_client={}):
+        # Expected to be called from a client's setup_dependent_environment(),
+        # with args extended to convey the client's compilers as needed.
+
+        if '+mkl' in self.spec or self.provides('mkl'):
+            # Spack's env philosophy demands that we replicate some of the
+            # settings normally handled by file_to_source ...
+            #
+            # TODO: Why is setup_environment() [which uses file_to_source()]
+            # not called as a matter of course upon entering the current
+            # function? (guarding against multiple calls notwithstanding)
+            #
+            # Use a local dict to facilitate debug_print():
+            env_mods = {
+                'MKLROOT': self.normalize_path('mkl'),
+                'SPACK_COMPILER_EXTRA_RPATHS': self.component_lib_dir('mkl'),
+            }
+
+            spack_env.set('MKLROOT', env_mods['MKLROOT'])
+            spack_env.append_path('SPACK_COMPILER_EXTRA_RPATHS',
+                                  env_mods['SPACK_COMPILER_EXTRA_RPATHS'])
+
+            debug_print("adding/modifying spack_env:", env_mods)
+
+        if '+mpi' in self.spec or self.provides('mpi'):
+            if compilers_of_client:
+                self.mpi_setup_dependent_environment(
+                    spack_env, run_env, dependent_spec, compilers_of_client)
+                # We could forego this nonce function and inline its code here,
+                # but (a) it sisters mpi_compiler_wrappers() [needed twice]
+                # which performs dizzyingly similar but necessarily different
+                # actions, and (b) function code leaves a bit more breathing
+                # room within the suffocating corset of flake8 line length.
+            else:
+                raise InstallError('compilers_of_client arg required for MPI')
+
+    def setup_dependent_package(self, module, dep_spec):
+        # https://spack.readthedocs.io/en/latest/spack.html#spack.package.PackageBase.setup_dependent_package
+        # Reminder: "module" refers to Python module.
+        # Called before the install() method of dependents.
+
+        if '+mpi' in self.spec or self.provides('mpi'):
+            compiler_wrapper_commands = self.mpi_compiler_wrappers
+            self.spec.mpicc  = compiler_wrapper_commands['MPICC']
+            self.spec.mpicxx = compiler_wrapper_commands['MPICXX']
+            self.spec.mpif77 = compiler_wrapper_commands['MPIF77']
+            self.spec.mpifc  = compiler_wrapper_commands['MPIFC']
+            debug_print(("spec '%s' received .mpi* properties:" % self.spec),
+                        compiler_wrapper_commands)
+
+    # ---------------------------------------------------------------------
+    # Specifics for installation phase
+    # ---------------------------------------------------------------------
+    @property
     def global_license_file(self):
-        """Returns the path where a global license file should be stored.
+        """Returns the path where a Spack-global license file should be stored.
 
         All Intel software shares the same license, so we store it in a
         common 'intel' directory."""
-        return join_path(self.global_license_dir, 'intel',
-                         os.path.basename(self.license_files[0]))
+        return os.path.join(self.global_license_dir, 'intel', 'license.lic')
+
+    @property
+    def _determine_license_type(self):
+        '''Provide appropriate license tokens for the installer (silent.cfg).
+        '''
+        # See:
+        #   ./README-intel.rst, section "Details for licensing tokens".
+        #   ./build_systems/README-intel.rst, section "Licenses"
+        #
+        # Ideally, we just tell the installer to look around on the system.
+        # Thankfully, we neither need to care nor emulate where it looks:
+        license_type = {'ACTIVATION_TYPE': 'exist_lic', }
+
+        # However (and only), if the spack-internal Intel license file has been
+        # populated beyond its templated explanatory comments, proffer it to
+        # the installer instead:
+        f = self.global_license_file
+        if os.path.isfile(f):
+            # The file will have been created upon self.license_required AND
+            # self.license_files having been populated, so the "if" is usually
+            # true by the time the present function runs; ../hooks/licensing.py
+            with open(f) as fh:
+                if re.search(r'^[ \t]*[^' + self.license_comment + '\n]',
+                             fh.read(), re.MULTILINE):
+                    license_type = {
+                        'ACTIVATION_TYPE': 'license_file',
+                        'ACTIVATION_LICENSE_FILE': f,
+                    }
+
+        debug_print(license_type)
+        return license_type
 
     def configure(self, spec, prefix):
-        """Writes the ``silent.cfg`` file used to configure the installation.
+        '''Generates the silent.cfg file to pass to installer.sh.
 
         See https://software.intel.com/en-us/articles/configuration-file-format
-        """
-        # Patterns used to check silent configuration file
-        #
-        # anythingpat - any string
-        # filepat     - the file location pattern (/path/to/license.lic)
-        # lspat       - the license server address pattern (0123@hostname)
-        # snpat       - the serial number pattern (ABCD-01234567)
-        config = {
-            # Accept EULA, valid values are: {accept, decline}
-            'ACCEPT_EULA': 'accept',
+        '''
 
-            # Optional error behavior, valid values are: {yes, no}
-            'CONTINUE_WITH_OPTIONAL_ERROR': 'yes',
-
-            # Install location, valid values are: {/opt/intel, filepat}
-            'PSET_INSTALL_DIR': prefix,
+        # Both tokens AND values of the configuration file are validated during
+        # the run of the underlying binary installer. Any unknown token or
+        # unacceptable value will cause that installer to fail.  Notably, this
+        # applies to trying to specify a license for a product that does not
+        # require one.
+        #
+        # Fortunately, the validator is a script from a solid code base that is
+        # only lightly adapted to the token vocabulary of each product and
+        # release.  Let's get that script so we can preempt its objections.
+        #
+        # Rather than running the script on a trial file and dissecting its
+        # pronouncements, let's brazenly skim it for supported tokens and build
+        # our configuration accordingly. We can do this because the tokens are
+        # quite long and specific.
 
-            # Continue with overwrite of existing installation directory,
-            # valid values are: {yes, no}
-            'CONTINUE_WITH_INSTALLDIR_OVERWRITE': 'yes',
+        validator_code = open('pset/check.awk', 'r').read()
+        # Let's go a little further and distill the tokens (plus some noise).
+        tokenlike_words = set(re.findall(r'[A-Z_]{4,}', validator_code))
 
-            # List of components to install,
-            # valid values are: {ALL, DEFAULTS, anythingpat}
-            'COMPONENTS': ';'.join(self._filtered_components),
+        # NB: .cfg files generated with the "--duplicate filename" option have
+        # the COMPONENTS string begin with a separator - do not worry about it.
+        components_joined = ';'.join(self._filtered_components)
+        nonrpm_db_dir = os.path.join(prefix, 'nonrpm-db')
 
-            # Installation mode, valid values are: {install, repair, uninstall}
-            'PSET_MODE': 'install',
+        config_draft = {
+            # Basics first - these should be accepted in all products.
+            'ACCEPT_EULA':                          'accept',
+            'PSET_MODE':                            'install',
+            'CONTINUE_WITH_OPTIONAL_ERROR':         'yes',
+            'CONTINUE_WITH_INSTALLDIR_OVERWRITE':   'yes',
+            'SIGNING_ENABLED':                      'no',
 
-            # Directory for non-RPM database, valid values are: {filepat}
-            'NONRPM_DB_DIR': prefix,
+            # Highly variable package specifics:
+            'PSET_INSTALL_DIR':                     prefix,
+            'NONRPM_DB_DIR':                        nonrpm_db_dir,
+            'COMPONENTS':                           components_joined,
 
-            # Perform validation of digital signatures of RPM files,
-            # valid values are: {yes, no}
-            'SIGNING_ENABLED': 'no',
+            # Conditional tokens; the first is supported post-2015 only.
+            # Ignore ia32; most recent products don't even provide it.
+            'ARCH_SELECTED':                        'INTEL64',   # was: 'ALL'
 
-            # Select target architecture of your applications,
-            # valid values are: {IA32, INTEL64, ALL}
-            'ARCH_SELECTED': 'ALL',
+            # 'ism' component -- see uninstall_ism(); also varies by release.
+            'PHONEHOME_SEND_USAGE_DATA':            'no',
+            # Ah, as of 2018.2, that somewhat loaded term got replaced by one
+            # in business-speak. We uphold our preference, both out of general
+            # principles and for technical reasons like overhead and non-routed
+            # compute nodes.
+            'INTEL_SW_IMPROVEMENT_PROGRAM_CONSENT': 'no',
         }
+        # Deal with licensing only if truly needed.
+        # NB: Token was 'ACTIVATION' pre ~2013, so basically irrelevant here.
+        if 'ACTIVATION_TYPE' in tokenlike_words:
+            config_draft.update(self._determine_license_type)
 
-        # Not all Intel software requires a license. Trying to specify
-        # one anyway will cause the installation to fail.
-        if self.license_required:
-            config.update({
-                # License file or license server,
-                # valid values are: {lspat, filepat}
-                'ACTIVATION_LICENSE_FILE': self.global_license_file,
-
-                # Activation type, valid values are: {exist_lic,
-                # license_server, license_file, trial_lic, serial_number}
-                'ACTIVATION_TYPE': 'license_file',
-
-                # Intel(R) Software Improvement Program opt-in,
-                # valid values are: {yes, no}
-                'PHONEHOME_SEND_USAGE_DATA': 'no',
-            })
-
-        with open('silent.cfg', 'w') as cfg:
-            for key in config:
-                cfg.write('{0}={1}\n'.format(key, config[key]))
+        # Write sorted *by token* so the file looks less like a hash dump.
+        f = open('silent.cfg', 'w')
+        for token, value in sorted(config_draft.items()):
+            if token in tokenlike_words:
+                f.write('%s=%s\n' % (token, value))
+        f.close()
 
     def install(self, spec, prefix):
-        """Runs the ``install.sh`` installation script."""
+        '''Runs Intel's install.sh installation script. Afterwards, save the
+        installer config and logs to <prefix>/.spack
+        '''
+        # prepare
+        tmpdir = tempfile.mkdtemp(prefix='spack-intel-')
 
         install_script = Executable('./install.sh')
+        install_script.add_default_env('TMPDIR', tmpdir)
+
+        # perform
         install_script('--silent', 'silent.cfg')
 
+        # preserve config and logs
+        dst = os.path.join(self.prefix, '.spack')
+        install('silent.cfg', dst)
+        for f in glob.glob('%s/intel*log' % tmpdir):
+            install(f, dst)
+
+    @run_after('install')
+    def configure_rpath(self):
+        if '+rpath' not in self.spec:
+            return
+
+        # https://software.intel.com/en-us/cpp-compiler-18.0-developer-guide-and-reference-using-configuration-files
+        compilers_bin_dir = self.component_bin_dir('compiler')
+        compilers_lib_dir = self.component_lib_dir('compiler')
+
+        for compiler_name in 'icc icpc ifort'.split():
+            f = os.path.join(compilers_bin_dir, compiler_name)
+            if not os.path.isfile(f):
+                raise InstallError(
+                    'Cannot find compiler command to configure rpath:\n\t' + f)
+
+            compiler_cfg = os.path.abspath(f + '.cfg')
+            with open(compiler_cfg, 'w') as fh:
+                fh.write('-Xlinker -rpath={0}\n'.format(compilers_lib_dir))
+
     @run_after('install')
-    def save_silent_cfg(self):
-        """Copies the silent.cfg configuration file to ``<prefix>/.spack``."""
-        install('silent.cfg', join_path(self.prefix, '.spack'))
+    def filter_compiler_wrappers(self):
+        if (('+mpi' in self.spec or self.provides('mpi')) and
+                '~newdtags' in self.spec):
+            bin_dir = self.component_bin_dir('mpi')
+            for f in 'mpif77 mpif90 mpigcc mpigxx mpiicc mpiicpc ' \
+                     'mpiifort'.split():
+                f = os.path.join(bin_dir, f)
+                filter_file('-Xlinker --enable-new-dtags', ' ', f, string=True)
+
+    @run_after('install')
+    def uninstall_ism(self):
+        # The "Intel(R) Software Improvement Program" [ahem] gets installed,
+        # apparently regardless of PHONEHOME_SEND_USAGE_DATA.
+        #
+        # https://software.intel.com/en-us/articles/software-improvement-program
+        # https://software.intel.com/en-us/forums/intel-c-compiler/topic/506959
+        # Hubert H. (Intel)  Mon, 03/10/2014 - 03:02 wrote:
+        #  "... you can also uninstall the Intel(R) Software Manager
+        #  completely: <installdir>/intel/ism/uninstall.sh"
+
+        f = os.path.join(self.normalize_path('ism'), 'uninstall.sh')
+        if os.path.isfile(f):
+            tty.warn('Uninstalling "Intel Software Improvement Program"'
+                     'component')
+            uninstall = Executable(f)
+            uninstall('--silent')
+
+        # TODO? also try
+        #   ~/intel/ism/uninstall --silent
+
+        debug_print(os.getcwd())
+        return
 
     # Check that self.prefix is there after installation
     run_after('install')(PackageBase.sanity_check_prefix)
diff --git a/lib/spack/spack/build_systems/makefile.py b/lib/spack/spack/build_systems/makefile.py
index 286b702fc9..1dd25bbd08 100644
--- a/lib/spack/spack/build_systems/makefile.py
+++ b/lib/spack/spack/build_systems/makefile.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 import inspect
 
diff --git a/lib/spack/spack/build_systems/meson.py b/lib/spack/spack/build_systems/meson.py
new file mode 100644
index 0000000000..929248d7f9
--- /dev/null
+++ b/lib/spack/spack/build_systems/meson.py
@@ -0,0 +1,171 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+import inspect
+import os
+
+from llnl.util.filesystem import working_dir
+from spack.directives import depends_on, variant
+from spack.package import PackageBase, run_after
+
+
+class MesonPackage(PackageBase):
+    """Specialized class for packages built using Meson
+
+    For more information on the Meson build system, see:
+    https://mesonbuild.com/
+
+    This class provides three phases that can be overridden:
+
+        1. :py:meth:`~.MesonPackage.meson`
+        2. :py:meth:`~.MesonPackage.build`
+        3. :py:meth:`~.MesonPackage.install`
+
+    They all have sensible defaults and for many packages the only thing
+    necessary will be to override :py:meth:`~.MesonPackage.meson_args`.
+    For a finer tuning you may also override:
+
+        +-----------------------------------------------+--------------------+
+        | **Method**                                    | **Purpose**        |
+        +===============================================+====================+
+        | :py:meth:`~.MesonPackage.root_mesonlists_dir` | Location of the    |
+        |                                               | root MesonLists.txt|
+        +-----------------------------------------------+--------------------+
+        | :py:meth:`~.MesonPackage.build_directory`     | Directory where to |
+        |                                               | build the package  |
+        +-----------------------------------------------+--------------------+
+
+
+    """
+    #: Phases of a Meson package
+    phases = ['meson', 'build', 'install']
+    #: This attribute is used in UI queries that need to know the build
+    #: system base class
+    build_system_class = 'MesonPackage'
+
+    build_targets = []
+    install_targets = ['install']
+
+    build_time_test_callbacks = ['check']
+
+    variant('buildtype', default='release',
+            description='Meson build type',
+            values=('plain', 'debug', 'debugoptimized', 'release', 'minsize'))
+
+    depends_on('meson', type='build')
+    depends_on('ninja', type='build')
+
+    @property
+    def archive_files(self):
+        """Files to archive for packages based on Meson"""
+        return [os.path.join(self.build_directory, 'meson-logs/meson-log.txt')]
+
+    @property
+    def root_mesonlists_dir(self):
+        """The relative path to the directory containing meson.build
+
+        This path is relative to the root of the extracted tarball,
+        not to the ``build_directory``. Defaults to the current directory.
+
+        :return: directory containing meson.build
+        """
+        return self.stage.source_path
+
+    @property
+    def std_meson_args(self):
+        """Standard meson arguments provided as a property for
+        convenience of package writers
+
+        :return: standard meson arguments
+        """
+        # standard Meson arguments
+        std_meson_args = MesonPackage._std_args(self)
+        std_meson_args += getattr(self, 'meson_flag_args', [])
+        return std_meson_args
+
+    @staticmethod
+    def _std_args(pkg):
+        """Computes the standard meson arguments for a generic package"""
+
+        try:
+            build_type = pkg.spec.variants['buildtype'].value
+        except KeyError:
+            build_type = 'release'
+
+        args = [
+            '--prefix={0}'.format(pkg.prefix),
+            # If we do not specify libdir explicitly, Meson chooses something
+            # like lib/x86_64-linux-gnu, which causes problems when trying to
+            # find libraries and pkg-config files.
+            # See https://github.com/mesonbuild/meson/issues/2197
+            '--libdir={0}'.format(pkg.prefix.lib),
+            '--buildtype={0}'.format(build_type),
+            '--strip',
+        ]
+
+        return args
+
+    def flags_to_build_system_args(self, flags):
+        """Produces a list of all command line arguments to pass the specified
+        compiler flags to meson."""
+        # Has to be dynamic attribute due to caching
+        setattr(self, 'meson_flag_args', [])
+
+    @property
+    def build_directory(self):
+        """Returns the directory to use when building the package
+
+        :return: directory where to build the package
+        """
+        return os.path.join(self.stage.source_path, 'spack-build')
+
+    def meson_args(self):
+        """Produces a list containing all the arguments that must be passed to
+        meson, except:
+
+        * ``--prefix``
+        * ``--libdir``
+        * ``--buildtype``
+        * ``--strip``
+
+        which will be set automatically.
+
+        :return: list of arguments for meson
+        """
+        return []
+
+    def meson(self, spec, prefix):
+        """Runs ``meson`` in the build directory"""
+        options = [os.path.abspath(self.root_mesonlists_dir)]
+        options += self.std_meson_args
+        options += self.meson_args()
+        with working_dir(self.build_directory, create=True):
+            inspect.getmodule(self).meson(*options)
+
+    def build(self, spec, prefix):
+        """Make the build targets"""
+        options = ['-v']
+        options += self.build_targets
+        with working_dir(self.build_directory):
+            inspect.getmodule(self).ninja(*options)
+
+    def install(self, spec, prefix):
+        """Make the install targets"""
+        with working_dir(self.build_directory):
+            inspect.getmodule(self).ninja(*self.install_targets)
+
+    run_after('build')(PackageBase._run_default_build_time_test_callbacks)
+
+    def check(self):
+        """Searches the Meson-generated file for the target ``test``
+        and runs it if found.
+        """
+        with working_dir(self.build_directory):
+            self._if_ninja_target_execute('test')
+            self._if_ninja_target_execute('check')
+
+    # Check that self.prefix is there after installation
+    run_after('install')(PackageBase.sanity_check_prefix)
diff --git a/lib/spack/spack/build_systems/octave.py b/lib/spack/spack/build_systems/octave.py
new file mode 100644
index 0000000000..ffcbb98c2a
--- /dev/null
+++ b/lib/spack/spack/build_systems/octave.py
@@ -0,0 +1,52 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import inspect
+
+from spack.directives import depends_on, extends
+from spack.package import PackageBase, run_after
+
+
+class OctavePackage(PackageBase):
+    """Specialized class for Octave packages. See
+    https://www.gnu.org/software/octave/doc/v4.2.0/Installing-and-Removing-Packages.html
+    for more information.
+
+    This class provides the following phases that can be overridden:
+
+    1. :py:meth:`~.OctavePackage.install`
+
+    """
+    # Default phases
+    phases = ['install']
+
+    # To be used in UI queries that require to know which
+    # build-system class we are using
+    build_system_class = 'OctavePackage'
+
+    extends('octave')
+    depends_on('octave', type=('build', 'run'))
+
+    def setup_environment(self, spack_env, run_env):
+        """Set up the compile and runtime environments for a package."""
+        # octave does not like those environment variables to be set:
+        spack_env.unset('CC')
+        spack_env.unset('CXX')
+        spack_env.unset('FC')
+
+    def install(self, spec, prefix):
+        """Install the package from the archive file"""
+        inspect.getmodule(self).octave(
+            '--quiet',
+            '--norc',
+            '--built-in-docstrings-file=/dev/null',
+            '--texi-macros-file=/dev/null',
+            '--eval', 'pkg prefix %s; pkg install %s' %
+            (prefix, self.stage.archive_file))
+
+    # Testing
+
+    # Check that self.prefix is there after installation
+    run_after('install')(PackageBase.sanity_check_prefix)
diff --git a/lib/spack/spack/build_systems/perl.py b/lib/spack/spack/build_systems/perl.py
index fe845a45db..f2b088f25d 100644
--- a/lib/spack/spack/build_systems/perl.py
+++ b/lib/spack/spack/build_systems/perl.py
@@ -1,32 +1,12 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 import inspect
 import os
 
-from llnl.util.filesystem import join_path
 from spack.directives import depends_on, extends
 from spack.package import PackageBase, run_after
 from spack.util.executable import Executable
@@ -88,7 +68,7 @@ class PerlPackage(PackageBase):
         elif os.path.isfile('Build.PL'):
             self.build_method = 'Build.PL'
             self.build_executable = Executable(
-                join_path(self.stage.source_path, 'Build'))
+                os.path.join(self.stage.source_path, 'Build'))
         else:
             raise RuntimeError('Unknown build_method for perl package')
 
diff --git a/lib/spack/spack/build_systems/python.py b/lib/spack/spack/build_systems/python.py
index b07a196fff..bf469cee23 100644
--- a/lib/spack/spack/build_systems/python.py
+++ b/lib/spack/spack/build_systems/python.py
@@ -1,35 +1,19 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 import inspect
 import os
+import shutil
 
 from spack.directives import depends_on, extends
 from spack.package import PackageBase, run_after
 
-from llnl.util.filesystem import working_dir
+from llnl.util.filesystem import (working_dir, get_filetype, filter_file,
+                                  path_contains_subdirectory, same_path)
+from llnl.util.lang import match_predicate
 
 
 class PythonPackage(PackageBase):
@@ -75,7 +59,7 @@ class PythonPackage(PackageBase):
 
     .. code-block:: console
 
-       $ python setup.py --no-user-cfg <phase>
+       $ python -s setup.py --no-user-cfg <phase>
 
     Each phase also has a <phase_args> function that can pass arguments to
     this call. All of these functions are empty except for the ``install_args``
@@ -116,6 +100,8 @@ class PythonPackage(PackageBase):
 
     depends_on('python', type=('build', 'run'))
 
+    py_namespace = None
+
     def setup_file(self):
         """Returns the name of the setup file to use."""
         return 'setup.py'
@@ -132,7 +118,7 @@ class PythonPackage(PackageBase):
         setup = self.setup_file()
 
         with working_dir(self.build_directory):
-            self.python(setup, '--no-user-cfg', *args, **kwargs)
+            self.python('-s', setup, '--no-user-cfg', *args, **kwargs)
 
     def _setup_command_available(self, command):
         """Determines whether or not a setup.py command exists.
@@ -152,7 +138,7 @@ class PythonPackage(PackageBase):
         python = inspect.getmodule(self).python
         setup = self.setup_file()
 
-        python(setup, '--no-user-cfg', command, '--help', **kwargs)
+        python('-s', setup, '--no-user-cfg', command, '--help', **kwargs)
         return python.returncode == 0
 
     # The following phases and their descriptions come from:
@@ -237,9 +223,15 @@ class PythonPackage(PackageBase):
         # Spack manages the package directory on its own by symlinking
         # extensions into the site-packages directory, so we don't really
         # need the .pth files or egg directories, anyway.
+        #
+        # We need to make sure this is only for build dependencies. A package
+        # such as py-basemap will not build properly with this flag since
+        # it does not use setuptools to build and those does not recognize
+        # the --single-version-externally-managed flag
         if ('py-setuptools' == spec.name or          # this is setuptools, or
-            'py-setuptools' in spec._dependencies):  # it's an immediate dep
-            args += ['--single-version-externally-managed', '--root=/']
+            'py-setuptools' in spec._dependencies and  # it's an immediate dep
+            'build' in spec._dependencies['py-setuptools'].deptypes):
+                args += ['--single-version-externally-managed', '--root=/']
 
         return args
 
@@ -389,7 +381,7 @@ class PythonPackage(PackageBase):
 
         # Make sure we are importing the installed modules,
         # not the ones in the current directory
-        with working_dir('..'):
+        with working_dir('spack-test', create=True):
             for module in self.import_modules:
                 self.python('-c', 'import {0}'.format(module))
 
@@ -397,3 +389,66 @@ class PythonPackage(PackageBase):
 
     # Check that self.prefix is there after installation
     run_after('install')(PackageBase.sanity_check_prefix)
+
+    def view_file_conflicts(self, view, merge_map):
+        """Report all file conflicts, excepting special cases for python.
+           Specifically, this does not report errors for duplicate
+           __init__.py files for packages in the same namespace.
+        """
+        conflicts = list(dst for src, dst in merge_map.items()
+                         if os.path.exists(dst))
+
+        if conflicts and self.py_namespace:
+            ext_map = view.extensions_layout.extension_map(self.extendee_spec)
+            namespaces = set(
+                x.package.py_namespace for x in ext_map.values())
+            namespace_re = (
+                r'site-packages/{0}/__init__.py'.format(self.py_namespace))
+            find_namespace = match_predicate(namespace_re)
+            if self.py_namespace in namespaces:
+                conflicts = list(
+                    x for x in conflicts if not find_namespace(x))
+
+        return conflicts
+
+    def add_files_to_view(self, view, merge_map):
+        bin_dir = self.spec.prefix.bin
+        python_prefix = self.extendee_spec.prefix
+        global_view = same_path(python_prefix, view.root)
+        for src, dst in merge_map.items():
+            if os.path.exists(dst):
+                continue
+            elif global_view or not path_contains_subdirectory(src, bin_dir):
+                view.link(src, dst)
+            elif not os.path.islink(src):
+                shutil.copy2(src, dst)
+                if 'script' in get_filetype(src):
+                    filter_file(
+                        python_prefix, os.path.abspath(view.root), dst)
+            else:
+                orig_link_target = os.path.realpath(src)
+                new_link_target = os.path.abspath(merge_map[orig_link_target])
+                view.link(new_link_target, dst)
+
+    def remove_files_from_view(self, view, merge_map):
+        ignore_namespace = False
+        if self.py_namespace:
+            ext_map = view.extensions_layout.extension_map(self.extendee_spec)
+            remaining_namespaces = set(
+                spec.package.py_namespace for name, spec in ext_map.items()
+                if name != self.name)
+            if self.py_namespace in remaining_namespaces:
+                namespace_init = match_predicate(
+                    r'site-packages/{0}/__init__.py'.format(self.py_namespace))
+                ignore_namespace = True
+
+        bin_dir = self.spec.prefix.bin
+        global_view = self.extendee_spec.prefix == view.root
+        for src, dst in merge_map.items():
+            if ignore_namespace and namespace_init(dst):
+                continue
+
+            if global_view or not path_contains_subdirectory(src, bin_dir):
+                view.remove_file(src, dst)
+            else:
+                os.remove(dst)
diff --git a/lib/spack/spack/build_systems/qmake.py b/lib/spack/spack/build_systems/qmake.py
index 70b53664dc..054d84f4b8 100644
--- a/lib/spack/spack/build_systems/qmake.py
+++ b/lib/spack/spack/build_systems/qmake.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 import inspect
 
diff --git a/lib/spack/spack/build_systems/r.py b/lib/spack/spack/build_systems/r.py
index 05a66427ec..32bad7bac6 100644
--- a/lib/spack/spack/build_systems/r.py
+++ b/lib/spack/spack/build_systems/r.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 import inspect
 
diff --git a/lib/spack/spack/build_systems/scons.py b/lib/spack/spack/build_systems/scons.py
index 0476362e17..a7bc5c6374 100644
--- a/lib/spack/spack/build_systems/scons.py
+++ b/lib/spack/spack/build_systems/scons.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 import inspect
 
diff --git a/lib/spack/spack/build_systems/waf.py b/lib/spack/spack/build_systems/waf.py
index 2097e1680f..ee00d175b0 100644
--- a/lib/spack/spack/build_systems/waf.py
+++ b/lib/spack/spack/build_systems/waf.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 import inspect
 
diff --git a/lib/spack/spack/caches.py b/lib/spack/spack/caches.py
new file mode 100644
index 0000000000..1d74e9dc3b
--- /dev/null
+++ b/lib/spack/spack/caches.py
@@ -0,0 +1,51 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+"""Caches used by Spack to store data"""
+import os
+
+import llnl.util.lang
+
+import spack.paths
+import spack.config
+import spack.fetch_strategy
+import spack.util.file_cache
+from spack.util.path import canonicalize_path
+
+
+def _misc_cache():
+    """The ``misc_cache`` is Spack's cache for small data.
+
+    Currently the ``misc_cache`` stores indexes for virtual dependency
+    providers and for which packages provide which tags.
+    """
+    path = spack.config.get('config:misc_cache')
+    if not path:
+        path = os.path.join(spack.paths.user_config_path, 'cache')
+    path = canonicalize_path(path)
+
+    return spack.util.file_cache.FileCache(path)
+
+
+#: Spack's cache for small data
+misc_cache = llnl.util.lang.Singleton(_misc_cache)
+
+
+def _fetch_cache():
+    """Filesystem cache of downloaded archives.
+
+    This prevents Spack from repeatedly fetch the same files when
+    building the same package different ways or multiple times.
+    """
+    path = spack.config.get('config:source_cache')
+    if not path:
+        path = os.path.join(spack.paths.var_path, "cache")
+    path = canonicalize_path(path)
+
+    return spack.fetch_strategy.FsCache(path)
+
+
+#: Spack's local cache for downloaded source archives
+fetch_cache = llnl.util.lang.Singleton(_fetch_cache)
diff --git a/lib/spack/spack/cmd/__init__.py b/lib/spack/spack/cmd/__init__.py
index 39eb4c2ae1..2963c053e4 100644
--- a/lib/spack/spack/cmd/__init__.py
+++ b/lib/spack/spack/cmd/__init__.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from __future__ import print_function
 
 import os
@@ -34,19 +15,12 @@ from llnl.util.tty.colify import colify
 from llnl.util.tty.color import colorize
 from llnl.util.filesystem import working_dir
 
-import spack
 import spack.config
+import spack.paths
 import spack.spec
 import spack.store
+from spack.error import SpackError
 
-#
-# Settings for commands that modify configuration
-#
-# Commands that modify configuration by default modify the *highest*
-# priority scope.
-default_modify_scope = spack.config.highest_precedence_scope().name
-# Commands that list configuration list *all* scopes by default.
-default_list_scope = None
 
 # cmd has a submodule called "list" so preserve the python list module
 python_list = list
@@ -57,14 +31,40 @@ ignore_files = r'^\.|^__init__.py$|^#'
 SETUP_PARSER = "setup_parser"
 DESCRIPTION = "description"
 
-command_path = os.path.join(spack.lib_path, "spack", "cmd")
+#: Names of all commands
+all_commands = []
+
+
+def python_name(cmd_name):
+    """Convert ``-`` to ``_`` in command name, to make a valid identifier."""
+    return cmd_name.replace("-", "_")
 
-commands = []
-for file in os.listdir(command_path):
-    if file.endswith(".py") and not re.search(ignore_files, file):
-        cmd = re.sub(r'.py$', '', file)
-        commands.append(cmd)
-commands.sort()
+
+def cmd_name(python_name):
+    """Convert module name (with ``_``) to command name (with ``-``)."""
+    return python_name.replace('_', '-')
+
+
+#: global, cached list of all commands -- access through all_commands()
+_all_commands = None
+
+
+def all_commands():
+    """Get a sorted list of all spack commands.
+
+    This will list the lib/spack/spack/cmd directory and find the
+    commands there to construct the list.  It does not actually import
+    the python files -- just gets the names.
+    """
+    global _all_commands
+    if _all_commands is None:
+        _all_commands = []
+        for file in os.listdir(spack.paths.command_path):
+            if file.endswith(".py") and not re.search(ignore_files, file):
+                cmd = re.sub(r'.py$', '', file)
+                _all_commands.append(cmd_name(cmd))
+        _all_commands.sort()
+    return _all_commands
 
 
 def remove_options(parser, *options):
@@ -76,33 +76,38 @@ def remove_options(parser, *options):
                 break
 
 
-def get_python_name(name):
-    """Commands can have '-' in their names, unlike Python identifiers."""
-    return name.replace("-", "_")
-
+def get_module(cmd_name):
+    """Imports the module for a particular command name and returns it.
 
-def get_module(name):
-    """Imports the module for a particular command name and returns it."""
-    module_name = "%s.%s" % (__name__, name)
+    Args:
+        cmd_name (str): name of the command for which to get a module
+            (contains ``-``, not ``_``).
+    """
+    pname = python_name(cmd_name)
+    module_name = "%s.%s" % (__name__, pname)
     module = __import__(module_name,
-                        fromlist=[name, SETUP_PARSER, DESCRIPTION],
+                        fromlist=[pname, SETUP_PARSER, DESCRIPTION],
                         level=0)
 
     attr_setdefault(module, SETUP_PARSER, lambda *args: None)  # null-op
     attr_setdefault(module, DESCRIPTION, "")
 
-    fn_name = get_python_name(name)
-    if not hasattr(module, fn_name):
+    if not hasattr(module, pname):
         tty.die("Command module %s (%s) must define function '%s'." %
-                (module.__name__, module.__file__, fn_name))
+                (module.__name__, module.__file__, pname))
 
     return module
 
 
-def get_command(name):
-    """Imports the command's function from a module and returns it."""
-    python_name = get_python_name(name)
-    return getattr(get_module(python_name), python_name)
+def get_command(cmd_name):
+    """Imports the command's function from a module and returns it.
+
+    Args:
+        cmd_name (str): name of the command for which to get a module
+            (contains ``-``, not ``_``).
+    """
+    pname = python_name(cmd_name)
+    return getattr(get_module(pname), pname)
 
 
 def parse_specs(args, **kwargs):
@@ -111,24 +116,30 @@ def parse_specs(args, **kwargs):
     """
     concretize = kwargs.get('concretize', False)
     normalize = kwargs.get('normalize', False)
+    tests = kwargs.get('tests', False)
 
     try:
         specs = spack.spec.parse(args)
         for spec in specs:
             if concretize:
-                spec.concretize()  # implies normalize
+                spec.concretize(tests=tests)  # implies normalize
             elif normalize:
-                spec.normalize()
+                spec.normalize(tests=tests)
 
         return specs
 
-    except spack.parse.ParseError as e:
-        tty.error(e.message, e.string, e.pos * " " + "^")
-        sys.exit(1)
+    except spack.spec.SpecParseError as e:
+        msg = e.message + "\n" + str(e.string) + "\n"
+        msg += (e.pos + 2) * " " + "^"
+        raise SpackError(msg)
 
     except spack.spec.SpecError as e:
-        tty.error(e.message)
-        sys.exit(1)
+
+        msg = e.message
+        if e.long_message:
+            msg += e.long_message
+
+        raise SpackError(msg)
 
 
 def elide_list(line_list, max_num=10):
@@ -164,7 +175,8 @@ def disambiguate_spec(spec):
 
 
 def gray_hash(spec, length):
-    return colorize('@K{%s}' % spec.dag_hash(length))
+    h = spec.dag_hash(length) if spec.concrete else '-' * length
+    return colorize('@K{%s}' % h)
 
 
 def display_specs(specs, args=None, **kwargs):
@@ -197,7 +209,10 @@ def display_specs(specs, args=None, **kwargs):
         namespace (bool): Print namespaces along with names
         show_flags (bool): Show compiler flags with specs
         variants (bool): Show variants with specs
-
+        indent (int): indent each line this much
+        decorators (dict): dictionary mappng specs to decorators
+        header_callback (function): called at start of arch/compiler sections
+        all_headers (bool): show headers even when arch/compiler aren't defined
     """
     def get_arg(name, default=None):
         """Prefer kwargs, then args, then default."""
@@ -208,19 +223,27 @@ def display_specs(specs, args=None, **kwargs):
         else:
             return default
 
-    mode      = get_arg('mode', 'short')
-    hashes    = get_arg('long', False)
-    namespace = get_arg('namespace', False)
-    flags     = get_arg('show_flags', False)
+    mode          = get_arg('mode', 'short')
+    hashes        = get_arg('long', False)
+    namespace     = get_arg('namespace', False)
+    flags         = get_arg('show_flags', False)
     full_compiler = get_arg('show_full_compiler', False)
-    variants  = get_arg('variants', False)
+    variants      = get_arg('variants', False)
+    all_headers   = get_arg('all_headers', False)
+
+    decorator     = get_arg('decorator', None)
+    if decorator is None:
+        decorator = lambda s, f: f
+
+    indent = get_arg('indent', 0)
+    ispace = indent * ' '
 
     hlen = 7
     if get_arg('very_long', False):
         hashes = True
         hlen = None
 
-    nfmt = '.' if namespace else '_'
+    nfmt = '{fullpackage}' if namespace else '{package}'
     ffmt = ''
     if full_compiler or flags:
         ffmt += '$%'
@@ -232,30 +255,46 @@ def display_specs(specs, args=None, **kwargs):
 
     # Make a dict with specs keyed by architecture and compiler.
     index = index_by(specs, ('architecture', 'compiler'))
+    transform = {'package': decorator, 'fullpackage': decorator}
 
     # Traverse the index and print out each package
     for i, (architecture, compiler) in enumerate(sorted(index)):
         if i > 0:
             print()
 
-        header = "%s{%s} / %s{%s}" % (spack.spec.architecture_color,
-                                      architecture, spack.spec.compiler_color,
-                                      compiler)
-        tty.hline(colorize(header), char='-')
+        header = "%s{%s} / %s{%s}" % (
+            spack.spec.architecture_color,
+            architecture if architecture else 'no arch',
+            spack.spec.compiler_color,
+            compiler if compiler else 'no compiler')
+
+        # Sometimes we want to display specs that are not yet concretized.
+        # If they don't have a compiler / architecture attached to them,
+        # then skip the header
+        if all_headers or (architecture is not None or compiler is not None):
+            sys.stdout.write(ispace)
+            tty.hline(colorize(header), char='-')
 
         specs = index[(architecture, compiler)]
         specs.sort()
 
-        abbreviated = [s.cformat(format_string) for s in specs]
         if mode == 'paths':
             # Print one spec per line along with prefix path
+            abbreviated = [s.cformat(format_string, transform=transform)
+                           for s in specs]
             width = max(len(s) for s in abbreviated)
             width += 2
-            format = "    %%-%ds%%s" % width
 
             for abbrv, spec in zip(abbreviated, specs):
-                prefix = gray_hash(spec, hlen) if hashes else ''
-                print(prefix + (format % (abbrv, spec.prefix)))
+                # optional hash prefix for paths
+                h = gray_hash(spec, hlen) if hashes else ''
+
+                # only show prefix for concrete specs
+                prefix = spec.prefix if spec.concrete else ''
+
+                # print it all out at once
+                fmt = "%%s%%s    %%-%ds%%s" % width
+                print(fmt % (ispace, h, abbrv, prefix))
 
         elif mode == 'deps':
             for spec in specs:
@@ -265,24 +304,25 @@ def display_specs(specs, args=None, **kwargs):
                     prefix=(lambda s: gray_hash(s, hlen)) if hashes else None))
 
         elif mode == 'short':
-            # Print columns of output if not printing flags
-            if not flags and not full_compiler:
+            def fmt(s):
+                string = ""
+                if hashes:
+                    string += gray_hash(s, hlen) + ' '
+                string += s.cformat(
+                    '$%s$@%s' % (nfmt, vfmt), transform=transform)
+                return string
 
-                def fmt(s):
-                    string = ""
-                    if hashes:
-                        string += gray_hash(s, hlen) + ' '
-                    string += s.cformat('$-%s$@%s' % (nfmt, vfmt))
-
-                    return string
+            if not flags and not full_compiler:
+                # Print columns of output if not printing flags
+                colify((fmt(s) for s in specs), indent=indent)
 
-                colify(fmt(s) for s in specs)
-            # Print one entry per line if including flags
             else:
+                # Print one entry per line if including flags
                 for spec in specs:
                     # Print the hash if necessary
                     hsh = gray_hash(spec, hlen) + ' ' if hashes else ''
-                    print(hsh + spec.cformat(format_string) + '\n')
+                    print(ispace + hsh + spec.cformat(
+                        format_string, transform=transform))
 
         else:
             raise ValueError(
@@ -292,5 +332,5 @@ def display_specs(specs, args=None, **kwargs):
 
 def spack_is_git_repo():
     """Ensure that this instance of Spack is a git clone."""
-    with working_dir(spack.prefix):
+    with working_dir(spack.paths.prefix):
         return os.path.isdir('.git')
diff --git a/lib/spack/spack/cmd/activate.py b/lib/spack/spack/cmd/activate.py
index a5909df9fb..de6bbc3ecc 100644
--- a/lib/spack/spack/cmd/activate.py
+++ b/lib/spack/spack/cmd/activate.py
@@ -1,32 +1,14 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import argparse
+
 import llnl.util.tty as tty
-import spack
+
 import spack.cmd
-from spack.directory_layout import YamlViewExtensionsLayout
+from spack.filesystem_view import YamlFilesystemView
 
 description = "activate a package extension"
 section = "extensions"
@@ -54,11 +36,17 @@ def activate(parser, args):
     if not spec.package.is_extension:
         tty.die("%s is not an extension." % spec.name)
 
-    layout = spack.store.extensions
-    if args.view is not None:
-        layout = YamlViewExtensionsLayout(args.view, spack.store.layout)
+    if args.view:
+        target = args.view
+    else:
+        target = spec.package.extendee_spec.prefix
+
+    view = YamlFilesystemView(target, spack.store.layout)
 
-    if spec.package.is_activated(extensions_layout=layout):
-        tty.die("Package %s is already activated." % specs[0].short_spec)
+    if spec.package.is_activated(view):
+        tty.msg("Package %s is already activated." % specs[0].short_spec)
+        return
 
-    spec.package.do_activate(extensions_layout=layout)
+    # TODO: refactor FilesystemView.add_extension and use that here (so there
+    # aren't two ways of activating extensions)
+    spec.package.do_activate(view, with_dependencies=not args.force)
diff --git a/lib/spack/spack/cmd/add.py b/lib/spack/spack/cmd/add.py
new file mode 100644
index 0000000000..6dc903ae68
--- /dev/null
+++ b/lib/spack/spack/cmd/add.py
@@ -0,0 +1,33 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import argparse
+
+import llnl.util.tty as tty
+
+import spack.cmd
+import spack.environment as ev
+
+
+description = 'add a spec to an environment'
+section = "environments"
+level = "long"
+
+
+def setup_parser(subparser):
+    subparser.add_argument(
+        'specs', nargs=argparse.REMAINDER, help="specs of packages to add")
+
+
+def add(parser, args):
+    env = ev.get_env(args, 'add')
+
+    for spec in spack.cmd.parse_specs(args.specs):
+        if not env.add(spec):
+            tty.msg("Package {0} was already added to {1}"
+                    .format(spec.name, env.name))
+        else:
+            tty.msg('Adding %s to environment %s' % (spec, env.name))
+    env.write()
diff --git a/lib/spack/spack/cmd/arch.py b/lib/spack/spack/cmd/arch.py
index c8f844e4c1..46a2306ed5 100644
--- a/lib/spack/spack/cmd/arch.py
+++ b/lib/spack/spack/cmd/arch.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from __future__ import print_function
 
 import spack.architecture as architecture
@@ -35,11 +16,24 @@ def setup_parser(subparser):
     parts = subparser.add_mutually_exclusive_group()
     parts.add_argument(
         '-p', '--platform', action='store_true', default=False,
-        help="print only the platform")
+        help='print only the platform')
+    parts.add_argument(
+        '-o', '--operating-system', action='store_true', default=False,
+        help='print only the operating system')
+    parts.add_argument(
+        '-t', '--target', action='store_true', default=False,
+        help='print only the target')
 
 
 def arch(parser, args):
+    arch = architecture.Arch(
+        architecture.platform(), 'default_os', 'default_target')
+
     if args.platform:
-        print(architecture.platform())
+        print(arch.platform)
+    elif args.operating_system:
+        print(arch.platform_os)
+    elif args.target:
+        print(arch.target)
     else:
-        print(architecture.sys_type())
+        print(arch)
diff --git a/lib/spack/spack/cmd/blame.py b/lib/spack/spack/cmd/blame.py
index a4f75da19a..a385817f9f 100644
--- a/lib/spack/spack/cmd/blame.py
+++ b/lib/spack/spack/cmd/blame.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 import re
 
@@ -30,7 +11,8 @@ from llnl.util.lang import pretty_date
 from llnl.util.filesystem import working_dir
 from llnl.util.tty.colify import colify_table
 
-import spack
+import spack.paths
+import spack.repo
 from spack.util.executable import which
 from spack.cmd import spack_is_git_repo
 
@@ -67,7 +49,7 @@ def blame(parser, args):
     blame_file = None
     if os.path.isfile(args.package_name):
         path = os.path.realpath(args.package_name)
-        if path.startswith(spack.prefix):
+        if path.startswith(spack.paths.prefix):
             blame_file = path
 
     if not blame_file:
@@ -75,7 +57,7 @@ def blame(parser, args):
         blame_file = pkg.module.__file__.rstrip('c')  # .pyc -> .py
 
     # get git blame for the package
-    with working_dir(spack.prefix):
+    with working_dir(spack.paths.prefix):
         if args.view == 'git':
             git('blame', blame_file)
             return
diff --git a/lib/spack/spack/cmd/bootstrap.py b/lib/spack/spack/cmd/bootstrap.py
index b41b568fb3..ee09298cb2 100644
--- a/lib/spack/spack/cmd/bootstrap.py
+++ b/lib/spack/spack/cmd/bootstrap.py
@@ -1,30 +1,12 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import llnl.util.tty as tty
-import spack
-import spack.cmd
+
+import spack.repo
+import spack.spec
 import spack.cmd.common.arguments as arguments
 
 description = "Bootstrap packages needed for spack to run smoothly"
@@ -35,16 +17,14 @@ level = "long"
 def setup_parser(subparser):
     subparser.add_argument(
         '-j', '--jobs', action='store', type=int,
-        help="explicitly set number of make jobs. default is #cpus")
+        help="explicitly set number of make jobs (default: #cpus)")
     subparser.add_argument(
         '--keep-prefix', action='store_true', dest='keep_prefix',
         help="don't remove the install prefix if installation fails")
     subparser.add_argument(
         '--keep-stage', action='store_true', dest='keep_stage',
         help="don't remove the build stage if installation succeeds")
-    subparser.add_argument(
-        '-n', '--no-checksum', action='store_true', dest='no_checksum',
-        help="do not check packages against checksum")
+    arguments.add_common_arguments(subparser, ['no_checksum'])
     subparser.add_argument(
         '-v', '--verbose', action='store_true', dest='verbose',
         help="display verbose build output while installing")
@@ -52,11 +32,6 @@ def setup_parser(subparser):
     cd_group = subparser.add_mutually_exclusive_group()
     arguments.add_common_arguments(cd_group, ['clean', 'dirty'])
 
-    subparser.add_argument(
-        '--run-tests', action='store_true', dest='run_tests',
-        help="run package level tests during installation"
-    )
-
 
 def bootstrap(parser, args, **kwargs):
     kwargs.update({
@@ -64,7 +39,6 @@ def bootstrap(parser, args, **kwargs):
         'keep_stage': args.keep_stage,
         'install_deps': 'dependencies',
         'make_jobs': args.jobs,
-        'run_tests': args.run_tests,
         'verbose': args.verbose,
         'dirty': args.dirty
     })
@@ -81,7 +55,7 @@ def bootstrap(parser, args, **kwargs):
                     "package %s" % (requirement, installed_specs[0]))
         else:
             # Install requirement
-            spec_to_install = spack.Spec(requirement_dict[requirement])
+            spec_to_install = spack.spec.Spec(requirement_dict[requirement])
             spec_to_install.concretize()
             tty.msg("Installing %s to satisfy requirement for %s" %
                     (spec_to_install, requirement))
diff --git a/lib/spack/spack/cmd/build.py b/lib/spack/spack/cmd/build.py
index 08fb9f1350..13b5621cd4 100644
--- a/lib/spack/spack/cmd/build.py
+++ b/lib/spack/spack/cmd/build.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import spack.cmd.configure as cfg
 
 from spack.build_systems.autotools import AutotoolsPackage
@@ -31,6 +12,7 @@ from spack.build_systems.scons import SConsPackage
 from spack.build_systems.waf import WafPackage
 from spack.build_systems.python import PythonPackage
 from spack.build_systems.perl import PerlPackage
+from spack.build_systems.meson import MesonPackage
 
 description = 'stops at build stage when installing a package, if possible'
 section = "build"
@@ -45,6 +27,7 @@ build_system_to_phase = {
     WafPackage: 'build',
     PythonPackage: 'build',
     PerlPackage: 'build',
+    MesonPackage: 'build',
 }
 
 
diff --git a/lib/spack/spack/cmd/build_env.py b/lib/spack/spack/cmd/build_env.py
new file mode 100644
index 0000000000..cb87bbc620
--- /dev/null
+++ b/lib/spack/spack/cmd/build_env.py
@@ -0,0 +1,59 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from __future__ import print_function
+
+import argparse
+import os
+
+import llnl.util.tty as tty
+import spack.build_environment as build_environment
+import spack.cmd
+import spack.cmd.common.arguments as arguments
+
+description = "show install environment for a spec, and run commands"
+section = "build"
+level = "long"
+
+
+def setup_parser(subparser):
+    arguments.add_common_arguments(subparser, ['clean', 'dirty'])
+    subparser.add_argument(
+        'spec', nargs=argparse.REMAINDER,
+        help="specs of package environment to emulate")
+
+
+def build_env(parser, args):
+    if not args.spec:
+        tty.die("spack build-env requires a spec.")
+
+    # Specs may have spaces in them, so if they do, require that the
+    # caller put a '--' between the spec and the command to be
+    # executed.  If there is no '--', assume that the spec is the
+    # first argument.
+    sep = '--'
+    if sep in args.spec:
+        s = args.spec.index(sep)
+        spec = args.spec[:s]
+        cmd = args.spec[s + 1:]
+    else:
+        spec = args.spec[0]
+        cmd = args.spec[1:]
+
+    specs = spack.cmd.parse_specs(spec, concretize=True)
+    if len(specs) > 1:
+        tty.die("spack build-env only takes one spec.")
+    spec = specs[0]
+
+    build_environment.setup_package(spec.package, args.dirty)
+
+    if not cmd:
+        # If no command act like the "env" command and print out env vars.
+        for key, val in os.environ.items():
+            print("%s=%s" % (key, val))
+
+    else:
+        # Otherwise execute the command with the new environment
+        os.execvp(cmd[0], cmd)
diff --git a/lib/spack/spack/cmd/buildcache.py b/lib/spack/spack/cmd/buildcache.py
index 653c59074a..dc9f736a7e 100644
--- a/lib/spack/spack/cmd/buildcache.py
+++ b/lib/spack/spack/cmd/buildcache.py
@@ -1,41 +1,20 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import argparse
 
-import os
 import llnl.util.tty as tty
 
-import spack
 import spack.cmd
+import spack.repo
+import spack.store
+import spack.spec
 import spack.binary_distribution as bindist
-from spack.binary_distribution import NoOverwriteException, NoGpgException
-from spack.binary_distribution import NoKeyException, PickKeyException
-from spack.binary_distribution import NoVerifyException, NoChecksumException
 
-description = "Create, download and install build cache files."
-section = "caching"
+description = "create, download and install binary packages"
+section = "packaging"
 level = "long"
 
 
@@ -43,15 +22,18 @@ def setup_parser(subparser):
     setup_parser.parser = subparser
     subparsers = subparser.add_subparsers(help='buildcache sub-commands')
 
-    create = subparsers.add_parser('create')
+    create = subparsers.add_parser('create', help=createtarball.__doc__)
     create.add_argument('-r', '--rel', action='store_true',
                         help="make all rpaths relative" +
                              " before creating tarballs.")
     create.add_argument('-f', '--force', action='store_true',
                         help="overwrite tarball if it exists.")
-    create.add_argument('-y', '--yes-to-all', action='store_true',
-                        help="answer yes to all create unsigned " +
-                             "buildcache questions")
+    create.add_argument('-u', '--unsigned', action='store_true',
+                        help="create unsigned buildcache" +
+                             " tarballs for testing")
+    create.add_argument('-a', '--allow_root', action='store_true',
+                        help="allow install root string in binary files " +
+                             "after RPATH substitution")
     create.add_argument('-k', '--key', metavar='key',
                         type=str, default=None,
                         help="Key for signing.")
@@ -63,18 +45,23 @@ def setup_parser(subparser):
         help="specs of packages to create buildcache for")
     create.set_defaults(func=createtarball)
 
-    install = subparsers.add_parser('install')
+    install = subparsers.add_parser('install', help=installtarball.__doc__)
     install.add_argument('-f', '--force', action='store_true',
                          help="overwrite install directory if it exists.")
-    install.add_argument('-y', '--yes-to-all', action='store_true',
-                         help="answer yes to all install unsigned " +
-                              "buildcache questions")
+    install.add_argument('-m', '--multiple', action='store_true',
+                         help="allow all matching packages ")
+    install.add_argument('-a', '--allow_root', action='store_true',
+                         help="allow install root string in binary files " +
+                              "after RPATH substitution")
+    install.add_argument('-u', '--unsigned', action='store_true',
+                         help="install unsigned buildcache" +
+                              " tarballs for testing")
     install.add_argument(
         'packages', nargs=argparse.REMAINDER,
-        help="specs of packages to install biuldache for")
+        help="specs of packages to install buildcache for")
     install.set_defaults(func=installtarball)
 
-    listcache = subparsers.add_parser('list')
+    listcache = subparsers.add_parser('list', help=listspecs.__doc__)
     listcache.add_argument('-f', '--force', action='store_true',
                            help="force new download of specs")
     listcache.add_argument(
@@ -82,13 +69,13 @@ def setup_parser(subparser):
         help="specs of packages to search for")
     listcache.set_defaults(func=listspecs)
 
-    dlkeys = subparsers.add_parser('keys')
+    dlkeys = subparsers.add_parser('keys', help=getkeys.__doc__)
     dlkeys.add_argument(
         '-i', '--install', action='store_true',
         help="install Keys pulled from mirror")
     dlkeys.add_argument(
-        '-y', '--yes-to-all', action='store_true',
-        help="answer yes to all trust questions")
+        '-t', '--trust', action='store_true',
+        help="trust all downloaded keys")
     dlkeys.add_argument('-f', '--force', action='store_true',
                         help="force new download of keys")
     dlkeys.set_defaults(func=getkeys)
@@ -179,26 +166,18 @@ def match_downloaded_specs(pkgs, allow_multiple_matches=False, force=False):
 
 
 def createtarball(args):
+    """create a binary package from an existing install"""
     if not args.packages:
         tty.die("build cache file creation requires at least one" +
                 " installed package argument")
     pkgs = set(args.packages)
     specs = set()
-    outdir = os.getcwd()
+    outdir = '.'
     if args.directory:
         outdir = args.directory
     signkey = None
     if args.key:
         signkey = args.key
-    yes_to_all = False
-    force = False
-    relative = False
-    if args.yes_to_all:
-        yes_to_all = True
-    if args.force:
-        force = True
-    if args.rel:
-        relative = True
 
     matches = find_matching_specs(pkgs, False, False)
     for match in matches:
@@ -219,38 +198,21 @@ def createtarball(args):
                     tty.msg('adding dependency %s' % node.format())
                     specs.add(node)
 
+    tty.msg('writing tarballs to %s/build_cache' % outdir)
+
     for spec in specs:
         tty.msg('creating binary cache file for package %s ' % spec.format())
-        try:
-            bindist.build_tarball(spec, outdir, force,
-                                  relative, yes_to_all, signkey)
-        except NoOverwriteException as e:
-            tty.warn("%s exists, use -f to force overwrite." % e)
-        except NoGpgException:
-            tty.die("gpg2 is not available,"
-                    " use -y to create unsigned build caches")
-        except NoKeyException:
-            tty.die("no default key available for signing,"
-                    " use -y to create unsigned build caches"
-                    " or spack gpg init to create a default key")
-        except PickKeyException:
-            tty.die("multi keys available for signing,"
-                    " use -y to create unsigned build caches"
-                    " or -k <key hash> to pick a key")
+        bindist.build_tarball(spec, outdir, args.force, args.rel,
+                              args.unsigned, args.allow_root, signkey)
 
 
 def installtarball(args):
+    """install from a binary package"""
     if not args.packages:
         tty.die("build cache file installation requires" +
                 " at least one package spec argument")
     pkgs = set(args.packages)
-    yes_to_all = False
-    if args.yes_to_all:
-        yes_to_all = True
-    force = False
-    if args.force:
-        force = True
-    matches = match_downloaded_specs(pkgs, yes_to_all, force)
+    matches = match_downloaded_specs(pkgs, args.multiple, args.force)
 
     for match in matches:
         install_tarball(match, args)
@@ -261,41 +223,27 @@ def install_tarball(spec, args):
     if s.external or s.virtual:
         tty.warn("Skipping external or virtual package %s" % spec.format())
         return
-    yes_to_all = False
-    if args.yes_to_all:
-        yes_to_all = True
-    force = False
-    if args.force:
-        force = True
     for d in s.dependencies(deptype=('link', 'run')):
         tty.msg("Installing buildcache for dependency spec %s" % d)
         install_tarball(d, args)
     package = spack.repo.get(spec)
-    if s.concrete and package.installed and not force:
-        tty.warn("Package for spec %s already installed." % spec.format(),
-                 " Use -f flag to overwrite.")
+    if s.concrete and package.installed and not args.force:
+        tty.warn("Package for spec %s already installed." % spec.format())
     else:
         tarball = bindist.download_tarball(spec)
         if tarball:
             tty.msg('Installing buildcache for spec %s' % spec.format())
-            try:
-                bindist.extract_tarball(spec, tarball, yes_to_all, force)
-            except NoOverwriteException as e:
-                tty.warn("%s exists. use -f to force overwrite." % e.args)
-            except NoVerifyException:
-                tty.die("Package spec file failed signature verification,"
-                        " use -y flag to install build cache")
-            except NoChecksumException:
-                tty.die("Package tarball failed checksum verification,"
-                        " use -y flag to install build cache")
-            finally:
-                spack.store.db.reindex(spack.store.layout)
+            bindist.extract_tarball(spec, tarball, args.allow_root,
+                                    args.unsigned, args.force)
+            spack.hooks.post_install(spec)
+            spack.store.store.reindex()
         else:
             tty.die('Download of binary cache file for spec %s failed.' %
                     spec.format())
 
 
 def listspecs(args):
+    """list binary packages available from mirrors"""
     specs = bindist.get_specs(args.force)
     if args.packages:
         pkgs = set(args.packages)
@@ -318,16 +266,8 @@ def listspecs(args):
 
 
 def getkeys(args):
-    install = False
-    if args.install:
-        install = True
-    yes_to_all = False
-    if args.yes_to_all:
-        yes_to_all = True
-    force = False
-    if args.force:
-        force = True
-    bindist.get_keys(install, yes_to_all, force)
+    """get public keys available on mirrors"""
+    bindist.get_keys(args.install, args.trust, args.force)
 
 
 def buildcache(parser, args):
diff --git a/lib/spack/spack/cmd/cd.py b/lib/spack/spack/cmd/cd.py
index bf86ba573d..b2dae30fd8 100644
--- a/lib/spack/spack/cmd/cd.py
+++ b/lib/spack/spack/cmd/cd.py
@@ -1,32 +1,14 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.cmd.common import print_module_placeholder_help
+
 import spack.cmd.location
-import spack.modules
 
 description = "cd to spack directories in the shell"
-section = "environment"
+section = "developer"
 level = "long"
 
 
@@ -38,4 +20,4 @@ def setup_parser(subparser):
 
 
 def cd(parser, args):
-    spack.modules.print_help()
+    print_module_placeholder_help()
diff --git a/lib/spack/spack/cmd/checksum.py b/lib/spack/spack/cmd/checksum.py
index 4a930ac5d0..19bfde49bd 100644
--- a/lib/spack/spack/cmd/checksum.py
+++ b/lib/spack/spack/cmd/checksum.py
@@ -1,34 +1,16 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from __future__ import print_function
 
 import argparse
 
 import llnl.util.tty as tty
-import spack
+
 import spack.cmd
+import spack.repo
 import spack.util.crypto
 import spack.util.web
 from spack.util.naming import valid_fully_qualified_module_name
@@ -54,8 +36,7 @@ def setup_parser(subparser):
 def checksum(parser, args):
     # Make sure the user provided a package and not a URL
     if not valid_fully_qualified_module_name(args.package):
-        tty.die("`spack checksum` accepts package names, not URLs. "
-                "Use `spack md5 <url>` instead.")
+        tty.die("`spack checksum` accepts package names, not URLs.")
 
     # Get the package we're going to generate checksums for
     pkg = spack.repo.get(args.package)
diff --git a/lib/spack/spack/cmd/clean.py b/lib/spack/spack/cmd/clean.py
index 62359aaa42..5d3d39997f 100644
--- a/lib/spack/spack/cmd/clean.py
+++ b/lib/spack/spack/cmd/clean.py
@@ -1,33 +1,20 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import argparse
+import os
+import shutil
 
 import llnl.util.tty as tty
 
-import spack
+import spack.caches
 import spack.cmd
+import spack.repo
+import spack.stage
+from spack.paths import lib_path, var_path
+
 
 description = "remove temporary build files and/or downloaded archives"
 section = "build"
@@ -35,9 +22,9 @@ level = "long"
 
 
 class AllClean(argparse.Action):
-    """Activates flags -s -d and -m simultaneously"""
+    """Activates flags -s -d -m and -p simultaneously"""
     def __call__(self, parser, namespace, values, option_string=None):
-        parser.parse_args(['-sdm'], namespace=namespace)
+        parser.parse_args(['-sdmp'], namespace=namespace)
 
 
 def setup_parser(subparser):
@@ -51,7 +38,10 @@ def setup_parser(subparser):
         '-m', '--misc-cache', action='store_true',
         help="remove long-lived caches, like the virtual package index")
     subparser.add_argument(
-        '-a', '--all', action=AllClean, help="equivalent to -sdm", nargs=0
+        '-p', '--python-cache', action='store_true',
+        help="remove .pyc, .pyo files and __pycache__ folders")
+    subparser.add_argument(
+        '-a', '--all', action=AllClean, help="equivalent to -sdmp", nargs=0
     )
     subparser.add_argument(
         'specs',
@@ -61,9 +51,9 @@ def setup_parser(subparser):
 
 
 def clean(parser, args):
-
     # If nothing was set, activate the default
-    if not any([args.specs, args.stage, args.downloads, args.misc_cache]):
+    if not any([args.specs, args.stage, args.downloads, args.misc_cache,
+                args.python_cache]):
         args.stage = True
 
     # Then do the cleaning falling through the cases
@@ -81,8 +71,23 @@ def clean(parser, args):
 
     if args.downloads:
         tty.msg('Removing cached downloads')
-        spack.fetch_cache.destroy()
+        spack.caches.fetch_cache.destroy()
 
     if args.misc_cache:
         tty.msg('Removing cached information on repositories')
-        spack.misc_cache.destroy()
+        spack.caches.misc_cache.destroy()
+
+    if args.python_cache:
+        tty.msg('Removing python cache files')
+        for directory in [lib_path, var_path]:
+            for root, dirs, files in os.walk(directory):
+                for f in files:
+                    if f.endswith('.pyc') or f.endswith('.pyo'):
+                        fname = os.path.join(root, f)
+                        tty.debug('Removing {0}'.format(fname))
+                        os.remove(fname)
+                for d in dirs:
+                    if d == '__pycache__':
+                        dname = os.path.join(root, d)
+                        tty.debug('Removing {0}'.format(dname))
+                        shutil.rmtree(dname)
diff --git a/lib/spack/spack/cmd/clone.py b/lib/spack/spack/cmd/clone.py
index 1394368f0b..9926bf016e 100644
--- a/lib/spack/spack/cmd/clone.py
+++ b/lib/spack/spack/cmd/clone.py
@@ -1,33 +1,14 @@
-##############################################################################
-# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 
 import llnl.util.tty as tty
 from llnl.util.filesystem import mkdirp, working_dir
 
-import spack
+import spack.paths
 from spack.util.executable import ProcessError, which
 
 _SPACK_UPSTREAM = 'https://github.com/spack/spack'
@@ -43,11 +24,11 @@ def setup_parser(subparser):
         help="name of the remote to clone from", default='origin')
     subparser.add_argument(
         'prefix',
-        help="names of prefix where we should install spack")
+        help="name of prefix where we should install spack")
 
 
 def get_origin_info(remote):
-    git_dir = os.path.join(spack.prefix, '.git')
+    git_dir = os.path.join(spack.paths.prefix, '.git')
     git = which('git', required=True)
     try:
         branch = git('symbolic-ref', '--short', 'HEAD', output=str)
diff --git a/lib/spack/spack/cmd/commands.py b/lib/spack/spack/cmd/commands.py
new file mode 100644
index 0000000000..bf29b3f096
--- /dev/null
+++ b/lib/spack/spack/cmd/commands.py
@@ -0,0 +1,123 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from __future__ import print_function
+
+import sys
+import re
+import argparse
+
+from llnl.util.argparsewriter import ArgparseWriter, ArgparseRstWriter
+
+import spack.main
+from spack.main import section_descriptions
+
+
+description = "list available spack commands"
+section = "developer"
+level = "long"
+
+
+#: list of command formatters
+formatters = {}
+
+
+def formatter(func):
+    """Decorator used to register formatters"""
+    formatters[func.__name__] = func
+    return func
+
+
+def setup_parser(subparser):
+    subparser.add_argument(
+        '--format', default='names', choices=formatters,
+        help='format to be used to print the output (default: names)')
+    subparser.add_argument(
+        'documented_commands', nargs=argparse.REMAINDER,
+        help='list of documented commands to cross-references')
+
+
+class SpackArgparseRstWriter(ArgparseRstWriter):
+    """RST writer tailored for spack documentation."""
+
+    def __init__(self, documented_commands, out=sys.stdout):
+        super(SpackArgparseRstWriter, self).__init__(out)
+        self.documented = documented_commands if documented_commands else []
+
+    def usage(self, *args):
+        super(SpackArgparseRstWriter, self).usage(*args)
+        cmd = re.sub(' ', '-', self.parser.prog)
+        if cmd in self.documented:
+            self.line()
+            self.line(':ref:`More documentation <cmd-%s>`' % cmd)
+
+
+class SubcommandWriter(ArgparseWriter):
+    def begin_command(self, prog):
+        print('    ' * self.level + prog)
+
+
+@formatter
+def subcommands(args):
+    parser = spack.main.make_argument_parser()
+    spack.main.add_all_commands(parser)
+    SubcommandWriter().write(parser)
+
+
+def rst_index(out=sys.stdout):
+    out.write('\n')
+
+    index = spack.main.index_commands()
+    sections = index['long']
+
+    dmax = max(len(section_descriptions.get(s, s)) for s in sections) + 2
+    cmax = max(len(c) for _, c in sections.items()) + 60
+
+    row = "%s  %s\n" % ('=' * dmax, '=' * cmax)
+    line = '%%-%ds  %%s\n' % dmax
+
+    out.write(row)
+    out.write(line % (" Category ", " Commands "))
+    out.write(row)
+    for section, commands in sorted(sections.items()):
+        description = section_descriptions.get(section, section)
+
+        for i, cmd in enumerate(sorted(commands)):
+            description = description.capitalize() if i == 0 else ''
+            ref = ':ref:`%s <spack-%s>`' % (cmd, cmd)
+            comma = ',' if i != len(commands) - 1 else ''
+            bar = '| ' if i % 8 == 0 else '  '
+            out.write(line % (description, bar + ref + comma))
+    out.write(row)
+
+
+@formatter
+def rst(args):
+    # print an index to each command
+    rst_index()
+    print()
+
+    # create a parser with all commands
+    parser = spack.main.make_argument_parser()
+    spack.main.add_all_commands(parser)
+
+    # get documented commands from the command line
+    documented_commands = set(args.documented_commands)
+
+    # print sections for each command and subcommand
+    SpackArgparseRstWriter(documented_commands).write(parser, root=1)
+
+
+@formatter
+def names(args):
+    for cmd in spack.cmd.all_commands():
+        print(cmd)
+
+
+def commands(parser, args):
+
+    # Print to stdout
+    formatters[args.format](args)
+    return
diff --git a/lib/spack/spack/cmd/common/__init__.py b/lib/spack/spack/cmd/common/__init__.py
index bb4e45438e..40fee516d1 100644
--- a/lib/spack/spack/cmd/common/__init__.py
+++ b/lib/spack/spack/cmd/common/__init__.py
@@ -1,46 +1,37 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-import spack
+
+import spack.paths
 from llnl.util import tty
 
 
+shell_init_instructions = [
+    "To initialize spack's shell commands:",
+    "",
+    "    # for bash and zsh",
+    "    . %s/setup-env.sh" % spack.paths.share_path,
+    "",
+    "    # for csh and tcsh",
+    "    setenv SPACK_ROOT %s" % spack.paths.prefix,
+    "    source %s/setup-env.csh" % spack.paths.share_path, ""
+]
+
+
 def print_module_placeholder_help():
     """
     For use by commands to tell user how to activate shell support.
     """
-    tty.msg("This command requires spack's shell integration.", "",
-            "To initialize spack's shell commands, you must run one of",
-            "the commands below.  Choose the right command for your shell.",
-            "", "For bash and zsh:",
-            "    . %s/setup-env.sh" % spack.share_path, "",
-            "For csh and tcsh:", "    setenv SPACK_ROOT %s" % spack.prefix,
-            "    source %s/setup-env.csh" % spack.share_path, "",
-            "This exposes a 'spack' shell function, which you can use like",
-            "    $ spack load package-foo", "",
-            "Running the Spack executable directly (for example, invoking",
-            "./bin/spack) will bypass the shell function and print this",
-            "placeholder message, even if you have sourced one of the above",
-            "shell integration scripts.")
+    msg = [
+        "This command requires spack's shell integration.", ""
+    ] + shell_init_instructions + [
+        "This exposes a 'spack' shell function, which you can use like",
+        "    $ spack load package-foo", "",
+        "Running the Spack executable directly (for example, invoking",
+        "./bin/spack) will bypass the shell function and print this",
+        "placeholder message, even if you have sourced one of the above",
+        "shell integration scripts."
+    ]
+    tty.msg(*msg)
diff --git a/lib/spack/spack/cmd/common/arguments.py b/lib/spack/spack/cmd/common/arguments.py
index 6628ec4190..b3b8773e00 100644
--- a/lib/spack/spack/cmd/common/arguments.py
+++ b/lib/spack/spack/cmd/common/arguments.py
@@ -1,31 +1,14 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 import argparse
 
 import spack.cmd
+import spack.config
+import spack.environment as ev
 import spack.modules
 import spack.spec
 import spack.store
@@ -52,7 +35,7 @@ def add_common_arguments(parser, list_of_arguments):
 
 
 class ConstraintAction(argparse.Action):
-    """Constructs a list of specs based on a constraint given on the command line
+    """Constructs a list of specs based on constraints from the command line
 
     An instance of this class is supposed to be used as an argument action
     in a parser. It will read a constraint and will attach a function to the
@@ -60,7 +43,6 @@ class ConstraintAction(argparse.Action):
 
     To obtain the specs from a command the function must be called.
     """
-
     def __call__(self, parser, namespace, values, option_string=None):
         # Query specs from command line
         self.values = values
@@ -70,45 +52,30 @@ class ConstraintAction(argparse.Action):
     def _specs(self, **kwargs):
         qspecs = spack.cmd.parse_specs(self.values)
 
+        # If an environment is provided, we'll restrict the search to
+        # only its installed packages.
+        env = ev._active_environment
+        if env:
+            kwargs['hashes'] = set(env.all_hashes())
+
         # return everything for an empty query.
         if not qspecs:
             return spack.store.db.query(**kwargs)
 
         # Return only matching stuff otherwise.
-        specs = set()
+        specs = {}
         for spec in qspecs:
             for s in spack.store.db.query(spec, **kwargs):
-                specs.add(s)
-        return sorted(specs)
+                # This is fast for already-concrete specs
+                specs[s.dag_hash()] = s
 
-
-class CleanOrDirtyAction(argparse.Action):
-    """Sets the dirty flag in the current namespace"""
-
-    def __init__(self, *args, **kwargs):
-        kwargs['default'] = spack.dirty
-        super(CleanOrDirtyAction, self).__init__(*args, **kwargs)
-
-    def __call__(self, parser, namespace, values, option_string=None):
-        if option_string == '--clean':
-            setattr(namespace, self.dest, False)
-        elif option_string == '--dirty':
-            setattr(namespace, self.dest, True)
-        else:
-            msg = 'expected "--dirty" or "--clean" [got {0} instead]'
-            raise argparse.ArgumentError(msg.format(option_string))
+        return sorted(specs.values())
 
 
 _arguments['constraint'] = Args(
     'constraint', nargs=argparse.REMAINDER, action=ConstraintAction,
     help='constraint to select a subset of installed packages')
 
-_arguments['module_type'] = Args(
-    '-m', '--module-type',
-    choices=spack.modules.module_types.keys(),
-    action='append',
-    help='type of module file. More than one choice is allowed [default: tcl]')  # NOQA: ignore=E501
-
 _arguments['yes_to_all'] = Args(
     '-y', '--yes-to-all', action='store_true', dest='yes_to_all',
     help='assume "yes" is the answer to every confirmation request')
@@ -117,22 +84,24 @@ _arguments['recurse_dependencies'] = Args(
     '-r', '--dependencies', action='store_true', dest='recurse_dependencies',
     help='recursively traverse spec dependencies')
 
+_arguments['recurse_dependents'] = Args(
+    '-R', '--dependents', action='store_true', dest='dependents',
+    help='also uninstall any packages that depend on the ones given '
+    'via command line')
+
 _arguments['clean'] = Args(
     '--clean',
-    action=CleanOrDirtyAction,
+    action='store_false',
+    default=spack.config.get('config:dirty'),
     dest='dirty',
-    help='sanitize the environment from variables that can affect how ' +
-         ' packages find libraries or headers',
-    nargs=0
-)
+    help='unset harmful variables in the build environment (default)')
 
 _arguments['dirty'] = Args(
     '--dirty',
-    action=CleanOrDirtyAction,
+    action='store_true',
+    default=spack.config.get('config:dirty'),
     dest='dirty',
-    help='maintain the current environment without trying to sanitize it',
-    nargs=0
-)
+    help='preserve user environment in the spack build environment (danger!)')
 
 _arguments['long'] = Args(
     '-l', '--long', action='store_true',
@@ -142,6 +111,24 @@ _arguments['very_long'] = Args(
     '-L', '--very-long', action='store_true',
     help='show full dependency hashes as well as versions')
 
+_arguments['jobs'] = Args(
+    '-j', '--jobs', action='store', type=int, dest='jobs',
+    help="explicitely set number of make jobs. default is #cpus")
+
 _arguments['tags'] = Args(
     '-t', '--tags', action='append',
     help='filter a package query by tags')
+
+_arguments['jobs'] = Args(
+    '-j', '--jobs', action='store', type=int, dest="jobs",
+    help="explicitly set number of make jobs, default is #cpus.")
+
+_arguments['install_status'] = Args(
+    '-I', '--install-status', action='store_true', default=False,
+    help='show install status of packages. packages can be: '
+         'installed [+], missing and needed by an installed package [-], '
+         'or not installed (no annotation)')
+
+_arguments['no_checksum'] = Args(
+    '-n', '--no-checksum', action='store_true', default=False,
+    help="do not use checksums to verify downloadeded files (unsafe)")
diff --git a/lib/spack/spack/cmd/compiler.py b/lib/spack/spack/cmd/compiler.py
index e7be196b1f..bf2e1687f8 100644
--- a/lib/spack/spack/cmd/compiler.py
+++ b/lib/spack/spack/cmd/compiler.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from __future__ import print_function
 
 import argparse
@@ -46,7 +27,8 @@ def setup_parser(subparser):
     sp = subparser.add_subparsers(
         metavar='SUBCOMMAND', dest='compiler_command')
 
-    scopes = spack.config.config_scopes
+    scopes = spack.config.scopes()
+    scopes_metavar = spack.config.scopes_metavar
 
     # Find
     find_parser = sp.add_parser(
@@ -54,7 +36,8 @@ def setup_parser(subparser):
         help='search the system for compilers to add to Spack configuration')
     find_parser.add_argument('add_paths', nargs=argparse.REMAINDER)
     find_parser.add_argument(
-        '--scope', choices=scopes, default=spack.cmd.default_modify_scope,
+        '--scope', choices=scopes, metavar=scopes_metavar,
+        default=spack.config.default_modify_scope(),
         help="configuration scope to modify")
 
     # Remove
@@ -65,20 +48,23 @@ def setup_parser(subparser):
         help='remove ALL compilers that match spec')
     remove_parser.add_argument('compiler_spec')
     remove_parser.add_argument(
-        '--scope', choices=scopes, default=spack.cmd.default_modify_scope,
+        '--scope', choices=scopes, metavar=scopes_metavar,
+        default=spack.config.default_modify_scope(),
         help="configuration scope to modify")
 
     # List
     list_parser = sp.add_parser('list', help='list available compilers')
     list_parser.add_argument(
-        '--scope', choices=scopes, default=spack.cmd.default_list_scope,
+        '--scope', choices=scopes, metavar=scopes_metavar,
+        default=spack.config.default_list_scope(),
         help="configuration scope to read from")
 
     # Info
     info_parser = sp.add_parser('info', help='show compiler paths')
     info_parser.add_argument('compiler_spec')
     info_parser.add_argument(
-        '--scope', choices=scopes, default=spack.cmd.default_list_scope,
+        '--scope', choices=scopes, metavar=scopes_metavar,
+        default=spack.config.default_list_scope(),
         help="configuration scope to read from")
 
 
@@ -109,7 +95,9 @@ def compiler_find(args):
                                                 init_config=False)
         n = len(new_compilers)
         s = 's' if n > 1 else ''
-        filename = spack.config.get_config_filename(args.scope, 'compilers')
+
+        config = spack.config.config
+        filename = config.get_config_filename(args.scope, 'compilers')
         tty.msg("Added %d new compiler%s to %s" % (n, s, filename))
         colify(reversed(sorted(c.spec for c in new_compilers)), indent=4)
     else:
diff --git a/lib/spack/spack/cmd/compilers.py b/lib/spack/spack/cmd/compilers.py
index 7895d11d94..7510e24b7e 100644
--- a/lib/spack/spack/cmd/compilers.py
+++ b/lib/spack/spack/cmd/compilers.py
@@ -1,28 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-import spack
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import spack.config
 from spack.cmd.compiler import compiler_list
 
 description = "list available compilers"
@@ -31,8 +12,12 @@ level = "short"
 
 
 def setup_parser(subparser):
-    subparser.add_argument('--scope', choices=spack.config.config_scopes,
-                           help="configuration scope to read/modify")
+    scopes = spack.config.scopes()
+    scopes_metavar = spack.config.scopes_metavar
+
+    subparser.add_argument(
+        '--scope', choices=scopes, metavar=scopes_metavar,
+        help="configuration scope to read/modify")
 
 
 def compilers(parser, args):
diff --git a/lib/spack/spack/cmd/concretize.py b/lib/spack/spack/cmd/concretize.py
new file mode 100644
index 0000000000..728718e502
--- /dev/null
+++ b/lib/spack/spack/cmd/concretize.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import spack.environment as ev
+
+description = 'concretize an environment and write a lockfile'
+section = "environments"
+level = "long"
+
+
+def setup_parser(subparser):
+    subparser.add_argument(
+        '-f', '--force', action='store_true',
+        help="Re-concretize even if already concretized.")
+
+
+def concretize(parser, args):
+    env = ev.get_env(args, 'concretize')
+    env.concretize(force=args.force)
+    env.write()
diff --git a/lib/spack/spack/cmd/config.py b/lib/spack/spack/cmd/config.py
index f2325e73e0..4fd21768c8 100644
--- a/lib/spack/spack/cmd/config.py
+++ b/lib/spack/spack/cmd/config.py
@@ -1,28 +1,17 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from __future__ import print_function
+import os
+
+import llnl.util.tty as tty
+
 import spack.config
+import spack.environment as ev
+
+from spack.util.editor import editor
 
 description = "get and set configuration options"
 section = "config"
@@ -30,9 +19,13 @@ level = "long"
 
 
 def setup_parser(subparser):
+    scopes = spack.config.scopes()
+    scopes_metavar = spack.config.scopes_metavar
+
     # User can only choose one
-    subparser.add_argument('--scope', choices=spack.config.config_scopes,
-                           help="configuration scope to read/modify")
+    subparser.add_argument(
+        '--scope', choices=scopes, metavar=scopes_metavar,
+        help="configuration scope to read/modify")
 
     sp = subparser.add_subparsers(metavar='SUBCOMMAND', dest='config_command')
 
@@ -40,34 +33,102 @@ def setup_parser(subparser):
     get_parser.add_argument('section',
                             help="configuration section to print. "
                                  "options: %(choices)s",
+                            nargs='?',
                             metavar='SECTION',
                             choices=spack.config.section_schemas)
 
+    blame_parser = sp.add_parser(
+        'blame', help='print configuration annotated with source file:line')
+    blame_parser.add_argument('section',
+                              help="configuration section to print. "
+                              "options: %(choices)s",
+                              metavar='SECTION',
+                              choices=spack.config.section_schemas)
+
     edit_parser = sp.add_parser('edit', help='edit configuration file')
     edit_parser.add_argument('section',
                              help="configuration section to edit. "
                                   "options: %(choices)s",
                              metavar='SECTION',
+                             nargs='?',
                              choices=spack.config.section_schemas)
+    edit_parser.add_argument(
+        '--print-file', action='store_true',
+        help="print the file name that would be edited")
+
+
+def _get_scope_and_section(args):
+    """Extract config scope and section from arguments."""
+    scope = args.scope
+    section = args.section
+
+    # w/no args and an active environment, point to env manifest
+    if not args.section:
+        env = ev.get_env(args, 'config edit', required=False)
+        if env:
+            scope = env.env_file_config_scope_name()
+
+    # set scope defaults
+    elif not args.scope:
+        if section == 'compilers':
+            scope = spack.config.default_modify_scope()
+        else:
+            scope = 'user'
+
+    return scope, section
 
 
 def config_get(args):
-    spack.config.print_section(args.section)
+    """Dump merged YAML configuration for a specific section.
 
+    With no arguments and an active environment, print the contents of
+    the environment's manifest file (spack.yaml).
 
-def config_edit(args):
-    if not args.scope:
-        if args.section == 'compilers':
-            args.scope = spack.cmd.default_modify_scope
+    """
+    scope, section = _get_scope_and_section(args)
+
+    if scope and scope.startswith('env:'):
+        config_file = spack.config.config.get_config_filename(scope, section)
+        if os.path.exists(config_file):
+            with open(config_file) as f:
+                print(f.read())
         else:
-            args.scope = 'user'
-    if not args.section:
-        args.section = None
-    config_file = spack.config.get_config_filename(args.scope, args.section)
-    spack.editor(config_file)
+            tty.die('environment has no %s file' % ev.manifest_name)
+
+    elif section is not None:
+        spack.config.config.print_section(section)
+
+    else:
+        tty.die('`spack config get` requires a section argument '
+                'or an active environment.')
+
+
+def config_blame(args):
+    """Print out line-by-line blame of merged YAML."""
+    spack.config.config.print_section(args.section, blame=True)
+
+
+def config_edit(args):
+    """Edit the configuration file for a specific scope and config section.
+
+    With no arguments and an active environment, edit the spack.yaml for
+    the active environment.
+
+    """
+    scope, section = _get_scope_and_section(args)
+    if not scope and not section:
+        tty.die('`spack config edit` requires a section argument '
+                'or an active environment.')
+
+    config_file = spack.config.config.get_config_filename(scope, section)
+    if args.print_file:
+        print(config_file)
+    else:
+        editor(config_file)
 
 
 def config(parser, args):
     action = {'get': config_get,
+              'blame': config_blame,
               'edit': config_edit}
     action[args.config_command](args)
diff --git a/lib/spack/spack/cmd/configure.py b/lib/spack/spack/cmd/configure.py
index 346fc71bdc..668d16dafd 100644
--- a/lib/spack/spack/cmd/configure.py
+++ b/lib/spack/spack/cmd/configure.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import argparse
 
 import llnl.util.tty as tty
@@ -34,6 +15,7 @@ from spack.build_systems.qmake import QMakePackage
 from spack.build_systems.waf import WafPackage
 from spack.build_systems.perl import PerlPackage
 from spack.build_systems.intel import IntelPackage
+from spack.build_systems.meson import MesonPackage
 
 description = 'stage and configure a package but do not install'
 section = "build"
@@ -47,6 +29,7 @@ build_system_to_phase = {
     WafPackage: 'configure',
     PerlPackage: 'configure',
     IntelPackage: 'configure',
+    MesonPackage: 'meson',
 }
 
 
@@ -79,7 +62,7 @@ def _stop_at_phase_during_install(args, calling_fn, phase_mapping):
         # Install package dependencies if needed
         parser = argparse.ArgumentParser()
         inst.setup_parser(parser)
-        tty.msg('Checking dependencies for {0}'.format(args.package))
+        tty.msg('Checking dependencies for {0}'.format(args.package[0]))
         cli_args = ['-v'] if args.verbose else []
         install_args = parser.parse_args(cli_args + ['--only=dependencies'])
         install_args.package = args.package
diff --git a/lib/spack/spack/cmd/create.py b/lib/spack/spack/cmd/create.py
index 2e67b7648b..880bdb05a8 100644
--- a/lib/spack/spack/cmd/create.py
+++ b/lib/spack/spack/cmd/create.py
@@ -1,39 +1,21 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from __future__ import print_function
 
 import os
 import re
 
 import llnl.util.tty as tty
-import spack
+from llnl.util.filesystem import mkdirp
+
 import spack.cmd
 import spack.util.web
-from llnl.util.filesystem import mkdirp
-from spack.repository import Repo
+import spack.repo
 from spack.spec import Spec
+from spack.util.editor import editor
 from spack.util.executable import which, ProcessError
 from spack.util.naming import mod_to_class
 from spack.util.naming import simplify_name, valid_fully_qualified_module_name
@@ -46,30 +28,14 @@ level = "short"
 
 
 package_template = '''\
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+# ----------------------------------------------------------------------------
+# If you submit this package back to Spack as a pull request,
+# please first remove this boilerplate and all FIXME comments.
 #
 # This is a template package file for Spack.  We've put "FIXME"
 # next to all the things you'll want to change. Once you've handled
@@ -82,9 +48,8 @@ package_template = '''\
 #     spack edit {name}
 #
 # See the Spack documentation for more information on packaging.
-# If you submit this package back to Spack as a pull request,
-# please first remove this boilerplate and all FIXME comments.
-#
+# ----------------------------------------------------------------------------
+
 from spack import *
 
 
@@ -194,6 +159,18 @@ class CMakePackageTemplate(PackageTemplate):
         return args"""
 
 
+class MesonPackageTemplate(PackageTemplate):
+    """Provides appropriate overrides for meson-based packages"""
+
+    base_class_name = 'MesonPackage'
+
+    body = """\
+    def meson_args(self):
+        # FIXME: If not needed delete this function
+        args = []
+        return args"""
+
+
 class QMakePackageTemplate(PackageTemplate):
     """Provides appropriate overrides for QMake-based packages"""
 
@@ -332,21 +309,14 @@ class PerlbuildPackageTemplate(PerlmakePackageTemplate):
 class OctavePackageTemplate(PackageTemplate):
     """Provides appropriate overrides for octave packages"""
 
+    base_class_name = 'OctavePackage'
+
     dependencies = """\
     extends('octave')
 
     # FIXME: Add additional dependencies if required.
     # depends_on('octave-foo', type=('build', 'run'))"""
 
-    body = """\
-    def install(self, spec, prefix):
-        # FIXME: Add logic to build and install here.
-        octave('--quiet', '--norc',
-               '--built-in-docstrings-file=/dev/null',
-               '--texi-macros-file=/dev/null',
-               '--eval', 'pkg prefix {0}; pkg install {1}'.format(
-                   prefix, self.stage.archive_file))"""
-
     def __init__(self, name, *args):
         # If the user provided `--name octave-splines`, don't rename it
         # octave-octave-splines
@@ -395,6 +365,7 @@ templates = {
     'octave':     OctavePackageTemplate,
     'makefile':   MakefilePackageTemplate,
     'intel':      IntelPackageTemplate,
+    'meson':      MesonPackageTemplate,
     'generic':    PackageTemplate,
 }
 
@@ -464,6 +435,8 @@ class BuildSystemGuesser:
             (r'/Makefile\.PL$',       'perlmake'),
             (r'/.*\.pro$',            'qmake'),
             (r'/(GNU)?[Mm]akefile$',  'makefile'),
+            (r'/DESCRIPTION$',        'octave'),
+            (r'/meson\.build$',       'meson'),
         ]
 
         # Peek inside the compressed file.
@@ -654,17 +627,17 @@ def get_repository(args, name):
     # Figure out where the new package should live
     repo_path = args.repo
     if repo_path is not None:
-        repo = Repo(repo_path)
+        repo = spack.repo.Repo(repo_path)
         if spec.namespace and spec.namespace != repo.namespace:
             tty.die("Can't create package with namespace {0} in repo with "
-                    "namespace {0}".format(spec.namespace, repo.namespace))
+                    "namespace {1}".format(spec.namespace, repo.namespace))
     else:
         if spec.namespace:
-            repo = spack.repo.get_repo(spec.namespace, None)
+            repo = spack.repo.path.get_repo(spec.namespace, None)
             if not repo:
                 tty.die("Unknown namespace: '{0}'".format(spec.namespace))
         else:
-            repo = spack.repo.first_repo()
+            repo = spack.repo.path.first_repo()
 
     # Set the namespace on the spec if it's not there already
     if not spec.namespace:
@@ -681,8 +654,8 @@ def create(parser, args):
     build_system = get_build_system(args, guesser)
 
     # Create the package template object
-    PackageClass = templates[build_system]
-    package = PackageClass(name, url, versions)
+    package_class = templates[build_system]
+    package = package_class(name, url, versions)
     tty.msg("Created template for {0} package".format(package.name))
 
     # Create a directory for the new package
@@ -699,4 +672,4 @@ def create(parser, args):
     tty.msg("Created package file: {0}".format(pkg_path))
 
     # Open up the new package file in your $EDITOR
-    spack.editor(pkg_path)
+    editor(pkg_path)
diff --git a/lib/spack/spack/cmd/deactivate.py b/lib/spack/spack/cmd/deactivate.py
index ae5241dfe8..ef450b1c94 100644
--- a/lib/spack/spack/cmd/deactivate.py
+++ b/lib/spack/spack/cmd/deactivate.py
@@ -1,34 +1,14 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import argparse
 import llnl.util.tty as tty
 
-import spack
 import spack.cmd
 import spack.store
-from spack.directory_layout import YamlViewExtensionsLayout
+from spack.filesystem_view import YamlFilesystemView
 from spack.graph import topological_sort
 
 description = "deactivate a package extension"
@@ -60,24 +40,29 @@ def deactivate(parser, args):
     spec = spack.cmd.disambiguate_spec(specs[0])
     pkg = spec.package
 
-    layout = spack.store.extensions
-    if args.view is not None:
-        layout = YamlViewExtensionsLayout(args.view, spack.store.layout)
+    if args.view:
+        target = args.view
+    elif pkg.is_extension:
+        target = pkg.extendee_spec.prefix
+    elif pkg.extendable:
+        target = spec.prefix
+
+    view = YamlFilesystemView(target, spack.store.layout)
 
     if args.all:
         if pkg.extendable:
             tty.msg("Deactivating all extensions of %s" % pkg.spec.short_spec)
             ext_pkgs = spack.store.db.activated_extensions_for(
-                spec, extensions_layout=layout)
+                spec, view.extensions_layout)
 
             for ext_pkg in ext_pkgs:
                 ext_pkg.spec.normalize()
-                if ext_pkg.is_activated():
-                    ext_pkg.do_deactivate(force=True, extensions_layout=layout)
+                if ext_pkg.is_activated(view):
+                    ext_pkg.do_deactivate(view, force=True)
 
         elif pkg.is_extension:
             if not args.force and \
-               not spec.package.is_activated(extensions_layout=layout):
+               not spec.package.is_activated(view):
                 tty.die("%s is not activated." % pkg.spec.short_spec)
 
             tty.msg("Deactivating %s and all dependencies." %
@@ -90,11 +75,8 @@ def deactivate(parser, args):
                 espec = index[name]
                 epkg = espec.package
                 if epkg.extends(pkg.extendee_spec):
-                    if epkg.is_activated(extensions_layout=layout) or \
-                       args.force:
-
-                        epkg.do_deactivate(
-                            force=args.force, extensions_layout=layout)
+                    if epkg.is_activated(view) or args.force:
+                        epkg.do_deactivate(view, force=args.force)
 
         else:
             tty.die(
@@ -107,7 +89,7 @@ def deactivate(parser, args):
                     "Did you mean 'spack deactivate --all'?")
 
         if not args.force and \
-           not spec.package.is_activated(extensions_layout=layout):
+           not spec.package.is_activated(view):
             tty.die("Package %s is not activated." % specs[0].short_spec)
 
-        spec.package.do_deactivate(force=args.force, extensions_layout=layout)
+        spec.package.do_deactivate(view, force=args.force)
diff --git a/lib/spack/spack/cmd/debug.py b/lib/spack/spack/cmd/debug.py
index 1d3e645a29..e1fa227371 100644
--- a/lib/spack/spack/cmd/debug.py
+++ b/lib/spack/spack/cmd/debug.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 import re
 from datetime import datetime
@@ -30,7 +11,7 @@ from glob import glob
 import llnl.util.tty as tty
 from llnl.util.filesystem import working_dir
 
-import spack
+import spack.paths
 from spack.util.executable import which
 
 description = "debugging commands for troubleshooting Spack"
@@ -52,7 +33,7 @@ def _debug_tarball_suffix():
     if not git:
         return 'nobranch-nogit-%s' % suffix
 
-    with working_dir(spack.spack_root):
+    with working_dir(spack.paths.prefix):
         if not os.path.isdir('.git'):
             return 'nobranch.nogit.%s' % suffix
 
@@ -76,14 +57,14 @@ def create_db_tarball(args):
     tarball_name = "spack-db.%s.tar.gz" % _debug_tarball_suffix()
     tarball_path = os.path.abspath(tarball_name)
 
-    base = os.path.basename(spack.store.root)
+    base = os.path.basename(str(spack.store.root))
     transform_args = []
     if 'GNU' in tar('--version', output=str):
         transform_args = ['--transform', 's/^%s/%s/' % (base, tarball_name)]
     else:
         transform_args = ['-s', '/^%s/%s/' % (base, tarball_name)]
 
-    wd = os.path.dirname(spack.store.root)
+    wd = os.path.dirname(str(spack.store.root))
     with working_dir(wd):
         files = [spack.store.db._index_path]
         files += glob('%s/*/*/*/.spack/spec.yaml' % base)
diff --git a/lib/spack/spack/cmd/dependencies.py b/lib/spack/spack/cmd/dependencies.py
index 95183fa318..fe66bef1df 100644
--- a/lib/spack/spack/cmd/dependencies.py
+++ b/lib/spack/spack/cmd/dependencies.py
@@ -1,34 +1,15 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import argparse
 
 import llnl.util.tty as tty
 from llnl.util.tty.colify import colify
 
-import spack
 import spack.store
+import spack.repo
 import spack.cmd
 
 description = "show dependencies of a package"
@@ -43,7 +24,10 @@ def setup_parser(subparser):
         "instead of possible dependencies of a package.")
     subparser.add_argument(
         '-t', '--transitive', action='store_true', default=False,
-        help="Show all transitive dependencies.")
+        help="show all transitive dependencies")
+    subparser.add_argument(
+        '-V', '--no-expand-virtuals', action='store_false', default=True,
+        dest="expand_virtuals", help="do not expand virtual dependencies")
     subparser.add_argument(
         'spec', nargs=argparse.REMAINDER, help="spec or package name")
 
@@ -70,13 +54,15 @@ def dependencies(parser, args):
         if not spec.virtual:
             packages = [spec.package]
         else:
-            packages = [spack.repo.get(s.name)
-                        for s in spack.repo.providers_for(spec)]
+            packages = [
+                spack.repo.get(s.name)
+                for s in spack.repo.path.providers_for(spec)]
 
         dependencies = set()
         for pkg in packages:
             dependencies.update(
-                set(pkg.possible_dependencies(args.transitive)))
+                set(pkg.possible_dependencies(
+                    args.transitive, args.expand_virtuals)))
 
         if spec.name in dependencies:
             dependencies.remove(spec.name)
diff --git a/lib/spack/spack/cmd/dependents.py b/lib/spack/spack/cmd/dependents.py
index 1ad3c0a3b9..46397ed5f0 100644
--- a/lib/spack/spack/cmd/dependents.py
+++ b/lib/spack/spack/cmd/dependents.py
@@ -1,33 +1,14 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import argparse
 
 import llnl.util.tty as tty
 from llnl.util.tty.colify import colify
 
-import spack
+import spack.repo
 import spack.store
 import spack.cmd
 
@@ -57,14 +38,14 @@ def inverted_dependencies():
        actual dependents.
     """
     dag = {}
-    for pkg in spack.repo.all_packages():
+    for pkg in spack.repo.path.all_packages():
         dag.setdefault(pkg.name, set())
         for dep in pkg.dependencies:
             deps = [dep]
 
             # expand virtuals if necessary
-            if spack.repo.is_virtual(dep):
-                deps += [s.name for s in spack.repo.providers_for(dep)]
+            if spack.repo.path.is_virtual(dep):
+                deps += [s.name for s in spack.repo.path.providers_for(dep)]
 
             for d in deps:
                 dag.setdefault(d, set()).add(pkg.name)
diff --git a/lib/spack/spack/cmd/diy.py b/lib/spack/spack/cmd/diy.py
index ba5c7eb954..39282b3b2d 100644
--- a/lib/spack/spack/cmd/diy.py
+++ b/lib/spack/spack/cmd/diy.py
@@ -1,47 +1,34 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import sys
 import os
 import argparse
 
 import llnl.util.tty as tty
 
-import spack
+import spack.config
 import spack.cmd
+import spack.repo
 import spack.cmd.common.arguments as arguments
 from spack.stage import DIYStage
 
 description = "do-it-yourself: build from an existing source directory"
-section = "developer"
+section = "build"
 level = "long"
 
 
 def setup_parser(subparser):
+    arguments.add_common_arguments(subparser, ['jobs'])
+    subparser.add_argument(
+        '-d', '--source-path', dest='source_path', default=None,
+        help="path to source directory. defaults to the current directory")
     subparser.add_argument(
         '-i', '--ignore-dependencies', action='store_true', dest='ignore_deps',
         help="don't try to install dependencies of requested packages")
+    arguments.add_common_arguments(subparser, ['no_checksum'])
     subparser.add_argument(
         '--keep-prefix', action='store_true',
         help="do not remove the install prefix if installation fails")
@@ -63,12 +50,16 @@ def diy(self, args):
     if not args.spec:
         tty.die("spack diy requires a package spec argument.")
 
+    if args.jobs is not None:
+        if args.jobs <= 0:
+            tty.die("the -j option must be a positive integer")
+
     specs = spack.cmd.parse_specs(args.spec)
     if len(specs) > 1:
         tty.die("spack diy only takes one spec.")
 
     spec = specs[0]
-    if not spack.repo.exists(spec.name):
+    if not spack.repo.path.exists(spec.name):
         tty.die("No package for '{0}' was found.".format(spec.name),
                 "  Use `spack create` to create a new package")
 
@@ -85,13 +76,20 @@ def diy(self, args):
         tty.msg("Uninstall or try adding a version suffix for this DIY build.")
         sys.exit(1)
 
+    source_path = args.source_path
+    if source_path is None:
+        source_path = os.getcwd()
+    source_path = os.path.abspath(source_path)
+
     # Forces the build to run out of the current directory.
-    package.stage = DIYStage(os.getcwd())
+    package.stage = DIYStage(source_path)
 
-    # TODO: make this an argument, not a global.
-    spack.do_checksum = False
+    # disable checksumming if requested
+    if args.no_checksum:
+        spack.config.set('config:checksum', False, scope='command_line')
 
     package.do_install(
+        make_jobs=args.jobs,
         keep_prefix=args.keep_prefix,
         install_deps=not args.ignore_deps,
         verbose=not args.quiet,
diff --git a/lib/spack/spack/cmd/docs.py b/lib/spack/spack/cmd/docs.py
index 02096a0020..9af6a37d7c 100644
--- a/lib/spack/spack/cmd/docs.py
+++ b/lib/spack/spack/cmd/docs.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import webbrowser
 
 description = 'open spack documentation in a web browser'
diff --git a/lib/spack/spack/cmd/edit.py b/lib/spack/spack/cmd/edit.py
index 48d423a97e..ddc49753af 100644
--- a/lib/spack/spack/cmd/edit.py
+++ b/lib/spack/spack/cmd/edit.py
@@ -1,36 +1,18 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
+import glob
 
 import llnl.util.tty as tty
-from llnl.util.filesystem import join_path
 
-import spack
 import spack.cmd
+import spack.paths
+import spack.repo
 from spack.spec import Spec
-from spack.repository import Repo
+from spack.util.editor import editor
 
 description = "open package files in $EDITOR"
 section = "packaging"
@@ -47,11 +29,11 @@ def edit_package(name, repo_path, namespace):
     """
     # Find the location of the package
     if repo_path:
-        repo = Repo(repo_path)
+        repo = spack.repo.Repo(repo_path)
     elif namespace:
-        repo = spack.repo.get_repo(namespace)
+        repo = spack.repo.path.get_repo(namespace)
     else:
-        repo = spack.repo
+        repo = spack.repo.path
     path = repo.filename_for_package_name(name)
 
     spec = Spec(name)
@@ -64,7 +46,7 @@ def edit_package(name, repo_path, namespace):
         tty.die("No package for '{0}' was found.".format(spec.name),
                 "  Use `spack create` to create a new package")
 
-    spack.editor(path)
+    editor(path)
 
 
 def setup_parser(subparser):
@@ -74,19 +56,23 @@ def setup_parser(subparser):
     # Edits package files by default
     excl_args.add_argument(
         '-b', '--build-system', dest='path', action='store_const',
-        const=spack.build_systems_path,
+        const=spack.paths.build_systems_path,
         help="Edit the build system with the supplied name.")
     excl_args.add_argument(
         '-c', '--command', dest='path', action='store_const',
-        const=spack.cmd.command_path,
+        const=spack.paths.command_path,
         help="edit the command with the supplied name")
     excl_args.add_argument(
+        '-d', '--docs', dest='path', action='store_const',
+        const=os.path.join(spack.paths.lib_path, 'docs'),
+        help="edit the docs with the supplied name")
+    excl_args.add_argument(
         '-t', '--test', dest='path', action='store_const',
-        const=spack.test_path,
+        const=spack.paths.test_path,
         help="edit the test with the supplied name")
     excl_args.add_argument(
         '-m', '--module', dest='path', action='store_const',
-        const=spack.module_path,
+        const=spack.paths.module_path,
         help="edit the main spack module with the supplied name")
 
     # Options for editing packages
@@ -106,18 +92,36 @@ def edit(parser, args):
     name = args.name
 
     # By default, edit package files
-    path = spack.packages_path
+    path = spack.paths.packages_path
 
     # If `--command`, `--test`, or `--module` is chosen, edit those instead
     if args.path:
         path = args.path
         if name:
-            path = join_path(path, name + ".py")
+            # convert command names to python module name
+            if path == spack.paths.command_path:
+                name = spack.cmd.python_name(name)
+
+            path = os.path.join(path, name)
             if not os.path.exists(path):
-                tty.die("No command for '{0}' was found.".format(name))
-        spack.editor(path)
+                files = glob.glob(path + '*')
+                blacklist = ['.pyc', '~']  # blacklist binaries and backups
+                files = list(filter(
+                    lambda x: all(s not in x for s in blacklist), files))
+                if len(files) > 1:
+                    m = 'Multiple files exist with the name {0}.'.format(name)
+                    m += ' Please specify a suffix. Files are:\n\n'
+                    for f in files:
+                        m += '        ' + os.path.basename(f) + '\n'
+                    tty.die(m)
+                if not files:
+                    tty.die("No file for '{0}' was found in {1}".format(name,
+                                                                        path))
+                path = files[0]  # already confirmed only one entry in files
+
+        editor(path)
     elif name:
         edit_package(name, args.repo, args.namespace)
     else:
         # By default open the directory where packages live
-        spack.editor(path)
+        editor(path)
diff --git a/lib/spack/spack/cmd/env.py b/lib/spack/spack/cmd/env.py
index 14432c4dd0..c8b9c169b5 100644
--- a/lib/spack/spack/cmd/env.py
+++ b/lib/spack/spack/cmd/env.py
@@ -1,78 +1,364 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import os
+import sys
+
+import llnl.util.tty as tty
+import llnl.util.filesystem as fs
+from llnl.util.tty.colify import colify
+from llnl.util.tty.color import colorize
+
+import spack.config
+import spack.schema.env
+import spack.cmd.install
+import spack.cmd.uninstall
+import spack.cmd.modules
+import spack.cmd.common.arguments as arguments
+import spack.environment as ev
+import spack.util.string as string
+
+description = "manage virtual environments"
+section = "environments"
+level = "short"
+
+
+#: List of subcommands of `spack env`
+subcommands = [
+    'activate',
+    'deactivate',
+    'create',
+    ['remove', 'rm'],
+    ['list', 'ls'],
+    ['status', 'st'],
+    'loads',
+]
+
+
 #
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+# env activate
 #
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
+def env_activate_setup_parser(subparser):
+    """set the current environment"""
+    shells = subparser.add_mutually_exclusive_group()
+    shells.add_argument(
+        '--sh', action='store_const', dest='shell', const='sh',
+        help="print sh commands to activate the environment")
+    shells.add_argument(
+        '--csh', action='store_const', dest='shell', const='csh',
+        help="print csh commands to activate the environment")
+    shells.add_argument(
+        '-d', '--dir', action='store_true', default=False,
+        help="force spack to treat env as a directory, not a name")
+
+    subparser.add_argument(
+        '-p', '--prompt', action='store_true', default=False,
+        help="decorate the command line prompt when activating")
+    subparser.add_argument(
+        metavar='env', dest='activate_env',
+        help='name of environment to activate')
+
+
+def env_activate(args):
+    env = args.activate_env
+    if not args.shell:
+        msg = [
+            "This command works best with Spack's shell support",
+            ""
+        ] + spack.cmd.common.shell_init_instructions + [
+            'Or, if you want to use `spack env activate` without initializing',
+            'shell support, you can run one of these:',
+            '',
+            '    eval `spack env activate --sh %s`   # for bash/sh' % env,
+            '    eval `spack env activate --csh %s`  # for csh/tcsh' % env,
+        ]
+        tty.msg(*msg)
+        return 1
+
+    if ev.exists(env) and not args.dir:
+        spack_env = ev.root(env)
+        short_name = env
+        env_prompt = '[%s]' % env
+
+    elif ev.is_env_dir(env):
+        spack_env = os.path.abspath(env)
+        short_name = os.path.basename(os.path.abspath(env))
+        env_prompt = '[%s]' % short_name
+
+    else:
+        tty.die("No such environment: '%s'" % env)
+
+    if spack_env == os.environ.get('SPACK_ENV'):
+        tty.die("Environment %s is already active" % args.activate_env)
+
+    if args.shell == 'csh':
+        # TODO: figure out how to make color work for csh
+        sys.stdout.write('setenv SPACK_ENV %s;\n' % spack_env)
+        sys.stdout.write('alias despacktivate "spack env deactivate";\n')
+        if args.prompt:
+            sys.stdout.write('if (! $?SPACK_OLD_PROMPT ) '
+                             'setenv SPACK_OLD_PROMPT "${prompt}";\n')
+            sys.stdout.write('set prompt="%s ${prompt}";\n' % env_prompt)
+
+    else:
+        if 'color' in os.environ['TERM']:
+            env_prompt = colorize('@G{%s} ' % env_prompt, color=True)
+
+        sys.stdout.write('export SPACK_ENV=%s;\n' % spack_env)
+        sys.stdout.write("alias despacktivate='spack env deactivate';\n")
+        if args.prompt:
+            sys.stdout.write('if [ -z "${SPACK_OLD_PS1}" ]; then\n')
+            sys.stdout.write('export SPACK_OLD_PS1="${PS1}"; fi;\n')
+            sys.stdout.write('export PS1="%s ${PS1}";\n' % env_prompt)
+
+
 #
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
+# env deactivate
 #
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-from __future__ import print_function
+def env_deactivate_setup_parser(subparser):
+    """deactivate any active environment in the shell"""
+    shells = subparser.add_mutually_exclusive_group()
+    shells.add_argument(
+        '--sh', action='store_const', dest='shell', const='sh',
+        help="print sh commands to deactivate the environment")
+    shells.add_argument(
+        '--csh', action='store_const', dest='shell', const='csh',
+        help="print csh commands to deactivate the environment")
 
-import argparse
-import os
 
-import llnl.util.tty as tty
-import spack.build_environment as build_env
-import spack.cmd
-import spack.cmd.common.arguments as arguments
+def env_deactivate(args):
+    if not args.shell:
+        msg = [
+            "This command works best with Spack's shell support",
+            ""
+        ] + spack.cmd.common.shell_init_instructions + [
+            'Or, if you want to use `spack env activate` without initializing',
+            'shell support, you can run one of these:',
+            '',
+            '    eval `spack env deactivate --sh`   # for bash/sh',
+            '    eval `spack env deactivate --csh`  # for csh/tcsh',
+        ]
+        tty.msg(*msg)
+        return 1
 
-description = "show install environment for a spec, and run commands"
-section = "build"
-level = "long"
+    if 'SPACK_ENV' not in os.environ:
+        tty.die('No environment is currently active.')
 
+    if args.shell == 'csh':
+        sys.stdout.write('unsetenv SPACK_ENV;\n')
+        sys.stdout.write('if ( $?SPACK_OLD_PROMPT ) '
+                         'set prompt="$SPACK_OLD_PROMPT" && '
+                         'unsetenv SPACK_OLD_PROMPT;\n')
+        sys.stdout.write('unalias despacktivate;\n')
 
-def setup_parser(subparser):
-    arguments.add_common_arguments(subparser, ['clean', 'dirty'])
+    else:
+        sys.stdout.write('unset SPACK_ENV; export SPACK_ENV;\n')
+        sys.stdout.write('unalias despacktivate;\n')
+        sys.stdout.write('if [ -n "$SPACK_OLD_PS1" ]; then\n')
+        sys.stdout.write('export PS1="$SPACK_OLD_PS1";\n')
+        sys.stdout.write('unset SPACK_OLD_PS1; export SPACK_OLD_PS1;\n')
+        sys.stdout.write('fi;\n')
+
+
+#
+# env create
+#
+def env_create_setup_parser(subparser):
+    """create a new environment"""
+    subparser.add_argument(
+        'create_env', metavar='ENV', help='name of environment to create')
+    subparser.add_argument(
+        '-d', '--dir', action='store_true',
+        help='create an environment in a specific directory')
     subparser.add_argument(
-        'spec', nargs=argparse.REMAINDER,
-        help="specs of package environment to emulate")
+        'envfile', nargs='?', default=None,
+        help='optional init file; can be spack.yaml or spack.lock')
 
 
-def env(parser, args):
-    if not args.spec:
-        tty.die("spack env requires a spec.")
-
-    # Specs may have spaces in them, so if they do, require that the
-    # caller put a '--' between the spec and the command to be
-    # executed.  If there is no '--', assume that the spec is the
-    # first argument.
-    sep = '--'
-    if sep in args.spec:
-        s = args.spec.index(sep)
-        spec = args.spec[:s]
-        cmd = args.spec[s + 1:]
+def env_create(args):
+    if args.envfile:
+        with open(args.envfile) as f:
+            _env_create(args.create_env, f, args.dir)
     else:
-        spec = args.spec[0]
-        cmd = args.spec[1:]
+        _env_create(args.create_env, None, args.dir)
+
+
+def _env_create(name_or_path, init_file=None, dir=False):
+    """Create a new environment, with an optional yaml description.
+
+    Arguments:
+        name_or_path (str): name of the environment to create, or path to it
+        init_file (str or file): optional initialization file -- can be
+            spack.yaml or spack.lock
+        dir (bool): if True, create an environment in a directory instead
+            of a named environment
+    """
+    if dir:
+        env = ev.Environment(name_or_path, init_file)
+        env.write()
+        tty.msg("Created environment in %s" % env.path)
+    else:
+        env = ev.create(name_or_path, init_file)
+        env.write()
+        tty.msg("Created environment '%s' in %s" % (name_or_path, env.path))
+    return env
+
+
+#
+# env remove
+#
+def env_remove_setup_parser(subparser):
+    """remove an existing environment"""
+    subparser.add_argument(
+        'rm_env', metavar='ENV', nargs='+',
+        help='environment(s) to remove')
+    arguments.add_common_arguments(subparser, ['yes_to_all'])
+
+
+def env_remove(args):
+    """Remove a *named* environment.
+
+    This removes an environment managed by Spack. Directory environments
+    and `spack.yaml` files embedded in repositories should be removed
+    manually.
+    """
+    read_envs = []
+    for env_name in args.rm_env:
+        env = ev.read(env_name)
+        read_envs.append(env)
+
+    if not args.yes_to_all:
+        answer = tty.get_yes_or_no(
+            'Really remove %s %s?' % (
+                string.plural(len(args.rm_env), 'environment', show_n=False),
+                string.comma_and(args.rm_env)),
+            default=False)
+        if not answer:
+            tty.die("Will not remove any environments")
+
+    for env in read_envs:
+        if env.active:
+            tty.die("Environment %s can't be removed while activated.")
+
+        env.destroy()
+        tty.msg("Successfully removed environment '%s'" % env.name)
+
+
+#
+# env list
+#
+def env_list_setup_parser(subparser):
+    """list available environments"""
 
-    specs = spack.cmd.parse_specs(spec, concretize=True)
-    if len(specs) > 1:
-        tty.die("spack env only takes one spec.")
-    spec = specs[0]
 
-    build_env.setup_package(spec.package, args.dirty)
+def env_list(args):
+    names = ev.all_environment_names()
 
-    if not cmd:
-        # If no command act like the "env" command and print out env vars.
-        for key, val in os.environ.items():
-            print("%s=%s" % (key, val))
+    color_names = []
+    for name in names:
+        if ev.active(name):
+            name = colorize('@*g{%s}' % name)
+        color_names.append(name)
 
+    # say how many there are if writing to a tty
+    if sys.stdout.isatty():
+        if not names:
+            tty.msg('No environments')
+        else:
+            tty.msg('%d environments' % len(names))
+
+    colify(color_names, indent=4)
+
+
+#
+# env status
+#
+def env_status_setup_parser(subparser):
+    """print whether there is an active environment"""
+
+
+def env_status(args):
+    env = ev.get_env(args, 'env status', required=False)
+    if env:
+        if env.path == os.getcwd():
+            tty.msg('Using %s in current directory: %s'
+                    % (ev.manifest_name, env.path))
+        else:
+            tty.msg('In environment %s' % env.name)
     else:
-        # Otherwise execute the command with the new environment
-        os.execvp(cmd[0], cmd)
+        tty.msg('No active environment')
+
+
+#
+# env loads
+#
+def env_loads_setup_parser(subparser):
+    """list modules for an installed environment '(see spack module loads)'"""
+    subparser.add_argument(
+        'env', nargs='?', help='name of env to generate loads file for')
+    subparser.add_argument(
+        '-m', '--module-type', choices=('tcl', 'lmod'),
+        help='type of module system to generate loads for')
+    spack.cmd.modules.add_loads_arguments(subparser)
+
+
+def env_loads(args):
+    env = ev.get_env(args, 'env loads')
+
+    # Set the module types that have been selected
+    module_type = args.module_type
+    if module_type is None:
+        # If no selection has been made select all of them
+        module_type = 'tcl'
+
+    recurse_dependencies = args.recurse_dependencies
+    args.recurse_dependencies = False
+
+    loads_file = fs.join_path(env.path, 'loads')
+    with open(loads_file, 'w') as f:
+        specs = env._get_environment_specs(
+            recurse_dependencies=recurse_dependencies)
+
+        spack.cmd.modules.loads(module_type, specs, args, f)
+
+    print('To load this environment, type:')
+    print('   source %s' % loads_file)
+
+
+#: Dictionary mapping subcommand names and aliases to functions
+subcommand_functions = {}
+
+
+#
+# spack env
+#
+def setup_parser(subparser):
+    sp = subparser.add_subparsers(metavar='SUBCOMMAND', dest='env_command')
+
+    for name in subcommands:
+        if isinstance(name, (list, tuple)):
+            name, aliases = name[0], name[1:]
+        else:
+            aliases = []
+
+        # add commands to subcommands dict
+        function_name = 'env_%s' % name
+        function = globals()[function_name]
+        for alias in [name] + aliases:
+            subcommand_functions[alias] = function
+
+        # make a subparser and run the command's setup function on it
+        setup_parser_cmd_name = 'env_%s_setup_parser' % name
+        setup_parser_cmd = globals()[setup_parser_cmd_name]
+
+        subsubparser = sp.add_parser(
+            name, aliases=aliases, help=setup_parser_cmd.__doc__)
+        setup_parser_cmd(subsubparser)
+
+
+def env(parser, args):
+    """Look for a function called environment_<name> and call it."""
+    action = subcommand_functions[args.env_command]
+    action(args)
diff --git a/lib/spack/spack/cmd/extensions.py b/lib/spack/spack/cmd/extensions.py
index 6d36511691..a564248d63 100644
--- a/lib/spack/spack/cmd/extensions.py
+++ b/lib/spack/spack/cmd/extensions.py
@@ -1,37 +1,18 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import argparse
 
 import llnl.util.tty as tty
 from llnl.util.tty.colify import colify
 
-import spack
 import spack.cmd
 import spack.cmd.find
+import spack.repo
 import spack.store
-from spack.directory_layout import YamlViewExtensionsLayout
+from spack.filesystem_view import YamlFilesystemView
 
 description = "list extensions for package"
 section = "extensions"
@@ -105,7 +86,7 @@ def extensions(parser, args):
     if show_packages:
         #
         # List package names of extensions
-        extensions = spack.repo.extensions_for(spec)
+        extensions = spack.repo.path.extensions_for(spec)
         if not extensions:
             tty.msg("%s has no extensions." % spec.cshort_spec)
         else:
@@ -113,16 +94,19 @@ def extensions(parser, args):
             tty.msg("%d extensions:" % len(extensions))
             colify(ext.name for ext in extensions)
 
-    layout = spack.store.extensions
-    if args.view is not None:
-        layout = YamlViewExtensionsLayout(args.view, spack.store.layout)
+    if args.view:
+        target = args.view
+    else:
+        target = spec.prefix
+
+    view = YamlFilesystemView(target, spack.store.layout)
 
     if show_installed:
         #
         # List specs of installed extensions.
         #
-        installed = [s.spec
-                     for s in spack.store.db.installed_extensions_for(spec)]
+        installed = [
+            s.spec for s in spack.store.db.installed_extensions_for(spec)]
 
         if show_all:
             print
@@ -136,7 +120,7 @@ def extensions(parser, args):
         #
         # List specs of activated extensions.
         #
-        activated = layout.extension_map(spec)
+        activated = view.extensions_layout.extension_map(spec)
         if show_all:
             print
         if not activated:
diff --git a/lib/spack/spack/cmd/fetch.py b/lib/spack/spack/cmd/fetch.py
index e3956b125a..6682cfaaa8 100644
--- a/lib/spack/spack/cmd/fetch.py
+++ b/lib/spack/spack/cmd/fetch.py
@@ -1,33 +1,16 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import argparse
 
 import llnl.util.tty as tty
 
-import spack
 import spack.cmd
+import spack.config
+import spack.repo
+import spack.cmd.common.arguments as arguments
 
 description = "fetch archives for packages"
 section = "build"
@@ -35,9 +18,7 @@ level = "long"
 
 
 def setup_parser(subparser):
-    subparser.add_argument(
-        '-n', '--no-checksum', action='store_true', dest='no_checksum',
-        help="do not check packages against checksum")
+    arguments.add_common_arguments(subparser, ['no_checksum'])
     subparser.add_argument(
         '-m', '--missing', action='store_true',
         help="fetch only missing (not yet installed) dependencies")
@@ -54,7 +35,7 @@ def fetch(parser, args):
         tty.die("fetch requires at least one package argument")
 
     if args.no_checksum:
-        spack.do_checksum = False
+        spack.config.set('config:checksum', False, scope='command_line')
 
     specs = spack.cmd.parse_specs(args.packages, concretize=True)
     for spec in specs:
diff --git a/lib/spack/spack/cmd/find.py b/lib/spack/spack/cmd/find.py
index 71102563c3..b1ea65dfc1 100644
--- a/lib/spack/spack/cmd/find.py
+++ b/lib/spack/spack/cmd/find.py
@@ -1,33 +1,18 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-import sys
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+from __future__ import print_function
 
 import llnl.util.tty as tty
-import spack
+import llnl.util.tty.color as color
+import llnl.util.lang
+
+import spack.environment as ev
+import spack.repo
 import spack.cmd.common.arguments as arguments
 from spack.cmd import display_specs
+from spack.util.string import plural
 
 description = "list and search installed packages"
 section = "basic"
@@ -54,8 +39,12 @@ def setup_parser(subparser):
         const='deps',
         help='show full dependency DAG of installed packages')
 
-    arguments.add_common_arguments(subparser, ['long', 'very_long', 'tags'])
+    arguments.add_common_arguments(
+        subparser, ['long', 'very_long', 'tags'])
 
+    subparser.add_argument('-c', '--show-concretized',
+                           action='store_true',
+                           help='show concretized specs in an environment')
     subparser.add_argument('-f', '--show-flags',
                            action='store_true',
                            dest='show_flags',
@@ -66,11 +55,11 @@ def setup_parser(subparser):
                            help='show full compiler specs')
     implicit_explicit = subparser.add_mutually_exclusive_group()
     implicit_explicit.add_argument(
-        '-e', '--explicit',
+        '-x', '--explicit',
         action='store_true',
         help='show only specs that were installed explicitly')
     implicit_explicit.add_argument(
-        '-E', '--implicit',
+        '-X', '--implicit',
         action='store_true',
         help='show only specs that were installed as dependencies')
     subparser.add_argument(
@@ -96,6 +85,14 @@ def setup_parser(subparser):
                            action='store_true',
                            help='show fully qualified package names')
 
+    subparser.add_argument(
+        '--start-date',
+        help='earliest date of installation [YYYY-MM-DD]'
+    )
+    subparser.add_argument(
+        '--end-date', help='latest date of installation [YYYY-MM-DD]'
+    )
+
     arguments.add_common_arguments(subparser, ['constraint'])
 
 
@@ -114,15 +111,52 @@ def query_arguments(args):
     if args.implicit:
         explicit = False
     q_args = {'installed': installed, 'known': known, "explicit": explicit}
+
+    # Time window of installation
+    for attribute in ('start_date', 'end_date'):
+        date = getattr(args, attribute)
+        if date:
+            q_args[attribute] = llnl.util.lang.pretty_string_to_date(date)
+
     return q_args
 
 
+def setup_env(env):
+    """Create a function for decorating specs when in an environment."""
+
+    def strip_build(seq):
+        return set(s.copy(deps=('link', 'run')) for s in seq)
+
+    added = set(strip_build(env.added_specs()))
+    roots = set(strip_build(env.roots()))
+    removed = set(strip_build(env.removed_specs()))
+
+    def decorator(spec, fmt):
+        # add +/-/* to show added/removed/root specs
+        if any(spec.dag_hash() == r.dag_hash() for r in roots):
+            return color.colorize('@*{%s}' % fmt)
+        elif spec in removed:
+            return color.colorize('@K{%s}' % fmt)
+        else:
+            return '%s' % fmt
+
+    return decorator, added, roots, removed
+
+
 def find(parser, args):
     q_args = query_arguments(args)
-    query_specs = args.specs(**q_args)
+    results = args.specs(**q_args)
+
+    decorator = lambda s, f: f
+    added = set()
+    removed = set()
+
+    env = ev.get_env(args, 'find', required=False)
+    if env:
+        decorator, added, roots, removed = setup_env(env)
 
     # Exit early if no package matches the constraint
-    if not query_specs and args.constraint:
+    if not results and args.constraint:
         msg = "No package matches the query: {0}"
         msg = msg.format(' '.join(args.constraint))
         tty.msg(msg)
@@ -130,11 +164,28 @@ def find(parser, args):
 
     # If tags have been specified on the command line, filter by tags
     if args.tags:
-        packages_with_tags = spack.repo.packages_with_tags(*args.tags)
-        query_specs = [x for x in query_specs if x.name in packages_with_tags]
+        packages_with_tags = spack.repo.path.packages_with_tags(*args.tags)
+        results = [x for x in results if x.name in packages_with_tags]
 
     # Display the result
-    if sys.stdout.isatty():
-        tty.msg("%d installed packages." % len(query_specs))
+    if env:
+        tty.msg('In environment %s' % env.name)
+
+        if not env.user_specs:
+            tty.msg('No root specs')
+        else:
+            tty.msg('Root specs')
+            display_specs(
+                env.user_specs, args,
+                decorator=lambda s, f: color.colorize('@*{%s}' % f))
+        print()
+
+        if args.show_concretized:
+            tty.msg('Concretized roots')
+            display_specs(
+                env.specs_by_hash.values(), args, decorator=decorator)
+            print()
+
+    tty.msg("%s" % plural(len(results), 'installed package'))
 
-    display_specs(query_specs, args)
+    display_specs(results, args, decorator=decorator, all_headers=True)
diff --git a/lib/spack/spack/cmd/flake8.py b/lib/spack/spack/cmd/flake8.py
index 887348e9f6..7049d622f2 100644
--- a/lib/spack/spack/cmd/flake8.py
+++ b/lib/spack/spack/cmd/flake8.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from __future__ import print_function
 
 import re
@@ -33,7 +14,7 @@ import argparse
 
 from llnl.util.filesystem import working_dir, mkdirp
 
-import spack
+import spack.paths
 from spack.util.executable import which
 
 
@@ -53,7 +34,7 @@ def is_package(f):
 
 
 #: List of directories to exclude from checks.
-exclude_directories = [spack.external_path]
+exclude_directories = [spack.paths.external_path]
 
 
 #: This is a dict that maps:
@@ -226,7 +207,7 @@ def setup_parser(subparser):
         help="send filtered files to stdout as well as temp files")
     subparser.add_argument(
         '-r', '--root-relative', action='store_true', default=False,
-        help="print root-relative paths (default is cwd-relative)")
+        help="print root-relative paths (default: cwd-relative)")
     subparser.add_argument(
         '-U', '--no-untracked', dest='untracked', action='store_false',
         default=True, help="exclude untracked files from checks")
@@ -243,11 +224,12 @@ def flake8(parser, args):
         if file_list:
             def prefix_relative(path):
                 return os.path.relpath(
-                    os.path.abspath(os.path.realpath(path)), spack.prefix)
+                    os.path.abspath(os.path.realpath(path)),
+                    spack.paths.prefix)
 
             file_list = [prefix_relative(p) for p in file_list]
 
-        with working_dir(spack.prefix):
+        with working_dir(spack.paths.prefix):
             if not file_list:
                 file_list = changed_files(args)
 
@@ -261,7 +243,7 @@ def flake8(parser, args):
 
         # filter files into a temporary directory with exemptions added.
         for filename in file_list:
-            src_path = os.path.join(spack.prefix, filename)
+            src_path = os.path.join(spack.paths.prefix, filename)
             dest_path = os.path.join(temp, filename)
             filter_file(src_path, dest_path, args.output)
 
@@ -275,13 +257,14 @@ def flake8(parser, args):
             if file_list:
                 output += flake8(
                     '--format', 'pylint',
-                    '--config=%s' % os.path.join(spack.prefix, '.flake8'),
+                    '--config=%s' % os.path.join(spack.paths.prefix,
+                                                 '.flake8'),
                     *file_list, fail_on_error=False, output=str)
                 returncode |= flake8.returncode
             if package_file_list:
                 output += flake8(
                     '--format', 'pylint',
-                    '--config=%s' % os.path.join(spack.prefix,
+                    '--config=%s' % os.path.join(spack.paths.prefix,
                                                  '.flake8_packages'),
                     *package_file_list, fail_on_error=False, output=str)
                 returncode |= flake8.returncode
@@ -293,7 +276,8 @@ def flake8(parser, args):
             # print results relative to current working directory
             def cwd_relative(path):
                 return '{0}: ['.format(os.path.relpath(
-                    os.path.join(spack.prefix, path.group(1)), os.getcwd()))
+                    os.path.join(
+                        spack.paths.prefix, path.group(1)), os.getcwd()))
 
             for line in output.split('\n'):
                 print(re.sub(r'^(.*): \[', cwd_relative, line))
diff --git a/lib/spack/spack/cmd/gpg.py b/lib/spack/spack/cmd/gpg.py
index b16df52e8f..6b81ce885d 100644
--- a/lib/spack/spack/cmd/gpg.py
+++ b/lib/spack/spack/cmd/gpg.py
@@ -1,34 +1,16 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-from spack.util.gpg import Gpg
-import argparse
-import spack
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
+import argparse
+
+import spack.paths
+from spack.util.gpg import Gpg
 
 description = "handle GPG actions for spack"
-section = "developer"
+section = "packaging"
 level = "long"
 
 
@@ -148,7 +130,7 @@ def gpg_trust(args):
 def gpg_init(args):
     import_dir = args.import_dir
     if import_dir is None:
-        import_dir = spack.gpg_keys_path
+        import_dir = spack.paths.gpg_keys_path
 
     for root, _, filenames in os.walk(import_dir):
         for filename in filenames:
diff --git a/lib/spack/spack/cmd/graph.py b/lib/spack/spack/cmd/graph.py
index 16bd6a38a1..6830c90bae 100644
--- a/lib/spack/spack/cmd/graph.py
+++ b/lib/spack/spack/cmd/graph.py
@@ -1,34 +1,15 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from __future__ import print_function
 
 import argparse
 import llnl.util.tty as tty
 
-import spack
 import spack.cmd
+import spack.config
 import spack.store
 from spack.dependency import all_deptypes, canonical_deptype
 from spack.graph import graph_dot, graph_ascii
@@ -98,7 +79,8 @@ def graph(parser, args):
         graph_dot(specs, static=args.static, deptype=deptype)
 
     elif specs:  # ascii is default: user doesn't need to provide it explicitly
-        graph_ascii(specs[0], debug=spack.debug, deptype=deptype)
+        debug = spack.config.get('config:debug')
+        graph_ascii(specs[0], debug=debug, deptype=deptype)
         for spec in specs[1:]:
             print()  # extra line bt/w independent graphs
-            graph_ascii(spec, debug=spack.debug)
+            graph_ascii(spec, debug=debug)
diff --git a/lib/spack/spack/cmd/help.py b/lib/spack/spack/cmd/help.py
index a76ef3a083..ab1a5b5c45 100644
--- a/lib/spack/spack/cmd/help.py
+++ b/lib/spack/spack/cmd/help.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import sys
 from llnl.util.tty.color import colorize
 
@@ -59,9 +40,9 @@ spec expression syntax:
       @B{variant=value1,value2,value3}  set multi-value <variant> values
 
     architecture variants:
-      @m{target=target}                 specific <target> processor
-      @m{os=operating_system}           specific <operating_system>
       @m{platform=platform}             linux, darwin, cray, bgq, etc.
+      @m{os=operating_system}           specific <operating_system>
+      @m{target=target}                 specific <target> processor
       @m{arch=platform-os-target}       shortcut for all three above
 
     cross-compiling:
diff --git a/lib/spack/spack/cmd/info.py b/lib/spack/spack/cmd/info.py
index e53d607704..d4e1f9e5d3 100644
--- a/lib/spack/spack/cmd/info.py
+++ b/lib/spack/spack/cmd/info.py
@@ -1,39 +1,20 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from __future__ import print_function
 
 import textwrap
-
 from six.moves import zip_longest
 
+import llnl.util.tty.color as color
 from llnl.util.tty.colify import colify
 
-import llnl.util.tty.color as color
-import spack
-import spack.fetch_strategy as fs
+import spack.repo
 import spack.spec
+import spack.fetch_strategy as fs
+
 
 description = 'get detailed information on a particular package'
 section = 'basic'
@@ -156,7 +137,7 @@ def print_text_info(pkg):
     color.cprint('')
     color.cprint(section_title('Description:'))
     if pkg.__doc__:
-        color.cprint(pkg.format_doc(indent=4))
+        color.cprint(color.cescape(pkg.format_doc(indent=4)))
     else:
         color.cprint("    None")
 
@@ -195,14 +176,14 @@ def print_text_info(pkg):
         preferred = sorted(pkg.versions, key=key_fn).pop()
 
         f = fs.for_package_version(pkg, preferred)
-        line = version('    {0}'.format(pad(preferred))) + str(f)
+        line = version('    {0}'.format(pad(preferred))) + color.cescape(f)
         color.cprint(line)
         color.cprint('')
         color.cprint(section_title('Safe versions:  '))
 
         for v in reversed(sorted(pkg.versions)):
             f = fs.for_package_version(pkg, v)
-            line = version('    {0}'.format(pad(v))) + str(f)
+            line = version('    {0}'.format(pad(v))) + color.cescape(f)
             color.cprint(line)
 
     color.cprint('')
diff --git a/lib/spack/spack/cmd/install.py b/lib/spack/spack/cmd/install.py
index 86acd580d7..d42988303f 100644
--- a/lib/spack/spack/cmd/install.py
+++ b/lib/spack/spack/cmd/install.py
@@ -1,52 +1,55 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import argparse
-import codecs
-import functools
 import os
-import platform
 import shutil
 import sys
-import time
-import xml.dom.minidom
-import xml.etree.ElementTree as ET
 
 import llnl.util.filesystem as fs
 import llnl.util.tty as tty
-import spack
+
+import spack.build_environment
 import spack.cmd
 import spack.cmd.common.arguments as arguments
-from spack.build_environment import InstallError
-from spack.fetch_strategy import FetchError
-from spack.package import PackageBase
+import spack.environment as ev
+import spack.fetch_strategy
+import spack.paths
+import spack.report
+from spack.error import SpackError
+
 
 description = "build and install packages"
 section = "build"
 level = "short"
 
 
+def update_kwargs_from_args(args, kwargs):
+    """Parse cli arguments and construct a dictionary
+    that will be passed to Package.do_install API"""
+
+    kwargs.update({
+        'keep_prefix': args.keep_prefix,
+        'keep_stage': args.keep_stage,
+        'restage': not args.dont_restage,
+        'install_source': args.install_source,
+        'make_jobs': args.jobs,
+        'verbose': args.verbose,
+        'fake': args.fake,
+        'dirty': args.dirty,
+        'use_cache': args.use_cache
+    })
+    if hasattr(args, 'setup'):
+        setups = set()
+        for arglist_s in args.setup:
+            for arg in [x.strip() for x in arglist_s.split(',')]:
+                setups.add(arg)
+        kwargs['setup'] = setups
+        tty.msg('Setup={0}'.format(kwargs['setup']))
+
+
 def setup_parser(subparser):
     subparser.add_argument(
         '--only',
@@ -58,9 +61,7 @@ the default is to install the package along with all its dependencies.
 alternatively one can decide to install only the package or only
 the dependencies"""
     )
-    subparser.add_argument(
-        '-j', '--jobs', action='store', type=int,
-        help="explicitly set number of make jobs. default is #cpus")
+    arguments.add_common_arguments(subparser, ['jobs', 'install_status'])
     subparser.add_argument(
         '--overwrite', action='store_true',
         help="reinstall an existing spec, even if it has dependents")
@@ -71,20 +72,24 @@ the dependencies"""
         '--keep-stage', action='store_true',
         help="don't remove the build stage if installation succeeds")
     subparser.add_argument(
-        '--restage', action='store_true',
-        help="if a partial install is detected, delete prior state")
-    subparser.add_argument(
-        '--use-cache', action='store_true', dest='use_cache',
-        help="check for pre-built Spack packages in mirrors")
+        '--dont-restage', action='store_true',
+        help="if a partial install is detected, don't delete prior state")
+
+    cache_group = subparser.add_mutually_exclusive_group()
+    cache_group.add_argument(
+        '--use-cache', action='store_true', dest='use_cache', default=True,
+        help="check for pre-built Spack packages in mirrors (default)")
+    cache_group.add_argument(
+        '--no-cache', action='store_false', dest='use_cache', default=True,
+        help="do not check for pre-built Spack packages in mirrors")
+
     subparser.add_argument(
         '--show-log-on-error', action='store_true',
         help="print full build log to stderr if build fails")
     subparser.add_argument(
         '--source', action='store_true', dest='install_source',
         help="install source files in prefix")
-    subparser.add_argument(
-        '-n', '--no-checksum', action='store_true',
-        help="do not check packages against checksum")
+    arguments.add_common_arguments(subparser, ['no_checksum'])
     subparser.add_argument(
         '-v', '--verbose', action='store_true',
         help="display verbose build output while installing")
@@ -92,7 +97,11 @@ the dependencies"""
         '--fake', action='store_true',
         help="fake install for debug purposes.")
     subparser.add_argument(
-        '-f', '--file', action='store_true',
+        '--only-concrete', action='store_true', default=False,
+        help='(with environment) only install already concretized specs')
+    subparser.add_argument(
+        '-f', '--file', action='append', default=[],
+        dest='specfiles', metavar='SPEC_YAML_FILE',
         help="install from file. Read specs to install from .yaml files")
 
     cd_group = subparser.add_mutually_exclusive_group()
@@ -119,7 +128,7 @@ packages. If neither are chosen, don't run tests for any packages."""
     subparser.add_argument(
         '--log-format',
         default=None,
-        choices=['junit'],
+        choices=spack.report.valid_formats,
         help="format to be used for log files"
     )
     subparser.add_argument(
@@ -127,237 +136,49 @@ packages. If neither are chosen, don't run tests for any packages."""
         default=None,
         help="filename for the log file. if not passed a default will be used"
     )
+    subparser.add_argument(
+        '--cdash-upload-url',
+        default=None,
+        help="CDash URL where reports will be uploaded"
+    )
     arguments.add_common_arguments(subparser, ['yes_to_all'])
 
 
-# Needed for test cases
-class TestResult(object):
-    PASSED = 0
-    FAILED = 1
-    SKIPPED = 2
-    ERRORED = 3
-
-
-class TestSuite(object):
-    def __init__(self, spec):
-        self.root = ET.Element('testsuite')
-        self.tests = []
-        self.spec = spec
-
-    def append(self, item):
-        if not isinstance(item, TestCase):
-            raise TypeError(
-                'only TestCase instances may be appended to TestSuite'
-            )
-        self.tests.append(item)  # Append the item to the list of tests
-
-    def dump(self, filename):
-        # Prepare the header for the entire test suite
-        number_of_errors = sum(
-            x.result_type == TestResult.ERRORED for x in self.tests
-        )
-        self.root.set('errors', str(number_of_errors))
-        number_of_failures = sum(
-            x.result_type == TestResult.FAILED for x in self.tests
-        )
-        self.root.set('failures', str(number_of_failures))
-        self.root.set('tests', str(len(self.tests)))
-        self.root.set('name', self.spec.short_spec)
-        self.root.set('hostname', platform.node())
-
-        for item in self.tests:
-            self.root.append(item.element)
-
-        with codecs.open(filename, 'wb', 'utf-8') as file:
-            xml_string = ET.tostring(self.root)
-            xml_string = xml.dom.minidom.parseString(xml_string).toprettyxml()
-            file.write(xml_string)
-
-
-class TestCase(object):
-
-    results = {
-        TestResult.PASSED: None,
-        TestResult.SKIPPED: 'skipped',
-        TestResult.FAILED: 'failure',
-        TestResult.ERRORED: 'error',
-    }
-
-    def __init__(self, classname, name):
-        self.element = ET.Element('testcase')
-        self.element.set('classname', str(classname))
-        self.element.set('name', str(name))
-        self.result_type = None
-
-    def set_duration(self, duration):
-        self.element.set('time', str(duration))
-
-    def set_result(self, result_type,
-                   message=None, error_type=None, text=None):
-        self.result_type = result_type
-        result = TestCase.results[self.result_type]
-        if result is not None and result is not TestResult.PASSED:
-            subelement = ET.SubElement(self.element, result)
-            if error_type is not None:
-                subelement.set('type', error_type)
-            if message is not None:
-                subelement.set('message', str(message))
-            if text is not None:
-                subelement.text = text
-
-
-def fetch_text(path):
-    if not os.path.exists(path):
-        return ''
-
-    with codecs.open(path, 'rb', 'utf-8') as f:
-        return '\n'.join(
-            list(line.strip() for line in f.readlines())
-        )
-
-
-def junit_output(spec, test_suite):
-    # Cycle once and for all on the dependencies and skip
-    # the ones that are already installed. This ensures that
-    # for the same spec, the same number of entries will be
-    # displayed in the XML report
-    for x in spec.traverse(order='post'):
-        package = spack.repo.get(x)
-        if package.installed:
-            test_case = TestCase(package.name, x.short_spec)
-            test_case.set_duration(0.0)
-            test_case.set_result(
-                TestResult.SKIPPED,
-                message='Skipped [already installed]',
-                error_type='already_installed'
-            )
-            test_suite.append(test_case)
-
-    def decorator(func):
-        @functools.wraps(func)
-        def wrapper(self, *args, ** kwargs):
-
-            # Check if the package has been installed already
-            if self.installed:
-                return
-
-            test_case = TestCase(self.name, self.spec.short_spec)
-            # Try to install the package
-            try:
-                # If already installed set the spec as skipped
-                start_time = time.time()
-                # PackageBase.do_install
-                func(self, *args, **kwargs)
-                duration = time.time() - start_time
-                test_case.set_duration(duration)
-                test_case.set_result(TestResult.PASSED)
-            except InstallError:
-                # Check if the package relies on dependencies that
-                # did not install
-                duration = time.time() - start_time
-                test_case.set_duration(duration)
-                if [x for x in self.spec.dependencies(('link', 'run')) if not spack.repo.get(x).installed]:  # NOQA: ignore=E501
-                    test_case.set_duration(0.0)
-                    test_case.set_result(
-                        TestResult.SKIPPED,
-                        message='Skipped [failed dependencies]',
-                        error_type='dep_failed'
-                    )
-                else:
-                    # An InstallError is considered a failure (the recipe
-                    # didn't work correctly)
-                    text = fetch_text(self.build_log_path)
-                    test_case.set_result(
-                        TestResult.FAILED,
-                        message='Installation failure',
-                        text=text
-                    )
-            except FetchError:
-                # A FetchError is considered an error as
-                # we didn't even start building
-                duration = time.time() - start_time
-                test_case.set_duration(duration)
-                text = fetch_text(self.build_log_path)
-                test_case.set_result(
-                    TestResult.FAILED,
-                    message='Unable to fetch package',
-                    text=text
-                )
-            except Exception:
-                # Anything else is also an error
-                duration = time.time() - start_time
-                test_case.set_duration(duration)
-                text = fetch_text(self.build_log_path)
-                test_case.set_result(
-                    TestResult.FAILED,
-                    message='Unexpected exception thrown during install',
-                    text=text
-                )
-            except BaseException:
-                # Anything else is also an error
-                duration = time.time() - start_time
-                test_case.set_duration(duration)
-                text = fetch_text(self.build_log_path)
-                test_case.set_result(
-                    TestResult.FAILED,
-                    message='Unknown error',
-                    text=text
-                )
-
-            # Try to get the log
-            test_suite.append(test_case)
-        return wrapper
-    return decorator
-
-
 def default_log_file(spec):
     """Computes the default filename for the log file and creates
     the corresponding directory if not present
     """
     fmt = 'test-{x.name}-{x.version}-{hash}.xml'
     basename = fmt.format(x=spec, hash=spec.dag_hash())
-    dirname = fs.join_path(spack.var_path, 'junit-report')
+    dirname = fs.os.path.join(spack.paths.var_path, 'junit-report')
     fs.mkdirp(dirname)
-    return fs.join_path(dirname, basename)
-
+    return fs.os.path.join(dirname, basename)
 
-def install_spec(cli_args, kwargs, spec):
 
-    saved_do_install = PackageBase.do_install
-    decorator = lambda fn: fn
+def install_spec(cli_args, kwargs, abstract_spec, spec):
+    """Do the actual installation."""
 
-    # Check if we were asked to produce some log for dashboards
-    if cli_args.log_format is not None:
-        # Compute the filename for logging
-        log_filename = cli_args.log_file
-        if not log_filename:
-            log_filename = default_log_file(spec)
-
-        # Create the test suite in which to log results
-        test_suite = TestSuite(spec)
-
-        # Temporarily decorate PackageBase.do_install to monitor
-        # recursive calls.
-        decorator = junit_output(spec, test_suite)
+    # handle active environment, if any
+    def install(spec, kwargs):
+        env = ev.get_env(cli_args, 'install', required=False)
+        if env:
+            env.install(abstract_spec, spec, **kwargs)
+            env.write()
+        else:
+            spec.package.do_install(**kwargs)
 
-    # Do the actual installation
     try:
-        # decorate the install if necessary
-        PackageBase.do_install = decorator(PackageBase.do_install)
-
         if cli_args.things_to_install == 'dependencies':
             # Install dependencies as-if they were installed
             # for root (explicit=False in the DB)
             kwargs['explicit'] = False
             for s in spec.dependencies():
-                p = spack.repo.get(s)
-                p.do_install(**kwargs)
+                install(s, kwargs)
         else:
-            package = spack.repo.get(spec)
             kwargs['explicit'] = True
-            package.do_install(**kwargs)
+            install(spec, kwargs)
 
-    except InstallError as e:
+    except spack.build_environment.InstallError as e:
         if cli_args.show_log_on_error:
             e.print_context()
             if not os.path.exists(e.pkg.build_log_path):
@@ -368,94 +189,114 @@ def install_spec(cli_args, kwargs, spec):
                     shutil.copyfileobj(log, sys.stderr)
         raise
 
-    finally:
-        PackageBase.do_install = saved_do_install
-
-    # Dump test output if asked to
-    if cli_args.log_format is not None:
-        test_suite.dump(log_filename)
-
 
 def install(parser, args, **kwargs):
-    if not args.package:
-        tty.die("install requires at least one package argument")
+    if not args.package and not args.specfiles:
+        # if there are no args but an active environment or spack.yaml file
+        # then install the packages from it.
+        env = ev.get_env(args, 'install', required=False)
+        if env:
+            if not args.only_concrete:
+                env.concretize()
+                env.write()
+            tty.msg("Installing environment %s" % env.name)
+            env.install_all(args)
+            return
+        else:
+            tty.die("install requires a package argument or a spack.yaml file")
 
     if args.jobs is not None:
         if args.jobs <= 0:
             tty.die("The -j option must be a positive integer!")
 
     if args.no_checksum:
-        spack.do_checksum = False        # TODO: remove this global.
+        spack.config.set('config:checksum', False, scope='command_line')
 
     # Parse cli arguments and construct a dictionary
     # that will be passed to Package.do_install API
+    update_kwargs_from_args(args, kwargs)
     kwargs.update({
-        'keep_prefix': args.keep_prefix,
-        'keep_stage': args.keep_stage,
-        'restage': args.restage,
-        'install_source': args.install_source,
-        'install_deps': 'dependencies' in args.things_to_install,
-        'make_jobs': args.jobs,
-        'verbose': args.verbose,
-        'fake': args.fake,
-        'dirty': args.dirty,
-        'use_cache': args.use_cache
+        'install_dependencies': ('dependencies' in args.things_to_install),
+        'install_package': ('package' in args.things_to_install)
     })
 
     if args.run_tests:
         tty.warn("Deprecated option: --run-tests: use --test=all instead")
 
-    specs = spack.cmd.parse_specs(args.package)
+    # 1. Abstract specs from cli
+    reporter = spack.report.collect_info(args.log_format,
+                                         ' '.join(args.package),
+                                         args.cdash_upload_url)
+    if args.log_file:
+        reporter.filename = args.log_file
+
+    abstract_specs = spack.cmd.parse_specs(args.package)
+    tests = False
     if args.test == 'all' or args.run_tests:
-        spack.package_testing.test_all()
+        tests = True
     elif args.test == 'root':
-        for spec in specs:
-            spack.package_testing.test(spec.name)
-
-    # Spec from cli
-    specs = []
-    if args.file:
-        for file in args.package:
-            with open(file, 'r') as f:
-                specs.append(spack.spec.Spec.from_yaml(f))
-    else:
-        specs = spack.cmd.parse_specs(args.package, concretize=True)
+        tests = [spec.name for spec in abstract_specs]
+    kwargs['tests'] = tests
+
+    try:
+        specs = spack.cmd.parse_specs(
+            args.package, concretize=True, tests=tests)
+    except SpackError as e:
+        reporter.concretization_report(e.message)
+        raise
+
+    # 2. Concrete specs from yaml files
+    for file in args.specfiles:
+        with open(file, 'r') as f:
+            s = spack.spec.Spec.from_yaml(f)
+
+        if s.concretized().dag_hash() != s.dag_hash():
+            msg = 'skipped invalid file "{0}". '
+            msg += 'The file does not contain a concrete spec.'
+            tty.warn(msg.format(file))
+            continue
+
+        specs.append(s.concretized())
+
     if len(specs) == 0:
-        tty.error('The `spack install` command requires a spec to install.')
-
-    if args.overwrite:
-        # If we asked to overwrite an existing spec we must ensure that:
-        # 1. We have only one spec
-        # 2. The spec is already installed
-        assert len(specs) == 1, \
-            "only one spec is allowed when overwriting an installation"
-
-        spec = specs[0]
-        t = spack.store.db.query(spec)
-        assert len(t) == 1, "to overwrite a spec you must install it first"
-
-        # Give the user a last chance to think about overwriting an already
-        # existing installation
-        if not args.yes_to_all:
-            tty.msg('The following package will be reinstalled:\n')
-
-            display_args = {
-                'long': True,
-                'show_flags': True,
-                'variants': True
-            }
-
-            spack.cmd.display_specs(t, **display_args)
-            answer = tty.get_yes_or_no(
-                'Do you want to proceed?', default=False
-            )
-            if not answer:
-                tty.die('Reinstallation aborted.')
-
-        with fs.replace_directory_transaction(specs[0].prefix):
-            install_spec(args, kwargs, specs[0])
-
-    else:
-
-        for spec in specs:
-            install_spec(args, kwargs, spec)
+        tty.die('The `spack install` command requires a spec to install.')
+
+    if not args.log_file and not reporter.filename:
+        reporter.filename = default_log_file(specs[0])
+    reporter.specs = specs
+    with reporter:
+        if args.overwrite:
+            # If we asked to overwrite an existing spec we must ensure that:
+            # 1. We have only one spec
+            # 2. The spec is already installed
+            assert len(specs) == 1, \
+                "only one spec is allowed when overwriting an installation"
+
+            spec = specs[0]
+            t = spack.store.db.query(spec)
+            assert len(t) == 1, "to overwrite a spec you must install it first"
+
+            # Give the user a last chance to think about overwriting an already
+            # existing installation
+            if not args.yes_to_all:
+                tty.msg('The following package will be reinstalled:\n')
+
+                display_args = {
+                    'long': True,
+                    'show_flags': True,
+                    'variants': True
+                }
+
+                spack.cmd.display_specs(t, **display_args)
+                answer = tty.get_yes_or_no(
+                    'Do you want to proceed?', default=False
+                )
+                if not answer:
+                    tty.die('Reinstallation aborted.')
+
+            with fs.replace_directory_transaction(specs[0].prefix):
+                install_spec(args, kwargs, abstract_specs[0], specs[0])
+
+        else:
+            for abstract, concrete in zip(abstract_specs, specs):
+                install_spec(args, kwargs, abstract, concrete)
diff --git a/lib/spack/spack/cmd/license.py b/lib/spack/spack/cmd/license.py
new file mode 100644
index 0000000000..df208d8bbe
--- /dev/null
+++ b/lib/spack/spack/cmd/license.py
@@ -0,0 +1,156 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from __future__ import print_function
+
+import os
+import re
+
+import llnl.util.tty as tty
+
+import spack.paths
+from spack.util.executable import which
+
+description = 'list and check license headers on files in spack'
+section = "developer"
+level = "long"
+
+#: need the git command to check new files
+git = which('git')
+
+#: SPDX license id must appear in the first <license_lines> lines of a file
+license_lines = 6
+
+#: Spack's license identifier
+apache2_mit_spdx = "(Apache-2.0 OR MIT)"
+
+#: regular expressions for licensed files.
+licensed_files = [
+    # spack scripts
+    r'^bin/spack$',
+    r'^bin/spack-python$',
+    r'^bin/sbang$',
+
+    # all of spack core
+    r'^lib/spack/spack/.*\.py$',
+    r'^lib/spack/spack/.*\.sh$',
+    r'^lib/spack/llnl/.*\.py$',
+    r'^lib/spack/env/cc$',
+
+    # rst files in documentation
+    r'^lib/spack/docs/(?!command_index|spack|llnl).*\.rst$',
+    r'^lib/spack/docs/.*\.py$',
+
+    # 2 files in external
+    r'^lib/spack/external/__init__.py$',
+    r'^lib/spack/external/ordereddict_backport.py$',
+
+    # shell scripts in share
+    r'^share/spack/.*\.sh$',
+    r'^share/spack/.*\.bash$',
+    r'^share/spack/.*\.csh$',
+    r'^share/spack/qa/run-[^/]*$',
+
+    # all packages
+    r'^var/spack/repos/.*/package.py$'
+]
+
+#: licensed files that can have LGPL language in them
+#: so far, just this command -- so it can find LGPL things elsewhere
+lgpl_exceptions = [
+    r'lib/spack/spack/cmd/license.py',
+    r'lib/spack/spack/test/cmd/license.py',
+]
+
+
+def _all_spack_files(root=spack.paths.prefix):
+    """Generates root-relative paths of all files in the spack repository."""
+    for cur_root, folders, files in os.walk(root):
+        for filename in files:
+            path = os.path.join(cur_root, filename)
+            yield os.path.relpath(path, root)
+
+
+def _licensed_files(root=spack.paths.prefix):
+    for relpath in _all_spack_files(root):
+        if any(regex.match(relpath) for regex in licensed_files):
+            yield relpath
+
+
+def list_files(args):
+    """list files in spack that should have license headers"""
+    for relpath in _licensed_files():
+        print(os.path.join(spack.paths.spack_root, relpath))
+
+
+def verify(args):
+    """verify that files in spack have the right license header"""
+    errors = 0
+    missing = 0
+    old_license = 0
+
+    for relpath in _licensed_files(args.root):
+        path = os.path.join(args.root, relpath)
+        with open(path) as f:
+            lines = [line for line in f]
+
+        if not any(re.match(regex, relpath) for regex in lgpl_exceptions):
+            if any(re.match(r'^# This program is free software', line)
+                   for line in lines):
+                print('%s: has old LGPL license header' % path)
+                old_license += 1
+                continue
+
+        # how we'll find licenses in files
+        spdx_expr = r'SPDX-License-Identifier: ([^\n]*)'
+
+        # check first <license_lines> lines for required header
+        first_n_lines = ''.join(lines[:license_lines])
+        match = re.search(spdx_expr, first_n_lines)
+
+        if not match:
+            print('%s: no license header' % path)
+            missing += 1
+            continue
+
+        correct = apache2_mit_spdx
+        actual = match.group(1)
+        if actual != correct:
+            print("%s: labeled as '%s', but should be '%s'"
+                  % (path, actual, correct))
+            errors += 1
+            continue
+
+    if any([errors, missing, old_license]):
+        tty.die(
+            '%d improperly licensed files' % (errors + missing + old_license),
+            'files with no SPDX-License-Identifier:      %d' % missing,
+            'files with wrong SPDX-License-Identifier:   %d' % errors,
+            'files with old license header:              %d' % old_license)
+    else:
+        tty.msg('No license issues found.')
+
+
+def setup_parser(subparser):
+    sp = subparser.add_subparsers(metavar='SUBCOMMAND', dest='license_command')
+    sp.add_parser('list-files', help=list_files.__doc__)
+
+    verify_parser = sp.add_parser('verify', help=verify.__doc__)
+    verify_parser.add_argument(
+        '--root', action='store', default=spack.paths.prefix,
+        help='scan a different prefix for license issues')
+
+
+def license(parser, args):
+    if not git:
+        tty.die('spack license requires git in your environment')
+
+    licensed_files[:] = [re.compile(regex) for regex in licensed_files]
+
+    commands = {
+        'list-files': list_files,
+        'verify': verify,
+    }
+    return commands[args.license_command](args)
diff --git a/lib/spack/spack/cmd/list.py b/lib/spack/spack/cmd/list.py
index 3549de361a..f486f46a4f 100644
--- a/lib/spack/spack/cmd/list.py
+++ b/lib/spack/spack/cmd/list.py
@@ -1,41 +1,25 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from __future__ import print_function
+from __future__ import division
 
 import argparse
 import cgi
 import fnmatch
 import re
 import sys
+import math
 
 from six import StringIO
 
 import llnl.util.tty as tty
 from llnl.util.tty.colify import colify
 
-import spack
+import spack.dependency
+import spack.repo
 import spack.cmd.common.arguments as arguments
 
 description = "list and search available packages"
@@ -113,23 +97,35 @@ def name_only(pkgs):
     colify(pkgs, indent=indent)
 
 
-@formatter
-def rst(pkgs):
-    """Print out information on all packages in restructured text."""
+def github_url(pkg):
+    """Link to a package file on github."""
+    url = 'https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/{0}/package.py'
+    return url.format(pkg.name)
+
 
-    def github_url(pkg):
-        """Link to a package file on github."""
-        url = 'https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/{0}/package.py'
-        return url.format(pkg.name)
+def rst_table(elts):
+    """Print out a RST-style table."""
+    cols = StringIO()
+    ncol, widths = colify(elts, output=cols, tty=True)
+    header = ' '.join('=' * (w - 1) for w in widths)
+    return '%s\n%s%s' % (header, cols.getvalue(), header)
 
-    def rst_table(elts):
-        """Print out a RST-style table."""
-        cols = StringIO()
-        ncol, widths = colify(elts, output=cols, tty=True)
-        header = ' '.join('=' * (w - 1) for w in widths)
-        return '%s\n%s%s' % (header, cols.getvalue(), header)
 
-    pkg_names = pkgs
+def rows_for_ncols(elts, ncols):
+    """Print out rows in a table with ncols of elts laid out vertically."""
+    clen = int(math.ceil(len(elts) / ncols))
+    for r in range(clen):
+        row = []
+        for c in range(ncols):
+            i = c * clen + r
+            row.append(elts[i] if i < len(elts) else None)
+        yield row
+
+
+@formatter
+def rst(pkg_names):
+    """Print out information on all packages in restructured text."""
+
     pkgs = [spack.repo.get(name) for name in pkg_names]
 
     print('.. _package-list:')
@@ -170,7 +166,7 @@ def rst(pkgs):
                                    reversed(sorted(pkg.versions))))
             print()
 
-        for deptype in spack.all_deptypes:
+        for deptype in spack.dependency.all_deptypes:
             deps = pkg.dependencies_of_type(deptype)
             if deps:
                 print('%s Dependencies' % deptype.capitalize())
@@ -183,6 +179,102 @@ def rst(pkgs):
         print()
 
 
+@formatter
+def html(pkg_names):
+    """Print out information on all packages in Sphinx HTML.
+
+    This is intended to be inlined directly into Sphinx documentation.
+    We write HTML instead of RST for speed; generating RST from *all*
+    packages causes the Sphinx build to take forever. Including this as
+    raw HTML is much faster.
+    """
+
+    # Read in all packages
+    pkgs = [spack.repo.get(name) for name in pkg_names]
+
+    # Start at 2 because the title of the page from Sphinx is id1.
+    span_id = 2
+
+    # HTML header with an increasing id span
+    def head(n, span_id, title, anchor=None):
+        if anchor is None:
+            anchor = title
+        print(('<span id="id%d"></span>'
+               '<h1>%s<a class="headerlink" href="#%s" '
+               'title="Permalink to this headline">&para;</a>'
+               '</h1>') % (span_id, title, anchor))
+
+    # Start with the number of packages, skipping the title and intro
+    # blurb, which we maintain in the RST file.
+    print('<p>')
+    print('Spack currently has %d mainline packages:' % len(pkgs))
+    print('</p>')
+
+    # Table of links to all packages
+    print('<table border="1" class="docutils">')
+    print('<tbody valign="top">')
+    for i, row in enumerate(rows_for_ncols(pkg_names, 3)):
+        print('<tr class="row-odd">' if i % 2 == 0 else
+              '<tr class="row-even">')
+        for name in row:
+            print('<td>')
+            print('<a class="reference internal" href="#%s">%s</a></td>'
+                  % (name, name))
+            print('</td>')
+        print('</tr>')
+    print('</tbody>')
+    print('</table>')
+    print('<hr class="docutils"/>')
+
+    # Output some text for each package.
+    for pkg in pkgs:
+        print('<div class="section" id="%s">' % pkg.name)
+        head(2, span_id, pkg.name)
+        span_id += 1
+
+        print('<dl class="docutils">')
+
+        print('<dt>Homepage:</dt>')
+        print('<dd><ul class="first last simple">')
+        print(('<li>'
+               '<a class="reference external" href="%s">%s</a>'
+               '</li>') % (pkg.homepage, cgi.escape(pkg.homepage)))
+        print('</ul></dd>')
+
+        print('<dt>Spack package:</dt>')
+        print('<dd><ul class="first last simple">')
+        print(('<li>'
+               '<a class="reference external" href="%s">%s/package.py</a>'
+               '</li>') % (github_url(pkg), pkg.name))
+        print('</ul></dd>')
+
+        if pkg.versions:
+            print('<dt>Versions:</dt>')
+            print('<dd>')
+            print(', '.join(str(v) for v in reversed(sorted(pkg.versions))))
+            print('</dd>')
+
+        for deptype in spack.dependency.all_deptypes:
+            deps = pkg.dependencies_of_type(deptype)
+            if deps:
+                print('<dt>%s Dependencies:</dt>' % deptype.capitalize())
+                print('<dd>')
+                print(', '.join(
+                    d if d not in pkg_names else
+                    '<a class="reference internal" href="#%s">%s</a>' % (d, d)
+                    for d in deps))
+                print('</dd>')
+
+        print('<dt>Description:</dt>')
+        print('<dd>')
+        print(cgi.escape(pkg.format_doc(indent=2)))
+        print('</dd>')
+        print('</dl>')
+
+        print('<hr class="docutils"/>')
+        print('</div>')
+
+
 def list(parser, args):
     # Retrieve the names of all the packages
     pkgs = set(spack.repo.all_package_names())
@@ -191,7 +283,8 @@ def list(parser, args):
 
     # Filter by tags
     if args.tags:
-        packages_with_tags = set(spack.repo.packages_with_tags(*args.tags))
+        packages_with_tags = set(
+            spack.repo.path.packages_with_tags(*args.tags))
         sorted_packages = set(sorted_packages) & packages_with_tags
         sorted_packages = sorted(sorted_packages)
 
diff --git a/lib/spack/spack/cmd/load.py b/lib/spack/spack/cmd/load.py
index 61c7003855..87822edb25 100644
--- a/lib/spack/spack/cmd/load.py
+++ b/lib/spack/spack/cmd/load.py
@@ -1,32 +1,13 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import argparse
-from spack.cmd.common import print_module_placeholder_help
+from spack.cmd.common import print_module_placeholder_help, arguments
 
 description = "add package to environment using `module load`"
-section = "environment"
+section = "modules"
 level = "short"
 
 
@@ -36,7 +17,8 @@ def setup_parser(subparser):
     subparser.add_argument(
         'spec', nargs=argparse.REMAINDER,
         help="spec of package to load with modules "
-             "(if -, read specs from STDIN)")
+    )
+    arguments.add_common_arguments(subparser, ['recurse_dependencies'])
 
 
 def load(parser, args):
diff --git a/lib/spack/spack/cmd/location.py b/lib/spack/spack/cmd/location.py
index 99ce4d4fc3..a878f63df8 100644
--- a/lib/spack/spack/cmd/location.py
+++ b/lib/spack/spack/cmd/location.py
@@ -1,37 +1,21 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from __future__ import print_function
 
+import os
 import argparse
 import llnl.util.tty as tty
 
-import spack
 import spack.cmd
+import spack.environment
+import spack.paths
+import spack.repo
 
-description = "print out locations of various directories used by Spack"
-section = "environment"
+description = "print out locations of packages and spack directories"
+section = "basic"
 level = "long"
 
 
@@ -65,6 +49,9 @@ def setup_parser(subparser):
         '-b', '--build-dir', action='store_true',
         help="checked out or expanded source directory for a spec "
              "(requires it to be staged first)")
+    directories.add_argument(
+        '-e', '--env', action='store',
+        help="location of an environment managed by spack")
 
     subparser.add_argument(
         'spec', nargs=argparse.REMAINDER,
@@ -73,16 +60,22 @@ def setup_parser(subparser):
 
 def location(parser, args):
     if args.module_dir:
-        print(spack.module_path)
+        print(spack.paths.module_path)
 
     elif args.spack_root:
-        print(spack.prefix)
+        print(spack.paths.prefix)
+
+    elif args.env:
+        path = spack.environment.root(args.env)
+        if not os.path.isdir(path):
+            tty.die("no such environment: '%s'" % args.env)
+        print(path)
 
     elif args.packages:
-        print(spack.repo.first_repo().root)
+        print(spack.repo.path.first_repo().root)
 
     elif args.stages:
-        print(spack.stage_path)
+        print(spack.paths.stage_path)
 
     else:
         specs = spack.cmd.parse_specs(args.spec)
@@ -101,7 +94,7 @@ def location(parser, args):
 
             if args.package_dir:
                 # This one just needs the spec name.
-                print(spack.repo.dirname_for_package_name(spec.name))
+                print(spack.repo.path.dirname_for_package_name(spec.name))
 
             else:
                 # These versions need concretized specs.
diff --git a/lib/spack/spack/cmd/log_parse.py b/lib/spack/spack/cmd/log_parse.py
new file mode 100644
index 0000000000..ac7db768bf
--- /dev/null
+++ b/lib/spack/spack/cmd/log_parse.py
@@ -0,0 +1,63 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import sys
+
+import llnl.util.tty as tty
+from spack.util.log_parse import parse_log_events, make_log_context
+
+description = "filter errors and warnings from build logs"
+section = "build"
+level = "long"
+
+event_types = ('errors', 'warnings')
+
+
+def setup_parser(subparser):
+    subparser.add_argument(
+        '--show', action='store', default='errors',
+        help="comma-separated list of what to show; options: errors, warnings")
+    subparser.add_argument(
+        '-c', '--context', action='store', type=int, default=3,
+        help="lines of context to show around lines of interest")
+    subparser.add_argument(
+        '-p', '--profile', action='store_true',
+        help="print out a profile of time spent in regexes during parse")
+    subparser.add_argument(
+        '-w', '--width', action='store', type=int, default=None,
+        help="wrap width: auto-size to terminal by default; 0 for no wrap")
+    subparser.add_argument(
+        '-j', '--jobs', action='store', type=int, default=None,
+        help="number of jobs to parse log file (default: 1 for short logs, "
+        "ncpus for long logs)")
+
+    subparser.add_argument(
+        'file', help="a log file containing build output, or - for stdin")
+
+
+def log_parse(parser, args):
+    input = args.file
+    if args.file == '-':
+        input = sys.stdin
+
+    errors, warnings = parse_log_events(
+        input, args.context, args.jobs, args.profile)
+    if args.profile:
+        return
+
+    types = [s.strip() for s in args.show.split(',')]
+    for e in types:
+        if e not in event_types:
+            tty.die('Invalid event type: %s' % e)
+
+    events = []
+    if 'errors' in types:
+        events.extend(errors)
+        print('%d errors' % len(errors))
+    if 'warnings' in types:
+        events.extend(warnings)
+        print('%d warnings' % len(warnings))
+
+    print(make_log_context(events, args.width))
diff --git a/lib/spack/spack/cmd/md5.py b/lib/spack/spack/cmd/md5.py
deleted file mode 100644
index 824e88373c..0000000000
--- a/lib/spack/spack/cmd/md5.py
+++ /dev/null
@@ -1,92 +0,0 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-import argparse
-import hashlib
-import os
-from six.moves.urllib.parse import urlparse
-
-import llnl.util.tty as tty
-import spack.util.crypto
-from spack.stage import Stage, FailedDownloadError
-
-description = "calculate md5 checksums for files/urls"
-section = "packaging"
-level = "long"
-
-
-def setup_parser(subparser):
-    setup_parser.parser = subparser
-    subparser.add_argument('files', nargs=argparse.REMAINDER,
-                           help="files/urls to checksum")
-
-
-def compute_checksum(url, algo):
-    algo = getattr(hashlib, algo)
-
-    if not os.path.isfile(url):
-        with Stage(url) as stage:
-            stage.fetch()
-            value = spack.util.crypto.checksum(algo, stage.archive_file)
-    else:
-        value = spack.util.crypto.checksum(algo, url)
-    return value
-
-
-def normalized(files):
-    for p in files:
-        result = urlparse(p)
-        value = p
-        if not result.scheme:
-            value = os.path.abspath(p)
-        yield value
-
-
-def do_checksum(parser, args, algo):
-    if not args.files:
-        setup_parser.parser.print_help()
-        return 1
-
-    urls = [x for x in normalized(args.files)]
-    results = []
-    for url in urls:
-        try:
-            checksum = compute_checksum(url, algo)
-            results.append((checksum, url))
-        except FailedDownloadError as e:
-            tty.warn("Failed to fetch %s" % url)
-            tty.warn("%s" % e)
-        except IOError as e:
-            tty.warn("Error when reading %s" % url)
-            tty.warn("%s" % e)
-
-    # Dump the hashes last, without interleaving them with downloads
-    checksum = 'checksum' if len(results) == 1 else 'checksums'
-    tty.msg("%d %s %s:" % (len(results), algo, checksum))
-    for checksum, url in results:
-        print("{0}  {1}".format(checksum, url))
-
-
-def md5(parser, args):
-    do_checksum(parser, args, 'md5')
diff --git a/lib/spack/spack/cmd/mirror.py b/lib/spack/spack/cmd/mirror.py
index 35d31adb2d..4d70df431b 100644
--- a/lib/spack/spack/cmd/mirror.py
+++ b/lib/spack/spack/cmd/mirror.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 from datetime import datetime
 
@@ -29,23 +10,23 @@ import argparse
 import llnl.util.tty as tty
 from llnl.util.tty.colify import colify
 
-import spack
 import spack.cmd
+import spack.concretize
 import spack.config
 import spack.mirror
+import spack.repo
+import spack.cmd.common.arguments as arguments
 from spack.spec import Spec
 from spack.error import SpackError
 from spack.util.spack_yaml import syaml_dict
 
-description = "manage mirrors"
+description = "manage mirrors (source and binary)"
 section = "config"
 level = "long"
 
 
 def setup_parser(subparser):
-    subparser.add_argument(
-        '-n', '--no-checksum', action='store_true', dest='no_checksum',
-        help="do not check fetched packages against checksum")
+    arguments.add_common_arguments(subparser, ['no_checksum'])
 
     sp = subparser.add_subparsers(
         metavar='SUBCOMMAND', dest='mirror_command')
@@ -67,7 +48,9 @@ def setup_parser(subparser):
         const=1, default=0,
         help="only fetch one 'preferred' version per spec, not all known")
 
-    scopes = spack.config.config_scopes
+    # used to construct scope arguments below
+    scopes = spack.config.scopes()
+    scopes_metavar = spack.config.scopes_metavar
 
     # Add
     add_parser = sp.add_parser('add', help=mirror_add.__doc__)
@@ -75,7 +58,8 @@ def setup_parser(subparser):
     add_parser.add_argument(
         'url', help="url of mirror directory from 'spack mirror create'")
     add_parser.add_argument(
-        '--scope', choices=scopes, default=spack.cmd.default_modify_scope,
+        '--scope', choices=scopes, metavar=scopes_metavar,
+        default=spack.config.default_modify_scope(),
         help="configuration scope to modify")
 
     # Remove
@@ -83,13 +67,15 @@ def setup_parser(subparser):
                                   help=mirror_remove.__doc__)
     remove_parser.add_argument('name')
     remove_parser.add_argument(
-        '--scope', choices=scopes, default=spack.cmd.default_modify_scope,
+        '--scope', choices=scopes, metavar=scopes_metavar,
+        default=spack.config.default_modify_scope(),
         help="configuration scope to modify")
 
     # List
     list_parser = sp.add_parser('list', help=mirror_list.__doc__)
     list_parser.add_argument(
-        '--scope', choices=scopes, default=spack.cmd.default_list_scope,
+        '--scope', choices=scopes, metavar=scopes_metavar,
+        default=spack.config.default_list_scope(),
         help="configuration scope to read from")
 
 
@@ -99,7 +85,7 @@ def mirror_add(args):
     if url.startswith('/'):
         url = 'file://' + url
 
-    mirrors = spack.config.get_config('mirrors', scope=args.scope)
+    mirrors = spack.config.get('mirrors', scope=args.scope)
     if not mirrors:
         mirrors = syaml_dict()
 
@@ -113,14 +99,14 @@ def mirror_add(args):
     items = [(n, u) for n, u in mirrors.items()]
     items.insert(0, (args.name, url))
     mirrors = syaml_dict(items)
-    spack.config.update_config('mirrors', mirrors, scope=args.scope)
+    spack.config.set('mirrors', mirrors, scope=args.scope)
 
 
 def mirror_remove(args):
     """Remove a mirror by name."""
     name = args.name
 
-    mirrors = spack.config.get_config('mirrors', scope=args.scope)
+    mirrors = spack.config.get('mirrors', scope=args.scope)
     if not mirrors:
         mirrors = syaml_dict()
 
@@ -128,13 +114,13 @@ def mirror_remove(args):
         tty.die("No mirror with name %s" % name)
 
     old_value = mirrors.pop(name)
-    spack.config.update_config('mirrors', mirrors, scope=args.scope)
+    spack.config.set('mirrors', mirrors, scope=args.scope)
     tty.msg("Removed mirror %s with url %s" % (name, old_value))
 
 
 def mirror_list(args):
     """Print out available mirrors to the console."""
-    mirrors = spack.config.get_config('mirrors', scope=args.scope)
+    mirrors = spack.config.get('mirrors', scope=args.scope)
     if not mirrors:
         tty.msg("No mirrors configured.")
         return
@@ -164,56 +150,61 @@ def mirror_create(args):
     """Create a directory to be used as a spack mirror, and fill it with
        package archives."""
     # try to parse specs from the command line first.
-    specs = spack.cmd.parse_specs(args.specs, concretize=True)
-
-    # If there is a file, parse each line as a spec and add it to the list.
-    if args.file:
-        if specs:
-            tty.die("Cannot pass specs on the command line with --file.")
-        specs = _read_specs_from_file(args.file)
-
-    # If nothing is passed, use all packages.
-    if not specs:
-        specs = [Spec(n) for n in spack.repo.all_package_names()]
-        specs.sort(key=lambda s: s.format("$_$@").lower())
-
-    # If the user asked for dependencies, traverse spec DAG get them.
-    if args.dependencies:
-        new_specs = set()
-        for spec in specs:
-            spec.concretize()
-            for s in spec.traverse():
-                new_specs.add(s)
-        specs = list(new_specs)
-
-    # Default name for directory is spack-mirror-<DATESTAMP>
-    directory = args.directory
-    if not directory:
-        timestamp = datetime.now().strftime("%Y-%m-%d")
-        directory = 'spack-mirror-' + timestamp
-
-    # Make sure nothing is in the way.
-    existed = False
-    if os.path.isfile(directory):
-        tty.error("%s already exists and is a file." % directory)
-    elif os.path.isdir(directory):
-        existed = True
-
-    # Actually do the work to create the mirror
-    present, mirrored, error = spack.mirror.create(
-        directory, specs, num_versions=args.one_version_per_spec)
-    p, m, e = len(present), len(mirrored), len(error)
-
-    verb = "updated" if existed else "created"
-    tty.msg(
-        "Successfully %s mirror in %s" % (verb, directory),
-        "Archive stats:",
-        "  %-4d already present"  % p,
-        "  %-4d added"            % m,
-        "  %-4d failed to fetch." % e)
-    if error:
-        tty.error("Failed downloads:")
-        colify(s.cformat("$_$@") for s in error)
+    with spack.concretize.concretizer.disable_compiler_existence_check():
+        specs = spack.cmd.parse_specs(args.specs, concretize=True)
+
+        # If there is a file, parse each line as a spec and add it to the list.
+        if args.file:
+            if specs:
+                tty.die("Cannot pass specs on the command line with --file.")
+            specs = _read_specs_from_file(args.file)
+
+        # If nothing is passed, use all packages.
+        if not specs:
+            specs = [Spec(n) for n in spack.repo.all_package_names()]
+            specs.sort(key=lambda s: s.format("$_$@").lower())
+
+        # If the user asked for dependencies, traverse spec DAG get them.
+        if args.dependencies:
+            new_specs = set()
+            for spec in specs:
+                spec.concretize()
+                for s in spec.traverse():
+                    new_specs.add(s)
+            specs = list(new_specs)
+
+        # Skip external specs, as they are already installed
+        external_specs = [s for s in specs if s.external]
+        specs = [s for s in specs if not s.external]
+
+        for spec in external_specs:
+            msg = 'Skipping {0} as it is an external spec.'
+            tty.msg(msg.format(spec.cshort_spec))
+
+        # Default name for directory is spack-mirror-<DATESTAMP>
+        directory = args.directory
+        if not directory:
+            timestamp = datetime.now().strftime("%Y-%m-%d")
+            directory = 'spack-mirror-' + timestamp
+
+        # Make sure nothing is in the way.
+        existed = os.path.isdir(directory)
+
+        # Actually do the work to create the mirror
+        present, mirrored, error = spack.mirror.create(
+            directory, specs, num_versions=args.one_version_per_spec)
+        p, m, e = len(present), len(mirrored), len(error)
+
+        verb = "updated" if existed else "created"
+        tty.msg(
+            "Successfully %s mirror in %s" % (verb, directory),
+            "Archive stats:",
+            "  %-4d already present"  % p,
+            "  %-4d added"            % m,
+            "  %-4d failed to fetch." % e)
+        if error:
+            tty.error("Failed downloads:")
+            colify(s.cformat("$_$@") for s in error)
 
 
 def mirror(parser, args):
diff --git a/lib/spack/spack/cmd/module.py b/lib/spack/spack/cmd/module.py
index 1ebead1f58..c71f84ef7d 100644
--- a/lib/spack/spack/cmd/module.py
+++ b/lib/spack/spack/cmd/module.py
@@ -1,357 +1,67 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-from __future__ import print_function
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-import collections
-import os
-import shutil
-import spack.modules
+import argparse
 
-import spack.cmd
-from llnl.util import filesystem, tty
-from spack.cmd.common import arguments
+import llnl.util.tty as tty
+
+import spack.cmd.modules.dotkit
+import spack.cmd.modules.lmod
+import spack.cmd.modules.tcl
 
 description = "manipulate module files"
-section = "environment"
+section = "modules"
 level = "short"
 
 
-#: Dictionary that will be populated with the list of sub-commands
-#: Each sub-command must be callable and accept 3 arguments:
-#:
-#:   - mtype : the type of the module file
-#:   - specs : the list of specs to be processed
-#:   - args : namespace containing the parsed command line arguments
-callbacks = {}
-
+_subcommands = {}
 
-def subcommand(subparser_name):
-    """Registers a function in the callbacks dictionary"""
-    def decorator(callback):
-        callbacks[subparser_name] = callback
-        return callback
-    return decorator
+_deprecated_commands = ('refresh', 'find', 'rm', 'loads')
 
 
 def setup_parser(subparser):
-    sp = subparser.add_subparsers(metavar='SUBCOMMAND', dest='subparser_name')
+    sp = subparser.add_subparsers(metavar='SUBCOMMAND', dest='module_command')
+    spack.cmd.modules.dotkit.add_command(sp, _subcommands)
+    spack.cmd.modules.lmod.add_command(sp, _subcommands)
+    spack.cmd.modules.tcl.add_command(sp, _subcommands)
 
-    # spack module refresh
-    refresh_parser = sp.add_parser('refresh', help='regenerate module files')
-    refresh_parser.add_argument(
-        '--delete-tree',
-        help='delete the module file tree before refresh',
-        action='store_true'
-    )
-    arguments.add_common_arguments(
-        refresh_parser, ['constraint', 'module_type', 'yes_to_all']
-    )
+    for name in _deprecated_commands:
+        add_deprecated_command(sp, name)
 
-    # spack module find
-    find_parser = sp.add_parser('find', help='find module files for packages')
-    arguments.add_common_arguments(find_parser, ['constraint', 'module_type'])
 
-    # spack module rm
-    rm_parser = sp.add_parser('rm', help='remove module files')
-    arguments.add_common_arguments(
-        rm_parser, ['constraint', 'module_type', 'yes_to_all']
+def add_deprecated_command(subparser, name):
+    parser = subparser.add_parser(name)
+    parser.add_argument(
+        '-m', '--module-type', help=argparse.SUPPRESS,
+        choices=spack.modules.module_types.keys(), action='append'
     )
 
-    # spack module loads
-    loads_parser = sp.add_parser(
-        'loads',
-        help='prompt the list of modules associated with a constraint'
-    )
-    loads_parser.add_argument(
-        '--input-only', action='store_false', dest='shell',
-        help='generate input for module command (instead of a shell script)'
-    )
-    loads_parser.add_argument(
-        '-p', '--prefix', dest='prefix', default='',
-        help='prepend to module names when issuing module load commands'
-    )
-    loads_parser.add_argument(
-        '-x', '--exclude', dest='exclude', action='append', default=[],
-        help="exclude package from output; may be specified multiple times"
-    )
-    arguments.add_common_arguments(
-        loads_parser, ['constraint', 'module_type', 'recurse_dependencies']
-    )
-
-
-class MultipleSpecsMatch(Exception):
-    """Raised when multiple specs match a constraint, in a context where
-    this is not allowed.
-    """
-
-
-class NoSpecMatches(Exception):
-    """Raised when no spec matches a constraint, in a context where
-    this is not allowed.
-    """
-
-
-class MultipleModuleTypes(Exception):
-    """Raised when multiple module types match a cli request, in a context
-    where this is not allowed.
-    """
-
-
-def one_module_or_raise(module_types):
-    """Ensures exactly one module type has been selected, or raises the
-    appropriate exception.
-    """
-    # Ensure a single module type has been selected
-    if len(module_types) > 1:
-        raise MultipleModuleTypes()
-    return module_types[0]
-
-
-def one_spec_or_raise(specs):
-    """Ensures exactly one spec has been selected, or raises the appropriate
-    exception.
-    """
-    # Ensure a single spec matches the constraint
-    if len(specs) == 0:
-        raise NoSpecMatches()
-    if len(specs) > 1:
-        raise MultipleSpecsMatch()
-
-    # Get the spec and module type
-    return specs[0]
-
-
-@subcommand('loads')
-def loads(module_types, specs, args):
-    """Prompt the list of modules associated with a list of specs"""
-
-    module_type = one_module_or_raise(module_types)
-
-    # Get a comprehensive list of specs
-    if args.recurse_dependencies:
-        specs_from_user_constraint = specs[:]
-        specs = []
-        # FIXME : during module file creation nodes seem to be visited
-        # FIXME : multiple times even if cover='nodes' is given. This
-        # FIXME : work around permits to get a unique list of spec anyhow.
-        # FIXME : (same problem as in spack/modules.py)
-        seen = set()
-        seen_add = seen.add
-        for spec in specs_from_user_constraint:
-            specs.extend(
-                [item for item in spec.traverse(order='post', cover='nodes')
-                 if not (item in seen or seen_add(item))]
-            )
-
-    module_cls = spack.modules.module_types[module_type]
-    modules = [
-        (spec, module_cls(spec).layout.use_name)
-        for spec in specs if os.path.exists(module_cls(spec).layout.filename)
-    ]
-
-    module_commands = {
-        'tcl': 'module load ',
-        'lmod': 'module load ',
-        'dotkit': 'dotkit use '
-    }
-
-    d = {
-        'command': '' if not args.shell else module_commands[module_type],
-        'prefix': args.prefix
-    }
-
-    exclude_set = set(args.exclude)
-    prompt_template = '{comment}{exclude}{command}{prefix}{name}'
-    for spec, mod in modules:
-        d['exclude'] = '## ' if spec.name in exclude_set else ''
-        d['comment'] = '' if not args.shell else '# {0}\n'.format(
-            spec.format())
-        d['name'] = mod
-        print(prompt_template.format(**d))
-
-
-@subcommand('find')
-def find(module_types, specs, args):
-    """Returns the module file "use" name if there's a single match. Raises
-    error messages otherwise.
-    """
-
-    spec = one_spec_or_raise(specs)
-    module_type = one_module_or_raise(module_types)
-
-    # Check if the module file is present
-    writer = spack.modules.module_types[module_type](spec)
-    if not os.path.isfile(writer.layout.filename):
-        msg = 'Even though {1} is installed, '
-        msg += 'no {0} module has been generated for it.'
-        tty.die(msg.format(module_type, spec))
-
-    # ... and if it is print its use name
-    print(writer.layout.use_name)
-
-
-@subcommand('rm')
-def rm(module_types, specs, args):
-    """Deletes the module files associated with every spec in specs, for every
-    module type in module types.
-    """
-    for module_type in module_types:
-
-        module_cls = spack.modules.module_types[module_type]
-        module_exist = lambda x: os.path.exists(module_cls(x).layout.filename)
-
-        specs_with_modules = [spec for spec in specs if module_exist(spec)]
-
-        modules = [module_cls(spec) for spec in specs_with_modules]
-
-        if not modules:
-            tty.die('No module file matches your query')
-
-        # Ask for confirmation
-        if not args.yes_to_all:
-            msg = 'You are about to remove {0} module files for:\n'
-            tty.msg(msg.format(module_type))
-            spack.cmd.display_specs(specs_with_modules, long=True)
-            print('')
-            answer = tty.get_yes_or_no('Do you want to proceed?')
-            if not answer:
-                tty.die('Will not remove any module files')
-
-        # Remove the module files
-        for s in modules:
-            s.remove()
-
-
-@subcommand('refresh')
-def refresh(module_types, specs, args):
-    """Regenerates the module files for every spec in specs and every module
-    type in module types.
-    """
-
-    # Prompt a message to the user about what is going to change
-    if not specs:
-        tty.msg('No package matches your query')
-        return
-
-    if not args.yes_to_all:
-        msg = 'You are about to regenerate {types} module files for:\n'
-        types = ', '.join(module_types)
-        tty.msg(msg.format(types=types))
-        spack.cmd.display_specs(specs, long=True)
-        print('')
-        answer = tty.get_yes_or_no('Do you want to proceed?')
-        if not answer:
-            tty.die('Module file regeneration aborted.')
-
-    # Cycle over the module types and regenerate module files
-    for module_type in module_types:
-
-        cls = spack.modules.module_types[module_type]
-
-        writers = [
-            cls(spec) for spec in specs if spack.repo.exists(spec.name)
-        ]  # skip unknown packages.
-
-        # Filter blacklisted packages early
-        writers = [x for x in writers if not x.conf.blacklisted]
-
-        # Detect name clashes in module files
-        file2writer = collections.defaultdict(list)
-        for item in writers:
-            file2writer[item.layout.filename].append(item)
-
-        if len(file2writer) != len(writers):
-            message = 'Name clashes detected in module files:\n'
-            for filename, writer_list in file2writer.items():
-                if len(writer_list) > 1:
-                    message += '\nfile: {0}\n'.format(filename)
-                    for x in writer_list:
-                        message += 'spec: {0}\n'.format(x.spec.format())
-            tty.error(message)
-            tty.error('Operation aborted')
-            raise SystemExit(1)
-
-        if len(writers) == 0:
-            msg = 'Nothing to be done for {0} module files.'
-            tty.msg(msg.format(module_type))
-            continue
-
-        # If we arrived here we have at least one writer
-        module_type_root = writers[0].layout.dirname()
-        # Proceed regenerating module files
-        tty.msg('Regenerating {name} module files'.format(name=module_type))
-        if os.path.isdir(module_type_root) and args.delete_tree:
-            shutil.rmtree(module_type_root, ignore_errors=False)
-        filesystem.mkdirp(module_type_root)
-        for x in writers:
-            try:
-                x.write(overwrite=True)
-            except Exception as e:
-                msg = 'Could not write module file [{0}]'
-                tty.warn(msg.format(x.layout.filename))
-                tty.warn('\t--> {0} <--'.format(str(e)))
-
-
-def module(parser, args):
-
-    # Qualifiers to be used when querying the db for specs
-    constraint_qualifiers = {
-        'refresh': {
-            'installed': True,
-            'known': True
-        },
-    }
-    query_args = constraint_qualifiers.get(args.subparser_name, {})
 
-    # Get the specs that match the query from the DB
-    specs = args.specs(**query_args)
+def handle_deprecated_command(args, unknown_args):
+    command = args.module_command
+    unknown = ' '.join(unknown_args)
 
-    # Set the module types that have been selected
-    module_types = args.module_type
-    if module_types is None:
-        # If no selection has been made select all of them
-        module_types = ['tcl']
+    module_types = args.module_type or ['tcl']
 
-    module_types = list(set(module_types))
+    msg = '`spack module {0} {1}` has moved. Use these commands instead:\n'
+    msg = msg.format(command, ' '.join('-m ' + x for x in module_types))
+    for x in module_types:
+        msg += '\n\t$ spack module {0} {1} {2}'.format(x, command, unknown)
+    msg += '\n'
+    tty.die(msg)
 
-    try:
 
-        callbacks[args.subparser_name](module_types, specs, args)
+def module(parser, args, unknown_args):
 
-    except MultipleSpecsMatch:
-        msg = "the constraint '{query}' matches multiple packages:\n"
-        for s in specs:
-            msg += '\t' + s.cformat() + '\n'
-        tty.error(msg.format(query=args.constraint))
-        tty.die('In this context exactly **one** match is needed: please specify your constraints better.')  # NOQA: ignore=E501
+    # Here we permit unknown arguments to intercept deprecated calls
+    if args.module_command in _deprecated_commands:
+        handle_deprecated_command(args, unknown_args)
 
-    except NoSpecMatches:
-        msg = "the constraint '{query}' matches no package."
-        tty.error(msg.format(query=args.constraint))
-        tty.die('In this context exactly **one** match is needed: please specify your constraints better.')  # NOQA: ignore=E501
+    # Fail if unknown arguments are present, once we excluded a deprecated
+    # command
+    if unknown_args:
+        tty.die('unrecognized arguments: {0}'.format(' '.join(unknown_args)))
 
-    except MultipleModuleTypes:
-        msg = "this command needs exactly **one** module type active."
-        tty.die(msg)
+    _subcommands[args.module_command](parser, args)
diff --git a/lib/spack/spack/cmd/modules/__init__.py b/lib/spack/spack/cmd/modules/__init__.py
new file mode 100644
index 0000000000..f8f883e42e
--- /dev/null
+++ b/lib/spack/spack/cmd/modules/__init__.py
@@ -0,0 +1,335 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+"""Implementation details of the ``spack module`` command."""
+
+import collections
+import os.path
+import shutil
+import sys
+
+from llnl.util import filesystem, tty
+
+import spack.cmd
+import spack.modules
+import spack.repo
+
+import spack.cmd.common.arguments as arguments
+
+description = "manipulate module files"
+section = "environment"
+level = "short"
+
+
+def setup_parser(subparser):
+    sp = subparser.add_subparsers(metavar='SUBCOMMAND', dest='subparser_name')
+
+    refresh_parser = sp.add_parser('refresh', help='regenerate module files')
+    refresh_parser.add_argument(
+        '--delete-tree',
+        help='delete the module file tree before refresh',
+        action='store_true'
+    )
+    arguments.add_common_arguments(
+        refresh_parser, ['constraint', 'yes_to_all']
+    )
+
+    find_parser = sp.add_parser('find', help='find module files for packages')
+    find_parser.add_argument(
+        '--full-path',
+        help='display full path to module file',
+        action='store_true'
+    )
+    arguments.add_common_arguments(
+        find_parser, ['constraint', 'recurse_dependencies']
+    )
+
+    rm_parser = sp.add_parser('rm', help='remove module files')
+    arguments.add_common_arguments(
+        rm_parser, ['constraint', 'yes_to_all']
+    )
+
+    loads_parser = sp.add_parser(
+        'loads',
+        help='prompt the list of modules associated with a constraint'
+    )
+    add_loads_arguments(loads_parser)
+    arguments.add_common_arguments(loads_parser, ['constraint'])
+
+    return sp
+
+
+def add_loads_arguments(subparser):
+    subparser.add_argument(
+        '--input-only', action='store_false', dest='shell',
+        help='generate input for module command (instead of a shell script)'
+    )
+    subparser.add_argument(
+        '-p', '--prefix', dest='prefix', default='',
+        help='prepend to module names when issuing module load commands'
+    )
+    subparser.add_argument(
+        '-x', '--exclude', dest='exclude', action='append', default=[],
+        help="exclude package from output; may be specified multiple times"
+    )
+    arguments.add_common_arguments(
+        subparser, ['recurse_dependencies']
+    )
+
+
+class MultipleSpecsMatch(Exception):
+    """Raised when multiple specs match a constraint, in a context where
+    this is not allowed.
+    """
+
+
+class NoSpecMatches(Exception):
+    """Raised when no spec matches a constraint, in a context where
+    this is not allowed.
+    """
+
+
+def one_spec_or_raise(specs):
+    """Ensures exactly one spec has been selected, or raises the appropriate
+    exception.
+    """
+    # Ensure a single spec matches the constraint
+    if len(specs) == 0:
+        raise NoSpecMatches()
+    if len(specs) > 1:
+        raise MultipleSpecsMatch()
+
+    # Get the spec and module type
+    return specs[0]
+
+
+def loads(module_type, specs, args, out=sys.stdout):
+    """Prompt the list of modules associated with a list of specs"""
+
+    # Get a comprehensive list of specs
+    if args.recurse_dependencies:
+        specs_from_user_constraint = specs[:]
+        specs = []
+        # FIXME : during module file creation nodes seem to be visited
+        # FIXME : multiple times even if cover='nodes' is given. This
+        # FIXME : work around permits to get a unique list of spec anyhow.
+        # FIXME : (same problem as in spack/modules.py)
+        seen = set()
+        seen_add = seen.add
+        for spec in specs_from_user_constraint:
+            specs.extend(
+                [item for item in spec.traverse(order='post', cover='nodes')
+                 if not (item in seen or seen_add(item))]
+            )
+
+    module_cls = spack.modules.module_types[module_type]
+    modules = [
+        (spec, module_cls(spec).layout.use_name)
+        for spec in specs if os.path.exists(module_cls(spec).layout.filename)
+    ]
+
+    module_commands = {
+        'tcl': 'module load ',
+        'lmod': 'module load ',
+        'dotkit': 'use '
+    }
+
+    d = {
+        'command': '' if not args.shell else module_commands[module_type],
+        'prefix': args.prefix
+    }
+
+    exclude_set = set(args.exclude)
+    prompt_template = '{comment}{exclude}{command}{prefix}{name}'
+    for spec, mod in modules:
+        d['exclude'] = '## ' if spec.name in exclude_set else ''
+        d['comment'] = '' if not args.shell else '# {0}\n'.format(
+            spec.format())
+        d['name'] = mod
+        out.write(prompt_template.format(**d))
+        out.write('\n')
+
+
+def find(module_type, specs, args):
+    """Returns the module file "use" name if there's a single match. Raises
+    error messages otherwise.
+    """
+
+    spec = one_spec_or_raise(specs)
+
+    # Check if the module file is present
+    def module_exists(spec):
+        writer = spack.modules.module_types[module_type](spec)
+        return os.path.isfile(writer.layout.filename)
+
+    if not module_exists(spec):
+        msg = 'Even though {1} is installed, '
+        msg += 'no {0} module has been generated for it.'
+        tty.die(msg.format(module_type, spec))
+
+    # Check if we want to recurse and load all dependencies. In that case
+    # modify the list of specs adding all the dependencies in post order
+    if args.recurse_dependencies:
+        specs = [
+            item for item in spec.traverse(order='post', cover='nodes')
+            if module_exists(item)
+        ]
+
+    # ... and if it is print its use name or full-path if requested
+    def module_str(specs):
+        modules = []
+        for x in specs:
+            writer = spack.modules.module_types[module_type](x)
+            if args.full_path:
+                modules.append(writer.layout.filename)
+            else:
+                modules.append(writer.layout.use_name)
+
+        return ' '.join(modules)
+
+    print(module_str(specs))
+
+
+def rm(module_type, specs, args):
+    """Deletes the module files associated with every spec in specs, for every
+    module type in module types.
+    """
+
+    module_cls = spack.modules.module_types[module_type]
+    module_exist = lambda x: os.path.exists(module_cls(x).layout.filename)
+
+    specs_with_modules = [spec for spec in specs if module_exist(spec)]
+
+    modules = [module_cls(spec) for spec in specs_with_modules]
+
+    if not modules:
+        tty.die('No module file matches your query')
+
+    # Ask for confirmation
+    if not args.yes_to_all:
+        msg = 'You are about to remove {0} module files for:\n'
+        tty.msg(msg.format(module_type))
+        spack.cmd.display_specs(specs_with_modules, long=True)
+        print('')
+        answer = tty.get_yes_or_no('Do you want to proceed?')
+        if not answer:
+            tty.die('Will not remove any module files')
+
+    # Remove the module files
+    for s in modules:
+        s.remove()
+
+
+def refresh(module_type, specs, args):
+    """Regenerates the module files for every spec in specs and every module
+    type in module types.
+    """
+
+    # Prompt a message to the user about what is going to change
+    if not specs:
+        tty.msg('No package matches your query')
+        return
+
+    if not args.yes_to_all:
+        msg = 'You are about to regenerate {types} module files for:\n'
+        tty.msg(msg.format(types=module_type))
+        spack.cmd.display_specs(specs, long=True)
+        print('')
+        answer = tty.get_yes_or_no('Do you want to proceed?')
+        if not answer:
+            tty.die('Module file regeneration aborted.')
+
+    # Cycle over the module types and regenerate module files
+
+    cls = spack.modules.module_types[module_type]
+
+    # Skip unknown packages.
+    writers = [
+        cls(spec) for spec in specs
+        if spack.repo.path.exists(spec.name)]
+
+    # Filter blacklisted packages early
+    writers = [x for x in writers if not x.conf.blacklisted]
+
+    # Detect name clashes in module files
+    file2writer = collections.defaultdict(list)
+    for item in writers:
+        file2writer[item.layout.filename].append(item)
+
+    if len(file2writer) != len(writers):
+        message = 'Name clashes detected in module files:\n'
+        for filename, writer_list in file2writer.items():
+            if len(writer_list) > 1:
+                message += '\nfile: {0}\n'.format(filename)
+                for x in writer_list:
+                    message += 'spec: {0}\n'.format(x.spec.format())
+        tty.error(message)
+        tty.error('Operation aborted')
+        raise SystemExit(1)
+
+    if len(writers) == 0:
+        msg = 'Nothing to be done for {0} module files.'
+        tty.msg(msg.format(module_type))
+        return
+
+    # If we arrived here we have at least one writer
+    module_type_root = writers[0].layout.dirname()
+    # Proceed regenerating module files
+    tty.msg('Regenerating {name} module files'.format(name=module_type))
+    if os.path.isdir(module_type_root) and args.delete_tree:
+        shutil.rmtree(module_type_root, ignore_errors=False)
+    filesystem.mkdirp(module_type_root)
+    for x in writers:
+        try:
+            x.write(overwrite=True)
+        except Exception as e:
+            msg = 'Could not write module file [{0}]'
+            tty.warn(msg.format(x.layout.filename))
+            tty.warn('\t--> {0} <--'.format(str(e)))
+
+
+#: Dictionary populated with the list of sub-commands.
+#: Each sub-command must be callable and accept 3 arguments:
+#:
+#:   - module_type: the type of module it refers to
+#:   - specs : the list of specs to be processed
+#:   - args : namespace containing the parsed command line arguments
+callbacks = {
+    'refresh': refresh,
+    'rm': rm,
+    'find': find,
+    'loads': loads
+}
+
+
+def modules_cmd(parser, args, module_type, callbacks=callbacks):
+
+    # Qualifiers to be used when querying the db for specs
+    constraint_qualifiers = {
+        'refresh': {
+            'installed': True,
+            'known': True
+        },
+    }
+    query_args = constraint_qualifiers.get(args.subparser_name, {})
+
+    # Get the specs that match the query from the DB
+    specs = args.specs(**query_args)
+
+    try:
+
+        callbacks[args.subparser_name](module_type, specs, args)
+
+    except MultipleSpecsMatch:
+        msg = "the constraint '{query}' matches multiple packages:\n"
+        for s in specs:
+            msg += '\t' + s.cformat(format_string='$/ $_$@$+$%@+$+$=') + '\n'
+        tty.error(msg.format(query=args.constraint))
+        tty.die('In this context exactly **one** match is needed: please specify your constraints better.')  # NOQA: ignore=E501
+
+    except NoSpecMatches:
+        msg = "the constraint '{query}' matches no package."
+        tty.error(msg.format(query=args.constraint))
+        tty.die('In this context exactly **one** match is needed: please specify your constraints better.')  # NOQA: ignore=E501
diff --git a/lib/spack/spack/cmd/modules/dotkit.py b/lib/spack/spack/cmd/modules/dotkit.py
new file mode 100644
index 0000000000..159defe3a6
--- /dev/null
+++ b/lib/spack/spack/cmd/modules/dotkit.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import functools
+
+import spack.cmd.modules
+
+
+def add_command(parser, command_dict):
+    dotkit_parser = parser.add_parser(
+        'dotkit', help='manipulate dotkit module files'
+    )
+    spack.cmd.modules.setup_parser(dotkit_parser)
+
+    command_dict['dotkit'] = functools.partial(
+        spack.cmd.modules.modules_cmd, module_type='dotkit'
+    )
diff --git a/lib/spack/spack/cmd/modules/lmod.py b/lib/spack/spack/cmd/modules/lmod.py
new file mode 100644
index 0000000000..33be5bc85b
--- /dev/null
+++ b/lib/spack/spack/cmd/modules/lmod.py
@@ -0,0 +1,50 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import functools
+import os
+
+import llnl.util.filesystem
+import spack.cmd.common.arguments
+import spack.cmd.modules
+
+
+def add_command(parser, command_dict):
+    lmod_parser = parser.add_parser(
+        'lmod', help='manipulate hierarchical module files'
+    )
+    sp = spack.cmd.modules.setup_parser(lmod_parser)
+
+    # Set default module file for a package
+    setdefault_parser = sp.add_parser(
+        'setdefault', help='set the default module file for a package'
+    )
+    spack.cmd.common.arguments.add_common_arguments(
+        setdefault_parser, ['constraint']
+    )
+
+    callbacks = dict(spack.cmd.modules.callbacks.items())
+    callbacks['setdefault'] = setdefault
+
+    command_dict['lmod'] = functools.partial(
+        spack.cmd.modules.modules_cmd, module_type='lmod', callbacks=callbacks
+    )
+
+
+def setdefault(module_type, specs, args):
+    """Set the default module file, when multiple are present"""
+    # For details on the underlying mechanism see:
+    #
+    # https://lmod.readthedocs.io/en/latest/060_locating.html#marking-a-version-as-default
+    #
+    spack.cmd.modules.one_spec_or_raise(specs)
+    writer = spack.modules.module_types['lmod'](specs[0])
+
+    module_folder = os.path.dirname(writer.layout.filename)
+    module_basename = os.path.basename(writer.layout.filename)
+    with llnl.util.filesystem.working_dir(module_folder):
+        if os.path.exists('default') and os.path.islink('default'):
+            os.remove('default')
+        os.symlink(module_basename, 'default')
diff --git a/lib/spack/spack/cmd/modules/tcl.py b/lib/spack/spack/cmd/modules/tcl.py
new file mode 100644
index 0000000000..c300584505
--- /dev/null
+++ b/lib/spack/spack/cmd/modules/tcl.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import functools
+
+import spack.cmd.modules
+
+
+def add_command(parser, command_dict):
+    tcl_parser = parser.add_parser(
+        'tcl', help='manipulate non-hierarchical module files'
+    )
+    spack.cmd.modules.setup_parser(tcl_parser)
+
+    command_dict['tcl'] = functools.partial(
+        spack.cmd.modules.modules_cmd, module_type='tcl'
+    )
diff --git a/lib/spack/spack/cmd/patch.py b/lib/spack/spack/cmd/patch.py
index b19acfcde4..6de45cccb5 100644
--- a/lib/spack/spack/cmd/patch.py
+++ b/lib/spack/spack/cmd/patch.py
@@ -1,32 +1,15 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import argparse
 
 import llnl.util.tty as tty
+
+import spack.repo
 import spack.cmd
-import spack
+import spack.cmd.common.arguments as arguments
 
 
 description = "patch expanded archive sources in preparation for install"
@@ -35,9 +18,7 @@ level = "long"
 
 
 def setup_parser(subparser):
-    subparser.add_argument(
-        '-n', '--no-checksum', action='store_true', dest='no_checksum',
-        help="do not check downloaded packages against checksum")
+    arguments.add_common_arguments(subparser, ['no_checksum'])
     subparser.add_argument(
         'packages', nargs=argparse.REMAINDER,
         help="specs of packages to stage")
@@ -48,7 +29,7 @@ def patch(parser, args):
         tty.die("patch requires at least one package argument")
 
     if args.no_checksum:
-        spack.do_checksum = False
+        spack.config.set('config:checksum', False, scope='command_line')
 
     specs = spack.cmd.parse_specs(args.packages, concretize=True)
     for spec in specs:
diff --git a/lib/spack/spack/cmd/pkg.py b/lib/spack/spack/cmd/pkg.py
index 9591b58acd..e73c1ec61e 100644
--- a/lib/spack/spack/cmd/pkg.py
+++ b/lib/spack/spack/cmd/pkg.py
@@ -1,37 +1,19 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from __future__ import print_function
 
 import os
-
 import argparse
+
 import llnl.util.tty as tty
 from llnl.util.tty.colify import colify
 from llnl.util.filesystem import working_dir
 
-import spack
+import spack.paths
+import spack.repo
 from spack.util.executable import which
 from spack.cmd import spack_is_git_repo
 
@@ -78,11 +60,11 @@ def setup_parser(subparser):
 
 
 def list_packages(rev):
-    pkgpath = os.path.join(spack.packages_path, 'packages')
-    relpath = pkgpath[len(spack.prefix + os.path.sep):] + os.path.sep
+    pkgpath = os.path.join(spack.paths.packages_path, 'packages')
+    relpath = pkgpath[len(spack.paths.prefix + os.path.sep):] + os.path.sep
 
     git = which('git', required=True)
-    with working_dir(spack.prefix):
+    with working_dir(spack.paths.prefix):
         output = git('ls-tree', '--full-tree', '--name-only', rev, relpath,
                      output=str)
     return sorted(line[len(relpath):] for line in output.split('\n') if line)
@@ -90,14 +72,14 @@ def list_packages(rev):
 
 def pkg_add(args):
     for pkg_name in args.packages:
-        filename = spack.repo.filename_for_package_name(pkg_name)
+        filename = spack.repo.path.filename_for_package_name(pkg_name)
         if not os.path.isfile(filename):
             tty.die("No such package: %s.  Path does not exist:" %
                     pkg_name, filename)
 
         git = which('git', required=True)
-        with working_dir(spack.prefix):
-            git('-C', spack.packages_path, 'add', filename)
+        with working_dir(spack.paths.prefix):
+            git('-C', spack.paths.packages_path, 'add', filename)
 
 
 def pkg_list(args):
diff --git a/lib/spack/spack/cmd/providers.py b/lib/spack/spack/cmd/providers.py
index de45e20ec5..f20966c4d3 100644
--- a/lib/spack/spack/cmd/providers.py
+++ b/lib/spack/spack/cmd/providers.py
@@ -1,33 +1,15 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-import argparse
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import six
+import sys
 
-from llnl.util.tty.colify import colify
+import llnl.util.tty.colify as colify
 
-import spack
 import spack.cmd
+import spack.repo
 
 description = "list packages that provide a particular virtual package"
 section = "basic"
@@ -35,11 +17,46 @@ level = "long"
 
 
 def setup_parser(subparser):
+    subparser.epilog = 'If called without argument returns ' \
+                       'the list of all valid virtual packages'
     subparser.add_argument(
-        'vpkg_spec', metavar='VPACKAGE_SPEC', nargs=argparse.REMAINDER,
-        help='find packages that provide this virtual package')
+        'virtual_package',
+        nargs='*',
+        help='find packages that provide this virtual package'
+    )
 
 
 def providers(parser, args):
-    for spec in spack.cmd.parse_specs(args.vpkg_spec):
-        colify(sorted(spack.repo.providers_for(spec)), indent=4)
+    valid_virtuals = sorted(spack.repo.path.provider_index.providers.keys())
+
+    buffer = six.StringIO()
+    isatty = sys.stdout.isatty()
+    if isatty:
+        buffer.write('Virtual packages:\n')
+    colify.colify(valid_virtuals, output=buffer, tty=isatty, indent=4)
+    valid_virtuals_str = buffer.getvalue()
+
+    # If called without arguments, list all the virtual packages
+    if not args.virtual_package:
+        print(valid_virtuals_str)
+        return
+
+    # Otherwise, parse the specs from command line
+    specs = spack.cmd.parse_specs(args.virtual_package)
+
+    # Check prerequisites
+    non_virtual = [
+        str(s) for s in specs if not s.virtual or s.name not in valid_virtuals
+    ]
+    if non_virtual:
+        msg = 'non-virtual specs cannot be part of the query '
+        msg += '[{0}]\n'.format(', '.join(non_virtual))
+        msg += valid_virtuals_str
+        raise ValueError(msg)
+
+    # Display providers
+    for spec in specs:
+        if sys.stdout.isatty():
+            print("{0}:".format(spec))
+        spack.cmd.display_specs(sorted(spack.repo.path.providers_for(spec)))
+        print('')
diff --git a/lib/spack/spack/cmd/pydoc.py b/lib/spack/spack/cmd/pydoc.py
index 093b16f66a..e17d548475 100644
--- a/lib/spack/spack/cmd/pydoc.py
+++ b/lib/spack/spack/cmd/pydoc.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 description = "run pydoc from within spack"
 section = "developer"
diff --git a/lib/spack/spack/cmd/python.py b/lib/spack/spack/cmd/python.py
index 8bdb796efa..fbd5c788fe 100644
--- a/lib/spack/spack/cmd/python.py
+++ b/lib/spack/spack/cmd/python.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 import sys
 import code
@@ -30,7 +11,6 @@ import platform
 
 import spack
 
-
 description = "launch an interpreter as spack would launch a command"
 section = "developer"
 level = "long"
diff --git a/lib/spack/spack/cmd/reindex.py b/lib/spack/spack/cmd/reindex.py
index 6babec60d5..4dcae1c678 100644
--- a/lib/spack/spack/cmd/reindex.py
+++ b/lib/spack/spack/cmd/reindex.py
@@ -1,34 +1,14 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-import spack
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import spack.store
-description = "rebuild Spack's package database"
 
+description = "rebuild Spack's package database"
 section = "admin"
 level = "long"
 
 
 def reindex(parser, args):
-    spack.store.db.reindex(spack.store.layout)
+    spack.store.store.reindex()
diff --git a/lib/spack/spack/cmd/remove.py b/lib/spack/spack/cmd/remove.py
new file mode 100644
index 0000000000..ec0b2cd218
--- /dev/null
+++ b/lib/spack/spack/cmd/remove.py
@@ -0,0 +1,39 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import argparse
+
+import llnl.util.tty as tty
+
+import spack.cmd
+import spack.environment as ev
+
+
+description = 'remove specs from an environment'
+section = "environments"
+level = "long"
+
+
+def setup_parser(subparser):
+    subparser.add_argument(
+        '-a', '--all', action='store_true',
+        help="remove all specs from (clear) the environment")
+    subparser.add_argument(
+        '-f', '--force', action='store_true',
+        help="remove concretized spec (if any) immediately")
+    subparser.add_argument(
+        'specs', nargs=argparse.REMAINDER, help="specs to be removed")
+
+
+def remove(parser, args):
+    env = ev.get_env(args, 'remove')
+
+    if args.all:
+        env.clear()
+    else:
+        for spec in spack.cmd.parse_specs(args.specs):
+            tty.msg('Removing %s from environment %s' % (spec, env.name))
+            env.remove(spec, force=args.force)
+    env.write()
diff --git a/lib/spack/spack/cmd/repo.py b/lib/spack/spack/cmd/repo.py
index 0b5ced1642..8ce9ea9351 100644
--- a/lib/spack/spack/cmd/repo.py
+++ b/lib/spack/spack/cmd/repo.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from __future__ import print_function
 
 import os
@@ -30,7 +11,7 @@ import llnl.util.tty as tty
 
 import spack.spec
 import spack.config
-from spack.repository import Repo, create_repo, canonicalize_path, RepoError
+from spack.repo import Repo, create_repo, canonicalize_path, RepoError
 
 description = "manage package source repositories"
 section = "config"
@@ -39,7 +20,8 @@ level = "long"
 
 def setup_parser(subparser):
     sp = subparser.add_subparsers(metavar='SUBCOMMAND', dest='repo_command')
-    scopes = spack.config.config_scopes
+    scopes = spack.config.scopes()
+    scopes_metavar = spack.config.scopes_metavar
 
     # Create
     create_parser = sp.add_parser('create', help=repo_create.__doc__)
@@ -52,7 +34,8 @@ def setup_parser(subparser):
     # List
     list_parser = sp.add_parser('list', help=repo_list.__doc__)
     list_parser.add_argument(
-        '--scope', choices=scopes, default=spack.cmd.default_list_scope,
+        '--scope', choices=scopes, metavar=scopes_metavar,
+        default=spack.config.default_list_scope(),
         help="configuration scope to read from")
 
     # Add
@@ -60,7 +43,8 @@ def setup_parser(subparser):
     add_parser.add_argument(
         'path', help="path to a Spack package repository directory")
     add_parser.add_argument(
-        '--scope', choices=scopes, default=spack.cmd.default_modify_scope,
+        '--scope', choices=scopes, metavar=scopes_metavar,
+        default=spack.config.default_modify_scope(),
         help="configuration scope to modify")
 
     # Remove
@@ -70,7 +54,8 @@ def setup_parser(subparser):
         'path_or_namespace',
         help="path or namespace of a Spack package repository")
     remove_parser.add_argument(
-        '--scope', choices=scopes, default=spack.cmd.default_modify_scope,
+        '--scope', choices=scopes, metavar=scopes_metavar,
+        default=spack.config.default_modify_scope(),
         help="configuration scope to modify")
 
 
@@ -101,7 +86,7 @@ def repo_add(args):
     repo = Repo(canon_path)
 
     # If that succeeds, finally add it to the configuration.
-    repos = spack.config.get_config('repos', args.scope)
+    repos = spack.config.get('repos', scope=args.scope)
     if not repos:
         repos = []
 
@@ -109,13 +94,13 @@ def repo_add(args):
         tty.die("Repository is already registered with Spack: %s" % path)
 
     repos.insert(0, canon_path)
-    spack.config.update_config('repos', repos, args.scope)
+    spack.config.set('repos', repos, args.scope)
     tty.msg("Added repo with namespace '%s'." % repo.namespace)
 
 
 def repo_remove(args):
     """Remove a repository from Spack's configuration."""
-    repos = spack.config.get_config('repos', args.scope)
+    repos = spack.config.get('repos', scope=args.scope)
     path_or_namespace = args.path_or_namespace
 
     # If the argument is a path, remove that repository from config.
@@ -124,7 +109,7 @@ def repo_remove(args):
         repo_canon_path = canonicalize_path(repo_path)
         if canon_path == repo_canon_path:
             repos.remove(repo_path)
-            spack.config.update_config('repos', repos, args.scope)
+            spack.config.set('repos', repos, args.scope)
             tty.msg("Removed repository %s" % repo_path)
             return
 
@@ -134,7 +119,7 @@ def repo_remove(args):
             repo = Repo(path)
             if repo.namespace == path_or_namespace:
                 repos.remove(path)
-                spack.config.update_config('repos', repos, args.scope)
+                spack.config.set('repos', repos, args.scope)
                 tty.msg("Removed repository %s with namespace '%s'."
                         % (repo.root, repo.namespace))
                 return
@@ -147,7 +132,7 @@ def repo_remove(args):
 
 def repo_list(args):
     """Show registered repositories and their namespaces."""
-    roots = spack.config.get_config('repos', args.scope)
+    roots = spack.config.get('repos', scope=args.scope)
     repos = []
     for r in roots:
         try:
diff --git a/lib/spack/spack/cmd/restage.py b/lib/spack/spack/cmd/restage.py
index 992aa40951..e2b77167b1 100644
--- a/lib/spack/spack/cmd/restage.py
+++ b/lib/spack/spack/cmd/restage.py
@@ -1,33 +1,14 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import argparse
 
 import llnl.util.tty as tty
 
-import spack
 import spack.cmd
+import spack.repo
 
 description = "revert checked out package source code"
 section = "build"
diff --git a/lib/spack/spack/cmd/setup.py b/lib/spack/spack/cmd/setup.py
index 01b40dda80..5620f8904c 100644
--- a/lib/spack/spack/cmd/setup.py
+++ b/lib/spack/spack/cmd/setup.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import argparse
 import copy
 import os
@@ -29,17 +10,20 @@ import string
 import sys
 
 import llnl.util.tty as tty
-import spack
+from llnl.util.filesystem import set_executable
+
+import spack.repo
 import spack.store
+import spack.build_systems.cmake
 import spack.cmd
 import spack.cmd.install as install
 import spack.cmd.common.arguments as arguments
-from llnl.util.filesystem import set_executable
-from spack import which
+from spack.util.executable import which
+
 from spack.stage import DIYStage
 
 description = "create a configuration script and module, but don't build"
-section = "developer"
+section = "build"
 level = "long"
 
 
@@ -47,6 +31,7 @@ def setup_parser(subparser):
     subparser.add_argument(
         '-i', '--ignore-dependencies', action='store_true', dest='ignore_deps',
         help="do not try to install dependencies of requested packages")
+    arguments.add_common_arguments(subparser, ['no_checksum'])
     subparser.add_argument(
         '-v', '--verbose', action='store_true', dest='verbose',
         help="display verbose build output while installing")
@@ -134,7 +119,7 @@ def setup(self, args):
     # Take a write lock before checking for existence.
     with spack.store.db.write_transaction():
         spec = specs[0]
-        if not spack.repo.exists(spec.name):
+        if not spack.repo.path.exists(spec.name):
             tty.die("No package for '{0}' was found.".format(spec.name),
                     "  Use `spack create` to create a new package")
         if not spec.versions.concrete:
@@ -144,20 +129,19 @@ def setup(self, args):
 
         spec.concretize()
         package = spack.repo.get(spec)
-        if not isinstance(package, spack.CMakePackage):
+        if not isinstance(package, spack.build_systems.cmake.CMakePackage):
             tty.die(
                 'Support for {0} derived packages not yet implemented'.format(
-                    package.build_system_class
-                )
-            )
+                    package.build_system_class))
 
         # It's OK if the package is already installed.
 
         # Forces the build to run out of the current directory.
         package.stage = DIYStage(os.getcwd())
 
-        # TODO: make this an argument, not a global.
-        spack.do_checksum = False
+        # disable checksumming if requested
+        if args.no_checksum:
+            spack.config.set('config:checksum', False, scope='command_line')
 
         # Install dependencies if requested to do so
         if not args.ignore_deps:
@@ -169,12 +153,14 @@ def setup(self, args):
                 namespace=inst_args
             )
             install.install(parser, inst_args)
+
         # Generate spconfig.py
         tty.msg(
             'Generating spconfig.py [{0}]'.format(package.spec.cshort_spec)
         )
         dirty = args.dirty
         write_spconfig(package, dirty)
+
         # Install this package to register it in the DB and permit
         # module file regeneration
         inst_args = copy.deepcopy(args)
diff --git a/lib/spack/spack/cmd/sha256.py b/lib/spack/spack/cmd/sha256.py
deleted file mode 100644
index 9b9b962e46..0000000000
--- a/lib/spack/spack/cmd/sha256.py
+++ /dev/null
@@ -1,40 +0,0 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-import argparse
-from spack.cmd.md5 import do_checksum
-
-description = "calculate sha256 checksums for files/urls"
-section = "packaging"
-level = "long"
-
-
-def setup_parser(subparser):
-    setup_parser.parser = subparser
-    subparser.add_argument('files', nargs=argparse.REMAINDER,
-                           help="files/urls to checksum")
-
-
-def sha256(parser, args):
-    do_checksum(parser, args, 'sha256')
diff --git a/lib/spack/spack/cmd/spec.py b/lib/spack/spack/cmd/spec.py
index 722987c35e..cc5172beb6 100644
--- a/lib/spack/spack/cmd/spec.py
+++ b/lib/spack/spack/cmd/spec.py
@@ -1,30 +1,15 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from __future__ import print_function
 
 import argparse
+import sys
+
+import llnl.util.tty as tty
+
 import spack
 import spack.cmd
 import spack.cmd.common.arguments as arguments
@@ -35,7 +20,8 @@ level = "short"
 
 
 def setup_parser(subparser):
-    arguments.add_common_arguments(subparser, ['long', 'very_long'])
+    arguments.add_common_arguments(
+        subparser, ['long', 'very_long', 'install_status'])
     subparser.add_argument(
         '-y', '--yaml', action='store_true', default=False,
         help='print concrete spec as YAML')
@@ -46,11 +32,7 @@ def setup_parser(subparser):
     subparser.add_argument(
         '-N', '--namespaces', action='store_true', default=False,
         help='show fully qualified package names')
-    subparser.add_argument(
-        '-I', '--install-status', action='store_true', default=False,
-        help='show install status of packages. packages can be: '
-             'installed [+], missing and needed by an installed package [-], '
-             'or not installed (no annotation)')
+
     subparser.add_argument(
         '-t', '--types', action='store_true', default=False,
         help='show dependency types')
@@ -62,29 +44,29 @@ def spec(parser, args):
     name_fmt = '$.' if args.namespaces else '$_'
     kwargs = {'cover': args.cover,
               'format': name_fmt + '$@$%@+$+$=',
-              'hashes': args.long or args.very_long,
               'hashlen': None if args.very_long else 7,
               'show_types': args.types,
               'install_status': args.install_status}
 
+    if not args.specs:
+        tty.die("spack spec requires at least one spec")
+
     for spec in spack.cmd.parse_specs(args.specs):
         # With -y, just print YAML to output.
         if args.yaml:
-            if spec.name in spack.repo:
+            if spec.name in spack.repo.path or spec.virtual:
                 spec.concretize()
-            print(spec.to_yaml())
+
+            # use write because to_yaml already has a newline.
+            sys.stdout.write(spec.to_yaml())
             continue
 
-        # Print some diagnostic info by default.
+        kwargs['hashes'] = False  # Always False for input spec
         print("Input spec")
         print("--------------------------------")
         print(spec.tree(**kwargs))
 
-        print("Normalized")
-        print("--------------------------------")
-        spec.normalize()
-        print(spec.tree(**kwargs))
-
+        kwargs['hashes'] = args.long or args.very_long
         print("Concretized")
         print("--------------------------------")
         spec.concretize()
diff --git a/lib/spack/spack/cmd/stage.py b/lib/spack/spack/cmd/stage.py
index 3456e9290e..68f2486b0d 100644
--- a/lib/spack/spack/cmd/stage.py
+++ b/lib/spack/spack/cmd/stage.py
@@ -1,32 +1,16 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import argparse
 
 import llnl.util.tty as tty
-import spack
+
+import spack.environment as ev
+import spack.repo
 import spack.cmd
+import spack.cmd.common.arguments as arguments
 
 description = "expand downloaded archive in preparation for install"
 section = "build"
@@ -34,9 +18,7 @@ level = "long"
 
 
 def setup_parser(subparser):
-    subparser.add_argument(
-        '-n', '--no-checksum', action='store_true', dest='no_checksum',
-        help="do not check downloaded packages against checksum")
+    arguments.add_common_arguments(subparser, ['no_checksum'])
     subparser.add_argument(
         '-p', '--path', dest='path',
         help="path to stage package, does not add to spack tree")
@@ -47,10 +29,18 @@ def setup_parser(subparser):
 
 def stage(parser, args):
     if not args.specs:
-        tty.die("stage requires at least one package argument")
+        env = ev.get_env(args, 'stage', required=False)
+        if env:
+            tty.msg("Staging specs from environment %s" % env.name)
+            for spec in env.specs_by_hash.values():
+                for dep in spec.traverse():
+                    dep.package.do_stage()
+            return
+        else:
+            tty.die("`spack stage` requires a spec or an active environment")
 
     if args.no_checksum:
-        spack.do_checksum = False
+        spack.config.set('config:checksum', False, scope='command_line')
 
     specs = spack.cmd.parse_specs(args.specs, concretize=True)
     for spec in specs:
diff --git a/lib/spack/spack/cmd/test.py b/lib/spack/spack/cmd/test.py
index d25a851237..40f2d6f8b2 100644
--- a/lib/spack/spack/cmd/test.py
+++ b/lib/spack/spack/cmd/test.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from __future__ import print_function
 
 import sys
@@ -34,7 +15,7 @@ from six import StringIO
 from llnl.util.filesystem import working_dir
 from llnl.util.tty.colify import colify
 
-import spack
+import spack.paths
 
 description = "run spack's unit tests"
 section = "developer"
@@ -96,8 +77,8 @@ def test(parser, args, unknown_args):
         pytest.main(['-h'])
         return
 
-    # pytest.ini lives in the root of the spack repository.
-    with working_dir(spack.prefix):
+    # pytest.ini lives in lib/spack/spack/test
+    with working_dir(spack.paths.test_path):
         # --list and --long-list print the test output better.
         if args.list or args.long_list:
             do_list(args, unknown_args)
diff --git a/lib/spack/spack/cmd/uninstall.py b/lib/spack/spack/cmd/uninstall.py
index 0cb79340eb..81e8437999 100644
--- a/lib/spack/spack/cmd/uninstall.py
+++ b/lib/spack/spack/cmd/uninstall.py
@@ -1,37 +1,21 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from __future__ import print_function
 
 import argparse
 
-import spack
 import spack.cmd
+import spack.environment as ev
+import spack.package
+import spack.cmd.common.arguments as arguments
+import spack.repo
 import spack.store
-import spack.repository
 
 from llnl.util import tty
+from llnl.util.tty.colify import colify
 
 description = "remove installed packages"
 section = "build"
@@ -46,31 +30,30 @@ error_message = """You can either:
 display_args = {
     'long': True,
     'show_flags': True,
-    'variants': True
+    'variants': True,
+    'indent': 4,
 }
 
 
-def setup_parser(subparser):
+def add_common_arguments(subparser):
     subparser.add_argument(
         '-f', '--force', action='store_true', dest='force',
-        help="remove regardless of whether other packages depend on this one")
-
-    subparser.add_argument(
-        '-a', '--all', action='store_true', dest='all',
-        help="USE CAREFULLY. remove ALL installed packages that match each "
-             "supplied spec. i.e., if you say uninstall `libelf`,"
-             " ALL versions of `libelf` are uninstalled. if no spec is "
-             "supplied all installed software will be uninstalled. this "
-             "is both useful and dangerous, like rm -r")
+        help="remove regardless of whether other packages or environments "
+        "depend on this one")
+    arguments.add_common_arguments(
+        subparser, ['recurse_dependents', 'yes_to_all'])
 
-    subparser.add_argument(
-        '-R', '--dependents', action='store_true', dest='dependents',
-        help='also uninstall any packages that depend on the ones given '
-             'via command line')
 
+def setup_parser(subparser):
+    add_common_arguments(subparser)
     subparser.add_argument(
-        '-y', '--yes-to-all', action='store_true', dest='yes_to_all',
-        help='assume "yes" is the answer to every confirmation requested')
+        '-a', '--all', action='store_true', dest='all',
+        help="USE CAREFULLY. Remove ALL installed packages that match each "
+        "supplied spec. i.e., if you `uninstall --all libelf`,"
+        " ALL versions of `libelf` are uninstalled. If no spec is "
+        "supplied, all installed packages will be uninstalled. "
+        "If used in an environment, all packages in the environment "
+        "will be uninstalled.")
 
     subparser.add_argument(
         'packages',
@@ -78,22 +61,26 @@ def setup_parser(subparser):
         help="specs of packages to uninstall")
 
 
-def find_matching_specs(specs, allow_multiple_matches=False, force=False):
+def find_matching_specs(env, specs, allow_multiple_matches=False, force=False):
     """Returns a list of specs matching the not necessarily
        concretized specs given from cli
 
     Args:
-        specs: list of specs to be matched against installed packages
-        allow_multiple_matches : if True multiple matches are admitted
+        env (Environment): active environment, or ``None`` if there is not one
+        specs (list): list of specs to be matched against installed packages
+        allow_multiple_matches (bool): if True multiple matches are admitted
 
     Return:
         list of specs
     """
+    # constrain uninstall resolution to current environment if one is active
+    hashes = env.all_hashes() if env else None
+
     # List of specs that match expressions given via command line
     specs_from_cli = []
     has_errors = False
     for spec in specs:
-        matching = spack.store.db.query(spec)
+        matching = spack.store.db.query(spec, hashes=hashes)
         # For each spec provided, make sure it refers to only one package.
         # Fail and ask user to be unambiguous if it doesn't
         if not allow_multiple_matches and len(matching) > 1:
@@ -105,54 +92,125 @@ def find_matching_specs(specs, allow_multiple_matches=False, force=False):
 
         # No installed package matches the query
         if len(matching) == 0 and spec is not any:
-            tty.error('{0} does not match any installed packages.'.format(
-                spec))
-            has_errors = True
+            if env:
+                pkg_type = "packages in environment '%s'" % env.name
+            else:
+                pkg_type = 'installed packages'
+            tty.die('{0} does not match any {1}.'.format(spec, pkg_type))
 
         specs_from_cli.extend(matching)
+
     if has_errors:
         tty.die(error_message)
 
     return specs_from_cli
 
 
-def installed_dependents(specs):
-    """Returns a dictionary that maps a spec with a list of its
-    installed dependents
+def installed_dependents(specs, env):
+    """Map each spec to a list of its installed dependents.
 
     Args:
-        specs: list of specs to be checked for dependents
+        specs (list): list of Specs
+        env (Environment): the active environment, or None
+
+    Returns:
+        (tuple of dicts): two mappings: one from specs to their dependent
+            environments in the active environment (or global scope if
+            there is no environment), and one from specs to their
+            dependents in *inactive* environments (empty if there is no
+            environment
+
+    """
+    active_dpts = {}
+    inactive_dpts = {}
+
+    env_hashes = set(env.all_hashes()) if env else set()
+
+    for spec in specs:
+        installed = spack.store.db.installed_relatives(
+            spec, direction='parents', transitive=True)
+
+        # separate installed dependents into dpts in this environment and
+        # dpts that are outside this environment
+        for dpt in installed:
+            if dpt not in specs:
+                if not env or dpt.dag_hash() in env_hashes:
+                    active_dpts.setdefault(spec, set()).add(dpt)
+                else:
+                    inactive_dpts.setdefault(spec, set()).add(dpt)
+
+    return active_dpts, inactive_dpts
+
 
+def dependent_environments(specs):
+    """Map each spec to environments that depend on it.
+
+    Args:
+        specs (list): list of Specs
     Returns:
-        dictionary of installed dependents
+        (dict): mapping from spec to lists of dependent Environments
+
     """
     dependents = {}
-    for item in specs:
-        installed = spack.store.db.installed_relatives(item, 'parents', True)
-        lst = [x for x in installed if x not in specs]
-        if lst:
-            lst = list(set(lst))
-            dependents[item] = lst
+    for env in ev.all_environments():
+        hashes = set(env.all_hashes())
+        for spec in specs:
+            if spec.dag_hash() in hashes:
+                dependents.setdefault(spec, []).append(env)
     return dependents
 
 
-def do_uninstall(specs, force):
+def inactive_dependent_environments(spec_envs):
+    """Strip the active environment from a dependent map.
+
+    Take the output of ``dependent_environment()`` and remove the active
+    environment from all mappings.  Remove any specs in the map that now
+    have no dependent environments.  Return the result.
+
+    Args:
+        (dict): mapping from spec to lists of dependent Environments
+    Returns:
+        (dict): mapping from spec to lists of *inactive* dependent Environments
     """
-    Uninstalls all the specs in a list.
+    spec_inactive_envs = {}
+    for spec, de_list in spec_envs.items():
+        inactive = [de for de in de_list if not de.active]
+        if inactive:
+            spec_inactive_envs[spec] = inactive
+
+    return spec_inactive_envs
+
+
+def _remove_from_env(spec, env):
+    """Remove a spec from an environment if it is a root."""
+    try:
+        # try removing the spec from the current active
+        # environment. this will fail if the spec is not a root
+        env.remove(spec, force=True)
+    except ev.SpackEnvironmentError:
+        pass  # ignore non-root specs
+
+
+def do_uninstall(env, specs, force):
+    """Uninstalls all the specs in a list.
 
     Args:
-        specs: list of specs to be uninstalled
-        force: force uninstallation (boolean)
+        env (Environment): active environment, or ``None`` if there is not one
+        specs (list): list of specs to be uninstalled
+        force (bool): force uninstallation (boolean)
     """
     packages = []
     for item in specs:
         try:
             # should work if package is known to spack
             packages.append(item.package)
-        except spack.repository.UnknownEntityError:
+        except spack.repo.UnknownEntityError:
             # The package.py file has gone away -- but still
             # want to uninstall.
-            spack.Package.uninstall_by_spec(item, force=True)
+            spack.package.Package.uninstall_by_spec(item, force=True)
+
+        if env:
+            _remove_from_env(item, env)
 
     # Sort packages to be uninstalled by the number of installed dependents
     # This ensures we do things in the right order
@@ -165,57 +223,113 @@ def do_uninstall(specs, force):
     for item in packages:
         item.do_uninstall(force=force)
 
+    # write any changes made to the active environment
+    if env:
+        env.write()
 
-def get_uninstall_list(args):
-    specs = [any]
-    if args.packages:
-        specs = spack.cmd.parse_specs(args.packages)
 
+def get_uninstall_list(args, specs, env):
     # Gets the list of installed specs that match the ones give via cli
-    # takes care of '-a' is given in the cli
-    uninstall_list = find_matching_specs(specs, args.all, args.force)
-
-    # Takes care of '-d'
-    dependent_list = installed_dependents(uninstall_list)
-
-    # Process dependent_list and update uninstall_list
-    has_error = False
-    if dependent_list and not args.dependents and not args.force:
-        for spec, lst in dependent_list.items():
-            tty.error("Will not uninstall %s" % spec.cformat("$_$@$%@$/"))
-            print('')
-            print('The following packages depend on it:')
-            spack.cmd.display_specs(lst, **display_args)
-            print('')
-            has_error = True
+    # args.all takes care of the case where '-a' is given in the cli
+    uninstall_list = find_matching_specs(env, specs, args.all, args.force)
+
+    # Takes care of '-R'
+    active_dpts, inactive_dpts = installed_dependents(uninstall_list, env)
+
+    # if we are in the global scope, we complain if you try to remove a
+    # spec that's in an environment.  If we're in an environment, we'll
+    # just *remove* it from the environment, so we ignore this
+    # error when *in* an environment
+    spec_envs = dependent_environments(uninstall_list)
+    spec_envs = inactive_dependent_environments(spec_envs)
+
+    # Process spec_dependents and update uninstall_list
+    has_error = not args.force and (
+        (active_dpts and not args.dependents)  # dependents in the current env
+        or (not env and spec_envs)  # there are environments that need specs
+    )
+
+    # say why each problem spec is needed
+    if has_error:
+        specs = set(active_dpts)
+        if not env:
+            specs.update(set(spec_envs))  # environments depend on this
+
+        for i, spec in enumerate(sorted(specs)):
+            # space out blocks of reasons
+            if i > 0:
+                print()
+
+            tty.info("Will not uninstall %s" % spec.cformat("$_$@$%@$/"),
+                     format='*r')
+
+            dependents = active_dpts.get(spec)
+            if dependents:
+                print('The following packages depend on it:')
+                spack.cmd.display_specs(dependents, **display_args)
+
+            if not env:
+                envs = spec_envs.get(spec)
+                if envs:
+                    print('It is used by the following environments:')
+                    colify([e.name for e in envs], indent=4)
+
+        msgs = []
+        if active_dpts:
+            msgs.append(
+                'use `spack uninstall --dependents` to remove dependents too')
+        if spec_envs:
+            msgs.append('use `spack env remove` to remove from environments')
+        print()
+        tty.die('There are still dependents.', *msgs)
+
     elif args.dependents:
-        for key, lst in dependent_list.items():
+        for spec, lst in active_dpts.items():
             uninstall_list.extend(lst)
         uninstall_list = list(set(uninstall_list))
-    if has_error:
-        tty.die('Use `spack uninstall --dependents` '
-                'to uninstall these dependencies as well.')
 
-    return uninstall_list
+    # only force-remove (don't completely uninstall) specs that still
+    # have external dependent envs or pkgs
+    removes = set(inactive_dpts)
+    if env:
+        removes.update(spec_envs)
 
+    # remove anything in removes from the uninstall list
+    uninstall_list = set(uninstall_list) - removes
 
-def uninstall(parser, args):
-    if not args.packages and not args.all:
-        tty.die('uninstall requires at least one package argument.',
-                '  Use `spack uninstall --all` to uninstall ALL packages.')
+    return uninstall_list, removes
 
-    uninstall_list = get_uninstall_list(args)
 
-    if not uninstall_list:
+def uninstall_specs(args, specs):
+    env = ev.get_env(args, 'uninstall', required=False)
+
+    uninstall_list, remove_list = get_uninstall_list(args, specs, env)
+    anything_to_do = set(uninstall_list).union(set(remove_list))
+
+    if not anything_to_do:
         tty.warn('There are no package to uninstall.')
         return
 
     if not args.yes_to_all:
         tty.msg('The following packages will be uninstalled:\n')
-        spack.cmd.display_specs(uninstall_list, **display_args)
+        spack.cmd.display_specs(anything_to_do, **display_args)
         answer = tty.get_yes_or_no('Do you want to proceed?', default=False)
         if not answer:
             tty.die('Will not uninstall any packages.')
 
+    # just force-remove things in the remove list
+    for spec in remove_list:
+        _remove_from_env(spec, env)
+
     # Uninstall everything on the list
-    do_uninstall(uninstall_list, args.force)
+    do_uninstall(env, uninstall_list, args.force)
+
+
+def uninstall(parser, args):
+    if not args.packages and not args.all:
+        tty.die('uninstall requires at least one package argument.',
+                '  Use `spack uninstall --all` to uninstall ALL packages.')
+
+    # [any] here handles the --all case by forcing all specs to be returned
+    uninstall_specs(
+        args, spack.cmd.parse_specs(args.packages) if args.packages else [any])
diff --git a/lib/spack/spack/cmd/unload.py b/lib/spack/spack/cmd/unload.py
index 9820ff52d3..d8730aea92 100644
--- a/lib/spack/spack/cmd/unload.py
+++ b/lib/spack/spack/cmd/unload.py
@@ -1,32 +1,13 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import argparse
 from spack.cmd.common import print_module_placeholder_help
 
 description = "remove package from environment using `module unload`"
-section = "environment"
+section = "modules"
 level = "short"
 
 
diff --git a/lib/spack/spack/cmd/unuse.py b/lib/spack/spack/cmd/unuse.py
index 14ca4227d2..4aab78b17b 100644
--- a/lib/spack/spack/cmd/unuse.py
+++ b/lib/spack/spack/cmd/unuse.py
@@ -1,32 +1,13 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import argparse
 from spack.cmd.common import print_module_placeholder_help
 
 description = "remove package from environment using dotkit"
-section = "environment"
+section = "modules"
 level = "long"
 
 
diff --git a/lib/spack/spack/cmd/url.py b/lib/spack/spack/cmd/url.py
index a445810b69..8168ffe45f 100644
--- a/lib/spack/spack/cmd/url.py
+++ b/lib/spack/spack/cmd/url.py
@@ -1,32 +1,18 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-from __future__ import division, print_function
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+from __future__ import division, print_function
 from collections import defaultdict
+try:
+    from urllib.parse import urlparse
+except ImportError:
+    from urlparse import urlparse
 
-import spack
+import spack.fetch_strategy as fs
+import spack.repo
+import spack.util.crypto as crypto
 
 from llnl.util import tty
 from spack.url import parse_version_offset, parse_name_offset
@@ -87,12 +73,18 @@ def setup_parser(subparser):
         'summary',
         help='print a summary of how well we are parsing package urls')
 
+    # Stats
+    sp.add_parser(
+        'stats',
+        help='print statistics on versions and checksums for all packages')
+
 
 def url(parser, args):
     action = {
         'parse':   url_parse,
         'list':    url_list,
-        'summary': url_summary
+        'summary': url_summary,
+        'stats':   url_stats,
     }
 
     action[args.subcommand](args)
@@ -144,7 +136,7 @@ def url_list(args):
     urls = set()
 
     # Gather set of URLs from all packages
-    for pkg in spack.repo.all_packages():
+    for pkg in spack.repo.path.all_packages():
         url = getattr(pkg.__class__, 'url', None)
         urls = url_list_parsing(args, urls, url, pkg)
 
@@ -178,7 +170,7 @@ def url_summary(args):
     tty.msg('Generating a summary of URL parsing in Spack...')
 
     # Loop through all packages
-    for pkg in spack.repo.all_packages():
+    for pkg in spack.repo.path.all_packages():
         urls = set()
 
         url = getattr(pkg.__class__, 'url', None)
@@ -227,7 +219,7 @@ def url_summary(args):
 
     print()
     print('    Index  Count  Regular Expression')
-    for ni in name_regex_dict:
+    for ni in sorted(name_regex_dict.keys()):
         print('    {0:>3}: {1:>6}   r{2!r}'.format(
             ni, name_count_dict[ni], name_regex_dict[ni]))
     print()
@@ -236,7 +228,7 @@ def url_summary(args):
 
     print()
     print('    Index  Count  Regular Expression')
-    for vi in version_regex_dict:
+    for vi in sorted(version_regex_dict.keys()):
         print('    {0:>3}: {1:>6}   r{2!r}'.format(
             vi, version_count_dict[vi], version_regex_dict[vi]))
     print()
@@ -246,6 +238,77 @@ def url_summary(args):
             name_count_dict, version_count_dict)
 
 
+def url_stats(args):
+    stats = {}  # stats about fetchers in packages.
+    nvers = 0   # total number of versions
+    npkgs = 0   # total number of packages
+
+    def inc(fstype, category, attr=None):
+        """Increment statistics in the stats dict."""
+        categories = stats.setdefault(fstype, {})
+        if attr:
+            cat_stats = categories.setdefault(category, {})
+            val = cat_stats.setdefault(attr, 0)
+            stats[fstype][category][attr] = val + 1
+        else:
+            val = categories.setdefault(category, 0)
+            stats[fstype][category] = val + 1
+
+    # over all packages
+    for pkg in spack.repo.path.all_packages():
+        npkgs += 1
+
+        # look at each version
+        for v, args in pkg.versions.items():
+            # figure out what type of fetcher it is
+            fetcher = fs.for_package_version(pkg, v)
+            nvers += 1
+
+            fstype = fetcher.url_attr
+            inc(fstype, 'total')
+
+            # put some special stats in for particular types of fetchers.
+            if fstype == 'git':
+                if 'commit' in args:
+                    inc('git', 'security', 'commit')
+                else:
+                    inc('git', 'security', 'no commit')
+            elif fstype == 'url':
+                for h in crypto.hashes:
+                    if h in args:
+                        inc('url', 'checksums', h)
+                        break
+                else:
+                    if 'checksum' in args:
+                        h = crypto.hash_algo_for_digest(args['checksum'])
+                        inc('url', 'checksums', h)
+                    else:
+                        inc('url', 'checksums', 'no checksum')
+
+                # parse out the URL scheme (https/http/ftp/etc.)
+                urlinfo = urlparse(fetcher.url)
+                inc('url', 'schemes', urlinfo.scheme)
+
+    # print a nice summary table
+    tty.msg("%d total versions for %d packages:" % (nvers, npkgs))
+    line_width = 36
+    print("-" * line_width)
+    for fetcher, fetcher_stats in sorted(stats.items(), reverse=True):
+        fs_total = fetcher_stats['total']
+        fs_pct = float(fs_total) / nvers * 100
+        print("%-22s%5d%8.1f%%" % (fetcher, fs_total, fs_pct))
+
+        for category, cat_stats in sorted(fetcher_stats.items(), reverse=True):
+            if category == 'total':
+                continue
+            print("  %s" % category)
+
+            for name, number in sorted(cat_stats.items(), reverse=True):
+                pct = float(number) / fs_total * 100
+                print("    %-18s%5d%8.1f%%" % (name, number, pct))
+        print("-" * line_width)
+
+
 def print_name_and_version(url):
     """Prints a URL. Underlines the detected name with dashes and
     the detected version with tildes.
diff --git a/lib/spack/spack/cmd/use.py b/lib/spack/spack/cmd/use.py
index 956f5c6cbc..80ae80329a 100644
--- a/lib/spack/spack/cmd/use.py
+++ b/lib/spack/spack/cmd/use.py
@@ -1,32 +1,13 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import argparse
-from spack.cmd.common import print_module_placeholder_help
+from spack.cmd.common import print_module_placeholder_help, arguments
 
 description = "add package to environment using dotkit"
-section = "environment"
+section = "modules"
 level = "long"
 
 
@@ -36,6 +17,7 @@ def setup_parser(subparser):
     subparser.add_argument(
         'spec', nargs=argparse.REMAINDER,
         help='spec of package to use with dotkit')
+    arguments.add_common_arguments(subparser, ['recurse_dependencies'])
 
 
 def use(parser, args):
diff --git a/lib/spack/spack/cmd/versions.py b/lib/spack/spack/cmd/versions.py
index 9c6f2d1ead..007e86c164 100644
--- a/lib/spack/spack/cmd/versions.py
+++ b/lib/spack/spack/cmd/versions.py
@@ -1,32 +1,14 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from __future__ import print_function
 
 from llnl.util.tty.colify import colify
 import llnl.util.tty as tty
-import spack
+
+import spack.repo
 
 description = "list available versions of a package"
 section = "packaging"
@@ -41,20 +23,27 @@ def setup_parser(subparser):
 def versions(parser, args):
     pkg = spack.repo.get(args.package)
 
+    tty.msg('Safe versions (already checksummed):')
+
     safe_versions = pkg.versions
+
+    if not safe_versions:
+        print('  Found no versions for {0}'.format(pkg.name))
+        tty.debug('Manually add versions to the package.')
+    else:
+        colify(sorted(safe_versions, reverse=True), indent=2)
+
+    tty.msg('Remote versions (not yet checksummed):')
+
     fetched_versions = pkg.fetch_remote_versions()
     remote_versions = set(fetched_versions).difference(safe_versions)
 
-    tty.msg("Safe versions (already checksummed):")
-    colify(sorted(safe_versions, reverse=True), indent=2)
-
-    tty.msg("Remote versions (not yet checksummed):")
     if not remote_versions:
         if not fetched_versions:
-            print("  Found no versions for %s" % pkg.name)
-            tty.debug("Check the list_url and list_depth attribute on the "
-                      "package to help Spack find versions.")
+            print('  Found no versions for {0}'.format(pkg.name))
+            tty.debug('Check the list_url and list_depth attributes of the '
+                      'package to help Spack find versions.')
         else:
-            print("  Found no unchecksummed versions for %s" % pkg.name)
+            print('  Found no unchecksummed versions for {0}'.format(pkg.name))
     else:
         colify(sorted(remote_versions, reverse=True), indent=2)
diff --git a/lib/spack/spack/cmd/view.py b/lib/spack/spack/cmd/view.py
index 13005053ff..9768458f02 100644
--- a/lib/spack/spack/cmd/view.py
+++ b/lib/spack/spack/cmd/view.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 '''Produce a "view" of a Spack DAG.
 
 A "view" is file hierarchy representing the union of a number of
@@ -52,16 +33,17 @@ All operations on views are performed via proxy objects such as
 YamlFilesystemView.
 
 '''
-
 import os
-import spack
+
+import llnl.util.tty as tty
+from llnl.util.link_tree import MergeConflictError
+
 import spack.cmd
 import spack.store
 from spack.filesystem_view import YamlFilesystemView
-import llnl.util.tty as tty
 
 description = "produce a single-rooted directory view of packages"
-section = "environment"
+section = "environments"
 level = "short"
 
 actions_link = ["symlink", "add", "soft", "hardlink", "hard"]
@@ -172,6 +154,7 @@ def setup_parser(sp):
 def view(parser, args):
     'Produce a view of a set of packages.'
 
+    specs = spack.cmd.parse_specs(args.specs)
     path = args.path[0]
 
     view = YamlFilesystemView(
@@ -189,26 +172,32 @@ def view(parser, args):
 
     elif args.action in actions_link:
         # only link commands need to disambiguate specs
-        specs = [spack.cmd.disambiguate_spec(s) for s in args.specs]
+        specs = [spack.cmd.disambiguate_spec(s) for s in specs]
 
     elif args.action in actions_status:
         # no specs implies all
-        if len(args.specs) == 0:
+        if len(specs) == 0:
             specs = view.get_all_specs()
         else:
-            specs = relaxed_disambiguate(args.specs, view)
+            specs = relaxed_disambiguate(specs, view)
 
     else:
         # status and remove can map the name to packages in view
-        specs = relaxed_disambiguate(args.specs, view)
+        specs = relaxed_disambiguate(specs, view)
 
     with_dependencies = args.dependencies.lower() in ['true', 'yes']
 
     # Map action to corresponding functionality
     if args.action in actions_link:
-        view.add_specs(*specs,
-                       with_dependencies=with_dependencies,
-                       exclude=args.exclude)
+        try:
+            view.add_specs(*specs,
+                           with_dependencies=with_dependencies,
+                           exclude=args.exclude)
+        except MergeConflictError:
+            tty.info("Some file blocked the merge, adding the '-i' flag will "
+                     "ignore this conflict. For more information see e.g. "
+                     "https://github.com/spack/spack/issues/9029")
+            raise
 
     elif args.action in actions_remove:
         view.remove_specs(*specs,
diff --git a/lib/spack/spack/compiler.py b/lib/spack/spack/compiler.py
index e19601116f..3bca4d1eae 100644
--- a/lib/spack/spack/compiler.py
+++ b/lib/spack/spack/compiler.py
@@ -1,38 +1,18 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 import re
 import itertools
 
 import llnl.util.tty as tty
-from llnl.util.filesystem import join_path
+import llnl.util.multiproc as mp
 
 import spack.error
 import spack.spec
 import spack.architecture
-from spack.util.multiproc import parmap
 from spack.util.executable import Executable, ProcessError
 from spack.util.environment import get_path
 
@@ -179,40 +159,40 @@ class Compiler(object):
     @property
     def openmp_flag(self):
         # If it is not overridden, assume it is not supported and warn the user
-        tty.die(
-            "The compiler you have chosen does not currently support OpenMP.",
-            "If you think it should, please edit the compiler subclass and",
-            "submit a pull request or issue.")
+        raise UnsupportedCompilerFlag(self, "OpenMP", "openmp_flag")
+
+    # This property should be overridden in the compiler subclass if
+    # C++98 is not the default standard for that compiler
+    @property
+    def cxx98_flag(self):
+        return ""
 
     # This property should be overridden in the compiler subclass if
     # C++11 is supported by that compiler
     @property
     def cxx11_flag(self):
         # If it is not overridden, assume it is not supported and warn the user
-        tty.die(
-            "The compiler you have chosen does not currently support C++11.",
-            "If you think it should, please edit the compiler subclass and",
-            "submit a pull request or issue.")
+        raise UnsupportedCompilerFlag(self,
+                                      "the C++11 standard",
+                                      "cxx11_flag")
 
     # This property should be overridden in the compiler subclass if
     # C++14 is supported by that compiler
     @property
     def cxx14_flag(self):
         # If it is not overridden, assume it is not supported and warn the user
-        tty.die(
-            "The compiler you have chosen does not currently support C++14.",
-            "If you think it should, please edit the compiler subclass and",
-            "submit a pull request or issue.")
+        raise UnsupportedCompilerFlag(self,
+                                      "the C++14 standard",
+                                      "cxx14_flag")
 
     # This property should be overridden in the compiler subclass if
     # C++17 is supported by that compiler
     @property
     def cxx17_flag(self):
         # If it is not overridden, assume it is not supported and warn the user
-        tty.die(
-            "The compiler you have chosen does not currently support C++17.",
-            "If you think it should, please edit the compiler subclass and",
-            "submit a pull request or issue.")
+        raise UnsupportedCompilerFlag(self,
+                                      "the C++17 standard",
+                                      "cxx17_flag")
 
     #
     # Compiler classes have methods for querying the version of
@@ -270,7 +250,7 @@ class Compiler(object):
 
             files = os.listdir(directory)
             for exe in files:
-                full_path = join_path(directory, exe)
+                full_path = os.path.join(directory, exe)
 
                 prod = itertools.product(prefixes, compiler_names, suffixes)
                 for pre, name, suf in prod:
@@ -278,27 +258,11 @@ class Compiler(object):
 
                     match = re.match(regex, exe)
                     if match:
-                        key = (full_path,) + match.groups()
+                        key = (full_path,) + match.groups() + (detect_version,)
                         checks.append(key)
 
-        def check(key):
-            try:
-                full_path, prefix, suffix = key
-                version = detect_version(full_path)
-                return (version, prefix, suffix, full_path)
-            except ProcessError as e:
-                tty.debug(
-                    "Couldn't get version for compiler %s" % full_path, e)
-                return None
-            except Exception as e:
-                # Catching "Exception" here is fine because it just
-                # means something went wrong running a candidate executable.
-                tty.debug("Error while executing candidate compiler %s"
-                          % full_path,
-                          "%s: %s" % (e.__class__.__name__, e))
-                return None
-
-        successful = [k for k in parmap(check, checks) if k is not None]
+        successful = [k for k in mp.parmap(_get_versioned_tuple, checks)
+                      if k is not None]
 
         # The 'successful' list is ordered like the input paths.
         # Reverse it here so that the dict creation (last insert wins)
@@ -322,6 +286,28 @@ class Compiler(object):
                 str(self.operating_system)))))
 
 
+def _get_versioned_tuple(compiler_check_tuple):
+    full_path, prefix, suffix, detect_version = compiler_check_tuple
+    try:
+        version = detect_version(full_path)
+        if (not version) or (not str(version).strip()):
+            tty.debug(
+                "Couldn't get version for compiler %s" % full_path)
+            return None
+        return (version, prefix, suffix, full_path)
+    except ProcessError as e:
+        tty.debug(
+            "Couldn't get version for compiler %s" % full_path, e)
+        return None
+    except Exception as e:
+        # Catching "Exception" here is fine because it just
+        # means something went wrong running a candidate executable.
+        tty.debug("Error while executing candidate compiler %s"
+                  % full_path,
+                  "%s: %s" % (e.__class__.__name__, e))
+        return None
+
+
 class CompilerAccessError(spack.error.SpackError):
 
     def __init__(self, path):
@@ -334,3 +320,19 @@ class InvalidCompilerError(spack.error.SpackError):
     def __init__(self):
         super(InvalidCompilerError, self).__init__(
             "Compiler has no executables.")
+
+
+class UnsupportedCompilerFlag(spack.error.SpackError):
+
+    def __init__(self, compiler, feature, flag_name, ver_string=None):
+        super(UnsupportedCompilerFlag, self).__init__(
+            "{0} ({1}) does not support {2} (as compiler.{3})."
+            .format(compiler.name,
+                    ver_string if ver_string else compiler.version,
+                    feature,
+                    flag_name),
+            "If you think it should, please edit the compiler.{0} subclass to"
+            .format(compiler.name) +
+            " implement the {0} property and submit a pull request or issue."
+            .format(flag_name)
+        )
diff --git a/lib/spack/spack/compilers/__init__.py b/lib/spack/spack/compilers/__init__.py
index f251889f83..188b7fd329 100644
--- a/lib/spack/spack/compilers/__init__.py
+++ b/lib/spack/spack/compilers/__init__.py
@@ -1,41 +1,21 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """This module contains functions related to finding compilers on the
 system and configuring Spack to use multiple compilers.
 """
-import imp
+import os
 
 from llnl.util.lang import list_modules
-from llnl.util.filesystem import join_path
 
-import spack
+import spack.paths
 import spack.error
 import spack.spec
 import spack.config
 import spack.architecture
-
+import spack.util.imp as simp
 from spack.util.naming import mod_to_class
 
 _imported_compilers_module = 'spack.compilers'
@@ -88,9 +68,9 @@ def get_compiler_config(scope=None, init_config=True):
         compilers_dict = []
         for compiler in compilers:
             compilers_dict.append(_to_dict(compiler))
-        spack.config.update_config('compilers', compilers_dict, scope=scope)
+        spack.config.set('compilers', compilers_dict, scope=scope)
 
-    config = spack.config.get_config('compilers', scope=scope)
+    config = spack.config.get('compilers', scope=scope)
     # Update the configuration if there are currently no compilers
     # configured.  Avoid updating automatically if there ARE site
     # compilers configured but no user ones.
@@ -98,15 +78,15 @@ def get_compiler_config(scope=None, init_config=True):
         if scope is None:
             # We know no compilers were configured in any scope.
             init_compiler_config()
-            config = spack.config.get_config('compilers', scope=scope)
+            config = spack.config.get('compilers', scope=scope)
         elif scope == 'user':
             # Check the site config and update the user config if
             # nothing is configured at the site level.
-            site_config = spack.config.get_config('compilers', scope='site')
-            sys_config = spack.config.get_config('compilers', scope='system')
+            site_config = spack.config.get('compilers', scope='site')
+            sys_config = spack.config.get('compilers', scope='system')
             if not site_config and not sys_config:
                 init_compiler_config()
-                config = spack.config.get_config('compilers', scope=scope)
+                config = spack.config.get('compilers', scope=scope)
         return config
     elif config:
         return config
@@ -116,11 +96,12 @@ def get_compiler_config(scope=None, init_config=True):
 
 def compiler_config_files():
     config_files = list()
-    for scope in spack.config.config_scopes:
-        config = spack.config.get_config('compilers', scope=scope)
-        if config:
-            config_files.append(spack.config.config_scopes[scope]
-                                .get_section_filename('compilers'))
+    config = spack.config.config
+    for scope in config.file_scopes:
+        name = scope.name
+        compiler_config = config.get('compilers', scope=name)
+        if compiler_config:
+            config_files.append(config.get_config_filename(name, 'compilers'))
     return config_files
 
 
@@ -136,7 +117,7 @@ def add_compilers_to_config(compilers, scope=None, init_config=True):
         compiler_config.append(_to_dict(compiler))
     global _cache_config_file
     _cache_config_file = compiler_config
-    spack.config.update_config('compilers', compiler_config, scope)
+    spack.config.set('compilers', compiler_config, scope=scope)
 
 
 @_auto_compiler_spec
@@ -161,7 +142,7 @@ def remove_compiler_from_config(compiler_spec, scope=None):
     _cache_config_file = filtered_compiler_config
     if len(filtered_compiler_config) == config_length:  # No items removed
         CompilerSpecInsufficientlySpecificError(compiler_spec)
-    spack.config.update_config('compilers', filtered_compiler_config, scope)
+    spack.config.set('compilers', filtered_compiler_config, scope=scope)
 
 
 def all_compilers_config(scope=None, init_config=True):
@@ -204,7 +185,8 @@ def supported_compilers():
        See available_compilers() to get a list of all the available
        versions of supported compilers.
     """
-    return sorted(name for name in list_modules(spack.compilers_path))
+    return sorted(
+        name for name in list_modules(spack.paths.compilers_path))
 
 
 @_auto_compiler_spec
@@ -337,17 +319,18 @@ def compiler_for_spec(compiler_spec, arch_spec):
 
 @_auto_compiler_spec
 def get_compiler_duplicates(compiler_spec, arch_spec):
-    config_scopes = spack.config.config_scopes
-    scope_to_compilers = dict()
-    for scope in config_scopes:
+    config = spack.config.config
+
+    scope_to_compilers = {}
+    for scope in config.scopes:
         compilers = compilers_for_spec(compiler_spec, arch_spec=arch_spec,
                                        scope=scope, use_cache=False)
         if compilers:
             scope_to_compilers[scope] = compilers
 
-    cfg_file_to_duplicates = dict()
+    cfg_file_to_duplicates = {}
     for scope, compilers in scope_to_compilers.items():
-        config_file = config_scopes[scope].get_section_filename('compilers')
+        config_file = config.get_config_filename(scope, 'compilers')
         cfg_file_to_duplicates[config_file] = compilers
 
     return cfg_file_to_duplicates
@@ -357,8 +340,8 @@ def class_for_compiler_name(compiler_name):
     """Given a compiler module name, get the corresponding Compiler class."""
     assert(supported(compiler_name))
 
-    file_path = join_path(spack.compilers_path, compiler_name + ".py")
-    compiler_mod = imp.load_source(_imported_compilers_module, file_path)
+    file_path = os.path.join(spack.paths.compilers_path, compiler_name + ".py")
+    compiler_mod = simp.load_source(_imported_compilers_module, file_path)
     cls = getattr(compiler_mod, mod_to_class(compiler_name))
 
     # make a note of the name in the module so we can get to it easily.
diff --git a/lib/spack/spack/compilers/arm.py b/lib/spack/spack/compilers/arm.py
new file mode 100644
index 0000000000..f80dba7ea1
--- /dev/null
+++ b/lib/spack/spack/compilers/arm.py
@@ -0,0 +1,73 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import re
+
+from spack.compiler import Compiler, _version_cache
+from spack.util.executable import Executable
+
+
+class Arm(Compiler):
+    # Subclasses use possible names of C compiler
+    cc_names = ['armclang']
+
+    # Subclasses use possible names of C++ compiler
+    cxx_names = ['armclang++']
+
+    # Subclasses use possible names of Fortran 77 compiler
+    f77_names = ['armflang']
+
+    # Subclasses use possible names of Fortran 90 compiler
+    fc_names = ['armflang']
+
+    # Named wrapper links within lib/spack/env
+    link_paths = {'cc': 'clang/clang',
+                  'cxx': 'clang/clang++',
+                  'f77': 'clang/flang',
+                  'fc': 'clang/flang'}
+
+    @property
+    def openmp_flag(self):
+        return "-fopenmp"
+
+    @property
+    def cxx11_flag(self):
+        return "-std=c++11"
+
+    @property
+    def cxx14_flag(self):
+        return "-std=c++14"
+
+    @property
+    def cxx17_flag(self):
+        return "-std=c++1z"
+
+    @property
+    def pic_flag(self):
+        return "-fPIC"
+
+    @classmethod
+    def default_version(cls, comp):
+        if comp not in _version_cache:
+            compiler = Executable(comp)
+            output = compiler('--version', output=str, error=str)
+
+            ver = 'unknown'
+            match = re.search(r'Arm C/C++/Fortran Compiler version ([^ )]+)',
+                              output)
+            if match:
+                ver = match.group(1)
+
+            _version_cache[comp] = ver
+
+        return _version_cache[comp]
+
+    @classmethod
+    def fc_version(cls, fc):
+        return cls.default_version(fc)
+
+    @classmethod
+    def f77_version(cls, f77):
+        return cls.fc_version(f77)
diff --git a/lib/spack/spack/compilers/cce.py b/lib/spack/spack/compilers/cce.py
index 7bb95492ad..879f6432ef 100644
--- a/lib/spack/spack/compilers/cce.py
+++ b/lib/spack/spack/compilers/cce.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack.compiler import Compiler, get_compiler_version
 
 
diff --git a/lib/spack/spack/compilers/clang.py b/lib/spack/spack/compilers/clang.py
index a748bd95bd..6f6f462559 100644
--- a/lib/spack/spack/compilers/clang.py
+++ b/lib/spack/spack/compilers/clang.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import re
 import os
 import sys
@@ -29,12 +10,31 @@ from shutil import copytree, ignore_patterns
 
 import llnl.util.tty as tty
 
-import spack
-from spack.compiler import Compiler, _version_cache
+import spack.paths
+from spack.compiler import Compiler, _version_cache, UnsupportedCompilerFlag
 from spack.util.executable import Executable
 from spack.version import ver
 
 
+#: compiler symlink mappings for mixed f77 compilers
+f77_mapping = [
+    ('gfortran', 'clang/gfortran'),
+    ('xlf_r', 'xl_r/xlf_r'),
+    ('xlf', 'xl/xlf'),
+    ('pgfortran', 'pgi/pgfortran'),
+    ('ifort', 'intel/ifort')
+]
+
+#: compiler symlink mappings for mixed f90/fc compilers
+fc_mapping = [
+    ('gfortran', 'clang/gfortran'),
+    ('xlf90_r', 'xl_r/xlf90_r'),
+    ('xlf90', 'xl/xlf90'),
+    ('pgfortran', 'pgi/pgfortran'),
+    ('ifort', 'intel/ifort')
+]
+
+
 class Clang(Compiler):
     # Subclasses use possible names of C compiler
     cc_names = ['clang']
@@ -43,23 +43,36 @@ class Clang(Compiler):
     cxx_names = ['clang++']
 
     # Subclasses use possible names of Fortran 77 compiler
-    f77_names = ['flang', 'gfortran']
+    f77_names = ['flang', 'gfortran', 'xlf_r']
 
     # Subclasses use possible names of Fortran 90 compiler
-    fc_names = ['flang', 'gfortran']
+    fc_names = ['flang', 'gfortran', 'xlf90_r']
 
-    # Named wrapper links within spack.build_env_path
-    link_paths = {'cc': 'clang/clang',
-                  'cxx': 'clang/clang++'}
+    # Clang has support for using different fortran compilers with the
+    # clang executable.
+    @property
+    def link_paths(self):
+        # clang links are always the same
+        link_paths = {'cc': 'clang/clang',
+                      'cxx': 'clang/clang++'}
+
+        # fortran links need to look at the actual compiler names from
+        # compilers.yaml to figure out which named symlink to use
+        for compiler_name, link_path in f77_mapping:
+            if self.f77 and compiler_name in self.f77:
+                link_paths['f77'] = link_path
+                break
+        else:
+            link_paths['f77'] = 'clang/flang'
 
-    if sys.platform == 'darwin':
-        # Use default wrappers for fortran, in case provided in
-        # compilers.yaml
-        link_paths['f77'] = 'clang/gfortran'
-        link_paths['fc'] = 'clang/gfortran'
-    else:
-        link_paths['f77'] = 'clang/flang'
-        link_paths['fc'] = 'clang/flang'
+        for compiler_name, link_path in fc_mapping:
+            if self.fc and compiler_name in self.fc:
+                link_paths['fc'] = link_path
+                break
+        else:
+            link_paths['fc'] = 'clang/flang'
+
+        return link_paths
 
     @property
     def is_apple(self):
@@ -69,7 +82,10 @@ class Clang(Compiler):
     @property
     def openmp_flag(self):
         if self.is_apple:
-            tty.die("Clang from Apple does not support Openmp yet.")
+            raise UnsupportedCompilerFlag(self,
+                                          "OpenMP",
+                                          "openmp_flag",
+                                          "Xcode {0}".format(self.version))
         else:
             return "-fopenmp"
 
@@ -77,14 +93,20 @@ class Clang(Compiler):
     def cxx11_flag(self):
         if self.is_apple:
             # Adapted from CMake's AppleClang-CXX rules
-            # Spack's AppleClang detection only valid form Xcode >= 4.6
+            # Spack's AppleClang detection only valid from Xcode >= 4.6
             if self.version < ver('4.0.0'):
-                tty.die("Only Apple LLVM 4.0 and above support c++11")
+                raise UnsupportedCompilerFlag(self,
+                                              "the C++11 standard",
+                                              "cxx11_flag",
+                                              "Xcode < 4.0.0")
             else:
                 return "-std=c++11"
         else:
             if self.version < ver('3.3'):
-                tty.die("Only Clang 3.3 and above support c++11.")
+                raise UnsupportedCompilerFlag(self,
+                                              "the C++11 standard",
+                                              "cxx11_flag",
+                                              "< 3.3")
             else:
                 return "-std=c++11"
 
@@ -93,14 +115,20 @@ class Clang(Compiler):
         if self.is_apple:
             # Adapted from CMake's rules for AppleClang
             if self.version < ver('5.1.0'):
-                tty.die("Only Apple LLVM 5.1 and above support c++14.")
+                raise UnsupportedCompilerFlag(self,
+                                              "the C++14 standard",
+                                              "cxx14_flag",
+                                              "Xcode < 5.1.0")
             elif self.version < ver('6.1.0'):
                 return "-std=c++1y"
             else:
                 return "-std=c++14"
         else:
             if self.version < ver('3.4'):
-                tty.die("Only Clang 3.4 and above support c++14.")
+                raise UnsupportedCompilerFlag(self,
+                                              "the C++14 standard",
+                                              "cxx14_flag",
+                                              "< 3.5")
             elif self.version < ver('3.5'):
                 return "-std=c++1y"
             else:
@@ -111,14 +139,22 @@ class Clang(Compiler):
         if self.is_apple:
             # Adapted from CMake's rules for AppleClang
             if self.version < ver('6.1.0'):
-                tty.die("Only Apple LLVM 6.1 and above support c++17.")
+                raise UnsupportedCompilerFlag(self,
+                                              "the C++17 standard",
+                                              "cxx17_flag",
+                                              "Xcode < 6.1.0")
             else:
                 return "-std=c++1z"
         else:
             if self.version < ver('3.5'):
-                tty.die("Only Clang 3.5 and above support c++17.")
-            else:
+                raise UnsupportedCompilerFlag(self,
+                                              "the C++17 standard",
+                                              "cxx17_flag",
+                                              "< 5.0")
+            elif self.version < ver('5.0'):
                 return "-std=c++1z"
+            else:
+                return "-std=c++17"
 
     @property
     def pic_flag(self):
@@ -228,7 +264,7 @@ class Clang(Compiler):
             raise OSError(msg)
 
         real_root = os.path.dirname(os.path.dirname(real_root))
-        developer_root = os.path.join(spack.stage_path,
+        developer_root = os.path.join(spack.paths.stage_path,
                                       'xcode-select',
                                       self.name,
                                       str(self.version))
@@ -267,8 +303,9 @@ class Clang(Compiler):
                 for fname in os.listdir(dev_dir):
                     if fname in bins:
                         os.unlink(os.path.join(dev_dir, fname))
-                        os.symlink(os.path.join(spack.build_env_path, 'cc'),
-                                   os.path.join(dev_dir, fname))
+                        os.symlink(
+                            os.path.join(spack.paths.build_env_path, 'cc'),
+                            os.path.join(dev_dir, fname))
 
             os.symlink(developer_root, xcode_link)
 
diff --git a/lib/spack/spack/compilers/gcc.py b/lib/spack/spack/compilers/gcc.py
index b97d8b2e24..241a8d97e6 100644
--- a/lib/spack/spack/compilers/gcc.py
+++ b/lib/spack/spack/compilers/gcc.py
@@ -1,31 +1,11 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-import llnl.util.tty as tty
-
-import spack
-from spack.compiler import Compiler, get_compiler_version
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import spack.compilers.clang
+from spack.compiler import \
+    Compiler, get_compiler_version, UnsupportedCompilerFlag
 from spack.version import ver
 
 
@@ -47,7 +27,7 @@ class Gcc(Compiler):
     # Old compatibility versions may contain XY suffixes.
     suffixes = [r'-mp-\d\.\d', r'-\d\.\d', r'-\d', r'\d\d']
 
-    # Named wrapper links within spack.build_env_path
+    # Named wrapper links within build_env_path
     link_paths = {'cc': 'gcc/gcc',
                   'cxx': 'gcc/g++',
                   'f77': 'gcc/gfortran',
@@ -61,9 +41,19 @@ class Gcc(Compiler):
         return "-fopenmp"
 
     @property
+    def cxx98_flag(self):
+        if self.version < ver('6.0'):
+            return ""
+        else:
+            return "-std=c++98"
+
+    @property
     def cxx11_flag(self):
         if self.version < ver('4.3'):
-            tty.die("Only gcc 4.3 and above support c++11.")
+            raise UnsupportedCompilerFlag(self,
+                                          "the C++11 standard",
+                                          "cxx11_flag",
+                                          " < 4.3")
         elif self.version < ver('4.7'):
             return "-std=c++0x"
         else:
@@ -72,18 +62,28 @@ class Gcc(Compiler):
     @property
     def cxx14_flag(self):
         if self.version < ver('4.8'):
-            tty.die("Only gcc 4.8 and above support c++14.")
+            raise UnsupportedCompilerFlag(self,
+                                          "the C++14 standard",
+                                          "cxx14_flag",
+                                          "< 4.8")
         elif self.version < ver('4.9'):
             return "-std=c++1y"
-        else:
+        elif self.version < ver('6.0'):
             return "-std=c++14"
+        else:
+            return ""
 
     @property
     def cxx17_flag(self):
         if self.version < ver('5.0'):
-            tty.die("Only gcc 5.0 and above support c++17.")
-        else:
+            raise UnsupportedCompilerFlag(self,
+                                          "the C++17 standard",
+                                          "cxx17_flag",
+                                          "< 5.0")
+        elif self.version < ver('6.0'):
             return "-std=c++1z"
+        else:
+            return "-std=c++17"
 
     @property
     def pic_flag(self):
@@ -113,7 +113,7 @@ class Gcc(Compiler):
             return 'unknown'
 
         version = super(Gcc, cls).default_version(cc)
-        if version in ['7']:
+        if ver(version) >= ver('7'):
             version = get_compiler_version(cc, '-dumpfullversion')
         return version
 
@@ -142,7 +142,7 @@ class Gcc(Compiler):
         version = get_compiler_version(
             fc, '-dumpversion',
             r'(?:GNU Fortran \(GCC\) )?([\d.]+)')
-        if version in ['7']:
+        if ver(version) >= ver('7'):
             version = get_compiler_version(fc, '-dumpfullversion')
         return version
 
diff --git a/lib/spack/spack/compilers/intel.py b/lib/spack/spack/compilers/intel.py
index b66436ecc0..53d78d09a1 100644
--- a/lib/spack/spack/compilers/intel.py
+++ b/lib/spack/spack/compilers/intel.py
@@ -1,30 +1,10 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-import llnl.util.tty as tty
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-from spack.compiler import Compiler, get_compiler_version
+from spack.compiler import \
+    Compiler, get_compiler_version, UnsupportedCompilerFlag
 from spack.version import ver
 
 
@@ -41,7 +21,7 @@ class Intel(Compiler):
     # Subclasses use possible names of Fortran 90 compiler
     fc_names = ['ifort']
 
-    # Named wrapper links within spack.build_env_path
+    # Named wrapper links within build_env_path
     link_paths = {'cc': 'intel/icc',
                   'cxx': 'intel/icpc',
                   'f77': 'intel/ifort',
@@ -60,7 +40,11 @@ class Intel(Compiler):
     @property
     def cxx11_flag(self):
         if self.version < ver('11.1'):
-            tty.die("Only intel 11.1 and above support c++11.")
+            raise UnsupportedCompilerFlag(self,
+                                          "the C++11 standard",
+                                          "cxx11_flag",
+                                          "< 11.1")
+
         elif self.version < ver('13'):
             return "-std=c++0x"
         else:
@@ -70,7 +54,10 @@ class Intel(Compiler):
     def cxx14_flag(self):
         # Adapted from CMake's Intel-CXX rules.
         if self.version < ver('15'):
-            tty.die("Only intel 15.0 and above support c++14.")
+            raise UnsupportedCompilerFlag(self,
+                                          "the C++14 standard",
+                                          "cxx14_flag",
+                                          "< 15")
         elif self.version < ver('15.0.2'):
             return "-std=c++1y"
         else:
diff --git a/lib/spack/spack/compilers/nag.py b/lib/spack/spack/compilers/nag.py
index 20688b67ef..18e5634bfd 100644
--- a/lib/spack/spack/compilers/nag.py
+++ b/lib/spack/spack/compilers/nag.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack.compiler import Compiler, get_compiler_version
 
 
@@ -38,7 +19,7 @@ class Nag(Compiler):
     # Subclasses use possible names of Fortran 90 compiler
     fc_names = ['nagfor']
 
-    # Named wrapper links within spack.build_env_path
+    # Named wrapper links within build_env_path
     # Use default wrappers for C and C++, in case provided in compilers.yaml
     link_paths = {
         'cc': 'cc',
@@ -72,7 +53,7 @@ class Nag(Compiler):
         return '-Wl,-Wl,,-rpath,,'
 
     @classmethod
-    def default_version(self, comp):
+    def default_version(cls, comp):
         """The ``-V`` option works for nag compilers.
         Output looks like this::
 
diff --git a/lib/spack/spack/compilers/pgi.py b/lib/spack/spack/compilers/pgi.py
index 0a90c4202d..a224e3ea6f 100644
--- a/lib/spack/spack/compilers/pgi.py
+++ b/lib/spack/spack/compilers/pgi.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack.compiler import Compiler, get_compiler_version
 
 
@@ -38,7 +19,7 @@ class Pgi(Compiler):
     # Subclasses use possible names of Fortran 90 compiler
     fc_names = ['pgfortran', 'pgf95', 'pgf90']
 
-    # Named wrapper links within spack.build_env_path
+    # Named wrapper links within build_env_path
     link_paths = {'cc': 'pgi/pgcc',
                   'cxx': 'pgi/pgc++',
                   'f77': 'pgi/pgfortran',
diff --git a/lib/spack/spack/compilers/xl.py b/lib/spack/spack/compilers/xl.py
index 827ffeba1b..2f7085fca5 100644
--- a/lib/spack/spack/compilers/xl.py
+++ b/lib/spack/spack/compilers/xl.py
@@ -1,30 +1,10 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-import llnl.util.tty as tty
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-from spack.compiler import Compiler, get_compiler_version
+from spack.compiler import \
+    Compiler, get_compiler_version, UnsupportedCompilerFlag
 from spack.version import ver
 
 
@@ -41,7 +21,7 @@ class Xl(Compiler):
     # Subclasses use possible names of Fortran 90 compiler
     fc_names = ['xlf90', 'xlf95', 'xlf2003', 'xlf2008']
 
-    # Named wrapper links within spack.build_env_path
+    # Named wrapper links within build_env_path
     link_paths = {'cc': 'xl/xlc',
                   'cxx': 'xl/xlc++',
                   'f77': 'xl/xlf',
@@ -54,7 +34,10 @@ class Xl(Compiler):
     @property
     def cxx11_flag(self):
         if self.version < ver('13.1'):
-            tty.die("Only xlC 13.1 and above have some c++11 support.")
+            raise UnsupportedCompilerFlag(self,
+                                          "the C++11 standard",
+                                          "cxx11_flag",
+                                          "< 13.1")
         else:
             return "-qlanglvl=extended0x"
 
@@ -112,6 +95,12 @@ class Xl(Compiler):
            older version of AIX and linux on power.
         """
         fver = get_compiler_version(fc, '-qversion', r'([0-9]?[0-9]\.[0-9])')
+        if fver >= 16:
+            """Starting with version 16.1, the XL C and Fortran compilers
+               have the same version.  So no need to downgrade the Fortran
+               compiler version to match that of the C compiler version.
+            """
+            return str(fver)
         cver = float(fver) - 2
         if cver < 10:
             cver = cver - 0.1
diff --git a/lib/spack/spack/compilers/xl_r.py b/lib/spack/spack/compilers/xl_r.py
index 1afaa45e63..18ffe0631d 100644
--- a/lib/spack/spack/compilers/xl_r.py
+++ b/lib/spack/spack/compilers/xl_r.py
@@ -1,31 +1,10 @@
-##############################################################################
-# Copyright (c) 2016, International Business Machines Corporation
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Serban Maerean, serban@us.ibm.com based on a similar file,
-# spack/lib/spack/spack/compilers/xl.py, produced by Todd Gamblin,
-# tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-import llnl.util.tty as tty
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-from spack.compiler import Compiler, get_compiler_version
+from spack.compiler import \
+    Compiler, get_compiler_version, UnsupportedCompilerFlag
 from spack.version import ver
 
 
@@ -42,7 +21,7 @@ class XlR(Compiler):
     # Subclasses use possible names of Fortran 90 compiler
     fc_names = ['xlf90_r', 'xlf95_r', 'xlf2003_r', 'xlf2008_r']
 
-    # Named wrapper links within spack.build_env_path
+    # Named wrapper links within build_env_path
     link_paths = {'cc': 'xl_r/xlc_r',
                   'cxx': 'xl_r/xlc++_r',
                   'f77': 'xl_r/xlf_r',
@@ -55,7 +34,10 @@ class XlR(Compiler):
     @property
     def cxx11_flag(self):
         if self.version < ver('13.1'):
-            tty.die("Only xlC 13.1 and above have some c++11 support.")
+            raise UnsupportedCompilerFlag(self,
+                                          "the C++11 standard",
+                                          "cxx11_flag",
+                                          "< 13.1")
         else:
             return "-qlanglvl=extended0x"
 
@@ -72,7 +54,7 @@ class XlR(Compiler):
         return "-qzerosize"
 
     @classmethod
-    def default_version(self, comp):
+    def default_version(cls, comp):
         """The '-qversion' is the standard option fo XL compilers.
            Output looks like this::
 
@@ -113,6 +95,12 @@ class XlR(Compiler):
            older version of AIX and linux on power.
         """
         fver = get_compiler_version(fc, '-qversion', r'([0-9]?[0-9]\.[0-9])')
+        if fver >= 16:
+            """Starting with version 16.1, the XL C and Fortran compilers
+               have the same version.  So no need to downgrade the Fortran
+               compiler version to match that of the C compiler version.
+            """
+            return str(fver)
         cver = float(fver) - 2
         if cver < 10:
             cver = cver - 0.1
diff --git a/lib/spack/spack/concretize.py b/lib/spack/spack/concretize.py
index 3b1e83cb5b..4b12588c56 100644
--- a/lib/spack/spack/concretize.py
+++ b/lib/spack/spack/concretize.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """
 Functions here are used to take abstract specs and make them concrete.
 For example, if a spec asks for a version between 1.8 and 1.9, these
@@ -36,9 +17,13 @@ TODO: make this customizable and allow users to configure
 from __future__ import print_function
 from itertools import chain
 from functools_backport import reverse_order
+from contextlib import contextmanager
 from six import iteritems
 
-import spack
+import llnl.util.lang
+
+import spack.repo
+import spack.abi
 import spack.spec
 import spack.compilers
 import spack.architecture
@@ -47,11 +32,30 @@ from spack.version import ver, Version, VersionList, VersionRange
 from spack.package_prefs import PackagePrefs, spec_externals, is_spec_buildable
 
 
-class DefaultConcretizer(object):
-    """This class doesn't have any state, it just provides some methods for
-       concretization.  You can subclass it to override just some of the
-       default concretization strategies, or you can override all of them.
+#: Concretizer singleton
+concretizer = llnl.util.lang.Singleton(lambda: Concretizer())
+
+
+#: impements rudimentary logic for ABI compatibility
+_abi = llnl.util.lang.Singleton(lambda: spack.abi.ABI())
+
+
+class Concretizer(object):
+    """You can subclass this class to override some of the default
+       concretization strategies, or you can override all of them.
     """
+    def __init__(self):
+        # controls whether we check that compiler versions actually exist
+        # during concretization. Used for testing and for mirror creation
+        self.check_for_compiler_existence = True
+
+    @contextmanager
+    def disable_compiler_existence_check(self):
+        saved = self.check_for_compiler_existence
+        self.check_for_compiler_existence = False
+        yield
+        self.check_for_compiler_existence = saved
+
     def _valid_virtuals_and_externals(self, spec):
         """Returns a list of candidate virtual dep providers and external
            packages that coiuld be used to concretize a spec.
@@ -63,7 +67,7 @@ class DefaultConcretizer(object):
         pref_key = lambda spec: 0  # no-op pref key
 
         if spec.virtual:
-            candidates = spack.repo.providers_for(spec)
+            candidates = spack.repo.path.providers_for(spec)
             if not candidates:
                 raise spack.spec.UnsatisfiableProviderSpecError(
                     candidates[0], spec)
@@ -124,8 +128,8 @@ class DefaultConcretizer(object):
         return sorted(candidates,
                       reverse=True,
                       key=lambda spec: (
-                          spack.abi.compatible(spec, abi_exemplar, loose=True),
-                          spack.abi.compatible(spec, abi_exemplar)))
+                          _abi.compatible(spec, abi_exemplar, loose=True),
+                          _abi.compatible(spec, abi_exemplar)))
 
     def concretize_version(self, spec):
         """If the spec is already concrete, return.  Otherwise take
@@ -214,27 +218,29 @@ class DefaultConcretizer(object):
         DAG has an architecture, then use the root otherwise use the defaults
         on the platform.
         """
-        root_arch = spec.root.architecture
-        sys_arch = spack.spec.ArchSpec(spack.architecture.sys_type())
+        try:
+            # Get the nearest architecture with any fields set
+            nearest = next(p for p in spec.traverse(direction='parents')
+                           if (p.architecture and p is not spec))
+            nearest_arch = nearest.architecture
+        except StopIteration:
+            # Default to the system architecture if nothing set
+            nearest_arch = spack.spec.ArchSpec(spack.architecture.sys_type())
+
         spec_changed = False
 
+        # ensure type safety for the architecture
         if spec.architecture is None:
-            spec.architecture = spack.spec.ArchSpec(sys_arch)
+            spec.architecture = spack.spec.ArchSpec()
             spec_changed = True
 
-        default_archs = list(x for x in [root_arch, sys_arch] if x)
-        for arch in default_archs:
-            if spec.architecture.concrete:
-                break
-
-            replacement_fields = [k for k, v in iteritems(arch.to_cmp_dict())
-                                  if v and not getattr(spec.architecture, k)]
-            for field in replacement_fields:
-                setattr(spec.architecture, field, getattr(arch, field))
-                spec_changed = True
-
-        if not spec.architecture.concrete:
-            raise InsufficientArchitectureInfoError(spec, default_archs)
+        # replace each of the fields (platform, os, target) separately
+        nearest_dict = nearest_arch.to_cmp_dict()
+        replacement_fields = [k for k, v in iteritems(nearest_dict)
+                              if v and not getattr(spec.architecture, k)]
+        for field in replacement_fields:
+            setattr(spec.architecture, field, getattr(nearest_arch, field))
+            spec_changed = True
 
         return spec_changed
 
@@ -283,14 +289,9 @@ class DefaultConcretizer(object):
         def _proper_compiler_style(cspec, aspec):
             return spack.compilers.compilers_for_spec(cspec, arch_spec=aspec)
 
-        all_compiler_specs = spack.compilers.all_compiler_specs()
-        if not all_compiler_specs:
-            raise spack.compilers.NoCompilersError()
-
-        if (spec.compiler and
-            spec.compiler.concrete and
-                spec.compiler in all_compiler_specs):
-            if not _proper_compiler_style(spec.compiler, spec.architecture):
+        if spec.compiler and spec.compiler.concrete:
+            if (self.check_for_compiler_existence and not
+                    _proper_compiler_style(spec.compiler, spec.architecture)):
                 _compiler_concretization_failure(
                     spec.compiler, spec.architecture)
             return False
@@ -302,6 +303,22 @@ class DefaultConcretizer(object):
         assert(other_spec)
 
         # Check if the compiler is already fully specified
+        if (other_compiler and other_compiler.concrete and
+                not self.check_for_compiler_existence):
+            spec.compiler = other_compiler.copy()
+            return True
+
+        all_compiler_specs = spack.compilers.all_compiler_specs()
+        if not all_compiler_specs:
+            # If compiler existence checking is disabled, then we would have
+            # exited by now if there were sufficient hints to form a full
+            # compiler spec. Therefore even if compiler existence checking is
+            # disabled, compilers must be available at this point because the
+            # available compilers are used to choose a compiler. If compiler
+            # existence checking is enabled then some compiler must exist in
+            # order to complete the spec.
+            raise spack.compilers.NoCompilersError()
+
         if other_compiler in all_compiler_specs:
             spec.compiler = other_compiler.copy()
             if not _proper_compiler_style(spec.compiler, spec.architecture):
@@ -377,8 +394,13 @@ class DefaultConcretizer(object):
         # Include the compiler flag defaults from the config files
         # This ensures that spack will detect conflicts that stem from a change
         # in default compiler flags.
-        compiler = spack.compilers.compiler_for_spec(
-            spec.compiler, spec.architecture)
+        try:
+            compiler = spack.compilers.compiler_for_spec(
+                spec.compiler, spec.architecture)
+        except spack.compilers.NoCompilerForSpecError:
+            if self.check_for_compiler_existence:
+                raise
+            return ret
         for flag in compiler.flags:
             config_flags = set(compiler.flags.get(flag, []))
             flags = set(spec.compiler_flags.get(flag, []))
diff --git a/lib/spack/spack/config.py b/lib/spack/spack/config.py
index 4be407fd68..2ecd669cfe 100644
--- a/lib/spack/spack/config.py
+++ b/lib/spack/spack/config.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """This module implements Spack's configuration file handling.
 
 This implements Spack's configuration system, which handles merging
@@ -53,28 +34,34 @@ import copy
 import os
 import re
 import sys
+import multiprocessing
+from contextlib import contextmanager
 from six import string_types
 from six import iteritems
-
-import yaml
-import jsonschema
-from yaml.error import MarkedYAMLError
-from jsonschema import Draft4Validator, validators
 from ordereddict_backport import OrderedDict
 
+import ruamel.yaml as yaml
+from ruamel.yaml.error import MarkedYAMLError
+
+import llnl.util.lang
 import llnl.util.tty as tty
 from llnl.util.filesystem import mkdirp
 
-import spack
+import spack.paths
 import spack.architecture
+import spack.schema.compilers
+import spack.schema.mirrors
+import spack.schema.repos
+import spack.schema.packages
+import spack.schema.modules
+import spack.schema.config
 from spack.error import SpackError
-import spack.schema
 
 # Hacked yaml for configuration files preserves line numbers.
 import spack.util.spack_yaml as syaml
 
 
-"""Dict from section names -> schema for that section."""
+#: Dict from section names -> schema for that section
 section_schemas = {
     'compilers': spack.schema.compilers.schema,
     'mirrors': spack.schema.mirrors.schema,
@@ -84,20 +71,51 @@ section_schemas = {
     'config': spack.schema.config.schema,
 }
 
-"""OrderedDict of config scopes keyed by name.
-   Later scopes will override earlier scopes.
-"""
-config_scopes = OrderedDict()
+#: Builtin paths to configuration files in Spack
+configuration_paths = (
+    # Default configuration scope is the lowest-level scope. These are
+    # versioned with Spack and can be overridden by systems, sites or users
+    ('defaults', os.path.join(spack.paths.etc_path, 'spack', 'defaults')),
+
+    # System configuration is per machine.
+    # No system-level configs should be checked into spack by default
+    ('system', os.path.join(spack.paths.system_etc_path, 'spack')),
+
+    # Site configuration is per spack instance, for sites or projects
+    # No site-level configs should be checked into spack by default.
+    ('site', os.path.join(spack.paths.etc_path, 'spack')),
+
+    # User configuration can override both spack defaults and site config
+    ('user', spack.paths.user_config_path)
+)
+
+#: Hard-coded default values for some key configuration options.
+#: This ensures that Spack will still work even if config.yaml in
+#: the defaults scope is removed.
+config_defaults = {
+    'config': {
+        'debug': False,
+        'verify_ssl': True,
+        'checksum': True,
+        'dirty': False,
+        'build_jobs': multiprocessing.cpu_count(),
+    }
+}
 
+#: metavar to use for commands that accept scopes
+#: this is shorter and more readable than listing all choices
+scopes_metavar = '{defaults,system,site,user}[/PLATFORM]'
 
-def validate_section_name(section):
-    """Exit if the section is not a valid section."""
-    if section not in section_schemas:
-        tty.die("Invalid config section: '%s'. Options are: %s"
-                % (section, " ".join(section_schemas.keys())))
+
+def first_existing(dictionary, keys):
+    """Get the value of the first key in keys that is in the dictionary."""
+    try:
+        return next(k for k in keys if k in dictionary)
+    except StopIteration:
+        raise KeyError("None of %s is in dict!" % keys)
 
 
-def extend_with_default(validator_class):
+def _extend_with_default(validator_class):
     """Add support for the 'default' attr for properties and patternProperties.
 
        jsonschema does not handle this out of the box -- it only
@@ -106,6 +124,7 @@ def extend_with_default(validator_class):
        commented out.
 
     """
+    import jsonschema
     validate_properties = validator_class.VALIDATORS["properties"]
     validate_pattern_properties = validator_class.VALIDATORS[
         "patternProperties"]
@@ -113,7 +132,8 @@ def extend_with_default(validator_class):
     def set_defaults(validator, properties, instance, schema):
         for property, subschema in iteritems(properties):
             if "default" in subschema:
-                instance.setdefault(property, subschema["default"])
+                instance.setdefault(
+                    property, copy.deepcopy(subschema["default"]))
         for err in validate_properties(
                 validator, properties, instance, schema):
             yield err
@@ -124,34 +144,18 @@ def extend_with_default(validator_class):
                 if isinstance(instance, dict):
                     for key, val in iteritems(instance):
                         if re.match(property, key) and val is None:
-                            instance[key] = subschema["default"]
+                            instance[key] = copy.deepcopy(subschema["default"])
 
         for err in validate_pattern_properties(
                 validator, properties, instance, schema):
             yield err
 
-    return validators.extend(validator_class, {
+    return jsonschema.validators.extend(validator_class, {
         "properties": set_defaults,
         "patternProperties": set_pp_defaults
     })
 
 
-DefaultSettingValidator = extend_with_default(Draft4Validator)
-
-
-def validate_section(data, schema):
-    """Validate data read in from a Spack YAML file.
-
-    This leverages the line information (start_mark, end_mark) stored
-    on Spack YAML structures.
-
-    """
-    try:
-        DefaultSettingValidator(schema).validate(data)
-    except jsonschema.ValidationError as e:
-        raise ConfigFormatError(e, data)
-
-
 class ConfigScope(object):
     """This class represents a configuration scope.
 
@@ -164,13 +168,8 @@ class ConfigScope(object):
         self.path = path           # path to directory containing configs.
         self.sections = syaml.syaml_dict()  # sections read from config files.
 
-        # Register in a dict of all ConfigScopes
-        # TODO: make this cleaner.  Mocking up for testing is brittle.
-        global config_scopes
-        config_scopes[name] = self
-
     def get_section_filename(self, section):
-        validate_section_name(section)
+        _validate_section_name(section)
         return os.path.join(self.path, "%s.yaml" % section)
 
     def get_section(self, section):
@@ -184,13 +183,13 @@ class ConfigScope(object):
     def write_section(self, section):
         filename = self.get_section_filename(section)
         data = self.get_section(section)
+        _validate(data, section_schemas[section])
+
         try:
             mkdirp(self.path)
             with open(filename, 'w') as f:
-                validate_section(data, section_schemas[section])
+                _validate(data, section_schemas[section])
                 syaml.dump(data, stream=f, default_flow_style=False)
-        except jsonschema.ValidationError as e:
-            raise ConfigSanityError(e, data)
         except (yaml.YAMLError, IOError) as e:
             raise ConfigFileError(
                 "Error writing to config file: '%s'" % str(e))
@@ -203,61 +202,514 @@ class ConfigScope(object):
         return '<ConfigScope: %s: %s>' % (self.name, self.path)
 
 
-#
-# Below are configuration scopes.
-#
-# Each scope can have per-platfom overrides in subdirectories of the
-# configuration directory.
-#
-_platform = spack.architecture.platform().name
+class SingleFileScope(ConfigScope):
+    """This class represents a configuration scope in a single YAML file."""
+    def __init__(self, name, path, schema, yaml_path=None):
+        """Similar to ``ConfigScope`` but can be embedded in another schema.
+
+        Arguments:
+            schema (dict): jsonschema for the file to read
+            yaml_path (list): list of dict keys in the schema where
+                config data can be found;
+
+        Elements of ``yaml_path`` can be tuples or lists to represent an
+        "or" of keys (e.g. "env" or "spack" is ``('env', 'spack')``)
+
+        """
+        super(SingleFileScope, self).__init__(name, path)
+        self._raw_data = None
+        self.schema = schema
+        self.yaml_path = yaml_path or []
+
+    def get_section_filename(self, section):
+        return self.path
+
+    def get_section(self, section):
+        # read raw data from the file, which looks like:
+        # {
+        #   'config': {
+        #      ... data ...
+        #   },
+        #   'packages': {
+        #      ... data ...
+        #   },
+        # }
+        if self._raw_data is None:
+            self._raw_data = _read_config_file(self.path, self.schema)
+            if self._raw_data is None:
+                return None
+
+            for key in self.yaml_path:
+                if self._raw_data is None:
+                    return None
+
+                # support tuples as "or" in the yaml path
+                if isinstance(key, (list, tuple)):
+                    key = first_existing(self._raw_data, key)
+
+                self._raw_data = self._raw_data[key]
+
+        # data in self.sections looks (awkwardly) like this:
+        # {
+        #   'config': {
+        #      'config': {
+        #         ... data ...
+        #       }
+        #   },
+        #   'packages': {
+        #      'packages': {
+        #         ... data ...
+        #      }
+        #   }
+        # }
+        #
+        # UNLESS there is no section, in which case it is stored as:
+        # {
+        #   'config': None,
+        #   ...
+        # }
+        value = self._raw_data.get(section)
+        self.sections.setdefault(
+            section, None if value is None else {section: value})
+        return self.sections[section]
+
+    def write_section(self, section):
+        _validate(self.sections, self.schema)
+        try:
+            parent = os.path.dirname(self.path)
+            mkdirp(parent)
 
-"""Default configuration scope is the lowest-level scope. These are
-   versioned with Spack and can be overridden by systems, sites or users."""
-_defaults_path = os.path.join(spack.etc_path, 'spack', 'defaults')
-ConfigScope('defaults', _defaults_path)
-ConfigScope('defaults/%s' % _platform, os.path.join(_defaults_path, _platform))
+            tmp = os.path.join(parent, '.%s.tmp' % self.path)
+            with open(tmp, 'w') as f:
+                syaml.dump(self.sections, stream=f, default_flow_style=False)
+            os.path.move(tmp, self.path)
+        except (yaml.YAMLError, IOError) as e:
+            raise ConfigFileError(
+                "Error writing to config file: '%s'" % str(e))
 
-"""System configuration is per machine.
-   No system-level configs should be checked into spack by default"""
-_system_path = os.path.join(spack.system_etc_path, 'spack')
-ConfigScope('system', _system_path)
-ConfigScope('system/%s' % _platform, os.path.join(_system_path, _platform))
+    def __repr__(self):
+        return '<SingleFileScope: %s: %s>' % (self.name, self.path)
 
-"""Site configuration is per spack instance, for sites or projects.
-   No site-level configs should be checked into spack by default."""
-_site_path = os.path.join(spack.etc_path, 'spack')
-ConfigScope('site', _site_path)
-ConfigScope('site/%s' % _platform, os.path.join(_site_path, _platform))
 
-"""User configuration can override both spack defaults and site config."""
-_user_path = spack.user_config_path
-ConfigScope('user', _user_path)
-ConfigScope('user/%s' % _platform, os.path.join(_user_path, _platform))
+class ImmutableConfigScope(ConfigScope):
+    """A configuration scope that cannot be written to.
 
+    This is used for ConfigScopes passed on the command line.
+    """
 
-def highest_precedence_scope():
-    """Get the scope with highest precedence (prefs will override others)."""
-    return config_scopes.values()[-1]
+    def write_section(self, section):
+        raise ConfigError("Cannot write to immutable scope %s" % self)
 
+    def __repr__(self):
+        return '<ImmutableConfigScope: %s: %s>' % (self.name, self.path)
 
-def validate_scope(scope):
-    """Ensure that scope is valid, and return a valid scope if it is None.
 
-       This should be used by routines in ``config.py`` to validate
-       scope name arguments, and to determine a default scope where no
-       scope is specified.
+class InternalConfigScope(ConfigScope):
+    """An internal configuration scope that is not persisted to a file.
 
+    This is for spack internal use so that command-line options and
+    config file settings are accessed the same way, and Spack can easily
+    override settings from files.
     """
-    if scope is None:
-        # default to the scope with highest precedence.
-        return highest_precedence_scope()
+    def __init__(self, name, data=None):
+        super(InternalConfigScope, self).__init__(name, None)
+        self.sections = syaml.syaml_dict()
+
+        if data:
+            for section in data:
+                dsec = data[section]
+                _validate({section: dsec}, section_schemas[section])
+                self.sections[section] = _mark_internal(
+                    syaml.syaml_dict({section: dsec}), name)
 
-    elif scope in config_scopes:
-        return config_scopes[scope]
+    def get_section_filename(self, section):
+        raise NotImplementedError(
+            "Cannot get filename for InternalConfigScope.")
+
+    def get_section(self, section):
+        """Just reads from an internal dictionary."""
+        if section not in self.sections:
+            self.sections[section] = None
+        return self.sections[section]
+
+    def write_section(self, section):
+        """This only validates, as the data is already in memory."""
+        data = self.get_section(section)
+        if data is not None:
+            _validate(data, section_schemas[section])
+        self.sections[section] = _mark_internal(data, self.name)
+
+    def __repr__(self):
+        return '<InternalConfigScope: %s>' % self.name
+
+
+class Configuration(object):
+    """A full Spack configuration, from a hierarchy of config files.
+
+    This class makes it easy to add a new scope on top of an existing one.
+    """
+
+    def __init__(self, *scopes):
+        """Initialize a configuration with an initial list of scopes.
+
+        Args:
+            scopes (list of ConfigScope): list of scopes to add to this
+                Configuration, ordered from lowest to highest precedence
+
+        """
+        self.scopes = OrderedDict()
+        for scope in scopes:
+            self.push_scope(scope)
+
+    def push_scope(self, scope):
+        """Add a higher precedence scope to the Configuration."""
+        cmd_line_scope = None
+        if self.scopes:
+            highest_precedence_scope = list(self.scopes.values())[-1]
+            if highest_precedence_scope.name == 'command_line':
+                # If the command-line scope is present, it should always
+                # be the scope of highest precedence
+                cmd_line_scope = self.pop_scope()
+
+        self.scopes[scope.name] = scope
+        if cmd_line_scope:
+            self.scopes['command_line'] = cmd_line_scope
+
+    def pop_scope(self):
+        """Remove the highest precedence scope and return it."""
+        name, scope = self.scopes.popitem(last=True)
+        return scope
+
+    def remove_scope(self, scope_name):
+        return self.scopes.pop(scope_name)
+
+    @property
+    def file_scopes(self):
+        """List of writable scopes with an associated file."""
+        return [s for s in self.scopes.values() if type(s) == ConfigScope]
+
+    def highest_precedence_scope(self):
+        """Non-internal scope with highest precedence."""
+        return next(reversed(self.file_scopes), None)
+
+    def _validate_scope(self, scope):
+        """Ensure that scope is valid in this configuration.
+
+        This should be used by routines in ``config.py`` to validate
+        scope name arguments, and to determine a default scope where no
+        scope is specified.
+
+        Raises:
+            ValueError: if ``scope`` is not valid
+
+        Returns:
+            ConfigScope: a valid ConfigScope if ``scope`` is ``None`` or valid
+        """
+        if scope is None:
+            # default to the scope with highest precedence.
+            return self.highest_precedence_scope()
+
+        elif scope in self.scopes:
+            return self.scopes[scope]
+
+        else:
+            raise ValueError("Invalid config scope: '%s'.  Must be one of %s"
+                             % (scope, self.scopes.keys()))
+
+    def get_config_filename(self, scope, section):
+        """For some scope and section, get the name of the configuration file.
+        """
+        scope = self._validate_scope(scope)
+        return scope.get_section_filename(section)
+
+    def clear_caches(self):
+        """Clears the caches for configuration files,
+
+        This will cause files to be re-read upon the next request."""
+        for scope in self.scopes.values():
+            scope.clear()
+
+    def update_config(self, section, update_data, scope=None):
+        """Update the configuration file for a particular scope.
+
+        Overwrites contents of a section in a scope with update_data,
+        then writes out the config file.
+
+        update_data should have the top-level section name stripped off
+        (it will be re-added).  Data itself can be a list, dict, or any
+        other yaml-ish structure.
+        """
+        _validate_section_name(section)  # validate section name
+        scope = self._validate_scope(scope)  # get ConfigScope object
+
+        # read only the requested section's data.
+        scope.sections[section] = {section: update_data}
+        scope.write_section(section)
+
+    def get_config(self, section, scope=None):
+        """Get configuration settings for a section.
+
+        If ``scope`` is ``None`` or not provided, return the merged contents
+        of all of Spack's configuration scopes.  If ``scope`` is provided,
+        return only the confiugration as specified in that scope.
+
+        This off the top-level name from the YAML section.  That is, for a
+        YAML config file that looks like this::
+
+           config:
+             install_tree: $spack/opt/spack
+             module_roots:
+               lmod:   $spack/share/spack/lmod
+
+        ``get_config('config')`` will return::
+
+           { 'install_tree': '$spack/opt/spack',
+             'module_roots: {
+                 'lmod': '$spack/share/spack/lmod'
+             }
+           }
+
+        """
+        _validate_section_name(section)
+
+        if scope is None:
+            scopes = self.scopes.values()
+        else:
+            scopes = [self._validate_scope(scope)]
+
+        merged_section = syaml.syaml_dict()
+        for scope in scopes:
+            # read potentially cached data from the scope.
+
+            data = scope.get_section(section)
+
+            # Skip empty configs
+            if not data or not isinstance(data, dict):
+                continue
+
+            if section not in data:
+                continue
+
+            merged_section = _merge_yaml(merged_section, data)
+
+        # no config files -- empty config.
+        if section not in merged_section:
+            return {}
+
+        # take the top key off before returning.
+        return merged_section[section]
+
+    def get(self, path, default=None, scope=None):
+        """Get a config section or a single value from one.
+
+        Accepts a path syntax that allows us to grab nested config map
+        entries.  Getting the 'config' section would look like::
+
+            spack.config.get('config')
+
+        and the ``dirty`` section in the ``config`` scope would be::
+
+            spack.config.get('config:dirty')
+
+        We use ``:`` as the separator, like YAML objects.
+    """
+        # TODO: Currently only handles maps. Think about lists if neded.
+        section, _, rest = path.partition(':')
+
+        value = self.get_config(section, scope=scope)
+        if not rest:
+            return value
+
+        parts = rest.split(':')
+        while parts:
+            key = parts.pop(0)
+            value = value.get(key, default)
+
+        return value
+
+    def set(self, path, value, scope=None):
+        """Convenience function for setting single values in config files.
+
+        Accepts the path syntax described in ``get()``.
+        """
+        section, _, rest = path.partition(':')
+
+        if not rest:
+            self.update_config(section, value, scope=scope)
+        else:
+            section_data = self.get_config(section, scope=scope)
+
+            parts = rest.split(':')
+            data = section_data
+            while len(parts) > 1:
+                key = parts.pop(0)
+                data = data[key]
+            data[parts[0]] = value
+
+            self.update_config(section, section_data, scope=scope)
+
+    def __iter__(self):
+        """Iterate over scopes in this configuration."""
+        for scope in self.scopes.values():
+            yield scope
+
+    def print_section(self, section, blame=False):
+        """Print a configuration to stdout."""
+        try:
+            data = syaml.syaml_dict()
+            data[section] = self.get_config(section)
+            syaml.dump(
+                data, stream=sys.stdout, default_flow_style=False, blame=blame)
+        except (yaml.YAMLError, IOError):
+            raise ConfigError("Error reading configuration: %s" % section)
 
+
+@contextmanager
+def override(path_or_scope, value=None):
+    """Simple way to override config settings within a context.
+
+    Arguments:
+        path_or_scope (ConfigScope or str): scope or single option to override
+        value (object, optional): value for the single option
+
+    Temporarily push a scope on the current configuration, then remove it
+    after the context completes. If a single option is provided, create
+    an internal config scope for it and push/pop that scope.
+
+    """
+    if isinstance(path_or_scope, ConfigScope):
+        overrides = path_or_scope
+        config.push_scope(path_or_scope)
     else:
-        raise ValueError("Invalid config scope: '%s'.  Must be one of %s"
-                         % (scope, config_scopes.keys()))
+        overrides = InternalConfigScope('overrides')
+        config.push_scope(overrides)
+        config.set(path_or_scope, value, scope='overrides')
+
+    yield config
+
+    scope = config.remove_scope(overrides.name)
+    assert scope is overrides
+
+
+#: configuration scopes added on the command line
+#: set by ``spack.main.main()``.
+command_line_scopes = []
+
+
+def _add_platform_scope(cfg, scope_type, name, path):
+    """Add a platform-specific subdirectory for the current platform."""
+    platform = spack.architecture.platform().name
+    plat_name = '%s/%s' % (name, platform)
+    plat_path = os.path.join(path, platform)
+    cfg.push_scope(scope_type(plat_name, plat_path))
+
+
+def _add_command_line_scopes(cfg, command_line_scopes):
+    """Add additional scopes from the --config-scope argument.
+
+    Command line scopes are named after their position in the arg list.
+    """
+    for i, path in enumerate(command_line_scopes):
+        # We ensure that these scopes exist and are readable, as they are
+        # provided on the command line by the user.
+        if not os.path.isdir(path):
+            raise ConfigError("config scope is not a directory: '%s'" % path)
+        elif not os.access(path, os.R_OK):
+            raise ConfigError("config scope is not readable: '%s'" % path)
+
+        # name based on order on the command line
+        name = 'cmd_scope_%d' % i
+        cfg.push_scope(ImmutableConfigScope(name, path))
+        _add_platform_scope(cfg, ImmutableConfigScope, name, path)
+
+
+def _config():
+    """Singleton Configuration instance.
+
+    This constructs one instance associated with this module and returns
+    it. It is bundled inside a function so that configuratoin can be
+    initialized lazily.
+
+    Return:
+        (Configuration): object for accessing spack configuration
+
+    """
+    cfg = Configuration()
+
+    # first do the builtin, hardcoded defaults
+    defaults = InternalConfigScope('_builtin', config_defaults)
+    cfg.push_scope(defaults)
+
+    # add each scope and its platform-specific directory
+    for name, path in configuration_paths:
+        cfg.push_scope(ConfigScope(name, path))
+
+        # Each scope can have per-platfom overrides in subdirectories
+        _add_platform_scope(cfg, ConfigScope, name, path)
+
+    # add command-line scopes
+    _add_command_line_scopes(cfg, command_line_scopes)
+
+    # we make a special scope for spack commands so that they can
+    # override configuration options.
+    cfg.push_scope(InternalConfigScope('command_line'))
+
+    return cfg
+
+
+#: This is the singleton configuration instance for Spack.
+config = llnl.util.lang.Singleton(_config)
+
+
+def get(path, default=None, scope=None):
+    """Module-level wrapper for ``Configuration.get()``."""
+    return config.get(path, default, scope)
+
+
+def set(path, value, scope=None):
+    """Convenience function for getting single values in config files.
+
+    Accepts the path syntax described in ``get()``.
+    """
+    return config.set(path, value, scope)
+
+
+def scopes():
+    """Convenience function to get list of configuration scopes."""
+    return config.scopes
+
+
+def _validate_section_name(section):
+    """Exit if the section is not a valid section."""
+    if section not in section_schemas:
+        raise ConfigSectionError(
+            "Invalid config section: '%s'. Options are: %s"
+            % (section, " ".join(section_schemas.keys())))
+
+
+def _validate(data, schema, set_defaults=True):
+    """Validate data read in from a Spack YAML file.
+
+    Arguments:
+        data (dict or list): data read from a Spack YAML file
+        schema (dict or list): jsonschema to validate data
+        set_defaults (bool): whether to set defaults based on the schema
+
+    This leverages the line information (start_mark, end_mark) stored
+    on Spack YAML structures.
+
+    """
+    import jsonschema
+
+    if not hasattr(_validate, 'validator'):
+        default_setting_validator = _extend_with_default(
+            jsonschema.Draft4Validator)
+        _validate.validator = default_setting_validator
+
+    try:
+        _validate.validator(schema).validate(data)
+    except jsonschema.ValidationError as e:
+        raise ConfigFormatError(e, data)
 
 
 def _read_config_file(filename, schema):
@@ -279,7 +731,7 @@ def _read_config_file(filename, schema):
             data = _mark_overrides(syaml.load(f))
 
         if data:
-            validate_section(data, schema)
+            _validate(data, schema)
         return data
 
     except MarkedYAMLError as e:
@@ -291,14 +743,7 @@ def _read_config_file(filename, schema):
             "Error reading configuration file %s: %s" % (filename, str(e)))
 
 
-def clear_config_caches():
-    """Clears the caches for configuration files, which will cause them
-       to be re-read upon the next request"""
-    for scope in config_scopes.values():
-        scope.clear()
-
-
-def override(string):
+def _override(string):
     """Test if a spack YAML string is an override.
 
     See ``spack_yaml`` for details.  Keys in Spack YAML can end in `::`,
@@ -311,7 +756,7 @@ def override(string):
 
 def _mark_overrides(data):
     if isinstance(data, list):
-        return [_mark_overrides(elt) for elt in data]
+        return syaml.syaml_list(_mark_overrides(elt) for elt in data)
 
     elif isinstance(data, dict):
         marked = syaml.syaml_dict()
@@ -326,6 +771,26 @@ def _mark_overrides(data):
         return data
 
 
+def _mark_internal(data, name):
+    """Add a simple name mark to raw YAML/JSON data.
+
+    This is used by `spack config blame` to show where config lines came from.
+    """
+    if isinstance(data, dict):
+        d = syaml.syaml_dict((_mark_internal(k, name), _mark_internal(v, name))
+                             for k, v in data.items())
+    elif isinstance(data, list):
+        d = syaml.syaml_list(_mark_internal(e, name) for e in data)
+    else:
+        d = syaml.syaml_type(data)
+
+    if syaml.markable(d):
+        d._start_mark = yaml.Mark(name, None, None, None, None, None)
+        d._end_mark = yaml.Mark(name, None, None, None, None, None)
+
+    return d
+
+
 def _merge_yaml(dest, source):
     """Merges source into dest; entries in source take precedence over dest.
 
@@ -357,13 +822,28 @@ def _merge_yaml(dest, source):
 
     # Source dict is merged into dest.
     elif they_are(dict):
+        # track keys for marking
+        key_marks = {}
+
         for sk, sv in iteritems(source):
-            if override(sk) or sk not in dest:
+            if _override(sk) or sk not in dest:
                 # if sk ended with ::, or if it's new, completely override
                 dest[sk] = copy.copy(sv)
             else:
                 # otherwise, merge the YAML
                 dest[sk] = _merge_yaml(dest[sk], source[sk])
+
+            # this seems unintuitive, but see below. We need this because
+            # Python dicts do not overwrite keys on insert, and we want
+            # to copy mark information on source keys to dest.
+            key_marks[sk] = sk
+
+        # ensure that keys are marked in the destination.  the key_marks dict
+        # ensures we can get the actual source key objects from dest keys
+        for dk in dest.keys():
+            if dk in key_marks:
+                syaml.mark(dk, key_marks[dk])
+
         return dest
 
     # In any other case, overwrite with a copy of the source value.
@@ -371,154 +851,105 @@ def _merge_yaml(dest, source):
         return copy.copy(source)
 
 
-def get_config(section, scope=None):
-    """Get configuration settings for a section.
-
-    If ``scope`` is ``None`` or not provided, return the merged contents
-    of all of Spack's configuration scopes.  If ``scope`` is provided,
-    return only the confiugration as specified in that scope.
-
-    This off the top-level name from the YAML section.  That is, for a
-    YAML config file that looks like this::
-
-       config:
-         install_tree: $spack/opt/spack
-         module_roots:
-           lmod:   $spack/share/spack/lmod
-
-    ``get_config('config')`` will return::
-
-       { 'install_tree': '$spack/opt/spack',
-         'module_roots: {
-             'lmod': '$spack/share/spack/lmod'
-         }
-       }
+#
+# Settings for commands that modify configuration
+#
+def default_modify_scope():
+    """Return the config scope that commands should modify by default.
 
+    Commands that modify configuration by default modify the *highest*
+    priority scope.
     """
-    validate_section_name(section)
-    merged_section = syaml.syaml_dict()
-
-    if scope is None:
-        scopes = config_scopes.values()
-    else:
-        scopes = [validate_scope(scope)]
-
-    for scope in scopes:
-        # read potentially cached data from the scope.
-
-        data = scope.get_section(section)
-
-        # Skip empty configs
-        if not data or not isinstance(data, dict):
-            continue
-
-        if section not in data:
-            tty.warn("Skipping bad configuration file: '%s'" % scope.path)
-            continue
-
-        merged_section = _merge_yaml(merged_section, data)
+    return spack.config.config.highest_precedence_scope().name
 
-    # no config files -- empty config.
-    if section not in merged_section:
-        return {}
 
-    # take the top key off before returning.
-    return merged_section[section]
-
-
-def get_config_filename(scope, section):
-    """For some scope and section, get the name of the configuration file"""
-    scope = validate_scope(scope)
-    return scope.get_section_filename(section)
-
-
-def update_config(section, update_data, scope=None):
-    """Update the configuration file for a particular scope.
-
-       Overwrites contents of a section in a scope with update_data,
-       then writes out the config file.
-
-       update_data should have the top-level section name stripped off
-       (it will be re-added).  Data itself can be a list, dict, or any
-       other yaml-ish structure.
+def default_list_scope():
+    """Return the config scope that is listed by default.
 
+    Commands that list configuration list *all* scopes (merged) by default.
     """
-    validate_section_name(section)  # validate section name
-    scope = validate_scope(scope)  # get ConfigScope object from string.
+    return None
 
-    # read in the config to ensure we've got current data
-    configuration = get_config(section)
 
-    if isinstance(update_data, list):
-        configuration = update_data
-    else:
-        configuration.update(update_data)
+class ConfigError(SpackError):
+    """Superclass for all Spack config related errors."""
 
-    # read only the requested section's data.
-    scope.sections[section] = {section: configuration}
-    scope.write_section(section)
 
+class ConfigSectionError(ConfigError):
+    """Error for referring to a bad config section name in a configuration."""
 
-def print_section(section):
-    """Print a configuration to stdout."""
-    try:
-        data = syaml.syaml_dict()
-        data[section] = get_config(section)
-        syaml.dump(data, stream=sys.stdout, default_flow_style=False)
-    except (yaml.YAMLError, IOError):
-        raise ConfigError("Error reading configuration: %s" % section)
 
+class ConfigFileError(ConfigError):
+    """Issue reading or accessing a configuration file."""
 
-class ConfigError(SpackError):
-    pass
 
+class ConfigFormatError(ConfigError):
+    """Raised when a configuration format does not match its schema."""
 
-class ConfigFileError(ConfigError):
-    pass
+    def __init__(self, validation_error, data, filename=None, line=None):
+        self.filename = filename  # record this for ruamel.yaml
 
+        location = '<unknown file>'
 
-def get_path(path, data):
-    if path:
-        return get_path(path[1:], data[path[0]])
-    else:
-        return data
+        # spack yaml has its own file/line marks -- try to find them
+        if not filename and not line:
+            mark = self._get_mark(validation_error, data)
+            if mark:
+                filename = mark.name
+                line = mark.line + 1
 
+        if filename:
+            location = '%s' % filename
+        if line is not None:
+            location += ':%d' % line
 
-class ConfigFormatError(ConfigError):
-    """Raised when a configuration format does not match its schema."""
+        message = '%s: %s' % (location, validation_error.message)
+        super(ConfigError, self).__init__(message)
 
-    def __init__(self, validation_error, data):
-        # Try to get line number from erroneous instance and its parent
-        instance_mark = getattr(validation_error.instance, '_start_mark', None)
-        parent_mark = getattr(validation_error.parent, '_start_mark', None)
-        path = [str(s) for s in getattr(validation_error, 'path', None)]
+    def _get_mark(self, validation_error, data):
+        """Get the file/line mark fo a validation error from a Spack YAML file.
+        """
+        def _get_mark_or_first_member_mark(obj):
+            # mark of object itelf
+            mark = getattr(obj, '_start_mark', None)
+            if mark:
+                return mark
+
+            # mark of first member if it is a container
+            if isinstance(obj, (list, dict)):
+                first_member = next(iter(obj), None)
+                if first_member:
+                    mark = getattr(first_member, '_start_mark', None)
+                    if mark:
+                        return mark
+
+        # Try various places, starting with instance and parent
+        for obj in (validation_error.instance, validation_error.parent):
+            mark = _get_mark_or_first_member_mark(obj)
+            if mark:
+                return mark
+
+        def get_path(path, data):
+            if path:
+                return get_path(path[1:], data[path[0]])
+            else:
+                return data
 
         # Try really hard to get the parent (which sometimes is not
         # set) This digs it out of the validated structure if it's not
         # on the validation_error.
-        if path and not parent_mark:
-            parent_path = list(path)[:-1]
-            parent = get_path(parent_path, data)
+        path = validation_error.path
+        if path:
+            parent = get_path(list(path)[:-1], data)
             if path[-1] in parent:
                 if isinstance(parent, dict):
-                    keylist = parent.keys()
+                    keylist = list(parent.keys())
                 elif isinstance(parent, list):
                     keylist = parent
                 idx = keylist.index(path[-1])
-                parent_mark = getattr(keylist[idx], '_start_mark', None)
-
-        if instance_mark:
-            location = '%s:%d' % (instance_mark.name, instance_mark.line + 1)
-        elif parent_mark:
-            location = '%s:%d' % (parent_mark.name, parent_mark.line + 1)
-        elif path:
-            location = 'At ' + ':'.join(path)
-        else:
-            location = '<unknown line>'
-
-        message = '%s: %s' % (location, validation_error.message)
-        super(ConfigError, self).__init__(message)
-
+                mark = getattr(keylist[idx], '_start_mark', None)
+                if mark:
+                    return mark
 
-class ConfigSanityError(ConfigFormatError):
-    """Same as ConfigFormatError, raised when config is written by Spack."""
+        # give up and return None if nothing worked
+        return None
diff --git a/lib/spack/spack/database.py b/lib/spack/spack/database.py
index fd4aae00cd..33942c362f 100644
--- a/lib/spack/spack/database.py
+++ b/lib/spack/spack/database.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """Spack's installation tracking database.
 
 The database serves two purposes:
@@ -39,6 +20,8 @@ provides a cache and a sanity checking mechanism for what is in the
 filesystem.
 
 """
+import datetime
+import time
 import os
 import sys
 import socket
@@ -46,21 +29,22 @@ import contextlib
 from six import string_types
 from six import iteritems
 
-from yaml.error import MarkedYAMLError, YAMLError
+from ruamel.yaml.error import MarkedYAMLError, YAMLError
 
 import llnl.util.tty as tty
-from llnl.util.filesystem import join_path, mkdirp
-from llnl.util.lock import Lock, WriteTransaction, ReadTransaction
+from llnl.util.filesystem import mkdirp
 
 import spack.store
-import spack.repository
+import spack.repo
 import spack.spec
 import spack.util.spack_yaml as syaml
 import spack.util.spack_json as sjson
+from spack.filesystem_view import YamlFilesystemView
 from spack.util.crypto import bit_length
 from spack.directory_layout import DirectoryLayoutError
 from spack.error import SpackError
 from spack.version import Version
+from spack.util.lock import Lock, WriteTransaction, ReadTransaction, LockError
 
 
 # DB goes in this directory underneath the root
@@ -70,12 +54,17 @@ _db_dirname = '.spack-db'
 _db_version = Version('0.9.3')
 
 # Timeout for spack database locks in seconds
-_db_lock_timeout = 60
+_db_lock_timeout = 120
 
 # Types of dependencies tracked by the database
 _tracked_deps = ('link', 'run')
 
 
+def _now():
+    """Returns the time since the epoch"""
+    return time.time()
+
+
 def _autospec(function):
     """Decorator that automatically converts the argument of a single-arg
        function to a Spec."""
@@ -103,14 +92,31 @@ class InstallRecord(object):
     actually remove from the database until a spec has no installed
     dependents left.
 
+    Args:
+        spec (Spec): spec tracked by the install record
+        path (str): path where the spec has been installed
+        installed (bool): whether or not the spec is currently installed
+        ref_count (int): number of specs that depend on this one
+        explicit (bool, optional): whether or not this spec was explicitly
+            installed, or pulled-in as a dependency of something else
+        installation_time (time, optional): time of the installation
     """
 
-    def __init__(self, spec, path, installed, ref_count=0, explicit=False):
+    def __init__(
+            self,
+            spec,
+            path,
+            installed,
+            ref_count=0,
+            explicit=False,
+            installation_time=None
+    ):
         self.spec = spec
         self.path = str(path)
         self.installed = bool(installed)
         self.ref_count = ref_count
         self.explicit = explicit
+        self.installation_time = installation_time or _now()
 
     def to_dict(self):
         return {
@@ -118,14 +124,15 @@ class InstallRecord(object):
             'path': self.path,
             'installed': self.installed,
             'ref_count': self.ref_count,
-            'explicit': self.explicit
+            'explicit': self.explicit,
+            'installation_time': self.installation_time
         }
 
     @classmethod
     def from_dict(cls, spec, dictionary):
-        d = dictionary
-        return InstallRecord(spec, d['path'], d['installed'], d['ref_count'],
-                             d.get('explicit', False))
+        d = dict(dictionary.items())
+        d.pop('spec', None)
+        return InstallRecord(spec, **d)
 
 
 class Database(object):
@@ -159,37 +166,48 @@ class Database(object):
 
         if db_dir is None:
             # If the db_dir is not provided, default to within the db root.
-            self._db_dir = join_path(self.root, _db_dirname)
+            self._db_dir = os.path.join(self.root, _db_dirname)
         else:
             # Allow customizing the database directory location for testing.
             self._db_dir = db_dir
 
         # Set up layout of database files within the db dir
-        self._old_yaml_index_path = join_path(self._db_dir, 'index.yaml')
-        self._index_path = join_path(self._db_dir, 'index.json')
-        self._lock_path = join_path(self._db_dir, 'lock')
+        self._old_yaml_index_path = os.path.join(self._db_dir, 'index.yaml')
+        self._index_path = os.path.join(self._db_dir, 'index.json')
+        self._lock_path = os.path.join(self._db_dir, 'lock')
 
         # This is for other classes to use to lock prefix directories.
-        self.prefix_lock_path = join_path(self._db_dir, 'prefix_lock')
+        self.prefix_lock_path = os.path.join(self._db_dir, 'prefix_lock')
 
         # Create needed directories and files
         if not os.path.exists(self._db_dir):
             mkdirp(self._db_dir)
 
         # initialize rest of state.
-        self.lock = Lock(self._lock_path)
+        self.db_lock_timeout = (
+            spack.config.get('config:db_lock_timeout') or _db_lock_timeout)
+        self.package_lock_timeout = (
+            spack.config.get('config:package_lock_timeout') or None)
+        tty.debug('DATABASE LOCK TIMEOUT: {0}s'.format(
+                  str(self.db_lock_timeout)))
+        timeout_format_str = ('{0}s'.format(str(self.package_lock_timeout))
+                              if self.package_lock_timeout else 'No timeout')
+        tty.debug('PACKAGE LOCK TIMEOUT: {0}'.format(
+                  str(timeout_format_str)))
+        self.lock = Lock(self._lock_path,
+                         default_timeout=self.db_lock_timeout)
         self._data = {}
 
         # whether there was an error at the start of a read transaction
         self._error = None
 
-    def write_transaction(self, timeout=_db_lock_timeout):
+    def write_transaction(self):
         """Get a write lock context manager for use in a `with` block."""
-        return WriteTransaction(self.lock, self._read, self._write, timeout)
+        return WriteTransaction(self.lock, self._read, self._write)
 
-    def read_transaction(self, timeout=_db_lock_timeout):
+    def read_transaction(self):
         """Get a read lock context manager for use in a `with` block."""
-        return ReadTransaction(self.lock, self._read, timeout=timeout)
+        return ReadTransaction(self.lock, self._read)
 
     def prefix_lock(self, spec):
         """Get a lock on a particular spec's installation directory.
@@ -210,26 +228,44 @@ class Database(object):
         if prefix not in self._prefix_locks:
             self._prefix_locks[prefix] = Lock(
                 self.prefix_lock_path,
-                spec.dag_hash_bit_prefix(bit_length(sys.maxsize)), 1)
+                start=spec.dag_hash_bit_prefix(bit_length(sys.maxsize)),
+                length=1,
+                default_timeout=self.package_lock_timeout)
 
         return self._prefix_locks[prefix]
 
     @contextlib.contextmanager
     def prefix_read_lock(self, spec):
         prefix_lock = self.prefix_lock(spec)
+        prefix_lock.acquire_read()
+
         try:
-            prefix_lock.acquire_read(60)
             yield self
-        finally:
+        except LockError:
+            # This addresses the case where a nested lock attempt fails inside
+            # of this context manager
+            raise
+        except (Exception, KeyboardInterrupt):
+            prefix_lock.release_read()
+            raise
+        else:
             prefix_lock.release_read()
 
     @contextlib.contextmanager
     def prefix_write_lock(self, spec):
         prefix_lock = self.prefix_lock(spec)
+        prefix_lock.acquire_write()
+
         try:
-            prefix_lock.acquire_write(60)
             yield self
-        finally:
+        except LockError:
+            # This addresses the case where a nested lock attempt fails inside
+            # of this context manager
+            raise
+        except (Exception, KeyboardInterrupt):
+            prefix_lock.release_write()
+            raise
+        else:
             prefix_lock.release_write()
 
     def _write_to_file(self, stream):
@@ -347,7 +383,7 @@ class Database(object):
         def invalid_record(hash_key, error):
             msg = ("Invalid record in Spack database: "
                    "hash: %s, cause: %s: %s")
-            msg %= (hash_key, type(e).__name__, str(e))
+            msg %= (hash_key, type(error).__name__, str(error))
             raise CorruptDatabaseError(msg, self._index_path)
 
         # Build up the database in three passes:
@@ -409,7 +445,7 @@ class Database(object):
                 self._data = {}
 
         transaction = WriteTransaction(
-            self.lock, _read_suppress_error, self._write, _db_lock_timeout
+            self.lock, _read_suppress_error, self._write
         )
 
         with transaction:
@@ -442,12 +478,18 @@ class Database(object):
                     tty.debug(
                         'RECONSTRUCTING FROM SPEC.YAML: {0}'.format(spec))
                     explicit = True
+                    inst_time = os.stat(spec.prefix).st_ctime
                     if old_data is not None:
                         old_info = old_data.get(spec.dag_hash())
                         if old_info is not None:
                             explicit = old_info.explicit
+                            inst_time = old_info.installation_time
 
-                    self._add(spec, directory_layout, explicit=explicit)
+                    extra_args = {
+                        'explicit': explicit,
+                        'installation_time': inst_time
+                    }
+                    self._add(spec, directory_layout, **extra_args)
 
                     processed_specs.add(spec)
 
@@ -479,7 +521,8 @@ class Database(object):
                             kwargs = {
                                 'spec': entry.spec,
                                 'directory_layout': layout,
-                                'explicit': entry.explicit
+                                'explicit': entry.explicit,
+                                'installation_time': entry.installation_time  # noqa: E501
                             }
                             self._add(**kwargs)
                             processed_specs.add(entry.spec)
@@ -566,7 +609,7 @@ class Database(object):
             if os.access(self._db_dir, os.R_OK | os.W_OK):
                 # if we can write, then read AND write a JSON file.
                 self._read_from_file(self._old_yaml_index_path, format='yaml')
-                with WriteTransaction(self.lock, timeout=_db_lock_timeout):
+                with WriteTransaction(self.lock):
                     self._write(None, None, None)
             else:
                 # Read chck for a YAML file if we can't find JSON.
@@ -575,27 +618,56 @@ class Database(object):
         else:
             # The file doesn't exist, try to traverse the directory.
             # reindex() takes its own write lock, so no lock here.
-            with WriteTransaction(self.lock, timeout=_db_lock_timeout):
+            with WriteTransaction(self.lock):
                 self._write(None, None, None)
             self.reindex(spack.store.layout)
 
-    def _add(self, spec, directory_layout=None, explicit=False):
+    def _add(
+            self,
+            spec,
+            directory_layout=None,
+            explicit=False,
+            installation_time=None
+    ):
         """Add an install record for this spec to the database.
 
         Assumes spec is installed in ``layout.path_for_spec(spec)``.
 
         Also ensures dependencies are present and updated in the DB as
-        either intsalled or missing.
+        either installed or missing.
+
+        Args:
+            spec: spec to be added
+            directory_layout: layout of the spec installation
+            **kwargs:
+
+                explicit
+                    Possible values: True, False, any
+
+                    A spec that was installed following a specific user
+                    request is marked as explicit. If instead it was
+                    pulled-in as a dependency of a user requested spec
+                    it's considered implicit.
+
+                installation_time
+                    Date and time of installation
 
         """
         if not spec.concrete:
             raise NonConcreteSpecAddError(
                 "Specs added to DB must be concrete.")
 
+        # Retrieve optional arguments
+        installation_time = installation_time or _now()
+
         for dep in spec.dependencies(_tracked_deps):
             dkey = dep.dag_hash()
             if dkey not in self._data:
-                self._add(dep, directory_layout, explicit=False)
+                extra_args = {
+                    'explicit': False,
+                    'installation_time': installation_time
+                }
+                self._add(dep, directory_layout, **extra_args)
 
         key = spec.dag_hash()
         if key not in self._data:
@@ -613,8 +685,13 @@ class Database(object):
 
             # Create a new install record with no deps initially.
             new_spec = spec.copy(deps=False)
+            extra_args = {
+                'explicit': explicit,
+                'installation_time': installation_time
+            }
             self._data[key] = InstallRecord(
-                new_spec, path, installed, ref_count=0, explicit=explicit)
+                new_spec, path, installed, ref_count=0, **extra_args
+            )
 
             # Connect dependencies from the DB to the new copy.
             for name, dep in iteritems(spec.dependencies_dict(_tracked_deps)):
@@ -757,7 +834,8 @@ class Database(object):
         the given spec
         """
         if extensions_layout is None:
-            extensions_layout = spack.store.extensions
+            view = YamlFilesystemView(extendee_spec.prefix, spack.store.layout)
+            extensions_layout = view.extensions_layout
         for spec in self.query():
             try:
                 extensions_layout.check_activated(extendee_spec, spec)
@@ -766,48 +844,68 @@ class Database(object):
                 continue
             # TODO: conditional way to do this instead of catching exceptions
 
-    def query(self, query_spec=any, known=any, installed=True, explicit=any):
-        """Run a query on the database.
-
-        ``query_spec``
-            Queries iterate through specs in the database and return
-            those that satisfy the supplied ``query_spec``.  If
-            query_spec is `any`, This will match all specs in the
-            database.  If it is a spec, we'll evaluate
-            ``spec.satisfies(query_spec)``.
-
-        The query can be constrained by two additional attributes:
-
-        ``known``
-            Possible values: True, False, any
-
-            Specs that are "known" are those for which Spack can
-            locate a ``package.py`` file -- i.e., Spack "knows" how to
-            install them.  Specs that are unknown may represent
-            packages that existed in a previous version of Spack, but
-            have since either changed their name or been removed.
-
-        ``installed``
-            Possible values: True, False, any
-
-            Specs for which a prefix exists are "installed". A spec
-            that is NOT installed will be in the database if some
-            other spec depends on it but its installation has gone
-            away since Spack installed it.
-
-        TODO: Specs are a lot like queries.  Should there be a
-              wildcard spec object, and should specs have attributes
-              like installed and known that can be queried?  Or are
-              these really special cases that only belong here?
+    def query(
+            self,
+            query_spec=any,
+            known=any,
+            installed=True,
+            explicit=any,
+            start_date=None,
+            end_date=None,
+            hashes=None
+    ):
+        """Run a query on the database
+
+        Args:
+            query_spec: queries iterate through specs in the database and
+                return those that satisfy the supplied ``query_spec``. If
+                query_spec is `any`, This will match all specs in the
+                database.  If it is a spec, we'll evaluate
+                ``spec.satisfies(query_spec)``
+
+            known (bool or any, optional): Specs that are "known" are those
+                for which Spack can locate a ``package.py`` file -- i.e.,
+                Spack "knows" how to install them.  Specs that are unknown may
+                represent packages that existed in a previous version of
+                Spack, but have since either changed their name or
+                been removed
+
+            installed (bool or any, optional): Specs for which a prefix exists
+                are "installed". A spec that is NOT installed will be in the
+                database if some other spec depends on it but its installation
+                has gone away since Spack installed it.
+
+            explicit (bool or any, optional): A spec that was installed
+                following a specific user request is marked as explicit. If
+                instead it was pulled-in as a dependency of a user requested
+                spec it's considered implicit.
+
+            start_date (datetime, optional): filters the query discarding
+                specs that have been installed before ``start_date``.
+
+            end_date (datetime, optional): filters the query discarding
+                specs that have been installed after ``end_date``.
+
+            hashes (container): list or set of hashes that we can use to
+                restrict the search
+
+        Returns:
+            list of specs that match the query
 
         """
+        # TODO: Specs are a lot like queries.  Should there be a
+        # TODO: wildcard spec object, and should specs have attributes
+        # TODO: like installed and known that can be queried?  Or are
+        # TODO: these really special cases that only belong here?
+
+        # TODO: handling of hashes restriction is not particularly elegant.
         with self.read_transaction():
             # Just look up concrete specs with hashes; no fancy search.
-            if (isinstance(query_spec, spack.spec.Spec) and
-                query_spec._concrete):
+            if isinstance(query_spec, spack.spec.Spec) and query_spec.concrete:
 
                 hash_key = query_spec.dag_hash()
-                if hash_key in self._data:
+                if (hash_key in self._data and
+                    (not hashes or hash_key in hashes)):
                     return [self._data[hash_key].spec]
                 else:
                     return []
@@ -815,14 +913,29 @@ class Database(object):
             # Abstract specs require more work -- currently we test
             # against everything.
             results = []
+            start_date = start_date or datetime.datetime.min
+            end_date = end_date or datetime.datetime.max
+
             for key, rec in self._data.items():
+                if hashes is not None and rec.spec.dag_hash() not in hashes:
+                    continue
+
                 if installed is not any and rec.installed != installed:
                     continue
+
                 if explicit is not any and rec.explicit != explicit:
                     continue
-                if known is not any and spack.repo.exists(
+
+                if known is not any and spack.repo.path.exists(
                         rec.spec.name) != known:
                     continue
+
+                inst_date = datetime.datetime.fromtimestamp(
+                    rec.installation_time
+                )
+                if not (start_date < inst_date < end_date):
+                    continue
+
                 if query_spec is any or rec.spec.satisfies(query_spec):
                     results.append(rec.spec)
 
@@ -835,7 +948,8 @@ class Database(object):
         query. Returns None if no installed package matches.
 
         """
-        concrete_specs = self.query(query_spec, known, installed)
+        concrete_specs = self.query(
+            query_spec, known=known, installed=installed)
         assert len(concrete_specs) <= 1
         return concrete_specs[0] if concrete_specs else None
 
diff --git a/lib/spack/spack/dependency.py b/lib/spack/spack/dependency.py
index 99a16c9d45..34b9a85537 100644
--- a/lib/spack/spack/dependency.py
+++ b/lib/spack/spack/dependency.py
@@ -1,32 +1,13 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """Data structures that represent Spack's dependency relationships.
 """
 from six import string_types
 
-import spack
+import spack.spec
 
 
 #: The types of dependency relationships that Spack understands.
@@ -72,7 +53,7 @@ class Dependency(object):
     This class differs from ``spack.spec.DependencySpec`` because it
     represents metadata at the ``Package`` level.
     ``spack.spec.DependencySpec`` is a descriptor for an actual package
-    confiuguration, while ``Dependency`` is a descriptor for a package's
+    configuration, while ``Dependency`` is a descriptor for a package's
     dependency *requirements*.
 
     A dependency is a requirement for a configuration of another package
diff --git a/lib/spack/spack/directives.py b/lib/spack/spack/directives.py
index 7255875541..9125d55e9a 100644
--- a/lib/spack/spack/directives.py
+++ b/lib/spack/spack/directives.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """This package contains directives that can be used within a package.
 
 Directives are functions that can be called inside a package
@@ -48,24 +29,20 @@ The available directives are:
 
 import collections
 import functools
-import inspect
 import os.path
 import re
 from six import string_types
 
 import llnl.util.lang
-from llnl.util.filesystem import join_path
 
-import spack
 import spack.error
 import spack.spec
 import spack.url
+import spack.variant
 from spack.dependency import Dependency, default_deptype, canonical_deptype
 from spack.fetch_strategy import from_kwargs
 from spack.patch import Patch
 from spack.resource import Resource
-from spack.spec import Spec, parse_anonymous_spec
-from spack.variant import Variant
 from spack.version import Version
 
 __all__ = []
@@ -74,7 +51,7 @@ __all__ = []
 reserved_names = ['patches']
 
 
-class DirectiveMetaMixin(type):
+class DirectiveMeta(type):
     """Flushes the directives that were temporarily stored in the staging
     area into the package.
     """
@@ -83,7 +60,7 @@ class DirectiveMetaMixin(type):
     _directive_names = set()
     _directives_to_be_executed = []
 
-    def __new__(mcs, name, bases, attr_dict):
+    def __new__(cls, name, bases, attr_dict):
         # Initialize the attribute containing the list of directives
         # to be executed. Here we go reversed because we want to execute
         # commands:
@@ -107,27 +84,27 @@ class DirectiveMetaMixin(type):
 
         # Move things to be executed from module scope (where they
         # are collected first) to class scope
-        if DirectiveMetaMixin._directives_to_be_executed:
+        if DirectiveMeta._directives_to_be_executed:
             attr_dict['_directives_to_be_executed'].extend(
-                DirectiveMetaMixin._directives_to_be_executed)
-            DirectiveMetaMixin._directives_to_be_executed = []
+                DirectiveMeta._directives_to_be_executed)
+            DirectiveMeta._directives_to_be_executed = []
 
-        return super(DirectiveMetaMixin, mcs).__new__(
-            mcs, name, bases, attr_dict)
+        return super(DirectiveMeta, cls).__new__(
+            cls, name, bases, attr_dict)
 
     def __init__(cls, name, bases, attr_dict):
         # The class is being created: if it is a package we must ensure
         # that the directives are called on the class to set it up
-        module = inspect.getmodule(cls)
-        if 'spack.pkg' in module.__name__:
+
+        if 'spack.pkg' in cls.__module__:
             # Package name as taken
             # from llnl.util.lang.get_calling_module_name
-            pkg_name = module.__name__.split('.')[-1]
+            pkg_name = cls.__module__.split('.')[-1]
             setattr(cls, 'name', pkg_name)
 
             # Ensure the presence of the dictionaries associated
             # with the directives
-            for d in DirectiveMetaMixin._directive_names:
+            for d in DirectiveMeta._directive_names:
                 setattr(cls, d, {})
 
             # Lazily execute directives
@@ -136,9 +113,9 @@ class DirectiveMetaMixin(type):
 
             # Ignore any directives executed *within* top-level
             # directives by clearing out the queue they're appended to
-            DirectiveMetaMixin._directives_to_be_executed = []
+            DirectiveMeta._directives_to_be_executed = []
 
-        super(DirectiveMetaMixin, cls).__init__(name, bases, attr_dict)
+        super(DirectiveMeta, cls).__init__(name, bases, attr_dict)
 
     @staticmethod
     def directive(dicts=None):
@@ -188,7 +165,7 @@ class DirectiveMetaMixin(type):
             message = "dicts arg must be list, tuple, or string. Found {0}"
             raise TypeError(message.format(type(dicts)))
         # Add the dictionary names if not already there
-        DirectiveMetaMixin._directive_names |= set(dicts)
+        DirectiveMeta._directive_names |= set(dicts)
 
         # This decorator just returns the directive functions
         def _decorator(decorated_function):
@@ -202,7 +179,7 @@ class DirectiveMetaMixin(type):
                 # This allows nested directive calls in packages.  The
                 # caller can return the directive if it should be queued.
                 def remove_directives(arg):
-                    directives = DirectiveMetaMixin._directives_to_be_executed
+                    directives = DirectiveMeta._directives_to_be_executed
                     if isinstance(arg, (list, tuple)):
                         # Descend into args that are lists or tuples
                         for a in arg:
@@ -228,32 +205,32 @@ class DirectiveMetaMixin(type):
                 if not isinstance(values, collections.Sequence):
                     values = (values, )
 
-                DirectiveMetaMixin._directives_to_be_executed.extend(values)
+                DirectiveMeta._directives_to_be_executed.extend(values)
 
                 # wrapped function returns same result as original so
                 # that we can nest directives
                 return result
-
             return _wrapper
 
         return _decorator
 
 
-directive = DirectiveMetaMixin.directive
+directive = DirectiveMeta.directive
 
 
 @directive('versions')
 def version(ver, checksum=None, **kwargs):
-    """Adds a version and metadata describing how to fetch it.
-    Metadata is just stored as a dict in the package's versions
-    dictionary.  Package must turn it into a valid fetch strategy
-    later.
+    """Adds a version and metadata describing how to fetch its source code.
+
+    Metadata is stored as a dict of ``kwargs`` in the package class's
+    ``versions`` dictionary.
+
+    The ``dict`` of arguments is turned into a valid fetch strategy
+    later. See ``spack.fetch_strategy.for_package_version()``.
     """
     def _execute_version(pkg):
-        # TODO: checksum vs md5 distinction is confusing -- fix this.
-        # special case checksum for backward compatibility
         if checksum:
-            kwargs['md5'] = checksum
+            kwargs['checksum'] = checksum
 
         # Store kwargs for the package to later with a fetch_strategy.
         pkg.versions[Version(ver)] = kwargs
@@ -267,9 +244,9 @@ def _depends_on(pkg, spec, when=None, type=default_deptype, patches=None):
     # If when is None or True make sure the condition is always satisfied
     if when is None or when is True:
         when = pkg.name
-    when_spec = parse_anonymous_spec(when, pkg.name)
+    when_spec = spack.spec.parse_anonymous_spec(when, pkg.name)
 
-    dep_spec = Spec(spec)
+    dep_spec = spack.spec.Spec(spec)
     if pkg.name == dep_spec.name:
         raise CircularReferenceError(
             "Package '%s' cannot depend on itself." % pkg.name)
@@ -330,7 +307,7 @@ def conflicts(conflict_spec, when=None, msg=None):
     def _execute_conflicts(pkg):
         # If when is not specified the conflict always holds
         condition = pkg.name if when is None else when
-        when_spec = parse_anonymous_spec(condition, pkg.name)
+        when_spec = spack.spec.parse_anonymous_spec(condition, pkg.name)
 
         # Save in a list the conflicts and the associated custom messages
         when_spec_list = pkg.conflicts.setdefault(conflict_spec, [])
@@ -362,13 +339,14 @@ def depends_on(spec, when=None, type=default_deptype, patches=None):
 
 @directive(('extendees', 'dependencies'))
 def extends(spec, **kwargs):
-    """Same as depends_on, but dependency is symlinked into parent prefix.
+    """Same as depends_on, but allows symlinking into dependency's
+    prefix tree.
 
     This is for Python and other language modules where the module
     needs to be installed into the prefix of the Python installation.
     Spack handles this by installing modules into their own prefix,
     but allowing ONE module version to be symlinked into a parent
-    Python install at a time.
+    Python install at a time, using ``spack activate``.
 
     keyword arguments can be passed to extends() so that extension
     packages can pass parameters to the extendee's extension
@@ -381,9 +359,9 @@ def extends(spec, **kwargs):
         #     msg = 'Packages can extend at most one other package.'
         #     raise DirectiveError(directive, msg)
 
-        when = kwargs.pop('when', pkg.name)
+        when = kwargs.get('when', pkg.name)
         _depends_on(pkg, spec, when=when)
-        pkg.extendees[spec] = (Spec(spec), kwargs)
+        pkg.extendees[spec] = (spack.spec.Spec(spec), kwargs)
     return _execute_extends
 
 
@@ -395,7 +373,7 @@ def provides(*specs, **kwargs):
     """
     def _execute_provides(pkg):
         spec_string = kwargs.get('when', pkg.name)
-        provider_spec = parse_anonymous_spec(spec_string, pkg.name)
+        provider_spec = spack.spec.parse_anonymous_spec(spec_string, pkg.name)
 
         for string in specs:
             for provided_spec in spack.spec.parse(string):
@@ -432,7 +410,8 @@ def patch(url_or_filename, level=1, when=None, working_dir=".", **kwargs):
     """
     def _execute_patch(pkg_or_dep):
         constraint = pkg_or_dep.name if when is None else when
-        when_spec = parse_anonymous_spec(constraint, pkg_or_dep.name)
+        when_spec = spack.spec.parse_anonymous_spec(
+            constraint, pkg_or_dep.name)
 
         # if this spec is identical to some other, then append this
         # patch to the existing list.
@@ -492,7 +471,7 @@ def variant(
             msg = "Invalid variant name in {0}: '{1}'"
             raise DirectiveError(directive, msg.format(pkg.name, name))
 
-        pkg.variants[name] = Variant(
+        pkg.variants[name] = spack.variant.Variant(
             name, default, description, values, multi, validator
         )
     return _execute_variant
@@ -522,24 +501,24 @@ def resource(**kwargs):
 
         # Check if the path is relative
         if os.path.isabs(destination):
-            message = 'The destination keyword of a resource directive '
-            'can\'t be an absolute path.\n'
+            message = ('The destination keyword of a resource directive '
+                       'can\'t be an absolute path.\n')
             message += "\tdestination : '{dest}\n'".format(dest=destination)
             raise RuntimeError(message)
 
         # Check if the path falls within the main package stage area
         test_path = 'stage_folder_root'
         normalized_destination = os.path.normpath(
-            join_path(test_path, destination)
+            os.path.join(test_path, destination)
         )  # Normalized absolute path
 
         if test_path not in normalized_destination:
-            message = "The destination folder of a resource must fall "
-            "within the main package stage directory.\n"
+            message = ("The destination folder of a resource must fall "
+                       "within the main package stage directory.\n")
             message += "\tdestination : '{dest}'\n".format(dest=destination)
             raise RuntimeError(message)
 
-        when_spec = parse_anonymous_spec(when, pkg.name)
+        when_spec = spack.spec.parse_anonymous_spec(when, pkg.name)
         resources = pkg.resources.setdefault(when_spec, [])
         name = kwargs.get('name')
         fetcher = from_kwargs(**kwargs)
diff --git a/lib/spack/spack/directory_layout.py b/lib/spack/spack/directory_layout.py
index e07db0ede4..9fc0c08d22 100644
--- a/lib/spack/spack/directory_layout.py
+++ b/lib/spack/spack/directory_layout.py
@@ -1,37 +1,19 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 import shutil
 import glob
 import tempfile
-import yaml
 import re
 
-from llnl.util.filesystem import join_path, mkdirp
+import ruamel.yaml as yaml
 
-import spack
+from llnl.util.filesystem import mkdirp, chgrp
+
+import spack.config
 import spack.spec
 from spack.error import SpackError
 
@@ -128,7 +110,6 @@ class ExtensionsLayout(object):
     """
     def __init__(self, root, **kwargs):
         self.root = root
-        self.link = kwargs.get("link", os.symlink)
 
     def add_extension(self, spec, ext_spec):
         """Add to the list of currently installed extensions."""
@@ -227,7 +208,7 @@ class YamlDirectoryLayout(DirectoryLayout):
             with open(path) as f:
                 spec = spack.spec.Spec.from_yaml(f)
         except Exception as e:
-            if spack.debug:
+            if spack.config.get('config:debug'):
                 raise
             raise SpecReadError(
                 'Unable to read file: %s' % path, 'Cause: ' + str(e))
@@ -239,22 +220,22 @@ class YamlDirectoryLayout(DirectoryLayout):
     def spec_file_path(self, spec):
         """Gets full path to spec file"""
         _check_concrete(spec)
-        return join_path(self.metadata_path(spec), self.spec_file_name)
+        return os.path.join(self.metadata_path(spec), self.spec_file_name)
 
     def metadata_path(self, spec):
-        return join_path(self.path_for_spec(spec), self.metadata_dir)
+        return os.path.join(self.path_for_spec(spec), self.metadata_dir)
 
     def build_log_path(self, spec):
-        return join_path(self.path_for_spec(spec), self.metadata_dir,
-                         self.build_log_name)
+        return os.path.join(self.path_for_spec(spec), self.metadata_dir,
+                            self.build_log_name)
 
     def build_env_path(self, spec):
-        return join_path(self.path_for_spec(spec), self.metadata_dir,
-                         self.build_env_name)
+        return os.path.join(self.path_for_spec(spec), self.metadata_dir,
+                            self.build_env_name)
 
     def build_packages_path(self, spec):
-        return join_path(self.path_for_spec(spec), self.metadata_dir,
-                         self.packages_dir)
+        return os.path.join(self.path_for_spec(spec), self.metadata_dir,
+                            self.packages_dir)
 
     def create_install_directory(self, spec):
         _check_concrete(spec)
@@ -263,7 +244,19 @@ class YamlDirectoryLayout(DirectoryLayout):
         if prefix:
             raise InstallDirectoryAlreadyExistsError(prefix)
 
-        mkdirp(self.metadata_path(spec))
+        # Create install directory with properly configured permissions
+        # Cannot import at top of file
+        from spack.package_prefs import get_package_dir_permissions
+        from spack.package_prefs import get_package_group
+        group = get_package_group(spec)
+        perms = get_package_dir_permissions(spec)
+        mkdirp(spec.prefix, mode=perms)
+        if group:
+            chgrp(spec.prefix, group)
+            # Need to reset the sticky group bit after chgrp
+            os.chmod(spec.prefix, perms)
+
+        mkdirp(self.metadata_path(spec), mode=perms)
         self.write_spec(spec, self.spec_file_path(spec))
 
     def check_installed(self, spec):
@@ -302,7 +295,7 @@ class YamlDirectoryLayout(DirectoryLayout):
 
         path_elems = ["*"] * len(self.path_scheme.split(os.sep))
         path_elems += [self.metadata_dir, self.spec_file_name]
-        pattern = join_path(self.root, *path_elems)
+        pattern = os.path.join(self.root, *path_elems)
         spec_files = glob.glob(pattern)
         return [self.read_spec(s) for s in spec_files]
 
@@ -313,14 +306,14 @@ class YamlDirectoryLayout(DirectoryLayout):
         return by_hash
 
 
-class YamlExtensionsLayout(ExtensionsLayout):
-    """Implements globally activated extensions within a YamlDirectoryLayout.
+class YamlViewExtensionsLayout(ExtensionsLayout):
+    """Maintain extensions within a view.
     """
     def __init__(self, root, layout):
         """layout is the corresponding YamlDirectoryLayout object for which
            we implement extensions.
         """
-        super(YamlExtensionsLayout, self).__init__(root)
+        super(YamlViewExtensionsLayout, self).__init__(root)
         self.layout = layout
         self.extension_file_name = 'extensions.yaml'
 
@@ -354,19 +347,29 @@ class YamlExtensionsLayout(ExtensionsLayout):
             raise NoSuchExtensionError(spec, ext_spec)
 
     def extension_file_path(self, spec):
-        """Gets full path to an installed package's extension file"""
+        """Gets full path to an installed package's extension file, which
+           keeps track of all the extensions for that package which have been
+           added to this view.
+        """
         _check_concrete(spec)
-        return join_path(self.layout.metadata_path(spec),
-                         self.extension_file_name)
+        normalize_path = lambda p: (
+            os.path.abspath(p).rstrip(os.path.sep))
+        if normalize_path(spec.prefix) == normalize_path(self.root):
+            # For backwards compatibility, when the root is the extended
+            # package's installation directory, do not include the spec name
+            # as a subdirectory.
+            components = [self.root, self.layout.metadata_dir,
+                          self.extension_file_name]
+        else:
+            components = [self.root, self.layout.metadata_dir, spec.name,
+                          self.extension_file_name]
+        return os.path.join(*components)
 
     def extension_map(self, spec):
         """Defensive copying version of _extension_map() for external API."""
         _check_concrete(spec)
         return self._extension_map(spec).copy()
 
-    def extendee_target_directory(self, extendee):
-        return extendee.prefix
-
     def remove_extension(self, spec, ext_spec):
         _check_concrete(spec)
         _check_concrete(ext_spec)
@@ -419,6 +422,8 @@ class YamlExtensionsLayout(ExtensionsLayout):
 
         # Create a temp file in the same directory as the actual file.
         dirname, basename = os.path.split(path)
+        mkdirp(dirname)
+
         tmp = tempfile.NamedTemporaryFile(
             prefix=basename, dir=dirname, delete=False)
 
@@ -436,23 +441,6 @@ class YamlExtensionsLayout(ExtensionsLayout):
         os.rename(tmp.name, path)
 
 
-class YamlViewExtensionsLayout(YamlExtensionsLayout):
-    """Governs the directory layout present when creating filesystem views in a
-    certain root folder.
-
-    Meant to replace YamlDirectoryLayout when working with filesystem views.
-    """
-
-    def extension_file_path(self, spec):
-        """Gets the full path to an installed package's extension file."""
-        _check_concrete(spec)
-        return join_path(self.root, self.layout.metadata_dir, spec.name,
-                         self.extension_file_name)
-
-    def extendee_target_directory(self, extendee):
-        return self.root
-
-
 class DirectoryLayoutError(SpackError):
     """Superclass for directory layout errors."""
 
@@ -492,7 +480,7 @@ class InstallDirectoryAlreadyExistsError(DirectoryLayoutError):
 
     def __init__(self, path):
         super(InstallDirectoryAlreadyExistsError, self).__init__(
-            "Install path %s already exists!")
+            "Install path %s already exists!" % path)
 
 
 class SpecReadError(DirectoryLayoutError):
diff --git a/lib/spack/spack/environment.py b/lib/spack/spack/environment.py
index d85c67d7fc..40d63eaa0e 100644
--- a/lib/spack/spack/environment.py
+++ b/lib/spack/spack/environment.py
@@ -1,559 +1,906 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-import collections
-import inspect
-import json
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
+import re
 import sys
-import os.path
-import subprocess
+import shutil
 
+import jsonschema
+import ruamel.yaml
 
-class NameModifier(object):
+import llnl.util.filesystem as fs
+import llnl.util.tty as tty
 
-    def __init__(self, name, **kwargs):
-        self.name = name
-        self.args = {'name': name}
-        self.args.update(kwargs)
+import spack.error
+import spack.repo
+import spack.schema.env
+import spack.spec
+import spack.util.spack_json as sjson
+import spack.config
+from spack.spec import Spec
 
-    def update_args(self, **kwargs):
-        self.__dict__.update(kwargs)
-        self.args.update(kwargs)
 
+#: environment variable used to indicate the active environment
+spack_env_var = 'SPACK_ENV'
 
-class NameValueModifier(object):
 
-    def __init__(self, name, value, **kwargs):
-        self.name = name
-        self.value = value
-        self.separator = kwargs.get('separator', ':')
-        self.args = {'name': name, 'value': value, 'separator': self.separator}
-        self.args.update(kwargs)
+#: currently activated environment
+_active_environment = None
 
-    def update_args(self, **kwargs):
-        self.__dict__.update(kwargs)
-        self.args.update(kwargs)
 
+#: path where environments are stored in the spack tree
+env_path = os.path.join(spack.paths.var_path, 'environments')
 
-class SetEnv(NameValueModifier):
 
-    def execute(self):
-        os.environ[self.name] = str(self.value)
+#: Name of the input yaml file for an environment
+manifest_name = 'spack.yaml'
 
 
-class AppendFlagsEnv(NameValueModifier):
+#: Name of the input yaml file for an environment
+lockfile_name = 'spack.lock'
 
-    def execute(self):
-        if self.name in os.environ and os.environ[self.name]:
-            os.environ[self.name] += self.separator + str(self.value)
-        else:
-            os.environ[self.name] = str(self.value)
 
+#: Name of the directory where environments store repos, logs, views
+env_subdir_name = '.spack-env'
 
-class UnsetEnv(NameModifier):
 
-    def execute(self):
-        # Avoid throwing if the variable was not set
-        os.environ.pop(self.name, None)
+#: default spack.yaml file to put in new environments
+default_manifest_yaml = """\
+# This is a Spack Environment file.
+#
+# It describes a set of packages to be installed, along with
+# configuration settings.
+spack:
+  # add package specs to the `specs` list
+  specs:
+  -
+"""
+#: regex for validating enviroment names
+valid_environment_name_re = r'^\w[\w-]*$'
 
+#: version of the lockfile format. Must increase monotonically.
+lockfile_format_version = 1
 
-class SetPath(NameValueModifier):
+#: legal first keys in the spack.yaml manifest file
+env_schema_keys = ('spack', 'env')
 
-    def execute(self):
-        string_path = concatenate_paths(self.value, separator=self.separator)
-        os.environ[self.name] = string_path
+#: jsonschema validator for environments
+_validator = None
 
 
-class AppendPath(NameValueModifier):
+def valid_env_name(name):
+    return re.match(valid_environment_name_re, name)
 
-    def execute(self):
-        environment_value = os.environ.get(self.name, '')
-        directories = environment_value.split(
-            self.separator) if environment_value else []
-        directories.append(os.path.normpath(self.value))
-        os.environ[self.name] = self.separator.join(directories)
 
+def validate_env_name(name):
+    if not valid_env_name(name):
+        raise ValueError((
+            "'%s': names must start with a letter, and only contain "
+            "letters, numbers, _, and -.") % name)
+    return name
 
-class PrependPath(NameValueModifier):
 
-    def execute(self):
-        environment_value = os.environ.get(self.name, '')
-        directories = environment_value.split(
-            self.separator) if environment_value else []
-        directories = [os.path.normpath(self.value)] + directories
-        os.environ[self.name] = self.separator.join(directories)
+def activate(env, use_env_repo=False):
+    """Activate an environment.
 
+    To activate an environment, we add its configuration scope to the
+    existing Spack configuration, and we set active to the current
+    environment.
 
-class RemovePath(NameValueModifier):
+    Arguments:
+        env (Environment): the environment to activate
+        use_env_repo (bool): use the packages exactly as they appear in the
+            environment's repository
 
-    def execute(self):
-        environment_value = os.environ.get(self.name, '')
-        directories = environment_value.split(
-            self.separator) if environment_value else []
-        directories = [os.path.normpath(x) for x in directories
-                       if x != os.path.normpath(self.value)]
-        os.environ[self.name] = self.separator.join(directories)
+    TODO: Add support for views here.  Activation should set up the shell
+    TODO: environment to use the activated spack environment.
+    """
+    global _active_environment
+
+    _active_environment = env
+    prepare_config_scope(_active_environment)
+    if use_env_repo:
+        spack.repo.path.put_first(_active_environment.repo)
+
+    tty.debug("Using environmennt '%s'" % _active_environment.name)
 
 
-class EnvironmentModifications(object):
-    """Keeps track of requests to modify the current environment.
+def deactivate():
+    """Undo any configuration or repo settings modified by ``activate()``.
 
-    Each call to a method to modify the environment stores the extra
-    information on the caller in the request:
+    Returns:
+        (bool): True if an environment was deactivated, False if no
+        environment was active.
 
-        * 'filename' : filename of the module where the caller is defined
-        * 'lineno': line number where the request occurred
-        * 'context' : line of code that issued the request that failed
     """
+    global _active_environment
 
-    def __init__(self, other=None):
-        """Initializes a new instance, copying commands from 'other'
-        if it is not None.
+    if not _active_environment:
+        return
 
-        Args:
-            other (EnvironmentModifications): list of environment modifications
-                to be extended (optional)
-        """
-        self.env_modifications = []
-        if other is not None:
-            self.extend(other)
-
-    def __iter__(self):
-        return iter(self.env_modifications)
-
-    def __len__(self):
-        return len(self.env_modifications)
-
-    def extend(self, other):
-        self._check_other(other)
-        self.env_modifications.extend(other.env_modifications)
-
-    @staticmethod
-    def _check_other(other):
-        if not isinstance(other, EnvironmentModifications):
-            raise TypeError(
-                'other must be an instance of EnvironmentModifications')
-
-    def _get_outside_caller_attributes(self):
-        stack = inspect.stack()
-        try:
-            _, filename, lineno, _, context, index = stack[2]
-            context = context[index].strip()
-        except Exception:
-            filename = 'unknown file'
-            lineno = 'unknown line'
-            context = 'unknown context'
-        args = {'filename': filename, 'lineno': lineno, 'context': context}
-        return args
-
-    def set(self, name, value, **kwargs):
-        """Stores a request to set an environment variable.
-
-        Args:
-            name: name of the environment variable to be set
-            value: value of the environment variable
-        """
-        kwargs.update(self._get_outside_caller_attributes())
-        item = SetEnv(name, value, **kwargs)
-        self.env_modifications.append(item)
+    deactivate_config_scope(_active_environment)
 
-    def append_flags(self, name, value, sep=' ', **kwargs):
-        """
-        Stores in the current object a request to append to an env variable
+    # use _repo so we only remove if a repo was actually constructed
+    if _active_environment._repo:
+        spack.repo.path.remove(_active_environment._repo)
 
-        Args:
-            name: name of the environment variable to be appended to
-            value: value to append to the environment variable
-        Appends with spaces separating different additions to the variable
-        """
-        kwargs.update(self._get_outside_caller_attributes())
-        kwargs.update({'separator': sep})
-        item = AppendFlagsEnv(name, value, **kwargs)
-        self.env_modifications.append(item)
+    tty.debug("Deactivated environmennt '%s'" % _active_environment.name)
+    _active_environment = None
 
-    def unset(self, name, **kwargs):
-        """Stores a request to unset an environment variable.
 
-        Args:
-            name: name of the environment variable to be set
-        """
-        kwargs.update(self._get_outside_caller_attributes())
-        item = UnsetEnv(name, **kwargs)
-        self.env_modifications.append(item)
+def find_environment(args):
+    """Find active environment from args, spack.yaml, or environment variable.
 
-    def set_path(self, name, elements, **kwargs):
-        """Stores a request to set a path generated from a list.
+    This is called in ``spack.main`` to figure out which environment to
+    activate.
 
-        Args:
-            name: name o the environment variable to be set.
-            elements: elements of the path to set.
-        """
-        kwargs.update(self._get_outside_caller_attributes())
-        item = SetPath(name, elements, **kwargs)
-        self.env_modifications.append(item)
+    Check for an environment in this order:
+        1. via ``spack -e ENV`` or ``spack -D DIR`` (arguments)
+        2. as a spack.yaml file in the current directory, or
+        3. via a path in the SPACK_ENV environment variable.
 
-    def append_path(self, name, path, **kwargs):
-        """Stores a request to append a path to a path list.
+    If an environment is found, read it in.  If not, return None.
 
-        Args:
-            name: name of the path list in the environment
-            path: path to be appended
-        """
-        kwargs.update(self._get_outside_caller_attributes())
-        item = AppendPath(name, path, **kwargs)
-        self.env_modifications.append(item)
+    Arguments:
+        args (Namespace): argparse namespace wtih command arguments
 
-    def prepend_path(self, name, path, **kwargs):
-        """Same as `append_path`, but the path is pre-pended.
+    Returns:
+        (Environment): a found environment, or ``None``
+    """
+    # try arguments
+    env = getattr(args, 'env', None)
 
-        Args:
-            name: name of the path list in the environment
-            path: path to be pre-pended
-        """
-        kwargs.update(self._get_outside_caller_attributes())
-        item = PrependPath(name, path, **kwargs)
-        self.env_modifications.append(item)
+    # treat env as a name
+    if env:
+        if exists(env):
+            return read(env)
 
-    def remove_path(self, name, path, **kwargs):
-        """Stores a request to remove a path from a path list.
+    else:
+        # if env was specified, see if it is a dirctory otherwise, look
+        # at env_dir (env and env_dir are mutually exclusive)
+        env = getattr(args, 'env_dir', None)
 
-        Args:
-            name: name of the path list in the environment
-            path: path to be removed
-        """
-        kwargs.update(self._get_outside_caller_attributes())
-        item = RemovePath(name, path, **kwargs)
-        self.env_modifications.append(item)
+        # if no argument, look for a manifest file
+        if not env:
+            if os.path.exists(manifest_name):
+                env = os.getcwd()
 
-    def group_by_name(self):
-        """Returns a dict of the modifications grouped by variable name.
+            # if no env, env_dir, or manifest try the environment
+            if not env:
+                env = os.environ.get(spack_env_var)
 
-        Returns:
-            dict mapping the environment variable name to the modifications to
-            be done on it
+                # nothing was set; there's no active environment
+                if not env:
+                    return None
+
+    # if we get here, env isn't the name of a spack environment; it has
+    # to be a path to an environment, or there is something wrong.
+    if is_env_dir(env):
+        return Environment(env)
+
+    raise SpackEnvironmentError('no environment in %s' % env)
+
+
+def get_env(args, cmd_name, required=True):
+    """Used by commands to get the active environment.
+
+    This first checks for an ``env`` argument, then looks at the
+    ``active`` environment.  We check args first because Spack's
+    subcommand arguments are parsed *after* the ``-e`` and ``-D``
+    arguments to ``spack``.  So there may be an ``env`` argument that is
+    *not* the active environment, and we give it precedence.
+
+    This is used by a number of commands for determining whether there is
+    an active environment.
+
+    If an environment is not found *and* is required, print an error
+    message that says the calling command *needs* an active environment.
+
+    Arguments:
+        args (Namespace): argparse namespace wtih command arguments
+        cmd_name (str): name of calling command
+        required (bool): if ``False``, return ``None`` if no environment
+            is found instead of raising an exception.
+
+    Returns:
+        (Environment): if there is an arg or active environment
+    """
+    # try argument first
+    env = getattr(args, 'env', None)
+    if env:
+        if exists(env):
+            return read(env)
+        elif is_env_dir(env):
+            return Environment(env)
+        else:
+            raise SpackEnvironmentError('no environment in %s' % env)
+
+    # try the active environment. This is set by find_environment() (above)
+    if _active_environment:
+        return _active_environment
+    elif not required:
+        return None
+    else:
+        tty.die(
+            '`spack %s` requires an environment' % cmd_name,
+            'activate an environment first:',
+            '    spack env activate ENV',
+            'or use:',
+            '    spack -e ENV %s ...' % cmd_name)
+
+
+def root(name):
+    """Get the root directory for an environment by name."""
+    validate_env_name(name)
+    return os.path.join(env_path, name)
+
+
+def exists(name):
+    """Whether an environment with this name exists or not."""
+    if not valid_env_name(name):
+        return False
+    return os.path.isdir(root(name))
+
+
+def active(name):
+    """True if the named environment is active."""
+    return _active_environment and name == _active_environment.name
+
+
+def is_env_dir(path):
+    """Whether a directory contains a spack environment."""
+    return os.path.isdir(path) and os.path.exists(
+        os.path.join(path, manifest_name))
+
+
+def read(name):
+    """Get an environment with the supplied name."""
+    validate_env_name(name)
+    if not exists(name):
+        raise SpackEnvironmentError("no such environment '%s'" % name)
+    return Environment(root(name))
+
+
+def create(name, init_file=None):
+    """Create a named environment in Spack."""
+    validate_env_name(name)
+    if exists(name):
+        raise SpackEnvironmentError("'%s': environment already exists" % name)
+    return Environment(root(name), init_file)
+
+
+def config_dict(yaml_data):
+    """Get the configuration scope section out of an spack.yaml"""
+    key = spack.config.first_existing(yaml_data, env_schema_keys)
+    return yaml_data[key]
+
+
+def all_environment_names():
+    """List the names of environments that currently exist."""
+    # just return empty if the env path does not exist.  A read-only
+    # operation like list should not try to create a directory.
+    if not os.path.exists(env_path):
+        return []
+
+    candidates = sorted(os.listdir(env_path))
+    names = []
+    for candidate in candidates:
+        yaml_path = os.path.join(root(candidate), manifest_name)
+        if valid_env_name(candidate) and os.path.exists(yaml_path):
+            names.append(candidate)
+    return names
+
+
+def all_environments():
+    """Generator for all named Environments."""
+    for name in all_environment_names():
+        yield read(name)
+
+
+def validate(data, filename=None):
+    global _validator
+    if _validator is None:
+        _validator = jsonschema.Draft4Validator(spack.schema.env.schema)
+    try:
+        _validator.validate(data)
+    except jsonschema.ValidationError as e:
+        raise spack.config.ConfigFormatError(
+            e, data, filename, e.instance.lc.line + 1)
+
+
+def _read_yaml(str_or_file):
+    """Read YAML from a file for round-trip parsing."""
+    data = ruamel.yaml.load(str_or_file, ruamel.yaml.RoundTripLoader)
+    filename = getattr(str_or_file, 'name', None)
+    validate(data, filename)
+    return data
+
+
+def _write_yaml(data, str_or_file):
+    """Write YAML to a file preserving comments and dict order."""
+    filename = getattr(str_or_file, 'name', None)
+    validate(data, filename)
+    ruamel.yaml.dump(data, str_or_file, Dumper=ruamel.yaml.RoundTripDumper,
+                     default_flow_style=False)
+
+
+class Environment(object):
+    def __init__(self, path, init_file=None):
+        """Create a new environment.
+
+        The environment can be optionally initialized with either a
+        spack.yaml or spack.lock file.
+
+        Arguments:
+            path (str): path to the root directory of this environment
+            init_file (str or file object): filename or file object to
+                initialize the environment
         """
-        modifications = collections.defaultdict(list)
-        for item in self:
-            modifications[item.name].append(item)
-        return modifications
+        self.path = os.path.abspath(path)
+        self.clear()
+
+        if init_file:
+            # initialize the environment from a file if provided
+            with fs.open_if_filename(init_file) as f:
+                if hasattr(f, 'name') and f.name.endswith('.lock'):
+                    # Initialize the environment from a lockfile
+                    self._read_lockfile(f)
+                    self._set_user_specs_from_lockfile()
+                    self.yaml = _read_yaml(default_manifest_yaml)
+                else:
+                    # Initialize the environment from a spack.yaml file
+                    self._read_manifest(f)
+        else:
+            # read lockfile, if it exists
+            if os.path.exists(self.lock_path):
+                with open(self.lock_path) as f:
+                    self._read_lockfile(f)
+
+            if os.path.exists(self.manifest_path):
+                # read the spack.yaml file, if exists
+                with open(self.manifest_path) as f:
+                    self._read_manifest(f)
+
+            elif self.concretized_user_specs:
+                # if not, take user specs from the lockfile
+                self._set_user_specs_from_lockfile()
+                self.yaml = _read_yaml(default_manifest_yaml)
+            else:
+                # if there's no manifest or lockfile, use the default
+                self._read_manifest(default_manifest_yaml)
+
+    def _read_manifest(self, f):
+        """Read manifest file and set up user specs."""
+        self.yaml = _read_yaml(f)
+        spec_list = config_dict(self.yaml).get('specs')
+        if spec_list:
+            self.user_specs = [Spec(s) for s in spec_list if s]
+
+    def _set_user_specs_from_lockfile(self):
+        """Copy user_specs from a read-in lockfile."""
+        self.user_specs = [Spec(s) for s in self.concretized_user_specs]
 
     def clear(self):
+        self.user_specs = []              # current user specs
+        self.concretized_user_specs = []  # user specs from last concretize
+        self.concretized_order = []       # roots of last concretize, in order
+        self.specs_by_hash = {}           # concretized specs by hash
+        self.new_specs = []               # write packages for these on write()
+        self._repo = None                 # RepoPath for this env (memoized)
+        self._previous_active = None      # previously active environment
+
+    @property
+    def internal(self):
+        """Whether this environment is managed by Spack."""
+        return self.path.startswith(env_path)
+
+    @property
+    def name(self):
+        """Human-readable representation of the environment.
+
+        This is the path for directory environments, and just the name
+        for named environments.
         """
-        Clears the current list of modifications
+        if self.internal:
+            return os.path.basename(self.path)
+        else:
+            return self.path
+
+    @property
+    def active(self):
+        """True if this environment is currently active."""
+        return _active_environment and self.path == _active_environment.path
+
+    @property
+    def manifest_path(self):
+        """Path to spack.yaml file in this environment."""
+        return os.path.join(self.path, manifest_name)
+
+    @property
+    def lock_path(self):
+        """Path to spack.lock file in this environment."""
+        return os.path.join(self.path, lockfile_name)
+
+    @property
+    def env_subdir_path(self):
+        """Path to directory where the env stores repos, logs, views."""
+        return os.path.join(self.path, env_subdir_name)
+
+    @property
+    def repos_path(self):
+        return os.path.join(self.path, env_subdir_name, 'repos')
+
+    @property
+    def log_path(self):
+        return os.path.join(self.path, env_subdir_name, 'logs')
+
+    @property
+    def repo(self):
+        if self._repo is None:
+            self._repo = make_repo_path(self.repos_path)
+        return self._repo
+
+    def included_config_scopes(self):
+        """List of included configuration scopes from the environment.
+
+        Scopes are listed in the YAML file in order from highest to
+        lowest precedence, so configuration from earlier scope will take
+        precedence over later ones.
+
+        This routine returns them in the order they should be pushed onto
+        the internal scope stack (so, in reverse, from lowest to highest).
         """
-        self.env_modifications.clear()
-
-    def apply_modifications(self):
-        """Applies the modifications and clears the list."""
-        modifications = self.group_by_name()
-        # Apply modifications one variable at a time
-        for name, actions in sorted(modifications.items()):
-            for x in actions:
-                x.execute()
-
-    @staticmethod
-    def from_sourcing_file(filename, *args, **kwargs):
-        """Returns modifications that would be made by sourcing a file.
-
-        Parameters:
-            filename (str): The file to source
-            *args (list of str): Arguments to pass on the command line
-
-        Keyword Arguments:
-            shell (str): The shell to use (default: ``bash``)
-            shell_options (str): Options passed to the shell (default: ``-c``)
-            source_command (str): The command to run (default: ``source``)
-            suppress_output (str): Redirect used to suppress output of command
-                (default: ``&> /dev/null``)
-            concatenate_on_success (str): Operator used to execute a command
-                only when the previous command succeeds (default: ``&&``)
+        scopes = []
+
+        # load config scopes added via 'include:', in reverse so that
+        # highest-precedence scopes are last.
+        includes = config_dict(self.yaml).get('include', [])
+        for i, config_path in enumerate(reversed(includes)):
+            # allow paths to contain environment variables
+            config_path = config_path.format(**os.environ)
+
+            # treat relative paths as relative to the environment
+            if not os.path.isabs(config_path):
+                config_path = os.path.join(self.path, config_path)
+                config_path = os.path.normpath(os.path.realpath(config_path))
+
+            if os.path.isdir(config_path):
+                # directories are treated as regular ConfigScopes
+                config_name = 'env:%s:%s' % (
+                    self.name, os.path.basename(config_path))
+                scope = spack.config.ConfigScope(config_name, config_path)
+            else:
+                # files are assumed to be SingleFileScopes
+                base, ext = os.path.splitext(os.path.basename(config_path))
+                config_name = 'env:%s:%s' % (self.name, base)
+                scope = spack.config.SingleFileScope(
+                    config_name, config_path, spack.schema.merged.schema)
+
+            scopes.append(scope)
+
+        return scopes
+
+    def env_file_config_scope_name(self):
+        """Name of the config scope of this environment's manifest file."""
+        return 'env:%s' % self.name
+
+    def env_file_config_scope(self):
+        """Get the configuration scope for the environment's manifest file."""
+        config_name = self.env_file_config_scope_name()
+        return spack.config.SingleFileScope(config_name,
+                                            self.manifest_path,
+                                            spack.schema.env.schema,
+                                            [env_schema_keys])
+
+    def config_scopes(self):
+        """A list of all configuration scopes for this environment."""
+        return self.included_config_scopes() + [self.env_file_config_scope()]
+
+    def destroy(self):
+        """Remove this environment from Spack entirely."""
+        shutil.rmtree(self.path)
+
+    def add(self, user_spec):
+        """Add a single user_spec (non-concretized) to the Environment
 
         Returns:
-            EnvironmentModifications: an object that, if executed, has
-                the same effect on the environment as sourcing the file
+            (bool): True if the spec was added, False if it was already
+                present and did not need to be added
+
         """
-        # Check if the file actually exists
-        if not os.path.isfile(filename):
-            msg = 'Trying to source non-existing file: {0}'.format(filename)
-            raise RuntimeError(msg)
-
-        # Kwargs parsing and default values
-        shell                  = kwargs.get('shell', '/bin/bash')
-        shell_options          = kwargs.get('shell_options', '-c')
-        source_command         = kwargs.get('source_command', 'source')
-        suppress_output        = kwargs.get('suppress_output', '&> /dev/null')
-        concatenate_on_success = kwargs.get('concatenate_on_success', '&&')
-
-        source_file = [source_command, filename]
-        source_file.extend(args)
-        source_file = ' '.join(source_file)
-
-        dump_cmd = 'import os, json; print(json.dumps(dict(os.environ)))'
-        dump_environment = 'python -c "{0}"'.format(dump_cmd)
-
-        # Construct the command that will be executed
-        command = [
-            shell,
-            shell_options,
-            ' '.join([
-                source_file, suppress_output,
-                concatenate_on_success, dump_environment,
-            ]),
-        ]
-
-        # Try to source the file
-        proc = subprocess.Popen(
-            command, stdout=subprocess.PIPE, env=os.environ)
-        proc.wait()
-
-        if proc.returncode != 0:
-            msg = 'Sourcing file {0} returned a non-zero exit code'.format(
-                filename)
-            raise RuntimeError(msg)
-
-        output = ''.join([line.decode('utf-8') for line in proc.stdout])
-
-        # Construct dictionaries of the environment before and after
-        # sourcing the file, so that we can diff them.
-        env_before = dict(os.environ)
-        env_after = json.loads(output)
-
-        # If we're in python2, convert to str objects instead of unicode
-        # like json gives us.  We can't put unicode in os.environ anyway.
-        if sys.version_info[0] < 3:
-            env_after = dict((k.encode('utf-8'), v.encode('utf-8'))
-                             for k, v in env_after.items())
-
-        # Filter variables that are not related to sourcing a file
-        to_be_filtered = 'SHLVL', '_', 'PWD', 'OLDPWD', 'PS2'
-        for d in env_after, env_before:
-            for name in to_be_filtered:
-                d.pop(name, None)
-
-        # Fill the EnvironmentModifications instance
-        env = EnvironmentModifications()
-
-        # New variables
-        new_variables = set(env_after) - set(env_before)
-        # Variables that have been unset
-        unset_variables = set(env_before) - set(env_after)
-        # Variables that have been modified
-        common_variables = set(
-            env_before).intersection(set(env_after))
-        modified_variables = [x for x in common_variables
-                              if env_before[x] != env_after[x]]
-
-        def return_separator_if_any(*args):
-            separators = ':', ';'
-            for separator in separators:
-                for arg in args:
-                    if separator in arg:
-                        return separator
-            return None
-
-        # Add variables to env.
-        # Assume that variables with 'PATH' in the name or that contain
-        # separators like ':' or ';' are more likely to be paths
-        for x in new_variables:
-            sep = return_separator_if_any(env_after[x])
-            if sep:
-                env.prepend_path(x, env_after[x], separator=sep)
-            elif 'PATH' in x:
-                env.prepend_path(x, env_after[x])
-            else:
-                # We just need to set the variable to the new value
-                env.set(x, env_after[x])
-
-        for x in unset_variables:
-            env.unset(x)
-
-        for x in modified_variables:
-            before = env_before[x]
-            after = env_after[x]
-            sep = return_separator_if_any(before, after)
-            if sep:
-                before_list = before.split(sep)
-                after_list = after.split(sep)
-
-                # Filter out empty strings
-                before_list = list(filter(None, before_list))
-                after_list = list(filter(None, after_list))
-
-                # Paths that have been removed
-                remove_list = [
-                    ii for ii in before_list if ii not in after_list]
-                # Check that nothing has been added in the middle of
-                # before_list
-                remaining_list = [
-                    ii for ii in before_list if ii in after_list]
-                try:
-                    start = after_list.index(remaining_list[0])
-                    end = after_list.index(remaining_list[-1])
-                    search = sep.join(after_list[start:end + 1])
-                except IndexError:
-                    env.prepend_path(x, env_after[x])
-
-                if search not in before:
-                    # We just need to set the variable to the new value
-                    env.prepend_path(x, env_after[x])
-                else:
-                    try:
-                        prepend_list = after_list[:start]
-                    except KeyError:
-                        prepend_list = []
-                    try:
-                        append_list = after_list[end + 1:]
-                    except KeyError:
-                        append_list = []
-
-                    for item in remove_list:
-                        env.remove_path(x, item)
-                    for item in append_list:
-                        env.append_path(x, item)
-                    for item in prepend_list:
-                        env.prepend_path(x, item)
-            else:
-                # We just need to set the variable to the new value
-                env.set(x, env_after[x])
+        spec = Spec(user_spec)
+        if not spec.name:
+            raise SpackEnvironmentError(
+                'cannot add anonymous specs to an environment!')
+        elif not spack.repo.path.exists(spec.name):
+            raise SpackEnvironmentError('no such package: %s' % spec.name)
+
+        existing = set(s for s in self.user_specs if s.name == spec.name)
+        if not existing:
+            self.user_specs.append(spec)
+        return bool(not existing)
+
+    def remove(self, query_spec, force=False):
+        """Remove specs from an environment that match a query_spec"""
+        query_spec = Spec(query_spec)
+
+        # try abstract specs first
+        matches = []
+        if not query_spec.concrete:
+            matches = [s for s in self.user_specs if s.satisfies(query_spec)]
+
+        if not matches:
+            # concrete specs match against concrete specs in the env
+            specs_hashes = zip(
+                self.concretized_user_specs, self.concretized_order)
+            matches = [
+                s for s, h in specs_hashes if query_spec.dag_hash() == h]
+
+        if not matches:
+            raise SpackEnvironmentError("Not found: {0}".format(query_spec))
+
+        for spec in matches:
+            if spec in self.user_specs:
+                self.user_specs.remove(spec)
+
+            if force and spec in self.concretized_user_specs:
+                i = self.concretized_user_specs.index(spec)
+                del self.concretized_user_specs[i]
+
+                dag_hash = self.concretized_order[i]
+                del self.concretized_order[i]
+                del self.specs_by_hash[dag_hash]
+
+    def concretize(self, force=False):
+        """Concretize user_specs in this environment.
+
+        Only concretizes specs that haven't been concretized yet unless
+        force is ``True``.
+
+        This only modifies the environment in memory. ``write()`` will
+        write out a lockfile containing concretized specs.
+
+        Arguments:
+            force (bool): re-concretize ALL specs, even those that were
+               already concretized
+        """
+        if force:
+            # Clear previously concretized specs
+            self.concretized_user_specs = []
+            self.concretized_order = []
+            self.specs_by_hash = {}
+
+        # keep any concretized specs whose user specs are still in the manifest
+        old_concretized_user_specs = self.concretized_user_specs
+        old_concretized_order = self.concretized_order
+        old_specs_by_hash = self.specs_by_hash
+
+        self.concretized_user_specs = []
+        self.concretized_order = []
+        self.specs_by_hash = {}
+
+        for s, h in zip(old_concretized_user_specs, old_concretized_order):
+            if s in self.user_specs:
+                concrete = old_specs_by_hash[h]
+                self._add_concrete_spec(s, concrete, new=False)
+
+        # concretize any new user specs that we haven't concretized yet
+        for uspec in self.user_specs:
+            if uspec not in old_concretized_user_specs:
+                tty.msg('Concretizing %s' % uspec)
+                concrete = uspec.concretized()
+                self._add_concrete_spec(uspec, concrete)
+
+                # Display concretized spec to the user
+                sys.stdout.write(concrete.tree(
+                    recurse_dependencies=True, install_status=True,
+                    hashlen=7, hashes=True))
+
+    def install(self, user_spec, concrete_spec=None, **install_args):
+        """Install a single spec into an environment.
+
+        This will automatically concretize the single spec, but it won't
+        affect other as-yet unconcretized specs.
+        """
+        spec = Spec(user_spec)
 
-        return env
+        if self.add(spec):
+            concrete = concrete_spec if concrete_spec else spec.concretized()
+            self._add_concrete_spec(spec, concrete)
+        else:
+            # spec might be in the user_specs, but not installed.
+            spec = next(s for s in self.user_specs if s.name == spec.name)
+            concrete = self.specs_by_hash.get(spec.dag_hash())
+            if not concrete:
+                concrete = spec.concretized()
+                self._add_concrete_spec(spec, concrete)
 
+        concrete.package.do_install(**install_args)
 
-def concatenate_paths(paths, separator=':'):
-    """Concatenates an iterable of paths into a string of paths separated by
-    separator, defaulting to colon.
+    def _add_concrete_spec(self, spec, concrete, new=True):
+        """Called when a new concretized spec is added to the environment.
 
-    Args:
-        paths: iterable of paths
-        separator: the separator to use, default ':'
+        This ensures that all internal data structures are kept in sync.
 
-    Returns:
-        string
-    """
-    return separator.join(str(item) for item in paths)
+        Arguments:
+            spec (Spec): user spec that resulted in the concrete spec
+            concrete (Spec): spec concretized within this environment
+            new (bool): whether to write this spec's package to the env
+                repo on write()
+        """
+        assert concrete.concrete
+
+        # when a spec is newly concretized, we need to make a note so
+        # that we can write its package to the env repo on write()
+        if new:
+            self.new_specs.append(concrete)
+
+        # update internal lists of specs
+        self.concretized_user_specs.append(spec)
+
+        h = concrete.dag_hash()
+        self.concretized_order.append(h)
+        self.specs_by_hash[h] = concrete
+
+    def install_all(self, args=None):
+        """Install all concretized specs in an environment."""
+
+        # Make sure log directory exists
+        log_path = self.log_path
+        fs.mkdirp(log_path)
+
+        for concretized_hash in self.concretized_order:
+            spec = self.specs_by_hash[concretized_hash]
+
+            # Parse cli arguments and construct a dictionary
+            # that will be passed to Package.do_install API
+            kwargs = dict()
+            if args:
+                spack.cmd.install.update_kwargs_from_args(args, kwargs)
+
+            with fs.working_dir(self.path):
+                spec.package.do_install(**kwargs)
+
+                # Link the resulting log file into logs dir
+                build_log_link = os.path.join(
+                    log_path, '%s-%s.log' % (spec.name, spec.dag_hash(7)))
+                if os.path.exists(build_log_link):
+                    os.remove(build_log_link)
+                os.symlink(spec.package.build_log_path, build_log_link)
+
+    def all_specs_by_hash(self):
+        """Map of hashes to spec for all specs in this environment."""
+        hashes = {}
+        for h in self.concretized_order:
+            specs = self.specs_by_hash[h].traverse(deptype=('link', 'run'))
+            for spec in specs:
+                hashes[spec.dag_hash()] = spec
+        return hashes
+
+    def all_specs(self):
+        """Return all specs, even those a user spec would shadow."""
+        return sorted(self.all_specs_by_hash().values())
+
+    def all_hashes(self):
+        """Return all specs, even those a user spec would shadow."""
+        return list(self.all_specs_by_hash().keys())
+
+    def roots(self):
+        """Specs explicitly requested by the user *in this environment*.
+
+        Yields both added and installed specs that have user specs in
+        `spack.yaml`.
+        """
+        concretized = dict(self.concretized_specs())
+        for spec in self.user_specs:
+            concrete = concretized.get(spec)
+            yield concrete if concrete else spec
 
+    def added_specs(self):
+        """Specs that are not yet installed.
 
-def set_or_unset_not_first(variable, changes, errstream):
-    """Check if we are going to set or unset something after other
-    modifications have already been requested.
-    """
-    indexes = [ii for ii, item in enumerate(changes)
-               if ii != 0 and
-               not item.args.get('force', False) and
-               type(item) in [SetEnv, UnsetEnv]]
-    if indexes:
-        good = '\t    \t{context} at {filename}:{lineno}'
-        nogood = '\t--->\t{context} at {filename}:{lineno}'
-        message = "Suspicious requests to set or unset '{var}' found"
-        errstream(message.format(var=variable))
-        for ii, item in enumerate(changes):
-            print_format = nogood if ii in indexes else good
-            errstream(print_format.format(**item.args))
-
-
-def validate(env, errstream):
-    """Validates the environment modifications to check for the presence of
-    suspicious patterns. Prompts a warning for everything that was found.
-
-    Current checks:
-    - set or unset variables after other changes on the same variable
-
-    Args:
-        env: list of environment modifications
-    """
-    modifications = env.group_by_name()
-    for variable, list_of_changes in sorted(modifications.items()):
-        set_or_unset_not_first(variable, list_of_changes, errstream)
+        Yields the user spec for non-concretized specs, and the concrete
+        spec for already concretized but not yet installed specs.
+        """
+        concretized = dict(self.concretized_specs())
+        for spec in self.user_specs:
+            concrete = concretized.get(spec)
+            if not concrete:
+                yield spec
+            elif not concrete.package.installed:
+                yield concrete
+
+    def concretized_specs(self):
+        """Tuples of (user spec, concrete spec) for all concrete specs."""
+        for s, h in zip(self.concretized_user_specs, self.concretized_order):
+            yield (s, self.specs_by_hash[h])
+
+    def removed_specs(self):
+        """Tuples of (user spec, concrete spec) for all specs that will be
+           removed on nexg concretize."""
+        needed = set()
+        for s, c in self.concretized_specs():
+            if s in self.user_specs:
+                for d in c.traverse():
+                    needed.add(d)
+
+        for s, c in self.concretized_specs():
+            for d in c.traverse():
+                if d not in needed:
+                    yield d
+
+    def _get_environment_specs(self, recurse_dependencies=True):
+        """Returns the specs of all the packages in an environment.
+
+        If these specs appear under different user_specs, only one copy
+        is added to the list returned.
+        """
+        package_to_spec = {}
+        spec_list = list()
+
+        for spec_hash in self.concretized_order:
+            spec = self.specs_by_hash[spec_hash]
 
+            specs = (spec.traverse(deptype=('link', 'run'))
+                     if recurse_dependencies else (spec,))
 
-def filter_environment_blacklist(env, variables):
-    """Generator that filters out any change to environment variables present in
-    the input list.
+            for dep in specs:
+                prior = package_to_spec.get(dep.name)
+                if prior and prior != dep:
+                    tty.debug("{0} takes priority over {1}"
+                              .format(package_to_spec[dep.name].format(),
+                                      dep.format()))
+                else:
+                    package_to_spec[dep.name] = dep
+                    spec_list.append(dep)
+
+        return spec_list
+
+    def _to_lockfile_dict(self):
+        """Create a dictionary to store a lockfile for this environment."""
+        concrete_specs = {}
+        for spec in self.specs_by_hash.values():
+            for s in spec.traverse():
+                dag_hash = s.dag_hash()
+                if dag_hash not in concrete_specs:
+                    concrete_specs[dag_hash] = s.to_node_dict(all_deps=True)
+
+        hash_spec_list = zip(
+            self.concretized_order, self.concretized_user_specs)
+
+        # this is the lockfile we'll write out
+        data = {
+            # metadata about the format
+            '_meta': {
+                'file-type': 'spack-lockfile',
+                'lockfile-version': lockfile_format_version,
+            },
+
+            # users specs + hashes are the 'roots' of the environment
+            'roots': [{
+                'hash': h,
+                'spec': str(s)
+            } for h, s in hash_spec_list],
+
+            # Concrete specs by hash, including dependencies
+            'concrete_specs': concrete_specs,
+        }
+
+        return data
+
+    def _read_lockfile(self, file_or_json):
+        """Read a lockfile from a file or from a raw string."""
+        lockfile_dict = sjson.load(file_or_json)
+        self._read_lockfile_dict(lockfile_dict)
+
+    def _read_lockfile_dict(self, d):
+        """Read a lockfile dictionary into this environment."""
+        roots = d['roots']
+        self.concretized_user_specs = [Spec(r['spec']) for r in roots]
+        self.concretized_order = [r['hash'] for r in roots]
+
+        json_specs_by_hash = d['concrete_specs']
+        root_hashes = set(self.concretized_order)
+
+        specs_by_hash = {}
+        for dag_hash, node_dict in json_specs_by_hash.items():
+            specs_by_hash[dag_hash] = Spec.from_node_dict(node_dict)
+
+        for dag_hash, node_dict in json_specs_by_hash.items():
+            for dep_name, dep_hash, deptypes in (
+                    Spec.dependencies_from_node_dict(node_dict)):
+                specs_by_hash[dag_hash]._add_dependency(
+                    specs_by_hash[dep_hash], deptypes)
+
+        self.specs_by_hash = dict(
+            (x, y) for x, y in specs_by_hash.items() if x in root_hashes)
+
+    def write(self):
+        """Writes an in-memory environment to its location on disk.
+
+        This will also write out package files for each newly concretized spec.
+        """
+        # ensure path in var/spack/environments
+        fs.mkdirp(self.path)
+
+        if self.specs_by_hash:
+            # ensure the prefix/.env directory exists
+            fs.mkdirp(self.env_subdir_path)
+
+            for spec in self.new_specs:
+                for dep in spec.traverse():
+                    if not dep.concrete:
+                        raise ValueError('specs passed to environment.write() '
+                                         'must be concrete!')
+
+                    root = os.path.join(self.repos_path, dep.namespace)
+                    repo = spack.repo.create_or_construct(root, dep.namespace)
+                    pkg_dir = repo.dirname_for_package_name(dep.name)
+
+                    fs.mkdirp(pkg_dir)
+                    spack.repo.path.dump_provenance(dep, pkg_dir)
+            self.new_specs = []
+
+            # write the lock file last
+            with fs.write_tmp_and_move(self.lock_path) as f:
+                sjson.dump(self._to_lockfile_dict(), stream=f)
+        else:
+            if os.path.exists(self.lock_path):
+                os.unlink(self.lock_path)
 
-    Args:
-        env: list of environment modifications
-        variables: list of variable names to be filtered
+        # invalidate _repo cache
+        self._repo = None
 
-    Returns:
-        items in env if they are not in variables
-    """
-    for item in env:
-        if item.name not in variables:
-            yield item
+        # put the new user specs in the YAML
+        yaml_spec_list = config_dict(self.yaml).setdefault('specs', [])
+        yaml_spec_list[:] = [str(s) for s in self.user_specs]
 
+        # if all that worked, write out the manifest file at the top level
+        with fs.write_tmp_and_move(self.manifest_path) as f:
+            _write_yaml(self.yaml, f)
 
-def inspect_path(root, inspections, exclude=None):
-    """Inspects ``root`` to search for the subdirectories in ``inspections``.
-    Adds every path found to a list of prepend-path commands and returns it.
+    def __enter__(self):
+        self._previous_active = _active_environment
+        activate(self)
+        return
 
-    Args:
-        root (str): absolute path where to search for subdirectories
+    def __exit__(self, exc_type, exc_val, exc_tb):
+        deactivate()
+        if self._previous_active:
+            activate(self._previous_active)
 
-        inspections (dict): maps relative paths to a list of environment
-            variables that will be modified if the path exists. The
-            modifications are not performed immediately, but stored in a
-            command object that is returned to client
 
-        exclude (callable): optional callable. If present it must accept an
-            absolute path and return True if it should be excluded from the
-            inspection
+def make_repo_path(root):
+    """Make a RepoPath from the repo subdirectories in an environment."""
+    path = spack.repo.RepoPath()
 
-    Examples:
+    if os.path.isdir(root):
+        for repo_root in os.listdir(root):
+            repo_root = os.path.join(root, repo_root)
 
-    The following lines execute an inspection in ``/usr`` to search for
-    ``/usr/include`` and ``/usr/lib64``. If found we want to prepend
-    ``/usr/include`` to ``CPATH`` and ``/usr/lib64`` to ``MY_LIB64_PATH``.
+            if not os.path.isdir(repo_root):
+                continue
 
-        .. code-block:: python
+            repo = spack.repo.Repo(repo_root)
+            path.put_last(repo)
 
-            # Set up the dictionary containing the inspection
-            inspections = {
-                'include': ['CPATH'],
-                'lib64': ['MY_LIB64_PATH']
-            }
+    return path
 
-            # Get back the list of command needed to modify the environment
-            env = inspect_path('/usr', inspections)
 
-            # Eventually execute the commands
-            env.apply_modifications()
+def prepare_config_scope(env):
+    """Add env's scope to the global configuration search path."""
+    for scope in env.config_scopes():
+        spack.config.config.push_scope(scope)
 
-    Returns:
-        instance of EnvironmentModifications containing the requested
-        modifications
-    """
-    if exclude is None:
-        exclude = lambda x: False
 
-    env = EnvironmentModifications()
-    # Inspect the prefix to check for the existence of common directories
-    for relative_path, variables in inspections.items():
-        expected = os.path.join(root, relative_path)
+def deactivate_config_scope(env):
+    """Remove any scopes from env from the global config path."""
+    for scope in env.config_scopes():
+        spack.config.config.remove_scope(scope.name)
 
-        if os.path.isdir(expected) and not exclude(expected):
-            for variable in variables:
-                env.prepend_path(variable, expected)
 
-    return env
+class SpackEnvironmentError(spack.error.SpackError):
+    """Superclass for all errors to do with Spack environments."""
diff --git a/lib/spack/spack/error.py b/lib/spack/spack/error.py
index 4a1278b6fe..e53536d819 100644
--- a/lib/spack/spack/error.py
+++ b/lib/spack/spack/error.py
@@ -1,34 +1,19 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from __future__ import print_function
 
 import sys
+import inspect
 
 import llnl.util.tty as tty
-import spack
-import inspect
+
+
+#: whether we should write stack traces or short error messages
+#: this is module-scoped because it needs to be set very early
+debug = False
 
 
 class SpackError(Exception):
@@ -59,7 +44,7 @@ class SpackError(Exception):
         """Print extended debug information about this exception.
 
         This is usually printed when the top-level Spack error handler
-        calls ``die()``, but it acn be called separately beforehand if a
+        calls ``die()``, but it can be called separately beforehand if a
         lower-level error handler needs to print error context and
         continue without raising the exception to the top level.
         """
@@ -73,7 +58,7 @@ class SpackError(Exception):
             sys.stderr.write('\n')
 
         # stack trace, etc. in debug mode.
-        if spack.debug:
+        if debug:
             if self.traceback:
                 # exception came from a build child, already got
                 # traceback in child, so print it.
diff --git a/lib/spack/spack/fetch_strategy.py b/lib/spack/spack/fetch_strategy.py
index 30e6823207..8cabfa10ac 100644
--- a/lib/spack/spack/fetch_strategy.py
+++ b/lib/spack/spack/fetch_strategy.py
@@ -1,27 +1,8 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """
 Fetch strategies are used to download source code into a staging area
 in order to build it.  They need to define the following methods:
@@ -49,14 +30,14 @@ from functools import wraps
 from six import string_types, with_metaclass
 
 import llnl.util.tty as tty
-from llnl.util.filesystem import working_dir, mkdirp, join_path
+from llnl.util.filesystem import working_dir, mkdirp
 
-import spack
+import spack.config
 import spack.error
 import spack.util.crypto as crypto
 import spack.util.pattern as pattern
 from spack.util.executable import which
-from spack.util.string import comma_or
+from spack.util.string import comma_and, quote
 from spack.version import Version, ver
 from spack.util.compression import decompressor_for, extension
 
@@ -89,7 +70,15 @@ class FSMeta(type):
 class FetchStrategy(with_metaclass(FSMeta, object)):
     """Superclass of all fetch strategies."""
     enabled = False  # Non-abstract subclasses should be enabled.
-    required_attributes = None  # Attributes required in version() args.
+
+    #: The URL attribute must be specified either at the package class
+    #: level, or as a keyword argument to ``version()``.  It is used to
+    #: distinguish fetchers for different versions in the package DSL.
+    url_attr = None
+
+    #: Optional attributes can be used to distinguish fetchers when :
+    #: classes have multiple ``url_attrs`` at the top-level.
+    optional_attrs = []  # optional attributes in version() args.
 
     def __init__(self):
         # The stage is initialized late, so that fetch strategies can be
@@ -141,6 +130,14 @@ class FetchStrategy(with_metaclass(FSMeta, object)):
             bool: True if can cache, False otherwise.
         """
 
+    def source_id(self):
+        """A unique ID for the source.
+
+        The returned value is added to the content which determines the full
+        hash for a package using `str()`.
+        """
+        raise NotImplementedError
+
     def __str__(self):  # Should be human readable URL.
         return "FetchStrategy.__str___"
 
@@ -148,7 +145,7 @@ class FetchStrategy(with_metaclass(FSMeta, object)):
     # arguments in packages.
     @classmethod
     def matches(cls, args):
-        return any(k in args for k in cls.required_attributes)
+        return cls.url_attr in args
 
 
 @pattern.composite(interface=FetchStrategy)
@@ -160,27 +157,35 @@ class FetchStrategyComposite(object):
     matches = FetchStrategy.matches
     set_stage = FetchStrategy.set_stage
 
+    def source_id(self):
+        component_ids = tuple(i.source_id() for i in self)
+        if all(component_ids):
+            return component_ids
+
 
 class URLFetchStrategy(FetchStrategy):
     """FetchStrategy that pulls source code from a URL for an archive,
        checks the archive against a checksum,and decompresses the archive.
     """
     enabled = True
-    required_attributes = ['url']
+    url_attr = 'url'
+
+    # these are checksum types. The generic 'checksum' is deprecated for
+    # specific hash names, but we need it for backward compatibility
+    optional_attrs = list(crypto.hashes.keys()) + ['checksum']
 
-    def __init__(self, url=None, digest=None, **kwargs):
+    def __init__(self, url=None, checksum=None, **kwargs):
         super(URLFetchStrategy, self).__init__()
 
-        # If URL or digest are provided in the kwargs, then prefer
-        # those values.
-        self.url = kwargs.get('url', None)
-        if not self.url:
-            self.url = url
+        # Prefer values in kwargs to the positionals.
+        self.url = kwargs.get('url', url)
 
-        self.digest = next((kwargs[h] for h in crypto.hashes if h in kwargs),
-                           None)
-        if not self.digest:
-            self.digest = digest
+        # digest can be set as the first argument, or from an explicit
+        # kwarg by the hash name.
+        self.digest = kwargs.get('checksum', checksum)
+        for h in self.optional_attrs:
+            if h in kwargs:
+                self.digest = kwargs[h]
 
         self.expand_archive = kwargs.get('expand', True)
         self.extra_curl_options = kwargs.get('curl_options', [])
@@ -197,6 +202,9 @@ class URLFetchStrategy(FetchStrategy):
             self._curl = which('curl', required=True)
         return self._curl
 
+    def source_id(self):
+        return self.digest
+
     @_needs_stage
     def fetch(self):
         if self.archive_file:
@@ -227,7 +235,7 @@ class URLFetchStrategy(FetchStrategy):
             self.url,
         ]
 
-        if spack.insecure:
+        if not spack.config.get('config:verify_ssl'):
             curl_args.append('-k')
 
         if sys.stdout.isatty():
@@ -276,15 +284,16 @@ class URLFetchStrategy(FetchStrategy):
         # Check if we somehow got an HTML file rather than the archive we
         # asked for.  We only look at the last content type, to handle
         # redirects properly.
-        content_types = re.findall(r'Content-Type:[^\r\n]+', headers)
+        content_types = re.findall(r'Content-Type:[^\r\n]+', headers,
+                                   flags=re.IGNORECASE)
         if content_types and 'text/html' in content_types[-1]:
-            tty.warn("The contents of ",
-                     (self.archive_file if self.archive_file is not None
-                      else "the archive"),
-                     " look like HTML.",
-                     "The checksum will likely be bad.  If it is, you can use",
-                     "'spack clean <package>' to remove the bad archive, then",
-                     "fix your internet gateway issue and install again.")
+            msg = ("The contents of {0} look like HTML. Either the URL "
+                   "you are trying to use does not exist or you have an "
+                   "internet gateway issue. You can remove the bad archive "
+                   "using 'spack clean <package>', then try again using "
+                   "the correct URL.")
+            tty.warn(msg.format(self.archive_file or "the archive"))
+
         if save_file:
             os.rename(partial_file, save_file)
 
@@ -403,9 +412,6 @@ class URLFetchStrategy(FetchStrategy):
 class CacheURLFetchStrategy(URLFetchStrategy):
     """The resource associated with a cache URL may be out of date."""
 
-    def __init__(self, *args, **kwargs):
-        super(CacheURLFetchStrategy, self).__init__(*args, **kwargs)
-
     @_needs_stage
     def fetch(self):
         path = re.sub('^file://', '', self.url)
@@ -436,35 +442,38 @@ class CacheURLFetchStrategy(URLFetchStrategy):
 
 
 class VCSFetchStrategy(FetchStrategy):
+    """Superclass for version control system fetch strategies.
+
+    Like all fetchers, VCS fetchers are identified by the attributes
+    passed to the ``version`` directive.  The optional_attrs for a VCS
+    fetch strategy represent types of revisions, e.g. tags, branches,
+    commits, etc.
+
+    The required attributes (git, svn, etc.) are used to specify the URL
+    and to distinguish a VCS fetch strategy from a URL fetch strategy.
 
-    def __init__(self, name, *rev_types, **kwargs):
+    """
+
+    def __init__(self, **kwargs):
         super(VCSFetchStrategy, self).__init__()
-        self.name = name
 
         # Set a URL based on the type of fetch strategy.
-        self.url = kwargs.get(name, None)
+        self.url = kwargs.get(self.url_attr, None)
         if not self.url:
             raise ValueError(
-                "%s requires %s argument." % (self.__class__, name))
+                "%s requires %s argument." % (self.__class__, self.url_attr))
 
-        # Ensure that there's only one of the rev_types
-        if sum(k in kwargs for k in rev_types) > 1:
-            raise ValueError(
-                "Supply only one of %s to fetch with %s" % (
-                    comma_or(rev_types), name
-                ))
-
-        # Set attributes for each rev type.
-        for rt in rev_types:
-            setattr(self, rt, kwargs.get(rt, None))
+        for attr in self.optional_attrs:
+            setattr(self, attr, kwargs.get(attr, None))
 
     @_needs_stage
     def check(self):
-        tty.msg("No checksum needed when fetching with %s" % self.name)
+        tty.msg("No checksum needed when fetching with %s" % self.url_attr)
 
     @_needs_stage
     def expand(self):
-        tty.debug("Source fetched with %s is already expanded." % self.name)
+        tty.debug(
+            "Source fetched with %s is already expanded." % self.url_attr)
 
     @_needs_stage
     def archive(self, destination, **kwargs):
@@ -501,15 +510,15 @@ class GoFetchStrategy(VCSFetchStrategy):
     Go get does not natively support versions, they can be faked with git
     """
     enabled = True
-    required_attributes = ('go', )
+    url_attr = 'go'
 
     def __init__(self, **kwargs):
         # Discards the keywords in kwargs that may conflict with the next
         # call to __init__
         forwarded_args = copy.copy(kwargs)
         forwarded_args.pop('name', None)
+        super(GoFetchStrategy, self).__init__(**forwarded_args)
 
-        super(GoFetchStrategy, self).__init__('go', **forwarded_args)
         self._go = None
 
     @property
@@ -525,7 +534,7 @@ class GoFetchStrategy(VCSFetchStrategy):
 
     @_needs_stage
     def fetch(self):
-        tty.msg("Trying to get go resource:", self.url)
+        tty.msg("Getting go resource:", self.url)
 
         with working_dir(self.stage.path):
             try:
@@ -567,16 +576,16 @@ class GitFetchStrategy(VCSFetchStrategy):
         * ``commit``: Particular commit hash in the repo
     """
     enabled = True
-    required_attributes = ('git', )
+    url_attr = 'git'
+    optional_attrs = ['tag', 'branch', 'commit', 'submodules']
 
     def __init__(self, **kwargs):
         # Discards the keywords in kwargs that may conflict with the next call
         # to __init__
         forwarded_args = copy.copy(kwargs)
         forwarded_args.pop('name', None)
+        super(GitFetchStrategy, self).__init__(**forwarded_args)
 
-        super(GitFetchStrategy, self).__init__(
-            'git', 'tag', 'branch', 'commit', **forwarded_args)
         self._git = None
         self.submodules = kwargs.get('submodules', False)
 
@@ -592,7 +601,7 @@ class GitFetchStrategy(VCSFetchStrategy):
 
             # If the user asked for insecure fetching, make that work
             # with git as well.
-            if spack.insecure:
+            if not spack.config.get('config:verify_ssl'):
                 self._git.add_default_env('GIT_SSL_NO_VERIFY', 'true')
 
         return self._git
@@ -601,6 +610,16 @@ class GitFetchStrategy(VCSFetchStrategy):
     def cachable(self):
         return bool(self.commit or self.tag)
 
+    def source_id(self):
+        return self.commit or self.tag
+
+    def get_source_id(self):
+        if not self.branch:
+            return
+        output = self.git('ls-remote', self.url, self.branch, output=str)
+        if output:
+            return output.split()[0]
+
     def fetch(self):
         if self.stage.source_path:
             tty.msg("Already fetched %s" % self.stage.source_path)
@@ -614,20 +633,20 @@ class GitFetchStrategy(VCSFetchStrategy):
         elif self.branch:
             args = 'on branch %s' % self.branch
 
-        tty.msg("Trying to clone git repository: %s %s" % (self.url, args))
+        tty.msg("Cloning git repository: %s %s" % (self.url, args))
 
         git = self.git
         if self.commit:
             # Need to do a regular clone and check out everything if
             # they asked for a particular commit.
             with working_dir(self.stage.path):
-                if spack.debug:
+                if spack.config.get('config:debug'):
                     git('clone', self.url)
                 else:
                     git('clone', '--quiet', self.url)
 
             with working_dir(self.stage.source_path):
-                if spack.debug:
+                if spack.config.get('config:debug'):
                     git('checkout', self.commit)
                 else:
                     git('checkout', '--quiet', self.commit)
@@ -635,7 +654,7 @@ class GitFetchStrategy(VCSFetchStrategy):
         else:
             # Can be more efficient if not checking out a specific commit.
             args = ['clone']
-            if not spack.debug:
+            if not spack.config.get('config:debug'):
                 args.append('--quiet')
 
             # If we want a particular branch ask for it.
@@ -673,7 +692,7 @@ class GitFetchStrategy(VCSFetchStrategy):
                         # pull --tags returns a "special" error code of 1 in
                         # older versions that we have to ignore.
                         # see: https://github.com/git/git/commit/19d122b
-                        if spack.debug:
+                        if spack.config.get('config:debug'):
                             git('pull', '--tags', ignore_errors=1)
                             git('checkout', self.tag)
                         else:
@@ -683,7 +702,7 @@ class GitFetchStrategy(VCSFetchStrategy):
         with working_dir(self.stage.source_path):
             # Init submodules if the user asked for them.
             if self.submodules:
-                if spack.debug:
+                if spack.config.get('config:debug'):
                     git('submodule', 'update', '--init', '--recursive')
                 else:
                     git('submodule', '--quiet', 'update', '--init',
@@ -695,7 +714,7 @@ class GitFetchStrategy(VCSFetchStrategy):
     @_needs_stage
     def reset(self):
         with working_dir(self.stage.source_path):
-            if spack.debug:
+            if spack.config.get('config:debug'):
                 self.git('checkout', '.')
                 self.git('clean', '-f')
             else:
@@ -719,16 +738,16 @@ class SvnFetchStrategy(VCSFetchStrategy):
                    revision='1641')
     """
     enabled = True
-    required_attributes = ['svn']
+    url_attr = 'svn'
+    optional_attrs = ['revision']
 
     def __init__(self, **kwargs):
         # Discards the keywords in kwargs that may conflict with the next call
         # to __init__
         forwarded_args = copy.copy(kwargs)
         forwarded_args.pop('name', None)
+        super(SvnFetchStrategy, self).__init__(**forwarded_args)
 
-        super(SvnFetchStrategy, self).__init__(
-            'svn', 'revision', **forwarded_args)
         self._svn = None
         if self.revision is not None:
             self.revision = str(self.revision)
@@ -743,13 +762,25 @@ class SvnFetchStrategy(VCSFetchStrategy):
     def cachable(self):
         return bool(self.revision)
 
+    def source_id(self):
+        return self.revision
+
+    def get_source_id(self):
+        output = self.svn('info', self.url, output=str)
+        if not output:
+            return None
+        lines = output.split('\n')
+        for line in lines:
+            if line.startswith('Revision:'):
+                return line.split()[-1]
+
     @_needs_stage
     def fetch(self):
         if self.stage.source_path:
             tty.msg("Already fetched %s" % self.stage.source_path)
             return
 
-        tty.msg("Trying to check out svn repository: %s" % self.url)
+        tty.msg("Checking out subversion repository: %s" % self.url)
 
         args = ['checkout', '--force', '--quiet']
         if self.revision:
@@ -807,16 +838,16 @@ class HgFetchStrategy(VCSFetchStrategy):
         * ``revision``: Particular revision, branch, or tag.
     """
     enabled = True
-    required_attributes = ['hg']
+    url_attr = 'hg'
+    optional_attrs = ['revision']
 
     def __init__(self, **kwargs):
         # Discards the keywords in kwargs that may conflict with the next call
         # to __init__
         forwarded_args = copy.copy(kwargs)
         forwarded_args.pop('name', None)
+        super(HgFetchStrategy, self).__init__(**forwarded_args)
 
-        super(HgFetchStrategy, self).__init__(
-            'hg', 'revision', **forwarded_args)
         self._hg = None
 
     @property
@@ -838,6 +869,14 @@ class HgFetchStrategy(VCSFetchStrategy):
     def cachable(self):
         return bool(self.revision)
 
+    def source_id(self):
+        return self.revision
+
+    def get_source_id(self):
+        output = self.hg('id', self.url, output=str)
+        if output:
+            return output.strip()
+
     @_needs_stage
     def fetch(self):
         if self.stage.source_path:
@@ -847,11 +886,11 @@ class HgFetchStrategy(VCSFetchStrategy):
         args = []
         if self.revision:
             args.append('at revision %s' % self.revision)
-        tty.msg("Trying to clone Mercurial repository:", self.url, *args)
+        tty.msg("Cloning mercurial repository:", self.url, *args)
 
         args = ['clone']
 
-        if spack.insecure:
+        if not spack.config.get('config:verify_ssl'):
             args.append('--insecure')
 
         args.append(self.url)
@@ -911,47 +950,112 @@ def from_kwargs(**kwargs):
     for fetcher in all_strategies:
         if fetcher.matches(kwargs):
             return fetcher(**kwargs)
-    # Raise an error in case we can't instantiate any known strategy
-    message = "Cannot instantiate any FetchStrategy"
-    long_message = message + " from the given arguments : {arguments}".format(
-        srguments=kwargs)
-    raise FetchError(message, long_message)
 
+    raise InvalidArgsError(**kwargs)
+
+
+def check_pkg_attributes(pkg):
+    """Find ambiguous top-level fetch attributes in a package.
+
+    Currently this only ensures that two or more VCS fetch strategies are
+    not specified at once.
+    """
+    # a single package cannot have URL attributes for multiple VCS fetch
+    # strategies *unless* they are the same attribute.
+    conflicts = set([s.url_attr for s in all_strategies
+                     if hasattr(pkg, s.url_attr)])
+
+    # URL isn't a VCS fetch method. We can use it with a VCS method.
+    conflicts -= set(['url'])
+
+    if len(conflicts) > 1:
+        raise FetcherConflict(
+            'Package %s cannot specify %s together. Pick at most one.'
+            % (pkg.name, comma_and(quote(conflicts))))
 
-def args_are_for(args, fetcher):
-    fetcher.matches(args)
+
+def _check_version_attributes(fetcher, pkg, version):
+    """Ensure that the fetcher for a version is not ambiguous.
+
+    This assumes that we have already determined the fetcher for the
+    specific version using ``for_package_version()``
+    """
+    all_optionals = set(a for s in all_strategies for a in s.optional_attrs)
+
+    args = pkg.versions[version]
+    extra = set(args) - set(fetcher.optional_attrs) - set([fetcher.url_attr])
+    extra.intersection_update(all_optionals)
+
+    if extra:
+        legal_attrs = [fetcher.url_attr] + list(fetcher.optional_attrs)
+        raise FetcherConflict(
+            "%s version '%s' has extra arguments: %s"
+            % (pkg.name, version, comma_and(quote(extra))),
+            "Valid arguments for a %s fetcher are: \n    %s"
+            % (fetcher.url_attr, comma_and(quote(legal_attrs))))
+
+
+def _extrapolate(pkg, version):
+    """Create a fetcher from an extrapolated URL for this version."""
+    try:
+        return URLFetchStrategy(pkg.url_for_version(version))
+    except spack.package.NoURLError:
+        msg = ("Can't extrapolate a URL for version %s "
+               "because package %s defines no URLs")
+        raise ExtrapolationError(msg % (version, pkg.name))
+
+
+def _from_merged_attrs(fetcher, pkg, version):
+    """Create a fetcher from merged package and version attributes."""
+    if fetcher.url_attr == 'url':
+        url = pkg.url_for_version(version)
+    else:
+        url = getattr(pkg, fetcher.url_attr)
+
+    attrs = {fetcher.url_attr: url}
+    attrs.update(pkg.versions[version])
+    return fetcher(**attrs)
 
 
 def for_package_version(pkg, version):
     """Determine a fetch strategy based on the arguments supplied to
        version() in the package description."""
-    # If it's not a known version, extrapolate one.
+    check_pkg_attributes(pkg)
+
+    if not isinstance(version, Version):
+        version = Version(version)
+
+    # If it's not a known version, try to extrapolate one by URL
     if version not in pkg.versions:
-        url = pkg.url_for_version(version)
-        if not url:
-            raise InvalidArgsError(pkg, version)
-        return URLFetchStrategy(url)
+        return _extrapolate(pkg, version)
 
     # Grab a dict of args out of the package version dict
     args = pkg.versions[version]
 
-    # Test all strategies against per-version arguments.
+    # If the version specifies a `url_attr` directly, use that.
     for fetcher in all_strategies:
-        if fetcher.matches(args):
+        if fetcher.url_attr in args:
+            _check_version_attributes(fetcher, pkg, version)
             return fetcher(**args)
 
-    # If nothing matched for a *specific* version, test all strategies
-    # against
+    # if a version's optional attributes imply a particular fetch
+    # strategy, and we have the `url_attr`, then use that strategy.
     for fetcher in all_strategies:
-        attrs = dict((attr, getattr(pkg, attr, None))
-                     for attr in fetcher.required_attributes)
-        if 'url' in attrs:
-            attrs['url'] = pkg.url_for_version(version)
-        attrs.update(args)
-        if fetcher.matches(attrs):
-            return fetcher(**attrs)
+        if hasattr(pkg, fetcher.url_attr) or fetcher.url_attr == 'url':
+            optionals = fetcher.optional_attrs
+            if optionals and any(a in args for a in optionals):
+                _check_version_attributes(fetcher, pkg, version)
+                return _from_merged_attrs(fetcher, pkg, version)
+
+    # if the optional attributes tell us nothing, then use any `url_attr`
+    # on the package.  This prefers URL vs. VCS, b/c URLFetchStrategy is
+    # defined first in this file.
+    for fetcher in all_strategies:
+        if hasattr(pkg, fetcher.url_attr):
+            _check_version_attributes(fetcher, pkg, version)
+            return _from_merged_attrs(fetcher, pkg, version)
 
-    raise InvalidArgsError(pkg, version)
+    raise InvalidArgsError(pkg, version, **args)
 
 
 def from_list_url(pkg):
@@ -962,15 +1066,25 @@ def from_list_url(pkg):
         try:
             versions = pkg.fetch_remote_versions()
             try:
+                # get a URL, and a checksum if we have it
                 url_from_list = versions[pkg.version]
-                digest = None
-                if pkg.version in pkg.versions:
-                    digest = pkg.versions[pkg.version].get('md5', None)
-                return URLFetchStrategy(url=url_from_list, digest=digest)
+                checksum = None
+
+                # try to find a known checksum for version, from the package
+                version = pkg.version
+                if version in pkg.versions:
+                    args = pkg.versions[version]
+                    checksum = next(
+                        (v for k, v in args.items() if k in crypto.hashes),
+                        args.get('checksum'))
+
+                # construct a fetcher
+                return URLFetchStrategy(url_from_list, checksum)
             except KeyError:
-                tty.msg("Can not find version %s in url_list" %
-                        pkg.version)
+                tty.msg("Cannot find version %s in url_list" % pkg.version)
+
         except BaseException:
+            # TODO: Don't catch BaseException here! Be more specific.
             tty.msg("Could not determine url from list_url.")
 
 
@@ -979,7 +1093,7 @@ class FsCache(object):
     def __init__(self, root):
         self.root = os.path.abspath(root)
 
-    def store(self, fetcher, relativeDst):
+    def store(self, fetcher, relative_dest):
         # skip fetchers that aren't cachable
         if not fetcher.cachable:
             return
@@ -988,12 +1102,12 @@ class FsCache(object):
         if isinstance(fetcher, CacheURLFetchStrategy):
             return
 
-        dst = join_path(self.root, relativeDst)
+        dst = os.path.join(self.root, relative_dest)
         mkdirp(os.path.dirname(dst))
         fetcher.archive(dst)
 
-    def fetcher(self, targetPath, digest, **kwargs):
-        path = join_path(self.root, targetPath)
+    def fetcher(self, target_path, digest, **kwargs):
+        path = os.path.join(self.root, target_path)
         return CacheURLFetchStrategy(path, digest, **kwargs)
 
     def destroy(self):
@@ -1024,12 +1138,24 @@ class NoDigestError(FetchError):
     """Raised after attempt to checksum when URL has no digest."""
 
 
+class ExtrapolationError(FetchError):
+    """Raised when we can't extrapolate a version for a package."""
+
+
+class FetcherConflict(FetchError):
+    """Raised for packages with invalid fetch attributes."""
+
+
 class InvalidArgsError(FetchError):
-    def __init__(self, pkg, version):
-        msg = ("Could not construct a fetch strategy for package %s at "
-               "version %s")
-        msg %= (pkg.name, version)
-        super(InvalidArgsError, self).__init__(msg)
+    """Raised when a version can't be deduced from a set of arguments."""
+    def __init__(self, pkg=None, version=None, **args):
+        msg = "Could not guess a fetch strategy"
+        if pkg:
+            msg += ' for {pkg}'.format(pkg=pkg)
+            if version:
+                msg += '@{version}'.format(version=version)
+        long_msg = 'with arguments: {args}'.format(args=args)
+        super(InvalidArgsError, self).__init__(msg, long_msg)
 
 
 class ChecksumError(FetchError):
diff --git a/lib/spack/spack/filesystem_view.py b/lib/spack/spack/filesystem_view.py
index 9be55e381b..d3e9878b32 100644
--- a/lib/spack/spack/filesystem_view.py
+++ b/lib/spack/spack/filesystem_view.py
@@ -1,38 +1,19 @@
-##############################################################################
-# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import filecmp
 import functools as ft
 import os
 import re
 import shutil
 import sys
 
-from llnl.util.filesystem import join_path
-from llnl.util.link_tree import LinkTree
+from llnl.util.link_tree import LinkTree, MergeConflictError
 from llnl.util import tty
+from llnl.util.lang import match_predicate
 
-import spack
 import spack.spec
 import spack.store
 from spack.directory_layout import ExtensionAlreadyInstalledError
@@ -94,7 +75,7 @@ class FilesystemView(object):
 
     def add_extension(self, spec):
         """
-            Add (link) an extension in this view.
+            Add (link) an extension in this view. Does not add dependencies.
         """
         raise NotImplementedError
 
@@ -225,17 +206,9 @@ class YamlFilesystemView(FilesystemView):
                      % colorize_spec(spec))
             return True
 
-        try:
-            if not spec.package.is_activated(self.extensions_layout):
-                spec.package.do_activate(
-                    verbose=self.verbose,
-                    extensions_layout=self.extensions_layout)
-
-        except ExtensionAlreadyInstalledError:
-            # As we use sets in add_specs(), the order in which packages get
-            # activated is essentially random. So this spec might have already
-            # been activated as dependency of another package -> fail silently
-            pass
+        if not spec.package.is_activated(self):
+            spec.package.do_activate(
+                self, verbose=self.verbose, with_dependencies=False)
 
         # make sure the meta folder is linked as well (this is not done by the
         # extension-activation mechnism)
@@ -273,29 +246,66 @@ class YamlFilesystemView(FilesystemView):
                                         long=False)
                 return False
 
-        tree = LinkTree(spec.prefix)
+        self.merge(spec)
 
-        if not self.ignore_conflicts:
-            conflict = tree.find_conflict(self.root)
-            if conflict is not None:
-                tty.error(self._croot +
-                          "Cannot link package %s, file already exists: %s"
-                          % (spec.name, conflict))
-                return False
-
-        conflicts = tree.merge(self.root, link=self.link,
-                               ignore=ignore_metadata_dir,
-                               ignore_conflicts=self.ignore_conflicts)
         self.link_meta_folder(spec)
 
-        if self.ignore_conflicts:
-            for c in conflicts:
-                tty.warn(self._croot + "Could not link: %s" % c)
-
         if self.verbose:
             tty.info(self._croot + 'Linked package: %s' % colorize_spec(spec))
         return True
 
+    def merge(self, spec, ignore=None):
+        pkg = spec.package
+        view_source = pkg.view_source()
+        view_dst = pkg.view_destination(self)
+
+        tree = LinkTree(view_source)
+
+        ignore = ignore or (lambda f: False)
+        ignore_file = match_predicate(
+            self.layout.hidden_file_paths, ignore)
+
+        # check for dir conflicts
+        conflicts = tree.find_dir_conflicts(view_dst, ignore_file)
+
+        merge_map = tree.get_file_map(view_dst, ignore_file)
+        if not self.ignore_conflicts:
+            conflicts.extend(pkg.view_file_conflicts(self, merge_map))
+
+        if conflicts:
+            raise MergeConflictError(conflicts[0])
+
+        # merge directories with the tree
+        tree.merge_directories(view_dst, ignore_file)
+
+        pkg.add_files_to_view(self, merge_map)
+
+    def unmerge(self, spec, ignore=None):
+        pkg = spec.package
+        view_source = pkg.view_source()
+        view_dst = pkg.view_destination(self)
+
+        tree = LinkTree(view_source)
+
+        ignore = ignore or (lambda f: False)
+        ignore_file = match_predicate(
+            self.layout.hidden_file_paths, ignore)
+
+        merge_map = tree.get_file_map(view_dst, ignore_file)
+        pkg.remove_files_from_view(self, merge_map)
+
+        # now unmerge the directory tree
+        tree.unmerge_directories(view_dst, ignore_file)
+
+    def remove_file(self, src, dest):
+        if not os.path.islink(dest):
+            raise ValueError("%s is not a link tree!" % dest)
+        # remove if dest is a hardlink/symlink to src; this will only
+        # be false if two packages are merged into a prefix and have a
+        # conflicting file
+        if filecmp.cmp(src, dest, shallow=True):
+            os.remove(dest)
+
     def check_added(self, spec):
         assert spec.concrete
         return spec == self.get_spec(spec)
@@ -363,11 +373,11 @@ class YamlFilesystemView(FilesystemView):
 
         # The spec might have been deactivated as depdency of another package
         # already
-        if spec.package.is_activated(self.extensions_layout):
+        if spec.package.is_activated(self):
             spec.package.do_deactivate(
+                self,
                 verbose=self.verbose,
-                remove_dependents=with_dependents,
-                extensions_layout=self.extensions_layout)
+                remove_dependents=with_dependents)
         self.unlink_meta_folder(spec)
 
     def remove_standalone(self, spec):
@@ -379,15 +389,15 @@ class YamlFilesystemView(FilesystemView):
                      'Skipping package not linked in view: %s' % spec.name)
             return
 
-        tree = LinkTree(spec.prefix)
-        tree.unmerge(self.root, ignore=ignore_metadata_dir)
+        self.unmerge(spec)
         self.unlink_meta_folder(spec)
 
         if self.verbose:
             tty.info(self._croot + 'Removed package: %s' % colorize_spec(spec))
 
     def get_all_specs(self):
-        dotspack = join_path(self.root, spack.store.layout.metadata_dir)
+        dotspack = os.path.join(self.root,
+                                spack.store.layout.metadata_dir)
         if os.path.exists(dotspack):
             return list(filter(None, map(self.get_spec, os.listdir(dotspack))))
         else:
@@ -404,12 +414,14 @@ class YamlFilesystemView(FilesystemView):
 
     def get_path_meta_folder(self, spec):
         "Get path to meta folder for either spec or spec name."
-        return join_path(self.root, spack.store.layout.metadata_dir,
-                         getattr(spec, "name", spec))
+        return os.path.join(self.root,
+                            spack.store.layout.metadata_dir,
+                            getattr(spec, "name", spec))
 
     def get_spec(self, spec):
         dotspack = self.get_path_meta_folder(spec)
-        filename = join_path(dotspack, spack.store.layout.spec_file_name)
+        filename = os.path.join(dotspack,
+                                spack.store.layout.spec_file_name)
 
         try:
             with open(filename, "r") as f:
@@ -541,7 +553,3 @@ def get_dependencies(specs):
     retval = set()
     set(map(retval.update, (set(s.traverse()) for s in specs)))
     return retval
-
-
-def ignore_metadata_dir(f):
-    return f in spack.store.layout.hidden_file_paths
diff --git a/lib/spack/spack/graph.py b/lib/spack/spack/graph.py
index 896bf15e36..6b65932e7d 100644
--- a/lib/spack/spack/graph.py
+++ b/lib/spack/spack/graph.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """Functions for graphing DAGs of dependencies.
 
 This file contains code for graphing DAGs of software packages
@@ -543,7 +524,9 @@ def graph_dot(specs, deptype='all', static=False, out=None):
 
     # Static graph includes anything a package COULD depend on.
     if static:
-        names = set.union(*[s.package.possible_dependencies() for s in specs])
+        names = set.union(*[
+            s.package.possible_dependencies(expand_virtuals=False)
+            for s in specs])
         specs = [Spec(name) for name in names]
 
     labeled = set()
diff --git a/lib/spack/spack/hooks/__init__.py b/lib/spack/spack/hooks/__init__.py
index 5bf4110608..b25dfeade2 100644
--- a/lib/spack/spack/hooks/__init__.py
+++ b/lib/spack/spack/hooks/__init__.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """This package contains modules with hooks for various stages in the
    Spack install process.  You can add modules here and they'll be
    executed by package at various times during the package lifecycle.
@@ -41,20 +22,20 @@
    systems (e.g. modules, dotkit, etc.) or to add other custom
    features.
 """
-import imp
+import os.path
 
-import spack
-from llnl.util.filesystem import join_path
+import spack.paths
+import spack.util.imp as simp
 from llnl.util.lang import memoized, list_modules
 
 
 @memoized
 def all_hook_modules():
     modules = []
-    for name in list_modules(spack.hooks_path):
+    for name in list_modules(spack.paths.hooks_path):
         mod_name = __name__ + '.' + name
-        path = join_path(spack.hooks_path, name) + ".py"
-        mod = imp.load_source(mod_name, path)
+        path = os.path.join(spack.paths.hooks_path, name) + ".py"
+        mod = simp.load_source(mod_name, path)
         modules.append(mod)
 
     return modules
diff --git a/lib/spack/spack/hooks/case_consistency.py b/lib/spack/spack/hooks/case_consistency.py
deleted file mode 100644
index 54139cb039..0000000000
--- a/lib/spack/spack/hooks/case_consistency.py
+++ /dev/null
@@ -1,110 +0,0 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-from __future__ import absolute_import
-
-import os
-import re
-import platform
-
-from llnl.util.filesystem import working_dir
-
-import spack
-from spack.cmd import spack_is_git_repo
-from spack.util.executable import which, ProcessError
-
-
-def pre_run():
-    if platform.system() != "Darwin":
-        return
-
-    try:
-        repo = spack.repo.get_repo('builtin')
-        git_case_consistency_check(repo.packages_path)
-    except spack.repository.UnknownNamespaceError:
-        pass
-
-
-def git_case_consistency_check(path):
-    """Re-sync case of files in a directory with git.
-
-    On case-insensitive but case-preserving filesystems like Mac OS X,
-    Git doesn't properly rename files that only had their case changed.
-
-    This checks files in a directory against git and does a
-    case-restoring rename (actually two renames, e.g.::
-
-        name -> tmp -> NAME
-
-    We use this in Spack to ensure package directories are named
-    correctly.
-
-    TODO: this check can probably be removed once package names have been
-    TODO: lowercase for a long while.
-
-    """
-    # Don't bother fixing case if Spack isn't in a git repository
-    if not spack_is_git_repo():
-        return
-
-    git = which('git', required=False)
-    if not git:
-        return
-
-    with working_dir(path):
-        try:
-            git_filenames = git('ls-tree', '--name-only', 'HEAD', output=str)
-            git_filenames = set(re.split(r'\s+', git_filenames.strip()))
-        except ProcessError:
-            return  # Ignore errors calling git
-
-        lower_to_mixed = {}
-        for fn in git_filenames:
-            lower = fn.lower()
-            mixed = lower_to_mixed.setdefault(lower, [])
-            mixed.append(fn)
-
-        # Iterate through all actual files and make sure their names are
-        # the same as corresponding names in git
-        actual_filenames = os.listdir('.')
-        for actual in actual_filenames:
-            lower = actual.lower()
-
-            # not tracked by git
-            if lower not in lower_to_mixed:
-                continue
-
-            # Don't know what to do with multiple matches
-            if len(lower_to_mixed[lower]) != 1:
-                continue
-
-            # Skip if case is already correct
-            git_name = lower_to_mixed[lower][0]
-            if git_name == actual:
-                continue
-
-            # restore case with two renames
-            tmp_name = actual + '.spack.tmp'
-            os.rename(actual, tmp_name)
-            os.rename(tmp_name, git_name)
diff --git a/lib/spack/spack/hooks/extensions.py b/lib/spack/spack/hooks/extensions.py
index 7865c34dc0..271e01ab2e 100644
--- a/lib/spack/spack/hooks/extensions.py
+++ b/lib/spack/spack/hooks/extensions.py
@@ -1,27 +1,10 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import spack
+from spack.filesystem_view import YamlFilesystemView
 
 
 def pre_uninstall(spec):
@@ -29,6 +12,9 @@ def pre_uninstall(spec):
     assert spec.concrete
 
     if pkg.is_extension:
-        if pkg.is_activated():
+        target = pkg.extendee_spec.prefix
+        view = YamlFilesystemView(target, spack.store.layout)
+
+        if pkg.is_activated(view):
             # deactivate globally
             pkg.do_deactivate(force=True)
diff --git a/lib/spack/spack/hooks/licensing.py b/lib/spack/spack/hooks/licensing.py
index 9b5a2728ed..bc4d0c2ee2 100644
--- a/lib/spack/spack/hooks/licensing.py
+++ b/lib/spack/spack/hooks/licensing.py
@@ -1,32 +1,14 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 
-import spack
 import llnl.util.tty as tty
-from llnl.util.filesystem import join_path, mkdirp
+from llnl.util.filesystem import mkdirp
+
+from spack.util.editor import editor
 
 
 def pre_install(spec):
@@ -55,7 +37,7 @@ def set_up_license(pkg):
             # Create a new license file
             write_license_file(pkg, license_path)
             # Open up file in user's favorite $EDITOR for editing
-            spack.editor(license_path)
+            editor(license_path)
             tty.msg("Added global license file %s" % license_path)
         else:
             # Use already existing license file
@@ -84,63 +66,74 @@ def write_license_file(pkg, license_path):
     Comments give suggestions on alternative methods of
     installing a license."""
 
-    comment = pkg.license_comment
+    # License files
+    linktargets = ""
+    for f in pkg.license_files:
+        linktargets += "\t%s\n" % f
 
-    # Global license directory may not already exist
-    if not os.path.exists(os.path.dirname(license_path)):
-        os.makedirs(os.path.dirname(license_path))
-    license = open(license_path, 'w')
+    # Environment variables
+    envvars = ""
+    if pkg.license_vars:
+        for varname in pkg.license_vars:
+            envvars += "\t%s\n" % varname
 
-    # License files
-    license.write("""\
-{0} A license is required to use {1}.
-{0}
-{0} The recommended solution is to store your license key in this global
-{0} license file. After installation, the following symlink(s) will be
-{0} added to point to this file (relative to the installation prefix):
-{0}
-""".format(comment, pkg.name))
+    # Documentation
+    url = ""
+    if pkg.license_url:
+        url += "\t%s\n" % pkg.license_url
 
-    for filename in pkg.license_files:
-        license.write("{0}\t{1}\n".format(comment, filename))
+    # Assemble. NB: pkg.license_comment will be prepended upon output.
+    txt = """
+ A license is required to use package '{0}'.
 
-    license.write("{0}\n".format(comment))
+ * If your system is already properly configured for such a license, save this
+   file UNCHANGED. The system may be configured if:
 
-    # Environment variables
-    if pkg.license_vars:
-        license.write("""\
-{0} Alternatively, use one of the following environment variable(s):
-{0}
-""".format(comment))
+    - A license file is installed in a default location.
+""".format(pkg.name)
 
-        for var in pkg.license_vars:
-            license.write("{0}\t{1}\n".format(comment, var))
+    if envvars:
+        txt += """\
+    - One of the following environment variable(s) is set for you, possibly via
+      a module file:
 
-        license.write("""\
 {0}
-{0} If you choose to store your license in a non-standard location, you may
-{0} set one of these variable(s) to the full pathname to the license file, or
-{0} port@host if you store your license keys on a dedicated license server.
-{0} You will likely want to set this variable in a module file so that it
-{0} gets loaded every time someone tries to use {1}.
-{0}
-""".format(comment, pkg.name))
+""".format(envvars)
+
+    txt += """\
+ * Otherwise, depending on the license you have, enter AT THE BEGINNING of
+   this file:
+
+   - the contents of your license file, or
+   - the address(es) of your license server.
+
+   After installation, the following symlink(s) will be added to point to
+   this Spack-global file (relative to the installation prefix).
 
-    # Documentation
-    if pkg.license_url:
-        license.write("""\
-{0} For further information on how to acquire a license, please refer to:
-{0}
-{0}\t{1}
 {0}
-""".format(comment, pkg.license_url))
+""".format(linktargets)
+
+    if url:
+        txt += """\
+ * For further information on licensing, see:
 
-    license.write("""\
-{0} You may enter your license below.
+{0}
+""".format(url)
 
-""".format(comment))
+    txt += """\
+ Recap:
+ - You may not need to modify this file at all.
+ - Otherwise, enter your license or server address AT THE BEGINNING.
+"""
+    # Global license directory may not already exist
+    if not os.path.exists(os.path.dirname(license_path)):
+        os.makedirs(os.path.dirname(license_path))
 
-    license.close()
+    # Output
+    with open(license_path, 'w') as f:
+        for line in txt.splitlines():
+            f.write("{0}{1}\n".format(pkg.license_comment, line))
+        f.close()
 
 
 def post_install(spec):
@@ -156,7 +149,8 @@ def symlink_license(pkg):
     """Create local symlinks that point to the global license file."""
     target = pkg.global_license_file
     for filename in pkg.license_files:
-        link_name = join_path(pkg.prefix, filename)
+        link_name = os.path.join(pkg.prefix, filename)
+        link_name = os.path.abspath(link_name)
         license_dir = os.path.dirname(link_name)
         if not os.path.exists(license_dir):
             mkdirp(license_dir)
diff --git a/lib/spack/spack/hooks/module_file_generation.py b/lib/spack/spack/hooks/module_file_generation.py
index 6858b0874e..5581b20b64 100644
--- a/lib/spack/spack/hooks/module_file_generation.py
+++ b/lib/spack/spack/hooks/module_file_generation.py
@@ -1,33 +1,14 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import spack.modules
 import spack.modules.common
 import llnl.util.tty as tty
 
 try:
-    enabled = spack.modules.common.configuration['enable']
+    enabled = spack.config.get('modules:enable')
 except KeyError:
     tty.debug('NO MODULE WRITTEN: list of enabled module files is empty')
     enabled = []
diff --git a/lib/spack/spack/hooks/permissions_setters.py b/lib/spack/spack/hooks/permissions_setters.py
new file mode 100644
index 0000000000..ceb6105c16
--- /dev/null
+++ b/lib/spack/spack/hooks/permissions_setters.py
@@ -0,0 +1,45 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import os
+
+from llnl.util.filesystem import chmod_x, chgrp
+
+from spack.package_prefs import get_package_permissions, get_package_group
+from spack.package_prefs import get_package_dir_permissions
+
+
+def forall_files(path, fn, args, dir_args=None):
+    """Apply function to all files in directory, with file as first arg.
+
+    Does not apply to the root dir. Does not apply to links"""
+    for root, dirs, files in os.walk(path):
+        for d in dirs:
+            if not os.path.islink(os.path.join(root, d)):
+                if dir_args:
+                    fn(os.path.join(root, d), *dir_args)
+                else:
+                    fn(os.path.join(root, d), *args)
+        for f in files:
+            if not os.path.islink(os.path.join(root, d)):
+                fn(os.path.join(root, f), *args)
+
+
+def chmod_real_entries(path, perms):
+    # Don't follow links so we don't change things outside the prefix
+    if not os.path.islink(path):
+        chmod_x(path, perms)
+
+
+def post_install(spec):
+    if not spec.external:
+        perms = get_package_permissions(spec)
+        dir_perms = get_package_dir_permissions(spec)
+        group = get_package_group(spec)
+
+        forall_files(spec.prefix, chmod_real_entries, [perms], [dir_perms])
+
+        if group:
+            forall_files(spec.prefix, chgrp, [group])
diff --git a/lib/spack/spack/hooks/sbang.py b/lib/spack/spack/hooks/sbang.py
index 887dfdc5b9..e03c397d6f 100644
--- a/lib/spack/spack/hooks/sbang.py
+++ b/lib/spack/spack/hooks/sbang.py
@@ -1,34 +1,15 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 import stat
 import re
 
 import llnl.util.tty as tty
 
-import spack
+import spack.paths
 import spack.modules
 
 # Character limit for shebang line.  Using Linux's 127 characters
@@ -56,7 +37,7 @@ def filter_shebang(path):
         original = original_file.read()
 
     # This line will be prepended to file
-    new_sbang_line = '#!/bin/bash %s/bin/sbang\n' % spack.spack_root
+    new_sbang_line = '#!/bin/bash %s/bin/sbang\n' % spack.paths.prefix
 
     # Skip files that are already using sbang.
     if original.startswith(new_sbang_line):
diff --git a/lib/spack/spack/hooks/yaml_version_check.py b/lib/spack/spack/hooks/yaml_version_check.py
index 338d2e51e7..a6978673ac 100644
--- a/lib/spack/spack/hooks/yaml_version_check.py
+++ b/lib/spack/spack/hooks/yaml_version_check.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """Yaml Version Check is a module for ensuring that config file
 formats are compatible with the current version of Spack."""
 import os.path
@@ -36,8 +17,9 @@ def pre_run():
 
 
 def check_compiler_yaml_version():
-    config_scopes = spack.config.config_scopes
-    for scope in config_scopes.values():
+    config = spack.config.config
+
+    for scope in config.file_scopes:
         file_name = os.path.join(scope.path, 'compilers.yaml')
         data = None
         if os.path.isfile(file_name):
@@ -45,8 +27,8 @@ def check_compiler_yaml_version():
                 data = syaml.load(f)
 
         if data:
-            compilers = data['compilers']
-            if len(compilers) > 0:
+            compilers = data.get('compilers')
+            if compilers and len(compilers) > 0:
                 if (not isinstance(compilers, list) or
                     'operating_system' not in compilers[0]['compiler']):
                     new_file = os.path.join(scope.path, '_old_compilers.yaml')
diff --git a/lib/spack/spack/main.py b/lib/spack/spack/main.py
index c3e1ea4506..4f77cd986d 100644
--- a/lib/spack/spack/main.py
+++ b/lib/spack/spack/main.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """This is the implementation of the Spack command line executable.
 
 In a normal Spack installation, this is invoked from the bin/spack script
@@ -30,6 +11,7 @@ after the system path is set up.
 from __future__ import print_function
 
 import sys
+import re
 import os
 import inspect
 import pstats
@@ -37,32 +19,47 @@ import argparse
 from six import StringIO
 
 import llnl.util.tty as tty
+import llnl.util.tty.color as color
 from llnl.util.tty.log import log_output
 
 import spack
+import spack.architecture
+import spack.config
 import spack.cmd
+import spack.environment as ev
+import spack.hooks
+import spack.paths
+import spack.repo
+import spack.store
+import spack.util.debug
+import spack.util.path
 from spack.error import SpackError
 
 
-# names of profile statistics
+#: names of profile statistics
 stat_names = pstats.Stats.sort_arg_dict_default
 
-# help levels in order of detail (i.e., number of commands shown)
+#: top-level aliases for Spack commands
+aliases = {
+    'rm': 'remove'
+}
+
+#: help levels in order of detail (i.e., number of commands shown)
 levels = ['short', 'long']
 
-# intro text for help at different levels
+#: intro text for help at different levels
 intro_by_level = {
     'short': 'These are common spack commands:',
     'long':  'Complete list of spack commands:',
 }
 
-# control top-level spack options shown in basic vs. advanced help
+#: control top-level spack options shown in basic vs. advanced help
 options_by_level = {
     'short': ['h', 'k', 'V', 'color'],
     'long': 'all'
 }
 
-# Longer text for each section, to show in help
+#: Longer text for each section, to show in help
 section_descriptions = {
     'admin':       'administration',
     'basic':       'query packages',
@@ -76,37 +73,42 @@ section_descriptions = {
     'system':      'system',
 }
 
-# preferential command order for some sections (e.g., build pipeline is
-# in execution order, not alphabetical)
+#: preferential command order for some sections (e.g., build pipeline is
+#: in execution order, not alphabetical)
 section_order = {
     'basic': ['list', 'info', 'find'],
     'build': ['fetch', 'stage', 'patch', 'configure', 'build', 'restage',
-              'install', 'uninstall', 'clean']
+              'install', 'uninstall', 'clean'],
+    'packaging': ['create', 'edit']
 }
 
-# Properties that commands are required to set.
+#: Properties that commands are required to set.
 required_command_properties = ['level', 'section', 'description']
 
+#: Recorded directory where spack command was originally invoked
+spack_working_dir = None
+
 
 def set_working_dir():
     """Change the working directory to getcwd, or spack prefix if no cwd."""
+    global spack_working_dir
     try:
-        spack.spack_working_dir = os.getcwd()
+        spack_working_dir = os.getcwd()
     except OSError:
-        os.chdir(spack.spack_prefix)
-        spack.spack_working_dir = spack.spack_prefix
+        os.chdir(spack.paths.prefix)
+        spack_working_dir = spack.paths.prefix
 
 
 def add_all_commands(parser):
     """Add all spack subcommands to the parser."""
-    for cmd in spack.cmd.commands:
+    for cmd in spack.cmd.all_commands():
         parser.add_command(cmd)
 
 
 def index_commands():
     """create an index of commands by section for this help level"""
     index = {}
-    for command in spack.cmd.commands:
+    for command in spack.cmd.all_commands():
         cmd_module = spack.cmd.get_module(command)
 
         # make sure command modules have required properties
@@ -127,6 +129,22 @@ def index_commands():
     return index
 
 
+class SpackHelpFormatter(argparse.RawTextHelpFormatter):
+    def _format_actions_usage(self, actions, groups):
+        """Formatter with more concise usage strings."""
+        usage = super(
+            SpackHelpFormatter, self)._format_actions_usage(actions, groups)
+
+        # compress single-character flags that are not mutually exclusive
+        # at the beginning of the usage string
+        chars = ''.join(re.findall(r'\[-(.)\]', usage))
+        usage = re.sub(r'\[-.\] ?', '', usage)
+        if chars:
+            return '[-%s] %s' % (chars, usage)
+        else:
+            return usage
+
+
 class SpackArgumentParser(argparse.ArgumentParser):
     def format_help_sections(self, level):
         """Format help on sections for a particular verbosity level.
@@ -149,7 +167,7 @@ class SpackArgumentParser(argparse.ArgumentParser):
             self.actions = self._subparsers._actions[-1]._get_subactions()
 
         # make a set of commands not yet added.
-        remaining = set(spack.cmd.commands)
+        remaining = set(spack.cmd.all_commands())
 
         def add_group(group):
             formatter.start_section(group.title)
@@ -159,11 +177,11 @@ class SpackArgumentParser(argparse.ArgumentParser):
 
         def add_subcommand_group(title, commands):
             """Add informational help group for a specific subcommand set."""
-            cmd_set = set(commands)
+            cmd_set = set(c for c in commands)
 
             # make a dict of commands of interest
-            cmds = dict((action.metavar, action) for action in self.actions
-                        if action.metavar in cmd_set)
+            cmds = dict((a.dest, a) for a in self.actions
+                        if a.dest in cmd_set)
 
             # add commands to a group in order, and add the group
             group = argparse._ArgumentGroup(self, title=title)
@@ -182,14 +200,11 @@ class SpackArgumentParser(argparse.ArgumentParser):
             new_actions = [opts[letter] for letter in show_options]
             self._optionals._group_actions = new_actions
 
-        options = ''.join(opt.option_strings[0].strip('-')
-                          for opt in self._optionals._group_actions)
-
-        index = index_commands()
-
-        # usage
-        formatter.add_text(
-            "usage: %s [-%s] <command> [...]" % (self.prog, options))
+        # custom, more concise usage for top level
+        help_options = self._optionals._group_actions
+        help_options = help_options + [self._positionals._group_actions[-1]]
+        formatter.add_usage(
+            self.usage, help_options, self._mutually_exclusive_groups)
 
         # description
         formatter.add_text(self.description)
@@ -198,7 +213,9 @@ class SpackArgumentParser(argparse.ArgumentParser):
         formatter.add_text(intro_by_level[level])
 
         # add argument groups based on metadata in commands
+        index = index_commands()
         sections = index[level]
+
         for section in sorted(sections):
             if section == 'help':
                 continue   # Cover help in the epilog.
@@ -226,7 +243,7 @@ class SpackArgumentParser(argparse.ArgumentParser):
         # epilog
         formatter.add_text("""\
 {help}:
-  spack help -a          list all available commands
+  spack help --all       list all commands and options
   spack help <command>   help on a specific command
   spack help --spec      help on the spec syntax
   spack docs             open http://spack.rtfd.io/ in a browser"""
@@ -235,11 +252,20 @@ class SpackArgumentParser(argparse.ArgumentParser):
         # determine help from format above
         return formatter.format_help()
 
-    def add_command(self, name):
-        """Add one subcommand to this parser."""
-        # convert CLI command name to python module name
-        name = spack.cmd.get_python_name(name)
+    def add_subparsers(self, **kwargs):
+        """Ensure that sensible defaults are propagated to subparsers"""
+        kwargs.setdefault('metavar', 'SUBCOMMAND')
+        sp = super(SpackArgumentParser, self).add_subparsers(**kwargs)
+        old_add_parser = sp.add_parser
+
+        def add_parser(name, **kwargs):
+            kwargs.setdefault('formatter_class', SpackHelpFormatter)
+            return old_add_parser(name, **kwargs)
+        sp.add_parser = add_parser
+        return sp
 
+    def add_command(self, cmd_name):
+        """Add one subcommand to this parser."""
         # lazily initialize any subparsers
         if not hasattr(self, 'subparsers'):
             # remove the dummy "command" argument.
@@ -250,12 +276,18 @@ class SpackArgumentParser(argparse.ArgumentParser):
 
         # each command module implements a parser() function, to which we
         # pass its subparser for setup.
-        module = spack.cmd.get_module(name)
-        cmd_name = name.replace('_', '-')
+        module = spack.cmd.get_module(cmd_name)
+
+        # build a list of aliases
+        alias_list = [k for k, v in aliases.items() if v == cmd_name]
+
         subparser = self.subparsers.add_parser(
-            cmd_name, help=module.description, description=module.description)
+            cmd_name, aliases=alias_list,
+            help=module.description, description=module.description)
         module.setup_parser(subparser)
-        return module
+
+        # return the callable function for the command
+        return spack.cmd.get_command(cmd_name)
 
     def format_help(self, level='short'):
         if self.prog == 'spack':
@@ -267,43 +299,89 @@ class SpackArgumentParser(argparse.ArgumentParser):
             return super(SpackArgumentParser, self).format_help()
 
 
-def make_argument_parser():
+def make_argument_parser(**kwargs):
     """Create an basic argument parser without any subcommands added."""
     parser = SpackArgumentParser(
-        formatter_class=argparse.RawTextHelpFormatter, add_help=False,
+        formatter_class=SpackHelpFormatter, add_help=False,
         description=(
             "A flexible package manager that supports multiple versions,\n"
-            "configurations, platforms, and compilers."))
+            "configurations, platforms, and compilers."),
+        **kwargs)
 
     # stat names in groups of 7, for nice wrapping.
     stat_lines = list(zip(*(iter(stat_names),) * 7))
 
-    parser.add_argument('-h', '--help', action='store_true',
-                        help="show this help message and exit")
-    parser.add_argument('--color', action='store', default='auto',
-                        choices=('always', 'never', 'auto'),
-                        help="when to colorize output; default is auto")
-    parser.add_argument('-d', '--debug', action='store_true',
-                        help="write out debug logs during compile")
-    parser.add_argument('-D', '--pdb', action='store_true',
-                        help="run spack under the pdb debugger")
-    parser.add_argument('-k', '--insecure', action='store_true',
-                        help="do not check ssl certificates when downloading")
-    parser.add_argument('-m', '--mock', action='store_true',
-                        help="use mock packages instead of real ones")
-    parser.add_argument('-p', '--profile', action='store_true',
-                        help="profile execution using cProfile")
-    parser.add_argument('-P', '--sorted-profile', default=None, metavar="STAT",
-                        help="profile and sort by one or more of:\n[%s]" %
-                        ',\n '.join([', '.join(line) for line in stat_lines]))
-    parser.add_argument('--lines', default=20, action='store',
-                        help="lines of profile output; default 20; or 'all'")
-    parser.add_argument('-v', '--verbose', action='store_true',
-                        help="print additional output during builds")
-    parser.add_argument('-s', '--stacktrace', action='store_true',
-                        help="add stacktraces to all printed statements")
-    parser.add_argument('-V', '--version', action='store_true',
-                        help='show version number and exit')
+    parser.add_argument(
+        '-h', '--help',
+        dest='help', action='store_const', const='short', default=None,
+        help="show this help message and exit")
+    parser.add_argument(
+        '-H', '--all-help',
+        dest='help', action='store_const', const='long', default=None,
+        help="show help for all commands (same as spack help --all)")
+    parser.add_argument(
+        '--color', action='store', default='auto',
+        choices=('always', 'never', 'auto'),
+        help="when to colorize output (default: auto)")
+    parser.add_argument(
+        '-C', '--config-scope', dest='config_scopes', action='append',
+        metavar='DIR', help="add a custom configuration scope")
+    parser.add_argument(
+        '-d', '--debug', action='store_true',
+        help="write out debug logs during compile")
+    parser.add_argument(
+        '--pdb', action='store_true',
+        help="run spack under the pdb debugger")
+
+    env_group = parser.add_mutually_exclusive_group()
+    env_group.add_argument(
+        '-e', '--env', dest='env', metavar='ENV', action='store',
+        help="run with a specific environment (see spack env)")
+    env_group.add_argument(
+        '-D', '--env-dir', dest='env_dir', metavar='DIR', action='store',
+        help="run with an environment directory (ignore named environments)")
+    env_group.add_argument(
+        '-E', '--no-env', dest='no_env', action='store_true',
+        help="run without any environments activated (see spack env)")
+    parser.add_argument(
+        '--use-env-repo', action='store_true',
+        help="when running in an environment, use its package repository")
+
+    parser.add_argument(
+        '-k', '--insecure', action='store_true',
+        help="do not check ssl certificates when downloading")
+    parser.add_argument(
+        '-l', '--enable-locks', action='store_true', dest='locks',
+        default=None, help="use filesystem locking (default)")
+    parser.add_argument(
+        '-L', '--disable-locks', action='store_false', dest='locks',
+        help="do not use filesystem locking (unsafe)")
+    parser.add_argument(
+        '-m', '--mock', action='store_true',
+        help="use mock packages instead of real ones")
+    parser.add_argument(
+        '-p', '--profile', action='store_true', dest='spack_profile',
+        help="profile execution using cProfile")
+    parser.add_argument(
+        '--sorted-profile', default=None, metavar="STAT",
+        help="profile and sort by one or more of:\n[%s]" %
+        ',\n '.join([', '.join(line) for line in stat_lines]))
+    parser.add_argument(
+        '--lines', default=20, action='store',
+        help="lines of profile output or 'all' (default: 20)")
+    parser.add_argument(
+        '-v', '--verbose', action='store_true',
+        help="print additional output during builds")
+    parser.add_argument(
+        '--stacktrace', action='store_true',
+        help="add stacktraces to all printed statements")
+    parser.add_argument(
+        '-V', '--version', action='store_true',
+        help='show version number and exit')
+    parser.add_argument(
+        '--print-shell-vars', action='store',
+        help="print info needed by setup-env.[c]sh")
+
     return parser
 
 
@@ -313,23 +391,30 @@ def setup_main_options(args):
     tty.set_verbose(args.verbose)
     tty.set_debug(args.debug)
     tty.set_stacktrace(args.stacktrace)
-    spack.debug = args.debug
 
-    if spack.debug:
-        import spack.util.debug as debug
-        debug.register_interrupt_handler()
+    # debug must be set first so that it can even affect behvaior of
+    # errors raised by spack.config.
+    if args.debug:
+        spack.error.debug = True
+        spack.util.debug.register_interrupt_handler()
+        spack.config.set('config:debug', True, scope='command_line')
+
+    # override lock configuration if passed on command line
+    if args.locks is not None:
+        spack.util.lock.check_lock_safety(spack.paths.prefix)
+        spack.config.set('config:locks', False, scope='command_line')
 
     if args.mock:
-        from spack.repository import RepoPath
-        spack.repo.swap(RepoPath(spack.mock_packages_path))
+        rp = spack.repo.RepoPath(spack.paths.mock_packages_path)
+        spack.repo.set_path(rp)
 
     # If the user asked for it, don't check ssl certs.
     if args.insecure:
         tty.warn("You asked for --insecure. Will NOT check SSL certificates.")
-        spack.insecure = True
+        spack.config.set('config:verify_ssl', False, scope='command_line')
 
     # when to use color (takes always, auto, or never)
-    tty.color.set_color_when(args.color)
+    color.set_color_when(args.color)
 
 
 def allows_unknown_args(command):
@@ -345,7 +430,7 @@ def allows_unknown_args(command):
     return (argcount == 3 and varnames[2] == 'unknown_args')
 
 
-def _invoke_spack_command(command, parser, args, unknown_args):
+def _invoke_command(command, parser, args, unknown_args):
     """Run a spack command *without* setting spack global options."""
     if allows_unknown_args(command):
         return_val = command(parser, args, unknown_args)
@@ -369,12 +454,15 @@ class SpackCommand(object):
     Use this to invoke Spack commands directly from Python and check
     their output.
     """
-    def __init__(self, command):
-        """Create a new SpackCommand that invokes ``command`` when called."""
+    def __init__(self, command_name):
+        """Create a new SpackCommand that invokes ``command_name`` when called.
+
+        Args:
+            command_name (str): name of the command to invoke
+        """
         self.parser = make_argument_parser()
-        self.parser.add_command(command)
-        self.command_name = command
-        self.command = spack.cmd.get_command(command)
+        self.command = self.parser.add_command(command_name)
+        self.command_name = command_name
 
     def __call__(self, *argv, **kwargs):
         """Invoke this SpackCommand.
@@ -388,7 +476,7 @@ class SpackCommand(object):
         Returns:
             (str): combined output and error as a string
 
-        On return, if ``fail_on_error`` is False, return value of comman
+        On return, if ``fail_on_error`` is False, return value of command
         is set in ``returncode`` property, and the error is set in the
         ``error`` property.  Otherwise, raise an error.
         """
@@ -404,7 +492,7 @@ class SpackCommand(object):
         out = StringIO()
         try:
             with log_output(out):
-                self.returncode = _invoke_spack_command(
+                self.returncode = _invoke_command(
                     self.command, self.parser, args, unknown)
 
         except SystemExit as e:
@@ -424,30 +512,6 @@ class SpackCommand(object):
         return out.getvalue()
 
 
-def _main(command, parser, args, unknown_args):
-    """Run a spack command *and* set spack globaloptions."""
-    # many operations will fail without a working directory.
-    set_working_dir()
-
-    # only setup main options in here, after the real parse (we'll get it
-    # wrong if we do it after the initial, partial parse)
-    setup_main_options(args)
-    spack.hooks.pre_run()
-
-    # Now actually execute the command
-    try:
-        return _invoke_spack_command(command, parser, args, unknown_args)
-    except SpackError as e:
-        e.die()  # gracefully die on any SpackErrors
-    except Exception as e:
-        if spack.debug:
-            raise
-        tty.die(str(e))
-    except KeyboardInterrupt:
-        sys.stderr.write('\n')
-        tty.die("Keyboard interrupt.")
-
-
 def _profile_wrapper(command, parser, args, unknown_args):
     import cProfile
 
@@ -470,7 +534,7 @@ def _profile_wrapper(command, parser, args, unknown_args):
         # make a profiler and run the code.
         pr = cProfile.Profile()
         pr.enable()
-        return _main(command, parser, args, unknown_args)
+        return _invoke_command(command, parser, args, unknown_args)
 
     finally:
         pr.disable()
@@ -481,6 +545,46 @@ def _profile_wrapper(command, parser, args, unknown_args):
         stats.print_stats(nlines)
 
 
+def print_setup_info(*info):
+    """Print basic information needed by setup-env.[c]sh.
+
+    Args:
+        info (list of str): list of things to print: comma-separated list
+            of 'csh', 'sh', or 'modules'
+
+    This is in ``main.py`` to make it fast; the setup scripts need to
+    invoke spack in login scripts, and it needs to be quick.
+
+    """
+    shell = 'csh' if 'csh' in info else 'sh'
+
+    def shell_set(var, value):
+        if shell == 'sh':
+            print("%s='%s'" % (var, value))
+        elif shell == 'csh':
+            print("set %s = '%s'" % (var, value))
+        else:
+            tty.die('shell must be sh or csh')
+
+    # print sys type
+    shell_set('_sp_sys_type', spack.architecture.sys_type())
+
+    # print roots for all module systems
+    module_roots = spack.config.get('config:module_roots')
+    for name, path in module_roots.items():
+        path = spack.util.path.canonicalize_path(path)
+        shell_set('_sp_%s_root' % name, path)
+
+    # print environment module system if available. This can be expensive
+    # on clusters, so skip it if not needed.
+    if 'modules' in info:
+        specs = spack.store.db.query('environment-modules')
+        if specs:
+            shell_set('_sp_module_prefix', specs[-1].prefix)
+        else:
+            shell_set('_sp_module_prefix', 'not_installed')
+
+
 def main(argv=None):
     """This is the entry point for the Spack command.
 
@@ -496,55 +600,85 @@ def main(argv=None):
     parser.add_argument('command', nargs=argparse.REMAINDER)
     args, unknown = parser.parse_known_args(argv)
 
+    # activate an environment if one was specified on the command line
+    if not args.no_env:
+        env = ev.find_environment(args)
+        if env:
+            ev.activate(env, args.use_env_repo)
+
+    # make spack.config aware of any command line configuration scopes
+    if args.config_scopes:
+        spack.config.command_line_scopes = args.config_scopes
+
+    if args.print_shell_vars:
+        print_setup_info(*args.print_shell_vars.split(','))
+        return 0
+
     # Just print help and exit if run with no arguments at all
     no_args = (len(sys.argv) == 1) if argv is None else (len(argv) == 0)
     if no_args:
         parser.print_help()
         return 1
 
-    # -h and -V are special as they do not require a command, but all the
-    # other options do nothing without a command.
-    if not args.command:
-        if args.version:
-            print(spack.spack_version)
-            return 0
-        else:
-            parser.print_help()
-            return 0 if args.help else 1
-
-    # Try to load the particular command the caller asked for.  If there
-    # is no module for it, just die.
-    command_name = spack.cmd.get_python_name(args.command[0])
-    try:
-        parser.add_command(command_name)
-    except ImportError:
-        if spack.debug:
-            raise
-        tty.die("Unknown command: %s" % args.command[0])
-
-    # Re-parse with the proper sub-parser added.
-    args, unknown = parser.parse_known_args()
-
-    # we now know whether options go with spack or the command
+    # -h, -H, and -V are special as they do not require a command, but
+    # all the other options do nothing without a command.
     if args.version:
         print(spack.spack_version)
         return 0
     elif args.help:
-        parser.print_help()
+        sys.stdout.write(parser.format_help(level=args.help))
         return 0
+    elif not args.command:
+        parser.print_help()
+        return 1
 
-    # now we can actually execute the command.
-    command = spack.cmd.get_command(command_name)
     try:
-        if args.profile or args.sorted_profile:
+        # ensure options on spack command come before everything
+        setup_main_options(args)
+
+        # Try to load the particular command the caller asked for.  If there
+        # is no module for it, just die.
+        cmd_name = args.command[0]
+        cmd_name = aliases.get(cmd_name, cmd_name)
+
+        try:
+            command = parser.add_command(cmd_name)
+        except ImportError:
+            if spack.config.get('config:debug'):
+                raise
+            tty.die("Unknown command: %s" % args.command[0])
+
+        # Re-parse with the proper sub-parser added.
+        args, unknown = parser.parse_known_args()
+
+        # many operations will fail without a working directory.
+        set_working_dir()
+
+        # pre-run hooks happen after we know we have a valid working dir
+        spack.hooks.pre_run()
+
+        # now we can actually execute the command.
+        if args.spack_profile or args.sorted_profile:
             _profile_wrapper(command, parser, args, unknown)
         elif args.pdb:
             import pdb
-            pdb.runctx('_main(command, parser, args, unknown)',
+            pdb.runctx('_invoke_command(command, parser, args, unknown)',
                        globals(), locals())
             return 0
         else:
-            return _main(command, parser, args, unknown)
+            return _invoke_command(command, parser, args, unknown)
+
+    except SpackError as e:
+        e.die()  # gracefully die on any SpackErrors
+
+    except Exception as e:
+        if spack.config.get('config:debug'):
+            raise
+        tty.die(str(e))
+
+    except KeyboardInterrupt:
+        sys.stderr.write('\n')
+        tty.die("Keyboard interrupt.")
 
     except SystemExit as e:
         return e.code
diff --git a/lib/spack/spack/mirror.py b/lib/spack/spack/mirror.py
index f8cedc38b4..3310bc53fb 100644
--- a/lib/spack/spack/mirror.py
+++ b/lib/spack/spack/mirror.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """
 This file contains code for creating spack mirror directories.  A
 mirror is an organized hierarchy containing specially named archive
@@ -33,9 +14,9 @@ to download packages directly from a mirror (e.g., on an intranet).
 import sys
 import os
 import llnl.util.tty as tty
-from llnl.util.filesystem import mkdirp, join_path
+from llnl.util.filesystem import mkdirp
 
-import spack
+import spack.config
 import spack.error
 import spack.url as url
 import spack.fetch_strategy as fs
@@ -44,7 +25,7 @@ from spack.version import VersionList
 from spack.util.compression import allowed_archive
 
 
-def mirror_archive_filename(spec, fetcher, resourceId=None):
+def mirror_archive_filename(spec, fetcher, resource_id=None):
     """Get the name of the spec's archive in the mirror."""
     if not spec.version.concrete:
         raise ValueError("mirror.path requires spec with concrete version.")
@@ -87,18 +68,18 @@ Spack not to expand it with the following syntax:
         # Otherwise we'll make a .tar.gz ourselves
         ext = 'tar.gz'
 
-    if resourceId:
-        filename = "%s-%s" % (resourceId, spec.version) + ".%s" % ext
+    if resource_id:
+        filename = "%s-%s" % (resource_id, spec.version) + ".%s" % ext
     else:
         filename = "%s-%s" % (spec.package.name, spec.version) + ".%s" % ext
 
     return filename
 
 
-def mirror_archive_path(spec, fetcher, resourceId=None):
+def mirror_archive_path(spec, fetcher, resource_id=None):
     """Get the relative path to the spec's archive within a mirror."""
-    return join_path(
-        spec.name, mirror_archive_filename(spec, fetcher, resourceId))
+    return os.path.join(
+        spec.name, mirror_archive_filename(spec, fetcher, resource_id))
 
 
 def get_matching_versions(specs, **kwargs):
@@ -222,12 +203,12 @@ def add_single_spec(spec, mirror_root, categories, **kwargs):
                 fetcher = stage.fetcher
                 if ii == 0:
                     # create a subdirectory for the current package@version
-                    archive_path = os.path.abspath(join_path(
+                    archive_path = os.path.abspath(os.path.join(
                         mirror_root, mirror_archive_path(spec, fetcher)))
                     name = spec.cformat("$_$@")
                 else:
                     resource = stage.resource
-                    archive_path = os.path.abspath(join_path(
+                    archive_path = os.path.abspath(os.path.join(
                         mirror_root,
                         mirror_archive_path(spec, fetcher, resource.name)))
                     name = "{resource} ({pkg}).".format(
@@ -255,7 +236,7 @@ def add_single_spec(spec, mirror_root, categories, **kwargs):
             categories['mirrored'].append(spec)
 
     except Exception as e:
-        if spack.debug:
+        if spack.config.get('config:debug'):
             sys.excepthook(*sys.exc_info())
         else:
             tty.warn(
diff --git a/lib/spack/spack/mixins.py b/lib/spack/spack/mixins.py
new file mode 100644
index 0000000000..bae8ec7494
--- /dev/null
+++ b/lib/spack/spack/mixins.py
@@ -0,0 +1,194 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+"""This module contains additional behavior that can be attached to any given
+package.
+"""
+import collections
+import os
+
+import llnl.util.filesystem
+
+__all__ = [
+    'filter_compiler_wrappers'
+]
+
+
+class PackageMixinsMeta(type):
+    """This metaclass serves the purpose of implementing a declarative syntax
+    for package mixins.
+
+    Mixins are implemented below in the form of a function. Each one of them
+    needs to register a callable that takes a single argument to be run
+    before or after a certain phase. This callable is basically a method that
+    gets implicitly attached to the package class by calling the mixin.
+    """
+
+    _methods_to_be_added = {}
+    _add_method_before = collections.defaultdict(list)
+    _add_method_after = collections.defaultdict(list)
+
+    @staticmethod
+    def register_method_before(fn, phase):
+        """Registers a method to be run before a certain phase.
+
+        Args:
+            fn: function taking a single argument (self)
+            phase (str): phase before which fn must run
+        """
+        PackageMixinsMeta._methods_to_be_added[fn.__name__] = fn
+        PackageMixinsMeta._add_method_before[phase].append(fn)
+
+    @staticmethod
+    def register_method_after(fn, phase):
+        """Registers a method to be run after a certain phase.
+
+        Args:
+            fn: function taking a single argument (self)
+            phase (str): phase after which fn must run
+        """
+        PackageMixinsMeta._methods_to_be_added[fn.__name__] = fn
+        PackageMixinsMeta._add_method_after[phase].append(fn)
+
+    def __init__(cls, name, bases, attr_dict):
+
+        # Add the methods to the class being created
+        if PackageMixinsMeta._methods_to_be_added:
+            attr_dict.update(PackageMixinsMeta._methods_to_be_added)
+            PackageMixinsMeta._methods_to_be_added.clear()
+
+        attr_fmt = '_InstallPhase_{0}'
+
+        # Copy the phases that needs it to the most derived classes
+        # in order not to interfere with other packages in the hierarchy
+        phases_to_be_copied = list(
+            PackageMixinsMeta._add_method_before.keys()
+        )
+        phases_to_be_copied += list(
+            PackageMixinsMeta._add_method_after.keys()
+        )
+
+        for phase in phases_to_be_copied:
+
+            attr_name = attr_fmt.format(phase)
+
+            # Here we want to get the attribute directly from the class (not
+            # from the instance), so that we can modify it and add the mixin
+            # method to the pipeline.
+            phase = getattr(cls, attr_name)
+
+            # Due to MRO, we may have taken a method from a parent class
+            # and modifying it may influence other packages in unwanted
+            # manners. Solve the problem by copying the phase into the most
+            # derived class.
+            setattr(cls, attr_name, phase.copy())
+
+        # Insert the methods in the appropriate position
+        # in the installation pipeline.
+
+        for phase in PackageMixinsMeta._add_method_before:
+
+            attr_name = attr_fmt.format(phase)
+            phase_obj = getattr(cls, attr_name)
+            fn_list = PackageMixinsMeta._add_method_after[phase]
+
+            for f in fn_list:
+                phase_obj.run_before.append(f)
+
+        # Flush the dictionary for the next class
+        PackageMixinsMeta._add_method_before.clear()
+
+        for phase in PackageMixinsMeta._add_method_after:
+
+            attr_name = attr_fmt.format(phase)
+            phase_obj = getattr(cls, attr_name)
+            fn_list = PackageMixinsMeta._add_method_after[phase]
+
+            for f in fn_list:
+                phase_obj.run_after.append(f)
+
+        # Flush the dictionary for the next class
+        PackageMixinsMeta._add_method_after.clear()
+
+        super(PackageMixinsMeta, cls).__init__(name, bases, attr_dict)
+
+
+def filter_compiler_wrappers(*files, **kwargs):
+    """Substitutes any path referring to a Spack compiler wrapper with the
+    path of the underlying compiler that has been used.
+
+    If this isn't done, the files will have CC, CXX, F77, and FC set to
+    Spack's generic cc, c++, f77, and f90. We want them to be bound to
+    whatever compiler they were built with.
+
+    Args:
+        *files: files to be filtered relative to the search root (which is,
+            by default, the installation prefix)
+
+        **kwargs: allowed keyword arguments
+
+            after
+                specifies after which phase the files should be
+                filtered (defaults to 'install')
+
+            relative_root
+                path relative to prefix where to start searching for
+                the files to be filtered. If not set the install prefix
+                wil be used as the search root. **It is highly recommended
+                to set this, as searching from the installation prefix may
+                affect performance severely in some cases**.
+
+            ignore_absent, backup
+                these two keyword arguments, if present, will be forwarded
+                to ``filter_file`` (see its documentation for more information
+                on their behavior)
+
+            recursive
+                this keyword argument, if present, will be forwarded to
+                ``find`` (see its documentation for more information on the
+                behavior)
+    """
+    after = kwargs.get('after', 'install')
+    relative_root = kwargs.get('relative_root', None)
+
+    filter_kwargs = {
+        'ignore_absent': kwargs.get('ignore_absent', True),
+        'backup': kwargs.get('backup', False),
+        'string': True
+    }
+
+    find_kwargs = {
+        'recursive': kwargs.get('recursive', False)
+    }
+
+    def _filter_compiler_wrappers_impl(self):
+        # Compute the absolute path of the search root
+        root = os.path.join(
+            self.prefix, relative_root
+        ) if relative_root else self.prefix
+
+        # Compute the absolute path of the files to be filtered and
+        # remove links from the list.
+        abs_files = llnl.util.filesystem.find(root, files, **find_kwargs)
+        abs_files = [x for x in abs_files if not os.path.islink(x)]
+
+        x = llnl.util.filesystem.FileFilter(*abs_files)
+
+        replacements = [
+            ('CC', self.compiler.cc),
+            ('CXX', self.compiler.cxx),
+            ('F77', self.compiler.f77),
+            ('FC', self.compiler.fc)
+        ]
+        for env_var, compiler_path in replacements:
+            if env_var in os.environ:
+                x.filter(os.environ[env_var], compiler_path, **filter_kwargs)
+
+        # Remove this linking flag if present (it turns RPATH into RUNPATH)
+        x.filter('-Wl,--enable-new-dtags', '', **filter_kwargs)
+
+    PackageMixinsMeta.register_method_after(
+        _filter_compiler_wrappers_impl, after
+    )
diff --git a/lib/spack/spack/modules/__init__.py b/lib/spack/spack/modules/__init__.py
index 47802092a5..edafb2e57b 100644
--- a/lib/spack/spack/modules/__init__.py
+++ b/lib/spack/spack/modules/__init__.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """This package contains code for creating environment modules, which can
 include dotkits, TCL non-hierarchical modules, LUA hierarchical modules, and
 others.
diff --git a/lib/spack/spack/modules/common.py b/lib/spack/spack/modules/common.py
index 86abaae7c3..482c3e1321 100644
--- a/lib/spack/spack/modules/common.py
+++ b/lib/spack/spack/modules/common.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """Here we consolidate the logic for creating an abstract description
 of the information that module systems need.
 
@@ -56,22 +37,23 @@ import re
 import six
 import llnl.util.filesystem
 import llnl.util.tty as tty
-import spack
+
+import spack.paths
 import spack.build_environment as build_environment
-import spack.environment
+import spack.util.environment
 import spack.tengine as tengine
 import spack.util.path
 import spack.util.environment
 import spack.error
 
-#: Root folders where the various module files should be written
-roots = spack.config.get_config('config').get('module_roots', {})
+#: config section for this file
+configuration = spack.config.get('modules')
 
-#: Merged modules.yaml as a dictionary
-configuration = spack.config.get_config('modules')
+#: Root folders where the various module files should be written
+roots = spack.config.get('config:module_roots', {})
 
 #: Inspections that needs to be done on spec prefixes
-prefix_inspections = configuration.get('prefix_inspections', {})
+prefix_inspections = spack.config.get('modules:prefix_inspections', {})
 
 #: Valid tokens for naming scheme and env variable names
 _valid_tokens = (
@@ -191,7 +173,7 @@ def merge_config_rules(configuration, spec):
         if constraint.endswith(':'):
             constraint = constraint.strip(':')
             override = True
-        if spec.satisfies(constraint):
+        if spec.satisfies(constraint, strict=True):
             if override:
                 spec_configuration = {}
             update_dictionary_extending_lists(spec_configuration, action)
@@ -229,7 +211,7 @@ def root_path(name):
     Returns:
         root folder for module file installation
     """
-    path = roots.get(name, os.path.join(spack.share_path, name))
+    path = roots.get(name, os.path.join(spack.paths.share_path, name))
     return spack.util.path.canonicalize_path(path)
 
 
@@ -274,7 +256,7 @@ class BaseConfiguration(object):
         """List of environment modifications that should be done in the
         module.
         """
-        env_mods = spack.environment.EnvironmentModifications()
+        env_mods = spack.util.environment.EnvironmentModifications()
         actions = self.conf.get('environment', {})
 
         def process_arglist(arglist):
@@ -518,14 +500,14 @@ class BaseContext(tengine.Context):
     def environment_modifications(self):
         """List of environment modifications to be processed."""
         # Modifications guessed inspecting the spec prefix
-        env = spack.environment.inspect_path(
+        env = spack.util.environment.inspect_path(
             self.spec.prefix,
             prefix_inspections,
             exclude=spack.util.environment.is_system_path
         )
 
         # Modifications that are coded at package level
-        _ = spack.environment.EnvironmentModifications()
+        _ = spack.util.environment.EnvironmentModifications()
         # TODO : the code down below is quite similar to
         # TODO : build_environment.setup_package and needs to be factored out
         # TODO : to a single place
@@ -564,7 +546,7 @@ class BaseContext(tengine.Context):
         # tokens uppercase.
         transform = {}
         for token in _valid_tokens:
-            transform[token] = str.upper
+            transform[token] = lambda spec, string: str.upper(string)
 
         for x in env:
             # Ensure all the tokens are valid in this context
diff --git a/lib/spack/spack/modules/dotkit.py b/lib/spack/spack/modules/dotkit.py
index e1374292d6..156a267b4f 100644
--- a/lib/spack/spack/modules/dotkit.py
+++ b/lib/spack/spack/modules/dotkit.py
@@ -1,35 +1,17 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """This module implements the classes necessary to generate dotkit modules."""
 import os.path
 
+import spack.config
 from .common import BaseConfiguration, BaseFileLayout
-from .common import BaseContext, BaseModuleFileWriter, configuration
+from .common import BaseContext, BaseModuleFileWriter
 
 #: Dotkit specific part of the configuration
-configuration = configuration.get('dotkit', {})
+configuration = spack.config.get('modules:dotkit', {})
 
 #: Caches the configuration {spec_hash: configuration}
 configuration_registry = {}
diff --git a/lib/spack/spack/modules/lmod.py b/lib/spack/spack/modules/lmod.py
index db221b8da3..ffea55184f 100644
--- a/lib/spack/spack/modules/lmod.py
+++ b/lib/spack/spack/modules/lmod.py
@@ -1,42 +1,25 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 import os.path
+
 import llnl.util.lang as lang
+import itertools
+import collections
+
+import spack.config
 import spack.compilers
 import spack.spec
 import spack.error
-import itertools
-import collections
 import spack.tengine as tengine
 
 from .common import BaseConfiguration, BaseFileLayout
-from .common import BaseContext, BaseModuleFileWriter, configuration
+from .common import BaseContext, BaseModuleFileWriter
 
-#: LMOD specific part of the configuration
-configuration = configuration.get('lmod', {})
+#: TCL specific part of the configuration
+configuration = spack.config.get('modules:lmod', {})
 
 #: Caches the configuration {spec_hash: configuration}
 configuration_registry = {}
@@ -63,6 +46,46 @@ def make_context(spec):
     return LmodContext(conf)
 
 
+def guess_core_compilers(store=False):
+    """Guesses the list of core compilers installed in the system.
+
+    Args:
+        store (bool): if True writes the core compilers to the
+            modules.yaml configuration file
+
+    Returns:
+        List of core compilers, if found, or None
+    """
+    core_compilers = []
+    for compiler_config in spack.compilers.all_compilers_config():
+        try:
+            compiler = compiler_config['compiler']
+            # A compiler is considered to be a core compiler if any of the
+            # C, C++ or Fortran compilers reside in a system directory
+            is_system_compiler = any(
+                os.path.dirname(x) in spack.util.environment.system_dirs
+                for x in compiler['paths'].values() if x is not None
+            )
+            if is_system_compiler:
+                core_compilers.append(str(compiler['spec']))
+        except (KeyError, TypeError, AttributeError):
+            continue
+
+    if store and core_compilers:
+        # If we asked to store core compilers, update the entry
+        # in the default modify scope (i.e. within the directory hierarchy
+        # of Spack itself)
+        modules_cfg = spack.config.get(
+            'modules', scope=spack.config.default_modify_scope()
+        )
+        modules_cfg.setdefault('lmod', {})['core_compilers'] = core_compilers
+        spack.config.set(
+            'modules', modules_cfg, scope=spack.config.default_modify_scope()
+        )
+
+    return core_compilers or None
+
+
 class LmodConfiguration(BaseConfiguration):
     """Configuration class for lmod module files."""
 
@@ -75,12 +98,12 @@ class LmodConfiguration(BaseConfiguration):
                 specified in the configuration file or the sequence
                 is empty
         """
-        value = configuration.get('core_compilers')
-        if value is None:
-            msg = "'core_compilers' key not found in configuration file"
-            raise CoreCompilersNotFoundError(msg)
+        value = configuration.get(
+            'core_compilers'
+        ) or guess_core_compilers(store=True)
+
         if not value:
-            msg = "'core_compilers' list cannot be empty"
+            msg = 'the key "core_compilers" must be set in modules.yaml'
             raise CoreCompilersNotFoundError(msg)
         return value
 
diff --git a/lib/spack/spack/modules/tcl.py b/lib/spack/spack/modules/tcl.py
index e3085f5d79..bec4e27d4a 100644
--- a/lib/spack/spack/modules/tcl.py
+++ b/lib/spack/spack/modules/tcl.py
@@ -1,41 +1,23 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """This module implements the classes necessary to generate TCL
 non-hierarchical modules.
 """
 import os.path
 import string
-import spack.tengine as tengine
 
 import llnl.util.tty as tty
 
+import spack.config
+import spack.tengine as tengine
 from .common import BaseConfiguration, BaseFileLayout
-from .common import BaseContext, BaseModuleFileWriter, configuration
+from .common import BaseContext, BaseModuleFileWriter
 
 #: TCL specific part of the configuration
-configuration = configuration.get('tcl', {})
+configuration = spack.config.get('modules:tcl', {})
 
 #: Caches the configuration {spec_hash: configuration}
 configuration_registry = {}
diff --git a/lib/spack/spack/multimethod.py b/lib/spack/spack/multimethod.py
index 78d547a69a..a66abe7bf7 100644
--- a/lib/spack/spack/multimethod.py
+++ b/lib/spack/spack/multimethod.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """This module contains utilities for using multi-methods in
 spack. You can think of multi-methods like overloaded methods --
 they're methods with the same name, and we need to select a version
diff --git a/lib/spack/spack/operating_systems/__init__.py b/lib/spack/spack/operating_systems/__init__.py
index 8922701e9f..4f442db458 100644
--- a/lib/spack/spack/operating_systems/__init__.py
+++ b/lib/spack/spack/operating_systems/__init__.py
@@ -1,24 +1,4 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
diff --git a/lib/spack/spack/operating_systems/cnk.py b/lib/spack/spack/operating_systems/cnk.py
index 008e5fc33b..aca4e869f4 100644
--- a/lib/spack/spack/operating_systems/cnk.py
+++ b/lib/spack/spack/operating_systems/cnk.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack.architecture import OperatingSystem
 
 
diff --git a/lib/spack/spack/operating_systems/cnl.py b/lib/spack/spack/operating_systems/cnl.py
index d64e4d06dc..d0d4e037be 100644
--- a/lib/spack/spack/operating_systems/cnl.py
+++ b/lib/spack/spack/operating_systems/cnl.py
@@ -1,35 +1,14 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import re
 
 import llnl.util.tty as tty
+import llnl.util.multiproc as mp
 
-import spack.spec
-import spack.compilers
 from spack.architecture import OperatingSystem
-from spack.util.multiproc import parmap
 from spack.util.module_cmd import get_module_cmd
 
 
@@ -42,16 +21,27 @@ class Cnl(OperatingSystem):
     """
 
     def __init__(self):
-        name = 'CNL'
-        version = '10'
+        name = 'cnl'
+        version = self._detect_crayos_version()
         super(Cnl, self).__init__(name, version)
 
     def __str__(self):
-        return self.name
+        return self.name + str(self.version)
+
+    def _detect_crayos_version(self):
+        modulecmd = get_module_cmd()
+        output = modulecmd("avail", "PrgEnv-", output=str, error=str)
+        matches = re.findall(r'PrgEnv-\w+/(\d+).\d+.\d+', output)
+        major_versions = set(matches)
+        latest_version = max(major_versions)
+        return latest_version
 
     def find_compilers(self, *paths):
+        # function-local so that cnl doesn't depend on spack.config
+        import spack.compilers
+
         types = spack.compilers.all_compiler_types()
-        compiler_lists = parmap(
+        compiler_lists = mp.parmap(
             lambda cmp_cls: self.find_compiler(cmp_cls, *paths), types)
 
         # ensure all the version calls we made are cached in the parent
@@ -60,6 +50,9 @@ class Cnl(OperatingSystem):
         return clist
 
     def find_compiler(self, cmp_cls, *paths):
+        # function-local so that cnl doesn't depend on spack.config
+        import spack.spec
+
         compilers = []
         if cmp_cls.PrgEnv:
             if not cmp_cls.PrgEnv_compiler:
diff --git a/lib/spack/spack/operating_systems/cray_frontend.py b/lib/spack/spack/operating_systems/cray_frontend.py
index d761a758ef..116a4ec802 100644
--- a/lib/spack/spack/operating_systems/cray_frontend.py
+++ b/lib/spack/spack/operating_systems/cray_frontend.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 
 from spack.operating_systems.linux_distro import LinuxDistro
@@ -61,7 +42,7 @@ class CrayFrontend(LinuxDistro):
             # 'intel', 'cce', 'gcc', etc.) will also be unloaded since they are
             # specified as prerequisites in the PrgEnv-* modulefiles.
             modulecmd = get_module_cmd()
-            exec (compile(
+            exec(compile(
                 modulecmd('unload', prg_env, output=str, error=os.devnull),
                 '<string>', 'exec'))
 
diff --git a/lib/spack/spack/operating_systems/linux_distro.py b/lib/spack/spack/operating_systems/linux_distro.py
index 723b4d5447..a12e08671e 100644
--- a/lib/spack/spack/operating_systems/linux_distro.py
+++ b/lib/spack/spack/operating_systems/linux_distro.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import re
 from spack.architecture import OperatingSystem
 
diff --git a/lib/spack/spack/operating_systems/mac_os.py b/lib/spack/spack/operating_systems/mac_os.py
index a5577fa39d..d50cbf32be 100644
--- a/lib/spack/spack/operating_systems/mac_os.py
+++ b/lib/spack/spack/operating_systems/mac_os.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import platform as py_platform
 
 from spack.architecture import OperatingSystem
@@ -29,7 +10,7 @@ from spack.version import Version
 
 
 # FIXME: store versions inside OperatingSystem as a Version instead of string
-def macOS_version():
+def macos_version():
     """temporary workaround to return a macOS version as a Version object
     """
     return Version('.'.join(py_platform.mac_ver()[0].split('.')[:2]))
@@ -54,7 +35,8 @@ class MacOs(OperatingSystem):
                         "10.10": "yosemite",
                         "10.11": "elcapitan",
                         "10.12": "sierra",
-                        "10.13": "highsierra"}
+                        "10.13": "highsierra",
+                        "10.14": "mojave"}
 
         mac_ver = '.'.join(py_platform.mac_ver()[0].split('.')[:2])
         name = mac_releases.get(mac_ver, "macos")
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index 18091f2e69..279ed89d04 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -1,41 +1,21 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-"""
-This is where most of the action happens in Spack.
-See the Package docs for detailed instructions on how the class works
-and on how to write your own packages.
-
-The spack package structure is based strongly on Homebrew
-(http://wiki.github.com/mxcl/homebrew/), mainly because
-Homebrew makes it very easy to create packages.  For a complete
-rundown on spack and how it differs from homebrew, look at the
-README.
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+"""This is where most of the action happens in Spack.
+
+The spack package class structure is based strongly on Homebrew
+(http://brew.sh/), mainly because Homebrew makes it very easy to create
+packages.
+
 """
+import base64
 import contextlib
 import copy
 import functools
+import glob
+import hashlib
 import inspect
 import os
 import re
@@ -46,33 +26,40 @@ import time
 from six import StringIO
 from six import string_types
 from six import with_metaclass
+from ordereddict_backport import OrderedDict
 
 import llnl.util.tty as tty
-import spack
+
+import spack.config
+import spack.paths
 import spack.store
 import spack.compilers
 import spack.directives
+import spack.directory_layout
 import spack.error
 import spack.fetch_strategy as fs
 import spack.hooks
 import spack.mirror
-import spack.repository
+import spack.mixins
+import spack.repo
 import spack.url
 import spack.util.web
 import spack.multimethod
 import spack.binary_distribution as binary_distribution
 
-from llnl.util.filesystem import mkdirp, join_path, touch, ancestor
+from llnl.util.filesystem import mkdirp, touch, chgrp
 from llnl.util.filesystem import working_dir, install_tree, install
 from llnl.util.lang import memoized
 from llnl.util.link_tree import LinkTree
 from llnl.util.tty.log import log_output
 from llnl.util.tty.color import colorize
-from spack import directory_layout
+from spack.filesystem_view import YamlFilesystemView
 from spack.util.executable import which
 from spack.stage import Stage, ResourceStage, StageComposite
 from spack.util.environment import dump_environment
+from spack.util.package_hash import package_hash
 from spack.version import Version
+from spack.package_prefs import get_package_dir_permissions, get_package_group
 
 """Allowed URL schemes for spack packages."""
 _ALLOWED_URL_SCHEMES = ["http", "https", "ftp", "file", "git"]
@@ -141,7 +128,10 @@ class InstallPhase(object):
             return other
 
 
-class PackageMeta(spack.directives.DirectiveMetaMixin):
+class PackageMeta(
+    spack.directives.DirectiveMeta,
+    spack.mixins.PackageMixinsMeta
+):
     """Conveniently transforms attributes to permit extensible phases
 
     Iterates over the attribute 'phases' and creates / updates private
@@ -152,7 +142,7 @@ class PackageMeta(spack.directives.DirectiveMetaMixin):
     _InstallPhase_run_before = {}
     _InstallPhase_run_after = {}
 
-    def __new__(mcs, name, bases, attr_dict):
+    def __new__(cls, name, bases, attr_dict):
 
         if 'phases' in attr_dict:
             # Turn the strings in 'phases' into InstallPhase instances
@@ -165,7 +155,7 @@ class PackageMeta(spack.directives.DirectiveMetaMixin):
         def _flush_callbacks(check_name):
             # Name of the attribute I am going to check it exists
             attr_name = PackageMeta.phase_fmt.format(check_name)
-            checks = getattr(mcs, attr_name)
+            checks = getattr(cls, attr_name)
             if checks:
                 for phase_name, funcs in checks.items():
                     try:
@@ -182,18 +172,21 @@ class PackageMeta(spack.directives.DirectiveMetaMixin):
                                 PackageMeta.phase_fmt.format(phase_name),
                                 None
                             )
+                            if phase is not None:
+                                break
+
                         attr_dict[PackageMeta.phase_fmt.format(
                             phase_name)] = phase.copy()
                         phase = attr_dict[
                             PackageMeta.phase_fmt.format(phase_name)]
                     getattr(phase, check_name).extend(funcs)
                 # Clear the attribute for the next class
-                setattr(mcs, attr_name, {})
+                setattr(cls, attr_name, {})
 
         _flush_callbacks('run_before')
         _flush_callbacks('run_after')
 
-        return super(PackageMeta, mcs).__new__(mcs, name, bases, attr_dict)
+        return super(PackageMeta, cls).__new__(cls, name, bases, attr_dict)
 
     @staticmethod
     def register_callback(check_type, *phases):
@@ -247,215 +240,91 @@ def on_package_attributes(**attr_dict):
     return _execute_under_condition
 
 
-class PackageBase(with_metaclass(PackageMeta, object)):
-    """This is the superclass for all spack packages.
-
-    ***The Package class***
-
-    Package is where the bulk of the work of installing packages is done.
-
-    A package defines how to fetch, verfiy (via, e.g., md5), build, and
-    install a piece of software.  A Package also defines what other
-    packages it depends on, so that dependencies can be installed along
-    with the package itself.  Packages are written in pure python.
-
-    Packages are all submodules of spack.packages.  If spack is installed
-    in ``$prefix``, all of its python files are in ``$prefix/lib/spack``.
-    Most of them are in the spack module, so all the packages live in
-    ``$prefix/lib/spack/spack/packages``.
-
-    All you have to do to create a package is make a new subclass of Package
-    in this directory.  Spack automatically scans the python files there
-    and figures out which one to import when you invoke it.
-
-    **An example package**
-
-    Let's look at the cmake package to start with.  This package lives in
-    ``$prefix/var/spack/repos/builtin/packages/cmake/package.py``:
-
-    .. code-block:: python
-
-       from spack import *
-       class Cmake(Package):
-           homepage  = 'https://www.cmake.org'
-           url       = 'http://www.cmake.org/files/v2.8/cmake-2.8.10.2.tar.gz'
-           md5       = '097278785da7182ec0aea8769d06860c'
-
-           def install(self, spec, prefix):
-               configure('--prefix=%s'   % prefix,
-                         '--parallel=%s' % make_jobs)
-               make()
-               make('install')
-
-    **Naming conventions**
-
-    There are two names you should care about:
-
-    1. The module name, ``cmake``.
-
-       * User will refers to this name, e.g. 'spack install cmake'.
-       * It can include ``_``, ``-``, and numbers (it can even start with a
-         number).
-
-    2. The class name, "Cmake".  This is formed by converting `-` or
-       ``_`` in the module name to camel case.  If the name starts with
-       a number, we prefix the class name with ``_``. Examples:
-
-          ===========  ==========
-          Module Name  Class Name
-          ===========  ==========
-          foo_bar      FooBar
-          docbook-xml  DocbookXml
-          FooBar       Foobar
-          3proxy       _3proxy
-          ===========  ==========
-
-        The class name is what spack looks for when it loads a package module.
-
-    **Required Attributes**
-
-    Aside from proper naming, here is the bare minimum set of things you
-    need when you make a package:
-
-    homepage:
-        informational URL, so that users know what they're
-        installing.
-
-    url or url_for_version(self, version):
-      If url, then the URL of the source archive that spack will fetch.
-      If url_for_version(), then a method returning the URL required
-      to fetch a particular version.
-
-    install():
-        This function tells spack how to build and install the
-        software it downloaded.
-
-    **Optional Attributes**
-
-    You can also optionally add these attributes, if needed:
-
-        list_url:
-            Webpage to scrape for available version strings. Default is the
-            directory containing the tarball; use this if the default isn't
-            correct so that invoking 'spack versions' will work for this
-            package.
-
-        url_version(self, version):
-            When spack downloads packages at particular versions, it just
-            converts version to string with str(version).  Override this if
-            your package needs special version formatting in its URL.  boost
-            is an example of a package that needs this.
-
-    ***Creating Packages***
-
-    As a package creator, you can probably ignore most of the preceding
-    information, because you can use the 'spack create' command to do it
-    all automatically.
-
-    You as the package creator generally only have to worry about writing
-    your install function and specifying dependencies.
-
-    **spack create**
-
-    Most software comes in nicely packaged tarballs, like this one
-
-    http://www.cmake.org/files/v2.8/cmake-2.8.10.2.tar.gz
-
-    Taking a page from homebrew, spack deduces pretty much everything it
-    needs to know from the URL above.  If you simply type this::
-
-        spack create http://www.cmake.org/files/v2.8/cmake-2.8.10.2.tar.gz
-
-    Spack will download the tarball, generate an md5 hash, figure out the
-    version and the name of the package from the URL, and create a new
-    package file for you with all the names and attributes set correctly.
+class PackageViewMixin(object):
+    """This collects all functionality related to adding installed Spack
+    package to views. Packages can customize how they are added to views by
+    overriding these functions.
+    """
+    def view_source(self):
+        """The source root directory that will be added to the view: files are
+        added such that their path relative to the view destination matches
+        their path relative to the view source.
+        """
+        return self.spec.prefix
 
-    Once this skeleton code is generated, spack pops up the new package in
-    your $EDITOR so that you can modify the parts that need changes.
+    def view_destination(self, view):
+        """The target root directory: each file is added relative to this
+        directory.
+        """
+        return view.root
 
-    **Dependencies**
+    def view_file_conflicts(self, view, merge_map):
+        """Report any files which prevent adding this package to the view. The
+        default implementation looks for any files which already exist.
+        Alternative implementations may allow some of the files to exist in
+        the view (in this case they would be omitted from the results).
+        """
+        return set(dst for dst in merge_map.values() if os.path.exists(dst))
 
-    If your package requires another in order to build, you can specify that
-    like this:
+    def add_files_to_view(self, view, merge_map):
+        """Given a map of package files to destination paths in the view, add
+        the files to the view. By default this adds all files. Alternative
+        implementations may skip some files, for example if other packages
+        linked into the view already include the file.
+        """
+        for src, dst in merge_map.items():
+            if not os.path.exists(dst):
+                view.link(src, dst)
+
+    def remove_files_from_view(self, view, merge_map):
+        """Given a map of package files to files currently linked in the view,
+        remove the files from the view. The default implementation removes all
+        files. Alternative implementations may not remove all files. For
+        example if two packages include the same file, it should only be
+        removed when both packages are removed.
+        """
+        for src, dst in merge_map.items():
+            view.remove_file(src, dst)
 
-    .. code-block:: python
 
-       class Stackwalker(Package):
-           ...
-           depends_on("libdwarf")
-           ...
-
-    This tells spack that before it builds stackwalker, it needs to build
-    the libdwarf package as well.  Note that this is the module name, not
-    the class name (The class name is really only used by spack to find
-    your package).
-
-    Spack will download an install each dependency before it installs your
-    package.  In addtion, it will add -L, -I, and rpath arguments to your
-    compiler and linker for each dependency.  In most cases, this allows you
-    to avoid specifying any dependencies in your configure or cmake line;
-    you can just run configure or cmake without any additional arguments and
-    it will find the dependencies automatically.
-
-    **The Install Function**
-
-    The install function is designed so that someone not too terribly familiar
-    with Python could write a package installer.  For example, we put a number
-    of commands in install scope that you can use almost like shell commands.
-    These include make, configure, cmake, rm, rmtree, mkdir, mkdirp, and
-    others.
-
-    You can see above in the cmake script that these commands are used to run
-    configure and make almost like they're used on the command line.  The
-    only difference is that they are python function calls and not shell
-    commands.
-
-    It may be puzzling to you where the commands and functions in install live.
-    They are NOT instance variables on the class; this would require us to
-    type 'self.' all the time and it makes the install code unnecessarily long.
-    Rather, spack puts these commands and variables in *module* scope for your
-    Package subclass.  Since each package has its own module, this doesn't
-    pollute other namespaces, and it allows you to more easily implement an
-    install function.
-
-    For a full list of commands and variables available in module scope, see
-    the add_commands_to_module() function in this class. This is where most
-    of them are created and set on the module.
-
-    **Parallel Builds**
-
-    By default, Spack will run make in parallel when you run make() in your
-    install function.  Spack figures out how many cores are available on
-    your system and runs make with -j<cores>.  If you do not want this
-    behavior, you can explicitly mark a package not to use parallel make:
+class PackageBase(with_metaclass(PackageMeta, PackageViewMixin, object)):
+    """This is the superclass for all spack packages.
 
-    .. code-block:: python
+    ***The Package class***
 
-       class SomePackage(Package):
-           ...
-           parallel = False
-           ...
+    A package defines how to fetch, verify (via, e.g., sha256), build,
+    and install a piece of software.  A Package also defines what other
+    packages it depends on, so that dependencies can be installed along
+    with the package itself.  Packages are written in pure python by
+    users of Spack.
 
-    This changes the default behavior so that make is sequential.  If you still
-    want to build some parts in parallel, you can do this in your install
-    function:
+    There are two main parts of a Spack package:
 
-    .. code-block:: python
+      1. **The package class**.  Classes contain ``directives``, which are
+         special functions, that add metadata (versions, patches,
+         dependencies, and other information) to packages (see
+         ``directives.py``). Directives provide the constraints that are
+         used as input to the concretizer.
 
-       make(parallel=True)
+      2. **Package instances**. Once instantiated, a package is
+         essentially an installer for a particular piece of
+         software. Spack calls methods like ``do_install()`` on the
+         ``Package`` object, and it uses those to drive user-implemented
+         methods like ``patch()``, ``install()``, and other build steps.
+         To install software, An instantiated package needs a *concrete*
+         spec, which guides the behavior of the various install methods.
 
-    Likewise, if you do not supply parallel = True in your Package, you can
-    keep the default parallel behavior and run make like this when you want a
-    sequential build:
+    Packages are imported from repos (see ``repo.py``).
 
-    .. code-block:: python
+    **Package DSL**
 
-       make(parallel=False)
+    Look in ``lib/spack/docs`` or check https://spack.readthedocs.io for
+    the full documentation of the package domain-specific language.  That
+    used to be partially documented here, but as it grew, the docs here
+    became increasingly out of date.
 
     **Package Lifecycle**
 
-    This section is really only for developers of new spack commands.
-
     A package's lifecycle over a run of Spack looks something like this:
 
     .. code-block:: python
@@ -481,8 +350,15 @@ class PackageBase(with_metaclass(PackageMeta, object)):
     package writers to override, and doing so may break the functionality
     of the Package class.
 
-    Package creators override functions like install() (all of them do this),
-    clean() (some of them do this), and others to provide custom behavior.
+    Package creators have a lot of freedom, and they could technically
+    override anything in this class.  That is not usually required.
+
+    For most use cases.  Package creators typically just add attributes
+    like ``url`` and ``homepage``, or functions like ``install()``.
+    There are many custom ``Package`` subclasses in the
+    ``spack.build_systems`` package that make things even easier for
+    specific build systems.
+
     """
     #
     # These are default values for instance variables.
@@ -492,7 +368,7 @@ class PackageBase(with_metaclass(PackageMeta, object)):
     parallel = True
 
     #: # jobs to use for parallel make. If set, overrides default of ncpus.
-    make_jobs = spack.build_jobs
+    make_jobs = None
 
     #: By default do not run tests within package's install()
     run_tests = False
@@ -518,6 +394,12 @@ class PackageBase(with_metaclass(PackageMeta, object)):
     #: directories, sanity checks will fail.
     sanity_check_is_dir = []
 
+    #: List of glob expressions. Each expression must either be
+    #: absolute or relative to the package source path.
+    #: Matching artifacts found at the end of the build process will
+    #: be copied in the same directory tree as build.env and build.out.
+    archive_files = []
+
     #
     # Set default licensing information
     #
@@ -556,6 +438,10 @@ class PackageBase(with_metaclass(PackageMeta, object)):
     #: Do not include @ here in order not to unnecessarily ping the users.
     maintainers = []
 
+    #: List of attributes which affect do not affect a package's content.
+    metadata_attrs = ['homepage', 'url', 'list_url', 'extendable', 'parallel',
+                      'make_jobs']
+
     def __init__(self, spec):
         # this determines how the package should be built.
         self.spec = spec
@@ -584,24 +470,6 @@ class PackageBase(with_metaclass(PackageMeta, object)):
         except ValueError as e:
             raise ValueError("In package %s: %s" % (self.name, e.message))
 
-        # stage used to build this package.
-        self._stage = None
-
-        # Init fetch strategy and url to None
-        self._fetcher = None
-        self.url = getattr(self.__class__, 'url', None)
-
-        # Fix up self.url if this package fetches with a URLFetchStrategy.
-        # This makes self.url behave sanely.
-        if self.spec.versions.concrete:
-            # TODO: this is a really roundabout way of determining the type
-            # TODO: of fetch to do. figure out a more sane fetch
-            # TODO: strategy/package init order (right now it's conflated with
-            # TODO: stage, package, and the tests make assumptions)
-            f = fs.for_package_version(self, self.version)
-            if isinstance(f, fs.URLFetchStrategy):
-                self.url = self.url_for_version(self.spec.version)
-
         # Set a default list URL (place to find available versions)
         if not hasattr(self, 'list_url'):
             self.list_url = None
@@ -609,40 +477,53 @@ class PackageBase(with_metaclass(PackageMeta, object)):
         if not hasattr(self, 'list_depth'):
             self.list_depth = 0
 
-        # Set up some internal variables for timing.
+        # init internal variables
+        self._stage = None
+        self._fetcher = None
+
+        # Set up timing variables
         self._fetch_time = 0.0
         self._total_time = 0.0
 
         if self.is_extension:
             spack.repo.get(self.extendee_spec)._check_extendable()
 
-        self.extra_args = {}
+        super(PackageBase, self).__init__()
 
-    def possible_dependencies(self, transitive=True, visited=None):
-        """Return set of possible transitive dependencies of this package.
+    def possible_dependencies(
+            self, transitive=True, expand_virtuals=True, visited=None):
+        """Return set of possible dependencies of this package.
+
+        Note: the set returned *includes* the package itself.
 
         Args:
-            transitive (bool): include all transitive dependencies if True,
+            transitive (bool): return all transitive dependencies if True,
                 only direct dependencies if False.
+            expand_virtuals (bool): expand virtual dependencies into all
+                possible implementations.
+            visited (set): set of names of dependencies visited so far.
         """
         if visited is None:
-            visited = set()
-
-        visited.add(self.name)
-        for name in self.dependencies:
-            spec = spack.spec.Spec(name)
+            visited = set([self.name])
 
-            if not spec.virtual:
-                visited.add(name)
-                if transitive:
-                    pkg = spack.repo.get(name)
-                    pkg.possible_dependencies(transitive, visited)
+        for i, name in enumerate(self.dependencies):
+            if spack.repo.path.is_virtual(name):
+                if expand_virtuals:
+                    providers = spack.repo.path.providers_for(name)
+                    dep_names = [spec.name for spec in providers]
+                else:
+                    visited.add(name)
+                    continue
             else:
-                for provider in spack.repo.providers_for(spec):
-                    visited.add(provider.name)
+                dep_names = [name]
+
+            for dep_name in dep_names:
+                if dep_name not in visited:
+                    visited.add(dep_name)
                     if transitive:
-                        pkg = spack.repo.get(provider.name)
-                        pkg.possible_dependencies(transitive, visited)
+                        pkg = spack.repo.get(dep_name)
+                        pkg.possible_dependencies(
+                            transitive, expand_virtuals, visited)
 
         return visited
 
@@ -655,8 +536,7 @@ class PackageBase(with_metaclass(PackageMeta, object)):
     def global_license_dir(self):
         """Returns the directory where global license files for all
            packages are stored."""
-        spack_root = ancestor(__file__, 4)
-        return join_path(spack_root, 'etc', 'spack', 'licenses')
+        return os.path.join(spack.paths.prefix, 'etc', 'spack', 'licenses')
 
     @property
     def global_license_file(self):
@@ -664,8 +544,8 @@ class PackageBase(with_metaclass(PackageMeta, object)):
            particular package should be stored."""
         if not self.license_files:
             return
-        return join_path(self.global_license_dir, self.name,
-                         os.path.basename(self.license_files[0]))
+        return os.path.join(self.global_license_dir, self.name,
+                            os.path.basename(self.license_files[0]))
 
     @property
     def version(self):
@@ -675,33 +555,46 @@ class PackageBase(with_metaclass(PackageMeta, object)):
 
     @memoized
     def version_urls(self):
-        """Return a list of URLs for different versions of this
-           package, sorted by version.  A version's URL only appears
-           in this list if it has an explicitly defined URL."""
-        version_urls = {}
-        for v in sorted(self.versions):
-            args = self.versions[v]
+        """OrderedDict of explicitly defined URLs for versions of this package.
+
+        Return:
+           An OrderedDict (version -> URL) different versions of this
+           package, sorted by version.
+
+        A version's URL only appears in the result if it has an an
+        explicitly defined ``url`` argument. So, this list may be empty
+        if a package only defines ``url`` at the top level.
+        """
+        version_urls = OrderedDict()
+        for v, args in sorted(self.versions.items()):
             if 'url' in args:
                 version_urls[v] = args['url']
         return version_urls
 
     def nearest_url(self, version):
-        """Finds the URL for the next lowest version with a URL.
-           If there is no lower version with a URL, uses the
-           package url property. If that isn't there, uses a
-           *higher* URL, and if that isn't there raises an error.
+        """Finds the URL with the "closest" version to ``version``.
+
+        This uses the following precedence order:
+
+          1. Find the next lowest or equal version with a URL.
+          2. If no lower URL, return the next *higher* URL.
+          3. If no higher URL, return None.
+
         """
         version_urls = self.version_urls()
-        url = getattr(self.__class__, 'url', None)
 
-        for v in version_urls:
-            if v > version and url:
-                break
-            if version_urls[v]:
-                url = version_urls[v]
-        return url
+        if version in version_urls:
+            return version_urls[version]
+
+        last_url = None
+        for v, u in self.version_urls().items():
+            if v > version:
+                if last_url:
+                    return last_url
+            last_url = u
+
+        return last_url
 
-    # TODO: move this out of here and into some URL extrapolation module?
     def url_for_version(self, version):
         """Returns a URL from which the specified version of this package
         may be downloaded.
@@ -714,18 +607,24 @@ class PackageBase(with_metaclass(PackageMeta, object)):
         if not isinstance(version, Version):
             version = Version(version)
 
-        cls = self.__class__
-        if not (hasattr(cls, 'url') or self.version_urls()):
-            raise NoURLError(cls)
-
         # If we have a specific URL for this version, don't extrapolate.
         version_urls = self.version_urls()
         if version in version_urls:
             return version_urls[version]
 
-        # If we have no idea, try to substitute the version.
+        # If no specific URL, use the default, class-level URL
+        default_url = getattr(self, 'url', None)
+
+        # if no exact match AND no class-level default, use the nearest URL
+        if not default_url:
+            default_url = self.nearest_url(version)
+
+            # if there are NO URLs to go by, then we can't do anything
+            if not default_url:
+                raise NoURLError(self.__class__)
+
         return spack.url.substitute_version(
-            self.nearest_url(version), self.url_version(version))
+            default_url, self.url_version(version))
 
     def _make_resource_stage(self, root_stage, fetcher, resource):
         resource_stage_folder = self._resource_stage(resource)
@@ -794,11 +693,17 @@ class PackageBase(with_metaclass(PackageMeta, object)):
 
     @property
     def env_path(self):
-        return os.path.join(self.stage.source_path, 'spack-build.env')
+        if self.stage.source_path is None:
+            return None
+        else:
+            return os.path.join(self.stage.source_path, 'spack-build.env')
 
     @property
     def log_path(self):
-        return os.path.join(self.stage.source_path, 'spack-build.out')
+        if self.stage.source_path is None:
+            return None
+        else:
+            return os.path.join(self.stage.source_path, 'spack-build.out')
 
     def _make_fetcher(self):
         # Construct a composite fetcher that always contains at least
@@ -903,13 +808,12 @@ class PackageBase(with_metaclass(PackageMeta, object)):
         s = self.extendee_spec
         return s and spec.satisfies(s)
 
-    def is_activated(self, extensions_layout=None):
+    def is_activated(self, view):
         """Return True if package is activated."""
         if not self.is_extension:
             raise ValueError(
-                "is_extension called on package that is not an extension.")
-        if extensions_layout is None:
-            extensions_layout = spack.store.extensions
+                "is_activated called on package that is not an extension.")
+        extensions_layout = view.extensions_layout
         exts = extensions_layout.extension_map(self.extendee_spec)
         return (self.name in exts) and (exts[self.name] == self.spec)
 
@@ -917,11 +821,30 @@ class PackageBase(with_metaclass(PackageMeta, object)):
         """
         True if this package provides a virtual package with the specified name
         """
-        return any(s.name == vpkg_name for s in self.provided)
+        return any(
+            any(self.spec.satisfies(c) for c in constraints)
+            for s, constraints in self.provided.items() if s.name == vpkg_name
+        )
 
     @property
     def installed(self):
-        return os.path.isdir(self.prefix)
+        """Installation status of a package.
+
+        Returns:
+            True if the package has been installed, False otherwise.
+        """
+        has_prefix = os.path.isdir(self.prefix)
+        try:
+            # If the spec is in the DB, check the installed
+            # attribute of the record
+            rec = spack.store.db.get_record(self.spec)
+            db_says_installed = rec.installed
+        except KeyError:
+            # If the spec is not in the DB, the method
+            #  above raises a Key error
+            db_says_installed = False
+
+        return has_prefix and db_says_installed
 
     @property
     def prefix(self):
@@ -971,7 +894,8 @@ class PackageBase(with_metaclass(PackageMeta, object)):
             raise ValueError("Can only fetch concrete packages.")
 
         start_time = time.time()
-        if spack.do_checksum and self.version not in self.versions:
+        checksum = spack.config.get('config:checksum')
+        if checksum and self.version not in self.versions:
             tty.warn("There is no checksum on file to fetch %s safely." %
                      self.spec.cformat('$_$@'))
 
@@ -993,7 +917,7 @@ class PackageBase(with_metaclass(PackageMeta, object)):
         self.stage.fetch(mirror_only)
         self._fetch_time = time.time() - start_time
 
-        if spack.do_checksum and self.version in self.versions:
+        if checksum and self.version in self.versions:
             self.stage.check()
 
         self.stage.cache_local()
@@ -1065,9 +989,9 @@ class PackageBase(with_metaclass(PackageMeta, object)):
         # Construct paths to special files in the archive dir used to
         # keep track of whether patches were successfully applied.
         archive_dir = self.stage.source_path
-        good_file = join_path(archive_dir, '.spack_patched')
-        no_patches_file = join_path(archive_dir, '.spack_no_patches')
-        bad_file = join_path(archive_dir, '.spack_patch_failed')
+        good_file = os.path.join(archive_dir, '.spack_patched')
+        no_patches_file = os.path.join(archive_dir, '.spack_no_patches')
+        bad_file = os.path.join(archive_dir, '.spack_patch_failed')
 
         # If we encounter an archive that failed to patch, restage it
         # so that we can apply all the patches again.
@@ -1129,6 +1053,34 @@ class PackageBase(with_metaclass(PackageMeta, object)):
         else:
             touch(no_patches_file)
 
+    def content_hash(self, content=None):
+        """Create a hash based on the sources and logic used to build the
+        package. This includes the contents of all applied patches and the
+        contents of applicable functions in the package subclass."""
+        if not self.spec.concrete:
+            err_msg = ("Cannot invoke content_hash on a package"
+                       " if the associated spec is not concrete")
+            raise spack.error.SpackError(err_msg)
+
+        hash_content = list()
+        source_id = fs.for_package_version(self, self.version).source_id()
+        if not source_id:
+            # TODO? in cases where a digest or source_id isn't available,
+            # should this attempt to download the source and set one? This
+            # probably only happens for source repositories which are
+            # referenced by branch name rather than tag or commit ID.
+            message = 'Missing a source id for {s.name}@{s.version}'
+            tty.warn(message.format(s=self))
+            hash_content.append(''.encode('utf-8'))
+        else:
+            hash_content.append(source_id.encode('utf-8'))
+        hash_content.extend(':'.join((p.sha256, str(p.level))).encode('utf-8')
+                            for p in self.spec.patches)
+        hash_content.append(package_hash(self.spec, content))
+        return base64.b32encode(
+            hashlib.sha256(bytes().join(
+                sorted(hash_content))).digest()).lower()
+
     @property
     def namespace(self):
         namespace, dot, module = self.__module__.rpartition('.')
@@ -1138,65 +1090,139 @@ class PackageBase(with_metaclass(PackageMeta, object)):
         """Make a fake install directory containing fake executables,
         headers, and libraries."""
 
-        name = self.name
-        library_name = 'lib' + self.name
+        command = self.name
+        header = self.name
+        library = self.name
+
+        # Avoid double 'lib' for packages whose names already start with lib
+        if not self.name.startswith('lib'):
+            library = 'lib' + library
+
         dso_suffix = '.dylib' if sys.platform == 'darwin' else '.so'
         chmod = which('chmod')
 
+        # Install fake command
         mkdirp(self.prefix.bin)
-        touch(join_path(self.prefix.bin, name))
-        chmod('+x', join_path(self.prefix.bin, name))
+        touch(os.path.join(self.prefix.bin, command))
+        chmod('+x', os.path.join(self.prefix.bin, command))
 
+        # Install fake header file
         mkdirp(self.prefix.include)
-        touch(join_path(self.prefix.include, name + '.h'))
+        touch(os.path.join(self.prefix.include, header + '.h'))
 
+        # Install fake shared and static libraries
         mkdirp(self.prefix.lib)
-        touch(join_path(self.prefix.lib, library_name + dso_suffix))
-        touch(join_path(self.prefix.lib, library_name + '.a'))
+        for suffix in [dso_suffix, '.a']:
+            touch(os.path.join(self.prefix.lib, library + suffix))
 
+        # Install fake man page
         mkdirp(self.prefix.man.man1)
 
         packages_dir = spack.store.layout.build_packages_path(self.spec)
         dump_packages(self.spec, packages_dir)
 
-    def _if_make_target_execute(self, target):
-        try:
-            # Check if we have a makefile
-            file = [x for x in ('Makefile', 'makefile') if os.path.exists(x)]
-            file = file.pop()
-        except IndexError:
+    def _has_make_target(self, target):
+        """Checks to see if 'target' is a valid target in a Makefile.
+
+        Parameters:
+            target (str): the target to check for
+
+        Returns:
+            bool: True if 'target' is found, else False
+        """
+        make = inspect.getmodule(self).make
+
+        # Check if we have a Makefile
+        for makefile in ['GNUmakefile', 'Makefile', 'makefile']:
+            if os.path.exists(makefile):
+                break
+        else:
             tty.msg('No Makefile found in the build directory')
-            return
+            return False
 
-        # Check if 'target' is in the makefile
-        regex = re.compile('^' + target + ':')
-        with open(file, 'r') as f:
-            matches = [line for line in f.readlines() if regex.match(line)]
+        # Check if 'target' is a valid target.
+        #
+        # `make -n target` performs a "dry run". It prints the commands that
+        # would be run but doesn't actually run them. If the target does not
+        # exist, you will see one of the following error messages:
+        #
+        # GNU Make:
+        #     make: *** No rule to make target `test'.  Stop.
+        #           *** No rule to make target 'test'.  Stop.
+        #
+        # BSD Make:
+        #     make: don't know how to make test. Stop
+        missing_target_msgs = [
+            "No rule to make target `{0}'.  Stop.",
+            "No rule to make target '{0}'.  Stop.",
+            "don't know how to make {0}. Stop",
+        ]
+
+        kwargs = {
+            'fail_on_error': False,
+            'output': os.devnull,
+            'error': str,
+        }
+
+        stderr = make('-n', target, **kwargs)
+
+        for missing_target_msg in missing_target_msgs:
+            if missing_target_msg.format(target) in stderr:
+                tty.msg("Target '" + target + "' not found in " + makefile)
+                return False
 
-        if not matches:
-            tty.msg("Target '" + target + ":' not found in Makefile")
-            return
+        return True
 
-        # Execute target
-        inspect.getmodule(self).make(target)
+    def _if_make_target_execute(self, target, *args, **kwargs):
+        """Runs ``make target`` if 'target' is a valid target in the Makefile.
+
+        Parameters:
+            target (str): the target to potentially execute
+        """
+        if self._has_make_target(target):
+            # Execute target
+            inspect.getmodule(self).make(target, *args, **kwargs)
 
-    def _if_ninja_target_execute(self, target):
-        # Check if we have a ninja build script
+    def _has_ninja_target(self, target):
+        """Checks to see if 'target' is a valid target in a Ninja build script.
+
+        Parameters:
+            target (str): the target to check for
+
+        Returns:
+            bool: True if 'target' is found, else False
+        """
+        ninja = inspect.getmodule(self).ninja
+
+        # Check if we have a Ninja build script
         if not os.path.exists('build.ninja'):
-            tty.msg('No ninja build script found in the build directory')
-            return
+            tty.msg('No Ninja build script found in the build directory')
+            return False
 
-        # Check if 'target' is in the ninja build script
-        regex = re.compile('^build ' + target + ':')
-        with open('build.ninja', 'r') as f:
-            matches = [line for line in f.readlines() if regex.match(line)]
+        # Get a list of all targets in the Ninja build script
+        # https://ninja-build.org/manual.html#_extra_tools
+        all_targets = ninja('-t', 'targets', 'all', output=str).split('\n')
+
+        # Check if 'target' is a valid target
+        matches = [line for line in all_targets
+                   if line.startswith(target + ':')]
 
         if not matches:
-            tty.msg("Target 'build " + target + ":' not found in build.ninja")
-            return
+            tty.msg("Target '" + target + "' not found in build.ninja")
+            return False
+
+        return True
+
+    def _if_ninja_target_execute(self, target, *args, **kwargs):
+        """Runs ``ninja target`` if 'target' is a valid target in the Ninja
+        build script.
 
-        # Execute target
-        inspect.getmodule(self).ninja(target)
+        Parameters:
+            target (str): the target to potentially execute
+        """
+        if self._has_ninja_target(target):
+            # Execute target
+            inspect.getmodule(self).ninja(target, *args, **kwargs)
 
     def _get_needed_resources(self):
         resources = []
@@ -1279,8 +1305,10 @@ class PackageBase(with_metaclass(PackageMeta, object)):
         tty.msg('Installing %s from binary cache' % self.name)
         tarball = binary_distribution.download_tarball(binary_spec)
         binary_distribution.extract_tarball(
-            binary_spec, tarball, yes_to_all=False, force=False)
-        spack.store.db.add(self.spec, spack.store.layout, explicit=explicit)
+            binary_spec, tarball, allow_root=False,
+            unsigned=False, force=False)
+        spack.store.db.add(
+            self.spec, spack.store.layout, explicit=explicit)
         return True
 
     def do_install(self,
@@ -1293,6 +1321,7 @@ class PackageBase(with_metaclass(PackageMeta, object)):
                    make_jobs=None,
                    fake=False,
                    explicit=False,
+                   tests=False,
                    dirty=None,
                    **kwargs):
         """Called by commands to install a package and its dependencies.
@@ -1318,6 +1347,8 @@ class PackageBase(with_metaclass(PackageMeta, object)):
             fake (bool): Don't really build; install fake stub files instead.
             explicit (bool): True if package was explicitly installed, False
                 if package was implicitly installed (as a dependency).
+            tests (bool or list or set): False to run no tests, True to test
+                all packages, or a list of package names to run tests for some
             dirty (bool): Don't clean the build environment before installing.
             force (bool): Install again, even if already installed.
         """
@@ -1343,6 +1374,11 @@ class PackageBase(with_metaclass(PackageMeta, object)):
                 msg = '{0.name} is already installed in {0.prefix}'
                 tty.msg(msg.format(self))
                 rec = spack.store.db.get_record(self.spec)
+                # In case the stage directory has already been created,
+                # this ensures it's removed after we checked that the spec
+                # is installed
+                if keep_stage is False:
+                    self.stage.destroy()
                 return self._update_explicit_entry_in_db(rec, explicit)
 
         self._do_install_pop_kwargs(kwargs)
@@ -1361,12 +1397,13 @@ class PackageBase(with_metaclass(PackageMeta, object)):
                     skip_patch=skip_patch,
                     verbose=verbose,
                     make_jobs=make_jobs,
+                    tests=tests,
                     dirty=dirty,
                     **kwargs)
 
         tty.msg(colorize('@*{Installing} @*g{%s}' % self.name))
 
-        if kwargs.get('use_cache', False):
+        if kwargs.get('use_cache', True):
             if self.try_install_from_binary_cache(explicit):
                 tty.msg('Successfully installed %s from binary cache'
                         % self.name)
@@ -1377,8 +1414,9 @@ class PackageBase(with_metaclass(PackageMeta, object)):
             tty.msg('No binary for %s found: installing from source'
                     % self.name)
 
-        # Set run_tests flag before starting build.
-        self.run_tests = spack.package_testing.check(self.name)
+        # Set run_tests flag before starting build
+        self.run_tests = (tests is True or
+                          tests and self.name in tests)
 
         # Set parallelism before starting build.
         self.make_jobs = make_jobs
@@ -1419,7 +1457,7 @@ class PackageBase(with_metaclass(PackageMeta, object)):
                 else:
                     source_path = self.stage.source_path
                     if install_source and os.path.isdir(source_path):
-                        src_target = join_path(
+                        src_target = os.path.join(
                             self.spec.prefix, 'share', self.name, 'src')
                         tty.msg('Copying source to {0}'.format(src_target))
                         install_tree(self.stage.source_path, src_target)
@@ -1462,10 +1500,27 @@ class PackageBase(with_metaclass(PackageMeta, object)):
             # preserve verbosity across runs
             return echo
 
+        # hook that allow tests to inspect this Package before installation
+        # see unit_test_check() docs.
+        if not self.unit_test_check():
+            return
+
         try:
             # Create the install prefix and fork the build process.
             if not os.path.exists(self.prefix):
                 spack.store.layout.create_install_directory(self.spec)
+            else:
+                # Set the proper group for the prefix
+                group = get_package_group(self.spec)
+                if group:
+                    chgrp(self.prefix, group)
+                # Set the proper permissions.
+                # This has to be done after group because changing groups blows
+                # away the sticky group bit on the directory
+                mode = os.stat(self.prefix).st_mode
+                perms = get_package_dir_permissions(self.spec)
+                if mode != perms:
+                    os.chmod(self.prefix, perms)
 
             # Fork a child to do the actual installation
             # we preserve verbosity settings across installs.
@@ -1479,7 +1534,7 @@ class PackageBase(with_metaclass(PackageMeta, object)):
             spack.store.db.add(
                 self.spec, spack.store.layout, explicit=explicit
             )
-        except directory_layout.InstallDirectoryAlreadyExistsError:
+        except spack.directory_layout.InstallDirectoryAlreadyExistsError:
             # Abort install if install directory exists.
             # But do NOT remove it (you'd be overwriting someone else's stuff)
             tty.warn("Keeping existing install prefix in place.")
@@ -1501,14 +1556,38 @@ class PackageBase(with_metaclass(PackageMeta, object)):
             # check the filesystem for it.
             self.stage.created = False
 
+    def unit_test_check(self):
+        """Hook for unit tests to assert things about package internals.
+
+        Unit tests can override this function to perform checks after
+        ``Package.install`` and all post-install hooks run, but before
+        the database is updated.
+
+        The overridden function may indicate that the install procedure
+        should terminate early (before updating the database) by
+        returning ``False`` (or any value such that ``bool(result)`` is
+        ``False``).
+
+        Return:
+            (bool): ``True`` to continue, ``False`` to skip ``install()``
+        """
+        return True
+
     def check_for_unfinished_installation(
             self, keep_prefix=False, restage=False):
         """Check for leftover files from partially-completed prior install to
-           prepare for a new install attempt. Options control whether these
-           files are reused (vs. destroyed). This function considers a package
-           fully-installed if there is a DB entry for it (in that way, it is
-           more strict than Package.installed). The return value is used to
-           indicate when the prefix exists but the install is not complete.
+        prepare for a new install attempt.
+
+        Options control whether these files are reused (vs. destroyed).
+
+        Args:
+            keep_prefix (bool): True if the installation prefix needs to be
+                kept, False otherwise
+            restage (bool): False if the stage has to be kept, True otherwise
+
+        Returns:
+            True if the prefix exists but the install is not complete, False
+            otherwise.
         """
         if self.spec.external:
             raise ExternalPackageError("Attempted to repair external spec %s" %
@@ -1529,7 +1608,7 @@ class PackageBase(with_metaclass(PackageMeta, object)):
                     partial = True
 
         stage_is_managed_in_spack = self.stage.path.startswith(
-            spack.stage_path)
+            spack.paths.stage_path)
         if restage and stage_is_managed_in_spack:
             self.stage.destroy()
             self.stage.create()
@@ -1564,8 +1643,54 @@ class PackageBase(with_metaclass(PackageMeta, object)):
             # FIXME : this potentially catches too many things...
             pass
 
+        # Archive the whole stdout + stderr for the package
         install(self.log_path, log_install_path)
+        # Archive the environment used for the build
         install(self.env_path, env_install_path)
+        # Finally, archive files that are specific to each package
+        with working_dir(self.stage.source_path):
+            errors = StringIO()
+            target_dir = os.path.join(
+                spack.store.layout.metadata_path(self.spec),
+                'archived-files')
+
+            for glob_expr in self.archive_files:
+                # Check that we are trying to copy things that are
+                # in the source_path tree (not arbitrary files)
+                abs_expr = os.path.realpath(glob_expr)
+                if os.path.realpath(self.stage.source_path) not in abs_expr:
+                    errors.write(
+                        '[OUTSIDE SOURCE PATH]: {0}\n'.format(glob_expr)
+                    )
+                    continue
+                # Now that we are sure that the path is within the correct
+                # folder, make it relative and check for matches
+                if os.path.isabs(glob_expr):
+                    glob_expr = os.path.relpath(
+                        glob_expr, self.stage.source_path
+                    )
+                files = glob.glob(glob_expr)
+                for f in files:
+                    try:
+                        target = os.path.join(target_dir, f)
+                        # We must ensure that the directory exists before
+                        # copying a file in
+                        mkdirp(os.path.dirname(target))
+                        install(f, target)
+                    except Exception:
+                        # Here try to be conservative, and avoid discarding
+                        # the whole install procedure because of copying a
+                        # single file failed
+                        errors.write('[FAILED TO ARCHIVE]: {0}'.format(f))
+
+            if errors.getvalue():
+                error_file = os.path.join(target_dir, 'errors.txt')
+                mkdirp(target_dir)
+                with open(error_file, 'w') as err:
+                    err.write(errors.getvalue())
+                tty.warn('Errors occurred when archiving files.\n\t'
+                         'See: {0}'.format(error_file))
+
         dump_packages(self.spec, packages_dir)
 
     def sanity_check_prefix(self):
@@ -1597,7 +1722,7 @@ class PackageBase(with_metaclass(PackageMeta, object)):
         if self.installed:
             return spack.store.layout.build_log_path(self.spec)
         else:
-            return join_path(self.stage.source_path, 'spack-build.out')
+            return os.path.join(self.stage.source_path, 'spack-build.out')
 
     @property
     def module(self):
@@ -1607,6 +1732,31 @@ class PackageBase(with_metaclass(PackageMeta, object)):
         return __import__(self.__class__.__module__,
                           fromlist=[self.__class__.__name__])
 
+    @classmethod
+    def inject_flags(cls, name, flags):
+        """
+        flag_handler that injects all flags through the compiler wrapper.
+        """
+        return (flags, None, None)
+
+    @classmethod
+    def env_flags(cls, name, flags):
+        """
+        flag_handler that adds all flags to canonical environment variables.
+        """
+        return (None, flags, None)
+
+    @classmethod
+    def build_system_flags(cls, name, flags):
+        """
+        flag_handler that passes flags to the build system arguments.  Any
+        package using `build_system_flags` must also implement
+        `flags_to_build_system_args`, or derive from a class that
+        implements it.  Currently, AutotoolsPackage and CMakePackage
+        implement it.
+        """
+        return (None, None, flags)
+
     def setup_environment(self, spack_env, run_env):
         """Set up the compile and runtime environments for a package.
 
@@ -1707,28 +1857,6 @@ class PackageBase(with_metaclass(PackageMeta, object)):
         """
         pass
 
-    def inject_flags(self, name, flags):
-        """
-        flag_handler that injects all flags through the compiler wrapper.
-        """
-        return (flags, None, None)
-
-    def env_flags(self, name, flags):
-        """
-        flag_handler that adds all flags to canonical environment variables.
-        """
-        return (None, flags, None)
-
-    def build_system_flags(self, name, flags):
-        """
-        flag_handler that passes flags to the build system arguments.  Any
-        package using `build_system_flags` must also implement
-        `flags_to_build_system_args`, or derive from a class that
-        implements it.  Currently, AutotoolsPackage and CMakePackage
-        implement it.
-        """
-        return (None, None, flags)
-
     flag_handler = inject_flags
     # The flag handler method is called for each of the allowed compiler flags.
     # It returns a triple of inject_flags, env_flags, build_system_flags.
@@ -1770,7 +1898,7 @@ class PackageBase(with_metaclass(PackageMeta, object)):
         # Try to get the pcakage for the spec
         try:
             pkg = spec.package
-        except spack.repository.UnknownEntityError:
+        except spack.repo.UnknownEntityError:
             pkg = None
 
         # Pre-uninstall hook runs first.
@@ -1819,82 +1947,80 @@ class PackageBase(with_metaclass(PackageMeta, object)):
             raise ActivationError("%s does not extend %s!" %
                                   (self.name, self.extendee.name))
 
-    def do_activate(self, force=False, verbose=True, extensions_layout=None):
+    def do_activate(self, view=None, with_dependencies=True, verbose=True):
         """Called on an extension to invoke the extendee's activate method.
 
         Commands should call this routine, and should not call
         activate() directly.
         """
+        if verbose:
+            tty.msg('Activating extension {0} for {1}'.format(
+                self.spec.cshort_spec, self.extendee_spec.cshort_spec))
+
         self._sanity_check_extension()
+        if not view:
+            view = YamlFilesystemView(
+                self.extendee_spec.prefix, spack.store.layout)
 
-        if extensions_layout is None:
-            extensions_layout = spack.store.extensions
+        extensions_layout = view.extensions_layout
 
         extensions_layout.check_extension_conflict(
             self.extendee_spec, self.spec)
 
         # Activate any package dependencies that are also extensions.
-        if not force:
+        if with_dependencies:
             for spec in self.dependency_activations():
-                if not spec.package.is_activated(
-                        extensions_layout=extensions_layout):
+                if not spec.package.is_activated(view):
                     spec.package.do_activate(
-                        force=force, verbose=verbose,
-                        extensions_layout=extensions_layout)
+                        view, with_dependencies=with_dependencies,
+                        verbose=verbose)
 
         self.extendee_spec.package.activate(
-            self, extensions_layout=extensions_layout, **self.extendee_args)
+            self, view, **self.extendee_args)
 
         extensions_layout.add_extension(self.extendee_spec, self.spec)
 
         if verbose:
-            tty.msg(
-                "Activated extension %s for %s" %
-                (self.spec.short_spec,
-                 self.extendee_spec.cformat("$_$@$+$%@")))
+            tty.debug('Activated extension {0} for {1}'.format(
+                self.spec.cshort_spec, self.extendee_spec.cshort_spec))
 
     def dependency_activations(self):
         return (spec for spec in self.spec.traverse(root=False, deptype='run')
                 if spec.package.extends(self.extendee_spec))
 
-    def activate(self, extension, **kwargs):
-        """Make extension package usable by linking all its files to a target
-        provided by the directory layout (depending if the user wants to
-        activate globally or in a specified file system view).
-
-        Package authors can override this method to support other
-        extension mechanisms.  Spack internals (commands, hooks, etc.)
-        should call do_activate() method so that proper checks are
-        always executed.
-
+    def activate(self, extension, view, **kwargs):
         """
-        extensions_layout = kwargs.get("extensions_layout",
-                                       spack.store.extensions)
-        target = extensions_layout.extendee_target_directory(self)
+        Add the extension to the specified view.
 
-        def ignore(filename):
-            return (filename in spack.store.layout.hidden_file_paths or
-                    kwargs.get('ignore', lambda f: False)(filename))
+        Package authors can override this function to maintain some
+        centralized state related to the set of activated extensions
+        for a package.
 
-        tree = LinkTree(extension.prefix)
-        conflict = tree.find_conflict(target, ignore=ignore)
-        if conflict:
-            raise ExtensionConflictError(conflict)
-
-        tree.merge(target, ignore=ignore, link=extensions_layout.link)
+        Spack internals (commands, hooks, etc.) should call
+        do_activate() method so that proper checks are always executed.
+        """
+        view.merge(extension.spec, ignore=kwargs.get('ignore', None))
 
-    def do_deactivate(self, **kwargs):
-        """Called on the extension to invoke extendee's deactivate() method.
+    def do_deactivate(self, view=None, **kwargs):
+        """Remove this extension package from the specified view. Called
+        on the extension to invoke extendee's deactivate() method.
 
         `remove_dependents=True` deactivates extensions depending on this
         package instead of raising an error.
         """
         self._sanity_check_extension()
         force = kwargs.get('force', False)
-        verbose = kwargs.get("verbose", True)
-        remove_dependents = kwargs.get("remove_dependents", False)
-        extensions_layout = kwargs.get("extensions_layout",
-                                       spack.store.extensions)
+        verbose = kwargs.get('verbose', True)
+        remove_dependents = kwargs.get('remove_dependents', False)
+
+        if verbose:
+            tty.msg('Deactivating extension {0} for {1}'.format(
+                self.spec.cshort_spec, self.extendee_spec.cshort_spec))
+
+        if not view:
+            view = YamlFilesystemView(
+                self.extendee_spec.prefix, spack.store.layout)
+        extensions_layout = view.extensions_layout
 
         # Allow a force deactivate to happen.  This can unlink
         # spurious files if something was corrupted.
@@ -1912,49 +2038,41 @@ class PackageBase(with_metaclass(PackageMeta, object)):
                         if remove_dependents:
                             aspec.package.do_deactivate(**kwargs)
                         else:
-                            msg = ("Cannot deactivate %s because %s is "
-                                   "activated and depends on it.")
-                            raise ActivationError(
-                                msg % (self.spec.cshort_spec,
-                                       aspec.cshort_spec))
+                            msg = ('Cannot deactivate {0} because {1} is '
+                                   'activated and depends on it')
+                            raise ActivationError(msg.format(
+                                self.spec.cshort_spec, aspec.cshort_spec))
 
         self.extendee_spec.package.deactivate(
-            self,
-            extensions_layout=extensions_layout,
-            **self.extendee_args)
+            self, view, **self.extendee_args)
 
         # redundant activation check -- makes SURE the spec is not
         # still activated even if something was wrong above.
-        if self.is_activated(extensions_layout):
+        if self.is_activated(view):
             extensions_layout.remove_extension(
                 self.extendee_spec, self.spec)
 
         if verbose:
-            tty.msg(
-                "Deactivated extension %s for %s" %
-                (self.spec.short_spec,
-                 self.extendee_spec.cformat("$_$@$+$%@")))
+            tty.debug('Deactivated extension {0} for {1}'.format(
+                self.spec.cshort_spec, self.extendee_spec.cshort_spec))
 
-    def deactivate(self, extension, **kwargs):
-        """Unlinks all files from extension out of this package's install dir
-        or the corresponding filesystem view.
+    def deactivate(self, extension, view, **kwargs):
+        """
+        Remove all extension files from the specified view.
 
         Package authors can override this method to support other
         extension mechanisms.  Spack internals (commands, hooks, etc.)
         should call do_deactivate() method so that proper checks are
         always executed.
-
         """
-        extensions_layout = kwargs.get("extensions_layout",
-                                       spack.store.extensions)
-        target = extensions_layout.extendee_target_directory(self)
+        view.unmerge(extension.spec, ignore=kwargs.get('ignore', None))
 
-        def ignore(filename):
-            return (filename in spack.store.layout.hidden_file_paths or
-                    kwargs.get('ignore', lambda f: False)(filename))
-
-        tree = LinkTree(extension.prefix)
-        tree.unmerge(target, ignore=ignore)
+    def view(self):
+        """Create a view with the prefix of this package as the root.
+        Extensions added to this view will modify the installation prefix of
+        this package.
+        """
+        return YamlFilesystemView(self.prefix, spack.store.layout)
 
     def do_restage(self):
         """Reverts expanded/checked out source to a pristine state."""
@@ -1980,8 +2098,15 @@ class PackageBase(with_metaclass(PackageMeta, object)):
 
     @property
     def all_urls(self):
+        """A list of all URLs in a package.
+
+        Check both class-level and version-specific URLs.
+
+        Returns:
+            list: a list of URLs
+        """
         urls = []
-        if self.url:
+        if hasattr(self, 'url') and self.url:
             urls.append(self.url)
 
         for args in self.versions.values():
@@ -1990,10 +2115,15 @@ class PackageBase(with_metaclass(PackageMeta, object)):
         return urls
 
     def fetch_remote_versions(self):
-        """Try to find remote versions of this package using the
-           list_url and any other URLs described in the package file."""
+        """Find remote versions of this package.
+
+        Uses ``list_url`` and any other URLs listed in the package file.
+
+        Returns:
+            dict: a dictionary mapping versions to URLs
+        """
         if not self.all_urls:
-            raise spack.util.web.VersionFetchError(self.__class__)
+            return {}
 
         try:
             return spack.util.web.find_versions_of_archive(
@@ -2063,6 +2193,11 @@ class PackageBase(with_metaclass(PackageMeta, object)):
                 tty.warn(msg.format(name))
 
 
+inject_flags = PackageBase.inject_flags
+env_flags = PackageBase.env_flags
+build_system_flags = PackageBase.build_system_flags
+
+
 class Package(PackageBase):
     """General purpose class with a single ``install``
     phase that needs to be coded by packagers.
@@ -2125,7 +2260,7 @@ def dump_packages(spec, path):
             # Locate the dependency package in the install tree and find
             # its provenance information.
             source = spack.store.layout.build_packages_path(node)
-            source_repo_root = join_path(source, node.namespace)
+            source_repo_root = os.path.join(source, node.namespace)
 
             # There's no provenance installed for the source package.  Skip it.
             # User can always get something current from the builtin repo.
@@ -2134,25 +2269,25 @@ def dump_packages(spec, path):
 
             # Create a source repo and get the pkg directory out of it.
             try:
-                source_repo = spack.repository.Repo(source_repo_root)
+                source_repo = spack.repo.Repo(source_repo_root)
                 source_pkg_dir = source_repo.dirname_for_package_name(
                     node.name)
-            except spack.repository.RepoError:
+            except spack.repo.RepoError:
                 tty.warn("Warning: Couldn't copy in provenance for %s" %
                          node.name)
 
         # Create a destination repository
-        dest_repo_root = join_path(path, node.namespace)
+        dest_repo_root = os.path.join(path, node.namespace)
         if not os.path.exists(dest_repo_root):
-            spack.repository.create_repo(dest_repo_root)
-        repo = spack.repository.Repo(dest_repo_root)
+            spack.repo.create_repo(dest_repo_root)
+        repo = spack.repo.Repo(dest_repo_root)
 
         # Get the location of the package in the dest repo.
         dest_pkg_dir = repo.dirname_for_package_name(node.name)
         if node is not spec:
             install_tree(source_pkg_dir, dest_pkg_dir)
         else:
-            spack.repo.dump_provenance(node, dest_pkg_dir)
+            spack.repo.path.dump_provenance(node, dest_pkg_dir)
 
 
 def print_pkg(message):
@@ -2197,7 +2332,6 @@ class ExternalPackageError(InstallError):
 
 class PackageStillNeededError(InstallError):
     """Raised when package is still needed by another on uninstall."""
-
     def __init__(self, spec, dependents):
         super(PackageStillNeededError, self).__init__("Cannot uninstall %s" %
                                                       spec)
@@ -2207,14 +2341,12 @@ class PackageStillNeededError(InstallError):
 
 class PackageError(spack.error.SpackError):
     """Raised when something is wrong with a package definition."""
-
     def __init__(self, message, long_msg=None):
         super(PackageError, self).__init__(message, long_msg)
 
 
 class PackageVersionError(PackageError):
     """Raised when a version URL cannot automatically be determined."""
-
     def __init__(self, version):
         super(PackageVersionError, self).__init__(
             "Cannot determine a URL automatically for version %s" % version,
@@ -2230,26 +2362,17 @@ class NoURLError(PackageError):
 
 
 class ExtensionError(PackageError):
-
-    pass
-
-
-class ExtensionConflictError(ExtensionError):
-
-    def __init__(self, path):
-        super(ExtensionConflictError, self).__init__(
-            "Extension blocked by file: %s" % path)
+    """Superclass for all errors having to do with extension packages."""
 
 
 class ActivationError(ExtensionError):
-
+    """Raised when there are problems activating an extension."""
     def __init__(self, msg, long_msg=None):
         super(ActivationError, self).__init__(msg, long_msg)
 
 
 class DependencyConflictError(spack.error.SpackError):
     """Raised when the dependencies cannot be flattened as asked for."""
-
     def __init__(self, conflict):
         super(DependencyConflictError, self).__init__(
             "%s conflicts with another file in the flattened directory." % (
diff --git a/lib/spack/spack/package_prefs.py b/lib/spack/spack/package_prefs.py
index 489e87b9b0..bd400b1eb8 100644
--- a/lib/spack/spack/package_prefs.py
+++ b/lib/spack/spack/package_prefs.py
@@ -1,37 +1,20 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import stat
+
 from six import string_types
 from six import iteritems
 
 from llnl.util.lang import classproperty
 
-import spack
+import spack.repo
 import spack.error
 from spack.util.path import canonicalize_path
 from spack.version import VersionList
-
+from spack.config import ConfigError
 
 _lesser_spec_types = {'compiler': spack.spec.CompilerSpec,
                       'version': VersionList}
@@ -44,14 +27,14 @@ def _spec_type(component):
 
 def get_packages_config():
     """Wrapper around get_packages_config() to validate semantics."""
-    config = spack.config.get_config('packages')
+    config = spack.config.get('packages')
 
     # Get a list of virtuals from packages.yaml.  Note that because we
     # check spack.repo, this collects virtuals that are actually provided
     # by sometihng, not just packages/names that don't exist.
     # So, this won't include, e.g., 'all'.
     virtuals = [(pkg_name, pkg_name._start_mark) for pkg_name in config
-                if spack.repo.is_virtual(pkg_name)]
+                if spack.repo.path.is_virtual(pkg_name)]
 
     # die if there are virtuals in `packages.py`
     if virtuals:
@@ -204,25 +187,6 @@ class PackagePrefs(object):
                     if name in pkg.variants)
 
 
-class PackageTesting(object):
-    def __init__(self):
-        self.packages_to_test = set()
-        self._test_all = False
-
-    def test(self, package_name):
-        self.packages_to_test.add(package_name)
-
-    def test_all(self):
-        self._test_all = True
-
-    def clear(self):
-        self._test_all = False
-        self.packages_to_test.clear()
-
-    def check(self, package_name):
-        return self._test_all or (package_name in self.packages_to_test)
-
-
 def spec_externals(spec):
     """Return a list of external specs (w/external directory path filled in),
        one for each known external installation."""
@@ -271,5 +235,79 @@ def is_spec_buildable(spec):
     return allpkgs[spec.name]['buildable']
 
 
+def get_package_dir_permissions(spec):
+    """Return the permissions configured for the spec.
+
+    Include the GID bit if group permissions are on. This makes the group
+    attribute sticky for the directory. Package-specific settings take
+    precedent over settings for ``all``"""
+    perms = get_package_permissions(spec)
+    if perms & stat.S_IRWXG:
+        perms |= stat.S_ISGID
+    return perms
+
+
+def get_package_permissions(spec):
+    """Return the permissions configured for the spec.
+
+    Package-specific settings take precedence over settings for ``all``"""
+
+    # Get read permissions level
+    for name in (spec.name, 'all'):
+        try:
+            readable = spack.config.get('packages:%s:permissions:read' % name,
+                                        '')
+            if readable:
+                break
+        except AttributeError:
+            readable = 'world'
+
+    # Get write permissions level
+    for name in (spec.name, 'all'):
+        try:
+            writable = spack.config.get('packages:%s:permissions:write' % name,
+                                        '')
+            if writable:
+                break
+        except AttributeError:
+            writable = 'user'
+
+    perms = stat.S_IRWXU
+    if readable in ('world', 'group'):  # world includes group
+        perms |= stat.S_IRGRP | stat.S_IXGRP
+    if readable == 'world':
+        perms |= stat.S_IROTH | stat.S_IXOTH
+
+    if writable in ('world', 'group'):
+        if readable == 'user':
+            raise ConfigError('Writable permissions may not be more' +
+                              ' permissive than readable permissions.\n' +
+                              '      Violating package is %s' % spec.name)
+        perms |= stat.S_IWGRP
+    if writable == 'world':
+        if readable != 'world':
+            raise ConfigError('Writable permissions may not be more' +
+                              ' permissive than readable permissions.\n' +
+                              '      Violating package is %s' % spec.name)
+        perms |= stat.S_IWOTH
+
+    return perms
+
+
+def get_package_group(spec):
+    """Return the unix group associated with the spec.
+
+    Package-specific settings take precedence over settings for ``all``"""
+    for name in (spec.name, 'all'):
+        try:
+            group = spack.config.get('packages:%s:permissions:group' % name,
+                                     '')
+            if group:
+                break
+        except AttributeError:
+            group = ''
+    return group
+
+
 class VirtualInPackagesYAMLError(spack.error.SpackError):
     """Raised when a disallowed virtual is found in packages.yaml"""
diff --git a/lib/spack/spack/package_test.py b/lib/spack/spack/package_test.py
index e3f2e82d03..29edfc6d38 100644
--- a/lib/spack/spack/package_test.py
+++ b/lib/spack/spack/package_test.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 from spack.util.executable import which, Executable
 
diff --git a/lib/spack/spack/parse.py b/lib/spack/spack/parse.py
index 1bdefde7a4..0b3d81d5a1 100644
--- a/lib/spack/spack/parse.py
+++ b/lib/spack/spack/parse.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import re
 import shlex
 import sys
diff --git a/lib/spack/spack/patch.py b/lib/spack/spack/patch.py
index 2fea1d9aff..a865d429a4 100644
--- a/lib/spack/spack/patch.py
+++ b/lib/spack/spack/patch.py
@@ -1,33 +1,13 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 import os.path
 import inspect
 import hashlib
 
-import spack
 import spack.error
 import spack.fetch_strategy as fs
 import spack.stage
@@ -154,7 +134,7 @@ class UrlPatch(Patch):
         if self.archive_sha256:
             fetch_digest = self.archive_sha256
 
-        fetcher = fs.URLFetchStrategy(self.url, digest=fetch_digest)
+        fetcher = fs.URLFetchStrategy(self.url, fetch_digest)
         mirror = os.path.join(
             os.path.dirname(stage.mirror_path),
             os.path.basename(self.url))
diff --git a/lib/spack/spack/paths.py b/lib/spack/spack/paths.py
new file mode 100644
index 0000000000..d1d1d27136
--- /dev/null
+++ b/lib/spack/spack/paths.py
@@ -0,0 +1,61 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+"""Defines paths that are part of Spack's directory structure.
+
+Do not import other ``spack`` modules here. This module is used
+throughout Spack and should bring in a minimal number of external
+dependencies.
+"""
+import os
+from llnl.util.filesystem import ancestor
+
+
+#: This file lives in $prefix/lib/spack/spack/__file__
+prefix = ancestor(__file__, 4)
+
+#: synonym for prefix
+spack_root = prefix
+
+#: bin directory in the spack prefix
+bin_path = os.path.join(prefix, "bin")
+
+#: The spack script itself
+spack_script = os.path.join(bin_path, "spack")
+
+# spack directory hierarchy
+lib_path              = os.path.join(prefix, "lib", "spack")
+external_path         = os.path.join(lib_path, "external")
+build_env_path        = os.path.join(lib_path, "env")
+module_path           = os.path.join(lib_path, "spack")
+command_path          = os.path.join(module_path, "cmd")
+platform_path         = os.path.join(module_path, 'platforms')
+compilers_path        = os.path.join(module_path, "compilers")
+build_systems_path    = os.path.join(module_path, 'build_systems')
+operating_system_path = os.path.join(module_path, 'operating_systems')
+test_path             = os.path.join(module_path, "test")
+hooks_path            = os.path.join(module_path, "hooks")
+var_path              = os.path.join(prefix, "var", "spack")
+stage_path            = os.path.join(var_path, "stage")
+repos_path            = os.path.join(var_path, "repos")
+share_path            = os.path.join(prefix, "share", "spack")
+
+# Paths to built-in Spack repositories.
+packages_path      = os.path.join(repos_path, "builtin")
+mock_packages_path = os.path.join(repos_path, "builtin.mock")
+
+#: User configuration location
+user_config_path = os.path.expanduser('~/.spack')
+
+
+opt_path        = os.path.join(prefix, "opt")
+etc_path        = os.path.join(prefix, "etc")
+system_etc_path = '/etc'
+
+# GPG paths.
+gpg_keys_path      = os.path.join(var_path, "gpg")
+mock_gpg_data_path = os.path.join(var_path, "gpg.mock", "data")
+mock_gpg_keys_path = os.path.join(var_path, "gpg.mock", "keys")
+gpg_path           = os.path.join(opt_path, "spack", "gpg")
diff --git a/lib/spack/spack/pkgkit.py b/lib/spack/spack/pkgkit.py
new file mode 100644
index 0000000000..39d1855a01
--- /dev/null
+++ b/lib/spack/spack/pkgkit.py
@@ -0,0 +1,49 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+# flake8: noqa: F401
+"""pkgkit is a set of useful build tools and directives for packages.
+
+Everything in this module is automatically imported into Spack package files.
+"""
+import llnl.util.filesystem
+from llnl.util.filesystem import *
+
+from spack.package import Package, run_before, run_after, on_package_attributes
+from spack.package import inject_flags, env_flags, build_system_flags
+from spack.build_systems.makefile import MakefilePackage
+from spack.build_systems.aspell_dict import AspellDictPackage
+from spack.build_systems.autotools import AutotoolsPackage
+from spack.build_systems.cmake import CMakePackage
+from spack.build_systems.cuda import CudaPackage
+from spack.build_systems.qmake import QMakePackage
+from spack.build_systems.scons import SConsPackage
+from spack.build_systems.waf import WafPackage
+from spack.build_systems.octave import OctavePackage
+from spack.build_systems.python import PythonPackage
+from spack.build_systems.r import RPackage
+from spack.build_systems.perl import PerlPackage
+from spack.build_systems.intel import IntelPackage
+from spack.build_systems.meson import MesonPackage
+
+from spack.mixins import filter_compiler_wrappers
+
+from spack.version import Version, ver
+
+from spack.spec import Spec
+
+from spack.dependency import all_deptypes
+
+from spack.multimethod import when
+
+import spack.directives
+from spack.directives import *
+
+import spack.util.executable
+from spack.util.executable import *
+
+from spack.package import \
+    install_dependency_symlinks, flatten_dependencies, \
+    DependencyConflictError, InstallError, ExternalPackageError
diff --git a/lib/spack/spack/platforms/__init__.py b/lib/spack/spack/platforms/__init__.py
index 8922701e9f..4f442db458 100644
--- a/lib/spack/spack/platforms/__init__.py
+++ b/lib/spack/spack/platforms/__init__.py
@@ -1,24 +1,4 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
diff --git a/lib/spack/spack/platforms/bgq.py b/lib/spack/spack/platforms/bgq.py
index f0dfe1dd14..9763dfadb3 100644
--- a/lib/spack/spack/platforms/bgq.py
+++ b/lib/spack/spack/platforms/bgq.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 from spack.architecture import Platform, Target
 from spack.operating_systems.linux_distro import LinuxDistro
@@ -53,5 +34,5 @@ class Bgq(Platform):
         self.add_operating_system(str(back_distro), back_distro)
 
     @classmethod
-    def detect(self):
+    def detect(cls):
         return os.path.exists('/bgsys')
diff --git a/lib/spack/spack/platforms/cray.py b/lib/spack/spack/platforms/cray.py
index 095a426b22..2190552e2b 100644
--- a/lib/spack/spack/platforms/cray.py
+++ b/lib/spack/spack/platforms/cray.py
@@ -1,37 +1,17 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 import re
 import llnl.util.tty as tty
-from spack import build_env_path
+from spack.paths import build_env_path
 from spack.util.executable import which
 from spack.architecture import Platform, Target, NoPlatformError
 from spack.operating_systems.cray_frontend import CrayFrontend
 from spack.operating_systems.cnl import Cnl
-from llnl.util.filesystem import join_path
-from spack.util.module_cmd import get_module_cmd
+from spack.util.module_cmd import get_module_cmd, unload_module
 
 
 def _get_modules_in_modulecmd_output(output):
@@ -103,12 +83,23 @@ class Cray(Platform):
         """ Change the linker to default dynamic to be more
             similar to linux/standard linker behavior
         """
+        # Unload these modules to prevent any silent linking or unnecessary
+        # I/O profiling in the case of darshan.
+        modules_to_unload = ["cray-mpich", "darshan", "cray-libsci"]
+        for module in modules_to_unload:
+            unload_module(module)
+
         env.set('CRAYPE_LINK_TYPE', 'dynamic')
-        cray_wrapper_names = join_path(build_env_path, 'cray')
+        cray_wrapper_names = os.path.join(build_env_path, 'cray')
+
         if os.path.isdir(cray_wrapper_names):
             env.prepend_path('PATH', cray_wrapper_names)
             env.prepend_path('SPACK_ENV_PATH', cray_wrapper_names)
 
+        # Makes spack installed pkg-config work on Crays
+        env.append_path("PKG_CONFIG_PATH", "/usr/lib64/pkgconfig")
+        env.append_path("PKG_CONFIG_PATH", "/usr/local/lib64/pkgconfig")
+
     @classmethod
     def detect(cls):
         return os.environ.get('CRAYPE_VERSION') is not None
diff --git a/lib/spack/spack/platforms/darwin.py b/lib/spack/spack/platforms/darwin.py
index be2a1e7e41..1a793e4ed2 100644
--- a/lib/spack/spack/platforms/darwin.py
+++ b/lib/spack/spack/platforms/darwin.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import platform
 from spack.architecture import Platform, Target
 from spack.operating_systems.mac_os import MacOs
@@ -45,5 +26,5 @@ class Darwin(Platform):
         self.add_operating_system(str(mac_os), mac_os)
 
     @classmethod
-    def detect(self):
+    def detect(cls):
         return 'darwin' in platform.system().lower()
diff --git a/lib/spack/spack/platforms/linux.py b/lib/spack/spack/platforms/linux.py
index 4913be4ed2..2c36c24ebc 100644
--- a/lib/spack/spack/platforms/linux.py
+++ b/lib/spack/spack/platforms/linux.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import platform
 from spack.architecture import Platform, Target
 from spack.operating_systems.linux_distro import LinuxDistro
@@ -49,5 +30,5 @@ class Linux(Platform):
         self.add_operating_system(str(linux_dist), linux_dist)
 
     @classmethod
-    def detect(self):
+    def detect(cls):
         return 'linux' in platform.system().lower()
diff --git a/lib/spack/spack/platforms/test.py b/lib/spack/spack/platforms/test.py
index 3a4d2c00ad..18d283347f 100644
--- a/lib/spack/spack/platforms/test.py
+++ b/lib/spack/spack/platforms/test.py
@@ -1,29 +1,10 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack.architecture import Platform, Target
-from spack.architecture import OperatingSystem as OS
+from spack.architecture import OperatingSystem
 
 
 class Test(Platform):
@@ -41,9 +22,11 @@ class Test(Platform):
         self.add_target(self.default, Target(self.default))
         self.add_target(self.front_end, Target(self.front_end))
 
-        self.add_operating_system(self.default_os, OS('debian', 6))
-        self.add_operating_system(self.front_os, OS('redhat', 6))
+        self.add_operating_system(
+            self.default_os, OperatingSystem('debian', 6))
+        self.add_operating_system(
+            self.front_os, OperatingSystem('redhat', 6))
 
     @classmethod
-    def detect(self):
+    def detect(cls):
         return True
diff --git a/lib/spack/spack/provider_index.py b/lib/spack/spack/provider_index.py
index 21bde7ce5c..222f98c0d9 100644
--- a/lib/spack/spack/provider_index.py
+++ b/lib/spack/spack/provider_index.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """
 The ``virtual`` module contains utility classes for virtual dependencies.
 """
@@ -29,11 +10,9 @@ from itertools import product as iproduct
 from six import iteritems
 from pprint import pformat
 
-import spack.util.spack_yaml as syaml
-from yaml.error import MarkedYAMLError
-
-import spack
 import spack.error
+import spack.util.spack_yaml as syaml
+from ruamel.yaml.error import MarkedYAMLError
 
 
 class ProviderIndex(object):
diff --git a/lib/spack/spack/relocate.py b/lib/spack/spack/relocate.py
index 1f62c70231..664551740a 100644
--- a/lib/spack/spack/relocate.py
+++ b/lib/spack/spack/relocate.py
@@ -1,38 +1,31 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 import os
 import platform
 import re
-import spack
+import spack.repo
 import spack.cmd
-from spack.util.executable import Executable
+from spack.util.executable import Executable, ProcessError
 from llnl.util.filesystem import filter_file
 import llnl.util.tty as tty
 
 
+class InstallRootStringException(spack.error.SpackError):
+    """
+    Raised when the relocated binary still has the install root string.
+    """
+    def __init__(self, file_path, root_path):
+        super(InstallRootStringException, self).__init__(
+            "\n %s \ncontains string\n %s \n"
+            "after replacing it in rpaths.\n"
+            "Package should not be relocated.\n Use -a to override." %
+            (file_path, root_path))
+
+
 def get_patchelf():
     """
     Builds and installs spack patchelf package on linux platforms
@@ -56,10 +49,15 @@ def get_existing_elf_rpaths(path_name):
     as a list of strings.
     """
     if platform.system() == 'Linux':
-        command = Executable(get_patchelf())
-        output = command('--print-rpath', '%s' %
-                         path_name, output=str, err=str)
-        return output.rstrip('\n').split(':')
+        patchelf = Executable(get_patchelf())
+        try:
+            output = patchelf('--print-rpath', '%s' %
+                              path_name, output=str, error=str)
+            return output.rstrip('\n').split(':')
+        except ProcessError as e:
+            tty.debug('patchelf --print-rpath produced an error on %s' %
+                      path_name, e)
+            return []
     else:
         tty.die('relocation not supported for this platform')
     return
@@ -81,6 +79,29 @@ def get_relative_rpaths(path_name, orig_dir, orig_rpaths):
     return rel_rpaths
 
 
+def set_placeholder(dirname):
+    """
+    return string of @'s with same length
+    """
+    return '@' * len(dirname)
+
+
+def get_placeholder_rpaths(path_name, orig_rpaths):
+    """
+    Replaces original layout root dir with a placeholder string in all rpaths.
+    """
+    rel_rpaths = []
+    orig_dir = spack.store.layout.root
+    for rpath in orig_rpaths:
+        if re.match(orig_dir, rpath):
+            placeholder = set_placeholder(orig_dir)
+            rel = re.sub(orig_dir, placeholder, rpath)
+            rel_rpaths.append('%s' % rel)
+        else:
+            rel_rpaths.append(rpath)
+    return rel_rpaths
+
+
 def macho_get_paths(path_name):
     """
     Examines the output of otool -l path_name for these three fields:
@@ -116,7 +137,7 @@ def macho_get_paths(path_name):
 def macho_make_paths_relative(path_name, old_dir, rpaths, deps, idpath):
     """
     Replace old_dir with relative path from dirname(path_name)
-    in rpaths and deps; idpaths are replaced with @rpath/basebane(path_name);
+    in rpaths and deps; idpaths are replaced with @rpath/libname as needed;
     replacement are returned.
     """
     new_idpath = None
@@ -139,6 +160,34 @@ def macho_make_paths_relative(path_name, old_dir, rpaths, deps, idpath):
     return (new_rpaths, new_deps, new_idpath)
 
 
+def macho_make_paths_placeholder(rpaths, deps, idpath):
+    """
+    Replace old_dir with a placeholder of the same length
+    in rpaths and deps and idpaths is needed.
+    replacement are returned.
+    """
+    new_idpath = None
+    old_dir = spack.store.layout.root
+    placeholder = set_placeholder(old_dir)
+    if idpath:
+        new_idpath = re.sub(old_dir, placeholder, idpath)
+    new_rpaths = list()
+    new_deps = list()
+    for rpath in rpaths:
+        if re.match(old_dir, rpath):
+            ph = re.sub(old_dir, placeholder, rpath)
+            new_rpaths.append('%s' % ph)
+        else:
+            new_rpaths.append(rpath)
+    for dep in deps:
+        if re.match(old_dir, dep):
+            ph = re.sub(old_dir, placeholder, dep)
+            new_deps.append('%s' % ph)
+        else:
+            new_deps.append(dep)
+    return (new_rpaths, new_deps, new_idpath)
+
+
 def macho_replace_paths(old_dir, new_dir, rpaths, deps, idpath):
     """
     Replace old_dir with new_dir in rpaths, deps and idpath
@@ -174,38 +223,44 @@ def modify_macho_object(cur_path, rpaths, deps, idpath,
     if 'libgcc_' in cur_path:
         return
     install_name_tool = Executable('install_name_tool')
+    args = []
     if new_idpath:
-        install_name_tool('-id', new_idpath, str(cur_path),
-                          output=str, err=str)
+        args.extend(['-id', new_idpath])
 
     for orig, new in zip(deps, new_deps):
-        install_name_tool('-change', orig, new, str(cur_path))
+        args.extend(['-change', orig, new])
 
     for orig, new in zip(rpaths, new_rpaths):
-        install_name_tool('-rpath', orig, new, str(cur_path))
+        args.extend(['-rpath', orig, new])
+    args.append(str(cur_path))
+    install_name_tool(*args)
     return
 
 
-def get_filetype(path_name):
+def strings_contains_installroot(path_name, root_dir):
     """
-    Return the output of file path_name as a string to identify file type.
+    Check if the file contain the install root string.
     """
-    file = Executable('file')
-    file.add_default_env('LC_ALL', 'C')
-    output = file('-b', '-h', '%s' % path_name,
-                  output=str, err=str)
-    return output.strip()
+    strings = Executable('strings')
+    output = strings('%s' % path_name,
+                     output=str, err=str)
+    return (root_dir in output)
 
 
-def modify_elf_object(path_name, orig_rpath, new_rpath):
+def modify_elf_object(path_name, new_rpaths):
     """
     Replace orig_rpath with new_rpath in RPATH of elf object path_name
     """
     if platform.system() == 'Linux':
-        new_joined = ':'.join(new_rpath)
+        new_joined = ':'.join(new_rpaths)
         patchelf = Executable(get_patchelf())
-        patchelf('--force-rpath', '--set-rpath', '%s' % new_joined,
-                 '%s' % path_name, output=str, cmd=str)
+        try:
+            patchelf('--force-rpath', '--set-rpath', '%s' % new_joined,
+                     '%s' % path_name, output=str, error=str)
+        except ProcessError as e:
+            tty.die('patchelf --set-rpath %s failed' %
+                    path_name, e)
+            pass
     else:
         tty.die('relocation not supported for this platform')
 
@@ -237,33 +292,68 @@ def needs_text_relocation(filetype):
     return ("text" in filetype)
 
 
-def relocate_binary(path_names, old_dir, new_dir):
+def relocate_binary(path_names, old_dir, new_dir, allow_root):
     """
     Change old_dir to new_dir in RPATHs of elf or mach-o files
+    Account for the case where old_dir is now a placeholder
     """
+    placeholder = set_placeholder(old_dir)
     if platform.system() == 'Darwin':
         for path_name in path_names:
-            rpaths, deps, idpath = macho_get_paths(path_name)
-            new_rpaths, new_deps, new_idpath = macho_replace_paths(old_dir,
-                                                                   new_dir,
-                                                                   rpaths,
-                                                                   deps,
-                                                                   idpath)
+            (rpaths, deps, idpath) = macho_get_paths(path_name)
+            # new style buildaches with placeholder in binaries
+            if (deps[0].startswith(placeholder) or
+                rpaths[0].startswith(placeholder) or
+                (idpath and idpath.startswith(placeholder))):
+                (new_rpaths,
+                 new_deps,
+                 new_idpath) = macho_replace_paths(placeholder,
+                                                   new_dir,
+                                                   rpaths,
+                                                   deps,
+                                                   idpath)
+            # old style buildcaches with original install root in binaries
+            else:
+                (new_rpaths,
+                 new_deps,
+                 new_idpath) = macho_replace_paths(old_dir,
+                                                   new_dir,
+                                                   rpaths,
+                                                   deps,
+                                                   idpath)
             modify_macho_object(path_name,
                                 rpaths, deps, idpath,
                                 new_rpaths, new_deps, new_idpath)
+            if (not allow_root and
+                old_dir != new_dir and
+                strings_contains_installroot(path_name, old_dir)):
+                    raise InstallRootStringException(path_name, old_dir)
+
     elif platform.system() == 'Linux':
         for path_name in path_names:
             orig_rpaths = get_existing_elf_rpaths(path_name)
-            new_rpaths = substitute_rpath(orig_rpaths, old_dir, new_dir)
-            modify_elf_object(path_name, orig_rpaths, new_rpaths)
+            if orig_rpaths:
+                if orig_rpaths[0].startswith(placeholder):
+                    # new style buildaches with placeholder in binaries
+                    new_rpaths = substitute_rpath(orig_rpaths,
+                                                  placeholder, new_dir)
+                else:
+                    # old style buildcaches with original install
+                    # root in binaries
+                    new_rpaths = substitute_rpath(orig_rpaths,
+                                                  old_dir, new_dir)
+                modify_elf_object(path_name, new_rpaths)
+                if (not allow_root and
+                    old_dir != new_dir and
+                    strings_contains_installroot(path_name, old_dir)):
+                        raise InstallRootStringException(path_name, old_dir)
     else:
         tty.die("Relocation not implemented for %s" % platform.system())
 
 
-def make_binary_relative(cur_path_names, orig_path_names, old_dir):
+def make_binary_relative(cur_path_names, orig_path_names, old_dir, allow_root):
     """
-    Make RPATHs relative to old_dir in given elf or mach-o files
+    Replace old RPATHs with paths relative to old_dir in binary files
     """
     if platform.system() == 'Darwin':
         for cur_path, orig_path in zip(cur_path_names, orig_path_names):
@@ -275,16 +365,56 @@ def make_binary_relative(cur_path_names, orig_path_names, old_dir):
             modify_macho_object(cur_path,
                                 rpaths, deps, idpath,
                                 new_rpaths, new_deps, new_idpath)
+            if (not allow_root and
+                strings_contains_installroot(cur_path)):
+                    raise InstallRootStringException(cur_path)
     elif platform.system() == 'Linux':
         for cur_path, orig_path in zip(cur_path_names, orig_path_names):
             orig_rpaths = get_existing_elf_rpaths(cur_path)
-            new_rpaths = get_relative_rpaths(orig_path, old_dir,
-                                             orig_rpaths)
-            modify_elf_object(cur_path, orig_rpaths, new_rpaths)
+            if orig_rpaths:
+                new_rpaths = get_relative_rpaths(orig_path, old_dir,
+                                                 orig_rpaths)
+                modify_elf_object(cur_path, new_rpaths)
+                if (not allow_root and
+                    strings_contains_installroot(cur_path, old_dir)):
+                        raise InstallRootStringException(cur_path, old_dir)
     else:
         tty.die("Prelocation not implemented for %s" % platform.system())
 
 
+def make_binary_placeholder(cur_path_names, allow_root):
+    """
+    Replace old install root in RPATHs with placeholder in binary files
+    """
+    if platform.system() == 'Darwin':
+        for cur_path in cur_path_names:
+            rpaths, deps, idpath = macho_get_paths(cur_path)
+            (new_rpaths,
+             new_deps,
+             new_idpath) = macho_make_paths_placeholder(rpaths, deps, idpath)
+            modify_macho_object(cur_path,
+                                rpaths, deps, idpath,
+                                new_rpaths, new_deps, new_idpath)
+            if (not allow_root and
+                strings_contains_installroot(cur_path,
+                                             spack.store.layout.root)):
+                raise InstallRootStringException(
+                    cur_path, spack.store.layout.root)
+    elif platform.system() == 'Linux':
+        for cur_path in cur_path_names:
+            orig_rpaths = get_existing_elf_rpaths(cur_path)
+            if orig_rpaths:
+                new_rpaths = get_placeholder_rpaths(cur_path, orig_rpaths)
+                modify_elf_object(cur_path, new_rpaths)
+                if (not allow_root and
+                    strings_contains_installroot(
+                        cur_path, spack.store.layout.root)):
+                    raise InstallRootStringException(
+                        cur_path, spack.store.layout.root)
+    else:
+        tty.die("Placeholder not implemented for %s" % platform.system())
+
+
 def relocate_text(path_names, old_dir, new_dir):
     """
     Replace old path with new path in text file path_name
diff --git a/lib/spack/spack/repository.py b/lib/spack/spack/repo.py
index e38af165f9..7e5a297664 100644
--- a/lib/spack/spack/repository.py
+++ b/lib/spack/spack/repo.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import collections
 import os
 import stat
@@ -29,10 +10,11 @@ import shutil
 import errno
 import sys
 import inspect
-import imp
 import re
 import traceback
 import json
+from contextlib import contextmanager
+from six import string_types
 
 try:
     from collections.abc import Mapping
@@ -41,24 +23,25 @@ except ImportError:
 
 from types import ModuleType
 
-import yaml
+import ruamel.yaml as yaml
 
 import llnl.util.lang
 import llnl.util.tty as tty
-from llnl.util.filesystem import mkdirp, join_path, install
+from llnl.util.filesystem import mkdirp, install
 
-import spack
+import spack.config
+import spack.caches
 import spack.error
 import spack.spec
+import spack.util.imp as simp
 from spack.provider_index import ProviderIndex
 from spack.util.path import canonicalize_path
 from spack.util.naming import NamespaceTrie, valid_module_name
 from spack.util.naming import mod_to_class, possible_spack_module_names
 
-#
-# Super-namespace for all packages.
-# Package modules are imported as spack.pkg.<namespace>.<pkg-name>.
-#
+
+#: Super-namespace for all packages.
+#: Package modules are imported as spack.pkg.<namespace>.<pkg-name>.
 repo_namespace     = 'spack.pkg'
 
 #
@@ -69,9 +52,25 @@ repo_index_name    = 'index.yaml'  # Top-level filename for repository index.
 packages_dir_name  = 'packages'    # Top-level repo directory containing pkgs.
 package_file_name  = 'package.py'  # Filename for packages in a repository.
 
-# Guaranteed unused default value for some functions.
+#: Guaranteed unused default value for some functions.
 NOT_PROVIDED = object()
 
+#: Code in ``_package_prepend`` is prepended to imported packages.
+#:
+#: Spack packages were originally expected to call `from spack import *`
+#: themselves, but it became difficult to manage and imports in the Spack
+#: core the top-level namespace polluted by package symbols this way.  To
+#: solve this, the top-level ``spack`` package contains very few symbols
+#: of its own, and importing ``*`` is essentially a no-op.  The common
+#: routines and directives that packages need are now in ``spack.pkgkit``,
+#: and the import system forces packages to automatically include
+#: this. This way, old packages that call ``from spack import *`` will
+#: continue to work without modification, but it's no longer required.
+#:
+#: TODO: At some point in the future, consider removing ``from spack import *``
+#: TODO: from packages and shifting to from ``spack.pkgkit import *``
+_package_prepend = 'from spack.pkgkit import *'
+
 
 def _autospec(function):
     """Decorator that automatically converts the argument of a single-arg
@@ -114,8 +113,7 @@ class FastPackageChecker(Mapping):
     _paths_cache = {}
 
     def __init__(self, packages_path):
-
-        #: The path of the repository managed by this instance
+        # The path of the repository managed by this instance
         self.packages_path = packages_path
 
         # If the cache we need is not there yet, then build it appropriately
@@ -138,7 +136,7 @@ class FastPackageChecker(Mapping):
         cache = {}
         for pkg_name in os.listdir(self.packages_path):
             # Skip non-directories in the package root.
-            pkg_dir = join_path(self.packages_path, pkg_name)
+            pkg_dir = os.path.join(self.packages_path, pkg_name)
 
             # Warn about invalid names that look like packages.
             if not valid_module_name(pkg_name):
@@ -220,8 +218,7 @@ class TagIndex(Mapping):
             pkg_name (str): name of the package to be removed from the index
 
         """
-
-        package = spack.repo.get(pkg_name)
+        package = path.get(pkg_name)
 
         # Remove the package from the list of packages, if present
         for pkg_list in self._tag_dict.values():
@@ -252,7 +249,8 @@ def make_provider_index_cache(packages_path, namespace):
     cache_filename = 'providers/{0}-index.yaml'.format(namespace)
 
     # Compute which packages needs to be updated in the cache
-    index_mtime = spack.misc_cache.mtime(cache_filename)
+    misc_cache = spack.caches.misc_cache
+    index_mtime = misc_cache.mtime(cache_filename)
 
     needs_update = [
         x for x, sinfo in fast_package_checker.items()
@@ -260,19 +258,19 @@ def make_provider_index_cache(packages_path, namespace):
     ]
 
     # Read the old ProviderIndex, or make a new one.
-    index_existed = spack.misc_cache.init_entry(cache_filename)
+    index_existed = misc_cache.init_entry(cache_filename)
 
     if index_existed and not needs_update:
 
         # If the provider index exists and doesn't need an update
         # just read from it
-        with spack.misc_cache.read_transaction(cache_filename) as f:
+        with misc_cache.read_transaction(cache_filename) as f:
             index = ProviderIndex.from_yaml(f)
 
     else:
 
         # Otherwise we need a write transaction to update it
-        with spack.misc_cache.write_transaction(cache_filename) as (old, new):
+        with misc_cache.write_transaction(cache_filename) as (old, new):
 
             index = ProviderIndex.from_yaml(old) if old else ProviderIndex()
 
@@ -305,7 +303,8 @@ def make_tag_index_cache(packages_path, namespace):
     cache_filename = 'tags/{0}-index.json'.format(namespace)
 
     # Compute which packages needs to be updated in the cache
-    index_mtime = spack.misc_cache.mtime(cache_filename)
+    misc_cache = spack.caches.misc_cache
+    index_mtime = misc_cache.mtime(cache_filename)
 
     needs_update = [
         x for x, sinfo in fast_package_checker.items()
@@ -313,19 +312,19 @@ def make_tag_index_cache(packages_path, namespace):
     ]
 
     # Read the old ProviderIndex, or make a new one.
-    index_existed = spack.misc_cache.init_entry(cache_filename)
+    index_existed = misc_cache.init_entry(cache_filename)
 
     if index_existed and not needs_update:
 
         # If the provider index exists and doesn't need an update
         # just read from it
-        with spack.misc_cache.read_transaction(cache_filename) as f:
+        with misc_cache.read_transaction(cache_filename) as f:
             index = TagIndex.from_json(f)
 
     else:
 
         # Otherwise we need a write transaction to update it
-        with spack.misc_cache.write_transaction(cache_filename) as (old, new):
+        with misc_cache.write_transaction(cache_filename) as (old, new):
 
             index = TagIndex.from_json(old) if old else TagIndex()
 
@@ -341,88 +340,62 @@ def make_tag_index_cache(packages_path, namespace):
 class RepoPath(object):
     """A RepoPath is a list of repos that function as one.
 
-       It functions exactly like a Repo, but it operates on the
-       combined results of the Repos in its list instead of on a
-       single package repository.
+    It functions exactly like a Repo, but it operates on the combined
+    results of the Repos in its list instead of on a single package
+    repository.
+
+    Args:
+        repos (list): list Repo objects or paths to put in this RepoPath
+
+    Optional Args:
+        repo_namespace (str): super-namespace for all packages in this
+            RepoPath (used when importing repos as modules)
     """
 
-    def __init__(self, *repo_dirs, **kwargs):
-        # super-namespace for all packages in the RepoPath
+    def __init__(self, *repos, **kwargs):
         self.super_namespace = kwargs.get('namespace', repo_namespace)
 
         self.repos = []
         self.by_namespace = NamespaceTrie()
-        self.by_path = {}
 
         self._all_package_names = None
         self._provider_index = None
 
-        # If repo_dirs is empty, just use the configuration
-        if not repo_dirs:
-            import spack.config
-            repo_dirs = spack.config.get_config('repos')
-            if not repo_dirs:
-                raise NoRepoConfiguredError(
-                    "Spack configuration contains no package repositories.")
-
         # Add each repo to this path.
-        for root in repo_dirs:
+        for repo in repos:
             try:
-                repo = Repo(root, self.super_namespace)
+                if isinstance(repo, string_types):
+                    repo = Repo(repo, self.super_namespace)
                 self.put_last(repo)
             except RepoError as e:
-                tty.warn("Failed to initialize repository at '%s'." % root,
+                tty.warn("Failed to initialize repository: '%s'." % repo,
                          e.message,
                          "To remove the bad repository, run this command:",
-                         "    spack repo rm %s" % root)
-
-    def swap(self, other):
-        """Convenience function to make swapping repositories easier.
-
-        This is currently used by mock tests.
-        TODO: Maybe there is a cleaner way.
-
-        """
-        attrs = ['repos',
-                 'by_namespace',
-                 'by_path',
-                 '_all_package_names',
-                 '_provider_index']
-        for attr in attrs:
-            tmp = getattr(self, attr)
-            setattr(self, attr, getattr(other, attr))
-            setattr(other, attr, tmp)
-
-    def _add(self, repo):
-        """Add a repository to the namespace and path indexes.
-
-        Checks for duplicates -- two repos can't have the same root
-        directory, and they provide have the same namespace.
-
-        """
-        if repo.root in self.by_path:
-            raise DuplicateRepoError("Duplicate repository: '%s'" % repo.root)
-
-        if repo.namespace in self.by_namespace:
-            raise DuplicateRepoError(
-                "Package repos '%s' and '%s' both provide namespace %s"
-                % (repo.root, self.by_namespace[repo.namespace].root,
-                   repo.namespace))
-
-        # Add repo to the pkg indexes
-        self.by_namespace[repo.full_namespace] = repo
-        self.by_path[repo.root] = repo
+                         "    spack repo rm %s" % repo)
 
     def put_first(self, repo):
         """Add repo first in the search path."""
-        self._add(repo)
+        if isinstance(repo, RepoPath):
+            for r in reversed(repo.repos):
+                self.put_first(r)
+            return
+
         self.repos.insert(0, repo)
+        self.by_namespace[repo.full_namespace] = repo
 
     def put_last(self, repo):
         """Add repo last in the search path."""
-        self._add(repo)
+        if isinstance(repo, RepoPath):
+            for r in repo.repos:
+                self.put_last(r)
+            return
+
         self.repos.append(repo)
 
+        # don't mask any higher-precedence repos with same namespace
+        if repo.full_namespace not in self.by_namespace:
+            self.by_namespace[repo.full_namespace] = repo
+
     def remove(self, repo):
         """Remove a repo from the search path."""
         if repo in self.repos:
@@ -648,18 +621,18 @@ class Repo(object):
                 raise BadRepoError(msg)
 
         # Validate repository layout.
-        self.config_file = join_path(self.root, repo_config_name)
+        self.config_file = os.path.join(self.root, repo_config_name)
         check(os.path.isfile(self.config_file),
               "No %s found in '%s'" % (repo_config_name, root))
 
-        self.packages_path = join_path(self.root, packages_dir_name)
+        self.packages_path = os.path.join(self.root, packages_dir_name)
         check(os.path.isdir(self.packages_path),
               "No directory '%s' found in '%s'" % (repo_config_name, root))
 
         # Read configuration and validate namespace
         config = self._read_config()
         check('namespace' in config, '%s must define a namespace.'
-              % join_path(root, repo_config_name))
+              % os.path.join(root, repo_config_name))
 
         self.namespace = config['namespace']
         check(re.match(r'[a-zA-Z][a-zA-Z0-9_.]+', self.namespace),
@@ -683,7 +656,7 @@ class Repo(object):
         self._instances = {}
 
         # Maps that goes from package name to corresponding file stat
-        self._fast_package_checker = FastPackageChecker(self.packages_path)
+        self._fast_package_checker = None
 
         # Index of virtual dependencies, computed lazily
         self._provider_index = None
@@ -819,7 +792,7 @@ class Repo(object):
                     % (self.config_file, self.root))
 
     @_autospec
-    def get(self, spec, new=False):
+    def get(self, spec):
         if not self.exists(spec.name):
             raise UnknownPackageError(spec.name)
 
@@ -828,18 +801,18 @@ class Repo(object):
                 "Repository %s does not contain package %s"
                 % (self.namespace, spec.fullname))
 
-        key = hash(spec)
-        if new or key not in self._instances:
-            package_class = self.get_pkg_class(spec.name)
-            try:
-                copy = spec.copy()  # defensive copy.  Package owns its spec.
-                self._instances[key] = package_class(copy)
-            except Exception:
-                if spack.debug:
-                    sys.excepthook(*sys.exc_info())
-                raise FailedConstructorError(spec.fullname, *sys.exc_info())
-
-        return self._instances[key]
+        package_class = self.get_pkg_class(spec.name)
+        try:
+            return package_class(spec)
+        except spack.error.SpackError:
+            # pass these through as their error messages will be fine.
+            raise
+        except Exception:
+            # make sure other errors in constructors hit the error
+            # handler by wrapping them
+            if spack.config.get('config:debug'):
+                sys.excepthook(*sys.exc_info())
+            raise FailedConstructorError(spec.fullname, *sys.exc_info())
 
     @_autospec
     def dump_provenance(self, spec, path):
@@ -917,7 +890,7 @@ class Repo(object):
         """Get the directory name for a particular package.  This is the
            directory that contains its package.py file."""
         self._check_namespace(spec)
-        return join_path(self.packages_path, spec.name)
+        return os.path.join(self.packages_path, spec.name)
 
     @_autospec
     def filename_for_package_name(self, spec):
@@ -931,11 +904,17 @@ class Repo(object):
         """
         self._check_namespace(spec)
         pkg_dir = self.dirname_for_package_name(spec.name)
-        return join_path(pkg_dir, package_file_name)
+        return os.path.join(pkg_dir, package_file_name)
+
+    @property
+    def _pkg_checker(self):
+        if self._fast_package_checker is None:
+            self._fast_package_checker = FastPackageChecker(self.packages_path)
+        return self._fast_package_checker
 
     def all_package_names(self):
         """Returns a sorted list of all package names in the Repo."""
-        return sorted(self._fast_package_checker.keys())
+        return sorted(self._pkg_checker.keys())
 
     def packages_with_tags(self, *tags):
         v = set(self.all_package_names())
@@ -957,7 +936,7 @@ class Repo(object):
 
     def exists(self, pkg_name):
         """Whether a package with the supplied name exists."""
-        return pkg_name in self._fast_package_checker
+        return pkg_name in self._pkg_checker
 
     def is_virtual(self, pkg_name):
         """True if the package with this name is virtual, False otherwise."""
@@ -987,7 +966,15 @@ class Repo(object):
             # e.g., spack.pkg.builtin.mpich
             fullname = "%s.%s" % (self.full_namespace, pkg_name)
 
-            module = imp.load_source(fullname, file_path)
+            try:
+                module = simp.load_source(fullname, file_path,
+                                          prepend=_package_prepend)
+            except SyntaxError as e:
+                # SyntaxError strips the path from the filename so we need to
+                # manually construct the error message in order to give the
+                # user the correct package.py where the syntax error is located
+                raise SyntaxError('invalid syntax in {0:}, line {1:}'
+                                  ''.format(file_path, e.lineno))
             module.__package__ = self.full_namespace
             module.__loader__ = self
             self._modules[pkg_name] = module
@@ -1084,6 +1071,78 @@ def create_repo(root, namespace=None):
     return full_path, namespace
 
 
+def create_or_construct(path, namespace=None):
+    """Create a repository, or just return a Repo if it already exists."""
+    if not os.path.exists(path):
+        mkdirp(path)
+        create_repo(path, namespace)
+    return Repo(path, namespace)
+
+
+def _path():
+    """Get the singleton RepoPath instance for Spack.
+
+    Create a RepoPath, add it to sys.meta_path, and return it.
+
+    TODO: consider not making this a singleton.
+    """
+    repo_dirs = spack.config.get('repos')
+    if not repo_dirs:
+        raise NoRepoConfiguredError(
+            "Spack configuration contains no package repositories.")
+
+    path = RepoPath(*repo_dirs)
+    sys.meta_path.append(path)
+    return path
+
+
+#: Singleton repo path instance
+path = llnl.util.lang.Singleton(_path)
+
+
+def get(spec):
+    """Convenience wrapper around ``spack.repo.get()``."""
+    return path.get(spec)
+
+
+def all_package_names():
+    """Convenience wrapper around ``spack.repo.all_package_names()``."""
+    return path.all_package_names()
+
+
+def set_path(repo):
+    """Set the path singleton to a specific value.
+
+    Overwrite ``path`` and register it as an importer in
+    ``sys.meta_path`` if it is a ``Repo`` or ``RepoPath``.
+    """
+    global path
+    path = repo
+
+    # make the new repo_path an importer if needed
+    append = isinstance(repo, (Repo, RepoPath))
+    if append:
+        sys.meta_path.append(repo)
+    return append
+
+
+@contextmanager
+def swap(repo_path):
+    """Temporarily use another RepoPath."""
+    global path
+
+    # swap out _path for repo_path
+    saved = path
+    remove_from_meta = set_path(repo_path)
+
+    yield
+
+    # restore _path and sys.meta_path
+    if remove_from_meta:
+        sys.meta_path.remove(repo_path)
+    path = saved
+
+
 class RepoError(spack.error.SpackError):
     """Superclass for repository-related errors."""
 
@@ -1100,10 +1159,6 @@ class BadRepoError(RepoError):
     """Raised when repo layout is invalid."""
 
 
-class DuplicateRepoError(RepoError):
-    """Raised when duplicate repos are added to a RepoPath."""
-
-
 class UnknownEntityError(RepoError):
     """Raised when we encounter a package spack doesn't have."""
 
diff --git a/lib/spack/spack/report.py b/lib/spack/spack/report.py
new file mode 100644
index 0000000000..74e5caf194
--- /dev/null
+++ b/lib/spack/spack/report.py
@@ -0,0 +1,267 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+"""Tools to produce reports of spec installations"""
+import codecs
+import collections
+import functools
+import time
+import traceback
+
+import llnl.util.lang
+import spack.build_environment
+import spack.fetch_strategy
+import spack.package
+from spack.reporter import Reporter
+from spack.reporters.cdash import CDash
+from spack.reporters.junit import JUnit
+
+report_writers = {
+    None: Reporter,
+    'junit': JUnit,
+    'cdash': CDash
+}
+
+#: Allowed report formats
+valid_formats = list(report_writers.keys())
+
+__all__ = [
+    'valid_formats',
+    'collect_info'
+]
+
+
+def fetch_package_log(pkg):
+    try:
+        with codecs.open(pkg.build_log_path, 'r', 'utf-8') as f:
+            return ''.join(f.readlines())
+    except Exception:
+        return 'Cannot open build log for {0}'.format(
+            pkg.spec.cshort_spec
+        )
+
+
+class InfoCollector(object):
+    """Decorates PackageBase.do_install to collect information
+    on the installation of certain specs.
+
+    When exiting the context this change will be rolled-back.
+
+    The data collected is available through the ``specs``
+    attribute once exited, and it's organized as a list where
+    each item represents the installation of one of the spec.
+
+    Args:
+        specs (list of Spec): specs whose install information will
+           be recorded
+    """
+    #: Backup of PackageBase.do_install
+    _backup_do_install = spack.package.PackageBase.do_install
+
+    def __init__(self, specs):
+        #: Specs that will be installed
+        self.input_specs = specs
+        #: This is where we record the data that will be included
+        #: in our report.
+        self.specs = []
+
+    def __enter__(self):
+        # Initialize the spec report with the data that is available upfront.
+        for input_spec in self.input_specs:
+            name_fmt = '{0}_{1}'
+            name = name_fmt.format(input_spec.name,
+                                   input_spec.dag_hash(length=7))
+
+            spec = {
+                'name': name,
+                'nerrors': None,
+                'nfailures': None,
+                'npackages': None,
+                'time': None,
+                'timestamp': time.strftime(
+                    "%a, %d %b %Y %H:%M:%S", time.gmtime()
+                ),
+                'properties': [],
+                'packages': []
+            }
+
+            self.specs.append(spec)
+
+            Property = collections.namedtuple('Property', ['name', 'value'])
+            spec['properties'].append(
+                Property('architecture', input_spec.architecture)
+            )
+            spec['properties'].append(
+                Property('compiler', input_spec.compiler))
+
+            # Check which specs are already installed and mark them as skipped
+            for dep in filter(lambda x: x.package.installed,
+                              input_spec.traverse()):
+                package = {
+                    'name': dep.name,
+                    'id': dep.dag_hash(),
+                    'elapsed_time': '0.0',
+                    'result': 'skipped',
+                    'message': 'Spec already installed'
+                }
+                spec['packages'].append(package)
+
+        def gather_info(do_install):
+            """Decorates do_install to gather useful information for
+            a CI report.
+
+            It's defined here to capture the environment and build
+            this context as the installations proceed.
+            """
+            @functools.wraps(do_install)
+            def wrapper(pkg, *args, **kwargs):
+
+                # We accounted before for what is already installed
+                installed_on_entry = pkg.installed
+
+                package = {
+                    'name': pkg.name,
+                    'id': pkg.spec.dag_hash(),
+                    'elapsed_time': None,
+                    'result': None,
+                    'message': None
+                }
+
+                start_time = time.time()
+                value = None
+                try:
+
+                    value = do_install(pkg, *args, **kwargs)
+                    package['result'] = 'success'
+                    package['stdout'] = fetch_package_log(pkg)
+                    if installed_on_entry:
+                        return
+
+                except spack.build_environment.InstallError as e:
+                    # An InstallError is considered a failure (the recipe
+                    # didn't work correctly)
+                    package['result'] = 'failure'
+                    package['stdout'] = fetch_package_log(pkg)
+                    package['message'] = e.message or 'Installation failure'
+                    package['exception'] = e.traceback
+
+                except (Exception, BaseException) as e:
+                    # Everything else is an error (the installation
+                    # failed outside of the child process)
+                    package['result'] = 'error'
+                    package['stdout'] = fetch_package_log(pkg)
+                    package['message'] = str(e) or 'Unknown error'
+                    package['exception'] = traceback.format_exc()
+
+                finally:
+                    package['elapsed_time'] = time.time() - start_time
+
+                # Append the package to the correct spec report. In some
+                # cases it may happen that a spec that is asked to be
+                # installed explicitly will also be installed as a
+                # dependency of another spec. In this case append to both
+                # spec reports.
+                for s in llnl.util.lang.dedupe([pkg.spec.root, pkg.spec]):
+                    name = name_fmt.format(s.name, s.dag_hash(length=7))
+                    try:
+                        item = next((
+                            x for x in self.specs
+                            if x['name'] == name
+                        ))
+                        item['packages'].append(package)
+                    except StopIteration:
+                        pass
+
+                return value
+
+            return wrapper
+
+        spack.package.PackageBase.do_install = gather_info(
+            spack.package.PackageBase.do_install
+        )
+
+    def __exit__(self, exc_type, exc_val, exc_tb):
+
+        # Restore the original method in PackageBase
+        spack.package.PackageBase.do_install = InfoCollector._backup_do_install
+
+        for spec in self.specs:
+            spec['npackages'] = len(spec['packages'])
+            spec['nfailures'] = len(
+                [x for x in spec['packages'] if x['result'] == 'failure']
+            )
+            spec['nerrors'] = len(
+                [x for x in spec['packages'] if x['result'] == 'error']
+            )
+            spec['time'] = sum([
+                float(x['elapsed_time']) for x in spec['packages']
+            ])
+
+
+class collect_info(object):
+    """Collects information to build a report while installing
+    and dumps it on exit.
+
+    If the format name is not ``None``, this context manager
+    decorates PackageBase.do_install when entering the context
+    and unrolls the change when exiting.
+
+    Within the context, only the specs that are passed to it
+    on initialization will be recorded for the report. Data from
+    other specs will be discarded.
+
+    Examples:
+
+        .. code-block:: python
+
+            # The file 'junit.xml' is written when exiting
+            # the context
+            specs = [Spec('hdf5').concretized()]
+            with collect_info(specs, 'junit', 'junit.xml'):
+                # A report will be generated for these specs...
+                for spec in specs:
+                    spec.do_install()
+                # ...but not for this one
+                Spec('zlib').concretized().do_install()
+
+    Args:
+        format_name (str or None): one of the supported formats
+        install_command (str): the command line passed to spack
+        cdash_upload_url (str or None): where to upload the report
+
+    Raises:
+        ValueError: when ``format_name`` is not in ``valid_formats``
+    """
+    def __init__(self, format_name, install_command, cdash_upload_url):
+        self.filename = None
+        if cdash_upload_url:
+            self.format_name = 'cdash'
+            self.filename = 'cdash_report'
+        else:
+            self.format_name = format_name
+        # Check that the format is valid.
+        if self.format_name not in valid_formats:
+            raise ValueError('invalid report type: {0}'
+                             .format(self.format_name))
+        self.report_writer = report_writers[self.format_name](
+            install_command, cdash_upload_url)
+
+    def concretization_report(self, msg):
+        self.report_writer.concretization_report(self.filename, msg)
+
+    def __enter__(self):
+        if self.format_name:
+            # Start the collector and patch PackageBase.do_install
+            self.collector = InfoCollector(self.specs)
+            self.collector.__enter__()
+
+    def __exit__(self, exc_type, exc_val, exc_tb):
+        if self.format_name:
+            # Close the collector and restore the
+            # original PackageBase.do_install
+            self.collector.__exit__(exc_type, exc_val, exc_tb)
+
+            report_data = {'specs': self.collector.specs}
+            self.report_writer.build_report(self.filename, report_data)
diff --git a/lib/spack/spack/reporter.py b/lib/spack/spack/reporter.py
new file mode 100644
index 0000000000..17efe23637
--- /dev/null
+++ b/lib/spack/spack/reporter.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+__all__ = ['Reporter']
+
+
+class Reporter(object):
+    """Base class for report writers."""
+
+    def __init__(self, install_command, cdash_upload_url):
+        self.install_command = install_command
+        self.cdash_upload_url = cdash_upload_url
+
+    def build_report(self, filename, report_data):
+        pass
+
+    def concretization_report(self, filename, msg):
+        pass
diff --git a/lib/spack/spack/reporters/__init__.py b/lib/spack/spack/reporters/__init__.py
new file mode 100644
index 0000000000..4f442db458
--- /dev/null
+++ b/lib/spack/spack/reporters/__init__.py
@@ -0,0 +1,4 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
diff --git a/lib/spack/spack/reporters/cdash.py b/lib/spack/spack/reporters/cdash.py
new file mode 100644
index 0000000000..e27d7e9728
--- /dev/null
+++ b/lib/spack/spack/reporters/cdash.py
@@ -0,0 +1,199 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+import codecs
+import hashlib
+import os.path
+import platform
+import re
+import socket
+import time
+import xml.sax.saxutils
+from six import text_type
+from six.moves.urllib.request import build_opener, HTTPHandler, Request
+
+import spack.build_environment
+import spack.fetch_strategy
+import spack.package
+from spack.reporter import Reporter
+from spack.util.crypto import checksum
+from spack.util.log_parse import parse_log_events
+
+__all__ = ['CDash']
+
+# Mapping Spack phases to the corresponding CTest/CDash phase.
+map_phases_to_cdash = {
+    'autoreconf': 'configure',
+    'cmake':      'configure',
+    'configure':  'configure',
+    'edit':       'configure',
+    'build':      'build',
+    'install':    'build'
+}
+
+# Initialize data structures common to each phase's report.
+cdash_phases = set(map_phases_to_cdash.values())
+
+
+class CDash(Reporter):
+    """Generate reports of spec installations for CDash.
+
+    To use this reporter, pass the ``--cdash-upload-url`` argument to
+    ``spack install``::
+
+        spack install --cdash-upload-url=\\
+            https://mydomain.com/cdash/submit.php?project=Spack <spec>
+
+    In this example, results will be uploaded to the *Spack* project on the
+    CDash instance hosted at https://mydomain.com/cdash.
+    """
+
+    def __init__(self, install_command, cdash_upload_url):
+        Reporter.__init__(self, install_command, cdash_upload_url)
+        self.template_dir = os.path.join('reports', 'cdash')
+        self.hostname = socket.gethostname()
+        self.osname = platform.system()
+        self.starttime = int(time.time())
+        # TODO: remove hardcoded use of Experimental here.
+        #       Make the submission model configurable.
+        self.buildstamp = time.strftime("%Y%m%d-%H%M-Experimental",
+                                        time.localtime(self.starttime))
+
+    def build_report(self, filename, report_data):
+        self.initialize_report(filename, report_data)
+
+        for phase in cdash_phases:
+            report_data[phase] = {}
+            report_data[phase]['log'] = ""
+            report_data[phase]['status'] = 0
+            report_data[phase]['starttime'] = self.starttime
+            report_data[phase]['endtime'] = self.starttime
+
+        # Track the phases we perform so we know what reports to create.
+        phases_encountered = []
+
+        # Parse output phase-by-phase.
+        phase_regexp = re.compile(r"Executing phase: '(.*)'")
+        for spec in report_data['specs']:
+            for package in spec['packages']:
+                if 'stdout' in package:
+                    current_phase = ''
+                    cdash_phase = ''
+                    for line in package['stdout'].splitlines():
+                        match = phase_regexp.search(line)
+                        if match:
+                            current_phase = match.group(1)
+                            if current_phase not in map_phases_to_cdash:
+                                current_phase = ''
+                                continue
+                            cdash_phase = \
+                                map_phases_to_cdash[current_phase]
+                            if cdash_phase not in phases_encountered:
+                                phases_encountered.append(cdash_phase)
+                            report_data[cdash_phase]['log'] += \
+                                text_type("{0} output for {1}:\n".format(
+                                    cdash_phase, package['name']))
+                        elif cdash_phase:
+                            report_data[cdash_phase]['log'] += \
+                                xml.sax.saxutils.escape(line) + "\n"
+
+        # Move the build phase to the front of the list if it occurred.
+        # This supports older versions of CDash that expect this phase
+        # to be reported before all others.
+        if "build" in phases_encountered:
+            build_pos = phases_encountered.index("build")
+            phases_encountered.insert(0, phases_encountered.pop(build_pos))
+
+        for phase in phases_encountered:
+            errors, warnings = parse_log_events(
+                report_data[phase]['log'].splitlines())
+            nerrors = len(errors)
+
+            if phase == 'configure' and nerrors > 0:
+                report_data[phase]['status'] = 1
+
+            if phase == 'build':
+                # Convert log output from ASCII to Unicode and escape for XML.
+                def clean_log_event(event):
+                    event = vars(event)
+                    event['text'] = xml.sax.saxutils.escape(event['text'])
+                    event['pre_context'] = xml.sax.saxutils.escape(
+                        '\n'.join(event['pre_context']))
+                    event['post_context'] = xml.sax.saxutils.escape(
+                        '\n'.join(event['post_context']))
+                    # source_file and source_line_no are either strings or
+                    # the tuple (None,).  Distinguish between these two cases.
+                    if event['source_file'][0] is None:
+                        event['source_file'] = ''
+                        event['source_line_no'] = ''
+                    else:
+                        event['source_file'] = xml.sax.saxutils.escape(
+                            event['source_file'])
+                    return event
+
+                report_data[phase]['errors'] = []
+                report_data[phase]['warnings'] = []
+                for error in errors:
+                    report_data[phase]['errors'].append(clean_log_event(error))
+                for warning in warnings:
+                    report_data[phase]['warnings'].append(
+                        clean_log_event(warning))
+
+            # Write the report.
+            report_name = phase.capitalize() + ".xml"
+            phase_report = os.path.join(filename, report_name)
+
+            with codecs.open(phase_report, 'w', 'utf-8') as f:
+                env = spack.tengine.make_environment()
+                site_template = os.path.join(self.template_dir, 'Site.xml')
+                t = env.get_template(site_template)
+                f.write(t.render(report_data))
+
+                phase_template = os.path.join(self.template_dir, report_name)
+                t = env.get_template(phase_template)
+                f.write(t.render(report_data))
+            self.upload(phase_report)
+
+    def concretization_report(self, filename, msg):
+        report_data = {}
+        self.initialize_report(filename, report_data)
+        report_data['starttime'] = self.starttime
+        report_data['endtime'] = self.starttime
+        report_data['msg'] = msg
+
+        env = spack.tengine.make_environment()
+        update_template = os.path.join(self.template_dir, 'Update.xml')
+        t = env.get_template(update_template)
+        output_filename = os.path.join(filename, 'Update.xml')
+        with open(output_filename, 'w') as f:
+            f.write(t.render(report_data))
+        self.upload(output_filename)
+
+    def initialize_report(self, filename, report_data):
+        if not os.path.exists(filename):
+            os.mkdir(filename)
+        report_data['install_command'] = self.install_command
+        report_data['buildstamp'] = self.buildstamp
+        report_data['hostname'] = self.hostname
+        report_data['osname'] = self.osname
+
+    def upload(self, filename):
+        if not self.cdash_upload_url:
+            return
+
+        # Compute md5 checksum for the contents of this file.
+        md5sum = checksum(hashlib.md5, filename, block_size=8192)
+
+        opener = build_opener(HTTPHandler)
+        with open(filename, 'rb') as f:
+            url = "{0}&MD5={1}".format(self.cdash_upload_url, md5sum)
+            request = Request(url, data=f)
+            request.add_header('Content-Type', 'text/xml')
+            request.add_header('Content-Length', os.path.getsize(filename))
+            # By default, urllib2 only support GET and POST.
+            # CDash needs expects this file to be uploaded via PUT.
+            request.get_method = lambda: 'PUT'
+            url = opener.open(request)
diff --git a/lib/spack/spack/reporters/junit.py b/lib/spack/spack/reporters/junit.py
new file mode 100644
index 0000000000..264da413f0
--- /dev/null
+++ b/lib/spack/spack/reporters/junit.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import os
+import os.path
+
+import spack.build_environment
+import spack.fetch_strategy
+import spack.package
+from spack.reporter import Reporter
+
+__all__ = ['JUnit']
+
+
+class JUnit(Reporter):
+    """Generate reports of spec installations for JUnit."""
+
+    def __init__(self, install_command, cdash_upload_url):
+        Reporter.__init__(self, install_command, cdash_upload_url)
+        self.template_file = os.path.join('reports', 'junit.xml')
+
+    def build_report(self, filename, report_data):
+        # Write the report
+        with open(filename, 'w') as f:
+            env = spack.tengine.make_environment()
+            t = env.get_template(self.template_file)
+            f.write(t.render(report_data))
diff --git a/lib/spack/spack/resource.py b/lib/spack/spack/resource.py
index 35ae0170e6..da697d4b2f 100644
--- a/lib/spack/spack/resource.py
+++ b/lib/spack/spack/resource.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """Describes an optional resource needed for a build.
 
 Typically a bunch of sources that can be built in-tree within another
diff --git a/lib/spack/spack/schema/__init__.py b/lib/spack/spack/schema/__init__.py
index 764dbd23bc..b7a90827f2 100644
--- a/lib/spack/spack/schema/__init__.py
+++ b/lib/spack/spack/schema/__init__.py
@@ -1,33 +1,6 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-"""This module contains jsonschema files for all of Spack's YAML formats.
-"""
-from llnl.util.lang import list_modules
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-# Automatically bring in all sub-modules
-__all__ = []
-for mod in list_modules(__path__[0]):
-    __import__('%s.%s' % (__name__, mod))
-    __all__.append(mod)
+"""This module contains jsonschema files for all of Spack's YAML formats."""
diff --git a/lib/spack/spack/schema/compilers.py b/lib/spack/spack/schema/compilers.py
index caa0d27662..139462d2d4 100644
--- a/lib/spack/spack/schema/compilers.py
+++ b/lib/spack/spack/schema/compilers.py
@@ -1,43 +1,23 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """Schema for compilers.yaml configuration file.
 
 .. literalinclude:: ../spack/schema/compilers.py
-   :lines: 32-
+   :lines: 13-
 """
 
 
-schema = {
-    '$schema': 'http://json-schema.org/schema#',
-    'title': 'Spack compiler configuration file schema',
-    'type': 'object',
-    'additionalProperties': False,
-    'patternProperties': {
-        'compilers': {
-            'type': 'array',
-            'items': {
+#: Properties for inclusion in other schemas
+properties = {
+    'compilers': {
+        'type': 'array',
+        'items': [{
+            'type': 'object',
+            'additionalProperties': False,
+            'properties': {
                 'compiler': {
                     'type': 'object',
                     'additionalProperties': False,
@@ -75,6 +55,7 @@ schema = {
                                                      {'type': 'null'}]}}},
                         'spec': {'type': 'string'},
                         'operating_system': {'type': 'string'},
+                        'target': {'type': 'string'},
                         'alias': {'anyOf': [{'type': 'string'},
                                             {'type': 'null'}]},
                         'modules': {'anyOf': [{'type': 'string'},
@@ -88,8 +69,37 @@ schema = {
                                 'set': {
                                     'type': 'object',
                                     'patternProperties': {
-                                        r'\w[\w-]*': {  # variable name
-                                            'type': 'string'
+                                        # Variable name
+                                        r'\w[\w-]*': {
+                                            'anyOf': [{'type': 'string'},
+                                                      {'type': 'number'}]
+                                        }
+                                    }
+                                },
+                                'unset': {
+                                    'type': 'object',
+                                    'patternProperties': {
+                                        # Variable name
+                                        r'\w[\w-]*': {'type': 'null'}
+                                    }
+                                },
+                                'prepend-path': {
+                                    'type': 'object',
+                                    'patternProperties': {
+                                        # Variable name
+                                        r'\w[\w-]*': {
+                                            'anyOf': [{'type': 'string'},
+                                                      {'type': 'number'}]
+                                        }
+                                    }
+                                },
+                                'append-path': {
+                                    'type': 'object',
+                                    'patternProperties': {
+                                        # Variable name
+                                        r'\w[\w-]*': {
+                                            'anyOf': [{'type': 'string'},
+                                                      {'type': 'number'}]
                                         }
                                     }
                                 }
@@ -100,9 +110,19 @@ schema = {
                             'default': [],
                             'items': {'type': 'string'}
                         }
-                    },
-                },
-            },
-        },
-    },
+                    }
+                }
+            }
+        }]
+    }
+}
+
+
+#: Full schema with metadata
+schema = {
+    '$schema': 'http://json-schema.org/schema#',
+    'title': 'Spack compiler configuration file schema',
+    'type': 'object',
+    'additionalProperties': False,
+    'properties': properties,
 }
diff --git a/lib/spack/spack/schema/config.py b/lib/spack/spack/schema/config.py
index 57a1c075b1..0558a7a9ae 100644
--- a/lib/spack/spack/schema/config.py
+++ b/lib/spack/spack/schema/config.py
@@ -1,73 +1,70 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """Schema for config.yaml configuration file.
 
 .. literalinclude:: ../spack/schema/config.py
-   :lines: 32-
+   :lines: 13-
 """
 
 
+#: Properties for inclusion in other schemas
+properties = {
+    'config': {
+        'type': 'object',
+        'default': {},
+        'properties': {
+            'install_tree': {'type': 'string'},
+            'install_hash_length': {'type': 'integer', 'minimum': 1},
+            'install_path_scheme': {'type': 'string'},
+            'build_stage': {
+                'oneOf': [
+                    {'type': 'string'},
+                    {'type': 'array',
+                     'items': {'type': 'string'}}],
+            },
+            'template_dirs': {
+                'type': 'array',
+                'items': {'type': 'string'}
+            },
+            'module_roots': {
+                'type': 'object',
+                'additionalProperties': False,
+                'properties': {
+                    'tcl': {'type': 'string'},
+                    'lmod': {'type': 'string'},
+                    'dotkit': {'type': 'string'},
+                },
+            },
+            'source_cache': {'type': 'string'},
+            'misc_cache': {'type': 'string'},
+            'verify_ssl': {'type': 'boolean'},
+            'debug': {'type': 'boolean'},
+            'checksum': {'type': 'boolean'},
+            'locks': {'type': 'boolean'},
+            'dirty': {'type': 'boolean'},
+            'build_language': {'type': 'string'},
+            'build_jobs': {'type': 'integer', 'minimum': 1},
+            'ccache': {'type': 'boolean'},
+            'db_lock_timeout': {'type': 'integer', 'minimum': 1},
+            'package_lock_timeout': {
+                'anyOf': [
+                    {'type': 'integer', 'minimum': 1},
+                    {'type': 'null'}
+                ],
+            },
+        },
+    },
+}
+
+
+#: Full schema with metadata
 schema = {
     '$schema': 'http://json-schema.org/schema#',
-    'title': 'Spack module file configuration file schema',
+    'title': 'Spack core configuration file schema',
     'type': 'object',
     'additionalProperties': False,
-    'patternProperties': {
-        'config': {
-            'type': 'object',
-            'default': {},
-            'properties': {
-                'install_tree': {'type': 'string'},
-                'install_hash_length': {'type': 'integer', 'minimum': 1},
-                'install_path_scheme': {'type': 'string'},
-                'build_stage': {
-                    'oneOf': [
-                        {'type': 'string'},
-                        {'type': 'array',
-                         'items': {'type': 'string'}}],
-                },
-                'template_dirs': {
-                    'type': 'array',
-                    'items': {'type': 'string'}
-                },
-                'module_roots': {
-                    'type': 'object',
-                    'additionalProperties': False,
-                    'properties': {
-                        'tcl': {'type': 'string'},
-                        'lmod': {'type': 'string'},
-                        'dotkit': {'type': 'string'},
-                    },
-                },
-                'source_cache': {'type': 'string'},
-                'misc_cache': {'type': 'string'},
-                'verify_ssl': {'type': 'boolean'},
-                'checksum': {'type': 'boolean'},
-                'dirty': {'type': 'boolean'},
-                'build_jobs': {'type': 'integer', 'minimum': 1},
-            }
-        },
-    },
+    'properties': properties,
 }
diff --git a/lib/spack/spack/schema/env.py b/lib/spack/spack/schema/env.py
new file mode 100644
index 0000000000..7b6ad602f7
--- /dev/null
+++ b/lib/spack/spack/schema/env.py
@@ -0,0 +1,57 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+"""Schema for env.yaml configuration file.
+
+.. literalinclude:: ../spack/schema/env.py
+   :lines: 36-
+"""
+from llnl.util.lang import union_dicts
+
+import spack.schema.merged
+import spack.schema.modules
+
+
+schema = {
+    '$schema': 'http://json-schema.org/schema#',
+    'title': 'Spack environment file schema',
+    'definitions': spack.schema.modules.definitions,
+    'type': 'object',
+    'additionalProperties': False,
+    'patternProperties': {
+        '^env|spack$': {
+            'type': 'object',
+            'default': {},
+            'additionalProperties': False,
+            'properties': union_dicts(
+                # merged configuration scope schemas
+                spack.schema.merged.properties,
+                # extra environment schema properties
+                {
+                    'include': {
+                        'type': 'array',
+                        'items': {
+                            'type': 'string'
+                        },
+                    },
+                    'specs': {
+                        # Specs is a list of specs, which can have
+                        # optional additional properties in a sub-dict
+                        'type': 'array',
+                        'default': [],
+                        'additionalProperties': False,
+                        'items': {
+                            'anyOf': [
+                                {'type': 'string'},
+                                {'type': 'null'},
+                                {'type': 'object'},
+                            ]
+                        }
+                    }
+                }
+            )
+        }
+    }
+}
diff --git a/lib/spack/spack/schema/merged.py b/lib/spack/spack/schema/merged.py
new file mode 100644
index 0000000000..4505728076
--- /dev/null
+++ b/lib/spack/spack/schema/merged.py
@@ -0,0 +1,40 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+"""Schema for configuration merged into one file.
+
+.. literalinclude:: ../spack/schema/merged.py
+   :lines: 40-
+"""
+from llnl.util.lang import union_dicts
+
+import spack.schema.compilers
+import spack.schema.config
+import spack.schema.mirrors
+import spack.schema.modules
+import spack.schema.packages
+import spack.schema.repos
+
+
+#: Properties for inclusion in other schemas
+properties = union_dicts(
+    spack.schema.compilers.properties,
+    spack.schema.config.properties,
+    spack.schema.mirrors.properties,
+    spack.schema.modules.properties,
+    spack.schema.packages.properties,
+    spack.schema.repos.properties
+)
+
+
+#: Full schema with metadata
+schema = {
+    '$schema': 'http://json-schema.org/schema#',
+    'title': 'Spack merged configuration file schema',
+    'definitions': spack.schema.modules.definitions,
+    'type': 'object',
+    'additionalProperties': False,
+    'properties': properties,
+}
diff --git a/lib/spack/spack/schema/mirrors.py b/lib/spack/spack/schema/mirrors.py
index b826bc251c..345f43db66 100644
--- a/lib/spack/spack/schema/mirrors.py
+++ b/lib/spack/spack/schema/mirrors.py
@@ -1,48 +1,33 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """Schema for mirrors.yaml configuration file.
 
 .. literalinclude:: ../spack/schema/mirrors.py
-   :lines: 32-
+   :lines: 13-
 """
 
 
+#: Properties for inclusion in other schemas
+properties = {
+    'mirrors': {
+        'type': 'object',
+        'default': {},
+        'additionalProperties': False,
+        'patternProperties': {
+            r'\w[\w-]*': {'type': 'string'},
+        },
+    },
+}
+
+
+#: Full schema with metadata
 schema = {
     '$schema': 'http://json-schema.org/schema#',
     'title': 'Spack mirror configuration file schema',
     'type': 'object',
     'additionalProperties': False,
-    'patternProperties': {
-        r'mirrors': {
-            'type': 'object',
-            'default': {},
-            'additionalProperties': False,
-            'patternProperties': {
-                r'\w[\w-]*': {
-                    'type': 'string'},
-            },
-        },
-    },
+    'properties': properties,
 }
diff --git a/lib/spack/spack/schema/modules.py b/lib/spack/spack/schema/modules.py
index 08380f0789..0a54856105 100644
--- a/lib/spack/spack/schema/modules.py
+++ b/lib/spack/spack/schema/modules.py
@@ -1,182 +1,179 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """Schema for modules.yaml configuration file.
 
 .. literalinclude:: ../spack/schema/modules.py
-   :lines: 32-
+   :lines: 13-
 """
 
 
-schema = {
-    '$schema': 'http://json-schema.org/schema#',
-    'title': 'Spack module file configuration file schema',
-    'type': 'object',
-    'additionalProperties': False,
-    'definitions': {
-        'array_of_strings': {
-            'type': 'array',
-            'default': [],
-            'items': {
+#: Definitions for parts of module schema
+definitions = {
+    'array_of_strings': {
+        'type': 'array',
+        'default': [],
+        'items': {
+            'type': 'string'
+        }
+    },
+    'dictionary_of_strings': {
+        'type': 'object',
+        'patternProperties': {
+            r'\w[\w-]*': {  # key
                 'type': 'string'
             }
-        },
-        'dictionary_of_strings': {
-            'type': 'object',
-            'patternProperties': {
-                r'\w[\w-]*': {  # key
-                    'type': 'string'
-                }
-            }
-        },
-        'dependency_selection': {
-            'type': 'string',
-            'enum': ['none', 'direct', 'all']
-        },
-        'module_file_configuration': {
-            'type': 'object',
-            'default': {},
-            'additionalProperties': False,
-            'properties': {
-                'filter': {
-                    'type': 'object',
-                    'default': {},
-                    'additionalProperties': False,
-                    'properties': {
-                        'environment_blacklist': {
-                            'type': 'array',
-                            'default': [],
-                            'items': {
-                                'type': 'string'
-                            }
+        }
+    },
+    'dependency_selection': {
+        'type': 'string',
+        'enum': ['none', 'direct', 'all']
+    },
+    'module_file_configuration': {
+        'type': 'object',
+        'default': {},
+        'additionalProperties': False,
+        'properties': {
+            'filter': {
+                'type': 'object',
+                'default': {},
+                'additionalProperties': False,
+                'properties': {
+                    'environment_blacklist': {
+                        'type': 'array',
+                        'default': [],
+                        'items': {
+                            'type': 'string'
                         }
                     }
+                }
+            },
+            'template': {
+                'type': 'string'
+            },
+            'autoload': {
+                '$ref': '#/definitions/dependency_selection'},
+            'prerequisites': {
+                '$ref': '#/definitions/dependency_selection'},
+            'conflict': {
+                '$ref': '#/definitions/array_of_strings'},
+            'load': {
+                '$ref': '#/definitions/array_of_strings'},
+            'suffixes': {
+                '$ref': '#/definitions/dictionary_of_strings'},
+            'environment': {
+                'type': 'object',
+                'default': {},
+                'additionalProperties': False,
+                'properties': {
+                    'set': {
+                        '$ref': '#/definitions/dictionary_of_strings'},
+                    'unset': {
+                        '$ref': '#/definitions/array_of_strings'},
+                    'prepend_path': {
+                        '$ref': '#/definitions/dictionary_of_strings'},
+                    'append_path': {
+                        '$ref': '#/definitions/dictionary_of_strings'}
+                }
+            }
+        }
+    },
+    'module_type_configuration': {
+        'type': 'object',
+        'default': {},
+        'anyOf': [
+            {'properties': {
+                'verbose': {
+                    'type': 'boolean',
+                    'default': False
                 },
-                'template': {
-                    'type': 'string'
+                'hash_length': {
+                    'type': 'integer',
+                    'minimum': 0,
+                    'default': 7
                 },
-                'autoload': {
-                    '$ref': '#/definitions/dependency_selection'},
-                'prerequisites': {
-                    '$ref': '#/definitions/dependency_selection'},
-                'conflict': {
+                'whitelist': {
                     '$ref': '#/definitions/array_of_strings'},
-                'load': {
+                'blacklist': {
                     '$ref': '#/definitions/array_of_strings'},
-                'suffixes': {
-                    '$ref': '#/definitions/dictionary_of_strings'},
-                'environment': {
-                    'type': 'object',
-                    'default': {},
-                    'additionalProperties': False,
-                    'properties': {
-                        'set': {
-                            '$ref': '#/definitions/dictionary_of_strings'},
-                        'unset': {
-                            '$ref': '#/definitions/array_of_strings'},
-                        'prepend_path': {
-                            '$ref': '#/definitions/dictionary_of_strings'},
-                        'append_path': {
-                            '$ref': '#/definitions/dictionary_of_strings'}
-                    }
+                'blacklist_implicits': {
+                    'type': 'boolean',
+                    'default': False
+                },
+                'naming_scheme': {
+                    'type': 'string'  # Can we be more specific here?
                 }
-            }
-        },
-        'module_type_configuration': {
-            'type': 'object',
-            'default': {},
-            'anyOf': [
-                {'properties': {
-                    'verbose': {
-                        'type': 'boolean',
-                        'default': False
-                    },
-                    'hash_length': {
-                        'type': 'integer',
-                        'minimum': 0,
-                        'default': 7
-                    },
-                    'whitelist': {
-                        '$ref': '#/definitions/array_of_strings'},
-                    'blacklist': {
-                        '$ref': '#/definitions/array_of_strings'},
-                    'naming_scheme': {
-                        'type': 'string'  # Can we be more specific here?
-                    }
-                }},
-                {'patternProperties': {
+            }},
+            {'patternProperties': {
+                r'\w[\w-]*': {
+                    '$ref': '#/definitions/module_file_configuration'
+                }
+            }}
+        ]
+    }
+}
+
+
+# Properties for inclusion into other schemas (requires definitions)
+properties = {
+    'modules': {
+        'type': 'object',
+        'default': {},
+        'additionalProperties': False,
+        'properties': {
+            'prefix_inspections': {
+                'type': 'object',
+                'patternProperties': {
+                    # prefix-relative path to be inspected for existence
                     r'\w[\w-]*': {
-                        '$ref': '#/definitions/module_file_configuration'
-                    }
-                }}
-            ]
-        }
-    },
-    'patternProperties': {
-        r'modules': {
-            'type': 'object',
-            'default': {},
-            'additionalProperties': False,
-            'properties': {
-                'prefix_inspections': {
-                    'type': 'object',
-                    'patternProperties': {
-                        # prefix-relative path to be inspected for existence
-                        r'\w[\w-]*': {
-                            '$ref': '#/definitions/array_of_strings'}}},
-                'enable': {
-                    'type': 'array',
-                    'default': [],
-                    'items': {
-                        'type': 'string',
-                        'enum': ['tcl', 'dotkit', 'lmod']}},
-                'lmod': {
-                    'allOf': [
-                        # Base configuration
-                        {'$ref': '#/definitions/module_type_configuration'},
-                        {
-                            'core_compilers': {
-                                '$ref': '#/definitions/array_of_strings'
-                            },
-                            'hierarchical_scheme': {
-                                '$ref': '#/definitions/array_of_strings'
-                            }
-                        }  # Specific lmod extensions
-                    ]},
-                'tcl': {
-                    'allOf': [
-                        # Base configuration
-                        {'$ref': '#/definitions/module_type_configuration'},
-                        {}  # Specific tcl extensions
-                    ]},
-                'dotkit': {
-                    'allOf': [
-                        # Base configuration
-                        {'$ref': '#/definitions/module_type_configuration'},
-                        {}  # Specific dotkit extensions
-                    ]},
-            }
+                        '$ref': '#/definitions/array_of_strings'}}},
+            'enable': {
+                'type': 'array',
+                'default': [],
+                'items': {
+                    'type': 'string',
+                    'enum': ['tcl', 'dotkit', 'lmod']}},
+            'lmod': {
+                'allOf': [
+                    # Base configuration
+                    {'$ref': '#/definitions/module_type_configuration'},
+                    {
+                        'core_compilers': {
+                            '$ref': '#/definitions/array_of_strings'
+                        },
+                        'hierarchical_scheme': {
+                            '$ref': '#/definitions/array_of_strings'
+                        }
+                    }  # Specific lmod extensions
+                ]
+            },
+            'tcl': {
+                'allOf': [
+                    # Base configuration
+                    {'$ref': '#/definitions/module_type_configuration'},
+                    {}  # Specific tcl extensions
+                ]
+            },
+            'dotkit': {
+                'allOf': [
+                    # Base configuration
+                    {'$ref': '#/definitions/module_type_configuration'},
+                    {}  # Specific dotkit extensions
+                ]
+            },
         },
     },
 }
+
+
+#: Full schema with metadata
+schema = {
+    '$schema': 'http://json-schema.org/schema#',
+    'title': 'Spack module file configuration file schema',
+    'definitions': definitions,
+    'type': 'object',
+    'additionalProperties': False,
+    'properties': properties,
+}
diff --git a/lib/spack/spack/schema/packages.py b/lib/spack/spack/schema/packages.py
index 70773c8aef..c762a75ba4 100644
--- a/lib/spack/spack/schema/packages.py
+++ b/lib/spack/spack/schema/packages.py
@@ -1,90 +1,93 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """Schema for packages.yaml configuration files.
 
 .. literalinclude:: ../spack/schema/packages.py
-   :lines: 32-
+   :lines: 13-
 """
 
 
-schema = {
-    '$schema': 'http://json-schema.org/schema#',
-    'title': 'Spack package configuration file schema',
-    'type': 'object',
-    'additionalProperties': False,
-    'patternProperties': {
-        r'packages': {
-            'type': 'object',
-            'default': {},
-            'additionalProperties': False,
-            'patternProperties': {
-                r'\w[\w-]*': {  # package name
-                    'type': 'object',
-                    'default': {},
-                    'additionalProperties': False,
-                    'properties': {
-                        'version': {
-                            'type': 'array',
-                            'default': [],
-                            # version strings
-                            'items': {'anyOf': [{'type': 'string'},
-                                                {'type': 'number'}]}},
-                        'compiler': {
-                            'type': 'array',
-                            'default': [],
-                            'items': {'type': 'string'}},  # compiler specs
-                        'buildable': {
-                            'type':  'boolean',
-                            'default': True,
-                        },
-                        'modules': {
-                            'type': 'object',
-                            'default': {},
-                        },
-                        'providers': {
-                            'type':  'object',
-                            'default': {},
-                            'additionalProperties': False,
-                            'patternProperties': {
-                                r'\w[\w-]*': {
-                                    'type': 'array',
-                                    'default': [],
-                                    'items': {'type': 'string'}, }, }, },
-                        'paths': {
-                            'type': 'object',
-                            'default': {},
-                        },
-                        'variants': {
-                            'oneOf': [
-                                {'type': 'string'},
-                                {'type': 'array',
-                                 'items': {'type': 'string'}}],
+#: Properties for inclusion in other schemas
+properties = {
+    'packages': {
+        'type': 'object',
+        'default': {},
+        'additionalProperties': False,
+        'patternProperties': {
+            r'\w[\w-]*': {  # package name
+                'type': 'object',
+                'default': {},
+                'additionalProperties': False,
+                'properties': {
+                    'version': {
+                        'type': 'array',
+                        'default': [],
+                        # version strings
+                        'items': {'anyOf': [{'type': 'string'},
+                                            {'type': 'number'}]}},
+                    'compiler': {
+                        'type': 'array',
+                        'default': [],
+                        'items': {'type': 'string'}},  # compiler specs
+                    'buildable': {
+                        'type':  'boolean',
+                        'default': True,
+                    },
+                    'permissions': {
+                        'type': 'object',
+                        'additionalProperties': False,
+                        'properties': {
+                            'read': {
+                                'type':  'string',
+                                'enum': ['user', 'group', 'world'],
+                            },
+                            'write': {
+                                'type':  'string',
+                                'enum': ['user', 'group', 'world'],
+                            },
+                            'group': {
+                                'type':  'string',
+                            },
                         },
                     },
+                    'modules': {
+                        'type': 'object',
+                        'default': {},
+                    },
+                    'providers': {
+                        'type':  'object',
+                        'default': {},
+                        'additionalProperties': False,
+                        'patternProperties': {
+                            r'\w[\w-]*': {
+                                'type': 'array',
+                                'default': [],
+                                'items': {'type': 'string'}, }, }, },
+                    'paths': {
+                        'type': 'object',
+                        'default': {},
+                    },
+                    'variants': {
+                        'oneOf': [
+                            {'type': 'string'},
+                            {'type': 'array',
+                             'items': {'type': 'string'}}],
+                    },
                 },
             },
         },
     },
 }
+
+
+#: Full schema with metadata
+schema = {
+    '$schema': 'http://json-schema.org/schema#',
+    'title': 'Spack package configuration file schema',
+    'type': 'object',
+    'additionalProperties': False,
+    'properties': properties,
+}
diff --git a/lib/spack/spack/schema/repos.py b/lib/spack/spack/schema/repos.py
index bdd1dfc5cf..1ee0457d99 100644
--- a/lib/spack/spack/schema/repos.py
+++ b/lib/spack/spack/schema/repos.py
@@ -1,45 +1,30 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """Schema for repos.yaml configuration file.
 
 .. literalinclude:: ../spack/schema/repos.py
-   :lines: 32-
+   :lines: 13-
 """
 
 
+#: Properties for inclusion in other schemas
+properties = {
+    'repos': {
+        'type': 'array',
+        'default': [],
+        'items': {'type': 'string'},
+    },
+}
+
+
+#: Full schema with metadata
 schema = {
     '$schema': 'http://json-schema.org/schema#',
     'title': 'Spack repository configuration file schema',
     'type': 'object',
     'additionalProperties': False,
-    'patternProperties': {
-        r'repos': {
-            'type': 'array',
-            'default': [],
-            'items': {
-                'type': 'string'},
-        },
-    },
+    'properties': properties,
 }
diff --git a/lib/spack/spack/spec.py b/lib/spack/spack/spec.py
index e29c1bed3c..f8991413cd 100644
--- a/lib/spack/spack/spec.py
+++ b/lib/spack/spack/spec.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """
 Spack allows very fine-grained control over how packages are installed and
 over how they are built and configured.  To make this easy, it has its own
@@ -114,11 +95,12 @@ from llnl.util.lang import key_ordering, HashableMap, ObjectWrapper, dedupe
 from llnl.util.lang import check_kwargs
 from llnl.util.tty.color import cwrite, colorize, cescape, get_color_when
 
-import spack
 import spack.architecture
+import spack.compiler
 import spack.compilers as compilers
 import spack.error
 import spack.parse
+import spack.repo
 import spack.store
 import spack.util.spack_json as sjson
 import spack.util.spack_yaml as syaml
@@ -138,7 +120,7 @@ from spack.variant import VariantMap, UnknownVariantError
 from spack.variant import DuplicateVariantError
 from spack.variant import UnsatisfiableVariantSpecError
 from spack.version import VersionList, VersionRange, Version, ver
-from yaml.error import MarkedYAMLError
+from ruamel.yaml.error import MarkedYAMLError
 
 __all__ = [
     'Spec',
@@ -183,7 +165,7 @@ hash_color = '@K'              #: color for highlighting package hashes
 
 #: This map determines the coloring of specs when using color output.
 #: We make the fields different colors to enhance readability.
-#: See spack.color for descriptions of the color codes.
+#: See llnl.util.tty.color for descriptions of the color codes.
 color_formats = {'%': compiler_color,
                  '@': version_color,
                  '=': architecture_color,
@@ -689,7 +671,7 @@ def _headers_default_handler(descriptor, spec, cls):
     Raises:
         RuntimeError: If no headers are found
     """
-    headers = find_headers('*', root=spec.prefix.include, recurse=True)
+    headers = find_headers('*', root=spec.prefix.include, recursive=True)
 
     if headers:
         return headers
@@ -702,7 +684,8 @@ def _libs_default_handler(descriptor, spec, cls):
     """Default handler when looking for the 'libs' attribute.
 
     Tries to search for ``lib{spec.name}`` recursively starting from
-    ``spec.prefix``.
+    ``spec.prefix``. If ``spec.name`` starts with ``lib``, searches for
+    ``{spec.name}`` instead.
 
     Parameters:
         descriptor (ForwardQueryToPackage): descriptor that triggered the call
@@ -727,33 +710,34 @@ def _libs_default_handler(descriptor, spec, cls):
     # depending on which one exists (there is a possibility, of course, to
     # get something like 'libabcXabc.so, but for now we consider this
     # unlikely).
-    name = 'lib' + spec.name.replace('-', '?')
-
-    if '+shared' in spec:
-        libs = find_libraries(
-            name, root=spec.prefix, shared=True, recurse=True
-        )
-    elif '~shared' in spec:
-        libs = find_libraries(
-            name, root=spec.prefix, shared=False, recurse=True
-        )
-    else:
-        # Prefer shared
-        libs = find_libraries(
-            name, root=spec.prefix, shared=True, recurse=True
-        )
-        if libs:
-            return libs
-
-        libs = find_libraries(
-            name, root=spec.prefix, shared=False, recurse=True
-        )
+    name = spec.name.replace('-', '?')
+
+    # Avoid double 'lib' for packages whose names already start with lib
+    if not name.startswith('lib'):
+        name = 'lib' + name
+
+    # To speedup the search for external packages configured e.g. in /usr,
+    # perform first non-recursive search in prefix.lib then in prefix.lib64 and
+    # finally search all of prefix recursively. The search stops when the first
+    # match is found.
+    prefix = spec.prefix
+    search_paths = [(prefix.lib, False), (prefix.lib64, False), (prefix, True)]
+
+    # If '+shared' search only for shared library; if '~shared' search only for
+    # static library; otherwise, first search for shared and then for static.
+    search_shared = [True] if ('+shared' in spec) else \
+        ([False] if ('~shared' in spec) else [True, False])
+
+    for shared in search_shared:
+        for path, recursive in search_paths:
+            libs = find_libraries(
+                name, root=path, shared=shared, recursive=recursive
+            )
+            if libs:
+                return libs
 
-    if libs:
-        return libs
-    else:
-        msg = 'Unable to recursively locate {0} libraries in {1}'
-        raise RuntimeError(msg.format(spec.name, spec.prefix))
+    msg = 'Unable to recursively locate {0} libraries in {1}'
+    raise RuntimeError(msg.format(spec.name, prefix))
 
 
 class ForwardQueryToPackage(object):
@@ -770,10 +754,6 @@ class ForwardQueryToPackage(object):
                 instance
         """
         self.attribute_name = attribute_name
-        # Turn the default handler into a function with the right
-        # signature that always returns None
-        if default_handler is None:
-            default_handler = lambda descriptor, spec, cls: None
         self.default = default_handler
 
     def __get__(self, instance, cls):
@@ -792,8 +772,11 @@ class ForwardQueryToPackage(object):
 
         The first call that produces a value will stop the chain.
 
-        If no call can handle the request or a None value is produced,
-        then AttributeError is raised.
+        If no call can handle the request then AttributeError is raised with a
+        message indicating that no relevant attribute exists.
+        If a call returns None, an AttributeError is raised with a message
+        indicating a query failure, e.g. that library files were not found in a
+        'libs' query.
         """
         pkg = instance.package
         try:
@@ -814,34 +797,53 @@ class ForwardQueryToPackage(object):
         # Try to get the generic method from Package
         callbacks_chain.append(lambda: getattr(pkg, self.attribute_name))
         # Final resort : default callback
-        callbacks_chain.append(lambda: self.default(self, instance, cls))
+        if self.default is not None:
+            callbacks_chain.append(lambda: self.default(self, instance, cls))
 
         # Trigger the callbacks in order, the first one producing a
         # value wins
         value = None
+        message = None
         for f in callbacks_chain:
             try:
                 value = f()
+                # A callback can return None to trigger an error indicating
+                # that the query failed.
+                if value is None:
+                    msg  = "Query of package '{name}' for '{attrib}' failed\n"
+                    msg += "\tprefix : {spec.prefix}\n"
+                    msg += "\tspec : {spec}\n"
+                    msg += "\tqueried as : {query.name}\n"
+                    msg += "\textra parameters : {query.extra_parameters}"
+                    message = msg.format(
+                        name=pkg.name, attrib=self.attribute_name,
+                        spec=instance, query=instance.last_query)
+                else:
+                    return value
                 break
             except AttributeError:
                 pass
-        # 'None' value raises AttributeError : this permits to 'disable'
-        # the call in a particular package by returning None from the
-        # queried attribute, or will trigger an exception if  things
-        # searched for were not found
-        if value is None:
-            fmt = '\'{name}\' package has no relevant attribute \'{query}\'\n'  # NOQA: ignore=E501
-            fmt += '\tspec : \'{spec}\'\n'
-            fmt += '\tqueried as : \'{spec.last_query.name}\'\n'
-            fmt += '\textra parameters : \'{spec.last_query.extra_parameters}\'\n'  # NOQA: ignore=E501
-            message = fmt.format(
-                name=pkg.name,
-                query=self.attribute_name,
-                spec=instance
-            )
+        # value is 'None'
+        if message is not None:
+            # Here we can use another type of exception. If we do that, the
+            # unit test 'test_getitem_exceptional_paths' in the file
+            # lib/spack/spack/test/spec_dag.py will need to be updated to match
+            # the type.
             raise AttributeError(message)
-
-        return value
+        # 'None' value at this point means that there are no appropriate
+        # properties defined and no default handler, or that all callbacks
+        # raised AttributeError. In this case, we raise AttributeError with an
+        # appropriate message.
+        fmt = '\'{name}\' package has no relevant attribute \'{query}\'\n'  # NOQA: ignore=E501
+        fmt += '\tspec : \'{spec}\'\n'
+        fmt += '\tqueried as : \'{spec.last_query.name}\'\n'
+        fmt += '\textra parameters : \'{spec.last_query.extra_parameters}\'\n'  # NOQA: ignore=E501
+        message = fmt.format(
+            name=pkg.name,
+            query=self.attribute_name,
+            spec=instance
+        )
+        raise AttributeError(message)
 
     def __set__(self, instance, value):
         cls_name = type(instance).__name__
@@ -884,6 +886,9 @@ class SpecBuildInterface(ObjectWrapper):
 @key_ordering
 class Spec(object):
 
+    #: Cache for spec's prefix, computed lazily in the corresponding property
+    _prefix = None
+
     @staticmethod
     def from_literal(spec_dict, normal=True):
         """Builds a Spec from a dictionary containing the spec literal.
@@ -1064,6 +1069,8 @@ class Spec(object):
         self.external_path = kwargs.get('external_path', None)
         self.external_module = kwargs.get('external_module', None)
 
+        self._full_hash = kwargs.get('full_hash', None)
+
     @property
     def external(self):
         return bool(self.external_path) or bool(self.external_module)
@@ -1194,14 +1201,16 @@ class Spec(object):
 
     @property
     def package(self):
-        return spack.repo.get(self)
+        if not self._package:
+            self._package = spack.repo.get(self)
+        return self._package
 
     @property
     def package_class(self):
         """Internal package call gets only the class object for a package.
            Use this to just get package metadata.
         """
-        return spack.repo.get_pkg_class(self.fullname)
+        return spack.repo.path.get_pkg_class(self.fullname)
 
     @property
     def virtual(self):
@@ -1217,7 +1226,7 @@ class Spec(object):
     @staticmethod
     def is_virtual(name):
         """Test if a name is virtual without requiring a Spec."""
-        return (name is not None) and (not spack.repo.exists(name))
+        return (name is not None) and (not spack.repo.path.exists(name))
 
     @property
     def concrete(self):
@@ -1374,12 +1383,13 @@ class Spec(object):
 
     @property
     def prefix(self):
-        if hasattr(self, 'test_prefix'):
-            return Prefix(self.test_prefix)
-        return Prefix(spack.store.layout.path_for_spec(self))
+        if self._prefix is None:
+            self.prefix = spack.store.layout.path_for_spec(self)
+        return self._prefix
 
-    def _set_test_prefix(self, val):
-        self.test_prefix = val
+    @prefix.setter
+    def prefix(self, value):
+        self._prefix = Prefix(value)
 
     def dag_hash(self, length=None):
         """Return a hash of the entire spec DAG, including connectivity."""
@@ -1402,7 +1412,26 @@ class Spec(object):
         """Get the first <bits> bits of the DAG hash as an integer type."""
         return base32_prefix_bits(self.dag_hash(), bits)
 
-    def to_node_dict(self):
+    def full_hash(self, length=None):
+        if not self.concrete:
+            raise SpecError("Spec is not concrete: " + str(self))
+
+        if not self._full_hash:
+            yaml_text = syaml.dump(
+                self.to_node_dict(hash_function=lambda s: s.full_hash()),
+                default_flow_style=True, width=maxint)
+            package_hash = self.package.content_hash()
+            sha = hashlib.sha1(yaml_text.encode('utf-8') + package_hash)
+
+            b32_hash = base64.b32encode(sha.digest()).lower()
+            if sys.version_info[0] >= 3:
+                b32_hash = b32_hash.decode('utf-8')
+
+            self._full_hash = b32_hash
+
+        return self._full_hash[:length]
+
+    def to_node_dict(self, hash_function=None, all_deps=False):
         d = syaml_dict()
 
         if self.versions:
@@ -1422,6 +1451,7 @@ class Spec(object):
                 v.yaml_entry() for _, v in self.variants.items()
             )
         )
+
         params.update(sorted(self.compiler_flags.items()))
         if params:
             d['parameters'] = params
@@ -1429,27 +1459,45 @@ class Spec(object):
         if self.external:
             d['external'] = {
                 'path': self.external_path,
-                'module': bool(self.external_module)
+                'module': self.external_module
             }
 
+        if not self._concrete:
+            d['concrete'] = False
+
+        if 'patches' in self.variants:
+            variant = self.variants['patches']
+            if hasattr(variant, '_patches_in_order_of_appearance'):
+                d['patches'] = variant._patches_in_order_of_appearance
+
         # TODO: restore build dependencies here once we have less picky
         # TODO: concretization.
-        deps = self.dependencies_dict(deptype=('link', 'run'))
+        if all_deps:
+            deptypes = ('link', 'run', 'build')
+        else:
+            deptypes = ('link', 'run')
+        deps = self.dependencies_dict(deptype=deptypes)
         if deps:
+            if hash_function is None:
+                hash_function = lambda s: s.dag_hash()
             d['dependencies'] = syaml_dict([
                 (name,
                  syaml_dict([
-                     ('hash', dspec.spec.dag_hash()),
+                     ('hash', hash_function(dspec.spec)),
                      ('type', sorted(str(s) for s in dspec.deptypes))])
                  ) for name, dspec in sorted(deps.items())
             ])
 
         return syaml_dict([(self.name, d)])
 
-    def to_dict(self):
+    def to_dict(self, all_deps=False):
+        if all_deps:
+            deptypes = ('link', 'run', 'build')
+        else:
+            deptypes = ('link', 'run')
         node_list = []
-        for s in self.traverse(order='pre', deptype=('link', 'run')):
-            node = s.to_node_dict()
+        for s in self.traverse(order='pre', deptype=deptypes):
+            node = s.to_node_dict(all_deps=all_deps)
             node[s.name]['hash'] = s.dag_hash()
             node_list.append(node)
 
@@ -1467,7 +1515,7 @@ class Spec(object):
         name = next(iter(node))
         node = node[name]
 
-        spec = Spec(name)
+        spec = Spec(name, full_hash=node.get('full_hash', None))
         spec.namespace = node.get('namespace', None)
         spec._hash = node.get('hash', None)
 
@@ -1513,12 +1561,34 @@ class Spec(object):
             spec.external_path = None
             spec.external_module = None
 
+        # specs read in are concrete unless marked abstract
+        spec._concrete = node.get('concrete', True)
+
+        if 'patches' in node:
+            patches = node['patches']
+            if len(patches) > 0:
+                mvar = spec.variants.setdefault(
+                    'patches', MultiValuedVariant('patches', ())
+                )
+                mvar.value = patches
+                # FIXME: Monkey patches mvar to store patches order
+                mvar._patches_in_order_of_appearance = patches
+
         # Don't read dependencies here; from_node_dict() is used by
         # from_yaml() to read the root *and* each dependency spec.
 
         return spec
 
     @staticmethod
+    def dependencies_from_node_dict(node):
+        name = next(iter(node))
+        node = node[name]
+        if 'dependencies' not in node:
+            return
+        for t in Spec.read_yaml_dep_specs(node['dependencies']):
+            yield t
+
+    @staticmethod
     def read_yaml_dep_specs(dependency_dict):
         """Read the DependencySpec portion of a YAML-formatted Spec.
 
@@ -1630,13 +1700,15 @@ class Spec(object):
             # to presets below, their constraints will all be merged, but we'll
             # still need to select a concrete package later.
             if not self.virtual:
+                import spack.concretize
+                concretizer = spack.concretize.concretizer
                 changed |= any(
-                    (spack.concretizer.concretize_architecture(self),
-                     spack.concretizer.concretize_compiler(self),
-                     spack.concretizer.concretize_compiler_flags(
-                         self),  # has to be concretized after compiler
-                     spack.concretizer.concretize_version(self),
-                     spack.concretizer.concretize_variants(self)))
+                    (concretizer.concretize_architecture(self),
+                     concretizer.concretize_compiler(self),
+                     # flags must be concretized after compiler
+                     concretizer.concretize_compiler_flags(self),
+                     concretizer.concretize_version(self),
+                     concretizer.concretize_variants(self)))
             presets[self.name] = self
 
         visited.add(self.name)
@@ -1697,8 +1769,9 @@ class Spec(object):
                 if not replacement:
                     # Get a list of possible replacements in order of
                     # preference.
-                    candidates = spack.concretizer.choose_virtual_or_external(
-                        spec)
+                    import spack.concretize
+                    concretizer = spack.concretize.concretizer
+                    candidates = concretizer.choose_virtual_or_external(spec)
 
                     # Try the replacements in order, skipping any that cause
                     # satisfiability problems.
@@ -1760,26 +1833,21 @@ class Spec(object):
 
         return changed
 
-    def concretize(self):
+    def concretize(self, tests=False):
         """A spec is concrete if it describes one build of a package uniquely.
         This will ensure that this spec is concrete.
 
+        Args:
+            tests (list or bool): list of packages that will need test
+                dependencies, or True/False for test all/none
+
         If this spec could describe more than one version, variant, or build
         of a package, this will add constraints to make it concrete.
 
         Some rigorous validation and checks are also performed on the spec.
         Concretizing ensures that it is self-consistent and that it's
-        consistent with requirements of its pacakges. See flatten() and
+        consistent with requirements of its packages. See flatten() and
         normalize() for more details on this.
-
-        It also ensures that:
-
-        .. code-block:: python
-
-            for x in self.traverse():
-                assert x.package.spec == x
-
-        which may not be true *during* the concretization step.
         """
         if not self.name:
             raise SpecError("Attempting to concretize anonymous spec")
@@ -1790,13 +1858,26 @@ class Spec(object):
         changed = True
         force = False
 
+        user_spec_deps = self.flat_dependencies(copy=False)
+
         while changed:
-            changes = (self.normalize(force),
+            changes = (self.normalize(force, tests=tests,
+                                      user_spec_deps=user_spec_deps),
                        self._expand_virtual_packages(),
                        self._concretize_helper())
             changed = any(changes)
             force = True
 
+        visited_user_specs = set()
+        for dep in self.traverse():
+            visited_user_specs.add(dep.name)
+            visited_user_specs.update(x.name for x in dep.package.provided)
+
+        extra = set(user_spec_deps.keys()).difference(visited_user_specs)
+        if extra:
+            raise InvalidDependencyError(
+                self.name + " does not depend on " + comma_or(extra))
+
         for s in self.traverse():
             # After concretizing, assign namespaces to anything left.
             # Note that this doesn't count as a "change".  The repository
@@ -1807,7 +1888,7 @@ class Spec(object):
             # we can do it as late as possible to allow as much
             # compatibility across repositories as possible.
             if s.namespace is None:
-                s.namespace = spack.repo.repo_for_pkg(s.name).namespace
+                s.namespace = spack.repo.path.repo_for_pkg(s.name).namespace
 
             if s.concrete:
                 continue
@@ -1850,10 +1931,11 @@ class Spec(object):
                 mvar.value = mvar.value + tuple(patches)
                 # FIXME: Monkey patches mvar to store patches order
                 p = getattr(mvar, '_patches_in_order_of_appearance', [])
-                mvar._patches_in_order_of_appearance = dedupe(p + patches)
+                mvar._patches_in_order_of_appearance = list(
+                    dedupe(p + patches))
 
         for s in self.traverse():
-            if s.external_module:
+            if s.external_module and not s.external_path:
                 compiler = spack.compilers.compiler_for_spec(
                     s.compiler, s.architecture)
                 for mod in compiler.modules:
@@ -1868,19 +1950,14 @@ class Spec(object):
         # there are declared conflicts
         matches = []
         for x in self.traverse():
-            for conflict_spec, when_list in x.package.conflicts.items():
-                if x.satisfies(conflict_spec):
+            for conflict_spec, when_list in x.package_class.conflicts.items():
+                if x.satisfies(conflict_spec, strict=True):
                     for when_spec, msg in when_list:
-                        if x.satisfies(when_spec):
+                        if x.satisfies(when_spec, strict=True):
                             matches.append((x, conflict_spec, when_spec, msg))
         if matches:
             raise ConflictsInSpecError(self, matches)
 
-        # At this point the spec-package mutual references should
-        # be self-consistent
-        for x in self.traverse():
-            x.package.spec = x
-
     def _mark_concrete(self, value=True):
         """Mark this spec and its dependencies as concrete.
 
@@ -1897,7 +1974,7 @@ class Spec(object):
         """This is a non-destructive version of concretize().  First clones,
            then returns a concrete version of this package without modifying
            this package. """
-        clone = self.copy()
+        clone = self.copy(caches=False)
         clone.concretize()
         return clone
 
@@ -1964,8 +2041,7 @@ class Spec(object):
         If no conditions are True (and we don't depend on it), return
         ``(None, None)``.
         """
-        pkg = spack.repo.get(self.fullname)
-        conditions = pkg.dependencies[name]
+        conditions = self.package_class.dependencies[name]
 
         substitute_abstract_variants(self)
         # evaluate when specs to figure out constraints on the dependency.
@@ -2017,7 +2093,7 @@ class Spec(object):
                 raise UnsatisfiableProviderSpecError(required[0], vdep)
 
     def _merge_dependency(
-            self, dependency, visited, spec_deps, provider_index):
+            self, dependency, visited, spec_deps, provider_index, tests):
         """Merge dependency information from a Package into this Spec.
 
         Args:
@@ -2113,10 +2189,10 @@ class Spec(object):
             self._add_dependency(spec_dependency, dependency.type)
 
         changed |= spec_dependency._normalize_helper(
-            visited, spec_deps, provider_index)
+            visited, spec_deps, provider_index, tests)
         return changed
 
-    def _normalize_helper(self, visited, spec_deps, provider_index):
+    def _normalize_helper(self, visited, spec_deps, provider_index, tests):
         """Recursive helper function for _normalize."""
         if self.name in visited:
             return False
@@ -2132,22 +2208,28 @@ class Spec(object):
         any_change = False
         changed = True
 
-        pkg = spack.repo.get(self.fullname)
         while changed:
             changed = False
-            for dep_name in pkg.dependencies:
+            for dep_name in self.package_class.dependencies:
                 # Do we depend on dep_name?  If so pkg_dep is not None.
                 dep = self._evaluate_dependency_conditions(dep_name)
+
                 # If dep is a needed dependency, merge it.
-                if dep and (spack.package_testing.check(self.name) or
-                            set(dep.type) - set(['test'])):
-                    changed |= self._merge_dependency(
-                        dep, visited, spec_deps, provider_index)
+                if dep:
+                    merge = (
+                        # caller requested test dependencies
+                        tests is True or (tests and self.name in tests) or
+                        # this is not a test-only dependency
+                        dep.type - set(['test']))
+
+                    if merge:
+                        changed |= self._merge_dependency(
+                            dep, visited, spec_deps, provider_index, tests)
             any_change |= changed
 
         return any_change
 
-    def normalize(self, force=False):
+    def normalize(self, force=False, tests=False, user_spec_deps=None):
         """When specs are parsed, any dependencies specified are hanging off
            the root, and ONLY the ones that were explicitly provided are there.
            Normalization turns a partial flat spec into a DAG, where:
@@ -2176,26 +2258,34 @@ class Spec(object):
 
         # Ensure first that all packages & compilers in the DAG exist.
         self.validate_or_raise()
-        # Get all the dependencies into one DependencyMap
-        spec_deps = self.flat_dependencies(copy=False)
+        # Clear the DAG and collect all dependencies in the DAG, which will be
+        # reapplied as constraints. All dependencies collected this way will
+        # have been created by a previous execution of 'normalize'.
+        # A dependency extracted here will only be reintegrated if it is
+        # discovered to apply according to _normalize_helper, so
+        # user-specified dependencies are recorded separately in case they
+        # refer to specs which take several normalization passes to
+        # materialize.
+        all_spec_deps = self.flat_dependencies(copy=False)
+
+        if user_spec_deps:
+            for name, spec in user_spec_deps.items():
+                if name not in all_spec_deps:
+                    all_spec_deps[name] = spec
+                else:
+                    all_spec_deps[name].constrain(spec)
 
         # Initialize index of virtual dependency providers if
         # concretize didn't pass us one already
         provider_index = ProviderIndex(
-            [s for s in spec_deps.values()], restrict=True)
+            [s for s in all_spec_deps.values()], restrict=True)
 
         # traverse the package DAG and fill out dependencies according
         # to package files & their 'when' specs
         visited = set()
 
-        any_change = self._normalize_helper(visited, spec_deps, provider_index)
-
-        # If there are deps specified but not visited, they're not
-        # actually deps of this package.  Raise an error.
-        extra = set(spec_deps.keys()).difference(visited)
-        if extra:
-            raise InvalidDependencyError(
-                self.name + " does not depend on " + comma_or(extra))
+        any_change = self._normalize_helper(
+            visited, all_spec_deps, provider_index, tests)
 
         # Mark the spec as normal once done.
         self._normal = True
@@ -2412,7 +2502,7 @@ class Spec(object):
         if not self.virtual and other.virtual:
             try:
                 pkg = spack.repo.get(self.fullname)
-            except spack.repository.UnknownEntityError:
+            except spack.repo.UnknownEntityError:
                 # If we can't get package info on this spec, don't treat
                 # it as a provider of this vdep.
                 return False
@@ -2552,7 +2642,7 @@ class Spec(object):
         # FIXME: concretization to store the order of patches somewhere.
         # FIXME: Needs to be refactored in a cleaner way.
         for sha256 in self.variants['patches']._patches_in_order_of_appearance:
-            patch = self.package.lookup_patch(sha256)
+            patch = self.package_class.lookup_patch(sha256)
             if patch:
                 patches.append(patch)
                 continue
@@ -2560,7 +2650,7 @@ class Spec(object):
             # if not found in this package, check immediate dependents
             # for dependency patches
             for dep_spec in self._dependents.values():
-                patch = dep_spec.parent.package.lookup_patch(sha256)
+                patch = dep_spec.parent.package_class.lookup_patch(sha256)
 
                 if patch:
                     patches.append(patch)
@@ -2606,6 +2696,8 @@ class Spec(object):
                        self.external_module != other.external_module and
                        self.compiler_flags != other.compiler_flags)
 
+        self._package = None
+
         # Local node attributes get copied first.
         self.name = other.name
         self.versions = other.versions.copy()
@@ -2618,6 +2710,15 @@ class Spec(object):
         self.compiler_flags = other.compiler_flags.copy()
         self.compiler_flags.spec = self
         self.variants = other.variants.copy()
+
+        # FIXME: we manage _patches_in_order_of_appearance specially here
+        # to keep it from leaking out of spec.py, but we should figure
+        # out how to handle it more elegantly in the Variant classes.
+        for k, v in other.variants.items():
+            patches = getattr(v, '_patches_in_order_of_appearance', None)
+            if patches:
+                self.variants[k]._patches_in_order_of_appearance = patches
+
         self.variants.spec = self
         self.external_path = other.external_path
         self.external_module = other.external_module
@@ -2638,16 +2739,18 @@ class Spec(object):
                 deptypes = deps
             self._dup_deps(other, deptypes, caches)
 
+        self._concrete = other._concrete
+
         if caches:
             self._hash = other._hash
             self._cmp_key_cache = other._cmp_key_cache
             self._normal = other._normal
-            self._concrete = other._concrete
+            self._full_hash = other._full_hash
         else:
             self._hash = None
             self._cmp_key_cache = None
             self._normal = False
-            self._concrete = False
+            self._full_hash = None
 
         return changed
 
@@ -2813,7 +2916,7 @@ class Spec(object):
         """Comparison key for just *this node* and not its deps."""
         return (self.name,
                 self.namespace,
-                self.versions,
+                tuple(self.versions),
                 self.variants,
                 self.architecture,
                 self.compiler,
@@ -2871,6 +2974,7 @@ class Spec(object):
         You can also use full-string versions, which elide the prefixes::
 
             ${PACKAGE}       Package name
+            ${FULLPACKAGE}   Full package name (with namespace)
             ${VERSION}       Version
             ${COMPILER}      Full compiler string
             ${COMPILERNAME}  Compiler name
@@ -2878,6 +2982,9 @@ class Spec(object):
             ${COMPILERFLAGS} Compiler flags
             ${OPTIONS}       Options
             ${ARCHITECTURE}  Architecture
+            ${PLATFORM}      Platform
+            ${OS}            Operating System
+            ${TARGET}        Target
             ${SHA1}          Dependencies 8-char sha1 prefix
             ${HASH:len}      DAG hash with optional length specifier
 
@@ -2885,6 +2992,7 @@ class Spec(object):
             ${SPACK_INSTALL} The default spack install directory,
                              ${SPACK_PREFIX}/opt
             ${PREFIX}        The package prefix
+            ${NAMESPACE}     The package namespace
 
         Note these are case-insensitive: for example you can specify either
         ``${PACKAGE}`` or ``${package}``.
@@ -2898,11 +3006,9 @@ class Spec(object):
         Args:
             format_string (str): string containing the format to be expanded
 
-            **kwargs (dict): the following list of keywords is supported
-
-                - color (bool): True if returned string is colored
-
-                - transform (dict): maps full-string formats to a callable \
+        Keyword Args:
+            color (bool): True if returned string is colored
+            transform (dict): maps full-string formats to a callable \
                 that accepts a string and returns another one
 
         Examples:
@@ -2922,16 +3028,18 @@ class Spec(object):
         color = kwargs.get('color', False)
 
         # Dictionary of transformations for named tokens
-        token_transforms = {}
-        token_transforms.update(kwargs.get('transform', {}))
+        token_transforms = dict(
+            (k.upper(), v) for k, v in kwargs.get('transform', {}).items())
 
         length = len(format_string)
         out = StringIO()
         named = escape = compiler = False
         named_str = fmt = ''
 
-        def write(s, c):
-            f = color_formats[c] + cescape(s) + '@.'
+        def write(s, c=None):
+            f = cescape(s)
+            if c is not None:
+                f = color_formats[c] + f + '@.'
             cwrite(f, stream=out, color=color)
 
         iterator = enumerate(format_string)
@@ -2951,7 +3059,8 @@ class Spec(object):
                     name = self.name if self.name else ''
                     out.write(fmt % name)
                 elif c == '.':
-                    out.write(fmt % self.fullname)
+                    name = self.fullname if self.fullname else ''
+                    out.write(fmt % name)
                 elif c == '@':
                     if self.versions and self.versions != _any_version:
                         write(fmt % (c + str(self.versions)), c)
@@ -3006,50 +3115,63 @@ class Spec(object):
                 #
                 # The default behavior is to leave the string unchanged
                 # (`lambda x: x` is the identity function)
-                token_transform = token_transforms.get(named_str, lambda x: x)
+                transform = token_transforms.get(named_str, lambda s, x: x)
 
                 if named_str == 'PACKAGE':
                     name = self.name if self.name else ''
-                    write(fmt % token_transform(name), '@')
-                if named_str == 'VERSION':
+                    write(fmt % transform(self, name))
+                elif named_str == 'FULLPACKAGE':
+                    name = self.fullname if self.fullname else ''
+                    write(fmt % transform(self, name))
+                elif named_str == 'VERSION':
                     if self.versions and self.versions != _any_version:
-                        write(fmt % token_transform(str(self.versions)), '@')
+                        write(fmt % transform(self, str(self.versions)), '@')
                 elif named_str == 'COMPILER':
                     if self.compiler:
-                        write(fmt % token_transform(self.compiler), '%')
+                        write(fmt % transform(self, self.compiler), '%')
                 elif named_str == 'COMPILERNAME':
                     if self.compiler:
-                        write(fmt % token_transform(self.compiler.name), '%')
+                        write(fmt % transform(self, self.compiler.name), '%')
                 elif named_str in ['COMPILERVER', 'COMPILERVERSION']:
                     if self.compiler:
                         write(
-                            fmt % token_transform(self.compiler.versions),
+                            fmt % transform(self, self.compiler.versions),
                             '%'
                         )
                 elif named_str == 'COMPILERFLAGS':
                     if self.compiler:
                         write(
-                            fmt % token_transform(str(self.compiler_flags)),
+                            fmt % transform(self, str(self.compiler_flags)),
                             '%'
                         )
                 elif named_str == 'OPTIONS':
                     if self.variants:
-                        write(fmt % token_transform(str(self.variants)), '+')
-                elif named_str == 'ARCHITECTURE':
+                        write(fmt % transform(self, str(self.variants)), '+')
+                elif named_str in ["ARCHITECTURE", "PLATFORM", "TARGET", "OS"]:
                     if self.architecture and str(self.architecture):
-                        write(
-                            fmt % token_transform(str(self.architecture)),
-                            '='
-                        )
+                        if named_str == "ARCHITECTURE":
+                            write(
+                                fmt % transform(self, str(self.architecture)),
+                                '='
+                            )
+                        elif named_str == "PLATFORM":
+                            platform = str(self.architecture.platform)
+                            write(fmt % transform(self, platform), '=')
+                        elif named_str == "OS":
+                            operating_sys = str(self.architecture.platform_os)
+                            write(fmt % transform(self, operating_sys), '=')
+                        elif named_str == "TARGET":
+                            target = str(self.architecture.target)
+                            write(fmt % transform(self, target), '=')
                 elif named_str == 'SHA1':
                     if self.dependencies:
-                        out.write(fmt % token_transform(str(self.dag_hash(7))))
+                        out.write(fmt % transform(self, str(self.dag_hash(7))))
                 elif named_str == 'SPACK_ROOT':
-                    out.write(fmt % token_transform(spack.prefix))
+                    out.write(fmt % transform(self, spack.paths.prefix))
                 elif named_str == 'SPACK_INSTALL':
-                    out.write(fmt % token_transform(spack.store.root))
+                    out.write(fmt % transform(self, spack.store.root))
                 elif named_str == 'PREFIX':
-                    out.write(fmt % token_transform(self.prefix))
+                    out.write(fmt % transform(self, self.prefix))
                 elif named_str.startswith('HASH'):
                     if named_str.startswith('HASH:'):
                         _, hashlen = named_str.split(':')
@@ -3057,6 +3179,8 @@ class Spec(object):
                     else:
                         hashlen = None
                     out.write(fmt % (self.dag_hash(hashlen)))
+                elif named_str == 'NAMESPACE':
+                    out.write(fmt % transform(self.namespace))
 
                 named = False
 
@@ -3078,7 +3202,7 @@ class Spec(object):
         return self.format(*args, **kwargs)
 
     def dep_string(self):
-        return ''.join("^" + dep.format() for dep in self.sorted_deps())
+        return ''.join(" ^" + dep.format() for dep in self.sorted_deps())
 
     def __str__(self):
         ret = self.format() + self.dep_string()
@@ -3117,7 +3241,8 @@ class Spec(object):
         fmt = kwargs.pop('format', '$_$@$%@+$+$=')
         prefix = kwargs.pop('prefix', None)
         show_types = kwargs.pop('show_types', False)
-        deptypes = kwargs.pop('deptypes', ('build', 'link'))
+        deptypes = kwargs.pop('deptypes', 'all')
+        recurse_dependencies = kwargs.pop('recurse_dependencies', True)
         check_kwargs(kwargs, self.tree)
 
         out = ""
@@ -3135,7 +3260,7 @@ class Spec(object):
             if install_status:
                 status = node._install_status()
                 if status is None:
-                    out += "     "  # Package isn't installed
+                    out += colorize("@K{ - }  ", color=color)  # not installed
                 elif status:
                     out += colorize("@g{[+]}  ", color=color)  # installed
                 else:
@@ -3145,18 +3270,32 @@ class Spec(object):
                 out += colorize('@K{%s}  ', color=color) % node.dag_hash(hlen)
 
             if show_types:
+                types = set()
+                if cover == 'nodes':
+                    # when only covering nodes, we merge dependency types
+                    # from all dependents before showing them.
+                    for name, ds in node.dependents_dict().items():
+                        if ds.deptypes:
+                            types.update(set(ds.deptypes))
+                elif dep_spec.deptypes:
+                    # when covering edges or paths, we show dependency
+                    # types only for the edge through which we visited
+                    types = set(dep_spec.deptypes)
+
                 out += '['
-                if dep_spec.deptypes:
-                    for t in all_deptypes:
-                        out += ''.join(t[0] if t in dep_spec.deptypes else ' ')
-                else:
-                    out += ' ' * len(all_deptypes)
+                for t in all_deptypes:
+                    out += ''.join(t[0] if t in types else ' ')
                 out += ']  '
 
             out += ("    " * d)
             if d > 0:
                 out += "^"
             out += node.format(fmt, color=color) + "\n"
+
+            # Check if we wanted just the first line
+            if not recurse_dependencies:
+                break
+
         return out
 
     def __repr__(self):
@@ -3370,8 +3509,10 @@ class SpecParser(spack.parse.Parser):
         spec._hash = None
         spec._cmp_key_cache = None
 
+        spec._package = None
         spec._normal = False
         spec._concrete = False
+        spec._full_hash = None
 
         # record this so that we know whether version is
         # unspecified or not.
diff --git a/lib/spack/spack/stage.py b/lib/spack/spack/stage.py
index 19eca53d1d..32cdaa0090 100644
--- a/lib/spack/spack/stage.py
+++ b/lib/spack/spack/stage.py
@@ -1,28 +1,10 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
+import stat
 import sys
 import errno
 import hashlib
@@ -34,13 +16,14 @@ from six import iteritems
 from six.moves.urllib.parse import urljoin
 
 import llnl.util.tty as tty
-import llnl.util.lock
-from llnl.util.filesystem import mkdirp, join_path, can_access
+from llnl.util.filesystem import mkdirp, can_access
 from llnl.util.filesystem import remove_if_dead_link, remove_linked_tree
 
-import spack
+import spack.paths
+import spack.caches
 import spack.config
 import spack.error
+import spack.util.lock
 import spack.fetch_strategy as fs
 import spack.util.pattern as pattern
 from spack.util.path import canonicalize_path
@@ -83,8 +66,7 @@ def get_tmp_root():
         return None
 
     if _tmp_root is None:
-        config = spack.config.get_config('config')
-        candidates = config['build_stage']
+        candidates = spack.config.get('config:build_stage')
         if isinstance(candidates, string_types):
             candidates = [candidates]
 
@@ -93,7 +75,7 @@ def get_tmp_root():
             raise StageError("No accessible stage paths in %s", candidates)
 
         # Return None to indicate we're using a local staging area.
-        if path == canonicalize_path(spack.stage_path):
+        if path == canonicalize_path(spack.paths.stage_path):
             _use_tmp_stage = False
             return None
 
@@ -145,10 +127,6 @@ class Stage(object):
         finally:
             stage.destroy()         # Explicitly destroy the stage directory.
 
-    If spack.use_tmp_stage is True, spack will attempt to create
-    stages in a tmp directory.  Otherwise, stages are created directly
-    in spack.stage_path.
-
     There are two kinds of stages: named and unnamed.  Named stages
     can persist between runs of spack, e.g. if you fetched a tarball
     but didn't finish building it, you won't have to fetch it again.
@@ -216,7 +194,7 @@ class Stage(object):
         if path is not None:
             self.path = path
         else:
-            self.path = join_path(spack.stage_path, self.name)
+            self.path = os.path.join(spack.paths.stage_path, self.name)
 
         # Flag to decide whether to delete the stage folder on exit or not
         self.keep = keep
@@ -229,9 +207,9 @@ class Stage(object):
             if self.name not in Stage.stage_locks:
                 sha1 = hashlib.sha1(self.name.encode('utf-8')).digest()
                 lock_id = prefix_bits(sha1, bit_length(sys.maxsize))
-                stage_lock_path = join_path(spack.stage_path, '.lock')
+                stage_lock_path = os.path.join(spack.paths.stage_path, '.lock')
 
-                Stage.stage_locks[self.name] = llnl.util.lock.Lock(
+                Stage.stage_locks[self.name] = spack.util.lock.Lock(
                     stage_lock_path, lock_id, 1)
 
             self._lock = Stage.stage_locks[self.name]
@@ -377,7 +355,7 @@ class Stage(object):
         # TODO: CompositeFetchStrategy here.
         self.skip_checksum_for_mirror = True
         if self.mirror_path:
-            mirrors = spack.config.get_config('mirrors')
+            mirrors = spack.config.get('mirrors')
 
             # Join URLs of mirror roots with mirror paths. Because
             # urljoin() will strip everything past the final '/' in
@@ -408,7 +386,7 @@ class Stage(object):
                         url, digest, expand=expand, extension=extension))
             if self.default_fetcher.cachable:
                 fetchers.insert(
-                    0, spack.fetch_cache.fetcher(
+                    0, spack.caches.fetch_cache.fetcher(
                         self.mirror_path, digest, expand=expand,
                         extension=extension))
 
@@ -436,9 +414,9 @@ class Stage(object):
                 tty.debug(e)
                 continue
         else:
-            errMessage = "All fetchers failed for %s" % self.name
+            err_msg = "All fetchers failed for %s" % self.name
             self.fetcher = self.default_fetcher
-            raise fs.FetchError(errMessage, None)
+            raise fs.FetchError(err_msg, None)
 
     def check(self):
         """Check the downloaded archive against a checksum digest.
@@ -455,7 +433,7 @@ class Stage(object):
             self.fetcher.check()
 
     def cache_local(self):
-        spack.fetch_cache.store(self.fetcher, self.mirror_path)
+        spack.caches.fetch_cache.store(self.fetcher, self.mirror_path)
 
     def expand_archive(self):
         """Changes to the stage directory and attempt to expand the downloaded
@@ -478,17 +456,13 @@ class Stage(object):
         """Creates the stage directory.
 
         If get_tmp_root() is None, the stage directory is created
-        directly under spack.stage_path, otherwise this will attempt to
+        directly under spack.paths.stage_path, otherwise this will attempt to
         create a stage in a temporary directory and link it into
-        spack.stage_path.
-
-        Spack will use the first writable location in spack.tmp_dirs
-        to create a stage. If there is no valid location in tmp_dirs,
-        fall back to making the stage inside spack.stage_path.
+        spack.paths.stage_path.
 
         """
         # Create the top-level stage directory
-        mkdirp(spack.stage_path)
+        mkdirp(spack.paths.stage_path)
         remove_if_dead_link(self.path)
 
         # If a tmp_root exists then create a directory there and then link it
@@ -496,11 +470,13 @@ class Stage(object):
         if self._need_to_create_path():
             tmp_root = get_tmp_root()
             if tmp_root is not None:
+                # tempfile.mkdtemp already sets mode 0700
                 tmp_dir = tempfile.mkdtemp('', _stage_prefix, tmp_root)
                 tty.debug('link %s -> %s' % (self.path, tmp_dir))
                 os.symlink(tmp_dir, self.path)
             else:
-                mkdirp(self.path)
+                # emulate file permissions for tempfile.mkdtemp
+                mkdirp(self.path, mode=stat.S_IRWXU)
         # Make sure we can actually do something with the stage we made.
         ensure_access(self.path)
         self.created = True
@@ -546,7 +522,7 @@ class ResourceStage(Stage):
         if not isinstance(placement, dict):
             placement = {'': placement}
 
-        target_path = join_path(
+        target_path = os.path.join(
             root_stage.source_path, resource.destination)
 
         try:
@@ -558,15 +534,15 @@ class ResourceStage(Stage):
                 raise
 
         for key, value in iteritems(placement):
-            destination_path = join_path(target_path, value)
-            source_path = join_path(self.source_path, key)
+            destination_path = os.path.join(target_path, value)
+            source_path = os.path.join(self.source_path, key)
 
             if not os.path.exists(destination_path):
                 tty.info('Moving resource stage\n\tsource : '
                          '{stage}\n\tdestination : {destination}'.format(
                              stage=source_path, destination=destination_path
                          ))
-                shutil.move(source_path, destination_path)
+                shutil.move(os.path.realpath(source_path), destination_path)
 
 
 @pattern.composite(method_list=[
@@ -651,11 +627,11 @@ class DIYStage(object):
 
 def _get_mirrors():
     """Get mirrors from spack configuration."""
-    config = spack.config.get_config('mirrors')
+    config = spack.config.get('mirrors')
     return [val for name, val in iteritems(config)]
 
 
-def ensure_access(file=spack.stage_path):
+def ensure_access(file=spack.paths.stage_path):
     """Ensure we can access a directory and die with an error if we can't."""
     if not can_access(file):
         tty.die("Insufficient permissions for %s" % file)
@@ -663,9 +639,9 @@ def ensure_access(file=spack.stage_path):
 
 def purge():
     """Remove all build directories in the top-level stage path."""
-    if os.path.isdir(spack.stage_path):
-        for stage_dir in os.listdir(spack.stage_path):
-            stage_path = join_path(spack.stage_path, stage_dir)
+    if os.path.isdir(spack.paths.stage_path):
+        for stage_dir in os.listdir(spack.paths.stage_path):
+            stage_path = os.path.join(spack.paths.stage_path, stage_dir)
             remove_linked_tree(stage_path)
 
 
diff --git a/lib/spack/spack/store.py b/lib/spack/spack/store.py
index a9a607150f..9deb208956 100644
--- a/lib/spack/spack/store.py
+++ b/lib/spack/spack/store.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """Components that manage Spack's installation tree.
 
 An install tree, or "build store" consists of two parts:
@@ -43,38 +24,63 @@ configuration.
 
 """
 import os
-import spack
+
+import llnl.util.lang
+
+import spack.paths
 import spack.config
-from spack.util.path import canonicalize_path
-from spack.database import Database
-from spack.directory_layout import YamlDirectoryLayout
-from spack.directory_layout import YamlExtensionsLayout
+import spack.util.path
+import spack.database
+import spack.directory_layout
 
-__author__ = "Benedikt Hegner (CERN)"
-__all__ = ['db', 'extensions', 'layout', 'root']
+#: default installation root, relative to the Spack install path
+default_root = os.path.join(spack.paths.opt_path, 'spack')
 
-#
-# Read in the config
-#
-config = spack.config.get_config("config")
 
-#
-# Set up the install path
-#
-root = canonicalize_path(
-    config.get('install_tree', os.path.join(spack.opt_path, 'spack')))
+class Store(object):
+    """A store is a path full of installed Spack packages.
 
-#
-# Set up the installed packages database
-#
-db = Database(root)
+    Stores consist of packages installed according to a
+    ``DirectoryLayout``, along with an index, or _database_ of their
+    contents.  The directory layout controls what paths look like and how
+    Spack ensures that each uniqe spec gets its own unique directory (or
+    not, though we don't recommend that). The database is a signle file
+    that caches metadata for the entire Spack installation.  It prevents
+    us from having to spider the install tree to figure out what's there.
 
-#
-# This controls how spack lays out install prefixes and
-# stage directories.
-#
-layout = YamlDirectoryLayout(root,
-                             hash_len=config.get('install_hash_length'),
-                             path_scheme=config.get('install_path_scheme'))
+    Args:
+        root (str): path to the root of the install tree
+        path_scheme (str): expression according to guidelines in
+            ``spack.util.path`` that describes how to construct a path to
+            a package prefix in this store
+        hash_length (int): length of the hashes used in the directory
+            layout; spec hash suffixes will be truncated to this length
+    """
+    def __init__(self, root, path_scheme=None, hash_length=None):
+        self.root = root
+        self.db = spack.database.Database(root)
+        self.layout = spack.directory_layout.YamlDirectoryLayout(
+            root, hash_len=hash_length, path_scheme=path_scheme)
+
+    def reindex(self):
+        """Convenience function to reindex the store DB with its own layout."""
+        return self.db.reindex(self.layout)
+
+
+def _store():
+    """Get the singleton store instance."""
+    root = spack.config.get('config:install_tree', default_root)
+    root = spack.util.path.canonicalize_path(root)
+
+    return Store(root,
+                 spack.config.get('config:install_path_scheme'),
+                 spack.config.get('config:install_hash_length'))
+
+
+#: Singleton store instance
+store = llnl.util.lang.Singleton(_store)
 
-extensions = YamlExtensionsLayout(root, layout)
+# convenience accessors for parts of the singleton store
+root = llnl.util.lang.LazyReference(lambda: store.root)
+db = llnl.util.lang.LazyReference(lambda: store.db)
+layout = llnl.util.lang.LazyReference(lambda: store.layout)
diff --git a/lib/spack/spack/tengine.py b/lib/spack/spack/tengine.py
index 44c62521b1..fa8e8f283f 100644
--- a/lib/spack/spack/tengine.py
+++ b/lib/spack/spack/tengine.py
@@ -1,34 +1,16 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 import textwrap
 
 import jinja2
 import llnl.util.lang
 import six
-import spack
+
+import spack.config
+from spack.util.path import canonicalize_path
 
 
 TemplateNotFound = jinja2.TemplateNotFound
@@ -42,10 +24,10 @@ class ContextMeta(type):
     #: by the class that is being defined
     _new_context_properties = []
 
-    def __new__(mcs, name, bases, attr_dict):
+    def __new__(cls, name, bases, attr_dict):
         # Merge all the context properties that are coming from base classes
         # into a list without duplicates.
-        context_properties = list(mcs._new_context_properties)
+        context_properties = list(cls._new_context_properties)
         for x in bases:
             try:
                 context_properties.extend(x.context_properties)
@@ -54,20 +36,20 @@ class ContextMeta(type):
         context_properties = list(llnl.util.lang.dedupe(context_properties))
 
         # Flush the list
-        mcs._new_context_properties = []
+        cls._new_context_properties = []
 
         # Attach the list to the class being created
         attr_dict['context_properties'] = context_properties
 
-        return super(ContextMeta, mcs).__new__(mcs, name, bases, attr_dict)
+        return super(ContextMeta, cls).__new__(cls, name, bases, attr_dict)
 
     @classmethod
-    def context_property(mcs, func):
+    def context_property(cls, func):
         """Decorator that adds a function name to the list of new context
         properties, and then returns a property.
         """
         name = func.__name__
-        mcs._new_context_properties.append(name)
+        cls._new_context_properties.append(name)
         return property(func)
 
 
@@ -90,7 +72,8 @@ def make_environment(dirs=None):
     """Returns an configured environment for template rendering."""
     if dirs is None:
         # Default directories where to search for templates
-        dirs = spack.template_dirs
+        dirs = [canonicalize_path(d)
+                for d in spack.config.get('config:template_dirs')]
     # Loader for the templates
     loader = jinja2.FileSystemLoader(dirs)
     # Environment of the template engine
diff --git a/lib/spack/spack/test/__init__.py b/lib/spack/spack/test/__init__.py
index 8922701e9f..4f442db458 100644
--- a/lib/spack/spack/test/__init__.py
+++ b/lib/spack/spack/test/__init__.py
@@ -1,24 +1,4 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
diff --git a/lib/spack/spack/test/architecture.py b/lib/spack/spack/test/architecture.py
index 18bf7d66c5..33a002faad 100644
--- a/lib/spack/spack/test/architecture.py
+++ b/lib/spack/spack/test/architecture.py
@@ -1,34 +1,15 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """ Test checks if the architecture class is created correctly and also that
     the functions are looking for the correct architecture name
 """
 import itertools
 import os
 import platform as py_platform
-import spack
+
 import spack.architecture
 from spack.spec import Spec
 from spack.platforms.cray import Cray
diff --git a/lib/spack/spack/test/build_environment.py b/lib/spack/spack/test/build_environment.py
index 37664aa35e..e055bbf99c 100644
--- a/lib/spack/spack/test/build_environment.py
+++ b/lib/spack/spack/test/build_environment.py
@@ -1,41 +1,24 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 import pytest
 
-import spack
-from llnl.util.filesystem import join_path
+import spack.build_environment
+import spack.spec
+from spack.paths import build_env_path
 from spack.build_environment import dso_suffix, _static_to_shared_library
 from spack.util.executable import Executable
+from spack.util.spack_yaml import syaml_dict, syaml_str
 
 
 @pytest.fixture
 def build_environment():
-    cc = Executable(join_path(spack.build_env_path, "cc"))
-    cxx = Executable(join_path(spack.build_env_path, "c++"))
-    fc = Executable(join_path(spack.build_env_path, "fc"))
+    cc = Executable(os.path.join(build_env_path, "cc"))
+    cxx = Executable(os.path.join(build_env_path, "c++"))
+    fc = Executable(os.path.join(build_env_path, "fc"))
 
     realcc = "/bin/mycc"
     prefix = "/spack-test-prefix"
@@ -57,6 +40,8 @@ def build_environment():
     os.environ['SPACK_F77_RPATH_ARG'] = "-Wl,-rpath,"
     os.environ['SPACK_FC_RPATH_ARG']  = "-Wl,-rpath,"
 
+    os.environ['SPACK_SYSTEM_DIRS'] = '/usr/include /usr/lib'
+
     if 'SPACK_DEPENDENCIES' in os.environ:
         del os.environ['SPACK_DEPENDENCIES']
 
@@ -66,7 +51,8 @@ def build_environment():
                  'SPACK_ENV_PATH', 'SPACK_DEBUG_LOG_DIR',
                  'SPACK_COMPILER_SPEC', 'SPACK_SHORT_SPEC',
                  'SPACK_CC_RPATH_ARG', 'SPACK_CXX_RPATH_ARG',
-                 'SPACK_F77_RPATH_ARG', 'SPACK_FC_RPATH_ARG'):
+                 'SPACK_F77_RPATH_ARG', 'SPACK_FC_RPATH_ARG',
+                 'SPACK_SYSTEM_DIRS'):
         del os.environ[name]
 
 
@@ -95,5 +81,137 @@ def test_static_to_shared_library(build_environment):
                 shared_lib = '{0}.{1}'.format(
                     os.path.splitext(static_lib)[0], dso_suffix)
 
-            assert output == expected[arch].format(
-                static_lib, shared_lib, os.path.basename(shared_lib))
+            assert set(output.split()) == set(expected[arch].format(
+                static_lib, shared_lib, os.path.basename(shared_lib)).split())
+
+
+@pytest.mark.regression('8345')
+@pytest.mark.usefixtures('config', 'mock_packages')
+def test_cc_not_changed_by_modules(monkeypatch):
+
+    s = spack.spec.Spec('cmake')
+    s.concretize()
+    pkg = s.package
+
+    def _set_wrong_cc(x):
+        os.environ['CC'] = 'NOT_THIS_PLEASE'
+        os.environ['ANOTHER_VAR'] = 'THIS_IS_SET'
+
+    monkeypatch.setattr(
+        spack.build_environment, 'load_module', _set_wrong_cc
+    )
+    monkeypatch.setattr(
+        pkg.compiler, 'modules', ['some_module']
+    )
+
+    spack.build_environment.setup_package(pkg, False)
+
+    assert os.environ['CC'] != 'NOT_THIS_PLEASE'
+    assert os.environ['ANOTHER_VAR'] == 'THIS_IS_SET'
+
+
+@pytest.mark.usefixtures('config', 'mock_packages')
+def test_compiler_config_modifications(monkeypatch):
+    s = spack.spec.Spec('cmake')
+    s.concretize()
+    pkg = s.package
+
+    os.environ['SOME_VAR_STR'] = ''
+    os.environ['SOME_VAR_NUM'] = '0'
+    os.environ['PATH_LIST'] = '/path/third:/path/forth'
+    os.environ['EMPTY_PATH_LIST'] = ''
+    os.environ.pop('NEW_PATH_LIST', None)
+
+    env_mod = syaml_dict()
+    set_cmd = syaml_dict()
+    env_mod[syaml_str('set')] = set_cmd
+
+    set_cmd[syaml_str('SOME_VAR_STR')] = syaml_str('SOME_STR')
+    set_cmd[syaml_str('SOME_VAR_NUM')] = 1
+
+    monkeypatch.setattr(pkg.compiler, 'environment', env_mod)
+    spack.build_environment.setup_package(pkg, False)
+    assert os.environ['SOME_VAR_STR'] == 'SOME_STR'
+    assert os.environ['SOME_VAR_NUM'] == str(1)
+
+    env_mod = syaml_dict()
+    unset_cmd = syaml_dict()
+    env_mod[syaml_str('unset')] = unset_cmd
+
+    unset_cmd[syaml_str('SOME_VAR_STR')] = None
+
+    monkeypatch.setattr(pkg.compiler, 'environment', env_mod)
+    assert 'SOME_VAR_STR' in os.environ
+    spack.build_environment.setup_package(pkg, False)
+    assert 'SOME_VAR_STR' not in os.environ
+
+    env_mod = syaml_dict()
+    set_cmd = syaml_dict()
+    env_mod[syaml_str('set')] = set_cmd
+    append_cmd = syaml_dict()
+    env_mod[syaml_str('append-path')] = append_cmd
+    unset_cmd = syaml_dict()
+    env_mod[syaml_str('unset')] = unset_cmd
+    prepend_cmd = syaml_dict()
+    env_mod[syaml_str('prepend-path')] = prepend_cmd
+
+    set_cmd[syaml_str('EMPTY_PATH_LIST')] = syaml_str('/path/middle')
+
+    append_cmd[syaml_str('PATH_LIST')] = syaml_str('/path/last')
+    append_cmd[syaml_str('EMPTY_PATH_LIST')] = syaml_str('/path/last')
+    append_cmd[syaml_str('NEW_PATH_LIST')] = syaml_str('/path/last')
+
+    unset_cmd[syaml_str('SOME_VAR_NUM')] = None
+
+    prepend_cmd[syaml_str('PATH_LIST')] = syaml_str('/path/first:/path/second')
+    prepend_cmd[syaml_str('EMPTY_PATH_LIST')] = syaml_str('/path/first')
+    prepend_cmd[syaml_str('NEW_PATH_LIST')] = syaml_str('/path/first')
+    prepend_cmd[syaml_str('SOME_VAR_NUM')] = syaml_str('/8')
+
+    assert 'SOME_VAR_NUM' in os.environ
+    monkeypatch.setattr(pkg.compiler, 'environment', env_mod)
+    spack.build_environment.setup_package(pkg, False)
+    # Check that the order of modifications is respected and the
+    # variable was unset before it was prepended.
+    assert os.environ['SOME_VAR_NUM'] == '/8'
+
+    expected = '/path/first:/path/second:/path/third:/path/forth:/path/last'
+    assert os.environ['PATH_LIST'] == expected
+
+    expected = '/path/first:/path/middle:/path/last'
+    assert os.environ['EMPTY_PATH_LIST'] == expected
+
+    expected = '/path/first:/path/last'
+    assert os.environ['NEW_PATH_LIST'] == expected
+
+    os.environ.pop('SOME_VAR_STR', None)
+    os.environ.pop('SOME_VAR_NUM', None)
+    os.environ.pop('PATH_LIST', None)
+    os.environ.pop('EMPTY_PATH_LIST', None)
+    os.environ.pop('NEW_PATH_LIST', None)
+
+
+@pytest.mark.regression('9107')
+def test_spack_paths_before_module_paths(config, mock_packages, monkeypatch):
+    s = spack.spec.Spec('cmake')
+    s.concretize()
+    pkg = s.package
+
+    module_path = '/path/to/module'
+
+    def _set_wrong_cc(x):
+        os.environ['PATH'] = module_path + ':' + os.environ['PATH']
+
+    monkeypatch.setattr(
+        spack.build_environment, 'load_module', _set_wrong_cc
+    )
+    monkeypatch.setattr(
+        pkg.compiler, 'modules', ['some_module']
+    )
+
+    spack.build_environment.setup_package(pkg, False)
+
+    spack_path = os.path.join(spack.paths.prefix, 'lib/spack/env')
+    paths = os.environ['PATH'].split(':')
+
+    assert paths.index(spack_path) < paths.index(module_path)
diff --git a/lib/spack/spack/test/build_system_guess.py b/lib/spack/spack/test/build_system_guess.py
index b23b66a846..1e11543823 100644
--- a/lib/spack/spack/test/build_system_guess.py
+++ b/lib/spack/spack/test/build_system_guess.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 import pytest
 import spack.cmd.create
@@ -45,6 +26,7 @@ import spack.stage
         ('GNUmakefile',    'makefile'),
         ('makefile',       'makefile'),
         ('Makefile',       'makefile'),
+        ('meson.build',    'meson'),
         ('foobar',         'generic')
     ]
 )
diff --git a/lib/spack/spack/test/build_systems.py b/lib/spack/spack/test/build_systems.py
index 72b88f3f26..3bf2390139 100644
--- a/lib/spack/spack/test/build_systems.py
+++ b/lib/spack/spack/test/build_systems.py
@@ -1,36 +1,107 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-import spack
+import glob
+import os
 import pytest
 
-from spack.build_environment import get_std_cmake_args
+import spack.repo
+from llnl.util.filesystem import working_dir
+from spack.build_environment import get_std_cmake_args, setup_package
 from spack.spec import Spec
+from spack.util.executable import which
+
+
+DATA_PATH = os.path.join(spack.paths.test_path, 'data')
+
+
+@pytest.mark.parametrize(
+    'directory',
+    glob.iglob(os.path.join(DATA_PATH, 'make', 'affirmative', '*'))
+)
+def test_affirmative_make_check(directory, config, mock_packages):
+    """Tests that Spack correctly detects targets in a Makefile."""
+
+    # Get a fake package
+    s = Spec('mpich')
+    s.concretize()
+    pkg = spack.repo.get(s)
+    setup_package(pkg, False)
+
+    with working_dir(directory):
+        assert pkg._has_make_target('check')
+
+        pkg._if_make_target_execute('check')
+
+
+@pytest.mark.parametrize(
+    'directory',
+    glob.iglob(os.path.join(DATA_PATH, 'make', 'negative', '*'))
+)
+@pytest.mark.regression('9067')
+def test_negative_make_check(directory, config, mock_packages):
+    """Tests that Spack correctly ignores false positives in a Makefile."""
+
+    # Get a fake package
+    s = Spec('mpich')
+    s.concretize()
+    pkg = spack.repo.get(s)
+    setup_package(pkg, False)
+
+    with working_dir(directory):
+        assert not pkg._has_make_target('check')
+
+        pkg._if_make_target_execute('check')
+
+
+@pytest.mark.skipif(not which('ninja'), reason='ninja is not installed')
+@pytest.mark.parametrize(
+    'directory',
+    glob.iglob(os.path.join(DATA_PATH, 'ninja', 'affirmative', '*'))
+)
+def test_affirmative_ninja_check(directory, config, mock_packages):
+    """Tests that Spack correctly detects targets in a Ninja build script."""
+
+    # Get a fake package
+    s = Spec('mpich')
+    s.concretize()
+    pkg = spack.repo.get(s)
+    setup_package(pkg, False)
+
+    with working_dir(directory):
+        assert pkg._has_ninja_target('check')
+
+        pkg._if_ninja_target_execute('check')
+
+        # Clean up Ninja files
+        for filename in glob.iglob('.ninja_*'):
+            os.remove(filename)
+
+
+@pytest.mark.skipif(not which('ninja'), reason='ninja is not installed')
+@pytest.mark.parametrize(
+    'directory',
+    glob.iglob(os.path.join(DATA_PATH, 'ninja', 'negative', '*'))
+)
+def test_negative_ninja_check(directory, config, mock_packages):
+    """Tests that Spack correctly ignores false positives in a Ninja
+    build script."""
+
+    # Get a fake package
+    s = Spec('mpich')
+    s.concretize()
+    pkg = spack.repo.get(s)
+    setup_package(pkg, False)
+
+    with working_dir(directory):
+        assert not pkg._has_ninja_target('check')
+
+        pkg._if_ninja_target_execute('check')
 
 
-def test_cmake_std_args(config, builtin_mock):
+def test_cmake_std_args(config, mock_packages):
     # Call the function on a CMakePackage instance
     s = Spec('cmake-client')
     s.concretize()
@@ -44,7 +115,7 @@ def test_cmake_std_args(config, builtin_mock):
     assert get_std_cmake_args(pkg)
 
 
-@pytest.mark.usefixtures('config', 'builtin_mock')
+@pytest.mark.usefixtures('config', 'mock_packages')
 class TestAutotoolsPackage(object):
 
     def test_with_or_without(self):
diff --git a/lib/spack/spack/test/cc.py b/lib/spack/spack/test/cc.py
index 671379c717..eb51021eac 100644
--- a/lib/spack/spack/test/cc.py
+++ b/lib/spack/spack/test/cc.py
@@ -1,42 +1,23 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """
 This test checks that the Spack cc compiler wrapper is parsing
 arguments correctly.
 """
 import os
-import unittest
-import tempfile
-import shutil
+import pytest
 
-import spack
-from llnl.util.filesystem import mkdirp, join_path
+from spack.paths import build_env_path
+from spack.util.environment import system_dirs, set_env
 from spack.util.executable import Executable
 
+#
 # Complicated compiler test command
-test_command = [
+#
+test_args = [
     '-I/test/include', '-L/test/lib', '-L/other/lib', '-I/other/include',
     'arg1',
     '-Wl,--start-group',
@@ -45,344 +26,525 @@ test_command = [
     '-llib1', '-llib2',
     'arg4',
     '-Wl,--end-group',
-    '-Xlinker', '-rpath', '-Xlinker', '/third/rpath', '-Xlinker',
-    '-rpath', '-Xlinker', '/fourth/rpath',
+    '-Xlinker', '-rpath', '-Xlinker', '/third/rpath',
+    '-Xlinker', '-rpath', '-Xlinker', '/fourth/rpath',
     '-llib3', '-llib4',
     'arg5', 'arg6']
 
+#
+# Pieces of the test command above, as they should be parsed out.
+#
+# `_wl_rpaths` are for the compiler (with -Wl,), and `_rpaths` are raw
+# -rpath arguments for the linker.
+#
+test_include_paths = [
+    '-I/test/include', '-I/other/include']
+
+test_library_paths = [
+    '-L/test/lib', '-L/other/lib']
 
-class CompilerWrapperTest(unittest.TestCase):
-
-    def setUp(self):
-        self.cc = Executable(join_path(spack.build_env_path, "cc"))
-        self.ld = Executable(join_path(spack.build_env_path, "ld"))
-        self.cpp = Executable(join_path(spack.build_env_path, "cpp"))
-        self.cxx = Executable(join_path(spack.build_env_path, "c++"))
-        self.fc = Executable(join_path(spack.build_env_path, "fc"))
-
-        self.realcc = "/bin/mycc"
-        self.prefix = "/spack-test-prefix"
-
-        os.environ['SPACK_CC'] = self.realcc
-        os.environ['SPACK_CXX'] = self.realcc
-        os.environ['SPACK_FC'] = self.realcc
-
-        os.environ['SPACK_PREFIX'] = self.prefix
-        os.environ['SPACK_ENV_PATH'] = "test"
-        os.environ['SPACK_DEBUG_LOG_DIR'] = "."
-        os.environ['SPACK_DEBUG_LOG_ID'] = "foo-hashabc"
-        os.environ['SPACK_COMPILER_SPEC'] = "gcc@4.4.7"
-        os.environ['SPACK_SHORT_SPEC'] = (
-            "foo@1.2 arch=linux-rhel6-x86_64 /hashabc")
-
-        os.environ['SPACK_CC_RPATH_ARG']  = "-Wl,-rpath,"
-        os.environ['SPACK_CXX_RPATH_ARG'] = "-Wl,-rpath,"
-        os.environ['SPACK_F77_RPATH_ARG'] = "-Wl,-rpath,"
-        os.environ['SPACK_FC_RPATH_ARG']  = "-Wl,-rpath,"
-
-        # Make some fake dependencies
-        self.tmp_deps = tempfile.mkdtemp()
-        self.dep1 = join_path(self.tmp_deps, 'dep1')
-        self.dep2 = join_path(self.tmp_deps, 'dep2')
-        self.dep3 = join_path(self.tmp_deps, 'dep3')
-        self.dep4 = join_path(self.tmp_deps, 'dep4')
-
-        mkdirp(join_path(self.dep1, 'include'))
-        mkdirp(join_path(self.dep1, 'lib'))
-
-        mkdirp(join_path(self.dep2, 'lib64'))
-
-        mkdirp(join_path(self.dep3, 'include'))
-        mkdirp(join_path(self.dep3, 'lib64'))
-
-        mkdirp(join_path(self.dep4, 'include'))
-
-        if 'SPACK_DEPENDENCIES' in os.environ:
-            del os.environ['SPACK_DEPENDENCIES']
-
-    def tearDown(self):
-        shutil.rmtree(self.tmp_deps, True)
-
-    def check_cc(self, command, args, expected):
-        os.environ['SPACK_TEST_COMMAND'] = command
-        self.assertEqual(self.cc(*args, output=str).strip(), expected)
-
-    def check_cxx(self, command, args, expected):
-        os.environ['SPACK_TEST_COMMAND'] = command
-        self.assertEqual(self.cxx(*args, output=str).strip(), expected)
-
-    def check_fc(self, command, args, expected):
-        os.environ['SPACK_TEST_COMMAND'] = command
-        self.assertEqual(self.fc(*args, output=str).strip(), expected)
-
-    def check_ld(self, command, args, expected):
-        os.environ['SPACK_TEST_COMMAND'] = command
-        self.assertEqual(self.ld(*args, output=str).strip(), expected)
-
-    def check_cpp(self, command, args, expected):
-        os.environ['SPACK_TEST_COMMAND'] = command
-        self.assertEqual(self.cpp(*args, output=str).strip(), expected)
-
-    def test_vcheck_mode(self):
-        self.check_cc('dump-mode', ['-I/include', '--version'], "vcheck")
-        self.check_cc('dump-mode', ['-I/include', '-V'], "vcheck")
-        self.check_cc('dump-mode', ['-I/include', '-v'], "vcheck")
-        self.check_cc('dump-mode', ['-I/include', '-dumpversion'], "vcheck")
-        self.check_cc('dump-mode', ['-I/include', '--version', '-c'], "vcheck")
-        self.check_cc('dump-mode', ['-I/include',
-                                    '-V', '-o', 'output'], "vcheck")
-
-    def test_cpp_mode(self):
-        self.check_cc('dump-mode', ['-E'], "cpp")
-        self.check_cpp('dump-mode', [], "cpp")
-
-    def test_as_mode(self):
-        self.check_cc('dump-mode', ['-S'], "as")
-
-    def test_ccld_mode(self):
-        self.check_cc('dump-mode', [], "ccld")
-        self.check_cc('dump-mode', ['foo.c', '-o', 'foo'], "ccld")
-        self.check_cc('dump-mode', ['foo.c', '-o',
-                                    'foo', '-Wl,-rpath,foo'], "ccld")
-        self.check_cc(
-            'dump-mode',
-            ['foo.o', 'bar.o', 'baz.o', '-o', 'foo', '-Wl,-rpath,foo'],
-            "ccld")
-
-    def test_ld_mode(self):
-        self.check_ld('dump-mode', [], "ld")
-        self.check_ld(
-            'dump-mode',
-            ['foo.o', 'bar.o', 'baz.o', '-o', 'foo', '-Wl,-rpath,foo'],
-            "ld")
-
-    def test_flags(self):
-        os.environ['SPACK_LDFLAGS'] = '-L foo'
-        os.environ['SPACK_LDLIBS'] = '-lfoo'
-        os.environ['SPACK_CPPFLAGS'] = '-g -O1'
-        os.environ['SPACK_CFLAGS'] = '-Wall'
-        os.environ['SPACK_CXXFLAGS'] = '-Werror'
-        os.environ['SPACK_FFLAGS'] = '-w'
-
-        # Test ldflags added properly in ld mode
-        self.check_ld('dump-args', test_command,
-                      "ld " +
-                      '-rpath ' + self.prefix + '/lib ' +
-                      '-rpath ' + self.prefix + '/lib64 ' +
-                      '-L foo ' +
-                      ' '.join(test_command) + ' ' +
-                      '-lfoo')
-
-        # Test cppflags added properly in cpp mode
-        self.check_cpp('dump-args', test_command,
-                       "cpp " +
-                       '-g -O1 ' +
-                       ' '.join(test_command))
-
-        # Test ldflags, cppflags, and language specific flags are added in
-        # proper order
-        self.check_cc('dump-args', test_command,
-                      self.realcc + ' ' +
-                      '-Wl,-rpath,' + self.prefix + '/lib ' +
-                      '-Wl,-rpath,' + self.prefix + '/lib64 ' +
-                      '-g -O1 ' +
-                      '-Wall ' +
-                      '-L foo ' +
-                      ' '.join(test_command) + ' ' +
-                      '-lfoo')
-
-        self.check_cxx('dump-args', test_command,
-                       self.realcc + ' ' +
-                       '-Wl,-rpath,' + self.prefix + '/lib ' +
-                       '-Wl,-rpath,' + self.prefix + '/lib64 ' +
-                       '-g -O1 ' +
-                       '-Werror ' +
-                       '-L foo ' +
-                       ' '.join(test_command) + ' ' +
-                       '-lfoo')
-
-        self.check_fc('dump-args', test_command,
-                      self.realcc + ' ' +
-                      '-Wl,-rpath,' + self.prefix + '/lib ' +
-                      '-Wl,-rpath,' + self.prefix + '/lib64 ' +
-                      '-w ' +
-                      '-g -O1 ' +
-                      '-L foo ' +
-                      ' '.join(test_command) + ' ' +
-                      '-lfoo')
-
-        del os.environ['SPACK_CFLAGS']
-        del os.environ['SPACK_CXXFLAGS']
-        del os.environ['SPACK_FFLAGS']
-        del os.environ['SPACK_CPPFLAGS']
-        del os.environ['SPACK_LDFLAGS']
-        del os.environ['SPACK_LDLIBS']
-
-    def test_dep_rpath(self):
-        """Ensure RPATHs for root package are added."""
-        self.check_cc('dump-args', test_command,
-                      self.realcc + ' ' +
-                      '-Wl,-rpath,' + self.prefix + '/lib ' +
-                      '-Wl,-rpath,' + self.prefix + '/lib64 ' +
-                      ' '.join(test_command))
-
-    def test_dep_include(self):
-        """Ensure a single dependency include directory is added."""
-        os.environ['SPACK_DEPENDENCIES'] = self.dep4
-        os.environ['SPACK_RPATH_DEPS'] = os.environ['SPACK_DEPENDENCIES']
-        os.environ['SPACK_LINK_DEPS'] = os.environ['SPACK_DEPENDENCIES']
-        self.check_cc('dump-args', test_command,
-                      self.realcc + ' ' +
-                      '-Wl,-rpath,' + self.prefix + '/lib ' +
-                      '-Wl,-rpath,' + self.prefix + '/lib64 ' +
-                      '-I' + self.dep4 + '/include ' +
-                      ' '.join(test_command))
-
-    def test_dep_lib(self):
-        """Ensure a single dependency RPATH is added."""
-        os.environ['SPACK_DEPENDENCIES'] = self.dep2
-        os.environ['SPACK_RPATH_DEPS'] = os.environ['SPACK_DEPENDENCIES']
-        os.environ['SPACK_LINK_DEPS'] = os.environ['SPACK_DEPENDENCIES']
-        self.check_cc('dump-args', test_command,
-                      self.realcc + ' ' +
-                      '-Wl,-rpath,' + self.prefix + '/lib ' +
-                      '-Wl,-rpath,' + self.prefix + '/lib64 ' +
-                      '-L' + self.dep2 + '/lib64 ' +
-                      '-Wl,-rpath,' + self.dep2 + '/lib64 ' +
-                      ' '.join(test_command))
-
-    def test_dep_lib_no_rpath(self):
-        """Ensure a single dependency link flag is added with no dep RPATH."""
-        os.environ['SPACK_DEPENDENCIES'] = self.dep2
-        os.environ['SPACK_LINK_DEPS'] = os.environ['SPACK_DEPENDENCIES']
-        self.check_cc('dump-args', test_command,
-                      self.realcc + ' ' +
-                      '-Wl,-rpath,' + self.prefix + '/lib ' +
-                      '-Wl,-rpath,' + self.prefix + '/lib64 ' +
-                      '-L' + self.dep2 + '/lib64 ' +
-                      ' '.join(test_command))
-
-    def test_dep_lib_no_lib(self):
-        """Ensure a single dependency RPATH is added with no -L."""
-        os.environ['SPACK_DEPENDENCIES'] = self.dep2
-        os.environ['SPACK_RPATH_DEPS'] = os.environ['SPACK_DEPENDENCIES']
-        self.check_cc('dump-args', test_command,
-                      self.realcc + ' ' +
-                      '-Wl,-rpath,' + self.prefix + '/lib ' +
-                      '-Wl,-rpath,' + self.prefix + '/lib64 ' +
-                      '-Wl,-rpath,' + self.dep2 + '/lib64 ' +
-                      ' '.join(test_command))
-
-    def test_all_deps(self):
-        """Ensure includes and RPATHs for all deps are added. """
-        os.environ['SPACK_DEPENDENCIES'] = ':'.join([
-            self.dep1, self.dep2, self.dep3, self.dep4])
-        os.environ['SPACK_RPATH_DEPS'] = os.environ['SPACK_DEPENDENCIES']
-        os.environ['SPACK_LINK_DEPS'] = os.environ['SPACK_DEPENDENCIES']
-
-        # This is probably more constrained than it needs to be; it
-        # checks order within prepended args and doesn't strictly have
-        # to.  We could loosen that if it becomes necessary
-        self.check_cc('dump-args', test_command,
-                      self.realcc + ' ' +
-                      '-Wl,-rpath,' + self.prefix + '/lib ' +
-                      '-Wl,-rpath,' + self.prefix + '/lib64 ' +
-
-                      '-I' + self.dep4 + '/include ' +
-
-                      '-L' + self.dep3 + '/lib64 ' +
-                      '-Wl,-rpath,' + self.dep3 + '/lib64 ' +
-                      '-I' + self.dep3 + '/include ' +
-
-                      '-L' + self.dep2 + '/lib64 ' +
-                      '-Wl,-rpath,' + self.dep2 + '/lib64 ' +
-
-                      '-L' + self.dep1 + '/lib ' +
-                      '-Wl,-rpath,' + self.dep1 + '/lib ' +
-                      '-I' + self.dep1 + '/include ' +
-
-                      ' '.join(test_command))
-
-    def test_ld_deps(self):
-        """Ensure no (extra) -I args or -Wl, are passed in ld mode."""
-        os.environ['SPACK_DEPENDENCIES'] = ':'.join([
-            self.dep1, self.dep2, self.dep3, self.dep4])
-        os.environ['SPACK_RPATH_DEPS'] = os.environ['SPACK_DEPENDENCIES']
-        os.environ['SPACK_LINK_DEPS'] = os.environ['SPACK_DEPENDENCIES']
-
-        self.check_ld('dump-args', test_command,
-                      'ld ' +
-                      '-rpath ' + self.prefix + '/lib ' +
-                      '-rpath ' + self.prefix + '/lib64 ' +
-
-                      '-L' + self.dep3 + '/lib64 ' +
-                      '-rpath ' + self.dep3 + '/lib64 ' +
-
-                      '-L' + self.dep2 + '/lib64 ' +
-                      '-rpath ' + self.dep2 + '/lib64 ' +
-
-                      '-L' + self.dep1 + '/lib ' +
-                      '-rpath ' + self.dep1 + '/lib ' +
-
-                      ' '.join(test_command))
-
-    def test_ld_deps_no_rpath(self):
-        """Ensure SPACK_RPATH_DEPS controls RPATHs for ld."""
-        os.environ['SPACK_DEPENDENCIES'] = ':'.join([
-            self.dep1, self.dep2, self.dep3, self.dep4])
-        os.environ['SPACK_LINK_DEPS'] = os.environ['SPACK_DEPENDENCIES']
-
-        self.check_ld('dump-args', test_command,
-                      'ld ' +
-                      '-rpath ' + self.prefix + '/lib ' +
-                      '-rpath ' + self.prefix + '/lib64 ' +
-
-                      '-L' + self.dep3 + '/lib64 ' +
-                      '-L' + self.dep2 + '/lib64 ' +
-                      '-L' + self.dep1 + '/lib ' +
-
-                      ' '.join(test_command))
-
-    def test_ld_deps_no_link(self):
-        """Ensure SPACK_LINK_DEPS controls -L for ld."""
-        os.environ['SPACK_DEPENDENCIES'] = ':'.join([
-            self.dep1, self.dep2, self.dep3, self.dep4])
-        os.environ['SPACK_RPATH_DEPS'] = os.environ['SPACK_DEPENDENCIES']
-
-        self.check_ld('dump-args', test_command,
-                      'ld ' +
-                      '-rpath ' + self.prefix + '/lib ' +
-                      '-rpath ' + self.prefix + '/lib64 ' +
-
-                      '-rpath ' + self.dep3 + '/lib64 ' +
-                      '-rpath ' + self.dep2 + '/lib64 ' +
-                      '-rpath ' + self.dep1 + '/lib ' +
-
-                      ' '.join(test_command))
-
-    def test_ld_deps_reentrant(self):
-        """Make sure ld -r is handled correctly on OS's where it doesn't
-           support rpaths."""
-        os.environ['SPACK_DEPENDENCIES'] = ':'.join([self.dep1])
-        os.environ['SPACK_RPATH_DEPS'] = os.environ['SPACK_DEPENDENCIES']
-        os.environ['SPACK_LINK_DEPS'] = os.environ['SPACK_DEPENDENCIES']
+test_wl_rpaths = [
+    '-Wl,-rpath,/first/rpath', '-Wl,-rpath,/second/rpath',
+    '-Wl,-rpath,/third/rpath', '-Wl,-rpath,/fourth/rpath']
 
-        os.environ['SPACK_SHORT_SPEC'] = "foo@1.2=linux-x86_64"
-        reentrant_test_command = ['-r'] + test_command
-        self.check_ld('dump-args', reentrant_test_command,
-                      'ld ' +
-                      '-rpath ' + self.prefix + '/lib ' +
-                      '-rpath ' + self.prefix + '/lib64 ' +
+test_rpaths = [
+    '-rpath', '/first/rpath', '-rpath', '/second/rpath',
+    '-rpath', '/third/rpath', '-rpath', '/fourth/rpath']
 
-                      '-L' + self.dep1 + '/lib ' +
-                      '-rpath ' + self.dep1 + '/lib ' +
+test_args_without_paths = [
+    'arg1',
+    '-Wl,--start-group',
+    'arg2', 'arg3', '-llib1', '-llib2', 'arg4',
+    '-Wl,--end-group',
+    '-llib3', '-llib4', 'arg5', 'arg6']
 
-                      '-r ' +
-                      ' '.join(test_command))
+#: The prefix of the package being mock installed
+pkg_prefix = '/spack-test-prefix'
 
+#
+# Expected RPATHs for the package itself.  The package is expected to
+# have only one of /lib or /lib64, but we add both b/c we can't know
+# before installing.
+#
+pkg_wl_rpaths = [
+    '-Wl,-rpath,' + pkg_prefix + '/lib',
+    '-Wl,-rpath,' + pkg_prefix + '/lib64']
+
+pkg_rpaths = [
+    '-rpath', '/spack-test-prefix/lib',
+    '-rpath', '/spack-test-prefix/lib64']
+
+# Compilers to use during tests
+cc = Executable(os.path.join(build_env_path, "cc"))
+ld = Executable(os.path.join(build_env_path, "ld"))
+cpp = Executable(os.path.join(build_env_path, "cpp"))
+cxx = Executable(os.path.join(build_env_path, "c++"))
+fc = Executable(os.path.join(build_env_path, "fc"))
+
+#: the "real" compiler the wrapper is expected to invoke
+real_cc = '/bin/mycc'
+
+# mock flags to use in the wrapper environment
+spack_cppflags = ['-g', '-O1', '-DVAR=VALUE']
+spack_cflags   = ['-Wall']
+spack_cxxflags = ['-Werror']
+spack_fflags   = ['-w']
+spack_ldflags  = ['-L', 'foo']
+spack_ldlibs   = ['-lfoo']
+
+
+@pytest.fixture(scope='session')
+def wrapper_environment():
+    with set_env(
+            SPACK_CC=real_cc,
+            SPACK_CXX=real_cc,
+            SPACK_FC=real_cc,
+            SPACK_PREFIX=pkg_prefix,
+            SPACK_ENV_PATH='test',
+            SPACK_DEBUG_LOG_DIR='.',
+            SPACK_DEBUG_LOG_ID='foo-hashabc',
+            SPACK_COMPILER_SPEC='gcc@4.4.7',
+            SPACK_SHORT_SPEC='foo@1.2 arch=linux-rhel6-x86_64 /hashabc',
+            SPACK_SYSTEM_DIRS=':'.join(system_dirs),
+            SPACK_CC_RPATH_ARG='-Wl,-rpath,',
+            SPACK_CXX_RPATH_ARG='-Wl,-rpath,',
+            SPACK_F77_RPATH_ARG='-Wl,-rpath,',
+            SPACK_FC_RPATH_ARG='-Wl,-rpath,',
+            SPACK_DEPENDENCIES=None):
+        yield
+
+
+@pytest.fixture()
+def wrapper_flags():
+    with set_env(
+            SPACK_CPPFLAGS=' '.join(spack_cppflags),
+            SPACK_CFLAGS=' '.join(spack_cflags),
+            SPACK_CXXFLAGS=' '.join(spack_cxxflags),
+            SPACK_FFLAGS=' '.join(spack_fflags),
+            SPACK_LDFLAGS=' '.join(spack_ldflags),
+            SPACK_LDLIBS=' '.join(spack_ldlibs)):
+        yield
+
+
+@pytest.fixture(scope='session')
+def dep1(tmpdir_factory):
+    path = tmpdir_factory.mktemp('cc-dep1')
+    path.mkdir('include')
+    path.mkdir('lib')
+    yield str(path)
+
+
+@pytest.fixture(scope='session')
+def dep2(tmpdir_factory):
+    path = tmpdir_factory.mktemp('cc-dep2')
+    path.mkdir('lib64')
+    yield str(path)
+
+
+@pytest.fixture(scope='session')
+def dep3(tmpdir_factory):
+    path = tmpdir_factory.mktemp('cc-dep3')
+    path.mkdir('include')
+    path.mkdir('lib64')
+    yield str(path)
+
+
+@pytest.fixture(scope='session')
+def dep4(tmpdir_factory):
+    path = tmpdir_factory.mktemp('cc-dep4')
+    path.mkdir('include')
+    yield str(path)
+
+
+pytestmark = pytest.mark.usefixtures('wrapper_environment')
+
+
+def check_args(cc, args, expected):
+    """Check output arguments that cc produces when called with args.
+
+    This assumes that cc will print debug command output with one element
+    per line, so that we see whether arguments that should (or shouldn't)
+    contain spaces are parsed correctly.
+    """
+    with set_env(SPACK_TEST_COMMAND='dump-args'):
+        assert expected == cc(*args, output=str).strip().split('\n')
+
+
+def dump_mode(cc, args):
+    """Make cc dump the mode it detects, and return it."""
+    with set_env(SPACK_TEST_COMMAND='dump-mode'):
+        return cc(*args, output=str).strip()
+
+
+def test_vcheck_mode():
+    assert dump_mode(cc, ['-I/include', '--version']) == 'vcheck'
+    assert dump_mode(cc, ['-I/include', '-V']) == 'vcheck'
+    assert dump_mode(cc, ['-I/include', '-v']) == 'vcheck'
+    assert dump_mode(cc, ['-I/include', '-dumpversion']) == 'vcheck'
+    assert dump_mode(cc, ['-I/include', '--version', '-c']) == 'vcheck'
+    assert dump_mode(cc, ['-I/include', '-V', '-o', 'output']) == 'vcheck'
+
+
+def test_cpp_mode():
+    assert dump_mode(cc, ['-E']) == 'cpp'
+    assert dump_mode(cxx, ['-E']) == 'cpp'
+    assert dump_mode(cpp, []) == 'cpp'
+
+
+def test_as_mode():
+    assert dump_mode(cc, ['-S']) == 'as'
+
+
+def test_ccld_mode():
+    assert dump_mode(cc, []) == 'ccld'
+    assert dump_mode(cc, ['foo.c', '-o', 'foo']) == 'ccld'
+    assert dump_mode(cc, ['foo.c', '-o', 'foo', '-Wl,-rpath,foo']) == 'ccld'
+    assert dump_mode(cc, [
+        'foo.o', 'bar.o', 'baz.o', '-o', 'foo', '-Wl,-rpath,foo']) == 'ccld'
+
+
+def test_ld_mode():
+    assert dump_mode(ld, []) == 'ld'
+    assert dump_mode(ld, [
+        'foo.o', 'bar.o', 'baz.o', '-o', 'foo', '-Wl,-rpath,foo']) == 'ld'
+
+
+def test_ld_flags(wrapper_flags):
+    check_args(
+        ld, test_args,
+        ['ld'] +
+        spack_ldflags +
+        test_include_paths +
+        test_library_paths +
+        test_rpaths +
+        pkg_rpaths +
+        test_args_without_paths +
+        spack_ldlibs)
+
+
+def test_cpp_flags(wrapper_flags):
+    check_args(
+        cpp, test_args,
+        ['cpp'] +
+        spack_cppflags +
+        test_include_paths +
+        test_library_paths +
+        test_args_without_paths)
+
+
+def test_cc_flags(wrapper_flags):
+    check_args(
+        cc, test_args,
+        [real_cc] +
+        spack_cppflags +
+        spack_cflags +
+        spack_ldflags +
+        test_include_paths +
+        test_library_paths +
+        test_wl_rpaths +
+        pkg_wl_rpaths +
+        test_args_without_paths +
+        spack_ldlibs)
+
+
+def test_cxx_flags(wrapper_flags):
+    check_args(
+        cxx, test_args,
+        [real_cc] +
+        spack_cppflags +
+        spack_cxxflags +
+        spack_ldflags +
+        test_include_paths +
+        test_library_paths +
+        test_wl_rpaths +
+        pkg_wl_rpaths +
+        test_args_without_paths +
+        spack_ldlibs)
+
+
+def test_fc_flags(wrapper_flags):
+    check_args(
+        fc, test_args,
+        [real_cc] +
+        spack_fflags +
+        spack_cppflags +
+        spack_ldflags +
+        test_include_paths +
+        test_library_paths +
+        test_wl_rpaths +
+        pkg_wl_rpaths +
+        test_args_without_paths +
+        spack_ldlibs)
+
+
+def test_dep_rpath():
+    """Ensure RPATHs for root package are added."""
+    check_args(
+        cc, test_args,
+        [real_cc] +
+        test_include_paths +
+        test_library_paths +
+        test_wl_rpaths +
+        pkg_wl_rpaths +
+        test_args_without_paths)
+
+
+def test_dep_include(dep4):
+    """Ensure a single dependency include directory is added."""
+    with set_env(SPACK_DEPENDENCIES=dep4,
+                 SPACK_RPATH_DEPS=dep4,
+                 SPACK_LINK_DEPS=dep4):
+        check_args(
+            cc, test_args,
+            [real_cc] +
+            test_include_paths +
+            ['-I' + dep4 + '/include'] +
+            test_library_paths +
+            test_wl_rpaths +
+            pkg_wl_rpaths +
+            test_args_without_paths)
+
+
+def test_dep_lib(dep2):
+    """Ensure a single dependency RPATH is added."""
+    with set_env(SPACK_DEPENDENCIES=dep2,
+                 SPACK_RPATH_DEPS=dep2,
+                 SPACK_LINK_DEPS=dep2):
+        check_args(
+            cc, test_args,
+            [real_cc] +
+            test_include_paths +
+            test_library_paths +
+            ['-L' + dep2 + '/lib64'] +
+            test_wl_rpaths +
+            pkg_wl_rpaths +
+            ['-Wl,-rpath,' + dep2 + '/lib64'] +
+            test_args_without_paths)
+
+
+def test_dep_lib_no_rpath(dep2):
+    """Ensure a single dependency link flag is added with no dep RPATH."""
+    with set_env(SPACK_DEPENDENCIES=dep2,
+                 SPACK_LINK_DEPS=dep2):
+        check_args(
+            cc, test_args,
+            [real_cc] +
+            test_include_paths +
+            test_library_paths +
+            ['-L' + dep2 + '/lib64'] +
+            test_wl_rpaths +
+            pkg_wl_rpaths +
+            test_args_without_paths)
+
+
+def test_dep_lib_no_lib(dep2):
+    """Ensure a single dependency RPATH is added with no -L."""
+    with set_env(SPACK_DEPENDENCIES=dep2,
+                 SPACK_RPATH_DEPS=dep2):
+        check_args(
+            cc, test_args,
+            [real_cc] +
+            test_include_paths +
+            test_library_paths +
+            test_wl_rpaths +
+            pkg_wl_rpaths +
+            ['-Wl,-rpath,' + dep2 + '/lib64'] +
+            test_args_without_paths)
+
+
+def test_ccld_deps(dep1, dep2, dep3, dep4):
+    """Ensure all flags are added in ccld mode."""
+    deps = ':'.join((dep1, dep2, dep3, dep4))
+    with set_env(SPACK_DEPENDENCIES=deps,
+                 SPACK_RPATH_DEPS=deps,
+                 SPACK_LINK_DEPS=deps):
+        check_args(
+            cc, test_args,
+            [real_cc] +
+            test_include_paths +
+            ['-I' + dep1 + '/include',
+             '-I' + dep3 + '/include',
+             '-I' + dep4 + '/include'] +
+            test_library_paths +
+            ['-L' + dep1 + '/lib',
+             '-L' + dep2 + '/lib64',
+             '-L' + dep3 + '/lib64'] +
+            test_wl_rpaths +
+            pkg_wl_rpaths +
+            ['-Wl,-rpath,' + dep1 + '/lib',
+             '-Wl,-rpath,' + dep2 + '/lib64',
+             '-Wl,-rpath,' + dep3 + '/lib64'] +
+            test_args_without_paths)
+
+
+def test_cc_deps(dep1, dep2, dep3, dep4):
+    """Ensure -L and RPATHs are not added in cc mode."""
+    deps = ':'.join((dep1, dep2, dep3, dep4))
+    with set_env(SPACK_DEPENDENCIES=deps,
+                 SPACK_RPATH_DEPS=deps,
+                 SPACK_LINK_DEPS=deps):
+        check_args(
+            cc, ['-c'] + test_args,
+            [real_cc] +
+            test_include_paths +
+            ['-I' + dep1 + '/include',
+             '-I' + dep3 + '/include',
+             '-I' + dep4 + '/include'] +
+            test_library_paths +
+            ['-c'] +
+            test_args_without_paths)
+
+
+def test_ccld_with_system_dirs(dep1, dep2, dep3, dep4):
+    """Ensure all flags are added in ccld mode."""
+    deps = ':'.join((dep1, dep2, dep3, dep4))
+    with set_env(SPACK_DEPENDENCIES=deps,
+                 SPACK_RPATH_DEPS=deps,
+                 SPACK_LINK_DEPS=deps):
+
+        sys_path_args = ['-I/usr/include',
+                         '-L/usr/local/lib',
+                         '-Wl,-rpath,/usr/lib64',
+                         '-I/usr/local/include',
+                         '-L/lib64/']
+        check_args(
+            cc, sys_path_args + test_args,
+            [real_cc] +
+            test_include_paths +
+            ['-I' + dep1 + '/include',
+             '-I' + dep3 + '/include',
+             '-I' + dep4 + '/include'] +
+            ['-I/usr/include',
+             '-I/usr/local/include'] +
+            test_library_paths +
+            ['-L' + dep1 + '/lib',
+             '-L' + dep2 + '/lib64',
+             '-L' + dep3 + '/lib64'] +
+            ['-L/usr/local/lib',
+             '-L/lib64/'] +
+            test_wl_rpaths +
+            pkg_wl_rpaths +
+            ['-Wl,-rpath,' + dep1 + '/lib',
+             '-Wl,-rpath,' + dep2 + '/lib64',
+             '-Wl,-rpath,' + dep3 + '/lib64'] +
+            ['-Wl,-rpath,/usr/lib64'] +
+            test_args_without_paths)
+
+
+def test_ld_deps(dep1, dep2, dep3, dep4):
+    """Ensure no (extra) -I args or -Wl, are passed in ld mode."""
+    deps = ':'.join((dep1, dep2, dep3, dep4))
+    with set_env(SPACK_DEPENDENCIES=deps,
+                 SPACK_RPATH_DEPS=deps,
+                 SPACK_LINK_DEPS=deps):
+        check_args(
+            ld, test_args,
+            ['ld'] +
+            test_include_paths +
+            test_library_paths +
+            ['-L' + dep1 + '/lib',
+             '-L' + dep2 + '/lib64',
+             '-L' + dep3 + '/lib64'] +
+            test_rpaths +
+            pkg_rpaths +
+            ['-rpath', dep1 + '/lib',
+             '-rpath', dep2 + '/lib64',
+             '-rpath', dep3 + '/lib64'] +
+            test_args_without_paths)
+
+
+def test_ld_deps_no_rpath(dep1, dep2, dep3, dep4):
+    """Ensure SPACK_LINK_DEPS controls -L for ld."""
+    deps = ':'.join((dep1, dep2, dep3, dep4))
+    with set_env(SPACK_DEPENDENCIES=deps,
+                 SPACK_LINK_DEPS=deps):
+        check_args(
+            ld, test_args,
+            ['ld'] +
+            test_include_paths +
+            test_library_paths +
+            ['-L' + dep1 + '/lib',
+             '-L' + dep2 + '/lib64',
+             '-L' + dep3 + '/lib64'] +
+            test_rpaths +
+            pkg_rpaths +
+            test_args_without_paths)
+
+
+def test_ld_deps_no_link(dep1, dep2, dep3, dep4):
+    """Ensure SPACK_RPATH_DEPS controls -rpath for ld."""
+    deps = ':'.join((dep1, dep2, dep3, dep4))
+    with set_env(SPACK_DEPENDENCIES=deps,
+                 SPACK_RPATH_DEPS=deps):
+        check_args(
+            ld, test_args,
+            ['ld'] +
+            test_include_paths +
+            test_library_paths +
+            test_rpaths +
+            pkg_rpaths +
+            ['-rpath', dep1 + '/lib',
+             '-rpath', dep2 + '/lib64',
+             '-rpath', dep3 + '/lib64'] +
+            test_args_without_paths)
+
+
+def test_ld_deps_partial(dep1):
+    """Make sure ld -r (partial link) is handled correctly on OS's where it
+       doesn't accept rpaths.
+    """
+    with set_env(SPACK_DEPENDENCIES=dep1,
+                 SPACK_RPATH_DEPS=dep1,
+                 SPACK_LINK_DEPS=dep1):
+        # TODO: do we need to add RPATHs on other platforms like Linux?
+        # TODO: Can't we treat them the same?
+        os.environ['SPACK_SHORT_SPEC'] = "foo@1.2=linux-x86_64"
+        check_args(
+            ld, ['-r'] + test_args,
+            ['ld'] +
+            test_include_paths +
+            test_library_paths +
+            ['-L' + dep1 + '/lib'] +
+            test_rpaths +
+            pkg_rpaths +
+            ['-rpath', dep1 + '/lib'] +
+            ['-r'] +
+            test_args_without_paths)
+
+        # rpaths from the underlying command will still appear
+        # Spack will not add its own rpaths.
         os.environ['SPACK_SHORT_SPEC'] = "foo@1.2=darwin-x86_64"
-        self.check_ld('dump-args', reentrant_test_command,
-                      'ld ' +
-                      '-L' + self.dep1 + '/lib ' +
-                      '-r ' +
-                      ' '.join(test_command))
+        check_args(
+            ld, ['-r'] + test_args,
+            ['ld'] +
+            test_include_paths +
+            test_library_paths +
+            ['-L' + dep1 + '/lib'] +
+            test_rpaths +
+            ['-r'] +
+            test_args_without_paths)
+
+
+def test_ccache_prepend_for_cc():
+    with set_env(SPACK_CCACHE_BINARY='ccache'):
+        check_args(
+            cc, test_args,
+            ['ccache'] +  # ccache prepended in cc mode
+            [real_cc] +
+            test_include_paths +
+            test_library_paths +
+            test_wl_rpaths +
+            pkg_wl_rpaths +
+            test_args_without_paths)
+
+
+def test_no_ccache_prepend_for_fc():
+    check_args(
+        fc, test_args,
+        # no ccache for Fortran
+        [real_cc] +
+        test_include_paths +
+        test_library_paths +
+        test_wl_rpaths +
+        pkg_wl_rpaths +
+        test_args_without_paths)
diff --git a/lib/spack/spack/test/cmd/__init__.py b/lib/spack/spack/test/cmd/__init__.py
deleted file mode 100644
index 8922701e9f..0000000000
--- a/lib/spack/spack/test/cmd/__init__.py
+++ /dev/null
@@ -1,24 +0,0 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
diff --git a/lib/spack/spack/test/cmd/activate.py b/lib/spack/spack/test/cmd/activate.py
new file mode 100644
index 0000000000..86abd80342
--- /dev/null
+++ b/lib/spack/spack/test/cmd/activate.py
@@ -0,0 +1,42 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.main import SpackCommand
+
+activate = SpackCommand('activate')
+deactivate = SpackCommand('deactivate')
+install = SpackCommand('install')
+extensions = SpackCommand('extensions')
+
+
+def test_activate(
+        mock_packages, mock_archive, mock_fetch, config,
+        install_mockery):
+    install('extension1')
+    activate('extension1')
+    output = extensions('--show', 'activated', 'extendee')
+    assert 'extension1' in output
+
+
+def test_deactivate(
+        mock_packages, mock_archive, mock_fetch, config,
+        install_mockery):
+    install('extension1')
+    activate('extension1')
+    deactivate('extension1')
+    output = extensions('--show', 'activated', 'extendee')
+    assert 'extension1' not in output
+
+
+def test_deactivate_all(
+        mock_packages, mock_archive, mock_fetch, config,
+        install_mockery):
+    install('extension1')
+    install('extension2')
+    activate('extension1')
+    activate('extension2')
+    deactivate('--all', 'extendee')
+    output = extensions('--show', 'activated', 'extendee')
+    assert 'extension1' not in output
diff --git a/lib/spack/spack/test/cmd/arch.py b/lib/spack/spack/test/cmd/arch.py
new file mode 100644
index 0000000000..1f3c14f059
--- /dev/null
+++ b/lib/spack/spack/test/cmd/arch.py
@@ -0,0 +1,36 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.main import SpackCommand
+
+
+arch = SpackCommand('arch')
+
+
+def test_arch():
+    """Sanity check ``spack arch`` to make sure it works."""
+
+    arch()
+
+
+def test_arch_platform():
+    """Sanity check ``spack arch --platform`` to make sure it works."""
+
+    arch('-p')
+    arch('--platform')
+
+
+def test_arch_operating_system():
+    """Sanity check ``spack arch --operating-system`` to make sure it works."""
+
+    arch('-o')
+    arch('--operating-system')
+
+
+def test_arch_target():
+    """Sanity check ``spack arch --target`` to make sure it works."""
+
+    arch('-t')
+    arch('--target')
diff --git a/lib/spack/spack/test/cmd/blame.py b/lib/spack/spack/test/cmd/blame.py
index 1f7d9e81a8..244fd14a6a 100644
--- a/lib/spack/spack/test/cmd/blame.py
+++ b/lib/spack/spack/test/cmd/blame.py
@@ -1,32 +1,13 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import pytest
 
 from llnl.util.filesystem import working_dir
 
-import spack
+import spack.paths
 import spack.cmd
 from spack.main import SpackCommand
 from spack.util.executable import which
@@ -38,7 +19,7 @@ pytestmark = pytest.mark.skipif(
 blame = SpackCommand('blame')
 
 
-def test_blame_by_modtime(builtin_mock):
+def test_blame_by_modtime(mock_packages):
     """Sanity check the blame command to make sure it works."""
     out = blame('--time', 'mpich')
     assert 'LAST_COMMIT' in out
@@ -46,7 +27,7 @@ def test_blame_by_modtime(builtin_mock):
     assert 'EMAIL' in out
 
 
-def test_blame_by_percent(builtin_mock):
+def test_blame_by_percent(mock_packages):
     """Sanity check the blame command to make sure it works."""
     out = blame('--percent', 'mpich')
     assert 'LAST_COMMIT' in out
@@ -54,16 +35,16 @@ def test_blame_by_percent(builtin_mock):
     assert 'EMAIL' in out
 
 
-def test_blame_file(builtin_mock):
+def test_blame_file(mock_packages):
     """Sanity check the blame command to make sure it works."""
-    with working_dir(spack.prefix):
+    with working_dir(spack.paths.prefix):
         out = blame('bin/spack')
     assert 'LAST_COMMIT' in out
     assert 'AUTHOR' in out
     assert 'EMAIL' in out
 
 
-def test_blame_by_git(builtin_mock, capfd):
+def test_blame_by_git(mock_packages, capfd):
     """Sanity check the blame command to make sure it works."""
     with capfd.disabled():
         out = blame('--git', 'mpich')
diff --git a/lib/spack/spack/test/cmd/build_env.py b/lib/spack/spack/test/cmd/build_env.py
new file mode 100644
index 0000000000..a84d2b8ff5
--- /dev/null
+++ b/lib/spack/spack/test/cmd/build_env.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import pytest
+
+from spack.main import SpackCommand, SpackCommandError
+
+info = SpackCommand('build-env')
+
+
+@pytest.mark.parametrize('pkg', [
+    ('zlib',),
+    ('zlib', '--')
+])
+@pytest.mark.usefixtures('config')
+def test_it_just_runs(pkg):
+    info(*pkg)
+
+
+@pytest.mark.parametrize('pkg,error_cls', [
+    ('zlib libszip', SpackCommandError),
+    ('', IndexError)
+])
+@pytest.mark.usefixtures('config')
+def test_it_just_fails(pkg, error_cls):
+    with pytest.raises(error_cls):
+        info(pkg)
diff --git a/lib/spack/spack/test/cmd/cd.py b/lib/spack/spack/test/cmd/cd.py
new file mode 100644
index 0000000000..cab460012a
--- /dev/null
+++ b/lib/spack/spack/test/cmd/cd.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.main import SpackCommand
+
+
+cd = SpackCommand('cd')
+
+
+def test_cd():
+    """Sanity check the cd command to make sure it works."""
+
+    out = cd()
+
+    assert "To initialize spack's shell commands:" in out
diff --git a/lib/spack/spack/test/cmd/clean.py b/lib/spack/spack/test/cmd/clean.py
index 3cb5044949..edc2c111f6 100644
--- a/lib/spack/spack/test/cmd/clean.py
+++ b/lib/spack/spack/test/cmd/clean.py
@@ -1,29 +1,11 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import pytest
-import spack
+import spack.stage
+import spack.caches
 import spack.main
 import spack.package
 
@@ -42,18 +24,22 @@ def mock_calls_for_clean(monkeypatch):
 
     monkeypatch.setattr(spack.package.PackageBase, 'do_clean', Counter())
     monkeypatch.setattr(spack.stage, 'purge', Counter())
-    monkeypatch.setattr(spack.fetch_cache, 'destroy', Counter(), raising=False)
-    monkeypatch.setattr(spack.misc_cache, 'destroy', Counter())
+    monkeypatch.setattr(
+        spack.caches.fetch_cache, 'destroy', Counter(), raising=False)
+    monkeypatch.setattr(
+        spack.caches.misc_cache, 'destroy', Counter())
 
 
 @pytest.mark.usefixtures(
-    'builtin_mock', 'config', 'mock_calls_for_clean'
+    'mock_packages', 'config', 'mock_calls_for_clean'
 )
 @pytest.mark.parametrize('command_line,counters', [
     ('mpileaks', [1, 0, 0, 0]),
-    ('-s', [0, 1, 0, 0]),
-    ('-sd', [0, 1, 1, 0]),
-    ('-a', [0, 1, 1, 1]),
+    ('-s',       [0, 1, 0, 0]),
+    ('-sd',      [0, 1, 1, 0]),
+    ('-m',       [0, 0, 0, 1]),
+    ('-a',       [0, 1, 1, 1]),
+    ('',         [0, 0, 0, 0]),
 ])
 def test_function_calls(command_line, counters):
 
@@ -64,5 +50,5 @@ def test_function_calls(command_line, counters):
     # number of times
     assert spack.package.PackageBase.do_clean.call_count == counters[0]
     assert spack.stage.purge.call_count == counters[1]
-    assert spack.fetch_cache.destroy.call_count == counters[2]
-    assert spack.misc_cache.destroy.call_count == counters[3]
+    assert spack.caches.fetch_cache.destroy.call_count == counters[2]
+    assert spack.caches.misc_cache.destroy.call_count == counters[3]
diff --git a/lib/spack/spack/test/cmd/commands.py b/lib/spack/spack/test/cmd/commands.py
new file mode 100644
index 0000000000..0b693a1bab
--- /dev/null
+++ b/lib/spack/spack/test/cmd/commands.py
@@ -0,0 +1,51 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import re
+
+from llnl.util.argparsewriter import ArgparseWriter
+
+import spack.cmd
+import spack.main
+from spack.main import SpackCommand
+
+commands = SpackCommand('commands')
+
+parser = spack.main.make_argument_parser()
+spack.main.add_all_commands(parser)
+
+
+def test_commands_by_name():
+    """Test default output of spack commands."""
+    out = commands()
+    assert out.strip().split('\n') == sorted(spack.cmd.all_commands())
+
+
+def test_subcommands():
+    """Test subcommand traversal."""
+    out = commands('--format=subcommands')
+    assert 'spack mirror create' in out
+    assert 'spack buildcache list' in out
+    assert 'spack repo add' in out
+    assert 'spack pkg diff' in out
+    assert 'spack url parse' in out
+    assert 'spack view symlink' in out
+
+    class Subcommands(ArgparseWriter):
+        def begin_command(self, prog):
+            assert prog in out
+
+    Subcommands().write(parser)
+
+
+def test_rst():
+    """Do some simple sanity checks of the rst writer."""
+    out = commands('--format=rst')
+
+    class Subcommands(ArgparseWriter):
+        def begin_command(self, prog):
+            assert prog in out
+            assert re.sub(r' ', '-', prog) in out
+    Subcommands().write(parser)
diff --git a/lib/spack/spack/test/cmd/config.py b/lib/spack/spack/test/cmd/config.py
new file mode 100644
index 0000000000..493236709b
--- /dev/null
+++ b/lib/spack/spack/test/cmd/config.py
@@ -0,0 +1,93 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import os
+
+from llnl.util.filesystem import mkdirp
+
+import spack.config
+import spack.environment as ev
+from spack.main import SpackCommand
+
+config = SpackCommand('config')
+
+
+def test_get_config_scope(mock_config):
+    assert config('get', 'compilers').strip() == 'compilers: {}'
+
+
+def test_get_config_scope_merged(mock_config):
+    low_path = mock_config.scopes['low'].path
+    high_path = mock_config.scopes['high'].path
+
+    mkdirp(low_path)
+    mkdirp(high_path)
+
+    with open(os.path.join(low_path, 'repos.yaml'), 'w') as f:
+        f.write('''\
+repos:
+- repo3
+''')
+
+    with open(os.path.join(high_path, 'repos.yaml'), 'w') as f:
+        f.write('''\
+repos:
+- repo1
+- repo2
+''')
+
+    assert config('get', 'repos').strip() == '''repos:
+- repo1
+- repo2
+- repo3'''
+
+
+def test_config_edit():
+    """Ensure `spack config edit` edits the right paths."""
+    dms = spack.config.default_modify_scope()
+    dms_path = spack.config.config.scopes[dms].path
+    user_path = spack.config.config.scopes['user'].path
+
+    comp_path = os.path.join(dms_path, 'compilers.yaml')
+    repos_path = os.path.join(user_path, 'repos.yaml')
+
+    assert config('edit', '--print-file', 'compilers').strip() == comp_path
+    assert config('edit', '--print-file', 'repos').strip() == repos_path
+
+
+def test_config_get_gets_spack_yaml(mutable_mock_env_path):
+    env = ev.create('test')
+
+    config('get', fail_on_error=False)
+    assert config.returncode == 1
+
+    with env:
+        config('get', fail_on_error=False)
+        assert config.returncode == 1
+
+        env.write()
+
+        assert 'mpileaks' not in config('get')
+
+        env.add('mpileaks')
+        env.write()
+
+        assert 'mpileaks' in config('get')
+
+
+def test_config_edit_edits_spack_yaml(mutable_mock_env_path):
+    env = ev.create('test')
+    with env:
+        assert config('edit', '--print-file').strip() == env.manifest_path
+
+
+def test_config_edit_fails_correctly_with_no_env(mutable_mock_env_path):
+    output = config('edit', '--print-file', fail_on_error=False)
+    assert "requires a section argument or an active environment" in output
+
+
+def test_config_get_fails_correctly_with_no_env(mutable_mock_env_path):
+    output = config('get', fail_on_error=False)
+    assert "requires a section argument or an active environment" in output
diff --git a/lib/spack/spack/test/cmd/debug.py b/lib/spack/spack/test/cmd/debug.py
new file mode 100644
index 0000000000..5189487265
--- /dev/null
+++ b/lib/spack/spack/test/cmd/debug.py
@@ -0,0 +1,40 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import os
+import os.path
+
+from spack.main import SpackCommand
+from spack.util.executable import which
+
+debug = SpackCommand('debug')
+
+
+def test_create_db_tarball(tmpdir, database):
+    with tmpdir.as_cwd():
+        debug('create-db-tarball')
+
+        # get the first non-dotfile to avoid coverage files in the directory
+        files = os.listdir(os.getcwd())
+        tarball_name = next(f for f in files if not f.startswith('.'))
+
+        # debug command made an archive
+        assert os.path.exists(tarball_name)
+
+        # print contents of archive
+        tar = which('tar')
+        contents = tar('tzf', tarball_name, output=str)
+
+        # DB file is included
+        assert 'index.json' in contents
+
+        # spec.yamls from all installs are included
+        for spec in database.query():
+            # externals won't have a spec.yaml
+            if spec.external:
+                continue
+
+            spec_suffix = '%s/.spack/spec.yaml' % spec.dag_hash()
+            assert spec_suffix in contents
diff --git a/lib/spack/spack/test/cmd/dependencies.py b/lib/spack/spack/test/cmd/dependencies.py
index 737a74caae..0583050812 100644
--- a/lib/spack/spack/test/cmd/dependencies.py
+++ b/lib/spack/spack/test/cmd/dependencies.py
@@ -1,32 +1,14 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import re
+import pytest
 
 from llnl.util.tty.color import color_when
 
-import spack
+import spack.store
 from spack.main import SpackCommand
 
 dependencies = SpackCommand('dependencies')
@@ -35,14 +17,14 @@ mpis = ['mpich', 'mpich2', 'multi-provider-mpi', 'zmpi']
 mpi_deps = ['fake']
 
 
-def test_immediate_dependencies(builtin_mock):
+def test_immediate_dependencies(mock_packages):
     out = dependencies('mpileaks')
     actual = set(re.split(r'\s+', out.strip()))
     expected = set(['callpath'] + mpis)
     assert expected == actual
 
 
-def test_transitive_dependencies(builtin_mock):
+def test_transitive_dependencies(mock_packages):
     out = dependencies('--transitive', 'mpileaks')
     actual = set(re.split(r'\s+', out.strip()))
     expected = set(
@@ -50,7 +32,8 @@ def test_transitive_dependencies(builtin_mock):
     assert expected == actual
 
 
-def test_immediate_installed_dependencies(builtin_mock, database):
+@pytest.mark.db
+def test_immediate_installed_dependencies(mock_packages, database):
     with color_when(False):
         out = dependencies('--installed', 'mpileaks^mpich')
 
@@ -63,7 +46,8 @@ def test_immediate_installed_dependencies(builtin_mock, database):
     assert expected == hashes
 
 
-def test_transitive_installed_dependencies(builtin_mock, database):
+@pytest.mark.db
+def test_transitive_installed_dependencies(mock_packages, database):
     with color_when(False):
         out = dependencies('--installed', '--transitive', 'mpileaks^zmpi')
 
diff --git a/lib/spack/spack/test/cmd/dependents.py b/lib/spack/spack/test/cmd/dependents.py
index acd64ec3d4..70019aa476 100644
--- a/lib/spack/spack/test/cmd/dependents.py
+++ b/lib/spack/spack/test/cmd/dependents.py
@@ -1,45 +1,28 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import re
 
+import pytest
+
 from llnl.util.tty.color import color_when
 
-import spack
+import spack.store
 from spack.main import SpackCommand
 
 dependents = SpackCommand('dependents')
 
 
-def test_immediate_dependents(builtin_mock):
+def test_immediate_dependents(mock_packages):
     out = dependents('libelf')
     actual = set(re.split(r'\s+', out.strip()))
     assert actual == set(['dyninst', 'libdwarf',
                           'patch-a-dependency', 'patch-several-dependencies'])
 
 
-def test_transitive_dependents(builtin_mock):
+def test_transitive_dependents(mock_packages):
     out = dependents('--transitive', 'libelf')
     actual = set(re.split(r'\s+', out.strip()))
     assert actual == set(
@@ -48,7 +31,8 @@ def test_transitive_dependents(builtin_mock):
          'patch-a-dependency', 'patch-several-dependencies'])
 
 
-def test_immediate_installed_dependents(builtin_mock, database):
+@pytest.mark.db
+def test_immediate_installed_dependents(mock_packages, database):
     with color_when(False):
         out = dependents('--installed', 'libelf')
 
@@ -64,7 +48,8 @@ def test_immediate_installed_dependents(builtin_mock, database):
     assert expected == hashes
 
 
-def test_transitive_installed_dependents(builtin_mock, database):
+@pytest.mark.db
+def test_transitive_installed_dependents(mock_packages, database):
     with color_when(False):
         out = dependents('--installed', '--transitive', 'fake')
 
diff --git a/lib/spack/spack/test/cmd/env.py b/lib/spack/spack/test/cmd/env.py
index 18d64b454b..76210bc562 100644
--- a/lib/spack/spack/test/cmd/env.py
+++ b/lib/spack/spack/test/cmd/env.py
@@ -1,48 +1,596 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import os
+from six import StringIO
+
 import pytest
 
-from spack.main import SpackCommand, SpackCommandError
+import llnl.util.filesystem as fs
+
+import spack.modules
+import spack.environment as ev
+from spack.cmd.env import _env_create
+from spack.spec import Spec
+from spack.main import SpackCommand
+
+
+# everything here uses the mock_env_path
+pytestmark = pytest.mark.usefixtures(
+    'mutable_mock_env_path', 'config', 'mutable_mock_packages')
+
+env        = SpackCommand('env')
+install    = SpackCommand('install')
+add        = SpackCommand('add')
+remove     = SpackCommand('remove')
+concretize = SpackCommand('concretize')
+stage      = SpackCommand('stage')
+uninstall  = SpackCommand('uninstall')
+find       = SpackCommand('find')
+
+
+def test_add():
+    e = ev.create('test')
+    e.add('mpileaks')
+    assert Spec('mpileaks') in e.user_specs
+
+
+def test_env_list():
+    env('create', 'foo')
+    env('create', 'bar')
+    env('create', 'baz')
+
+    out = env('list')
+
+    assert 'foo' in out
+    assert 'bar' in out
+    assert 'baz' in out
+
+
+def test_env_remove(capfd):
+    env('create', 'foo')
+    env('create', 'bar')
+
+    out = env('list')
+    assert 'foo' in out
+    assert 'bar' in out
+
+    foo = ev.read('foo')
+    with foo:
+        with pytest.raises(spack.main.SpackCommandError):
+            with capfd.disabled():
+                env('remove', '-y', 'foo')
+        assert 'foo' in env('list')
+
+    env('remove', '-y', 'foo')
+    out = env('list')
+    assert 'foo' not in out
+    assert 'bar' in out
+
+    env('remove', '-y', 'bar')
+    out = env('list')
+    assert 'foo' not in out
+    assert 'bar' not in out
+
+
+def test_concretize():
+    e = ev.create('test')
+    e.add('mpileaks')
+    e.concretize()
+    env_specs = e._get_environment_specs()
+    assert any(x.name == 'mpileaks' for x in env_specs)
+
+
+def test_env_install_all(install_mockery, mock_fetch):
+    e = ev.create('test')
+    e.add('cmake-client')
+    e.concretize()
+    e.install_all()
+    env_specs = e._get_environment_specs()
+    spec = next(x for x in env_specs if x.name == 'cmake-client')
+    assert spec.package.installed
+
+
+def test_env_install_single_spec(install_mockery, mock_fetch):
+    env('create', 'test')
+    install = SpackCommand('install')
+
+    e = ev.read('test')
+    with e:
+        install('cmake-client')
+
+    e = ev.read('test')
+    assert e.user_specs[0].name == 'cmake-client'
+    assert e.concretized_user_specs[0].name == 'cmake-client'
+    assert e.specs_by_hash[e.concretized_order[0]].name == 'cmake-client'
+
+
+def test_env_install_same_spec_twice(install_mockery, mock_fetch, capfd):
+    env('create', 'test')
+
+    e = ev.read('test')
+    with capfd.disabled():
+        with e:
+            install('cmake-client')
+            out = install('cmake-client')
+            assert 'is already installed in' in out
+
+
+def test_remove_after_concretize():
+    e = ev.create('test')
+
+    e.add('mpileaks')
+    e.concretize()
+
+    e.add('python')
+    e.concretize()
+
+    e.remove('mpileaks')
+    assert Spec('mpileaks') not in e.user_specs
+    env_specs = e._get_environment_specs()
+    assert any(s.name == 'mpileaks' for s in env_specs)
+
+    e.add('mpileaks')
+    assert any(s.name == 'mpileaks' for s in e.user_specs)
+
+    e.remove('mpileaks', force=True)
+    assert Spec('mpileaks') not in e.user_specs
+    env_specs = e._get_environment_specs()
+    assert not any(s.name == 'mpileaks' for s in env_specs)
+
+
+def test_remove_command():
+    env('create', 'test')
+    assert 'test' in env('list')
+
+    with ev.read('test'):
+        add('mpileaks')
+        assert 'mpileaks' in find()
+        assert 'mpileaks@' not in find()
+        assert 'mpileaks@' not in find('--show-concretized')
+
+    with ev.read('test'):
+        remove('mpileaks')
+        assert 'mpileaks' not in find()
+        assert 'mpileaks@' not in find()
+        assert 'mpileaks@' not in find('--show-concretized')
+
+    with ev.read('test'):
+        add('mpileaks')
+        assert 'mpileaks' in find()
+        assert 'mpileaks@' not in find()
+        assert 'mpileaks@' not in find('--show-concretized')
+
+    with ev.read('test'):
+        concretize()
+        assert 'mpileaks' in find()
+        assert 'mpileaks@' not in find()
+        assert 'mpileaks@' in find('--show-concretized')
+
+    with ev.read('test'):
+        remove('mpileaks')
+        assert 'mpileaks' not in find()
+        # removed but still in last concretized specs
+        assert 'mpileaks@' in find('--show-concretized')
+
+    with ev.read('test'):
+        concretize()
+        assert 'mpileaks' not in find()
+        assert 'mpileaks@' not in find()
+        # now the lockfile is regenerated and it's gone.
+        assert 'mpileaks@' not in find('--show-concretized')
+
+
+def test_environment_status(capfd, tmpdir):
+    with capfd.disabled():
+        with tmpdir.as_cwd():
+            assert 'No active environment' in env('status')
+
+            with ev.create('test'):
+                assert 'In environment test' in env('status')
+
+            with ev.Environment('local_dir'):
+                assert os.path.join(os.getcwd(), 'local_dir') in env('status')
+
+                e = ev.Environment('myproject')
+                e.write()
+                with tmpdir.join('myproject').as_cwd():
+                    with e:
+                        assert 'in current directory' in env('status')
+
+
+def test_to_lockfile_dict():
+    e = ev.create('test')
+    e.add('mpileaks')
+    e.concretize()
+    context_dict = e._to_lockfile_dict()
+
+    e_copy = ev.create('test_copy')
+
+    e_copy._read_lockfile_dict(context_dict)
+    assert e.specs_by_hash == e_copy.specs_by_hash
+
+
+def test_env_repo():
+    e = ev.create('test')
+    e.add('mpileaks')
+    e.write()
+
+    with ev.read('test'):
+        concretize()
+
+    package = e.repo.get('mpileaks')
+    assert package.name == 'mpileaks'
+    assert package.namespace == 'spack.pkg.builtin.mock'
+
+
+def test_user_removed_spec():
+    """Ensure a user can remove from any position in the spack.yaml file."""
+    initial_yaml = StringIO("""\
+env:
+  specs:
+  - mpileaks
+  - hypre
+  - libelf
+""")
+
+    before = ev.create('test', initial_yaml)
+    before.concretize()
+    before.write()
+
+    # user modifies yaml externally to spack and removes hypre
+    with open(before.manifest_path, 'w') as f:
+        f.write("""\
+env:
+  specs:
+  - mpileaks
+  - libelf
+""")
+
+    after = ev.read('test')
+    after.concretize()
+    after.write()
+
+    env_specs = after._get_environment_specs()
+    read = ev.read('test')
+    env_specs = read._get_environment_specs()
+
+    assert not any(x.name == 'hypre' for x in env_specs)
+
+
+def test_init_from_lockfile(tmpdir):
+    """Test that an environment can be instantiated from a lockfile."""
+    initial_yaml = StringIO("""\
+env:
+  specs:
+  - mpileaks
+  - hypre
+  - libelf
+""")
+    e1 = ev.create('test', initial_yaml)
+    e1.concretize()
+    e1.write()
+
+    e2 = ev.Environment(str(tmpdir), e1.lock_path)
+
+    for s1, s2 in zip(e1.user_specs, e2.user_specs):
+        assert s1 == s2
+
+    for h1, h2 in zip(e1.concretized_order, e2.concretized_order):
+        assert h1 == h2
+        assert e1.specs_by_hash[h1] == e2.specs_by_hash[h2]
+
+    for s1, s2 in zip(e1.concretized_user_specs, e2.concretized_user_specs):
+        assert s1 == s2
+
+
+def test_init_from_yaml(tmpdir):
+    """Test that an environment can be instantiated from a lockfile."""
+    initial_yaml = StringIO("""\
+env:
+  specs:
+  - mpileaks
+  - hypre
+  - libelf
+""")
+    e1 = ev.create('test', initial_yaml)
+    e1.concretize()
+    e1.write()
+
+    e2 = ev.Environment(str(tmpdir), e1.manifest_path)
+
+    for s1, s2 in zip(e1.user_specs, e2.user_specs):
+        assert s1 == s2
+
+    assert not e2.concretized_order
+    assert not e2.concretized_user_specs
+    assert not e2.specs_by_hash
+
+
+def test_init_with_file_and_remove(tmpdir):
+    """Ensure a user can remove from any position in the spack.yaml file."""
+    path = tmpdir.join('spack.yaml')
+
+    with tmpdir.as_cwd():
+        with open(str(path), 'w') as f:
+            f.write("""\
+env:
+  specs:
+  - mpileaks
+""")
+
+        env('create', 'test', 'spack.yaml')
+
+    out = env('list')
+    assert 'test' in out
+
+    with ev.read('test'):
+        assert 'mpileaks' in find()
+
+    env('remove', '-y', 'test')
+
+    out = env('list')
+    assert 'test' not in out
+
+
+def test_env_with_config():
+    test_config = """\
+env:
+  specs:
+  - mpileaks
+  packages:
+    mpileaks:
+      version: [2.2]
+"""
+    spack.package_prefs.PackagePrefs.clear_caches()
+
+    _env_create('test', StringIO(test_config))
+
+    e = ev.read('test')
+    ev.prepare_config_scope(e)
+    e.concretize()
+
+    assert any(x.satisfies('mpileaks@2.2')
+               for x in e._get_environment_specs())
+
+
+def test_env_with_included_config_file():
+    test_config = """\
+env:
+  include:
+  - ./included-config.yaml
+  specs:
+  - mpileaks
+"""
+    spack.package_prefs.PackagePrefs.clear_caches()
+
+    _env_create('test', StringIO(test_config))
+    e = ev.read('test')
+
+    with open(os.path.join(e.path, 'included-config.yaml'), 'w') as f:
+        f.write("""\
+packages:
+  mpileaks:
+    version: [2.2]
+""")
+
+    ev.prepare_config_scope(e)
+    e.concretize()
+
+    assert any(x.satisfies('mpileaks@2.2')
+               for x in e._get_environment_specs())
+
+
+def test_env_with_included_config_scope():
+    config_scope_path = os.path.join(ev.root('test'), 'config')
+    test_config = """\
+env:
+  include:
+  - %s
+  specs:
+  - mpileaks
+""" % config_scope_path
+
+    spack.package_prefs.PackagePrefs.clear_caches()
+    _env_create('test', StringIO(test_config))
+
+    e = ev.read('test')
+
+    fs.mkdirp(config_scope_path)
+    with open(os.path.join(config_scope_path, 'packages.yaml'), 'w') as f:
+        f.write("""\
+packages:
+  mpileaks:
+    version: [2.2]
+""")
+
+    ev.prepare_config_scope(e)
+    e.concretize()
+
+    assert any(x.satisfies('mpileaks@2.2')
+               for x in e._get_environment_specs())
+
+
+def test_env_config_precedence():
+    test_config = """\
+env:
+  packages:
+    libelf:
+      version: [0.8.12]
+  include:
+  - ./included-config.yaml
+  specs:
+  - mpileaks
+"""
+
+    spack.package_prefs.PackagePrefs.clear_caches()
+
+    _env_create('test', StringIO(test_config))
+    e = ev.read('test')
+
+    with open(os.path.join(e.path, 'included-config.yaml'), 'w') as f:
+        f.write("""\
+packages:
+  mpileaks:
+    version: [2.2]
+  libelf:
+    version: [0.8.11]
+""")
+
+    ev.prepare_config_scope(e)
+    e.concretize()
+
+    # ensure included scope took effect
+    assert any(
+        x.satisfies('mpileaks@2.2') for x in e._get_environment_specs())
+
+    # ensure env file takes precedence
+    assert any(
+        x.satisfies('libelf@0.8.12') for x in e._get_environment_specs())
+
+
+def test_included_config_precedence():
+    test_config = """\
+env:
+  include:
+  - ./high-config.yaml  # this one should take precedence
+  - ./low-config.yaml
+  specs:
+  - mpileaks
+"""
+    spack.package_prefs.PackagePrefs.clear_caches()
+
+    _env_create('test', StringIO(test_config))
+    e = ev.read('test')
+
+    with open(os.path.join(e.path, 'high-config.yaml'), 'w') as f:
+        f.write("""\
+packages:
+  libelf:
+    version: [0.8.10]  # this should override libelf version below
+""")
+
+    with open(os.path.join(e.path, 'low-config.yaml'), 'w') as f:
+        f.write("""\
+packages:
+  mpileaks:
+    version: [2.2]
+  libelf:
+    version: [0.8.12]
+""")
+
+    ev.prepare_config_scope(e)
+    e.concretize()
+
+    assert any(
+        x.satisfies('mpileaks@2.2') for x in e._get_environment_specs())
+
+    assert any(
+        [x.satisfies('libelf@0.8.10') for x in e._get_environment_specs()])
+
+
+def test_bad_env_yaml_format(tmpdir):
+    filename = str(tmpdir.join('spack.yaml'))
+    with open(filename, 'w') as f:
+        f.write("""\
+env:
+  spacks:
+    - mpileaks
+""")
+
+    with tmpdir.as_cwd():
+        with pytest.raises(spack.config.ConfigFormatError) as e:
+            env('create', 'test', './spack.yaml')
+        assert './spack.yaml:2' in str(e)
+        assert "'spacks' was unexpected" in str(e)
+
+
+def test_env_loads(install_mockery, mock_fetch):
+    env('create', 'test')
+
+    with ev.read('test'):
+        add('mpileaks')
+        concretize()
+        install('--fake')
+
+    with ev.read('test'):
+        env('loads', 'test')
+
+    e = ev.read('test')
+
+    loads_file = os.path.join(e.path, 'loads')
+    assert os.path.exists(loads_file)
+
+    with open(loads_file) as f:
+        contents = f.read()
+        assert 'module load mpileaks' in contents
+
+
+@pytest.mark.disable_clean_stage_check
+def test_stage(mock_stage, mock_fetch, install_mockery):
+    env('create', 'test')
+    with ev.read('test'):
+        add('mpileaks')
+        add('zmpi')
+        concretize()
+        stage()
+
+    root = str(mock_stage)
+
+    def check_stage(spec):
+        spec = Spec(spec).concretized()
+        for dep in spec.traverse():
+            stage_name = "%s-%s-%s" % (dep.name, dep.version, dep.dag_hash())
+            assert os.path.isdir(os.path.join(root, stage_name))
+
+    check_stage('mpileaks')
+    check_stage('zmpi')
+
+
+def test_env_commands_die_with_no_env_arg():
+    # these fail in argparse when given no arg
+    with pytest.raises(SystemExit):
+        env('create')
+    with pytest.raises(SystemExit):
+        env('remove')
+
+    # these have an optional env arg and raise errors via tty.die
+    with pytest.raises(spack.main.SpackCommandError):
+        env('loads')
+
+    # This should NOT raise an error with no environment
+    # it just tells the user there isn't an environment
+    env('status')
+
+
+def test_env_blocks_uninstall(mock_stage, mock_fetch, install_mockery):
+    env('create', 'test')
+    with ev.read('test'):
+        add('mpileaks')
+        install('--fake')
+
+    out = uninstall('mpileaks', fail_on_error=False)
+    assert uninstall.returncode == 1
+    assert 'used by the following environments' in out
 
-info = SpackCommand('env')
 
+def test_uninstall_removes_from_env(mock_stage, mock_fetch, install_mockery):
+    env('create', 'test')
+    with ev.read('test'):
+        add('mpileaks')
+        add('libelf')
+        install('--fake')
 
-@pytest.mark.parametrize('pkg', [
-    ('zlib',),
-    ('zlib', '--')
-])
-@pytest.mark.usefixtures('config')
-def test_it_just_runs(pkg):
-    info(*pkg)
+    test = ev.read('test')
+    assert any(s.name == 'mpileaks' for s in test.specs_by_hash.values())
+    assert any(s.name == 'libelf' for s in test.specs_by_hash.values())
 
+    with ev.read('test'):
+        uninstall('-ya')
 
-@pytest.mark.parametrize('pkg,error_cls', [
-    ('zlib libszip', SpackCommandError),
-    ('', IndexError)
-])
-@pytest.mark.usefixtures('config')
-def test_it_just_fails(pkg, error_cls):
-    with pytest.raises(error_cls):
-        info(pkg)
+    test = ev.read('test')
+    assert not test.specs_by_hash
+    assert not test.concretized_order
+    assert not test.user_specs
diff --git a/lib/spack/spack/test/cmd/find.py b/lib/spack/spack/test/cmd/find.py
index 69973e715b..6beaaa9b7e 100644
--- a/lib/spack/spack/test/cmd/find.py
+++ b/lib/spack/spack/test/cmd/find.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import argparse
 
 import pytest
@@ -62,7 +43,9 @@ def test_query_arguments():
         missing=False,
         unknown=False,
         explicit=False,
-        implicit=False
+        implicit=False,
+        start_date="2018-02-23",
+        end_date=None
     )
 
     q_args = query_arguments(args)
@@ -72,6 +55,8 @@ def test_query_arguments():
     assert q_args['installed'] is True
     assert q_args['known'] is any
     assert q_args['explicit'] is any
+    assert 'start_date' in q_args
+    assert 'end_date' not in q_args
 
     # Check that explicit works correctly
     args.explicit = True
@@ -84,27 +69,32 @@ def test_query_arguments():
     assert q_args['explicit'] is False
 
 
+@pytest.mark.db
 @pytest.mark.usefixtures('database', 'mock_display')
-class TestFindWithTags(object):
+def test_tag1(parser, specs):
+
+    args = parser.parse_args(['--tags', 'tag1'])
+    spack.cmd.find.find(parser, args)
 
-    def test_tag1(self, parser, specs):
+    assert len(specs) == 2
+    assert 'mpich' in [x.name for x in specs]
+    assert 'mpich2' in [x.name for x in specs]
 
-        args = parser.parse_args(['--tags', 'tag1'])
-        spack.cmd.find.find(parser, args)
 
-        assert len(specs) == 2
-        assert 'mpich' in [x.name for x in specs]
-        assert 'mpich2' in [x.name for x in specs]
+@pytest.mark.db
+@pytest.mark.usefixtures('database', 'mock_display')
+def test_tag2(parser, specs):
+    args = parser.parse_args(['--tags', 'tag2'])
+    spack.cmd.find.find(parser, args)
 
-    def test_tag2(self, parser, specs):
-        args = parser.parse_args(['--tags', 'tag2'])
-        spack.cmd.find.find(parser, args)
+    assert len(specs) == 1
+    assert 'mpich' in [x.name for x in specs]
 
-        assert len(specs) == 1
-        assert 'mpich' in [x.name for x in specs]
 
-    def test_tag2_tag3(self, parser, specs):
-        args = parser.parse_args(['--tags', 'tag2', '--tags', 'tag3'])
-        spack.cmd.find.find(parser, args)
+@pytest.mark.db
+@pytest.mark.usefixtures('database', 'mock_display')
+def test_tag2_tag3(parser, specs):
+    args = parser.parse_args(['--tags', 'tag2', '--tags', 'tag3'])
+    spack.cmd.find.find(parser, args)
 
-        assert len(specs) == 0
+    assert len(specs) == 0
diff --git a/lib/spack/spack/test/cmd/flake8.py b/lib/spack/spack/test/cmd/flake8.py
index 632351601d..295b1c544b 100644
--- a/lib/spack/spack/test/cmd/flake8.py
+++ b/lib/spack/spack/test/cmd/flake8.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import argparse
 import os
 import pytest
@@ -29,9 +10,9 @@ import sys
 
 from llnl.util.filesystem import FileFilter
 
-import spack
+import spack.paths
 from spack.cmd.flake8 import flake8, setup_parser, changed_files
-from spack.repository import Repo
+from spack.repo import Repo
 from spack.util.executable import which
 
 
@@ -50,7 +31,7 @@ def flake8_package():
     mock package, yields the filename, then undoes the
     change on cleanup.
     """
-    repo = Repo(spack.mock_packages_path)
+    repo = Repo(spack.paths.mock_packages_path)
     filename = repo.filename_for_package_name('flake8')
     package = FileFilter(filename)
 
@@ -69,7 +50,7 @@ def test_changed_files(parser, flake8_package):
     # changed_files returns file paths relative to the root
     # directory of Spack. Convert to absolute file paths.
     files = changed_files(args)
-    files = [os.path.join(spack.spack_root, path) for path in files]
+    files = [os.path.join(spack.paths.prefix, path) for path in files]
 
     # There will likely be other files that have changed
     # when these tests are run
diff --git a/lib/spack/spack/test/cmd/gpg.py b/lib/spack/spack/test/cmd/gpg.py
index ef2f64211a..e962b24c3f 100644
--- a/lib/spack/spack/test/cmd/gpg.py
+++ b/lib/spack/spack/test/cmd/gpg.py
@@ -1,31 +1,13 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 
 import pytest
-import spack
+
+from spack.paths import mock_gpg_data_path, mock_gpg_keys_path
 import spack.util.gpg as gpg_util
 from spack.main import SpackCommand
 from spack.util.executable import ProcessError
@@ -52,15 +34,16 @@ def has_gnupg2():
         return False
 
 
+@pytest.mark.maybeslow
 @pytest.mark.skipif(not has_gnupg2(),
                     reason='These tests require gnupg2')
 def test_gpg(gpg, tmpdir, testing_gpg_directory):
     # Verify a file with an empty keyring.
     with pytest.raises(ProcessError):
-        gpg('verify', os.path.join(spack.mock_gpg_data_path, 'content.txt'))
+        gpg('verify', os.path.join(mock_gpg_data_path, 'content.txt'))
 
     # Import the default key.
-    gpg('init', '--from', spack.mock_gpg_keys_path)
+    gpg('init', '--from', mock_gpg_keys_path)
 
     # List the keys.
     # TODO: Test the output here.
@@ -68,14 +51,14 @@ def test_gpg(gpg, tmpdir, testing_gpg_directory):
     gpg('list', '--signing')
 
     # Verify the file now that the key has been trusted.
-    gpg('verify', os.path.join(spack.mock_gpg_data_path, 'content.txt'))
+    gpg('verify', os.path.join(mock_gpg_data_path, 'content.txt'))
 
     # Untrust the default key.
     gpg('untrust', 'Spack testing')
 
     # Now that the key is untrusted, verification should fail.
     with pytest.raises(ProcessError):
-        gpg('verify', os.path.join(spack.mock_gpg_data_path, 'content.txt'))
+        gpg('verify', os.path.join(mock_gpg_data_path, 'content.txt'))
 
     # Create a file to test signing.
     test_path = tmpdir.join('to-sign.txt')
diff --git a/lib/spack/spack/test/cmd/graph.py b/lib/spack/spack/test/cmd/graph.py
new file mode 100644
index 0000000000..1601f24f92
--- /dev/null
+++ b/lib/spack/spack/test/cmd/graph.py
@@ -0,0 +1,64 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.main import SpackCommand, SpackCommandError
+
+import pytest
+
+
+graph = SpackCommand('graph')
+
+
+@pytest.mark.db
+@pytest.mark.usefixtures('mock_packages', 'database')
+def test_graph_ascii():
+    """Tests spack graph --ascii"""
+    graph('--ascii', 'dt-diamond')
+
+
+@pytest.mark.db
+@pytest.mark.usefixtures('mock_packages', 'database')
+def test_graph_dot():
+    """Tests spack graph --dot"""
+    graph('--dot', 'dt-diamond')
+
+
+@pytest.mark.db
+@pytest.mark.usefixtures('mock_packages', 'database')
+def test_graph_normalize():
+    """Tests spack graph --normalize"""
+    graph('--normalize', 'dt-diamond')
+
+
+@pytest.mark.db
+@pytest.mark.usefixtures('mock_packages', 'database')
+def test_graph_static():
+    """Tests spack graph --static"""
+    graph('--static', 'dt-diamond')
+
+
+@pytest.mark.db
+@pytest.mark.usefixtures('mock_packages', 'database')
+def test_graph_installed():
+    """Tests spack graph --installed"""
+
+    graph('--installed')
+
+    with pytest.raises(SpackCommandError):
+        graph('--installed', 'dt-diamond')
+
+
+@pytest.mark.db
+@pytest.mark.usefixtures('mock_packages', 'database')
+def test_graph_deptype():
+    """Tests spack graph --deptype"""
+    graph('--deptype', 'all', 'dt-diamond')
+
+
+def test_graph_no_specs():
+    """Tests spack graph with no arguments"""
+
+    with pytest.raises(SpackCommandError):
+        graph()
diff --git a/lib/spack/spack/test/cmd/help.py b/lib/spack/spack/test/cmd/help.py
new file mode 100644
index 0000000000..9747314403
--- /dev/null
+++ b/lib/spack/spack/test/cmd/help.py
@@ -0,0 +1,56 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import pytest
+
+from spack.main import SpackCommand
+
+
+@pytest.mark.xfail
+def test_reuse_after_help():
+    """Test `spack help` can be called twice with the same SpackCommand."""
+    help_cmd = SpackCommand('help')
+    help_cmd()
+
+    # This second invocation will somehow fail because the parser no
+    # longer works after add_all_commands() is called in
+    # SpackArgumentParser.format_help_sections().
+    #
+    # TODO: figure out why this doesn't work properly and change this
+    # test to use a single SpackCommand.
+    #
+    # It seems that parse_known_args() finds "too few arguments" the
+    # second time through b/c add_all_commands() ends up leaving extra
+    # positionals in the parser. But this used to work before we loaded
+    # commands lazily.
+    help_cmd()
+
+
+def test_help():
+    """Sanity check the help command to make sure it works."""
+    help_cmd = SpackCommand('help')
+    out = help_cmd()
+    assert 'These are common spack commands:' in out
+
+
+def test_help_all():
+    """Test the spack help --all flag"""
+    help_cmd = SpackCommand('help')
+    out = help_cmd('--all')
+    assert 'Complete list of spack commands:' in out
+
+
+def test_help_spec():
+    """Test the spack help --spec flag"""
+    help_cmd = SpackCommand('help')
+    out = help_cmd('--spec')
+    assert 'spec expression syntax:' in out
+
+
+def test_help_subcommand():
+    """Test the spack help subcommand argument"""
+    help_cmd = SpackCommand('help')
+    out = help_cmd('help')
+    assert 'get help on spack and its commands' in out
diff --git a/lib/spack/spack/test/cmd/info.py b/lib/spack/spack/test/cmd/info.py
index c406f6f78e..404c11befd 100644
--- a/lib/spack/spack/test/cmd/info.py
+++ b/lib/spack/spack/test/cmd/info.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import argparse
 
 import pytest
diff --git a/lib/spack/spack/test/cmd/install.py b/lib/spack/spack/test/cmd/install.py
index 7bd6ebc160..904472f243 100644
--- a/lib/spack/spack/test/cmd/install.py
+++ b/lib/spack/spack/test/cmd/install.py
@@ -1,40 +1,26 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import argparse
 import os
 import filecmp
+from six.moves import builtins
 
 import pytest
 
 import llnl.util.filesystem as fs
 
-import spack
+import spack.config
+import spack.package
 import spack.cmd.install
+from spack.error import SpackError
 from spack.spec import Spec
 from spack.main import SpackCommand
 
+from six.moves.urllib.error import HTTPError, URLError
+
 install = SpackCommand('install')
 
 
@@ -48,15 +34,13 @@ def parser():
 
 @pytest.fixture()
 def noop_install(monkeypatch):
-
     def noop(*args, **kwargs):
-        return
-
+        pass
     monkeypatch.setattr(spack.package.PackageBase, 'do_install', noop)
 
 
 def test_install_package_and_dependency(
-        tmpdir, builtin_mock, mock_archive, mock_fetch, config,
+        tmpdir, mock_packages, mock_archive, mock_fetch, config,
         install_mockery):
 
     with tmpdir.as_cwd():
@@ -71,39 +55,36 @@ def test_install_package_and_dependency(
     assert 'failures="0"' in content
     assert 'errors="0"' in content
 
-    s = Spec('libdwarf').concretized()
-    assert not spack.repo.get(s).stage.created
+
+@pytest.mark.disable_clean_stage_check
+def test_install_runtests_notests(monkeypatch, mock_packages, install_mockery):
+    def check(pkg):
+        assert not pkg.run_tests
+    monkeypatch.setattr(spack.package.PackageBase, 'unit_test_check', check)
+    install('-v', 'dttop')
 
 
-@pytest.mark.usefixtures('noop_install', 'builtin_mock', 'config')
-def test_install_runtests():
-    assert not spack.package_testing._test_all
-    assert not spack.package_testing.packages_to_test
+@pytest.mark.disable_clean_stage_check
+def test_install_runtests_root(monkeypatch, mock_packages, install_mockery):
+    def check(pkg):
+        assert pkg.run_tests == (pkg.name == 'dttop')
 
+    monkeypatch.setattr(spack.package.PackageBase, 'unit_test_check', check)
     install('--test=root', 'dttop')
-    assert not spack.package_testing._test_all
-    assert spack.package_testing.packages_to_test == set(['dttop'])
-
-    spack.package_testing.clear()
 
-    install('--test=all', 'a')
-    assert spack.package_testing._test_all
-    assert not spack.package_testing.packages_to_test
 
-    spack.package_testing.clear()
+@pytest.mark.disable_clean_stage_check
+def test_install_runtests_all(monkeypatch, mock_packages, install_mockery):
+    def check(pkg):
+        assert pkg.run_tests
 
+    monkeypatch.setattr(spack.package.PackageBase, 'unit_test_check', check)
+    install('--test=all', 'a')
     install('--run-tests', 'a')
-    assert spack.package_testing._test_all
-    assert not spack.package_testing.packages_to_test
-
-    spack.package_testing.clear()
-
-    assert not spack.package_testing._test_all
-    assert not spack.package_testing.packages_to_test
 
 
 def test_install_package_already_installed(
-        tmpdir, builtin_mock, mock_archive, mock_fetch, config,
+        tmpdir, mock_packages, mock_archive, mock_fetch, config,
         install_mockery):
 
     with tmpdir.as_cwd():
@@ -124,7 +105,7 @@ def test_install_package_already_installed(
 
 
 @pytest.mark.parametrize('arguments,expected', [
-    ([], spack.dirty),  # The default read from configuration file
+    ([], spack.config.get('config:dirty')),  # default from config file
     (['--clean'], False),
     (['--dirty'], True),
 ])
@@ -153,7 +134,7 @@ def test_package_output(tmpdir, capsys, install_mockery, mock_fetch):
 
 
 @pytest.mark.disable_clean_stage_check
-def test_install_output_on_build_error(builtin_mock, mock_archive, mock_fetch,
+def test_install_output_on_build_error(mock_packages, mock_archive, mock_fetch,
                                        config, install_mockery, capfd):
     # capfd interferes with Spack's capturing
     with capfd.disabled():
@@ -165,8 +146,8 @@ def test_install_output_on_build_error(builtin_mock, mock_archive, mock_fetch,
 
 
 @pytest.mark.disable_clean_stage_check
-def test_install_output_on_python_error(builtin_mock, mock_archive, mock_fetch,
-                                        config, install_mockery):
+def test_install_output_on_python_error(
+        mock_packages, mock_archive, mock_fetch, config, install_mockery):
     out = install('failing-build', fail_on_error=False)
     assert isinstance(install.error, spack.build_environment.ChildError)
     assert install.error.name == 'InstallError'
@@ -175,7 +156,7 @@ def test_install_output_on_python_error(builtin_mock, mock_archive, mock_fetch,
 
 @pytest.mark.disable_clean_stage_check
 def test_install_with_source(
-        builtin_mock, mock_archive, mock_fetch, config, install_mockery):
+        mock_packages, mock_archive, mock_fetch, config, install_mockery):
     """Verify that source has been copied into place."""
     install('--source', '--keep-stage', 'trivial-install-test-package')
     spec = Spec('trivial-install-test-package').concretized()
@@ -186,7 +167,7 @@ def test_install_with_source(
 
 
 @pytest.mark.disable_clean_stage_check
-def test_show_log_on_error(builtin_mock, mock_archive, mock_fetch,
+def test_show_log_on_error(mock_packages, mock_archive, mock_fetch,
                            config, install_mockery, capfd):
     """Make sure --show-log-on-error works."""
     with capfd.disabled():
@@ -202,7 +183,7 @@ def test_show_log_on_error(builtin_mock, mock_archive, mock_fetch,
 
 
 def test_install_overwrite(
-        builtin_mock, mock_archive, mock_fetch, config, install_mockery
+        mock_packages, mock_archive, mock_fetch, config, install_mockery
 ):
     # It's not possible to overwrite something that is not yet installed
     with pytest.raises(AssertionError):
@@ -234,3 +215,245 @@ def test_install_overwrite(
     assert os.path.exists(spec.prefix)
     assert fs.hash_directory(spec.prefix) == expected_md5
     assert fs.hash_directory(spec.prefix) != bad_md5
+
+
+@pytest.mark.usefixtures(
+    'mock_packages', 'mock_archive', 'mock_fetch', 'config', 'install_mockery',
+)
+def test_install_conflicts(conflict_spec):
+    # Make sure that spec with conflicts raises a SpackError
+    with pytest.raises(SpackError):
+        install(conflict_spec)
+
+
+@pytest.mark.usefixtures(
+    'mock_packages', 'mock_archive', 'mock_fetch', 'config', 'install_mockery',
+)
+def test_install_invalid_spec(invalid_spec):
+    # Make sure that invalid specs raise a SpackError
+    with pytest.raises(SpackError, match='Unexpected token'):
+        install(invalid_spec)
+
+
+@pytest.mark.usefixtures('noop_install', 'config')
+@pytest.mark.parametrize('spec,concretize,error_code', [
+    (Spec('mpi'), False, 1),
+    (Spec('mpi'), True, 0),
+    (Spec('boost'), False, 1),
+    (Spec('boost'), True, 0)
+])
+def test_install_from_file(spec, concretize, error_code, tmpdir):
+
+    if concretize:
+        spec.concretize()
+
+    specfile = tmpdir.join('spec.yaml')
+
+    with specfile.open('w') as f:
+        spec.to_yaml(f)
+
+    # Relative path to specfile (regression for #6906)
+    with fs.working_dir(specfile.dirname):
+        # A non-concrete spec will fail to be installed
+        install('-f', specfile.basename, fail_on_error=False)
+    assert install.returncode == error_code
+
+    # Absolute path to specfile (regression for #6983)
+    install('-f', str(specfile), fail_on_error=False)
+    assert install.returncode == error_code
+
+
+@pytest.mark.disable_clean_stage_check
+@pytest.mark.usefixtures(
+    'mock_packages', 'mock_archive', 'mock_fetch', 'config', 'install_mockery'
+)
+@pytest.mark.parametrize('exc_typename,msg', [
+    ('RuntimeError', 'something weird happened'),
+    ('ValueError', 'spec is not concrete')
+])
+def test_junit_output_with_failures(tmpdir, exc_typename, msg):
+    with tmpdir.as_cwd():
+        install(
+            '--log-format=junit', '--log-file=test.xml',
+            'raiser',
+            'exc_type={0}'.format(exc_typename),
+            'msg="{0}"'.format(msg)
+        )
+
+    files = tmpdir.listdir()
+    filename = tmpdir.join('test.xml')
+    assert filename in files
+
+    content = filename.open().read()
+
+    # Count failures and errors correctly
+    assert 'tests="1"' in content
+    assert 'failures="1"' in content
+    assert 'errors="0"' in content
+
+    # We want to have both stdout and stderr
+    assert '<system-out>' in content
+    assert msg in content
+
+
+@pytest.mark.disable_clean_stage_check
+@pytest.mark.parametrize('exc_typename,msg', [
+    ('RuntimeError', 'something weird happened'),
+    ('KeyboardInterrupt', 'Ctrl-C strikes again')
+])
+def test_junit_output_with_errors(
+        exc_typename, msg,
+        mock_packages, mock_archive, mock_fetch, install_mockery,
+        config, tmpdir, monkeypatch):
+
+    def just_throw(*args, **kwargs):
+        exc_type = getattr(builtins, exc_typename)
+        raise exc_type(msg)
+
+    monkeypatch.setattr(spack.package.PackageBase, 'do_install', just_throw)
+
+    with tmpdir.as_cwd():
+        install('--log-format=junit', '--log-file=test.xml', 'libdwarf')
+
+    files = tmpdir.listdir()
+    filename = tmpdir.join('test.xml')
+    assert filename in files
+
+    content = filename.open().read()
+
+    # Count failures and errors correctly
+    assert 'tests="1"' in content
+    assert 'failures="0"' in content
+    assert 'errors="1"' in content
+
+    # We want to have both stdout and stderr
+    assert '<system-out>' in content
+    assert msg in content
+
+
+@pytest.mark.usefixtures('noop_install', 'config')
+@pytest.mark.parametrize('clispecs,filespecs', [
+    [[],                  ['mpi']],
+    [[],                  ['mpi', 'boost']],
+    [['cmake'],           ['mpi']],
+    [['cmake', 'libelf'], []],
+    [['cmake', 'libelf'], ['mpi', 'boost']],
+])
+def test_install_mix_cli_and_files(clispecs, filespecs, tmpdir):
+
+    args = clispecs
+
+    for spec in filespecs:
+        filepath = tmpdir.join(spec + '.yaml')
+        args = ['-f', str(filepath)] + args
+        s = Spec(spec)
+        s.concretize()
+        with filepath.open('w') as f:
+            s.to_yaml(f)
+
+    install(*args, fail_on_error=False)
+    assert install.returncode == 0
+
+
+def test_extra_files_are_archived(mock_packages, mock_archive, mock_fetch,
+                                  config, install_mockery):
+    s = Spec('archive-files')
+    s.concretize()
+
+    install('archive-files')
+
+    archive_dir = os.path.join(
+        spack.store.layout.metadata_path(s), 'archived-files'
+    )
+    config_log = os.path.join(archive_dir, 'config.log')
+    assert os.path.exists(config_log)
+
+    errors_txt = os.path.join(archive_dir, 'errors.txt')
+    assert os.path.exists(errors_txt)
+
+
+@pytest.mark.disable_clean_stage_check
+def test_cdash_report_concretization_error(tmpdir, mock_fetch, install_mockery,
+                                           capfd, conflict_spec):
+    # capfd interferes with Spack's capturing
+    with capfd.disabled():
+        with tmpdir.as_cwd():
+            with pytest.raises(SpackError):
+                install(
+                    '--log-format=cdash',
+                    '--log-file=cdash_reports',
+                    conflict_spec)
+            report_dir = tmpdir.join('cdash_reports')
+            assert report_dir in tmpdir.listdir()
+            report_file = report_dir.join('Update.xml')
+            assert report_file in report_dir.listdir()
+            content = report_file.open().read()
+            assert '<UpdateReturnStatus>Conflicts in concretized spec' \
+                in content
+
+
+@pytest.mark.disable_clean_stage_check
+def test_cdash_upload_build_error(tmpdir, mock_fetch, install_mockery,
+                                  capfd):
+    # capfd interferes with Spack's capturing
+    with capfd.disabled():
+        with tmpdir.as_cwd():
+            with pytest.raises((HTTPError, URLError)):
+                install(
+                    '--log-format=cdash',
+                    '--log-file=cdash_reports',
+                    '--cdash-upload-url=http://localhost/fakeurl/submit.php?project=Spack',
+                    'build-error')
+            report_dir = tmpdir.join('cdash_reports')
+            assert report_dir in tmpdir.listdir()
+            report_file = report_dir.join('Build.xml')
+            assert report_file in report_dir.listdir()
+            content = report_file.open().read()
+            assert '<Text>configure: error: in /path/to/some/file:</Text>' in content
+
+
+@pytest.mark.disable_clean_stage_check
+def test_cdash_upload_clean_build(tmpdir, mock_fetch, install_mockery,
+                                  capfd):
+    # capfd interferes with Spack's capturing
+    with capfd.disabled():
+        with tmpdir.as_cwd():
+            with pytest.raises((HTTPError, URLError)):
+                install(
+                    '--log-file=cdash_reports',
+                    '--cdash-upload-url=http://localhost/fakeurl/submit.php?project=Spack',
+                    'a')
+            report_dir = tmpdir.join('cdash_reports')
+            assert report_dir in tmpdir.listdir()
+            report_file = report_dir.join('Build.xml')
+            assert report_file in report_dir.listdir()
+            content = report_file.open().read()
+            assert '</Build>' in content
+            assert '<Text>' not in content
+
+
+@pytest.mark.disable_clean_stage_check
+def test_build_error_output(tmpdir, mock_fetch, install_mockery, capfd):
+    with capfd.disabled():
+        msg = ''
+        try:
+            install('build-error')
+            assert False, "no exception was raised!"
+        except spack.build_environment.ChildError as e:
+            msg = e.long_message
+
+        assert 'configure: error: in /path/to/some/file:' in msg
+        assert 'configure: error: cannot run C compiled programs.' in msg
+
+
+@pytest.mark.disable_clean_stage_check
+def test_build_warning_output(tmpdir, mock_fetch, install_mockery, capfd):
+    with capfd.disabled():
+        msg = ''
+        try:
+            install('build-warnings')
+        except spack.build_environment.ChildError as e:
+            msg = e.long_message
+
+        assert 'WARNING: ALL CAPITAL WARNING!' in msg
+        assert 'foo.c:89: warning: some weird warning!' in msg
diff --git a/lib/spack/spack/test/cmd/license.py b/lib/spack/spack/test/cmd/license.py
new file mode 100644
index 0000000000..6294309c86
--- /dev/null
+++ b/lib/spack/spack/test/cmd/license.py
@@ -0,0 +1,68 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import os.path
+import re
+
+from llnl.util.filesystem import touch, mkdirp
+
+import spack.paths
+from spack.main import SpackCommand
+
+license = SpackCommand('license')
+
+
+def test_list_files():
+    files = license('list-files').strip().split('\n')
+    assert all(f.startswith(spack.paths.prefix) for f in files)
+    assert os.path.join(spack.paths.bin_path, 'spack') in files
+    assert os.path.abspath(__file__) in files
+
+
+def test_verify(tmpdir):
+    source_dir = tmpdir.join('lib', 'spack', 'spack')
+    mkdirp(str(source_dir))
+
+    no_header = source_dir.join('no_header.py')
+    touch(str(no_header))
+
+    lgpl_header = source_dir.join('lgpl_header.py')
+    with lgpl_header.open('w') as f:
+        f.write("""\
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: LGPL-2.1-only
+""")
+
+    old_lgpl_header = source_dir.join('old_lgpl_header.py')
+    with old_lgpl_header.open('w') as f:
+        f.write("""\
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+""")
+
+    correct_header = source_dir.join('correct_header.py')
+    with correct_header.open('w') as f:
+        f.write("""\
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+""")
+
+    out = license('verify', '--root', str(tmpdir), fail_on_error=False)
+
+    assert str(no_header) in out
+    assert str(lgpl_header) in out
+    assert str(old_lgpl_header) in out
+    assert str(correct_header) not in out
+    assert '3 improperly licensed files' in out
+    assert re.search('files with no SPDX-License-Identifier:\s*1', out)
+    assert re.search('files with wrong SPDX-License-Identifier:\s*1', out)
+    assert re.search('files with old license header:\s*1', out)
+
+    assert license.returncode == 1
diff --git a/lib/spack/spack/test/cmd/list.py b/lib/spack/spack/test/cmd/list.py
index 9fe335a6e3..a05ac8f04f 100644
--- a/lib/spack/spack/test/cmd/list.py
+++ b/lib/spack/spack/test/cmd/list.py
@@ -1,73 +1,61 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-import argparse
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 import pytest
-import spack.cmd.list
 
+from spack.main import SpackCommand
+
+list = SpackCommand('list')
+
+
+def test_list():
+    output = list()
+    assert 'cloverleaf3d' in output
+    assert 'hdf5' in output
 
-@pytest.fixture(scope='module')
-def parser():
-    """Returns the parser for the module command"""
-    prs = argparse.ArgumentParser()
-    spack.cmd.list.setup_parser(prs)
-    return prs
 
+def test_list_filter():
+    output = list('py-*')
+    assert 'py-numpy' in output
+    assert 'perl-file-copy-recursive' not in output
 
-@pytest.fixture()
-def pkg_names():
-    pkg_names = []
-    return pkg_names
+    output = list('py-')
+    assert 'py-numpy' in output
+    assert 'perl-file-copy-recursive' in output
 
 
-@pytest.fixture()
-def mock_name_only(monkeypatch, pkg_names):
+@pytest.mark.maybeslow
+def test_list_search_description():
+    output = list('--search-description', 'xml')
+    assert 'expat' in output
 
-    def name_only(x):
-        pkg_names.extend(x)
 
-    monkeypatch.setattr(spack.cmd.list, 'name_only', name_only)
-    monkeypatch.setitem(spack.cmd.list.formatters, 'name_only', name_only)
+def test_list_tags():
+    output = list('--tags', 'proxy-app')
+    assert 'cloverleaf3d' in output
+    assert 'hdf5' not in output
 
 
-@pytest.mark.usefixtures('mock_name_only')
-class TestListCommand(object):
+def test_list_format_name_only():
+    output = list('--format', 'name_only')
+    assert 'cloverleaf3d' in output
+    assert 'hdf5' in output
 
-    def test_list_without_filters(self, parser, pkg_names):
 
-        args = parser.parse_args([])
-        spack.cmd.list.list(parser, args)
+@pytest.mark.maybeslow
+def test_list_format_rst():
+    output = list('--format', 'rst')
+    assert '.. _cloverleaf3d:' in output
+    assert '.. _hdf5:' in output
 
-        assert pkg_names
-        assert 'cloverleaf3d' in pkg_names
-        assert 'hdf5' in pkg_names
 
-    def test_list_with_filters(self, parser, pkg_names):
-        args = parser.parse_args(['--tags', 'proxy-app'])
-        spack.cmd.list.list(parser, args)
+@pytest.mark.maybeslow
+def test_list_format_html():
+    output = list('--format', 'html')
+    assert '<div class="section" id="cloverleaf3d">' in output
+    assert '<h1>cloverleaf3d' in output
 
-        assert pkg_names
-        assert 'cloverleaf3d' in pkg_names
-        assert 'hdf5' not in pkg_names
+    assert '<div class="section" id="hdf5">' in output
+    assert '<h1>hdf5' in output
diff --git a/lib/spack/spack/test/cmd/mirror.py b/lib/spack/spack/test/cmd/mirror.py
new file mode 100644
index 0000000000..5122bf69b8
--- /dev/null
+++ b/lib/spack/spack/test/cmd/mirror.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import pytest
+
+from spack.main import SpackCommand
+
+mirror = SpackCommand('mirror')
+
+
+@pytest.mark.disable_clean_stage_check
+@pytest.mark.regression('8083')
+def test_regression_8083(tmpdir, capfd, mock_packages, mock_fetch, config):
+    with capfd.disabled():
+        output = mirror('create', '-d', str(tmpdir), 'externaltool')
+    assert 'Skipping' in output
+    assert 'as it is an external spec' in output
diff --git a/lib/spack/spack/test/cmd/module.py b/lib/spack/spack/test/cmd/module.py
index 0aa08b9aa6..3151594ea3 100644
--- a/lib/spack/spack/test/cmd/module.py
+++ b/lib/spack/spack/test/cmd/module.py
@@ -1,52 +1,22 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-import argparse
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os.path
 
 import pytest
-import spack.cmd.module as module
-import spack.modules as modules
-
-
-def _get_module_files(args):
 
-    files = []
-    specs = args.specs()
+import spack.main
+import spack.modules
 
-    for module_type in args.module_type:
-        writer_cls = modules.module_types[module_type]
-        files.extend([writer_cls(spec).layout.filename for spec in specs])
-    return files
+module = spack.main.SpackCommand('module')
 
 
-@pytest.fixture(scope='module')
-def parser():
-    """Returns the parser for the module command"""
-    parser = argparse.ArgumentParser()
-    module.setup_parser(parser)
-    return parser
+def _module_files(module_type, *specs):
+    specs = [spack.spec.Spec(x).concretized() for x in specs]
+    writer_cls = spack.modules.module_types[module_type]
+    return [writer_cls(spec).layout.filename for spec in specs]
 
 
 @pytest.fixture(
@@ -54,8 +24,7 @@ def parser():
         ['rm', 'doesnotexist'],  # Try to remove a non existing module
         ['find', 'mpileaks'],  # Try to find a module with multiple matches
         ['find', 'doesnotexist'],  # Try to find a module with no matches
-        # Try to find a module specifying more than one type
-        ['find', '-m', 'tcl', '-m', 'lmod', 'libelf'],
+        ['find', '--unkown_args'],  # Try to give an unknown argument
     ]
 )
 def failure_args(request):
@@ -63,62 +32,160 @@ def failure_args(request):
     return request.param
 
 
+@pytest.fixture(
+    params=['dotkit', 'tcl', 'lmod']
+)
+def module_type(request):
+    return request.param
+
+
 # TODO : test the --delete-tree option
 # TODO : this requires having a separate directory for test modules
 # TODO : add tests for loads and find to check the prompt format
 
+@pytest.mark.db
+def test_exit_with_failure(database, module_type, failure_args):
+    with pytest.raises(spack.main.SpackCommandError):
+        module(module_type, *failure_args)
+
 
-def test_exit_with_failure(database, parser, failure_args):
-    args = parser.parse_args(failure_args)
-    with pytest.raises(SystemExit):
-        module.module(parser, args)
+@pytest.mark.db
+@pytest.mark.parametrize('deprecated_command', [
+    ('refresh', '-m', 'tcl', 'mpileaks'),
+    ('rm', '-m', 'tcl', '-m', 'lmod', 'mpileaks'),
+    ('find', 'mpileaks'),
+])
+def test_deprecated_command(database, deprecated_command):
+    with pytest.raises(spack.main.SpackCommandError):
+        module(*deprecated_command)
 
 
-def test_remove_and_add_tcl(database, parser):
+@pytest.mark.db
+def test_remove_and_add(database, module_type):
     """Tests adding and removing a tcl module file."""
 
-    # Remove existing modules [tcl]
-    args = parser.parse_args(['rm', '-y', '-m', 'tcl', 'mpileaks'])
-    module_files = _get_module_files(args)
+    if module_type == 'lmod':
+        # TODO: Testing this with lmod requires mocking
+        # TODO: the core compilers
+        return
 
+    rm_cli_args = ['rm', '-y', 'mpileaks']
+    module_files = _module_files(module_type, 'mpileaks')
     for item in module_files:
         assert os.path.exists(item)
 
-    module.module(parser, args)
-
+    module(module_type, *rm_cli_args)
     for item in module_files:
         assert not os.path.exists(item)
 
-    # Add them back [tcl]
-    args = parser.parse_args(['refresh', '-y', '-m', 'tcl', 'mpileaks'])
-    module.module(parser, args)
-
+    module(module_type, 'refresh', '-y', 'mpileaks')
     for item in module_files:
         assert os.path.exists(item)
 
 
-def test_find(database, parser):
-    """Tests the 'spack module find' under a few common scenarios."""
-
-    # Try to find it for tcl module files
-    args = parser.parse_args(['find', '--module-type', 'tcl', 'libelf'])
-    module.module(parser, args)
-
-
-def test_remove_and_add_dotkit(database, parser):
-    """Tests adding and removing a dotkit module file."""
-
-    # Remove existing modules [dotkit]
-    args = parser.parse_args(['rm', '-y', '-m', 'dotkit', 'mpileaks'])
-    module_files = _get_module_files(args)
-    for item in module_files:
-        assert os.path.exists(item)
-    module.module(parser, args)
-    for item in module_files:
-        assert not os.path.exists(item)
-
-    # Add them back [dotkit]
-    args = parser.parse_args(['refresh', '-y', '-m', 'dotkit', 'mpileaks'])
-    module.module(parser, args)
-    for item in module_files:
-        assert os.path.exists(item)
+@pytest.mark.db
+@pytest.mark.parametrize('cli_args', [
+    ['libelf'],
+    ['--full-path', 'libelf']
+])
+def test_find(database, cli_args, module_type):
+    if module_type == 'lmod':
+        # TODO: Testing this with lmod requires mocking
+        # TODO: the core compilers
+        return
+
+    module(module_type, *(['find'] + cli_args))
+
+
+@pytest.mark.db
+@pytest.mark.usefixtures('database')
+@pytest.mark.regression('2215')
+def test_find_fails_on_multiple_matches():
+    # As we installed multiple versions of mpileaks, the command will
+    # fail because of multiple matches
+    out = module('tcl', 'find', 'mpileaks', fail_on_error=False)
+    assert module.returncode == 1
+    assert 'matches multiple packages' in out
+
+    # Passing multiple packages from the command line also results in the
+    # same failure
+    out = module(
+        'tcl', 'find', 'mpileaks ^mpich', 'libelf', fail_on_error=False
+    )
+    assert module.returncode == 1
+    assert 'matches multiple packages' in out
+
+
+@pytest.mark.db
+@pytest.mark.usefixtures('database')
+@pytest.mark.regression('2570')
+def test_find_fails_on_non_existing_packages():
+    # Another way the command might fail is if the package does not exist
+    out = module('tcl', 'find', 'doesnotexist', fail_on_error=False)
+    assert module.returncode == 1
+    assert 'matches no package' in out
+
+
+@pytest.mark.db
+@pytest.mark.usefixtures('database')
+def test_find_recursive():
+    # If we call find without options it should return only one module
+    out = module('tcl', 'find', 'mpileaks ^zmpi')
+    assert len(out.split()) == 1
+
+    # If instead we call it with the recursive option the length should
+    # be greater
+    out = module('tcl', 'find', '-r', 'mpileaks ^zmpi')
+    assert len(out.split()) > 1
+
+
+# Needed to make the 'module_configuration' fixture below work
+writer_cls = spack.modules.lmod.LmodModulefileWriter
+
+
+@pytest.mark.db
+def test_setdefault_command(
+        mutable_database, module_configuration
+):
+    module_configuration('autoload_direct')
+
+    # Install two different versions of a package
+    other_spec, preferred = 'a@1.0', 'a@2.0'
+
+    spack.spec.Spec(other_spec).concretized().package.do_install(fake=True)
+    spack.spec.Spec(preferred).concretized().package.do_install(fake=True)
+
+    writers = {
+        preferred: writer_cls(spack.spec.Spec(preferred).concretized()),
+        other_spec: writer_cls(spack.spec.Spec(other_spec).concretized())
+    }
+
+    # Create two module files for the same software
+    module('lmod', 'refresh', '-y', '--delete-tree', preferred, other_spec)
+
+    # Assert initial directory state: no link and all module files present
+    link_name = os.path.join(
+        os.path.dirname(writers[preferred].layout.filename),
+        'default'
+    )
+    for k in preferred, other_spec:
+        assert os.path.exists(writers[k].layout.filename)
+    assert not os.path.exists(link_name)
+
+    # Set the default to be the other spec
+    module('lmod', 'setdefault', other_spec)
+
+    # Check that a link named 'default' exists, and points to the right file
+    for k in preferred, other_spec:
+        assert os.path.exists(writers[k].layout.filename)
+    assert os.path.exists(link_name) and os.path.islink(link_name)
+    assert os.path.realpath(link_name) == writers[other_spec].layout.filename
+
+    # Reset the default to be the preferred spec
+    module('lmod', 'setdefault', preferred)
+
+    # Check that a link named 'default' exists, and points to the right file
+    for k in preferred, other_spec:
+        assert os.path.exists(writers[k].layout.filename)
+    assert os.path.exists(link_name) and os.path.islink(link_name)
+    assert os.path.realpath(link_name) == writers[preferred].layout.filename
diff --git a/lib/spack/spack/test/cmd/print_shell_vars.py b/lib/spack/spack/test/cmd/print_shell_vars.py
new file mode 100644
index 0000000000..3630c86a71
--- /dev/null
+++ b/lib/spack/spack/test/cmd/print_shell_vars.py
@@ -0,0 +1,46 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.main import print_setup_info
+
+
+def test_print_shell_vars_sh(capsys):
+    print_setup_info('sh')
+    out, _ = capsys.readouterr()
+
+    assert "_sp_sys_type=" in out
+    assert "_sp_tcl_root=" in out
+    assert "_sp_lmod_root=" in out
+    assert "_sp_module_prefix" not in out
+
+
+def test_print_shell_vars_csh(capsys):
+    print_setup_info('csh')
+    out, _ = capsys.readouterr()
+
+    assert "set _sp_sys_type = " in out
+    assert "set _sp_tcl_root = " in out
+    assert "set _sp_lmod_root = " in out
+    assert "set _sp_module_prefix = " not in out
+
+
+def test_print_shell_vars_sh_modules(capsys):
+    print_setup_info('sh', 'modules')
+    out, _ = capsys.readouterr()
+
+    assert "_sp_sys_type=" in out
+    assert "_sp_tcl_root=" in out
+    assert "_sp_lmod_root=" in out
+    assert "_sp_module_prefix=" in out
+
+
+def test_print_shell_vars_csh_modules(capsys):
+    print_setup_info('csh', 'modules')
+    out, _ = capsys.readouterr()
+
+    assert "set _sp_sys_type = " in out
+    assert "set _sp_tcl_root = " in out
+    assert "set _sp_lmod_root = " in out
+    assert "set _sp_module_prefix = " in out
diff --git a/lib/spack/spack/test/cmd/providers.py b/lib/spack/spack/test/cmd/providers.py
new file mode 100644
index 0000000000..f547607315
--- /dev/null
+++ b/lib/spack/spack/test/cmd/providers.py
@@ -0,0 +1,50 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+import pytest
+
+from spack.main import SpackCommand
+
+providers = SpackCommand('providers')
+
+
+@pytest.mark.parametrize('pkg', [
+    ('mpi',),
+    ('mpi@2',),
+    ('mpi', 'lapack'),
+    ('',)  # Lists all the available virtual packages
+])
+def test_it_just_runs(pkg):
+    providers(*pkg)
+
+
+@pytest.mark.parametrize('vpkg,provider_list', [
+    (('mpi',), ['intel-mpi',
+                'intel-parallel-studio',
+                'mpich',
+                'mpich@1:',
+                'mpich@3:',
+                'mvapich2',
+                'openmpi',
+                'openmpi@1.6.5',
+                'openmpi@1.7.5:',
+                'openmpi@2.0.0:',
+                'spectrum-mpi']),
+    (('D', 'awk'), ['ldc', 'gawk', 'mawk'])  # Call 2 virtual packages at once
+])
+def test_provider_lists(vpkg, provider_list):
+    output = providers(*vpkg)
+    for item in provider_list:
+        assert item in output
+
+
+@pytest.mark.parametrize('pkg,error_cls', [
+    ('zlib', ValueError),
+    ('foo', ValueError)  # Trying to call with a package that does not exist
+])
+def test_it_just_fails(pkg, error_cls):
+    with pytest.raises(error_cls):
+        providers(pkg)
diff --git a/lib/spack/spack/test/cmd/python.py b/lib/spack/spack/test/cmd/python.py
index 000535af8e..edfffb879c 100644
--- a/lib/spack/spack/test/cmd/python.py
+++ b/lib/spack/spack/test/cmd/python.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import spack
 from spack.main import SpackCommand
 
@@ -30,4 +11,4 @@ python = SpackCommand('python')
 
 def test_python():
     out = python('-c', 'import spack; print(spack.spack_version)')
-    assert out.strip() == str(spack.spack_version)
+    assert out.strip() == spack.spack_version
diff --git a/lib/spack/spack/test/cmd/spec.py b/lib/spack/spack/test/cmd/spec.py
new file mode 100644
index 0000000000..b67d2fd4d8
--- /dev/null
+++ b/lib/spack/spack/test/cmd/spec.py
@@ -0,0 +1,77 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import re
+import pytest
+
+import spack.spec
+from spack.main import SpackCommand
+
+pytestmark = pytest.mark.usefixtures('config', 'mutable_mock_packages')
+
+spec = SpackCommand('spec')
+
+
+def test_spec():
+    output = spec('mpileaks')
+
+    assert 'mpileaks@2.3' in output
+    assert 'callpath@1.0' in output
+    assert 'dyninst@8.2' in output
+    assert 'libdwarf@20130729' in output
+    assert 'libelf@0.8.1' in output
+    assert 'mpich@3.0.4' in output
+
+
+def test_spec_yaml():
+    output = spec('--yaml', 'mpileaks')
+
+    mpileaks = spack.spec.Spec.from_yaml(output)
+    assert 'mpileaks' in mpileaks
+    assert 'callpath' in mpileaks
+    assert 'dyninst' in mpileaks
+    assert 'libdwarf' in mpileaks
+    assert 'libelf' in mpileaks
+    assert 'mpich' in mpileaks
+
+
+def _parse_types(string):
+    """Parse deptypes for specs from `spack spec -t` output."""
+    lines = string.strip().split('\n')
+
+    result = {}
+    for line in lines:
+        match = re.match(r'\[([^]]*)\]\s*\^?([^@]*)@', line)
+        if match:
+            types, name = match.groups()
+            result.setdefault(name, []).append(types)
+            result[name] = sorted(result[name])
+    return result
+
+
+def test_spec_deptypes_nodes():
+    output = spec('--types', '--cover', 'nodes', 'dt-diamond')
+    types = _parse_types(output)
+
+    assert types['dt-diamond']        == ['    ']
+    assert types['dt-diamond-left']   == ['bl  ']
+    assert types['dt-diamond-right']  == ['bl  ']
+    assert types['dt-diamond-bottom'] == ['blr ']
+
+
+def test_spec_deptypes_edges():
+    output = spec('--types', '--cover', 'edges', 'dt-diamond')
+    types = _parse_types(output)
+
+    assert types['dt-diamond']        == ['    ']
+    assert types['dt-diamond-left']   == ['bl  ']
+    assert types['dt-diamond-right']  == ['bl  ']
+    assert types['dt-diamond-bottom'] == ['b   ', 'blr ']
+
+
+def test_spec_returncode():
+    with pytest.raises(spack.main.SpackCommandError):
+        spec()
+    assert spec.returncode == 1
diff --git a/lib/spack/spack/test/cmd/test_compiler_cmd.py b/lib/spack/spack/test/cmd/test_compiler_cmd.py
index e7a2186344..3ef12769f4 100644
--- a/lib/spack/spack/test/cmd/test_compiler_cmd.py
+++ b/lib/spack/spack/test/cmd/test_compiler_cmd.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import pytest
 import llnl.util.filesystem
 
@@ -63,7 +44,7 @@ done
     return str(tmpdir)
 
 
-@pytest.mark.usefixtures('config', 'builtin_mock')
+@pytest.mark.usefixtures('config', 'mock_packages')
 class TestCompilerCommand(object):
 
     def test_compiler_remove(self):
diff --git a/lib/spack/spack/test/cmd/uninstall.py b/lib/spack/spack/test/cmd/uninstall.py
index 096dfe74e4..1acf1ff20b 100644
--- a/lib/spack/spack/test/cmd/uninstall.py
+++ b/lib/spack/spack/test/cmd/uninstall.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import pytest
 import spack.store
 from spack.main import SpackCommand, SpackCommandError
@@ -39,19 +20,25 @@ class MockArgs(object):
         self.yes_to_all = True
 
 
-def test_multiple_matches(database):
+@pytest.mark.db
+@pytest.mark.usefixtures('database')
+def test_multiple_matches():
     """Test unable to uninstall when multiple matches."""
     with pytest.raises(SpackCommandError):
         uninstall('-y', 'mpileaks')
 
 
-def test_installed_dependents(database):
+@pytest.mark.db
+@pytest.mark.usefixtures('database')
+def test_installed_dependents():
     """Test can't uninstall when ther are installed dependents."""
     with pytest.raises(SpackCommandError):
         uninstall('-y', 'libelf')
 
 
-def test_recursive_uninstall(database):
+@pytest.mark.db
+@pytest.mark.usefixtures('database')
+def test_recursive_uninstall():
     """Test recursive uninstall."""
     uninstall('-y', '-a', '--dependents', 'callpath')
 
diff --git a/lib/spack/spack/test/cmd/url.py b/lib/spack/spack/test/cmd/url.py
index 84fcf90135..53f53a1b78 100644
--- a/lib/spack/spack/test/cmd/url.py
+++ b/lib/spack/spack/test/cmd/url.py
@@ -1,29 +1,12 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import re
 import pytest
+
+import spack.repo
 from spack.url import UndetectableVersionError
 from spack.main import SpackCommand
 from spack.cmd.url import name_parsed_correctly, version_parsed_correctly
@@ -44,8 +27,9 @@ def test_name_parsed_correctly():
     assert name_parsed_correctly(MyPackage('r-devtools',     []), 'devtools')
     assert name_parsed_correctly(MyPackage('py-numpy',       []), 'numpy')
     assert name_parsed_correctly(MyPackage('octave-splines', []), 'splines')
-    assert name_parsed_correctly(MyPackage('imagemagick',    []), 'ImageMagick')  # noqa
     assert name_parsed_correctly(MyPackage('th-data',        []), 'TH.data')
+    assert name_parsed_correctly(
+        MyPackage('imagemagick',    []), 'ImageMagick')
 
     # Expected False
     assert not name_parsed_correctly(MyPackage('',            []), 'hdf5')
@@ -53,7 +37,8 @@ def test_name_parsed_correctly():
     assert not name_parsed_correctly(MyPackage('yaml-cpp',    []), 'yamlcpp')
     assert not name_parsed_correctly(MyPackage('yamlcpp',     []), 'yaml-cpp')
     assert not name_parsed_correctly(MyPackage('r-py-parser', []), 'parser')
-    assert not name_parsed_correctly(MyPackage('oce',         []), 'oce-0.18.0')   # noqa
+    assert not name_parsed_correctly(
+        MyPackage('oce',         []), 'oce-0.18.0')
 
 
 def test_version_parsed_correctly():
@@ -70,7 +55,8 @@ def test_version_parsed_correctly():
     assert not version_parsed_correctly(MyPackage('', ['1.2.3']),  '1.2.4')
     assert not version_parsed_correctly(MyPackage('', ['3.4a']),   '3.4')
     assert not version_parsed_correctly(MyPackage('', ['3.4']),    '3.4b')
-    assert not version_parsed_correctly(MyPackage('', ['0.18.0']), 'oce-0.18.0')   # noqa
+    assert not version_parsed_correctly(
+        MyPackage('', ['0.18.0']), 'oce-0.18.0')
 
 
 def test_url_parse():
@@ -83,6 +69,7 @@ def test_url_with_no_version_fails():
         url('parse', 'http://www.netlib.org/voronoi/triangle.zip')
 
 
+@pytest.mark.network
 def test_url_list():
     out = url('list')
     total_urls = len(out.split('\n'))
@@ -112,14 +99,17 @@ def test_url_list():
     assert 0 < correct_version_urls < total_urls
 
 
+@pytest.mark.network
 def test_url_summary():
     """Test the URL summary command."""
     # test url_summary, the internal function that does the work
     (total_urls, correct_names, correct_versions,
      name_count_dict, version_count_dict) = url_summary(None)
 
-    assert 0 < correct_names    <= sum(name_count_dict.values())    <= total_urls  # noqa
-    assert 0 < correct_versions <= sum(version_count_dict.values()) <= total_urls  # noqa
+    assert (0 < correct_names <=
+            sum(name_count_dict.values()) <= total_urls)
+    assert (0 < correct_versions <=
+            sum(version_count_dict.values()) <= total_urls)
 
     # make sure it agrees with the actual command.
     out = url('summary')
@@ -134,3 +124,11 @@ def test_url_summary():
     out_correct_versions = int(
         re.search(r'Versions correctly parsed:\s*(\d+)', out).group(1))
     assert out_correct_versions == correct_versions
+
+
+def test_url_stats(capfd):
+    with capfd.disabled():
+        output = url('stats')
+        npkgs = '%d packages' % len(spack.repo.all_package_names())
+        assert npkgs in output
+        assert 'total versions' in output
diff --git a/lib/spack/spack/test/cmd/versions.py b/lib/spack/spack/test/cmd/versions.py
new file mode 100644
index 0000000000..45b62a14d6
--- /dev/null
+++ b/lib/spack/spack/test/cmd/versions.py
@@ -0,0 +1,45 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import pytest
+
+from spack.main import SpackCommand
+
+versions = SpackCommand('versions')
+
+
+@pytest.mark.network
+def test_remote_versions():
+    """Test a package for which remote versions should be available."""
+
+    versions('zlib')
+
+
+@pytest.mark.network
+def test_no_versions():
+    """Test a package for which no remote versions are available."""
+
+    versions('converge')
+
+
+@pytest.mark.network
+def test_no_unchecksummed_versions():
+    """Test a package for which no unchecksummed versions are available."""
+
+    versions('bzip2')
+
+
+@pytest.mark.network
+def test_versions_no_url():
+    """Test a package with versions but without a ``url`` attribute."""
+
+    versions('graphviz')
+
+
+@pytest.mark.network
+def test_no_versions_no_url():
+    """Test a package without versions or a ``url`` attribute."""
+
+    versions('opengl')
diff --git a/lib/spack/spack/test/cmd/view.py b/lib/spack/spack/test/cmd/view.py
index 9ab3e528d2..df6d7b92cc 100644
--- a/lib/spack/spack/test/cmd/view.py
+++ b/lib/spack/spack/test/cmd/view.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack.main import SpackCommand
 import os.path
 import pytest
@@ -34,7 +15,7 @@ view = SpackCommand('view')
 
 @pytest.mark.parametrize('cmd', ['hardlink', 'symlink', 'hard', 'add'])
 def test_view_link_type(
-        tmpdir, builtin_mock, mock_archive, mock_fetch, config,
+        tmpdir, mock_packages, mock_archive, mock_fetch, config,
         install_mockery, cmd):
     install('libdwarf')
     viewpath = str(tmpdir.mkdir('view_{0}'.format(cmd)))
@@ -45,7 +26,7 @@ def test_view_link_type(
 
 
 def test_view_external(
-        tmpdir, builtin_mock, mock_archive, mock_fetch, config,
+        tmpdir, mock_packages, mock_archive, mock_fetch, config,
         install_mockery):
     install('externaltool')
     viewpath = str(tmpdir.mkdir('view'))
@@ -54,7 +35,7 @@ def test_view_external(
 
 
 def test_view_extension(
-        tmpdir, builtin_mock, mock_archive, mock_fetch, config,
+        tmpdir, mock_packages, mock_archive, mock_fetch, config,
         install_mockery):
     install('extendee')
     install('extension1@1.0')
@@ -80,7 +61,7 @@ def test_view_extension(
 
 
 def test_view_extension_remove(
-        tmpdir, builtin_mock, mock_archive, mock_fetch, config,
+        tmpdir, mock_packages, mock_archive, mock_fetch, config,
         install_mockery):
     install('extendee')
     install('extension1@1.0')
@@ -99,7 +80,7 @@ def test_view_extension_remove(
 
 
 def test_view_extension_conflict(
-        tmpdir, builtin_mock, mock_archive, mock_fetch, config,
+        tmpdir, mock_packages, mock_archive, mock_fetch, config,
         install_mockery):
     install('extendee')
     install('extension1@1.0')
@@ -111,7 +92,7 @@ def test_view_extension_conflict(
 
 
 def test_view_extension_conflict_ignored(
-        tmpdir, builtin_mock, mock_archive, mock_fetch, config,
+        tmpdir, mock_packages, mock_archive, mock_fetch, config,
         install_mockery):
     install('extendee')
     install('extension1@1.0')
@@ -124,7 +105,7 @@ def test_view_extension_conflict_ignored(
 
 
 def test_view_extension_global_activation(
-        tmpdir, builtin_mock, mock_archive, mock_fetch, config,
+        tmpdir, mock_packages, mock_archive, mock_fetch, config,
         install_mockery):
     install('extendee')
     install('extension1@1.0')
@@ -153,7 +134,7 @@ def test_view_extension_global_activation(
 
 
 def test_view_extendee_with_global_activations(
-        tmpdir, builtin_mock, mock_archive, mock_fetch, config,
+        tmpdir, mock_packages, mock_archive, mock_fetch, config,
         install_mockery):
     install('extendee')
     install('extension1@1.0')
diff --git a/lib/spack/spack/test/compilers.py b/lib/spack/spack/test/compilers.py
index d172d56638..d7a1fa6743 100644
--- a/lib/spack/spack/test/compilers.py
+++ b/lib/spack/spack/test/compilers.py
@@ -1,52 +1,46 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-import pytest
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from copy import copy
 from six import iteritems
 
 import spack.spec
 import spack.compilers as compilers
+from spack.compiler import _get_versioned_tuple, Compiler
+
 
+def test_get_compiler_duplicates(config):
+    # In this case there is only one instance of the specified compiler in
+    # the test configuration (so it is not actually a duplicate), but the
+    # method behaves the same.
+    cfg_file_to_duplicates = compilers.get_compiler_duplicates(
+        'gcc@4.5.0', spack.spec.ArchSpec('cray-CNL-xeon'))
 
-@pytest.mark.usefixtures('config')
-class TestCompilers(object):
+    assert len(cfg_file_to_duplicates) == 1
+    cfg_file, duplicates = next(iteritems(cfg_file_to_duplicates))
+    assert len(duplicates) == 1
 
-    def test_get_compiler_duplicates(self):
-        # In this case there is only one instance of the specified compiler in
-        # the test configuration (so it is not actually a duplicate), but the
-        # method behaves the same.
-        cfg_file_to_duplicates = compilers.get_compiler_duplicates(
-            'gcc@4.5.0', spack.spec.ArchSpec('cray-CNL-xeon'))
-        assert len(cfg_file_to_duplicates) == 1
-        cfg_file, duplicates = next(iteritems(cfg_file_to_duplicates))
-        assert len(duplicates) == 1
 
-    def test_all_compilers(self):
-        all_compilers = compilers.all_compilers()
-        filtered = [x for x in all_compilers if str(x.spec) == 'clang@3.3']
-        filtered = [x for x in filtered if x.operating_system == 'SuSE11']
-        assert len(filtered) == 1
+def test_all_compilers(config):
+    all_compilers = compilers.all_compilers()
+    filtered = [x for x in all_compilers if str(x.spec) == 'clang@3.3']
+    filtered = [x for x in filtered if x.operating_system == 'SuSE11']
+    assert len(filtered) == 1
+
+
+def test_version_detection_is_empty():
+    no_version = lambda x: None
+    compiler_check_tuple = ('/usr/bin/gcc', '', r'\d\d', no_version)
+    assert not _get_versioned_tuple(compiler_check_tuple)
+
+
+def test_version_detection_is_successful():
+    version = lambda x: '4.9'
+    compiler_check_tuple = ('/usr/bin/gcc', '', r'\d\d', version)
+    assert _get_versioned_tuple(compiler_check_tuple) == (
+        '4.9', '', r'\d\d', '/usr/bin/gcc')
 
 
 def test_compiler_flags_from_config_are_grouped():
@@ -67,3 +61,169 @@ def test_compiler_flags_from_config_are_grouped():
 
     compiler = compilers.compiler_from_config_entry(compiler_entry)
     assert any(x == '-foo-flag foo-val' for x in compiler.flags['cflags'])
+
+
+# Test behavior of flags and UnsupportedCompilerFlag.
+
+# Utility function to test most flags.
+default_compiler_entry = {
+    'spec': 'clang@2.0.0-apple',
+    'operating_system': 'foo-os',
+    'paths': {
+        'cc': 'cc-path',
+        'cxx': 'cxx-path',
+        'fc': None,
+        'f77': None
+    },
+    'flags': {},
+    'modules': None
+}
+
+
+# Fake up a mock compiler where everything is defaulted.
+class MockCompiler(Compiler):
+    def __init__(self):
+        super(MockCompiler, self).__init__(
+            "badcompiler@1.0.0",
+            default_compiler_entry['operating_system'],
+            None,
+            [default_compiler_entry['paths']['cc'],
+             default_compiler_entry['paths']['cxx'],
+             default_compiler_entry['paths']['fc'],
+             default_compiler_entry['paths']['f77']])
+
+    @property
+    def name(self):
+        return "mockcompiler"
+
+    @property
+    def version(self):
+        return "1.0.0"
+
+
+# Get the desired flag from the specified compiler spec.
+def flag_value(flag, spec):
+    compiler = None
+    if spec is None:
+        compiler = MockCompiler()
+    else:
+        compiler_entry = copy(default_compiler_entry)
+        compiler_entry['spec'] = spec
+        # Disable faulty id()-based cache (issue #7647).
+        compilers._compiler_cache = {}
+        compiler = compilers.compiler_from_config_entry(compiler_entry)
+
+    return getattr(compiler, flag)
+
+
+# Utility function to verify that the expected exception is thrown for
+# an unsupported flag.
+def unsupported_flag_test(flag, spec=None):
+    caught_exception = None
+    try:
+        flag_value(flag, spec)
+    except spack.compiler.UnsupportedCompilerFlag:
+        caught_exception = True
+
+    assert(caught_exception and "Expected exception not thrown.")
+
+
+# Verify the expected flag value for the give compiler spec.
+def supported_flag_test(flag, flag_value_ref, spec=None):
+    assert(flag_value(flag, spec) == flag_value_ref)
+
+
+# Tests for UnsupportedCompilerFlag exceptions from default
+# implementations of flags.
+def test_default_flags():
+    unsupported_flag_test("openmp_flag")
+    unsupported_flag_test("cxx11_flag")
+    unsupported_flag_test("cxx14_flag")
+    unsupported_flag_test("cxx17_flag")
+    supported_flag_test("cxx98_flag", "")
+
+
+# Verify behavior of particular compiler definitions.
+def test_clang_flags():
+    # Common
+    supported_flag_test("pic_flag", "-fPIC", "gcc@4.0")
+
+    # Apple Clang.
+    unsupported_flag_test("openmp_flag", "clang@2.0.0-apple")
+    unsupported_flag_test("cxx11_flag", "clang@2.0.0-apple")
+    supported_flag_test("cxx11_flag", "-std=c++11", "clang@4.0.0-apple")
+    unsupported_flag_test("cxx14_flag", "clang@5.0.0-apple")
+    supported_flag_test("cxx14_flag", "-std=c++1y", "clang@5.1.0-apple")
+    supported_flag_test("cxx14_flag", "-std=c++14", "clang@6.1.0-apple")
+    unsupported_flag_test("cxx17_flag", "clang@6.0.0-apple")
+    supported_flag_test("cxx17_flag", "-std=c++1z", "clang@6.1.0-apple")
+
+    # non-Apple Clang.
+    supported_flag_test("openmp_flag", "-fopenmp", "clang@3.3")
+    unsupported_flag_test("cxx11_flag", "clang@3.2")
+    supported_flag_test("cxx11_flag", "-std=c++11", "clang@3.3")
+    unsupported_flag_test("cxx14_flag", "clang@3.3")
+    supported_flag_test("cxx14_flag", "-std=c++1y", "clang@3.4")
+    supported_flag_test("cxx14_flag", "-std=c++14", "clang@3.5")
+    unsupported_flag_test("cxx17_flag", "clang@3.4")
+    supported_flag_test("cxx17_flag", "-std=c++1z", "clang@3.5")
+    supported_flag_test("cxx17_flag", "-std=c++17", "clang@5.0")
+
+
+def test_cce_flags():
+    supported_flag_test("openmp_flag", "-h omp", "cce@1.0")
+    supported_flag_test("cxx11_flag", "-h std=c++11", "cce@1.0")
+    supported_flag_test("pic_flag", "-h PIC", "cce@1.0")
+
+
+def test_gcc_flags():
+    supported_flag_test("openmp_flag", "-fopenmp", "gcc@4.1")
+    supported_flag_test("cxx98_flag", "", "gcc@5.2")
+    supported_flag_test("cxx98_flag", "-std=c++98", "gcc@6.0")
+    unsupported_flag_test("cxx11_flag", "gcc@4.2")
+    supported_flag_test("cxx11_flag", "-std=c++0x", "gcc@4.3")
+    supported_flag_test("cxx11_flag", "-std=c++11", "gcc@4.7")
+    unsupported_flag_test("cxx14_flag", "gcc@4.7")
+    supported_flag_test("cxx14_flag", "-std=c++1y", "gcc@4.8")
+    supported_flag_test("cxx14_flag", "-std=c++14", "gcc@4.9")
+    supported_flag_test("cxx14_flag", "", "gcc@6.0")
+    unsupported_flag_test("cxx17_flag", "gcc@4.9")
+    supported_flag_test("pic_flag", "-fPIC", "gcc@4.0")
+
+
+def test_intel_flags():
+    supported_flag_test("openmp_flag", "-openmp", "intel@15.0")
+    supported_flag_test("openmp_flag", "-qopenmp", "intel@16.0")
+    unsupported_flag_test("cxx11_flag", "intel@11.0")
+    supported_flag_test("cxx11_flag", "-std=c++0x", "intel@12.0")
+    supported_flag_test("cxx11_flag", "-std=c++11", "intel@13")
+    unsupported_flag_test("cxx14_flag", "intel@14.0")
+    supported_flag_test("cxx14_flag", "-std=c++1y", "intel@15.0")
+    supported_flag_test("cxx14_flag", "-std=c++14", "intel@15.0.2")
+    supported_flag_test("pic_flag", "-fPIC", "intel@1.0")
+
+
+def test_nag_flags():
+    supported_flag_test("openmp_flag", "-openmp", "nag@1.0")
+    supported_flag_test("cxx11_flag", "-std=c++11", "nag@1.0")
+    supported_flag_test("pic_flag", "-PIC", "nag@1.0")
+
+
+def test_pgi_flags():
+    supported_flag_test("openmp_flag", "-mp", "pgi@1.0")
+    supported_flag_test("cxx11_flag", "-std=c++11", "pgi@1.0")
+    supported_flag_test("pic_flag", "-fpic", "pgi@1.0")
+
+
+def test_xl_flags():
+    supported_flag_test("openmp_flag", "-qsmp=omp", "xl@1.0")
+    unsupported_flag_test("cxx11_flag", "xl@13.0")
+    supported_flag_test("cxx11_flag", "-qlanglvl=extended0x", "xl@13.1")
+    supported_flag_test("pic_flag", "-qpic", "xl@1.0")
+
+
+def test_xl_r_flags():
+    supported_flag_test("openmp_flag", "-qsmp=omp", "xl_r@1.0")
+    unsupported_flag_test("cxx11_flag", "xl_r@13.0")
+    supported_flag_test("cxx11_flag", "-qlanglvl=extended0x", "xl_r@13.1")
+    supported_flag_test("pic_flag", "-qpic", "xl_r@1.0")
diff --git a/lib/spack/spack/test/concretize.py b/lib/spack/spack/test/concretize.py
index f0d5ae131f..d0574794b2 100644
--- a/lib/spack/spack/test/concretize.py
+++ b/lib/spack/spack/test/concretize.py
@@ -1,34 +1,19 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import pytest
-import spack
+import llnl.util.lang
+
 import spack.architecture
+import spack.repo
+
 from spack.concretize import find_spec
 from spack.spec import Spec, CompilerSpec
 from spack.spec import ConflictsInSpecError, SpecError
 from spack.version import ver
+from spack.test.conftest import MockPackage, MockPackageMultiRepo
 
 
 def check_spec(abstract, concrete):
@@ -94,20 +79,7 @@ def spec(request):
     return request.param
 
 
-@pytest.fixture(
-    params=[
-        'conflict%clang',
-        'conflict%clang+foo',
-        'conflict-parent%clang',
-        'conflict-parent@0.9^conflict~foo'
-    ]
-)
-def conflict_spec(request):
-    """Spec to be concretized"""
-    return request.param
-
-
-@pytest.mark.usefixtures('config', 'builtin_mock')
+@pytest.mark.usefixtures('config', 'mock_packages')
 class TestConcretize(object):
     def test_concretize(self, spec):
         check_concretize(spec)
@@ -158,11 +130,20 @@ class TestConcretize(object):
         concrete = check_concretize('mpileaks   ^mpich2@1.3.1:1.4')
         assert concrete['mpich2'].satisfies('mpich2@1.3.1:1.4')
 
+    def test_concretize_disable_compiler_existence_check(self):
+        with pytest.raises(spack.concretize.UnavailableCompilerVersionError):
+            check_concretize('dttop %gcc@100.100')
+
+        with spack.concretize.concretizer.disable_compiler_existence_check():
+            spec = check_concretize('dttop %gcc@100.100')
+            assert spec.satisfies('%gcc@100.100')
+            assert spec['dtlink3'].satisfies('%gcc@100.100')
+
     def test_concretize_with_provides_when(self):
         """Make sure insufficient versions of MPI are not in providers list when
         we ask for some advanced version.
         """
-        repo = spack.repo
+        repo = spack.repo.path
         assert not any(
             s.satisfies('mpich2@:1.0') for s in repo.providers_for('mpi@2.1')
         )
@@ -182,7 +163,7 @@ class TestConcretize(object):
     def test_provides_handles_multiple_providers_of_same_vesrion(self):
         """
         """
-        providers = spack.repo.providers_for('mpi@3.0')
+        providers = spack.repo.path.providers_for('mpi@3.0')
 
         # Note that providers are repo-specific, so we don't misinterpret
         # providers, but vdeps are not namespace-specific, so we can
@@ -203,6 +184,35 @@ class TestConcretize(object):
         assert set(client.compiler_flags['fflags']) == set(['-O0'])
         assert not set(cmake.compiler_flags['fflags'])
 
+    def test_architecture_inheritance(self):
+        """test_architecture_inheritance is likely to fail with an
+        UnavailableCompilerVersionError if the architecture is concretized
+        incorrectly.
+        """
+        spec = Spec('cmake-client %gcc@4.7.2 os=fe ^ cmake')
+        spec.concretize()
+        assert spec['cmake'].architecture == spec.architecture
+
+    def test_architecture_deep_inheritance(self):
+        """Make sure that indirect dependencies receive architecture
+        information from the root even when partial architecture information
+        is provided by an intermediate dependency.
+        """
+        default_dep = ('link', 'build')
+
+        bazpkg = MockPackage('bazpkg', [], [])
+        barpkg = MockPackage('barpkg', [bazpkg], [default_dep])
+        foopkg = MockPackage('foopkg', [barpkg], [default_dep])
+        mock_repo = MockPackageMultiRepo([foopkg, barpkg, bazpkg])
+
+        with spack.repo.swap(mock_repo):
+            spec = Spec('foopkg %clang@3.3 os=CNL target=footar' +
+                        ' ^barpkg os=SuSE11 ^bazpkg os=be')
+            spec.concretize()
+
+            for s in spec.traverse(root=False):
+                assert s.architecture.target == spec.architecture.target
+
     def test_compiler_flags_from_user_are_grouped(self):
         spec = Spec('a%gcc cflags="-O -foo-flag foo-val" platform=test')
         spec.concretize()
@@ -215,11 +225,12 @@ class TestConcretize(object):
         assert s['mpi'].version == ver('1.10.3')
 
     def test_concretize_two_virtuals(self):
+
         """Test a package with multiple virtual dependencies."""
         Spec('hypre').concretize()
 
     def test_concretize_two_virtuals_with_one_bound(
-            self, refresh_builtin_mock
+            self, mutable_mock_packages
     ):
         """Test a package with multiple virtual dependencies and one preset."""
         Spec('hypre ^openblas').concretize()
@@ -457,3 +468,44 @@ class TestConcretize(object):
         s._concrete = False
 
         assert not s.concrete
+
+    @pytest.mark.regression('7239')
+    def test_regression_issue_7239(self):
+        # Constructing a SpecBuildInterface from another SpecBuildInterface
+        # results in an inconsistent MRO
+
+        # Normal Spec
+        s = Spec('mpileaks')
+        s.concretize()
+
+        assert llnl.util.lang.ObjectWrapper not in type(s).__mro__
+
+        # Spec wrapped in a build interface
+        build_interface = s['mpileaks']
+        assert llnl.util.lang.ObjectWrapper in type(build_interface).__mro__
+
+        # Mimics asking the build interface from a build interface
+        build_interface = s['mpileaks']['mpileaks']
+        assert llnl.util.lang.ObjectWrapper in type(build_interface).__mro__
+
+    @pytest.mark.regression('7705')
+    def test_regression_issue_7705(self):
+        # spec.package.provides(name) doesn't account for conditional
+        # constraints in the concretized spec
+        s = Spec('simple-inheritance~openblas')
+        s.concretize()
+
+        assert not s.package.provides('lapack')
+
+    @pytest.mark.regression('7941')
+    def test_regression_issue_7941(self):
+        # The string representation of a spec containing
+        # an explicit multi-valued variant and a dependency
+        # might be parsed differently than the originating spec
+        s = Spec('a foobar=bar ^b')
+        t = Spec(str(s))
+
+        s.concretize()
+        t.concretize()
+
+        assert s.dag_hash() == t.dag_hash()
diff --git a/lib/spack/spack/test/concretize_preferences.py b/lib/spack/spack/test/concretize_preferences.py
index 164b21e072..dbf2b828ce 100644
--- a/lib/spack/spack/test/concretize_preferences.py
+++ b/lib/spack/spack/test/concretize_preferences.py
@@ -1,50 +1,55 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import pytest
+import stat
 
-import spack
+import spack.package_prefs
+import spack.repo
 import spack.util.spack_yaml as syaml
+from spack.config import ConfigScope, ConfigError
 from spack.spec import Spec
-import spack.package_prefs
 
 
 @pytest.fixture()
 def concretize_scope(config, tmpdir):
     """Adds a scope for concretization preferences"""
     tmpdir.ensure_dir('concretize')
-    spack.config.ConfigScope(
-        'concretize', str(tmpdir.join('concretize'))
-    )
+    config.push_scope(
+        ConfigScope('concretize', str(tmpdir.join('concretize'))))
+
     yield
-    # This is kind of weird, but that's how config scopes are
-    # set in ConfigScope.__init__
-    spack.config.config_scopes.pop('concretize')
+
+    config.pop_scope()
     spack.package_prefs.PackagePrefs.clear_caches()
+    spack.repo.path._provider_index = None
 
-    # reset provider index each time, too
-    spack.repo._provider_index = None
+
+@pytest.fixture()
+def configure_permissions():
+    conf = syaml.load("""\
+all:
+  permissions:
+    read: group
+    write: group
+    group: all
+mpich:
+  permissions:
+    read: user
+    write: user
+mpileaks:
+  permissions:
+    write: user
+    group: mpileaks
+callpath:
+  permissions:
+    write: world
+""")
+    spack.config.set('packages', conf, scope='concretize')
+
+    yield
 
 
 def concretize(abstract_spec):
@@ -54,7 +59,7 @@ def concretize(abstract_spec):
 def update_packages(pkgname, section, value):
     """Update config and reread package list"""
     conf = {pkgname: {section: value}}
-    spack.config.update_config('packages', conf, 'concretize')
+    spack.config.set('packages', conf, scope='concretize')
     spack.package_prefs.PackagePrefs.clear_caches()
 
 
@@ -64,7 +69,7 @@ def assert_variant_values(spec, **variants):
         assert concrete.variants[variant].value == value
 
 
-@pytest.mark.usefixtures('concretize_scope', 'builtin_mock')
+@pytest.mark.usefixtures('concretize_scope', 'mock_packages')
 class TestConcretizePreferences(object):
     def test_preferred_variants(self):
         """Test preferred variants are applied correctly
@@ -80,7 +85,7 @@ class TestConcretizePreferences(object):
             'mpileaks', debug=True, opt=True, shared=False, static=False
         )
 
-    def test_preferred_compilers(self, refresh_builtin_mock):
+    def test_preferred_compilers(self, mutable_mock_packages):
         """Test preferred compilers are applied correctly
         """
         update_packages('mpileaks', 'compiler', ['clang@3.3'])
@@ -136,7 +141,7 @@ mpi:
     paths:
       mpi-with-lapack@2.1: /path/to/lapack
 """)
-        spack.config.update_config('packages', conf, 'concretize')
+        spack.config.set('packages', conf, scope='concretize')
 
         # now when we get the packages.yaml config, there should be an error
         with pytest.raises(spack.package_prefs.VirtualInPackagesYAMLError):
@@ -148,7 +153,7 @@ mpi:
 all:
         variants: [+mpi]
 """)
-        spack.config.update_config('packages', conf, 'concretize')
+        spack.config.set('packages', conf, scope='concretize')
 
         # should be no error for 'all':
         spack.package_prefs.PackagePrefs.clear_caches()
@@ -170,9 +175,56 @@ mpich:
     paths:
         mpich@3.0.4: /dummy/path
 """)
-        spack.config.update_config('packages', conf, 'concretize')
+        spack.config.set('packages', conf, scope='concretize')
 
         # ensure that once config is in place, external is used
         spec = Spec('mpi')
         spec.concretize()
         assert spec['mpich'].external_path == '/dummy/path'
+
+    def test_config_permissions_from_all(self, configure_permissions):
+        # Although these aren't strictly about concretization, they are
+        # configured in the same file and therefore convenient to test here.
+        # Make sure we can configure readable and writable
+
+        # Test inheriting from 'all'
+        spec = Spec('zmpi')
+        perms = spack.package_prefs.get_package_permissions(spec)
+        assert perms == stat.S_IRWXU | stat.S_IRWXG
+
+        dir_perms = spack.package_prefs.get_package_dir_permissions(spec)
+        assert dir_perms == stat.S_IRWXU | stat.S_IRWXG | stat.S_ISGID
+
+        group = spack.package_prefs.get_package_group(spec)
+        assert group == 'all'
+
+    def test_config_permissions_from_package(self, configure_permissions):
+        # Test overriding 'all'
+        spec = Spec('mpich')
+        perms = spack.package_prefs.get_package_permissions(spec)
+        assert perms == stat.S_IRWXU
+
+        dir_perms = spack.package_prefs.get_package_dir_permissions(spec)
+        assert dir_perms == stat.S_IRWXU
+
+        group = spack.package_prefs.get_package_group(spec)
+        assert group == 'all'
+
+    def test_config_permissions_differ_read_write(self, configure_permissions):
+        # Test overriding group from 'all' and different readable/writable
+        spec = Spec('mpileaks')
+        perms = spack.package_prefs.get_package_permissions(spec)
+        assert perms == stat.S_IRWXU | stat.S_IRGRP | stat.S_IXGRP
+
+        dir_perms = spack.package_prefs.get_package_dir_permissions(spec)
+        expected = stat.S_IRWXU | stat.S_IRGRP | stat.S_IXGRP | stat.S_ISGID
+        assert dir_perms == expected
+
+        group = spack.package_prefs.get_package_group(spec)
+        assert group == 'mpileaks'
+
+    def test_config_perms_fail_write_gt_read(self, configure_permissions):
+        # Test failure for writable more permissive than readable
+        spec = Spec('callpath')
+        with pytest.raises(ConfigError):
+            spack.package_prefs.get_package_permissions(spec)
diff --git a/lib/spack/spack/test/config.py b/lib/spack/spack/test/config.py
index 2b7a7a5c08..1235d57f30 100644
--- a/lib/spack/spack/test/config.py
+++ b/lib/spack/spack/test/config.py
@@ -1,40 +1,94 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import os
 import collections
 import getpass
-import os
 import tempfile
+from six import StringIO
+
+from llnl.util.filesystem import touch, mkdirp
 
-import ordereddict_backport
 import pytest
-import spack
+import ruamel.yaml as yaml
+
+import spack.paths
 import spack.config
-import yaml
+import spack.schema.compilers
+import spack.schema.config
+import spack.schema.env
+import spack.schema.packages
+import spack.schema.mirrors
+import spack.schema.repos
+import spack.util.spack_yaml as syaml
 from spack.util.path import canonicalize_path
 
-# Some sample compiler config data
+
+# sample config data
+config_low = {
+    'config': {
+        'install_tree': 'install_tree_path',
+        'build_stage': ['path1', 'path2', 'path3']}}
+
+config_override_all = {
+    'config:': {
+        'install_tree:': 'override_all'}}
+
+config_override_key = {
+    'config': {
+        'install_tree:': 'override_key'}}
+
+config_merge_list = {
+    'config': {
+        'build_stage': ['patha', 'pathb']}}
+
+config_override_list = {
+    'config': {
+        'build_stage:': ['patha', 'pathb']}}
+
+
+@pytest.fixture()
+def write_config_file(tmpdir):
+    """Returns a function that writes a config file."""
+    def _write(config, data, scope):
+        config_yaml = tmpdir.join(scope, config + '.yaml')
+        config_yaml.ensure()
+        with config_yaml.open('w') as f:
+            yaml.dump(data, f)
+    return _write
+
+
+def check_compiler_config(comps, *compiler_names):
+    """Check that named compilers in comps match Spack's config."""
+    config = spack.config.get('compilers')
+    compiler_list = ['cc', 'cxx', 'f77', 'fc']
+    flag_list = ['cflags', 'cxxflags', 'fflags', 'cppflags',
+                 'ldflags', 'ldlibs']
+    param_list = ['modules', 'paths', 'spec', 'operating_system']
+    for compiler in config:
+        conf = compiler['compiler']
+        if conf['spec'] in compiler_names:
+            comp = next((c['compiler'] for c in comps if
+                         c['compiler']['spec'] == conf['spec']), None)
+            if not comp:
+                raise ValueError('Bad config spec')
+            for p in param_list:
+                assert conf[p] == comp[p]
+            for f in flag_list:
+                expected = comp.get('flags', {}).get(f, None)
+                actual = conf.get('flags', {}).get(f, None)
+                assert expected == actual
+            for c in compiler_list:
+                expected = comp['paths'][c]
+                actual = conf['paths'][c]
+                assert expected == actual
+
+
+#
+# Some sample compiler config data and tests.
+#
 a_comps = {
     'compilers': [
         {'compiler': {
@@ -139,240 +193,309 @@ b_comps = {
     ]
 }
 
-# Some Sample repo data
+
+@pytest.fixture()
+def compiler_specs():
+    """Returns a couple of compiler specs needed for the tests"""
+    a = [ac['compiler']['spec'] for ac in a_comps['compilers']]
+    b = [bc['compiler']['spec'] for bc in b_comps['compilers']]
+    CompilerSpecs = collections.namedtuple('CompilerSpecs', ['a', 'b'])
+    return CompilerSpecs(a=a, b=b)
+
+
+def test_write_key_in_memory(mock_config, compiler_specs):
+    # Write b_comps "on top of" a_comps.
+    spack.config.set('compilers', a_comps['compilers'], scope='low')
+    spack.config.set('compilers', b_comps['compilers'], scope='high')
+
+    # Make sure the config looks how we expect.
+    check_compiler_config(a_comps['compilers'], *compiler_specs.a)
+    check_compiler_config(b_comps['compilers'], *compiler_specs.b)
+
+
+def test_write_key_to_disk(mock_config, compiler_specs):
+    # Write b_comps "on top of" a_comps.
+    spack.config.set('compilers', a_comps['compilers'], scope='low')
+    spack.config.set('compilers', b_comps['compilers'], scope='high')
+
+    # Clear caches so we're forced to read from disk.
+    spack.config.config.clear_caches()
+
+    # Same check again, to ensure consistency.
+    check_compiler_config(a_comps['compilers'], *compiler_specs.a)
+    check_compiler_config(b_comps['compilers'], *compiler_specs.b)
+
+
+def test_write_to_same_priority_file(mock_config, compiler_specs):
+    # Write b_comps in the same file as a_comps.
+    spack.config.set('compilers', a_comps['compilers'], scope='low')
+    spack.config.set('compilers', b_comps['compilers'], scope='low')
+
+    # Clear caches so we're forced to read from disk.
+    spack.config.config.clear_caches()
+
+    # Same check again, to ensure consistency.
+    check_compiler_config(a_comps['compilers'], *compiler_specs.a)
+    check_compiler_config(b_comps['compilers'], *compiler_specs.b)
+
+
+#
+# Sample repo data and tests
+#
 repos_low = {'repos': ["/some/path"]}
 repos_high = {'repos': ["/some/other/path"]}
 
 
-# sample config data
-config_low = {
-    'config': {
+# repos
+def test_write_list_in_memory(mock_config):
+    spack.config.set('repos', repos_low['repos'], scope='low')
+    spack.config.set('repos', repos_high['repos'], scope='high')
+
+    config = spack.config.get('repos')
+    assert config == repos_high['repos'] + repos_low['repos']
+
+
+def test_substitute_config_variables(mock_config):
+    prefix = spack.paths.prefix.lstrip('/')
+
+    assert os.path.join(
+        '/foo/bar/baz', prefix
+    ) == canonicalize_path('/foo/bar/baz/$spack')
+
+    assert os.path.join(
+        spack.paths.prefix, 'foo/bar/baz'
+    ) == canonicalize_path('$spack/foo/bar/baz/')
+
+    assert os.path.join(
+        '/foo/bar/baz', prefix, 'foo/bar/baz'
+    ) == canonicalize_path('/foo/bar/baz/$spack/foo/bar/baz/')
+
+    assert os.path.join(
+        '/foo/bar/baz', prefix
+    ) == canonicalize_path('/foo/bar/baz/${spack}')
+
+    assert os.path.join(
+        spack.paths.prefix, 'foo/bar/baz'
+    ) == canonicalize_path('${spack}/foo/bar/baz/')
+
+    assert os.path.join(
+        '/foo/bar/baz', prefix, 'foo/bar/baz'
+    ) == canonicalize_path('/foo/bar/baz/${spack}/foo/bar/baz/')
+
+    assert os.path.join(
+        '/foo/bar/baz', prefix, 'foo/bar/baz'
+    ) != canonicalize_path('/foo/bar/baz/${spack/foo/bar/baz/')
+
+
+packages_merge_low = {
+    'packages': {
+        'foo': {
+            'variants': ['+v1']
+        },
+        'bar': {
+            'variants': ['+v2']
+        }
+    }
+}
+
+packages_merge_high = {
+    'packages': {
+        'foo': {
+            'version': ['a']
+        },
+        'bar': {
+            'version': ['b'],
+            'variants': ['+v3']
+        },
+        'baz': {
+            'version': ['c']
+        }
+    }
+}
+
+
+@pytest.mark.regression('7924')
+def test_merge_with_defaults(mock_config, write_config_file):
+    """This ensures that specified preferences merge with defaults as
+       expected. Originally all defaults were initialized with the
+       exact same object, which led to aliasing problems. Therefore
+       the test configs used here leave 'version' blank for multiple
+       packages in 'packages_merge_low'.
+    """
+    write_config_file('packages', packages_merge_low, 'low')
+    write_config_file('packages', packages_merge_high, 'high')
+    cfg = spack.config.get('packages')
+
+    assert cfg['foo']['version'] == ['a']
+    assert cfg['bar']['version'] == ['b']
+    assert cfg['baz']['version'] == ['c']
+
+
+def test_substitute_user(mock_config):
+    user = getpass.getuser()
+    assert '/foo/bar/' + user + '/baz' == canonicalize_path(
+        '/foo/bar/$user/baz'
+    )
+
+
+def test_substitute_tempdir(mock_config):
+    tempdir = tempfile.gettempdir()
+    assert tempdir == canonicalize_path('$tempdir')
+    assert tempdir + '/foo/bar/baz' == canonicalize_path(
+        '$tempdir/foo/bar/baz'
+    )
+
+
+def test_read_config(mock_config, write_config_file):
+    write_config_file('config', config_low, 'low')
+    assert spack.config.get('config') == config_low['config']
+
+
+def test_read_config_override_all(mock_config, write_config_file):
+    write_config_file('config', config_low, 'low')
+    write_config_file('config', config_override_all, 'high')
+    assert spack.config.get('config') == {
+        'install_tree': 'override_all'
+    }
+
+
+def test_read_config_override_key(mock_config, write_config_file):
+    write_config_file('config', config_low, 'low')
+    write_config_file('config', config_override_key, 'high')
+    assert spack.config.get('config') == {
+        'install_tree': 'override_key',
+        'build_stage': ['path1', 'path2', 'path3']
+    }
+
+
+def test_read_config_merge_list(mock_config, write_config_file):
+    write_config_file('config', config_low, 'low')
+    write_config_file('config', config_merge_list, 'high')
+    assert spack.config.get('config') == {
         'install_tree': 'install_tree_path',
-        'build_stage': ['path1', 'path2', 'path3']}}
+        'build_stage': ['patha', 'pathb', 'path1', 'path2', 'path3']
+    }
 
-config_override_all = {
-    'config:': {
-        'install_tree:': 'override_all'}}
 
-config_override_key = {
-    'config': {
-        'install_tree:': 'override_key'}}
+def test_read_config_override_list(mock_config, write_config_file):
+    write_config_file('config', config_low, 'low')
+    write_config_file('config', config_override_list, 'high')
+    assert spack.config.get('config') == {
+        'install_tree': 'install_tree_path',
+        'build_stage': ['patha', 'pathb']
+    }
 
-config_merge_list = {
-    'config': {
-        'build_stage': ['patha', 'pathb']}}
 
-config_override_list = {
-    'config': {
-        'build_stage:': ['patha', 'pathb']}}
+def test_internal_config_update(mock_config, write_config_file):
+    write_config_file('config', config_low, 'low')
 
+    before = mock_config.get('config')
+    assert before['install_tree'] == 'install_tree_path'
 
-def check_compiler_config(comps, *compiler_names):
-    """Check that named compilers in comps match Spack's config."""
-    config = spack.config.get_config('compilers')
-    compiler_list = ['cc', 'cxx', 'f77', 'fc']
-    flag_list = ['cflags', 'cxxflags', 'fflags', 'cppflags',
-                 'ldflags', 'ldlibs']
-    param_list = ['modules', 'paths', 'spec', 'operating_system']
-    for compiler in config:
-        conf = compiler['compiler']
-        if conf['spec'] in compiler_names:
-            comp = next((c['compiler'] for c in comps if
-                         c['compiler']['spec'] == conf['spec']), None)
-            if not comp:
-                raise ValueError('Bad config spec')
-            for p in param_list:
-                assert conf[p] == comp[p]
-            for f in flag_list:
-                expected = comp.get('flags', {}).get(f, None)
-                actual = conf.get('flags', {}).get(f, None)
-                assert expected == actual
-            for c in compiler_list:
-                expected = comp['paths'][c]
-                actual = conf['paths'][c]
-                assert expected == actual
+    # add an internal configuration scope
+    scope = spack.config.InternalConfigScope('command_line')
+    assert 'InternalConfigScope' in repr(scope)
 
+    mock_config.push_scope(scope)
 
-@pytest.fixture()
-def config(tmpdir):
-    """Mocks the configuration scope."""
-    spack.config.clear_config_caches()
-    real_scope = spack.config.config_scopes
-    spack.config.config_scopes = ordereddict_backport.OrderedDict()
-    for priority in ['low', 'high']:
-        spack.config.ConfigScope(priority, str(tmpdir.join(priority)))
-    Config = collections.namedtuple('Config', ['real', 'mock'])
-    yield Config(real=real_scope, mock=spack.config.config_scopes)
-    spack.config.config_scopes = real_scope
-    spack.config.clear_config_caches()
+    command_config = mock_config.get('config', scope='command_line')
+    command_config['install_tree'] = 'foo/bar'
 
+    mock_config.set('config', command_config, scope='command_line')
 
-@pytest.fixture()
-def write_config_file(tmpdir):
-    """Returns a function that writes a config file."""
-    def _write(config, data, scope):
-        config_yaml = tmpdir.join(scope, config + '.yaml')
-        config_yaml.ensure()
-        with config_yaml.open('w') as f:
-            yaml.dump(data, f)
-    return _write
+    after = mock_config.get('config')
+    assert after['install_tree'] == 'foo/bar'
 
 
-@pytest.fixture()
-def compiler_specs():
-    """Returns a couple of compiler specs needed for the tests"""
-    a = [ac['compiler']['spec'] for ac in a_comps['compilers']]
-    b = [bc['compiler']['spec'] for bc in b_comps['compilers']]
-    CompilerSpecs = collections.namedtuple('CompilerSpecs', ['a', 'b'])
-    return CompilerSpecs(a=a, b=b)
+def test_internal_config_filename(mock_config, write_config_file):
+    write_config_file('config', config_low, 'low')
+    mock_config.push_scope(spack.config.InternalConfigScope('command_line'))
 
+    with pytest.raises(NotImplementedError):
+        mock_config.get_config_filename('command_line', 'config')
 
-@pytest.mark.usefixtures('config')
-class TestConfig(object):
-
-    def test_write_list_in_memory(self):
-        spack.config.update_config('repos', repos_low['repos'], scope='low')
-        spack.config.update_config('repos', repos_high['repos'], scope='high')
-
-        config = spack.config.get_config('repos')
-        assert config == repos_high['repos'] + repos_low['repos']
-
-    def test_write_key_in_memory(self, compiler_specs):
-        # Write b_comps "on top of" a_comps.
-        spack.config.update_config(
-            'compilers', a_comps['compilers'], scope='low'
-        )
-        spack.config.update_config(
-            'compilers', b_comps['compilers'], scope='high'
-        )
-        # Make sure the config looks how we expect.
-        check_compiler_config(a_comps['compilers'], *compiler_specs.a)
-        check_compiler_config(b_comps['compilers'], *compiler_specs.b)
-
-    def test_write_key_to_disk(self, compiler_specs):
-        # Write b_comps "on top of" a_comps.
-        spack.config.update_config(
-            'compilers', a_comps['compilers'], scope='low'
-        )
-        spack.config.update_config(
-            'compilers', b_comps['compilers'], scope='high'
-        )
-        # Clear caches so we're forced to read from disk.
-        spack.config.clear_config_caches()
-        # Same check again, to ensure consistency.
-        check_compiler_config(a_comps['compilers'], *compiler_specs.a)
-        check_compiler_config(b_comps['compilers'], *compiler_specs.b)
-
-    def test_write_to_same_priority_file(self, compiler_specs):
-        # Write b_comps in the same file as a_comps.
-        spack.config.update_config(
-            'compilers', a_comps['compilers'], scope='low'
-        )
-        spack.config.update_config(
-            'compilers', b_comps['compilers'], scope='low'
-        )
-        # Clear caches so we're forced to read from disk.
-        spack.config.clear_config_caches()
-        # Same check again, to ensure consistency.
-        check_compiler_config(a_comps['compilers'], *compiler_specs.a)
-        check_compiler_config(b_comps['compilers'], *compiler_specs.b)
-
-    def check_canonical(self, var, expected):
-        """Ensure that <expected> is substituted properly for <var> in strings
-           containing <var> in various positions."""
-        path = '/foo/bar/baz'
-
-        self.assertEqual(canonicalize_path(var + path),
-                         expected + path)
-
-        self.assertEqual(canonicalize_path(path + var),
-                         path + '/' + expected)
-
-        self.assertEqual(canonicalize_path(path + var + path),
-                         expected + path)
-
-    def test_substitute_config_variables(self):
-        prefix = spack.prefix.lstrip('/')
-
-        assert os.path.join(
-            '/foo/bar/baz', prefix
-        ) == canonicalize_path('/foo/bar/baz/$spack')
-
-        assert os.path.join(
-            spack.prefix, 'foo/bar/baz'
-        ) == canonicalize_path('$spack/foo/bar/baz/')
-
-        assert os.path.join(
-            '/foo/bar/baz', prefix, 'foo/bar/baz'
-        ) == canonicalize_path('/foo/bar/baz/$spack/foo/bar/baz/')
-
-        assert os.path.join(
-            '/foo/bar/baz', prefix
-        ) == canonicalize_path('/foo/bar/baz/${spack}')
-
-        assert os.path.join(
-            spack.prefix, 'foo/bar/baz'
-        ) == canonicalize_path('${spack}/foo/bar/baz/')
-
-        assert os.path.join(
-            '/foo/bar/baz', prefix, 'foo/bar/baz'
-        ) == canonicalize_path('/foo/bar/baz/${spack}/foo/bar/baz/')
-
-        assert os.path.join(
-            '/foo/bar/baz', prefix, 'foo/bar/baz'
-        ) != canonicalize_path('/foo/bar/baz/${spack/foo/bar/baz/')
-
-    def test_substitute_user(self):
-        user = getpass.getuser()
-        assert '/foo/bar/' + user + '/baz' == canonicalize_path(
-            '/foo/bar/$user/baz'
-        )
-
-    def test_substitute_tempdir(self):
-        tempdir = tempfile.gettempdir()
-        assert tempdir == canonicalize_path('$tempdir')
-        assert tempdir + '/foo/bar/baz' == canonicalize_path(
-            '$tempdir/foo/bar/baz'
-        )
-
-    def test_read_config(self, write_config_file):
-        write_config_file('config', config_low, 'low')
-        assert spack.config.get_config('config') == config_low['config']
-
-    def test_read_config_override_all(self, write_config_file):
-        write_config_file('config', config_low, 'low')
-        write_config_file('config', config_override_all, 'high')
-        assert spack.config.get_config('config') == {
-            'install_tree': 'override_all'
-        }
 
-    def test_read_config_override_key(self, write_config_file):
-        write_config_file('config', config_low, 'low')
-        write_config_file('config', config_override_key, 'high')
-        assert spack.config.get_config('config') == {
-            'install_tree': 'override_key',
-            'build_stage': ['path1', 'path2', 'path3']
+def test_mark_internal():
+    data = {
+        'config': {
+            'bool': False,
+            'int': 6,
+            'numbers': [1, 2, 3],
+            'string': 'foo',
+            'dict': {
+                'more_numbers': [1, 2, 3],
+                'another_string': 'foo',
+                'another_int': 7,
+            }
         }
+    }
+
+    marked = spack.config._mark_internal(data, 'x')
+
+    # marked version should be equal to the original
+    assert data == marked
+
+    def assert_marked(obj):
+        if type(obj) is bool:
+            return  # can't subclass bool, so can't mark it
+
+        assert hasattr(obj, '_start_mark') and obj._start_mark.name == 'x'
+        assert hasattr(obj, '_end_mark') and obj._end_mark.name == 'x'
+
+    # everything in the marked version should have marks
+    checks = (marked.keys(), marked.values(),
+              marked['config'].keys(), marked['config'].values(),
+              marked['config']['numbers'],
+              marked['config']['dict'].keys(),
+              marked['config']['dict'].values(),
+              marked['config']['dict']['more_numbers'])
 
-    def test_read_config_merge_list(self, write_config_file):
-        write_config_file('config', config_low, 'low')
-        write_config_file('config', config_merge_list, 'high')
-        assert spack.config.get_config('config') == {
-            'install_tree': 'install_tree_path',
-            'build_stage': ['patha', 'pathb', 'path1', 'path2', 'path3']
+    for seq in checks:
+        for obj in seq:
+            assert_marked(obj)
+
+
+def test_internal_config_from_data():
+    config = spack.config.Configuration()
+
+    # add an internal config initialized from an inline dict
+    config.push_scope(spack.config.InternalConfigScope('_builtin', {
+        'config': {
+            'verify_ssl': False,
+            'build_jobs': 6,
         }
+    }))
 
-    def test_read_config_override_list(self, write_config_file):
-        write_config_file('config', config_low, 'low')
-        write_config_file('config', config_override_list, 'high')
-        assert spack.config.get_config('config') == {
-            'install_tree': 'install_tree_path',
-            'build_stage': ['patha', 'pathb']
+    assert config.get('config:verify_ssl', scope='_builtin') is False
+    assert config.get('config:build_jobs', scope='_builtin') == 6
+
+    assert config.get('config:verify_ssl') is False
+    assert config.get('config:build_jobs') == 6
+
+    # push one on top and see what happens.
+    config.push_scope(spack.config.InternalConfigScope('higher', {
+        'config': {
+            'checksum': True,
+            'verify_ssl': True,
         }
+    }))
 
+    assert config.get('config:verify_ssl', scope='_builtin') is False
+    assert config.get('config:build_jobs', scope='_builtin') == 6
 
-def test_keys_are_ordered():
+    assert config.get('config:verify_ssl', scope='higher') is True
+    assert config.get('config:build_jobs', scope='higher') is None
 
+    assert config.get('config:verify_ssl') is True
+    assert config.get('config:build_jobs') == 6
+    assert config.get('config:checksum') is True
+
+    assert config.get('config:checksum', scope='_builtin') is None
+    assert config.get('config:checksum', scope='higher') is True
+
+
+def test_keys_are_ordered():
+    """Test that keys in Spack YAML files retain their order from the file."""
     expected_order = (
         'bin',
         'man',
@@ -388,7 +511,7 @@ def test_keys_are_ordered():
 
     config_scope = spack.config.ConfigScope(
         'modules',
-        os.path.join(spack.test_path, 'data', 'config')
+        os.path.join(spack.paths.test_path, 'data', 'config')
     )
 
     data = config_scope.get_section('modules')
@@ -397,3 +520,242 @@ def test_keys_are_ordered():
 
     for actual, expected in zip(prefix_inspections, expected_order):
         assert actual == expected
+
+
+def test_config_format_error(mutable_config):
+    """This is raised when we try to write a bad configuration."""
+    with pytest.raises(spack.config.ConfigFormatError):
+        spack.config.set('compilers', {'bad': 'data'}, scope='site')
+
+
+def get_config_error(filename, schema, yaml_string):
+    """Parse a YAML string and return the resulting ConfigFormatError.
+
+    Fail if there is no ConfigFormatError
+    """
+    with open(filename, 'w') as f:
+        f.write(yaml_string)
+
+    # parse and return error, or fail.
+    try:
+        spack.config._read_config_file(filename, schema)
+    except spack.config.ConfigFormatError as e:
+        return e
+    else:
+        pytest.fail('ConfigFormatError was not raised!')
+
+
+def test_config_parse_dict_in_list(tmpdir):
+    with tmpdir.as_cwd():
+        e = get_config_error(
+            'repos.yaml', spack.schema.repos.schema, """\
+repos:
+- https://foobar.com/foo
+- https://foobar.com/bar
+- error:
+  - abcdef
+- https://foobar.com/baz
+""")
+        assert "repos.yaml:4" in str(e)
+
+
+def test_config_parse_str_not_bool(tmpdir):
+    with tmpdir.as_cwd():
+        e = get_config_error(
+            'config.yaml', spack.schema.config.schema, """\
+config:
+    verify_ssl: False
+    checksum: foobar
+    dirty: True
+""")
+        assert "config.yaml:3" in str(e)
+
+
+def test_config_parse_list_in_dict(tmpdir):
+    with tmpdir.as_cwd():
+        e = get_config_error(
+            'mirrors.yaml', spack.schema.mirrors.schema, """\
+mirrors:
+    foo: http://foobar.com/baz
+    bar: http://barbaz.com/foo
+    baz: http://bazfoo.com/bar
+    travis: [1, 2, 3]
+""")
+        assert "mirrors.yaml:5" in str(e)
+
+
+def test_bad_config_section(mock_config):
+    """Test that getting or setting a bad section gives an error."""
+    with pytest.raises(spack.config.ConfigSectionError):
+        spack.config.set('foobar', 'foobar')
+
+    with pytest.raises(spack.config.ConfigSectionError):
+        spack.config.get('foobar')
+
+
+def test_bad_command_line_scopes(tmpdir, mock_config):
+    cfg = spack.config.Configuration()
+
+    with tmpdir.as_cwd():
+        with pytest.raises(spack.config.ConfigError):
+            spack.config._add_command_line_scopes(cfg, ['bad_path'])
+
+        touch('unreadable_file')
+        with pytest.raises(spack.config.ConfigError):
+            spack.config._add_command_line_scopes(cfg, ['unreadable_file'])
+
+        mkdirp('unreadable_dir')
+        with pytest.raises(spack.config.ConfigError):
+            try:
+                os.chmod('unreadable_dir', 0)
+                spack.config._add_command_line_scopes(cfg, ['unreadable_dir'])
+            finally:
+                os.chmod('unreadable_dir', 0o700)  # so tmpdir can be removed
+
+
+def test_add_command_line_scopes(tmpdir, mutable_config):
+    config_yaml = str(tmpdir.join('config.yaml'))
+    with open(config_yaml, 'w') as f:
+            f.write("""\
+config:
+    verify_ssl: False
+    dirty: False
+""")
+
+    spack.config._add_command_line_scopes(mutable_config, [str(tmpdir)])
+
+
+def test_immutable_scope(tmpdir):
+    config_yaml = str(tmpdir.join('config.yaml'))
+    with open(config_yaml, 'w') as f:
+        f.write("""\
+config:
+    install_tree: dummy_tree_value
+""")
+    scope = spack.config.ImmutableConfigScope('test', str(tmpdir))
+
+    data = scope.get_section('config')
+    assert data['config']['install_tree'] == 'dummy_tree_value'
+
+    with pytest.raises(spack.config.ConfigError):
+        scope.write_section('config')
+
+
+def test_single_file_scope(tmpdir, config):
+    env_yaml = str(tmpdir.join("env.yaml"))
+    with open(env_yaml, 'w') as f:
+        f.write("""\
+env:
+    config:
+        verify_ssl: False
+        dirty: False
+    packages:
+        libelf:
+            compiler: [ 'gcc@4.5.3' ]
+    repos:
+        - /x/y/z
+""")
+
+    scope = spack.config.SingleFileScope(
+        'env', env_yaml, spack.schema.env.schema, ['env'])
+
+    with spack.config.override(scope):
+        # from the single-file config
+        assert spack.config.get('config:verify_ssl') is False
+        assert spack.config.get('config:dirty') is False
+        assert spack.config.get('packages:libelf:compiler') == ['gcc@4.5.3']
+
+        # from the lower config scopes
+        assert spack.config.get('config:checksum') is True
+        assert spack.config.get('config:checksum') is True
+        assert spack.config.get('packages:externalmodule:buildable') is False
+        assert spack.config.get('repos') == [
+            '/x/y/z', '$spack/var/spack/repos/builtin']
+
+
+def check_schema(name, file_contents):
+    """Check a Spack YAML schema against some data"""
+    f = StringIO(file_contents)
+    data = syaml.load(f)
+    spack.config._validate(data, name)
+
+
+def test_good_env_yaml(tmpdir):
+    check_schema(spack.schema.env.schema, """\
+spack:
+    config:
+        verify_ssl: False
+        dirty: False
+    repos:
+        - ~/my/repo/location
+    mirrors:
+        remote: /foo/bar/baz
+    compilers:
+        - compiler:
+            spec: cce@2.1
+            operating_system: cnl
+            modules: []
+            paths:
+                cc: /path/to/cc
+                cxx: /path/to/cxx
+                fc: /path/to/fc
+                f77: /path/to/f77
+""")
+
+
+def test_bad_env_yaml(tmpdir):
+    with pytest.raises(spack.config.ConfigFormatError):
+        check_schema(spack.schema.env.schema, """\
+env:
+    foobar:
+        verify_ssl: False
+        dirty: False
+""")
+
+
+def test_bad_config_yaml(tmpdir):
+    with pytest.raises(spack.config.ConfigFormatError):
+        check_schema(spack.schema.config.schema, """\
+config:
+    verify_ssl: False
+    module_roots:
+        fmod: /some/fake/location
+""")
+
+
+def test_bad_mirrors_yaml(tmpdir):
+    with pytest.raises(spack.config.ConfigFormatError):
+        check_schema(spack.schema.mirrors.schema, """\
+mirrors:
+    local: True
+""")
+
+
+def test_bad_repos_yaml(tmpdir):
+    with pytest.raises(spack.config.ConfigFormatError):
+        check_schema(spack.schema.repos.schema, """\
+repos:
+    True
+""")
+
+
+def test_bad_compilers_yaml(tmpdir):
+    with pytest.raises(spack.config.ConfigFormatError):
+        check_schema(spack.schema.compilers.schema, """\
+compilers:
+    key_instead_of_list: 'value'
+""")
+
+    with pytest.raises(spack.config.ConfigFormatError):
+        check_schema(spack.schema.compilers.schema, """\
+compilers:
+    - shmompiler:
+         environment: /bad/value
+""")
+
+    with pytest.raises(spack.config.ConfigFormatError):
+        check_schema(spack.schema.compilers.schema, """\
+compilers:
+    - compiler:
+         fenfironfent: /bad/value
+""")
diff --git a/lib/spack/spack/test/conftest.py b/lib/spack/spack/test/conftest.py
index 5ac4de1851..ad0644da3e 100644
--- a/lib/spack/spack/test/conftest.py
+++ b/lib/spack/spack/test/conftest.py
@@ -1,49 +1,35 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import collections
 import copy
+import inspect
 import os
+import os.path
 import shutil
 import re
 
 import ordereddict_backport
-
 import py
 import pytest
+import ruamel.yaml as yaml
 
 from llnl.util.filesystem import remove_linked_tree
 
-import spack
 import spack.architecture
+import spack.config
+import spack.caches
 import spack.database
 import spack.directory_layout
+import spack.environment as ev
+import spack.paths
 import spack.platforms.test
-import spack.repository
+import spack.repo
 import spack.stage
 import spack.util.executable
-import spack.util.pattern
+from spack.util.pattern import Bunch
 from spack.dependency import Dependency
 from spack.package import PackageBase
 from spack.fetch_strategy import FetchStrategyComposite, URLFetchStrategy
@@ -53,6 +39,53 @@ from spack.version import Version
 
 
 #
+# Disable any activate Spack environment BEFORE all tests
+#
+@pytest.fixture(scope='session', autouse=True)
+def clean_user_environment():
+    env_var = ev.spack_env_var in os.environ
+    active = ev._active_environment
+
+    if env_var:
+        spack_env_value = os.environ.pop(ev.spack_env_var)
+    if active:
+        ev.deactivate()
+
+    yield
+
+    if env_var:
+        os.environ[ev.spack_env_var] = spack_env_value
+    if active:
+        ev.activate(active)
+
+
+# Hooks to add command line options or set other custom behaviors.
+# They must be placed here to be found by pytest. See:
+#
+# https://docs.pytest.org/en/latest/writing_plugins.html
+#
+def pytest_addoption(parser):
+    group = parser.getgroup("Spack specific command line options")
+    group.addoption(
+        '--fast', action='store_true', default=False,
+        help='runs only "fast" unit tests, instead of the whole suite')
+
+
+def pytest_collection_modifyitems(config, items):
+    if not config.getoption('--fast'):
+        # --fast not given, run all the tests
+        return
+
+    slow_tests = ['db', 'network', 'maybeslow']
+    skip_as_slow = pytest.mark.skip(
+        reason='skipped slow test [--fast command line option given]'
+    )
+    for item in items:
+        if any(x in item.keywords for x in slow_tests):
+            item.add_marker(skip_as_slow)
+
+
+#
 # These fixtures are applied to all tests
 #
 @pytest.fixture(scope='function', autouse=True)
@@ -77,11 +110,11 @@ def no_chdir():
 @pytest.fixture(scope='session', autouse=True)
 def mock_stage(tmpdir_factory):
     """Mocks up a fake stage directory for use by tests."""
-    stage_path = spack.stage_path
+    stage_path = spack.paths.stage_path
     new_stage = str(tmpdir_factory.mktemp('mock_stage'))
-    spack.stage_path = new_stage
+    spack.paths.stage_path = new_stage
     yield new_stage
-    spack.stage_path = stage_path
+    spack.paths.stage_path = stage_path
 
 
 @pytest.fixture(scope='session')
@@ -118,14 +151,14 @@ def check_for_leftover_stage_files(request, mock_stage, _ignore_stage_files):
     yield
 
     files_in_stage = set()
-    if os.path.exists(spack.stage_path):
+    if os.path.exists(spack.paths.stage_path):
         files_in_stage = set(
-            os.listdir(spack.stage_path)) - _ignore_stage_files
+            os.listdir(spack.paths.stage_path)) - _ignore_stage_files
 
     if 'disable_clean_stage_check' in request.keywords:
         # clean up after tests that are expected to be dirty
         for f in files_in_stage:
-            path = os.path.join(spack.stage_path, f)
+            path = os.path.join(spack.paths.stage_path, f)
             remove_whatever_it_is(path)
     else:
         _ignore_stage_files |= files_in_stage
@@ -134,14 +167,14 @@ def check_for_leftover_stage_files(request, mock_stage, _ignore_stage_files):
 
 @pytest.fixture(autouse=True)
 def mock_fetch_cache(monkeypatch):
-    """Substitutes spack.fetch_cache with a mock object that does nothing
+    """Substitutes spack.paths.fetch_cache with a mock object that does nothing
     and raises on fetch.
     """
     class MockCache(object):
-        def store(self, copyCmd, relativeDst):
+        def store(self, copy_cmd, relative_dest):
             pass
 
-        def fetcher(self, targetPath, digest, **kwargs):
+        def fetcher(self, target_path, digest, **kwargs):
             return MockCacheFetcher()
 
     class MockCacheFetcher(object):
@@ -154,7 +187,7 @@ def mock_fetch_cache(monkeypatch):
         def __str__(self):
             return "[mock fetch cache]"
 
-    monkeypatch.setattr(spack, 'fetch_cache', MockCache())
+    monkeypatch.setattr(spack.caches, 'fetch_cache', MockCache())
 
 
 # FIXME: The lines below should better be added to a fixture with
@@ -171,27 +204,23 @@ spack.architecture.platform = lambda: spack.platforms.test.Test()
 @pytest.fixture(scope='session')
 def repo_path():
     """Session scoped RepoPath object pointing to the mock repository"""
-    return spack.repository.RepoPath(spack.mock_packages_path)
+    return spack.repo.RepoPath(spack.paths.mock_packages_path)
 
 
 @pytest.fixture(scope='module')
-def builtin_mock(repo_path):
-    """Uses the 'builtin.mock' repository instead of 'builtin'"""
+def mock_packages(repo_path):
+    """Use the 'builtin.mock' repository instead of 'builtin'"""
     mock_repo = copy.deepcopy(repo_path)
-    spack.repo.swap(mock_repo)
-    BuiltinMock = collections.namedtuple('BuiltinMock', ['real', 'mock'])
-    # Confusing, but we swapped above
-    yield BuiltinMock(real=mock_repo, mock=spack.repo)
-    spack.repo.swap(mock_repo)
+    with spack.repo.swap(mock_repo):
+        yield
 
 
-@pytest.fixture()
-def refresh_builtin_mock(builtin_mock, repo_path):
-    """Refreshes the state of spack.repo"""
-    # Get back the real repository
+@pytest.fixture(scope='function')
+def mutable_mock_packages(mock_packages, repo_path):
+    """Function-scoped mock packages, for tests that need to modify them."""
     mock_repo = copy.deepcopy(repo_path)
-    spack.repo.swap(mock_repo)
-    return builtin_mock
+    with spack.repo.swap(mock_repo):
+        yield
 
 
 @pytest.fixture(scope='session')
@@ -215,17 +244,23 @@ def configuration_dir(tmpdir_factory, linux_os):
     directory path.
     """
     tmpdir = tmpdir_factory.mktemp('configurations')
+
     # Name of the yaml files in the test/data folder
-    test_path = py.path.local(spack.test_path)
+    test_path = py.path.local(spack.paths.test_path)
     compilers_yaml = test_path.join('data', 'compilers.yaml')
     packages_yaml = test_path.join('data', 'packages.yaml')
     config_yaml = test_path.join('data', 'config.yaml')
+    repos_yaml = test_path.join('data', 'repos.yaml')
+
     # Create temporary 'site' and 'user' folders
     tmpdir.ensure('site', dir=True)
     tmpdir.ensure('user', dir=True)
+
     # Copy the configurations that don't need further work
     packages_yaml.copy(tmpdir.join('site', 'packages.yaml'))
     config_yaml.copy(tmpdir.join('site', 'config.yaml'))
+    repos_yaml.copy(tmpdir.join('site', 'repos.yaml'))
+
     # Write the one that needs modifications
     content = ''.join(compilers_yaml.read()).format(linux_os)
     t = tmpdir.join('site', 'compilers.yaml')
@@ -238,149 +273,143 @@ def config(configuration_dir):
     """Hooks the mock configuration files into spack.config"""
     # Set up a mock config scope
     spack.package_prefs.PackagePrefs.clear_caches()
-    spack.config.clear_config_caches()
-    real_scope = spack.config.config_scopes
-    spack.config.config_scopes = ordereddict_backport.OrderedDict()
-    spack.config.ConfigScope('site', str(configuration_dir.join('site')))
-    spack.config.ConfigScope('system', str(configuration_dir.join('system')))
-    spack.config.ConfigScope('user', str(configuration_dir.join('user')))
-    Config = collections.namedtuple('Config', ['real', 'mock'])
-
-    yield Config(real=real_scope, mock=spack.config.config_scopes)
-
-    spack.config.config_scopes = real_scope
-    spack.config.clear_config_caches()
+
+    real_configuration = spack.config.config
+
+    test_scopes = [
+        spack.config.ConfigScope(name, str(configuration_dir.join(name)))
+        for name in ['site', 'system', 'user']]
+    test_scopes.append(spack.config.InternalConfigScope('command_line'))
+
+    spack.config.config = spack.config.Configuration(*test_scopes)
+
+    yield spack.config.config
+
+    spack.config.config = real_configuration
     spack.package_prefs.PackagePrefs.clear_caches()
 
 
-@pytest.fixture(scope='module')
-def database(tmpdir_factory, builtin_mock, config):
-    """Creates a mock database with some packages installed note that
-    the ref count for dyninst here will be 3, as it's recycled
-    across each install.
-    """
+@pytest.fixture(scope='function')
+def mutable_config(tmpdir_factory, configuration_dir, config):
+    """Like config, but tests can modify the configuration."""
+    spack.package_prefs.PackagePrefs.clear_caches()
 
-    # Here is what the mock DB looks like:
-    #
-    # o  mpileaks     o  mpileaks'    o  mpileaks''
-    # |\              |\              |\
-    # | o  callpath   | o  callpath'  | o  callpath''
-    # |/|             |/|             |/|
-    # o |  mpich      o |  mpich2     o |  zmpi
-    #   |               |             o |  fake
-    #   |               |               |
-    #   |               |______________/
-    #   | .____________/
-    #   |/
-    #   o  dyninst
-    #   |\
-    #   | o  libdwarf
-    #   |/
-    #   o  libelf
+    mutable_dir = tmpdir_factory.mktemp('mutable_config').join('tmp')
+    configuration_dir.copy(mutable_dir)
 
-    # Make a fake install directory
-    install_path = tmpdir_factory.mktemp('install_for_database')
-    spack_install_path = spack.store.root
+    real_configuration = spack.config.config
 
-    spack.store.root = str(install_path)
-    install_layout = spack.directory_layout.YamlDirectoryLayout(
-        str(install_path))
-    spack_install_layout = spack.store.layout
-    spack.store.layout = install_layout
+    spack.config.config = spack.config.Configuration(
+        *[spack.config.ConfigScope(name, str(mutable_dir))
+          for name in ['site', 'system', 'user']])
 
-    # Make fake database and fake install directory.
-    install_db = spack.database.Database(str(install_path))
-    spack_install_db = spack.store.db
-    spack.store.db = install_db
+    yield spack.config.config
 
-    Entry = collections.namedtuple('Entry', ['path', 'layout', 'db'])
-    Database = collections.namedtuple(
-        'Database', ['real', 'mock', 'install', 'uninstall', 'refresh'])
+    spack.config.config = real_configuration
+    spack.package_prefs.PackagePrefs.clear_caches()
 
-    real = Entry(
-        path=spack_install_path,
-        layout=spack_install_layout,
-        db=spack_install_db)
-    mock = Entry(path=install_path, layout=install_layout, db=install_db)
 
+@pytest.fixture()
+def mock_config(tmpdir):
+    """Mocks two configuration scopes: 'low' and 'high'."""
+    real_configuration = spack.config.config
+
+    spack.config.config = spack.config.Configuration(
+        *[spack.config.ConfigScope(name, str(tmpdir.join(name)))
+          for name in ['low', 'high']])
+
+    yield spack.config.config
+
+    spack.config.config = real_configuration
+
+
+def _populate(mock_db):
+    r"""Populate a mock database with packages.
+
+    Here is what the mock DB looks like:
+
+    o  mpileaks     o  mpileaks'    o  mpileaks''
+    |\              |\              |\
+    | o  callpath   | o  callpath'  | o  callpath''
+    |/|             |/|             |/|
+    o |  mpich      o |  mpich2     o |  zmpi
+      |               |             o |  fake
+      |               |               |
+      |               |______________/
+      | .____________/
+      |/
+      o  dyninst
+      |\
+      | o  libdwarf
+      |/
+      o  libelf
+    """
     def _install(spec):
-        s = spack.spec.Spec(spec)
-        s.concretize()
+        s = spack.spec.Spec(spec).concretized()
         pkg = spack.repo.get(s)
-        pkg.do_install(fake=True)
-
-    def _uninstall(spec):
-        spec.package.do_uninstall(spec)
-
-    def _refresh():
-        with spack.store.db.write_transaction():
-            for spec in spack.store.db.query():
-                _uninstall(spec)
-            _install('mpileaks ^mpich')
-            _install('mpileaks ^mpich2')
-            _install('mpileaks ^zmpi')
-            _install('externaltest')
-
-    t = Database(
-        real=real,
-        mock=mock,
-        install=_install,
-        uninstall=_uninstall,
-        refresh=_refresh)
+        pkg.do_install(fake=True, explicit=True)
 
     # Transaction used to avoid repeated writes.
-    with spack.store.db.write_transaction():
-        t.install('mpileaks ^mpich')
-        t.install('mpileaks ^mpich2')
-        t.install('mpileaks ^zmpi')
-        t.install('externaltest')
+    with mock_db.write_transaction():
+        _install('mpileaks ^mpich')
+        _install('mpileaks ^mpich2')
+        _install('mpileaks ^zmpi')
+        _install('externaltest')
 
-    yield t
 
-    with spack.store.db.write_transaction():
-        for spec in spack.store.db.query():
+@pytest.fixture(scope='module')
+def database(tmpdir_factory, mock_packages, config):
+    """Creates a mock database with some packages installed note that
+    the ref count for dyninst here will be 3, as it's recycled
+    across each install.
+    """
+    # save the real store
+    real_store = spack.store.store
+
+    # Make a fake install directory
+    install_path = tmpdir_factory.mktemp('install_for_database')
+
+    # Make fake store (database and install layout)
+    tmp_store = spack.store.Store(str(install_path))
+    spack.store.store = tmp_store
+
+    _populate(tmp_store.db)
+
+    yield tmp_store.db
+
+    with tmp_store.db.write_transaction():
+        for spec in tmp_store.db.query():
             if spec.package.installed:
-                t.uninstall(spec)
+                PackageBase.uninstall_by_spec(spec, force=True)
             else:
-                spack.store.db.remove(spec)
+                tmp_store.db.remove(spec)
 
     install_path.remove(rec=1)
-    spack.store.root = spack_install_path
-    spack.store.layout = spack_install_layout
-    spack.store.db = spack_install_db
+    spack.store.store = real_store
 
 
-@pytest.fixture()
-def refresh_db_on_exit(database):
-    """"Restores the state of the database after a test."""
-    yield
-    database.refresh()
+@pytest.fixture(scope='function')
+def mutable_database(database):
+    """For tests that need to modify the database instance."""
+    yield database
+    with database.write_transaction():
+        for spec in spack.store.db.query():
+            PackageBase.uninstall_by_spec(spec, force=True)
+    _populate(database)
 
 
-@pytest.fixture()
-def install_mockery(tmpdir, config, builtin_mock):
+@pytest.fixture(scope='function')
+def install_mockery(tmpdir, config, mock_packages):
     """Hooks a fake install directory, DB, and stage directory into Spack."""
-    layout = spack.store.layout
-    extensions = spack.store.extensions
-    db = spack.store.db
-    new_opt = str(tmpdir.join('opt'))
-
-    # Use a fake install directory to avoid conflicts bt/w
-    # installed pkgs and mock packages.
-    spack.store.layout = spack.directory_layout.YamlDirectoryLayout(new_opt)
-    spack.store.extensions = spack.directory_layout.YamlExtensionsLayout(
-        new_opt, spack.store.layout)
-    spack.store.db = spack.database.Database(new_opt)
-
-    # We use a fake package, so skip the checksum.
-    spack.do_checksum = False
-    yield
-    # Turn checksumming back on
-    spack.do_checksum = True
-    # Restore Spack's layout.
-    spack.store.layout = layout
-    spack.store.extensions = extensions
-    spack.store.db = db
+    real_store = spack.store.store
+    spack.store.store = spack.store.Store(str(tmpdir.join('opt')))
+
+    # We use a fake package, so temporarily disable checksumming
+    with spack.config.override('config:checksum', False):
+        yield
+
+    tmpdir.join('opt').remove()
+    spack.store.store = real_store
 
 
 @pytest.fixture()
@@ -399,6 +428,45 @@ def mock_fetch(mock_archive):
     PackageBase.fetcher = orig_fn
 
 
+@pytest.fixture()
+def module_configuration(monkeypatch, request):
+    """Reads the module configuration file from the mock ones prepared
+    for tests and monkeypatches the right classes to hook it in.
+    """
+    # Class of the module file writer
+    writer_cls = getattr(request.module, 'writer_cls')
+    # Module where the module file writer is defined
+    writer_mod = inspect.getmodule(writer_cls)
+    # Key for specific settings relative to this module type
+    writer_key = str(writer_mod.__name__).split('.')[-1]
+    # Root folder for configuration
+    root_for_conf = os.path.join(
+        spack.paths.test_path, 'data', 'modules', writer_key
+    )
+
+    def _impl(filename):
+
+        file = os.path.join(root_for_conf, filename + '.yaml')
+        with open(file) as f:
+            configuration = yaml.load(f)
+
+        monkeypatch.setattr(
+            spack.modules.common,
+            'configuration',
+            configuration
+        )
+        monkeypatch.setattr(
+            writer_mod,
+            'configuration',
+            configuration[writer_key]
+        )
+        monkeypatch.setattr(
+            writer_mod,
+            'configuration_registry',
+            {}
+        )
+    return _impl
+
 ##########
 # Fake archives and repositories
 ##########
@@ -503,7 +571,6 @@ def mock_git_repository(tmpdir_factory):
         r1 = rev_hash(branch)
         r1_file = branch_file
 
-    Bunch = spack.util.pattern.Bunch
     checks = {
         'master': Bunch(
             revision='master', file=r0_file, args={'git': str(repodir)}
@@ -556,7 +623,6 @@ def mock_hg_repository(tmpdir_factory):
         hg('commit', '-m' 'revision 1', '-u', 'test')
         r1 = get_rev()
 
-    Bunch = spack.util.pattern.Bunch
     checks = {
         'default': Bunch(
             revision=r1, file=r1_file, args={'hg': str(repodir)}
@@ -613,7 +679,6 @@ def mock_svn_repository(tmpdir_factory):
         r0 = '1'
         r1 = '2'
 
-    Bunch = spack.util.pattern.Bunch
     checks = {
         'default': Bunch(
             revision=r1, file=r1_file, args={'svn': url}),
@@ -634,6 +699,15 @@ def mock_svn_repository(tmpdir_factory):
     yield t
 
 
+@pytest.fixture()
+def mutable_mock_env_path(tmpdir_factory):
+    """Fixture for mocking the internal spack environments directory."""
+    saved_path = spack.environment.env_path
+    spack.environment.env_path = str(tmpdir_factory.mktemp('mock-env-path'))
+    yield spack.environment.env_path
+    spack.environment.env_path = saved_path
+
+
 ##########
 # Mock packages
 ##########
@@ -652,7 +726,11 @@ class MockPackage(object):
             if not conditions or dep.name not in conditions:
                 self.dependencies[dep.name] = {Spec(name): d}
             else:
-                self.dependencies[dep.name] = {Spec(conditions[dep.name]): d}
+                dep_conditions = conditions[dep.name]
+                dep_conditions = dict(
+                    (Spec(x), Dependency(self, Spec(y), type=dtype))
+                    for x, y in dep_conditions.items())
+                self.dependencies[dep.name] = dep_conditions
 
         if versions:
             self.versions = versions
@@ -690,3 +768,33 @@ class MockPackageMultiRepo(object):
         import collections
         Repo = collections.namedtuple('Repo', ['namespace'])
         return Repo('mockrepo')
+
+##########
+# Specs of various kind
+##########
+
+
+@pytest.fixture(
+    params=[
+        'conflict%clang',
+        'conflict%clang+foo',
+        'conflict-parent%clang',
+        'conflict-parent@0.9^conflict~foo'
+    ]
+)
+def conflict_spec(request):
+    """Specs which violate constraints specified with the "conflicts"
+    directive in the "conflict" package.
+    """
+    return request.param
+
+
+@pytest.fixture(
+    params=[
+        'conflict%~'
+    ]
+)
+def invalid_spec(request):
+    """Specs that do not parse cleanly due to invalid formatting.
+    """
+    return request.param
diff --git a/lib/spack/spack/test/data/config.yaml b/lib/spack/spack/test/data/config.yaml
index ab925f4f6b..2fcd10ad97 100644
--- a/lib/spack/spack/test/data/config.yaml
+++ b/lib/spack/spack/test/data/config.yaml
@@ -1,7 +1,7 @@
 config:
   install_tree: $spack/opt/spack
   template_dirs:
-  - $spack/templates
+  - $spack/share/spack/templates
   - $spack/lib/spack/spack/test/data/templates
   - $spack/lib/spack/spack/test/data/templates_again
   build_stage:
diff --git a/lib/spack/spack/test/data/directory_search/a/foobar.txt b/lib/spack/spack/test/data/directory_search/a/foobar.txt
new file mode 100644
index 0000000000..e69de29bb2
--- /dev/null
+++ b/lib/spack/spack/test/data/directory_search/a/foobar.txt
diff --git a/lib/spack/spack/test/data/directory_search/b/bar.txp b/lib/spack/spack/test/data/directory_search/b/bar.txp
new file mode 100644
index 0000000000..e69de29bb2
--- /dev/null
+++ b/lib/spack/spack/test/data/directory_search/b/bar.txp
diff --git a/lib/spack/spack/test/data/directory_search/c/bar.txt b/lib/spack/spack/test/data/directory_search/c/bar.txt
new file mode 100644
index 0000000000..e69de29bb2
--- /dev/null
+++ b/lib/spack/spack/test/data/directory_search/c/bar.txt
diff --git a/lib/spack/spack/test/data/make/affirmative/capital_makefile/Makefile b/lib/spack/spack/test/data/make/affirmative/capital_makefile/Makefile
new file mode 100644
index 0000000000..a580687aa0
--- /dev/null
+++ b/lib/spack/spack/test/data/make/affirmative/capital_makefile/Makefile
@@ -0,0 +1,3 @@
+# Tests that Spack checks for Makefile
+
+check:
diff --git a/lib/spack/spack/test/data/make/affirmative/check_test/Makefile b/lib/spack/spack/test/data/make/affirmative/check_test/Makefile
new file mode 100644
index 0000000000..bbd931b84c
--- /dev/null
+++ b/lib/spack/spack/test/data/make/affirmative/check_test/Makefile
@@ -0,0 +1,3 @@
+# Tests that Spack detects target when it is the first of two targets
+
+check test:
diff --git a/lib/spack/spack/test/data/make/affirmative/expansion/Makefile b/lib/spack/spack/test/data/make/affirmative/expansion/Makefile
new file mode 100644
index 0000000000..e73101f01a
--- /dev/null
+++ b/lib/spack/spack/test/data/make/affirmative/expansion/Makefile
@@ -0,0 +1,5 @@
+# Tests that Spack can handle variable expansion targets
+
+TARGETS = check
+
+$(TARGETS):
diff --git a/lib/spack/spack/test/data/make/affirmative/gnu_makefile/GNUmakefile b/lib/spack/spack/test/data/make/affirmative/gnu_makefile/GNUmakefile
new file mode 100644
index 0000000000..77ea4d0972
--- /dev/null
+++ b/lib/spack/spack/test/data/make/affirmative/gnu_makefile/GNUmakefile
@@ -0,0 +1,3 @@
+# Tests that Spack checks for GNUmakefile
+
+check:
diff --git a/lib/spack/spack/test/data/make/affirmative/include/Makefile b/lib/spack/spack/test/data/make/affirmative/include/Makefile
new file mode 100644
index 0000000000..f24ab957cb
--- /dev/null
+++ b/lib/spack/spack/test/data/make/affirmative/include/Makefile
@@ -0,0 +1,3 @@
+# Tests that Spack detects targets in include files
+
+include make.mk
diff --git a/lib/spack/spack/test/data/make/affirmative/include/make.mk b/lib/spack/spack/test/data/make/affirmative/include/make.mk
new file mode 100644
index 0000000000..76e4478aae
--- /dev/null
+++ b/lib/spack/spack/test/data/make/affirmative/include/make.mk
@@ -0,0 +1 @@
+check:
diff --git a/lib/spack/spack/test/data/make/affirmative/lowercase_makefile/makefile b/lib/spack/spack/test/data/make/affirmative/lowercase_makefile/makefile
new file mode 100644
index 0000000000..942f8ab96e
--- /dev/null
+++ b/lib/spack/spack/test/data/make/affirmative/lowercase_makefile/makefile
@@ -0,0 +1,3 @@
+# Tests that Spack checks for makefile
+
+check:
diff --git a/lib/spack/spack/test/data/make/affirmative/prerequisites/Makefile b/lib/spack/spack/test/data/make/affirmative/prerequisites/Makefile
new file mode 100644
index 0000000000..22b42f3f83
--- /dev/null
+++ b/lib/spack/spack/test/data/make/affirmative/prerequisites/Makefile
@@ -0,0 +1,5 @@
+# Tests that Spack detects a target even if it is followed by prerequisites
+
+check: check-recursive
+
+check-recursive:
diff --git a/lib/spack/spack/test/data/make/affirmative/spaces/Makefile b/lib/spack/spack/test/data/make/affirmative/spaces/Makefile
new file mode 100644
index 0000000000..c9b5d4d920
--- /dev/null
+++ b/lib/spack/spack/test/data/make/affirmative/spaces/Makefile
@@ -0,0 +1,3 @@
+# Tests that Spack allows spaces following the target name
+
+check    :
diff --git a/lib/spack/spack/test/data/make/affirmative/test_check/Makefile b/lib/spack/spack/test/data/make/affirmative/test_check/Makefile
new file mode 100644
index 0000000000..5924d7d702
--- /dev/null
+++ b/lib/spack/spack/test/data/make/affirmative/test_check/Makefile
@@ -0,0 +1,3 @@
+# Tests that Spack detects target when it is the second of two targets
+
+test check:
diff --git a/lib/spack/spack/test/data/make/affirmative/three_targets/Makefile b/lib/spack/spack/test/data/make/affirmative/three_targets/Makefile
new file mode 100644
index 0000000000..96d7eff3af
--- /dev/null
+++ b/lib/spack/spack/test/data/make/affirmative/three_targets/Makefile
@@ -0,0 +1,3 @@
+# Tests that Spack detects a target if it is in the middle of a list
+
+foo check bar:
diff --git a/lib/spack/spack/test/data/make/negative/no_makefile/readme.txt b/lib/spack/spack/test/data/make/negative/no_makefile/readme.txt
new file mode 100644
index 0000000000..836ad0edb6
--- /dev/null
+++ b/lib/spack/spack/test/data/make/negative/no_makefile/readme.txt
@@ -0,0 +1,3 @@
+# Tests that Spack ignores directories without a Makefile
+
+check:
diff --git a/lib/spack/spack/test/data/make/negative/partial_match/Makefile b/lib/spack/spack/test/data/make/negative/partial_match/Makefile
new file mode 100644
index 0000000000..ea315731eb
--- /dev/null
+++ b/lib/spack/spack/test/data/make/negative/partial_match/Makefile
@@ -0,0 +1,11 @@
+# Tests that Spack ignores targets that contain a partial match
+
+checkinstall:
+
+installcheck:
+
+foo-check-bar:
+
+foo_check_bar:
+
+foo/check/bar:
diff --git a/lib/spack/spack/test/data/make/negative/variable/Makefile b/lib/spack/spack/test/data/make/negative/variable/Makefile
new file mode 100644
index 0000000000..586aea18dc
--- /dev/null
+++ b/lib/spack/spack/test/data/make/negative/variable/Makefile
@@ -0,0 +1,5 @@
+# Tests that Spack ignores variable definitions
+
+check = FOO
+
+check := BAR
diff --git a/lib/spack/spack/test/data/modules/lmod/module_path_separator.yaml b/lib/spack/spack/test/data/modules/lmod/module_path_separator.yaml
new file mode 100644
index 0000000000..208554968f
--- /dev/null
+++ b/lib/spack/spack/test/data/modules/lmod/module_path_separator.yaml
@@ -0,0 +1,5 @@
+enable:
+  - lmod
+lmod:
+  core_compilers:
+    - 'clang@3.3'
diff --git a/lib/spack/spack/test/data/modules/tcl/autoload_with_constraints.yaml b/lib/spack/spack/test/data/modules/tcl/autoload_with_constraints.yaml
new file mode 100644
index 0000000000..52796cad5b
--- /dev/null
+++ b/lib/spack/spack/test/data/modules/tcl/autoload_with_constraints.yaml
@@ -0,0 +1,8 @@
+enable:
+  - tcl
+tcl:
+  ^mpich2:
+    autoload: 'direct'
+
+  ^python:
+    autoload: 'direct'
diff --git a/lib/spack/spack/test/data/modules/tcl/blacklist_implicits.yaml b/lib/spack/spack/test/data/modules/tcl/blacklist_implicits.yaml
new file mode 100644
index 0000000000..4d5fbfb04a
--- /dev/null
+++ b/lib/spack/spack/test/data/modules/tcl/blacklist_implicits.yaml
@@ -0,0 +1,6 @@
+enable:
+  - tcl
+tcl:
+  blacklist_implicits: true
+  all:
+    autoload: 'direct'
diff --git a/lib/spack/spack/test/data/ninja/.gitignore b/lib/spack/spack/test/data/ninja/.gitignore
new file mode 100644
index 0000000000..50e58f24cc
--- /dev/null
+++ b/lib/spack/spack/test/data/ninja/.gitignore
@@ -0,0 +1,2 @@
+.ninja_deps
+.ninja_log
diff --git a/lib/spack/spack/test/data/ninja/affirmative/check_test/build.ninja b/lib/spack/spack/test/data/ninja/affirmative/check_test/build.ninja
new file mode 100644
index 0000000000..e3af305dbe
--- /dev/null
+++ b/lib/spack/spack/test/data/ninja/affirmative/check_test/build.ninja
@@ -0,0 +1,6 @@
+# Tests that Spack detects target when it is the first of two targets
+
+rule cc
+  command = true
+
+build check test: cc
diff --git a/lib/spack/spack/test/data/ninja/affirmative/include/build.ninja b/lib/spack/spack/test/data/ninja/affirmative/include/build.ninja
new file mode 100644
index 0000000000..c9ce4e61a6
--- /dev/null
+++ b/lib/spack/spack/test/data/ninja/affirmative/include/build.ninja
@@ -0,0 +1,3 @@
+# Tests that Spack can handle targets in include files
+
+include include.ninja
diff --git a/lib/spack/spack/test/data/ninja/affirmative/include/include.ninja b/lib/spack/spack/test/data/ninja/affirmative/include/include.ninja
new file mode 100644
index 0000000000..8a0d0f7c1d
--- /dev/null
+++ b/lib/spack/spack/test/data/ninja/affirmative/include/include.ninja
@@ -0,0 +1,4 @@
+rule cc
+  command = true
+
+build check: cc
diff --git a/lib/spack/spack/test/data/ninja/affirmative/simple/build.ninja b/lib/spack/spack/test/data/ninja/affirmative/simple/build.ninja
new file mode 100644
index 0000000000..f002938b10
--- /dev/null
+++ b/lib/spack/spack/test/data/ninja/affirmative/simple/build.ninja
@@ -0,0 +1,6 @@
+# Tests that Spack can handle a simple Ninja build script
+
+rule cc
+  command = true
+
+build check: cc
diff --git a/lib/spack/spack/test/data/ninja/affirmative/spaces/build.ninja b/lib/spack/spack/test/data/ninja/affirmative/spaces/build.ninja
new file mode 100644
index 0000000000..dd59a9932f
--- /dev/null
+++ b/lib/spack/spack/test/data/ninja/affirmative/spaces/build.ninja
@@ -0,0 +1,6 @@
+# Tests that Spack allows spaces following the target name
+
+rule cc
+  command = true
+
+build check   : cc
diff --git a/lib/spack/spack/test/data/ninja/affirmative/subninja/build.ninja b/lib/spack/spack/test/data/ninja/affirmative/subninja/build.ninja
new file mode 100644
index 0000000000..19ef7e3509
--- /dev/null
+++ b/lib/spack/spack/test/data/ninja/affirmative/subninja/build.ninja
@@ -0,0 +1,3 @@
+# Tests that Spack can handle targets in subninja files
+
+subninja subninja.ninja
diff --git a/lib/spack/spack/test/data/ninja/affirmative/subninja/subninja.ninja b/lib/spack/spack/test/data/ninja/affirmative/subninja/subninja.ninja
new file mode 100644
index 0000000000..8a0d0f7c1d
--- /dev/null
+++ b/lib/spack/spack/test/data/ninja/affirmative/subninja/subninja.ninja
@@ -0,0 +1,4 @@
+rule cc
+  command = true
+
+build check: cc
diff --git a/lib/spack/spack/test/data/ninja/affirmative/test_check/build.ninja b/lib/spack/spack/test/data/ninja/affirmative/test_check/build.ninja
new file mode 100644
index 0000000000..6a3cd0b0ff
--- /dev/null
+++ b/lib/spack/spack/test/data/ninja/affirmative/test_check/build.ninja
@@ -0,0 +1,6 @@
+# Tests that Spack detects target when it is the second of two targets
+
+rule cc
+  command = true
+
+build test check: cc
diff --git a/lib/spack/spack/test/data/ninja/affirmative/three_targets/build.ninja b/lib/spack/spack/test/data/ninja/affirmative/three_targets/build.ninja
new file mode 100644
index 0000000000..bf9e14ed0b
--- /dev/null
+++ b/lib/spack/spack/test/data/ninja/affirmative/three_targets/build.ninja
@@ -0,0 +1,6 @@
+# Tests that Spack detects a target if it is in the middle of a list
+
+rule cc
+  command = true
+
+build foo check bar: cc
diff --git a/lib/spack/spack/test/data/ninja/negative/no_ninja/readme.txt b/lib/spack/spack/test/data/ninja/negative/no_ninja/readme.txt
new file mode 100644
index 0000000000..0a85aa7af8
--- /dev/null
+++ b/lib/spack/spack/test/data/ninja/negative/no_ninja/readme.txt
@@ -0,0 +1,8 @@
+# Tests that Spack ignores directories without a Ninja build script
+
+cflags = -Wall
+
+rule cc
+  command = gcc $cflags -c $in -o $out
+
+build check: cc foo.c
diff --git a/lib/spack/spack/test/data/ninja/negative/partial_match/build.ninja b/lib/spack/spack/test/data/ninja/negative/partial_match/build.ninja
new file mode 100644
index 0000000000..12efb5839a
--- /dev/null
+++ b/lib/spack/spack/test/data/ninja/negative/partial_match/build.ninja
@@ -0,0 +1,16 @@
+# Tests that Spack ignores targets that contain a partial match
+
+cflags = -Wall
+
+rule cc
+  command = gcc $cflags -c $in -o $out
+
+build installcheck: cc foo.c
+
+build checkinstall: cc foo.c
+
+build foo-check-bar: cc foo.c
+
+build foo_check_bar: cc foo.c
+
+build foo/check/bar: cc foo.c
diff --git a/lib/spack/spack/test/data/ninja/negative/rule/build.ninja b/lib/spack/spack/test/data/ninja/negative/rule/build.ninja
new file mode 100644
index 0000000000..2164bda6d9
--- /dev/null
+++ b/lib/spack/spack/test/data/ninja/negative/rule/build.ninja
@@ -0,0 +1,8 @@
+# Tests that Spack ignores rule names
+
+cflags = -Wall
+
+rule check
+  command = gcc $cflags -c $in -o $out
+
+build foo: check foo.c
diff --git a/lib/spack/spack/test/data/ninja/negative/variable/build.ninja b/lib/spack/spack/test/data/ninja/negative/variable/build.ninja
new file mode 100644
index 0000000000..73aafbf5bd
--- /dev/null
+++ b/lib/spack/spack/test/data/ninja/negative/variable/build.ninja
@@ -0,0 +1,8 @@
+# Tests that Spack ignores variable definitions
+
+check = -Wall
+
+rule cc
+  command = gcc $check -c $in -o $out
+
+build foo: cc foo.c
diff --git a/lib/spack/spack/test/data/packages.yaml b/lib/spack/spack/test/data/packages.yaml
index 923d63173a..c7256ddb33 100644
--- a/lib/spack/spack/test/data/packages.yaml
+++ b/lib/spack/spack/test/data/packages.yaml
@@ -3,6 +3,7 @@ packages:
     buildable: False
     paths:
       externaltool@1.0%gcc@4.5.0: /path/to/external_tool
+      externaltool@0.9%gcc@4.5.0: /usr
   externalvirtual:
     buildable: False
     paths:
diff --git a/lib/spack/spack/test/data/repos.yaml b/lib/spack/spack/test/data/repos.yaml
new file mode 100644
index 0000000000..4fbbfe9d62
--- /dev/null
+++ b/lib/spack/spack/test/data/repos.yaml
@@ -0,0 +1,2 @@
+repos:
+  - $spack/var/spack/repos/builtin
diff --git a/lib/spack/spack/test/data/sourceme_first.sh b/lib/spack/spack/test/data/sourceme_first.sh
index 7adf35e137..c9c8103816 100644
--- a/lib/spack/spack/test/data/sourceme_first.sh
+++ b/lib/spack/spack/test/data/sourceme_first.sh
@@ -1,29 +1,11 @@
 #!/usr/bin/env bash
-
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
 #
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
 
 export NEW_VAR='new'
 export UNSET_ME='overridden'
diff --git a/lib/spack/spack/test/data/sourceme_parameters.sh b/lib/spack/spack/test/data/sourceme_parameters.sh
index 8b60e944b3..1c63e06cd0 100644
--- a/lib/spack/spack/test/data/sourceme_parameters.sh
+++ b/lib/spack/spack/test/data/sourceme_parameters.sh
@@ -1,29 +1,11 @@
 #!/usr/bin/env bash
-
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
 #
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
 
 if [[ "$1" == "intel64" ]] ; then
     export FOO='intel64'
diff --git a/lib/spack/spack/test/data/sourceme_second.sh b/lib/spack/spack/test/data/sourceme_second.sh
index 37059707f8..bec2619e0d 100644
--- a/lib/spack/spack/test/data/sourceme_second.sh
+++ b/lib/spack/spack/test/data/sourceme_second.sh
@@ -1,29 +1,11 @@
 #!/usr/bin/env bash
-
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
 #
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
 
 export PATH_LIST='/path/first:/path/second:/path/fourth'
 unset EMPTY_PATH_LIST
diff --git a/lib/spack/spack/test/data/sourceme_unicode.sh b/lib/spack/spack/test/data/sourceme_unicode.sh
index b602dadbbc..61bfa19b90 100644
--- a/lib/spack/spack/test/data/sourceme_unicode.sh
+++ b/lib/spack/spack/test/data/sourceme_unicode.sh
@@ -1,29 +1,11 @@
 #!/usr/bin/env bash
-
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
 #
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
 
 # Set an environment variable with some unicode in it to ensure that
 # Spack can decode it.
diff --git a/lib/spack/spack/test/database.py b/lib/spack/spack/test/database.py
index 72ae6ad278..cc469301a8 100644
--- a/lib/spack/spack/test/database.py
+++ b/lib/spack/spack/test/database.py
@@ -1,43 +1,46 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """
 These tests check the database is functioning properly,
 both in memory and in its file
 """
+import datetime
+import functools
 import multiprocessing
 import os
 import pytest
 
 from llnl.util.tty.colify import colify
 
-import spack
+import spack.repo
 import spack.store
 from spack.test.conftest import MockPackageMultiRepo
 from spack.util.executable import Executable
 
 
+pytestmark = pytest.mark.db
+
+
+@pytest.fixture()
+def usr_folder_exists(monkeypatch):
+    """The ``/usr`` folder is assumed to be existing in some tests. This
+    fixture makes it such that its existence is mocked, so we have no
+    requirements on the system running tests.
+    """
+    isdir = os.path.isdir
+
+    @functools.wraps(os.path.isdir)
+    def mock_isdir(path):
+        if path == '/usr':
+            return True
+        return isdir(path)
+
+    monkeypatch.setattr(os.path, 'isdir', mock_isdir)
+
+
 def _print_ref_counts():
     """Print out all ref counts for the graph used here, for debugging"""
     recs = []
@@ -87,10 +90,10 @@ def _check_merkleiness():
                 assert seen[hash_key] == id(dep)
 
 
-def _check_db_sanity(install_db):
+def _check_db_sanity(database):
     """Utiilty function to check db against install layout."""
     pkg_in_layout = sorted(spack.store.layout.all_specs())
-    actual = sorted(install_db.query())
+    actual = sorted(database.query())
 
     externals = sorted([x for x in actual if x.external])
     nexpected = len(pkg_in_layout) + len(externals)
@@ -105,6 +108,36 @@ def _check_db_sanity(install_db):
     _check_merkleiness()
 
 
+def _check_remove_and_add_package(database, spec):
+    """Remove a spec from the DB, then add it and make sure everything's
+    still ok once it is added.  This checks that it was
+    removed, that it's back when added again, and that ref
+    counts are consistent.
+    """
+    original = database.query()
+    database._check_ref_counts()
+
+    # Remove spec
+    concrete_spec = database.remove(spec)
+    database._check_ref_counts()
+    remaining = database.query()
+
+    # ensure spec we removed is gone
+    assert len(original) - 1 == len(remaining)
+    assert all(s in original for s in remaining)
+    assert concrete_spec not in remaining
+
+    # add it back and make sure everything is ok.
+    database.add(concrete_spec, spack.store.layout)
+    installed = database.query()
+    assert concrete_spec in installed
+    assert installed == original
+
+    # sanity check against direcory layout and check ref counts.
+    _check_db_sanity(database)
+    database._check_ref_counts()
+
+
 def _mock_install(spec):
     s = spack.spec.Spec(spec)
     s.concretize()
@@ -120,28 +153,49 @@ def _mock_remove(spec):
 
 
 def test_default_queries(database):
-    install_db = database.mock.db
-    rec = install_db.get_record('zmpi')
+    # Testing a package whose name *doesn't* start with 'lib'
+    # to ensure the library has 'lib' prepended to the name
+    rec = database.get_record('zmpi')
 
     spec = rec.spec
 
     libraries = spec['zmpi'].libs
     assert len(libraries) == 1
+    assert libraries.names[0] == 'zmpi'
 
     headers = spec['zmpi'].headers
     assert len(headers) == 1
+    assert headers.names[0] == 'zmpi'
 
     command = spec['zmpi'].command
     assert isinstance(command, Executable)
     assert command.name == 'zmpi'
     assert os.path.exists(command.path)
 
+    # Testing a package whose name *does* start with 'lib'
+    # to ensure the library doesn't have a double 'lib' prefix
+    rec = database.get_record('libelf')
+
+    spec = rec.spec
+
+    libraries = spec['libelf'].libs
+    assert len(libraries) == 1
+    assert libraries.names[0] == 'elf'
+
+    headers = spec['libelf'].headers
+    assert len(headers) == 1
+    assert headers.names[0] == 'libelf'
+
+    command = spec['libelf'].command
+    assert isinstance(command, Executable)
+    assert command.name == 'libelf'
+    assert os.path.exists(command.path)
+
 
 def test_005_db_exists(database):
     """Make sure db cache file exists after creating."""
-    install_path = database.mock.path
-    index_file = install_path.join('.spack-db', 'index.json')
-    lock_file = install_path.join('.spack-db', 'lock')
+    index_file = os.path.join(database.root, '.spack-db', 'index.json')
+    lock_file = os.path.join(database.root, '.spack-db', 'lock')
     assert os.path.exists(str(index_file))
     assert os.path.exists(str(lock_file))
 
@@ -170,9 +224,15 @@ def test_010_all_install_sanity(database):
     assert len(libelf_specs) == 1
 
     # Query by dependency
-    assert len([s for s in all_specs if s.satisfies('mpileaks ^mpich')]) == 1
-    assert len([s for s in all_specs if s.satisfies('mpileaks ^mpich2')]) == 1
-    assert len([s for s in all_specs if s.satisfies('mpileaks ^zmpi')]) == 1
+    assert len(
+        [s for s in all_specs if s.satisfies('mpileaks ^mpich')]
+    ) == 1
+    assert len(
+        [s for s in all_specs if s.satisfies('mpileaks ^mpich2')]
+    ) == 1
+    assert len(
+        [s for s in all_specs if s.satisfies('mpileaks ^zmpi')]
+    ) == 1
 
 
 def test_015_write_and_read(database):
@@ -191,23 +251,20 @@ def test_015_write_and_read(database):
 
 def test_020_db_sanity(database):
     """Make sure query() returns what's actually in the db."""
-    install_db = database.mock.db
-    _check_db_sanity(install_db)
+    _check_db_sanity(database)
 
 
 def test_025_reindex(database):
     """Make sure reindex works and ref counts are valid."""
-    install_db = database.mock.db
-    spack.store.db.reindex(spack.store.layout)
-    _check_db_sanity(install_db)
-
+    spack.store.store.reindex()
+    _check_db_sanity(database)
 
-def test_030_db_sanity_from_another_process(database, refresh_db_on_exit):
-    install_db = database.mock.db
 
+def test_030_db_sanity_from_another_process(mutable_database):
     def read_and_modify():
-        _check_db_sanity(install_db)  # check that other process can read DB
-        with install_db.write_transaction():
+        # check that other process can read DB
+        _check_db_sanity(mutable_database)
+        with mutable_database.write_transaction():
             _mock_remove('mpileaks ^zmpi')
 
     p = multiprocessing.Process(target=read_and_modify, args=())
@@ -215,210 +272,181 @@ def test_030_db_sanity_from_another_process(database, refresh_db_on_exit):
     p.join()
 
     # ensure child process change is visible in parent process
-    with install_db.read_transaction():
-        assert len(install_db.query('mpileaks ^zmpi')) == 0
+    with mutable_database.read_transaction():
+        assert len(mutable_database.query('mpileaks ^zmpi')) == 0
 
 
 def test_040_ref_counts(database):
     """Ensure that we got ref counts right when we read the DB."""
-    install_db = database.mock.db
-    install_db._check_ref_counts()
+    database._check_ref_counts()
 
 
 def test_050_basic_query(database):
     """Ensure querying database is consistent with what is installed."""
-    install_db = database.mock.db
     # query everything
     assert len(spack.store.db.query()) == 16
 
     # query specs with multiple configurations
-    mpileaks_specs = install_db.query('mpileaks')
-    callpath_specs = install_db.query('callpath')
-    mpi_specs = install_db.query('mpi')
+    mpileaks_specs = database.query('mpileaks')
+    callpath_specs = database.query('callpath')
+    mpi_specs = database.query('mpi')
 
     assert len(mpileaks_specs) == 3
     assert len(callpath_specs) == 3
     assert len(mpi_specs) == 3
 
     # query specs with single configurations
-    dyninst_specs = install_db.query('dyninst')
-    libdwarf_specs = install_db.query('libdwarf')
-    libelf_specs = install_db.query('libelf')
+    dyninst_specs = database.query('dyninst')
+    libdwarf_specs = database.query('libdwarf')
+    libelf_specs = database.query('libelf')
 
     assert len(dyninst_specs) == 1
     assert len(libdwarf_specs) == 1
     assert len(libelf_specs) == 1
 
     # Query by dependency
-    assert len(install_db.query('mpileaks ^mpich')) == 1
-    assert len(install_db.query('mpileaks ^mpich2')) == 1
-    assert len(install_db.query('mpileaks ^zmpi')) == 1
+    assert len(database.query('mpileaks ^mpich')) == 1
+    assert len(database.query('mpileaks ^mpich2')) == 1
+    assert len(database.query('mpileaks ^zmpi')) == 1
 
-
-def _check_remove_and_add_package(install_db, spec):
-    """Remove a spec from the DB, then add it and make sure everything's
-    still ok once it is added.  This checks that it was
-    removed, that it's back when added again, and that ref
-    counts are consistent.
-    """
-    original = install_db.query()
-    install_db._check_ref_counts()
-
-    # Remove spec
-    concrete_spec = install_db.remove(spec)
-    install_db._check_ref_counts()
-    remaining = install_db.query()
-
-    # ensure spec we removed is gone
-    assert len(original) - 1 == len(remaining)
-    assert all(s in original for s in remaining)
-    assert concrete_spec not in remaining
-
-    # add it back and make sure everything is ok.
-    install_db.add(concrete_spec, spack.store.layout)
-    installed = install_db.query()
-    assert concrete_spec in installed
-    assert installed == original
-
-    # sanity check against direcory layout and check ref counts.
-    _check_db_sanity(install_db)
-    install_db._check_ref_counts()
+    # Query by date
+    assert len(database.query(start_date=datetime.datetime.min)) == 16
+    assert len(database.query(start_date=datetime.datetime.max)) == 0
+    assert len(database.query(end_date=datetime.datetime.min)) == 0
+    assert len(database.query(end_date=datetime.datetime.max)) == 16
 
 
 def test_060_remove_and_add_root_package(database):
-    install_db = database.mock.db
-    _check_remove_and_add_package(install_db, 'mpileaks ^mpich')
+    _check_remove_and_add_package(database, 'mpileaks ^mpich')
 
 
 def test_070_remove_and_add_dependency_package(database):
-    install_db = database.mock.db
-    _check_remove_and_add_package(install_db, 'dyninst')
+    _check_remove_and_add_package(database, 'dyninst')
 
 
 def test_080_root_ref_counts(database):
-    install_db = database.mock.db
-    rec = install_db.get_record('mpileaks ^mpich')
+    rec = database.get_record('mpileaks ^mpich')
 
     # Remove a top-level spec from the DB
-    install_db.remove('mpileaks ^mpich')
+    database.remove('mpileaks ^mpich')
 
     # record no longer in DB
-    assert install_db.query('mpileaks ^mpich', installed=any) == []
+    assert database.query('mpileaks ^mpich', installed=any) == []
 
     # record's deps have updated ref_counts
-    assert install_db.get_record('callpath ^mpich').ref_count == 0
-    assert install_db.get_record('mpich').ref_count == 1
+    assert database.get_record('callpath ^mpich').ref_count == 0
+    assert database.get_record('mpich').ref_count == 1
 
     # Put the spec back
-    install_db.add(rec.spec, spack.store.layout)
+    database.add(rec.spec, spack.store.layout)
 
     # record is present again
-    assert len(install_db.query('mpileaks ^mpich', installed=any)) == 1
+    assert len(database.query('mpileaks ^mpich', installed=any)) == 1
 
     # dependencies have ref counts updated
-    assert install_db.get_record('callpath ^mpich').ref_count == 1
-    assert install_db.get_record('mpich').ref_count == 2
+    assert database.get_record('callpath ^mpich').ref_count == 1
+    assert database.get_record('mpich').ref_count == 2
 
 
 def test_090_non_root_ref_counts(database):
-    install_db = database.mock.db
-
-    install_db.get_record('mpileaks ^mpich')
-    install_db.get_record('callpath ^mpich')
+    database.get_record('mpileaks ^mpich')
+    database.get_record('callpath ^mpich')
 
     # "force remove" a non-root spec from the DB
-    install_db.remove('callpath ^mpich')
+    database.remove('callpath ^mpich')
 
     # record still in DB but marked uninstalled
-    assert install_db.query('callpath ^mpich', installed=True) == []
-    assert len(install_db.query('callpath ^mpich', installed=any)) == 1
+    assert database.query('callpath ^mpich', installed=True) == []
+    assert len(database.query('callpath ^mpich', installed=any)) == 1
 
     # record and its deps have same ref_counts
-    assert install_db.get_record(
+    assert database.get_record(
         'callpath ^mpich', installed=any
     ).ref_count == 1
-    assert install_db.get_record('mpich').ref_count == 2
+    assert database.get_record('mpich').ref_count == 2
 
     # remove only dependent of uninstalled callpath record
-    install_db.remove('mpileaks ^mpich')
+    database.remove('mpileaks ^mpich')
 
     # record and parent are completely gone.
-    assert install_db.query('mpileaks ^mpich', installed=any) == []
-    assert install_db.query('callpath ^mpich', installed=any) == []
+    assert database.query('mpileaks ^mpich', installed=any) == []
+    assert database.query('callpath ^mpich', installed=any) == []
 
     # mpich ref count updated properly.
-    mpich_rec = install_db.get_record('mpich')
+    mpich_rec = database.get_record('mpich')
     assert mpich_rec.ref_count == 0
 
 
 def test_100_no_write_with_exception_on_remove(database):
-    install_db = database.mock.db
-
     def fail_while_writing():
-        with install_db.write_transaction():
+        with database.write_transaction():
             _mock_remove('mpileaks ^zmpi')
             raise Exception()
 
-    with install_db.read_transaction():
-        assert len(install_db.query('mpileaks ^zmpi', installed=any)) == 1
+    with database.read_transaction():
+        assert len(database.query('mpileaks ^zmpi', installed=any)) == 1
 
     with pytest.raises(Exception):
         fail_while_writing()
 
     # reload DB and make sure zmpi is still there.
-    with install_db.read_transaction():
-        assert len(install_db.query('mpileaks ^zmpi', installed=any)) == 1
+    with database.read_transaction():
+        assert len(database.query('mpileaks ^zmpi', installed=any)) == 1
 
 
 def test_110_no_write_with_exception_on_install(database):
-    install_db = database.mock.db
-
     def fail_while_writing():
-        with install_db.write_transaction():
+        with database.write_transaction():
             _mock_install('cmake')
             raise Exception()
 
-    with install_db.read_transaction():
-        assert install_db.query('cmake', installed=any) == []
+    with database.read_transaction():
+        assert database.query('cmake', installed=any) == []
 
     with pytest.raises(Exception):
         fail_while_writing()
 
     # reload DB and make sure cmake was not written.
-    with install_db.read_transaction():
-        assert install_db.query('cmake', installed=any) == []
+    with database.read_transaction():
+        assert database.query('cmake', installed=any) == []
 
 
-def test_115_reindex_with_packages_not_in_repo(database, refresh_db_on_exit):
-    install_db = database.mock.db
-
-    saved_repo = spack.repo
+def test_115_reindex_with_packages_not_in_repo(mutable_database):
     # Dont add any package definitions to this repository, the idea is that
-    # packages should not have to be defined in the repository once they are
-    # installed
-    mock_repo = MockPackageMultiRepo([])
-    try:
-        spack.repo = mock_repo
-        spack.store.db.reindex(spack.store.layout)
-        _check_db_sanity(install_db)
-    finally:
-        spack.repo = saved_repo
+    # packages should not have to be defined in the repository once they
+    # are installed
+    with spack.repo.swap(MockPackageMultiRepo([])):
+        spack.store.store.reindex()
+        _check_db_sanity(mutable_database)
 
 
 def test_external_entries_in_db(database):
-    install_db = database.mock.db
-
-    rec = install_db.get_record('mpileaks ^zmpi')
+    rec = database.get_record('mpileaks ^zmpi')
     assert rec.spec.external_path is None
     assert rec.spec.external_module is None
 
-    rec = install_db.get_record('externaltool')
+    rec = database.get_record('externaltool')
     assert rec.spec.external_path == '/path/to/external_tool'
     assert rec.spec.external_module is None
     assert rec.explicit is False
 
     rec.spec.package.do_install(fake=True, explicit=True)
-    rec = install_db.get_record('externaltool')
+    rec = database.get_record('externaltool')
     assert rec.spec.external_path == '/path/to/external_tool'
     assert rec.spec.external_module is None
     assert rec.explicit is True
+
+
+@pytest.mark.regression('8036')
+def test_regression_issue_8036(mutable_database, usr_folder_exists):
+    # The test ensures that the external package prefix is treated as
+    # existing. Even when the package prefix exists, the package should
+    # not be considered installed until it is added to the database with
+    # do_install.
+    s = spack.spec.Spec('externaltool@0.9')
+    s.concretize()
+    assert not s.package.installed
+
+    # Now install the external package and check again the `installed` property
+    s.package.do_install(fake=True)
+    assert s.package.installed
diff --git a/lib/spack/spack/test/directory_layout.py b/lib/spack/spack/test/directory_layout.py
index b166ea4eac..6584c3c636 100644
--- a/lib/spack/spack/test/directory_layout.py
+++ b/lib/spack/spack/test/directory_layout.py
@@ -1,39 +1,18 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """
 This test verifies that the Spack directory layout works properly.
 """
 import os
 import pytest
 
-from llnl.util.filesystem import join_path
-
-import spack
+import spack.paths
+import spack.repo
 from spack.directory_layout import YamlDirectoryLayout
 from spack.directory_layout import InvalidDirectoryLayoutParametersError
-from spack.repository import RepoPath
 from spack.spec import Spec
 
 # number of packages to test (to reduce test time)
@@ -74,13 +53,19 @@ def test_yaml_directory_layout_parameters(
     # Test path_scheme
     arch, compiler, package7 = path_7.split('/')
     scheme_package7 = "${PACKAGE}-${VERSION}-${HASH:7}"
-
     layout_package7 = YamlDirectoryLayout(str(tmpdir),
                                           path_scheme=scheme_package7)
     path_package7 = layout_package7.relative_path_for_spec(spec)
 
     assert(package7 == path_package7)
 
+    # Test separation of architecture
+    arch_scheme_package = "${PLATFORM}/${TARGET}/${OS}/${PACKAGE}/${VERSION}/${HASH:7}"   # NOQA: ignore=E501
+    layout_arch_package = YamlDirectoryLayout(str(tmpdir),
+                                              path_scheme=arch_scheme_package)
+    arch_path_package = layout_arch_package.relative_path_for_spec(spec)
+    assert(arch_path_package == spec.format(arch_scheme_package))
+
     # Ensure conflicting parameters caught
     with pytest.raises(InvalidDirectoryLayoutParametersError):
         YamlDirectoryLayout(str(tmpdir),
@@ -89,7 +74,7 @@ def test_yaml_directory_layout_parameters(
 
 
 def test_read_and_write_spec(
-        layout_and_dir, config, builtin_mock
+        layout_and_dir, config, mock_packages
 ):
     """This goes through each package in spack and creates a directory for
     it.  It then ensures that the spec for the directory's
@@ -98,7 +83,7 @@ def test_read_and_write_spec(
     layout.
     """
     layout, tmpdir = layout_and_dir
-    packages = list(spack.repo.all_packages())[:max_packages]
+    packages = list(spack.repo.path.all_packages())[:max_packages]
 
     for pkg in packages:
         if pkg.name.startswith('external'):
@@ -167,7 +152,7 @@ def test_read_and_write_spec(
 
 
 def test_handle_unknown_package(
-        layout_and_dir, config, builtin_mock
+        layout_and_dir, config, mock_packages
 ):
     """This test ensures that spack can at least do *some*
     operations with packages that are installed but that it
@@ -180,7 +165,7 @@ def test_handle_unknown_package(
     or query them again if the package goes away.
     """
     layout, _ = layout_and_dir
-    mock_db = RepoPath(spack.mock_packages_path)
+    mock_db = spack.repo.RepoPath(spack.paths.mock_packages_path)
 
     not_in_mock = set.difference(
         set(spack.repo.all_package_names()),
@@ -202,28 +187,25 @@ def test_handle_unknown_package(
         layout.create_install_directory(spec)
         installed_specs[spec] = layout.path_for_spec(spec)
 
-    spack.repo.swap(mock_db)
-
-    # Now check that even without the package files, we know
-    # enough to read a spec from the spec file.
-    for spec, path in installed_specs.items():
-        spec_from_file = layout.read_spec(
-            join_path(path, '.spack', 'spec.yaml')
-        )
-        # To satisfy these conditions, directory layouts need to
-        # read in concrete specs from their install dirs somehow.
-        assert path == layout.path_for_spec(spec_from_file)
-        assert spec == spec_from_file
-        assert spec.eq_dag(spec_from_file)
-        assert spec.dag_hash() == spec_from_file.dag_hash()
+    with spack.repo.swap(mock_db):
+        # Now check that even without the package files, we know
+        # enough to read a spec from the spec file.
+        for spec, path in installed_specs.items():
+            spec_from_file = layout.read_spec(
+                os.path.join(path, '.spack', 'spec.yaml'))
 
-    spack.repo.swap(mock_db)
+            # To satisfy these conditions, directory layouts need to
+            # read in concrete specs from their install dirs somehow.
+            assert path == layout.path_for_spec(spec_from_file)
+            assert spec == spec_from_file
+            assert spec.eq_dag(spec_from_file)
+            assert spec.dag_hash() == spec_from_file.dag_hash()
 
 
-def test_find(layout_and_dir, config, builtin_mock):
+def test_find(layout_and_dir, config, mock_packages):
     """Test that finding specs within an install layout works."""
     layout, _ = layout_and_dir
-    packages = list(spack.repo.all_packages())[:max_packages]
+    packages = list(spack.repo.path.all_packages())[:max_packages]
 
     # Create install prefixes for all packages in the list
     installed_specs = {}
diff --git a/lib/spack/spack/test/environment.py b/lib/spack/spack/test/environment_modifications.py
index c11c050820..a7941a30cb 100644
--- a/lib/spack/spack/test/environment.py
+++ b/lib/spack/spack/test/environment_modifications.py
@@ -1,35 +1,16 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 
 import pytest
-import spack.environment as environment
-from spack import spack_root
-from spack.environment import EnvironmentModifications
-from spack.environment import RemovePath, PrependPath, AppendPath
-from spack.environment import SetEnv, UnsetEnv
+import spack.util.environment as environment
+from spack.paths import spack_root
+from spack.util.environment import EnvironmentModifications
+from spack.util.environment import RemovePath, PrependPath, AppendPath
+from spack.util.environment import SetEnv, UnsetEnv
 from spack.util.environment import filter_system_paths, is_system_path
 
 
@@ -306,3 +287,22 @@ def test_source_files(files_to_be_sourced):
     assert modifications['PATH_LIST'][1].value == '/path/fourth'
     assert isinstance(modifications['PATH_LIST'][2], PrependPath)
     assert modifications['PATH_LIST'][2].value == '/path/first'
+
+
+@pytest.mark.regression('8345')
+def test_preserve_environment(prepare_environment_for_tests):
+    # UNSET_ME is defined, and will be unset in the context manager,
+    # NOT_SET is not in the environment and will be set within the
+    # context manager, PATH_LIST is set and will be changed.
+    with environment.preserve_environment('UNSET_ME', 'NOT_SET', 'PATH_LIST'):
+        os.environ['NOT_SET'] = 'a'
+        assert os.environ['NOT_SET'] == 'a'
+
+        del os.environ['UNSET_ME']
+        assert 'UNSET_ME' not in os.environ
+
+        os.environ['PATH_LIST'] = 'changed'
+
+    assert 'NOT_SET' not in os.environ
+    assert os.environ['UNSET_ME'] == 'foo'
+    assert os.environ['PATH_LIST'] == '/path/second:/path/third'
diff --git a/lib/spack/spack/test/flag_handlers.py b/lib/spack/spack/test/flag_handlers.py
index 80dad9c35e..de84a19008 100644
--- a/lib/spack/spack/test/flag_handlers.py
+++ b/lib/spack/spack/test/flag_handlers.py
@@ -1,33 +1,17 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import pytest
 import os
 
 import spack.spec
+import spack.repo
 import spack.build_environment
 
+from spack.pkgkit import inject_flags, env_flags, build_system_flags
+
 
 @pytest.fixture()
 def temp_env():
@@ -36,23 +20,23 @@ def temp_env():
     os.environ = old_env
 
 
-def add_O3_to_build_system_cflags(pkg, name, flags):
+def add_o3_to_build_system_cflags(pkg, name, flags):
     build_system_flags = []
     if name == 'cflags':
         build_system_flags.append('-O3')
     return (flags, None, build_system_flags)
 
 
-@pytest.mark.usefixtures('config')
+@pytest.mark.usefixtures('config', 'mock_packages')
 class TestFlagHandlers(object):
     def test_no_build_system_flags(self, temp_env):
         # Test that both autotools and cmake work getting no build_system flags
-        s1 = spack.spec.Spec('callpath')
+        s1 = spack.spec.Spec('cmake-client')
         s1.concretize()
         pkg1 = spack.repo.get(s1)
         spack.build_environment.setup_package(pkg1, False)
 
-        s2 = spack.spec.Spec('libelf')
+        s2 = spack.spec.Spec('patchelf')
         s2.concretize()
         pkg2 = spack.repo.get(s2)
         spack.build_environment.setup_package(pkg2, False)
@@ -69,7 +53,6 @@ class TestFlagHandlers(object):
         pkg = spack.repo.get(s)
         pkg.flag_handler = pkg.__class__.inject_flags
         spack.build_environment.setup_package(pkg, False)
-
         assert os.environ['SPACK_CPPFLAGS'] == '-g'
         assert 'CPPFLAGS' not in os.environ
 
@@ -77,7 +60,7 @@ class TestFlagHandlers(object):
         s = spack.spec.Spec('mpileaks cppflags=-g')
         s.concretize()
         pkg = spack.repo.get(s)
-        pkg.flag_handler = pkg.inject_flags
+        pkg.flag_handler = inject_flags
         spack.build_environment.setup_package(pkg, False)
 
         assert os.environ['SPACK_CPPFLAGS'] == '-g'
@@ -87,17 +70,17 @@ class TestFlagHandlers(object):
         s = spack.spec.Spec('mpileaks cppflags=-g')
         s.concretize()
         pkg = spack.repo.get(s)
-        pkg.flag_handler = pkg.env_flags
+        pkg.flag_handler = env_flags
         spack.build_environment.setup_package(pkg, False)
 
         assert os.environ['CPPFLAGS'] == '-g'
         assert 'SPACK_CPPFLAGS' not in os.environ
 
     def test_build_system_flags_cmake(self, temp_env):
-        s = spack.spec.Spec('callpath cppflags=-g')
+        s = spack.spec.Spec('cmake-client cppflags=-g')
         s.concretize()
         pkg = spack.repo.get(s)
-        pkg.flag_handler = pkg.build_system_flags
+        pkg.flag_handler = build_system_flags
         spack.build_environment.setup_package(pkg, False)
 
         assert 'SPACK_CPPFLAGS' not in os.environ
@@ -108,10 +91,10 @@ class TestFlagHandlers(object):
         assert set(pkg.cmake_flag_args) == expected
 
     def test_build_system_flags_autotools(self, temp_env):
-        s = spack.spec.Spec('libelf cppflags=-g')
+        s = spack.spec.Spec('patchelf cppflags=-g')
         s.concretize()
         pkg = spack.repo.get(s)
-        pkg.flag_handler = pkg.build_system_flags
+        pkg.flag_handler = build_system_flags
         spack.build_environment.setup_package(pkg, False)
 
         assert 'SPACK_CPPFLAGS' not in os.environ
@@ -123,7 +106,7 @@ class TestFlagHandlers(object):
         s = spack.spec.Spec('mpileaks cppflags=-g')
         s.concretize()
         pkg = spack.repo.get(s)
-        pkg.flag_handler = pkg.build_system_flags
+        pkg.flag_handler = build_system_flags
 
         # Test the command line flags method raises a NotImplementedError
         try:
@@ -133,10 +116,10 @@ class TestFlagHandlers(object):
             assert True
 
     def test_add_build_system_flags_autotools(self, temp_env):
-        s = spack.spec.Spec('libelf cppflags=-g')
+        s = spack.spec.Spec('patchelf cppflags=-g')
         s.concretize()
         pkg = spack.repo.get(s)
-        pkg.flag_handler = add_O3_to_build_system_cflags
+        pkg.flag_handler = add_o3_to_build_system_cflags
         spack.build_environment.setup_package(pkg, False)
 
         assert '-g' in os.environ['SPACK_CPPFLAGS']
@@ -145,10 +128,10 @@ class TestFlagHandlers(object):
         assert pkg.configure_flag_args == ['CFLAGS=-O3']
 
     def test_add_build_system_flags_cmake(self, temp_env):
-        s = spack.spec.Spec('callpath cppflags=-g')
+        s = spack.spec.Spec('cmake-client cppflags=-g')
         s.concretize()
         pkg = spack.repo.get(s)
-        pkg.flag_handler = add_O3_to_build_system_cflags
+        pkg.flag_handler = add_o3_to_build_system_cflags
         spack.build_environment.setup_package(pkg, False)
 
         assert '-g' in os.environ['SPACK_CPPFLAGS']
@@ -157,10 +140,10 @@ class TestFlagHandlers(object):
         assert pkg.cmake_flag_args == ['-DCMAKE_C_FLAGS=-O3']
 
     def test_ld_flags_cmake(self, temp_env):
-        s = spack.spec.Spec('callpath ldflags=-mthreads')
+        s = spack.spec.Spec('cmake-client ldflags=-mthreads')
         s.concretize()
         pkg = spack.repo.get(s)
-        pkg.flag_handler = pkg.build_system_flags
+        pkg.flag_handler = build_system_flags
         spack.build_environment.setup_package(pkg, False)
 
         assert 'SPACK_LDFLAGS' not in os.environ
@@ -173,10 +156,10 @@ class TestFlagHandlers(object):
         assert set(pkg.cmake_flag_args) == expected
 
     def test_ld_libs_cmake(self, temp_env):
-        s = spack.spec.Spec('callpath ldlibs=-lfoo')
+        s = spack.spec.Spec('cmake-client ldlibs=-lfoo')
         s.concretize()
         pkg = spack.repo.get(s)
-        pkg.flag_handler = pkg.build_system_flags
+        pkg.flag_handler = build_system_flags
         spack.build_environment.setup_package(pkg, False)
 
         assert 'SPACK_LDLIBS' not in os.environ
diff --git a/lib/spack/spack/test/git_fetch.py b/lib/spack/spack/test/git_fetch.py
index b28c553753..8171538756 100644
--- a/lib/spack/spack/test/git_fetch.py
+++ b/lib/spack/spack/test/git_fetch.py
@@ -1,32 +1,16 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 
 import pytest
-import spack
-from llnl.util.filesystem import working_dir, join_path, touch
+
+from llnl.util.filesystem import working_dir, touch
+
+import spack.repo
+import spack.config
 from spack.spec import Spec
 from spack.version import ver
 from spack.fetch_strategy import GitFetchStrategy
@@ -71,7 +55,7 @@ def test_fetch(type_of_test,
                secure,
                mock_git_repository,
                config,
-               refresh_builtin_mock,
+               mutable_mock_packages,
                git_version):
     """Tries to:
 
@@ -89,21 +73,18 @@ def test_fetch(type_of_test,
     # Construct the package under test
     spec = Spec('git-test')
     spec.concretize()
-    pkg = spack.repo.get(spec, new=True)
+    pkg = spack.repo.get(spec)
     pkg.versions[ver('git')] = t.args
 
     # Enter the stage directory and check some properties
     with pkg.stage:
-        try:
-            spack.insecure = secure
+        with spack.config.override('config:verify_ssl', secure):
             pkg.do_stage()
-        finally:
-            spack.insecure = False
 
         with working_dir(pkg.stage.source_path):
             assert h('HEAD') == h(t.revision)
 
-            file_path = join_path(pkg.stage.source_path, t.file)
+            file_path = os.path.join(pkg.stage.source_path, t.file)
             assert os.path.isdir(pkg.stage.source_path)
             assert os.path.isfile(file_path)
 
diff --git a/lib/spack/spack/test/graph.py b/lib/spack/spack/test/graph.py
index 7cd82c3a88..d1de8db8cb 100644
--- a/lib/spack/spack/test/graph.py
+++ b/lib/spack/spack/test/graph.py
@@ -1,34 +1,15 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from six import StringIO
 
 from spack.spec import Spec
 from spack.graph import AsciiGraph, topological_sort, graph_dot
 
 
-def test_topo_sort(builtin_mock):
+def test_topo_sort(mock_packages):
     """Test topo sort gives correct order."""
     s = Spec('mpileaks').normalized()
 
@@ -51,7 +32,7 @@ def test_topo_sort(builtin_mock):
     assert topo.index('libdwarf') < topo.index('libelf')
 
 
-def test_static_graph_mpileaks(builtin_mock):
+def test_static_graph_mpileaks(mock_packages):
     """Test a static spack graph for a simple package."""
     s = Spec('mpileaks').normalized()
 
@@ -75,7 +56,7 @@ def test_static_graph_mpileaks(builtin_mock):
     assert '  "dyninst" -> "libelf"\n'    in dot
 
 
-def test_dynamic_dot_graph_mpileaks(builtin_mock):
+def test_dynamic_dot_graph_mpileaks(mock_packages):
     """Test dynamically graphing the mpileaks package."""
     s = Spec('mpileaks').normalized()
 
@@ -111,7 +92,7 @@ def test_dynamic_dot_graph_mpileaks(builtin_mock):
     assert '  "%s" -> "%s"\n' % (dyninst_hash, libelf_hash)  in dot
 
 
-def test_ascii_graph_mpileaks(builtin_mock):
+def test_ascii_graph_mpileaks(mock_packages):
     """Test dynamically graphing the mpileaks package."""
     s = Spec('mpileaks').normalized()
 
diff --git a/lib/spack/spack/test/hg_fetch.py b/lib/spack/spack/test/hg_fetch.py
index 6a22502e86..b9fa6a1e6d 100644
--- a/lib/spack/spack/test/hg_fetch.py
+++ b/lib/spack/spack/test/hg_fetch.py
@@ -1,32 +1,16 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 
 import pytest
-import spack
-from llnl.util.filesystem import working_dir, join_path, touch
+
+from llnl.util.filesystem import working_dir, touch
+
+import spack.repo
+import spack.config
 from spack.spec import Spec
 from spack.version import ver
 from spack.util.executable import which
@@ -43,7 +27,7 @@ def test_fetch(
         secure,
         mock_hg_repository,
         config,
-        refresh_builtin_mock
+        mutable_mock_packages
 ):
     """Tries to:
 
@@ -61,21 +45,18 @@ def test_fetch(
     # Construct the package under test
     spec = Spec('hg-test')
     spec.concretize()
-    pkg = spack.repo.get(spec, new=True)
+    pkg = spack.repo.get(spec)
     pkg.versions[ver('hg')] = t.args
 
     # Enter the stage directory and check some properties
     with pkg.stage:
-        try:
-            spack.insecure = secure
+        with spack.config.override('config:verify_ssl', secure):
             pkg.do_stage()
-        finally:
-            spack.insecure = False
 
         with working_dir(pkg.stage.source_path):
             assert h() == t.revision
 
-            file_path = join_path(pkg.stage.source_path, t.file)
+            file_path = os.path.join(pkg.stage.source_path, t.file)
             assert os.path.isdir(pkg.stage.source_path)
             assert os.path.isfile(file_path)
 
diff --git a/lib/spack/spack/test/install.py b/lib/spack/spack/test/install.py
index 86b95459f4..a63c149d3d 100644
--- a/lib/spack/spack/test/install.py
+++ b/lib/spack/spack/test/install.py
@@ -1,31 +1,12 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 import pytest
 
-import spack
+import spack.repo
 import spack.store
 from spack.spec import Spec
 
@@ -132,7 +113,7 @@ def test_dont_add_patches_to_installed_package(install_mockery, mock_fetch):
 
 
 def test_installed_dependency_request_conflicts(
-        install_mockery, mock_fetch, refresh_builtin_mock):
+        install_mockery, mock_fetch, mutable_mock_packages):
     dependency = Spec('dependency-install')
     dependency.concretize()
     dependency.package.do_install()
diff --git a/lib/spack/spack/test/llnl/util/file_list.py b/lib/spack/spack/test/llnl/util/file_list.py
index f7d5dde4d3..e54e479e14 100644
--- a/lib/spack/spack/test/llnl/util/file_list.py
+++ b/lib/spack/spack/test/llnl/util/file_list.py
@@ -1,36 +1,18 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-import fnmatch
 import os
+import fnmatch
 
-import pytest
 import six
-import spack
+import pytest
+
 from llnl.util.filesystem import LibraryList, HeaderList
-from llnl.util.filesystem import find_libraries, find_headers
+from llnl.util.filesystem import find_libraries, find_headers, find
+
+import spack.paths
 
 
 @pytest.fixture()
@@ -211,40 +193,44 @@ class TestHeaderList(object):
 
 
 #: Directory where the data for the test below is stored
-search_dir = os.path.join(spack.test_path, 'data', 'directory_search')
+search_dir = os.path.join(spack.paths.test_path, 'data', 'directory_search')
 
 
 @pytest.mark.parametrize('search_fn,search_list,root,kwargs', [
-    (find_libraries, 'liba', search_dir, {'recurse': True}),
-    (find_libraries, ['liba'], search_dir, {'recurse': True}),
-    (find_libraries, 'libb', search_dir, {'recurse': True}),
-    (find_libraries, ['libc'], search_dir, {'recurse': True}),
-    (find_libraries, ['libc', 'liba'], search_dir, {'recurse': True}),
-    (find_libraries, ['liba', 'libc'], search_dir, {'recurse': True}),
-    (find_libraries, ['libc', 'libb', 'liba'], search_dir, {'recurse': True}),
-    (find_libraries, ['liba', 'libc'], search_dir, {'recurse': True}),
+    (find_libraries, 'liba', search_dir, {'recursive': True}),
+    (find_libraries, ['liba'], search_dir, {'recursive': True}),
+    (find_libraries, 'libb', search_dir, {'recursive': True}),
+    (find_libraries, ['libc'], search_dir, {'recursive': True}),
+    (find_libraries, ['libc', 'liba'], search_dir, {'recursive': True}),
+    (find_libraries, ['liba', 'libc'], search_dir, {'recursive': True}),
     (find_libraries,
      ['libc', 'libb', 'liba'],
      search_dir,
-     {'recurse': True, 'shared': False}
+     {'recursive': True}
      ),
-    (find_headers, 'a', search_dir, {'recurse': True}),
-    (find_headers, ['a'], search_dir, {'recurse': True}),
-    (find_headers, 'b', search_dir, {'recurse': True}),
-    (find_headers, ['c'], search_dir, {'recurse': True}),
-    (find_headers, ['c', 'a'], search_dir, {'recurse': True}),
-    (find_headers, ['a', 'c'], search_dir, {'recurse': True}),
-    (find_headers, ['c', 'b', 'a'], search_dir, {'recurse': True}),
-    (find_headers, ['a', 'c'], search_dir, {'recurse': True}),
+    (find_libraries, ['liba', 'libc'], search_dir, {'recursive': True}),
+    (find_libraries,
+     ['libc', 'libb', 'liba'],
+     search_dir,
+     {'recursive': True, 'shared': False}
+     ),
+    (find_headers, 'a', search_dir, {'recursive': True}),
+    (find_headers, ['a'], search_dir, {'recursive': True}),
+    (find_headers, 'b', search_dir, {'recursive': True}),
+    (find_headers, ['c'], search_dir, {'recursive': True}),
+    (find_headers, ['c', 'a'], search_dir, {'recursive': True}),
+    (find_headers, ['a', 'c'], search_dir, {'recursive': True}),
+    (find_headers, ['c', 'b', 'a'], search_dir, {'recursive': True}),
+    (find_headers, ['a', 'c'], search_dir, {'recursive': True}),
     (find_libraries,
      ['liba', 'libd'],
      os.path.join(search_dir, 'b'),
-     {'recurse': False}
+     {'recursive': False}
      ),
     (find_headers,
      ['b', 'd'],
      os.path.join(search_dir, 'b'),
-     {'recurse': False}
+     {'recursive': False}
      ),
 ])
 def test_searching_order(search_fn, search_list, root, kwargs):
@@ -258,7 +244,7 @@ def test_searching_order(search_fn, search_list, root, kwargs):
     # Now reverse the result and start discarding things
     # as soon as you have matches. In the end the list should
     # be emptied.
-    L = list(reversed(result))
+    rlist = list(reversed(result))
 
     # At this point make sure the search list is a sequence
     if isinstance(search_list, six.string_types):
@@ -267,11 +253,28 @@ def test_searching_order(search_fn, search_list, root, kwargs):
     # Discard entries in the order they appear in search list
     for x in search_list:
         try:
-            while fnmatch.fnmatch(L[-1], x) or x in L[-1]:
-                L.pop()
+            while fnmatch.fnmatch(rlist[-1], x) or x in rlist[-1]:
+                rlist.pop()
         except IndexError:
             # List is empty
             pass
 
     # List should be empty here
-    assert len(L) == 0
+    assert len(rlist) == 0
+
+
+@pytest.mark.parametrize('root,search_list,kwargs,expected', [
+    (search_dir, '*/*bar.tx?', {'recursive': False}, [
+        os.path.join(search_dir, 'a/foobar.txt'),
+        os.path.join(search_dir, 'b/bar.txp'),
+        os.path.join(search_dir, 'c/bar.txt'),
+    ]),
+    (search_dir, '*/*bar.tx?', {'recursive': True}, [
+        os.path.join(search_dir, 'a/foobar.txt'),
+        os.path.join(search_dir, 'b/bar.txp'),
+        os.path.join(search_dir, 'c/bar.txt'),
+    ])
+])
+def test_find_with_globbing(root, search_list, kwargs, expected):
+    matches = find(root, search_list, **kwargs)
+    assert sorted(matches) == sorted(expected)
diff --git a/lib/spack/spack/test/llnl/util/filesystem.py b/lib/spack/spack/test/llnl/util/filesystem.py
new file mode 100644
index 0000000000..33857854fe
--- /dev/null
+++ b/lib/spack/spack/test/llnl/util/filesystem.py
@@ -0,0 +1,217 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+"""Tests for ``llnl/util/filesystem.py``"""
+
+import llnl.util.filesystem as fs
+import os
+import stat
+import pytest
+
+
+@pytest.fixture()
+def stage(tmpdir_factory):
+    """Creates a stage with the directory structure for the tests."""
+
+    s = tmpdir_factory.mktemp('filesystem_test')
+
+    with s.as_cwd():
+        # Create source file hierarchy
+        fs.touchp('source/1')
+        fs.touchp('source/a/b/2')
+        fs.touchp('source/a/b/3')
+        fs.touchp('source/c/4')
+        fs.touchp('source/c/d/5')
+        fs.touchp('source/c/d/6')
+        fs.touchp('source/c/d/e/7')
+
+        # Create symlinks
+        os.symlink(os.path.abspath('source/1'), 'source/2')
+        os.symlink('b/2', 'source/a/b2')
+        os.symlink('a/b', 'source/f')
+
+        # Create destination directory
+        fs.mkdirp('dest')
+
+    yield s
+
+
+class TestCopy:
+    """Tests for ``filesystem.copy``"""
+
+    def test_file_dest(self, stage):
+        """Test using a filename as the destination."""
+
+        with fs.working_dir(str(stage)):
+            fs.copy('source/1', 'dest/1')
+
+            assert os.path.exists('dest/1')
+
+    def test_dir_dest(self, stage):
+        """Test using a directory as the destination."""
+
+        with fs.working_dir(str(stage)):
+            fs.copy('source/1', 'dest')
+
+            assert os.path.exists('dest/1')
+
+
+def check_added_exe_permissions(src, dst):
+    src_mode = os.stat(src).st_mode
+    dst_mode = os.stat(dst).st_mode
+    for perm in [stat.S_IXUSR, stat.S_IXGRP, stat.S_IXOTH]:
+        if src_mode & perm:
+            assert dst_mode & perm
+
+
+class TestInstall:
+    """Tests for ``filesystem.install``"""
+
+    def test_file_dest(self, stage):
+        """Test using a filename as the destination."""
+
+        with fs.working_dir(str(stage)):
+            fs.install('source/1', 'dest/1')
+
+            assert os.path.exists('dest/1')
+            check_added_exe_permissions('source/1', 'dest/1')
+
+    def test_dir_dest(self, stage):
+        """Test using a directory as the destination."""
+
+        with fs.working_dir(str(stage)):
+            fs.install('source/1', 'dest')
+
+            assert os.path.exists('dest/1')
+            check_added_exe_permissions('source/1', 'dest/1')
+
+
+class TestCopyTree:
+    """Tests for ``filesystem.copy_tree``"""
+
+    def test_existing_dir(self, stage):
+        """Test copying to an existing directory."""
+
+        with fs.working_dir(str(stage)):
+            fs.copy_tree('source', 'dest')
+
+            assert os.path.exists('dest/a/b/2')
+
+    def test_non_existing_dir(self, stage):
+        """Test copying to a non-existing directory."""
+
+        with fs.working_dir(str(stage)):
+            fs.copy_tree('source', 'dest/sub/directory')
+
+            assert os.path.exists('dest/sub/directory/a/b/2')
+
+    def test_symlinks_true(self, stage):
+        """Test copying with symlink preservation."""
+
+        with fs.working_dir(str(stage)):
+            fs.copy_tree('source', 'dest', symlinks=True)
+
+            assert os.path.exists('dest/2')
+            assert os.path.islink('dest/2')
+
+            assert os.path.exists('dest/a/b2')
+            with fs.working_dir('dest/a'):
+                assert os.path.exists(os.readlink('b2'))
+
+            assert (os.path.realpath('dest/f/2') ==
+                    os.path.abspath('dest/a/b/2'))
+            assert os.path.realpath('dest/2') == os.path.abspath('dest/1')
+
+    def test_symlinks_true_ignore(self, stage):
+        """Test copying when specifying relative paths that should be ignored
+        """
+        with fs.working_dir(str(stage)):
+            ignore = lambda p: p in ['c/d/e', 'a']
+            fs.copy_tree('source', 'dest', symlinks=True, ignore=ignore)
+            assert not os.path.exists('dest/a')
+            assert os.path.exists('dest/c/d')
+            assert not os.path.exists('dest/c/d/e')
+
+    def test_symlinks_false(self, stage):
+        """Test copying without symlink preservation."""
+
+        with fs.working_dir(str(stage)):
+            fs.copy_tree('source', 'dest', symlinks=False)
+
+            assert os.path.exists('dest/2')
+            assert not os.path.islink('dest/2')
+
+
+class TestInstallTree:
+    """Tests for ``filesystem.install_tree``"""
+
+    def test_existing_dir(self, stage):
+        """Test installing to an existing directory."""
+
+        with fs.working_dir(str(stage)):
+            fs.install_tree('source', 'dest')
+
+            assert os.path.exists('dest/a/b/2')
+
+    def test_non_existing_dir(self, stage):
+        """Test installing to a non-existing directory."""
+
+        with fs.working_dir(str(stage)):
+            fs.install_tree('source', 'dest/sub/directory')
+
+            assert os.path.exists('dest/sub/directory/a/b/2')
+
+    def test_symlinks_true(self, stage):
+        """Test installing with symlink preservation."""
+
+        with fs.working_dir(str(stage)):
+            fs.install_tree('source', 'dest', symlinks=True)
+
+            assert os.path.exists('dest/2')
+            assert os.path.islink('dest/2')
+
+    def test_symlinks_false(self, stage):
+        """Test installing without symlink preservation."""
+
+        with fs.working_dir(str(stage)):
+            fs.install_tree('source', 'dest', symlinks=False)
+
+            assert os.path.exists('dest/2')
+            assert not os.path.islink('dest/2')
+
+
+def test_move_transaction_commit(tmpdir):
+
+    fake_library = tmpdir.mkdir('lib').join('libfoo.so')
+    fake_library.write('Just some fake content.')
+
+    old_md5 = fs.hash_directory(str(tmpdir))
+
+    with fs.replace_directory_transaction(str(tmpdir.join('lib'))):
+        fake_library = tmpdir.mkdir('lib').join('libfoo.so')
+        fake_library.write('Other content.')
+        new_md5 = fs.hash_directory(str(tmpdir))
+
+    assert old_md5 != fs.hash_directory(str(tmpdir))
+    assert new_md5 == fs.hash_directory(str(tmpdir))
+
+
+def test_move_transaction_rollback(tmpdir):
+
+    fake_library = tmpdir.mkdir('lib').join('libfoo.so')
+    fake_library.write('Just some fake content.')
+
+    h = fs.hash_directory(str(tmpdir))
+
+    try:
+        with fs.replace_directory_transaction(str(tmpdir.join('lib'))):
+            assert h != fs.hash_directory(str(tmpdir))
+            fake_library = tmpdir.mkdir('lib').join('libfoo.so')
+            fake_library.write('Other content.')
+            raise RuntimeError('')
+    except RuntimeError:
+        pass
+
+    assert h == fs.hash_directory(str(tmpdir))
diff --git a/lib/spack/spack/test/llnl/util/lang.py b/lib/spack/spack/test/llnl/util/lang.py
index 37dc01ce53..eec75f036f 100644
--- a/lib/spack/spack/test/llnl/util/lang.py
+++ b/lib/spack/spack/test/llnl/util/lang.py
@@ -1,33 +1,21 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import pytest
+
 from datetime import datetime, timedelta
 
+import llnl.util.lang
 from llnl.util.lang import pretty_date, match_predicate
 
 
+@pytest.fixture()
+def now():
+    return datetime.now()
+
+
 def test_pretty_date():
     """Make sure pretty_date prints the right dates."""
     now = datetime.now()
@@ -75,6 +63,32 @@ def test_pretty_date():
     assert pretty_date(years, now) == "2 years ago"
 
 
+@pytest.mark.parametrize('delta,pretty_string', [
+    (timedelta(days=1), 'a day ago'),
+    (timedelta(days=1), 'yesterday'),
+    (timedelta(days=1), '1 day ago'),
+    (timedelta(weeks=1), '1 week ago'),
+    (timedelta(weeks=3), '3 weeks ago'),
+    (timedelta(days=30), '1 month ago'),
+    (timedelta(days=730), '2 years  ago'),
+])
+def test_pretty_string_to_date_delta(now, delta, pretty_string):
+    t1 = now - delta
+    t2 = llnl.util.lang.pretty_string_to_date(pretty_string, now)
+    assert t1 == t2
+
+
+@pytest.mark.parametrize('format,pretty_string', [
+    ('%Y', '2018'),
+    ('%Y-%m', '2015-03'),
+    ('%Y-%m-%d', '2015-03-28'),
+])
+def test_pretty_string_to_date(format, pretty_string):
+    t1 = datetime.strptime(pretty_string, format)
+    t2 = llnl.util.lang.pretty_string_to_date(pretty_string, now)
+    assert t1 == t2
+
+
 def test_match_predicate():
     matcher = match_predicate(lambda x: True)
     assert matcher('foo')
diff --git a/lib/spack/spack/test/llnl/util/link_tree.py b/lib/spack/spack/test/llnl/util/link_tree.py
index 59af3b8ad4..0c526512f9 100644
--- a/lib/spack/spack/test/llnl/util/link_tree.py
+++ b/lib/spack/spack/test/llnl/util/link_tree.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 
 import pytest
diff --git a/lib/spack/spack/test/llnl/util/lock.py b/lib/spack/spack/test/llnl/util/lock.py
index 0574adff51..1991c9640b 100644
--- a/lib/spack/spack/test/llnl/util/lock.py
+++ b/lib/spack/spack/test/llnl/util/lock.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """These tests ensure that our lock works correctly.
 
 This can be run in two ways.
@@ -62,19 +43,20 @@ actually on a shared filesystem.
 
 """
 import os
+import socket
 import shutil
 import tempfile
 import traceback
 import glob
 import getpass
 from contextlib import contextmanager
-from multiprocessing import Process
+from multiprocessing import Process, Queue
 
 import pytest
 
-from llnl.util.filesystem import join_path, touch
-from spack.util.multiproc import Barrier
-from llnl.util.lock import Lock, WriteTransaction, ReadTransaction, LockError
+import llnl.util.lock as lk
+import llnl.util.multiproc as mp
+from llnl.util.filesystem import touch
 
 
 #
@@ -127,12 +109,27 @@ This may need to be higher for some filesystems."""
 lock_fail_timeout = 0.1
 
 
+def make_readable(*paths):
+    for path in paths:
+        mode = 0o555 if os.path.isdir(path) else 0o444
+        os.chmod(path, mode)
+
+
+def make_writable(*paths):
+    for path in paths:
+        mode = 0o755 if os.path.isdir(path) else 0o744
+        os.chmod(path, mode)
+
+
 @contextmanager
-def read_only(path):
-    orginal_mode = os.stat(path).st_mode
-    os.chmod(path, 0o444)
+def read_only(*paths):
+    modes = [os.stat(p).st_mode for p in paths]
+    make_readable(*paths)
+
     yield
-    os.chmod(path, orginal_mode)
+
+    for path, mode in zip(paths, modes):
+        os.chmod(path, mode)
 
 
 @pytest.fixture(scope='session', params=locations)
@@ -171,6 +168,7 @@ def lock_dir(lock_test_directory):
         comm.barrier()
 
     if not mpi or comm.rank == 0:
+        make_writable(tempdir)
         shutil.rmtree(tempdir)
 
 
@@ -180,30 +178,51 @@ def private_lock_path(lock_dir):
 
     For other modes, it is the same as a shared lock.
     """
-    lock_file = join_path(lock_dir, 'lockfile')
+    lock_file = os.path.join(lock_dir, 'lockfile')
     if mpi:
         lock_file += '.%s' % comm.rank
+
     yield lock_file
 
+    if os.path.exists(lock_file):
+        make_writable(lock_dir, lock_file)
+        os.unlink(lock_file)
+
 
 @pytest.fixture
 def lock_path(lock_dir):
     """This lock is shared among all processes in a multiproc test."""
-    lock_file = join_path(lock_dir, 'lockfile')
+    lock_file = os.path.join(lock_dir, 'lockfile')
+
     yield lock_file
 
+    if os.path.exists(lock_file):
+        make_writable(lock_dir, lock_file)
+        os.unlink(lock_file)
+
+
+def test_poll_interval_generator():
+    interval_iter = iter(
+        lk.Lock._poll_interval_generator(_wait_times=[1, 2, 3]))
+    intervals = list(next(interval_iter) for i in range(100))
+    assert intervals == [1] * 20 + [2] * 40 + [3] * 40
 
-def local_multiproc_test(*functions):
+
+def local_multiproc_test(*functions, **kwargs):
     """Order some processes using simple barrier synchronization."""
-    b = Barrier(len(functions), timeout=barrier_timeout)
-    procs = [Process(target=f, args=(b,)) for f in functions]
+    b = mp.Barrier(len(functions), timeout=barrier_timeout)
+
+    args = (b,) + tuple(kwargs.get('extra_args', ()))
+    procs = [Process(target=f, args=args, name=f.__name__)
+             for f in functions]
 
     for p in procs:
         p.start()
 
     for p in procs:
         p.join()
-        assert p.exitcode == 0
+
+    assert all(p.exitcode == 0 for p in procs)
 
 
 def mpi_multiproc_test(*functions):
@@ -257,7 +276,7 @@ multiproc_test = mpi_multiproc_test if mpi else local_multiproc_test
 #
 def acquire_write(lock_path, start=0, length=0):
     def fn(barrier):
-        lock = Lock(lock_path, start, length)
+        lock = lk.Lock(lock_path, start, length)
         lock.acquire_write()  # grab exclusive lock
         barrier.wait()
         barrier.wait()  # hold the lock until timeout in other procs.
@@ -266,7 +285,7 @@ def acquire_write(lock_path, start=0, length=0):
 
 def acquire_read(lock_path, start=0, length=0):
     def fn(barrier):
-        lock = Lock(lock_path, start, length)
+        lock = lk.Lock(lock_path, start, length)
         lock.acquire_read()  # grab shared lock
         barrier.wait()
         barrier.wait()  # hold the lock until timeout in other procs.
@@ -275,9 +294,9 @@ def acquire_read(lock_path, start=0, length=0):
 
 def timeout_write(lock_path, start=0, length=0):
     def fn(barrier):
-        lock = Lock(lock_path, start, length)
+        lock = lk.Lock(lock_path, start, length)
         barrier.wait()  # wait for lock acquire in first process
-        with pytest.raises(LockError):
+        with pytest.raises(lk.LockTimeoutError):
             lock.acquire_write(lock_fail_timeout)
         barrier.wait()
     return fn
@@ -285,9 +304,9 @@ def timeout_write(lock_path, start=0, length=0):
 
 def timeout_read(lock_path, start=0, length=0):
     def fn(barrier):
-        lock = Lock(lock_path, start, length)
+        lock = lk.Lock(lock_path, start, length)
         barrier.wait()  # wait for lock acquire in first process
-        with pytest.raises(LockError):
+        with pytest.raises(lk.LockTimeoutError):
             lock.acquire_read(lock_fail_timeout)
         barrier.wait()
     return fn
@@ -527,9 +546,47 @@ def test_write_lock_timeout_with_multiple_readers_3_2_ranges(lock_path):
         timeout_write(lock_path, 5, 1))
 
 
-#
-# Test that read can be upgraded to write.
-#
+def test_read_lock_on_read_only_lockfile(lock_dir, lock_path):
+    """read-only directory, read-only lockfile."""
+    touch(lock_path)
+    with read_only(lock_path, lock_dir):
+        lock = lk.Lock(lock_path)
+
+        with lk.ReadTransaction(lock):
+            pass
+
+        with pytest.raises(lk.LockROFileError):
+            with lk.WriteTransaction(lock):
+                pass
+
+
+def test_read_lock_read_only_dir_writable_lockfile(lock_dir, lock_path):
+    """read-only directory, writable lockfile."""
+    touch(lock_path)
+    with read_only(lock_dir):
+        lock = lk.Lock(lock_path)
+
+        with lk.ReadTransaction(lock):
+            pass
+
+        with lk.WriteTransaction(lock):
+            pass
+
+
+def test_read_lock_no_lockfile(lock_dir, lock_path):
+    """read-only directory, no lockfile (so can't create)."""
+    with read_only(lock_dir):
+        lock = lk.Lock(lock_path)
+
+        with pytest.raises(lk.CantCreateLockError):
+            with lk.ReadTransaction(lock):
+                pass
+
+        with pytest.raises(lk.CantCreateLockError):
+            with lk.WriteTransaction(lock):
+                pass
+
+
 def test_upgrade_read_to_write(private_lock_path):
     """Test that a read lock can be upgraded to a write lock.
 
@@ -542,7 +599,7 @@ def test_upgrade_read_to_write(private_lock_path):
     # to begin wtih.
     touch(private_lock_path)
 
-    lock = Lock(private_lock_path)
+    lock = lk.Lock(private_lock_path)
     assert lock._reads == 0
     assert lock._writes == 0
 
@@ -567,16 +624,14 @@ def test_upgrade_read_to_write(private_lock_path):
     assert lock._file is None
 
 
-#
-# Test that read-only file can be read-locked but not write-locked.
-#
 def test_upgrade_read_to_write_fails_with_readonly_file(private_lock_path):
-    # ensure lock file exists the first time, so we open it read-only
-    # to begin wtih.
+    """Test that read-only file can be read-locked but not write-locked."""
+    # ensure lock file exists the first time
     touch(private_lock_path)
 
+    # open it read-only to begin wtih.
     with read_only(private_lock_path):
-        lock = Lock(private_lock_path)
+        lock = lk.Lock(private_lock_path)
         assert lock._reads == 0
         assert lock._writes == 0
 
@@ -585,7 +640,8 @@ def test_upgrade_read_to_write_fails_with_readonly_file(private_lock_path):
         assert lock._writes == 0
         assert lock._file.mode == 'r'
 
-        with pytest.raises(LockError):
+        # upgrade to writ here
+        with pytest.raises(lk.LockROFileError):
             lock.acquire_write()
 
 
@@ -595,7 +651,7 @@ def test_upgrade_read_to_write_fails_with_readonly_file(private_lock_path):
 #
 def test_complex_acquire_and_release_chain(lock_path):
     def p1(barrier):
-        lock = Lock(lock_path)
+        lock = lk.Lock(lock_path)
 
         lock.acquire_write()
         barrier.wait()  # ---------------------------------------- 1
@@ -603,7 +659,7 @@ def test_complex_acquire_and_release_chain(lock_path):
         barrier.wait()  # ---------------------------------------- 2
         lock.release_write()   # release and others acquire read
         barrier.wait()  # ---------------------------------------- 3
-        with pytest.raises(LockError):
+        with pytest.raises(lk.LockTimeoutError):
             lock.acquire_write(lock_fail_timeout)
         lock.acquire_read()
         barrier.wait()  # ---------------------------------------- 4
@@ -612,9 +668,9 @@ def test_complex_acquire_and_release_chain(lock_path):
 
         # p2 upgrades read to write
         barrier.wait()  # ---------------------------------------- 6
-        with pytest.raises(LockError):
+        with pytest.raises(lk.LockTimeoutError):
             lock.acquire_write(lock_fail_timeout)
-        with pytest.raises(LockError):
+        with pytest.raises(lk.LockTimeoutError):
             lock.acquire_read(lock_fail_timeout)
         barrier.wait()  # ---------------------------------------- 7
         # p2 releases write and read
@@ -624,9 +680,9 @@ def test_complex_acquire_and_release_chain(lock_path):
         barrier.wait()  # ---------------------------------------- 9
         # p3 upgrades read to write
         barrier.wait()  # ---------------------------------------- 10
-        with pytest.raises(LockError):
+        with pytest.raises(lk.LockTimeoutError):
             lock.acquire_write(lock_fail_timeout)
-        with pytest.raises(LockError):
+        with pytest.raises(lk.LockTimeoutError):
             lock.acquire_read(lock_fail_timeout)
         barrier.wait()  # ---------------------------------------- 11
         # p3 releases locks
@@ -636,13 +692,13 @@ def test_complex_acquire_and_release_chain(lock_path):
         lock.release_read()
 
     def p2(barrier):
-        lock = Lock(lock_path)
+        lock = lk.Lock(lock_path)
 
         # p1 acquires write
         barrier.wait()  # ---------------------------------------- 1
-        with pytest.raises(LockError):
+        with pytest.raises(lk.LockTimeoutError):
             lock.acquire_write(lock_fail_timeout)
-        with pytest.raises(LockError):
+        with pytest.raises(lk.LockTimeoutError):
             lock.acquire_read(lock_fail_timeout)
         barrier.wait()  # ---------------------------------------- 2
         lock.acquire_read()
@@ -664,9 +720,9 @@ def test_complex_acquire_and_release_chain(lock_path):
         barrier.wait()  # ---------------------------------------- 9
         # p3 upgrades read to write
         barrier.wait()  # ---------------------------------------- 10
-        with pytest.raises(LockError):
+        with pytest.raises(lk.LockTimeoutError):
             lock.acquire_write(lock_fail_timeout)
-        with pytest.raises(LockError):
+        with pytest.raises(lk.LockTimeoutError):
             lock.acquire_read(lock_fail_timeout)
         barrier.wait()  # ---------------------------------------- 11
         # p3 releases locks
@@ -676,13 +732,13 @@ def test_complex_acquire_and_release_chain(lock_path):
         lock.release_read()
 
     def p3(barrier):
-        lock = Lock(lock_path)
+        lock = lk.Lock(lock_path)
 
         # p1 acquires write
         barrier.wait()  # ---------------------------------------- 1
-        with pytest.raises(LockError):
+        with pytest.raises(lk.LockTimeoutError):
             lock.acquire_write(lock_fail_timeout)
-        with pytest.raises(LockError):
+        with pytest.raises(lk.LockTimeoutError):
             lock.acquire_read(lock_fail_timeout)
         barrier.wait()  # ---------------------------------------- 2
         lock.acquire_read()
@@ -694,9 +750,9 @@ def test_complex_acquire_and_release_chain(lock_path):
 
         # p2 upgrades read to write
         barrier.wait()  # ---------------------------------------- 6
-        with pytest.raises(LockError):
+        with pytest.raises(lk.LockTimeoutError):
             lock.acquire_write(lock_fail_timeout)
-        with pytest.raises(LockError):
+        with pytest.raises(lk.LockTimeoutError):
             lock.acquire_read(lock_fail_timeout)
         barrier.wait()  # ---------------------------------------- 7
         # p2 releases write & read
@@ -726,9 +782,9 @@ def test_transaction(lock_path):
         vals['exited'] = True
         vals['exception'] = (t or v or tb)
 
-    lock = Lock(lock_path)
+    lock = lk.Lock(lock_path)
     vals = {'entered': False, 'exited': False, 'exception': False}
-    with ReadTransaction(lock, enter_fn, exit_fn):
+    with lk.ReadTransaction(lock, enter_fn, exit_fn):
         pass
 
     assert vals['entered']
@@ -736,7 +792,7 @@ def test_transaction(lock_path):
     assert not vals['exception']
 
     vals = {'entered': False, 'exited': False, 'exception': False}
-    with WriteTransaction(lock, enter_fn, exit_fn):
+    with lk.WriteTransaction(lock, enter_fn, exit_fn):
         pass
 
     assert vals['entered']
@@ -752,14 +808,14 @@ def test_transaction_with_exception(lock_path):
         vals['exited'] = True
         vals['exception'] = (t or v or tb)
 
-    lock = Lock(lock_path)
+    lock = lk.Lock(lock_path)
 
     def do_read_with_exception():
-        with ReadTransaction(lock, enter_fn, exit_fn):
+        with lk.ReadTransaction(lock, enter_fn, exit_fn):
             raise Exception()
 
     def do_write_with_exception():
-        with WriteTransaction(lock, enter_fn, exit_fn):
+        with lk.WriteTransaction(lock, enter_fn, exit_fn):
             raise Exception()
 
     vals = {'entered': False, 'exited': False, 'exception': False}
@@ -791,11 +847,11 @@ def test_transaction_with_context_manager(lock_path):
         vals['exited_fn'] = True
         vals['exception_fn'] = (t or v or tb)
 
-    lock = Lock(lock_path)
+    lock = lk.Lock(lock_path)
 
     vals = {'entered': False, 'exited': False, 'exited_fn': False,
             'exception': False, 'exception_fn': False}
-    with ReadTransaction(lock, TestContextManager, exit_fn):
+    with lk.ReadTransaction(lock, TestContextManager, exit_fn):
         pass
 
     assert vals['entered']
@@ -806,7 +862,7 @@ def test_transaction_with_context_manager(lock_path):
 
     vals = {'entered': False, 'exited': False, 'exited_fn': False,
             'exception': False, 'exception_fn': False}
-    with ReadTransaction(lock, TestContextManager):
+    with lk.ReadTransaction(lock, TestContextManager):
         pass
 
     assert vals['entered']
@@ -817,7 +873,7 @@ def test_transaction_with_context_manager(lock_path):
 
     vals = {'entered': False, 'exited': False, 'exited_fn': False,
             'exception': False, 'exception_fn': False}
-    with WriteTransaction(lock, TestContextManager, exit_fn):
+    with lk.WriteTransaction(lock, TestContextManager, exit_fn):
         pass
 
     assert vals['entered']
@@ -828,7 +884,7 @@ def test_transaction_with_context_manager(lock_path):
 
     vals = {'entered': False, 'exited': False, 'exited_fn': False,
             'exception': False, 'exception_fn': False}
-    with WriteTransaction(lock, TestContextManager):
+    with lk.WriteTransaction(lock, TestContextManager):
         pass
 
     assert vals['entered']
@@ -851,14 +907,14 @@ def test_transaction_with_context_manager_and_exception(lock_path):
         vals['exited_fn'] = True
         vals['exception_fn'] = (t or v or tb)
 
-    lock = Lock(lock_path)
+    lock = lk.Lock(lock_path)
 
     def do_read_with_exception(exit_fn):
-        with ReadTransaction(lock, TestContextManager, exit_fn):
+        with lk.ReadTransaction(lock, TestContextManager, exit_fn):
             raise Exception()
 
     def do_write_with_exception(exit_fn):
-        with WriteTransaction(lock, TestContextManager, exit_fn):
+        with lk.WriteTransaction(lock, TestContextManager, exit_fn):
             raise Exception()
 
     vals = {'entered': False, 'exited': False, 'exited_fn': False,
@@ -900,3 +956,102 @@ def test_transaction_with_context_manager_and_exception(lock_path):
     assert vals['exception']
     assert not vals['exited_fn']
     assert not vals['exception_fn']
+
+
+def test_lock_debug_output(lock_path):
+    host = socket.getfqdn()
+
+    def p1(barrier, q1, q2):
+        # exchange pids
+        p1_pid = os.getpid()
+        q1.put(p1_pid)
+        p2_pid = q2.get()
+
+        # set up lock
+        lock = lk.Lock(lock_path, debug=True)
+
+        with lk.WriteTransaction(lock):
+            # p1 takes write lock and writes pid/host to file
+            barrier.wait()  # ------------------------------------ 1
+
+        assert lock.pid == p1_pid
+        assert lock.host == host
+
+        # wait for p2 to verify contents of file
+        barrier.wait()  # ---------------------------------------- 2
+
+        # wait for p2 to take a write lock
+        barrier.wait()  # ---------------------------------------- 3
+
+        # verify pid/host info again
+        with lk.ReadTransaction(lock):
+            assert lock.old_pid == p1_pid
+            assert lock.old_host == host
+
+            assert lock.pid == p2_pid
+            assert lock.host == host
+
+        barrier.wait()  # ---------------------------------------- 4
+
+    def p2(barrier, q1, q2):
+        # exchange pids
+        p2_pid = os.getpid()
+        p1_pid = q1.get()
+        q2.put(p2_pid)
+
+        # set up lock
+        lock = lk.Lock(lock_path, debug=True)
+
+        # p1 takes write lock and writes pid/host to file
+        barrier.wait()  # ---------------------------------------- 1
+
+        # verify that p1 wrote information to lock file
+        with lk.ReadTransaction(lock):
+            assert lock.pid == p1_pid
+            assert lock.host == host
+
+        barrier.wait()  # ---------------------------------------- 2
+
+        # take a write lock on the file and verify pid/host info
+        with lk.WriteTransaction(lock):
+            assert lock.old_pid == p1_pid
+            assert lock.old_host == host
+
+            assert lock.pid == p2_pid
+            assert lock.host == host
+
+            barrier.wait()  # ------------------------------------ 3
+
+        # wait for p1 to verify pid/host info
+        barrier.wait()  # ---------------------------------------- 4
+
+    q1, q2 = Queue(), Queue()
+    local_multiproc_test(p2, p1, extra_args=(q1, q2))
+
+
+def test_lock_with_no_parent_directory(tmpdir):
+    """Make sure locks work even when their parent directory does not exist."""
+    with tmpdir.as_cwd():
+        lock = lk.Lock('foo/bar/baz/lockfile')
+        with lk.WriteTransaction(lock):
+            pass
+
+
+def test_lock_in_current_directory(tmpdir):
+    """Make sure locks work even when their parent directory does not exist."""
+    with tmpdir.as_cwd():
+        # test we can create a lock in the current directory
+        lock = lk.Lock('lockfile')
+        for i in range(10):
+            with lk.ReadTransaction(lock):
+                pass
+            with lk.WriteTransaction(lock):
+                pass
+
+        # and that we can do the same thing after it's already there
+        lock = lk.Lock('lockfile')
+        for i in range(10):
+            with lk.ReadTransaction(lock):
+                pass
+            with lk.WriteTransaction(lock):
+                pass
diff --git a/lib/spack/spack/test/llnl/util/log.py b/lib/spack/spack/test/llnl/util/log.py
index 44f4f15131..530c4b8be6 100644
--- a/lib/spack/spack/test/llnl/util/log.py
+++ b/lib/spack/spack/test/llnl/util/log.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from __future__ import print_function
 import pytest
 
diff --git a/lib/spack/spack/test/make_executable.py b/lib/spack/spack/test/make_executable.py
index dd50746ade..08dbe4edf7 100644
--- a/lib/spack/spack/test/make_executable.py
+++ b/lib/spack/spack/test/make_executable.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """
 Tests for Spack's built-in parallel make support.
 
@@ -32,7 +13,6 @@ import shutil
 import tempfile
 import unittest
 
-from llnl.util.filesystem import join_path
 from spack.build_environment import MakeExecutable
 from spack.util.environment import path_put_first
 
@@ -42,7 +22,7 @@ class MakeExecutableTest(unittest.TestCase):
     def setUp(self):
         self.tmpdir = tempfile.mkdtemp()
 
-        make_exe = join_path(self.tmpdir, 'make')
+        make_exe = os.path.join(self.tmpdir, 'make')
         with open(make_exe, 'w') as f:
             f.write('#!/bin/sh\n')
             f.write('echo "$@"')
@@ -123,3 +103,10 @@ class MakeExecutableTest(unittest.TestCase):
                               output=str).strip(), '-j8 install')
 
         del os.environ['SPACK_NO_PARALLEL_MAKE']
+
+    def test_make_jobs_env(self):
+        make = MakeExecutable('make', 8)
+        dump_env = {}
+        self.assertEqual(make(output=str, jobs_env='MAKE_PARALLELISM',
+                              _dump_env=dump_env).strip(), '-j8')
+        self.assertEqual(dump_env['MAKE_PARALLELISM'], '8')
diff --git a/lib/spack/spack/test/mirror.py b/lib/spack/spack/test/mirror.py
index ec8a0d504c..d59f958481 100644
--- a/lib/spack/spack/test/mirror.py
+++ b/lib/spack/spack/test/mirror.py
@@ -1,40 +1,21 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import filecmp
 import os
 import pytest
 
-from llnl.util.filesystem import join_path
-
-import spack
+import spack.repo
 import spack.mirror
 import spack.util.executable
 from spack.spec import Spec
 from spack.stage import Stage
 from spack.util.executable import which
 
+pytestmark = pytest.mark.usefixtures('config', 'mutable_mock_packages')
+
 # paths in repos that shouldn't be in the mirror tarballs.
 exclude = ['.hg', '.git', '.svn']
 
@@ -66,10 +47,10 @@ def set_up_package(name, repository, url_attr):
 
 def check_mirror():
     with Stage('spack-mirror-test') as stage:
-        mirror_root = join_path(stage.path, 'test-mirror')
+        mirror_root = os.path.join(stage.path, 'test-mirror')
         # register mirror with spack config
         mirrors = {'spack-mirror-test': 'file://' + mirror_root}
-        spack.config.update_config('mirrors', mirrors)
+        spack.config.set('mirrors', mirrors)
         spack.mirror.create(mirror_root, repos, no_checksum=True)
 
         # Stage directory exists
@@ -77,7 +58,7 @@ def check_mirror():
 
         # check that there are subdirs for each package
         for name in repos:
-            subdir = join_path(mirror_root, name)
+            subdir = os.path.join(mirror_root, name)
             assert os.path.isdir(subdir)
 
             files = os.listdir(subdir)
@@ -88,72 +69,72 @@ def check_mirror():
                 spec = Spec(name).concretized()
                 pkg = spec.package
 
-                saved_checksum_setting = spack.do_checksum
-                with pkg.stage:
-                    # Stage the archive from the mirror and cd to it.
-                    spack.do_checksum = False
-                    pkg.do_stage(mirror_only=True)
-
-                    # Compare the original repo with the expanded archive
-                    original_path = mock_repo.path
-                    if 'svn' in name:
-                        # have to check out the svn repo to compare.
-                        original_path = join_path(
-                            mock_repo.path, 'checked_out')
-
-                        svn = which('svn', required=True)
-                        svn('checkout', mock_repo.url, original_path)
-
-                    dcmp = filecmp.dircmp(original_path, pkg.stage.source_path)
-                    # make sure there are no new files in the expanded
-                    # tarball
-                    assert not dcmp.right_only
-                    # and that all original files are present.
-                    assert all(l in exclude for l in dcmp.left_only)
-                    spack.do_checksum = saved_checksum_setting
-
-
-@pytest.mark.usefixtures('config', 'refresh_builtin_mock')
-class TestMirror(object):
-    def test_url_mirror(self, mock_archive):
-        set_up_package('trivial-install-test-package', mock_archive, 'url')
-        check_mirror()
-        repos.clear()
-
-    @pytest.mark.skipif(
-        not which('git'), reason='requires git to be installed')
-    def test_git_mirror(self, mock_git_repository):
-        set_up_package('git-test', mock_git_repository, 'git')
-        check_mirror()
-        repos.clear()
-
-    @pytest.mark.skipif(
-        not which('svn'), reason='requires subversion to be installed')
-    def test_svn_mirror(self, mock_svn_repository):
-        set_up_package('svn-test', mock_svn_repository, 'svn')
-        check_mirror()
-        repos.clear()
-
-    @pytest.mark.skipif(
-        not which('hg'), reason='requires mercurial to be installed')
-    def test_hg_mirror(self, mock_hg_repository):
-        set_up_package('hg-test', mock_hg_repository, 'hg')
-        check_mirror()
-        repos.clear()
-
-    @pytest.mark.skipif(
-        not all([which('svn'), which('hg'), which('git')]),
-        reason='requires subversion, git, and mercurial to be installed')
-    def test_all_mirror(
-            self,
-            mock_git_repository,
-            mock_svn_repository,
-            mock_hg_repository,
-            mock_archive):
-
-        set_up_package('git-test', mock_git_repository, 'git')
-        set_up_package('svn-test', mock_svn_repository, 'svn')
-        set_up_package('hg-test', mock_hg_repository, 'hg')
-        set_up_package('trivial-install-test-package', mock_archive, 'url')
-        check_mirror()
-        repos.clear()
+                with spack.config.override('config:checksum', False):
+                    with pkg.stage:
+                        pkg.do_stage(mirror_only=True)
+
+                        # Compare the original repo with the expanded archive
+                        original_path = mock_repo.path
+                        if 'svn' in name:
+                            # have to check out the svn repo to compare.
+                            original_path = os.path.join(
+                                mock_repo.path, 'checked_out')
+
+                            svn = which('svn', required=True)
+                            svn('checkout', mock_repo.url, original_path)
+
+                        dcmp = filecmp.dircmp(
+                            original_path, pkg.stage.source_path)
+
+                        # make sure there are no new files in the expanded
+                        # tarball
+                        assert not dcmp.right_only
+                        # and that all original files are present.
+                        assert all(l in exclude for l in dcmp.left_only)
+
+
+def test_url_mirror(mock_archive):
+    set_up_package('trivial-install-test-package', mock_archive, 'url')
+    check_mirror()
+    repos.clear()
+
+
+@pytest.mark.skipif(
+    not which('git'), reason='requires git to be installed')
+def test_git_mirror(mock_git_repository):
+    set_up_package('git-test', mock_git_repository, 'git')
+    check_mirror()
+    repos.clear()
+
+
+@pytest.mark.skipif(
+    not which('svn'), reason='requires subversion to be installed')
+def test_svn_mirror(mock_svn_repository):
+    set_up_package('svn-test', mock_svn_repository, 'svn')
+    check_mirror()
+    repos.clear()
+
+
+@pytest.mark.skipif(
+    not which('hg'), reason='requires mercurial to be installed')
+def test_hg_mirror(mock_hg_repository):
+    set_up_package('hg-test', mock_hg_repository, 'hg')
+    check_mirror()
+    repos.clear()
+
+
+@pytest.mark.skipif(
+    not all([which('svn'), which('hg'), which('git')]),
+    reason='requires subversion, git, and mercurial to be installed')
+def test_all_mirror(
+        mock_git_repository,
+        mock_svn_repository,
+        mock_hg_repository,
+        mock_archive):
+
+    set_up_package('git-test', mock_git_repository, 'git')
+    set_up_package('svn-test', mock_svn_repository, 'svn')
+    set_up_package('hg-test', mock_hg_repository, 'hg')
+    set_up_package('trivial-install-test-package', mock_archive, 'url')
+    check_mirror()
+    repos.clear()
diff --git a/lib/spack/spack/test/module_parsing.py b/lib/spack/spack/test/module_parsing.py
index 61e0ba1972..3ff7e764a9 100644
--- a/lib/spack/spack/test/module_parsing.py
+++ b/lib/spack/spack/test/module_parsing.py
@@ -1,34 +1,18 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import pytest
 import subprocess
 import os
-from spack.util.module_cmd import get_path_from_module
-from spack.util.module_cmd import get_argument_from_module_line
-from spack.util.module_cmd import get_module_cmd_from_bash
-from spack.util.module_cmd import get_module_cmd, ModuleError
+from spack.util.module_cmd import (
+    get_path_from_module,
+    get_path_from_module_contents,
+    get_path_arg_from_module_line,
+    get_module_cmd_from_bash,
+    get_module_cmd,
+    ModuleError)
 
 
 typeset_func = subprocess.Popen('module avail',
@@ -42,19 +26,20 @@ MODULE_NOT_DEFINED = b'not found' in typeset
 
 @pytest.fixture
 def save_env():
-    old_PATH = os.environ.get('PATH', None)
+    old_path = os.environ.get('PATH', None)
     old_bash_func = os.environ.get('BASH_FUNC_module()', None)
 
     yield
 
-    if old_PATH:
-        os.environ['PATH'] = old_PATH
+    if old_path:
+        os.environ['PATH'] = old_path
     if old_bash_func:
         os.environ['BASH_FUNC_module()'] = old_bash_func
 
 
 def test_get_path_from_module(save_env):
     lines = ['prepend-path LD_LIBRARY_PATH /path/to/lib',
+             'prepend-path CRAY_LD_LIBRARY_PATH /path/to/lib',
              'setenv MOD_DIR /path/to',
              'setenv LDFLAGS -Wl,-rpath/path/to/lib',
              'setenv LDFLAGS -L/path/to/lib',
@@ -64,7 +49,6 @@ def test_get_path_from_module(save_env):
         module_func = '() { eval `echo ' + line + ' bash filler`\n}'
         os.environ['BASH_FUNC_module()'] = module_func
         path = get_path_from_module('mod')
-
         assert path == '/path/to'
 
     os.environ['BASH_FUNC_module()'] = '() { eval $(echo fill bash $*)\n}'
@@ -73,6 +57,38 @@ def test_get_path_from_module(save_env):
     assert path is None
 
 
+def test_get_path_from_module_contents():
+    # A line with "MODULEPATH" appears early on, and the test confirms that it
+    # is not extracted as the package's path
+    module_show_output = """
+os.environ["MODULEPATH"] = "/path/to/modules1:/path/to/modules2";
+----------------------------------------------------------------------------
+   /root/cmake/3.9.2.lua:
+----------------------------------------------------------------------------
+help([[CMake Version 3.9.2
+]])
+whatis("Name: CMake")
+whatis("Version: 3.9.2")
+whatis("Category: Tools")
+whatis("URL: https://cmake.org/")
+prepend_path("PATH","/path/to/cmake-3.9.2/bin")
+prepend_path("MANPATH","/path/to/cmake/cmake-3.9.2/share/man")
+"""
+    module_show_lines = module_show_output.split('\n')
+    assert (get_path_from_module_contents(module_show_lines, 'cmake-3.9.2') ==
+            '/path/to/cmake-3.9.2')
+
+
+def test_pkg_dir_from_module_name():
+    module_show_lines = ['setenv FOO_BAR_DIR /path/to/foo-bar']
+
+    assert (get_path_from_module_contents(module_show_lines, 'foo-bar') ==
+            '/path/to/foo-bar')
+
+    assert (get_path_from_module_contents(module_show_lines, 'foo-bar/1.0') ==
+            '/path/to/foo-bar')
+
+
 def test_get_argument_from_module_line():
     lines = ['prepend-path LD_LIBRARY_PATH /lib/path',
              'prepend-path  LD_LIBRARY_PATH  /lib/path',
@@ -83,10 +99,10 @@ def test_get_argument_from_module_line():
     bad_lines = ['prepend_path(PATH,/lib/path)',
                  'prepend-path (LD_LIBRARY_PATH) /lib/path']
 
-    assert all(get_argument_from_module_line(l) == '/lib/path' for l in lines)
+    assert all(get_path_arg_from_module_line(l) == '/lib/path' for l in lines)
     for bl in bad_lines:
         with pytest.raises(ValueError):
-            get_argument_from_module_line(bl)
+            get_path_arg_from_module_line(bl)
 
 
 @pytest.mark.skipif(MODULE_NOT_DEFINED, reason='Depends on defined module fn')
diff --git a/lib/spack/spack/test/modules/common.py b/lib/spack/spack/test/modules/common.py
index 9c04dae649..63d3f562fd 100644
--- a/lib/spack/spack/test/modules/common.py
+++ b/lib/spack/spack/test/modules/common.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 import spack.modules.common
 
diff --git a/lib/spack/spack/test/modules/conftest.py b/lib/spack/spack/test/modules/conftest.py
index 35b5a30856..5e5133ec9c 100644
--- a/lib/spack/spack/test/modules/conftest.py
+++ b/lib/spack/spack/test/modules/conftest.py
@@ -1,37 +1,19 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+import os.path
 import collections
 import contextlib
 import inspect
-import os.path
-import yaml
 
-from six import StringIO
+import ruamel.yaml as yaml
 import pytest
-import spack
+from six import StringIO
+
+import spack.paths
+import spack.spec
 import spack.modules.common
 import spack.util.path
 
@@ -90,14 +72,6 @@ def modulefile_content(filename_dict, request):
 
 
 @pytest.fixture()
-def update_template_dirs(config, monkeypatch):
-    """Mocks the template directories for tests"""
-    dirs = spack.config.get_config('config')['template_dirs']
-    dirs = [spack.util.path.canonicalize_path(x) for x in dirs]
-    monkeypatch.setattr(spack, 'template_dirs', dirs)
-
-
-@pytest.fixture()
 def patch_configuration(monkeypatch, request):
     """Reads a configuration file from the mock ones prepared for tests
     and monkeypatches the right classes to hook it in.
@@ -110,7 +84,7 @@ def patch_configuration(monkeypatch, request):
     writer_key = str(writer_mod.__name__).split('.')[-1]
     # Root folder for configuration
     root_for_conf = os.path.join(
-        spack.test_path, 'data', 'modules', writer_key
+        spack.paths.test_path, 'data', 'modules', writer_key
     )
 
     def _impl(filename):
@@ -138,6 +112,14 @@ def patch_configuration(monkeypatch, request):
 
 
 @pytest.fixture()
+def update_template_dirs(config, monkeypatch):
+    """Mocks the template directories for tests"""
+    dirs = spack.config.get_config('config')['template_dirs']
+    dirs = [spack.util.path.canonicalize_path(x) for x in dirs]
+    monkeypatch.setattr(spack, 'template_dirs', dirs)
+
+
+@pytest.fixture()
 def factory(request):
     """Function that, given a spec string, returns an instance of the writer
     and the corresponding spec.
diff --git a/lib/spack/spack/test/modules/dotkit.py b/lib/spack/spack/test/modules/dotkit.py
index b27a9eecf7..f97bc14216 100644
--- a/lib/spack/spack/test/modules/dotkit.py
+++ b/lib/spack/spack/test/modules/dotkit.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 import pytest
 import spack.modules.dotkit
@@ -30,39 +11,37 @@ import spack.modules.dotkit
 writer_cls = spack.modules.dotkit.DotkitModulefileWriter
 
 
-@pytest.mark.usefixtures('config', 'builtin_mock')
+@pytest.mark.usefixtures('config', 'mock_packages')
 class TestDotkit(object):
 
-    def test_dotkit(self, modulefile_content, patch_configuration):
+    def test_dotkit(self, modulefile_content, module_configuration):
         """Tests the generation of a dotkit file that loads dependencies
         automatically.
         """
 
-        patch_configuration('autoload_direct')
+        module_configuration('autoload_direct')
         content = modulefile_content('mpileaks arch=x86-linux')
 
         assert '#c spack' in content
         assert '#d mpileaks @2.3' in content
         assert len([x for x in content if 'dk_op' in x]) == 2
 
-    @pytest.mark.usefixtures('update_template_dirs')
     def test_override_template_in_package(
-            self, modulefile_content, patch_configuration
+            self, modulefile_content, module_configuration
     ):
         """Tests overriding a template from and attribute in the package."""
 
-        patch_configuration('autoload_direct')
+        module_configuration('autoload_direct')
         content = modulefile_content('override-module-templates')
 
         assert 'Override successful!' in content
 
-    @pytest.mark.usefixtures('update_template_dirs')
     def test_override_template_in_modules_yaml(
-            self, modulefile_content, patch_configuration
+            self, modulefile_content, module_configuration
     ):
         """Tests overriding a template from `modules.yaml`"""
 
-        patch_configuration('override_template')
+        module_configuration('override_template')
 
         # Check that this takes precedence over an attribute in the package
         content = modulefile_content('override-module-templates')
diff --git a/lib/spack/spack/test/modules/lmod.py b/lib/spack/spack/test/modules/lmod.py
index 494a78e829..fe97ae9910 100644
--- a/lib/spack/spack/test/modules/lmod.py
+++ b/lib/spack/spack/test/modules/lmod.py
@@ -1,28 +1,10 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
+import re
 import pytest
 
 import spack.modules.lmod
@@ -52,14 +34,14 @@ def provider(request):
     return request.param
 
 
-@pytest.mark.usefixtures('config', 'builtin_mock',)
+@pytest.mark.usefixtures('config', 'mock_packages',)
 class TestLmod(object):
 
     def test_file_layout(
-            self, compiler, provider, factory, patch_configuration
+            self, compiler, provider, factory, module_configuration
     ):
         """Tests the layout of files in the hierarchy is the one expected."""
-        patch_configuration('complex_hierarchy')
+        module_configuration('complex_hierarchy')
         spec_string, services = provider
         module, spec = factory(spec_string + '%' + compiler)
 
@@ -91,10 +73,10 @@ class TestLmod(object):
         else:
             assert repetitions == 1
 
-    def test_simple_case(self, modulefile_content, patch_configuration):
+    def test_simple_case(self, modulefile_content, module_configuration):
         """Tests the generation of a simple TCL module file."""
 
-        patch_configuration('autoload_direct')
+        module_configuration('autoload_direct')
         content = modulefile_content(mpich_spec_string)
 
         assert '-- -*- lua -*-' in content
@@ -102,10 +84,10 @@ class TestLmod(object):
         assert 'whatis([[Version : 3.0.4]])' in content
         assert 'family("mpi")' in content
 
-    def test_autoload_direct(self, modulefile_content, patch_configuration):
+    def test_autoload_direct(self, modulefile_content, module_configuration):
         """Tests the automatic loading of direct dependencies."""
 
-        patch_configuration('autoload_direct')
+        module_configuration('autoload_direct')
         content = modulefile_content(mpileaks_spec_string)
 
         assert len([x for x in content if 'if not isloaded(' in x]) == 2
@@ -116,10 +98,10 @@ class TestLmod(object):
         messages = [x for x in content if 'LmodMessage("Autoloading' in x]
         assert len(messages) == 0
 
-    def test_autoload_all(self, modulefile_content, patch_configuration):
+    def test_autoload_all(self, modulefile_content, module_configuration):
         """Tests the automatic loading of all dependencies."""
 
-        patch_configuration('autoload_all')
+        module_configuration('autoload_all')
         content = modulefile_content(mpileaks_spec_string)
 
         assert len([x for x in content if 'if not isloaded(' in x]) == 5
@@ -129,10 +111,10 @@ class TestLmod(object):
         messages = [x for x in content if 'LmodMessage("Autoloading' in x]
         assert len(messages) == 5
 
-    def test_alter_environment(self, modulefile_content, patch_configuration):
+    def test_alter_environment(self, modulefile_content, module_configuration):
         """Tests modifications to run-time environment."""
 
-        patch_configuration('alter_environment')
+        module_configuration('alter_environment')
         content = modulefile_content('mpileaks platform=test target=x86_64')
 
         assert len(
@@ -151,31 +133,44 @@ class TestLmod(object):
         assert len([x for x in content if 'setenv("FOO", "foo")' in x]) == 0
         assert len([x for x in content if 'unsetenv("BAR")' in x]) == 0
 
-    def test_blacklist(self, modulefile_content, patch_configuration):
+    def test_prepend_path_separator(self, modulefile_content,
+                                    module_configuration):
+        """Tests modifications to run-time environment."""
+
+        module_configuration('module_path_separator')
+        content = modulefile_content('module-path-separator')
+
+        for line in content:
+            if re.match(r'[a-z]+_path\("COLON"', line):
+                assert line.endswith('"foo", ":")')
+            elif re.match(r'[a-z]+_path\("SEMICOLON"', line):
+                assert line.endswith('"bar", ";")')
+
+    def test_blacklist(self, modulefile_content, module_configuration):
         """Tests blacklisting the generation of selected modules."""
 
-        patch_configuration('blacklist')
+        module_configuration('blacklist')
         content = modulefile_content(mpileaks_spec_string)
 
         assert len([x for x in content if 'if not isloaded(' in x]) == 1
         assert len([x for x in content if 'load(' in x]) == 1
 
-    def test_no_hash(self, factory, patch_configuration):
+    def test_no_hash(self, factory, module_configuration):
         """Makes sure that virtual providers (in the hierarchy) always
         include a hash. Make sure that the module file for the spec
         does not include a hash if hash_length is 0.
         """
 
-        patch_configuration('no_hash')
+        module_configuration('no_hash')
         module, spec = factory(mpileaks_spec_string)
         path = module.layout.filename
         mpi_spec = spec['mpi']
 
-        mpiElement = "{0}/{1}-{2}/".format(
+        mpi_element = "{0}/{1}-{2}/".format(
             mpi_spec.name, mpi_spec.version, mpi_spec.dag_hash(length=7)
         )
 
-        assert mpiElement in path
+        assert mpi_element in path
 
         mpileaks_spec = spec
         mpileaks_element = "{0}/{1}.lua".format(
@@ -184,52 +179,50 @@ class TestLmod(object):
 
         assert path.endswith(mpileaks_element)
 
-    def test_no_core_compilers(self, factory, patch_configuration):
+    def test_no_core_compilers(self, factory, module_configuration):
         """Ensures that missing 'core_compilers' in the configuration file
         raises the right exception.
         """
 
         # In this case we miss the entry completely
-        patch_configuration('missing_core_compilers')
+        module_configuration('missing_core_compilers')
 
         module, spec = factory(mpileaks_spec_string)
         with pytest.raises(spack.modules.lmod.CoreCompilersNotFoundError):
             module.write()
 
         # Here we have an empty list
-        patch_configuration('core_compilers_empty')
+        module_configuration('core_compilers_empty')
 
         module, spec = factory(mpileaks_spec_string)
         with pytest.raises(spack.modules.lmod.CoreCompilersNotFoundError):
             module.write()
 
-    def test_non_virtual_in_hierarchy(self, factory, patch_configuration):
+    def test_non_virtual_in_hierarchy(self, factory, module_configuration):
         """Ensures that if a non-virtual is in hierarchy, an exception will
         be raised.
         """
-        patch_configuration('non_virtual_in_hierarchy')
+        module_configuration('non_virtual_in_hierarchy')
 
         module, spec = factory(mpileaks_spec_string)
         with pytest.raises(spack.modules.lmod.NonVirtualInHierarchyError):
             module.write()
 
-    @pytest.mark.usefixtures('update_template_dirs')
     def test_override_template_in_package(
-            self, modulefile_content, patch_configuration
+            self, modulefile_content, module_configuration
     ):
         """Tests overriding a template from and attribute in the package."""
 
-        patch_configuration('autoload_direct')
+        module_configuration('autoload_direct')
         content = modulefile_content('override-module-templates')
 
         assert 'Override successful!' in content
 
-    @pytest.mark.usefixtures('update_template_dirs')
     def test_override_template_in_modules_yaml(
-            self, modulefile_content, patch_configuration
+            self, modulefile_content, module_configuration
     ):
         """Tests overriding a template from `modules.yaml`"""
-        patch_configuration('override_template')
+        module_configuration('override_template')
 
         content = modulefile_content('override-module-templates')
         assert 'Override even better!' in content
@@ -246,3 +239,26 @@ class TestLmod(object):
         writer, spec = factory('externaltool')
 
         assert 'unknown' in writer.context.configure_options
+
+    def test_guess_core_compilers(
+            self, factory, module_configuration, monkeypatch
+    ):
+        """Check that we can guess core compilers."""
+
+        # In this case we miss the entry completely
+        module_configuration('missing_core_compilers')
+
+        # Our mock paths must be detected as system paths
+        monkeypatch.setattr(
+            spack.util.environment, 'system_dirs', ['/path/to']
+        )
+
+        # We don't want to really write into user configuration
+        # when running tests
+        def no_op_set(*args, **kwargs):
+            pass
+        monkeypatch.setattr(spack.config, 'set', no_op_set)
+
+        # Assert we have core compilers now
+        writer, _ = factory(mpileaks_spec_string)
+        assert writer.conf.core_compilers
diff --git a/lib/spack/spack/test/modules/tcl.py b/lib/spack/spack/test/modules/tcl.py
index 0a8dd99c76..b7b6a023ce 100644
--- a/lib/spack/spack/test/modules/tcl.py
+++ b/lib/spack/spack/test/modules/tcl.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 import pytest
 import spack.modules.common
@@ -36,21 +17,21 @@ libdwarf_spec_string = 'libdwarf arch=x64-linux'
 writer_cls = spack.modules.tcl.TclModulefileWriter
 
 
-@pytest.mark.usefixtures('config', 'builtin_mock')
+@pytest.mark.usefixtures('config', 'mock_packages')
 class TestTcl(object):
 
-    def test_simple_case(self, modulefile_content, patch_configuration):
+    def test_simple_case(self, modulefile_content, module_configuration):
         """Tests the generation of a simple TCL module file."""
 
-        patch_configuration('autoload_direct')
+        module_configuration('autoload_direct')
         content = modulefile_content(mpich_spec_string)
 
         assert 'module-whatis "mpich @3.0.4"' in content
 
-    def test_autoload_direct(self, modulefile_content, patch_configuration):
+    def test_autoload_direct(self, modulefile_content, module_configuration):
         """Tests the automatic loading of direct dependencies."""
 
-        patch_configuration('autoload_direct')
+        module_configuration('autoload_direct')
         content = modulefile_content(mpileaks_spec_string)
 
         assert len([x for x in content if 'is-loaded' in x]) == 2
@@ -70,10 +51,10 @@ class TestTcl(object):
         messages = [x for x in content if 'puts stderr "Autoloading' in x]
         assert len(messages) == 0
 
-    def test_autoload_all(self, modulefile_content, patch_configuration):
+    def test_autoload_all(self, modulefile_content, module_configuration):
         """Tests the automatic loading of all dependencies."""
 
-        patch_configuration('autoload_all')
+        module_configuration('autoload_all')
         content = modulefile_content(mpileaks_spec_string)
 
         assert len([x for x in content if 'is-loaded' in x]) == 5
@@ -94,27 +75,27 @@ class TestTcl(object):
         assert len(messages) == 2
 
     def test_prerequisites_direct(
-            self, modulefile_content, patch_configuration
+            self, modulefile_content, module_configuration
     ):
         """Tests asking direct dependencies as prerequisites."""
 
-        patch_configuration('prerequisites_direct')
+        module_configuration('prerequisites_direct')
         content = modulefile_content('mpileaks arch=x86-linux')
 
         assert len([x for x in content if 'prereq' in x]) == 2
 
-    def test_prerequisites_all(self, modulefile_content, patch_configuration):
+    def test_prerequisites_all(self, modulefile_content, module_configuration):
         """Tests asking all dependencies as prerequisites."""
 
-        patch_configuration('prerequisites_all')
+        module_configuration('prerequisites_all')
         content = modulefile_content('mpileaks arch=x86-linux')
 
         assert len([x for x in content if 'prereq' in x]) == 5
 
-    def test_alter_environment(self, modulefile_content, patch_configuration):
+    def test_alter_environment(self, modulefile_content, module_configuration):
         """Tests modifications to run-time environment."""
 
-        patch_configuration('alter_environment')
+        module_configuration('alter_environment')
         content = modulefile_content('mpileaks platform=test target=x86_64')
 
         assert len([x for x in content
@@ -143,10 +124,10 @@ class TestTcl(object):
         assert len([x for x in content if 'module load foo/bar' in x]) == 1
         assert len([x for x in content if 'setenv LIBDWARF_ROOT' in x]) == 1
 
-    def test_blacklist(self, modulefile_content, patch_configuration):
+    def test_blacklist(self, modulefile_content, module_configuration):
         """Tests blacklisting the generation of selected modules."""
 
-        patch_configuration('blacklist')
+        module_configuration('blacklist')
         content = modulefile_content('mpileaks ^zmpi')
 
         assert len([x for x in content if 'is-loaded' in x]) == 1
@@ -161,12 +142,12 @@ class TestTcl(object):
         assert len([x for x in content if 'is-loaded' in x]) == 1
         assert len([x for x in content if 'module load ' in x]) == 1
 
-    def test_naming_scheme(self, factory, patch_configuration):
+    def test_naming_scheme(self, factory, module_configuration):
         """Tests reading the correct naming scheme."""
 
         # This configuration has no error, so check the conflicts directives
         # are there
-        patch_configuration('conflicts')
+        module_configuration('conflicts')
 
         # Test we read the expected configuration for the naming scheme
         writer, _ = factory('mpileaks')
@@ -174,10 +155,10 @@ class TestTcl(object):
 
         assert writer.conf.naming_scheme == expected
 
-    def test_invalid_naming_scheme(self, factory, patch_configuration):
+    def test_invalid_naming_scheme(self, factory, module_configuration):
         """Tests the evaluation of an invalid naming scheme."""
 
-        patch_configuration('invalid_naming_scheme')
+        module_configuration('invalid_naming_scheme')
 
         # Test that having invalid tokens in the naming scheme raises
         # a RuntimeError
@@ -185,21 +166,21 @@ class TestTcl(object):
         with pytest.raises(RuntimeError):
             writer.layout.use_name
 
-    def test_invalid_token_in_env_name(self, factory, patch_configuration):
+    def test_invalid_token_in_env_name(self, factory, module_configuration):
         """Tests setting environment variables with an invalid name."""
 
-        patch_configuration('invalid_token_in_env_var_name')
+        module_configuration('invalid_token_in_env_var_name')
 
         writer, _ = factory('mpileaks')
         with pytest.raises(RuntimeError):
             writer.write()
 
-    def test_conflicts(self, modulefile_content, patch_configuration):
+    def test_conflicts(self, modulefile_content, module_configuration):
         """Tests adding conflicts to the module."""
 
         # This configuration has no error, so check the conflicts directives
         # are there
-        patch_configuration('conflicts')
+        module_configuration('conflicts')
         content = modulefile_content('mpileaks')
 
         assert len([x for x in content if x.startswith('conflict')]) == 2
@@ -207,13 +188,13 @@ class TestTcl(object):
         assert len([x for x in content if x == 'conflict intel/14.0.1']) == 1
 
         # This configuration is inconsistent, check an error is raised
-        patch_configuration('wrong_conflicts')
+        module_configuration('wrong_conflicts')
         with pytest.raises(SystemExit):
             modulefile_content('mpileaks')
 
-    def test_suffixes(self, patch_configuration, factory):
+    def test_suffixes(self, module_configuration, factory):
         """Tests adding suffixes to module file name."""
-        patch_configuration('suffix')
+        module_configuration('suffix')
 
         writer, spec = factory('mpileaks+debug arch=x86-linux')
         assert 'foo' in writer.layout.use_name
@@ -221,10 +202,10 @@ class TestTcl(object):
         writer, spec = factory('mpileaks~debug arch=x86-linux')
         assert 'bar' in writer.layout.use_name
 
-    def test_setup_environment(self, modulefile_content, patch_configuration):
+    def test_setup_environment(self, modulefile_content, module_configuration):
         """Tests the internal set-up of run-time environment."""
 
-        patch_configuration('suffix')
+        module_configuration('suffix')
         content = modulefile_content('mpileaks')
 
         assert len([x for x in content if 'setenv FOOBAR' in x]) == 1
@@ -241,23 +222,21 @@ class TestTcl(object):
             [x for x in content if 'setenv FOOBAR "callpath"' in x]
         ) == 1
 
-    @pytest.mark.usefixtures('update_template_dirs')
     def test_override_template_in_package(
-            self, modulefile_content, patch_configuration
+            self, modulefile_content, module_configuration
     ):
         """Tests overriding a template from and attribute in the package."""
 
-        patch_configuration('autoload_direct')
+        module_configuration('autoload_direct')
         content = modulefile_content('override-module-templates')
 
         assert 'Override successful!' in content
 
-    @pytest.mark.usefixtures('update_template_dirs')
     def test_override_template_in_modules_yaml(
-            self, modulefile_content, patch_configuration
+            self, modulefile_content, module_configuration
     ):
         """Tests overriding a template from `modules.yaml`"""
-        patch_configuration('override_template')
+        module_configuration('override_template')
 
         content = modulefile_content('override-module-templates')
         assert 'Override even better!' in content
@@ -265,15 +244,52 @@ class TestTcl(object):
         content = modulefile_content('mpileaks arch=x86-linux')
         assert 'Override even better!' in content
 
-    @pytest.mark.usefixtures('update_template_dirs')
     def test_extend_context(
-            self, modulefile_content, patch_configuration
+            self, modulefile_content, module_configuration
     ):
         """Tests using a package defined context"""
-        patch_configuration('autoload_direct')
+        module_configuration('autoload_direct')
         content = modulefile_content('override-context-templates')
 
         assert 'puts stderr "sentence from package"' in content
 
         short_description = 'module-whatis "This package updates the context for TCL modulefiles."'  # NOQA: ignore=E501
         assert short_description in content
+
+    @pytest.mark.regression('4400')
+    @pytest.mark.db
+    def test_blacklist_implicits(
+            self, modulefile_content, module_configuration, database
+    ):
+        module_configuration('blacklist_implicits')
+
+        # mpileaks has been installed explicitly when setting up
+        # the tests database
+        mpileaks_specs = database.query('mpileaks')
+        for item in mpileaks_specs:
+            writer = writer_cls(item)
+            assert not writer.conf.blacklisted
+
+        # callpath is a dependency of mpileaks, and has been pulled
+        # in implicitly
+        callpath_specs = database.query('callpath')
+        for item in callpath_specs:
+            writer = writer_cls(item)
+            assert writer.conf.blacklisted
+
+    @pytest.mark.regression('9624')
+    @pytest.mark.db
+    def test_autoload_with_constraints(
+            self, modulefile_content, module_configuration, database
+    ):
+        """Tests the automatic loading of direct dependencies."""
+
+        module_configuration('autoload_with_constraints')
+
+        # Test the mpileaks that should have the autoloaded dependencies
+        content = modulefile_content('mpileaks ^mpich2')
+        assert len([x for x in content if 'is-loaded' in x]) == 2
+
+        # Test the mpileaks that should NOT have the autoloaded dependencies
+        content = modulefile_content('mpileaks ^mpich')
+        assert len([x for x in content if 'is-loaded' in x]) == 0
diff --git a/lib/spack/spack/test/multimethod.py b/lib/spack/spack/test/multimethod.py
index 40519cccb1..de694c1498 100644
--- a/lib/spack/spack/test/multimethod.py
+++ b/lib/spack/spack/test/multimethod.py
@@ -1,40 +1,22 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """Test for multi_method dispatch."""
-import spack
 import pytest
+
+import spack.repo
 from spack.multimethod import NoSuchMethodError
 
 
-def test_no_version_match(builtin_mock):
+def test_no_version_match(mock_packages):
     pkg = spack.repo.get('multimethod@2.0')
     with pytest.raises(NoSuchMethodError):
         pkg.no_version_2()
 
 
-def test_one_version_match(builtin_mock):
+def test_one_version_match(mock_packages):
     pkg = spack.repo.get('multimethod@1.0')
     assert pkg.no_version_2() == 1
 
@@ -45,7 +27,7 @@ def test_one_version_match(builtin_mock):
     assert pkg.no_version_2() == 4
 
 
-def test_version_overlap(builtin_mock):
+def test_version_overlap(mock_packages):
     pkg = spack.repo.get('multimethod@2.0')
     assert pkg.version_overlap() == 1
 
@@ -53,7 +35,7 @@ def test_version_overlap(builtin_mock):
     assert pkg.version_overlap() == 2
 
 
-def test_mpi_version(builtin_mock):
+def test_mpi_version(mock_packages):
     pkg = spack.repo.get('multimethod^mpich@3.0.4')
     assert pkg.mpi_version() == 3
 
@@ -64,7 +46,7 @@ def test_mpi_version(builtin_mock):
     assert pkg.mpi_version() == 1
 
 
-def test_undefined_mpi_version(builtin_mock):
+def test_undefined_mpi_version(mock_packages):
     pkg = spack.repo.get('multimethod^mpich@0.4')
     assert pkg.mpi_version() == 1
 
@@ -72,7 +54,7 @@ def test_undefined_mpi_version(builtin_mock):
     assert pkg.mpi_version() == 1
 
 
-def test_default_works(builtin_mock):
+def test_default_works(mock_packages):
     pkg = spack.repo.get('multimethod%gcc')
     assert pkg.has_a_default() == 'gcc'
 
@@ -83,7 +65,7 @@ def test_default_works(builtin_mock):
     assert pkg.has_a_default() == 'default'
 
 
-def test_target_match(builtin_mock):
+def test_target_match(mock_packages):
     platform = spack.architecture.platform()
     targets = list(platform.targets.values())
     for target in targets[:-1]:
@@ -98,7 +80,7 @@ def test_target_match(builtin_mock):
             pkg.different_by_target()
 
 
-def test_dependency_match(builtin_mock):
+def test_dependency_match(mock_packages):
     pkg = spack.repo.get('multimethod^zmpi')
     assert pkg.different_by_dep() == 'zmpi'
 
@@ -111,7 +93,7 @@ def test_dependency_match(builtin_mock):
     assert pkg.different_by_dep() == 'mpich'
 
 
-def test_virtual_dep_match(builtin_mock):
+def test_virtual_dep_match(mock_packages):
     pkg = spack.repo.get('multimethod^mpich2')
     assert pkg.different_by_virtual_dep() == 2
 
@@ -119,7 +101,7 @@ def test_virtual_dep_match(builtin_mock):
     assert pkg.different_by_virtual_dep() == 1
 
 
-def test_multimethod_with_base_class(builtin_mock):
+def test_multimethod_with_base_class(mock_packages):
     pkg = spack.repo.get('multimethod@3')
     assert pkg.base_method() == "subclass_method"
 
diff --git a/lib/spack/spack/test/namespace_trie.py b/lib/spack/spack/test/namespace_trie.py
index fa38a76cc1..6c64c71f00 100644
--- a/lib/spack/spack/test/namespace_trie.py
+++ b/lib/spack/spack/test/namespace_trie.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import pytest
 
 import spack.util.naming
diff --git a/lib/spack/spack/test/optional_deps.py b/lib/spack/spack/test/optional_deps.py
index 23702a3410..bac942618b 100644
--- a/lib/spack/spack/test/optional_deps.py
+++ b/lib/spack/spack/test/optional_deps.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import pytest
 from spack.spec import Spec
 
@@ -107,14 +88,14 @@ def spec_and_expected(request):
     return spec, Spec.from_literal(d)
 
 
-def test_normalize(spec_and_expected, config, builtin_mock):
+def test_normalize(spec_and_expected, config, mock_packages):
     spec, expected = spec_and_expected
     spec = Spec(spec)
     spec.normalize()
     assert spec.eq_dag(expected, deptypes=False)
 
 
-def test_default_variant(config, builtin_mock):
+def test_default_variant(config, mock_packages):
     spec = Spec('optional-dep-test-3')
     spec.concretize()
     assert 'a' in spec
diff --git a/lib/spack/spack/test/package_hash.py b/lib/spack/spack/test/package_hash.py
new file mode 100644
index 0000000000..89fe8e9294
--- /dev/null
+++ b/lib/spack/spack/test/package_hash.py
@@ -0,0 +1,65 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.util.package_hash import package_hash, package_content
+from spack.spec import Spec
+
+
+def test_hash(tmpdir, mock_packages, config):
+    package_hash("hash-test1@1.2")
+
+
+def test_different_variants(tmpdir, mock_packages, config):
+    spec1 = Spec("hash-test1@1.2 +variantx")
+    spec2 = Spec("hash-test1@1.2 +varianty")
+    assert package_hash(spec1) == package_hash(spec2)
+
+
+def test_all_same_but_name(tmpdir, mock_packages, config):
+    spec1 = Spec("hash-test1@1.2")
+    spec2 = Spec("hash-test2@1.2")
+    compare_sans_name(True, spec1, spec2)
+
+    spec1 = Spec("hash-test1@1.2 +varianty")
+    spec2 = Spec("hash-test2@1.2 +varianty")
+    compare_sans_name(True, spec1, spec2)
+
+
+def test_all_same_but_archive_hash(tmpdir, mock_packages, config):
+    """
+    Archive hash is not intended to be reflected in Package hash.
+    """
+    spec1 = Spec("hash-test1@1.3")
+    spec2 = Spec("hash-test2@1.3")
+    compare_sans_name(True, spec1, spec2)
+
+
+def test_all_same_but_patch_contents(tmpdir, mock_packages, config):
+    spec1 = Spec("hash-test1@1.1")
+    spec2 = Spec("hash-test2@1.1")
+    compare_sans_name(True, spec1, spec2)
+
+
+def test_all_same_but_patches_to_apply(tmpdir, mock_packages, config):
+    spec1 = Spec("hash-test1@1.4")
+    spec2 = Spec("hash-test2@1.4")
+    compare_sans_name(True, spec1, spec2)
+
+
+def test_all_same_but_install(tmpdir, mock_packages, config):
+    spec1 = Spec("hash-test1@1.5")
+    spec2 = Spec("hash-test2@1.5")
+    compare_sans_name(False, spec1, spec2)
+
+
+def compare_sans_name(eq, spec1, spec2):
+    content1 = package_content(spec1)
+    content1 = content1.replace(spec1.package.__class__.__name__, '')
+    content2 = package_content(spec2)
+    content2 = content2.replace(spec2.package.__class__.__name__, '')
+    if eq:
+        assert content1 == content2
+    else:
+        assert content1 != content2
diff --git a/lib/spack/spack/test/package_sanity.py b/lib/spack/spack/test/package_sanity.py
index adc6867b72..a8c84bd70d 100644
--- a/lib/spack/spack/test/package_sanity.py
+++ b/lib/spack/spack/test/package_sanity.py
@@ -1,52 +1,35 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-"""This test does sanity checks on Spack's builtin package database."""
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+"""This test does sanity checks on Spack's builtin package database."""
 import re
 
-import spack
-from spack.repository import RepoPath
+import pytest
 
+import spack.paths
+import spack.repo
+import spack.fetch_strategy
 
-def check_db():
-    """Get all packages in a DB to make sure they work."""
+
+def check_repo():
+    """Get all packages in the builtin repo to make sure they work."""
     for name in spack.repo.all_package_names():
         spack.repo.get(name)
 
 
+@pytest.mark.maybeslow
 def test_get_all_packages():
     """Get all packages once and make sure that works."""
-    check_db()
+    check_repo()
 
 
 def test_get_all_mock_packages():
     """Get the mock packages once each too."""
-    db = RepoPath(spack.mock_packages_path)
-    spack.repo.swap(db)
-    check_db()
-    spack.repo.swap(db)
+    db = spack.repo.RepoPath(spack.paths.mock_packages_path)
+    with spack.repo.swap(db):
+        check_repo()
 
 
 def test_all_versions_are_lowercase():
@@ -57,3 +40,50 @@ def test_all_versions_are_lowercase():
             errors.append(name)
 
     assert len(errors) == 0
+
+
+def test_all_virtual_packages_have_default_providers():
+    """All virtual packages must have a default provider explicitly set."""
+    defaults = spack.config.get('packages', scope='defaults')
+    default_providers = defaults['all']['providers']
+    providers = spack.repo.path.provider_index.providers
+    default_providers_filename = \
+        spack.config.config.scopes['defaults'].get_section_filename('packages')
+    for provider in providers:
+        assert provider in default_providers, \
+            "all providers must have a default in %s" \
+            % default_providers_filename
+
+
+def test_package_version_consistency():
+    """Make sure all versions on builtin packages can produce a fetcher."""
+    for name in spack.repo.all_package_names():
+        pkg = spack.repo.get(name)
+        spack.fetch_strategy.check_pkg_attributes(pkg)
+        for version in pkg.versions:
+            assert spack.fetch_strategy.for_package_version(pkg, version)
+
+
+def test_no_fixme():
+    """Packages should not contain any boilerplate such as
+       FIXME or example.com."""
+    errors = []
+    fixme_regexes = [
+        r'remove this boilerplate',
+        r'FIXME: Put',
+        r'FIXME: Add',
+        r'example.com',
+    ]
+    for name in spack.repo.all_package_names():
+        repo = spack.repo.Repo(spack.paths.packages_path)
+        filename = repo.filename_for_package_name(name)
+        with open(filename, 'r') as package_file:
+            for i, line in enumerate(package_file):
+                pattern = next((r for r in fixme_regexes
+                                if re.search(r, line)), None)
+                if pattern:
+                    errors.append(
+                        "%s:%d: boilerplate needs to be removed: %s" %
+                        (filename, i, line.strip())
+                    )
+            assert [] == errors
diff --git a/lib/spack/spack/test/packages.py b/lib/spack/spack/test/packages.py
index 9533627b24..1206d274ce 100644
--- a/lib/spack/spack/test/packages.py
+++ b/lib/spack/spack/test/packages.py
@@ -1,37 +1,20 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-import spack
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import os.path
 import pytest
 
-from llnl.util.filesystem import join_path
-from spack.repository import Repo
+import spack.repo
+import spack.fetch_strategy
+from spack.paths import mock_packages_path
 from spack.util.naming import mod_to_class
 from spack.spec import Spec
+from spack.util.package_hash import package_content
 
 
-@pytest.mark.usefixtures('config', 'builtin_mock')
+@pytest.mark.usefixtures('config', 'mock_packages')
 class TestPackage(object):
     def test_load_package(self):
         spack.repo.get('mpich')
@@ -41,20 +24,20 @@ class TestPackage(object):
         assert pkg.name == 'mpich'
 
     def test_package_filename(self):
-        repo = Repo(spack.mock_packages_path)
+        repo = spack.repo.Repo(mock_packages_path)
         filename = repo.filename_for_package_name('mpich')
-        assert filename == join_path(
-            spack.mock_packages_path,
+        assert filename == os.path.join(
+            mock_packages_path,
             'packages',
             'mpich',
             'package.py'
         )
 
     def test_nonexisting_package_filename(self):
-        repo = Repo(spack.mock_packages_path)
+        repo = spack.repo.Repo(mock_packages_path)
         filename = repo.filename_for_package_name('some-nonexisting-package')
-        assert filename == join_path(
-            spack.mock_packages_path,
+        assert filename == os.path.join(
+            mock_packages_path,
             'packages',
             'some-nonexisting-package',
             'package.py'
@@ -67,6 +50,42 @@ class TestPackage(object):
         assert 'Pmgrcollective' == mod_to_class('PmgrCollective')
         assert '_3db' == mod_to_class('3db')
 
+    def test_content_hash_all_same_but_patch_contents(self):
+        spec1 = Spec("hash-test1@1.1")
+        spec2 = Spec("hash-test2@1.1")
+        spec1.concretize()
+        spec2.concretize()
+        content1 = package_content(spec1)
+        content1 = content1.replace(spec1.package.__class__.__name__, '')
+        content2 = package_content(spec2)
+        content2 = content2.replace(spec2.package.__class__.__name__, '')
+        assert spec1.package.content_hash(content=content1) != \
+            spec2.package.content_hash(content=content2)
+
+    def test_content_hash_different_variants(self):
+        spec1 = Spec("hash-test1@1.2 +variantx")
+        spec2 = Spec("hash-test2@1.2 ~variantx")
+        spec1.concretize()
+        spec2.concretize()
+        content1 = package_content(spec1)
+        content1 = content1.replace(spec1.package.__class__.__name__, '')
+        content2 = package_content(spec2)
+        content2 = content2.replace(spec2.package.__class__.__name__, '')
+        assert spec1.package.content_hash(content=content1) == \
+            spec2.package.content_hash(content=content2)
+
+    def test_all_same_but_archive_hash(self):
+        spec1 = Spec("hash-test1@1.3")
+        spec2 = Spec("hash-test2@1.3")
+        spec1.concretize()
+        spec2.concretize()
+        content1 = package_content(spec1)
+        content1 = content1.replace(spec1.package.__class__.__name__, '')
+        content2 = package_content(spec2)
+        content2 = content2.replace(spec2.package.__class__.__name__, '')
+        assert spec1.package.content_hash(content=content1) != \
+            spec2.package.content_hash(content=content2)
+
     # Below tests target direct imports of spack packages from the
     # spack.pkg namespace
     def test_import_package(self):
@@ -128,3 +147,209 @@ class TestPackage(object):
         import spack.pkg.builtin.mock                   # noqa
         import spack.pkg.builtin.mock as m              # noqa
         from spack.pkg.builtin import mock              # noqa
+
+
+@pytest.mark.regression('2737')
+def test_urls_for_versions(mock_packages, config):
+    """Version directive without a 'url' argument should use default url."""
+    for spec_str in ('url_override@0.9.0', 'url_override@1.0.0'):
+        s = Spec(spec_str).concretized()
+        url = s.package.url_for_version('0.9.0')
+        assert url == 'http://www.anothersite.org/uo-0.9.0.tgz'
+
+        url = s.package.url_for_version('1.0.0')
+        assert url == 'http://www.doesnotexist.org/url_override-1.0.0.tar.gz'
+
+        url = s.package.url_for_version('0.8.1')
+        assert url == 'http://www.doesnotexist.org/url_override-0.8.1.tar.gz'
+
+
+def test_url_for_version_with_no_urls():
+    pkg = spack.repo.get('git-test')
+    with pytest.raises(spack.package.NoURLError):
+        pkg.url_for_version('1.0')
+
+    with pytest.raises(spack.package.NoURLError):
+        pkg.url_for_version('1.1')
+
+
+def test_url_for_version_with_only_overrides(mock_packages, config):
+    spec = Spec('url-only-override')
+    spec.concretize()
+
+    pkg = spack.repo.get(spec)
+
+    # these exist and should just take the URL provided in the package
+    assert pkg.url_for_version('1.0.0') == 'http://a.example.com/url_override-1.0.0.tar.gz'
+    assert pkg.url_for_version('0.9.0') == 'http://b.example.com/url_override-0.9.0.tar.gz'
+    assert pkg.url_for_version('0.8.1') == 'http://c.example.com/url_override-0.8.1.tar.gz'
+
+    # these don't exist but should still work, even if there are only overrides
+    assert pkg.url_for_version('1.0.5') == 'http://a.example.com/url_override-1.0.5.tar.gz'
+    assert pkg.url_for_version('0.9.5') == 'http://b.example.com/url_override-0.9.5.tar.gz'
+    assert pkg.url_for_version('0.8.5') == 'http://c.example.com/url_override-0.8.5.tar.gz'
+    assert pkg.url_for_version('0.7.0') == 'http://c.example.com/url_override-0.7.0.tar.gz'
+
+
+def test_url_for_version_with_only_overrides_with_gaps(mock_packages, config):
+    spec = Spec('url-only-override-with-gaps')
+    spec.concretize()
+
+    pkg = spack.repo.get(spec)
+
+    # same as for url-only-override -- these are specific
+    assert pkg.url_for_version('1.0.0') == 'http://a.example.com/url_override-1.0.0.tar.gz'
+    assert pkg.url_for_version('0.9.0') == 'http://b.example.com/url_override-0.9.0.tar.gz'
+    assert pkg.url_for_version('0.8.1') == 'http://c.example.com/url_override-0.8.1.tar.gz'
+
+    # these don't have specific URLs, but should still work by extrapolation
+    assert pkg.url_for_version('1.0.5') == 'http://a.example.com/url_override-1.0.5.tar.gz'
+    assert pkg.url_for_version('0.9.5') == 'http://b.example.com/url_override-0.9.5.tar.gz'
+    assert pkg.url_for_version('0.8.5') == 'http://c.example.com/url_override-0.8.5.tar.gz'
+    assert pkg.url_for_version('0.7.0') == 'http://c.example.com/url_override-0.7.0.tar.gz'
+
+
+def test_git_top_level(mock_packages, config):
+    """Ensure that top-level git attribute can be used as a default."""
+    pkg = spack.repo.get('git-top-level')
+
+    fetcher = spack.fetch_strategy.for_package_version(pkg, '1.0')
+    assert isinstance(fetcher, spack.fetch_strategy.GitFetchStrategy)
+    assert fetcher.url == 'https://example.com/some/git/repo'
+
+
+def test_svn_top_level(mock_packages, config):
+    """Ensure that top-level svn attribute can be used as a default."""
+    pkg = spack.repo.get('svn-top-level')
+
+    fetcher = spack.fetch_strategy.for_package_version(pkg, '1.0')
+    assert isinstance(fetcher, spack.fetch_strategy.SvnFetchStrategy)
+    assert fetcher.url == 'https://example.com/some/svn/repo'
+
+
+def test_hg_top_level(mock_packages, config):
+    """Ensure that top-level hg attribute can be used as a default."""
+    pkg = spack.repo.get('hg-top-level')
+
+    fetcher = spack.fetch_strategy.for_package_version(pkg, '1.0')
+    assert isinstance(fetcher, spack.fetch_strategy.HgFetchStrategy)
+    assert fetcher.url == 'https://example.com/some/hg/repo'
+
+
+def test_no_extrapolate_without_url(mock_packages, config):
+    """Verify that we can't extrapolate versions for non-URL packages."""
+    pkg = spack.repo.get('git-top-level')
+
+    with pytest.raises(spack.fetch_strategy.ExtrapolationError):
+        spack.fetch_strategy.for_package_version(pkg, '1.1')
+
+
+def test_two_vcs_fetchers_top_level(mock_packages, config):
+    """Verify conflict when two VCS strategies are specified together."""
+
+    pkg = spack.repo.get('git-url-svn-top-level')
+    with pytest.raises(spack.fetch_strategy.FetcherConflict):
+        spack.fetch_strategy.for_package_version(pkg, '1.0')
+
+    pkg = spack.repo.get('git-svn-top-level')
+    with pytest.raises(spack.fetch_strategy.FetcherConflict):
+        spack.fetch_strategy.for_package_version(pkg, '1.0')
+
+
+def test_git_url_top_level_url_versions(mock_packages, config):
+    """Test URL fetch strategy inference when url is specified with git."""
+
+    pkg = spack.repo.get('git-url-top-level')
+
+    fetcher = spack.fetch_strategy.for_package_version(pkg, '2.0')
+    assert isinstance(fetcher, spack.fetch_strategy.URLFetchStrategy)
+    assert fetcher.url == 'https://example.com/some/tarball-2.0.tar.gz'
+    assert fetcher.digest == 'abc20'
+
+    fetcher = spack.fetch_strategy.for_package_version(pkg, '2.1')
+    assert isinstance(fetcher, spack.fetch_strategy.URLFetchStrategy)
+    assert fetcher.url == 'https://example.com/some/tarball-2.1.tar.gz'
+    assert fetcher.digest == 'abc21'
+
+    fetcher = spack.fetch_strategy.for_package_version(pkg, '2.2')
+    assert isinstance(fetcher, spack.fetch_strategy.URLFetchStrategy)
+    assert fetcher.url == 'https://www.example.com/foo2.2.tar.gz'
+    assert fetcher.digest == 'abc22'
+
+    fetcher = spack.fetch_strategy.for_package_version(pkg, '2.3')
+    assert isinstance(fetcher, spack.fetch_strategy.URLFetchStrategy)
+    assert fetcher.url == 'https://www.example.com/foo2.3.tar.gz'
+    assert fetcher.digest == 'abc23'
+
+
+def test_git_url_top_level_git_versions(mock_packages, config):
+    """Test git fetch strategy inference when url is specified with git."""
+
+    pkg = spack.repo.get('git-url-top-level')
+
+    fetcher = spack.fetch_strategy.for_package_version(pkg, '3.0')
+    assert isinstance(fetcher, spack.fetch_strategy.GitFetchStrategy)
+    assert fetcher.url == 'https://example.com/some/git/repo'
+    assert fetcher.tag == 'v3.0'
+    assert fetcher.commit is None
+    assert fetcher.branch is None
+
+    fetcher = spack.fetch_strategy.for_package_version(pkg, '3.1')
+    assert isinstance(fetcher, spack.fetch_strategy.GitFetchStrategy)
+    assert fetcher.url == 'https://example.com/some/git/repo'
+    assert fetcher.tag == 'v3.1'
+    assert fetcher.commit == 'abc31'
+    assert fetcher.branch is None
+
+    fetcher = spack.fetch_strategy.for_package_version(pkg, '3.2')
+    assert isinstance(fetcher, spack.fetch_strategy.GitFetchStrategy)
+    assert fetcher.url == 'https://example.com/some/git/repo'
+    assert fetcher.tag is None
+    assert fetcher.commit is None
+    assert fetcher.branch == 'releases/v3.2'
+
+    fetcher = spack.fetch_strategy.for_package_version(pkg, '3.3')
+    assert isinstance(fetcher, spack.fetch_strategy.GitFetchStrategy)
+    assert fetcher.url == 'https://example.com/some/git/repo'
+    assert fetcher.tag is None
+    assert fetcher.commit == 'abc33'
+    assert fetcher.branch == 'releases/v3.3'
+
+    fetcher = spack.fetch_strategy.for_package_version(pkg, '3.4')
+    assert isinstance(fetcher, spack.fetch_strategy.GitFetchStrategy)
+    assert fetcher.url == 'https://example.com/some/git/repo'
+    assert fetcher.tag is None
+    assert fetcher.commit == 'abc34'
+    assert fetcher.branch is None
+
+    fetcher = spack.fetch_strategy.for_package_version(pkg, 'submodules')
+    assert isinstance(fetcher, spack.fetch_strategy.GitFetchStrategy)
+    assert fetcher.url == 'https://example.com/some/git/repo'
+    assert fetcher.tag is None
+    assert fetcher.commit is None
+    assert fetcher.branch is None
+
+    fetcher = spack.fetch_strategy.for_package_version(pkg, 'develop')
+    assert isinstance(fetcher, spack.fetch_strategy.GitFetchStrategy)
+    assert fetcher.url == 'https://example.com/some/git/repo'
+    assert fetcher.tag is None
+    assert fetcher.commit is None
+    assert fetcher.branch == 'develop'
+
+
+def test_git_url_top_level_conflicts(mock_packages, config):
+    """Test git fetch strategy inference when url is specified with git."""
+
+    pkg = spack.repo.get('git-url-top-level')
+
+    with pytest.raises(spack.fetch_strategy.FetcherConflict):
+        spack.fetch_strategy.for_package_version(pkg, '1.0')
+
+    with pytest.raises(spack.fetch_strategy.FetcherConflict):
+        spack.fetch_strategy.for_package_version(pkg, '1.1')
+
+    with pytest.raises(spack.fetch_strategy.FetcherConflict):
+        spack.fetch_strategy.for_package_version(pkg, '1.2')
+
+    with pytest.raises(spack.fetch_strategy.FetcherConflict):
+        spack.fetch_strategy.for_package_version(pkg, '1.3')
diff --git a/lib/spack/spack/test/packaging.py b/lib/spack/spack/test/packaging.py
index 49e5138c89..ae7d7678ae 100644
--- a/lib/spack/spack/test/packaging.py
+++ b/lib/spack/spack/test/packaging.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """
 This test checks the binary packaging infrastructure
 """
@@ -34,14 +15,16 @@ import argparse
 
 from llnl.util.filesystem import mkdirp
 
-import spack
+import spack.repo
 import spack.store
 import spack.binary_distribution as bindist
 import spack.cmd.buildcache as buildcache
 from spack.spec import Spec
+from spack.paths import mock_gpg_keys_path
 from spack.fetch_strategy import URLFetchStrategy, FetchStrategyComposite
 from spack.util.executable import ProcessError
 from spack.relocate import needs_binary_relocation, needs_text_relocation
+from spack.relocate import strings_contains_installroot
 from spack.relocate import get_patchelf, relocate_text
 from spack.relocate import substitute_rpath, get_relative_rpaths
 from spack.relocate import macho_replace_paths, macho_make_paths_relative
@@ -72,7 +55,7 @@ def fake_fetchify(url, pkg):
 
 
 @pytest.mark.usefixtures('install_mockery', 'testing_gpg_directory')
-def test_packaging(mock_archive, tmpdir):
+def test_buildcache(mock_archive, tmpdir):
     # tweak patchelf to only do a download
     spec = Spec("patchelf")
     spec.concretize()
@@ -92,7 +75,7 @@ echo $PATH"""
     spec = Spec('trivial-install-test-package')
     spec.concretize()
     assert spec.concrete
-    pkg = spack.repo.get(spec)
+    pkg = spec.package
     fake_fetchify(mock_archive.url, pkg)
     pkg.do_install()
     pkghash = '/' + spec.dag_hash(7)
@@ -106,14 +89,13 @@ echo $PATH"""
     # put it directly into the mirror
 
     mirror_path = os.path.join(str(tmpdir), 'test-mirror')
-    specs = [spec]
     spack.mirror.create(
-        mirror_path, specs, no_checksum=True
+        mirror_path, specs=[], no_checksum=True
     )
 
     # register mirror with spack config
     mirrors = {'spack-mirror-test': 'file://' + mirror_path}
-    spack.config.update_config('mirrors', mirrors)
+    spack.config.set('mirrors', mirrors)
 
     stage = spack.stage.Stage(
         mirrors['spack-mirror-test'], name="build_cache", keep=True)
@@ -157,34 +139,34 @@ echo $PATH"""
     else:
         # create build cache without signing
         args = parser.parse_args(
-            ['create', '-d', mirror_path, '-y', str(spec)])
+            ['create', '-d', mirror_path, '-u', str(spec)])
         buildcache.buildcache(parser, args)
 
         # Uninstall the package
         pkg.do_uninstall(force=True)
 
         # install build cache without verification
-        args = parser.parse_args(['install', '-y', str(spec)])
+        args = parser.parse_args(['install', '-u', str(spec)])
         buildcache.install_tarball(spec, args)
 
         # test overwrite install without verification
-        args = parser.parse_args(['install', '-f', '-y', str(pkghash)])
+        args = parser.parse_args(['install', '-f', '-u', str(pkghash)])
         buildcache.buildcache(parser, args)
 
         # create build cache with relative path
         args = parser.parse_args(
-            ['create', '-d', mirror_path, '-f', '-r', '-y', str(pkghash)])
+            ['create', '-d', mirror_path, '-f', '-r', '-u', str(pkghash)])
         buildcache.buildcache(parser, args)
 
         # Uninstall the package
         pkg.do_uninstall(force=True)
 
         # install build cache
-        args = parser.parse_args(['install', '-y', str(spec)])
+        args = parser.parse_args(['install', '-u', str(spec)])
         buildcache.install_tarball(spec, args)
 
         # test overwrite install
-        args = parser.parse_args(['install', '-f', '-y', str(pkghash)])
+        args = parser.parse_args(['install', '-f', '-u', str(pkghash)])
         buildcache.buildcache(parser, args)
 
     # Validate the relocation information
@@ -201,7 +183,7 @@ echo $PATH"""
     buildcache.buildcache(parser, args)
 
     # Copy a key to the mirror to have something to download
-    shutil.copyfile(spack.mock_gpg_keys_path + '/external.key',
+    shutil.copyfile(mock_gpg_keys_path + '/external.key',
                     mirror_path + '/external.key')
 
     args = parser.parse_args(['keys'])
@@ -212,26 +194,29 @@ echo $PATH"""
 
     # unregister mirror with spack config
     mirrors = {}
-    spack.config.update_config('mirrors', mirrors)
+    spack.config.set('mirrors', mirrors)
     shutil.rmtree(mirror_path)
     stage.destroy()
 
+    # Remove cached binary specs since we deleted the mirror
+    bindist._cached_specs = None
 
-def test_relocate_text():
-    # Validate the text path replacement
-    old_dir = '/home/spack/opt/spack'
-    filename = 'dummy.txt'
-    with open(filename, "w") as script:
-        script.write(old_dir)
-        script.close()
-
-    filenames = [filename]
-    new_dir = '/opt/rh/devtoolset/'
-    relocate_text(filenames, old_dir, new_dir)
 
-    with open(filename, "r")as script:
-        for line in script:
-            assert(new_dir in line)
+def test_relocate_text(tmpdir):
+    with tmpdir.as_cwd():
+        # Validate the text path replacement
+        old_dir = '/home/spack/opt/spack'
+        filename = 'dummy.txt'
+        with open(filename, "w") as script:
+            script.write(old_dir)
+            script.close()
+        filenames = [filename]
+        new_dir = '/opt/rh/devtoolset/'
+        relocate_text(filenames, old_dir, new_dir)
+        with open(filename, "r")as script:
+            for line in script:
+                assert(new_dir in line)
+        assert(strings_contains_installroot(filename, old_dir) is False)
 
 
 def test_needs_relocation():
diff --git a/lib/spack/spack/test/patch.py b/lib/spack/spack/test/patch.py
index 6afb50bba0..e606c9113a 100644
--- a/lib/spack/spack/test/patch.py
+++ b/lib/spack/spack/test/patch.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 import sys
 import filecmp
@@ -29,8 +10,9 @@ import pytest
 
 from llnl.util.filesystem import working_dir, mkdirp
 
-import spack
+import spack.paths
 import spack.util.compression
+from spack.util.executable import Executable
 from spack.stage import Stage
 from spack.spec import Spec
 
@@ -39,11 +21,11 @@ from spack.spec import Spec
 def mock_stage(tmpdir, monkeypatch):
     # don't disrupt the spack install directory with tests.
     mock_path = str(tmpdir)
-    monkeypatch.setattr(spack, 'stage_path', mock_path)
+    monkeypatch.setattr(spack.paths, 'stage_path', mock_path)
     return mock_path
 
 
-data_path = os.path.join(spack.test_path, 'data', 'patch')
+data_path = os.path.join(spack.paths.test_path, 'data', 'patch')
 
 
 @pytest.mark.parametrize('filename, sha256, archive_sha256', [
@@ -93,7 +75,7 @@ third line
             assert filecmp.cmp('foo.txt', 'foo-expected.txt')
 
 
-def test_patch_in_spec(builtin_mock, config):
+def test_patch_in_spec(mock_packages, config):
     """Test whether patches in a package appear in the spec."""
     spec = Spec('patch')
     spec.concretize()
@@ -108,18 +90,34 @@ def test_patch_in_spec(builtin_mock, config):
             spec.variants['patches'].value)
 
 
-def test_patched_dependency(builtin_mock, config):
+def test_patched_dependency(
+        mock_packages, config, install_mockery, mock_fetch):
     """Test whether patched dependencies work."""
     spec = Spec('patch-a-dependency')
     spec.concretize()
     assert 'patches' in list(spec['libelf'].variants.keys())
 
-    # foo
-    assert (('b5bb9d8014a0f9b1d61e21e796d78dccdf1352f23cd32812f4850b878ae4944c',) ==
+    # make sure the patch makes it into the dependency spec
+    assert (('c45c1564f70def3fc1a6e22139f62cb21cd190cc3a7dbe6f4120fa59ce33dcb8',) ==
             spec['libelf'].variants['patches'].value)
 
+    # make sure the patch in the dependent's directory is applied to the
+    # dependency
+    libelf = spec['libelf']
+    pkg = libelf.package
+    pkg.do_patch()
+    with pkg.stage:
+        with working_dir(pkg.stage.source_path):
+            # output a Makefile with 'echo Patched!' as the default target
+            configure = Executable('./configure')
+            configure()
+
+            # Make sure the Makefile contains the patched text
+            with open('Makefile') as mf:
+                assert 'Patched!' in mf.read()
+
 
-def test_multiple_patched_dependencies(builtin_mock, config):
+def test_multiple_patched_dependencies(mock_packages, config):
     """Test whether multiple patched dependencies work."""
     spec = Spec('patch-several-dependencies')
     spec.concretize()
@@ -138,7 +136,7 @@ def test_multiple_patched_dependencies(builtin_mock, config):
             spec['fake'].variants['patches'].value)
 
 
-def test_conditional_patched_dependencies(builtin_mock, config):
+def test_conditional_patched_dependencies(mock_packages, config):
     """Test whether conditional patched dependencies work."""
     spec = Spec('patch-several-dependencies @1.0')
     spec.concretize()
@@ -166,7 +164,7 @@ def test_conditional_patched_dependencies(builtin_mock, config):
             spec['fake'].variants['patches'].value)
 
 
-def test_conditional_patched_deps_with_conditions(builtin_mock, config):
+def test_conditional_patched_deps_with_conditions(mock_packages, config):
     """Test whether conditional patched dependencies with conditions work."""
     spec = Spec('patch-several-dependencies @1.0 ^libdwarf@20111030')
     spec.concretize()
diff --git a/lib/spack/spack/test/pattern.py b/lib/spack/spack/test/pattern.py
index 72cabbbfd7..fc2c85735d 100644
--- a/lib/spack/spack/test/pattern.py
+++ b/lib/spack/spack/test/pattern.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 import pytest
 import spack.util.pattern as pattern
diff --git a/lib/spack/spack/test/provider_index.py b/lib/spack/spack/test/provider_index.py
index 985a1ae3f3..dfa9ef37fc 100644
--- a/lib/spack/spack/test/provider_index.py
+++ b/lib/spack/spack/test/provider_index.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """Tests for provider index cache files.
 
 Tests assume that mock packages provide this::
@@ -39,12 +20,12 @@ Tests assume that mock packages provide this::
 """
 from six import StringIO
 
-import spack
+import spack.repo
 from spack.provider_index import ProviderIndex
 from spack.spec import Spec
 
 
-def test_yaml_round_trip(builtin_mock):
+def test_yaml_round_trip(mock_packages):
     p = ProviderIndex(spack.repo.all_package_names())
 
     ostream = StringIO()
@@ -56,7 +37,7 @@ def test_yaml_round_trip(builtin_mock):
     assert p == q
 
 
-def test_providers_for_simple(builtin_mock):
+def test_providers_for_simple(mock_packages):
     p = ProviderIndex(spack.repo.all_package_names())
 
     blas_providers = p.providers_for('blas')
@@ -69,7 +50,7 @@ def test_providers_for_simple(builtin_mock):
     assert Spec('openblas-with-lapack') in lapack_providers
 
 
-def test_mpi_providers(builtin_mock):
+def test_mpi_providers(mock_packages):
     p = ProviderIndex(spack.repo.all_package_names())
 
     mpi_2_providers = p.providers_for('mpi@2')
@@ -82,13 +63,13 @@ def test_mpi_providers(builtin_mock):
     assert Spec('zmpi') in mpi_3_providers
 
 
-def test_equal(builtin_mock):
+def test_equal(mock_packages):
     p = ProviderIndex(spack.repo.all_package_names())
     q = ProviderIndex(spack.repo.all_package_names())
     assert p == q
 
 
-def test_copy(builtin_mock):
+def test_copy(mock_packages):
     p = ProviderIndex(spack.repo.all_package_names())
     q = p.copy()
     assert p == q
diff --git a/lib/spack/spack/test/pytest.ini b/lib/spack/spack/test/pytest.ini
new file mode 100644
index 0000000000..ccad5f86cc
--- /dev/null
+++ b/lib/spack/spack/test/pytest.ini
@@ -0,0 +1,9 @@
+# content of pytest.ini
+[pytest]
+addopts = --durations=20 -ra
+testpaths = .
+python_files = *.py
+markers =
+  db: tests that require creating a DB
+  network: tests that require access to the network
+  maybeslow: tests that may be slow (e.g. access a lot the filesystem, etc.)
diff --git a/lib/spack/spack/test/python_version.py b/lib/spack/spack/test/python_version.py
index b9bb18bfd2..4e2a4b41f1 100644
--- a/lib/spack/spack/test/python_version.py
+++ b/lib/spack/spack/test/python_version.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """Check that Spack complies with minimum supported python versions.
 
 We ensure that all Spack files work with Python2 >= 2.6 and Python3 >= 3.0.
@@ -37,8 +18,13 @@ import os
 import sys
 import re
 
+import pytest
+
 import llnl.util.tty as tty
-import spack
+
+import spack.paths
+from spack.paths import lib_path as spack_lib_path
+
 
 #
 # This test uses pyqver, by Greg Hewgill, which is a dual-source module.
@@ -53,10 +39,10 @@ if sys.version_info[0] < 3:
     exclude_paths = [
         # Jinja 2 has some 'async def' functions that are not treated correctly
         # by pyqver.py
-        os.path.join(spack.lib_path, 'external', 'jinja2', 'asyncfilters.py'),
-        os.path.join(spack.lib_path, 'external', 'jinja2', 'asyncsupport.py'),
-        os.path.join(spack.lib_path, 'external', 'yaml', 'lib3'),
-        os.path.join(spack.lib_path, 'external', 'pyqver3.py')]
+        os.path.join(spack_lib_path, 'external', 'jinja2', 'asyncfilters.py'),
+        os.path.join(spack_lib_path, 'external', 'jinja2', 'asyncsupport.py'),
+        os.path.join(spack_lib_path, 'external', 'yaml', 'lib3'),
+        os.path.join(spack_lib_path, 'external', 'pyqver3.py')]
 
 else:
     import pyqver3 as pyqver
@@ -66,10 +52,10 @@ else:
     exclude_paths = [
         # Jinja 2 has some 'async def' functions that are not treated correctly
         # by pyqver.py
-        os.path.join(spack.lib_path, 'external', 'jinja2', 'asyncfilters.py'),
-        os.path.join(spack.lib_path, 'external', 'jinja2', 'asyncsupport.py'),
-        os.path.join(spack.lib_path, 'external', 'yaml', 'lib'),
-        os.path.join(spack.lib_path, 'external', 'pyqver2.py')]
+        os.path.join(spack_lib_path, 'external', 'jinja2', 'asyncfilters.py'),
+        os.path.join(spack_lib_path, 'external', 'jinja2', 'asyncsupport.py'),
+        os.path.join(spack_lib_path, 'external', 'yaml', 'lib'),
+        os.path.join(spack_lib_path, 'external', 'pyqver2.py')]
 
 
 def pyfiles(search_paths, exclude=()):
@@ -83,7 +69,7 @@ def pyfiles(search_paths, exclude=()):
         python files in the search path.
     """
     # first file is the spack script.
-    yield spack.spack_file
+    yield spack.paths.spack_script
 
     # Iterate through the whole spack source tree.
     for path in search_paths:
@@ -133,8 +119,8 @@ def check_python_versions(files):
         messages = []
         for path in sorted(all_issues[v].keys()):
             short_path = path
-            if path.startswith(spack.prefix):
-                short_path = path[len(spack.prefix):]
+            if path.startswith(spack.paths.prefix):
+                short_path = path[len(spack.paths.prefix):]
 
             reasons = [r for r in set(all_issues[v][path]) if r]
             for lineno, cause in reasons:
@@ -154,11 +140,14 @@ def check_python_versions(files):
     assert not all_issues
 
 
+@pytest.mark.maybeslow
 def test_core_module_compatibility():
     """Test that all core spack modules work with supported Python versions."""
-    check_python_versions(pyfiles([spack.lib_path], exclude=exclude_paths))
+    check_python_versions(
+        pyfiles([spack_lib_path], exclude=exclude_paths))
 
 
+@pytest.mark.maybeslow
 def test_package_module_compatibility():
     """Test that all spack packages work with supported Python versions."""
-    check_python_versions(pyfiles([spack.packages_path]))
+    check_python_versions(pyfiles([spack.paths.packages_path]))
diff --git a/lib/spack/spack/test/repo.py b/lib/spack/spack/test/repo.py
index 7bf1291ec0..3dcb9eaf9f 100644
--- a/lib/spack/spack/test/repo.py
+++ b/lib/spack/spack/test/repo.py
@@ -1,38 +1,20 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-import spack
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 import pytest
 
+import spack.repo
+import spack.paths
+
 
 # Unlike the repo_path fixture defined in conftest, this has a test-level
 # scope rather than a session level scope, since we want to edit the
 # given RepoPath
 @pytest.fixture()
 def repo_for_test():
-    return spack.repository.RepoPath(spack.mock_packages_path)
+    return spack.repo.RepoPath(spack.paths.mock_packages_path)
 
 
 @pytest.fixture()
@@ -41,12 +23,12 @@ def extra_repo(tmpdir_factory):
     repo_dir = tmpdir_factory.mktemp(repo_namespace)
     repo_dir.ensure('packages', dir=True)
 
-    with open(str(repo_dir.join('repo.yaml')), 'w') as F:
-        F.write("""
+    with open(str(repo_dir.join('repo.yaml')), 'w') as f:
+        f.write("""
 repo:
   namespace: extra_test_repo
 """)
-    return spack.repository.Repo(str(repo_dir))
+    return spack.repo.Repo(str(repo_dir))
 
 
 def test_repo_getpkg(repo_for_test):
@@ -67,10 +49,10 @@ def test_repo_multi_getpkgclass(repo_for_test, extra_repo):
 
 
 def test_repo_pkg_with_unknown_namespace(repo_for_test):
-    with pytest.raises(spack.repository.UnknownNamespaceError):
+    with pytest.raises(spack.repo.UnknownNamespaceError):
         repo_for_test.get('unknown.a')
 
 
 def test_repo_unknown_pkg(repo_for_test):
-    with pytest.raises(spack.repository.UnknownPackageError):
+    with pytest.raises(spack.repo.UnknownPackageError):
         repo_for_test.get('builtin.mock.nonexistentpackage')
diff --git a/lib/spack/spack/test/sbang.py b/lib/spack/spack/test/sbang.py
index 6b583b187f..6e22483608 100644
--- a/lib/spack/spack/test/sbang.py
+++ b/lib/spack/spack/test/sbang.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """\
 Test that Spack's shebang filtering works correctly.
 """
@@ -34,7 +15,7 @@ import filecmp
 
 from llnl.util.filesystem import mkdirp
 
-import spack
+import spack.paths
 from spack.hooks.sbang import shebang_too_long, filter_shebangs_in_directory
 from spack.util.executable import which
 
@@ -47,7 +28,7 @@ lua_line_patched  = "--!/this/" + ('x' * 200) + "/is/lua\n"
 node_line         = "#!/this/" + ('x' * 200) + "/is/node\n"
 node_in_text      = ("line\n") * 100 + "lua\n" + ("line\n" * 100)
 node_line_patched = "//!/this/" + ('x' * 200) + "/is/node\n"
-sbang_line        = '#!/bin/bash %s/bin/sbang\n' % spack.spack_root
+sbang_line        = '#!/bin/bash %s/bin/sbang\n' % spack.paths.prefix
 last_line         = "last!\n"
 
 
diff --git a/lib/spack/spack/test/spack_yaml.py b/lib/spack/spack/test/spack_yaml.py
index 2bcb2b4ce9..b05aacf4b2 100644
--- a/lib/spack/spack/test/spack_yaml.py
+++ b/lib/spack/spack/test/spack_yaml.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """Test Spack's custom YAML format."""
 
 import pytest
@@ -68,10 +49,10 @@ def test_parse(data):
 def test_dict_order(data):
 
     expected_order = ['x86_64', 'some_list', 'another_list', 'some_key']
-    assert data['config_file'].keys() == expected_order
+    assert list(data['config_file'].keys()) == expected_order
 
     expected_order = ['foo', 'bar', 'baz']
-    assert data['config_file']['x86_64'].keys() == expected_order
+    assert list(data['config_file']['x86_64'].keys()) == expected_order
 
 
 def test_line_numbers(data):
diff --git a/lib/spack/spack/test/spec_dag.py b/lib/spack/spack/test/spec_dag.py
index 0f359d8291..7d29e5da34 100644
--- a/lib/spack/spack/test/spec_dag.py
+++ b/lib/spack/spack/test/spec_dag.py
@@ -1,32 +1,12 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """
 These tests check Spec DAG operations using dummy packages.
 """
 import pytest
-import spack
 import spack.architecture
 import spack.package
 
@@ -86,8 +66,6 @@ packages in the following spec DAG::
 w->y deptypes are (link, build), w->x and y->z deptypes are (test)
 
 """
-    saved_repo = spack.repo
-
     default = ('build', 'link')
     test_only = ('test',)
 
@@ -97,20 +75,53 @@ w->y deptypes are (link, build), w->x and y->z deptypes are (test)
     w = MockPackage('w', [x, y], [test_only, default])
 
     mock_repo = MockPackageMultiRepo([w, x, y, z])
-    try:
-        spack.package_testing.test(w.name)
-        spack.repo = mock_repo
+    with spack.repo.swap(mock_repo):
         spec = Spec('w')
-        spec.concretize()
+        spec.concretize(tests=(w.name,))
 
         assert ('x' in spec)
         assert ('z' not in spec)
-    finally:
-        spack.repo = saved_repo
-        spack.package_testing.clear()
 
 
-@pytest.mark.usefixtures('refresh_builtin_mock')
+@pytest.mark.usefixtures('config')
+def test_conditional_dep_with_user_constraints():
+    """This sets up packages X->Y such that X depends on Y conditionally. It
+    then constructs a Spec with X but with no constraints on X, so that the
+    initial normalization pass cannot determine whether the constraints are
+    met to add the dependency; this checks whether a user-specified constraint
+    on Y is applied properly.
+    """
+    default = ('build', 'link')
+
+    y = MockPackage('y', [], [])
+    x_on_y_conditions = {
+        y.name: {
+            'x@2:': 'y'
+        }
+    }
+    x = MockPackage('x', [y], [default], conditions=x_on_y_conditions)
+
+    mock_repo = MockPackageMultiRepo([x, y])
+    with spack.repo.swap(mock_repo):
+        spec = Spec('x ^y@2')
+        spec.concretize()
+
+        assert ('y@2' in spec)
+
+    with spack.repo.swap(mock_repo):
+        spec = Spec('x@1')
+        spec.concretize()
+
+        assert ('y' not in spec)
+
+    with spack.repo.swap(mock_repo):
+        spec = Spec('x')
+        spec.concretize()
+
+        assert ('y@3' in spec)
+
+
+@pytest.mark.usefixtures('mutable_mock_packages')
 class TestSpecDag(object):
 
     def test_conflicting_package_constraints(self, set_dependency):
@@ -308,18 +319,19 @@ class TestSpecDag(object):
         with pytest.raises(spack.spec.UnsatisfiableArchitectureSpecError):
             spec.normalize()
 
+    @pytest.mark.usefixtures('config')
     def test_invalid_dep(self):
         spec = Spec('libelf ^mpich')
         with pytest.raises(spack.spec.InvalidDependencyError):
-            spec.normalize()
+            spec.concretize()
 
         spec = Spec('libelf ^libdwarf')
         with pytest.raises(spack.spec.InvalidDependencyError):
-            spec.normalize()
+            spec.concretize()
 
         spec = Spec('mpich ^dyninst ^libelf')
         with pytest.raises(spack.spec.InvalidDependencyError):
-            spec.normalize()
+            spec.concretize()
 
     def test_equal(self):
         # Different spec structures to test for equality
diff --git a/lib/spack/spack/test/spec_semantics.py b/lib/spack/spack/test/spec_semantics.py
index 03f77992c5..d24c38fafc 100644
--- a/lib/spack/spack/test/spec_semantics.py
+++ b/lib/spack/spack/test/spec_semantics.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import spack.architecture
 import pytest
 
@@ -101,7 +82,7 @@ def check_invalid_constraint(spec, constraint):
         spec.constrain(constraint)
 
 
-@pytest.mark.usefixtures('config', 'builtin_mock')
+@pytest.mark.usefixtures('config', 'mock_packages')
 class TestSpecSematics(object):
     """This tests satisfies(), constrain() and other semantic operations
     on specs.
@@ -720,3 +701,45 @@ class TestSpecSematics(object):
 
         with pytest.raises(ValueError):
             Spec('libelf foo')
+
+    def test_spec_formatting(self):
+        spec = Spec("libelf cflags=-O2")
+        spec.concretize()
+
+        # Since the default is the full spec see if the string rep of
+        # spec is the same as the output of spec.format()
+        # ignoring whitespace (though should we?)
+        assert str(spec) == spec.format().strip()
+
+        # Testing named strings ie ${STRING} and whether we get
+        # the correct component
+        package_segments = [("${PACKAGE}", "name"),
+                            ("${VERSION}", "versions"),
+                            ("${COMPILER}", "compiler"),
+                            ("${COMPILERFLAGS}", "compiler_flags"),
+                            ("${OPTIONS}", "variants"),
+                            ("${ARCHITECTURE}", "architecture")]
+
+        compiler_segments = [("${COMPILERNAME}", "name"),
+                             ("${COMPILERVER}", "versions")]
+
+        architecture_segments = [("${PLATFORM}", "platform"),
+                                 ("${OS}", "platform_os"),
+                                 ("${TARGET}", "target")]
+
+        for named_str, prop in package_segments:
+            expected = getattr(spec, prop, "")
+            actual = spec.format(named_str)
+            assert str(expected) == actual
+
+        compiler = spec.compiler
+        for named_str, prop in compiler_segments:
+            expected = getattr(compiler, prop, "")
+            actual = spec.format(named_str)
+            assert str(expected) == actual
+
+        arch = spec.architecture
+        for named_str, prop in architecture_segments:
+            expected = getattr(arch, prop, "")
+            actual = spec.format(named_str)
+            assert str(expected) == actual
diff --git a/lib/spack/spack/test/spec_syntax.py b/lib/spack/spack/test/spec_syntax.py
index 009cb5c129..fc8cec097a 100644
--- a/lib/spack/spack/test/spec_syntax.py
+++ b/lib/spack/spack/test/spec_syntax.py
@@ -1,31 +1,12 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import pytest
 import shlex
 
-import spack
+import spack.store
 import spack.spec as sp
 from spack.parse import Token
 from spack.spec import Spec, parse, parse_anonymous_spec
@@ -94,7 +75,7 @@ class TestSpecSyntax(object):
     # Parse checks
     # ========================================================================
 
-    def check_parse(self, expected, spec=None, remove_arch=True):
+    def check_parse(self, expected, spec=None):
         """Assert that the provided spec is able to be parsed.
 
            If this is called with one argument, it assumes that the
@@ -152,14 +133,18 @@ class TestSpecSyntax(object):
         self.check_parse('@4.2: languages=go')
 
     def test_simple_dependence(self):
-        self.check_parse("openmpi^hwloc")
-        self.check_parse("openmpi^hwloc^libunwind")
+        self.check_parse("openmpi ^hwloc")
+        self.check_parse("openmpi ^hwloc", "openmpi^hwloc")
+
+        self.check_parse("openmpi ^hwloc ^libunwind")
+        self.check_parse("openmpi ^hwloc ^libunwind",
+                         "openmpi^hwloc^libunwind")
 
     def test_dependencies_with_versions(self):
-        self.check_parse("openmpi^hwloc@1.2e6")
-        self.check_parse("openmpi^hwloc@1.2e6:")
-        self.check_parse("openmpi^hwloc@:1.4b7-rc3")
-        self.check_parse("openmpi^hwloc@1.2e6:1.4b7-rc3")
+        self.check_parse("openmpi ^hwloc@1.2e6")
+        self.check_parse("openmpi ^hwloc@1.2e6:")
+        self.check_parse("openmpi ^hwloc@:1.4b7-rc3")
+        self.check_parse("openmpi ^hwloc@1.2e6:1.4b7-rc3")
 
     def test_multiple_specs(self):
         self.check_parse("mvapich emacs")
@@ -172,31 +157,33 @@ class TestSpecSyntax(object):
     def test_multiple_specs_long_second(self):
         self.check_parse('mvapich emacs@1.1.1%intel cflags="-O3"',
                          'mvapich emacs @1.1.1 %intel cflags=-O3')
-        self.check_parse('mvapich cflags="-O3 -fPIC" emacs^ncurses%intel')
+        self.check_parse('mvapich cflags="-O3 -fPIC" emacs ^ncurses%intel')
+        self.check_parse('mvapich cflags="-O3 -fPIC" emacs ^ncurses%intel',
+                         'mvapich cflags="-O3 -fPIC" emacs^ncurses%intel')
 
     def test_full_specs(self):
         self.check_parse(
             "mvapich_foo"
-            "^_openmpi@1.2:1.4,1.6%intel@12.1+debug~qt_4"
-            "^stackwalker@8.1_1e")
+            " ^_openmpi@1.2:1.4,1.6%intel@12.1+debug~qt_4"
+            " ^stackwalker@8.1_1e")
         self.check_parse(
             "mvapich_foo"
-            "^_openmpi@1.2:1.4,1.6%intel@12.1 debug=2 ~qt_4"
-            "^stackwalker@8.1_1e")
+            " ^_openmpi@1.2:1.4,1.6%intel@12.1 debug=2 ~qt_4"
+            " ^stackwalker@8.1_1e")
         self.check_parse(
             'mvapich_foo'
-            '^_openmpi@1.2:1.4,1.6%intel@12.1 cppflags="-O3" +debug~qt_4'
-            '^stackwalker@8.1_1e')
+            ' ^_openmpi@1.2:1.4,1.6%intel@12.1 cppflags="-O3" +debug~qt_4'
+            ' ^stackwalker@8.1_1e')
         self.check_parse(
             "mvapich_foo"
-            "^_openmpi@1.2:1.4,1.6%intel@12.1 debug=2 ~qt_4"
-            "^stackwalker@8.1_1e arch=test-redhat6-x86_32")
+            " ^_openmpi@1.2:1.4,1.6%intel@12.1 debug=2 ~qt_4"
+            " ^stackwalker@8.1_1e arch=test-redhat6-x86_32")
 
     def test_canonicalize(self):
         self.check_parse(
             "mvapich_foo"
-            "^_openmpi@1.2:1.4,1.6%intel@12.1:12.6+debug~qt_4"
-            "^stackwalker@8.1_1e",
+            " ^_openmpi@1.2:1.4,1.6%intel@12.1:12.6+debug~qt_4"
+            " ^stackwalker@8.1_1e",
 
             "mvapich_foo "
             "^_openmpi@1.6,1.2:1.4%intel@12.1:12.6+debug~qt_4 "
@@ -204,21 +191,21 @@ class TestSpecSyntax(object):
 
         self.check_parse(
             "mvapich_foo"
-            "^_openmpi@1.2:1.4,1.6%intel@12.1:12.6+debug~qt_4"
-            "^stackwalker@8.1_1e",
+            " ^_openmpi@1.2:1.4,1.6%intel@12.1:12.6+debug~qt_4"
+            " ^stackwalker@8.1_1e",
 
             "mvapich_foo "
             "^stackwalker@8.1_1e "
             "^_openmpi@1.6,1.2:1.4%intel@12.1:12.6~qt_4+debug")
 
         self.check_parse(
-            "x^y@1,2:3,4%intel@1,2,3,4+a~b+c~d+e~f",
+            "x ^y@1,2:3,4%intel@1,2,3,4+a~b+c~d+e~f",
             "x ^y~f+e~d+c~b+a@4,2:3,1%intel@4,3,2,1")
 
         self.check_parse(
             "x arch=test-redhat6-None "
-            "^y arch=test-None-x86_64 "
-            "^z arch=linux-None-None",
+            " ^y arch=test-None-x86_64 "
+            " ^z arch=linux-None-None",
 
             "x os=fe "
             "^y target=be "
@@ -226,12 +213,12 @@ class TestSpecSyntax(object):
 
         self.check_parse(
             "x arch=test-debian6-x86_64 "
-            "^y arch=test-debian6-x86_64",
+            " ^y arch=test-debian6-x86_64",
 
             "x os=default_os target=default_target "
             "^y os=default_os target=default_target")
 
-        self.check_parse("x^y", "x@: ^y@:")
+        self.check_parse("x ^y", "x@: ^y@:")
 
     def test_parse_errors(self):
         errors = ['x@@1.2', 'x ^y@@1.2', 'x@1.2::', 'x::']
@@ -253,17 +240,19 @@ class TestSpecSyntax(object):
             str(spec), spec.name + '@' + str(spec.version) +
             ' /' + spec.dag_hash()[:6])
 
+    @pytest.mark.db
     def test_spec_by_hash(self, database):
-        specs = database.mock.db.query()
+        specs = database.query()
         assert len(specs)  # make sure something's in the DB
 
         for spec in specs:
             self._check_hash_parse(spec)
 
+    @pytest.mark.db
     def test_dep_spec_by_hash(self, database):
-        mpileaks_zmpi = database.mock.db.query_one('mpileaks ^zmpi')
-        zmpi = database.mock.db.query_one('zmpi')
-        fake = database.mock.db.query_one('fake')
+        mpileaks_zmpi = database.query_one('mpileaks ^zmpi')
+        zmpi = database.query_one('zmpi')
+        fake = database.query_one('fake')
 
         assert 'fake' in mpileaks_zmpi
         assert 'zmpi' in mpileaks_zmpi
@@ -287,9 +276,10 @@ class TestSpecSyntax(object):
         assert 'fake' in mpileaks_hash_fake_and_zmpi
         assert mpileaks_hash_fake_and_zmpi['fake'] == fake
 
+    @pytest.mark.db
     def test_multiple_specs_with_hash(self, database):
-        mpileaks_zmpi = database.mock.db.query_one('mpileaks ^zmpi')
-        callpath_mpich2 = database.mock.db.query_one('callpath ^mpich2')
+        mpileaks_zmpi = database.query_one('mpileaks ^zmpi')
+        callpath_mpich2 = database.query_one('callpath ^mpich2')
 
         # name + hash + separate hash
         specs = sp.parse('mpileaks /' + mpileaks_zmpi.dag_hash() +
@@ -319,6 +309,7 @@ class TestSpecSyntax(object):
                          ' / ' + callpath_mpich2.dag_hash())
         assert len(specs) == 2
 
+    @pytest.mark.db
     def test_ambiguous_hash(self, database):
         x1 = Spec('a')
         x1._hash = 'xy'
@@ -326,8 +317,8 @@ class TestSpecSyntax(object):
         x2 = Spec('a')
         x2._hash = 'xx'
         x2._concrete = True
-        database.mock.db.add(x1, spack.store.layout)
-        database.mock.db.add(x2, spack.store.layout)
+        database.add(x1, spack.store.layout)
+        database.add(x2, spack.store.layout)
 
         # ambiguity in first hash character
         self._check_raises(AmbiguousHashError, ['/x'])
@@ -335,12 +326,13 @@ class TestSpecSyntax(object):
         # ambiguity in first hash character AND spec name
         self._check_raises(AmbiguousHashError, ['a/x'])
 
+    @pytest.mark.db
     def test_invalid_hash(self, database):
-        mpileaks_zmpi = database.mock.db.query_one('mpileaks ^zmpi')
-        zmpi = database.mock.db.query_one('zmpi')
+        mpileaks_zmpi = database.query_one('mpileaks ^zmpi')
+        zmpi = database.query_one('zmpi')
 
-        mpileaks_mpich = database.mock.db.query_one('mpileaks ^mpich')
-        mpich = database.mock.db.query_one('mpich')
+        mpileaks_mpich = database.query_one('mpileaks ^mpich')
+        mpich = database.query_one('mpich')
 
         # name + incompatible hash
         self._check_raises(InvalidHashError, [
@@ -352,9 +344,10 @@ class TestSpecSyntax(object):
             'mpileaks ^mpich /' + mpileaks_zmpi.dag_hash(),
             'mpileaks ^zmpi /' + mpileaks_mpich.dag_hash()])
 
+    @pytest.mark.db
     def test_nonexistent_hash(self, database):
         """Ensure we get errors for nonexistant hashes."""
-        specs = database.mock.db.query()
+        specs = database.query()
 
         # This hash shouldn't be in the test DB.  What are the odds :)
         no_such_hash = 'aaaaaaaaaaaaaaa'
@@ -365,6 +358,7 @@ class TestSpecSyntax(object):
             '/' + no_such_hash,
             'mpileaks /' + no_such_hash])
 
+    @pytest.mark.db
     def test_redundant_spec(self, database):
         """Check that redundant spec constraints raise errors.
 
@@ -372,11 +366,11 @@ class TestSpecSyntax(object):
         specs only raise errors if constraints cause a contradiction?
 
         """
-        mpileaks_zmpi = database.mock.db.query_one('mpileaks ^zmpi')
-        callpath_zmpi = database.mock.db.query_one('callpath ^zmpi')
-        dyninst = database.mock.db.query_one('dyninst')
+        mpileaks_zmpi = database.query_one('mpileaks ^zmpi')
+        callpath_zmpi = database.query_one('callpath ^zmpi')
+        dyninst = database.query_one('dyninst')
 
-        mpileaks_mpich2 = database.mock.db.query_one('mpileaks ^mpich2')
+        mpileaks_mpich2 = database.query_one('mpileaks ^mpich2')
 
         redundant_specs = [
             # redudant compiler
diff --git a/lib/spack/spack/test/spec_yaml.py b/lib/spack/spack/test/spec_yaml.py
index cefb737cfb..5e5ac37904 100644
--- a/lib/spack/spack/test/spec_yaml.py
+++ b/lib/spack/spack/test/spec_yaml.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """Test YAML serialization for specs.
 
 YAML format preserves DAG information in the spec.
@@ -46,13 +27,13 @@ def test_simple_spec():
     check_yaml_round_trip(spec)
 
 
-def test_normal_spec(builtin_mock):
+def test_normal_spec(mock_packages):
     spec = Spec('mpileaks+debug~opt')
     spec.normalize()
     check_yaml_round_trip(spec)
 
 
-def test_external_spec(config, builtin_mock):
+def test_external_spec(config, mock_packages):
     spec = Spec('externaltool')
     spec.concretize()
     check_yaml_round_trip(spec)
@@ -62,13 +43,13 @@ def test_external_spec(config, builtin_mock):
     check_yaml_round_trip(spec)
 
 
-def test_ambiguous_version_spec(builtin_mock):
+def test_ambiguous_version_spec(mock_packages):
     spec = Spec('mpileaks@1.0:5.0,6.1,7.3+debug~opt')
     spec.normalize()
     check_yaml_round_trip(spec)
 
 
-def test_concrete_spec(config, builtin_mock):
+def test_concrete_spec(config, mock_packages):
     spec = Spec('mpileaks+debug~opt')
     spec.concretize()
     check_yaml_round_trip(spec)
@@ -80,7 +61,7 @@ def test_yaml_multivalue():
     check_yaml_round_trip(spec)
 
 
-def test_yaml_subdag(config, builtin_mock):
+def test_yaml_subdag(config, mock_packages):
     spec = Spec('mpileaks^mpich+debug')
     spec.concretize()
     yaml_spec = Spec.from_yaml(spec.to_yaml())
@@ -89,7 +70,7 @@ def test_yaml_subdag(config, builtin_mock):
         assert spec[dep].eq_dag(yaml_spec[dep])
 
 
-def test_using_ordered_dict(builtin_mock):
+def test_using_ordered_dict(mock_packages):
     """ Checks that dicts are ordered
 
     Necessary to make sure that dag_hash is stable across python
@@ -122,7 +103,7 @@ def test_using_ordered_dict(builtin_mock):
 
 
 def test_ordered_read_not_required_for_consistent_dag_hash(
-        config, builtin_mock
+        config, mock_packages
 ):
     """Make sure ordered serialization isn't required to preserve hashes.
 
@@ -195,6 +176,16 @@ def test_ordered_read_not_required_for_consistent_dag_hash(
         assert spec.dag_hash() == round_trip_json_spec.dag_hash()
         assert spec.dag_hash() == round_trip_reversed_yaml_spec.dag_hash()
         assert spec.dag_hash() == round_trip_reversed_json_spec.dag_hash()
+        # full_hashes are equal
+        spec.concretize()
+        round_trip_yaml_spec.concretize()
+        round_trip_json_spec.concretize()
+        round_trip_reversed_yaml_spec.concretize()
+        round_trip_reversed_json_spec.concretize()
+        assert spec.full_hash() == round_trip_yaml_spec.full_hash()
+        assert spec.full_hash() == round_trip_json_spec.full_hash()
+        assert spec.full_hash() == round_trip_reversed_yaml_spec.full_hash()
+        assert spec.full_hash() == round_trip_reversed_json_spec.full_hash()
 
 
 def reverse_all_dicts(data):
diff --git a/lib/spack/spack/test/stage.py b/lib/spack/spack/test/stage.py
index 2117ef5462..971033472a 100644
--- a/lib/spack/spack/test/stage.py
+++ b/lib/spack/spack/test/stage.py
@@ -1,35 +1,17 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """Test that the Stage class works correctly."""
-import collections
 import os
-
-from llnl.util.filesystem import join_path, working_dir
+import collections
 
 import pytest
-import spack
+
+from llnl.util.filesystem import working_dir
+
+import spack.paths
 import spack.stage
 import spack.util.executable
 from spack.stage import Stage
@@ -42,9 +24,9 @@ def check_expand_archive(stage, stage_name, mock_archive):
     assert archive_name in os.listdir(stage_path)
     assert archive_dir in os.listdir(stage_path)
 
-    assert join_path(stage_path, archive_dir) == stage.source_path
+    assert os.path.join(stage_path, archive_dir) == stage.source_path
 
-    readme = join_path(stage_path, archive_dir, 'README.txt')
+    readme = os.path.join(stage_path, archive_dir, 'README.txt')
     assert os.path.isfile(readme)
     with open(readme) as file:
         'hello world!\n' == file.read()
@@ -54,7 +36,7 @@ def check_fetch(stage, stage_name):
     archive_name = 'test-files.tar.gz'
     stage_path = get_stage_path(stage, stage_name)
     assert archive_name in os.listdir(stage_path)
-    assert join_path(stage_path, archive_name) == stage.fetcher.archive_file
+    assert os.path.join(stage_path, archive_name) == stage.fetcher.archive_file
 
 
 def check_destroy(stage, stage_name):
@@ -101,31 +83,28 @@ def get_stage_path(stage, stage_name):
     """
     if stage_name is not None:
         # If it is a named stage, we know where the stage should be
-        return join_path(spack.stage_path, stage_name)
+        return os.path.join(spack.paths.stage_path, stage_name)
     else:
         # If it's unnamed, ensure that we ran mkdtemp in the right spot.
         assert stage.path is not None
-        assert stage.path.startswith(spack.stage_path)
+        assert stage.path.startswith(spack.paths.stage_path)
         return stage.path
 
 
 @pytest.fixture()
-def tmpdir_for_stage(mock_archive):
+def tmpdir_for_stage(mock_archive, mutable_config):
     """Uses a temporary directory for staging"""
-    current = spack.stage_path
-    spack.config.update_config(
+    current = spack.paths.stage_path
+    spack.config.set(
         'config',
         {'build_stage': [str(mock_archive.test_tmp_dir)]},
-        scope='user'
-    )
+        scope='user')
     yield
-    spack.config.update_config(
-        'config', {'build_stage': [current]}, scope='user'
-    )
+    spack.config.set('config', {'build_stage': [current]}, scope='user')
 
 
 @pytest.fixture()
-def mock_archive(tmpdir, monkeypatch):
+def mock_archive(tmpdir, monkeypatch, mutable_config):
     """Creates a mock archive with the structure expected by the tests"""
     # Mock up a stage area that looks like this:
     #
@@ -137,9 +116,8 @@ def mock_archive(tmpdir, monkeypatch):
     #
     test_tmp_path = tmpdir.join('tmp')
     # set _test_tmp_path as the default test directory to use for stages.
-    spack.config.update_config(
-        'config', {'build_stage': [str(test_tmp_path)]}, scope='user'
-    )
+    spack.config.set(
+        'config', {'build_stage': [str(test_tmp_path)]}, scope='user')
 
     archive_dir = tmpdir.join('test-files')
     archive_name = 'test-files.tar.gz'
@@ -202,7 +180,7 @@ def search_fn():
     return _Mock()
 
 
-@pytest.mark.usefixtures('builtin_mock')
+@pytest.mark.usefixtures('mock_packages')
 class TestStage(object):
 
     stage_name = 'spack-test-stage'
diff --git a/lib/spack/spack/test/svn_fetch.py b/lib/spack/spack/test/svn_fetch.py
index f00b0b8259..129c38587a 100644
--- a/lib/spack/spack/test/svn_fetch.py
+++ b/lib/spack/spack/test/svn_fetch.py
@@ -1,32 +1,16 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 
 import pytest
-import spack
-from llnl.util.filesystem import join_path, touch, working_dir
+
+from llnl.util.filesystem import touch, working_dir
+
+import spack.repo
+import spack.config
 from spack.spec import Spec
 from spack.version import ver
 from spack.util.executable import which
@@ -43,7 +27,7 @@ def test_fetch(
         secure,
         mock_svn_repository,
         config,
-        refresh_builtin_mock
+        mutable_mock_packages
 ):
     """Tries to:
 
@@ -61,21 +45,18 @@ def test_fetch(
     # Construct the package under test
     spec = Spec('svn-test')
     spec.concretize()
-    pkg = spack.repo.get(spec, new=True)
+    pkg = spack.repo.get(spec)
     pkg.versions[ver('svn')] = t.args
 
     # Enter the stage directory and check some properties
     with pkg.stage:
-        try:
-            spack.insecure = secure
+        with spack.config.override('config:verify_ssl', secure):
             pkg.do_stage()
-        finally:
-            spack.insecure = False
 
         with working_dir(pkg.stage.source_path):
             assert h() == t.revision
 
-            file_path = join_path(pkg.stage.source_path, t.file)
+            file_path = os.path.join(pkg.stage.source_path, t.file)
             assert os.path.isdir(pkg.stage.source_path)
             assert os.path.isfile(file_path)
 
diff --git a/lib/spack/spack/test/tengine.py b/lib/spack/spack/test/tengine.py
index 35979879e1..c9cfbc59d0 100644
--- a/lib/spack/spack/test/tengine.py
+++ b/lib/spack/spack/test/tengine.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 import pytest
 import spack.tengine as tengine
@@ -91,7 +72,7 @@ class TestTengineEnvironment(object):
     def test_template_retrieval(self):
         """Tests the template retrieval mechanism hooked into config files"""
         # Check the directories are correct
-        template_dirs = spack.config.get_config('config')['template_dirs']
+        template_dirs = spack.config.get('config:template_dirs')
         template_dirs = [canonicalize_path(x) for x in template_dirs]
         assert len(template_dirs) == 3
 
diff --git a/lib/spack/spack/test/test_activations.py b/lib/spack/spack/test/test_activations.py
index ec3562aaa6..35f1d0c87d 100644
--- a/lib/spack/spack/test/test_activations.py
+++ b/lib/spack/spack/test/test_activations.py
@@ -1,41 +1,29 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-import spack
-from llnl.util.filesystem import join_path
+import os
+import pytest
+import sys
+
+import spack.spec
+import spack.package
+from llnl.util.link_tree import MergeConflictError
+from spack.build_systems.python import PythonPackage
 from spack.directory_layout import YamlDirectoryLayout
 from spack.filesystem_view import YamlFilesystemView
+from spack.util.prefix import Prefix
 
-import os
-import pytest
+"""This includes tests for customized activation logic for specific packages
+   (e.g. python and perl).
+"""
 
 
-class FakeExtensionPackage(object):
+class FakeExtensionPackage(spack.package.PackageViewMixin):
     def __init__(self, name, prefix):
         self.name = name
-        self.prefix = prefix
+        self.prefix = Prefix(prefix)
         self.spec = FakeSpec(self)
 
 
@@ -44,10 +32,43 @@ class FakeSpec(object):
         self.name = package.name
         self.prefix = package.prefix
         self.hash = self.name
+        self.package = package
+        self.concrete = True
 
     def dag_hash(self):
         return self.hash
 
+    def __lt__(self, other):
+        return self.name < other.name
+
+
+class FakePythonExtensionPackage(FakeExtensionPackage):
+    def __init__(self, name, prefix, py_namespace, python_spec):
+        self.py_namespace = py_namespace
+        self.extendee_spec = python_spec
+        super(FakePythonExtensionPackage, self).__init__(name, prefix)
+
+    def add_files_to_view(self, view, merge_map):
+        if sys.version_info >= (3, 0):
+            add_fn = PythonPackage.add_files_to_view
+        else:
+            add_fn = PythonPackage.add_files_to_view.im_func
+        return add_fn(self, view, merge_map)
+
+    def view_file_conflicts(self, view, merge_map):
+        if sys.version_info >= (3, 0):
+            conflicts_fn = PythonPackage.view_file_conflicts
+        else:
+            conflicts_fn = PythonPackage.view_file_conflicts.im_func
+        return conflicts_fn(self, view, merge_map)
+
+    def remove_files_from_view(self, view, merge_map):
+        if sys.version_info >= (3, 0):
+            remove_fn = PythonPackage.remove_files_from_view
+        else:
+            remove_fn = PythonPackage.remove_files_from_view.im_func
+        return remove_fn(self, view, merge_map)
+
 
 def create_dir_structure(tmpdir, dir_structure):
     for fname, children in dir_structure.items():
@@ -75,7 +96,7 @@ def python_and_extension_dirs(tmpdir):
 
     python_spec = spack.spec.Spec('python@2.7.12')
     python_spec._concrete = True
-    python_spec.package.spec._set_test_prefix(str(python_prefix))
+    python_spec.package.spec.prefix = str(python_prefix)
 
     ext_dirs = {
         'bin/': {
@@ -97,32 +118,56 @@ def python_and_extension_dirs(tmpdir):
     create_dir_structure(ext_prefix, ext_dirs)
 
     easy_install_location = 'lib/python2.7/site-packages/easy-install.pth'
-    with open(join_path(ext_prefix, easy_install_location), 'w') as F:
-        F.write("""path/to/ext1.egg
+    with open(str(ext_prefix.join(easy_install_location)), 'w') as f:
+        f.write("""path/to/ext1.egg
 path/to/setuptools.egg""")
 
     return str(python_prefix), str(ext_prefix)
 
 
-def test_python_activation(tmpdir):
-    # Note the lib directory is based partly on the python version
-    python_spec = spack.spec.Spec('python@2.7.12')
-    python_spec._concrete = True
+@pytest.fixture()
+def namespace_extensions(tmpdir):
+    ext1_dirs = {
+        'bin/': {
+            'py-ext-tool1': None
+        },
+        'lib/': {
+            'python2.7/': {
+                'site-packages/': {
+                    'examplenamespace/': {
+                        '__init__.py': None,
+                        'ext1_sample.py': None
+                    }
+                }
+            }
+        }
+    }
 
-    python_name = 'python'
-    tmpdir.ensure(python_name, dir=True)
+    ext2_dirs = {
+        'bin/': {
+            'py-ext-tool2': None
+        },
+        'lib/': {
+            'python2.7/': {
+                'site-packages/': {
+                    'examplenamespace/': {
+                        '__init__.py': None,
+                        'ext2_sample.py': None
+                    }
+                }
+            }
+        }
+    }
 
-    python_prefix = str(tmpdir.join(python_name))
-    # Set the prefix on the package's spec reference because that is a copy of
-    # the original spec
-    python_spec.package.spec._set_test_prefix(python_prefix)
+    ext1_name = 'py-extension1'
+    ext1_prefix = tmpdir.join(ext1_name)
+    create_dir_structure(ext1_prefix, ext1_dirs)
 
-    ext_name = 'py-extension'
-    tmpdir.ensure(ext_name, dir=True)
-    ext_pkg = FakeExtensionPackage(ext_name, str(tmpdir.join(ext_name)))
+    ext2_name = 'py-extension2'
+    ext2_prefix = tmpdir.join(ext2_name)
+    create_dir_structure(ext2_prefix, ext2_dirs)
 
-    python_pkg = python_spec.package
-    python_pkg.activate(ext_pkg)
+    return str(ext1_prefix), str(ext2_prefix), 'examplenamespace'
 
 
 def test_python_activation_with_files(tmpdir, python_and_extension_dirs):
@@ -130,18 +175,18 @@ def test_python_activation_with_files(tmpdir, python_and_extension_dirs):
 
     python_spec = spack.spec.Spec('python@2.7.12')
     python_spec._concrete = True
-    python_spec.package.spec._set_test_prefix(python_prefix)
+    python_spec.package.spec.prefix = python_prefix
 
     ext_pkg = FakeExtensionPackage('py-extension', ext_prefix)
 
     python_pkg = python_spec.package
-    python_pkg.activate(ext_pkg)
+    python_pkg.activate(ext_pkg, python_pkg.view())
 
-    assert os.path.exists(join_path(python_prefix, 'bin/py-ext-tool'))
+    assert os.path.exists(os.path.join(python_prefix, 'bin/py-ext-tool'))
 
     easy_install_location = 'lib/python2.7/site-packages/easy-install.pth'
-    with open(join_path(python_prefix, easy_install_location), 'r') as F:
-        easy_install_contents = F.read()
+    with open(os.path.join(python_prefix, easy_install_location), 'r') as f:
+        easy_install_contents = f.read()
 
     assert 'ext1.egg' in easy_install_contents
     assert 'setuptools.egg' not in easy_install_contents
@@ -152,7 +197,7 @@ def test_python_activation_view(tmpdir, python_and_extension_dirs):
 
     python_spec = spack.spec.Spec('python@2.7.12')
     python_spec._concrete = True
-    python_spec.package.spec._set_test_prefix(python_prefix)
+    python_spec.package.spec.prefix = python_prefix
 
     ext_pkg = FakeExtensionPackage('py-extension', ext_prefix)
 
@@ -161,11 +206,112 @@ def test_python_activation_view(tmpdir, python_and_extension_dirs):
     view = YamlFilesystemView(view_dir, layout)
 
     python_pkg = python_spec.package
-    python_pkg.activate(ext_pkg, extensions_layout=view.extensions_layout)
+    python_pkg.activate(ext_pkg, view)
+
+    assert not os.path.exists(os.path.join(python_prefix, 'bin/py-ext-tool'))
+
+    assert os.path.exists(os.path.join(view_dir, 'bin/py-ext-tool'))
+
+
+def test_python_ignore_namespace_init_conflict(tmpdir, namespace_extensions):
+    """Test the view update logic in PythonPackage ignores conflicting
+       instances of __init__ for packages which are in the same namespace.
+    """
+    ext1_prefix, ext2_prefix, py_namespace = namespace_extensions
+
+    python_spec = spack.spec.Spec('python@2.7.12')
+    python_spec._concrete = True
+
+    ext1_pkg = FakePythonExtensionPackage(
+        'py-extension1', ext1_prefix, py_namespace, python_spec)
+    ext2_pkg = FakePythonExtensionPackage(
+        'py-extension2', ext2_prefix, py_namespace, python_spec)
+
+    view_dir = str(tmpdir.join('view'))
+    layout = YamlDirectoryLayout(view_dir)
+    view = YamlFilesystemView(view_dir, layout)
+
+    python_pkg = python_spec.package
+    python_pkg.activate(ext1_pkg, view)
+    # Normally handled by Package.do_activate, but here we activate directly
+    view.extensions_layout.add_extension(python_spec, ext1_pkg.spec)
+    python_pkg.activate(ext2_pkg, view)
+
+    f1 = 'lib/python2.7/site-packages/examplenamespace/ext1_sample.py'
+    f2 = 'lib/python2.7/site-packages/examplenamespace/ext2_sample.py'
+    init_file = 'lib/python2.7/site-packages/examplenamespace/__init__.py'
+
+    assert os.path.exists(os.path.join(view_dir, f1))
+    assert os.path.exists(os.path.join(view_dir, f2))
+    assert os.path.exists(os.path.join(view_dir, init_file))
+
+
+def test_python_keep_namespace_init(tmpdir, namespace_extensions):
+    """Test the view update logic in PythonPackage keeps the namespace
+       __init__ file as long as one package in the namespace still
+       exists.
+    """
+    ext1_prefix, ext2_prefix, py_namespace = namespace_extensions
+
+    python_spec = spack.spec.Spec('python@2.7.12')
+    python_spec._concrete = True
+
+    ext1_pkg = FakePythonExtensionPackage(
+        'py-extension1', ext1_prefix, py_namespace, python_spec)
+    ext2_pkg = FakePythonExtensionPackage(
+        'py-extension2', ext2_prefix, py_namespace, python_spec)
+
+    view_dir = str(tmpdir.join('view'))
+    layout = YamlDirectoryLayout(view_dir)
+    view = YamlFilesystemView(view_dir, layout)
+
+    python_pkg = python_spec.package
+    python_pkg.activate(ext1_pkg, view)
+    # Normally handled by Package.do_activate, but here we activate directly
+    view.extensions_layout.add_extension(python_spec, ext1_pkg.spec)
+    python_pkg.activate(ext2_pkg, view)
+    view.extensions_layout.add_extension(python_spec, ext2_pkg.spec)
+
+    f1 = 'lib/python2.7/site-packages/examplenamespace/ext1_sample.py'
+    init_file = 'lib/python2.7/site-packages/examplenamespace/__init__.py'
+
+    python_pkg.deactivate(ext1_pkg, view)
+    view.extensions_layout.remove_extension(python_spec, ext1_pkg.spec)
+
+    assert not os.path.exists(os.path.join(view_dir, f1))
+    assert os.path.exists(os.path.join(view_dir, init_file))
+
+    python_pkg.deactivate(ext2_pkg, view)
+    view.extensions_layout.remove_extension(python_spec, ext2_pkg.spec)
 
-    assert not os.path.exists(join_path(python_prefix, 'bin/py-ext-tool'))
+    assert not os.path.exists(os.path.join(view_dir, init_file))
 
-    assert os.path.exists(join_path(view_dir, 'bin/py-ext-tool'))
+
+def test_python_namespace_conflict(tmpdir, namespace_extensions):
+    """Test the view update logic in PythonPackage reports an error when two
+       python extensions with different namespaces have a conflicting __init__
+       file.
+    """
+    ext1_prefix, ext2_prefix, py_namespace = namespace_extensions
+    other_namespace = py_namespace + 'other'
+
+    python_spec = spack.spec.Spec('python@2.7.12')
+    python_spec._concrete = True
+
+    ext1_pkg = FakePythonExtensionPackage(
+        'py-extension1', ext1_prefix, py_namespace, python_spec)
+    ext2_pkg = FakePythonExtensionPackage(
+        'py-extension2', ext2_prefix, other_namespace, python_spec)
+
+    view_dir = str(tmpdir.join('view'))
+    layout = YamlDirectoryLayout(view_dir)
+    view = YamlFilesystemView(view_dir, layout)
+
+    python_pkg = python_spec.package
+    python_pkg.activate(ext1_pkg, view)
+    view.extensions_layout.add_extension(python_spec, ext1_pkg.spec)
+    with pytest.raises(MergeConflictError):
+        python_pkg.activate(ext2_pkg, view)
 
 
 @pytest.fixture()
@@ -189,7 +335,7 @@ def perl_and_extension_dirs(tmpdir):
 
     perl_spec = spack.spec.Spec('perl@5.24.1')
     perl_spec._concrete = True
-    perl_spec.package.spec._set_test_prefix(str(perl_prefix))
+    perl_spec.package.spec.prefix = str(perl_prefix)
 
     ext_dirs = {
         'bin/': {
@@ -225,14 +371,14 @@ def test_perl_activation(tmpdir):
     perl_prefix = str(tmpdir.join(perl_name))
     # Set the prefix on the package's spec reference because that is a copy of
     # the original spec
-    perl_spec.package.spec._set_test_prefix(perl_prefix)
+    perl_spec.package.spec.prefix = perl_prefix
 
     ext_name = 'perl-extension'
     tmpdir.ensure(ext_name, dir=True)
     ext_pkg = FakeExtensionPackage(ext_name, str(tmpdir.join(ext_name)))
 
     perl_pkg = perl_spec.package
-    perl_pkg.activate(ext_pkg)
+    perl_pkg.activate(ext_pkg, perl_pkg.view())
 
 
 def test_perl_activation_with_files(tmpdir, perl_and_extension_dirs):
@@ -240,14 +386,14 @@ def test_perl_activation_with_files(tmpdir, perl_and_extension_dirs):
 
     perl_spec = spack.spec.Spec('perl@5.24.1')
     perl_spec._concrete = True
-    perl_spec.package.spec._set_test_prefix(perl_prefix)
+    perl_spec.package.spec.prefix = perl_prefix
 
     ext_pkg = FakeExtensionPackage('perl-extension', ext_prefix)
 
     perl_pkg = perl_spec.package
-    perl_pkg.activate(ext_pkg)
+    perl_pkg.activate(ext_pkg, perl_pkg.view())
 
-    assert os.path.exists(join_path(perl_prefix, 'bin/perl-ext-tool'))
+    assert os.path.exists(os.path.join(perl_prefix, 'bin/perl-ext-tool'))
 
 
 def test_perl_activation_view(tmpdir, perl_and_extension_dirs):
@@ -255,7 +401,7 @@ def test_perl_activation_view(tmpdir, perl_and_extension_dirs):
 
     perl_spec = spack.spec.Spec('perl@5.24.1')
     perl_spec._concrete = True
-    perl_spec.package.spec._set_test_prefix(perl_prefix)
+    perl_spec.package.spec.prefix = perl_prefix
 
     ext_pkg = FakeExtensionPackage('perl-extension', ext_prefix)
 
@@ -264,8 +410,8 @@ def test_perl_activation_view(tmpdir, perl_and_extension_dirs):
     view = YamlFilesystemView(view_dir, layout)
 
     perl_pkg = perl_spec.package
-    perl_pkg.activate(ext_pkg, extensions_layout=view.extensions_layout)
+    perl_pkg.activate(ext_pkg, view)
 
-    assert not os.path.exists(join_path(perl_prefix, 'bin/perl-ext-tool'))
+    assert not os.path.exists(os.path.join(perl_prefix, 'bin/perl-ext-tool'))
 
-    assert os.path.exists(join_path(view_dir, 'bin/perl-ext-tool'))
+    assert os.path.exists(os.path.join(view_dir, 'bin/perl-ext-tool'))
diff --git a/lib/spack/spack/test/url_fetch.py b/lib/spack/spack/test/url_fetch.py
index 168bda5f64..f81521c2b0 100644
--- a/lib/spack/spack/test/url_fetch.py
+++ b/lib/spack/spack/test/url_fetch.py
@@ -1,33 +1,15 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 import pytest
 
 from llnl.util.filesystem import working_dir, is_exe
 
-import spack
+import spack.repo
+import spack.config
 from spack.fetch_strategy import from_list_url, URLFetchStrategy
 from spack.spec import Spec
 from spack.version import ver
@@ -45,13 +27,13 @@ def test_fetch(
         secure,
         checksum_type,
         config,
-        refresh_builtin_mock
+        mutable_mock_packages
 ):
     """Fetch an archive and make sure we can checksum it."""
     mock_archive.url
     mock_archive.path
 
-    algo = crypto.hashes[checksum_type]()
+    algo = crypto.hash_fun_for_algo(checksum_type)()
     with open(mock_archive.archive_file, 'rb') as f:
         algo.update(f.read())
     checksum = algo.hexdigest()
@@ -60,18 +42,15 @@ def test_fetch(
     spec = Spec('url-test')
     spec.concretize()
 
-    pkg = spack.repo.get('url-test', new=True)
+    pkg = spack.repo.get('url-test')
     pkg.url = mock_archive.url
     pkg.versions[ver('test')] = {checksum_type: checksum, 'url': pkg.url}
     pkg.spec = spec
 
     # Enter the stage directory and check some properties
     with pkg.stage:
-        try:
-            spack.insecure = secure
+        with spack.config.override('config:verify_ssl', secure):
             pkg.do_stage()
-        finally:
-            spack.insecure = False
 
         with working_dir(pkg.stage.source_path):
             assert os.path.exists('configure')
@@ -83,22 +62,71 @@ def test_fetch(
             assert 'echo Building...' in contents
 
 
-def test_from_list_url(builtin_mock, config):
-    pkg = spack.repo.get('url-list-test', new=True)
-    for ver_str in ['0.0.0', '1.0.0', '2.0.0',
-                    '3.0', '4.5', '2.0.0b2',
-                    '3.0a1', '4.5-rc5']:
-        spec = Spec('url-list-test@%s' % ver_str)
-        spec.concretize()
-        pkg.spec = spec
-        fetch_strategy = from_list_url(pkg)
-        assert isinstance(fetch_strategy, URLFetchStrategy)
-        assert (os.path.basename(fetch_strategy.url) ==
-                ('foo-' + ver_str + '.tar.gz'))
+def test_from_list_url(mock_packages, config):
+    pkg = spack.repo.get('url-list-test')
+
+    # These URLs are all in the url-list-test package and should have
+    # checksums taken from the package.
+    spec = Spec('url-list-test @0.0.0').concretized()
+    pkg = spack.repo.get(spec)
+    fetch_strategy = from_list_url(pkg)
+    assert isinstance(fetch_strategy, URLFetchStrategy)
+    assert os.path.basename(fetch_strategy.url) == 'foo-0.0.0.tar.gz'
+    assert fetch_strategy.digest == 'abc000'
+
+    spec = Spec('url-list-test @1.0.0').concretized()
+    pkg = spack.repo.get(spec)
+    fetch_strategy = from_list_url(pkg)
+    assert isinstance(fetch_strategy, URLFetchStrategy)
+    assert os.path.basename(fetch_strategy.url) == 'foo-1.0.0.tar.gz'
+    assert fetch_strategy.digest == 'abc100'
+
+    spec = Spec('url-list-test @3.0').concretized()
+    pkg = spack.repo.get(spec)
+    fetch_strategy = from_list_url(pkg)
+    assert isinstance(fetch_strategy, URLFetchStrategy)
+    assert os.path.basename(fetch_strategy.url) == 'foo-3.0.tar.gz'
+    assert fetch_strategy.digest == 'abc30'
+
+    spec = Spec('url-list-test @4.5').concretized()
+    pkg = spack.repo.get(spec)
+    fetch_strategy = from_list_url(pkg)
+    assert isinstance(fetch_strategy, URLFetchStrategy)
+    assert os.path.basename(fetch_strategy.url) == 'foo-4.5.tar.gz'
+    assert fetch_strategy.digest == 'abc45'
+
+    spec = Spec('url-list-test @2.0.0b2').concretized()
+    pkg = spack.repo.get(spec)
+    fetch_strategy = from_list_url(pkg)
+    assert isinstance(fetch_strategy, URLFetchStrategy)
+    assert os.path.basename(fetch_strategy.url) == 'foo-2.0.0b2.tar.gz'
+    assert fetch_strategy.digest == 'abc200b2'
+
+    spec = Spec('url-list-test @3.0a1').concretized()
+    pkg = spack.repo.get(spec)
+    fetch_strategy = from_list_url(pkg)
+    assert isinstance(fetch_strategy, URLFetchStrategy)
+    assert os.path.basename(fetch_strategy.url) == 'foo-3.0a1.tar.gz'
+    assert fetch_strategy.digest == 'abc30a1'
+
+    spec = Spec('url-list-test @4.5-rc5').concretized()
+    pkg = spack.repo.get(spec)
+    fetch_strategy = from_list_url(pkg)
+    assert isinstance(fetch_strategy, URLFetchStrategy)
+    assert os.path.basename(fetch_strategy.url) == 'foo-4.5-rc5.tar.gz'
+    assert fetch_strategy.digest == 'abc45rc5'
+
+    # this one is not in the url-list-test package.
+    spec = Spec('url-list-test @2.0.0').concretized()
+    pkg = spack.repo.get(spec)
+    fetch_strategy = from_list_url(pkg)
+    assert isinstance(fetch_strategy, URLFetchStrategy)
+    assert os.path.basename(fetch_strategy.url) == 'foo-2.0.0.tar.gz'
+    assert fetch_strategy.digest is None
 
 
 def test_hash_detection(checksum_type):
-    algo = crypto.hashes[checksum_type]()
+    algo = crypto.hash_fun_for_algo(checksum_type)()
     h = 'f' * (algo.digest_size * 2)  # hex -> bytes
     checker = crypto.Checker(h)
     assert checker.hash_name == checksum_type
diff --git a/lib/spack/spack/test/url_parse.py b/lib/spack/spack/test/url_parse.py
index 7a22205076..7dcdb36424 100644
--- a/lib/spack/spack/test/url_parse.py
+++ b/lib/spack/spack/test/url_parse.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """Tests Spack's ability to parse the name and version of a package
 based on its URL.
 """
@@ -43,6 +24,8 @@ from spack.version import Version
     ('jpegsrc.v9b', 'jpegsrc.v9b'),
     ('turbolinux702', 'turbolinux702'),
     ('converge_install_2.3.16', 'converge_install_2.3.16'),
+    # Download type - code, source
+    ('cistem-1.0.0-beta-source-code', 'cistem-1.0.0-beta'),
     # Download type - src
     ('apache-ant-1.9.7-src', 'apache-ant-1.9.7'),
     ('go1.7.4.src', 'go1.7.4'),
@@ -75,6 +58,8 @@ from spack.version import Version
     ('ncbi-blast-2.6.0+-src', 'ncbi-blast-2.6.0'),
     # License
     ('cppad-20170114.gpl', 'cppad-20170114'),
+    # Arch
+    ('pcraster-4.1.0_x86-64', 'pcraster-4.1.0'),
     # OS - linux
     ('astyle_2.04_linux', 'astyle_2.04'),
     # OS - unix
@@ -167,6 +152,7 @@ def test_url_strip_name_suffixes(url, version, expected):
     ('libxc', 58, '2.2.2', 64, 'http://www.tddft.org/programs/octopus/down.php?file=libxc/libxc-2.2.2.tar.gz'),
     # Version in suffix
     ('swiftsim', 36, '0.3.0', 76, 'http://gitlab.cosma.dur.ac.uk/swift/swiftsim/repository/archive.tar.gz?ref=v0.3.0'),
+    ('swiftsim', 55, '0.3.0', 95, 'https://gitlab.cosma.dur.ac.uk/api/v4/projects/swift%2Fswiftsim/repository/archive.tar.gz?sha=v0.3.0'),
     ('sionlib', 30, '1.7.1', 59, 'http://apps.fz-juelich.de/jsc/sionlib/download.php?version=1.7.1'),
     # Regex in name
     ('voro++', 40, '0.4.6', 47, 'http://math.lbl.gov/voro++/download/dir/voro++-0.4.6.tar.gz'),
@@ -207,14 +193,21 @@ def test_url_parse_offset(name, noffset, ver, voffset, path):
     ('git', '2.7.1', 'https://github.com/git/git/tarball/v2.7.1'),
     # name/zipball/vver.ver
     ('git', '2.7.1', 'https://github.com/git/git/zipball/v2.7.1'),
+
     # Common Repositories - gitlab downloads
 
     # name/repository/archive.ext?ref=vver.ver
     ('swiftsim', '0.3.0',
      'http://gitlab.cosma.dur.ac.uk/swift/swiftsim/repository/archive.tar.gz?ref=v0.3.0'),
+    # /api/v4/projects/NAMESPACE%2Fname/repository/archive.ext?sha=vver.ver
+    ('swiftsim', '0.3.0',
+     'https://gitlab.cosma.dur.ac.uk/api/v4/projects/swift%2Fswiftsim/repository/archive.tar.gz?sha=v0.3.0'),
     # name/repository/archive.ext?ref=name-ver.ver
     ('icet', '1.2.3',
      'https://gitlab.kitware.com/icet/icet/repository/archive.tar.gz?ref=IceT-1.2.3'),
+    # /api/v4/projects/NAMESPACE%2Fname/repository/archive.ext?sha=name-ver.ver
+    ('icet', '1.2.3',
+     'https://gitlab.kitware.com/api/v4/projects/icet%2Ficet/repository/archive.tar.bz2?sha=IceT-1.2.3'),
 
     # Common Repositories - bitbucket downloads
 
@@ -370,6 +363,7 @@ def test_url_parse_offset(name, noffset, ver, voffset, path):
     ('nextflow', '0.20.1', 'https://github.com/nextflow-io/nextflow/releases/download/v0.20.1/nextflow'),
     # suffix queries
     ('swiftsim', '0.3.0', 'http://gitlab.cosma.dur.ac.uk/swift/swiftsim/repository/archive.tar.gz?ref=v0.3.0'),
+    ('swiftsim', '0.3.0', 'https://gitlab.cosma.dur.ac.uk/api/v4/projects/swift%2Fswiftsim/repository/archive.tar.gz?sha=v0.3.0'),
     ('sionlib', '1.7.1', 'http://apps.fz-juelich.de/jsc/sionlib/download.php?version=1.7.1'),
     # stem queries
     ('slepc', '3.6.2', 'http://slepc.upv.es/download/download.php?filename=slepc-3.6.2.tar.gz'),
diff --git a/lib/spack/spack/test/url_substitution.py b/lib/spack/spack/test/url_substitution.py
index dcd26aad0d..a07a9bf6f0 100644
--- a/lib/spack/spack/test/url_substitution.py
+++ b/lib/spack/spack/test/url_substitution.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """Tests Spack's ability to substitute a different version into a URL."""
 
 import os
diff --git a/lib/spack/spack/test/file_cache.py b/lib/spack/spack/test/util/file_cache.py
index 7098b9673e..fc1391c8e6 100644
--- a/lib/spack/spack/test/file_cache.py
+++ b/lib/spack/spack/test/util/file_cache.py
@@ -1,32 +1,13 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """Test Spack's FileCache."""
 import os
 
 import pytest
-from spack.file_cache import FileCache
+from spack.util.file_cache import FileCache
 
 
 @pytest.fixture()
diff --git a/lib/spack/spack/test/util/filesystem.py b/lib/spack/spack/test/util/filesystem.py
deleted file mode 100644
index 86c243a97e..0000000000
--- a/lib/spack/spack/test/util/filesystem.py
+++ /dev/null
@@ -1,61 +0,0 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-
-import llnl.util.filesystem as fs
-
-
-def test_move_transaction_commit(tmpdir):
-
-    fake_library = tmpdir.mkdir('lib').join('libfoo.so')
-    fake_library.write('Just some fake content.')
-
-    old_md5 = fs.hash_directory(str(tmpdir))
-
-    with fs.replace_directory_transaction(str(tmpdir.join('lib'))):
-        fake_library = tmpdir.mkdir('lib').join('libfoo.so')
-        fake_library.write('Other content.')
-        new_md5 = fs.hash_directory(str(tmpdir))
-
-    assert old_md5 != fs.hash_directory(str(tmpdir))
-    assert new_md5 == fs.hash_directory(str(tmpdir))
-
-
-def test_move_transaction_rollback(tmpdir):
-
-    fake_library = tmpdir.mkdir('lib').join('libfoo.so')
-    fake_library.write('Just some fake content.')
-
-    h = fs.hash_directory(str(tmpdir))
-
-    try:
-        with fs.replace_directory_transaction(str(tmpdir.join('lib'))):
-            assert h != fs.hash_directory(str(tmpdir))
-            fake_library = tmpdir.mkdir('lib').join('libfoo.so')
-            fake_library.write('Other content.')
-            raise RuntimeError('')
-    except RuntimeError:
-        pass
-
-    assert h == fs.hash_directory(str(tmpdir))
diff --git a/lib/spack/spack/test/util/log_parser.py b/lib/spack/spack/test/util/log_parser.py
index 37642f7f1f..976b720fa8 100644
--- a/lib/spack/spack/test/util/log_parser.py
+++ b/lib/spack/spack/test/util/log_parser.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from ctest_log_parser import CTestLogParser
 
 
diff --git a/lib/spack/spack/test/util/prefix.py b/lib/spack/spack/test/util/prefix.py
index e1cda1f1e4..f312afbc29 100644
--- a/lib/spack/spack/test/util/prefix.py
+++ b/lib/spack/spack/test/util/prefix.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """Tests various features of :py:class:`spack.util.prefix.Prefix`"""
 
 from spack.util.prefix import Prefix
@@ -36,6 +17,35 @@ def test_prefix_attributes():
     assert prefix.include == '/usr/include'
 
 
+def test_prefix_join():
+    """Test prefix join  ``prefix.join(...)``"""
+    prefix = Prefix('/usr')
+
+    a1 = prefix.join('a_{0}'.format(1)).lib64
+    a2 = prefix.join('a-{0}'.format(1)).lib64
+    a3 = prefix.join('a.{0}'.format(1)).lib64
+
+    assert a1 == '/usr/a_1/lib64'
+    assert a2 == '/usr/a-1/lib64'
+    assert a3 == '/usr/a.1/lib64'
+
+    assert isinstance(a1, Prefix)
+    assert isinstance(a2, Prefix)
+    assert isinstance(a3, Prefix)
+
+    p1 = prefix.bin.join('executable.sh')
+    p2 = prefix.share.join('pkg-config').join('foo.pc')
+    p3 = prefix.join('dashed-directory').foo
+
+    assert p1 == '/usr/bin/executable.sh'
+    assert p2 == '/usr/share/pkg-config/foo.pc'
+    assert p3 == '/usr/dashed-directory/foo'
+
+    assert isinstance(p1, Prefix)
+    assert isinstance(p2, Prefix)
+    assert isinstance(p3, Prefix)
+
+
 def test_multilevel_attributes():
     """Test attributes of attributes, like ``prefix.share.man``"""
     prefix = Prefix('/usr/')
diff --git a/lib/spack/spack/test/util/spack_lock_wrapper.py b/lib/spack/spack/test/util/spack_lock_wrapper.py
new file mode 100644
index 0000000000..fd06d6b386
--- /dev/null
+++ b/lib/spack/spack/test/util/spack_lock_wrapper.py
@@ -0,0 +1,104 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+"""Tests for Spack's wrapper module around llnl.util.lock."""
+import os
+
+import pytest
+
+from llnl.util.filesystem import group_ids
+
+import spack.config
+import spack.util.lock as lk
+
+
+def test_disable_locking(tmpdir):
+    """Ensure that locks do no real locking when disabled."""
+    lock_path = str(tmpdir.join('lockfile'))
+
+    old_value = spack.config.get('config:locks')
+
+    with spack.config.override('config:locks', False):
+        lock = lk.Lock(lock_path)
+
+        lock.acquire_read()
+        assert not os.path.exists(lock_path)
+
+        lock.acquire_write()
+        assert not os.path.exists(lock_path)
+
+        lock.release_write()
+        assert not os.path.exists(lock_path)
+
+        lock.release_read()
+        assert not os.path.exists(lock_path)
+
+    assert old_value == spack.config.get('config:locks')
+
+
+def test_lock_checks_user(tmpdir):
+    """Ensure lock checks work with a self-owned, self-group repo."""
+    uid = os.getuid()
+    if uid not in group_ids():
+        pytest.skip("user has no group with gid == uid")
+
+    # self-owned, own group
+    tmpdir.chown(uid, uid)
+
+    # safe
+    path = str(tmpdir)
+    tmpdir.chmod(0o744)
+    lk.check_lock_safety(path)
+
+    # safe
+    tmpdir.chmod(0o774)
+    lk.check_lock_safety(path)
+
+    # unsafe
+    tmpdir.chmod(0o777)
+    with pytest.raises(spack.error.SpackError):
+        lk.check_lock_safety(path)
+
+    # safe
+    tmpdir.chmod(0o474)
+    lk.check_lock_safety(path)
+
+    # safe
+    tmpdir.chmod(0o477)
+    lk.check_lock_safety(path)
+
+
+def test_lock_checks_group(tmpdir):
+    """Ensure lock checks work with a self-owned, non-self-group repo."""
+    uid = os.getuid()
+    gid = next((g for g in group_ids() if g != uid), None)
+    if not gid:
+        pytest.skip("user has no group with gid != uid")
+
+    # self-owned, another group
+    tmpdir.chown(uid, gid)
+
+    # safe
+    path = str(tmpdir)
+    tmpdir.chmod(0o744)
+    lk.check_lock_safety(path)
+
+    # unsafe
+    tmpdir.chmod(0o774)
+    with pytest.raises(spack.error.SpackError):
+        lk.check_lock_safety(path)
+
+    # unsafe
+    tmpdir.chmod(0o777)
+    with pytest.raises(spack.error.SpackError):
+        lk.check_lock_safety(path)
+
+    # safe
+    tmpdir.chmod(0o474)
+    lk.check_lock_safety(path)
+
+    # safe
+    tmpdir.chmod(0o477)
+    lk.check_lock_safety(path)
diff --git a/lib/spack/spack/test/util/spack_yaml.py b/lib/spack/spack/test/util/spack_yaml.py
new file mode 100644
index 0000000000..d14e2de3a1
--- /dev/null
+++ b/lib/spack/spack/test/util/spack_yaml.py
@@ -0,0 +1,67 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import re
+
+import spack.config
+from spack.main import SpackCommand
+
+config_cmd = SpackCommand('config')
+
+
+def get_config_line(pattern, lines):
+    """Get a configuration line that matches a particular pattern."""
+    line = next((l for l in lines if re.search(pattern, l)), None)
+    assert line is not None, 'no such line!'
+    return line
+
+
+def check_blame(element, file_name, line=None):
+    """Check that `config blame config` gets right file/line for an element.
+
+    This runs `spack config blame config` and scrapes the output for a
+    particular YAML key. It thne checks that the requested file/line info
+    is also on that line.
+
+    Line is optional; if it is ``None`` we just check for the
+    ``file_name``, which may just be a name for a special config scope
+    like ``_builtin`` or ``command_line``.
+    """
+    output = config_cmd('blame', 'config')
+
+    blame_lines = output.rstrip().split('\n')
+    element_line = get_config_line(element + ':', blame_lines)
+
+    annotation = file_name
+    if line is not None:
+        annotation += ':%d' % line
+
+    assert file_name in element_line
+
+
+def test_config_blame(config):
+    """check blame info for elements in mock configuration."""
+    config_file = config.get_config_filename('site', 'config')
+
+    check_blame('install_tree', config_file, 2)
+    check_blame('source_cache', config_file, 11)
+    check_blame('misc_cache', config_file, 12)
+    check_blame('verify_ssl', config_file, 13)
+    check_blame('checksum', config_file, 14)
+    check_blame('dirty', config_file, 15)
+
+
+def test_config_blame_with_override(config):
+    """check blame for an element from an override scope"""
+    config_file = config.get_config_filename('site', 'config')
+
+    with spack.config.override('config:install_tree', 'foobar'):
+        check_blame('install_tree', 'overrides')
+
+        check_blame('source_cache', config_file, 11)
+        check_blame('misc_cache', config_file, 12)
+        check_blame('verify_ssl', config_file, 13)
+        check_blame('checksum', config_file, 14)
+        check_blame('dirty', config_file, 15)
diff --git a/lib/spack/spack/test/util/util_string.py b/lib/spack/spack/test/util/util_string.py
new file mode 100644
index 0000000000..205fd1105f
--- /dev/null
+++ b/lib/spack/spack/test/util/util_string.py
@@ -0,0 +1,14 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.util.string import plural
+
+
+def test_plural():
+    assert plural(0, 'thing') == '0 things'
+    assert plural(1, 'thing') == '1 thing'
+    assert plural(2, 'thing') == '2 things'
+    assert plural(1, 'thing', 'wombats') == '1 thing'
+    assert plural(2, 'thing', 'wombats') == '2 wombats'
diff --git a/lib/spack/spack/test/variant.py b/lib/spack/spack/test/variant.py
index 6bb7dc78e4..0bbab46efa 100644
--- a/lib/spack/spack/test/variant.py
+++ b/lib/spack/spack/test/variant.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 import pytest
 import numbers
diff --git a/lib/spack/spack/test/versions.py b/lib/spack/spack/test/versions.py
index c0136c41dc..1a56b921b3 100644
--- a/lib/spack/spack/test/versions.py
+++ b/lib/spack/spack/test/versions.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """These version tests were taken from the RPM source code.
 We try to maintain compatibility with RPM's version semantics
 where it makes sense.
@@ -488,6 +469,14 @@ def test_repr_and_str():
     check_repr_and_str('R2016a.2-3_4')
 
 
+def test_len():
+    a = Version('1.2.3.4')
+    assert len(a) == len(a.version)
+    assert(len(a) == 4)
+    b = Version('2018.0')
+    assert(len(b) == 2)
+
+
 def test_get_item():
     a = Version('0.1_2-3')
     assert isinstance(a[1], int)
diff --git a/lib/spack/spack/test/views.py b/lib/spack/spack/test/views.py
new file mode 100644
index 0000000000..827c9f0a3f
--- /dev/null
+++ b/lib/spack/spack/test/views.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import os
+
+from spack.spec import Spec
+
+
+def test_global_activation(install_mockery, mock_fetch):
+    """This test ensures that views which are maintained inside of an extendee
+       package's prefix are maintained as expected and are compatible with
+       global activations prior to #7152.
+    """
+    spec = Spec('extension1').concretized()
+    pkg = spec.package
+    pkg.do_install()
+    pkg.do_activate()
+
+    extendee_spec = spec['extendee']
+    extendee_pkg = spec['extendee'].package
+    view = extendee_pkg.view()
+    assert pkg.is_activated(view)
+
+    expected_path = os.path.join(
+        extendee_spec.prefix, '.spack', 'extensions.yaml')
+    assert (view.extensions_layout.extension_file_path(extendee_spec) ==
+            expected_path)
diff --git a/lib/spack/spack/test/web.py b/lib/spack/spack/test/web.py
index 82ca61f410..07e1f656fa 100644
--- a/lib/spack/spack/test/web.py
+++ b/lib/spack/spack/test/web.py
@@ -1,36 +1,17 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """Tests for web.py."""
 import os
 
-import spack
+import spack.paths
 from spack.util.web import spider, find_versions_of_archive
 from spack.version import ver
 
 
-web_data_path = os.path.join(spack.test_path, 'data', 'web')
+web_data_path = os.path.join(spack.paths.test_path, 'data', 'web')
 
 root = 'file://' + web_data_path + '/index.html'
 root_tarball = 'file://' + web_data_path + '/foo-0.0.0.tar.gz'
diff --git a/lib/spack/spack/url.py b/lib/spack/spack/url.py
index 5276b3165f..644ff53bbf 100644
--- a/lib/spack/spack/url.py
+++ b/lib/spack/spack/url.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """
 This module has methods for parsing names and versions of packages from URLs.
 The idea is to allow package creators to supply nothing more than the
@@ -90,9 +71,14 @@ def find_list_url(url):
         (r'(.*github\.com/[^/]+/[^/]+)',
          lambda m: m.group(1) + '/releases'),
 
-        # GitLab
+        # GitLab API endpoint
+        # e.g. https://gitlab.dkrz.de/api/v4/projects/k202009%2Flibaec/repository/archive.tar.gz?sha=v1.0.2
+        (r'(.*gitlab[^/]+)/api/v4/projects/([^/]+)%2F([^/]+)',
+         lambda m: m.group(1) + '/' + m.group(2) + '/' + m.group(3) + '/tags'),
+
+        # GitLab non-API endpoint
         # e.g. https://gitlab.dkrz.de/k202009/libaec/uploads/631e85bcf877c2dcaca9b2e6d6526339/libaec-1.0.0.tar.gz
-        (r'(.*gitlab[^/]+/[^/]+/[^/]+)',
+        (r'(.*gitlab[^/]+/(?!api/v4/projects)[^/]+/[^/]+)',
          lambda m: m.group(1) + '/tags'),
 
         # BitBucket
@@ -164,6 +150,7 @@ def strip_version_suffixes(path):
         # Download type
         '[Ii]nstall',
         'all',
+        'code',
         'src(_0)?',
         '[Ss]ources?',
         'file',
@@ -201,7 +188,7 @@ def strip_version_suffixes(path):
         'intel',
         'amd64',
         'x64',
-        'x86_64',
+        'x86[_-]64',
         'x86',
         'i[36]86',
         'ppc64(le)?',
@@ -226,7 +213,7 @@ def strip_version_suffixes(path):
         'intel',
         'amd64',
         'x64',
-        'x86_64',
+        'x86[_-]64',
         'x86',
         'i[36]86',
         'ppc64(le)?',
@@ -529,6 +516,9 @@ def parse_version_offset(path):
 
         # 9th Pass: Query strings
 
+        # e.g. https://gitlab.cosma.dur.ac.uk/api/v4/projects/swift%2Fswiftsim/repository/archive.tar.gz?sha=v0.3.0
+        (r'\?sha=[a-zA-Z+._-]*v?(\d[\da-zA-Z._-]*)$', suffix),
+
         # e.g. http://gitlab.cosma.dur.ac.uk/swift/swiftsim/repository/archive.tar.gz?ref=v0.3.0
         (r'\?ref=[a-zA-Z+._-]*v?(\d[\da-zA-Z._-]*)$', suffix),
 
@@ -640,9 +630,13 @@ def parse_name_offset(path, v=None):
         # e.g. https://github.com/nco/nco/archive/4.6.2.tar.gz
         (r'github\.com/[^/]+/([^/]+)', path),
 
-        # GitLab: gitlab.*/repo/name/
+        # GitLab API endpoint: gitlab.*/api/v4/projects/NAMESPACE%2Fname/
+        # e.g. https://gitlab.cosma.dur.ac.uk/api/v4/projects/swift%2Fswiftsim/repository/archive.tar.gz?sha=v0.3.0
+        (r'gitlab[^/]+/api/v4/projects/[^/]+%2F([^/]+)', path),
+
+        # GitLab non-API endpoint: gitlab.*/repo/name/
         # e.g. http://gitlab.cosma.dur.ac.uk/swift/swiftsim/repository/archive.tar.gz?ref=v0.3.0
-        (r'gitlab[^/]+/[^/]+/([^/]+)', path),
+        (r'gitlab[^/]+/(?!api/v4/projects)[^/]+/([^/]+)', path),
 
         # Bitbucket: bitbucket.org/repo/name/
         # e.g. https://bitbucket.org/glotzer/hoomd-blue/get/v1.3.3.tar.bz2
diff --git a/lib/spack/spack/util/__init__.py b/lib/spack/spack/util/__init__.py
index 8922701e9f..4f442db458 100644
--- a/lib/spack/spack/util/__init__.py
+++ b/lib/spack/spack/util/__init__.py
@@ -1,24 +1,4 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
diff --git a/lib/spack/spack/util/compression.py b/lib/spack/spack/util/compression.py
index 3b747e08c6..93c91dc49c 100644
--- a/lib/spack/spack/util/compression.py
+++ b/lib/spack/spack/util/compression.py
@@ -1,34 +1,15 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import re
 import os
 from itertools import product
 from spack.util.executable import which
 
 # Supported archive extensions.
-PRE_EXTS = ["tar"]
+PRE_EXTS = ["tar", "TAR"]
 EXTS     = ["gz", "bz2", "xz", "Z", "zip", "tgz"]
 
 # Add PRE_EXTS and EXTS last so that .tar.gz is matched *before* .tar or .gz
diff --git a/lib/spack/spack/util/crypto.py b/lib/spack/spack/util/crypto.py
index 13262be551..34e62e218a 100644
--- a/lib/spack/spack/util/crypto.py
+++ b/lib/spack/spack/util/crypto.py
@@ -1,41 +1,90 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import sys
 import hashlib
 
-"""Set of acceptable hashes that Spack will use."""
-hashes = dict((h, getattr(hashlib, h)) for h in [
-    'md5',
-    'sha1',
-    'sha224',
-    'sha256',
-    'sha384',
-    'sha512'])
+import llnl.util.tty as tty
+
+
+#: Set of hash algorithms that Spack can use, mapped to digest size in bytes
+hashes = {
+    'md5': 16,
+    'sha1': 20,
+    'sha224': 28,
+    'sha256': 32,
+    'sha384': 48,
+    'sha512': 64
+}
+
+
+#: size of hash digests in bytes, mapped to algoritm names
+_size_to_hash = dict((v, k) for k, v in hashes.items())
+
+
+#: List of deprecated hash functions. On some systems, these cannot be
+#: used without special options to hashlib.
+_deprecated_hash_algorithms = ['md5']
+
+
+#: cache of hash functions generated
+_hash_functions = {}
 
-"""Index for looking up hasher for a digest."""
-_size_to_hash = dict((h().digest_size, h) for h in hashes.values())
+
+class DeprecatedHash(object):
+    def __init__(self, hash_alg, alert_fn, disable_security_check):
+        self.hash_alg = hash_alg
+        self.alert_fn = alert_fn
+        self.disable_security_check = disable_security_check
+
+    def __call__(self, disable_alert=False):
+        if not disable_alert:
+            self.alert_fn("Deprecation warning: {0} checksums will not be"
+                          " supported in future Spack releases."
+                          .format(self.hash_alg))
+        if self.disable_security_check:
+            return hashlib.new(self.hash_alg, usedforsecurity=False)
+        else:
+            return hashlib.new(self.hash_alg)
+
+
+def hash_fun_for_algo(algo):
+    """Get a function that can perform the specified hash algorithm."""
+    hash_gen = _hash_functions.get(algo)
+    if hash_gen is None:
+        if algo in _deprecated_hash_algorithms:
+            try:
+                hash_gen = DeprecatedHash(
+                    algo, tty.debug, disable_security_check=False)
+
+                # call once to get a ValueError if usedforsecurity is needed
+                hash_gen(disable_alert=True)
+            except ValueError:
+                # Some systems may support the 'usedforsecurity' option
+                # so try with that (but display a warning when it is used)
+                hash_gen = DeprecatedHash(
+                    algo, tty.warn, disable_security_check=True)
+        else:
+            hash_gen = getattr(hashlib, algo)
+        _hash_functions[algo] = hash_gen
+
+    return hash_gen
+
+
+def hash_algo_for_digest(hexdigest):
+    """Gets name of the hash algorithm for a hex digest."""
+    bytes = len(hexdigest) / 2
+    if bytes not in _size_to_hash:
+        raise ValueError(
+            'Spack knows no hash algorithm for this digest: %s' % hexdigest)
+    return _size_to_hash[bytes]
+
+
+def hash_fun_for_digest(hexdigest):
+    """Gets a hash function corresponding to a hex digest."""
+    return hash_fun_for_algo(hash_algo_for_digest(hexdigest))
 
 
 def checksum(hashlib_algo, filename, **kwargs):
@@ -78,15 +127,8 @@ class Checker(object):
     def __init__(self, hexdigest, **kwargs):
         self.block_size = kwargs.get('block_size', 2**20)
         self.hexdigest = hexdigest
-        self.sum       = None
-
-        bytes = len(hexdigest) / 2
-        if bytes not in _size_to_hash:
-            raise ValueError(
-                'Spack knows no hash algorithm for this digest: %s'
-                % hexdigest)
-
-        self.hash_fun = _size_to_hash[bytes]
+        self.sum = None
+        self.hash_fun = hash_fun_for_digest(hexdigest)
 
     @property
     def hash_name(self):
diff --git a/lib/spack/spack/util/debug.py b/lib/spack/spack/util/debug.py
index 25f0600935..99c9770aa2 100644
--- a/lib/spack/spack/util/debug.py
+++ b/lib/spack/spack/util/debug.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """Debug signal handler: prints a stack trace and enters interpreter.
 
 ``register_interrupt_handler()`` enables a ctrl-C handler that prints
diff --git a/lib/spack/spack/util/editor.py b/lib/spack/spack/util/editor.py
new file mode 100644
index 0000000000..730eb9fa3a
--- /dev/null
+++ b/lib/spack/spack/util/editor.py
@@ -0,0 +1,35 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+"""Module for finding the user's preferred text editor.
+
+Defines one variable: ``editor``, which is a
+``spack.util.executable.Executable`` object that can be called to invoke
+the editor.
+
+If no ``editor`` is found, an ``EnvironmentError`` is raised when
+``editor`` is invoked.
+"""
+import os
+
+from spack.util.executable import Executable, which
+
+# Set up the user's editor
+# $EDITOR environment variable has the highest precedence
+editor = os.environ.get('EDITOR')
+
+# if editor is not set, use some sensible defaults
+if editor is not None:
+    editor = Executable(editor)
+else:
+    editor = which('vim', 'vi', 'emacs', 'nano')
+
+# If there is no editor, only raise an error if we actually try to use it.
+if not editor:
+    def editor_not_found(*args, **kwargs):
+        raise EnvironmentError(
+            'No text editor found! Please set the EDITOR environment variable '
+            'to your preferred text editor.')
+    editor = editor_not_found
diff --git a/lib/spack/spack/util/environment.py b/lib/spack/spack/util/environment.py
index 51f7f586ec..fc6d416e7e 100644
--- a/lib/spack/spack/util/environment.py
+++ b/lib/spack/spack/util/environment.py
@@ -1,28 +1,23 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+"""Utilities for setting and modifying environment variables."""
+import collections
+import contextlib
+import inspect
+import json
 import os
+import re
+import sys
+import os.path
+import subprocess
+
+import llnl.util.tty as tty
+
+from llnl.util.lang import dedupe
+
 
 system_paths = ['/', '/usr', '/usr/local']
 suffixes = ['bin', 'bin64', 'include', 'lib', 'lib64']
@@ -86,3 +81,635 @@ def dump_environment(path):
     with open(path, 'w') as env_file:
         for key, val in sorted(os.environ.items()):
             env_file.write('export %s="%s"\n' % (key, val))
+
+
+@contextlib.contextmanager
+def set_env(**kwargs):
+    """Temporarily sets and restores environment variables.
+
+    Variables can be set as keyword arguments to this function.
+    """
+    saved = {}
+    for var, value in kwargs.items():
+        if var in os.environ:
+            saved[var] = os.environ[var]
+
+        if value is None:
+            if var in os.environ:
+                del os.environ[var]
+        else:
+            os.environ[var] = value
+
+    yield
+
+    for var, value in kwargs.items():
+        if var in saved:
+            os.environ[var] = saved[var]
+        else:
+            if var in os.environ:
+                del os.environ[var]
+
+
+class NameModifier(object):
+
+    def __init__(self, name, **kwargs):
+        self.name = name
+        self.args = {'name': name}
+        self.args.update(kwargs)
+
+    def update_args(self, **kwargs):
+        self.__dict__.update(kwargs)
+        self.args.update(kwargs)
+
+
+class NameValueModifier(object):
+
+    def __init__(self, name, value, **kwargs):
+        self.name = name
+        self.value = value
+        self.separator = kwargs.get('separator', ':')
+        self.args = {'name': name, 'value': value, 'separator': self.separator}
+        self.args.update(kwargs)
+
+    def update_args(self, **kwargs):
+        self.__dict__.update(kwargs)
+        self.args.update(kwargs)
+
+
+class SetEnv(NameValueModifier):
+
+    def execute(self):
+        os.environ[self.name] = str(self.value)
+
+
+class AppendFlagsEnv(NameValueModifier):
+
+    def execute(self):
+        if self.name in os.environ and os.environ[self.name]:
+            os.environ[self.name] += self.separator + str(self.value)
+        else:
+            os.environ[self.name] = str(self.value)
+
+
+class UnsetEnv(NameModifier):
+
+    def execute(self):
+        # Avoid throwing if the variable was not set
+        os.environ.pop(self.name, None)
+
+
+class SetPath(NameValueModifier):
+
+    def execute(self):
+        string_path = concatenate_paths(self.value, separator=self.separator)
+        os.environ[self.name] = string_path
+
+
+class AppendPath(NameValueModifier):
+
+    def execute(self):
+        environment_value = os.environ.get(self.name, '')
+        directories = environment_value.split(
+            self.separator) if environment_value else []
+        directories.append(os.path.normpath(self.value))
+        os.environ[self.name] = self.separator.join(directories)
+
+
+class PrependPath(NameValueModifier):
+
+    def execute(self):
+        environment_value = os.environ.get(self.name, '')
+        directories = environment_value.split(
+            self.separator) if environment_value else []
+        directories = [os.path.normpath(self.value)] + directories
+        os.environ[self.name] = self.separator.join(directories)
+
+
+class RemovePath(NameValueModifier):
+
+    def execute(self):
+        environment_value = os.environ.get(self.name, '')
+        directories = environment_value.split(
+            self.separator) if environment_value else []
+        directories = [os.path.normpath(x) for x in directories
+                       if x != os.path.normpath(self.value)]
+        os.environ[self.name] = self.separator.join(directories)
+
+
+class EnvironmentModifications(object):
+    """Keeps track of requests to modify the current environment.
+
+    Each call to a method to modify the environment stores the extra
+    information on the caller in the request:
+
+        * 'filename' : filename of the module where the caller is defined
+        * 'lineno': line number where the request occurred
+        * 'context' : line of code that issued the request that failed
+    """
+
+    def __init__(self, other=None):
+        """Initializes a new instance, copying commands from 'other'
+        if it is not None.
+
+        Args:
+            other (EnvironmentModifications): list of environment modifications
+                to be extended (optional)
+        """
+        self.env_modifications = []
+        if other is not None:
+            self.extend(other)
+
+    def __iter__(self):
+        return iter(self.env_modifications)
+
+    def __len__(self):
+        return len(self.env_modifications)
+
+    def extend(self, other):
+        self._check_other(other)
+        self.env_modifications.extend(other.env_modifications)
+
+    @staticmethod
+    def _check_other(other):
+        if not isinstance(other, EnvironmentModifications):
+            raise TypeError(
+                'other must be an instance of EnvironmentModifications')
+
+    def _get_outside_caller_attributes(self):
+        stack = inspect.stack()
+        try:
+            _, filename, lineno, _, context, index = stack[2]
+            context = context[index].strip()
+        except Exception:
+            filename = 'unknown file'
+            lineno = 'unknown line'
+            context = 'unknown context'
+        args = {'filename': filename, 'lineno': lineno, 'context': context}
+        return args
+
+    def set(self, name, value, **kwargs):
+        """Stores a request to set an environment variable.
+
+        Args:
+            name: name of the environment variable to be set
+            value: value of the environment variable
+        """
+        kwargs.update(self._get_outside_caller_attributes())
+        item = SetEnv(name, value, **kwargs)
+        self.env_modifications.append(item)
+
+    def append_flags(self, name, value, sep=' ', **kwargs):
+        """
+        Stores in the current object a request to append to an env variable
+
+        Args:
+            name: name of the environment variable to be appended to
+            value: value to append to the environment variable
+        Appends with spaces separating different additions to the variable
+        """
+        kwargs.update(self._get_outside_caller_attributes())
+        kwargs.update({'separator': sep})
+        item = AppendFlagsEnv(name, value, **kwargs)
+        self.env_modifications.append(item)
+
+    def unset(self, name, **kwargs):
+        """Stores a request to unset an environment variable.
+
+        Args:
+            name: name of the environment variable to be set
+        """
+        kwargs.update(self._get_outside_caller_attributes())
+        item = UnsetEnv(name, **kwargs)
+        self.env_modifications.append(item)
+
+    def set_path(self, name, elements, **kwargs):
+        """Stores a request to set a path generated from a list.
+
+        Args:
+            name: name o the environment variable to be set.
+            elements: elements of the path to set.
+        """
+        kwargs.update(self._get_outside_caller_attributes())
+        item = SetPath(name, elements, **kwargs)
+        self.env_modifications.append(item)
+
+    def append_path(self, name, path, **kwargs):
+        """Stores a request to append a path to a path list.
+
+        Args:
+            name: name of the path list in the environment
+            path: path to be appended
+        """
+        kwargs.update(self._get_outside_caller_attributes())
+        item = AppendPath(name, path, **kwargs)
+        self.env_modifications.append(item)
+
+    def prepend_path(self, name, path, **kwargs):
+        """Same as `append_path`, but the path is pre-pended.
+
+        Args:
+            name: name of the path list in the environment
+            path: path to be pre-pended
+        """
+        kwargs.update(self._get_outside_caller_attributes())
+        item = PrependPath(name, path, **kwargs)
+        self.env_modifications.append(item)
+
+    def remove_path(self, name, path, **kwargs):
+        """Stores a request to remove a path from a path list.
+
+        Args:
+            name: name of the path list in the environment
+            path: path to be removed
+        """
+        kwargs.update(self._get_outside_caller_attributes())
+        item = RemovePath(name, path, **kwargs)
+        self.env_modifications.append(item)
+
+    def group_by_name(self):
+        """Returns a dict of the modifications grouped by variable name.
+
+        Returns:
+            dict mapping the environment variable name to the modifications to
+            be done on it
+        """
+        modifications = collections.defaultdict(list)
+        for item in self:
+            modifications[item.name].append(item)
+        return modifications
+
+    def clear(self):
+        """
+        Clears the current list of modifications
+        """
+        self.env_modifications.clear()
+
+    def apply_modifications(self):
+        """Applies the modifications and clears the list."""
+        modifications = self.group_by_name()
+        # Apply modifications one variable at a time
+        for name, actions in sorted(modifications.items()):
+            for x in actions:
+                x.execute()
+
+    @staticmethod
+    def from_sourcing_file(filename, *args, **kwargs):
+        """Returns modifications that would be made by sourcing a file.
+
+        Parameters:
+            filename (str): The file to source
+            *args (list of str): Arguments to pass on the command line
+
+        Keyword Arguments:
+            shell (str): The shell to use (default: ``bash``)
+            shell_options (str): Options passed to the shell (default: ``-c``)
+            source_command (str): The command to run (default: ``source``)
+            suppress_output (str): Redirect used to suppress output of command
+                (default: ``&> /dev/null``)
+            concatenate_on_success (str): Operator used to execute a command
+                only when the previous command succeeds (default: ``&&``)
+            blacklist ([str or re]): Ignore any modifications of these
+                variables (default: [])
+            whitelist ([str or re]): Always respect modifications of these
+                variables (default: []). Has precedence over blacklist.
+            clean (bool): In addition to removing empty entries,
+                also remove duplicate entries (default: False).
+
+        Returns:
+            EnvironmentModifications: an object that, if executed, has
+                the same effect on the environment as sourcing the file
+        """
+        # Check if the file actually exists
+        if not os.path.isfile(filename):
+            msg = 'Trying to source non-existing file: {0}'.format(filename)
+            raise RuntimeError(msg)
+
+        # Kwargs parsing and default values
+        shell                  = kwargs.get('shell', '/bin/bash')
+        shell_options          = kwargs.get('shell_options', '-c')
+        source_command         = kwargs.get('source_command', 'source')
+        suppress_output        = kwargs.get('suppress_output', '&> /dev/null')
+        concatenate_on_success = kwargs.get('concatenate_on_success', '&&')
+        blacklist              = kwargs.get('blacklist', [])
+        whitelist              = kwargs.get('whitelist', [])
+        clean                  = kwargs.get('clean', False)
+
+        source_file = [source_command, filename]
+        source_file.extend(args)
+        source_file = ' '.join(source_file)
+
+        dump_cmd = 'import os, json; print(json.dumps(dict(os.environ)))'
+        dump_environment = 'python -c "{0}"'.format(dump_cmd)
+
+        # Construct the command that will be executed
+        command = [
+            shell,
+            shell_options,
+            ' '.join([
+                source_file, suppress_output,
+                concatenate_on_success, dump_environment,
+            ]),
+        ]
+
+        # Try to source the file
+        proc = subprocess.Popen(
+            command, stdout=subprocess.PIPE, env=os.environ)
+        proc.wait()
+
+        if proc.returncode != 0:
+            msg = 'Sourcing file {0} returned a non-zero exit code'.format(
+                filename)
+            raise RuntimeError(msg)
+
+        output = ''.join([line.decode('utf-8') for line in proc.stdout])
+
+        # Construct dictionaries of the environment before and after
+        # sourcing the file, so that we can diff them.
+        env_before = dict(os.environ)
+        env_after = json.loads(output)
+
+        # If we're in python2, convert to str objects instead of unicode
+        # like json gives us.  We can't put unicode in os.environ anyway.
+        if sys.version_info[0] < 3:
+            env_after = dict((k.encode('utf-8'), v.encode('utf-8'))
+                             for k, v in env_after.items())
+
+        # Other variables unrelated to sourcing a file
+        blacklist.extend(['SHLVL', '_', 'PWD', 'OLDPWD', 'PS2'])
+
+        def set_intersection(fullset, *args):
+            # A set intersection using string literals and regexs
+            meta = '[' + re.escape('[$()*?[]^{|}') + ']'
+            subset = fullset & set(args)   # As literal
+            for name in args:
+                if re.search(meta, name):
+                    pattern = re.compile(name)
+                    for k in fullset:
+                        if re.match(pattern, k):
+                            subset.add(k)
+            return subset
+
+        for d in env_after, env_before:
+            # Retain (whitelist) has priority over prune (blacklist)
+            prune = set_intersection(set(d), *blacklist)
+            prune -= set_intersection(prune, *whitelist)
+            for k in prune:
+                d.pop(k, None)
+
+        # Fill the EnvironmentModifications instance
+        env = EnvironmentModifications()
+
+        # New variables
+        new_variables = list(set(env_after) - set(env_before))
+        # Variables that have been unset
+        unset_variables = list(set(env_before) - set(env_after))
+        # Variables that have been modified
+        common_variables = set(env_before).intersection(set(env_after))
+
+        modified_variables = [x for x in common_variables
+                              if env_before[x] != env_after[x]]
+
+        # Consistent output order - looks nicer, easier comparison...
+        new_variables.sort()
+        unset_variables.sort()
+        modified_variables.sort()
+
+        def return_separator_if_any(*args):
+            separators = ':', ';'
+            for separator in separators:
+                for arg in args:
+                    if separator in arg:
+                        return separator
+            return None
+
+        # Add variables to env.
+        # Assume that variables with 'PATH' in the name or that contain
+        # separators like ':' or ';' are more likely to be paths
+        for x in new_variables:
+            sep = return_separator_if_any(env_after[x])
+            if sep:
+                env.prepend_path(x, env_after[x], separator=sep)
+            elif 'PATH' in x:
+                env.prepend_path(x, env_after[x])
+            else:
+                # We just need to set the variable to the new value
+                env.set(x, env_after[x])
+
+        for x in unset_variables:
+            env.unset(x)
+
+        for x in modified_variables:
+            before = env_before[x]
+            after = env_after[x]
+            sep = return_separator_if_any(before, after)
+            if sep:
+                before_list = before.split(sep)
+                after_list = after.split(sep)
+
+                # Filter out empty strings
+                before_list = list(filter(None, before_list))
+                after_list = list(filter(None, after_list))
+
+                # Remove duplicate entries (worse matching, bloats env)
+                if clean:
+                    before_list = list(dedupe(before_list))
+                    after_list = list(dedupe(after_list))
+                    # The reassembled cleaned entries
+                    before = sep.join(before_list)
+                    after = sep.join(after_list)
+
+                # Paths that have been removed
+                remove_list = [
+                    ii for ii in before_list if ii not in after_list]
+                # Check that nothing has been added in the middle of
+                # before_list
+                remaining_list = [
+                    ii for ii in before_list if ii in after_list]
+                try:
+                    start = after_list.index(remaining_list[0])
+                    end = after_list.index(remaining_list[-1])
+                    search = sep.join(after_list[start:end + 1])
+                except IndexError:
+                    env.prepend_path(x, after)
+
+                if search not in before:
+                    # We just need to set the variable to the new value
+                    env.prepend_path(x, after)
+                else:
+                    try:
+                        prepend_list = after_list[:start]
+                        prepend_list.reverse()  # Preserve order after prepend
+                    except KeyError:
+                        prepend_list = []
+                    try:
+                        append_list = after_list[end + 1:]
+                    except KeyError:
+                        append_list = []
+
+                    for item in remove_list:
+                        env.remove_path(x, item)
+                    for item in append_list:
+                        env.append_path(x, item)
+                    for item in prepend_list:
+                        env.prepend_path(x, item)
+            else:
+                # We just need to set the variable to the new value
+                env.set(x, after)
+
+        return env
+
+
+def concatenate_paths(paths, separator=':'):
+    """Concatenates an iterable of paths into a string of paths separated by
+    separator, defaulting to colon.
+
+    Args:
+        paths: iterable of paths
+        separator: the separator to use, default ':'
+
+    Returns:
+        string
+    """
+    return separator.join(str(item) for item in paths)
+
+
+def set_or_unset_not_first(variable, changes, errstream):
+    """Check if we are going to set or unset something after other
+    modifications have already been requested.
+    """
+    indexes = [ii for ii, item in enumerate(changes)
+               if ii != 0 and
+               not item.args.get('force', False) and
+               type(item) in [SetEnv, UnsetEnv]]
+    if indexes:
+        good = '\t    \t{context} at {filename}:{lineno}'
+        nogood = '\t--->\t{context} at {filename}:{lineno}'
+        message = "Suspicious requests to set or unset '{var}' found"
+        errstream(message.format(var=variable))
+        for ii, item in enumerate(changes):
+            print_format = nogood if ii in indexes else good
+            errstream(print_format.format(**item.args))
+
+
+def validate(env, errstream):
+    """Validates the environment modifications to check for the presence of
+    suspicious patterns. Prompts a warning for everything that was found.
+
+    Current checks:
+    - set or unset variables after other changes on the same variable
+
+    Args:
+        env: list of environment modifications
+    """
+    modifications = env.group_by_name()
+    for variable, list_of_changes in sorted(modifications.items()):
+        set_or_unset_not_first(variable, list_of_changes, errstream)
+
+
+def filter_environment_blacklist(env, variables):
+    """Generator that filters out any change to environment variables present in
+    the input list.
+
+    Args:
+        env: list of environment modifications
+        variables: list of variable names to be filtered
+
+    Returns:
+        items in env if they are not in variables
+    """
+    for item in env:
+        if item.name not in variables:
+            yield item
+
+
+def inspect_path(root, inspections, exclude=None):
+    """Inspects ``root`` to search for the subdirectories in ``inspections``.
+    Adds every path found to a list of prepend-path commands and returns it.
+
+    Args:
+        root (str): absolute path where to search for subdirectories
+
+        inspections (dict): maps relative paths to a list of environment
+            variables that will be modified if the path exists. The
+            modifications are not performed immediately, but stored in a
+            command object that is returned to client
+
+        exclude (callable): optional callable. If present it must accept an
+            absolute path and return True if it should be excluded from the
+            inspection
+
+    Examples:
+
+    The following lines execute an inspection in ``/usr`` to search for
+    ``/usr/include`` and ``/usr/lib64``. If found we want to prepend
+    ``/usr/include`` to ``CPATH`` and ``/usr/lib64`` to ``MY_LIB64_PATH``.
+
+        .. code-block:: python
+
+            # Set up the dictionary containing the inspection
+            inspections = {
+                'include': ['CPATH'],
+                'lib64': ['MY_LIB64_PATH']
+            }
+
+            # Get back the list of command needed to modify the environment
+            env = inspect_path('/usr', inspections)
+
+            # Eventually execute the commands
+            env.apply_modifications()
+
+    Returns:
+        instance of EnvironmentModifications containing the requested
+        modifications
+    """
+    if exclude is None:
+        exclude = lambda x: False
+
+    env = EnvironmentModifications()
+    # Inspect the prefix to check for the existence of common directories
+    for relative_path, variables in inspections.items():
+        expected = os.path.join(root, relative_path)
+
+        if os.path.isdir(expected) and not exclude(expected):
+            for variable in variables:
+                env.prepend_path(variable, expected)
+
+    return env
+
+
+@contextlib.contextmanager
+def preserve_environment(*variables):
+    """Ensures that the value of the environment variables passed as
+    arguments is the same before entering to the context manager and after
+    exiting it.
+
+    Variables that are unset before entering the context manager will be
+    explicitly unset on exit.
+
+    Args:
+        variables (list of str): list of environment variables to be preserved
+    """
+    cache = {}
+    for var in variables:
+        # The environment variable to be preserved might not be there.
+        # In that case store None as a placeholder.
+        cache[var] = os.environ.get(var, None)
+
+    yield
+
+    for var in variables:
+        value = cache[var]
+        msg = '[PRESERVE_ENVIRONMENT]'
+        if value is not None:
+            # Print a debug statement if the value changed
+            if var not in os.environ:
+                msg += ' {0} was unset, will be reset to "{1}"'
+                tty.debug(msg.format(var, value))
+            elif os.environ[var] != value:
+                msg += ' {0} was set to "{1}", will be reset to "{2}"'
+                tty.debug(msg.format(var, os.environ[var], value))
+            os.environ[var] = value
+        elif var in os.environ:
+            msg += ' {0} was set to "{1}", will be unset'
+            tty.debug(msg.format(var, os.environ[var]))
+            del os.environ[var]
diff --git a/lib/spack/spack/util/executable.py b/lib/spack/spack/util/executable.py
index af516dc607..e1d7b49016 100644
--- a/lib/spack/spack/util/executable.py
+++ b/lib/spack/spack/util/executable.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 import re
 import subprocess
@@ -29,7 +10,7 @@ from six import string_types
 import sys
 
 import llnl.util.tty as tty
-import spack
+
 import spack.error
 
 __all__ = ['Executable', 'which', 'ProcessError']
@@ -93,7 +74,11 @@ class Executable(object):
             *args (str): Command-line arguments to the executable to run
 
         Keyword Arguments:
+            _dump_env (dict): Dict to be set to the environment actually
+                used (envisaged for testing purposes only)
             env (dict): The environment to run the executable with
+            extra_env (dict): Extra items to add to the environment
+                (neither requires nor precludes env)
             fail_on_error (bool): Raise an exception if the subprocess returns
                 an error. Default is True. The return code is available as
                 ``exe.returncode``
@@ -115,6 +100,7 @@ class Executable(object):
           for ``input``
 
         By default, the subprocess inherits the parent's file descriptors.
+
         """
         # Environment
         env_arg = kwargs.get('env', None)
@@ -124,6 +110,10 @@ class Executable(object):
         else:
             env = self.default_env.copy()
             env.update(env_arg)
+        env.update(kwargs.get('extra_env', {}))
+        if '_dump_env' in kwargs:
+            kwargs['_dump_env'].clear()
+            kwargs['_dump_env'].update(env)
 
         fail_on_error = kwargs.pop('fail_on_error', True)
         ignore_errors = kwargs.pop('ignore_errors', ())
@@ -177,18 +167,28 @@ class Executable(object):
                 env=env)
             out, err = proc.communicate()
 
-            rc = self.returncode = proc.returncode
-            if fail_on_error and rc != 0 and (rc not in ignore_errors):
-                raise ProcessError('Command exited with status %d:' %
-                                   proc.returncode, cmd_line)
-
+            result = None
             if output is str or error is str:
                 result = ''
                 if output is str:
                     result += to_str(out)
                 if error is str:
                     result += to_str(err)
-                return result
+
+            rc = self.returncode = proc.returncode
+            if fail_on_error and rc != 0 and (rc not in ignore_errors):
+                long_msg = cmd_line
+                if result:
+                    # If the output is not captured in the result, it will have
+                    # been stored either in the specified files (e.g. if
+                    # 'output' specifies a file) or written to the parent's
+                    # stdout/stderr (e.g. if 'output' is not specified)
+                    long_msg += '\n' + result
+
+                raise ProcessError('Command exited with status %d:' %
+                                   proc.returncode, long_msg)
+
+            return result
 
         except OSError as e:
             raise ProcessError(
diff --git a/lib/spack/spack/file_cache.py b/lib/spack/spack/util/file_cache.py
index 688f32a4ad..6e6ef3037f 100644
--- a/lib/spack/spack/file_cache.py
+++ b/lib/spack/spack/util/file_cache.py
@@ -1,34 +1,15 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 import shutil
 
-from llnl.util.filesystem import mkdirp, join_path
-from llnl.util.lock import Lock, ReadTransaction, WriteTransaction
+from llnl.util.filesystem import mkdirp
 
 from spack.error import SpackError
+from spack.util.lock import Lock, ReadTransaction, WriteTransaction
 
 
 class FileCache(object):
@@ -42,22 +23,29 @@ class FileCache(object):
 
     """
 
-    def __init__(self, root):
+    def __init__(self, root, timeout=120):
         """Create a file cache object.
 
         This will create the cache directory if it does not exist yet.
 
+        Args:
+            root: specifies the root directory where the cache stores files
+
+            timeout: when there is contention among multiple Spack processes
+                for cache files, this specifies how long Spack should wait
+                before assuming that there is a deadlock.
         """
         self.root = root.rstrip(os.path.sep)
         if not os.path.exists(self.root):
             mkdirp(self.root)
 
         self._locks = {}
+        self.lock_timeout = timeout
 
     def destroy(self):
         """Remove all files under the cache root."""
         for f in os.listdir(self.root):
-            path = join_path(self.root, f)
+            path = os.path.join(self.root, f)
             if os.path.isdir(path):
                 shutil.rmtree(path, True)
             else:
@@ -65,19 +53,20 @@ class FileCache(object):
 
     def cache_path(self, key):
         """Path to the file in the cache for a particular key."""
-        return join_path(self.root, key)
+        return os.path.join(self.root, key)
 
     def _lock_path(self, key):
         """Path to the file in the cache for a particular key."""
         keyfile = os.path.basename(key)
         keydir = os.path.dirname(key)
 
-        return join_path(self.root, keydir, '.' + keyfile + '.lock')
+        return os.path.join(self.root, keydir, '.' + keyfile + '.lock')
 
     def _get_lock(self, key):
         """Create a lock for a key, if necessary, and return a lock object."""
         if key not in self._locks:
-            self._locks[key] = Lock(self._lock_path(key))
+            self._locks[key] = Lock(self._lock_path(key),
+                                    default_timeout=self.lock_timeout)
         return self._locks[key]
 
     def init_entry(self, key):
@@ -130,7 +119,7 @@ class FileCache(object):
         """
         class WriteContextManager(object):
 
-            def __enter__(cm):
+            def __enter__(cm):  # noqa
                 cm.orig_filename = self.cache_path(key)
                 cm.orig_file = None
                 if os.path.exists(cm.orig_filename):
@@ -141,7 +130,7 @@ class FileCache(object):
 
                 return cm.orig_file, cm.tmp_file
 
-            def __exit__(cm, type, value, traceback):
+            def __exit__(cm, type, value, traceback):  # noqa
                 if cm.orig_file:
                     cm.orig_file.close()
                 cm.tmp_file.close()
diff --git a/lib/spack/spack/util/gpg.py b/lib/spack/spack/util/gpg.py
index 4af849fb3c..77979047b0 100644
--- a/lib/spack/spack/util/gpg.py
+++ b/lib/spack/spack/util/gpg.py
@@ -1,35 +1,15 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 import os
 
-import spack
+import spack.paths
 from spack.util.executable import Executable
 
 
-GNUPGHOME = spack.gpg_path
+GNUPGHOME = spack.paths.gpg_path
 
 
 class Gpg(object):
diff --git a/lib/spack/spack/util/imp/__init__.py b/lib/spack/spack/util/imp/__init__.py
new file mode 100644
index 0000000000..4d6ef756ca
--- /dev/null
+++ b/lib/spack/spack/util/imp/__init__.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+"""Consolidated module for all imports done by Spack.
+
+Many parts of Spack have to import Python code. This utility package
+wraps Spack's interface with Python's import system.
+
+We do this because Python's import system is confusing and changes from
+Python version to Python version, and we should be able to adapt our
+approach to the underlying implementation.
+
+Currently, this uses ``importlib.machinery`` where available and ``imp``
+when ``importlib`` is not completely usable.
+"""
+
+try:
+    from .importlib_importer import load_source  # noqa
+except ImportError:
+    from .imp_importer import load_source        # noqa
diff --git a/lib/spack/spack/util/imp/imp_importer.py b/lib/spack/spack/util/imp/imp_importer.py
new file mode 100644
index 0000000000..2949ef3b3e
--- /dev/null
+++ b/lib/spack/spack/util/imp/imp_importer.py
@@ -0,0 +1,67 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+"""Implementation of Spack imports that uses imp underneath.
+
+``imp`` is deprecated in newer versions of Python, but is the only option
+in Python 2.6.
+"""
+import imp
+import tempfile
+from contextlib import contextmanager
+
+
+@contextmanager
+def import_lock():
+    imp.acquire_lock()
+    yield
+    imp.release_lock()
+
+
+def load_source(full_name, path, prepend=None):
+    """Import a Python module from source.
+
+    Load the source file and add it to ``sys.modules``.
+
+    Args:
+        full_name (str): full name of the module to be loaded
+        path (str): path to the file that should be loaded
+        prepend (str, optional): some optional code to prepend to the
+            loaded module; e.g., can be used to inject import statements
+
+    Returns:
+        (ModuleType): the loaded module
+    """
+    with import_lock():
+        if prepend is None:
+            return imp.load_source(full_name, path)
+        else:
+            with prepend_open(path, text=prepend) as f:
+                return imp.load_source(full_name, path, f)
+
+
+@contextmanager
+def prepend_open(f, *args, **kwargs):
+    """Open a file for reading, but prepend with some text prepended
+
+    Arguments are same as for ``open()``, with one keyword argument,
+    ``text``, specifying the text to prepend.
+
+    We have to write and read a tempfile for the ``imp``-based importer,
+    as the ``file`` argument to ``imp.load_source()`` requires a
+    low-level file handle.
+
+    See the ``importlib``-based importer for a faster way to do this in
+    later versions of python.
+    """
+    text = kwargs.get('text', None)
+
+    with open(f, *args) as f:
+        with tempfile.NamedTemporaryFile(mode='w+') as tf:
+            if text:
+                tf.write(text + '\n')
+            tf.write(f.read())
+            tf.seek(0)
+            yield tf.file
diff --git a/lib/spack/spack/util/imp/importlib_importer.py b/lib/spack/spack/util/imp/importlib_importer.py
new file mode 100644
index 0000000000..a36d13e67b
--- /dev/null
+++ b/lib/spack/spack/util/imp/importlib_importer.py
@@ -0,0 +1,42 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+"""Implementation of Spack imports that uses importlib underneath.
+
+``importlib`` is only fully implemented in Python 3.
+"""
+from importlib.machinery import SourceFileLoader
+
+
+class PrependFileLoader(SourceFileLoader):
+    def __init__(self, full_name, path, prepend=None):
+        super(PrependFileLoader, self).__init__(full_name, path)
+        self.prepend = prepend
+
+    def get_data(self, path):
+        data = super(PrependFileLoader, self).get_data(path)
+        if path != self.path or self.prepend is None:
+            return data
+        else:
+            return self.prepend.encode() + b"\n" + data
+
+
+def load_source(full_name, path, prepend=None):
+    """Import a Python module from source.
+
+    Load the source file and add it to ``sys.modules``.
+
+    Args:
+        full_name (str): full name of the module to be loaded
+        path (str): path to the file that should be loaded
+        prepend (str, optional): some optional code to prepend to the
+            loaded module; e.g., can be used to inject import statements
+
+    Returns:
+        (ModuleType): the loaded module
+    """
+    # use our custom loader
+    loader = PrependFileLoader(full_name, path, prepend)
+    return loader.load_module()
diff --git a/lib/spack/spack/util/lock.py b/lib/spack/spack/util/lock.py
new file mode 100644
index 0000000000..05efe14d8d
--- /dev/null
+++ b/lib/spack/spack/util/lock.py
@@ -0,0 +1,74 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+"""Wrapper for ``llnl.util.lock`` allows locking to be enabled/disabled."""
+import os
+import stat
+
+import llnl.util.lock
+from llnl.util.lock import *  # noqa
+
+import spack.config
+import spack.error
+import spack.paths
+
+
+class Lock(llnl.util.lock.Lock):
+    """Lock that can be disabled.
+
+    This overrides the ``_lock()`` and ``_unlock()`` methods from
+    ``llnl.util.lock`` so that all the lock API calls will succeed, but
+    the actual locking mechanism can be disabled via ``_enable_locks``.
+    """
+    def __init__(self, *args, **kwargs):
+        super(Lock, self).__init__(*args, **kwargs)
+        self._enable = spack.config.get('config:locks', True)
+
+    def _lock(self, op, timeout=0):
+        if self._enable:
+            return super(Lock, self)._lock(op, timeout)
+        else:
+            return 0, 0
+
+    def _unlock(self):
+        """Unlock call that always succeeds."""
+        if self._enable:
+            super(Lock, self)._unlock()
+
+    def _debug(self, *args):
+        if self._enable:
+            super(Lock, self)._debug(*args)
+
+
+def check_lock_safety(path):
+    """Do some extra checks to ensure disabling locks is safe.
+
+    This will raise an error if ``path`` can is group- or world-writable
+    AND the current user can write to the directory (i.e., if this user
+    AND others could write to the path).
+
+    This is intended to run on the Spack prefix, but can be run on any
+    path for testing.
+    """
+    if os.access(path, os.W_OK):
+        stat_result = os.stat(path)
+        uid, gid = stat_result.st_uid, stat_result.st_gid
+        mode = stat_result[stat.ST_MODE]
+
+        writable = None
+        if (mode & stat.S_IWGRP) and (uid != gid):
+            # spack is group-writeable and the group is not the owner
+            writable = 'group'
+        elif (mode & stat.S_IWOTH):
+            # spack is world-writeable
+            writable = 'world'
+
+        if writable:
+            msg = "Refusing to disable locks: spack is {0}-writable.".format(
+                writable)
+            long_msg = (
+                "Running a shared spack without locks is unsafe. You must "
+                "restrict permissions on {0} or enable locks.").format(path)
+            raise spack.error.SpackError(msg, long_msg)
diff --git a/lib/spack/spack/util/log_parse.py b/lib/spack/spack/util/log_parse.py
index 1d5ad465fa..36b3312ec8 100644
--- a/lib/spack/spack/util/log_parse.py
+++ b/lib/spack/spack/util/log_parse.py
@@ -1,41 +1,29 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from __future__ import print_function
 
+import sys
 from six import StringIO
 
-from ctest_log_parser import CTestLogParser
-from llnl.util.tty.color import colorize
+from ctest_log_parser import CTestLogParser, BuildError, BuildWarning
+
+import llnl.util.tty as tty
+from llnl.util.tty.color import cescape, colorize
 
+__all__ = ['parse_log_events', 'make_log_context']
 
-def parse_log_events(stream, context=6):
+
+def parse_log_events(stream, context=6, jobs=None, profile=False):
     """Extract interesting events from a log file as a list of LogEvent.
 
     Args:
         stream (str or fileobject): build log name or file object
         context (int): lines of context to extract around each log event
+        jobs (int): number of jobs to parse with; default ncpus
+        profile (bool): print out profile information for parsing
 
     Returns:
         (tuple): two lists containig ``BuildError`` and
@@ -46,47 +34,87 @@ def parse_log_events(stream, context=6):
     that all the regex compilation is only done once.
     """
     if parse_log_events.ctest_parser is None:
-        parse_log_events.ctest_parser = CTestLogParser()
+        parse_log_events.ctest_parser = CTestLogParser(profile=profile)
 
-    return parse_log_events.ctest_parser.parse(stream, context)
+    result = parse_log_events.ctest_parser.parse(stream, context, jobs)
+    if profile:
+        parse_log_events.ctest_parser.print_timings()
+    return result
 
 
 #: lazily constructed CTest log parser
 parse_log_events.ctest_parser = None
 
 
-def make_log_context(log_events):
+def _wrap(text, width):
+    """Break text into lines of specific width."""
+    lines = []
+    pos = 0
+    while pos < len(text):
+        lines.append(text[pos:pos + width])
+        pos += width
+    return lines
+
+
+def make_log_context(log_events, width=None):
     """Get error context from a log file.
 
     Args:
         log_events (list of LogEvent): list of events created by
             ``ctest_log_parser.parse()``
-
+        width (int or None): wrap width; ``0`` for no limit; ``None`` to
+            auto-size for terminal
     Returns:
         str: context from the build log with errors highlighted
 
     Parses the log file for lines containing errors, and prints them out
     with line numbers and context.  Errors are highlighted with '>>' and
     with red highlighting (if color is enabled).
+
+    Events are sorted by line number before they are displayed.
     """
     error_lines = set(e.line_no for e in log_events)
+    log_events = sorted(log_events, key=lambda e: e.line_no)
+
+    num_width = len(str(max(error_lines))) + 4
+    line_fmt = '%%-%dd%%s' % num_width
+    indent = ' ' * (5 + num_width)
+
+    if width is None:
+        _, width = tty.terminal_size()
+    if width <= 0:
+        width = sys.maxsize
+    wrap_width = width - num_width - 6
 
     out = StringIO()
     next_line = 1
     for event in log_events:
         start = event.start
 
-        if start > next_line:
-            out.write('     [ ... ]\n')
+        if isinstance(event, BuildError):
+            color = 'R'
+        elif isinstance(event, BuildWarning):
+            color = 'Y'
+        else:
+            color = 'W'
+
+        if next_line != 1 and start > next_line:
+            out.write('\n     ...\n\n')
 
         if start < next_line:
             start = next_line
 
         for i in range(start, event.end):
+            # wrap to width
+            lines = _wrap(event[i], wrap_width)
+            lines[1:] = [indent + l for l in lines[1:]]
+            wrapped_line = line_fmt % (i, '\n'.join(lines))
+
             if i in error_lines:
-                out.write(colorize('  @R{>> %-6d%s}\n' % (i, event[i])))
+                out.write(colorize(
+                    '  @%s{>> %s}\n' % (color, cescape(wrapped_line))))
             else:
-                out.write('     %-6d%s\n' % (i, event[i]))
+                out.write('     %s\n' % wrapped_line)
 
         next_line = event.end
 
diff --git a/lib/spack/spack/util/module_cmd.py b/lib/spack/spack/util/module_cmd.py
index 00fc4ddc65..d195e0db9c 100644
--- a/lib/spack/spack/util/module_cmd.py
+++ b/lib/spack/spack/util/module_cmd.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """
 This module contains routines related to the module command for accessing and
 parsing environment modules.
@@ -115,6 +96,14 @@ def get_module_cmd_from_bash(bashopts=''):
     return module_cmd
 
 
+def unload_module(mod):
+    """Takes a module name and unloads the module from the environment. It does
+    not check whether conflicts arise from the unloaded module"""
+    modulecmd = get_module_cmd()
+    exec(compile(modulecmd('unload', mod, output=str, error=str), '<string>',
+                 'exec'))
+
+
 def load_module(mod):
     """Takes a module name and removes modules until it is possible to
     load that module. It then loads the provided module. Depends on the
@@ -130,14 +119,17 @@ def load_module(mod):
     text = modulecmd('show', mod, output=str, error=str).split()
     for i, word in enumerate(text):
         if word == 'conflict':
-            exec(compile(modulecmd('unload', text[i + 1], output=str,
-                                   error=str), '<string>', 'exec'))
+            unload_module(text[i + 1])
+
     # Load the module now that there are no conflicts
-    load = modulecmd('load', mod, output=str, error=str)
+    # Some module systems use stdout and some use stderr
+    load = modulecmd('load', mod, output=str, error='/dev/null')
+    if not load:
+        load = modulecmd('load', mod, error=str)
     exec(compile(load, '<string>', 'exec'))
 
 
-def get_argument_from_module_line(line):
+def get_path_arg_from_module_line(line):
     if '(' in line and ')' in line:
         # Determine which lua quote symbol is being used for the argument
         comma_index = line.index(',')
@@ -149,9 +141,10 @@ def get_argument_from_module_line(line):
             # Change error text to describe what is going on.
             raise ValueError("No lua quote symbol found in lmod module line.")
         words_and_symbols = line.split(lua_quote)
-        return words_and_symbols[-2]
+        path_arg = words_and_symbols[-2]
     else:
-        return line.split()[2]
+        path_arg = line.split()[2]
+    return path_arg
 
 
 def get_path_from_module(mod):
@@ -164,16 +157,35 @@ def get_path_from_module(mod):
     # Read the module
     text = modulecmd('show', mod, output=str, error=str).split('\n')
 
+    p = get_path_from_module_contents(text, mod)
+    if p and not os.path.exists(p):
+        tty.warn("Extracted path from module does not exist:"
+                 "\n\tExtracted path: " + p)
+    return p
+
+
+def get_path_from_module_contents(text, module_name):
+    tty.debug("Module name: " + module_name)
+    pkg_var_prefix = module_name.replace('-', '_').upper()
+    components = pkg_var_prefix.split('/')
+    # For modules with multiple components like foo/1.0.1, retrieve the package
+    # name "foo" from the module name
+    if len(components) > 1:
+        pkg_var_prefix = components[-2]
+    tty.debug("Package directory variable prefix: " + pkg_var_prefix)
+
     # If it sets the LD_LIBRARY_PATH or CRAY_LD_LIBRARY_PATH, use that
     for line in text:
-        if line.find('LD_LIBRARY_PATH') >= 0:
-            path = get_argument_from_module_line(line)
+        pattern = r'\W(CRAY_)?LD_LIBRARY_PATH'
+        if re.search(pattern, line):
+            path = get_path_arg_from_module_line(line)
             return path[:path.find('/lib')]
 
     # If it lists its package directory, return that
     for line in text:
-        if line.find(mod.upper() + '_DIR') >= 0:
-            return get_argument_from_module_line(line)
+        pattern = r'\W{0}_DIR'.format(pkg_var_prefix)
+        if re.search(pattern, line):
+            return get_path_arg_from_module_line(line)
 
     # If it lists a -rpath instruction, use that
     for line in text:
@@ -183,14 +195,15 @@ def get_path_from_module(mod):
 
     # If it lists a -L instruction, use that
     for line in text:
-        L = line.find('-L/')
-        if L >= 0:
-            return line[L + 2:line.find('/lib')]
+        lib_paths = line.find('-L/')
+        if lib_paths >= 0:
+            return line[lib_paths + 2:line.find('/lib')]
 
     # If it sets the PATH, use it
     for line in text:
-        if line.find('PATH') >= 0:
-            path = get_argument_from_module_line(line)
+        pattern = r'\WPATH'
+        if re.search(pattern, line):
+            path = get_path_arg_from_module_line(line)
             return path[:path.find('/bin')]
 
     # Unable to find module path
diff --git a/lib/spack/spack/util/naming.py b/lib/spack/spack/util/naming.py
index 78e368f06c..949189a3ca 100644
--- a/lib/spack/spack/util/naming.py
+++ b/lib/spack/spack/util/naming.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 # Need this because of spack.util.string
 from __future__ import absolute_import
 import string
@@ -29,7 +10,7 @@ import itertools
 import re
 from six import StringIO
 
-import spack
+import spack.error
 
 __all__ = [
     'mod_to_class',
diff --git a/lib/spack/spack/util/package_hash.py b/lib/spack/spack/util/package_hash.py
new file mode 100644
index 0000000000..c7354e97cf
--- /dev/null
+++ b/lib/spack/spack/util/package_hash.py
@@ -0,0 +1,133 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import ast
+import hashlib
+
+import spack.repo
+import spack.package
+import spack.directives
+import spack.error
+import spack.spec
+import spack.util.naming
+
+
+class RemoveDocstrings(ast.NodeTransformer):
+    """Transformer that removes docstrings from a Python AST."""
+    def remove_docstring(self, node):
+        if node.body:
+            if isinstance(node.body[0], ast.Expr) and \
+               isinstance(node.body[0].value, ast.Str):
+                node.body.pop(0)
+
+        self.generic_visit(node)
+        return node
+
+    def visit_FunctionDef(self, node):  # noqa
+        return self.remove_docstring(node)
+
+    def visit_ClassDef(self, node):  # noqa
+        return self.remove_docstring(node)
+
+    def visit_Module(self, node):  # noqa
+        return self.remove_docstring(node)
+
+
+class RemoveDirectives(ast.NodeTransformer):
+    """Remove Spack directives from a package AST."""
+    def __init__(self, spec):
+        self.spec = spec
+
+    def is_directive(self, node):
+        return (isinstance(node, ast.Expr) and
+                node.value and isinstance(node.value, ast.Call) and
+                node.value.func.id in spack.directives.__all__)
+
+    def is_spack_attr(self, node):
+        return (isinstance(node, ast.Assign) and
+                node.targets and isinstance(node.targets[0], ast.Name) and
+                node.targets[0].id in spack.package.Package.metadata_attrs)
+
+    def visit_ClassDef(self, node):  # noqa
+        if node.name == spack.util.naming.mod_to_class(self.spec.name):
+            node.body = [
+                c for c in node.body
+                if (not self.is_directive(c) and not self.is_spack_attr(c))]
+        return node
+
+
+class TagMultiMethods(ast.NodeVisitor):
+    """Tag @when-decorated methods in a spec."""
+    def __init__(self, spec):
+        self.spec = spec
+        self.methods = {}
+
+    def visit_FunctionDef(self, node):  # noqa
+        nodes = self.methods.setdefault(node.name, [])
+        if node.decorator_list:
+            dec = node.decorator_list[0]
+            if isinstance(dec, ast.Call) and dec.func.id == 'when':
+                cond = dec.args[0].s
+                nodes.append((node, self.spec.satisfies(cond, strict=True)))
+        else:
+            nodes.append((node, None))
+
+
+class ResolveMultiMethods(ast.NodeTransformer):
+    """Remove methods which do not exist if their @when is not satisfied."""
+    def __init__(self, methods):
+        self.methods = methods
+
+    def resolve(self, node):
+        if node.name not in self.methods:
+            raise PackageHashError(
+                "Future traversal visited new node: %s" % node.name)
+
+        result = None
+        for n, cond in self.methods[node.name]:
+            if cond:
+                return n
+            if cond is None:
+                result = n
+        return result
+
+    def visit_FunctionDef(self, node):  # noqa
+        if self.resolve(node) is node:
+            node.decorator_list = []
+            return node
+        return None
+
+
+def package_content(spec):
+    return ast.dump(package_ast(spec))
+
+
+def package_hash(spec, content=None):
+    if content is None:
+        content = package_content(spec)
+    return hashlib.sha256(content.encode('utf-8')).digest().lower()
+
+
+def package_ast(spec):
+    spec = spack.spec.Spec(spec)
+
+    filename = spack.repo.path.filename_for_package_name(spec.name)
+    with open(filename) as f:
+        text = f.read()
+        root = ast.parse(text)
+
+    root = RemoveDocstrings().visit(root)
+
+    RemoveDirectives(spec).visit(root)
+
+    fmm = TagMultiMethods(spec)
+    fmm.visit(root)
+
+    root = ResolveMultiMethods(fmm.methods).visit(root)
+    return root
+
+
+class PackageHashError(spack.error.SpackError):
+    """Raised for all errors encountered during package hashing."""
diff --git a/lib/spack/spack/util/path.py b/lib/spack/spack/util/path.py
index 9ce6c9306c..dc866984d6 100644
--- a/lib/spack/spack/util/path.py
+++ b/lib/spack/spack/util/path.py
@@ -1,42 +1,27 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """Utilities for managing paths in Spack.
+
+TODO: this is really part of spack.config. Consolidate it.
 """
 import os
 import re
-import spack
 import getpass
 import tempfile
 
+import spack.paths
+
+
 __all__ = [
     'substitute_config_variables',
     'canonicalize_path']
 
 # Substitutions to perform
 replacements = {
-    'spack': spack.prefix,
+    'spack': spack.paths.prefix,
     'user': getpass.getuser(),
     'tempdir': tempfile.gettempdir(),
 }
diff --git a/lib/spack/spack/util/pattern.py b/lib/spack/spack/util/pattern.py
index 3a85336bdc..32ee342135 100644
--- a/lib/spack/spack/util/pattern.py
+++ b/lib/spack/spack/util/pattern.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import inspect
 import collections
 import functools
diff --git a/lib/spack/spack/util/prefix.py b/lib/spack/spack/util/prefix.py
index d96b1c2449..60f8408b5a 100644
--- a/lib/spack/spack/util/prefix.py
+++ b/lib/spack/spack/util/prefix.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """
 This file contains utilities for managing the installation prefix of a package.
 """
@@ -44,6 +25,8 @@ class Prefix(str):
     /usr/share/man
     >>> prefix.foo.bar.baz
     /usr/foo/bar/baz
+    >>> prefix.join('dashed-directory').bin64
+    /usr/dashed-directory/bin64
 
     Prefix objects behave identically to strings. In fact, they
     subclass ``str``. So operators like ``+`` are legal::
@@ -55,3 +38,14 @@ class Prefix(str):
     """
     def __getattr__(self, attr):
         return Prefix(os.path.join(self, attr))
+
+    def join(self, string):
+        """Concatenates a string to a prefix.
+
+        Parameters:
+            string (str): the string to append to the prefix
+
+        Returns:
+            Prefix: the newly created installation prefix
+        """
+        return Prefix(os.path.join(self, string))
diff --git a/lib/spack/spack/util/spack_json.py b/lib/spack/spack/util/spack_json.py
index fbc514c14b..a56b6283d3 100644
--- a/lib/spack/spack/util/spack_json.py
+++ b/lib/spack/spack/util/spack_json.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """Simple wrapper around JSON to guarantee consistent use of load/dump. """
 import sys
 import json
@@ -59,7 +40,7 @@ def dump(data, stream=None):
 def _strify(data, ignore_dicts=False):
     # if this is a unicode string in python 2, return its string representation
     if sys.version_info[0] < 3:
-        if isinstance(data, unicode):
+        if isinstance(data, string_types):
             return data.encode('utf-8')
 
     # if this is a list of values, return list of byteified values
diff --git a/lib/spack/spack/util/spack_yaml.py b/lib/spack/spack/util/spack_yaml.py
index 476ed464f5..a1966664d9 100644
--- a/lib/spack/spack/util/spack_yaml.py
+++ b/lib/spack/spack/util/spack_yaml.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """Enhanced YAML parsing for Spack.
 
 - ``load()`` preserves YAML Marks on returned objects -- this allows
@@ -31,11 +12,15 @@
   default unorderd dict.
 
 """
-import yaml
-from yaml import Loader, Dumper
-from yaml.nodes import MappingNode, SequenceNode, ScalarNode
-from yaml.constructor import ConstructorError
 from ordereddict_backport import OrderedDict
+from six import string_types, StringIO
+
+import ruamel.yaml as yaml
+from ruamel.yaml import Loader, Dumper
+from ruamel.yaml.nodes import MappingNode, SequenceNode, ScalarNode
+from ruamel.yaml.constructor import ConstructorError
+
+from llnl.util.tty.color import colorize, clen, cextra
 
 import spack.error
 
@@ -60,10 +45,56 @@ class syaml_str(str):
     __repr__ = str.__repr__
 
 
+class syaml_int(int):
+    __repr__ = str.__repr__
+
+
+#: mapping from syaml type -> primitive type
+syaml_types = {
+    syaml_str: string_types,
+    syaml_int: int,
+    syaml_dict: dict,
+    syaml_list: list,
+}
+
+
+def syaml_type(obj):
+    """Get the corresponding syaml wrapper type for a primitive type.
+
+    Return:
+        (object): syaml-typed copy of object, or the obj if no wrapper
+    """
+    for syaml_t, t in syaml_types.items():
+        if type(obj) is not bool and isinstance(obj, t):
+            return syaml_t(obj) if type(obj) != syaml_t else obj
+    return obj
+
+
+def markable(obj):
+    """Whether an object can be marked."""
+    return type(obj) in syaml_types
+
+
 def mark(obj, node):
     """Add start and end markers to an object."""
-    obj._start_mark = node.start_mark
-    obj._end_mark = node.end_mark
+    if not markable(obj):
+        return
+
+    if hasattr(node, 'start_mark'):
+        obj._start_mark = node.start_mark
+    elif hasattr(node, '_start_mark'):
+        obj._start_mark = node._start_mark
+
+    if hasattr(node, 'end_mark'):
+        obj._end_mark = node.end_mark
+    elif hasattr(node, '_end_mark'):
+        obj._end_mark = node._end_mark
+
+
+def marked(obj):
+    """Whether an object has been marked by spack_yaml."""
+    return (hasattr(obj, '_start_mark') and obj._start_mark or
+            hasattr(obj, '_end_mark') and obj._end_mark)
 
 
 class OrderedLineLoader(Loader):
@@ -193,6 +224,7 @@ class OrderedLineDumper(Dumper):
                 node.flow_style = self.default_flow_style
             else:
                 node.flow_style = best_style
+
         return node
 
     def ignore_aliases(self, _data):
@@ -204,6 +236,87 @@ class OrderedLineDumper(Dumper):
 OrderedLineDumper.add_representer(syaml_dict, OrderedLineDumper.represent_dict)
 OrderedLineDumper.add_representer(syaml_list, OrderedLineDumper.represent_list)
 OrderedLineDumper.add_representer(syaml_str, OrderedLineDumper.represent_str)
+OrderedLineDumper.add_representer(syaml_int, OrderedLineDumper.represent_int)
+
+
+def file_line(mark):
+    """Format a mark as <file>:<line> information."""
+    result = mark.name
+    if mark.line:
+        result += ':' + str(mark.line)
+    return result
+
+
+#: Global for interactions between LineAnnotationDumper and dump_annotated().
+#: This is nasty but YAML doesn't give us many ways to pass arguments --
+#: yaml.dump() takes a class (not an instance) and instantiates the dumper
+#: itself, so we can't just pass an instance
+_annotations = []
+
+
+class LineAnnotationDumper(OrderedLineDumper):
+    """Dumper that generates per-line annotations.
+
+    Annotations are stored in the ``_annotations`` global.  After one
+    dump pass, the strings in ``_annotations`` will correspond one-to-one
+    with the lines output by the dumper.
+
+    LineAnnotationDumper records blame information after each line is
+    generated. As each line is parsed, it saves file/line info for each
+    object printed. At the end of each line, it creates an annotation
+    based on the saved mark and stores it in ``_annotations``.
+
+    For an example of how to use this, see ``dump_annotated()``, which
+    writes to a ``StringIO`` then joins the lines from that with
+    annotations.
+    """
+    saved = None
+
+    def __init__(self, *args, **kwargs):
+        super(LineAnnotationDumper, self).__init__(*args, **kwargs)
+        del _annotations[:]
+        self.colors = 'KgrbmcyGRBMCY'
+        self.filename_colors = {}
+
+    def process_scalar(self):
+        super(LineAnnotationDumper, self).process_scalar()
+        if marked(self.event.value):
+            self.saved = self.event.value
+
+    def represent_data(self, data):
+        """Force syaml_str to be passed through with marks."""
+        result = super(LineAnnotationDumper, self).represent_data(data)
+        if isinstance(result.value, string_types):
+            result.value = syaml_str(data)
+        mark(result.value, data)
+        return result
+
+    def write_stream_start(self):
+        super(LineAnnotationDumper, self).write_stream_start()
+        _annotations.append(colorize('@K{---}'))
+
+    def write_line_break(self):
+        super(LineAnnotationDumper, self).write_line_break()
+        if not self.saved:
+            return
+
+        # append annotations at the end of each line
+        if self.saved:
+            mark = self.saved._start_mark
+
+            color = self.filename_colors.get(mark.name)
+            if not color:
+                ncolors = len(self.colors)
+                color = self.colors[len(self.filename_colors) % ncolors]
+                self.filename_colors[mark.name] = color
+
+            fmt = '@%s{%%s}' % color
+            ann = fmt % mark.name
+            if mark.line is not None:
+                ann += ':@c{%s}' % (mark.line + 1)
+            _annotations.append(colorize(ann))
+        else:
+            _annotations.append('')
 
 
 def load(*args, **kwargs):
@@ -214,8 +327,36 @@ def load(*args, **kwargs):
 
 
 def dump(*args, **kwargs):
-    kwargs['Dumper'] = OrderedLineDumper
-    return yaml.dump(*args, **kwargs)
+    blame = kwargs.pop('blame', False)
+
+    if blame:
+        return dump_annotated(*args, **kwargs)
+    else:
+        kwargs['Dumper'] = OrderedLineDumper
+        return yaml.dump(*args, **kwargs)
+
+
+def dump_annotated(data, stream=None, *args, **kwargs):
+    kwargs['Dumper'] = LineAnnotationDumper
+
+    sio = StringIO()
+    yaml.dump(data, sio, *args, **kwargs)
+    lines = sio.getvalue().rstrip().split('\n')
+
+    getvalue = None
+    if stream is None:
+        stream = StringIO()
+        getvalue = stream.getvalue
+
+    # write out annotations and linees, accounting for color
+    width = max(clen(a) for a in _annotations)
+    formats = ['%%-%ds  %%s\n' % (width + cextra(a)) for a in _annotations]
+
+    for f, a, l in zip(formats, _annotations, lines):
+        stream.write(f % (a, l))
+
+    if getvalue:
+        return getvalue()
 
 
 class SpackYAMLError(spack.error.SpackError):
diff --git a/lib/spack/spack/util/string.py b/lib/spack/spack/util/string.py
index feb05a31a8..a85d50f50f 100644
--- a/lib/spack/spack/util/string.py
+++ b/lib/spack/spack/util/string.py
@@ -1,27 +1,7 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 
 def comma_list(sequence, article=''):
@@ -49,3 +29,29 @@ def comma_or(sequence):
 
 def comma_and(sequence):
     return comma_list(sequence, 'and')
+
+
+def quote(sequence, q="'"):
+    return ['%s%s%s' % (q, e, q) for e in sequence]
+
+
+def plural(n, singular, plural=None, show_n=True):
+    """Pluralize <singular> word by adding an s if n != 1.
+
+    Arguments:
+        n (int): number of things there are
+        singular (str): singular form of word
+        plural (str, optional): optional plural form, for when it's not just
+            singular + 's'
+        show_n (bool): whether to include n in the result string (default True)
+
+    Returns:
+        (str): "1 thing" if n == 1 or "n things" if n != 1
+    """
+    number = '%s ' % n if show_n else ''
+    if n == 1:
+        return "%s%s" % (number, singular)
+    elif plural is not None:
+        return "%s%s" % (number, plural)
+    else:
+        return "%s%ss" % (number, singular)
diff --git a/lib/spack/spack/util/web.py b/lib/spack/spack/util/web.py
index eadfc66ee0..b403e44d18 100644
--- a/lib/spack/spack/util/web.py
+++ b/lib/spack/spack/util/web.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from __future__ import print_function
 
 import re
@@ -49,8 +30,12 @@ except ImportError:
 
 import llnl.util.tty as tty
 
-import spack
+import spack.config
+import spack.cmd
+import spack.url
+import spack.stage
 import spack.error
+import spack.util.crypto
 from spack.util.compression import ALLOWED_ARCHIVE_TYPES
 
 
@@ -75,18 +60,30 @@ class LinkParser(HTMLParser):
 
 class NonDaemonProcess(multiprocessing.Process):
     """Process tha allows sub-processes, so pools can have sub-pools."""
-    def _get_daemon(self):
+    @property
+    def daemon(self):
         return False
 
-    def _set_daemon(self, value):
+    @daemon.setter
+    def daemon(self, value):
         pass
 
-    daemon = property(_get_daemon, _set_daemon)
 
+if sys.version_info[0] < 3:
+    class NonDaemonPool(multiprocessing.pool.Pool):
+        """Pool that uses non-daemon processes"""
+        Process = NonDaemonProcess
+else:
+
+    class NonDaemonContext(type(multiprocessing.get_context())):
+        Process = NonDaemonProcess
 
-class NonDaemonPool(multiprocessing.pool.Pool):
-    """Pool that uses non-daemon processes"""
-    Process = NonDaemonProcess
+    class NonDaemonPool(multiprocessing.pool.Pool):
+        """Pool that uses non-daemon processes"""
+
+        def __init__(self, *args, **kwargs):
+            kwargs['context'] = NonDaemonContext()
+            super(NonDaemonPool, self).__init__(*args, **kwargs)
 
 
 def _spider(url, visited, root, depth, max_depth, raise_on_error):
@@ -111,18 +108,19 @@ def _spider(url, visited, root, depth, max_depth, raise_on_error):
 
     try:
         context = None
-        if sys.version_info < (2, 7, 9) or \
-                ((3,) < sys.version_info < (3, 4, 3)):
-            if not spack.insecure:
+        verify_ssl = spack.config.get('config:verify_ssl')
+        pyver = sys.version_info
+        if (pyver < (2, 7, 9) or (3,) < pyver < (3, 4, 3)):
+            if verify_ssl:
                 tty.warn("Spack will not check SSL certificates. You need to "
                          "update your Python to enable certificate "
                          "verification.")
-        else:
+        elif verify_ssl:
             # We explicitly create default context to avoid error described in
             # https://blog.sucuri.net/2016/03/beware-unverified-tls-certificates-php-python.html
-            context = ssl._create_unverified_context() \
-                if spack.insecure \
-                else ssl.create_default_context()
+            context = ssl.create_default_context()
+        else:
+            context = ssl._create_unverified_context()
 
         # Make a HEAD request first to check the content type.  This lets
         # us ignore tarballs and gigantic files.
@@ -196,7 +194,7 @@ def _spider(url, visited, root, depth, max_depth, raise_on_error):
     except URLError as e:
         tty.debug(e)
 
-        if isinstance(e.reason, ssl.SSLError):
+        if hasattr(e, 'reason') and isinstance(e.reason, ssl.SSLError):
             tty.warn("Spack was unable to fetch url list due to a certificate "
                      "verification problem. You can try running spack -k, "
                      "which will not check SSL certificates. Use this at your "
@@ -281,6 +279,13 @@ def find_versions_of_archive(archive_urls, list_url=None, list_depth=0):
     for aurl in archive_urls:
         list_urls.add(spack.url.find_list_url(aurl))
 
+    # Add '/' to the end of the URL. Some web servers require this.
+    additional_list_urls = set()
+    for lurl in list_urls:
+        if not lurl.endswith('/'):
+            additional_list_urls.add(lurl + '/')
+    list_urls.update(additional_list_urls)
+
     # Grab some web pages to scrape.
     pages = {}
     links = set()
@@ -317,7 +322,7 @@ def find_versions_of_archive(archive_urls, list_url=None, list_depth=0):
         #   .sha256
         #   .sig
         # However, SourceForge downloads still need to end in '/download'.
-        url_regex += '(\/download)?$'
+        url_regex += r'(\/download)?$'
 
         regexes.append(url_regex)
 
@@ -392,7 +397,7 @@ def get_checksums_for_versions(
 
                 # Checksum the archive and add it to the list
                 version_hashes.append((version, spack.util.crypto.checksum(
-                    hashlib.md5, stage.archive_file)))
+                    hashlib.sha256, stage.archive_file)))
                 i += 1
         except spack.stage.FailedDownloadError:
             tty.msg("Failed to fetch {0}".format(url))
@@ -408,7 +413,7 @@ def get_checksums_for_versions(
 
     # Generate the version directives to put in a package.py
     version_lines = "\n".join([
-        "    version('{0}', {1}'{2}')".format(
+        "    version('{0}', {1}sha256='{2}')".format(
             v, ' ' * (max_len - len(str(v))), h) for v, h in version_hashes
     ])
 
diff --git a/lib/spack/spack/variant.py b/lib/spack/spack/variant.py
index 43a1ab4ae6..8f154139c5 100644
--- a/lib/spack/spack/variant.py
+++ b/lib/spack/spack/variant.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """The variant module contains data structures that are needed to manage
 variants both in packages and in specs.
 """
@@ -29,11 +10,12 @@ variants both in packages and in specs.
 import functools
 import inspect
 import re
+from six import StringIO
 
 import llnl.util.lang as lang
-import spack
+
+import spack.directives
 import spack.error as error
-from six import StringIO
 
 
 class Variant(object):
diff --git a/lib/spack/spack/version.py b/lib/spack/spack/version.py
index cef58d43f4..82d3927b64 100644
--- a/lib/spack/spack/version.py
+++ b/lib/spack/spack/version.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 """
 This module implements Version and version-ish objects.  These are:
 
@@ -51,6 +32,7 @@ from six import string_types
 
 from spack.util.spack_yaml import syaml_dict
 
+
 __all__ = ['Version', 'VersionRange', 'VersionList', 'ver']
 
 # Valid version characters
@@ -253,6 +235,9 @@ class Version(object):
     def __iter__(self):
         return iter(self.version)
 
+    def __len__(self):
+        return len(self.version)
+
     def __getitem__(self, idx):
         cls = type(self)
 
diff --git a/pytest.ini b/pytest.ini
deleted file mode 100644
index 0d8d2b271f..0000000000
--- a/pytest.ini
+++ /dev/null
@@ -1,5 +0,0 @@
-# content of pytest.ini
-[pytest]
-addopts = --durations=20 -ra
-testpaths = lib/spack/spack/test
-python_files = *.py
\ No newline at end of file
diff --git a/share/spack/csh/pathadd.csh b/share/spack/csh/pathadd.csh
index 1e0800c5f3..5e94d4a4c0 100644
--- a/share/spack/csh/pathadd.csh
+++ b/share/spack/csh/pathadd.csh
@@ -1,3 +1,8 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 ########################################################################
 # Prepends directories to path, if they exist.
 #      pathadd /path/to/dir            # add to PATH
diff --git a/share/spack/csh/spack.csh b/share/spack/csh/spack.csh
index 5acd190449..a773dd216b 100644
--- a/share/spack/csh/spack.csh
+++ b/share/spack/csh/spack.csh
@@ -1,3 +1,8 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 ########################################################################
 # This is a wrapper around the spack command that forwards calls to
 # 'spack use' and 'spack unuse' to shell functions.  This in turn
@@ -58,6 +63,47 @@ case cd:
         cd `\spack location $_sp_arg $_sp_args`
     endif
     breaksw
+case env:
+    shift _sp_args  # get rid of 'env'
+
+    set _sp_arg=""
+    [ $#_sp_args -gt 0 ] && set _sp_arg = ($_sp_args[1])
+
+    if ( "$_sp_arg" == "-h" ) then
+        \spack env -h
+    else
+        switch ($_sp_arg)
+            case activate:
+                set _sp_env_arg=""
+                [ $#_sp_args -gt 1 ] && set _sp_env_arg = ($_sp_args[2])
+
+                if ( "$_sp_env_arg" == "" || "$_sp_args" =~ "*--sh*" || "$_sp_args" =~ "*--csh*" || "$_sp_args" =~ "*-h*" ) then
+                    # no args or args contain -h/--help, --sh, or --csh: just execute
+                    \spack $_sp_flags env $_sp_args
+                else
+                    shift _sp_args  # consume 'activate' or 'deactivate'
+                    # actual call to activate: source the output
+                    eval `\spack $_sp_flags env activate --csh $_sp_args`
+                endif
+                breaksw
+            case deactivate:
+                set _sp_env_arg=""
+                [ $#_sp_args -gt 1 ] && set _sp_env_arg = ($_sp_args[2])
+
+                if ( "$_sp_env_arg" != "" ) then
+                    # with args: execute the command
+                    \spack $_sp_flags env $_sp_args
+                else
+                    # no args: source the output
+                    eval `\spack $_sp_flags env deactivate --csh`
+                endif
+                breaksw
+            default:
+                echo default
+                \spack $_sp_flags env $_sp_args
+                breaksw
+        endsw
+    endif
 case use:
 case unuse:
 case load:
@@ -74,25 +120,25 @@ case unload:
     # tool's commands to add/remove the result from the environment.
     switch ($_sp_subcommand)
         case "use":
-            set _sp_full_spec = ( "`\spack $_sp_flags module find --module-type dotkit $_sp_spec`" )
+            set _sp_full_spec = ( "`\spack $_sp_flags module dotkit find $_sp_spec`" )
             if ( $? == 0 ) then
                 use $_sp_module_args $_sp_full_spec
             endif
             breaksw
         case "unuse":
-            set _sp_full_spec = ( "`\spack $_sp_flags module find --module-type dotkit $_sp_spec`" )
+            set _sp_full_spec = ( "`\spack $_sp_flags module dotkit find $_sp_spec`" )
             if ( $? == 0 ) then
                 unuse $_sp_module_args $_sp_full_spec
             endif
             breaksw
         case "load":
-            set _sp_full_spec = ( "`\spack $_sp_flags module find --module-type tcl $_sp_spec`" )
+            set _sp_full_spec = ( "`\spack $_sp_flags module tcl find $_sp_spec`" )
             if ( $? == 0 ) then
                 module load $_sp_module_args $_sp_full_spec
             endif
             breaksw
         case "unload":
-            set _sp_full_spec = ( "`\spack $_sp_flags module find --module-type tcl $_sp_spec`" )
+            set _sp_full_spec = ( "`\spack $_sp_flags module tcl find $_sp_spec`" )
             if ( $? == 0 ) then
                 module unload $_sp_module_args $_sp_full_spec
             endif
@@ -108,3 +154,4 @@ endsw
 _sp_end:
 unset _sp_args _sp_full_spec _sp_modtype _sp_module_args
 unset _sp_sh_cmd _sp_spec _sp_subcommand _sp_flags
+unset _sp_arg _sp_env_arg
diff --git a/share/spack/docker/Dockerfile b/share/spack/docker/Dockerfile
new file mode 100644
index 0000000000..0c3b49f366
--- /dev/null
+++ b/share/spack/docker/Dockerfile
@@ -0,0 +1,132 @@
+ARG BASE
+
+FROM $BASE
+MAINTAINER Spack Maintainers <maintainers@spack.io>
+
+ARG BASE
+ARG DISTRO
+ARG DISTRO_VERSION
+
+ENV DOCKERFILE_BASE=$BASE                     \
+    DOCKERFILE_DISTRO=$DISTRO                 \
+    DOCKERFILE_DISTRO_VERSION=$DISTRO_VERSION \
+    SPACK_ROOT=/spack                         \
+    FORCE_UNSAFE_CONFIGURE=1                  \
+    DEBIAN_FRONTEND=noninteractive            \
+    container=docker
+
+COPY bin   $SPACK_ROOT/bin
+COPY etc   $SPACK_ROOT/etc
+COPY lib   $SPACK_ROOT/lib
+COPY share $SPACK_ROOT/share
+COPY var   $SPACK_ROOT/var
+RUN mkdir -p $SPACK_ROOT/opt/spack
+
+MASK PUSH
+MASK [[ $DISTRO == arch ]]
+RUN pacman -Sy --noconfirm                                     \
+        base-devel   ca-certificates curl   gcc                \
+        gcc-fortran  git             gnupg2 iproute2           \
+        make         openssh         python python-pip         \
+        sudo         tcl                                       \
+ && echo 'nobody ALL=(ALL) NOPASSWD: ALL' >                    \
+        /etc/sudoers.d/nobody-sudo                             \
+ && sudo -u nobody git clone --depth 1                         \
+        https://aur.archlinux.org/lua-posix.git /tmp/lua-posix \
+ && sudo -u nobody git clone --depth 1                         \
+        https://aur.archlinux.org/lmod.git /tmp/lmod           \
+ && (  cd /tmp/lua-posix                                       \
+    && sudo -u nobody makepkg -si --asdeps --noconfirm )       \
+ && (  cd /tmp/lmod                                            \
+    && sudo -u nobody makepkg -si --noconfirm )                \
+ && rm -rf /tmp/lua-posix /tmp/lmod /etc/sudoers.d/nobody-sudo
+
+MASK [[ $DISTRO =~ (centos|rhel.*) ]]
+RUN yum update -y
+
+  MASK PUSH
+  MASK [[ $DISTRO =~ rhel.* ]]
+  RUN yum install -y yum-conf-repos.noarch \
+   && yum update -y
+  MASK POP
+
+RUN yum install -y epel-release                               \
+ && yum update -y                                             \
+ && yum --enablerepo epel groupinstall -y "Development Tools" \
+ && yum --enablerepo epel install -y                          \
+         curl           findutils gcc-c++    gcc              \
+         gcc-gfortran   git       gnupg2     hostname         \
+         iproute        Lmod      make       patch            \
+         openssh-server python    python-pip tcl              \
+ && rm -rf /var/cache/yum                                     \
+ && yum clean all
+
+MASK [[ $DISTRO == fedora ]]
+RUN dnf update -y                                            \
+ && dnf group install -y "C Development Tools and Libraries" \
+ && dnf install -y                                           \
+        @development-tools                                   \
+        curl            findutils    gcc-c++     gcc         \
+        gcc-gfortran    git          gnupg2      hostname    \
+        iproute         Lmod         make        patch       \
+        openssh-server  python       tcl                     \
+ && dnf clean all
+
+MASK [[ $DISTRO == opensuse ]]
+RUN zypper -n ref                                              \
+ && zypper -n up --skip-interactive --no-recommends            \
+ && zypper -n install -l --no-recommends --type pattern        \
+        devel_basis  devel_C_C++                               \
+ && zypper -n install -l --no-recommends                       \
+        bash        bash-completion ca-certificates curl       \
+        findutils   gcc             gcc-locale      gcc-c++    \
+        gcc-fortran git             glibc-locale    gpg2       \
+        hostname    iproute         lua-lmod        make       \
+        patch       openssh         python          python-pip \
+        python-xml  tcl                                        \
+ && zypper clean                                               \
+ && rm -rf /var/cache/zypp/*
+
+MASK [[ $DISTRO == ubuntu ]]
+RUN apt-get -yqq update                                   \
+ && apt-get -yqq install                                  \
+        build-essential ca-certificates curl       g++    \
+        gcc             gfortran        git        gnupg2 \
+        iproute2        lmod            lua-posix  make   \
+        openssh-server  python          python-pip tcl
+
+  MASK PUSH
+  MASK [[ $DISTRO_VERSION == bionic ]]
+  # [WORKAROUND]
+  # https://bugs.launchpad.net/ubuntu/+source/lua-posix/+bug/1752082
+  RUN ln -s posix_c.so /usr/lib/x86_64-linux-gnu/lua/5.2/posix.so
+  MASK POP
+
+RUN rm -rf /var/lib/apt/lists/*
+
+MASK POP
+
+RUN rm -rf $SPACK_ROOT/.git                                          \
+ && pip install boto3                                                \
+ && (  echo ". /usr/share/lmod/lmod/init/bash"                       \
+    && echo ". $SPACK_ROOT/share/spack/setup-env.sh"                 \
+    && echo ". $SPACK_ROOT/share/spack/spack-completion.bash" )      \
+        >> /etc/profile.d/spack.sh                                   \
+ && ln -s $SPACK_ROOT/share/spack/docker/handle-ssh.sh               \
+        /etc/profile.d/handle-ssh.sh                                 \
+ && ln -s $SPACK_ROOT/share/spack/docker/handle-prompt.sh            \
+        /etc/profile.d/handle-prompt.sh                              \
+ && mkdir -p /root/.spack                                            \
+ && cp $SPACK_ROOT/share/spack/docker/modules.yaml                   \
+        /root/.spack/modules.yaml                                    \
+ && rm -rf /root/*.*
+
+MASK PUSH
+MASK [[ $DISTRO_VERSION =~ (centos|fedora|opensuse|rhel.*) ]]
+RUN rm -f /run/nologin
+MASK POP
+
+WORKDIR /root
+ENTRYPOINT ["bash", "/spack/share/spack/docker/entrypoint.bash"]
+CMD ["docker-shell"]
+
diff --git a/share/spack/docker/build-image.sh b/share/spack/docker/build-image.sh
new file mode 100755
index 0000000000..fb12bdb833
--- /dev/null
+++ b/share/spack/docker/build-image.sh
@@ -0,0 +1,84 @@
+#! /usr/bin/env bash
+#
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+script="$( basename "$0" )"
+cd "$( dirname "$0" )"
+
+if [ -z "$BASE_IMAGE" ] ; then
+    BASE_IMAGE="ubuntu"
+fi
+
+if [ -z "$BASE_TAG" ] ; then
+    BASE_TAG="latest"
+fi
+
+if [ -z "$DISTRO" ] ; then
+    DISTRO="${BASE_IMAGE}"
+fi
+
+if [ -z "$DISTRO_VERSION" ] ; then
+    DISTRO_VERSION="${BASE_TAG}"
+fi
+
+if [ -z "$BASE_NAME" ] ; then
+    BASE_NAME="${DISTRO}"
+fi
+
+if [ "$BASE_TAG" '=' 'latest' ] ; then
+    BASE_TAG=""
+fi
+
+if [ -n "$BASE_TAG" ] ; then
+    BASE_TAG=":${BASE_TAG}"
+fi
+
+TAG="spack/${BASE_NAME}${BASE_TAG}"
+
+export BASE_IMAGE BASE_TAG DISTRO DISTRO_VERSION BASE_NAME TAG
+
+if [ "$script" '=' 'run-image.sh' ] ; then
+    com="docker run --rm -ti"
+
+    if [ -z "$DISABLE_MOUNT" ] ; then
+        DISABLE_MOUNT=1
+        if [ -z "$*" ] ; then
+            DISABLE_MOUNT=0
+        fi
+    fi
+
+    if [ "$DISABLE_MOUNT" '==' 0 ] ; then
+        com="${com} -v \"$( readlink -f ../../.. ):/spack\""
+    fi
+
+    eval "exec ${com}" "${TAG}" "$@"
+elif [ "$script" '=' 'render-image-template.sh' ] ; then
+    ./dpp.bash Dockerfile
+elif [ "$script" '=' 'push-image.sh' ] ; then
+    docker push "${TAG}"
+    for tag in ${EXTRA_TAGS} ; do
+        docker push "spack/${BASE_NAME}:${tag}"
+    done
+else
+    tag_options="-t ${TAG}"
+    for tag in ${EXTRA_TAGS} ; do
+        tag_options="${tag_options} -t spack/${BASE_NAME}:${tag}"
+    done
+
+    cache_options=""
+    if docker pull "${TAG}" ; then
+        cache_options="--cache-from ${TAG}"
+    fi
+
+    exec ./render-image-template.sh |
+         docker build -f -                                           \
+                      ${cache_options}                               \
+                      ${tag_options}                                 \
+                      --build-arg BASE="${BASE_IMAGE}${BASE_TAG}"    \
+                      --build-arg DISTRO="${DISTRO}"                 \
+                      --build-arg DISTRO_VERSION="${DISTRO_VERSION}" \
+                      ../../..
+fi
diff --git a/share/spack/docker/config/arch.bash b/share/spack/docker/config/arch.bash
new file mode 100644
index 0000000000..3cb2951c4b
--- /dev/null
+++ b/share/spack/docker/config/arch.bash
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+unset DISTRO
+unset DISTRO_VERSION
+unset BASE_IMAGE
+unset BASE_NAME
+unset BASE_TAG
+unset TAG
+unset EXTRA_TAGS
+
+export BASE_IMAGE="base/archlinux"
+export BASE_NAME="archlinux"
+export BASE_TAG="2018.10.01"
+export DISTRO="arch"
+export EXTRA_TAGS="latest"
diff --git a/share/spack/docker/config/centos.bash b/share/spack/docker/config/centos.bash
new file mode 100644
index 0000000000..bef7ad276b
--- /dev/null
+++ b/share/spack/docker/config/centos.bash
@@ -0,0 +1,16 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+unset DISTRO
+unset DISTRO_VERSION
+unset BASE_IMAGE
+unset BASE_NAME
+unset BASE_TAG
+unset TAG
+unset EXTRA_TAGS
+
+export BASE_IMAGE=centos
+export BASE_TAG="7"
+export EXTRA_TAGS="latest"
diff --git a/share/spack/docker/config/fedora.bash b/share/spack/docker/config/fedora.bash
new file mode 100644
index 0000000000..fcf7425693
--- /dev/null
+++ b/share/spack/docker/config/fedora.bash
@@ -0,0 +1,16 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+unset DISTRO
+unset DISTRO_VERSION
+unset BASE_IMAGE
+unset BASE_NAME
+unset BASE_TAG
+unset TAG
+unset EXTRA_TAGS
+
+export BASE_IMAGE=fedora
+export BASE_TAG="24"
+export EXTRA_TAGS="latest"
diff --git a/share/spack/docker/config/opensuse.bash b/share/spack/docker/config/opensuse.bash
new file mode 100644
index 0000000000..b0e11c17ac
--- /dev/null
+++ b/share/spack/docker/config/opensuse.bash
@@ -0,0 +1,16 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+unset DISTRO
+unset DISTRO_VERSION
+unset BASE_IMAGE
+unset BASE_NAME
+unset BASE_TAG
+unset TAG
+unset EXTRA_TAGS
+
+export BASE_IMAGE=opensuse
+export BASE_TAG="tumbleweed"
+export EXTRA_TAGS="latest"
diff --git a/share/spack/docker/config/scilinux.bash b/share/spack/docker/config/scilinux.bash
new file mode 100644
index 0000000000..71fd737f69
--- /dev/null
+++ b/share/spack/docker/config/scilinux.bash
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+unset DISTRO
+unset BASE_IMAGE
+unset BASE_NAME
+unset BASE_TAG
+unset TAG
+unset EXTRA_TAGS
+
+export BASE_IMAGE=sl
+export BASE_TAG="7"
+export BASE_NAME=scilinux
+export DISTRO=rhel7
+export EXTRA_TAGS="latest"
diff --git a/share/spack/docker/config/ubuntu.bash b/share/spack/docker/config/ubuntu.bash
new file mode 100644
index 0000000000..588848fb40
--- /dev/null
+++ b/share/spack/docker/config/ubuntu.bash
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+unset DISTRO
+unset BASE_IMAGE
+unset BASE_NAME
+unset BASE_TAG
+unset TAG
+unset EXTRA_TAGS
+
+export BASE_IMAGE=ubuntu
+export BASE_TAG="bionic"
+export EXTRA_TAGS="latest"
diff --git a/share/spack/docker/dpp.bash b/share/spack/docker/dpp.bash
new file mode 100755
index 0000000000..f41a9c5260
--- /dev/null
+++ b/share/spack/docker/dpp.bash
@@ -0,0 +1,77 @@
+#! /usr/bin/env bash
+#
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+function prefix_tokens() {
+    line="$1" ; shift
+    nprefix="$1"
+
+    line="${line::$nprefix} "
+    echo "${line::$nprefix}"
+}
+
+
+# read file contents, or stdin
+cat "$1" |
+
+# remove blank lines
+grep -v '^ *$' |
+
+# remove leading whitespace
+sed 's/^ *//g' |
+
+# remove comments
+grep -v '^#.*' |
+
+# remove trailing whitespace
+sed 's/ *$//g' |
+
+# remove extraneous whitespace
+sed 's/  */ /g' |
+
+# mask out subsections
+(
+    stack_level=1
+    mask_level=1
+
+    while read LINE ; do
+        try_print=1
+
+        if [ "$( prefix_tokens "$LINE" 10 )" '=' 'MASK PUSH ' ] ; then
+            tmp="$stack_level"
+            stack_level="$(( stack_level + 1 ))"
+            if [ "$mask_level" '=' "$tmp" ] ; then
+                mask_level="$stack_level"
+            fi
+            try_print=0
+        elif [ "$( prefix_tokens "$LINE" 9 )" '=' 'MASK POP ' ] ; then
+            stack_level="$(( stack_level - 1 ))"
+            if [ "$mask_level" -gt "$stack_level" ] ; then
+                mask_level="$stack_level"
+            fi
+            try_print=0
+        elif [ "$( prefix_tokens "$LINE" 5 )" '=' 'MASK ' ] ; then
+            if [ "$(( mask_level + 1 ))" -ge "$stack_level" ] ; then
+                mask_level="$stack_level"
+                eval "${LINE:5}"
+                if [ "$?" '!=' 0 ] ; then
+                    mask_level="$(( mask_level - 1 ))"
+                fi
+            fi
+            try_print=0
+        fi
+
+        if [ "$stack_level" -lt 1 ] ; then
+            stack_level=1
+            mask_level=0
+        fi
+
+        if [ "$try_print" '=' 1 -a "$mask_level" '=' "$stack_level" ] ; then
+            echo "$LINE"
+        fi
+    done
+)
+
diff --git a/share/spack/docker/entrypoint.bash b/share/spack/docker/entrypoint.bash
new file mode 100755
index 0000000000..58d6281084
--- /dev/null
+++ b/share/spack/docker/entrypoint.bash
@@ -0,0 +1,43 @@
+#! /usr/bin/env bash -e
+#
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+if [ "$1" '=' 'docker-shell' ] ; then
+    if [ -t 0 ] ; then
+        exec bash -il
+    else
+        (
+            echo -n "It looks like you're trying to run an intractive shell"
+            echo -n " session, but either no psuedo-TTY is allocateed for this"
+            echo -n " container's STDIN, or it is closed."
+            echo
+
+            echo -n "Make sure you run docker with the --interactive and --tty"
+            echo -n " options."
+            echo
+        ) >&2
+
+        exit 1
+    fi
+else
+    exec 3>&1
+    exec 4>&2
+
+    exec 1>&-
+    exec 2>&-
+
+    source /etc/profile.d/spack.sh
+    source /etc/profile.d/handle-ssh.sh
+
+    exec 1>&3
+    exec 2>&4
+
+    exec 3>&-
+    exec 4>&-
+
+    spack "$@"
+    exit $?
+fi
diff --git a/share/spack/docker/handle-prompt.sh b/share/spack/docker/handle-prompt.sh
new file mode 100644
index 0000000000..d523ac3a31
--- /dev/null
+++ b/share/spack/docker/handle-prompt.sh
@@ -0,0 +1,169 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+if [ x$SPACK_PROMPT '!=' x0 ] ; then
+
+__tmp="`mktemp -d`"
+
+__trylock() {
+    local dir
+    dir="$__tmp/$1.lock"
+    mkdir "$dir" &>/dev/null
+    return $?
+}
+
+__queue_init() {
+    local r
+    local w
+
+    mkdir "$__tmp/$1.read.lock" ; r=$?
+    mkdir "$__tmp/$1.write.lock" ; w=$?
+
+    if [ "$r" '=' '0' -a "$w" '=' '0' ] ; then
+        return 0
+    else
+        return 1
+    fi
+}
+
+__queue_try_read() {
+    __trylock "$1.read"
+    return $?
+}
+
+__queue_try_write() {
+    __trylock "$1.write"
+    return $?
+}
+
+__queue_make_readable() {
+    rm -r "$__tmp/$1.read.lock" &>/dev/null
+    return $?
+}
+
+__queue_make_writable() {
+    rm -r "$__tmp/$1.write.lock" &>/dev/null
+    return $?
+}
+
+__read() {
+    cat "$__tmp/$1" 2> /dev/null
+    return $?
+}
+
+__write() {
+    cat > "$__tmp/$1" 2> /dev/null
+    return $?
+}
+
+__revparse_head() {
+    head="`git -C /spack rev-parse $@ HEAD 2>/dev/null`"
+    result="$?"
+    if [ "$result" '!=' '0' ] ; then
+        head="`git --git-dir=/spack/.git \\
+              --work-tree=/spack rev-parse $@ HEAD 2>/dev/null`"
+        result="$?"
+    fi
+
+    echo "$head"
+    return $result
+}
+
+__git_head() {
+    head="`__revparse_head --abbrev-ref`"
+    if [ "$?" '=' '0' ] ; then
+        if [ "$head" '=' 'HEAD' ] ; then
+            head="`__revparse_head | cut -c1-8`..."
+        fi
+
+        echo "$head"
+    fi
+}
+
+__update_prompt() {
+    local prompt
+    prompt=''
+    linux_distro="$DOCKERFILE_DISTRO"
+    if [ -n "$linux_distro" ] ; then
+        linux_distro='\[\e[1;34m\][\[\e[0;34m\]'"$linux_distro"'\[\e[1;34m\]]'
+        if [ -n "$prompt" ] ; then
+            prompt="$prompt "
+        fi
+        prompt="$prompt$linux_distro"
+    fi
+
+    git_head="`__git_head`"
+
+    if [ -n "$git_head" ] ; then
+        git_head='\[\e[1;32m\](\[\e[0;32m\]'"$git_head"'\[\e[1;32m\])'
+        if [ -n "$prompt" ] ; then
+            prompt="$prompt "
+        fi
+        prompt="$prompt$git_head"
+    fi
+
+    if [ -n "$prompt" ] ; then
+        prompt="$prompt "
+    fi
+    prompt="$prompt"'\[\e[0;m\]\W: '
+    echo "$prompt" | __write prompt
+}
+
+set -m
+(
+    __queue_init query
+    __queue_init prompt
+
+    __update_prompt
+    __queue_make_readable prompt
+
+    __queue_make_writable query
+
+    while sleep 0.010 ; do
+        last_q_time=''
+
+        while sleep 0.010 ; do
+            q_time="`date +%s%N`"
+            if __queue_try_read query ; then
+                last_q_time="$q_time"
+                __queue_make_writable query
+            fi
+
+            if [ -n "$last_q_time" -a \
+                "$(( (q_time - last_q_time)/10000000 > 100 ))" '=' '1' ] ; then
+                break
+            fi
+        done
+
+        __update_prompt
+        __queue_make_readable prompt
+    done
+) &>/dev/null &
+set +m
+
+__update_prompt_main_first_call=1
+__update_prompt_main() {
+    if [ "$__update_prompt_main_first_call" '=' '1' ] ; then
+        while sleep 0.001 ; do
+            if __queue_try_read prompt ; then
+                PS1="`__read prompt`"
+                break
+            fi
+        done
+        __update_prompt_main_first_call=0
+    else
+        if __queue_try_read prompt ; then
+            PS1="`__read prompt`"
+        fi
+    fi
+
+    if __queue_try_write query ; then
+        __queue_make_readable query
+    fi
+}
+
+PROMPT_COMMAND=__update_prompt_main
+
+fi # [ x$SPACK_PROMPT '!=' x0 ]
diff --git a/share/spack/docker/handle-ssh.sh b/share/spack/docker/handle-ssh.sh
new file mode 100644
index 0000000000..f2139897cb
--- /dev/null
+++ b/share/spack/docker/handle-ssh.sh
@@ -0,0 +1,41 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+uid="`id -u`"
+if [ "$uid" '=' '0' ] ; then
+    for key_type in dsa ecdsa ed25519 rsa ; do
+        private_key_file="/etc/ssh/ssh_host_${key_type}_key"
+        public_key_file="$private_key_file.pub"
+
+        if [ '!' -f "$private_key_file" ] ; then
+            ssh-keygen \
+                -q -t "$key_type" -N "" -f "$private_key_file"
+            chmod 600 "$private_key_file"
+            chmod 644 "$public_key_file"
+        fi
+    done
+
+    mkdir -p /var/run/sshd
+
+    pgrep -u 0 -U 0 sshd &> /dev/null
+    if [ '!' "$?" '=' '0' ] ; then
+        nohup /usr/sbin/sshd -f /etc/ssh/sshd_config < /dev/null &> /dev/null
+    fi
+fi
+
+if [ '!' -f "$HOME/.ssh/id_rsa" ] ; then
+    ssh-keygen \
+        -t rsa -C "spack.developer@docker.host" -N "" -f "$HOME/.ssh/id_rsa"
+    cat "$HOME/.ssh/id_rsa.pub" >> "$HOME/.ssh/authorized_keys"
+    chmod 600 "$HOME/.ssh/authorized_keys"
+
+    docker_ip="`ip address show dev eth0 |
+                grep inet |
+                cut -d' ' -f 6 |
+                cut -d/ -f 1`"
+
+    ssh-keyscan -t rsa 127.0.0.1 localhost "$docker_ip" "`hostname`" \
+        > "$HOME/.ssh/known_hosts" 2> /dev/null
+fi
diff --git a/share/spack/docker/modules.yaml b/share/spack/docker/modules.yaml
new file mode 100644
index 0000000000..02907ecc40
--- /dev/null
+++ b/share/spack/docker/modules.yaml
@@ -0,0 +1,6 @@
+modules:
+  enable:
+    - lmod
+  lmod:
+    core_compilers:
+      - gcc
diff --git a/share/spack/docker/push-image.sh b/share/spack/docker/push-image.sh
new file mode 120000
index 0000000000..9e5dfdf52d
--- /dev/null
+++ b/share/spack/docker/push-image.sh
@@ -0,0 +1 @@
+./build-image.sh
\ No newline at end of file
diff --git a/share/spack/docker/render-image-template.sh b/share/spack/docker/render-image-template.sh
new file mode 120000
index 0000000000..9e5dfdf52d
--- /dev/null
+++ b/share/spack/docker/render-image-template.sh
@@ -0,0 +1 @@
+./build-image.sh
\ No newline at end of file
diff --git a/share/spack/docker/run-image.sh b/share/spack/docker/run-image.sh
new file mode 120000
index 0000000000..b3fd71be24
--- /dev/null
+++ b/share/spack/docker/run-image.sh
@@ -0,0 +1 @@
+build-image.sh
\ No newline at end of file
diff --git a/share/spack/docs/docker/module-file-tutorial/Dockerfile b/share/spack/docs/docker/module-file-tutorial/Dockerfile
index a012492a98..8dfd51bf31 100644
--- a/share/spack/docs/docker/module-file-tutorial/Dockerfile
+++ b/share/spack/docs/docker/module-file-tutorial/Dockerfile
@@ -36,8 +36,7 @@ RUN spack install lmod && spack clean -a
 # Build a compiler
 RUN spack install gcc@7.2.0 && spack clean -a
 RUN /bin/bash -l -c ' \
-    spack load gcc@7.2.0 \
-    && spack compiler add'
+    spack compiler add $(spack location -i gcc@7.2.0)/bin'
 
 # Build the software on top of the compiler
 RUN spack install netlib-scalapack ^openmpi ^openblas %gcc@7.2.0 \
diff --git a/share/spack/docs/docker/module-file-tutorial/spack.sh b/share/spack/docs/docker/module-file-tutorial/spack.sh
index 54d095c717..a59bc7575f 100644
--- a/share/spack/docs/docker/module-file-tutorial/spack.sh
+++ b/share/spack/docs/docker/module-file-tutorial/spack.sh
@@ -1,3 +1,8 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 source $SPACK_ROOT/share/spack/setup-env.sh
 
 LMOD_DIR=$(spack location -i lmod)
diff --git a/share/spack/qa/run-build-tests b/share/spack/qa/run-build-tests
index b5d5aed28f..315c0b8e99 100755
--- a/share/spack/qa/run-build-tests
+++ b/share/spack/qa/run-build-tests
@@ -1,5 +1,11 @@
 #!/bin/bash -e
 #
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+#
 # Description:
 #     Runs Spack build smoke tests.  This installs a few packages that
 #     cover different parts of the build system.  It is not an exhaustive
@@ -11,6 +17,12 @@
 . "$(dirname $0)/setup.sh"
 check_dependencies ${coverage} git hg svn
 
+# Fetch the sources in a mirror, and add it to Spack
+mkdir -p ~/.mirror
+bin/spack mirror add travis ~/.mirror
+bin/spack mirror create -D -d ~/.mirror ${SPEC}
+
+
 # Move to root directory of Spack
 # Allows script to be run from anywhere
 cd "$SPACK_ROOT"
@@ -25,5 +37,4 @@ fi
 spack config get compilers
 
 # Run some build smoke tests, potentially with code coverage
-${coverage_run} bin/spack install -v ${SPEC}
-${coverage_combine}
+${coverage_run} bin/spack install ${SPEC}
diff --git a/share/spack/qa/run-doc-tests b/share/spack/qa/run-doc-tests
index c43779fcaf..6129243676 100755
--- a/share/spack/qa/run-doc-tests
+++ b/share/spack/qa/run-doc-tests
@@ -1,5 +1,11 @@
 #!/bin/bash -e
 #
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+#
 # Description:
 #     Builds Spack documentation and checks for
 #     possible syntax errors. Treats warnings as
diff --git a/share/spack/qa/run-flake8-tests b/share/spack/qa/run-flake8-tests
index 29fc15f9d7..f98cdb919c 100755
--- a/share/spack/qa/run-flake8-tests
+++ b/share/spack/qa/run-flake8-tests
@@ -1,5 +1,11 @@
 #!/bin/bash -e
 #
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+#
 # Description:
 #     Runs source code style checks on Spack.
 #     See $SPACK_ROOT/.flake8 for a list of
@@ -11,4 +17,8 @@
 . "$(dirname $0)/setup.sh"
 check_dependencies flake8
 
+# verify that the code style is correct
 spack flake8
+
+# verify that the license headers are present
+spack license verify
diff --git a/share/spack/qa/run-unit-tests b/share/spack/qa/run-unit-tests
index 87203ba915..7aae551f03 100755
--- a/share/spack/qa/run-unit-tests
+++ b/share/spack/qa/run-unit-tests
@@ -1,5 +1,11 @@
 #!/bin/bash -e
 #
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+#
 # Description:
 #     Runs Spack unit tests.
 #
@@ -25,8 +31,11 @@ ${coverage_run} bin/spack -h
 ${coverage_run} bin/spack help -a
 
 # Profile and print top 20 lines for a simple call to spack spec
-${coverage_run} bin/spack -p --lines 20 spec mpileaks
+${coverage_run} bin/spack -p --lines 20 spec mpileaks%gcc ^elfutils@0.170
 
 # Run unit tests with code coverage
-${coverage_run} bin/spack test "$@"
-${coverage_combine}
+extra_args=""
+if [[ -n "$@" ]]; then
+    extra_args="-k $@"
+fi
+${coverage_run} bin/spack test --verbose "$extra_args"
diff --git a/share/spack/qa/setup.sh b/share/spack/qa/setup.sh
index 98c79a0457..4f40904433 100755
--- a/share/spack/qa/setup.sh
+++ b/share/spack/qa/setup.sh
@@ -1,5 +1,11 @@
 #!/bin/bash -e
 #
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+#
 # Description:
 #     Common setup code to be sourced by Spack's test scripts.
 #
@@ -11,14 +17,12 @@ SPACK_ROOT="$QA_DIR/../../.."
 . "$SPACK_ROOT/share/spack/setup-env.sh"
 
 # Set up some variables for running coverage tests.
-if [[ "$COVERAGE" == true ]]; then
+if [[ "$TEST_SUITE" == "unit" || "$TEST_SUITE" == "build" ]]; then
     coverage=coverage
     coverage_run="coverage run"
-    coverage_combine="coverage combine"
 else
     coverage=""
     coverage_run=""
-    coverage_combine=""
 fi
 
 #
diff --git a/share/spack/setup-env.csh b/share/spack/setup-env.csh
index 6fc728daa8..4e471b1121 100755
--- a/share/spack/setup-env.csh
+++ b/share/spack/setup-env.csh
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 #
 # This file is part of Spack and sets up the spack environment for
@@ -39,15 +20,14 @@ if ($?SPACK_ROOT) then
     alias spack          'set _sp_args = (\!*); source $_spack_share_dir/csh/spack.csh'
     alias _spack_pathadd 'set _pa_args = (\!*) && source $_spack_share_dir/csh/pathadd.csh'
 
-    # Shamelessly stolen from setup-env.sh
-    set _sp_sys_type    = `$SPACK_ROOT/bin/spack python -c 'print(spack.architecture.sys_type())'`
-    set _sp_dotkit_root = `$SPACK_ROOT/bin/spack python -c "print(spack.util.path.canonicalize_path(spack.config.get_config('config').get('module_roots').get('dotkit')))"`
-    set _sp_tcl_root    = `$SPACK_ROOT/bin/spack python -c "print(spack.util.path.canonicalize_path(spack.config.get_config('config').get('module_roots').get('tcl')))"`
+    # Set variables needed by this script
+    _spack_pathadd PATH "$SPACK_ROOT/bin"
+    eval `spack --print-shell-vars csh`
 
     # Set up modules and dotkit search paths in the user environment
     _spack_pathadd DK_NODE    "$_sp_dotkit_root/$_sp_sys_type"
     _spack_pathadd MODULEPATH "$_sp_tcl_root/$_sp_sys_type"
-    _spack_pathadd PATH       "$SPACK_ROOT/bin"
 else
-    echo "ERROR: Sourcing spack setup-env.csh requires setting SPACK_ROOT to the root of your spack installation"
+    echo "ERROR: Sourcing spack setup-env.csh requires setting SPACK_ROOT to "
+    echo "       the root of your spack installation."
 endif
diff --git a/share/spack/setup-env.sh b/share/spack/setup-env.sh
index 21a7e00345..79688455bf 100755
--- a/share/spack/setup-env.sh
+++ b/share/spack/setup-env.sh
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 ########################################################################
 #
@@ -80,14 +61,22 @@ function spack {
         return
     fi
 
-    _sp_subcommand=$1; shift
-    _sp_spec="$@"
+    _sp_subcommand=""
+    if [ -n "$1" ]; then
+        _sp_subcommand="$1"
+        shift
+    fi
+    _sp_spec=("$@")
 
     # Filter out use and unuse.  For any other commands, just run the
     # command.
     case $_sp_subcommand in
         "cd")
-            _sp_arg="$1"; shift
+            _sp_arg=""
+            if [ -n "$1" ]; then
+                _sp_arg="$1"
+                shift
+            fi
             if [ "$_sp_arg" = "-h" ]; then
                 command spack cd -h
             else
@@ -100,6 +89,43 @@ function spack {
             fi
             return
             ;;
+        "env")
+            _sp_arg=""
+            if [ -n "$1" ]; then
+                _sp_arg="$1"
+                shift
+            fi
+
+            if [ "$_sp_arg" = "-h" ]; then
+                command spack env -h
+            else
+                case $_sp_arg in
+                    activate)
+                        _a="$@"
+                        if [ -z "$1" -o "${_a#*--sh}" != "$_a" -o "${_a#*--csh}" != "$_a" -o "${_a#*-h}" != "$_a" ]; then
+                            # no args or args contain -h/--help, --sh, or --csh: just execute
+                            command spack "${args[@]}"
+                        else
+                            # actual call to activate: source the output
+                            eval $(command spack $_sp_flags env activate --sh "$@")
+                        fi
+                        ;;
+                    deactivate)
+                        if [ -n "$1" ]; then
+                            # with args: execute the command
+                            command spack "${args[@]}"
+                        else
+                            # no args: source the output.
+                            eval $(command spack $_sp_flags env deactivate --sh)
+                        fi
+                        ;;
+                    *)
+                        command spack "${args[@]}"
+                        ;;
+                esac
+            fi
+            return
+            ;;
         "use"|"unuse"|"load"|"unload")
             # Shift any other args for use off before parsing spec.
             _sp_subcommand_args=""
@@ -113,7 +139,7 @@ function spack {
                 shift
             done
 
-            _sp_spec="$@"
+            _sp_spec=("$@")
 
             # Here the user has run use or unuse with a spec.  Find a matching
             # spec using 'spack module find', then use the appropriate module
@@ -121,20 +147,28 @@ function spack {
             # If spack module command comes back with an error, do nothing.
             case $_sp_subcommand in
                 "use")
-                    if _sp_full_spec=$(command spack $_sp_flags module loads --input-only $_sp_subcommand_args --module-type dotkit $_sp_spec); then
+                    if _sp_full_spec=$(command spack $_sp_flags module dotkit find $_sp_subcommand_args "${_sp_spec[@]}"); then
                         use $_sp_module_args $_sp_full_spec
+                    else
+                        $(exit 1)
                     fi ;;
                 "unuse")
-                    if _sp_full_spec=$(command spack $_sp_flags module loads --input-only $_sp_subcommand_args --module-type dotkit $_sp_spec); then
+                    if _sp_full_spec=$(command spack $_sp_flags module dotkit find $_sp_subcommand_args "${_sp_spec[@]}"); then
                         unuse $_sp_module_args $_sp_full_spec
+                    else
+                        $(exit 1)
                     fi ;;
                 "load")
-                    if _sp_full_spec=$(command spack $_sp_flags module loads --input-only $_sp_subcommand_args --module-type tcl $_sp_spec); then
+                    if _sp_full_spec=$(command spack $_sp_flags module tcl find $_sp_subcommand_args "${_sp_spec[@]}"); then
                         module load $_sp_module_args $_sp_full_spec
+                    else
+                        $(exit 1)
                     fi ;;
                 "unload")
-                    if _sp_full_spec=$(command spack $_sp_flags module loads --input-only $_sp_subcommand_args --module-type tcl $_sp_spec); then
+                    if _sp_full_spec=$(command spack $_sp_flags module tcl find $_sp_subcommand_args "${_sp_spec[@]}"); then
                         module unload $_sp_module_args $_sp_full_spec
+                    else
+                        $(exit 1)
                     fi ;;
             esac
             ;;
@@ -202,7 +236,7 @@ export SPACK_ROOT=${_sp_prefix}
 # Determine which shell is being used
 #
 function _spack_determine_shell() {
-	ps -p $$ | tail -n 1 | awk '{print $4}' | sed 's/^-//' | xargs basename
+	PS_FORMAT= ps -p $$ | tail -n 1 | awk '{print $4}' | sed 's/^-//' | xargs basename
 }
 export SPACK_SHELL=$(_spack_determine_shell)
 
@@ -218,27 +252,27 @@ if ! _spack_fn_exists use && ! _spack_fn_exists module; then
 	need_module="yes"
 fi;
 
+
 #
-# build and make available environment-modules
+# make available environment-modules
 #
 if [ "${need_module}" = "yes" ]; then
-    #check if environment-modules is installed
-    module_prefix="$(spack location -i "environment-modules" 2>&1 || echo "not_installed")"
-    module_prefix=$(echo "${module_prefix}" | tail -n 1)
-    if [ "${module_prefix}" != "not_installed" ]; then
+    eval `spack --print-shell-vars sh,modules`
+
+    # _sp_module_prefix is set by spack --print-sh-vars
+    if [ "${_sp_module_prefix}" != "not_installed" ]; then
         #activate it!
-        export MODULE_PREFIX=${module_prefix}
+        export MODULE_PREFIX=${_sp_module_prefix}
         _spack_pathadd PATH "${MODULE_PREFIX}/Modules/bin"
         module() { eval `${MODULE_PREFIX}/Modules/bin/modulecmd ${SPACK_SHELL} $*`; }
     fi;
+else
+    eval `spack --print-shell-vars sh`
 fi;
 
 #
-# Set up modules and dotkit search paths in the user environment
+# set module system roots
 #
-_sp_sys_type=$(spack-python -c 'print(spack.architecture.sys_type())')
-_sp_dotkit_root=$(spack-python -c "print(spack.util.path.canonicalize_path(spack.config.get_config('config').get('module_roots', {}).get('dotkit')))")
-_sp_tcl_root=$(spack-python -c "print(spack.util.path.canonicalize_path(spack.config.get_config('config').get('module_roots', {}).get('tcl')))")
 _spack_pathadd DK_NODE    "${_sp_dotkit_root%/}/$_sp_sys_type"
 _spack_pathadd MODULEPATH "${_sp_tcl_root%/}/$_sp_sys_type"
 
diff --git a/share/spack/spack-completion.bash b/share/spack/spack-completion.bash
index 56cbfef792..c157d836a4 100755
--- a/share/spack/spack-completion.bash
+++ b/share/spack/spack-completion.bash
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 # The following global variables are used/set by Bash programmable completion
 #     COMP_CWORD: An index into ${COMP_WORDS} of the word containing the
@@ -114,9 +95,9 @@ function _bash_completion_spack {
 function _spack {
     if $list_options
     then
-        compgen -W "-h --help -d --debug -D --pdb -k --insecure -m --mock -p
-                    --profile -v --verbose -s --stacktrace -V --version
-                    --color --color=always --color=auto --color=never" -- "$cur"
+        compgen -W "-h --help --color -d --debug -D --pdb -k --insecure
+                    -m --mock -p --profile -P --sorted-profile --lines
+                    -v --verbose -s --stacktrace -V --version" -- "$cur"
     else
         compgen -W "$(_subcommands)" -- "$cur"
     fi
@@ -125,24 +106,31 @@ function _spack {
 function _spack_activate {
     if $list_options
     then
-        compgen -W "-h --help -f --force" -- "$cur"
+        compgen -W "-h --help -f --force -v --view" -- "$cur"
     else
         compgen -W "$(_installed_packages)" -- "$cur"
     fi
 }
 
 function _spack_arch {
-    compgen -W "-h --help -p --platform" -- "$cur"
+    compgen -W "-h --help -p --platform -o --operating-system
+                -t --target" -- "$cur"
 }
 
-function _spack_bootstrap {
-    # FIXME: What does this command even do?
+function _spack_blame {
     if $list_options
     then
-        compgen -W "-h --help -r --remote" -- "$cur"
+        compgen -W "-h --help -t --time -p --percent -g --git" -- "$cur"
+    else
+        compgen -W "$(_all_packages)" -- "$cur"
     fi
 }
 
+function _spack_bootstrap {
+    compgen -W "-h --help -j --jobs --keep-prefix --keep-stage -n --no-checksum
+                -v --verbose --clean --dirty --run-tests" -- "$cur"
+}
+
 function _spack_build {
     if $list_options
     then
@@ -164,8 +152,8 @@ function _spack_buildcache {
 function _spack_buildcache_create {
     if $list_options
     then
-        compgen -W "-h --help -r --rel -f --force -y --yes-to-all -k --key
-                    -d --directory" -- "$cur"
+        compgen -W "-h --help -r --rel -f --force -u --unsigned -a --allow-root
+                    -k --key -d --directory" -- "$cur"
     else
         compgen -W "$(_all_packages)" -- "$cur"
     fi
@@ -174,23 +162,21 @@ function _spack_buildcache_create {
 function _spack_buildcache_install {
     if $list_options
     then
-        compgen -W "-h --help -f --force -y --yes-to-all" -- "$cur"
+        compgen -W "-h --help -f --force -m --multiple -a --allow-root -u
+                    --unsigned" -- "$cur"
     else
         compgen -W "$(_all_packages)" -- "$cur"
     fi
 }
 
 function _spack_buildcache_keys {
-    if $list_options
-    then
-        compgen -W "-h --help -i --install -y --yes-to-all" -- "$cur"
-    fi
+    compgen -W "-h --help -i --install -t --trust -f --force" -- "$cur"
 }
 
 function _spack_buildcache_list {
     if $list_options
     then
-        compgen -W "-h --help" -- "$cur"
+        compgen -W "-h --help -f --force" -- "$cur"
     else
         compgen -W "$(_all_packages)" -- "$cur"
     fi
@@ -220,12 +206,26 @@ function _spack_clean {
     if $list_options
     then
         compgen -W "-h --help -s --stage -d --downloads
-                   -m --misc-cache -a --all" -- "$cur"
+                    -m --misc-cache -a --all" -- "$cur"
     else
         compgen -W "$(_all_packages)" -- "$cur"
     fi
 }
 
+function _spack_clone {
+    if $list_options
+    then
+        compgen -W "-h --help -r --remote" -- "$cur"
+    fi
+}
+
+function _spack_commands {
+    if $list_options
+    then
+        compgen -W "-h --help --format" -- "$cur"
+    fi
+}
+
 function _spack_compiler {
     if $list_options
     then
@@ -315,14 +315,17 @@ function _spack_configure {
 }
 
 function _spack_create {
-    compgen -W "-h --help --keep-stage -n --name -t --template -r --repo
-                -N --namespace -f --force" -- "$cur"
+    if $list_options
+    then
+        compgen -W "-h --help --keep-stage -n --name -t --template -r --repo
+                    -N --namespace -f --force" -- "$cur"
+    fi
 }
 
 function _spack_deactivate {
     if $list_options
     then
-        compgen -W "-h --help -f --force -a --all" -- "$cur"
+        compgen -W "-h --help -f --force -v --view -a --all" -- "$cur"
     else
         compgen -W "$(_installed_packages)" -- "$cur"
     fi
@@ -341,10 +344,20 @@ function _spack_debug_create_db_tarball {
     compgen -W "-h --help" -- "$cur"
 }
 
+function _spack_dependencies {
+    if $list_options
+    then
+        compgen -W "-h --help -i --installed -t --transitive -V
+                    --no-expand-virtuals" -- "$cur"
+    else
+        compgen -W "$(_all_packages)" -- "$cur"
+    fi
+}
+
 function _spack_dependents {
     if $list_options
     then
-        compgen -W "-h --help" -- "$cur"
+        compgen -W "-h --help -i --installed -t --transitive" -- "$cur"
     else
         compgen -W "$(_all_packages)" -- "$cur"
     fi
@@ -360,16 +373,15 @@ function _spack_diy {
     fi
 }
 
-function _spack_doc {
-    # FIXME: What does this command even do?
+function _spack_docs {
     compgen -W "-h --help" -- "$cur"
 }
 
 function _spack_edit {
     if $list_options
     then
-        compgen -W "-h --help -b --build-system -c --command -t --test -m --module
-                    -r --repo -N --namespace" -- "$cur"
+        compgen -W "-h --help -b --build-system -c --command -d --docs -t
+                    --test -m --module -r --repo -N --namespace" -- "$cur"
     else
         compgen -W "$(_all_packages)" -- "$cur"
     fi
@@ -378,7 +390,7 @@ function _spack_edit {
 function _spack_env {
     if $list_options
     then
-        compgen -W "-h --help" -- "$cur"
+        compgen -W "-h --help --clean --dirty" -- "$cur"
     else
         compgen -W "$(_all_packages)" -- "$cur"
     fi
@@ -387,9 +399,11 @@ function _spack_env {
 function _spack_extensions {
     if $list_options
     then
-        compgen -W "-h --help -l --long -p --paths -d --deps" -- "$cur"
+        compgen -W "-h --help -l --long -p --paths -d --deps
+                    -s --show -v --view" -- "$cur"
     else
-        compgen -W "go-bootstrap go lua octave python r ruby rust" -- "$cur"
+        compgen -W "aspell go-bootstrap go lua matlab octave perl python r ruby
+                    rust tcl yorick" -- "$cur"
     fi
 }
 
@@ -406,10 +420,11 @@ function _spack_fetch {
 function _spack_find {
     if $list_options
     then
-        compgen -W "-h --help -s --short -p --paths -d --deps -l --long
-                    -L --very-long -f --show-flags --show-full-compiler
+        compgen -W "-h --help -s --short -p --paths -d --deps -l --long -L
+                    --very-long -t --tags -f --show-flags --show-full-compiler
                     -e --explicit -E --implicit -u --unknown -m --missing
-                    -v --variants -M --only-missing -N --namespace" -- "$cur"
+                    -v --variants -M --only-missing -N --namespace --start-date
+                    --end-date" -- "$cur"
     else
         compgen -W "$(_installed_packages)" -- "$cur"
     fi
@@ -418,11 +433,74 @@ function _spack_find {
 function _spack_flake8 {
     if $list_options
     then
-        compgen -W "-h --help -k --keep-temp -o --output
+        compgen -W "-h --help -b --base -k --keep-temp -a --all -o --output
                     -r --root-relative -U --no-untracked" -- "$cur"
     fi
 }
 
+function _spack_gpg {
+    if $list_options
+    then
+        compgen -W "-h --help" -- "$cur"
+    else
+        compgen -W "create export init list sign trust untrust verify" -- "$cur"
+    fi
+}
+
+function _spack_gpg_create {
+    if $list_options
+    then
+        compgen -W "-h --help --comment --expires --export" -- "$cur"
+    fi
+}
+
+function _spack_gpg_export {
+    if $list_options
+    then
+        compgen -W "-h --help" -- "$cur"
+    fi
+}
+
+function _spack_gpg_init {
+    compgen -W "-h --help" -- "$cur"
+}
+
+function _spack_gpg_list {
+    compgen -W "-h --help --trusted --signing" -- "$cur"
+}
+
+function _spack_gpg_sign {
+    if $list_options
+    then
+        compgen -W "-h --help --output --key --clearsign" -- "$cur"
+    else
+        compgen -W "$(installed_packages)" -- "$cur"
+    fi
+}
+
+function _spack_gpg_trust {
+    if $list_options
+    then
+        compgen -W "-h --help" -- "$cur"
+    fi
+}
+
+function _spack_gpg_untrust {
+    if $list_options
+    then
+        compgen -W "-h --help --signing" -- "$cur"
+    fi
+}
+
+function _spack_gpg_verify {
+    if $list_options
+    then
+        compgen -W "-h --help" -- "$cur"
+    else
+        compgen -W "$(installed_packages)" -- "$cur"
+    fi
+}
+
 function _spack_graph {
     if $list_options
     then
@@ -436,7 +514,7 @@ function _spack_graph {
 function _spack_help {
     if $list_options
     then
-        compgen -W "-h --help" -- "$cur"
+        compgen -W "-h --help -a --all --spec" -- "$cur"
     else
         compgen -W "$(_subcommands)" -- "$cur"
     fi
@@ -454,9 +532,11 @@ function _spack_info {
 function _spack_install {
     if $list_options
     then
-        compgen -W "-h --help --only -j --jobs --keep-prefix --keep-stage
-                    -n --no-checksum -v --verbose --fake --clean --dirty
-                    --run-tests --log-format --log-file --source" -- "$cur"
+        compgen -W "-h --help --only -j --jobs --overwrite --keep-prefix
+                    --keep-stage --dont-restage --use-cache --show-log-on-error
+                    --source -n --no-checksum -v --verbose --fake -f --file
+                    --clean --dirty --test --log-format --log-file
+                    -y --yes-to-all" -- "$cur"
     else
         compgen -W "$(_all_packages)" -- "$cur"
     fi
@@ -465,7 +545,8 @@ function _spack_install {
 function _spack_list {
     if $list_options
     then
-        compgen -W "-h --help -d --search-description --format" -- "$cur"
+        compgen -W "-h --help -d --search-description --format
+                    -t --tags" -- "$cur"
     else
         compgen -W "$(_all_packages)" -- "$cur"
     fi
@@ -491,10 +572,11 @@ function _spack_location {
     fi
 }
 
-function _spack_md5 {
+function _spack_log_parse {
     if $list_options
     then
-        compgen -W "-h --help" -- "$cur"
+        compgen -W "-h --help --show -c --context -p --profile -w --width
+                    -j --jobs" -- "$cur"
     fi
 }
 
@@ -537,49 +619,168 @@ function _spack_mirror_remove {
     fi
 }
 
+function _spack_mirror_rm {
+    # Alias to `spack mirror remove`
+    _spack_mirror_remove
+}
+
 function _spack_module {
     if $list_options
     then
         compgen -W "-h --help" -- "$cur"
     else
-        compgen -W "find loads refresh rm" -- "$cur"
+        compgen -W "lmod tcl dotkit" -- "$cur"
     fi
 }
 
-function _spack_module_find {
+function _spack_module_tcl {
     if $list_options
     then
-        compgen -W "-h --help -m --module-type" -- "$cur"
+        compgen -W "-h --help" -- "$cur"
+    else
+        compgen -W "refresh find rm loads" -- "$cur"
+    fi
+}
+
+
+function _spack_module_tcl_find {
+    if $list_options
+    then
+        compgen -W "-h --help --full-path -r --dependencies" -- "$cur"
     else
         compgen -W "$(_installed_packages)" -- "$cur"
     fi
 }
 
-function _spack_module_loads {
+function _spack_module_tcl_loads {
     if $list_options
     then
         compgen -W "-h --help --input-only -p --prefix -x --exclude
-                    -m --module-type -r --dependencies" -- "$cur"
+                    -r --dependencies" -- "$cur"
     else
         compgen -W "$(_installed_packages)" -- "$cur"
     fi
 
 }
 
-function _spack_module_refresh {
+function _spack_module_tcl_refresh {
     if $list_options
     then
-        compgen -W "-h --help --delete-tree -m --module-type
-                    -y --yes-to-all" -- "$cur"
+        compgen -W "-h --help --delete-tree -y --yes-to-all" -- "$cur"
+    else
+        compgen -W "$(_installed_packages)" -- "$cur"
+    fi
+}
+
+function _spack_module_tcl_rm {
+    if $list_options
+    then
+        compgen -W "-h --help -y --yes-to-all" -- "$cur"
+    else
+        compgen -W "$(_installed_packages)" -- "$cur"
+    fi
+}
+
+function _spack_module_dotkit {
+    if $list_options
+    then
+        compgen -W "-h --help" -- "$cur"
+    else
+        compgen -W "refresh find rm loads" -- "$cur"
+    fi
+}
+
+
+function _spack_module_dotkit_find {
+    if $list_options
+    then
+        compgen -W "-h --help --full-path -r --dependencies" -- "$cur"
+    else
+        compgen -W "$(_installed_packages)" -- "$cur"
+    fi
+}
+
+function _spack_module_dotkit_loads {
+    if $list_options
+    then
+        compgen -W "-h --help --input-only -p --prefix -x --exclude
+                    -r --dependencies" -- "$cur"
+    else
+        compgen -W "$(_installed_packages)" -- "$cur"
+    fi
+
+}
+
+function _spack_module_dotkit_refresh {
+    if $list_options
+    then
+        compgen -W "-h --help --delete-tree -y --yes-to-all" -- "$cur"
+    else
+        compgen -W "$(_installed_packages)" -- "$cur"
+    fi
+}
+
+function _spack_module_dotkit_rm {
+    if $list_options
+    then
+        compgen -W "-h --help -y --yes-to-all" -- "$cur"
+    else
+        compgen -W "$(_installed_packages)" -- "$cur"
+    fi
+}
+
+function _spack_module_lmod {
+    if $list_options
+    then
+        compgen -W "-h --help" -- "$cur"
+    else
+        compgen -W "refresh find rm loads setdefault" -- "$cur"
+    fi
+}
+
+
+function _spack_module_lmod_find {
+    if $list_options
+    then
+        compgen -W "-h --help --full-path -r --dependencies" -- "$cur"
+    else
+        compgen -W "$(_installed_packages)" -- "$cur"
+    fi
+}
+
+function _spack_module_lmod_loads {
+    if $list_options
+    then
+        compgen -W "-h --help --input-only -p --prefix -x --exclude
+                    -r --dependencies" -- "$cur"
+    else
+        compgen -W "$(_installed_packages)" -- "$cur"
+    fi
+
+}
+
+function _spack_module_lmod_refresh {
+    if $list_options
+    then
+        compgen -W "-h --help --delete-tree -y --yes-to-all" -- "$cur"
+    else
+        compgen -W "$(_installed_packages)" -- "$cur"
+    fi
+}
+
+function _spack_module_lmod_rm {
+    if $list_options
+    then
+        compgen -W "-h --help -y --yes-to-all" -- "$cur"
     else
         compgen -W "$(_installed_packages)" -- "$cur"
     fi
 }
 
-function _spack_module_rm {
+function _spack_module_lmod_setdefault {
     if $list_options
     then
-        compgen -W "-h --help -m --module-type -y --yes-to-all" -- "$cur"
+        compgen -W "-h --help" -- "$cur"
     else
         compgen -W "$(_installed_packages)" -- "$cur"
     fi
@@ -595,7 +796,6 @@ function _spack_patch {
 }
 
 function _spack_pkg {
-    # FIXME: What does this subcommand even do?
     if $list_options
     then
         compgen -W "-h --help" -- "$cur"
@@ -615,22 +815,34 @@ function _spack_pkg_add {
 
 function _spack_pkg_added {
     # FIXME: How to list git revisions?
-    compgen -W "-h --help" -- "$cur"
+    if $list_options
+    then
+        compgen -W "-h --help" -- "$cur"
+    fi
 }
 
 function _spack_pkg_diff {
     # FIXME: How to list git revisions?
-    compgen -W "-h --help" -- "$cur"
+    if $list_options
+    then
+        compgen -W "-h --help" -- "$cur"
+    fi
 }
 
 function _spack_pkg_list {
     # FIXME: How to list git revisions?
-    compgen -W "-h --help" -- "$cur"
+    if $list_options
+    then
+        compgen -W "-h --help" -- "$cur"
+    fi
 }
 
 function _spack_pkg_removed {
     # FIXME: How to list git revisions?
-    compgen -W "-h --help" -- "$cur"
+    if $list_options
+    then
+        compgen -W "-h --help" -- "$cur"
+    fi
 }
 
 function _spack_providers {
@@ -638,8 +850,14 @@ function _spack_providers {
     then
         compgen -W "-h --help" -- "$cur"
     else
-        compgen -W "awk blas daal elf golang ipp lapack mkl
-                    mpe mpi opencl openfoam pil scalapack" -- "$cur"
+        compgen -W "$(_providers)" -- "$cur"
+    fi
+}
+
+function _spack_pydoc {
+    if $list_options
+    then
+        compgen -W "-h --help" -- "$cur"
     fi
 }
 
@@ -787,7 +1005,10 @@ function _spack_url_list {
 }
 
 function _spack_url_parse {
-    compgen -W "-h --help -s --spider" -- "$cur"
+    if $list_options
+    then
+        compgen -W "-h --help -s --spider" -- "$cur"
+    fi
 }
 
 function _spack_url_summary {
@@ -841,14 +1062,14 @@ function _spack_view_hard {
 function _spack_view_hardlink {
     if $list_options
     then
-        compgen -W "-h --help" -- "$cur"
+        compgen -W "-h --help -i --ignore-conflicts" -- "$cur"
     fi
 }
 
 function _spack_view_remove {
     if $list_options
     then
-        compgen -W "-h --help" -- "$cur"
+        compgen -W "-h --help --no-remove-dependents -a --all" -- "$cur"
     fi
 }
 
@@ -877,14 +1098,14 @@ function _spack_view_status {
 function _spack_view_symlink {
     if $list_options
     then
-        compgen -W "-h --help" -- "$cur"
+        compgen -W "-h --help --ignore-conflicts" -- "$cur"
     fi
 }
 
 # Helper functions for subcommands
 
 function _subcommands {
-    spack help --all | grep "^  [a-z]" | awk '{print $1}' | grep -v spack
+    spack commands
 }
 
 function _all_packages {
@@ -892,14 +1113,17 @@ function _all_packages {
 }
 
 function _installed_packages {
-    # Perl one-liner used to strip out color codes
-    spack find | grep -v "^--" | perl -pe 's/\e\[?.*?[\@-~]//g'
+    spack --color=never find | grep -v "^--"
 }
 
 function _installed_compilers {
     spack compilers | egrep -v "^(-|=)"
 }
 
+function _providers {
+    spack providers
+}
+
 function _mirrors {
     spack mirror list | awk '{print $1}'
 }
diff --git a/templates/modules/modulefile.dk b/share/spack/templates/modules/modulefile.dk
index c3f6d2dce1..c3f6d2dce1 100644
--- a/templates/modules/modulefile.dk
+++ b/share/spack/templates/modules/modulefile.dk
diff --git a/templates/modules/modulefile.lua b/share/spack/templates/modules/modulefile.lua
index cf37595228..a8eae9bef1 100644
--- a/templates/modules/modulefile.lua
+++ b/share/spack/templates/modules/modulefile.lua
@@ -73,11 +73,11 @@ end
 {% block environment %}
 {% for command_name, cmd in environment_modifications %}
 {% if command_name == 'PrependPath' %}
-prepend_path("{{ cmd.name }}", "{{ cmd.value }}")
+prepend_path("{{ cmd.name }}", "{{ cmd.value }}", "{{ cmd.separator }}")
 {% elif command_name == 'AppendPath' %}
-append_path("{{ cmd.name }}", "{{ cmd.value }}")
+append_path("{{ cmd.name }}", "{{ cmd.value }}", "{{ cmd.separator }}")
 {% elif command_name == 'RemovePath' %}
-remove_path("{{ cmd.name }}", "{{ cmd.value }}")
+remove_path("{{ cmd.name }}", "{{ cmd.value }}", "{{ cmd.separator }}")
 {% elif command_name == 'SetEnv' %}
 setenv("{{ cmd.name }}", "{{ cmd.value }}")
 {% elif command_name == 'UnsetEnv' %}
diff --git a/templates/modules/modulefile.tcl b/share/spack/templates/modules/modulefile.tcl
index 833d8bf6c2..87edc10a64 100644
--- a/templates/modules/modulefile.tcl
+++ b/share/spack/templates/modules/modulefile.tcl
@@ -23,7 +23,7 @@ proc ModulesHelp { } {
 
 {% block autoloads %}
 {% for module in autoload %}
-if ![ is-loaded {{ module }} ] {{ '{' }}
+if {{ '{' }} [ module-info mode load ] && ![ is-loaded {{ module }} ] {{ '}' }} {{ '{' }}
 {% if verbose %}
     puts stderr "Autoloading {{ module }}"
 {% endif %}
diff --git a/share/spack/templates/reports/cdash/Build.xml b/share/spack/templates/reports/cdash/Build.xml
new file mode 100644
index 0000000000..1d184349b3
--- /dev/null
+++ b/share/spack/templates/reports/cdash/Build.xml
@@ -0,0 +1,27 @@
+  <Build>
+    <StartBuildTime>{{ build.starttime }}</StartBuildTime>
+    <BuildCommand>{{ install_command }}</BuildCommand>
+{% for warning in build.warnings %}
+    <Warning>
+      <BuildLogLine>{{ warning.line_no }}</BuildLogLine>
+      <Text>{{ warning.text }}</Text>
+      <SourceFile>{{ warning.source_file }}</SourceFile>
+      <SourceLineNumber>{{ warning.source_line_no }}</SourceLineNumber>
+      <PreContext>{{ warning.pre_context }}</PreContext>
+      <PostContext>{{ warning.post_context }}</PostContext>
+    </Warning>
+{% endfor %}
+{% for error in build.errors %}
+    <Error>
+      <BuildLogLine>{{ error.line_no }}</BuildLogLine>
+      <Text>{{ error.text }}</Text>
+      <SourceFile>{{ error.source_file }}</SourceFile>
+      <SourceLineNumber>{{ error.source_line_no }}</SourceLineNumber>
+      <PreContext>{{ error.pre_context }}</PreContext>
+      <PostContext>{{ error.post_context }}</PostContext>
+    </Error>
+{% endfor %}
+    <EndBuildTime>{{ build.endtime }}</EndBuildTime>
+    <ElapsedMinutes>0</ElapsedMinutes>
+  </Build>
+</Site>
diff --git a/share/spack/templates/reports/cdash/Configure.xml b/share/spack/templates/reports/cdash/Configure.xml
new file mode 100644
index 0000000000..0451279563
--- /dev/null
+++ b/share/spack/templates/reports/cdash/Configure.xml
@@ -0,0 +1,8 @@
+  <Configure>
+    <StartConfigureTime>{{ configure.starttime }}</StartConfigureTime>
+    <ConfigureCommand>{{ install_command }}</ConfigureCommand>
+    <Log>{{ configure.log }}</Log>
+    <ConfigureStatus>{{ configure.status }}</ConfigureStatus>
+    <EndConfigureTime>{{ configure.endtime }}</EndConfigureTime>
+  </Configure>
+</Site>
diff --git a/share/spack/templates/reports/cdash/Site.xml b/share/spack/templates/reports/cdash/Site.xml
new file mode 100644
index 0000000000..a47ffd34e6
--- /dev/null
+++ b/share/spack/templates/reports/cdash/Site.xml
@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<Site BuildName="{{ install_command }}"
+      BuildStamp="{{ buildstamp }}"
+      Name="{{ hostname }}"
+      OSName="{{ osname }}"
+>
+
diff --git a/share/spack/templates/reports/cdash/Update.xml b/share/spack/templates/reports/cdash/Update.xml
new file mode 100644
index 0000000000..39f3d6a337
--- /dev/null
+++ b/share/spack/templates/reports/cdash/Update.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<Update>
+  <Site>{{ hostname }}</Site>
+  <BuildName>{{ install_command }}</BuildName>
+  <BuildStamp>{{ buildstamp }}</BuildStamp>
+  <StartTime>{{ starttime }}</StartTime>
+  <EndTime>{{ endtime }}</EndTime>
+{% if msg %}
+  <UpdateReturnStatus>{{ msg }}</UpdateReturnStatus>
+{% endif %}
+</Update>
diff --git a/share/spack/templates/reports/junit.xml b/share/spack/templates/reports/junit.xml
new file mode 100644
index 0000000000..62e6db40c8
--- /dev/null
+++ b/share/spack/templates/reports/junit.xml
@@ -0,0 +1,51 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+    This file has been modeled after the basic
+    specifications at this url:
+
+    http://help.catchsoftware.com/display/ET/JUnit+Format
+-->
+<testsuites>
+{% for spec in specs %}
+    <testsuite name="{{ spec.name }}"
+               errors="{{ spec.nerrors }}"
+               tests="{{ spec.npackages }}"
+               failures="{{ spec.nfailures }}"
+               time="{{ spec.time }}"
+               timestamp="{{ spec.timestamp }}" >
+        <properties>
+{% for property in spec.properties %}
+            <property name="{{ property.name }}" value="{{ property.value }}" />
+{% endfor %}
+        </properties>
+{% for package in spec.packages %}
+        <testcase classname="{{ package.name }}"
+                  name="{{ package.id }}"
+                  time="{{ package.elapsed_time }}">
+{% if package.result == 'failure' %}
+            <failure message="{{ package.message }}">
+{{ package.exception }}
+            </failure>
+{% elif package.result == 'error' %}
+            <error message="{{ package.message }}">
+{{ package.exception }}
+            </error>
+{% elif package.result == 'skipped' %}
+            <skipped />
+{% endif %}
+{% if package.stdout %}
+            <system-out>
+{{ package.stdout }}
+            </system-out>
+{% endif %}
+{% if package.stderr %}
+            <system-err>
+{{ package.stderr }}
+            </system-err>
+{% endif %}
+        </testcase>
+{% endfor %}
+{# Add an error tag? #}
+    </testsuite>
+{% endfor %}
+</testsuites>
diff --git a/var/spack/repos/builtin.mock/packages/a/package.py b/var/spack/repos/builtin.mock/packages/a/package.py
index 468e839dec..a9197c94b0 100644
--- a/var/spack/repos/builtin.mock/packages/a/package.py
+++ b/var/spack/repos/builtin.mock/packages/a/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/archive-files/package.py b/var/spack/repos/builtin.mock/packages/archive-files/package.py
new file mode 100644
index 0000000000..5025d70d6b
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/archive-files/package.py
@@ -0,0 +1,34 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class ArchiveFiles(AutotoolsPackage):
+    """Simple package with one optional dependency"""
+
+    homepage = "http://www.example.com"
+    url = "http://www.example.com/a-1.0.tar.gz"
+
+    version('1.0', '0123456789abcdef0123456789abcdef')
+    version('2.0', '2.0_a_hash')
+
+    @property
+    def archive_files(self):
+        return super(ArchiveFiles, self).archive_files + ['../../outside.log']
+
+    def autoreconf(self, spec, prefix):
+        pass
+
+    def configure(self, spec, prefix):
+        pass
+
+    def build(self, spec, prefix):
+        mkdirp(self.build_directory)
+        config_log = join_path(self.build_directory, 'config.log')
+        touch(config_log)
+
+    def install(self, spec, prefix):
+        touch(join_path(prefix, 'deleteme'))
diff --git a/var/spack/repos/builtin.mock/packages/b/package.py b/var/spack/repos/builtin.mock/packages/b/package.py
index b352fa6f80..776240a31c 100644
--- a/var/spack/repos/builtin.mock/packages/b/package.py
+++ b/var/spack/repos/builtin.mock/packages/b/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/boost/package.py b/var/spack/repos/builtin.mock/packages/boost/package.py
index df50e18574..4398d445df 100644
--- a/var/spack/repos/builtin.mock/packages/boost/package.py
+++ b/var/spack/repos/builtin.mock/packages/boost/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/build-error/package.py b/var/spack/repos/builtin.mock/packages/build-error/package.py
index e0c1a9ee83..191cfe3b14 100644
--- a/var/spack/repos/builtin.mock/packages/build-error/package.py
+++ b/var/spack/repos/builtin.mock/packages/build-error/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/build-warnings/package.py b/var/spack/repos/builtin.mock/packages/build-warnings/package.py
new file mode 100644
index 0000000000..1ea58a2a1a
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/build-warnings/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class BuildWarnings(Package):
+    """This package's install fails but only emits warnings."""
+
+    homepage = "http://www.example.com/trivial_install"
+    url      = "http://www.unit-test-should-replace-this-url/trivial_install-1.0.tar.gz"
+
+    version('1.0', 'foobarbaz')
+
+    def install(self, spec, prefix):
+        with open('configure', 'w') as f:
+            f.write("""#!/bin/sh\n
+echo 'checking for gcc... /Users/gamblin2/src/spack/lib/spack/env/clang/clang'
+echo 'checking whether the C compiler works... yes'
+echo 'checking for C compiler default output file name... a.out'
+echo 'WARNING: ALL CAPITAL WARNING!'
+echo 'checking for suffix of executables...'
+echo 'foo.c:89: warning: some weird warning!'
+exit 1
+""")
+        configure()
diff --git a/var/spack/repos/builtin.mock/packages/c/package.py b/var/spack/repos/builtin.mock/packages/c/package.py
index 22132dd00d..5687635f7c 100644
--- a/var/spack/repos/builtin.mock/packages/c/package.py
+++ b/var/spack/repos/builtin.mock/packages/c/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/callpath/package.py b/var/spack/repos/builtin.mock/packages/callpath/package.py
index 19438e6277..27214741b7 100644
--- a/var/spack/repos/builtin.mock/packages/callpath/package.py
+++ b/var/spack/repos/builtin.mock/packages/callpath/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/canfail/package.py b/var/spack/repos/builtin.mock/packages/canfail/package.py
index b49bb3ce3e..777a9bd023 100644
--- a/var/spack/repos/builtin.mock/packages/canfail/package.py
+++ b/var/spack/repos/builtin.mock/packages/canfail/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/cmake-client/package.py b/var/spack/repos/builtin.mock/packages/cmake-client/package.py
index 2fde961376..4082d77055 100644
--- a/var/spack/repos/builtin.mock/packages/cmake-client/package.py
+++ b/var/spack/repos/builtin.mock/packages/cmake-client/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 
 from spack import *
diff --git a/var/spack/repos/builtin.mock/packages/cmake/package.py b/var/spack/repos/builtin.mock/packages/cmake/package.py
index 15ad5606b4..a589797d69 100644
--- a/var/spack/repos/builtin.mock/packages/cmake/package.py
+++ b/var/spack/repos/builtin.mock/packages/cmake/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
diff --git a/var/spack/repos/builtin.mock/packages/conflict-parent/package.py b/var/spack/repos/builtin.mock/packages/conflict-parent/package.py
index b8aaf55def..8f27d59ff5 100644
--- a/var/spack/repos/builtin.mock/packages/conflict-parent/package.py
+++ b/var/spack/repos/builtin.mock/packages/conflict-parent/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/conflict/package.py b/var/spack/repos/builtin.mock/packages/conflict/package.py
index 26f09d77ee..08d8c5df4b 100644
--- a/var/spack/repos/builtin.mock/packages/conflict/package.py
+++ b/var/spack/repos/builtin.mock/packages/conflict/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/conflicting-dependent/package.py b/var/spack/repos/builtin.mock/packages/conflicting-dependent/package.py
index 620d398d35..efa8ae9596 100644
--- a/var/spack/repos/builtin.mock/packages/conflicting-dependent/package.py
+++ b/var/spack/repos/builtin.mock/packages/conflicting-dependent/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/dependency-install/package.py b/var/spack/repos/builtin.mock/packages/dependency-install/package.py
index eeaf2ada11..2e40b8dc8d 100644
--- a/var/spack/repos/builtin.mock/packages/dependency-install/package.py
+++ b/var/spack/repos/builtin.mock/packages/dependency-install/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/dependent-install/package.py b/var/spack/repos/builtin.mock/packages/dependent-install/package.py
index 9bcc73d056..01a955d744 100644
--- a/var/spack/repos/builtin.mock/packages/dependent-install/package.py
+++ b/var/spack/repos/builtin.mock/packages/dependent-install/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/develop-test/package.py b/var/spack/repos/builtin.mock/packages/develop-test/package.py
index c546f701fd..7a28cc25be 100644
--- a/var/spack/repos/builtin.mock/packages/develop-test/package.py
+++ b/var/spack/repos/builtin.mock/packages/develop-test/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/direct-mpich/package.py b/var/spack/repos/builtin.mock/packages/direct-mpich/package.py
index 737570ffe8..44bd7d16b1 100644
--- a/var/spack/repos/builtin.mock/packages/direct-mpich/package.py
+++ b/var/spack/repos/builtin.mock/packages/direct-mpich/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/dt-diamond-bottom/package.py b/var/spack/repos/builtin.mock/packages/dt-diamond-bottom/package.py
index 7f55beb542..1c6b8d624d 100644
--- a/var/spack/repos/builtin.mock/packages/dt-diamond-bottom/package.py
+++ b/var/spack/repos/builtin.mock/packages/dt-diamond-bottom/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/dt-diamond-left/package.py b/var/spack/repos/builtin.mock/packages/dt-diamond-left/package.py
index 262008079c..f54086e8b3 100644
--- a/var/spack/repos/builtin.mock/packages/dt-diamond-left/package.py
+++ b/var/spack/repos/builtin.mock/packages/dt-diamond-left/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/dt-diamond-right/package.py b/var/spack/repos/builtin.mock/packages/dt-diamond-right/package.py
index cc0db5bff1..2a915a1f10 100644
--- a/var/spack/repos/builtin.mock/packages/dt-diamond-right/package.py
+++ b/var/spack/repos/builtin.mock/packages/dt-diamond-right/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/dt-diamond/package.py b/var/spack/repos/builtin.mock/packages/dt-diamond/package.py
index c3b0b9db57..a4dcdfd04b 100644
--- a/var/spack/repos/builtin.mock/packages/dt-diamond/package.py
+++ b/var/spack/repos/builtin.mock/packages/dt-diamond/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/dtbuild1/package.py b/var/spack/repos/builtin.mock/packages/dtbuild1/package.py
index bc00d4ed03..dfc71d5f89 100644
--- a/var/spack/repos/builtin.mock/packages/dtbuild1/package.py
+++ b/var/spack/repos/builtin.mock/packages/dtbuild1/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/dtbuild2/package.py b/var/spack/repos/builtin.mock/packages/dtbuild2/package.py
index 1a3eb57835..b91aa8bba3 100644
--- a/var/spack/repos/builtin.mock/packages/dtbuild2/package.py
+++ b/var/spack/repos/builtin.mock/packages/dtbuild2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/dtbuild3/package.py b/var/spack/repos/builtin.mock/packages/dtbuild3/package.py
index a03a04a523..8102ca80f0 100644
--- a/var/spack/repos/builtin.mock/packages/dtbuild3/package.py
+++ b/var/spack/repos/builtin.mock/packages/dtbuild3/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/dtlink1/package.py b/var/spack/repos/builtin.mock/packages/dtlink1/package.py
index 9c7e4bdebf..05885a00e0 100644
--- a/var/spack/repos/builtin.mock/packages/dtlink1/package.py
+++ b/var/spack/repos/builtin.mock/packages/dtlink1/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/dtlink2/package.py b/var/spack/repos/builtin.mock/packages/dtlink2/package.py
index 1a78a4879c..06bcb7bda7 100644
--- a/var/spack/repos/builtin.mock/packages/dtlink2/package.py
+++ b/var/spack/repos/builtin.mock/packages/dtlink2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/dtlink3/package.py b/var/spack/repos/builtin.mock/packages/dtlink3/package.py
index 8c53f3e2a0..58a9e9f995 100644
--- a/var/spack/repos/builtin.mock/packages/dtlink3/package.py
+++ b/var/spack/repos/builtin.mock/packages/dtlink3/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/dtlink4/package.py b/var/spack/repos/builtin.mock/packages/dtlink4/package.py
index 4d7a57b2da..10fbf0b033 100644
--- a/var/spack/repos/builtin.mock/packages/dtlink4/package.py
+++ b/var/spack/repos/builtin.mock/packages/dtlink4/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/dtlink5/package.py b/var/spack/repos/builtin.mock/packages/dtlink5/package.py
index 914e7655fb..a573555274 100644
--- a/var/spack/repos/builtin.mock/packages/dtlink5/package.py
+++ b/var/spack/repos/builtin.mock/packages/dtlink5/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/dtrun1/package.py b/var/spack/repos/builtin.mock/packages/dtrun1/package.py
index 738540ea52..865d8ee633 100644
--- a/var/spack/repos/builtin.mock/packages/dtrun1/package.py
+++ b/var/spack/repos/builtin.mock/packages/dtrun1/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/dtrun2/package.py b/var/spack/repos/builtin.mock/packages/dtrun2/package.py
index 84129c1732..6e207ba5ae 100644
--- a/var/spack/repos/builtin.mock/packages/dtrun2/package.py
+++ b/var/spack/repos/builtin.mock/packages/dtrun2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/dtrun3/package.py b/var/spack/repos/builtin.mock/packages/dtrun3/package.py
index ee0c4272e4..3d834c2749 100644
--- a/var/spack/repos/builtin.mock/packages/dtrun3/package.py
+++ b/var/spack/repos/builtin.mock/packages/dtrun3/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/dttop/package.py b/var/spack/repos/builtin.mock/packages/dttop/package.py
index 9bb83fff89..b68c3e1cd4 100644
--- a/var/spack/repos/builtin.mock/packages/dttop/package.py
+++ b/var/spack/repos/builtin.mock/packages/dttop/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/dtuse/package.py b/var/spack/repos/builtin.mock/packages/dtuse/package.py
index 3f8b0c9e98..c87d9e145d 100644
--- a/var/spack/repos/builtin.mock/packages/dtuse/package.py
+++ b/var/spack/repos/builtin.mock/packages/dtuse/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/dyninst/package.py b/var/spack/repos/builtin.mock/packages/dyninst/package.py
index d00f604d61..f6fdc5a432 100644
--- a/var/spack/repos/builtin.mock/packages/dyninst/package.py
+++ b/var/spack/repos/builtin.mock/packages/dyninst/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/e/package.py b/var/spack/repos/builtin.mock/packages/e/package.py
index a00d459e9f..12fc145e17 100644
--- a/var/spack/repos/builtin.mock/packages/e/package.py
+++ b/var/spack/repos/builtin.mock/packages/e/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/extendee/package.py b/var/spack/repos/builtin.mock/packages/extendee/package.py
index cae5f93bf3..ead0d8c9ec 100644
--- a/var/spack/repos/builtin.mock/packages/extendee/package.py
+++ b/var/spack/repos/builtin.mock/packages/extendee/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/extension1/package.py b/var/spack/repos/builtin.mock/packages/extension1/package.py
index f4999e9963..abb526459e 100644
--- a/var/spack/repos/builtin.mock/packages/extension1/package.py
+++ b/var/spack/repos/builtin.mock/packages/extension1/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os.path
 
diff --git a/var/spack/repos/builtin.mock/packages/extension2/package.py b/var/spack/repos/builtin.mock/packages/extension2/package.py
index 01f3f94636..0d4ce8b374 100644
--- a/var/spack/repos/builtin.mock/packages/extension2/package.py
+++ b/var/spack/repos/builtin.mock/packages/extension2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os.path
 
diff --git a/var/spack/repos/builtin.mock/packages/externalmodule/package.py b/var/spack/repos/builtin.mock/packages/externalmodule/package.py
index 5e9f8fda44..84b152a93b 100644
--- a/var/spack/repos/builtin.mock/packages/externalmodule/package.py
+++ b/var/spack/repos/builtin.mock/packages/externalmodule/package.py
@@ -1,28 +1,8 @@
-
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/externalprereq/package.py b/var/spack/repos/builtin.mock/packages/externalprereq/package.py
index 1890ab72d8..b14045afd2 100644
--- a/var/spack/repos/builtin.mock/packages/externalprereq/package.py
+++ b/var/spack/repos/builtin.mock/packages/externalprereq/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/externaltest/package.py b/var/spack/repos/builtin.mock/packages/externaltest/package.py
index 00cc553cbe..69484f5d54 100644
--- a/var/spack/repos/builtin.mock/packages/externaltest/package.py
+++ b/var/spack/repos/builtin.mock/packages/externaltest/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/externaltool/package.py b/var/spack/repos/builtin.mock/packages/externaltool/package.py
index c47c31ac66..6e8cb30f09 100644
--- a/var/spack/repos/builtin.mock/packages/externaltool/package.py
+++ b/var/spack/repos/builtin.mock/packages/externaltool/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,6 +11,7 @@ class Externaltool(Package):
     url      = "http://somewhere.com/tool-1.0.tar.gz"
 
     version('1.0', '1234567890abcdef1234567890abcdef')
+    version('0.9', '1234567890abcdef1234567890abcdef')
 
     depends_on('externalprereq')
 
diff --git a/var/spack/repos/builtin.mock/packages/externalvirtual/package.py b/var/spack/repos/builtin.mock/packages/externalvirtual/package.py
index d0b814d83b..a23743ca66 100644
--- a/var/spack/repos/builtin.mock/packages/externalvirtual/package.py
+++ b/var/spack/repos/builtin.mock/packages/externalvirtual/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/failing-build/package.py b/var/spack/repos/builtin.mock/packages/failing-build/package.py
index e61451253a..f332b86323 100644
--- a/var/spack/repos/builtin.mock/packages/failing-build/package.py
+++ b/var/spack/repos/builtin.mock/packages/failing-build/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/fake/package.py b/var/spack/repos/builtin.mock/packages/fake/package.py
index 6b264a4d55..6d6e133cb5 100644
--- a/var/spack/repos/builtin.mock/packages/fake/package.py
+++ b/var/spack/repos/builtin.mock/packages/fake/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/flake8/package.py b/var/spack/repos/builtin.mock/packages/flake8/package.py
index 4f2e9bd475..a38ede73f9 100644
--- a/var/spack/repos/builtin.mock/packages/flake8/package.py
+++ b/var/spack/repos/builtin.mock/packages/flake8/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/git-svn-top-level/package.py b/var/spack/repos/builtin.mock/packages/git-svn-top-level/package.py
new file mode 100644
index 0000000000..9864269a21
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/git-svn-top-level/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class GitSvnTopLevel(Package):
+    """Mock package that uses git for fetching."""
+    homepage = "http://www.git-fetch-example.com"
+
+    # can't have two VCS fetchers.
+    git = 'https://example.com/some/git/repo'
+    svn = 'https://example.com/some/svn/repo'
+
+    version('2.0')
+
+    def install(self, spec, prefix):
+        pass
diff --git a/var/spack/repos/builtin.mock/packages/git-test/package.py b/var/spack/repos/builtin.mock/packages/git-test/package.py
index 9378f72195..544168d53b 100644
--- a/var/spack/repos/builtin.mock/packages/git-test/package.py
+++ b/var/spack/repos/builtin.mock/packages/git-test/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/git-top-level/package.py b/var/spack/repos/builtin.mock/packages/git-top-level/package.py
new file mode 100644
index 0000000000..36a2852f32
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/git-top-level/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class GitTopLevel(Package):
+    """Mock package that uses git for fetching."""
+    homepage = "http://www.git-fetch-example.com"
+
+    git = 'https://example.com/some/git/repo'
+    version('1.0')
+
+    def install(self, spec, prefix):
+        pass
diff --git a/var/spack/repos/builtin.mock/packages/git-url-svn-top-level/package.py b/var/spack/repos/builtin.mock/packages/git-url-svn-top-level/package.py
new file mode 100644
index 0000000000..c737284fff
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/git-url-svn-top-level/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class GitUrlSvnTopLevel(Package):
+    """Mock package that uses git for fetching."""
+    homepage = "http://www.git-fetch-example.com"
+
+    # can't have two VCS fetchers.
+    url = 'https://example.com/some/tarball-1.0.tar.gz'
+    git = 'https://example.com/some/git/repo'
+    svn = 'https://example.com/some/svn/repo'
+
+    version('2.0')
+
+    def install(self, spec, prefix):
+        pass
diff --git a/var/spack/repos/builtin.mock/packages/git-url-top-level/package.py b/var/spack/repos/builtin.mock/packages/git-url-top-level/package.py
new file mode 100644
index 0000000000..8b41eda0eb
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/git-url-top-level/package.py
@@ -0,0 +1,43 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class GitUrlTopLevel(Package):
+    """Mock package that top-level git and url attributes.
+
+    This demonstrates how Spack infers fetch mechanisms from parameters
+    to the ``version`` directive.
+
+    """
+    homepage = "http://www.git-fetch-example.com"
+
+    git = 'https://example.com/some/git/repo'
+    url = 'https://example.com/some/tarball-1.0.tar.gz'
+
+    # These resolve to git fetchers
+    version('develop', branch='develop')
+    version('submodules', submodules=True)
+    version('3.4', commit='abc34')
+    version('3.3', branch='releases/v3.3', commit='abc33')
+    version('3.2', branch='releases/v3.2')
+    version('3.1', tag='v3.1', commit='abc31')
+    version('3.0', tag='v3.0')
+
+    # These resolve to URL fetchers
+    version('2.3', 'abc23', url='https://www.example.com/foo2.3.tar.gz')
+    version('2.2', sha256='abc22', url='https://www.example.com/foo2.2.tar.gz')
+    version('2.1', sha256='abc21')
+    version('2.0', 'abc20')
+
+    # These result in a FetcherConflict b/c we can't tell what to use
+    version('1.3', sha256='abc13', commit='abc13')
+    version('1.2', sha512='abc12', branch='releases/v1.2')
+    version('1.1', md5='abc11', tag='v1.1')
+    version('1.0', 'abc11', tag='abc123')
+
+    def install(self, spec, prefix):
+        pass
diff --git a/var/spack/repos/builtin.mock/packages/hash-test1/package.py b/var/spack/repos/builtin.mock/packages/hash-test1/package.py
new file mode 100644
index 0000000000..2fd44f07e4
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/hash-test1/package.py
@@ -0,0 +1,39 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+import os
+
+
+class HashTest1(Package):
+    """Used to test package hashing
+    """
+
+    homepage = "http://www.hashtest1.org"
+    url = "http://www.hashtest1.org/downloads/hashtest1-1.1.tar.bz2"
+
+    version('1.1', 'a' * 32)
+    version('1.2', 'b' * 32)
+    version('1.3', 'c' * 32)
+    version('1.4', 'd' * 32)
+
+    patch('patch1.patch', when="@1.1")
+    patch('patch2.patch', when="@1.4")
+
+    variant('variantx', default=False, description='Test variant X')
+    variant('varianty', default=False, description='Test variant Y')
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        pass
+
+    @when('@:1.4')
+    def install(self, spec, prefix):
+        print("install 1")
+        os.listdir(os.getcwd())
+
+    @when('@1.5')
+    def install(self, spec, prefix):
+        os.listdir(os.getcwd())
diff --git a/var/spack/repos/builtin.mock/packages/hash-test1/patch1.patch b/var/spack/repos/builtin.mock/packages/hash-test1/patch1.patch
new file mode 100644
index 0000000000..a333c82dfd
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/hash-test1/patch1.patch
@@ -0,0 +1 @@
+the contents of patch 1 (not a valid diff, but sufficient for testing)
diff --git a/var/spack/repos/builtin.mock/packages/hash-test1/patch2.patch b/var/spack/repos/builtin.mock/packages/hash-test1/patch2.patch
new file mode 100644
index 0000000000..9e292a10fe
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/hash-test1/patch2.patch
@@ -0,0 +1 @@
+the contents of patch 2 (not a valid diff, but sufficient for testing)
diff --git a/var/spack/repos/builtin.mock/packages/hash-test2/package.py b/var/spack/repos/builtin.mock/packages/hash-test2/package.py
new file mode 100644
index 0000000000..de08125bf6
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/hash-test2/package.py
@@ -0,0 +1,33 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+import os
+
+
+class HashTest2(Package):
+    """Used to test package hashing
+    """
+
+    homepage = "http://www.hashtest2.org"
+    url = "http://www.hashtest1.org/downloads/hashtest2-1.1.tar.bz2"
+
+    version('1.1', 'a' * 32)
+    version('1.2', 'b' * 32)
+    version('1.3', 'c' * 31 + 'x')  # Source hash differs from hash-test1@1.3
+    version('1.4', 'd' * 32)
+
+    patch('patch1.patch', when="@1.1")
+
+    variant('variantx', default=False, description='Test variant X')
+    variant('varianty', default=False, description='Test variant Y')
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        pass
+
+    def install(self, spec, prefix):
+        print("install 1")
+        os.listdir(os.getcwd())
diff --git a/var/spack/repos/builtin.mock/packages/hash-test2/patch1.patch b/var/spack/repos/builtin.mock/packages/hash-test2/patch1.patch
new file mode 100644
index 0000000000..bbfa868935
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/hash-test2/patch1.patch
@@ -0,0 +1,2 @@
+the different contents of patch 1 (not a valid diff, but sufficient for testing,
+and different from patch 1 of hash-test1)
diff --git a/var/spack/repos/builtin.mock/packages/hg-test/package.py b/var/spack/repos/builtin.mock/packages/hg-test/package.py
index 17d8379d1c..89a3286bea 100644
--- a/var/spack/repos/builtin.mock/packages/hg-test/package.py
+++ b/var/spack/repos/builtin.mock/packages/hg-test/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/hg-top-level/package.py b/var/spack/repos/builtin.mock/packages/hg-top-level/package.py
new file mode 100644
index 0000000000..225a2e852c
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/hg-top-level/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class HgTopLevel(Package):
+    """Test package that does fetching with mercurial."""
+    homepage = "http://www.hg-fetch-example.com"
+
+    hg = 'https://example.com/some/hg/repo'
+    version('1.0')
+
+    def install(self, spec, prefix):
+        pass
diff --git a/var/spack/repos/builtin.mock/packages/hypre/package.py b/var/spack/repos/builtin.mock/packages/hypre/package.py
index c815aca191..62133f48ac 100644
--- a/var/spack/repos/builtin.mock/packages/hypre/package.py
+++ b/var/spack/repos/builtin.mock/packages/hypre/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/indirect-mpich/package.py b/var/spack/repos/builtin.mock/packages/indirect-mpich/package.py
index 3b9b9caec1..902a8f7345 100644
--- a/var/spack/repos/builtin.mock/packages/indirect-mpich/package.py
+++ b/var/spack/repos/builtin.mock/packages/indirect-mpich/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/libdwarf/package.py b/var/spack/repos/builtin.mock/packages/libdwarf/package.py
index 726cb756a6..302e7f1eeb 100644
--- a/var/spack/repos/builtin.mock/packages/libdwarf/package.py
+++ b/var/spack/repos/builtin.mock/packages/libdwarf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 # Only build certain parts of dwarf because the other ones break.
diff --git a/var/spack/repos/builtin.mock/packages/libelf/package.py b/var/spack/repos/builtin.mock/packages/libelf/package.py
index 9cf8d152df..4fdd90e935 100644
--- a/var/spack/repos/builtin.mock/packages/libelf/package.py
+++ b/var/spack/repos/builtin.mock/packages/libelf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/mixedversions/package.py b/var/spack/repos/builtin.mock/packages/mixedversions/package.py
index 6e01fbc13b..ff564d5cb9 100644
--- a/var/spack/repos/builtin.mock/packages/mixedversions/package.py
+++ b/var/spack/repos/builtin.mock/packages/mixedversions/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/module-path-separator/package.py b/var/spack/repos/builtin.mock/packages/module-path-separator/package.py
new file mode 100644
index 0000000000..a7a4baabb7
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/module-path-separator/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class ModulePathSeparator(Package):
+    homepage = "http://www.llnl.gov"
+    url      = "http://www.llnl.gov/module-path-separator-1.0.tar.gz"
+
+    version(1.0, 'foobarbaz')
+
+    def install(self, spec, prefix):
+        pass
+
+    def setup_environment(self, senv, renv):
+        renv.append_path("COLON", "foo")
+        renv.prepend_path("COLON", "foo")
+        renv.remove_path("COLON", "foo")
+
+        renv.append_path("SEMICOLON", "bar", separator=";")
+        renv.prepend_path("SEMICOLON", "bar", separator=";")
+        renv.remove_path("SEMICOLON", "bar", separator=";")
diff --git a/var/spack/repos/builtin.mock/packages/mpich/package.py b/var/spack/repos/builtin.mock/packages/mpich/package.py
index f9dbf572c5..1ba68925d5 100644
--- a/var/spack/repos/builtin.mock/packages/mpich/package.py
+++ b/var/spack/repos/builtin.mock/packages/mpich/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/mpich2/package.py b/var/spack/repos/builtin.mock/packages/mpich2/package.py
index 92e72daa4a..9f7df9696f 100644
--- a/var/spack/repos/builtin.mock/packages/mpich2/package.py
+++ b/var/spack/repos/builtin.mock/packages/mpich2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/mpileaks/package.py b/var/spack/repos/builtin.mock/packages/mpileaks/package.py
index 6b5afafdb2..478da9f9b9 100644
--- a/var/spack/repos/builtin.mock/packages/mpileaks/package.py
+++ b/var/spack/repos/builtin.mock/packages/mpileaks/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/multi-provider-mpi/package.py b/var/spack/repos/builtin.mock/packages/multi-provider-mpi/package.py
index 9240671ba2..1b3e044f22 100644
--- a/var/spack/repos/builtin.mock/packages/multi-provider-mpi/package.py
+++ b/var/spack/repos/builtin.mock/packages/multi-provider-mpi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/multimethod-base/package.py b/var/spack/repos/builtin.mock/packages/multimethod-base/package.py
index 454f658adf..7b7d00b43b 100644
--- a/var/spack/repos/builtin.mock/packages/multimethod-base/package.py
+++ b/var/spack/repos/builtin.mock/packages/multimethod-base/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/multimethod/package.py b/var/spack/repos/builtin.mock/packages/multimethod/package.py
index 25a7ec7fca..3224d73fe9 100644
--- a/var/spack/repos/builtin.mock/packages/multimethod/package.py
+++ b/var/spack/repos/builtin.mock/packages/multimethod/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from six import string_types
 
 from spack import *
diff --git a/var/spack/repos/builtin.mock/packages/multivalue_variant/package.py b/var/spack/repos/builtin.mock/packages/multivalue_variant/package.py
index 0d27e31e44..1077f5f978 100644
--- a/var/spack/repos/builtin.mock/packages/multivalue_variant/package.py
+++ b/var/spack/repos/builtin.mock/packages/multivalue_variant/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/netlib-blas/package.py b/var/spack/repos/builtin.mock/packages/netlib-blas/package.py
index 48c99ba9d6..07bdbcb801 100644
--- a/var/spack/repos/builtin.mock/packages/netlib-blas/package.py
+++ b/var/spack/repos/builtin.mock/packages/netlib-blas/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/netlib-lapack/package.py b/var/spack/repos/builtin.mock/packages/netlib-lapack/package.py
index 9108e70cf0..2b12ee77ce 100644
--- a/var/spack/repos/builtin.mock/packages/netlib-lapack/package.py
+++ b/var/spack/repos/builtin.mock/packages/netlib-lapack/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/openblas-with-lapack/package.py b/var/spack/repos/builtin.mock/packages/openblas-with-lapack/package.py
index c73e65ac2b..5480507e1b 100644
--- a/var/spack/repos/builtin.mock/packages/openblas-with-lapack/package.py
+++ b/var/spack/repos/builtin.mock/packages/openblas-with-lapack/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/openblas/package.py b/var/spack/repos/builtin.mock/packages/openblas/package.py
index 8d41c8958a..d10b423626 100644
--- a/var/spack/repos/builtin.mock/packages/openblas/package.py
+++ b/var/spack/repos/builtin.mock/packages/openblas/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/optional-dep-test-2/package.py b/var/spack/repos/builtin.mock/packages/optional-dep-test-2/package.py
index 51bbb9761f..6f988410fa 100644
--- a/var/spack/repos/builtin.mock/packages/optional-dep-test-2/package.py
+++ b/var/spack/repos/builtin.mock/packages/optional-dep-test-2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/optional-dep-test-3/package.py b/var/spack/repos/builtin.mock/packages/optional-dep-test-3/package.py
index 48bf3820af..d1bf81a7fa 100644
--- a/var/spack/repos/builtin.mock/packages/optional-dep-test-3/package.py
+++ b/var/spack/repos/builtin.mock/packages/optional-dep-test-3/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/optional-dep-test/package.py b/var/spack/repos/builtin.mock/packages/optional-dep-test/package.py
index 48ffbf6765..af30815bc7 100644
--- a/var/spack/repos/builtin.mock/packages/optional-dep-test/package.py
+++ b/var/spack/repos/builtin.mock/packages/optional-dep-test/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/othervirtual/package.py b/var/spack/repos/builtin.mock/packages/othervirtual/package.py
index c7b0e72a01..db9a218767 100644
--- a/var/spack/repos/builtin.mock/packages/othervirtual/package.py
+++ b/var/spack/repos/builtin.mock/packages/othervirtual/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/override-context-templates/package.py b/var/spack/repos/builtin.mock/packages/override-context-templates/package.py
index 9f59ad0e7e..6ec1b26dfa 100644
--- a/var/spack/repos/builtin.mock/packages/override-context-templates/package.py
+++ b/var/spack/repos/builtin.mock/packages/override-context-templates/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/override-module-templates/package.py b/var/spack/repos/builtin.mock/packages/override-module-templates/package.py
index 6d877c7a76..090a889448 100644
--- a/var/spack/repos/builtin.mock/packages/override-module-templates/package.py
+++ b/var/spack/repos/builtin.mock/packages/override-module-templates/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/patch-a-dependency/foo.patch b/var/spack/repos/builtin.mock/packages/patch-a-dependency/foo.patch
deleted file mode 100644
index 257cc5642c..0000000000
--- a/var/spack/repos/builtin.mock/packages/patch-a-dependency/foo.patch
+++ /dev/null
@@ -1 +0,0 @@
-foo
diff --git a/var/spack/repos/builtin.mock/packages/patch-a-dependency/libelf.patch b/var/spack/repos/builtin.mock/packages/patch-a-dependency/libelf.patch
new file mode 100644
index 0000000000..02bfad9103
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/patch-a-dependency/libelf.patch
@@ -0,0 +1,11 @@
+--- patch-a-dependency/configure	2018-08-13 23:13:51.000000000 -0700
++++ patch-a-dependency/configure.patched	2018-08-13 23:14:15.000000000 -0700
+@@ -2,7 +2,7 @@
+ prefix=$(echo $1 | sed 's/--prefix=//')
+ cat > Makefile <<EOF
+ all:
+-	echo Building...
++	echo Patched!
+ 
+ install:
+ 	mkdir -p $prefix
diff --git a/var/spack/repos/builtin.mock/packages/patch-a-dependency/package.py b/var/spack/repos/builtin.mock/packages/patch-a-dependency/package.py
index fea0b27195..4b4f044504 100644
--- a/var/spack/repos/builtin.mock/packages/patch-a-dependency/package.py
+++ b/var/spack/repos/builtin.mock/packages/patch-a-dependency/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,7 +14,7 @@ class PatchADependency(Package):
 
     version('1.0', '0123456789abcdef0123456789abcdef')
 
-    depends_on('libelf', patches=patch('foo.patch'))
+    depends_on('libelf', patches=patch('libelf.patch'))
 
     def install(self, spec, prefix):
         pass
diff --git a/var/spack/repos/builtin.mock/packages/patch-several-dependencies/package.py b/var/spack/repos/builtin.mock/packages/patch-several-dependencies/package.py
index 73837449c6..fdd5cc30e7 100644
--- a/var/spack/repos/builtin.mock/packages/patch-several-dependencies/package.py
+++ b/var/spack/repos/builtin.mock/packages/patch-several-dependencies/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/patch/package.py b/var/spack/repos/builtin.mock/packages/patch/package.py
index 79b0943b24..cf0d2f1c63 100644
--- a/var/spack/repos/builtin.mock/packages/patch/package.py
+++ b/var/spack/repos/builtin.mock/packages/patch/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/patchelf/package.py b/var/spack/repos/builtin.mock/packages/patchelf/package.py
index d499199d3e..6b7205cb9a 100644
--- a/var/spack/repos/builtin.mock/packages/patchelf/package.py
+++ b/var/spack/repos/builtin.mock/packages/patchelf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/printing-package/package.py b/var/spack/repos/builtin.mock/packages/printing-package/package.py
index 815972f9eb..580e9727f1 100644
--- a/var/spack/repos/builtin.mock/packages/printing-package/package.py
+++ b/var/spack/repos/builtin.mock/packages/printing-package/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/python/package.py b/var/spack/repos/builtin.mock/packages/python/package.py
index f402be3b56..053c6d24f1 100644
--- a/var/spack/repos/builtin.mock/packages/python/package.py
+++ b/var/spack/repos/builtin.mock/packages/python/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/raiser/package.py b/var/spack/repos/builtin.mock/packages/raiser/package.py
new file mode 100644
index 0000000000..bbd4cb329b
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/raiser/package.py
@@ -0,0 +1,43 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from six.moves import builtins
+
+from spack import *
+
+
+class Raiser(Package):
+    """A package that can raise a built-in exception
+    of any kind with any message
+    """
+
+    homepage = "http://www.example.com"
+    url = "http://www.example.com/a-1.0.tar.gz"
+
+    version('1.0', '0123456789abcdef0123456789abcdef')
+    version('2.0', '2.0_a_hash')
+
+    variant(
+        'exc_type',
+        values=lambda x: isinstance(x, str),
+        default='RuntimeError',
+        description='type of the exception to be raised',
+        multi=False
+    )
+
+    variant(
+        'msg',
+        values=lambda x: isinstance(x, str),
+        default='Unknown Exception',
+        description='message that will be tied to the exception',
+        multi=False
+    )
+
+    def install(self, spec, prefix):
+        print('Raiser will raise ')
+        exc_typename = self.spec.variants['exc_type'].value
+        exc_type = getattr(builtins, exc_typename)
+        msg = self.spec.variants['msg'].value
+        raise exc_type(msg)
diff --git a/var/spack/repos/builtin.mock/packages/simple-inheritance/package.py b/var/spack/repos/builtin.mock/packages/simple-inheritance/package.py
index 3f135b002e..cd43575a01 100644
--- a/var/spack/repos/builtin.mock/packages/simple-inheritance/package.py
+++ b/var/spack/repos/builtin.mock/packages/simple-inheritance/package.py
@@ -1,3 +1,8 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/singlevalue-variant-dependent/package.py b/var/spack/repos/builtin.mock/packages/singlevalue-variant-dependent/package.py
index 60530e8202..c9cc385b6a 100644
--- a/var/spack/repos/builtin.mock/packages/singlevalue-variant-dependent/package.py
+++ b/var/spack/repos/builtin.mock/packages/singlevalue-variant-dependent/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/svn-test/package.py b/var/spack/repos/builtin.mock/packages/svn-test/package.py
index 1c4424dab5..b0ad42542b 100644
--- a/var/spack/repos/builtin.mock/packages/svn-test/package.py
+++ b/var/spack/repos/builtin.mock/packages/svn-test/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,7 +10,7 @@ class SvnTest(Package):
     """Mock package that uses svn for fetching."""
     url      = "http://www.example.com/svn-test-1.0.tar.gz"
 
-    version('svn', 'to-be-filled-in-by-test')
+    version('svn', svn='to-be-filled-in-by-test')
 
     def install(self, spec, prefix):
         pass
diff --git a/var/spack/repos/builtin.mock/packages/svn-top-level/package.py b/var/spack/repos/builtin.mock/packages/svn-top-level/package.py
new file mode 100644
index 0000000000..8acd54b66a
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/svn-top-level/package.py
@@ -0,0 +1,16 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class SvnTopLevel(Package):
+    """Mock package that uses svn for fetching."""
+
+    svn = 'https://example.com/some/svn/repo'
+    version('1.0')
+
+    def install(self, spec, prefix):
+        pass
diff --git a/var/spack/repos/builtin.mock/packages/trivial-install-test-package/package.py b/var/spack/repos/builtin.mock/packages/trivial-install-test-package/package.py
index eadba7064c..aad58f08e3 100644
--- a/var/spack/repos/builtin.mock/packages/trivial-install-test-package/package.py
+++ b/var/spack/repos/builtin.mock/packages/trivial-install-test-package/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/url-list-test/package.py b/var/spack/repos/builtin.mock/packages/url-list-test/package.py
index e77d203707..98d7af8425 100644
--- a/var/spack/repos/builtin.mock/packages/url-list-test/package.py
+++ b/var/spack/repos/builtin.mock/packages/url-list-test/package.py
@@ -1,49 +1,30 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 import os
-import spack
+import spack.paths
 
 
 class UrlListTest(Package):
     """Mock package with url_list."""
     homepage = "http://www.url-list-example.com"
 
-    web_data_path = os.path.join(spack.test_path, 'data', 'web')
+    web_data_path = os.path.join(spack.paths.test_path, 'data', 'web')
     url = 'file://' + web_data_path + '/foo-0.0.0.tar.gz'
     list_url = 'file://' + web_data_path + '/index.html'
     list_depth = 3
 
-    version('0.0.0')
-    version('1.0.0')
-    version('3.0')
-    version('4.5')
-    version('2.0.0b2')
-    version('3.0a1')
-    version('4.5-rc5')
+    version('0.0.0',   'abc000')
+    version('1.0.0',   'abc100')
+    version('3.0',     'abc30')
+    version('4.5',     'abc45')
+    version('2.0.0b2', 'abc200b2')
+    version('3.0a1',   'abc30a1')
+    version('4.5-rc5', 'abc45rc5')
 
     def install(self, spec, prefix):
         pass
diff --git a/var/spack/repos/builtin.mock/packages/url-only-override-with-gaps/package.py b/var/spack/repos/builtin.mock/packages/url-only-override-with-gaps/package.py
new file mode 100644
index 0000000000..bee39c0c72
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/url-only-override-with-gaps/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class UrlOnlyOverrideWithGaps(Package):
+    homepage = 'http://www.example.com'
+
+    version('1.0.5', 'abcdef0')
+    version('1.0.0', 'bcdef0a', url='http://a.example.com/url_override-1.0.0.tar.gz')
+    version('0.9.5', 'cdef0ab')
+    version('0.9.0', 'def0abc', url='http://b.example.com/url_override-0.9.0.tar.gz')
+    version('0.8.5', 'ef0abcd')
+    version('0.8.1', 'f0abcde', url='http://c.example.com/url_override-0.8.1.tar.gz')
+    version('0.7.0', '0abcdef')
diff --git a/var/spack/repos/builtin.mock/packages/url-only-override/package.py b/var/spack/repos/builtin.mock/packages/url-only-override/package.py
new file mode 100644
index 0000000000..e145285985
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/url-only-override/package.py
@@ -0,0 +1,14 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class UrlOnlyOverride(Package):
+    homepage = 'http://www.example.com'
+
+    version('1.0.0', 'cxyzab', url='http://a.example.com/url_override-1.0.0.tar.gz')
+    version('0.9.0', 'bcxyza', url='http://b.example.com/url_override-0.9.0.tar.gz')
+    version('0.8.1', 'cxyzab', url='http://c.example.com/url_override-0.8.1.tar.gz')
diff --git a/var/spack/repos/builtin.mock/packages/url-test/package.py b/var/spack/repos/builtin.mock/packages/url-test/package.py
index 113dc0714b..c16f345980 100644
--- a/var/spack/repos/builtin.mock/packages/url-test/package.py
+++ b/var/spack/repos/builtin.mock/packages/url-test/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/url_override/package.py b/var/spack/repos/builtin.mock/packages/url_override/package.py
new file mode 100644
index 0000000000..803afe5e33
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/url_override/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class UrlOverride(Package):
+    homepage = 'http://www.doesnotexist.org'
+    url      = 'http://www.doesnotexist.org/url_override-1.0.0.tar.gz'
+
+    version('1.0.0', 'cxyzab')
+    version('0.9.0', 'bcxyza', url='http://www.anothersite.org/uo-0.9.0.tgz')
+    version('0.8.1', 'cxyzab')
diff --git a/var/spack/repos/builtin.mock/packages/zmpi/package.py b/var/spack/repos/builtin.mock/packages/zmpi/package.py
index 99a750afc1..4546ed7335 100644
--- a/var/spack/repos/builtin.mock/packages/zmpi/package.py
+++ b/var/spack/repos/builtin.mock/packages/zmpi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/abinit/package.py b/var/spack/repos/builtin/packages/abinit/package.py
index 59040cd0d8..4902509d4e 100644
--- a/var/spack/repos/builtin/packages/abinit/package.py
+++ b/var/spack/repos/builtin/packages/abinit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 # Author: Matteo Giantomassi <matteo.giantomassiNOSPAM AT uclouvain.be>
 # Date: October 11, 2016
@@ -47,8 +28,10 @@ class Abinit(AutotoolsPackage):
     """
 
     homepage = 'http://www.abinit.org'
-    url      = 'http://ftp.abinit.org/abinit-8.0.8b.tar.gz'
+    url      = 'https://www.abinit.org/sites/default/files/packages/abinit-8.6.3.tar.gz'
 
+    version('8.8.2', '72d7046c7ff31b9f17afe050ecdfb3a5')
+    version('8.6.3', '6c34d2cec0cf0008dd25b8ec1b6d3ee8')
     version('8.2.2', '5f25250e06fdc0815c224ffd29858860')
     # Versions before 8.0.8b are not supported.
     version('8.0.8b', 'abc9e303bfa7f9f43f95598f87d84d5d')
diff --git a/var/spack/repos/builtin/packages/abyss/package.py b/var/spack/repos/builtin/packages/abyss/package.py
index 4a8aa0fb03..aabaf94400 100644
--- a/var/spack/repos/builtin/packages/abyss/package.py
+++ b/var/spack/repos/builtin/packages/abyss/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,11 +12,15 @@ class Abyss(AutotoolsPackage):
        is useful for assembling genomes up to 100 Mbases in size."""
 
     homepage = "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
-    url      = "https://github.com/bcgsc/abyss/archive/2.0.2.tar.gz"
+    url      = "https://github.com/bcgsc/abyss/releases/download/1.5.2/abyss-1.5.2.tar.gz"
 
-    version('2.0.2', 'bb3f8cebf121312bf81789d963b4ecc5')
+    version('2.0.2', '1623f55ad7f4586e80f6e74b1f27c798')
     version('1.5.2', '10d6d72d1a915e618d41a5cbbcf2364c')
 
+    variant('maxk', values=int, default=0, 
+            description='''set the maximum k-mer length.
+            This value must be a multiple of 32''')
+
     depends_on('autoconf', type='build')
     depends_on('automake', type='build')
 
@@ -44,6 +29,7 @@ class Abyss(AutotoolsPackage):
     depends_on('boost@:1.50.0,1.53.0:1.59.0', when='@:1.5.2')
     depends_on('sparsehash')
     depends_on('sqlite')
+    depends_on('libtool')
 
     conflicts('^intel-mpi')
     conflicts('^intel-parallel-studio+mpi')
@@ -51,9 +37,12 @@ class Abyss(AutotoolsPackage):
     conflicts('^spectrum-mpi')
 
     def configure_args(self):
+        maxk = int(self.spec.variants['maxk'].value)
         args = ['--with-boost=%s' % self.spec['boost'].prefix,
                 '--with-sqlite=%s' % self.spec['sqlite'].prefix,
                 '--with-mpi=%s' % self.spec['mpi'].prefix]
+        if maxk:
+                args.append('--enable-maxk=%s' % maxk)
         if self.spec['mpi'].name == 'mpich':
                 args.append('--enable-mpich')
         return args
diff --git a/var/spack/repos/builtin/packages/accfft/package.py b/var/spack/repos/builtin/packages/accfft/package.py
new file mode 100644
index 0000000000..3a59f11f27
--- /dev/null
+++ b/var/spack/repos/builtin/packages/accfft/package.py
@@ -0,0 +1,47 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Accfft(CMakePackage, CudaPackage):
+    """AccFFT extends existing FFT libraries for CUDA-enabled
+    Graphics Processing Units (GPUs) to distributed memory clusters
+    """
+
+    homepage = "http://accfft.org"
+    git      = "https://github.com/amirgholami/accfft.git"
+
+    version('develop', branch='master')
+
+    variant('pnetcdf', default=True, description='Add support for parallel NetCDF')
+    variant('shared', default=True, description='Enables the build of shared libraries')
+
+    # See: http://accfft.org/articles/install/#installing-dependencies
+    depends_on('fftw+float+double~mpi+openmp')
+
+    depends_on('parallel-netcdf', when='+pnetcdf')
+
+    parallel = False
+
+    def cmake_args(self):
+        spec = self.spec
+        args = [
+            '-DFFTW_ROOT={0}'.format(spec['fftw'].prefix),
+            '-DFFTW_USE_STATIC_LIBS=false',
+            '-DBUILD_GPU={0}'.format('true' if '+cuda' in spec else 'false'),
+            '-DBUILD_SHARED={0}'.format(
+                'true' if '+shared' in spec else 'false'
+            ),
+        ]
+
+        if '+cuda' in spec:
+            cuda_arch = [x for x in spec.variants['cuda_arch'].value if x]
+            if cuda_arch:
+                args.append('-DCUDA_NVCC_FLAGS={0}'.format(
+                    ' '.join(self.cuda_flags(cuda_arch))
+                ))
+
+        return args
diff --git a/var/spack/repos/builtin/packages/ack/package.py b/var/spack/repos/builtin/packages/ack/package.py
index ec1b6d2a22..c889d1f31e 100644
--- a/var/spack/repos/builtin/packages/ack/package.py
+++ b/var/spack/repos/builtin/packages/ack/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,6 +16,7 @@ class Ack(Package):
     homepage = "http://beyondgrep.com/"
     url      = "http://beyondgrep.com/ack-2.14-single-file"
 
+    version('2.22', 'eea9d4daef7c262751f15ca9b3b70317', expand=False)
     version('2.18', 'e8ebfd7a7ec8476bffd4686bf7b14fd7', expand=False)
     version('2.16', '7085b5a5c76fda43ff049410870c8535', expand=False)
     version('2.14', 'e74150a1609d28a70b450ef9cc2ed56b', expand=False)
diff --git a/var/spack/repos/builtin/packages/activeharmony/package.py b/var/spack/repos/builtin/packages/activeharmony/package.py
index d03d3f99eb..7c90f24a0d 100644
--- a/var/spack/repos/builtin/packages/activeharmony/package.py
+++ b/var/spack/repos/builtin/packages/activeharmony/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/adept-utils/package.py b/var/spack/repos/builtin/packages/adept-utils/package.py
index 3f704a4893..fcac87759a 100644
--- a/var/spack/repos/builtin/packages/adept-utils/package.py
+++ b/var/spack/repos/builtin/packages/adept-utils/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/adios/package.py b/var/spack/repos/builtin/packages/adios/package.py
index 1b0b88d167..2b93379129 100644
--- a/var/spack/repos/builtin/packages/adios/package.py
+++ b/var/spack/repos/builtin/packages/adios/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,15 +14,19 @@ class Adios(AutotoolsPackage):
     """
 
     homepage = "http://www.olcf.ornl.gov/center-projects/adios/"
-    url = "https://github.com/ornladios/ADIOS/archive/v1.12.0.tar.gz"
+    url      = "https://github.com/ornladios/ADIOS/archive/v1.12.0.tar.gz"
+    git      = "https://github.com/ornladios/ADIOS.git"
+
+    maintainers = ['ax3l']
 
-    version('develop', git='https://github.com/ornladios/ADIOS.git',
-            branch='master')
+    version('develop', branch='master')
+    version('1.13.1', '958aed11240d7f5a065ab5ee271ecb44')
+    version('1.13.0', '68af36b821debbdf4748b20320a990ce')
     version('1.12.0', '84a1c71b6698009224f6f748c5257fc9')
     version('1.11.1', '5639bfc235e50bf17ba9dafb14ea4185')
     version('1.11.0', '5eead5b2ccf962f5e6d5f254d29d5238')
     version('1.10.0', 'eff450a4c0130479417cfd63186957f3')
-    version('1.9.0', '310ff02388bbaa2b1c1710ee970b5678')
+    version('1.9.0',  '310ff02388bbaa2b1c1710ee970b5678')
 
     variant('shared', default=True,
             description='Builds a shared version of the library')
@@ -65,6 +50,10 @@ class Adios(AutotoolsPackage):
             description='Enable ZFP transform support')
     variant('sz', default=True,
             description='Enable SZ transform support')
+    variant('lz4', default=True,
+            description='Enable LZ4 transform support')
+    variant('blosc', default=True,
+            description='Enable Blosc transform support')
     # transports and serial file converters
     variant('hdf5', default=False,
             description='Enable parallel HDF5 transport and serial bp2h5 ' +
@@ -90,8 +79,12 @@ class Adios(AutotoolsPackage):
     depends_on('zlib', when='+zlib')
     depends_on('bzip2', when='+bzip2')
     depends_on('szip', when='+szip')
-    depends_on('sz@:1.4.10', when='+sz')
+    depends_on('sz@:1.4.10', when='@:1.12.0 +sz')
+    depends_on('sz@1.4.11.0:1.4.11.99', when='@1.13.0 +sz')
+    depends_on('sz@1.4.12.3:1.4.12.99', when='@1.13.1: +sz')
     depends_on('zfp@:0.5.0', when='+zfp')
+    depends_on('lz4', when='+lz4')
+    depends_on('c-blosc@1.12.0:', when='+blosc')
     # optional transports & file converters
     depends_on('hdf5@1.8:+hl+mpi', when='+hdf5')
     depends_on('netcdf', when='+netcdf')
@@ -153,7 +146,16 @@ class Adios(AutotoolsPackage):
         extra_args += self.with_or_without('infiniband')
 
         # Transforms
-        variants = ['zlib', 'bzip2', 'szip', 'zfp', 'sz']
+        variants = ['zlib', 'bzip2', 'szip']
+        if spec.satisfies('@1.11.0:'):
+            variants += ['zfp']
+        if spec.satisfies('@1.12.0:'):
+            variants += ['sz', 'lz4']
+        if spec.satisfies('@1.13.0:'):
+            extra_args += self.with_or_without(
+                'blosc',
+                activation_value=lambda x: spec['c-blosc'].prefix
+            )
 
         # External I/O libraries
         variants += ['hdf5', 'netcdf']
diff --git a/var/spack/repos/builtin/packages/adios2/package.py b/var/spack/repos/builtin/packages/adios2/package.py
index a222477c2d..a7ba1eec0b 100644
--- a/var/spack/repos/builtin/packages/adios2/package.py
+++ b/var/spack/repos/builtin/packages/adios2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,21 +11,27 @@ class Adios2(CMakePackage):
 
     homepage = "https://www.olcf.ornl.gov/center-projects/adios/"
     url      = "https://github.com/ornladios/ADIOS2/archive/v2.0.0.tar.gz"
+    git      = "https://github.com/ornladios/ADIOS2.git"
 
-    version('develop', branch='master',
-            git='https://github.com/ornladios/ADIOS2.git')
+    maintainers = ['ax3l']
 
+    version('develop', branch='master')
+    version('2.2.0', sha256='77058ea2ff7224dc02ea519733de42d89112cf21ffe7474fb2fa3c5696152948')
+    version('2.1.0', '431fa5b015349f1838b96b8f5a1cc8f8')
     version('2.0.0', 'da39655b51745d2c5f3f1e46c5abc4d7')
 
     variant('shared', default=True,
             description='Also build shared libraries')
     variant('mpi', default=True,
             description='Enable MPI')
-    # transforms (not yet implemented)
-    # variant('bzip2', default=True,
-    #         description='Enable BZip2 compression')
-    # variant('zfp', default=True,
-    #         description='Enable ZFP compression')
+    # transforms
+    variant('bzip2', default=True,
+            description='Enable BZip2 compression')
+    variant('zfp', default=True,
+            description='Enable ZFP compression')
+    # sz is broken in 2.2.0: https://github.com/ornladios/ADIOS2/issues/705
+    # variant('sz', default=True,
+    #         description='Enable SZ compression')
     # transport engines
     variant('dataman', default=True,
             description='Enable the DataMan engine for WAN transports')
@@ -58,6 +45,8 @@ class Adios2(CMakePackage):
     # language bindings
     variant('python', default=True,
             description='Enable the Python >= 2.7 bindings')
+    variant('fortran', default=True,
+            description='Enable the Fortran bindings')
 
     # requires mature C++11 implementations
     conflicts('%gcc@:4.7')
@@ -68,12 +57,17 @@ class Adios2(CMakePackage):
     conflicts('+dataman', when='~shared')
 
     depends_on('cmake@3.5.0:', type='build')
+    depends_on('pkgconfig', type='build', when='@2.2.0:')
+    # The included ffs requires bison and flex but using them makes
+    # the build fail due to an undefined reference.
+    # depends_on('bison', type='build', when='@2.2.0:')
+    # depends_on('flex', when='@2.2.0:')
 
     # contained in thirdparty/
     # depends_on('googletest')
     # depends_on('pugixml')
     # depends_on('kwsys')
-    # depends_on('nlohmannjson')
+    # depends_on('nlohmann-json')
     # depends_on('pybind11@2.1.1:', when='+python')
 
     depends_on('mpi', when='+mpi')
@@ -86,6 +80,7 @@ class Adios2(CMakePackage):
 
     depends_on('bzip2', when='+bzip2')
     depends_on('zfp', when='+zfp')
+    # depends_on('sz@:1.4.12', when='+sz')
 
     extends('python', when='+python')
     depends_on('python@2.7:', type=('build', 'run'), when='+python')
@@ -96,24 +91,31 @@ class Adios2(CMakePackage):
         spec = self.spec
 
         args = [
-            '-DADIOS2_BUILD_SHARED_LIBS:BOOL={0}'.format((
-                'ON' if '+shared' in spec else 'OFF')),
+            '-DADIOS2_BUILD_SHARED_LIBS:BOOL={0}'.format(
+                'ON' if '+shared' in spec else 'OFF'),
             '-DADIOS2_BUILD_TESTING=OFF',
-            '-DADIOS2_USE_MPI={0}'.format((
-                'ON' if '+mpi' in spec else 'OFF')),
-            '-DADIOS2_USE_BZip2={0}'.format((
-                'ON' if '+bzip2' in spec else 'OFF')),
-            '-DADIOS2_USE_ZFP={0}'.format((
-                'ON' if '+zfp' in spec else 'OFF')),
-            '-DADIOS2_USE_DataMan={0}'.format((
-                'ON' if '+dataman' in spec else 'OFF')),
-            '-DADIOS2_USE_ZeroMQ={0}'.format((
-                'ON' if '+dataman' in spec else 'OFF')),
-            '-DADIOS2_USE_HDF5={0}'.format((
-                'ON' if '+hdf5' in spec else 'OFF')),
-            '-DADIOS2_USE_ADIOS1={0}'.format((
-                'ON' if '+adios1' in spec else 'OFF')),
-            '-DADIOS2_USE_Python={0}'.format((
-                'ON' if '+python' in spec else 'OFF'))
+            '-DADIOS2_USE_MPI={0}'.format(
+                'ON' if '+mpi' in spec else 'OFF'),
+            '-DADIOS2_USE_BZip2={0}'.format(
+                'ON' if '+bzip2' in spec else 'OFF'),
+            '-DADIOS2_USE_ZFP={0}'.format(
+                'ON' if '+zfp' in spec else 'OFF'),
+            '-DADIOS2_USE_SZ={0}'.format(
+                'ON' if '+sz' in spec else 'OFF'),
+            '-DADIOS2_USE_DataMan={0}'.format(
+                'ON' if '+dataman' in spec else 'OFF'),
+            '-DADIOS2_USE_ZeroMQ={0}'.format(
+                'ON' if '+dataman' in spec else 'OFF'),
+            '-DADIOS2_USE_HDF5={0}'.format(
+                'ON' if '+hdf5' in spec else 'OFF'),
+            '-DADIOS2_USE_ADIOS1={0}'.format(
+                'ON' if '+adios1' in spec else 'OFF'),
+            '-DADIOS2_USE_Python={0}'.format(
+                'ON' if '+python' in spec else 'OFF'),
+            '-DADIOS2_USE_Fortran={0}'.format(
+                'ON' if '+fortran' in spec else 'OFF')
         ]
+        if spec.satisfies('+python'):
+            args.append('-DPYTHON_EXECUTABLE:FILEPATH=%s'
+                        % self.spec['python'].command.path)
         return args
diff --git a/var/spack/repos/builtin/packages/adlbx/package.py b/var/spack/repos/builtin/packages/adlbx/package.py
index dfe6dffb03..4f7e06d2c9 100644
--- a/var/spack/repos/builtin/packages/adlbx/package.py
+++ b/var/spack/repos/builtin/packages/adlbx/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -30,12 +11,21 @@ class Adlbx(AutotoolsPackage):
     """ADLB/X: Master-worker library + work stealing and data dependencies"""
 
     homepage = 'http://swift-lang.org/Swift-T'
-    url      = 'http://swift-lang.github.io/swift-t-downloads/adlbx-0.8.0.tar.gz'
+    url      = 'http://swift-lang.github.io/swift-t-downloads/spack/adlbx-0.0.0.tar.gz'
+
+    version('0.9.1', '07151ddef5fb83d8f4b40700013d9daf')
     version('0.8.0', '34ade59ce3be5bc296955231d47a27dd')
 
-    depends_on('exmcutils')
+    depends_on('exmcutils@:0.5.3', when='@:0.8.0')
+    depends_on('exmcutils', when='@0.9.1:')
     depends_on('mpi')
 
+    def setup_environment(self, spack_env, run_env):
+        spec = self.spec
+        spack_env.set('CC', spec['mpi'].mpicc)
+        spack_env.set('CXX', spec['mpi'].mpicxx)
+        spack_env.set('CXXLD', spec['mpi'].mpicxx)
+
     def configure_args(self):
         args = ['--with-c-utils=' + self.spec['exmcutils'].prefix]
         return args
diff --git a/var/spack/repos/builtin/packages/adol-c/package.py b/var/spack/repos/builtin/packages/adol-c/package.py
index 953cade297..7769dc13b7 100644
--- a/var/spack/repos/builtin/packages/adol-c/package.py
+++ b/var/spack/repos/builtin/packages/adol-c/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,14 +10,16 @@ class AdolC(AutotoolsPackage):
     """A package for the automatic differentiation of first and higher
     derivatives of vector functions in C and C++ programs by operator
     overloading."""
+
     homepage = "https://projects.coin-or.org/ADOL-C"
     url      = "http://www.coin-or.org/download/source/ADOL-C/ADOL-C-2.6.1.tgz"
+    git      = "https://gitlab.com/adol-c/adol-c.git"
 
-    version('develop',  git='https://gitlab.com/adol-c/adol-c.git',
-            branch='master')
+    version('develop',  branch='master')
     version('2.6.3', 'f78f67f70d5874830a1ad1c0f54e54f7')
     version('2.6.2', '0f9547584c99c0673e4f81cf64e8d865')
     version('2.6.1', '1032b28427d6e399af4610e78c0f087b')
+    version('2.5.2', '96f81b80e93cca57398066ea4afe28f0')
 
     variant('advanced_branching', default=False,
             description='Enable advanced branching to reduce retaping')
@@ -46,6 +29,7 @@ class AdolC(AutotoolsPackage):
     variant('openmp',   default=False, description='Enable OpenMP support')
     variant('sparse',   default=False, description='Enable sparse drivers')
     variant('examples', default=True,  description='Install examples')
+    variant('boost',    default=False, description='Enable boost')
 
     # Build dependencies
     depends_on('automake', type='build', when='@develop')
@@ -53,6 +37,18 @@ class AdolC(AutotoolsPackage):
     depends_on('libtool',  type='build', when='@develop')
     depends_on('m4',       type='build', when='@develop')
 
+    # Link dependencies
+    depends_on('boost+system', when='+boost')
+
+    # FIXME: add
+    #  --with-colpack=DIR      path to the colpack library and headers
+    #                       [default=system libraries]
+    #  --with-mpi-root=MPIROOT absolute path to the MPI root directory
+    #  --with-mpicc=MPICC      name of the MPI C++ compiler (default mpicc)
+    #  --with-mpicxx=MPICXX    name of the MPI C++ compiler (default mpicxx)
+    #  --with-ampi=AMPI_DIR    full path to the installation of adjoinable MPI
+    #                           (AMPI)
+
     patch('openmp_exam_261.patch', when='@2.6.1')
 
     def configure_args(self):
@@ -60,25 +56,34 @@ class AdolC(AutotoolsPackage):
 
         configure_args = []
 
+        if '+boost' in spec:
+            configure_args.append(
+                '--with-boost={0}'.format(spec['boost'].prefix)
+            )
+        else:
+            configure_args.append(
+                '--with-boost=no'
+            )
+
         if '+advanced_branching' in spec:
-            configure_args.extend([
+            configure_args.append(
                 '--enable-advanced-branching'
-            ])
+            )
 
         if '+atrig_erf' in spec:
-            configure_args.extend([
+            configure_args.append(
                 '--enable-atrig-erf'
-            ])
+            )
 
         if '+openmp' in spec:
-            configure_args.extend([
+            configure_args.append(
                 '--with-openmp-flag={0}'.format(self.compiler.openmp_flag)
-            ])
+            )
 
         if '+sparse' in spec:
-            configure_args.extend([
+            configure_args.append(
                 '--enable-sparse'
-            ])
+            )
 
         # We can simply use the bundled examples to check
         # whether Adol-C works as expected
@@ -88,9 +93,9 @@ class AdolC(AutotoolsPackage):
                 '--enable-addexa'  # Additional examples
             ])
             if '+openmp' in spec:
-                configure_args.extend([
+                configure_args.append(
                     '--enable-parexa'  # Parallel examples
-                ])
+                )
 
         return configure_args
 
diff --git a/var/spack/repos/builtin/packages/aegean/package.py b/var/spack/repos/builtin/packages/aegean/package.py
new file mode 100644
index 0000000000..a66c4d1e72
--- /dev/null
+++ b/var/spack/repos/builtin/packages/aegean/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Aegean(MakefilePackage):
+    """The AEGeAn Toolkit is designed for the Analysis and Evaluation of
+       Genome Annotations. The toolkit includes a variety of analysis programs
+       as well as a C library whose API provides access to AEGeAn's core
+       functions and data structures."""
+
+    homepage = "http://brendelgroup.github.io/AEGeAn/"
+    url      = "https://github.com/BrendelGroup/AEGeAn/archive/v0.15.2.tar.gz"
+
+    version('0.15.2', 'd7d73f5f132ff52340975b636564e949')
+
+    depends_on('genometools')
+
+    def edit(self, spec, prefix):
+        makefile = FileFilter('Makefile')
+        makefile.filter('/usr/local', prefix)
diff --git a/var/spack/repos/builtin/packages/aida/package.py b/var/spack/repos/builtin/packages/aida/package.py
new file mode 100644
index 0000000000..d2b2a22d72
--- /dev/null
+++ b/var/spack/repos/builtin/packages/aida/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Aida(Package):
+    """Abstract Interfaces for Data Analysis"""
+
+    homepage = "http://aida.freehep.org/"
+    url      = "ftp://ftp.slac.stanford.edu/software/freehep/AIDA/v3.2.1/aida-3.2.1.tar.gz"
+
+    version('3.2.1', sha256='c51da83e99c0985a7ef3e8bc5a60c3ae61f3ca603b61100c2438b4cdadd5bb2e')
+
+    def install(self, spec, prefix):
+        install_tree('src/cpp', prefix.include)
+        install_tree('lib', prefix)
diff --git a/var/spack/repos/builtin/packages/albany/package.py b/var/spack/repos/builtin/packages/albany/package.py
new file mode 100644
index 0000000000..ae8613d361
--- /dev/null
+++ b/var/spack/repos/builtin/packages/albany/package.py
@@ -0,0 +1,102 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Albany(CMakePackage):
+    """Albany is an implicit, unstructured grid, finite element code for the
+       solution and analysis of multiphysics problems.  The Albany repository
+       on the GitHub site contains hundreds of regression tests and examples
+       that demonstrate the code's capabilities on a wide variety of problems
+       including fluid mechanics, solid mechanics (elasticity and plasticity),
+       ice-sheet flow, quantum device modeling, and many other applications."""
+
+    homepage = "http://gahansen.github.io/Albany"
+    git      = "https://github.com/gahansen/Albany.git"
+
+    maintainers = ['gahansen']
+
+    version('develop', branch='master')
+
+    variant('lcm',          default=True,
+            description='Enable LCM')
+    variant('aeras',          default=False,
+            description='Enable AERAS')
+    variant('qcad',          default=False,
+            description='Enable QCAD')
+    variant('hydride',          default=False,
+            description='Enable HYDRIDE')
+    variant('lcm_spec',          default=False,
+            description='Enable LCM_SPECULATIVE')
+    variant('lame',          default=False,
+            description='Enable LAME')
+    variant('debug',          default=False,
+            description='Enable DEBUGGING')
+    variant('fpe',          default=False,
+            description='Enable CHECK_FPE')
+    variant('scorec',          default=False,
+            description='Enable SCOREC')
+    variant('felix',          default=False,
+            description='Enable FELIX')
+    variant('mor',          default=False,
+            description='Enable MOR')
+    variant('confgui',          default=False,
+            description='Enable Albany configuration (CI) GUI')
+    variant('ascr',          default=False,
+            description='Enable ALBANY_ASCR')
+    variant('perf',          default=False,
+            description='Enable PERFORMANCE_TESTS')
+    variant('64bit',          default=True,
+            description='Enable 64BIT')
+
+    # Add dependencies
+    depends_on('mpi')
+    depends_on('trilinos~superlu-dist+isorropia+tempus+rythmos+teko+intrepid+intrepid2+minitensor+phalanx+pnetcdf+nox+piro+rol+shards+stk+superlu@master,develop')
+
+    def cmake_args(self):
+        spec = self.spec
+        trilinos_dir = spec['trilinos'].prefix
+        options = []
+
+        options.extend([
+            '-DALBANY_TRILINOS_DIR:FILEPATH={0}'.format(trilinos_dir),
+            '-DINSTALL_ALBANY:BOOL=ON'
+        ])
+
+        options.extend([
+                       '-DENABLE_LCM:BOOL=%s' % (
+                           'ON' if '+lcm' in spec else 'OFF'),
+                       '-DENABLE_AERAS:BOOL=%s' % (
+                           'ON' if '+aeras' in spec else 'OFF'),
+                       '-DENABLE_QCAD:BOOL=%s' % (
+                           'ON' if '+qcad' in spec else 'OFF'),
+                       '-DENABLE_HYDRIDE:BOOL=%s' % (
+                           'ON' if '+hydride' in spec else 'OFF'),
+                       '-DENABLE_LCM_SPECULATIVE:BOOL=%s' % (
+                           'ON' if '+lcm_spec' in spec else 'OFF'),
+                       '-DENABLE_LAME:BOOL=%s' % (
+                           'ON' if '+lame' in spec else 'OFF'),
+                       '-DENABLE_DEBUGGING:BOOL=%s' % (
+                           'ON' if '+debug' in spec else 'OFF'),
+                       '-DENABLE_CHECK_FPE:BOOL=%s' % (
+                           'ON' if '+fpe' in spec else 'OFF'),
+                       '-DENABLE_SCOREC:BOOL=%s' % (
+                           'ON' if '+scorec' in spec else 'OFF'),
+                       '-DENABLE_FELIX:BOOL=%s' % (
+                           'ON' if '+felix' in spec else 'OFF'),
+                       '-DENABLE_MOR:BOOL=%s' % (
+                           'ON' if '+mor' in spec else 'OFF'),
+                       '-DENABLE_ALBANY_CI:BOOL=%s' % (
+                           'ON' if '+ci' in spec else 'OFF'),
+                       '-DENABLE_ASCR:BOOL=%s' % (
+                           'ON' if '+ascr' in spec else 'OFF'),
+                       '-DENABLE_PERFORMANCE_TESTS:BOOL=%s' % (
+                           'ON' if '+perf' in spec else 'OFF'),
+                       '-DENABLE_64BIT_INT:BOOL=%s' % (
+                           'ON' if '+64bit' in spec else 'OFF')
+                       ])
+
+        return options
diff --git a/var/spack/repos/builtin/packages/albert/package.py b/var/spack/repos/builtin/packages/albert/package.py
index d720f04650..c2d432fd36 100644
--- a/var/spack/repos/builtin/packages/albert/package.py
+++ b/var/spack/repos/builtin/packages/albert/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/alglib/package.py b/var/spack/repos/builtin/packages/alglib/package.py
index e470dba292..6842cbd8ad 100644
--- a/var/spack/repos/builtin/packages/alglib/package.py
+++ b/var/spack/repos/builtin/packages/alglib/package.py
@@ -1,31 +1,12 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
 import os
-import shutil
+import sys
 
 
 class Alglib(MakefilePackage):
@@ -47,7 +28,7 @@ class Alglib(MakefilePackage):
         make_file_src = join_path(os.path.dirname(self.module.__file__),
                                   'Makefile')
         make_file = join_path(self.stage.source_path, 'src', 'Makefile')
-        shutil.copy(make_file_src, make_file)
+        copy(make_file_src, make_file)
         filter_file(r'so', dso_suffix, make_file)
 
     def install(self, spec, prefix):
@@ -59,3 +40,9 @@ class Alglib(MakefilePackage):
             headers = glob.glob('*.h')
             for h in headers:
                 install(h, prefix.include)
+
+    @run_after('install')
+    def fix_darwin_install(self):
+        # The shared libraries are not installed correctly on Darwin:
+        if sys.platform == 'darwin':
+            fix_darwin_install_name(self.spec.prefix.lib)
diff --git a/var/spack/repos/builtin/packages/allinea-forge/package.py b/var/spack/repos/builtin/packages/allinea-forge/package.py
index a4a821737d..c0519014a8 100644
--- a/var/spack/repos/builtin/packages/allinea-forge/package.py
+++ b/var/spack/repos/builtin/packages/allinea-forge/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/allinea-reports/package.py b/var/spack/repos/builtin/packages/allinea-reports/package.py
index 69c881c369..a1da29ba47 100644
--- a/var/spack/repos/builtin/packages/allinea-reports/package.py
+++ b/var/spack/repos/builtin/packages/allinea-reports/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/allpaths-lg/package.py b/var/spack/repos/builtin/packages/allpaths-lg/package.py
index 69731045aa..3ec1e99418 100644
--- a/var/spack/repos/builtin/packages/allpaths-lg/package.py
+++ b/var/spack/repos/builtin/packages/allpaths-lg/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/alquimia/package.py b/var/spack/repos/builtin/packages/alquimia/package.py
index 983bab23f7..2b42e89db2 100644
--- a/var/spack/repos/builtin/packages/alquimia/package.py
+++ b/var/spack/repos/builtin/packages/alquimia/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,17 +11,21 @@ class Alquimia(CMakePackage):
     of mature geochemistry codes such as CrunchFlow and PFLOTRAN"""
 
     homepage = "https://github.com/LBL-EESA/alquimia-dev"
+    git      = "https://github.com/LBL-EESA/alquimia-dev.git"
 
-    version('xsdk-0.2.0', git='https://github.com/LBL-EESA/alquimia-dev.git', tag='xsdk-0.2.0')
-    version('develop', git='https://github.com/LBL-EESA/alquimia-dev.git')
+    version('develop')
+    version('xsdk-0.3.0', tag='xsdk-0.3.0')
+    version('xsdk-0.2.0', tag='xsdk-0.2.0')
 
     variant('shared', default=True,
             description='Enables the build of shared libraries')
 
     depends_on('mpi')
     depends_on('hdf5')
+    depends_on('pflotran@xsdk-0.3.0', when='@xsdk-0.3.0')
     depends_on('pflotran@xsdk-0.2.0', when='@xsdk-0.2.0')
     depends_on('pflotran@develop', when='@develop')
+    depends_on('petsc@3.8.0:', when='@xsdk-0.3.0')
     depends_on('petsc@xsdk-0.2.0', when='@xsdk-0.2.0')
     depends_on('petsc@develop', when='@develop')
 
diff --git a/var/spack/repos/builtin/packages/alsa-lib/package.py b/var/spack/repos/builtin/packages/alsa-lib/package.py
index 8e469e9ae7..48cf792548 100644
--- a/var/spack/repos/builtin/packages/alsa-lib/package.py
+++ b/var/spack/repos/builtin/packages/alsa-lib/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/aluminum/package.py b/var/spack/repos/builtin/packages/aluminum/package.py
new file mode 100644
index 0000000000..9700988217
--- /dev/null
+++ b/var/spack/repos/builtin/packages/aluminum/package.py
@@ -0,0 +1,43 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Aluminum(CMakePackage):
+    """Aluminum provides a generic interface to high-performance
+    communication libraries, with a focus on allreduce
+    algorithms. Blocking and non-blocking algorithms and GPU-aware
+    algorithms are supported. Aluminum also contains custom
+    implementations of select algorithms to optimize for certain
+    situations."""
+
+    homepage = "https://github.com/LLNL/Aluminum"
+    url      = "https://github.com/LLNL/Aluminum/archive/v0.1.tar.gz"
+    git      = "https://github.com/LLNL/Aluminum.git"
+
+    version('master', branch='master')
+    version('0.1', sha256='3880b736866e439dd94e6a61eeeb5bb2abccebbac82b82d52033bc6c94950bdb')
+
+    variant('gpu', default=False, description='Builds with support for GPUs via CUDA and cuDNN')
+    variant('nccl', default=False, description='Builds with support for NCCL communication lib')
+    variant('mpi_cuda', default=False, description='Builds with support for MPI-CUDA enabled library')
+
+    depends_on('cmake@3.9.0:', type='build')
+    depends_on('cuda', when='+gpu')
+    depends_on('cudnn', when='+gpu')
+    depends_on('cub', when='+gpu')
+    depends_on('mpi', when='~mpi_cuda')
+    depends_on('mpi +cuda', when='+mpi_cuda')
+    depends_on('nccl', when='+nccl')
+    depends_on('hwloc')
+
+    def cmake_args(self):
+        spec = self.spec
+        args = [
+            '-DALUMINUM_ENABLE_CUDA:BOOL=%s' % ('+gpu' in spec),
+            '-DALUMINUM_ENABLE_MPI_CUDA:BOOL=%s' % ('+mpi_cuda' in spec),
+            '-DALUMINUM_ENABLE_NCCL:BOOL=%s' % ('+nccl' in spec)]
+        return args
diff --git a/var/spack/repos/builtin/packages/amg/package.py b/var/spack/repos/builtin/packages/amg/package.py
index 5167347dc9..5a16aac3e0 100644
--- a/var/spack/repos/builtin/packages/amg/package.py
+++ b/var/spack/repos/builtin/packages/amg/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 0s2111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,11 +13,12 @@ class Amg(MakefilePackage):
     """
     tags = ['proxy-app', 'ecp-proxy-app']
 
-    homepage = "https://codesign.llnl.gov/amg2013.php"
-    git      = "https://github.com/LLNL/AMG"
+    homepage = "https://computation.llnl.gov/projects/co-design/amg2013"
+    git      = "https://github.com/LLNL/AMG.git"
 
-    version('1.0', git=git, tag='1.0')
-    version('develop', git=git, branch='master')
+    version('develop', branch='master')
+    version('1.1', tag='1.1')
+    version('1.0', tag='1.0')
 
     variant('openmp', default=True, description='Build with OpenMP support')
     variant('optflags', default=False, description='Additional optimizations')
diff --git a/var/spack/repos/builtin/packages/amg2013/package.py b/var/spack/repos/builtin/packages/amg2013/package.py
index 43e9277805..78a3ac71c9 100644
--- a/var/spack/repos/builtin/packages/amg2013/package.py
+++ b/var/spack/repos/builtin/packages/amg2013/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 0s2111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,11 +14,11 @@ class Amg2013(MakefilePackage):
     in the Center for Applied Scientific Computing (CASC) at LLNL.
     """
     tags = ['proxy-app']
-    homepage = "https://codesign.llnl.gov/amg2013.php"
-    url      = "https://codesign.llnl.gov/amg2013/amg2013.tgz"
+    homepage = "https://computation.llnl.gov/projects/co-design/amg2013"
+    url      = "https://computation.llnl.gov/projects/co-design/download/amg2013.tgz"
 
     version('master', '9d918d2a69528b83e6e0aba6ba601fef',
-            url='https://codesign.llnl.gov/amg2013/amg2013.tgz')
+            url='https://computation.llnl.gov/projects/co-design/download/amg2013.tgz')
 
     variant('openmp', default=True, description='Build with OpenMP support')
     variant('assumedpartition', default=False, description='Use assumed partition (for thousands of processors)')
diff --git a/var/spack/repos/builtin/packages/amp/package.py b/var/spack/repos/builtin/packages/amp/package.py
new file mode 100644
index 0000000000..c56d101a3a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/amp/package.py
@@ -0,0 +1,140 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Amp(CMakePackage):
+    """The Advanced Multi-Physics (AMP) package is an open source parallel
+    object-oriented computational framework that is designed with single
+    and multi-domain multi-physics applications in mind. AMP can be used
+    to build powerful and flexible multi-physics simulation algorithms
+    from lightweight operator, solver, linear algebra, material database,
+    discretization, and meshing components. The AMP design is meant to
+    enable existing investments in application codes to be leveraged without
+    having to adopt dramatically different data structures while developing
+    new computational science applications. Application components are
+    represented as discrete mathematical operators that only require a
+    minimal interface and through operator composition the incremental
+    development of complex parallel applications is enabled. AMP is meant
+    to allow application domain scientists, computer scientists and
+    mathematicians to simulate, collaborate, and conduct research on
+    various aspects of massively parallel simulation algorithms."""
+
+    homepage = "https://bitbucket.org/AdvancedMultiPhysics/amp"
+    hg       = homepage
+
+    version('develop')
+
+    # Everything should be compiled position independent (-fpic)
+    depends_on('blas')
+    depends_on('lapack')
+    depends_on('boost', when='+boost')
+    depends_on('petsc', when='+petsc')
+    depends_on('trilinos', when='+trilinos')
+    depends_on('hdf5', when='+hdf5')
+    depends_on('hdf5', when='+silo')
+    depends_on('silo', when='+silo')
+    depends_on('zlib', when="+zlib")
+
+    # MPI related dependencies
+    depends_on('mpi', when='+mpi')
+
+    def cmake_args(self):
+        spec = self.spec
+
+        options = []
+
+        # #################### Base Settings #######################
+
+        options.extend([
+            '-DTPL_URL=https://bitbucket.org/AdvancedMultiPhysics/tpl-builder',
+            '-DAMP_DATA_URL=https://bitbucket.org/AdvancedMultiPhysics/amp/downloads/AMP-Data.tar.gz',
+            '-DAMP_ENABLE_TESTS:BOOL=OFF',
+            '-DAMP_ENABLE_EXAMPLES:BOOL=OFF',
+            '-DAMP_ENABLE_CXX11:BOOL=ON',
+            '-DCXX_STD=11',
+            '-DBUILD_SHARED_LIBS:BOOL=%s' % (
+                'ON' if '+shared' in spec else 'OFF'),
+        ])
+
+        # #################### Compiler Settings #######################
+
+        if '+mpi' in spec:
+            options.extend([
+                '-DCMAKE_C_COMPILER=%s'       % spec['mpi'].mpicc,
+                '-DCMAKE_CXX_COMPILER=%s'     % spec['mpi'].mpicxx,
+                '-DCMAKE_Fortran_COMPILER=%s' % spec['mpi'].mpifc,
+                '-DUSE_MPI=0',
+                '-DMPI_COMPILER=1',
+                '-DMPIEXEC=$s'                % spec['mpi'].prefix.bin,
+            ])
+        else:
+            options.extend([
+                '-DCMAKE_C_COMPILER=%s'       % self.compiler.cc,
+                '-DCMAKE_CXX_COMPILER=%s'     % self.compiler.cxx,
+                '-DCMAKE_Fortran_COMPILER=%s' % self.compiler.fc,
+                '-DUSE_MPI=0',
+            ])
+
+        # ################## Third Party Libraries #####################
+
+        tpl_list = "LAPACK"
+        blas = spec['blas'].libs
+        lapack = spec['lapack'].libs
+        options.extend([
+            '-DTPL_LAPACK_INSTALL_DIR=%s' % spec['lapack'].prefix,
+            '-DTPL_BLAS_LIBRARY_NAMES=%s' % ';'.join(blas.names),
+            '-DTPL_BLAS_LIBRARY_DIRS=%s' % ';'.join(blas.directories),
+            '-DTPL_LAPACK_LIBRARY_NAMES=%s' % ';'.join(lapack.names),
+            '-DTPL_LAPACK_LIBRARY_DIRS=%s' % ';'.join(lapack.directories),
+        ])
+        if '+boost' in spec:
+            tpl_list = tpl_list + ";BOOST"
+            options.extend(['-DTPL_BOOST_INSTALL_DIR=%s' %
+                            spec['boost'].prefix, ])
+        if '+zlib' in spec:
+            tpl_list = tpl_list + ";ZLIB"
+            options.extend(['-DTPL_ZLIB_INSTALL_DIR=%s' %
+                            spec['zlib'].prefix, ])
+        if '+hdf5' in spec:
+            tpl_list = tpl_list + ";HDF5"
+            options.extend(['-DTPL_HDF5_INSTALL_DIR=%s' %
+                            spec['hdf5'].prefix, ])
+        if '+silo' in spec:
+            tpl_list = tpl_list + ";SILO"
+            options.extend(['-DTPL_SILO_INSTALL_DIR=%s' %
+                            spec['silo'].prefix, ])
+        if '+netcdf' in spec:
+            tpl_list = tpl_list + ";NETCDF"
+            options.extend(['-DTPL_NETCDF_INSTALL_DIR=%s' %
+                            spec['netcdf'].prefix, ])
+        if '+hypre' in spec:
+            tpl_list = tpl_list + ";HYPRE"
+            options.extend(['-DTPL_HYPRE_INSTALL_DIR=%s' %
+                            spec['hypre'].prefix, ])
+        if '+petsc' in spec:
+            tpl_list = tpl_list + ";PETSC"
+            options.extend(['-DTPL_PETSC_INSTALL_DIR=%s' %
+                            spec['petsc'].prefix, ])
+        if '+trilinos' in spec:
+            tpl_list = tpl_list + ";TRILINOS"
+            options.extend(['-DTPL_TRILINOS_INSTALL_DIR=%s' %
+                            spec['trilinos'].prefix, ])
+        if '+libmesh' in spec:
+            tpl_list = tpl_list + ";LIBMESH"
+            options.extend(['-DTPL_LIBMESH_INSTALL_DIR=%s' %
+                            spec['libmesh'].prefix, ])
+        if '+sundials' in spec:
+            tpl_list = tpl_list + ";SUNDIALS"
+            options.extend(['-DTPL_SUNDIALS_INSTALL_DIR=%s' %
+                            spec['sundials'].prefix, ])
+        if '+amp-timer' in spec:
+            tpl_list = tpl_list + ";TIMER"
+            options.extend(['-DTPL_TIMER_INSTALL_DIR=%s' %
+                            spec['amp-timer'].prefix, ])
+        options.extend(['-DTPL_LIST=%s' % tpl_list, ])
+
+        return options
diff --git a/var/spack/repos/builtin/packages/ampliconnoise/package.py b/var/spack/repos/builtin/packages/ampliconnoise/package.py
index 626ac16678..e70328fa1e 100644
--- a/var/spack/repos/builtin/packages/ampliconnoise/package.py
+++ b/var/spack/repos/builtin/packages/ampliconnoise/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/amr-exp-parabolic/package.py b/var/spack/repos/builtin/packages/amr-exp-parabolic/package.py
deleted file mode 100644
index 14d393ed27..0000000000
--- a/var/spack/repos/builtin/packages/amr-exp-parabolic/package.py
+++ /dev/null
@@ -1,95 +0,0 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-from spack import *
-import glob
-
-
-class AmrExpParabolic(MakefilePackage):
-    """Simplified block-structured adaptive mesh refinement algorithm
-    in two and three dimensions with subcycling in time.
-    The algorithm solves a linear advection diffusion equation
-    with a simple numerical method. This proxy app is intended to
-    capture the communication pattern of an explicit AMR algorithm
-    but does not represent an accurate characterization of
-    floating point effort or
-    relative costs of communication to computation."""
-
-    homepage = "https://ccse.lbl.gov/ExaCT/index.html"
-    url      = "https://ccse.lbl.gov/ExaCT/AMR_Exp_Parabolic.tgz"
-    tags     = ['proxy-app']
-
-    version(
-        'release', '330604d9cc755dad8a2cdfaa7ff8f6a4',
-        url='https://ccse.lbl.gov/ExaCT/AMR_Exp_Parabolic.tgz')
-
-    variant(
-        'debug', default=False, description='Turn on debugging')
-    variant(
-        'mpi', default=True, description='Build with MPI support')
-    variant(
-        'openmp', default=False,
-        description='Build with OpenMP support')
-    variant(
-        'prof', default=False, description='Use profiler')
-
-    depends_on('mpi', when='+mpi')
-    depends_on('gmake', type='build')
-
-    build_directory = 'MiniApps/AMR_Adv_Diff_F90'
-
-    def edit(self, spec, prefix):
-        def_file = FileFilter('Tools/F_mk/GMakedefs.mak')
-        def_file.filter('tdir = t/.*', 'tdir := t/$(suf)')
-        def_file.filter('hdir = t/.*', 'hdir := t/html')
-        def_file.filter('include $(BOXLIB_HOME)/Tools/F_mk/GMakeMPI.mak', '#')
-
-        if '+mpi' in spec:
-            def_file.filter('FC.*:=.*', 'FC = {0}'.format(spec['mpi'].mpifc))
-            def_file.filter('F90.*:=.*', 'F90 = {0}'.format(spec['mpi'].mpifc))
-            def_file.filter(
-                'mpi_include_dir =.*',
-                'mpi_include_dir = {0}'.format(spec['mpi'].prefix.include))
-            def_file.filter(
-                'mpi_lib_dir =.*',
-                'mpi_lib_dir = {0}'.format(spec['mpi'].prefix.lib))
-
-        with working_dir(self.build_directory):
-            makefile = FileFilter('GNUmakefile')
-            if '+debug' in spec:
-                makefile.filter('NDEBUG.*:= t', '#')
-            if '~mpi' in spec:
-                makefile.filter('MPI.*:= t', '#')
-            if '+openmp' in spec:
-                makefile.filter('OMP.*:=', 'OMP := t')
-            if '+prof' in spec:
-                makefile.filter('PROF.*:=', 'PROF := t')
-
-    def install(self, spec, prefix):
-        mkdirp(prefix.bin)
-        files = glob.glob(join_path(self.build_directory, '*.exe'))
-        for f in files:
-            install(f, prefix.bin)
-        install('README.txt', prefix)
-        install('license.txt', prefix)
diff --git a/var/spack/repos/builtin/packages/amrex/package.py b/var/spack/repos/builtin/packages/amrex/package.py
index 89533db2e6..abf1e54968 100644
--- a/var/spack/repos/builtin/packages/amrex/package.py
+++ b/var/spack/repos/builtin/packages/amrex/package.py
@@ -1,86 +1,73 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class Amrex(CMakePackage):
-    """AMReX is the successor to BoxLib.
-       It is a Block-Structured AMR Framework.
-    """
-
-    homepage = "https://ccse.lbl.gov/AMReX/index.html"
-    url      = "https://github.com/AMReX-Codes/amrex.git"
+    """AMReX is a publicly available software framework designed
+    for building massively parallel block- structured adaptive
+    mesh refinement (AMR) applications."""
 
-    version('17.06', git='https://github.com/AMReX-Codes/amrex.git', commit='836d3c7')
-    version('master', git='https://github.com/AMReX-Codes/amrex.git', tag='master')
-    version('develop', git='https://github.com/AMReX-Codes/amrex.git', tag='development')
+    homepage = "https://amrex-codes.github.io/amrex/"
+    git      = "https://github.com/AMReX-Codes/amrex.git"
 
-    variant('dims',
-        default='3',
-        values=('1', '2', '3'),
-        multi=False,
-        description='Number of spatial dimensions')
+    version('develop', branch='development')
+    version('18.10.1', commit='260b53169badaa760b91dfc60ea6b2ea3d9ccf06')  # tag:18.10.1
+    version('18.10', commit='d37a266c38092e1174096e245326e9eead1f4e03')  # tag:18.10
+    version('18.09.1', commit='88120db4736c325a2d3d2c291adacaffd3bf224b')  # tag:18.09.1
 
-    variant('prec',
-        default='DOUBLE',
-        values=('FLOAT', 'DOUBLE'),
-        multi=False,
-        description='Floating point precision')
-
-    variant('mpi', default=True, description='Enable MPI parallel support')
-    variant('openmp', default=False, description='Enable OpenMP parallel support')
-    variant('fortran', default=True, description='Enable Fortran support')
-    variant('debug', default=False, description='Enable debugging features')
-    variant('particles', default=False, description='Include particle classes in build')
+    # Config options
+    variant('dimensions', default='3',
+            description='Dimensionality', values=('2', '3'))
+    variant('shared',  default=False,
+            description='Build shared library')
+    variant('mpi',          default=True,
+            description='Build with MPI support')
+    variant('openmp',       default=False,
+            description='Build with OpenMP support')
+    variant('precision',  default='double',
+            description='Real precision (double/single)',
+            values=('single', 'double'))
+    variant('eb',  default=False,
+            description='Build Embedded Boundary classes')
+    variant('fortran',  default=False,
+            description='Build Fortran API')
+    variant('linear_solvers', default=True,
+            description='Build linear solvers')
+    variant('amrdata',    default=False,
+            description='Build data services')
+    variant('particles',  default=False,
+            description='Build particle classes')
+    variant('build_type', default='Release',
+            description='The build type to build',
+            values=('Debug', 'Release'))
 
+    # Build dependencies
     depends_on('mpi', when='+mpi')
+    depends_on('python@2.7:', type='build')
+    depends_on('cmake@3.5:',  type='build')
+    conflicts('%clang')
 
-    def cmake_args(self):
-        spec = self.spec
+    def cmake_is_on(self, option):
+        return 'ON' if option in self.spec else 'OFF'
 
-        cmake_args = [
-            '-DENABLE_POSITION_INDEPENDENT_CODE=ON',
-            '-DBL_SPACEDIM:INT=%d' % int(spec.variants['dims'].value),
-            '-DBL_PRECISION:STRING=%s' % spec.variants['prec'].value,
-            '-DENABLE_FMG=%s' % ('+fortran' in spec),
-            '-DENABLE_FBASELIB=%s' % ('+fortran' in spec),
-            '-DBL_DEBUG:INT=%d' % int('+debug' in spec),
-            '-DBL_USE_PARTICLES:INT=%d' % int('+particles' in spec),
-            '-DENABLE_MPI:INT=%d' % int('+mpi' in spec),
-            '-DENABLE_OpenMP:INT=%d' % int('+openmp' in spec),
+    def cmake_args(self):
+        args = [
+            '-DUSE_XSDK_DEFAULTS=ON',
+            '-DDIM:STRING=%s' % self.spec.variants['dimensions'].value,
+            '-DBUILD_SHARED_LIBS:BOOL=%s' % self.cmake_is_on('+shared'),
+            '-DENABLE_MPI:BOOL=%s' % self.cmake_is_on('+mpi'),
+            '-DENABLE_OMP:BOOL=%s' % self.cmake_is_on('+openmp'),
+            '-DXSDK_PRECISION:STRING=%s' %
+            self.spec.variants['precision'].value.upper(),
+            '-DENABLE_EB:BOOL=%s' % self.cmake_is_on('+eb'),
+            '-DXSDK_ENABLE_Fortran:BOOL=%s' % self.cmake_is_on('+fortran'),
+            '-DENABLE_LINEAR_SOLVERS:BOOL=%s' %
+            self.cmake_is_on('+linear_solvers'),
+            '-DENABLE_AMRDATA:BOOL=%s' % self.cmake_is_on('+amrdata'),
+            '-DENABLE_PARTICLES:BOOL=%s' % self.cmake_is_on('+particles')
         ]
-
-        if '+mpi' in spec:
-            cmake_args += [
-                '-DCMAKE_C_COMPILER=%s' % spec['mpi'].mpicc,
-                '-DCMAKE_CXX_COMPILER=%s' % spec['mpi'].mpicxx
-            ]
-            if '+fortran' in spec:
-                cmake_args += [
-                    '-DCMAKE_Fortran_COMPILER=%s' % spec['mpi'].mpifc
-                ]
-            cmake_args += ['-DENABLE_FORTRAN_MPI=%s' % ('+fortran' in spec)]
-
-        return cmake_args
+        return args
diff --git a/var/spack/repos/builtin/packages/amrvis/package.py b/var/spack/repos/builtin/packages/amrvis/package.py
new file mode 100644
index 0000000000..b9e69466d7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/amrvis/package.py
@@ -0,0 +1,192 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import glob
+
+
+class Amrvis(MakefilePackage):
+    """Amrvis is a visualization package specifically designed to
+       read and display output and profiling data from codes built
+       on the AMReX framework.
+    """
+
+    homepage = "https://github.com/AMReX-Codes/Amrvis"
+    git      = "https://github.com/AMReX-Codes/Amrvis.git"
+
+    version('master', tag='master')
+
+    variant(
+        'dims',
+        default='3',
+        values=('1', '2', '3'),
+        multi=False,
+        description='Number of spatial dimensions'
+    )
+    variant(
+        'prec',
+        default='DOUBLE',
+        values=('FLOAT', 'DOUBLE'),
+        multi=False,
+        description='Floating point precision'
+    )
+    variant('mpi', default=True, description='Enable MPI parallel support')
+    variant('debug', default=False, description='Enable debugging features')
+    variant('profiling', default=False,
+            description='Enable AMReX profiling features')
+
+    depends_on('gmake', type='build')
+    depends_on('mpi', when='+mpi')
+    depends_on('libsm')
+    depends_on('libice')
+    depends_on('libxpm')
+    depends_on('libx11')
+    depends_on('libxt')
+    depends_on('libxext')
+    depends_on('motif')
+    depends_on('flex')
+    depends_on('bison')
+
+    conflicts(
+        '+profiling', when='dims=1',
+        msg='Amrvis profiling support requires a 2D build'
+    )
+    conflicts(
+        '+profiling', when='dims=3',
+        msg='Amrvis profiling support requires a 2D build'
+    )
+
+    # Only doing gcc and clang at the moment.
+    # Intel currently fails searching for mpiicc, mpiicpc, etc.
+    for comp in ['%intel', '%cce', '%nag', '%pgi', '%xl', '%xl_r']:
+        conflicts(
+            comp,
+            msg='Amrvis currently only builds with gcc and clang'
+        )
+
+    # Need to clone AMReX into Amrvis because Amrvis uses AMReX's source
+    resource(name='amrex',
+             git='https://github.com/AMReX-Codes/amrex.git',
+             tag='master',
+             placement='amrex')
+
+    def edit(self, spec, prefix):
+        # Set all available makefile options to values we want
+        makefile = FileFilter('GNUmakefile')
+        makefile.filter(
+            r'^AMREX_HOME\s*\?=.*',
+            'AMREX_HOME = {0}'.format('./amrex')
+        )
+        makefile.filter(
+            r'^PRECISION\s*=.*',
+            'PRECISION = {0}'.format(spec.variants['prec'].value)
+        )
+        makefile.filter(
+            r'^DIM\s*=.*',
+            'DIM = {0}'.format(spec.variants['dims'].value)
+        )
+        makefile.filter(
+            r'^PROFILE\s*=.*',
+            'PROFILE = {0}'.format(
+                spec.variants['profiling'].value
+            ).upper()
+        )
+        makefile.filter(
+            r'^TRACE_PROFILE\s*=.*',
+            'TRACE_PROFILE = {0}'.format(
+                spec.variants['profiling'].value
+            ).upper()
+        )
+        makefile.filter(
+            r'^COMM_PROFILE\s*=.*',
+            'COMM_PROFILE = {0}'.format(
+                spec.variants['profiling'].value
+            ).upper()
+        )
+        makefile.filter(
+            r'^COMP\s*=.*',
+            'COMP = {0}'.format(self.compiler.name)
+        )
+        makefile.filter(
+            r'^DEBUG\s*=.*',
+            'DEBUG = {0}'.format(spec.variants['debug'].value).upper()
+        )
+        makefile.filter(
+            r'^USE_ARRAYVIEW\s*=.*',
+            'USE_ARRAY_VIEW = FALSE'
+        )
+        makefile.filter(
+            r'^USE_MPI\s*=.*',
+            'USE_MPI = {0}'.format(spec.variants['mpi'].value).upper()
+        )
+        makefile.filter(
+            r'^USE_CXX11\s*=.*',
+            'USE_CXX11 = TRUE'
+        )
+        makefile.filter(
+            r'^USE_VOLRENDER\s*=.*',
+            'USE_VOLRENDER = FALSE'
+        )
+        makefile.filter(
+            r'^USE_PARALLELVOLRENDER\s*=.*',
+            'USE_PARALLELVOLRENDER = FALSE'
+        )
+        makefile.filter(
+            r'^USE_PROFPARSER\s*=.*',
+            'USE_PROFPARSER = {0}'.format(
+                spec.variants['profiling'].value
+            ).upper()
+        )
+
+        # A bit risky here deleting all /usr and /opt X
+        # library default search paths in makefile
+        makefile.filter(
+            r'^.*\b(usr|opt)\b.*$',
+            '# Spack removed INCLUDE_LOCATIONS and LIBRARY_LOCATIONS'
+        )
+
+        # Read GNUmakefile into array
+        with open('GNUmakefile', 'r') as file:
+            contents = file.readlines()
+
+        # Edit GNUmakefile includes and libraries to point to Spack
+        # dependencies.
+        # The safest bet is to put the LIBRARY_LOCATIONS and
+        # INCLUDE_LOCATIONS at the beginning of the makefile.
+        line_offset = 0
+        count = 0
+        for lib in ['libsm', 'libice', 'libxpm', 'libx11',
+                    'libxt', 'libxext', 'motif']:
+            contents.insert(
+                line_offset + count,
+                'LIBRARY_LOCATIONS += {0}\n'.format(spec[lib].prefix.lib)
+            )
+            contents.insert(
+                line_offset + count + 1,
+                'INCLUDE_LOCATIONS += {0}\n'.format(spec[lib].prefix.include)
+            )
+            count += 1
+
+        # Write GNUmakefile
+        with open('GNUmakefile', 'w') as file:
+            file.writelines(contents)
+
+    def setup_environment(self, spack_env, run_env):
+        # We don't want an AMREX_HOME the user may have set already
+        spack_env.unset('AMREX_HOME')
+        # Help force Amrvis to not pick up random system compilers
+        if '+mpi' in self.spec:
+            spack_env.set('MPI_HOME', self.spec['mpi'].prefix)
+            spack_env.set('CC', self.spec['mpi'].mpicc)
+            spack_env.set('CXX', self.spec['mpi'].mpicxx)
+            spack_env.set('F77', self.spec['mpi'].mpif77)
+            spack_env.set('FC', self.spec['mpi'].mpifc)
+
+    def install(self, spec, prefix):
+        # Install exe manually
+        mkdirp(prefix.bin)
+        exes = glob.iglob('*.ex')
+        for exe in exes:
+            install(exe, prefix.bin)
diff --git a/var/spack/repos/builtin/packages/andi/package.py b/var/spack/repos/builtin/packages/andi/package.py
index 44c2644507..091cdc80ef 100644
--- a/var/spack/repos/builtin/packages/andi/package.py
+++ b/var/spack/repos/builtin/packages/andi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/angsd/package.py b/var/spack/repos/builtin/packages/angsd/package.py
index eb3e5e58f5..e39cc5e5a9 100644
--- a/var/spack/repos/builtin/packages/angsd/package.py
+++ b/var/spack/repos/builtin/packages/angsd/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,9 +16,11 @@ class Angsd(MakefilePackage):
     homepage = "https://github.com/ANGSD/angsd"
     url      = "https://github.com/ANGSD/angsd/archive/0.919.tar.gz"
 
+    version('0.921', '3702db035396db602c7f74728b1a5a1f')
     version('0.919', '79d342f49c24ac00d35934f2617048d4')
 
     depends_on('htslib')
+    conflicts('^htslib@1.6:', when='@0.919')
 
     def setup_environment(self, spack_env, run_env):
         run_env.set('R_LIBS', prefix.R)
diff --git a/var/spack/repos/builtin/packages/ant/package.py b/var/spack/repos/builtin/packages/ant/package.py
index 82478c481d..302ba94699 100644
--- a/var/spack/repos/builtin/packages/ant/package.py
+++ b/var/spack/repos/builtin/packages/ant/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,8 +15,7 @@ class Ant(Package):
     homepage = "http://ant.apache.org/"
     url = "https://archive.apache.org/dist/ant/source/apache-ant-1.9.7-src.tar.gz"
 
-    # 1.10.0 requires newer Java, not yet tested....
-    # version('1.10.0', '2260301bb7734e34d8b96f1a5fd7979c')
+    version('1.10.0', '2260301bb7734e34d8b96f1a5fd7979c')
     version('1.9.9',  '22c9d40dabafbec348aaada226581239')
     version('1.9.8',  '16253d516d5c33c4af9ef8fafcf1004b')
     version('1.9.7',  'a2fd9458c76700b7be51ef12f07d4bb1')
@@ -46,4 +26,4 @@ class Ant(Package):
     def install(self, spec, prefix):
         env['ANT_HOME'] = self.prefix
         bash = which('bash')
-        bash('./build.sh', 'install')
+        bash('./build.sh', 'install-lite')
diff --git a/var/spack/repos/builtin/packages/antlr/package.py b/var/spack/repos/builtin/packages/antlr/package.py
index 50324dd82c..70a21cd0f9 100644
--- a/var/spack/repos/builtin/packages/antlr/package.py
+++ b/var/spack/repos/builtin/packages/antlr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -51,6 +32,7 @@ class Antlr(AutotoolsPackage):
         spec = self.spec
 
         return [
+            '--disable-csharp',
             '--{0}-cxx'.format('enable' if '+cxx' in spec else 'disable'),
             '--{0}-java'.format('enable' if '+java' in spec else 'disable'),
             '--{0}-python'.format('enable' if '+python' in spec else 'disable')
diff --git a/var/spack/repos/builtin/packages/ants/package.py b/var/spack/repos/builtin/packages/ants/package.py
new file mode 100644
index 0000000000..866301c1e7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ants/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Ants(CMakePackage):
+    """ANTs extracts information from complex datasets that include imaging.
+       Paired with ANTsR (answer), ANTs is useful for managing, interpreting
+       and visualizing multidimensional data. ANTs is popularly considered a
+       state-of-the-art medical image registration and segmentation toolkit.
+       ANTs depends on the Insight ToolKit (ITK), a widely used medical image
+       processing library to which ANTs developers contribute.
+    """
+
+    homepage = "http://stnava.github.io/ANTs/"
+    url      = "https://github.com/ANTsX/ANTs/archive/v2.2.0.tar.gz"
+
+    version('2.2.0', '5661b949268100ac0f7baf6d2702b4dd')
+
+    def install(self, spec, prefix):
+        with working_dir(join_path('spack-build', 'ANTS-build'), create=False):
+            make("install")
+        install_tree('Scripts', prefix.bin)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.set('ANTSPATH', self.prefix.bin)
diff --git a/var/spack/repos/builtin/packages/ape/package.py b/var/spack/repos/builtin/packages/ape/package.py
index dd24c84e5e..c054c06106 100644
--- a/var/spack/repos/builtin/packages/ape/package.py
+++ b/var/spack/repos/builtin/packages/ape/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/aperture-photometry/APT.sh b/var/spack/repos/builtin/packages/aperture-photometry/APT.sh
new file mode 100644
index 0000000000..b51d30626b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/aperture-photometry/APT.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+# convenience wrapper for the aperture jar file
+java -jar APT.jar "$@"
+
diff --git a/var/spack/repos/builtin/packages/aperture-photometry/package.py b/var/spack/repos/builtin/packages/aperture-photometry/package.py
new file mode 100644
index 0000000000..82d4af33b0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/aperture-photometry/package.py
@@ -0,0 +1,32 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os.path
+
+
+class AperturePhotometry(Package):
+    """Aperture Photometry Tool APT is software for astronomical research"""
+
+    homepage = "http://www.aperturephotometry.org/aptool/"
+    url      = "http://www.aperturephotometry.org/aptool/wp-content/plugins/download-monitor/download.php?id=1"
+
+    version('2.7.2', '2beca6aac14c5e0a94d115f81edf0caa9ec83dc9d32893ea00ee376c9360deb0', extension='tar.gz')
+
+    depends_on('java')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        jar_file = 'APT.jar'
+        install(jar_file, prefix.bin)
+        java = join_path(self.spec['java'].prefix, 'bin', 'java')
+        script_sh = join_path(os.path.dirname(__file__), "APT.sh")
+        script = join_path(prefix.bin, "apt")
+        install(script_sh, script)
+        set_executable(script)
+        kwargs = {'ignore_absent': False, 'backup': False, 'string': False}
+        filter_file('^java', java, script, **kwargs)
+        filter_file('APT.jar', join_path(prefix.bin, 'APT.jar'),
+                    script, **kwargs)
diff --git a/var/spack/repos/builtin/packages/apex/package.py b/var/spack/repos/builtin/packages/apex/package.py
index 50f74f6220..b78b183021 100644
--- a/var/spack/repos/builtin/packages/apex/package.py
+++ b/var/spack/repos/builtin/packages/apex/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/apple-libunwind/package.py b/var/spack/repos/builtin/packages/apple-libunwind/package.py
new file mode 100644
index 0000000000..ced31d20e8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/apple-libunwind/package.py
@@ -0,0 +1,79 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class AppleLibunwind(Package):
+    """Placeholder package for Apple's analogue to non-GNU libunwind"""
+
+    homepage = "https://opensource.apple.com/source/libunwind/libunwind-35.3/"
+
+    provides('unwind')
+
+    # The 'conflicts' directive only accepts valid spack specs;
+    # platforms cannot be negated -- 'platform!=darwin' is not a valid
+    # spec -- so expressing a conflict for any platform that isn't
+    # Darwin must be expressed by listing a conflict with every
+    # platform that isn't Darwin/macOS
+    conflicts('platform=linux')
+    conflicts('platform=bgq')
+    conflicts('platform=cray')
+
+    # Override the fetcher method to throw a useful error message;
+    # avoids GitHub issue (#7061) in which the opengl placeholder
+    # package threw a generic, uninformative error during the `fetch`
+    # step,
+    @property
+    def fetcher(self):
+        msg = """This package is intended to be a placeholder for Apple's
+        system-provided, non-GNU-compatible libunwind library.
+
+        Add to your packages.yaml:
+
+        packages:
+          apple-libunwind:
+            paths:
+              apple-libunwind@35.3: /usr
+            buildable: False
+
+        """
+        raise InstallError(msg)
+
+    def install(self, spec, prefix):
+        pass
+
+    @property
+    def libs(self):
+        """Export the Apple libunwind library. The Apple libunwind library
+        cannot be linked to directly using an absolute path; doing so
+        will cause the linker to throw an error 'cannot link directly
+        with /usr/lib/system/libunwind.dylib' and the linker will
+        suggest linking with System.framework instead. Linking to this
+        framework is equivalent to linking with libSystem.dylib, which
+        can be confirmed on a macOS system by executing at a terminal
+        the command `ls -l
+        /System/Library/Frameworks/System.Framework` -- the file
+        "System" is a symlink to `/usr/lib/libSystem.B.dylib`, and
+        `/usr/lib/libSystem.dylib` also symlinks to this file.
+
+        Running `otool -L /usr/lib/libSystem.dylib` confirms that
+        it will link dynamically to `/usr/lib/system/libunwind.dylib`.
+
+        """
+        libs = find_libraries('libSystem',
+                              self.prefix.lib,
+                              shared=True, recursive=False)
+        if libs:
+            return libs
+        return None
+
+    @property
+    def headers(self):
+        """ Export the Apple libunwind header
+        """
+        hdrs = HeaderList(find(self.prefix.include, 'libunwind.h',
+                               recursive=False))
+        return hdrs or None
diff --git a/var/spack/repos/builtin/packages/applewmproto/package.py b/var/spack/repos/builtin/packages/applewmproto/package.py
index 170df5d570..231becb6b2 100644
--- a/var/spack/repos/builtin/packages/applewmproto/package.py
+++ b/var/spack/repos/builtin/packages/applewmproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Applewmproto(AutotoolsPackage):
 
     version('1.4.2', 'ecc8a4424a893ce120f5652dba62e9e6')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/appres/package.py b/var/spack/repos/builtin/packages/appres/package.py
index 87f5c2ff96..ab798eb4c2 100644
--- a/var/spack/repos/builtin/packages/appres/package.py
+++ b/var/spack/repos/builtin/packages/appres/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,5 +21,5 @@ class Appres(AutotoolsPackage):
     depends_on('libxt')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/apr-util/package.py b/var/spack/repos/builtin/packages/apr-util/package.py
index 1b68584530..0f237e8e6f 100644
--- a/var/spack/repos/builtin/packages/apr-util/package.py
+++ b/var/spack/repos/builtin/packages/apr-util/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/apr/package.py b/var/spack/repos/builtin/packages/apr/package.py
index f78b229229..a0e2e9f52e 100644
--- a/var/spack/repos/builtin/packages/apr/package.py
+++ b/var/spack/repos/builtin/packages/apr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/aragorn/package.py b/var/spack/repos/builtin/packages/aragorn/package.py
new file mode 100644
index 0000000000..3bd4878770
--- /dev/null
+++ b/var/spack/repos/builtin/packages/aragorn/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Aragorn(Package):
+    """ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide
+    sequences."""
+
+    homepage = "http://mbio-serv2.mbioekol.lu.se/ARAGORN"
+    url      = "http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/aragorn1.2.38.tgz"
+
+    version('1.2.38', '1df0ed600069e6f520e5cd989de1eaf0')
+
+    phases = ['build', 'install']
+
+    def build(self, spec, prefix):
+        cc = Executable(spack_cc)
+        cc('-O3', '-ffast-math', '-finline-functions',
+           '-oaragorn', 'aragorn' + format(spec.version.dotted) + '.c')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('aragorn', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/archer/package.py b/var/spack/repos/builtin/packages/archer/package.py
index 87ced1051a..fa326d13c7 100644
--- a/var/spack/repos/builtin/packages/archer/package.py
+++ b/var/spack/repos/builtin/packages/archer/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/argobots/package.py b/var/spack/repos/builtin/packages/argobots/package.py
new file mode 100644
index 0000000000..3df5a2039e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/argobots/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Argobots(AutotoolsPackage):
+    """Argobots, which was developed as a part of the Argo project, is
+    a lightweight runtime system that supports integrated computation
+    and data movement with massive concurrency. It will directly
+    leverage the lowest-level constructs in the hardware and OS:
+    lightweight notification mechanisms, data movement engines, memory
+    mapping, and data placement strategies. It consists of an
+    execution model and a memory model."""
+
+    homepage = "http://www.argobots.org/"
+    url      = "https://github.com/pmodels/argobots/releases/download/v1.0b1/argobots-1.0b1.tar.gz"
+
+    version("1.0b1", "5eeab7b2c639d08bbea22db3026cdf39")
+    version("1.0a1", "9d29d57d14d718f93b505178f6ba3e08")
diff --git a/var/spack/repos/builtin/packages/argp-standalone/argp-fmtstream.h.patch b/var/spack/repos/builtin/packages/argp-standalone/argp-fmtstream.h.patch
new file mode 100644
index 0000000000..b0a518fc67
--- /dev/null
+++ b/var/spack/repos/builtin/packages/argp-standalone/argp-fmtstream.h.patch
@@ -0,0 +1,11 @@
+--- argp-fmtstream.h.orig	2003-12-11 09:37:05.000000000 +0100
++++ argp-fmtstream.h	2011-08-12 11:56:43.000000000 +0200
+@@ -192,7 +192,7 @@
+ extern int _argp_fmtstream_ensure (argp_fmtstream_t __fs, size_t __amount);
+ extern int __argp_fmtstream_ensure (argp_fmtstream_t __fs, size_t __amount);
+ 
+-#ifdef __OPTIMIZE__
++#if defined(__OPTIMIZE__) && !defined(__clang__)
+ /* Inline versions of above routines.  */
+
+ #if !_LIBC
\ No newline at end of file
diff --git a/var/spack/repos/builtin/packages/argp-standalone/package.py b/var/spack/repos/builtin/packages/argp-standalone/package.py
new file mode 100644
index 0000000000..1f82edbf87
--- /dev/null
+++ b/var/spack/repos/builtin/packages/argp-standalone/package.py
@@ -0,0 +1,31 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class ArgpStandalone(AutotoolsPackage):
+    """Standalone version of the argp interface from glibc for parsing
+       unix-style arguments. """
+
+    homepage = "https://www.lysator.liu.se/~nisse/misc"
+    url      = "https://www.lysator.liu.se/~nisse/misc/argp-standalone-1.3.tar.gz"
+
+    version('1.3', '720704bac078d067111b32444e24ba69')
+
+    # Homebrew (https://github.com/Homebrew/homebrew-core) patches
+    # argp-standalone to work on Darwin; the patchfile below was taken
+    # from
+    # https://raw.githubusercontent.com/Homebrew/formula-patches/b5f0ad3/argp-standalone/patch-argp-fmtstream.h
+    patch('argp-fmtstream.h.patch', 0, 'platform=darwin', '.')
+
+    def install(self, spec, prefix):
+        make('install')
+        make('check')
+        mkdirp(self.spec.prefix.lib)
+        install('libargp.a', join_path(self.spec.prefix.lib, 'libargp.a'))
+        mkdirp(self.spec.prefix.include)
+        install('argp.h', join_path(self.spec.prefix.include, 'argp.h'))
diff --git a/var/spack/repos/builtin/packages/argtable/package.py b/var/spack/repos/builtin/packages/argtable/package.py
index f622e29837..cc280a1f7c 100644
--- a/var/spack/repos/builtin/packages/argtable/package.py
+++ b/var/spack/repos/builtin/packages/argtable/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/arlecore/package.py b/var/spack/repos/builtin/packages/arlecore/package.py
index 69de30423d..e873aa8ffb 100644
--- a/var/spack/repos/builtin/packages/arlecore/package.py
+++ b/var/spack/repos/builtin/packages/arlecore/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-import distutils.dir_util
 
 
 class Arlecore(Package):
@@ -37,4 +17,4 @@ class Arlecore(Package):
     depends_on('r', type=('build', 'run'))
 
     def install(self, spec, prefix):
-        distutils.dir_util.copy_tree(".", prefix)
+        install_tree('.', prefix)
diff --git a/var/spack/repos/builtin/packages/armadillo/package.py b/var/spack/repos/builtin/packages/armadillo/package.py
index 2037f552d8..f538b2a6ce 100644
--- a/var/spack/repos/builtin/packages/armadillo/package.py
+++ b/var/spack/repos/builtin/packages/armadillo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/arpack-ng/package.py b/var/spack/repos/builtin/packages/arpack-ng/package.py
index a784baf1cc..b6b87f58fe 100644
--- a/var/spack/repos/builtin/packages/arpack-ng/package.py
+++ b/var/spack/repos/builtin/packages/arpack-ng/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -54,8 +35,13 @@ class ArpackNg(Package):
     """
 
     homepage = 'https://github.com/opencollab/arpack-ng'
-    url = 'https://github.com/opencollab/arpack-ng/archive/3.3.0.tar.gz'
+    url      = 'https://github.com/opencollab/arpack-ng/archive/3.3.0.tar.gz'
+    git      = 'https://github.com/opencollab/arpack-ng.git'
 
+    version('develop', branch='master')
+    version('3.6.3', sha256='64f3551e5a2f8497399d82af3076b6a33bf1bc95fc46bbcabe66442db366f453')
+    version('3.6.2', sha256='673c8202de996fd3127350725eb1818e534db4e79de56d5dcee8c00768db599a')
+    version('3.6.0', 'f2607c1d5f80e922d55751fbed86a8ec')
     version('3.5.0', '9762c9ae6d739a9e040f8201b1578874')
     version('3.4.0', 'ae9ca13f2143a7ea280cb0e2fd4bfae4')
     version('3.3.0', 'ed3648a23f0a868a43ef44c97a21bad5')
@@ -91,7 +77,7 @@ class ArpackNg(Package):
             libraries = ['libparpack'] + libraries
 
         return find_libraries(
-            libraries, root=self.prefix, shared=True, recurse=True
+            libraries, root=self.prefix, shared=True, recursive=True
         )
 
     @when('@3.4.0:')
diff --git a/var/spack/repos/builtin/packages/arrow/package.py b/var/spack/repos/builtin/packages/arrow/package.py
new file mode 100644
index 0000000000..7610d1fae0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/arrow/package.py
@@ -0,0 +1,64 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Arrow(CMakePackage):
+    """A cross-language development platform for in-memory data.
+
+    This package contains the C++ bindings.
+    """
+
+    homepage = "http://arrow.apache.org"
+    url      = "https://github.com/apache/arrow/archive/apache-arrow-0.9.0.tar.gz"
+
+    version('0.11.0', '0ac629a7775d86108e403eb66d9f1a3d3bdd6b3a497a86228aa4e8143364b7cc')
+    version('0.9.0', 'ebbd36c362b9e1d398ca612f6d2531ec')
+    version('0.8.0', '56436f6f61ccc68686b7e0ea30bf4d09')
+
+    depends_on('boost@1.60:')
+    depends_on('cmake@3.2.0:', type='build')
+    depends_on('flatbuffers@1.8.0 build_type=Release')  # only Release contains flatc
+    depends_on('python', when='+python')
+    depends_on('py-numpy', when='+python')
+    depends_on('rapidjson')
+    depends_on('snappy~shared')
+    depends_on('zlib+pic')
+    depends_on('zstd+pic')
+
+    variant('build_type', default='Release',
+            description='CMake build type',
+            values=('Debug', 'FastDebug', 'Release'))
+    variant('python', default=False, description='Build Python interface')
+    variant('parquet', default=False, description='Build Parquet interface')
+
+    root_cmakelists_dir = 'cpp'
+
+    def patch(self):
+        """Prevent `-isystem /usr/include` from appearing, since this confuses gcc.
+        """
+        filter_file(r'(include_directories\()SYSTEM ',
+                    r'\1',
+                    'cpp/cmake_modules/ThirdpartyToolchain.cmake')
+
+    def cmake_args(self):
+        args = [
+            "-DARROW_USE_SSE=ON",
+            "-DARROW_BUILD_SHARED=ON",
+            "-DARROW_BUILD_STATIC=OFF",
+            "-DARROW_BUILD_TESTS=OFF",
+            "-DARROW_WITH_BROTLI=OFF",
+            "-DARROW_WITH_LZ4=OFF",
+        ]
+        if self.spec.satisfies('+python'):
+            args.append("-DARROW_PYTHON:BOOL=ON")
+        if self.spec.satisfies('+parquet'):
+            args.append("-DARROW_PARQUET:BOOL=ON")
+        for dep in ('flatbuffers', 'rapidjson', 'snappy', 'zlib', 'zstd'):
+            args.append("-D{0}_HOME={1}".format(dep.upper(),
+                                                self.spec[dep].prefix))
+        args.append("-DZLIB_LIBRARIES={0}".format(self.spec['zlib'].libs))
+        return args
diff --git a/var/spack/repos/builtin/packages/ascent/package.py b/var/spack/repos/builtin/packages/ascent/package.py
index 854bf1e909..22dd639c1a 100644
--- a/var/spack/repos/builtin/packages/ascent/package.py
+++ b/var/spack/repos/builtin/packages/ascent/package.py
@@ -1,28 +1,7 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack import *
 
@@ -47,14 +26,11 @@ class Ascent(Package):
     simulations."""
 
     homepage = "https://github.com/Alpine-DAV/ascent"
-    url      = "https://github.com/Alpine-DAV/ascent"
+    git      = "https://github.com/Alpine-DAV/ascent.git"
 
     maintainers = ['cyrush']
 
-    version('develop',
-            git='https://github.com/Alpine-DAV/ascent.git',
-            branch='develop',
-            submodules=True)
+    version('develop', branch='develop', submodules=True)
 
     ###########################################################################
     # package variants
@@ -78,7 +54,7 @@ class Ascent(Package):
     variant("tbb", default=True, description="Build tbb support")
     variant("cuda", default=False, description="Build cuda support")
 
-    variant("adios", default=True, description="Build Adios filter support")
+    variant("adios", default=False, description="Build Adios filter support")
 
     # variants for dev-tools (docs, etc)
     variant("doc", default=False, description="Build Conduit's documentation")
@@ -88,7 +64,7 @@ class Ascent(Package):
     ###########################################################################
 
     depends_on("cmake", when="+cmake")
-    depends_on("conduit")
+    depends_on("conduit@master")
 
     #######################
     # Python
@@ -97,9 +73,7 @@ class Ascent(Package):
     # causes duplicate state issues when running compiled python modules.
     depends_on("python+shared")
     extends("python", when="+python")
-    # TODO: blas and lapack are disabled due to build
-    # issues Cyrus experienced on OSX 10.11.6
-    depends_on("py-numpy~blas~lapack", when="+python", type=('build', 'run'))
+    depends_on("py-numpy", when="+python", type=('build', 'run'))
 
     #######################
     # MPI
@@ -125,7 +99,13 @@ class Ascent(Package):
         Build and install Conduit.
         """
         with working_dir('spack-build', create=True):
-            host_cfg_fname = self.create_host_config(spec, prefix)
+            py_site_pkgs_dir = None
+            if "+python" in spec:
+                py_site_pkgs_dir = site_packages_dir
+
+            host_cfg_fname = self.create_host_config(spec,
+                                                     prefix,
+                                                     py_site_pkgs_dir)
             cmake_args = []
             # if we have a static build, we need to avoid any of
             # spack's default cmake settings related to rpaths
@@ -140,12 +120,26 @@ class Ascent(Package):
             cmake(*cmake_args)
             make()
             make("install")
-            # TODO also copy host_cfg_fname into install
+            # install copy of host config for provenance
+            install(host_cfg_fname, prefix)
 
-    def create_host_config(self, spec, prefix):
+    def create_host_config(self, spec, prefix, py_site_pkgs_dir=None):
         """
         This method creates a 'host-config' file that specifies
         all of the options used to configure and build ascent.
+
+        For more details about 'host-config' files see:
+            http://ascent.readthedocs.io/en/latest/BuildingAscent.html
+
+        Note:
+          The `py_site_pkgs_dir` arg exists to allow a package that
+          subclasses this package provide a specific site packages
+          dir when calling this function. `py_site_pkgs_dir` should
+          be an absolute path or `None`.
+
+          This is necessary because the spack `site_packages_dir`
+          var will not exist in the base class. For more details
+          on this issue see: https://github.com/spack/spack/issues/6261
         """
 
         #######################
@@ -184,9 +178,9 @@ class Ascent(Package):
                 raise RuntimeError(msg)
             cmake_exe = cmake_exe.path
 
-        host_cfg_fname = "%s-%s-%s.cmake" % (socket.gethostname(),
-                                             sys_type,
-                                             spec.compiler)
+        host_cfg_fname = "%s-%s-%s-ascent.cmake" % (socket.gethostname(),
+                                                    sys_type,
+                                                    spec.compiler)
 
         cfg = open(host_cfg_fname, "w")
         cfg.write("##################################\n")
@@ -246,10 +240,10 @@ class Ascent(Package):
             cfg.write("# python from spack \n")
             cfg.write(cmake_cache_entry("PYTHON_EXECUTABLE",
                       spec['python'].command.path))
-            # install module to standard style site packages dir
-            # so we can support spack activate
-            cfg.write(cmake_cache_entry("PYTHON_MODULE_INSTALL_PREFIX",
-                                        site_packages_dir))
+            # only set dest python site packages dir if passed
+            if py_site_pkgs_dir:
+                cfg.write(cmake_cache_entry("PYTHON_MODULE_INSTALL_PREFIX",
+                                            py_site_pkgs_dir))
         else:
             cfg.write(cmake_cache_entry("ENABLE_PYTHON", "OFF"))
 
@@ -260,10 +254,6 @@ class Ascent(Package):
             sphinx_build_exe = join_path(spec['py-sphinx'].prefix.bin,
                                          "sphinx-build")
             cfg.write(cmake_cache_entry("SPHINX_EXECUTABLE", sphinx_build_exe))
-
-            cfg.write("# doxygen from uberenv\n")
-            doxygen_exe = spec['doxygen'].command.path
-            cfg.write(cmake_cache_entry("DOXYGEN_EXECUTABLE", doxygen_exe))
         else:
             cfg.write(cmake_cache_entry("ENABLE_DOCS", "OFF"))
 
@@ -280,6 +270,16 @@ class Ascent(Package):
                                         spec['mpi'].mpicxx))
             cfg.write(cmake_cache_entry("MPI_Fortran_COMPILER",
                                         spec['mpi'].mpifc))
+            mpiexe_bin = join_path(spec['mpi'].prefix.bin, 'mpiexec')
+            if os.path.isfile(mpiexe_bin):
+                # starting with cmake 3.10, FindMPI expects MPIEXEC_EXECUTABLE
+                # vs the older versions which expect MPIEXEC
+                if self.spec["cmake"].satisfies('@3.10:'):
+                    cfg.write(cmake_cache_entry("MPIEXEC_EXECUTABLE",
+                                                mpiexe_bin))
+                else:
+                    cfg.write(cmake_cache_entry("MPIEXEC",
+                                                mpiexe_bin))
         else:
             cfg.write(cmake_cache_entry("ENABLE_MPI", "OFF"))
 
diff --git a/var/spack/repos/builtin/packages/asciidoc/package.py b/var/spack/repos/builtin/packages/asciidoc/package.py
index 885fc02404..f186961cc1 100644
--- a/var/spack/repos/builtin/packages/asciidoc/package.py
+++ b/var/spack/repos/builtin/packages/asciidoc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/aspa/package.py b/var/spack/repos/builtin/packages/aspa/package.py
index 3686ffe4ea..2081ed73e1 100644
--- a/var/spack/repos/builtin/packages/aspa/package.py
+++ b/var/spack/repos/builtin/packages/aspa/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
 
@@ -32,12 +13,14 @@ class Aspa(MakefilePackage):
     demands upon the exascale ecosystem that need to be identified and
     quantified.
     """
-    tags = ['proxy-app']
+
     homepage = "http://www.exmatex.org/aspa.html"
-    url = "https://github.com/exmatex/ASPA/archive/master.tar.gz"
+    git      = "https://github.com/exmatex/ASPA.git"
+
+    tags = ['proxy-app']
+
+    version('master', branch='master')
 
-    version('master', git='https://github.com/exmatex/ASPA.git',
-            description='master')
     variant('mpi', default=True, description='Build with MPI Support')
 
     depends_on('lapack')
diff --git a/var/spack/repos/builtin/packages/aspcud/package.py b/var/spack/repos/builtin/packages/aspcud/package.py
new file mode 100644
index 0000000000..ca4ec49350
--- /dev/null
+++ b/var/spack/repos/builtin/packages/aspcud/package.py
@@ -0,0 +1,34 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Aspcud(CMakePackage):
+    """Aspcud: Package dependency solver
+
+       Aspcud is a solver for package dependencies. A package universe
+       and a request to install, remove, or upgrade packages have to
+       be encoded in the CUDF format. Such a CUDF document can then be
+       passed to aspcud along with an optimization criteria to obtain
+       a solution to the given package problem."""
+
+    homepage = "https://potassco.org/aspcud"
+    url      = "https://github.com/potassco/aspcud/archive/v1.9.4.tar.gz"
+
+    version('1.9.4', '35e5c663a25912e4bdc94f168e827ed2')
+
+    depends_on('boost', type=('build'))
+    depends_on('cmake', type=('build'))
+    depends_on('re2c', type=('build'))
+    depends_on('clingo')
+
+    def cmake_args(self):
+        spec = self.spec
+        gringo_path = join_path(spec['clingo'].prefix.bin, 'gringo')
+        clasp_path = join_path(spec['clingo'].prefix.bin, 'clasp')
+        args = ['-DASPCUD_GRINGO_PATH={0}'.format(gringo_path),
+                '-DASPCUD_CLASP_PATH={0}'.format(clasp_path)]
+        return args
diff --git a/var/spack/repos/builtin/packages/aspect/package.py b/var/spack/repos/builtin/packages/aspect/package.py
new file mode 100644
index 0000000000..a4ab96e8cc
--- /dev/null
+++ b/var/spack/repos/builtin/packages/aspect/package.py
@@ -0,0 +1,39 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Aspect(CMakePackage):
+    """Parallel, extendible finite element code to simulate convection in the
+    Earth's mantle and elsewhere."""
+
+    homepage = "https://aspect.geodynamics.org"
+    url      = "https://github.com/geodynamics/aspect/releases/download/v2.0.0/aspect-2.0.0.tar.gz"
+    git      = "https://github.com/geodynamics/aspect.git"
+
+    maintainers = ['tjhei']
+
+    version('develop', branch='master')
+    version('2.0.1', sha256='0bf5600c42afce9d39c1d285b0654ecfdeb0f30e9f3421651c95f54ca01ac165')
+    version('2.0.0', sha256='d485c07f54248e824bdfa35f3eec8971b65e8b7114552ffa2c771bc0dede8cc0')
+
+    variant('build_type', default='Release',
+            description='The build type to build',
+            values=('Debug', 'Release'))
+    variant('gui', default=False, description='Enable the deal.II parameter GUI')
+    variant('fpe', default=False, description='Enable floating point exception checks')
+
+    depends_on('dealii+p4est+trilinos+mpi')
+    depends_on('dealii-parameter-gui', when='+gui')
+
+    def cmake_args(self):
+        return [
+            '-DASPECT_USE_FP_EXCEPTIONS=%s' %
+            ('ON' if '+fpe' in self.spec else 'OFF')
+        ]
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.set('Aspect_DIR', self.prefix)
diff --git a/var/spack/repos/builtin/packages/aspell/darwin.patch b/var/spack/repos/builtin/packages/aspell/darwin.patch
new file mode 100644
index 0000000000..54ec257637
--- /dev/null
+++ b/var/spack/repos/builtin/packages/aspell/darwin.patch
@@ -0,0 +1,20 @@
++++ a/interfaces/cc/aspell.h
+--- b/interfaces/cc/aspell.h
+@@ -236,7 +236,7 @@
+ 
+ /******************************** errors ********************************/
+ 
+-
++#ifndef __cplusplus
+ extern const struct AspellErrorInfo * const aerror_other;
+ extern const struct AspellErrorInfo * const aerror_operation_not_supported;
+ extern const struct AspellErrorInfo * const   aerror_cant_copy;
+@@ -322,7 +322,7 @@
+ extern const struct AspellErrorInfo * const   aerror_bad_magic;
+ extern const struct AspellErrorInfo * const aerror_expression;
+ extern const struct AspellErrorInfo * const   aerror_invalid_expression;
+-
++#endif
+ 
+ /******************************* speller *******************************/
+ 
diff --git a/var/spack/repos/builtin/packages/aspell/package.py b/var/spack/repos/builtin/packages/aspell/package.py
index c24a50ef39..5dbe7ed301 100644
--- a/var/spack/repos/builtin/packages/aspell/package.py
+++ b/var/spack/repos/builtin/packages/aspell/package.py
@@ -1,31 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from llnl.util.link_tree import LinkTree
-import spack.store
-from spack.package import ExtensionError, ExtensionConflictError
 
 
 # See also: AspellDictPackage
@@ -40,46 +18,4 @@ class Aspell(AutotoolsPackage):
 
     version('0.60.6.1', 'e66a9c9af6a60dc46134fdacf6ce97d7')
 
-    # The dictionaries install all their bits into their prefix.lib dir,
-    # we want to link them into aspell's dict-dir.
-    # These are identical to what's in spack/package.py except
-    # for using:
-    #   - extension.prefix.lib instead of extension.prefix in LinkTree()
-    #   - dest_dir instead of self.prefix in tree.(find_conflict|merge)()
-    def activate(self, extension, **kwargs):
-        extensions_layout = kwargs.get("extensions_layout",
-                                       spack.store.extensions)
-        if extensions_layout is not spack.store.extensions:
-            raise ExtensionError(
-                'aspell does not support non-global extensions')
-
-        aspell = which(self.prefix.bin.aspell)
-        dest_dir = aspell('dump', 'config', 'dict-dir', output=str).strip()
-        tree = LinkTree(extension.prefix.lib)
-
-        def ignore(filename):
-            return (filename in spack.store.layout.hidden_file_paths or
-                    kwargs.get('ignore', lambda f: False)(filename))
-
-        conflict = tree.find_conflict(dest_dir, ignore=ignore)
-        if conflict:
-            raise ExtensionConflictError(conflict)
-
-        tree.merge(dest_dir, ignore=ignore)
-
-    def deactivate(self, extension, **kwargs):
-        extensions_layout = kwargs.get("extensions_layout",
-                                       spack.store.extensions)
-        if extensions_layout is not spack.store.extensions:
-            raise ExtensionError(
-                'aspell does not support non-global extensions')
-
-        aspell = which(self.prefix.bin.aspell)
-        dest_dir = aspell('dump', 'config', 'dict-dir', output=str).strip()
-
-        def ignore(filename):
-            return (filename in spack.store.layout.hidden_file_paths or
-                    kwargs.get('ignore', lambda f: False)(filename))
-
-        tree = LinkTree(extension.prefix.lib)
-        tree.unmerge(dest_dir, ignore=ignore)
+    patch('darwin.patch', when='platform=darwin')
diff --git a/var/spack/repos/builtin/packages/aspell6-de/package.py b/var/spack/repos/builtin/packages/aspell6-de/package.py
index 5a4b1c82d8..5468829058 100644
--- a/var/spack/repos/builtin/packages/aspell6-de/package.py
+++ b/var/spack/repos/builtin/packages/aspell6-de/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,6 +10,6 @@ class Aspell6De(AspellDictPackage):
     """German (de) dictionary for aspell."""
 
     homepage = "http://aspell.net/"
-    url      = "ftp://ftp.gnu.org/gnu/aspell/dict/de/aspell6-de-20030222-1.tar.bz2"
+    url      = "https://ftpmirror.gnu.org/aspell/dict/de/aspell6-de-20030222-1.tar.bz2"
 
     version('6-de-20030222-1', '5950c5c8a36fc93d4d7616591bace6a6')
diff --git a/var/spack/repos/builtin/packages/aspell6-en/package.py b/var/spack/repos/builtin/packages/aspell6-en/package.py
index 38d6caeabd..d49cb61188 100644
--- a/var/spack/repos/builtin/packages/aspell6-en/package.py
+++ b/var/spack/repos/builtin/packages/aspell6-en/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,6 +10,6 @@ class Aspell6En(AspellDictPackage):
     """English (en) dictionary for aspell."""
 
     homepage = "http://aspell.net/"
-    url      = "ftp://ftp.gnu.org/gnu/aspell/dict/en/aspell6-en-2017.01.22-0.tar.bz2"
+    url      = "https://ftpmirror.gnu.org/aspell/dict/en/aspell6-en-2017.01.22-0.tar.bz2"
 
     version('2017.01.22-0', 'a6e002076574de9dc4915967032a1dab')
diff --git a/var/spack/repos/builtin/packages/aspell6-es/package.py b/var/spack/repos/builtin/packages/aspell6-es/package.py
index 84a798d41a..3e11115e9a 100644
--- a/var/spack/repos/builtin/packages/aspell6-es/package.py
+++ b/var/spack/repos/builtin/packages/aspell6-es/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,6 +10,6 @@ class Aspell6Es(AspellDictPackage):
     """Spanish (es) dictionary for aspell."""
 
     homepage = "http://aspell.net/"
-    url      = "ftp://ftp.gnu.org/gnu/aspell/dict/es/aspell6-es-1.11-2.tar.bz2"
+    url      = "https://ftpmirror.gnu.org/aspell/dict/es/aspell6-es-1.11-2.tar.bz2"
 
     version('1.11-2', '8406336a89c64e47e96f4153d0af70c4')
diff --git a/var/spack/repos/builtin/packages/aspera-cli/package.py b/var/spack/repos/builtin/packages/aspera-cli/package.py
new file mode 100644
index 0000000000..3a903208f1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/aspera-cli/package.py
@@ -0,0 +1,34 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+from glob import glob
+
+
+class AsperaCli(Package):
+    """The Aspera CLI client for the Fast and Secure Protocol (FASP)."""
+
+    homepage = "https://asperasoft.com"
+    url      = "https://download.asperasoft.com/download/sw/cli/3.7.7/aspera-cli-3.7.7.608.927cce8-linux-64-release.sh"
+
+    version('3.7.7', 'e92140d809e7e65112a5d1cd49c442cf',
+            url='https://download.asperasoft.com/download/sw/cli/3.7.7/aspera-cli-3.7.7.608.927cce8-linux-64-release.sh',
+            expand=False)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PATH', self.prefix.cli.bin)
+
+    def install(self, spec, prefix):
+        runfile = glob(join_path(self.stage.path, 'aspera-cli*.sh'))[0]
+        # Update destination path
+        filter_file('INSTALL_DIR=~/.aspera',
+                    'INSTALL_DIR=%s' % prefix,
+                    runfile,
+                    string=True)
+        # Install
+        chmod = which('chmod')
+        chmod('+x', runfile)
+        runfile = which(runfile)
+        runfile()
diff --git a/var/spack/repos/builtin/packages/assimp/package.py b/var/spack/repos/builtin/packages/assimp/package.py
index dd9b414772..3852df5bc4 100644
--- a/var/spack/repos/builtin/packages/assimp/package.py
+++ b/var/spack/repos/builtin/packages/assimp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,12 +11,25 @@ class Assimp(CMakePackage):
     import various well-known 3D model formats in a uniform manner."""
 
     homepage = "https://www.assimp.org"
-    url      = "https://github.com/assimp/assimp/archive/v3.3.1.tar.gz"
+    url      = "https://github.com/assimp/assimp/archive/v4.0.1.tar.gz"
 
     version('4.0.1', '23a6301c728a413aafbfa1cca19ba91f')
 
+    variant('shared',  default=True,
+            description='Enables the build of shared libraries')
+
     depends_on('boost')
 
     def cmake_args(self):
-        args = ['-DASSIMP_BUILD_TESTS=OFF']
+        args = [
+            '-DASSIMP_BUILD_TESTS=OFF',
+            '-DBUILD_SHARED_LIBS:BOOL=%s' % (
+                'ON' if '+shared' in self.spec else 'OFF'),
+        ]
         return args
+
+    def flag_handler(self, name, flags):
+        flags = list(flags)
+        if name == 'cxxflags':
+            flags.append(self.compiler.cxx11_flag)
+        return (None, None, flags)
diff --git a/var/spack/repos/builtin/packages/astra/package.py b/var/spack/repos/builtin/packages/astra/package.py
index 694a394c69..267fedddf6 100644
--- a/var/spack/repos/builtin/packages/astra/package.py
+++ b/var/spack/repos/builtin/packages/astra/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/astral/package.py b/var/spack/repos/builtin/packages/astral/package.py
index 11d8b0ed23..8c9e25d1e9 100644
--- a/var/spack/repos/builtin/packages/astral/package.py
+++ b/var/spack/repos/builtin/packages/astral/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os.path
 
@@ -36,6 +17,7 @@ class Astral(Package):
     version('4.10.7', '38c81020570254e3f5c75d6c3c27fc6d')
 
     depends_on('java', type=('build', 'run'))
+    depends_on('zip', type='build')
 
     phases = ['build', 'install']
 
diff --git a/var/spack/repos/builtin/packages/astyle/package.py b/var/spack/repos/builtin/packages/astyle/package.py
index 62e7204168..862f6d8691 100644
--- a/var/spack/repos/builtin/packages/astyle/package.py
+++ b/var/spack/repos/builtin/packages/astyle/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import sys
 
@@ -32,12 +13,13 @@ class Astyle(MakefilePackage):
     """
 
     homepage = "http://astyle.sourceforge.net/"
-    # homepage is dead use Gentoo Mirror
-    # url = "http://downloads.sourceforge.net/project/astyle/astyle/astyle%202.04/astyle_2.04_linux.tar.gz"
-    url = "http://distfiles.gentoo.org/distfiles/astyle_3.0.1_linux.tar.gz"
+    url = "https://sourceforge.net/projects/astyle/files/astyle/astyle%203.0.1/astyle_3.0.1_linux.tar.gz"
+    # Gentoo alternative
+    # url = "http://distfiles.gentoo.org/distfiles/astyle_3.0.1_linux.tar.gz"
 
     maintainers = ['davydden']
 
+    version('3.1',    '7712622f62661b1d8cb1062d7fedc390')
     version('3.0.1',  'c301f09679efa2e1eb6e6b5fd33788b4')
     version('2.06',   'ff588e7fcede824591cf5b9085df109d')
     version('2.05.1', '4142d178047d7040da3e0e2f1b030a1a')
diff --git a/var/spack/repos/builtin/packages/at-spi2-atk/package.py b/var/spack/repos/builtin/packages/at-spi2-atk/package.py
new file mode 100644
index 0000000000..dc6bf63b6c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/at-spi2-atk/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class AtSpi2Atk(MesonPackage):
+    """The At-Spi2 Atk package contains a library that bridges ATK to
+       At-Spi2 D-Bus service."""
+
+    homepage = "http://www.linuxfromscratch.org/blfs/view/cvs/x/at-spi2-atk.html"
+    url      = "http://ftp.gnome.org/pub/gnome/sources/at-spi2-atk/2.26/at-spi2-atk-2.26.1.tar.xz"
+    list_url = "http://ftp.gnome.org/pub/gnome/sources/at-spi2-atk"
+    list_depth = 1
+
+    version('2.26.2', '355c7916a69513490cb83ad34016b169')
+    version('2.26.1', 'eeec6cead3350dca48a235271c105b3e')
+
+    depends_on('pkgconfig', type='build')
+    depends_on('at-spi2-core@2.28.0:')
+    depends_on('atk@2.28.1:')
+
+    def url_for_version(self, version):
+        """Handle gnome's version-based custom URLs."""
+        url = 'http://ftp.gnome.org/pub/gnome/sources/at-spi2-atk'
+        return url + '/%s/at-spi2-atk-%s.tar.xz' % (version.up_to(2), version)
diff --git a/var/spack/repos/builtin/packages/at-spi2-core/package.py b/var/spack/repos/builtin/packages/at-spi2-core/package.py
new file mode 100644
index 0000000000..868fae2270
--- /dev/null
+++ b/var/spack/repos/builtin/packages/at-spi2-core/package.py
@@ -0,0 +1,39 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class AtSpi2Core(MesonPackage):
+    """The At-Spi2 Core package provides a Service Provider Interface for the
+       Assistive Technologies available on the GNOME platform and a library
+       against which applications can be linked."""
+
+    homepage = "http://www.linuxfromscratch.org/blfs/view/cvs/x/at-spi2-core.html"
+    url      = "http://ftp.gnome.org/pub/gnome/sources/at-spi2-core/2.28/at-spi2-core-2.28.0.tar.xz"
+    list_url = "http://ftp.gnome.org/pub/gnome/sources/at-spi2-core"
+    list_depth = 1
+
+    version('2.28.0', '9c42f79636ed1c0e908b7483d789b32e')
+
+    depends_on('glib@2.56.1:')
+    depends_on('dbus@1.12.8:')
+    depends_on('libx11')
+    depends_on('libxi')
+    depends_on('libxtst', type='build')
+    depends_on('recordproto', type='build')
+    depends_on('inputproto', type='build')
+    depends_on('fixesproto', type='build')
+    depends_on('pkgconfig', type='build')
+    depends_on('python', type='build')
+
+    def url_for_version(self, version):
+        """Handle gnome's version-based custom URLs."""
+        url = 'http://ftp.gnome.org/pub/gnome/sources/at-spi2-core'
+        return url + '/%s/at-spi2-core-%s.tar.xz' % (version.up_to(2), version)
+
+    def setup_environment(self, spack_env, run_env):
+        # this avoids an "import site" error in the build
+        spack_env.unset('PYTHONHOME')
diff --git a/var/spack/repos/builtin/packages/atk/package.py b/var/spack/repos/builtin/packages/atk/package.py
index 93ce88bb8a..ba6a872a69 100644
--- a/var/spack/repos/builtin/packages/atk/package.py
+++ b/var/spack/repos/builtin/packages/atk/package.py
@@ -1,47 +1,33 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class Atk(AutotoolsPackage):
+class Atk(Package):
     """ATK provides the set of accessibility interfaces that are
        implemented by other toolkits and applications. Using the ATK
        interfaces, accessibility tools have full access to view and
        control running applications."""
     homepage = "https://developer.gnome.org/atk/"
-    url      = "http://ftp.gnome.org/pub/gnome/sources/atk/2.14/atk-2.14.0.tar.xz"
+    url      = "http://ftp.gnome.org/pub/gnome/sources/atk/2.28/atk-2.28.1.tar.xz"
+    list_url = "http://ftp.gnome.org/pub/gnome/sources/atk"
+    list_depth = 1
 
+    version('2.28.1', 'dfb5e7474220afa3f4ca7e45af9f3a11')
     version('2.20.0', '5187b0972f4d3905f285540b31395e20')
     version('2.14.0', 'ecb7ca8469a5650581b1227d78051b8b')
 
+    depends_on('meson', type='build', when='@2.28.0:')
     depends_on('glib')
-    depends_on('pkg-config', type='build')
+    depends_on('gettext')
+    depends_on('pkgconfig', type='build')
     depends_on('gobject-introspection')
 
     def url_for_version(self, version):
-        """Handle atk's version-based custom URLs."""
+        """Handle gnome's version-based custom URLs."""
         url = 'http://ftp.gnome.org/pub/gnome/sources/atk'
         return url + '/%s/atk-%s.tar.xz' % (version.up_to(2), version)
 
@@ -50,3 +36,19 @@ class Atk(AutotoolsPackage):
                                self.prefix.share)
         run_env.prepend_path("XDG_DATA_DIRS",
                              self.prefix.share)
+
+    def install(self, spec, prefix):
+        with working_dir('spack-build', create=True):
+            meson('..', *std_meson_args)
+            ninja('-v')
+            ninja('install')
+
+    @when('@:2.27')
+    def install(self, spec, prefix):
+        configure('--prefix={0}'.format(prefix))
+        make()
+        if self.run_tests:
+            make('check')
+        make('install')
+        if self.run_tests:
+            make('installcheck')
diff --git a/var/spack/repos/builtin/packages/atlas/package.py b/var/spack/repos/builtin/packages/atlas/package.py
index 7f5652bad4..0f624ae839 100644
--- a/var/spack/repos/builtin/packages/atlas/package.py
+++ b/var/spack/repos/builtin/packages/atlas/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 
 from spack import *
@@ -37,6 +18,12 @@ class Atlas(Package):
     """
     homepage = "http://math-atlas.sourceforge.net/"
 
+    version('3.11.39', '5f3252fa980f5f060f93edd4669321e2',
+            url='http://sourceforge.net/projects/math-atlas/files/Developer%20%28unstable%29/3.11.39/atlas3.11.39.tar.bz2')
+
+    version('3.11.34', '0b6c5389c095c4c8785fd0f724ec6825',
+            url='http://sourceforge.net/projects/math-atlas/files/Developer%20%28unstable%29/3.11.34/atlas3.11.34.tar.bz2')
+
     version('3.10.3', 'd6ce4f16c2ad301837cfb3dade2f7cef',
             url='https://sourceforge.net/projects/math-atlas/files/Stable/3.10.3/atlas3.10.3.tar.bz2')
 
@@ -50,9 +37,6 @@ class Atlas(Package):
              destination='spack-resource-lapack',
              when='@3:')
 
-    version('3.11.34', '0b6c5389c095c4c8785fd0f724ec6825',
-            url='http://sourceforge.net/projects/math-atlas/files/Developer%20%28unstable%29/3.11.34/atlas3.11.34.tar.bz2')
-
     variant('shared', default=True, description='Builds shared library')
 
     variant(
@@ -139,7 +123,7 @@ class Atlas(Package):
             to_find = ['liblapack'] + interfaces + ['libatlas']
             shared = False
         return find_libraries(
-            to_find, root=self.prefix, shared=shared, recurse=True
+            to_find, root=self.prefix, shared=shared, recursive=True
         )
 
     def install_test(self):
diff --git a/var/spack/repos/builtin/packages/atom-dft/package.py b/var/spack/repos/builtin/packages/atom-dft/package.py
new file mode 100644
index 0000000000..1c42382591
--- /dev/null
+++ b/var/spack/repos/builtin/packages/atom-dft/package.py
@@ -0,0 +1,32 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class AtomDft(MakefilePackage):
+    """ATOM is a program for DFT calculations in atoms and pseudopotential
+       generation."""
+
+    homepage = "https://departments.icmab.es/leem/siesta/Pseudopotentials/"
+    url      = "https://departments.icmab.es/leem/siesta/Pseudopotentials/Code/atom-4.2.6.tgz"
+
+    version('4.2.6', 'c0c80cf349f951601942ed6c7cb0256b')
+
+    depends_on('libgridxc')
+    depends_on('xmlf90')
+
+    def edit(self, spec, prefix):
+        copy('arch.make.sample', 'arch.make')
+
+    @property
+    def build_targets(self):
+        return ['XMLF90_ROOT=%s' % self.spec['xmlf90'].prefix,
+                'GRIDXC_ROOT=%s' % self.spec['libgridxc'].prefix,
+                'FC=fc']
+
+    def install(self, spec, prefix):
+        mkdir(prefix.bin)
+        install('atm', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/atompaw/package.py b/var/spack/repos/builtin/packages/atompaw/package.py
index c86a5c5de5..430f3a4248 100644
--- a/var/spack/repos/builtin/packages/atompaw/package.py
+++ b/var/spack/repos/builtin/packages/atompaw/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/atop/package.py b/var/spack/repos/builtin/packages/atop/package.py
index 6c59ee4dbe..9c8d73b693 100644
--- a/var/spack/repos/builtin/packages/atop/package.py
+++ b/var/spack/repos/builtin/packages/atop/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/augustus/package.py b/var/spack/repos/builtin/packages/augustus/package.py
index d79cde02c5..86cffa20f7 100644
--- a/var/spack/repos/builtin/packages/augustus/package.py
+++ b/var/spack/repos/builtin/packages/augustus/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,11 +11,12 @@ class Augustus(MakefilePackage):
        genomic sequences"""
 
     homepage = "http://bioinf.uni-greifswald.de/augustus/"
-    url      = "http://bioinf.uni-greifswald.de/augustus/binaries/augustus-3.3.tar.gz"
+    url      = "http://bioinf.uni-greifswald.de/augustus/binaries/augustus-3.3.1.tar.gz"
+    list_url = "http://bioinf.uni-greifswald.de/augustus/binaries/old"
 
-    version('3.3',   '9ebe494df78ebf6a43091cfc8551050c')
-    version('3.2.3', 'b8c47ea8d0c45aa7bb9a82626c8ff830',
-            url='http://bioinf.uni-greifswald.de/augustus/binaries/old/augustus-3.2.3.tar.gz')
+    version('3.3.1', '8363ece221c799eb169f47e545efb951')
+    version('3.3',   '93691d9aafc7d3d0e1adf31ec308507f')
+    version('3.2.3', 'b8c47ea8d0c45aa7bb9a82626c8ff830')
 
     depends_on('bamtools')
     depends_on('gsl')
@@ -48,18 +30,28 @@ class Augustus(MakefilePackage):
                             'bamtools'].prefix)
             makefile.filter('INCLUDES = *',
                             'INCLUDES = -I$(BAMTOOLS)/include/bamtools ')
-            makefile.filter('LIBS = -lbamtools -lz',
-                            'LIBS = $(BAMTOOLS)/lib/bamtools'
-                            '/libbamtools.a -lz')
+            if 'bamtools@2.5:' in spec:
+                makefile.filter('LIBS = -lbamtools -lz',
+                                'LIBS = $(BAMTOOLS)/lib64/'
+                                '/libbamtools.a -lz')
+            if 'bamtools@:2.4' in spec:
+                makefile.filter('LIBS = -lbamtools -lz',
+                                'LIBS = $(BAMTOOLS)/lib/bamtools'
+                                '/libbamtools.a -lz')
         with working_dir(join_path('auxprogs', 'bam2hints')):
             makefile = FileFilter('Makefile')
             makefile.filter('# Variable definition',
                             'BAMTOOLS = %s' % self.spec['bamtools'].prefix)
             makefile.filter('INCLUDES = /usr/include/bamtools',
                             'INCLUDES = $(BAMTOOLS)/include/bamtools')
-            makefile.filter('LIBS = -lbamtools -lz',
-                            'LIBS = $(BAMTOOLS)/lib/bamtools'
-                            '/libbamtools.a -lz')
+            if 'bamtools@2.5:' in spec:
+                makefile.filter('LIBS = -lbamtools -lz',
+                                'LIBS = $(BAMTOOLS)/lib64/'
+                                '/libbamtools.a -lz')
+            if 'bamtools@:2.4' in spec:
+                makefile.filter('LIBS = -lbamtools -lz',
+                                'LIBS = $(BAMTOOLS)/lib/bamtools'
+                                '/libbamtools.a -lz')
 
     def install(self, spec, prefix):
         install_tree('bin', join_path(self.spec.prefix, 'bin'))
diff --git a/var/spack/repos/builtin/packages/autoconf/package.py b/var/spack/repos/builtin/packages/autoconf/package.py
index f178a6e264..87d24bc680 100644
--- a/var/spack/repos/builtin/packages/autoconf/package.py
+++ b/var/spack/repos/builtin/packages/autoconf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,7 +10,7 @@ class Autoconf(AutotoolsPackage):
     """Autoconf -- system configuration part of autotools"""
 
     homepage = 'https://www.gnu.org/software/autoconf/'
-    url = 'http://ftp.gnu.org/gnu/autoconf/autoconf-2.69.tar.gz'
+    url      = 'https://ftpmirror.gnu.org/autoconf/autoconf-2.69.tar.gz'
 
     version('2.69', '82d05e03b93e45f5a39b828dc9c6c29b')
     version('2.62', '6c1f3b3734999035d77da5024aab4fbd')
@@ -55,12 +36,11 @@ class Autoconf(AutotoolsPackage):
         # We have to do this after install because otherwise the install
         # target will try to rebuild the binaries (filter_file updates the
         # timestamps)
-        perl = join_path(self.spec['perl'].prefix.bin, 'perl')
 
         # Revert sbang, so Spack's sbang hook can fix it up
         filter_file('^#! /usr/bin/env perl',
-                    '#! {0} -w'.format(perl),
-                    '{0}/autom4te'.format(self.prefix.bin),
+                    '#! {0} -w'.format(self.spec['perl'].command.path),
+                    self.prefix.bin.autom4te,
                     backup=False)
 
     def _make_executable(self, name):
diff --git a/var/spack/repos/builtin/packages/autodock-vina/package.py b/var/spack/repos/builtin/packages/autodock-vina/package.py
index 255839e894..5efacf02a5 100644
--- a/var/spack/repos/builtin/packages/autodock-vina/package.py
+++ b/var/spack/repos/builtin/packages/autodock-vina/package.py
@@ -1,30 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from shutil import copyfile
-from shutil import copymode
 import sys
 
 
@@ -66,7 +45,5 @@ class AutodockVina(MakefilePackage):
     def install(self, spec, prefix):
         with working_dir(self.build_directory):
             mkdirp(prefix.bin)
-            copyfile("vina", join_path(prefix.bin, "vina"))
-            copymode("vina", join_path(prefix.bin, "vina"))
-            copyfile("vina_split", join_path(prefix.bin, "vina_split"))
-            copymode("vina_split", join_path(prefix.bin, "vina_split"))
+            install('vina', prefix.bin)
+            install('vina_split', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/autofact/package.py b/var/spack/repos/builtin/packages/autofact/package.py
new file mode 100644
index 0000000000..0ad36c82dd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/autofact/package.py
@@ -0,0 +1,36 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import glob
+
+
+class Autofact(Package):
+    """An Automatic Functional Annotation and Classification Tool"""
+
+    homepage = "http://megasun.bch.umontreal.ca/Software/AutoFACT.htm"
+    url      = "http://megasun.bch.umontreal.ca/Software/AutoFACT_v3_4.tar"
+
+    version('3_4', sha256='1465d263b19adb42f01f6e636ac40ef1c2e3dbd63461f977b89da9493fe9c6f4')
+
+    depends_on('perl', type='run')
+    depends_on('perl-bio-perl', type='run')
+    depends_on('perl-io-string', type='run')
+    depends_on('perl-lwp', type='run')
+    depends_on('blast-plus', type='run')
+
+    def patch(self):
+        with working_dir('scripts'):
+            files = glob.iglob("*.pl")
+            for file in files:
+                change = FileFilter(file)
+                change.filter('usr/bin/perl', 'usr/bin/env perl')
+
+    def install(self, spec, prefix):
+        install_tree(self.stage.source_path, prefix)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PATH', self.prefix.scripts)
+        run_env.set('PATH2AUTOFACT', self.prefix)
diff --git a/var/spack/repos/builtin/packages/autogen/package.py b/var/spack/repos/builtin/packages/autogen/package.py
index 4198ab1589..5f4c893e45 100644
--- a/var/spack/repos/builtin/packages/autogen/package.py
+++ b/var/spack/repos/builtin/packages/autogen/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,7 +13,7 @@ class Autogen(AutotoolsPackage):
     synchronized."""
 
     homepage = "https://www.gnu.org/software/autogen/index.html"
-    url      = "https://ftp.gnu.org/gnu/autogen/rel5.18.12/autogen-5.18.12.tar.gz"
+    url      = "https://ftpmirror.gnu.org/autogen/rel5.18.12/autogen-5.18.12.tar.gz"
     list_url = "https://ftp.gnu.org/gnu/autogen"
     list_depth = 1
 
@@ -40,7 +21,7 @@ class Autogen(AutotoolsPackage):
 
     variant('xml', default=True, description='Enable XML support')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
 
     depends_on('guile@1.8:2.0')
     depends_on('libxml2', when='+xml')
diff --git a/var/spack/repos/builtin/packages/automaded/package.py b/var/spack/repos/builtin/packages/automaded/package.py
index 7b227afb9d..30ca8684cd 100644
--- a/var/spack/repos/builtin/packages/automaded/package.py
+++ b/var/spack/repos/builtin/packages/automaded/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/automake/package.py b/var/spack/repos/builtin/packages/automake/package.py
index 2140612b7f..94bd569614 100644
--- a/var/spack/repos/builtin/packages/automake/package.py
+++ b/var/spack/repos/builtin/packages/automake/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,8 +10,9 @@ class Automake(AutotoolsPackage):
     """Automake -- make file builder part of autotools"""
 
     homepage = 'http://www.gnu.org/software/automake/'
-    url      = 'http://ftp.gnu.org/gnu/automake/automake-1.15.tar.gz'
+    url      = 'https://ftpmirror.gnu.org/automake/automake-1.15.tar.gz'
 
+    version('1.16.1', '83cc2463a4080efd46a72ba2c9f6b8f5')
     version('1.15.1', '95df3f2d6eb8f81e70b8cb63a93c8853')
     version('1.15',   '716946a105ca228ab545fc37a70df3a3')
     version('1.14.1', 'd052a3e884631b9c7892f2efce542d75')
@@ -43,10 +25,14 @@ class Automake(AutotoolsPackage):
 
     def patch(self):
         # The full perl shebang might be too long
+        files_to_be_patched_fmt = 'bin/{0}.in'
+        if '@:1.15.1' in self.spec:
+            files_to_be_patched_fmt = 't/wrap/{0}.in'
+
         for file in ('aclocal', 'automake'):
             filter_file('^#!@PERL@ -w',
                         '#!/usr/bin/env perl',
-                        't/wrap/{0}.in'.format(file))
+                        files_to_be_patched_fmt.format(file))
 
     def _make_executable(self, name):
         return Executable(join_path(self.prefix.bin, name))
diff --git a/var/spack/repos/builtin/packages/axel/package.py b/var/spack/repos/builtin/packages/axel/package.py
new file mode 100644
index 0000000000..bd736b2db5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/axel/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Axel(AutotoolsPackage):
+    """Axel is a light command line download accelerator for Linux and Unix"""
+
+    homepage = "https://github.com/axel-download-accelerator/axel"
+    url      = "https://github.com/axel-download-accelerator/axel/archive/v2.16.1.tar.gz"
+
+    version('2.16.1', '3aaa7052458c66c1547bf1133609d0f2')
+
+    depends_on('m4', type='build')
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool', type='build')
+    depends_on('pkgconf', type='build')
+    depends_on('gettext')
+    depends_on('openssl')
diff --git a/var/spack/repos/builtin/packages/axl/package.py b/var/spack/repos/builtin/packages/axl/package.py
new file mode 100644
index 0000000000..c4118b58f7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/axl/package.py
@@ -0,0 +1,56 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+from spack.error import SpackError
+
+
+def async_api_validator(values):
+    if 'none' in values and len(values) != 1:
+        raise SpackError("The value 'none' is not usable"
+                         " with other async_api values.")
+    if 'ibm_bbapi' in values and 'cray_dw' in values:
+        raise SpackError("The 'ibm_bbapi' and 'cray_dw' asynchronous"
+                         " APIs are incompatible.")
+
+
+class Axl(CMakePackage):
+    """Asynchronous transfer library"""
+
+    homepage = "https://github.com/ECP-VeloC/AXL"
+    url      = "https://github.com/ECP-VeloC/AXL/archive/v0.1.0.zip"
+    git      = "https://github.com/ecp-veloc/axl.git"
+
+    tags = ['ecp']
+
+    version('master', branch='master')
+    version('0.1.1', sha256='7ec0417447c5a3cc0b6e46ff3f646984410c77e6c2081cf0c748781384be739b')
+
+    variant('async_api', default='daemon',
+            description="Set of async transfer APIs to enable",
+            values=['cray_dw', 'ibm_bbapi', 'daemon', 'none'], multi=True,
+            validator=async_api_validator)
+
+    # not-yet implemented functionality
+    conflicts('async_api=cray_dw', when='@0.1.0')
+    conflicts('async_api=ibm_bbapi', when='@0.1.0')
+
+    depends_on('kvtree')
+
+    def cmake_args(self):
+        args = []
+        if self.spec.satisfies('platform=cray'):
+            args.append("-DAXL_LINK_STATIC=ON")
+        args.append("-DWITH_KVTREE_PREFIX=%s" % self.spec['kvtree'].prefix)
+
+        apis = list(self.spec.variants['async_api'].value)
+        if 'daemon' in apis:
+            args.append('-DAXL_ASYNC_DAEMON=ON')
+            apis.remove('daemon')
+
+        for api in apis:
+            args.append('-DAXL_ASYNC_API={0}'.format(api))
+
+        return args
diff --git a/var/spack/repos/builtin/packages/bamdst/package.py b/var/spack/repos/builtin/packages/bamdst/package.py
new file mode 100644
index 0000000000..5f8c2b2b04
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bamdst/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Bamdst(MakefilePackage):
+    "Bamdst is a a lightweight bam file depth statistical tool."
+
+    homepage = "https://github.com/shiquan/bamdst"
+    git      = "https://github.com/shiquan/bamdst.git"
+
+    version('master', git='https://github.com/shiquan/bamdst.git')
+
+    depends_on('zlib')
+
+    parallel = False
+
+    def edit(self, spec, prefix):
+        makefile = FileFilter('Makefile')
+        makefile.filter('CC= .*', 'CC = cc')
+
+    def install(self, spec, prefix):
+        mkdir(prefix.bin)
+        install('bamdst', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/bamtools/package.py b/var/spack/repos/builtin/packages/bamtools/package.py
index a45cf38b80..4ad73eb78e 100644
--- a/var/spack/repos/builtin/packages/bamtools/package.py
+++ b/var/spack/repos/builtin/packages/bamtools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
@@ -32,6 +13,8 @@ class Bamtools(CMakePackage):
     homepage = "https://github.com/pezmaster31/bamtools"
     url      = "https://github.com/pezmaster31/bamtools/archive/v2.4.0.tar.gz"
 
+    version('2.5.1', '98e90632058f85bd5eed6088b3ff912e')
+    version('2.5.0', 'dd4185bdba6e3adf2c24b7f93a57233d')
     version('2.4.1', '41cadf513f2744256851accac2bc7baa')
     version('2.4.0', '6139d00c1b1fe88fe15d094d8a74d8b9')
     version('2.3.0', 'd327df4ba037d6eb8beef65d7da75ebc')
diff --git a/var/spack/repos/builtin/packages/bamutil/package.py b/var/spack/repos/builtin/packages/bamutil/package.py
index d739fe1f84..73a2d322ca 100644
--- a/var/spack/repos/builtin/packages/bamutil/package.py
+++ b/var/spack/repos/builtin/packages/bamutil/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,6 +17,8 @@ class Bamutil(MakefilePackage):
 
     version('1.0.13', '08b7d0bb1d60be104a11f0e54ddf4a79')
 
+    depends_on('zlib', type=('build', 'link'))
+
     # Looks like this will be fixed in 1.0.14.
     # https://github.com/statgen/libStatGen/issues/9
     patch('libstatgen-issue-9.patch', when='@1.0.13:')
diff --git a/var/spack/repos/builtin/packages/barrnap/package.py b/var/spack/repos/builtin/packages/barrnap/package.py
new file mode 100644
index 0000000000..3332b120a8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/barrnap/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Barrnap(Package):
+    """Barrnap predicts the location of ribosomal RNA genes in genomes."""
+
+    homepage = "https://github.com/tseemann/barrnap"
+    url      = "https://github.com/tseemann/barrnap/archive/0.8.tar.gz"
+
+    version('0.8', 'd02ccb800d60fa824bae946dd4fa2358')
+
+    depends_on('hmmer@3.1b:', type='run')
+
+    def install(self, spec, prefix):
+        install_tree('bin', prefix.bin)
+        install_tree('db', prefix.db)
diff --git a/var/spack/repos/builtin/packages/bash-completion/package.py b/var/spack/repos/builtin/packages/bash-completion/package.py
index 2e59e6247e..668bbc237e 100644
--- a/var/spack/repos/builtin/packages/bash-completion/package.py
+++ b/var/spack/repos/builtin/packages/bash-completion/package.py
@@ -1,37 +1,21 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class BashCompletion(AutotoolsPackage):
     """Programmable completion functions for bash."""
+
     homepage = "https://github.com/scop/bash-completion"
-    url = "https://github.com/scop/bash-completion/archive/2.3.tar.gz"
+    url      = "https://github.com/scop/bash-completion/archive/2.3.tar.gz"
+    git      = "https://github.com/scop/bash-completion.git"
 
+    version('develop', branch='master')
+    version('2.7', 'f72c9e2e877d188c3159956a3496a450e7279b76')
     version('2.3', '67e50f5f3c804350b43f2b664c33dde811d24292')
-    version('develop',  git='https://github.com/scop/bash-completion.git')
 
     # Build dependencies
     depends_on('automake', type='build')
@@ -41,6 +25,10 @@ class BashCompletion(AutotoolsPackage):
     # Other dependencies
     depends_on('bash@4.1:', type='run')
 
+    @run_before('install')
+    def create_install_directory(self):
+        mkdirp(join_path(self.prefix.share, 'bash-completion', 'completions'))
+
     @run_after('install')
     def show_message_to_user(self):
         prefix = self.prefix
diff --git a/var/spack/repos/builtin/packages/bash/package.py b/var/spack/repos/builtin/packages/bash/package.py
index 478edccd99..9903e1517d 100644
--- a/var/spack/repos/builtin/packages/bash/package.py
+++ b/var/spack/repos/builtin/packages/bash/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,8 +10,9 @@ class Bash(AutotoolsPackage):
     """The GNU Project's Bourne Again SHell."""
 
     homepage = "https://www.gnu.org/software/bash/"
-    url      = "https://ftp.gnu.org/gnu/bash/bash-4.4.tar.gz"
+    url      = "https://ftpmirror.gnu.org/bash/bash-4.4.tar.gz"
 
+    version('4.4.12', '7c112970cbdcadfc331e10eeb5f6aa41')
     version('4.4', '148888a7c95ac23705559b6f477dfe25')
     version('4.3', '81348932d5da294953e15d4814c74dd1')
 
@@ -49,3 +31,12 @@ class Bash(AutotoolsPackage):
 
     def check(self):
         make('tests')
+
+    @property
+    def install_targets(self):
+        args = ['install']
+
+        if self.spec.satisfies('@4.4:'):
+            args.append('install-headers')
+
+        return args
diff --git a/var/spack/repos/builtin/packages/bats/package.py b/var/spack/repos/builtin/packages/bats/package.py
index 4ee05c5a1c..d7ef4088ce 100644
--- a/var/spack/repos/builtin/packages/bats/package.py
+++ b/var/spack/repos/builtin/packages/bats/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/bazel/fix_env_handling-0.13.0.patch b/var/spack/repos/builtin/packages/bazel/fix_env_handling-0.13.0.patch
new file mode 100644
index 0000000000..31b4cf1a8e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bazel/fix_env_handling-0.13.0.patch
@@ -0,0 +1,129 @@
+--- a/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelConfiguration.java.orig	2018-05-23 12:11:29.319402761 +0200
++++ b/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelConfiguration.java	2018-05-23 12:35:21.817904301 +0200
+@@ -150,6 +150,126 @@
+       builder.put("PATH", null);
+       builder.put("LD_LIBRARY_PATH", null);
+     }
++
++      String spack_prefix = System.getenv("SPACK_PREFIX");
++      if (spack_prefix != null) {
++          builder.put("SPACK_PREFIX", spack_prefix);
++      }
++
++      String spack_env_path = System.getenv("SPACK_ENV_PATH");
++      if (spack_env_path != null) {
++          builder.put("SPACK_ENV_PATH", spack_env_path);
++      }
++
++      String spack_debug_log_id = System.getenv("SPACK_DEBUG_LOG_ID");
++      if (spack_debug_log_id != null) {
++          builder.put("SPACK_DEBUG_LOG_ID", spack_debug_log_id);
++      }
++
++      String spack_debug_log_dir = System.getenv("SPACK_DEBUG_LOG_DIR");
++      if (spack_debug_log_dir != null) {
++          builder.put("SPACK_DEBUG_LOG_DIR", spack_debug_log_dir);
++      }
++
++      String spack_compiler_spec = System.getenv("SPACK_COMPILER_SPEC");
++      if (spack_compiler_spec != null) {
++          builder.put("SPACK_COMPILER_SPEC", spack_compiler_spec);
++      }
++
++      String spack_cc_rpath_arg = System.getenv("SPACK_CC_RPATH_ARG");
++      if (spack_cc_rpath_arg != null) {
++          builder.put("SPACK_CC_RPATH_ARG", spack_cc_rpath_arg);
++      }
++
++      String spack_cxx_rpath_arg = System.getenv("SPACK_CXX_RPATH_ARG");
++      if (spack_cxx_rpath_arg != null) {
++          builder.put("SPACK_CXX_RPATH_ARG", spack_cxx_rpath_arg);
++      }
++
++      String spack_f77_rpath_arg = System.getenv("SPACK_F77_RPATH_ARG");
++      if (spack_f77_rpath_arg != null) {
++          builder.put("SPACK_F77_RPATH_ARG", spack_f77_rpath_arg);
++      }
++
++      String spack_fc_rpath_arg = System.getenv("SPACK_FC_RPATH_ARG");
++      if (spack_fc_rpath_arg != null) {
++          builder.put("SPACK_FC_RPATH_ARG", spack_fc_rpath_arg);
++      }
++
++      String spack_short_spec = System.getenv("SPACK_SHORT_SPEC");
++      if (spack_short_spec != null) {
++          builder.put("SPACK_SHORT_SPEC", spack_short_spec);
++      }
++
++      String spack_system_dirs = System.getenv("SPACK_SYSTEM_DIRS");
++      if (spack_system_dirs != null) {
++          builder.put("SPACK_SYSTEM_DIRS", spack_system_dirs);
++      }
++
++      String spack_cc = System.getenv("SPACK_CC");
++      if (spack_cc != null) {
++          builder.put("SPACK_CC", spack_cc);
++      }
++
++      String spack_cxx = System.getenv("SPACK_CXX");
++      if (spack_cxx != null) {
++          builder.put("SPACK_CXX", spack_cxx);
++      }
++
++      String spack_f77 = System.getenv("SPACK_F77");
++      if (spack_f77 != null) {
++          builder.put("SPACK_F77", spack_f77);
++      }
++
++      String spack_fc = System.getenv("SPACK_FC");
++      if (spack_fc != null) {
++          builder.put("SPACK_FC", spack_fc);
++      }
++
++      String spack_cflags = System.getenv("SPACK_CFLAGS");
++      if (spack_cflags != null) {
++          builder.put("SPACK_CFLAGS", spack_cflags);
++      }
++
++      String spack_cxxflags = System.getenv("SPACK_CXXFLAGS");
++      if (spack_cxxflags != null) {
++          builder.put("SPACK_CXXFLAGS", spack_cxxflags);
++      }
++
++      String spack_fcflags = System.getenv("SPACK_FCFLAGS");
++      if (spack_fcflags != null) {
++          builder.put("SPACK_FCFLAGS", spack_fcflags);
++      }
++
++      String spack_fflags = System.getenv("SPACK_FFLAGS");
++      if (spack_fflags != null) {
++          builder.put("SPACK_FFLAGS", spack_fflags);
++      }
++
++      String spack_ldflags = System.getenv("SPACK_LDFLAGS");
++      if (spack_ldflags != null) {
++          builder.put("SPACK_LDFLAGS", spack_ldflags);
++      }
++
++      String spack_ldlibs = System.getenv("SPACK_LDLIBS");
++      if (spack_ldlibs != null) {
++          builder.put("SPACK_LDLIBS", spack_ldlibs);
++      }
++
++      String spack_debug = System.getenv("SPACK_DEBUG");
++      if (spack_debug != null) {
++          builder.put("SPACK_DEBUG", spack_debug);
++      }
++
++      String spack_test_command = System.getenv("SPACK_TEST_COMMAND");
++      if (spack_test_command != null) {
++          builder.put("SPACK_TEST_COMMAND", spack_test_command);
++      }
++
++      String spack_dependencies = System.getenv("SPACK_DEPENDENCIES");
++      if (spack_dependencies != null) {
++          builder.put("SPACK_DEPENDENCIES", spack_dependencies);
++      }
+   }
+ 
+   private static PathFragment determineShellExecutable(OS os, PathFragment fromOption) {
diff --git a/var/spack/repos/builtin/packages/bazel/fix_env_handling-0.17.2.patch b/var/spack/repos/builtin/packages/bazel/fix_env_handling-0.17.2.patch
new file mode 100644
index 0000000000..89537387a6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bazel/fix_env_handling-0.17.2.patch
@@ -0,0 +1,131 @@
+diff --git a/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelRuleClassProvider.java b/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelRuleClassProvider.java
+index 72c40ac..2e73530 100755
+--- a/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelRuleClassProvider.java
++++ b/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelRuleClassProvider.java
+@@ -168,6 +168,126 @@ public class BazelRuleClassProvider {
+       env.put("PATH", null);
+     }
+ 
++    String spack_prefix = System.getenv("SPACK_PREFIX");
++    if (spack_prefix != null) {
++      env.put("SPACK_PREFIX", spack_prefix);
++    }
++
++    String spack_env_path = System.getenv("SPACK_ENV_PATH");
++    if (spack_env_path != null) {
++        env.put("SPACK_ENV_PATH", spack_env_path);
++    }
++
++    String spack_debug_log_id = System.getenv("SPACK_DEBUG_LOG_ID");
++    if (spack_debug_log_id != null) {
++        env.put("SPACK_DEBUG_LOG_ID", spack_debug_log_id);
++    }
++
++    String spack_debug_log_dir = System.getenv("SPACK_DEBUG_LOG_DIR");
++    if (spack_debug_log_dir != null) {
++        env.put("SPACK_DEBUG_LOG_DIR", spack_debug_log_dir);
++    }
++
++    String spack_compiler_spec = System.getenv("SPACK_COMPILER_SPEC");
++    if (spack_compiler_spec != null) {
++        env.put("SPACK_COMPILER_SPEC", spack_compiler_spec);
++    }
++
++    String spack_cc_rpath_arg = System.getenv("SPACK_CC_RPATH_ARG");
++    if (spack_cc_rpath_arg != null) {
++        env.put("SPACK_CC_RPATH_ARG", spack_cc_rpath_arg);
++    }
++
++    String spack_cxx_rpath_arg = System.getenv("SPACK_CXX_RPATH_ARG");
++    if (spack_cxx_rpath_arg != null) {
++        env.put("SPACK_CXX_RPATH_ARG", spack_cxx_rpath_arg);
++    }
++
++    String spack_f77_rpath_arg = System.getenv("SPACK_F77_RPATH_ARG");
++    if (spack_f77_rpath_arg != null) {
++        env.put("SPACK_F77_RPATH_ARG", spack_f77_rpath_arg);
++    }
++
++    String spack_fc_rpath_arg = System.getenv("SPACK_FC_RPATH_ARG");
++    if (spack_fc_rpath_arg != null) {
++        env.put("SPACK_FC_RPATH_ARG", spack_fc_rpath_arg);
++    }
++
++    String spack_short_spec = System.getenv("SPACK_SHORT_SPEC");
++    if (spack_short_spec != null) {
++        env.put("SPACK_SHORT_SPEC", spack_short_spec);
++    }
++
++    String spack_system_dirs = System.getenv("SPACK_SYSTEM_DIRS");
++    if (spack_system_dirs != null) {
++        env.put("SPACK_SYSTEM_DIRS", spack_system_dirs);
++    }
++
++    String spack_cc = System.getenv("SPACK_CC");
++    if (spack_cc != null) {
++        env.put("SPACK_CC", spack_cc);
++    }
++
++    String spack_cxx = System.getenv("SPACK_CXX");
++    if (spack_cxx != null) {
++        env.put("SPACK_CXX", spack_cxx);
++    }
++
++    String spack_f77 = System.getenv("SPACK_F77");
++    if (spack_f77 != null) {
++        env.put("SPACK_F77", spack_f77);
++    }
++
++    String spack_fc = System.getenv("SPACK_FC");
++    if (spack_fc != null) {
++        env.put("SPACK_FC", spack_fc);
++    }
++
++    String spack_cflags = System.getenv("SPACK_CFLAGS");
++    if (spack_cflags != null) {
++        env.put("SPACK_CFLAGS", spack_cflags);
++    }
++
++    String spack_cxxflags = System.getenv("SPACK_CXXFLAGS");
++    if (spack_cxxflags != null) {
++        env.put("SPACK_CXXFLAGS", spack_cxxflags);
++    }
++
++    String spack_fcflags = System.getenv("SPACK_FCFLAGS");
++    if (spack_fcflags != null) {
++        env.put("SPACK_FCFLAGS", spack_fcflags);
++    }
++
++    String spack_fflags = System.getenv("SPACK_FFLAGS");
++    if (spack_fflags != null) {
++        env.put("SPACK_FFLAGS", spack_fflags);
++    }
++
++    String spack_ldflags = System.getenv("SPACK_LDFLAGS");
++    if (spack_ldflags != null) {
++        env.put("SPACK_LDFLAGS", spack_ldflags);
++    }
++
++    String spack_ldlibs = System.getenv("SPACK_LDLIBS");
++    if (spack_ldlibs != null) {
++        env.put("SPACK_LDLIBS", spack_ldlibs);
++    }
++
++    String spack_debug = System.getenv("SPACK_DEBUG");
++    if (spack_debug != null) {
++        env.put("SPACK_DEBUG", spack_debug);
++    }
++
++    String spack_test_command = System.getenv("SPACK_TEST_COMMAND");
++    if (spack_test_command != null) {
++        env.put("SPACK_TEST_COMMAND", spack_test_command);
++    }
++
++    String spack_dependencies = System.getenv("SPACK_DEPENDENCIES");
++    if (spack_dependencies != null) {
++        env.put("SPACK_DEPENDENCIES", spack_dependencies);
++    }
++
+     // Shell environment variables specified via options take precedence over the
+     // ones inherited from the fragments. In the long run, these fragments will
+     // be replaced by appropriate default rc files anyway.
diff --git a/var/spack/repos/builtin/packages/bazel/fix_env_handling-0.9.0.patch b/var/spack/repos/builtin/packages/bazel/fix_env_handling-0.9.0.patch
new file mode 100644
index 0000000000..323748377f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bazel/fix_env_handling-0.9.0.patch
@@ -0,0 +1,126 @@
+diff --git a/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelConfiguration.java.orig b/home/jtang/spack/var/spack/stage/bazel-0.9.0-xcsfcyrpdn3df755cwpk4sxtfwjdv4ub/spack-expanded-archive/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelConfiguration.java
+index f1a7a1f..32cd181 100755
+--- a/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelConfiguration.java.orig
++++ b/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelConfiguration.java
+@@ -154,6 +154,121 @@ public class BazelConfiguration extends Fragment {
+       if (tmpdir != null) {
+         builder.put("TMPDIR", tmpdir);
+       }
++
++      String spack_prefix = System.getenv("SPACK_PREFIX");
++      if (spack_prefix != null) {
++          builder.put("SPACK_PREFIX", spack_prefix);
++      }
++
++      String spack_env_path = System.getenv("SPACK_ENV_PATH");
++      if (spack_env_path != null) {
++          builder.put("SPACK_ENV_PATH", spack_env_path);
++      }
++
++      String spack_debug_log_id = System.getenv("SPACK_DEBUG_LOG_ID");
++      if (spack_debug_log_id != null) {
++          builder.put("SPACK_DEBUG_LOG_ID", spack_debug_log_id);
++      }
++
++      String spack_debug_log_dir = System.getenv("SPACK_DEBUG_LOG_DIR");
++      if (spack_debug_log_dir != null) {
++          builder.put("SPACK_DEBUG_LOG_DIR", spack_debug_log_dir);
++      }
++
++      String spack_compiler_spec = System.getenv("SPACK_COMPILER_SPEC");
++      if (spack_compiler_spec != null) {
++          builder.put("SPACK_COMPILER_SPEC", spack_compiler_spec);
++      }
++
++      String spack_cc_rpath_arg = System.getenv("SPACK_CC_RPATH_ARG");
++      if (spack_cc_rpath_arg != null) {
++          builder.put("SPACK_CC_RPATH_ARG", spack_cc_rpath_arg);
++      }
++
++      String spack_cxx_rpath_arg = System.getenv("SPACK_CXX_RPATH_ARG");
++      if (spack_cxx_rpath_arg != null) {
++          builder.put("SPACK_CXX_RPATH_ARG", spack_cxx_rpath_arg);
++      }
++
++      String spack_f77_rpath_arg = System.getenv("SPACK_F77_RPATH_ARG");
++      if (spack_f77_rpath_arg != null) {
++          builder.put("SPACK_F77_RPATH_ARG", spack_f77_rpath_arg);
++      }
++
++      String spack_fc_rpath_arg = System.getenv("SPACK_FC_RPATH_ARG");
++      if (spack_fc_rpath_arg != null) {
++          builder.put("SPACK_FC_RPATH_ARG", spack_fc_rpath_arg);
++      }
++
++      String spack_short_spec = System.getenv("SPACK_SHORT_SPEC");
++      if (spack_short_spec != null) {
++          builder.put("SPACK_SHORT_SPEC", spack_short_spec);
++      }
++
++      String spack_cc = System.getenv("SPACK_CC");
++      if (spack_cc != null) {
++          builder.put("SPACK_CC", spack_cc);
++      }
++
++      String spack_cxx = System.getenv("SPACK_CXX");
++      if (spack_cxx != null) {
++          builder.put("SPACK_CXX", spack_cxx);
++      }
++
++      String spack_f77 = System.getenv("SPACK_F77");
++      if (spack_f77 != null) {
++          builder.put("SPACK_F77", spack_f77);
++      }
++
++      String spack_fc = System.getenv("SPACK_FC");
++      if (spack_fc != null) {
++          builder.put("SPACK_FC", spack_fc);
++      }
++
++      String spack_cflags = System.getenv("SPACK_CFLAGS");
++      if (spack_cflags != null) {
++          builder.put("SPACK_CFLAGS", spack_cflags);
++      }
++
++      String spack_cxxflags = System.getenv("SPACK_CXXFLAGS");
++      if (spack_cxxflags != null) {
++          builder.put("SPACK_CXXFLAGS", spack_cxxflags);
++      }
++
++      String spack_fcflags = System.getenv("SPACK_FCFLAGS");
++      if (spack_fcflags != null) {
++          builder.put("SPACK_FCFLAGS", spack_fcflags);
++      }
++
++      String spack_fflags = System.getenv("SPACK_FFLAGS");
++      if (spack_fflags != null) {
++          builder.put("SPACK_FFLAGS", spack_fflags);
++      }
++
++      String spack_ldflags = System.getenv("SPACK_LDFLAGS");
++      if (spack_ldflags != null) {
++          builder.put("SPACK_LDFLAGS", spack_ldflags);
++      }
++
++      String spack_ldlibs = System.getenv("SPACK_LDLIBS");
++      if (spack_ldlibs != null) {
++          builder.put("SPACK_LDLIBS", spack_ldlibs);
++      }
++
++      String spack_debug = System.getenv("SPACK_DEBUG");
++      if (spack_debug != null) {
++          builder.put("SPACK_DEBUG", spack_debug);
++      }
++
++      String spack_test_command = System.getenv("SPACK_TEST_COMMAND");
++      if (spack_test_command != null) {
++          builder.put("SPACK_TEST_COMMAND", spack_test_command);
++      }
++
++      String spack_dependencies = System.getenv("SPACK_DEPENDENCIES");
++      if (spack_dependencies != null) {
++          builder.put("SPACK_DEPENDENCIES", spack_dependencies);
++      }
+     }
+   }
+ 
diff --git a/var/spack/repos/builtin/packages/bazel/fix_env_handling.patch b/var/spack/repos/builtin/packages/bazel/fix_env_handling.patch
index 9be9f97d69..14deccf950 100644
--- a/var/spack/repos/builtin/packages/bazel/fix_env_handling.patch
+++ b/var/spack/repos/builtin/packages/bazel/fix_env_handling.patch
@@ -1,7 +1,7 @@
 diff -pu bazel-0.3.1/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelConfiguration.java bazel-0.3.1/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelConfiguration.java 
 --- bazel-0.3.1/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelConfiguration.java 2016-09-14 11:56:01.565756979 +0200
 +++ bazel-0.3.1/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelConfiguration.java	2016-09-14 12:04:13.292839801 +0200
-@@ -92,5 +92,115 @@ public class BazelConfiguration extends
+@@ -92,5 +92,120 @@ public class BazelConfiguration extends
      if (tmpdir != null) {
        builder.put("TMPDIR", tmpdir);
      }
@@ -16,6 +16,11 @@ diff -pu bazel-0.3.1/src/main/java/com/google/devtools/build/lib/bazel/rules/Baz
 +      builder.put("SPACK_ENV_PATH", spack_env_path);
 +    }
 +
++    String spack_debug_log_id = System.getenv("SPACK_DEBUG_LOG_ID");
++    if (spack_debug_log_id != null) {
++      builder.put("SPACK_DEBUG_LOG_ID", spack_debug_log_id);
++    }
++
 +    String spack_debug_log_dir = System.getenv("SPACK_DEBUG_LOG_DIR");
 +    if (spack_debug_log_dir != null) {
 +      builder.put("SPACK_DEBUG_LOG_DIR", spack_debug_log_dir);
diff --git a/var/spack/repos/builtin/packages/bazel/link.patch b/var/spack/repos/builtin/packages/bazel/link.patch
index 69d100f62c..5c8824b87d 100644
--- a/var/spack/repos/builtin/packages/bazel/link.patch
+++ b/var/spack/repos/builtin/packages/bazel/link.patch
@@ -1,6 +1,6 @@
 --- bazel-0.3.1/src/main/java/com/google/devtools/build/lib/rules/cpp/CppLinkAction.java	2016-07-29 10:22:16.000000000 +0200
 +++ bazel-0.3.1/src/main/java/com/google/devtools/build/lib/rules/cpp/CppLinkAction.java	2016-10-13 15:21:35.036617890 +0200
-@@ -214,6 +214,130 @@
+@@ -214,6 +214,135 @@
                .getParentDirectory()
                .getPathString());
      }
@@ -28,6 +28,11 @@
 +      result.put("SPACK_ENV_PATH", spack_env_path);
 +    }
 +
++    String spack_debug_log_id = System.getenv("SPACK_DEBUG_LOG_ID");
++    if (spack_debug_log_id != null) {
++      result.put("SPACK_DEBUG_LOG_ID", spack_debug_log_id);
++    }
++
 +    String spack_debug_log_dir = System.getenv("SPACK_DEBUG_LOG_DIR");
 +    if (spack_debug_log_dir != null) {
 +      result.put("SPACK_DEBUG_LOG_DIR", spack_debug_log_dir);
diff --git a/var/spack/repos/builtin/packages/bazel/package.py b/var/spack/repos/builtin/packages/bazel/package.py
index ff9817be97..9f34d3d52b 100644
--- a/var/spack/repos/builtin/packages/bazel/package.py
+++ b/var/spack/repos/builtin/packages/bazel/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 from multiprocessing import cpu_count
 from spack.util.environment import env_flag
@@ -32,8 +13,19 @@ class Bazel(Package):
     """Bazel is Google's own build tool"""
 
     homepage = "https://www.bazel.io"
-    url = "https://github.com/bazelbuild/bazel/releases/download/0.5.0/bazel-0.5.0-dist.zip"
-
+    url = "https://github.com/bazelbuild/bazel/releases/download/0.11.1/bazel-0.11.1-dist.zip"
+
+    version('0.17.2', '9805c0593e781295126af6b8be8cc7a9')
+    version('0.16.1', 'c333d903c5275286e79316eb19dd742d')
+    version('0.15.0', 'fb6b928b62f068697bd66ad6d13aad53')
+    version('0.14.1', '841900316b3ec9b996babe1c5b0b92e1')
+    version('0.13.0', '64a5124025c1618b550faec64a9b6fa3')
+    version('0.12.0', 'b5d67564ceecfe2005a885fe2ffe0da3')
+    version('0.11.1', '80daac6b100b7f8e2b17d133150eba44')
+    version('0.11.0', 'e6caf93a805b45c33367028e575b91dd')
+    version('0.10.1', 'a7e5b9576993b752e31bd2d3259a14c5')
+    version('0.10.0', 'c2f15b34255099d25e94fce7283e5cd2')
+    version('0.9.0', '7fda74c163108f7c180bbc513bc8123b')
     version('0.4.5', '2b737be42678900470ae9e48c975ac5b2296d9ae23c007bf118350dbe7c0552b')
     version('0.4.4', '5e7c52b89071efc41277e2f0057d258f')
     version('0.3.1', '5c959467484a7fc7dd2e5e4a1e8e866b')
@@ -42,12 +34,18 @@ class Bazel(Package):
     version('0.2.2b', '75081804f073cbd194da1a07b16cba5f')
     version('0.2.2', '644bc4ea7f429d835e74f255dc1054e6')
 
-    depends_on('java@8:')
+    depends_on('java@8:', type=('build', 'link', 'run'))
     depends_on('zip')
 
-    patch('fix_env_handling.patch')
+    patch('fix_env_handling.patch', when='@:0.4.5')
+    patch('fix_env_handling-0.9.0.patch', when='@0.9.0:0.12.0')
+    patch('fix_env_handling-0.13.0.patch', when='@0.13.0:0.13.999')
+    patch('fix_env_handling-0.17.2.patch', when='@0.14.0:')
     patch('link.patch')
-    patch('cc_configure.patch')
+    patch('cc_configure.patch', when='@:0.4.5')
+    patch('unix_cc_configure.patch', when='@0.9.0')
+    patch('unix_cc_configure-0.10.0.patch', when='@0.10.0:0.14.999')
+    patch('unix_cc_configure-0.17.2.patch', when='@0.15.0:')
 
     def url_for_version(self, version):
         if version >= Version('0.4.1'):
@@ -80,8 +78,8 @@ class Bazel(Package):
 
             def __call__(self, *args, **kwargs):
                 disable = env_flag(SPACK_NO_PARALLEL_MAKE)
-                parallel = ((not disable) and
-                            kwargs.get('parallel', self.jobs > 1))
+                parallel = ((not disable) and kwargs.get('parallel',
+                                                         self.jobs > 1))
 
                 jobs = "--jobs=1"
                 if parallel:
diff --git a/var/spack/repos/builtin/packages/bazel/unix_cc_configure-0.10.0.patch b/var/spack/repos/builtin/packages/bazel/unix_cc_configure-0.10.0.patch
new file mode 100644
index 0000000000..e375283fed
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bazel/unix_cc_configure-0.10.0.patch
@@ -0,0 +1,25 @@
+diff --git a/tools/cpp/unix_cc_configure.bzl.orig b/tools/cpp/unix_cc_configure.bzl
+index f67b9b5..cc952e0 100755
+--- a/tools/cpp/unix_cc_configure.bzl.orig
++++ b/tools/cpp/unix_cc_configure.bzl
+@@ -147,9 +147,18 @@ def get_escaped_cxx_inc_directories(repository_ctx, cc, additional_flags = []):
+   else:
+     inc_dirs = result.stderr[index1 + 1:index2].strip()
+ 
+-  return [_prepare_include_path(repository_ctx, _cxx_inc_convert(p))
+-          for p in inc_dirs.split("\n")]
++  default_inc_directories = [
++    _prepare_include_path(repository_ctx, _cxx_inc_convert(p))
++      for p in inc_dirs.split("\n")
++  ]
+ 
++  env = repository_ctx.os.environ
++  if "SPACK_DEPENDENCIES" in env:
++    for dep in env["SPACK_DEPENDENCIES"].split(":"):
++      path = dep + "/include"
++      default_inc_directories.append(path)
++
++  return default_inc_directories
+ 
+ def _is_option_supported(repository_ctx, cc, option):
+   """Checks that `option` is supported by the C compiler. Doesn't %-escape the option."""
diff --git a/var/spack/repos/builtin/packages/bazel/unix_cc_configure-0.17.2.patch b/var/spack/repos/builtin/packages/bazel/unix_cc_configure-0.17.2.patch
new file mode 100644
index 0000000000..d1a502a49a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bazel/unix_cc_configure-0.17.2.patch
@@ -0,0 +1,25 @@
+diff --git a/tools/cpp/unix_cc_configure.bzl b/tools/cpp/unix_cc_configure.bzl
+index 361931b..a79129b 100755
+--- a/tools/cpp/unix_cc_configure.bzl
++++ b/tools/cpp/unix_cc_configure.bzl
+@@ -145,11 +145,19 @@ def get_escaped_cxx_inc_directories(repository_ctx, cc, lang_flag, additional_fl
+     else:
+         inc_dirs = result.stderr[index1 + 1:index2].strip()
+ 
+-    return [
++    default_inc_directories = [
+         _prepare_include_path(repository_ctx, _cxx_inc_convert(p))
+         for p in inc_dirs.split("\n")
+     ]
+ 
++    env = repository_ctx.os.environ
++    if "SPACK_DEPENDENCIES" in env:
++        for dep in env["SPACK_DEPENDENCIES"].split(":"):
++            path = dep + "/include"
++            default_inc_directories.append(path)
++
++    return default_inc_directories
++
+ def _is_compiler_option_supported(repository_ctx, cc, option):
+     """Checks that `option` is supported by the C compiler. Doesn't %-escape the option."""
+     result = repository_ctx.execute([
diff --git a/var/spack/repos/builtin/packages/bazel/unix_cc_configure.patch b/var/spack/repos/builtin/packages/bazel/unix_cc_configure.patch
new file mode 100644
index 0000000000..3f14bc2fc0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bazel/unix_cc_configure.patch
@@ -0,0 +1,32 @@
+diff --git a/spack-expanded-archive/tools/cpp/unix_cc_configure.bzl.orig b/spack-expanded-archive/tools/cpp/unix_cc_configure.bzl
+old mode 100644
+new mode 100755
+index aa46f55..ae3c689
+--- spack-expanded-archive/tools/cpp/unix_cc_configure.bzl
++++ spack-expanded-archive/tools/cpp/unix_cc_configure.bzl
+@@ -117,9 +117,23 @@ def get_escaped_cxx_inc_directories(repository_ctx, cc):
+   else:
+     inc_dirs = result.stderr[index1 + 1:index2].strip()
+ 
+-  return [escape_string(repository_ctx.path(_cxx_inc_convert(p)))
+-          for p in inc_dirs.split("\n")]
++  default_inc_directories = [
++    escape_string(repository_ctx.path(_cxx_inc_convert(p)))
++          for p in inc_dirs.split("\n")
++  ]
+ 
++  env = repository_ctx.os.environ
++  if "SPACK_DEPENDENCIES" in env:
++    for dep in env["SPACK_DEPENDENCIES"].split(":"):
++      path = dep + "/include"
++      # path = repository_ctx.os.path.join(dep, "include")
++      # if not repository_ctx.os.path.exists(path):
++      #   continue
++      default_inc_directories.append(
++        repository_ctx.path(_cxx_inc_convert(path))
++      )
++
++  return default_inc_directories
+ 
+ def _add_option_if_supported(repository_ctx, cc, option):
+   """Checks that `option` is supported by the C compiler. Doesn't %-escape the option."""
diff --git a/var/spack/repos/builtin/packages/bbcp/package.py b/var/spack/repos/builtin/packages/bbcp/package.py
index f72b4fcb12..bd597decea 100644
--- a/var/spack/repos/builtin/packages/bbcp/package.py
+++ b/var/spack/repos/builtin/packages/bbcp/package.py
@@ -1,36 +1,18 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class Bbcp(Package):
     """Securely and quickly copy data from source to target"""
+
     homepage = "http://www.slac.stanford.edu/~abh/bbcp/"
+    git      = "http://www.slac.stanford.edu/~abh/bbcp/bbcp.git"
 
-    version('git', git='http://www.slac.stanford.edu/~abh/bbcp/bbcp.git',
-            branch="master")
+    version('git', branch='master')
 
     depends_on('zlib')
     depends_on('openssl')
diff --git a/var/spack/repos/builtin/packages/bbmap/package.py b/var/spack/repos/builtin/packages/bbmap/package.py
index 15d7d880c3..d73b72cc2f 100644
--- a/var/spack/repos/builtin/packages/bbmap/package.py
+++ b/var/spack/repos/builtin/packages/bbmap/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/bc/package.py b/var/spack/repos/builtin/packages/bc/package.py
new file mode 100644
index 0000000000..6f149e6fa9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bc/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Bc(AutotoolsPackage):
+    """bc is an arbitrary precision numeric processing language. Syntax is
+    similar to C, but differs in many substantial areas. It supports
+    interactive execution of statements."""
+
+    homepage = "https://www.gnu.org/software/bc"
+    url      = "https://ftpmirror.gnu.org/bc/bc-1.07.tar.gz"
+
+    version('1.07', 'e91638a947beadabf4d7770bdbb3d512')
+
+    depends_on('ed', type='build')
+    depends_on('texinfo', type='build')
+
+    parallel = False
diff --git a/var/spack/repos/builtin/packages/bcftools/package.py b/var/spack/repos/builtin/packages/bcftools/package.py
index b1cccc1f21..e49c7c4bd2 100644
--- a/var/spack/repos/builtin/packages/bcftools/package.py
+++ b/var/spack/repos/builtin/packages/bcftools/package.py
@@ -1,31 +1,12 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class Bcftools(Package):
+class Bcftools(AutotoolsPackage):
     """BCFtools is a set of utilities that manipulate variant calls in the
        Variant Call Format (VCF) and its binary counterpart BCF. All
        commands work transparently with both VCFs and BCFs, both
@@ -34,16 +15,20 @@ class Bcftools(Package):
     homepage = "http://samtools.github.io/bcftools/"
     url      = "https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2"
 
+    version('1.9', sha256='6f36d0e6f16ec4acf88649fb1565d443acf0ba40f25a9afd87f14d14d13070c8')
+    version('1.8', 'ba6c2fb7eb6dcb208f00ab8b22df475c')
+    version('1.7', 'c972db68d17af9da3a18963f4e5aeca8')
     version('1.6', 'c4dba1e8cb55db0f94b4c47724b4f9fa')
     version('1.4', '50ccf0a073bd70e99cdb3c8be830416e')
     version('1.3.1', '575001e9fca37cab0c7a7287ad4b1cdb')
     version('1.2', '8044bed8fce62f7072fc6835420f0906')
 
+    depends_on('libzip', when='@1.8:')
+
+    depends_on('htslib@1.9', when='@1.9')
+    depends_on('htslib@1.8', when='@1.8')
+    depends_on('htslib@1.7',   when='@1.7')
     depends_on('htslib@1.6',   when='@1.6')
     depends_on('htslib@1.4',   when='@1.4')
     depends_on('htslib@1.3.1', when='@1.3.1')
     depends_on('htslib@1.2', when='@1.2')
-
-    def install(self, spec, prefix):
-        make("prefix=%s" % prefix, "all")
-        make("prefix=%s" % prefix, "install")
diff --git a/var/spack/repos/builtin/packages/bcl2fastq2/package.py b/var/spack/repos/builtin/packages/bcl2fastq2/package.py
index 173bb050ff..f3eb3175ac 100644
--- a/var/spack/repos/builtin/packages/bcl2fastq2/package.py
+++ b/var/spack/repos/builtin/packages/bcl2fastq2/package.py
@@ -1,30 +1,11 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
-import shutil
+import glob
 import llnl.util.tty as tty
 
 
@@ -36,8 +17,9 @@ class Bcl2fastq2(Package):
        call (BCL) files from a sequencing run into FASTQ
        files."""
 
-    homepage = "https://support.illumina.com/downloads/bcl2fastq-conversion-software-v2-18.html"
+    homepage = "https://support.illumina.com/downloads/bcl2fastq-conversion-software-v2-20.html"
 
+    version('2.20.0.422', '4dc99f1af208498b7279b66556329488')
     version('2.19.1.403', 'baba7a02767fd868e87cb36781d2be26')
     version('2.18.0.12', 'fbe06492117f65609c41be0c27e3215c')
     # 2.17.1.14 is no longer distributed.  If you have a copy of the
@@ -65,12 +47,11 @@ class Bcl2fastq2(Package):
     # v2.19.1.403 is only available via ftp.
     # who knows what the future will hold.
     def url_for_version(self, version):
+        url = "ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/software/bcl2fastq/bcl2fastq2-v{0}-tar.zip"
         if version.string == '2.19.1.403':
-            return "ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/software/bcl2fastq/bcl2fastq2-v2.19.1-tar.zip"
+            return url.format(version.up_to(3).dotted)
         else:
-            url = "https://support.illumina.com/content/dam/illumina-support/documents/downloads/software/bcl2fastq/bcl2fastq2-v{0}-tar.zip"
-            # - required to change the version from dots to dashes.
-            return url.format(version.dashed)
+            return url.format(version.up_to(3).dashed)
 
     # Illumina tucks the source inside a gzipped tarball inside a zip
     # file.  We let the normal Spack expansion bit unzip the zip file,
@@ -91,12 +72,12 @@ class Bcl2fastq2(Package):
                 else:
                     tty.msg("Unpacking bcl2fastq2 tarball")
                     tty.msg("cwd sez: {0}".format(os.getcwd()))
-                    tarball = 'bcl2fastq2-v{0}.tar.gz'.format(
-                        self.version.dotted)
-                    shutil.move(join_path('spack-expanded-archive', tarball),
-                                '.')
+                    tarball = glob.glob(join_path('spack-expanded-archive',
+                                        'bcl2fastq2*.tar.gz'))[0]
+                    copy(tarball, '.')
                     os.rmdir('spack-expanded-archive')
                     tar = which('tar')
+                    tarball = os.path.basename(tarball)
                     tar('-xf', tarball)
                     tty.msg("Finished unpacking bcl2fastq2 tarball")
         return wrap
diff --git a/var/spack/repos/builtin/packages/bdftopcf/package.py b/var/spack/repos/builtin/packages/bdftopcf/package.py
index a85bcf5307..7140818204 100644
--- a/var/spack/repos/builtin/packages/bdftopcf/package.py
+++ b/var/spack/repos/builtin/packages/bdftopcf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,7 +21,7 @@ class Bdftopcf(AutotoolsPackage):
 
     depends_on('libxfont')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('xproto', type='build')
     depends_on('fontsproto', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/bdw-gc/package.py b/var/spack/repos/builtin/packages/bdw-gc/package.py
index 7971dae506..4246867f22 100644
--- a/var/spack/repos/builtin/packages/bdw-gc/package.py
+++ b/var/spack/repos/builtin/packages/bdw-gc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/bear/package.py b/var/spack/repos/builtin/packages/bear/package.py
index f3f46b1025..1117ef5aac 100644
--- a/var/spack/repos/builtin/packages/bear/package.py
+++ b/var/spack/repos/builtin/packages/bear/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/beast1/package.py b/var/spack/repos/builtin/packages/beast1/package.py
new file mode 100644
index 0000000000..f9c94650e4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/beast1/package.py
@@ -0,0 +1,33 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Beast1(Package):
+    """BEAST is a cross-platform program for Bayesian
+       analysis of molecular sequences using MCMC."""
+
+    homepage = "http://beast.community/"
+    url      = "https://github.com/beast-dev/beast-mcmc/releases/download/v1.8.4/BEASTv1.8.4.tgz"
+
+    version('1.10.0', 'bcf2f2c074319360ec8a2ebad57d2e57', 
+            url='https://github.com/beast-dev/beast-mcmc/releases/download/v1.10.0/BEAST_v1.10.0.tgz')
+    version('1.8.4', 'cb8752340c1f77a22d39ca4fe09687b0')
+
+    variant('beagle', default=True, description='Build with libbeagle support')
+
+    depends_on('java', type='run')
+    depends_on('libbeagle', type=('build', 'link', 'run'), when="+beagle")
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.set('BEAST1', self.prefix)
+
+    def install(self, spec, prefix):
+        install_tree('bin', prefix.bin)
+        install_tree('examples', prefix.examples)
+        install_tree('images', prefix.images)
+        install_tree('lib', prefix.lib)
+        install_tree('doc', prefix.doc)
diff --git a/var/spack/repos/builtin/packages/beast2/package.py b/var/spack/repos/builtin/packages/beast2/package.py
index 88066116a2..a5b8182e74 100644
--- a/var/spack/repos/builtin/packages/beast2/package.py
+++ b/var/spack/repos/builtin/packages/beast2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/bedops/package.py b/var/spack/repos/builtin/packages/bedops/package.py
new file mode 100644
index 0000000000..9e22dbbe10
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bedops/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Bedops(MakefilePackage):
+    """BEDOPS is an open-source command-line toolkit that performs highly
+    efficient and scalable Boolean and other set operations, statistical
+    calculations, archiving, conversion and other management of genomic data of
+    arbitrary scale."""
+
+    homepage = "https://bedops.readthedocs.io"
+    url      = "https://github.com/bedops/bedops/archive/v2.4.30.tar.gz"
+
+    version('2.4.35', 'b425b3e05fd4cd1024ef4dd8bf04b4e5')
+    version('2.4.34', 'fc467d96134a0efe8b134e638af87a1a')
+    version('2.4.30', '4e5d9f7b7e5432b28aef8d17a22cffab')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        make('install', "BINDIR=%s" % prefix.bin)
diff --git a/var/spack/repos/builtin/packages/bedtools2/package.py b/var/spack/repos/builtin/packages/bedtools2/package.py
index 5956491f1b..55d06175bb 100644
--- a/var/spack/repos/builtin/packages/bedtools2/package.py
+++ b/var/spack/repos/builtin/packages/bedtools2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,6 +15,8 @@ class Bedtools2(Package):
     homepage = "https://github.com/arq5x/bedtools2"
     url      = "https://github.com/arq5x/bedtools2/archive/v2.26.0.tar.gz"
 
+    version('2.27.1', '8e0afcab95a824e42a6e99c5436a8438')
+    version('2.27.0', '052f22eb214ef2e7e7981b3c01167302')
     version('2.26.0', '52227e7efa6627f0f95d7d734973233d')
     version('2.25.0', '534fb4a7bf0d0c3f05be52a0160d8e3d')
     version('2.23.0', '4fa3671b3a3891eefd969ad3509222e3')
diff --git a/var/spack/repos/builtin/packages/beforelight/package.py b/var/spack/repos/builtin/packages/beforelight/package.py
index 457c547a16..fcde1adb4c 100644
--- a/var/spack/repos/builtin/packages/beforelight/package.py
+++ b/var/spack/repos/builtin/packages/beforelight/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,5 +21,5 @@ class Beforelight(AutotoolsPackage):
     depends_on('libxscrnsaver')
     depends_on('libxt')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/benchmark/package.py b/var/spack/repos/builtin/packages/benchmark/package.py
index 8c4dc6ec1f..83abbde812 100644
--- a/var/spack/repos/builtin/packages/benchmark/package.py
+++ b/var/spack/repos/builtin/packages/benchmark/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,12 +11,14 @@ class Benchmark(CMakePackage):
 
     homepage = "https://github.com/google/benchmark"
     url      = "https://github.com/google/benchmark/archive/v1.1.0.tar.gz"
-
-    version('develop', branch='master',
-            git='https://github.com/google/benchmark.git')
+    git      = "https://github.com/google/benchmark.git"
 
     # first properly installed CMake config packages in
     # 1.2.0 release: https://github.com/google/benchmark/issues/363
+
+    version('develop', branch='master')
+    version('1.4.0', 'ccfaf2cd93ae20191b94f730b945423e')
+    version('1.3.0', '19ce86516ab82d6ad3b17173cf307aac')
     version('1.2.0', '48d0b090cd7a84af2c4a28c8dc963c74')
     version('1.1.0', '66b2a23076cf70739525be0092fc3ae3')
     version('1.0.0', '1474ff826f8cd68067258db75a0835b8')
@@ -45,6 +28,14 @@ class Benchmark(CMakePackage):
             values=('Debug', 'Release', 'RelWithDebInfo',
                     'MinSizeRel', 'Coverage'))
 
+    depends_on("cmake@2.8.11:", type="build", when="@:1.1.0")
+    depends_on("cmake@2.8.12:", type="build", when="@1.2.0:")
+
+    def cmake_args(self):
+        # No need for testing for the install
+        args = ["-DBENCHMARK_ENABLE_TESTING=OFF"]
+        return args
+
     def patch(self):
         filter_file(
             r'add_cxx_compiler_flag..fstrict.aliasing.',
diff --git a/var/spack/repos/builtin/packages/berkeley-db/package.py b/var/spack/repos/builtin/packages/berkeley-db/package.py
index 3962ef3472..bd47c239af 100644
--- a/var/spack/repos/builtin/packages/berkeley-db/package.py
+++ b/var/spack/repos/builtin/packages/berkeley-db/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/bertini/package.py b/var/spack/repos/builtin/packages/bertini/package.py
index dc3e746eae..3b9f9efd34 100644
--- a/var/spack/repos/builtin/packages/bertini/package.py
+++ b/var/spack/repos/builtin/packages/bertini/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/bib2xhtml/package.py b/var/spack/repos/builtin/packages/bib2xhtml/package.py
index 3c9bab772e..0a50a18004 100644
--- a/var/spack/repos/builtin/packages/bib2xhtml/package.py
+++ b/var/spack/repos/builtin/packages/bib2xhtml/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 from glob import glob
 
diff --git a/var/spack/repos/builtin/packages/bigreqsproto/package.py b/var/spack/repos/builtin/packages/bigreqsproto/package.py
index e271e12777..323ea99d6c 100644
--- a/var/spack/repos/builtin/packages/bigreqsproto/package.py
+++ b/var/spack/repos/builtin/packages/bigreqsproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Bigreqsproto(AutotoolsPackage):
 
     version('1.1.2', '9b83369ac7a5eb2bf54c8f34db043a0e')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/binutils/package.py b/var/spack/repos/builtin/packages/binutils/package.py
index c3c521bad8..59620e1cb2 100644
--- a/var/spack/repos/builtin/packages/binutils/package.py
+++ b/var/spack/repos/builtin/packages/binutils/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,11 +10,14 @@ class Binutils(AutotoolsPackage):
     """GNU binutils, which contain the linker, assembler, objdump and others"""
 
     homepage = "http://www.gnu.org/software/binutils/"
-    url      = "https://ftp.gnu.org/gnu/binutils/binutils-2.28.tar.bz2"
+    url      = "https://ftpmirror.gnu.org/binutils/binutils-2.28.tar.bz2"
 
+    version('2.31.1', 'ffcc382695bf947da6135e7436b8ed52d991cf270db897190f19d6f9838564d0')
+    version('2.29.1', '9af59a2ca3488823e453bb356fe0f113')
     version('2.28', '9e8340c96626b469a603c15c9d843727')
     version('2.27', '2869c9bf3e60ee97c74ac2a6bf4e9d68')
     version('2.26', '64146a0faa3b411ba774f47d41de239f')
+    version('2.25.1', sha256='b5b14added7d78a8d1ca70b5cb75fef57ce2197264f4f5835326b0df22ac9f22')
     version('2.25', 'd9f3303f802a5b6b0bb73a335ab89d66')
     version('2.24', 'e0f71a7b2ddab0f8612336ac81d9636b')
     version('2.23.2', '4f8fa651e35ef262edc01d60fb45702e')
@@ -43,29 +27,30 @@ class Binutils(AutotoolsPackage):
             description="enable plugins, needed for gold linker")
     variant('gold', default=True, description="build the gold linker")
     variant('libiberty', default=False, description='Also install libiberty.')
+    variant('nls', default=True, description='Enable Native Language Support')
 
-    patch('cr16.patch')
+    patch('cr16.patch', when='@:2.29.1')
     patch('update_symbol-2.26.patch', when='@2.26')
 
     depends_on('zlib')
+    depends_on('gettext', when='+nls')
 
-    depends_on('m4', type='build')
-    depends_on('flex', type='build')
-    depends_on('bison', type='build')
-    depends_on('gettext')
+    # Prior to 2.30, gold did not distribute the generated files and
+    # thus needs bison, even for a one-time build.
+    depends_on('m4', type='build', when='@:2.29.99 +gold')
+    depends_on('bison', type='build', when='@:2.29.99 +gold')
 
     def configure_args(self):
         spec = self.spec
 
         configure_args = [
-            '--with-system-zlib',
             '--disable-dependency-tracking',
             '--disable-werror',
-            '--enable-interwork',
             '--enable-multilib',
             '--enable-shared',
             '--enable-64-bit-bfd',
             '--enable-targets=all',
+            '--with-system-zlib',
             '--with-sysroot=/',
         ]
 
@@ -78,4 +63,15 @@ class Binutils(AutotoolsPackage):
         if '+libiberty' in spec:
             configure_args.append('--enable-install-libiberty')
 
+        if '+nls' in spec:
+            configure_args.append('--enable-nls')
+        else:
+            configure_args.append('--disable-nls')
+
+        # To avoid namespace collisions with Darwin/BSD system tools,
+        # prefix executables with "g", e.g., gar, gnm; see Homebrew
+        # https://github.com/Homebrew/homebrew-core/blob/master/Formula/binutils.rb
+        if spec.satisfies('platform=darwin'):
+            configure_args.append('--program-prefix=g')
+
         return configure_args
diff --git a/var/spack/repos/builtin/packages/bioawk/package.py b/var/spack/repos/builtin/packages/bioawk/package.py
index 386aa16953..3a5318bc70 100644
--- a/var/spack/repos/builtin/packages/bioawk/package.py
+++ b/var/spack/repos/builtin/packages/bioawk/package.py
@@ -1,30 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from shutil import copyfile
-from shutil import copymode
 
 
 class Bioawk(MakefilePackage):
@@ -45,7 +24,5 @@ class Bioawk(MakefilePackage):
 
     def install(self, spec, prefix):
         mkdirp(prefix.bin)
-        copyfile("bioawk", join_path(prefix.bin, "bioawk"))
-        copymode("bioawk", join_path(prefix.bin, "bioawk"))
-        copyfile("maketab", join_path(prefix.bin, "maketab"))
-        copymode("maketab", join_path(prefix.bin, "maketab"))
+        install('bioawk',  prefix.bin)
+        install('maketab', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/biopieces/package.py b/var/spack/repos/builtin/packages/biopieces/package.py
new file mode 100644
index 0000000000..c237fdf564
--- /dev/null
+++ b/var/spack/repos/builtin/packages/biopieces/package.py
@@ -0,0 +1,70 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Biopieces(Package):
+    """The Biopieces are a collection of bioinformatics tools that can be
+       pieced together in a very easy and flexible manner to perform both
+       simple and complex tasks."""
+
+    homepage = "http://maasha.github.io/biopieces/"
+    git      = "https://github.com/maasha/biopieces.git"
+
+    version('2016-04-12', commit='982f80f7c55e2cae67737d80fe35a4e784762856',
+            submodules=True)
+
+    depends_on('perl', type=('build', 'run'))
+    depends_on('perl-module-build', type=('build', 'run'))
+    depends_on('perl-bit-vector', type=('build', 'run'))
+    depends_on('perl-svg', type=('build', 'run'))
+    depends_on('perl-term-readkey', type=('build', 'run'))
+    depends_on('perl-time-hires', type=('build', 'run'))
+    depends_on('perl-dbi', type=('build', 'run'))
+    depends_on('perl-xml-parser', type=('build', 'run'))
+    depends_on('perl-carp-clan', type=('build', 'run'))
+    depends_on('perl-class-inspector', type=('build', 'run'))
+    depends_on('perl-html-parser', type=('build', 'run'))
+    depends_on('perl-lwp', type=('build', 'run'))
+    depends_on('perl-soap-lite', type=('build', 'run'))
+    depends_on('perl-uri', type=('build', 'run'))
+    depends_on('perl-inline', type=('build', 'run'))
+    depends_on('perl-inline-c', type=('build', 'run'))
+    depends_on('perl-parse-recdescent', type=('build', 'run'))
+    depends_on('perl-version', type=('build', 'run'))
+    depends_on('perl-dbfile', type=('build', 'run'))
+    depends_on('perl-dbd-mysql', type=('build', 'run'))
+
+    depends_on('ruby@1.9:')
+    depends_on('ruby-gnuplot')
+    depends_on('ruby-narray')
+    depends_on('ruby-rubyinline')
+    depends_on('ruby-terminal-table')
+
+    depends_on('python@2.6:', type=('build', 'run'))
+    depends_on('blast-plus')
+    depends_on('muscle')
+    depends_on('mummer')
+    depends_on('blat')
+    depends_on('vmatch')
+    depends_on('bowtie')
+    depends_on('bwa')
+    depends_on('usearch')
+    depends_on('velvet')
+    depends_on('idba')
+    depends_on('ray')
+    depends_on('scan-for-matches')
+
+    def install(self, spec, prefix):
+        install_tree('.', prefix)
+
+    def setup_environment(self, spack_env, run_env):
+        # Note: user will need to set environment variables on their own,
+        # dependent on where they will want data to be located:
+        #    BP_DATA - Contains genomic data etc.
+        #    BP_TMP - Required temporary directory
+        #    BP_LOG - Required log directory
+        run_env.prepend_path('BP_DIR', prefix)
diff --git a/var/spack/repos/builtin/packages/bismark/package.py b/var/spack/repos/builtin/packages/bismark/package.py
new file mode 100644
index 0000000000..4326c63fc6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bismark/package.py
@@ -0,0 +1,35 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Bismark(Package):
+    """A tool to map bisulfite converted sequence reads and determine cytosine
+    methylation states"""
+
+    homepage = "https://www.bioinformatics.babraham.ac.uk/projects/bismark"
+    url      = "https://github.com/FelixKrueger/Bismark/archive/0.19.0.tar.gz"
+
+    version('0.19.0', 'f403654aded77bf0d1dac1203867ded1')
+    version('0.18.2', '42334b7e3ed53ba246f30f1f846b4af8')
+
+    depends_on('bowtie2', type='run')
+    depends_on('perl', type='run')
+    depends_on('samtools', type='run')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('bam2nuc', prefix.bin)
+        install('bismark', prefix.bin)
+        install('bismark_genome_preparation', prefix.bin)
+        install('bismark_methylation_extractor', prefix.bin)
+        install('bismark2bedGraph', prefix.bin)
+        install('bismark2report', prefix.bin)
+        install('bismark2summary', prefix.bin)
+        install('coverage2cytosine', prefix.bin)
+        install('deduplicate_bismark', prefix.bin)
+        install('filter_non_conversion', prefix.bin)
+        install('NOMe_filtering', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/bison/package.py b/var/spack/repos/builtin/packages/bison/package.py
index 1cc2aacfaf..bd2b66d53d 100644
--- a/var/spack/repos/builtin/packages/bison/package.py
+++ b/var/spack/repos/builtin/packages/bison/package.py
@@ -1,29 +1,10 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from spack.operating_systems.mac_os import macOS_version
+from spack.operating_systems.mac_os import macos_version
 import sys
 
 
@@ -33,16 +14,20 @@ class Bison(AutotoolsPackage):
     generalized LR (GLR) parser employing LALR(1) parser tables."""
 
     homepage = "http://www.gnu.org/software/bison/"
-    url      = "http://ftp.gnu.org/gnu/bison/bison-3.0.4.tar.gz"
+    url      = "https://ftpmirror.gnu.org/bison/bison-3.0.4.tar.gz"
 
+    version('3.0.5', '41ad57813157b61bfa47e33067a9d6f0')
     version('3.0.4', 'a586e11cd4aff49c3ff6d3b6a4c9ccf8')
     version('2.7',   'ded660799e76fb1667d594de1f7a0da9')
 
+    depends_on('diffutils', type='build')
     depends_on('m4', type=('build', 'run'))
+    depends_on('perl', type='build')
+    depends_on('help2man', type='build')
 
     patch('pgi.patch', when='@3.0.4')
 
-    if sys.platform == 'darwin' and macOS_version() >= Version('10.13'):
+    if sys.platform == 'darwin' and macos_version() >= Version('10.13'):
         patch('secure_snprintf.patch', level=0, when='@3.0.4')
 
     build_directory = 'spack-build'
diff --git a/var/spack/repos/builtin/packages/bitmap/package.py b/var/spack/repos/builtin/packages/bitmap/package.py
index 2ea4613a53..cc0c49aade 100644
--- a/var/spack/repos/builtin/packages/bitmap/package.py
+++ b/var/spack/repos/builtin/packages/bitmap/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -41,5 +22,5 @@ class Bitmap(AutotoolsPackage):
 
     depends_on('xbitmaps', type='build')
     depends_on('xproto@7.0.25:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/blasr-libcpp/package.py b/var/spack/repos/builtin/packages/blasr-libcpp/package.py
new file mode 100644
index 0000000000..ceb7d642ff
--- /dev/null
+++ b/var/spack/repos/builtin/packages/blasr-libcpp/package.py
@@ -0,0 +1,54 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class BlasrLibcpp(Package):
+    """Blasr_libcpp is a library used by blasr
+    and other executables such as samtoh5,
+    loadPulses for analyzing PacBio sequences."""
+
+    homepage = "https://github.com/PacificBiosciences/blasr_libcpp"
+    url      = "https://github.com/PacificBiosciences/blasr_libcpp/archive/5.3.1.tar.gz"
+
+    version('5.3.1', 'ca770042cbca508d5ff12dff0d645045')
+
+    depends_on('pbbam')
+    depends_on('hdf5+cxx@1.8.12:1.8.99')
+    # maximum version is 1.8.20 currently. There doesn't appear to be a
+    # major version 1.9 and the 1.10.1 version doesn't build correctly.
+    # https://github.com/PacificBiosciences/blasr/issues/355
+
+    depends_on('python', type='build')
+
+    phases = ['configure', 'build', 'install']
+
+    def configure(self, spec, prefix):
+        configure_args = [
+            'PBBAM_INC={0}'.format(self.spec['pbbam'].prefix.include),
+            'PBBAM_LIB={0}'.format(self.spec['pbbam'].prefix.lib),
+            'HDF5_INC={0}'.format(self.spec['hdf5'].prefix.include),
+            'HDF5_LIB={0}'.format(self.spec['hdf5'].prefix.lib)
+        ]
+        python('configure.py', *configure_args)
+
+    def build(self, spec, prefix):
+        os.environ['CPLUS_INCLUDE_PATH'] = self.stage.source_path
+        make()
+
+    def install(self, spec, prefix):
+        install_tree('alignment', prefix.alignment)
+        install_tree('hdf', prefix.hdf)
+        install_tree('pbdata', prefix.pbdata)
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        spack_env.prepend_path('LD_LIBRARY_PATH',
+                               self.spec.prefix.hdf)
+        spack_env.prepend_path('LD_LIBRARY_PATH',
+                               self.spec.prefix.alignment)
+        spack_env.prepend_path('LD_LIBRARY_PATH',
+                               self.spec.prefix.pbdata)
diff --git a/var/spack/repos/builtin/packages/blasr/package.py b/var/spack/repos/builtin/packages/blasr/package.py
new file mode 100644
index 0000000000..b7bbd3790f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/blasr/package.py
@@ -0,0 +1,77 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class Blasr(Package):
+    """The PacBio long read aligner."""
+
+    homepage = "https://github.com/PacificBiosciences/blasr/wiki"
+    url      = "https://github.com/PacificBiosciences/blasr/archive/5.3.1.tar.gz"
+
+    version('5.3.1', '53c93f499aa4bc10781c87bafc33df2a') 
+
+    depends_on('ncurses')
+    depends_on('hdf5+cxx@1.8.12:1.8.99')
+    depends_on('htslib')
+    depends_on('zlib')
+    depends_on('boost')
+    depends_on('pbbam')
+    depends_on('blasr-libcpp')
+    depends_on('python', type='build')
+
+    phases = ['configure', 'build', 'install']
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PATH', self.spec.prefix.utils)
+        spack_env.prepend_path('CPATH', self.spec['blasr-libcpp'].prefix)
+        spack_env.prepend_path('CPATH', self.spec[
+                               'blasr-libcpp'].prefix.pbdata)
+        spack_env.prepend_path('CPATH', self.spec[
+                               'blasr-libcpp'].prefix.alignment)
+        spack_env.prepend_path('CPATH', self.spec['blasr-libcpp'].prefix.hdf)
+
+        # hdf has +mpi by default, so handle that possibility
+        if ('+mpi' in self.spec['hdf5']):
+            spack_env.set('CC', self.spec['mpi'].mpicc)
+            spack_env.set('CXX', self.spec['mpi'].mpicxx)
+
+    def configure(self, spec, prefix):
+        configure_args = [
+            'LIBPBDATA_INC={0}'.format(
+                self.spec['blasr-libcpp'].prefix),
+            'LIBPBDATA_LIB={0}'.format(
+                self.spec['blasr-libcpp'].prefix.pbdata),
+            'LIBBLASR_LIB={0}'.format(
+                self.spec['blasr-libcpp'].prefix.alignment),
+            'LIBBLASR_INC={0}'.format(
+                self.spec['blasr-libcpp'].prefix),
+            'LIBPBIHDF_INC={0}'.format(self.spec['blasr-libcpp'].prefix),
+            'LIBPBIHDF_LIB={0}'.format(self.spec['blasr-libcpp'].prefix.hdf),
+            'HDF5_INC={0}'.format(self.spec['hdf5'].prefix.include),
+            'HDF5_LIB={0}'.format(self.spec['hdf5'].prefix.lib),
+            '--shared'
+        ]
+        python('configure.py', *configure_args)
+
+    def build(self, spec, prefix):
+        os.environ['CPLUS_INCLUDE_PATH'] = join_path(
+            self.stage.source_path, 'include')
+        make()
+
+    def install(self, spec, prefix):
+        mkdir(prefix.utils)
+        mkdir(prefix.bin)
+        install('blasr', prefix.bin.blasr)
+        install('utils/loadPulses', prefix.utils)
+        install('utils/pls2fasta', prefix.utils)
+        install('utils/samFilter', prefix.utils)
+        install('utils/samtoh5', prefix.utils)
+        install('utils/samtom4', prefix.utils)
+        install('utils/sawriter', prefix.utils)
+        install('utils/sdpMatcher', prefix.utils)
+        install('utils/toAfg', prefix.utils)
diff --git a/var/spack/repos/builtin/packages/blast-plus/package.py b/var/spack/repos/builtin/packages/blast-plus/package.py
index 073eab24d1..3cc075f578 100644
--- a/var/spack/repos/builtin/packages/blast-plus/package.py
+++ b/var/spack/repos/builtin/packages/blast-plus/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 # This is a based largely on the Homebrew science formula:
 # https://github.com/Homebrew/homebrew-science/blob/master/blast.rb
@@ -42,6 +23,7 @@ class BlastPlus(AutotoolsPackage):
     homepage = "http://blast.ncbi.nlm.nih.gov/"
     url      = "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-src.tar.gz"
 
+    version('2.7.1', sha256='10a78d3007413a6d4c983d2acbf03ef84b622b82bd9a59c6bd9fbdde9d0298ca')
     version('2.6.0',  'c8ce8055b10c4d774d995f88c7cc6225')
     version('2.2.30', 'f8e9a5eb368173142fe6867208b73715')
 
@@ -107,6 +89,8 @@ class BlastPlus(AutotoolsPackage):
     depends_on('python', when='+python')
     depends_on('perl', when='+perl')
 
+    depends_on('lmdb', when='@2.7.1:')
+
     configure_directory = 'c++'
 
     def configure_args(self):
diff --git a/var/spack/repos/builtin/packages/blat/package.py b/var/spack/repos/builtin/packages/blat/package.py
index 60a33bbdff..8e0abb249f 100644
--- a/var/spack/repos/builtin/packages/blat/package.py
+++ b/var/spack/repos/builtin/packages/blat/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/blaze/package.py b/var/spack/repos/builtin/packages/blaze/package.py
index 2f175ff7d5..ffe65b85e2 100644
--- a/var/spack/repos/builtin/packages/blaze/package.py
+++ b/var/spack/repos/builtin/packages/blaze/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -35,8 +16,10 @@ class Blaze(Package):
     """
 
     homepage = "https://bitbucket.org/blaze-lib/blaze/overview"
-    url      = "https://bitbucket.org/blaze-lib/blaze/downloads/blaze-3.1.tar.gz"
+    url      = "https://bitbucket.org/blaze-lib/blaze/downloads/blaze-3.4.tar.gz"
 
+    version('3.4', sha256='fd474ab479e81d31edf27d4a529706b418f874caa7b046c67489128c20dda66f')
+    version('3.3', sha256='138cbb7b95775c10bf56a5ab3596a32205751299b19699984b6ed55b1bf989d0')
     version('3.2', '47bd4a4f1b6292f5a6f71ed9d5287480')
     version('3.1', '2938e015f0d274e8d62ee5c4c0c1e9f3')
     version('3.0', '0c4cefb0be7b5a27ed8a377941be1ab1')
diff --git a/var/spack/repos/builtin/packages/blis/package.py b/var/spack/repos/builtin/packages/blis/package.py
new file mode 100644
index 0000000000..771797d4b2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/blis/package.py
@@ -0,0 +1,117 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+# Although this looks like an Autotools package, it's not one. Refer to:
+# https://github.com/flame/blis/issues/17
+# https://github.com/flame/blis/issues/195
+# https://github.com/flame/blis/issues/197
+
+
+class Blis(Package):
+    """BLIS is a portable software framework for instantiating high-performance
+    BLAS-like dense linear algebra libraries. The framework was designed to
+    isolate essential kernels of computation that, when optimized, immediately
+    enable optimized implementations of most of its commonly used and
+    computationally intensive operations. BLIS is written in ISO C99 and
+    available under a new/modified/3-clause BSD license. While BLIS exports a
+    new BLAS-like API, it also includes a BLAS compatibility layer which gives
+    application developers access to BLIS implementations via traditional BLAS
+    routine calls. An object-based API unique to BLIS is also available."""
+
+    homepage = "https://github.com/flame/blis"
+    url      = "https://github.com/flame/blis/archive/0.4.0.tar.gz"
+    git      = "https://github.com/flame/blis.git"
+
+    version('develop', branch='master')
+    version('0.4.0', sha256='9c7efd75365a833614c01b5adfba93210f869d92e7649e0b5d9edc93fc20ea76')
+    version('0.3.2', sha256='b87e42c73a06107d647a890cbf12855925777dc7124b0c7698b90c5effa7f58f')
+    version('0.3.1', sha256='957f28d47c5cf71ffc62ce8cc1277e17e44d305b1c2fa8506b0b55617a9f28e4')
+    version('0.3.0', sha256='d34d17df7bdc2be8771fe0b7f867109fd10437ac91e2a29000a4a23164c7f0da')
+    version('0.2.2', sha256='4a7ecb56034fb20e9d1d8b16e2ef587abbc3d30cb728e70629ca7e795a7998e8')
+
+    depends_on('python@2.7:2.8,3.4:', type=('build', 'run'))
+
+    variant(
+        'threads', default='none',
+        description='Multithreading support',
+        values=('pthreads', 'openmp', 'none'),
+        multi=False
+    )
+
+    variant(
+        'blas', default=True,
+        description='BLAS compatibility',
+    )
+
+    variant(
+        'cblas', default=False,
+        description='CBLAS compatibility',
+    )
+
+    variant(
+        'shared', default=True,
+        description='Build shared library',
+    )
+
+    variant(
+        'static', default=True,
+        description='Build static library',
+    )
+
+    # TODO: add cpu variants. Currently using auto.
+    # If one knl, should the default be memkind ?
+
+    # BLIS has it's own API but can be made compatible with BLAS
+    # enabling CBLAS automatically enables BLAS.
+
+    provides('blas', when="+blas")
+    provides('blas', when="+cblas")
+
+    phases = ['configure', 'build', 'install']
+
+    def configure(self, spec, prefix):
+        config_args = []
+
+        config_args.append("--enable-threading=" +
+                           spec.variants['threads'].value)
+
+        if '+cblas' in spec:
+            config_args.append("--enable-cblas")
+        else:
+            config_args.append("--disable-cblas")
+
+        if '+blas' in spec:
+            config_args.append("--enable-blas")
+        else:
+            config_args.append("--disable-blas")
+
+        if '+shared' in spec:
+            config_args.append("--enable-shared")
+        else:
+            config_args.append("--disable-shared")
+
+        if '+static' in spec:
+            config_args.append("--enable-static")
+        else:
+            config_args.append("--disable-static")
+
+        # FIXME: add cpu isa variants.
+        config_args.append("auto")
+
+        configure("--prefix=" + prefix,
+                  *config_args)
+
+    def build(self, spec, prefix):
+        make()
+
+    @run_after('build')
+    @on_package_attributes(run_tests=True)
+    def check(self):
+        make('check')
+
+    def install(self, spec, prefix):
+        make('install')
diff --git a/var/spack/repos/builtin/packages/bliss/package.py b/var/spack/repos/builtin/packages/bliss/package.py
index 6604c2dc9a..42aef78a91 100644
--- a/var/spack/repos/builtin/packages/bliss/package.py
+++ b/var/spack/repos/builtin/packages/bliss/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/blitz/package.py b/var/spack/repos/builtin/packages/blitz/package.py
index 2cb9d8f5ab..cda7309b3e 100644
--- a/var/spack/repos/builtin/packages/blitz/package.py
+++ b/var/spack/repos/builtin/packages/blitz/package.py
@@ -1,36 +1,18 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class Blitz(AutotoolsPackage):
     """N-dimensional arrays for C++"""
     homepage = "http://github.com/blitzpp/blitz"
-    url = "https://github.com/blitzpp/blitz/tarball/1.0.0"
+    url = "https://github.com/blitzpp/blitz/archive/1.0.1.tar.gz"
 
-    version('1.0.0', '9f040b9827fe22228a892603671a77af')
+    version('1.0.1', 'fe43e2cf6c9258bc8b369264dd008971')
+    version('1.0.0', '971c43e22318bbfe8da016e6ef596234')
 
     build_targets = ['lib']
 
diff --git a/var/spack/repos/builtin/packages/bmake/package.py b/var/spack/repos/builtin/packages/bmake/package.py
new file mode 100644
index 0000000000..463a6e7134
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bmake/package.py
@@ -0,0 +1,34 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Bmake(Package):
+    """Portable version of NetBSD make(1)."""
+
+    homepage = "http://www.crufty.net/help/sjg/bmake.htm"
+    url      = "http://www.crufty.net/ftp/pub/sjg/bmake-20180512.tar.gz"
+
+    version('20180512', '48ba5933833a7f224d76ce482eedfec0')
+    version('20171207', '5d7f2f85f16c4a6ba34ceea68957447f')
+
+    phases = ['configure', 'build', 'install']
+
+    def patch(self):
+        # Do not pre-roff cat pages
+        filter_file('MANTARGET?', 'MANTARGET', 'mk/man.mk', string=True)
+
+    def configure(self, spec, prefix):
+        sh = which('sh')
+        sh('boot-strap', 'op=configure')
+
+    def build(self, spec, prefix):
+        sh = which('sh')
+        sh('boot-strap', 'op=build')
+
+    def install(self, spec, prefix):
+        sh = which('sh')
+        sh('boot-strap', '--prefix={0}'.format(prefix), 'op=install')
diff --git a/var/spack/repos/builtin/packages/bml/package.py b/var/spack/repos/builtin/packages/bml/package.py
index ee4b805d1b..ca00cf4a3d 100644
--- a/var/spack/repos/builtin/packages/bml/package.py
+++ b/var/spack/repos/builtin/packages/bml/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,13 +13,16 @@ class Bml(CMakePackage):
 
     homepage = "http://lanl.github.io/bml/"
     url      = "https://github.com/lanl/bml/tarball/v1.2.2"
+    git      = "https://github.com/lanl/bml.git"
 
+    version('develop', branch='master')
+    version('1.3.0', '2bf8546b27a89666dab3e8f4873cd117')
+    version('1.2.3', '8133137fb56a27fade44d1588449c2ac')
     version('1.2.2', 'c86959cb0188e9d0a9a2cbad03b2782d')
     version('1.1.0', '271adecee08aee678be9eeceee06b6fb')
-    version('develop', git='https://github.com/lanl/bml', branch='master')
 
     variant('shared', default=True, description='Build shared libs')
-    variant('mpi', default=False, description='Build with MPI Support')
+    variant('mpi', default=True, description='Build with MPI Support')
 
     conflicts('+mpi', when='@:1.2.2')
 
diff --git a/var/spack/repos/builtin/packages/bohrium/cxxadd.cpp b/var/spack/repos/builtin/packages/bohrium/cxxadd.cpp
new file mode 100644
index 0000000000..94c9287807
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bohrium/cxxadd.cpp
@@ -0,0 +1,24 @@
+#include <bhxx/bhxx.hpp>
+
+int main() {
+    const size_t dim = 3;
+    bhxx::BhArray<double> a({dim});
+    bhxx::BhArray<double> b({dim});
+    bhxx::BhArray<double> c({dim});
+
+    bhxx::identity(a, 1);
+    bhxx::identity(b, 2);
+    bhxx::add(c, a, b);
+
+    bhxx::Runtime::instance().sync(c.base);
+    bhxx::Runtime::instance().flush();
+
+    for (auto it = c.data(); it < c.data() + dim; ++it) {
+        if (*it != 3) {
+            std::cout << "Failure, values not as expected." << std::endl;
+            return 1;
+        }
+    }
+    std::cout << "Success!" << std::endl;
+    return 0;
+}
diff --git a/var/spack/repos/builtin/packages/bohrium/package.py b/var/spack/repos/builtin/packages/bohrium/package.py
new file mode 100644
index 0000000000..9df2ace777
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bohrium/package.py
@@ -0,0 +1,272 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+from spack.package_test import compare_output
+from spack.util.executable import Executable
+import llnl.util.tty as tty
+import os
+
+
+class Bohrium(CMakePackage, CudaPackage):
+    """Library for automatic acceleration of array operations"""
+
+    homepage = "http://bh107.org"
+    url      = "https://github.com/bh107/bohrium/archive/v0.9.0.tar.gz"
+    git      = "https://github.com/bh107/bohrium.git"
+
+    maintainers = ['mfherbst']
+
+    #
+    # Versions
+    #
+    version("develop", branch="master")
+    version('0.9.1', sha256='a8675db35ea4587ef12d5885a1aa19b59fd9c3f1366e239059de8b0f3cf51e04')
+    version('0.9.0', sha256='6f6379f1555de5a6a19138beac891a470df7df1fc9594e2b9404cf01b6e17d93')
+
+    #
+    # Variants
+    #
+    variant("cuda", default=True,
+            description="Build with CUDA code generator")
+    variant('opencl', default=True,
+            description="Build with OpenCL code generator")
+    variant('openmp', default=True,
+            description="Build with OpenMP code generator")
+
+    variant('node', default=True,
+            description="Build the node vector engine manager")
+    variant('proxy', default=False,
+            description="Build the proxy vector engine manager")
+    variant('python', default=True,
+            description="Build the numpy-like bridge "
+            "to enable use from python")
+    variant('cbridge', default=True,
+            description="Build the bridge interface towards plain C")
+
+    variant('blas', default=True,
+            description="Build with BLAS extension methods")
+    variant('lapack', default=True,
+            description="Build with LAPACK extension methods")
+    variant('opencv', default=True,
+            description="Build with OpenCV extension methods")
+
+    #
+    # Conflicts and extensions
+    #
+    conflicts('%intel')
+    conflicts('%clang@:3.5')
+    conflicts('%gcc@:4.7')
+    extends('python', when="+python")
+
+    # Bohrium needs at least one vector engine and
+    # at least one vector engine manager
+    conflicts('~node~proxy')
+    conflicts('~openmp~opencl~cuda')
+
+    #
+    # Dependencies
+    #
+    depends_on('cmake@2.8:', type="build")
+    depends_on('boost+system+serialization+filesystem+regex')
+
+    # cuda dependencies managed by CudaPackage class
+    depends_on('opencl', when="+opencl")
+
+    # NOTE The lapacke interface and hence netlib-lapack
+    #      is the strictly required lapack provider
+    #      for bohrium right now.
+    depends_on('netlib-lapack+lapacke', when="+lapack")
+    depends_on('blas', when="+blas")
+
+    # Make sure an appropriate opencv is used
+    depends_on('opencv+imgproc', when="+opencv")
+    depends_on('opencv+imgproc+cuda', when="+opencv+cuda")
+    depends_on('opencv+imgproc+openmp', when="+opencv+openmp")
+    depends_on('opencv+imgproc+openmp+cuda', when="+opencv+openmp+cuda")
+
+    depends_on('python', type="build", when="~python")
+    depends_on('python', type=("build", "link", "test"), when="+python")
+    depends_on('py-numpy', type=("build", "test", "run"), when="+python")
+    depends_on('swig', type="build", when="+python")
+    depends_on('py-cython', type="build", when="+python")
+
+    depends_on('zlib', when="+proxy")
+
+    @property
+    def config_file(self):
+        """Return the path of the Bohrium system-wide configuration file"""
+        return join_path(self.prefix.etc.bohrium, "config.ini")
+
+    #
+    # Settings and cmake cache
+    #
+    def cmake_args(self):
+        spec = self.spec
+
+        # Sanity check
+        cuda_arch = spec.variants['cuda_arch'].value
+        if "+cuda" in spec and len(cuda_arch) >= 1 and cuda_arch[0]:
+            # TODO Add cuda_arch support to Bohrium once the basic setup
+            #      via Spack works.
+            raise InstallError(
+                "Bohrium does not support setting the CUDA architecture yet."
+            )
+
+        args = [
+            # Choose a particular python version
+            "-DPYTHON_EXECUTABLE:FILEPATH=" + spec['python'].command.path,
+            #
+            # Hard-disable Jupyter, since this would override a config
+            # file in the user's home directory in some cases during
+            # the configuration stage.
+            "-DJUPYTER_FOUND=FALSE",
+            "-DJUPYTER_EXECUTABLE=FALSE",
+            #
+            # Force the configuration file to appear at a sensible place
+            "-DFORCE_CONFIG_PATH=" + os.path.dirname(self.config_file),
+            #
+            # Vector engine managers
+            "-DVEM_NODE=" + str("+node" in spec),
+            "-DVEM_PROXY=" + str("+proxy" in spec),
+            #
+            # Bridges and interfaces
+            "-DBRIDGE_BHXX=ON",
+            "-DBRIDGE_C=" + str("+cbridge" in spec or "+python" in spec),
+            "-DBRIDGE_NPBACKEND=" + str("+python" in spec),
+            "-DNO_PYTHON3=ON",  # Only build python version we provide
+        ]
+
+        #
+        # Vector engines
+        #
+        args += [
+            "-DVE_OPENCL=" + str("+opencl" in spec),
+            "-DVE_CUDA=" + str("+cuda" in spec),
+        ]
+
+        if "+openmp" in spec:
+            args += [
+                "-DVE_OPENMP=ON",
+                "-DOPENMP_FOUND=True",
+                "-DVE_OPENMP_COMPILER_CMD=" + self.compiler.cc,
+            ]
+        else:
+            args += ["-DVE_OPENMP=OFF", "-DOPENMP_FOUND=False"]
+
+        #
+        # Extension methods
+        #
+        if "+blas" in spec:
+            args += [
+                "-DEXT_BLAS=ON",
+                "-DCBLAS_FOUND=True",
+                "-DCBLAS_LIBRARIES=" + spec["blas"].libs.joined(";"),
+                "-DCBLAS_INCLUDES=" + spec["blas"].prefix.include,
+            ]
+        else:
+            args += ["-DEXT_BLAS=OFF", "-DDCBLAS_FOUND=False"]
+
+        if "+lapack" in spec:
+            args += [
+                "-DEXT_LAPACK=ON",
+                "-DLAPACKE_FOUND=True",
+                "-DLAPACKE_LIBRARIES=" + spec["lapack"].libs.joined(";"),
+                "-DLAPACKE_INCLUDE_DIR=" + spec["lapack"].prefix.include,
+            ]
+        else:
+            args += ["-DEXT_LAPACK=OFF", "-DLAPACKE_FOUND=False"]
+
+        if "+opencv" in spec:
+            args += [
+                "-DEXT_OPENCV=ON",
+                "-DOpenCV_FOUND=True",
+                "-DOpenCV_INCLUDE_DIRS=" + spec["opencv"].prefix.include,
+                "-DOpenCV_LIBS=" + spec["opencv"].libs.joined(";"),
+            ]
+        else:
+            args += ["-DEXT_OPENCV=OFF", "-DOpenCV_FOUND=False"]
+
+        # TODO Other extension methods are not ready yet,
+        #      because of missing packages in Spack
+        args += [
+            "-DEXT_CLBLAS=OFF",      # clBLAS missing
+            # Bohrium visualizer extension method
+            "-DEXT_VISUALIZER=OFF",  # freeglut missing
+        ]
+        return args
+
+    #
+    # Environment setup
+    #
+    def setup_environment(self, spack_env, run_env):
+        # Bohrium needs an extra include dir apart from
+        # the self.prefix.include dir
+        run_env.prepend_path("CPATH", self.prefix.include.bohrium)
+        run_env.set("BH_CONFIG", self.config_file)
+
+    #
+    # Quick tests
+    #
+    @run_after('install')
+    @on_package_attributes(run_tests=True)
+    def check_install(self):
+        spec = self.spec
+        test_env = {}
+
+        # Make sure the correct config is found
+        test_env["BH_CONFIG"] = self.config_file
+
+        # Remove the lib/spackenv directory from the PATH variable when
+        # executing the tests, becauses it messes with the JIT compilation
+        # inside Bohrium
+        paths = os.environ['PATH'].split(':')
+        paths = [p for p in paths if "spack/env" not in p]
+        test_env["PATH"] = ":".join(paths)
+
+        # Add the PYTHONPATH to bohrium to the PYTHONPATH environment
+        pythonpaths = [p for p in os.environ["PYTHONPATH"].split(":")]
+        pythonpaths.append(join_path(self.prefix,
+                                     spec['python'].package.site_packages_dir))
+        test_env["PYTHONPATH"] = ":".join(pythonpaths)
+
+        # Collect the stacks which should be available:
+        stacks = ["default"]
+        if "+openmp" in spec:
+            stacks.append("openmp")
+        if "+cuda" in spec:
+            stacks.append("cuda")
+        if "+opencl" in spec:
+            stacks.append("opencl")
+
+        # C++ compiler and compiler flags
+        cxx = Executable(self.compiler.cxx)
+        cxx_flags = ["-I", self.prefix.include,
+                     "-I", self.prefix.include.bohrium,
+                     "-L", self.prefix.lib, "-lbh", "-lbhxx"]
+
+        # Compile C++ test program
+        file_cxxadd = join_path(os.path.dirname(self.module.__file__),
+                                "cxxadd.cpp")
+        cxx("-o", "test_cxxadd", file_cxxadd, *cxx_flags)
+        test_cxxadd = Executable("./test_cxxadd")
+
+        # Build python test commandline
+        file_pyadd = join_path(os.path.dirname(self.module.__file__),
+                               "pyadd.py")
+        test_pyadd = Executable(spec['python'].command.path + " " + file_pyadd)
+
+        # Run tests for each available stack
+        for bh_stack in stacks:
+            tty.info("Testing with bohrium stack '" + bh_stack + "'")
+            test_env["BH_STACK"] = bh_stack
+
+            cpp_output = test_cxxadd(output=str, env=test_env)
+            compare_output(cpp_output, "Success!\n")
+
+            # Python test (if +python)
+            if "+python" in spec:
+                py_output = test_pyadd(output=str, env=test_env)
+                compare_output(py_output, "Success!\n")
diff --git a/var/spack/repos/builtin/packages/bohrium/pyadd.py b/var/spack/repos/builtin/packages/bohrium/pyadd.py
new file mode 100644
index 0000000000..fc9f6968df
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bohrium/pyadd.py
@@ -0,0 +1,10 @@
+#!/usr/bin/env python
+import bohrium as bh
+a = bh.array([1, 2, 3])
+b = bh.array([3, 4, 5])
+c = a + b
+
+if bh.all(c == bh.array([4, 6, 8])):
+    print("Success!")
+else:
+    print("Failure, values not as expected.")
diff --git a/var/spack/repos/builtin/packages/bolt/package.py b/var/spack/repos/builtin/packages/bolt/package.py
new file mode 100644
index 0000000000..5d24e1fa15
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bolt/package.py
@@ -0,0 +1,31 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Bolt(CMakePackage):
+    """BOLT targets a high-performing OpenMP implementation,
+    especially specialized for fine-grain parallelism. Unlike other
+    OpenMP implementations, BOLT utilizes a lightweight threading
+    model for its underlying threading mechanism. It currently adopts
+    Argobots, a new holistic, low-level threading and tasking runtime,
+    in order to overcome shortcomings of conventional OS-level
+    threads. The current BOLT implementation is based on the OpenMP
+    runtime in LLVM, and thus it can be used with LLVM/Clang, Intel
+    OpenMP compiler, and GCC."""
+
+    homepage = "http://www.bolt-omp.org/"
+    url      = "https://github.com/pmodels/bolt/releases/download/v1.0b1/bolt-1.0b1.tar.gz"
+
+    version("1.0b1", "df76beb3a7f13ae2dcaf9ab099eea87b")
+
+    def cmake_args(self):
+        options = [
+            '-DLIBOMP_USE_ITT_NOTIFY=off',
+            '-DLIBOMP_USE_ARGOBOTS=on'
+        ]
+
+        return options
diff --git a/var/spack/repos/builtin/packages/bookleaf-cpp/package.py b/var/spack/repos/builtin/packages/bookleaf-cpp/package.py
new file mode 100644
index 0000000000..394a79fab7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bookleaf-cpp/package.py
@@ -0,0 +1,50 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class BookleafCpp(CMakePackage):
+    """BookLeaf is a 2D unstructured hydrodynamics mini-app."""
+
+    homepage = "https://github.com/UK-MAC/BookLeaf_Cpp"
+    url      = "https://github.com/UK-MAC/BookLeaf_Cpp/archive/v2.0.tar.gz"
+    git      = "https://github.com/UK-MAC/BookLeaf_Cpp.git"
+
+    version('develop', branch='develop')
+
+    version('2.0.2', sha256='787ade5045415d71d9bad55fe9f93598f3a0548d13e2ff80e752cc99f62fe6d3')
+    version('2.0.1', '34a5a9e7b2b5ffc98562656a4406ba5b')
+    version('2.0',   '69819ebcbae5eaa63d1a4de2c77cac85')
+
+    variant('typhon', default=True, description='Use Typhon')
+    variant('parmetis', default=False, description='Use ParMETIS')
+    variant('silo', default=False, description='Use Silo')
+    variant('caliper', default=False, description='Use Caliper')
+
+    depends_on('caliper', when='+caliper')
+    depends_on('parmetis', when='+parmetis')
+    depends_on('silo', when='+silo')
+    depends_on('typhon', when='+typhon')
+    depends_on('mpi', when='+typhon')
+    depends_on('yaml-cpp@0.6.0:')
+
+    def cmake_args(self):
+        spec = self.spec
+        cmake_args = []
+
+        if '+typhon' in spec:
+            cmake_args.append('-DENABLE_TYPHON=ON')
+
+        if '+parmetis' in spec:
+            cmake_args.append('-DENABLE_PARMETIS=ON')
+
+        if '+silo' in spec:
+            cmake_args.append('-DENABLE_SILO=ON')
+
+        if '+caliper' in spec:
+            cmake_args.append('-DENABLE_CALIPER=ON')
+
+        return cmake_args
diff --git a/var/spack/repos/builtin/packages/boost/boost_1.67.0_pgi.patch b/var/spack/repos/builtin/packages/boost/boost_1.67.0_pgi.patch
new file mode 100644
index 0000000000..b2c7acaf6b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/boost/boost_1.67.0_pgi.patch
@@ -0,0 +1,13 @@
+--- a/libs/filesystem/src/operations.cpp
++++ b/libs/filesystem/src/operations.cpp
+@@ -2056,10 +2056,6 @@
+     return ok;
+   }
+ 
+-#if defined(__PGI) && defined(__USE_FILE_OFFSET64)
+-#define dirent dirent64
+-#endif
+-
+   error_code dir_itr_first(void *& handle, void *& buffer,
+     const char* dir, string& target,
+     fs::file_status &, fs::file_status &)
diff --git a/var/spack/repos/builtin/packages/boost/package.py b/var/spack/repos/builtin/packages/boost/package.py
index 6134456188..5b51187fea 100644
--- a/var/spack/repos/builtin/packages/boost/package.py
+++ b/var/spack/repos/builtin/packages/boost/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import sys
 import os
@@ -38,18 +19,16 @@ class Boost(Package):
     """
     homepage = "http://www.boost.org"
     url      = "http://downloads.sourceforge.net/project/boost/boost/1.55.0/boost_1_55_0.tar.bz2"
+    git      = "https://github.com/boostorg/boost.git"
     list_url = "http://sourceforge.net/projects/boost/files/boost/"
     list_depth = 1
 
-    version('develop',
-            git='https://github.com/boostorg/boost.git',
-            branch='develop',
-            submodules=True)
-
-    version('1.65.1', '41d7542ce40e171f3f7982aff008ff0d',
-            url='https://dl.bintray.com/boostorg/release/1.65.1/source/boost_1_65_1.tar.bz2')
-    version('1.65.0', '5512d3809801b0a1b9dd58447b70915d',
-            url='https://dl.bintray.com/boostorg/release/1.65.0/source/boost_1_65_0.tar.bz2')
+    version('develop', branch='develop', submodules=True)
+    version('1.68.0', '18863a7cae4d58ae85eb63d400f774f60a383411')
+    version('1.67.0', '694ae3f4f899d1a80eb7a3b31b33be73c423c1ae')
+    version('1.66.0', 'b6b284acde2ad7ed49b44e856955d7b1ea4e9459')
+    version('1.65.1', '41d7542ce40e171f3f7982aff008ff0d')
+    version('1.65.0', '5512d3809801b0a1b9dd58447b70915d')
     # NOTE: 1.64.0 seems fine for *most* applications, but if you need
     #       +python and +mpi, there seem to be errors with out-of-date
     #       API calls from mpi/python.
@@ -91,6 +70,7 @@ class Boost(Package):
     default_install_libs = set(['atomic',
                                 'chrono',
                                 'date_time',
+                                'exception',
                                 'filesystem',
                                 'graph',
                                 'iostreams',
@@ -119,6 +99,11 @@ class Boost(Package):
         variant(lib, default=(lib not in default_noinstall_libs),
                 description="Compile with {0} library".format(lib))
 
+    variant('cxxstd',
+            default='default',
+            values=('default', '98', '11', '14', '17'),
+            multi=False,
+            description='Use the specified C++ standard when building.')
     variant('debug', default=False,
             description='Switch to the debug version of Boost')
     variant('shared', default=True,
@@ -129,22 +114,24 @@ class Boost(Package):
             description="Build single-threaded versions of libraries")
     variant('icu', default=False,
             description="Build with Unicode and ICU suport")
-    variant('graph', default=False,
-            description="Build the Boost Graph library")
     variant('taggedlayout', default=False,
             description="Augment library names with build options")
     variant('versionedlayout', default=False,
             description="Augment library layout with versioned subdirs")
     variant('clanglibcpp', default=False,
             description='Compile with clang libc++ instead of libstdc++')
+    variant('numpy', default=False,
+            description='Build the Boost NumPy library (requires +python)')
 
     depends_on('icu4c', when='+icu')
     depends_on('python', when='+python')
     depends_on('mpi', when='+mpi')
     depends_on('bzip2', when='+iostreams')
     depends_on('zlib', when='+iostreams')
+    depends_on('py-numpy', when='+numpy', type=('build', 'run'))
 
     conflicts('+taggedlayout', when='+versionedlayout')
+    conflicts('+numpy', when='~python')
 
     # Patch fix from https://svn.boost.org/trac/boost/ticket/11856
     patch('boost_11856.patch', when='@1.60.0%gcc@4.4.7')
@@ -158,14 +145,19 @@ class Boost(Package):
     patch('xl_1_62_0_le.patch', when='@1.62.0%xl')
 
     # Patch fix from https://svn.boost.org/trac/boost/ticket/10125
-    patch('call_once_variadic.patch', when='@1.55.0:1.55.9999%gcc@5.0:5.9')
+    patch('call_once_variadic.patch', when='@1.54.0:1.55.9999%gcc@5.0:5.9')
 
     # Patch fix for PGI compiler
+    patch('boost_1.67.0_pgi.patch', when='@1.67.0%pgi')
     patch('boost_1.63.0_pgi.patch', when='@1.63.0%pgi')
     patch('boost_1.63.0_pgi_17.4_workaround.patch', when='@1.63.0%pgi@17.4')
 
     def url_for_version(self, version):
-        url = "http://downloads.sourceforge.net/project/boost/boost/{0}/boost_{1}.tar.bz2"
+        if version >= Version('1.63.0'):
+            url = "https://dl.bintray.com/boostorg/release/{0}/source/boost_{1}.tar.bz2"
+        else:
+            url = "http://downloads.sourceforge.net/project/boost/boost/{0}/boost_{1}.tar.bz2"
+
         return url.format(version.dotted, version.underscored)
 
     def determine_toolset(self, spec):
@@ -189,6 +181,10 @@ class Boost(Package):
         return 'gcc'
 
     def bjam_python_line(self, spec):
+        # avoid "ambiguous key" error
+        if spec.satisfies('@:1.58'):
+            return ''
+
         return 'using python : {0} : {1} : {2} : {3} ;\n'.format(
             spec['python'].version.up_to(2),
             spec['python'].command.path,
@@ -196,10 +192,10 @@ class Boost(Package):
             spec['python'].libs[0]
         )
 
-    def determine_bootstrap_options(self, spec, withLibs, options):
-        boostToolsetId = self.determine_toolset(spec)
-        options.append('--with-toolset=%s' % boostToolsetId)
-        options.append("--with-libraries=%s" % ','.join(withLibs))
+    def determine_bootstrap_options(self, spec, with_libs, options):
+        boost_toolset_id = self.determine_toolset(spec)
+        options.append('--with-toolset=%s' % boost_toolset_id)
+        options.append("--with-libraries=%s" % ','.join(with_libs))
 
         if '+python' in spec:
             options.append('--with-python=%s' % spec['python'].command.path)
@@ -213,7 +209,7 @@ class Boost(Package):
                 # error: duplicate initialization of intel-linux with the following parameters:  # noqa
                 # error: version = <unspecified>
                 # error: previous initialization at ./user-config.jam:1
-                f.write("using {0} : : {1} ;\n".format(boostToolsetId,
+                f.write("using {0} : : {1} ;\n".format(boost_toolset_id,
                                                        spack_cxx))
 
             if '+mpi' in spec:
@@ -235,6 +231,26 @@ class Boost(Package):
             if '+python' in spec:
                 f.write(self.bjam_python_line(spec))
 
+    def cxxstd_to_flag(self, std):
+        flag = ''
+        if self.spec.variants['cxxstd'].value == '98':
+            flag = self.compiler.cxx98_flag
+        elif self.spec.variants['cxxstd'].value == '11':
+            flag = self.compiler.cxx11_flag
+        elif self.spec.variants['cxxstd'].value == '14':
+            flag = self.compiler.cxx14_flag
+        elif self.spec.variants['cxxstd'].value == '17':
+            flag = self.compiler.cxx17_flag
+        elif self.spec.variants['cxxstd'].value == 'default':
+            # Let the compiler do what it usually does.
+            pass
+        else:
+            # The user has selected a (new?) legal value that we've
+            # forgotten to deal with here.
+            tty.die("INTERNAL ERROR: cannot accommodate unexpected variant ",
+                    "cxxstd={0}".format(spec.variants['cxxstd'].value))
+        return flag
+
     def determine_b2_options(self, spec, options):
         if '+debug' in spec:
             options.append('variant=debug')
@@ -251,16 +267,16 @@ class Boost(Package):
                 '-s', 'ZLIB_INCLUDE=%s' % spec['zlib'].prefix.include,
                 '-s', 'ZLIB_LIBPATH=%s' % spec['zlib'].prefix.lib])
 
-        linkTypes = ['static']
+        link_types = ['static']
         if '+shared' in spec:
-            linkTypes.append('shared')
+            link_types.append('shared')
 
-        threadingOpts = []
+        threading_opts = []
         if '+multithreaded' in spec:
-            threadingOpts.append('multi')
+            threading_opts.append('multi')
         if '+singlethreaded' in spec:
-            threadingOpts.append('single')
-        if not threadingOpts:
+            threading_opts.append('single')
+        if not threading_opts:
             raise RuntimeError("At least one of {singlethreaded, " +
                                "multithreaded} must be enabled")
 
@@ -269,13 +285,13 @@ class Boost(Package):
         elif '+versionedlayout' in spec:
             layout = 'versioned'
         else:
-            if len(threadingOpts) > 1:
+            if len(threading_opts) > 1:
                 raise RuntimeError("Cannot build both single and " +
                                    "multi-threaded targets with system layout")
             layout = 'system'
 
         options.extend([
-            'link=%s' % ','.join(linkTypes),
+            'link=%s' % ','.join(link_types),
             '--layout=%s' % layout
         ])
 
@@ -284,6 +300,19 @@ class Boost(Package):
                 'toolset=%s' % self.determine_toolset(spec)
             ])
 
+        # Other C++ flags.
+        cxxflags = []
+
+        # Deal with C++ standard.
+        if spec.satisfies('@1.66:'):
+            if spec.variants['cxxstd'].value != 'default':
+                options.append('cxxstd={0}'.format(
+                    spec.variants['cxxstd'].value))
+        else:  # Add to cxxflags for older Boost.
+            flag = self.cxxstd_to_flag(spec.variants['cxxstd'].value)
+            if flag:
+                cxxflags.append(flag)
+
         # clang is not officially supported for pre-compiled headers
         # and at least in clang 3.9 still fails to build
         #   http://www.boost.org/build/doc/html/bbv2/reference/precompiled_headers.html
@@ -291,11 +320,14 @@ class Boost(Package):
         if spec.satisfies('%clang'):
             options.extend(['pch=off'])
             if '+clanglibcpp' in spec:
+                cxxflags.append('-stdlib=libc++')
                 options.extend(['toolset=clang',
-                                'cxxflags="-stdlib=libc++"',
                                 'linkflags="-stdlib=libc++"'])
 
-        return threadingOpts
+        if cxxflags:
+            options.append('cxxflags="{0}"'.format(' '.join(cxxflags)))
+
+        return threading_opts
 
     def add_buildopt_symlinks(self, prefix):
         with working_dir(prefix.lib):
@@ -314,11 +346,11 @@ class Boost(Package):
             force_symlink('/usr/bin/libtool', join_path(newdir, 'libtool'))
             env['PATH'] = newdir + ':' + env['PATH']
 
-        withLibs = list()
+        with_libs = list()
         for lib in Boost.all_libs:
             if "+{0}".format(lib) in spec:
-                withLibs.append(lib)
-        if not withLibs:
+                with_libs.append(lib)
+        if not with_libs:
             # if no libraries are specified for compilation, then you dont have
             # to configure/build anything, just copy over to the prefix
             # directory.
@@ -330,25 +362,27 @@ class Boost(Package):
 
         # Remove libraries that the release version does not support
         if not spec.satisfies('@1.54.0:'):
-            withLibs.remove('log')
+            with_libs.remove('log')
         if not spec.satisfies('@1.53.0:'):
-            withLibs.remove('atomic')
+            with_libs.remove('atomic')
         if not spec.satisfies('@1.48.0:'):
-            withLibs.remove('locale')
+            with_libs.remove('locale')
         if not spec.satisfies('@1.47.0:'):
-            withLibs.remove('chrono')
+            with_libs.remove('chrono')
         if not spec.satisfies('@1.43.0:'):
-            withLibs.remove('random')
+            with_libs.remove('random')
+        if not spec.satisfies('@1.39.0:'):
+            with_libs.remove('exception')
         if '+graph' in spec and '+mpi' in spec:
-            withLibs.append('graph_parallel')
+            with_libs.append('graph_parallel')
 
         # to make Boost find the user-config.jam
-        env['BOOST_BUILD_PATH'] = './'
+        env['BOOST_BUILD_PATH'] = self.stage.source_path
 
         bootstrap = Executable('./bootstrap.sh')
 
         bootstrap_options = ['--prefix=%s' % prefix]
-        self.determine_bootstrap_options(spec, withLibs, bootstrap_options)
+        self.determine_bootstrap_options(spec, with_libs, bootstrap_options)
 
         bootstrap(*bootstrap_options)
 
@@ -360,15 +394,20 @@ class Boost(Package):
         # in 1.59 max jobs became dynamic
         if jobs > 64 and spec.satisfies('@:1.58'):
             jobs = 64
-        b2_options = ['-j', '%s' % jobs]
 
-        threadingOpts = self.determine_b2_options(spec, b2_options)
+        b2_options = [
+            '-j', '%s' % jobs,
+            '--user-config=%s' % os.path.join(
+                self.stage.source_path, 'user-config.jam')
+        ]
+
+        threading_opts = self.determine_b2_options(spec, b2_options)
 
         b2('--clean')
 
         # In theory it could be done on one call but it fails on
         # Boost.MPI if the threading options are not separated.
-        for threadingOpt in threadingOpts:
+        for threadingOpt in threading_opts:
             b2('install', 'threading=%s' % threadingOpt, *b2_options)
 
         if '+multithreaded' in spec and '~taggedlayout' in spec:
diff --git a/var/spack/repos/builtin/packages/boostmplcartesianproduct/package.py b/var/spack/repos/builtin/packages/boostmplcartesianproduct/package.py
index 7ddc65b439..d38609235c 100644
--- a/var/spack/repos/builtin/packages/boostmplcartesianproduct/package.py
+++ b/var/spack/repos/builtin/packages/boostmplcartesianproduct/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/bowtie/package.py b/var/spack/repos/builtin/packages/bowtie/package.py
index 8958352bd1..50f4c3e1cd 100644
--- a/var/spack/repos/builtin/packages/bowtie/package.py
+++ b/var/spack/repos/builtin/packages/bowtie/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/bowtie2/package.py b/var/spack/repos/builtin/packages/bowtie2/package.py
index 677020f60f..7b016710ed 100644
--- a/var/spack/repos/builtin/packages/bowtie2/package.py
+++ b/var/spack/repos/builtin/packages/bowtie2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 from glob import glob
 
@@ -33,6 +14,7 @@ class Bowtie2(Package):
     homepage = "bowtie-bio.sourceforge.net/bowtie2/index.shtml"
     url      = "http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.3.1/bowtie2-2.3.1-source.zip"
 
+    version('2.3.4.1', '8371bbb6eb02ae99c5cf633054265cb9')
     version('2.3.1', 'b4efa22612e98e0c23de3d2c9f2f2478')
     version('2.3.0', '3ab33f30f00f3c30fec1355b4e569ea2')
     version('2.2.5', '51fa97a862d248d7ee660efc1147c75f')
@@ -48,7 +30,7 @@ class Bowtie2(Package):
     patch('bowtie2-2.3.0.patch', when='@2.3.0', level=0)
 
     # seems to have trouble with 6's -std=gnu++14
-    conflicts('%gcc@6:')
+    conflicts('%gcc@6:', when='@:2.3.1')
 
     @run_before('install')
     def filter_sbang(self):
diff --git a/var/spack/repos/builtin/packages/boxlib/package.py b/var/spack/repos/builtin/packages/boxlib/package.py
index 833a027c29..c5f88f4896 100644
--- a/var/spack/repos/builtin/packages/boxlib/package.py
+++ b/var/spack/repos/builtin/packages/boxlib/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -49,7 +30,7 @@ class Boxlib(CMakePackage):
 
         options.extend([
             '-DBL_SPACEDIM=%d' % int(spec.variants['dims'].value),
-            '-DENABLE_POSITION_INDEPENDENT_CODE=ON',
+            '-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON',
             '-DENABLE_FBASELIB=ON',
             '-DCMAKE_C_COMPILER=%s' % spec['mpi'].mpicc,
             '-DCMAKE_CXX_COMPILER=%s' % spec['mpi'].mpicxx,
diff --git a/var/spack/repos/builtin/packages/bpp-core/package.py b/var/spack/repos/builtin/packages/bpp-core/package.py
index 96a775cb60..d52e51519d 100644
--- a/var/spack/repos/builtin/packages/bpp-core/package.py
+++ b/var/spack/repos/builtin/packages/bpp-core/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/bpp-phyl/package.py b/var/spack/repos/builtin/packages/bpp-phyl/package.py
index 3453f85a9d..9564468e3d 100644
--- a/var/spack/repos/builtin/packages/bpp-phyl/package.py
+++ b/var/spack/repos/builtin/packages/bpp-phyl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/bpp-seq/package.py b/var/spack/repos/builtin/packages/bpp-seq/package.py
index bd3219523f..bd16f0828d 100644
--- a/var/spack/repos/builtin/packages/bpp-seq/package.py
+++ b/var/spack/repos/builtin/packages/bpp-seq/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/bpp-suite/package.py b/var/spack/repos/builtin/packages/bpp-suite/package.py
index 13fc341cfa..acf0fadf2f 100644
--- a/var/spack/repos/builtin/packages/bpp-suite/package.py
+++ b/var/spack/repos/builtin/packages/bpp-suite/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/bracken/package.py b/var/spack/repos/builtin/packages/bracken/package.py
new file mode 100644
index 0000000000..ed48722a59
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bracken/package.py
@@ -0,0 +1,56 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Bracken(Package):
+    """Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly
+    accurate statistical method that computes the abundance of species in DNA
+    sequences from a metagenomics sample."""
+
+    homepage = "https://ccb.jhu.edu/software/bracken"
+    url      = "https://github.com/jenniferlu717/Bracken/archive/1.0.0.tar.gz"
+
+    version('1.0.0', 'bd91805655269c5f3becb8f8028bab6d')
+
+    depends_on('perl')
+    depends_on('python@2.7:')
+    depends_on('perl-exporter-tiny')
+    depends_on('perl-list-moreutils')
+    depends_on('perl-parallel-forkmanager')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install_tree('sample_data', prefix.sample_data)
+
+        filter_file(
+            r'#!/bin/env perl',
+            '#!/usr/bin/env perl',
+            'count-kmer-abundances.pl'
+        )
+
+        filter_file(
+            r'#!/usr/bin/python',
+            '#!/usr/bin/env python',
+            'est_abundance.py'
+        )
+
+        filter_file(
+            r'#!/usr/bin/python',
+            '#!/usr/bin/env python',
+            'generate_kmer_distribution.py'
+        )
+
+        files = (
+            'count-kmer-abundances.pl',
+            'est_abundance.py',
+            'generate_kmer_distribution.py',
+        )
+
+        chmod = which('chmod')
+        for name in files:
+            install(name, prefix.bin)
+            chmod('+x', join_path(self.prefix.bin, name))
diff --git a/var/spack/repos/builtin/packages/braker/package.py b/var/spack/repos/builtin/packages/braker/package.py
index 97fe9f710a..a295a4943a 100644
--- a/var/spack/repos/builtin/packages/braker/package.py
+++ b/var/spack/repos/builtin/packages/braker/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,12 +11,18 @@ class Braker(Package):
        that combines the advantages of GeneMark-ET and AUGUSTUS"""
 
     homepage = "http://exon.gatech.edu/braker1.html"
-    url      = "http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER1_v1.11.tar.gz"
+    url      = "http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER_v2.1.0.tar.gz"
+    list_url = "http://bioinf.uni-greifswald.de/augustus/binaries/old"
 
-    version('1.11', '297efe4cabdd239b710ac2c45d81f6a5')
+    version('2.1.0', '5f974abcceb9f96a11668fa20a6f6a56')
+    version('1.11', '297efe4cabdd239b710ac2c45d81f6a5',
+            url='http://bioinf.uni-greifswald.de/augustus/binaries/old/BRAKER1_v1.11.tar.gz')
 
     depends_on('perl', type=('build', 'run'))
-    depends_on('augustus')
+    depends_on('perl-scalar-util-numeric', type=('build', 'run'))
+    depends_on('perl-parallel-forkmanager', type=('build', 'run'))
+    depends_on('perl-file-which', type=('build', 'run'))
+    depends_on('augustus@3.2.3')
     depends_on('genemark-et')
     depends_on('bamtools')
     depends_on('samtools')
diff --git a/var/spack/repos/builtin/packages/branson/package.py b/var/spack/repos/builtin/packages/branson/package.py
index 7eedf7135e..b87e91f08a 100644
--- a/var/spack/repos/builtin/packages/branson/package.py
+++ b/var/spack/repos/builtin/packages/branson/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,13 +13,14 @@ class Branson(CMakePackage):
 
     homepage = "https://github.com/lanl/branson"
     url      = "https://github.com/lanl/branson/archive/1.01.zip"
+    git      = "https://github.com/lanl/branson.git"
 
     tags = ['proxy-app']
 
-    version('develop', git='https://github.com/lanl/branson', branch='develop')
+    version('develop', branch='develop')
     version('1.01', 'cf7095a887a8dd7d417267615bd0452a')
 
-    depends_on('mpi')
+    depends_on('mpi@2:')
     depends_on('boost')
     depends_on('metis')
     depends_on('parmetis')
diff --git a/var/spack/repos/builtin/packages/breakdancer/package.py b/var/spack/repos/builtin/packages/breakdancer/package.py
new file mode 100644
index 0000000000..c068094d6a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/breakdancer/package.py
@@ -0,0 +1,52 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Breakdancer(CMakePackage):
+    """BreakDancer-1.3.6, released under GPLv3, is a perl/Cpp package that
+    provides genome-wide detection of structural variants from next generation
+    paired-end sequencing reads. It includes two complementary programs.
+    BreakDancerMax predicts five types of structural variants: insertions,
+    deletions, inversions, inter- and intra-chromosomal translocations from
+    next-generation short paired-end sequencing reads using read pairs that are
+    mapped with unexpected separation distances or orientation.
+    BreakDancerMini focuses on detecting small indels (usually between 10bp and
+    100bp) using normally mapped read pairs.."""
+
+    homepage = "http://gmt.genome.wustl.edu/packages/breakdancer"
+    url      = "https://github.com/genome/breakdancer/archive/v1.4.5.tar.gz"
+
+    version('1.4.5', sha256='5d74f3a90f5c69026ebb4cf4cb9ccc51ec8dd49ac7a88595a1efabd5a73e92b6')
+    version('master', submodules='true', 
+            git='https://github.com/genome/breakdancer.git', preferred=True)
+
+    phases = ['edit', 'cmake', 'build', 'install']
+
+    depends_on('zlib')
+
+    depends_on('perl-statistics-descriptive', type='run')
+    depends_on('perl-math-cdf', type='run')
+    depends_on('perl-gd-graph', type='run')
+    depends_on('perl-gdgraph-histogram', type='run')
+    depends_on('perl-list-moreutils', type='run')
+    depends_on('perl-exporter-tiny', type='run')
+
+    # TODO: remove git submodules, and depend on boost & samtools
+
+    parallel = False
+
+    def setup_environment(self, spack_env, run_env):
+        # get the perl tools in the path
+        run_env.prepend_path('PATH', self.prefix.lib)
+
+    def edit(self, spec, prefix):
+        # perl tools end up in a silly lib subdirectory, fixing that
+        filter_file(r'set\(SUPPORT_LIBDIR lib\/breakdancer-max\$ \
+                    \{EXE_VERSION_SUFFIX\}\)',
+                    'set(SUPPORT_LIBDIR lib)',
+                    join_path(self.stage.source_path,
+                              'perl', 'CMakeLists.txt'))
diff --git a/var/spack/repos/builtin/packages/breseq/package.py b/var/spack/repos/builtin/packages/breseq/package.py
new file mode 100644
index 0000000000..6e406fba6a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/breseq/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Breseq(AutotoolsPackage):
+    """breseq is a computational pipeline for finding mutations relative to a
+    reference sequence in short-read DNA re-sequencing data for haploid
+    microbial-sized genomes."""
+
+    homepage = "http://barricklab.org/breseq"
+    url      = "https://github.com/barricklab/breseq/archive/v0.31.1.tar.gz"
+
+    version('0.31.1', 'a4e602d5481f8692833ba3d5a3cd0394')
+
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool', type='build')
+    depends_on('m4', type='build')
+
+    depends_on('bedtools2', type='run')
+    depends_on('r', type='run')
diff --git a/var/spack/repos/builtin/packages/brigand/package.py b/var/spack/repos/builtin/packages/brigand/package.py
index 4c946d4f66..f92b2814b3 100644
--- a/var/spack/repos/builtin/packages/brigand/package.py
+++ b/var/spack/repos/builtin/packages/brigand/package.py
@@ -1,41 +1,20 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
 
 class Brigand(Package):
-    """
-    Brigand Meta-programming library
-    """
+    """Brigand Meta-programming library"""
 
     homepage = "https://github.com/edouarda/brigand"
     url      = "https://github.com/edouarda/brigand/archive/1.0.0.tar.gz"
+    git      = "https://github.com/edouarda/brigand.git"
 
-    version('master', git='https://github.com/edouarda/brigand.git',
-            branch='master')
+    version('master', branch='master')
     version('1.3.0', '0bea9713b3b712229aed289e218d577b')
     version('1.2.0', '32c0f73e7e666d33ff123334f5c9c92f')
     version('1.1.0', '073b7c8e2cbda3a81bbeb1ea5b9ca0eb')
diff --git a/var/spack/repos/builtin/packages/bsseeker2/package.py b/var/spack/repos/builtin/packages/bsseeker2/package.py
index 48b2fc1e6f..f066a3e7ea 100644
--- a/var/spack/repos/builtin/packages/bsseeker2/package.py
+++ b/var/spack/repos/builtin/packages/bsseeker2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/bucky/package.py b/var/spack/repos/builtin/packages/bucky/package.py
index eeac2ab2b6..98b71eb8ec 100644
--- a/var/spack/repos/builtin/packages/bucky/package.py
+++ b/var/spack/repos/builtin/packages/bucky/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/bumpversion/package.py b/var/spack/repos/builtin/packages/bumpversion/package.py
new file mode 100644
index 0000000000..66dff78fc9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bumpversion/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Bumpversion(PythonPackage):
+    """Version-bump your software with a single command."""
+
+    homepage = "https://pypi.python.org/pypi/bumpversion"
+    url      = "https://pypi.io/packages/source/b/bumpversion/bumpversion-0.5.0.tar.gz"
+
+    version('0.5.3', 'c66a3492eafcf5ad4b024be9fca29820')
+    version('0.5.0', '222ba619283d6408ce1bfbb0b5b542f3')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/busco/package.py b/var/spack/repos/builtin/packages/busco/package.py
index 2b50abb40a..e0d56e6d81 100644
--- a/var/spack/repos/builtin/packages/busco/package.py
+++ b/var/spack/repos/builtin/packages/busco/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,10 +11,16 @@ class Busco(PythonPackage):
        Universal Single-Copy Orthologs"""
 
     homepage = "http://busco.ezlab.org/"
-    url      = "https://gitlab.com/ezlab/busco"
+    url      = "https://gitlab.com/api/v4/projects/ezlab%2Fbusco/repository/archive.tar.gz?sha=2.0.1"
+    git      = "https://gitlab.com/ezlab/busco.git"
+
+    # TODO: check the installation procedure for version 3.0.2
+    # and uncomment the following line
+    # version('3.0.2', '31d80042bb7e96422843fa43d0acbd21')
 
-    version('3.0.1', git='https://gitlab.com/ezlab/busco.git', commit='078252e00399550d7b0e8941cd4d986c8e868a83')
-    version('2.0.1', git='https://gitlab.com/ezlab/busco.git', commit='89aa1ab2527f03a87a214ca90a504ad236582a11')
+    # There is no tag for version 3.0.1
+    version('3.0.1', commit='078252e00399550d7b0e8941cd4d986c8e868a83')
+    version('2.0.1', '4dbcc8a0c18fa8f8312c103eb2fbb4e2')
 
     depends_on('python', type=('build', 'run'))
     depends_on('blast-plus')
diff --git a/var/spack/repos/builtin/packages/butter/package.py b/var/spack/repos/builtin/packages/butter/package.py
index 602f68c5b5..787a4aa759 100644
--- a/var/spack/repos/builtin/packages/butter/package.py
+++ b/var/spack/repos/builtin/packages/butter/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/bwa/package.py b/var/spack/repos/builtin/packages/bwa/package.py
index 7f260fcdc9..c32dbaa72a 100644
--- a/var/spack/repos/builtin/packages/bwa/package.py
+++ b/var/spack/repos/builtin/packages/bwa/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,12 +12,10 @@ class Bwa(Package):
     homepage = "http://github.com/lh3/bwa"
     url      = "https://github.com/lh3/bwa/releases/download/v0.7.15/bwa-0.7.15.tar.bz2"
 
-    version('0.7.17', '82cba7ef695538e6a38b9d4156837381',
-            url="https://github.com/lh3/bwa/releases/download/v0.7.17/bwa-0.7.17.tar.bz2")
-    version('0.7.15', 'fcf470a46a1dbe2f96a1c5b87c530554',
-            url="https://github.com/lh3/bwa/releases/download/v0.7.15/bwa-0.7.15.tar.bz2")
-    version('0.7.13', 'f094f609438511766c434178a3635ab4',
-            url="https://github.com/lh3/bwa/releases/download/v0.7.13/bwa-0.7.13.tar.bz2")
+    version('0.7.17', '82cba7ef695538e6a38b9d4156837381')
+    version('0.7.16a', 'c5115c9a5ea0406848500e4b23a7708c')
+    version('0.7.15', 'fcf470a46a1dbe2f96a1c5b87c530554')
+    version('0.7.13', 'f094f609438511766c434178a3635ab4')
     version('0.7.12', 'e24a587baaad411d5da89516ad7a261a',
             url='https://github.com/lh3/bwa/archive/0.7.12.tar.gz')
 
diff --git a/var/spack/repos/builtin/packages/bwtool/package.py b/var/spack/repos/builtin/packages/bwtool/package.py
new file mode 100644
index 0000000000..d1505bc50f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bwtool/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Bwtool(AutotoolsPackage):
+    """bwtool is a command-line utility for bigWig files."""
+
+    homepage = "https://github.com/CRG-Barcelona/bwtool"
+    url      = "https://github.com/CRG-Barcelona/bwtool/archive/1.0.tar.gz"
+
+    version('1.0', 'cdd7a34ae457b587edfe7dc8a0bdbedd')
+
+    depends_on('libbeato')
diff --git a/var/spack/repos/builtin/packages/byobu/package.py b/var/spack/repos/builtin/packages/byobu/package.py
index 90f91db9e3..d81b641490 100644
--- a/var/spack/repos/builtin/packages/byobu/package.py
+++ b/var/spack/repos/builtin/packages/byobu/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -32,6 +13,8 @@ class Byobu(AutotoolsPackage):
     homepage = "http://www.byobu.co"
     url      = "https://launchpad.net/byobu/trunk/5.123/+download/byobu_5.123.orig.tar.gz"
 
+    version('5.127', '4bafc7cb69ff5b0ab6998816d58cd1ef7175e5de75abc1dd7ffd6d5288a4f63b')
+    version('5.125', 'f90f15771325e8be9360f301b52182d2')
     version('5.123', '961e0072c01c78c9ce4c20d1aa1b0dc4')
 
     depends_on('tmux', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/bzip2/package.py b/var/spack/repos/builtin/packages/bzip2/package.py
index d44e97207f..2f89b73b8e 100644
--- a/var/spack/repos/builtin/packages/bzip2/package.py
+++ b/var/spack/repos/builtin/packages/bzip2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,27 +13,33 @@ class Bzip2(Package):
     compressors), whilst being around twice as fast at compression
     and six times faster at decompression."""
 
-    homepage = "http://www.bzip.org"
-    url      = "http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz"
-    list_url = "http://www.bzip.org/downloads.html"
+    # FIXME: The bzip.org domain has expired:
+    # https://lwn.net/Articles/762264/
+    # This package will need to be updated when a new home is found.
+    homepage = "https://sourceware.org/bzip2/"
+    url      = "https://fossies.org/linux/misc/bzip2-1.0.6.tar.gz"
 
     version('1.0.6', '00b516f4704d4a7cb50a1d97e6e8e15b')
 
     variant('shared', default=True, description='Enables the build of shared libraries.')
 
+    depends_on('diffutils', type='build')
+
     # override default implementation
     @property
     def libs(self):
         shared = '+shared' in self.spec
         return find_libraries(
-            'libbz2', root=self.prefix, shared=shared, recurse=True
+            'libbz2', root=self.prefix, shared=shared, recursive=True
         )
 
     def patch(self):
         # bzip2 comes with two separate Makefiles for static and dynamic builds
         # Tell both to use Spack's compiler wrapper instead of GCC
-        filter_file(r'^CC=gcc', 'CC=cc', 'Makefile')
-        filter_file(r'^CC=gcc', 'CC=cc', 'Makefile-libbz2_so')
+        filter_file(r'^CC=gcc', 'CC={0}'.format(spack_cc), 'Makefile')
+        filter_file(
+            r'^CC=gcc', 'CC={0}'.format(spack_cc), 'Makefile-libbz2_so'
+        )
 
         # The Makefiles use GCC flags that are incompatible with PGI
         if self.compiler.name == 'pgi':
diff --git a/var/spack/repos/builtin/packages/c-blosc/package.py b/var/spack/repos/builtin/packages/c-blosc/package.py
index 8bc5a76ef7..fd2ecc70cb 100644
--- a/var/spack/repos/builtin/packages/c-blosc/package.py
+++ b/var/spack/repos/builtin/packages/c-blosc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 import sys
 
@@ -33,6 +14,7 @@ class CBlosc(CMakePackage):
     homepage = "http://www.blosc.org"
     url      = "https://github.com/Blosc/c-blosc/archive/v1.11.1.tar.gz"
 
+    version('1.12.1', '6fa4ecb7ef70803a190dd386bf4a2e93')
     version('1.11.1', 'e236550640afa50155f3881f2d300206')
     version('1.9.2',  'dd2d83069d74b36b8093f1c6b49defc5')
     version('1.9.1',  '7d708d3daadfacf984a87b71b1734ce2')
@@ -45,6 +27,8 @@ class CBlosc(CMakePackage):
     depends_on('cmake@2.8.10:', type='build')
     depends_on('snappy')
     depends_on('zlib')
+    depends_on('zstd')
+    depends_on('lz4')
 
     def cmake_args(self):
         args = []
@@ -54,6 +38,12 @@ class CBlosc(CMakePackage):
         else:
             args.append('-DDEACTIVATE_AVX2=ON')
 
+        if self.spec.satisfies('@1.12.0:'):
+            args.append('-DPREFER_EXTERNAL_SNAPPY=ON')
+            args.append('-DPREFER_EXTERNAL_ZLIB=ON')
+            args.append('-DPREFER_EXTERNAL_ZSTD=ON')
+            args.append('-DPREFER_EXTERNAL_LZ4=ON')
+
         return args
 
     @run_after('install')
diff --git a/var/spack/repos/builtin/packages/c-lime/package.py b/var/spack/repos/builtin/packages/c-lime/package.py
new file mode 100644
index 0000000000..916f95ffd6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/c-lime/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class CLime(AutotoolsPackage):
+    """LIME (which can stand for Lattice QCD Interchange Message Encapsulation
+       or more generally, Large Internet Message Encapsulation) is a simple
+       packaging scheme for combining records containing ASCII and/or binary
+       data."""
+
+    homepage = "https://usqcd-software.github.io/c-lime/"
+    url      = "https://github.com/usqcd-software/c-lime/archive/qio2-3-9.tar.gz"
+
+    version('2-3-9', '28257e7ae75dc68c7c920e3e16db0ec9')
diff --git a/var/spack/repos/builtin/packages/cabana/package.py b/var/spack/repos/builtin/packages/cabana/package.py
new file mode 100644
index 0000000000..115bdf6a2b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cabana/package.py
@@ -0,0 +1,36 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Cabana(CMakePackage):
+    """The Exascale Co-Design Center for Particle Applications Toolkit
+    """
+    homepage = "https://github.com/ECP-copa/Cabana"
+    git      = "https://github.com/ECP-copa/Cabana.git"
+    url      = "https://github.com/ECP-copa/Cabana/archive/0.1.0.tar.gz"
+
+    version('develop', branch='master')
+    version('0.1.0', sha256='3280712facf6932b9d1aff375b24c932abb9f60a8addb0c0a1950afd0cb9b9cf')
+    version('0.1.0-rc0', sha256='73754d38aaa0c2a1e012be6959787108fec142294774c23f70292f59c1bdc6c5')
+
+    variant('serial', default=True, description="enable Serial backend (default)")
+    variant('openmp', default=False, description="enable OpenMP backend")
+
+    depends_on("cmake@3.9:", type='build')
+    depends_on("kokkos+serial", when="+serial")
+    depends_on("kokkos+openmp", when="+openmp")
+
+    def cmake_args(self):
+        options = [
+            '-DCabana_ENABLE_TESTING=ON',
+            '-DCabana_ENABLE_Serial=%s'  % (
+                'On' if '+serial'  in self.spec else 'Off'),
+            '-DCabana_ENABLE_OpenMP=%s'  % (
+                'On' if '+openmp'  in self.spec else 'Off')
+        ]
+
+        return options
diff --git a/var/spack/repos/builtin/packages/caffe/package.py b/var/spack/repos/builtin/packages/caffe/package.py
index 730b293adb..97e3e643cc 100644
--- a/var/spack/repos/builtin/packages/caffe/package.py
+++ b/var/spack/repos/builtin/packages/caffe/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/cairo/package.py b/var/spack/repos/builtin/packages/cairo/package.py
index ec04e5ed38..b6c9deabe6 100644
--- a/var/spack/repos/builtin/packages/cairo/package.py
+++ b/var/spack/repos/builtin/packages/cairo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,6 +12,7 @@ class Cairo(AutotoolsPackage):
     homepage = "http://cairographics.org"
     url      = "http://cairographics.org/releases/cairo-1.14.8.tar.xz"
 
+    version('1.14.12', '490025a0ba0622a853010f49fb6343f29fb70b9b')
     version('1.14.8', 'c6f7b99986f93c9df78653c3e6a3b5043f65145e')
     version('1.14.0', '53cf589b983412ea7f78feee2e1ba9cea6e3ebae')
 
@@ -45,7 +27,7 @@ class Cairo(AutotoolsPackage):
     depends_on("glib")
     depends_on("pixman")
     depends_on("freetype")
-    depends_on("pkg-config", type="build")
+    depends_on("pkgconfig", type="build")
     depends_on("fontconfig@2.10.91:")  # Require newer version of fontconfig.
 
     def configure_args(self):
diff --git a/var/spack/repos/builtin/packages/cairomm/package.py b/var/spack/repos/builtin/packages/cairomm/package.py
new file mode 100644
index 0000000000..323288ea5a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cairomm/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Cairomm(AutotoolsPackage):
+    """Cairomm is a C++ wrapper for the cairo graphics library."""
+
+    homepage = "https://www.cairographics.org/cairomm/"
+    url      = "https://cairographics.org/releases/cairomm-1.6.4.tar.gz"
+
+    version('1.6.4', '63561c62536173a98f03005dfe55c90e')
+    version('1.6.2', 'eac5d159e4cba98e32ea174483dee24e')
+
+    depends_on('cairo')
+    depends_on('libsigcpp')
diff --git a/var/spack/repos/builtin/packages/caliper/package.py b/var/spack/repos/builtin/packages/caliper/package.py
index e3fff54e6f..5896cfb420 100644
--- a/var/spack/repos/builtin/packages/caliper/package.py
+++ b/var/spack/repos/builtin/packages/caliper/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 import sys
@@ -36,13 +17,18 @@ class Caliper(CMakePackage):
     """
 
     homepage = "https://github.com/LLNL/Caliper"
-    url      = ""
+    git      = "https://github.com/LLNL/Caliper.git"
+
+    version('master')
+    version('1.7.0', tag='v1.7.0')
+    # version 1.6.0 is broken b/c it downloads the wrong gotcha version
+    version('1.6.0', tag='v1.6.0')
 
-    version('master', git='https://github.com/LLNL/Caliper.git')
+    is_linux = sys.platform.startswith('linux')
 
-    variant('mpi', default=True, 
+    variant('mpi', default=True,
             description='Enable MPI wrappers')
-    variant('dyninst', default=False, 
+    variant('dyninst', default=False,
             description='Enable symbol translation support with dyninst')
     # libunwind has some issues on Mac
     variant('callpath', default=sys.platform != 'darwin',
@@ -50,14 +36,23 @@ class Caliper(CMakePackage):
     # pthread_self() signature is incompatible with PAPI_thread_init() on Mac
     variant('papi', default=sys.platform != 'darwin',
             description='Enable PAPI service')
+    variant('libpfm', default=is_linux,
+            description='Enable libpfm (perf_events) service')
     # gotcha doesn't work on Mac
     variant('gotcha', default=sys.platform != 'darwin',
             description='Enable GOTCHA support')
+    variant('sampler', default=is_linux,
+            description='Enable sampling support on Linux')
+    variant('sosflow', default=False,
+            description='Enable SOSflow support')
 
+    depends_on('gotcha@1.0:', when='+gotcha')
     depends_on('dyninst', when='+dyninst')
     depends_on('papi', when='+papi')
+    depends_on('libpfm4', when='+libpfm')
     depends_on('mpi', when='+mpi')
-    depends_on('libunwind', when='+callpath')
+    depends_on('unwind', when='+callpath')
+    depends_on('sosflow', when='+sosflow')
 
     depends_on('cmake', type='build')
     depends_on('python', type='build')
@@ -67,17 +62,28 @@ class Caliper(CMakePackage):
 
         args = [
             '-DBUILD_TESTING=Off',
-            '-DWITH_DOCS=Off',
-            '-DWITH_TEST_APPS=Off',
+            '-DBUILD_DOCS=Off',
             '-DWITH_DYNINST=%s'  % ('On' if '+dyninst'  in spec else 'Off'),
             '-DWITH_CALLPATH=%s' % ('On' if '+callpath' in spec else 'Off'),
             '-DWITH_GOTCHA=%s'   % ('On' if '+gotcha'   in spec else 'Off'),
             '-DWITH_PAPI=%s'     % ('On' if '+papi'     in spec else 'Off'),
-            '-DWITH_MPI=%s'      % ('On' if '+mpi'      in spec else 'Off')
+            '-DWITH_LIBPFM=%s'   % ('On' if '+libpfm'   in spec else 'Off'),
+            '-DWITH_SOSFLOW=%s'  % ('On' if '+sosflow'  in spec else 'Off'),
+            '-DWITH_SAMPLER=%s'  % ('On' if '+sampler'  in spec else 'Off'),
+            '-DWITH_MPI=%s'      % ('On' if '+mpi'      in spec else 'Off'),
+            '-DWITH_MPIT=%s' % ('On' if spec.satisfies('^mpi@3:') else 'Off')
         ]
 
+        if '+gotcha' in spec:
+            args.append('-DUSE_EXTERNAL_GOTCHA=True')
         if '+papi' in spec:
-            args.append('-DPAPI_PREFIX=%s' % spec['papi'].prefix)
+            args.append('-DPAPI_PREFIX=%s'    % spec['papi'].prefix)
+        if '+libpfm' in spec:
+            args.append('-DLIBPFM_INSTALL=%s' % spec['libpfm4'].prefix)
+        if '+sosflow' in spec:
+            args.append('-DSOS_PREFIX=%s'     % spec['sosflow'].prefix)
+        if '+callpath' in spec:
+            args.append('-DLIBUNWIND_PREFIX=%s' % spec['libunwind'].prefix)
 
         if '+mpi' in spec:
             args.append('-DMPI_C_COMPILER=%s' % spec['mpi'].mpicc)
diff --git a/var/spack/repos/builtin/packages/callpath/package.py b/var/spack/repos/builtin/packages/callpath/package.py
index a9cb2bf420..479a2d0abc 100644
--- a/var/spack/repos/builtin/packages/callpath/package.py
+++ b/var/spack/repos/builtin/packages/callpath/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/camellia/package.py b/var/spack/repos/builtin/packages/camellia/package.py
new file mode 100644
index 0000000000..c97a74a0d3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/camellia/package.py
@@ -0,0 +1,44 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Camellia(CMakePackage):
+    """Camellia: user-friendly MPI-parallel adaptive finite element package,
+       with support for DPG and other hybrid methods, built atop Trilinos.
+    """
+
+    homepage = "https://bitbucket.org/nateroberts/Camellia"
+    git      = "https://bitbucket.org/nateroberts/camellia.git"
+
+    maintainers = ['CamelliaDPG']
+
+    version('master', branch='master')
+
+    variant('moab', default=True, description='Compile with MOAB to include support for reading standard mesh formats')
+
+    depends_on('trilinos+amesos+amesos2+belos+epetra+epetraext+exodus+ifpack+ifpack2+intrepid+intrepid2+kokkos+ml+muelu+sacado+shards+teuchos+tpetra+zoltan+mumps+superlu-dist+hdf5+zlib+pnetcdf@master,12.12.1:')
+    depends_on('moab@:4', when='+moab')
+    depends_on('hdf5@:1.8')
+    depends_on('mpi')
+
+    def cmake_args(self):
+        spec = self.spec
+        options = [
+            '-DTrilinos_PATH:PATH=%s' % spec['trilinos'].prefix,
+            '-DMPI_DIR:PATH=%s' % spec['mpi'].prefix,
+            '-DBUILD_FOR_INSTALL:BOOL=ON'
+        ]
+
+        if '+moab' in spec:
+            options.extend([
+                '-DENABLE_MOAB:BOOL=ON',
+                '-DMOAB_PATH:PATH=%s' % spec['moab'].prefix
+            ])
+        else:
+            options.append('-DENABLE_MOAB:BOOL=OFF')
+
+        return options
diff --git a/var/spack/repos/builtin/packages/candle-benchmarks/package.py b/var/spack/repos/builtin/packages/candle-benchmarks/package.py
index 7e5650c6f3..6b15e5ebec 100644
--- a/var/spack/repos/builtin/packages/candle-benchmarks/package.py
+++ b/var/spack/repos/builtin/packages/candle-benchmarks/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,17 +14,23 @@ class CandleBenchmarks(Package):
 
     tags = ['proxy-app', 'ecp-proxy-app']
 
-    version('1.0', '6eced30dc15374bc9f90a86d0396e470')
+    version('0.1', sha256='767f74f43ee3a5d4e0f26750f2a96b8433e25a9cd4f2d29938ac8acf263ab58d')
+    version('0.0', '6eced30dc15374bc9f90a86d0396e470')
+
+    variant('mpi', default=True, description='Build with MPI support')
 
-    depends_on('python@2.7:')
+    extends('python@2.7:')
     depends_on('py-theano +gpu', type=('build', 'run'))
     depends_on('py-keras', type=('build', 'run'))
-    depends_on('py-matplotlib +image', type=('build', 'run'))
+    depends_on('py-matplotlib +image@:2.2.3', type=('build', 'run'))
     depends_on('py-tqdm', type=('build', 'run'))
     depends_on('py-scikit-learn', type=('build', 'run'))
-    depends_on('opencv@3.2.0: +core +highgui +imgproc +jpeg +png +tiff +zlib +python -dnn')
+    depends_on('opencv@3.2.0: +core +highgui +imgproc +jpeg +png +tiff +zlib +python -dnn ~eigen ~gtk')
     depends_on('py-mdanalysis', type=('build', 'run'))
-    depends_on('py-mpi4py', type=('build', 'run'))
+    depends_on('py-mpi4py', when='+mpi', type=('build', 'run'))
+    depends_on('py-h5py~mpi', when='~mpi', type=('build', 'run'))
+    depends_on('py-h5py+mpi', when='+mpi', type=('build', 'run'))
+    depends_on('py-requests', type=('build', 'run'))
 
     # see #3244, but use external for now
     # depends_on('tensorflow')
diff --git a/var/spack/repos/builtin/packages/cantera/package.py b/var/spack/repos/builtin/packages/cantera/package.py
index 03dece3af8..b710163870 100644
--- a/var/spack/repos/builtin/packages/cantera/package.py
+++ b/var/spack/repos/builtin/packages/cantera/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
diff --git a/var/spack/repos/builtin/packages/canu/package.py b/var/spack/repos/builtin/packages/canu/package.py
index 0198246e72..1aec3384df 100644
--- a/var/spack/repos/builtin/packages/canu/package.py
+++ b/var/spack/repos/builtin/packages/canu/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,6 +13,7 @@ class Canu(MakefilePackage):
     homepage = "http://canu.readthedocs.io/"
     url      = "https://github.com/marbl/canu/archive/v1.5.tar.gz"
 
+    version('1.7.1', sha256='c314659c929ee05fd413274f391463a93f19b8337eabb7ee5de1ecfc061caafa')
     version('1.5', '65df275baa28ecf11b15dfd7343361e3')
 
     depends_on('gnuplot', type='run')
@@ -39,23 +21,14 @@ class Canu(MakefilePackage):
     depends_on('perl', type='run')
 
     build_directory = 'src'
+    build_targets = ['clean']
 
     def patch(self):
         # Use our perl, not whatever is in the environment
-        perl = self.spec['perl'].prefix.bin.perl
         filter_file(r'^#!/usr/bin/env perl',
-                    '#!{0}'.format(perl),
+                    '#!{0}'.format(self.spec['perl'].command.path),
                     'src/pipelines/canu.pl')
 
     def install(self, spec, prefix):
-        # replicate the Makefile logic here:
-        # https://github.com/marbl/canu/blob/master/src/Makefile#L344
-        uname = which('uname')
-        ostype = uname(output=str).strip()
-        machinetype = uname('-m', output=str).strip()
-        if machinetype == 'x86_64':
-            machinetype = 'amd64'
-        target_dir = '{0}-{1}'.format(ostype, machinetype)
-        bin = join_path(target_dir, 'bin')
-
-        install_tree(bin, prefix.bin)
+        with working_dir(self.build_directory):
+            make('all', 'TARGET_DIR={0}'.format(prefix))
diff --git a/var/spack/repos/builtin/packages/cap3/package.py b/var/spack/repos/builtin/packages/cap3/package.py
index 13568b40cd..e0d760ccbd 100644
--- a/var/spack/repos/builtin/packages/cap3/package.py
+++ b/var/spack/repos/builtin/packages/cap3/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/cares/package.py b/var/spack/repos/builtin/packages/cares/package.py
index ab3691be16..36c155a95e 100644
--- a/var/spack/repos/builtin/packages/cares/package.py
+++ b/var/spack/repos/builtin/packages/cares/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,10 +11,9 @@ class Cares(CMakePackage):
 
     homepage = "https://c-ares.haxx.se"
     url      = "https://github.com/c-ares/c-ares/archive/cares-1_13_0.tar.gz"
+    git      = "https://github.com/c-ares/c-ares.git"
 
-    version('develop', branch='master',
-            git='https://github.com/c-ares/c-ares.git')
-
+    version('develop', branch='master')
     version('1.13.0', 'cdb21052a7eb85261da22f83c0654cfd')
 
     def url_for_version(self, version):
diff --git a/var/spack/repos/builtin/packages/cask/package.py b/var/spack/repos/builtin/packages/cask/package.py
index e1ffe284e7..ba4d29d845 100644
--- a/var/spack/repos/builtin/packages/cask/package.py
+++ b/var/spack/repos/builtin/packages/cask/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 # Based on Homebrew's formula:
 # https://github.com/Homebrew/homebrew-core/blob/master/Formula/cask.rb
diff --git a/var/spack/repos/builtin/packages/casper/package.py b/var/spack/repos/builtin/packages/casper/package.py
new file mode 100644
index 0000000000..39754fe3b1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/casper/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Casper(MakefilePackage):
+    """CASPER (Context-Aware Scheme for Paired-End Read) is state-of-the art
+       merging tool in terms of accuracy and robustness. Using this
+       sophisticated merging method, we could get elongated reads from the
+       forward and reverse reads."""
+
+    homepage = "http://best.snu.ac.kr/casper/index.php?name=main"
+    url      = "http://best.snu.ac.kr/casper/program/casper_v0.8.2.tar.gz"
+
+    version('0.8.2', '9e83d32ff46b876f33eb1d7b545ec9c2')
+
+    depends_on('jellyfish@2.2.3:')
+    depends_on('boost')
+
+    conflicts('%gcc@7.1.0')
+
+    def install(self, spec, prefix):
+        install_tree('.', prefix)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PATH', self.spec.prefix)
diff --git a/var/spack/repos/builtin/packages/catalyst/package.py b/var/spack/repos/builtin/packages/catalyst/package.py
new file mode 100644
index 0000000000..d9be7b17dd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/catalyst/package.py
@@ -0,0 +1,152 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+import subprocess
+import llnl.util.tty as tty
+
+
+class Catalyst(CMakePackage):
+    """Catalyst is an in situ use case library, with an adaptable application
+    programming interface (API), that orchestrates the alliance between
+    simulation and analysis and/or visualization tasks."""
+
+    homepage = 'http://www.paraview.org'
+    url      = "http://www.paraview.org/files/v5.5/ParaView-v5.5.2.tar.gz"
+    _urlfmt_gz = 'http://www.paraview.org/files/v{0}/ParaView-v{1}{2}.tar.gz'
+    _urlfmt_xz = 'http://www.paraview.org/files/v{0}/ParaView-v{1}{2}.tar.xz' 
+
+    version('5.5.2', '7eb93c31a1e5deb7098c3b4275e53a4a')
+    version('5.5.1', 'a7d92a45837b67c3371006cc45163277')
+    version('5.5.0', 'a8f2f41edadffdcc89b37fdc9aa7f005')
+    version('5.4.1', '4030c70477ec5a85aa72d6fc86a30753')
+    version('5.4.0', 'b92847605bac9036414b644f33cb7163')
+    version('5.3.0', '68fbbbe733aa607ec13d1db1ab5eba71')
+    version('5.2.0', '4570d1a2a183026adb65b73c7125b8b0')
+    version('5.1.2', '44fb32fc8988fcdfbc216c9e40c3e925')
+    version('5.0.1', 'fdf206113369746e2276b95b257d2c9b')
+    version('4.4.0', 'fa1569857dd680ebb4d7ff89c2227378')
+
+    variant('python', default=False, description='Enable Python support')
+    variant('essentials', default=False, description='Enable Essentials support')
+    variant('extras', default=False, description='Enable Extras support')
+    variant('rendering', default=False, description='Enable Vtk Rendering support')
+
+    depends_on('git')
+    depends_on('mpi')
+    depends_on('python@2:2.8', when='+python', type=("build", "link", "run"))
+    depends_on('python', when='~python', type=("build"))
+    depends_on('mesa', when='+rendering')
+    depends_on("libx11", when='+rendering')
+    depends_on("libxt", when='+rendering')
+    depends_on('cmake@3.3:', type='build')
+
+    def url_for_version(self, version):
+        """Handle ParaView version-based custom URLs."""
+        if version < Version('5.1.0'):
+            return self._urlfmt_gz.format(version.up_to(2), version, '-source')
+        elif version < Version('5.6.0'):
+            return self._urlfmt_gz.format(version.up_to(2), version, '')
+        else:
+            return self._urlfmt_xz.format(version.up_to(2), version, '')
+
+    def do_stage(self, mirror_only=False):
+        """Unpacks and expands the fetched tarball.
+        Then, generate the catalyst source files."""
+        super(Catalyst, self).do_stage(mirror_only)
+
+        # extract the catalyst part
+        paraview_dir = os.path.join(self.stage.path,
+                                    'ParaView-v' + str(self.version))
+        catalyst_script = os.path.join(paraview_dir, 'Catalyst', 'catalyze.py')
+        catalyst_source_dir = os.path.abspath(self.root_cmakelists_dir)
+
+        command = ['python', catalyst_script,
+                   '-r', paraview_dir]
+
+        catalyst_edition = os.path.join(paraview_dir, 'Catalyst',
+                                        'Editions', 'Base')
+        command.append('-i')
+        command.append(catalyst_edition)
+        if '+python' in self.spec:
+            catalyst_edition = os.path.join(paraview_dir, 'Catalyst',
+                                            'Editions', 'Enable-Python')
+            command.append('-i')
+            command.append(catalyst_edition)
+        if '+essentials' in self.spec:
+            catalyst_edition = os.path.join(paraview_dir, 'Catalyst',
+                                            'Editions', 'Essentials')
+            command.append('-i')
+            command.append(catalyst_edition)
+        if '+extras' in self.spec:
+            catalyst_edition = os.path.join(paraview_dir, 'Catalyst',
+                                            'Editions', 'Extras')
+            command.append('-i')
+            command.append(catalyst_edition)
+        if '+rendering' in self.spec:
+            catalyst_edition = os.path.join(paraview_dir, 'Catalyst',
+                                            'Editions', 'Rendering-Base')
+            command.append('-i')
+            command.append(catalyst_edition)
+
+        command.append('-o')
+        command.append(catalyst_source_dir)
+
+        if not os.path.isdir(catalyst_source_dir):
+            os.mkdir(catalyst_source_dir)
+            subprocess.check_call(command)
+            tty.msg("Generated catalyst source in %s" % self.stage.path)
+        else:
+            tty.msg("Already generated %s in %s" % (self.name,
+                                                    self.stage.path))
+
+    def setup_environment(self, spack_env, run_env):
+        if os.path.isdir(self.prefix.lib64):
+            lib_dir = self.prefix.lib64
+        else:
+            lib_dir = self.prefix.lib
+        paraview_version = 'paraview-%s' % self.spec.version.up_to(2)
+        run_env.prepend_path('LIBRARY_PATH', join_path(lib_dir,
+                             paraview_version))
+        run_env.prepend_path('LD_LIBRARY_PATH', join_path(lib_dir,
+                             paraview_version))
+
+    @property
+    def root_cmakelists_dir(self):
+        """The relative path to the directory containing CMakeLists.txt
+
+        This path is relative to the root of the extracted tarball,
+        not to the ``build_directory``. Defaults to the current directory.
+
+        :return: directory containing CMakeLists.txt
+        """
+        return os.path.join(self.stage.path, 'Catalyst-v' + str(self.version))
+
+    @property
+    def build_directory(self):
+        """Returns the directory to use when building the package
+
+        :return: directory where to build the package
+        """
+        return join_path(os.path.abspath(self.root_cmakelists_dir),
+                         'spack-build')
+
+    def cmake_args(self):
+        """Populate cmake arguments for Catalyst."""
+        cmake_args = [
+            '-DPARAVIEW_GIT_DESCRIBE=v%s' % str(self.version)
+        ]
+        return cmake_args
+
+    def cmake(self, spec, prefix):
+        """Runs ``cmake`` in the build directory through the cmake.sh script"""
+        cmake_script_path = os.path.join(
+            os.path.abspath(self.root_cmakelists_dir),
+            'cmake.sh')
+        with working_dir(self.build_directory, create=True):
+            subprocess.check_call([cmake_script_path,
+                                   os.path.abspath(self.root_cmakelists_dir)] +
+                                  self.cmake_args() + self.std_cmake_args)
diff --git a/var/spack/repos/builtin/packages/catch/package.py b/var/spack/repos/builtin/packages/catch/package.py
index 37e8d69aaf..0db27a853d 100644
--- a/var/spack/repos/builtin/packages/catch/package.py
+++ b/var/spack/repos/builtin/packages/catch/package.py
@@ -1,55 +1,66 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class Catch(Package):
+class Catch(CMakePackage):
     """Catch tests"""
 
-    homepage = "https://github.com/philsquared/Catch"
-    url = "https://github.com/philsquared/Catch/archive/v1.3.0.tar.gz"
-
-    version('1.9.4', '110b9173d7f766487fed5b710836c7216a781568')
-    version('1.9.3', 'dc0cd0b344d8ccb1190ac3447efcb49c9b43d497')
-    version('1.9.2', '0580f57edd2b33ec671488dc7b6151f9e360c8c9')
-    version('1.9.1', '10784fc4c3786dfc3bd222fb3f9b048b6d68f186')
-    version('1.9.0', '62f07506d4a381d1730d494b71cff0396b9eb3d6')
-    version('1.8.2', '45a7598a8e5c47bc09fb73eec205ffe0885983dc')
-    version('1.8.1', 'd4e302f712fb7e75ce6f05b436dbaf21dca40030')
-    version('1.8.0', '26064092b5682c9c997b04015ed1565f0e198827')
-    version('1.7.2', '13018db2f0f0395456f695b0d0fbc490662e3467')
-    version('1.7.1', 'f82e11a5cdfef2d36b5687ff5970d383f9e76490')
-    version('1.7.0', 'fe39f5b3eb07a5dd0e3f84a1335ceca7de8982e6')
-    version('1.6.1', '7d46961a3131655b986123f8a1f439a04a0af623')
-    version('1.6.0', '890a3b21085d796e13c3bfaf4b6c6f1d06e4a52e')
-    version('1.5.9', '8bc32146a5a2789cd3d3ce2893772e32f412f1b1')
-    version('1.5.0', 'c87397846ea5126febd39f513b413e32f9ed552b')
-    version('1.4.0', 'c165406968fbfb46949885da571cd528c62c4d9a')
-    version('1.3.5', '31553ba6e4bd0cc61e0507d6754847e354699284')
-    version('1.3.0', 'e13694aaff72817d02af8ed27d077cd261b6e857')
+    homepage = "https://github.com/catchorg/Catch2"
+    url = "https://github.com/catchorg/Catch2/archive/v1.3.0.tar.gz"
+
+    variant('single_header', default=True,
+            description='Install a single header only.')
+
+    # - "make install" was added in 1.7.0
+    # - pkg-config package was added in 2.0.1
+    # - CMake config package was added in 2.1.2
+    conflicts('~single_header', when='@:1.6.1')
+
+    version('2.4.0', sha256='ab176de36b886a33aa745fcf34642eac853bf677bda518a88655dc750c72d756')
+    version('2.3.0', sha256='aaf6bbf81ce8522131bae2ea4d013a77b003bbb2017614f5872d5787687f8f5f')
+    # releases 2.3.0+ changed to "catch2/catch.hpp" header
+    version('2.2.1', '54e56803c84890636bd7fe6c3856b104')
+    version('2.1.0', '70b44068976d46d48f3cd8796f675691d3bc726b')
+    version('2.0.1', '5c191a031edebd0525640ed2f38cbf64bacb1803')
+    version('1.12.1', '7d89cffd9d61f4fdcbdb373b70cc92d1')
+    version('1.12.0', '8fb0a64144a2c1572dd930254c7bbdf504ecbe2d')
+    version('1.11.0', '3c03a022d8ba8dbbc931e1ce9fb28faec4890b8d')
+    version('1.10.0', 'c2033ca00b616e7e703623c68220cf5a8e12bba4')
+    version('1.9.7', '7ea41b48a23bd83f377f05a9dfde2be230cfc1b4')
+    version('1.9.6', 'e6ae3a50c6e4da64410979dcd4b2bb3f7ba1c364')
+    version('1.9.5', '7ba2bb12b5398b8b9ab7a7907f4cd345a55e179a')
+    version('1.9.4', 'b48fce35161160def587bd0d8f0e95969b20b786')
+    version('1.9.3', 'c0db82118496a2dd0637aad352f31d9356bffc28')
+    version('1.9.2', '627fd94d466c0f71ba84010adf82771ed3ce85c7')
+    version('1.9.1', '331e4a5cd32fe4c36b4bea15e5198346f18b5c3f')
+    version('1.9.0', '5bb46e99eea39224189a8a0442ec7790c635a7b0')
+    version('1.8.2', '34b8a2da76befeeaeafc393569538222605dda51')
+    version('1.8.1', 'd5f4ae9603fe27c313bc5b5b23c233bdce5c57f7')
+    version('1.8.0', '7fa6bfc50e6dbb6fd1352f41496650d56a86ac1a')
+    version('1.7.2', '45b0ab04b6da75ce56de25a81f0b0de4c7a62179')
+    version('1.7.1', '3a55985aacd5a5ff8a87c1490bbf65f0122647dc')
+    version('1.7.0', '6f9869cc066721d525bb03e8a9423b806c362140')
+    version('1.6.1', 'e88de5b611c07d5d402142d3dc20b63350fdf76c')
+    version('1.6.0', '21273cbed050b8d4785231d04812d5addf5b71b7')
+    version('1.5.9', '341bee0b642f0dc9bb6fb41243a068239468b703')
+    version('1.5.0', '2d14342c72f12b3f4b975cf6aa8594c8ad43d773')
+    version('1.4.0', '3b3b76a842508386be40d73849627bbe12fb5b7f')
+    version('1.3.5', '2cfd78bce21368355c7d3880df88716084df2186')
+    version('1.3.0', '24cd4e6518273fea20becd47a2e1edbee7ec209a')
+
+    @when('+single_header')
+    def cmake(self, spec, prefix):
+        pass
+
+    @when('+single_header')
+    def build(self, spec, prefix):
+        pass
 
+    @when('+single_header')
     def install(self, spec, prefix):
         mkdirp(prefix.include)
         install(join_path('single_include', 'catch.hpp'), prefix.include)
diff --git a/var/spack/repos/builtin/packages/cbench/package.py b/var/spack/repos/builtin/packages/cbench/package.py
index c090907af7..d7bd1a7eb7 100644
--- a/var/spack/repos/builtin/packages/cbench/package.py
+++ b/var/spack/repos/builtin/packages/cbench/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -50,27 +31,27 @@ class Cbench(MakefilePackage):
     conflicts('%xl')
     conflicts('%xl_r')
 
-    def edit(self, spec, prefix):
+    def setup_environment(self, build_env, run_env):
         # The location of the Cbench source tree
-        env['CBENCHOME'] = self.stage.source_path
+        build_env.set('CBENCHOME', self.stage.source_path)
 
         # The location that will contain all of your tests and their results
-        env['CBENCHTEST'] = prefix
+        build_env.set('CBENCHTEST', self.prefix)
 
         # The location of the system MPI tree
-        env['MPIHOME'] = spec['mpi'].prefix
+        build_env.set('MPIHOME', self.spec['mpi'].prefix)
 
         # Pick the compiler collection/chain you want to compile with.
         # Examples include: intel, gcc, pgi.
-        env['COMPILERCOLLECTION'] = self.compiler.name
+        build_env.set('COMPILERCOLLECTION', self.compiler.name)
 
         # Linking flags for BLAS/LAPACK and FFTW
-        env['BLASLIB']   = spec['blas'].libs.ld_flags
-        env['LAPACKLIB'] = spec['lapack'].libs.ld_flags
-        env['FFTWLIB']   = spec['fftw'].libs.ld_flags
+        build_env.set('BLASLIB', self.spec['blas'].libs.ld_flags)
+        build_env.set('LAPACKLIB', self.spec['lapack'].libs.ld_flags)
+        build_env.set('FFTWLIB', self.spec['fftw'].libs.ld_flags)
 
         # The number of make jobs (commands) to run simultaneously
-        env['JOBS'] = str(make_jobs)
+        build_env.set('JOBS', str(make_jobs))
 
     @run_before('build')
     @on_package_attributes(run_tests=True)
diff --git a/var/spack/repos/builtin/packages/cblas/package.py b/var/spack/repos/builtin/packages/cblas/package.py
index 05a3ddb43e..3a36664103 100644
--- a/var/spack/repos/builtin/packages/cblas/package.py
+++ b/var/spack/repos/builtin/packages/cblas/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -42,10 +23,10 @@ class Cblas(Package):
     def patch(self):
         mf = FileFilter('Makefile.in')
 
-        mf.filter('^BLLIB =.*', 'BLLIB = %s/libblas.a' %
-                  self.spec['blas'].prefix.lib)
+        mf.filter('^BLLIB =.*', 'BLLIB = {0}'.format(
+                  ' '.join(self.spec['blas'].libs.libraries)))
         mf.filter('^CC =.*', 'CC = cc')
-        mf.filter('^FC =.*', 'FC = f90')
+        mf.filter('^FC =.*', 'FC = fc')
 
     def install(self, spec, prefix):
         make('all')
@@ -53,6 +34,6 @@ class Cblas(Package):
         mkdirp(prefix.include)
 
         # Rename the generated lib file to libcblas.a
-        install('./lib/cblas_LINUX.a', '%s/libcblas.a' % prefix.lib)
-        install('./include/cblas.h', '%s' % prefix.include)
-        install('./include/cblas_f77.h', '%s' % prefix.include)
+        install('lib/cblas_LINUX.a', prefix.lib.join('libcblas.a'))
+        install('include/cblas.h', prefix.include)
+        install('include/cblas_f77.h', prefix.include)
diff --git a/var/spack/repos/builtin/packages/cbtf-argonavis-gui/package.py b/var/spack/repos/builtin/packages/cbtf-argonavis-gui/package.py
index 42f40c63ea..3d4f039371 100644
--- a/var/spack/repos/builtin/packages/cbtf-argonavis-gui/package.py
+++ b/var/spack/repos/builtin/packages/cbtf-argonavis-gui/package.py
@@ -1,46 +1,10 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-##########################################################################
-# Copyright (c) 2015-2017 Krell Institute. All Rights Reserved.
-#
-# This program is free software; you can redistribute it and/or modify it under
-# the terms of the GNU General Public License as published by the Free Software
-# Foundation; either version 2 of the License, or (at your option) any later
-# version.
-#
-# This program is distributed in the hope that it will be useful, but WITHOUT
-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-# FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
-# details.
-#
-# You should have received a copy of the GNU General Public License along with
-# this program; if not, write to the Free Software Foundation, Inc., 59 Temple
-# Place, Suite 330, Boston, MA  02111-1307  USA
-##########################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack import *
+import os
 
 
 class CbtfArgonavisGui(QMakePackage):
@@ -48,21 +12,43 @@ class CbtfArgonavisGui(QMakePackage):
        performance information by loading in the Sqlite database files.
     """
     homepage = "http://sourceforge.net/p/cbtf/wiki/Home/"
+    git      = "https://github.com/OpenSpeedShop/cbtf-argonavis-gui.git"
+
+    version('develop', branch='master')
+    version('1.3.0.0', branch='1.3.0.0')
+
+    depends_on("cmake@3.0.2:", type='build')
+
+    depends_on('qt@5.10.0:', when='@develop')
+    depends_on('qt@5.10.0', when='@1.3.0.0:9999')
 
-    version('0.8.1', branch='master',
-            git='https://github.com/OpenSpeedShop/cbtf-argonavis-gui.git')
+    depends_on("boost@1.66.0:")
+
+    # For MRNet
+    depends_on("mrnet@5.0.1-3:+lwthreads", when='@develop')
+    depends_on("mrnet@5.0.1-3+lwthreads", when='@1.3.0.0:9999')
+
+    # Dependencies for the openspeedshop cbtf packages.
+    depends_on("cbtf@develop", when='@develop')
+    depends_on("cbtf@1.9.1.0:9999", when='@1.3.0.0:9999')
+
+    depends_on("cbtf-krell@develop", when='@develop')
+    depends_on("cbtf-krell@1.9.1.0:9999", when='@1.3.0.0:9999')
+
+    depends_on("cbtf-argonavis@develop", when='@develop')
+    depends_on("cbtf-argonavis@1.9.1.0:9999", when='@1.3.0.0:9999')
 
-    depends_on("cmake@3.0.2", type='build')
-    depends_on("openspeedshop+cuda gui='qt4'")
-    depends_on('qt@4.8.6:')
-    depends_on("boost@1.50.0:1.59.0")
-    depends_on("cbtf")
-    depends_on("cbtf-krell")
-    depends_on("cbtf-argonavis")
     depends_on("cuda")
-    depends_on("mrnet@5.0.1:+lwthreads")
-    depends_on("xerces-c@3.1.1:")
-    depends_on("graphviz")
+
+    depends_on("openspeedshop-utils+cuda@develop", when='@develop')
+    depends_on("openspeedshop-utils@2.3.1.3:+cuda", when='@1.3.0.0:9999')
+
+    # For Xerces-C
+    depends_on("xerces-c")
+
+    depends_on("graphviz@2.40.1:", when='@develop')
+    depends_on("graphviz@2.40.1", when='@1.3.0.0:9999')
+
     depends_on("qtgraph")
 
     parallel = False
@@ -74,7 +60,7 @@ class CbtfArgonavisGui(QMakePackage):
         spack_env.set('CBTF_KRELL_ROOT', self.spec['cbtf-krell'].prefix)
         spack_env.set('CBTF_ARGONAVIS_ROOT',
                       self.spec['cbtf-argonavis'].prefix)
-        spack_env.set('OSS_CBTF_ROOT', self.spec['openspeedshop'].prefix)
+        spack_env.set('OSS_CBTF_ROOT', self.spec['openspeedshop-utils'].prefix)
         spack_env.set('GRAPHVIZ_ROOT', self.spec['graphviz'].prefix)
         spack_env.set('QTGRAPHLIB_ROOT', self.spec['qtgraph'].prefix)
         spack_env.set('KRELL_ROOT_MRNET', self.spec['mrnet'].prefix)
@@ -83,14 +69,21 @@ class CbtfArgonavisGui(QMakePackage):
 
         # The implementor of qtgraph has set up the library and include
         # paths in a non-conventional way.  We reflect that here.
+        # What library suffix should be used based on library existence
+        if os.path.isdir(self.spec['qtgraph'].prefix.lib64):
+            qtgraph_lib_dir = self.spec['qtgraph'].prefix.lib64
+        else:
+            qtgraph_lib_dir = self.spec['qtgraph'].prefix.lib
+
         run_env.prepend_path(
             'LD_LIBRARY_PATH', join_path(
-                self.spec['qtgraph'].prefix.lib64,
+                qtgraph_lib_dir,
                 '{0}'.format(self.spec['qt'].version.up_to(3))))
+
         # The openspeedshop libraries are needed to actually load the
         # performance information into the GUI.
         run_env.prepend_path(
-            'LD_LIBRARY_PATH', self.spec['openspeedshop'].prefix.lib64)
+            'LD_LIBRARY_PATH', self.spec['openspeedshop-utils'].prefix.lib64)
 
     def qmake_args(self):
         options = ['-o', 'Makefile', 'openss-gui.pro']
diff --git a/var/spack/repos/builtin/packages/cbtf-argonavis/package.py b/var/spack/repos/builtin/packages/cbtf-argonavis/package.py
index a335754537..f56e01e46f 100644
--- a/var/spack/repos/builtin/packages/cbtf-argonavis/package.py
+++ b/var/spack/repos/builtin/packages/cbtf-argonavis/package.py
@@ -1,44 +1,7 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-##########################################################################
-# Copyright (c) 2015-2017 Krell Institute. All Rights Reserved.
-#
-# This program is free software; you can redistribute it and/or modify it under
-# the terms of the GNU General Public License as published by the Free Software
-# Foundation; either version 2 of the License, or (at your option) any later
-# version.
-#
-# This program is distributed in the hope that it will be useful, but WITHOUT
-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-# FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
-# details.
-#
-# You should have received a copy of the GNU General Public License along with
-# this program; if not, write to the Free Software Foundation, Inc., 59 Temple
-# Place, Suite 330, Boston, MA  02111-1307  USA
-##########################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack import *
 
@@ -46,22 +9,71 @@ from spack import *
 class CbtfArgonavis(CMakePackage):
     """CBTF Argo Navis project contains the CUDA collector and supporting
        libraries that was done as a result of a DOE SBIR grant.
-
     """
     homepage = "http://sourceforge.net/p/cbtf/wiki/Home/"
+    git      = "https://github.com/OpenSpeedShop/cbtf-argonavis.git"
 
-    version('1.8', branch='master',
-            git='https://github.com/OpenSpeedShop/cbtf-argonavis.git')
+    version('develop', branch='master')
+    version('1.9.2', branch='1.9.2')
+    version('1.9.1.2', branch='1.9.1.2')
+    version('1.9.1.1', branch='1.9.1.1')
+    version('1.9.1.0', branch='1.9.1.0')
 
+    variant('cti', default=False,
+            description="Build MRNet with the CTI startup option")
+    variant('crayfe', default=False,
+            description="build only the FE tool using the runtime_dir \
+                         to point to target build.")
+    variant('runtime', default=False,
+            description="build only the runtime libraries and collectors.")
     variant('build_type', default='None', values=('None'),
             description='CMake build type')
 
     depends_on("cmake@3.0.2:", type='build')
-    depends_on("boost@1.50.0:1.59.0")
-    depends_on("papi")
-    depends_on("mrnet@5.0.1:+lwthreads")
-    depends_on("cbtf")
-    depends_on("cbtf-krell")
+
+    # To specify ^elfutils@0.170 on the command line spack
+    # apparently needs/wants this dependency explicity here
+    # even though it is referenced downstream
+    depends_on("elf", type="link")
+
+    # For boost
+    depends_on("boost@1.66.0:")
+
+    # For MRNet
+    depends_on("mrnet@5.0.1-3:+cti", when='@develop+cti')
+    depends_on("mrnet@5.0.1-3:+lwthreads", when='@develop~cti')
+    depends_on("mrnet@5.0.1-3+cti", when='@1.9.1.0:9999+cti')
+    depends_on("mrnet@5.0.1-3+lwthreads", when='@1.9.1.0:9999~cti')
+
+    # For CBTF
+    depends_on("cbtf@develop", when='@develop')
+    depends_on("cbtf@1.9.1.0:9999", when='@1.9.1.0:9999')
+
+    # For CBTF with cti
+    depends_on("cbtf@develop+cti", when='@develop+cti')
+    depends_on("cbtf@1.9.1.0:9999+cti", when='@1.9.1.0:9999+cti')
+
+    # For CBTF with runtime
+    depends_on("cbtf@develop+runtime", when='@develop+runtime')
+    depends_on("cbtf@1.9.1.0:9999+runtime", when='@1.9.1.0:9999+runtime')
+
+    # For libmonitor
+    depends_on("libmonitor@2013.02.18+krellpatch")
+
+    # For PAPI
+    depends_on("papi@5.4.1:")
+
+    # For CBTF-KRELL
+    depends_on("cbtf-krell@develop", when='@develop')
+    depends_on("cbtf-krell@1.9.1.0:9999", when='@1.9.1.0:9999')
+
+    depends_on('cbtf-krell@develop+cti', when='@develop+cti')
+    depends_on('cbtf-krell@1.9.1.0:9999+cti', when='@1.9.1.0:9999+cti')
+
+    depends_on('cbtf-krell@develop+runtime', when='@develop+runtime')
+    depends_on('cbtf-krell@1.9.1.0:9999+runtime', when='@1.9.1.0:9999+runtime')
+
+    # For CUDA
     depends_on("cuda")
 
     parallel = False
@@ -87,6 +99,17 @@ class CbtfArgonavis(CMakePackage):
             '-DBoost_DIR=%s' % spec['boost'].prefix,
             '-DBOOST_LIBRARYDIR=%s' % spec['boost'].prefix.lib,
             '-DMRNET_DIR=%s' % spec['mrnet'].prefix,
+            '-DLIBMONITOR_DIR=%s' % spec['libmonitor'].prefix,
             '-DBoost_NO_SYSTEM_PATHS=ON']
 
         return cmake_args
+
+    def setup_environment(self, spack_env, run_env):
+        """Set up the compile and runtime environments for a package."""
+
+        run_env.prepend_path(
+            'LD_LIBRARY_PATH',
+            self.spec['cuda'].prefix + '/extras/CUPTI/lib64')
+        spack_env.prepend_path(
+            'LD_LIBRARY_PATH',
+            self.spec['cuda'].prefix + '/extras/CUPTI/lib64')
diff --git a/var/spack/repos/builtin/packages/cbtf-krell/package.py b/var/spack/repos/builtin/packages/cbtf-krell/package.py
index 1716d83188..b30a4a6649 100644
--- a/var/spack/repos/builtin/packages/cbtf-krell/package.py
+++ b/var/spack/repos/builtin/packages/cbtf-krell/package.py
@@ -1,46 +1,11 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-##########################################################################
-# Copyright (c) 2015-2017 Krell Institute. All Rights Reserved.
-#
-# This program is free software; you can redistribute it and/or modify it under
-# the terms of the GNU General Public License as published by the Free Software
-# Foundation; either version 2 of the License, or (at your option) any later
-# version.
-#
-# This program is distributed in the hope that it will be useful, but WITHOUT
-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-# FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
-# details.
-#
-# You should have received a copy of the GNU General Public License along with
-# this program; if not, write to the Free Software Foundation, Inc., 59 Temple
-# Place, Suite 330, Boston, MA  02111-1307  USA
-##########################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack import *
+import spack
+import spack.store
 
 
 class CbtfKrell(CMakePackage):
@@ -48,12 +13,15 @@ class CbtfKrell(CMakePackage):
        CBTF project.  These contributions include many performance data
        collectors and support libraries as well as some example tools
        that drive the data collection at HPC levels of scale.
-
     """
     homepage = "http://sourceforge.net/p/cbtf/wiki/Home/"
+    git      = "https://github.com/OpenSpeedShop/cbtf-krell.git"
 
-    version('1.8', branch='master',
-            git='https://github.com/OpenSpeedShop/cbtf-krell.git')
+    version('develop', branch='master')
+    version('1.9.2', branch='1.9.2')
+    version('1.9.1.2', branch='1.9.1.2')
+    version('1.9.1.1', branch='1.9.1.1')
+    version('1.9.1.0', branch='1.9.1.0')
 
     # MPI variants
     variant('openmpi', default=False,
@@ -68,32 +36,62 @@ class CbtfKrell(CMakePackage):
             description="Build mpi experiment collector for mpich2 MPI.")
     variant('mpich', default=False,
             description="Build mpi experiment collector for mpich MPI.")
+    variant('runtime', default=False,
+            description="build only the runtime libraries and collectors.")
     variant('build_type', default='None', values=('None'),
             description='CMake build type')
+    variant('cti', default=False,
+            description="Build MRNet with the CTI startup option")
+    variant('crayfe', default=False,
+            description="build only the FE tool using the runtime_dir \
+                         to point to target build.")
 
     # Dependencies for cbtf-krell
     depends_on("cmake@3.0.2:", type='build')
 
-    # For binutils service
+    # For binutils
     depends_on("binutils")
 
-    # collectionTool
-    depends_on("boost@1.50.0:1.59.0")
-    depends_on("dyninst@9.3.2")
-    depends_on("mrnet@5.0.1:+lwthreads")
+    # For boost
+    depends_on("boost@1.66.0:")
+
+    # For Dyninst
+    depends_on("dyninst@develop", when='@develop')
+    depends_on("dyninst@10:", when='@1.9.1.0:9999')
+
+    # For MRNet
+    depends_on("mrnet@5.0.1-3:+cti", when='@develop+cti', type=('build', 'link', 'run'))
+    depends_on("mrnet@5.0.1-3:+lwthreads", when='@develop', type=('build', 'link', 'run'))
 
-    depends_on("xerces-c@3.1.1:")
-    depends_on("cbtf")
+    depends_on("mrnet@5.0.1-3+cti", when='@1.9.1.0:9999+cti', type=('build', 'link', 'run'))
+    depends_on("mrnet@5.0.1-3+lwthreads", when='@1.9.1.0:9999', type=('build', 'link', 'run'))
+
+    # For Xerces-C
+    depends_on("xerces-c")
+
+    # For CBTF
+    depends_on("cbtf@develop", when='@develop', type=('build', 'link', 'run'))
+    depends_on("cbtf@1.9.1.0:9999", when='@1.9.1.0:9999', type=('build', 'link', 'run'))
+
+    # For CBTF with cti
+    depends_on("cbtf@develop+cti", when='@develop+cti', type=('build', 'link', 'run'))
+    depends_on("cbtf@1.9.1.0:9999+cti", when='@1.9.1.0:9999+cti', type=('build', 'link', 'run'))
+
+    # For CBTF with runtime
+    depends_on("cbtf@develop+runtime", when='@develop+runtime', type=('build', 'link', 'run'))
+    depends_on("cbtf@1.9.1.0:9999+runtime", when='@1.9.1.0:9999+runtime', type=('build', 'link', 'run'))
 
     # for services and collectors
-    depends_on("libmonitor+krellpatch")
-    depends_on("libunwind")
-    depends_on("papi")
-    depends_on("llvm-openmp-ompt@towards_tr4+standalone")
+    depends_on("libmonitor@2013.02.18+krellpatch")
+
+    depends_on("libunwind", when='@develop')
+    depends_on("libunwind@1.2.1", when='@1.9.1.0:9999')
+
+    depends_on("papi@5.4.1:")
+
+    depends_on("llvm-openmp-ompt@tr6_forwards+standalone")
 
     # MPI Installations
-    # These have not worked either for build or execution, commenting out for
-    # now
     depends_on("openmpi", when='+openmpi')
     depends_on("mpich", when='+mpich')
     depends_on("mpich2", when='+mpich2')
@@ -101,36 +99,97 @@ class CbtfKrell(CMakePackage):
     depends_on("mvapich", when='+mvapich')
     depends_on("mpt", when='+mpt')
 
+    depends_on("python", when='@develop', type=('build', 'run'))
+    depends_on("python@2.7.14:2.7.15", when='@2.3.1.3:9999', type=('build', 'run'))
+
+    depends_on("gotcha")
+
     parallel = False
 
     build_directory = 'build_cbtf_krell'
 
-    def set_mpi_cmakeOptions(self, spec, cmakeOptions):
-        # Appends to cmakeOptions the options that will enable the appropriate
+    def set_rt_only_cmake_options(self, spec, cmake_options):
+        # Appends to cmake_options the options that will enable the appropriate
         # MPI implementations
 
-        MPIOptions = []
+        rt_only_options = []
+        rt_only_options.append('-DRUNTIME_ONLY=true')
+        cmake_options.extend(rt_only_options)
+
+    def set_mpi_cmake_options(self, spec, cmake_options):
+        # Appends to cmake_options the options that will enable the appropriate
+        # MPI implementations
+
+        mpi_options = []
 
         # openmpi
-        if '+openmpi' in spec:
-            MPIOptions.append('-DOPENMPI_DIR=%s' % spec['openmpi'].prefix)
+        if spec.satisfies('+openmpi'):
+            mpi_options.append('-DOPENMPI_DIR=%s' % spec['openmpi'].prefix)
         # mpich
-        if '+mpich' in spec:
-            MPIOptions.append('-DMPICH_DIR=%s' % spec['mpich'].prefix)
+        if spec.satisfies('+mpich'):
+            mpi_options.append('-DMPICH_DIR=%s' % spec['mpich'].prefix)
         # mpich2
-        if '+mpich2' in spec:
-            MPIOptions.append('-DMPICH2_DIR=%s' % spec['mpich2'].prefix)
+        if spec.satisfies('+mpich2'):
+            mpi_options.append('-DMPICH2_DIR=%s' % spec['mpich2'].prefix)
         # mvapich
-        if '+mvapich' in spec:
-            MPIOptions.append('-DMVAPICH_DIR=%s' % spec['mvapich'].prefix)
+        if spec.satisfies('+mvapich'):
+            mpi_options.append('-DMVAPICH_DIR=%s' % spec['mvapich'].prefix)
         # mvapich2
-        if '+mvapich2' in spec:
-            MPIOptions.append('-DMVAPICH2_DIR=%s' % spec['mvapich2'].prefix)
+        if spec.satisfies('+mvapich2'):
+            mpi_options.append('-DMVAPICH2_DIR=%s' % spec['mvapich2'].prefix)
         # mpt
-        if '+mpt' in spec:
-            MPIOptions.append('-DMPT_DIR=%s' % spec['mpt'].prefix)
+        if spec.satisfies('+mpt'):
+            mpi_options.append('-DMPT_DIR=%s' % spec['mpt'].prefix)
+
+        cmake_options.extend(mpi_options)
+
+    def set_cray_login_node_cmake_options(self, spec, cmake_options):
+        # Appends to cmake_options the options that will enable
+        # the appropriate Cray login node libraries
+
+        cray_login_node_options = []
+        rt_platform = "cray"
+        # How do we get the compute node (CNL) cbtf package
+        # install directory path. spec['cbtf'].prefix is the
+        # login node path for this build, as we are building
+        # the login node components with this spack invocation. We
+        # need these paths to be the ones created in the CNL
+        # spack invocation.
+        be_cbtf = spack.store.db.query_one('cbtf arch=cray-CNL-haswell')
+        be_cbtfk = spack.store.db.query_one('cbtf-krell arch=cray-CNL-haswell')
+        be_papi = spack.store.db.query_one('papi arch=cray-CNL-haswell')
+        be_boost = spack.store.db.query_one('boost arch=cray-CNL-haswell')
+        be_mont = spack.store.db.query_one('libmonitor arch=cray-CNL-haswell')
+        be_unw = spack.store.db.query_one('libunwind arch=cray-CNL-haswell')
+        be_xer = spack.store.db.query_one('xerces-c arch=cray-CNL-haswell')
+        be_dyn = spack.store.db.query_one('dyninst arch=cray-CNL-haswell')
+        be_mrnet = spack.store.db.query_one('mrnet arch=cray-CNL-haswell')
 
-        cmakeOptions.extend(MPIOptions)
+        cray_login_node_options.append(
+            '-DCN_RUNTIME_PLATFORM=%s' % rt_platform)
+
+        # Use install directories as CMAKE args for the building
+        # of login cbtf-krell
+        cray_login_node_options.append(
+            '-DCBTF_CN_RUNTIME_DIR=%s' % be_cbtf.prefix)
+        cray_login_node_options.append(
+            '-DCBTF_KRELL_CN_RUNTIME_DIR=%s' % be_cbtfk.prefix)
+        cray_login_node_options.append(
+            '-DPAPI_CN_RUNTIME_DIR=%s' % be_papi.prefix)
+        cray_login_node_options.append(
+            '-DBOOST_CN_RUNTIME_DIR=%s' % be_boost.prefix)
+        cray_login_node_options.append(
+            '-DLIBMONITOR_CN_RUNTIME_DIR=%s' % be_mont.prefix)
+        cray_login_node_options.append(
+            '-DLIBUNWIND_CN_RUNTIME_DIR=%s' % be_unw.prefix)
+        cray_login_node_options.append(
+            '-DXERCESC_CN_RUNTIME_DIR=%s' % be_xer.prefix)
+        cray_login_node_options.append(
+            '-DDYNINST_CN_RUNTIME_DIR=%s' % be_dyn.prefix)
+        cray_login_node_options.append(
+            '-DMRNET_CN_RUNTIME_DIR=%s' % be_mrnet.prefix)
+
+        cmake_options.extend(cray_login_node_options)
 
     def cmake_args(self):
         spec = self.spec
@@ -151,9 +210,52 @@ class CbtfKrell(CMakePackage):
             '-DMRNET_DIR=%s' % spec['mrnet'].prefix,
             '-DDYNINST_DIR=%s' % spec['dyninst'].prefix,
             '-DLIBIOMP_DIR=%s' % spec['llvm-openmp-ompt'].prefix,
+            '-DGOTCHA_DIR=%s' % spec['gotcha'].prefix,
             '-DXERCESC_DIR=%s' % spec['xerces-c'].prefix]
 
+        if self.spec.satisfies('+runtime'):
+            self.set_rt_only_cmake_options(spec, cmake_args)
+
         # Add any MPI implementations coming from variant settings
-        self.set_mpi_cmakeOptions(spec, cmake_args)
+        self.set_mpi_cmake_options(spec, cmake_args)
+
+        if self.spec.satisfies('+crayfe'):
+            # We need to build target/compute node components/libraries first
+            # then pass those libraries to the cbtf-krell login node build
+            self.set_cray_login_node_cmake_options(spec, cmake_args)
 
         return cmake_args
+
+    def setup_environment(self, spack_env, run_env):
+        """Set up the compile and runtime environments for a package."""
+
+        # Environment settings for cbtf-krell, bin is automatically
+        # added to the path in the module file
+        run_env.prepend_path('PATH', self.prefix.sbin)
+
+        run_env.set('XPLAT_RSH', 'ssh')
+        run_env.set('MRNET_COMM_PATH', self.prefix.sbin.cbtf_mrnet_commnode)
+
+        # Set CBTF_MPI_IMPLEMENTATON to the appropriate mpi implementation
+        # This is needed by CBTF tools to deploy the correct
+        # mpi runtimes for cbtfsummary
+        # Users may have to set the CBTF_MPI_IMPLEMENTATION variable
+        # manually if multiple mpi's are specified in the build
+
+        if self.spec.satisfies('+mpich'):
+            run_env.set('CBTF_MPI_IMPLEMENTATION', "mpich")
+
+        if self.spec.satisfies('+mvapich'):
+            run_env.set('CBTF_MPI_IMPLEMENTATION', "mvapich")
+
+        if self.spec.satisfies('+mvapich2'):
+            run_env.set('CBTF_MPI_IMPLEMENTATION', "mvapich2")
+
+        if self.spec.satisfies('+mpt'):
+            run_env.set('CBTF_MPI_IMPLEMENTATION', "mpt")
+
+        if self.spec.satisfies('+openmpi'):
+            run_env.set('CBTF_MPI_IMPLEMENTATION', "openmpi")
+
+        run_env.set('CBTF_MRNET_BACKEND_PATH',
+                    self.prefix.sbin.cbtf_libcbtf_mrnet_backend)
diff --git a/var/spack/repos/builtin/packages/cbtf-lanl/package.py b/var/spack/repos/builtin/packages/cbtf-lanl/package.py
index 19b00e00df..460c845552 100644
--- a/var/spack/repos/builtin/packages/cbtf-lanl/package.py
+++ b/var/spack/repos/builtin/packages/cbtf-lanl/package.py
@@ -1,44 +1,7 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-##########################################################################
-# Copyright (c) 2015-2017 Krell Institute. All Rights Reserved.
-#
-# This program is free software; you can redistribute it and/or modify it under
-# the terms of the GNU General Public License as published by the Free Software
-# Foundation; either version 2 of the License, or (at your option) any later
-# version.
-#
-# This program is distributed in the hope that it will be useful, but WITHOUT
-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-# FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
-# details.
-#
-# You should have received a copy of the GNU General Public License along with
-# this program; if not, write to the Free Software Foundation, Inc., 59 Temple
-# Place, Suite 330, Boston, MA  02111-1307  USA
-##########################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack import *
 
@@ -46,20 +9,57 @@ from spack import *
 class CbtfLanl(CMakePackage):
     """CBTF LANL project contains a memory tool and data center type system
        command monitoring tool."""
+
     homepage = "http://sourceforge.net/p/cbtf/wiki/Home/"
+    git      = "https://github.com/OpenSpeedShop/cbtf-lanl.git"
 
-    version('1.8', branch='master',
-            git='http://git.code.sf.net/p/cbtf-lanl/cbtf-lanl')
+    version('develop', branch='master')
+    version('1.9.2', branch='1.9.2')
+    version('1.9.1.2', branch='1.9.1.2')
+    version('1.9.1.1', branch='1.9.1.1')
+    version('1.9.1.0', branch='1.9.1.0')
 
     variant('build_type', default='None', values=('None'),
             description='CMake build type')
 
+    variant('runtime', default=False,
+            description="build only the runtime libraries and collectors.")
+
+    variant('cti', default=False,
+            description="Build MRNet with the CTI startup option")
+
     depends_on("cmake@3.0.2:", type='build')
-    # Dependencies for cbtf-krell
-    depends_on("mrnet@5.0.1:+lwthreads")
-    depends_on("xerces-c@3.1.1:")
-    depends_on("cbtf")
-    depends_on("cbtf-krell")
+
+    # For MRNet
+    depends_on("mrnet@5.0.1-3:+cti", when='@develop+cti')
+    depends_on("mrnet@5.0.1-3:+lwthreads", when='@develop')
+    depends_on("mrnet@5.0.1-3+cti", when='@1.9.1.0:9999+cti')
+    depends_on("mrnet@5.0.1-3+lwthreads", when='@1.9.1.0:9999')
+
+    # For Xerces-C
+    depends_on("xerces-c")
+
+    # For CBTF
+    depends_on("cbtf@develop", when='@develop')
+    depends_on("cbtf@1.9.1.0:9999", when='@1.9.1.0:9999')
+
+    # For CBTF with cti
+    depends_on("cbtf@develop+cti", when='@develop+cti')
+    depends_on("cbtf@1.9.1.0:9999+cti", when='@1.9.1.0:9999+cti')
+
+    # For CBTF with runtime
+    depends_on("cbtf@develop+runtime", when='@develop+runtime')
+    depends_on("cbtf@1.9.1.0:9999+runtime", when='@1.9.1.0:9999+runtime')
+
+    # For CBTF-KRELL
+    depends_on("cbtf-krell@develop", when='@develop')
+    depends_on("cbtf-krell@1.9.1.0:9999", when='@1.9.1.0:9999')
+
+    depends_on('cbtf-krell@develop+cti', when='@develop+cti')
+    depends_on('cbtf-krell@1.9.1.0:9999+cti', when='@1.9.1.0:9999+cti')
+
+    depends_on('cbtf-krell@develop+runtime', when='@develop+runtime')
+    depends_on('cbtf-krell@1.9.1.0:9999+runtime', when='@1.9.1.0:9999+runtime')
 
     parallel = False
 
diff --git a/var/spack/repos/builtin/packages/cbtf/package.py b/var/spack/repos/builtin/packages/cbtf/package.py
index 2f0b3b275d..ba6cbd7477 100644
--- a/var/spack/repos/builtin/packages/cbtf/package.py
+++ b/var/spack/repos/builtin/packages/cbtf/package.py
@@ -1,44 +1,7 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-##########################################################################
-# Copyright (c) 2015-2017 Krell Institute. All Rights Reserved.
-#
-# This program is free software; you can redistribute it and/or modify it under
-# the terms of the GNU General Public License as published by the Free Software
-# Foundation; either version 2 of the License, or (at your option) any later
-# version.
-#
-# This program is distributed in the hope that it will be useful, but WITHOUT
-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-# FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
-# details.
-#
-# You should have received a copy of the GNU General Public License along with
-# this program; if not, write to the Free Software Foundation, Inc., 59 Temple
-# Place, Suite 330, Boston, MA  02111-1307  USA
-##########################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack import *
 
@@ -51,22 +14,38 @@ class Cbtf(CMakePackage):
 
     """
     homepage = "http://sourceforge.net/p/cbtf/wiki/Home"
+    git      = "https://github.com/OpenSpeedShop/cbtf.git"
 
-    # Use when the git repository is available
-    version('1.8', branch='master',
-            git='https://github.com/OpenSpeedShop/cbtf.git')
+    version('develop', branch='master')
+    version('1.9.2', branch='1.9.2')
+    version('1.9.1.2', branch='1.9.1.2')
+    version('1.9.1.1', branch='1.9.1.1')
+    version('1.9.1.0', branch='1.9.1.0')
+
+    variant('cti', default=False,
+            description="Build MRNet with the CTI startup option")
 
     variant('runtime', default=False,
             description="build only the runtime libraries and collectors.")
+
     variant('build_type', default='None', values=('None'),
             description='CMake build type')
 
     depends_on("cmake@3.0.2:", type='build')
-    depends_on("boost@1.50.0:1.59.0")
-    depends_on("mrnet@5.0.1:+lwthreads")
-    depends_on("xerces-c@3.1.1:")
-    # Work around for spack libxml2 package bug, take off python when fixed
-    depends_on("libxml2+python")
+
+    depends_on("boost@1.66.0:")
+
+    # For MRNet
+    depends_on("mrnet@5.0.1-3:+cti", when='@develop+cti')
+    depends_on("mrnet@5.0.1-3:+lwthreads", when='@develop')
+    depends_on("mrnet@5.0.1-3+cti", when='@1.9.1.0:9999+cti')
+    depends_on("mrnet@5.0.1-3+lwthreads", when='@1.9.1.0:9999')
+
+    # For Xerces-C
+    depends_on("xerces-c")
+
+    # For XML2
+    depends_on("libxml2")
 
     parallel = False
 
@@ -83,7 +62,8 @@ class Cbtf(CMakePackage):
 
         compile_flags = "-O2 -g"
 
-        if '+runtime' in spec:
+        if spec.satisfies('+runtime'):
+
             # Install message tag include file for use in Intel MIC
             # cbtf-krell build
             # FIXME
diff --git a/var/spack/repos/builtin/packages/ccache/package.py b/var/spack/repos/builtin/packages/ccache/package.py
index 44b45fbea9..6446768e4f 100644
--- a/var/spack/repos/builtin/packages/ccache/package.py
+++ b/var/spack/repos/builtin/packages/ccache/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/cctools/package.py b/var/spack/repos/builtin/packages/cctools/package.py
index 997a6ba6df..63cc6a83b0 100644
--- a/var/spack/repos/builtin/packages/cctools/package.py
+++ b/var/spack/repos/builtin/packages/cctools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/cdbfasta/package.py b/var/spack/repos/builtin/packages/cdbfasta/package.py
index f3aafbe20a..11bccc8f9d 100644
--- a/var/spack/repos/builtin/packages/cdbfasta/package.py
+++ b/var/spack/repos/builtin/packages/cdbfasta/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,11 @@ class Cdbfasta(MakefilePackage):
     """Fast indexing and retrieval of fasta records from flat file databases"""
 
     homepage = "https://github.com/gpertea/cdbfasta"
-    url      = "https://github.com/gpertea/cdbfasta"
+    git      = "https://github.com/gpertea/cdbfasta.git"
+
+    version('2017-03-16', commit='b3e481fe02dfbc767a3842bcb1b687c60376a5e8')
 
-    version('2017-03-16', git='https://github.com/gpertea/cdbfasta.git', commit='b3e481fe02dfbc767a3842bcb1b687c60376a5e8')
+    depends_on('zlib')
 
     def install(self, spec, prefix):
         mkdirp(prefix.bin)
diff --git a/var/spack/repos/builtin/packages/cdd/package.py b/var/spack/repos/builtin/packages/cdd/package.py
index cf720577ea..706ee1876d 100644
--- a/var/spack/repos/builtin/packages/cdd/package.py
+++ b/var/spack/repos/builtin/packages/cdd/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/cddlib/package.py b/var/spack/repos/builtin/packages/cddlib/package.py
index 360089272e..328f76bd61 100644
--- a/var/spack/repos/builtin/packages/cddlib/package.py
+++ b/var/spack/repos/builtin/packages/cddlib/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/cdhit/package.py b/var/spack/repos/builtin/packages/cdhit/package.py
index 64f4940606..14857581bf 100644
--- a/var/spack/repos/builtin/packages/cdhit/package.py
+++ b/var/spack/repos/builtin/packages/cdhit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/cdo/package.py b/var/spack/repos/builtin/packages/cdo/package.py
index ccf0769ff1..68a23730ea 100644
--- a/var/spack/repos/builtin/packages/cdo/package.py
+++ b/var/spack/repos/builtin/packages/cdo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,6 +15,12 @@ class Cdo(AutotoolsPackage):
     url = 'https://code.mpimet.mpg.de/attachments/download/12760/cdo-1.7.2.tar.gz'
     list_url = 'https://code.mpimet.mpg.de/projects/cdo/files'
 
+    maintainers = ['skosukhin']
+
+    version('1.9.5', '0c60f2c94dc5c76421ecf363153a5043')
+    version('1.9.4', '377c9e5aa7d8cbcb4a6c558abb2eb053')
+    version('1.9.3', '13ae222164413dbd53532b03b072def5')
+    version('1.9.2', '38e68d34f0b5b44a52c3241be6831423')
     version('1.9.1', 'e60a89f268ba24cee5c461f2c217829e')
     version('1.9.0', '2d88561b3b4a880df0422a62e5027e40')
     version('1.8.2', '6a2e2f99b7c67ee9a512c40a8d4a7121')
@@ -133,8 +120,13 @@ class Cdo(AutotoolsPackage):
 
         config_args += self.enable_or_disable('openmp')
 
-        # Workaround for a problem in CDO
+        # Starting version 1.9.0 CDO is a C++ program but it uses the C
+        # interface of HDF5 without the parallel features. To avoid
+        # unnecessary dependencies on mpi's cxx library, we need to set the
+        # following flags. This works for OpenMPI, MPICH, MVAPICH, Intel MPI,
+        # IBM Spectrum MPI, bullx MPI, and Cray MPI.
         if self.spec.satisfies('@1.9:+hdf5^hdf5+mpi'):
-            config_args.append('CXX=' + self.spec['mpi'].mpicxx)
+            config_args.append(
+                'CPPFLAGS=-DOMPI_SKIP_MPICXX -DMPICH_SKIP_MPICXX')
 
         return config_args
diff --git a/var/spack/repos/builtin/packages/ceed/README.md b/var/spack/repos/builtin/packages/ceed/README.md
new file mode 100644
index 0000000000..74bcae1d17
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ceed/README.md
@@ -0,0 +1,3 @@
+This is a bundle for the CEED software suite.
+
+See https://ceed.exascaleproject.org for details.
diff --git a/var/spack/repos/builtin/packages/ceed/package.py b/var/spack/repos/builtin/packages/ceed/package.py
new file mode 100644
index 0000000000..94d4d98545
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ceed/package.py
@@ -0,0 +1,92 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class Ceed(Package):
+    """Ceed is a collection of benchmarks, miniapps, software libraries and
+       APIs for efficient high-order finite element and spectral element
+       discretizations for exascale applications developed in the Department of
+       Energy (DOE) and partially supported by the Exascale Computing Project
+       (ECP). This is a Spack bundle package that installs the CEED software
+       components."""
+
+    homepage = "https://ceed.exascaleproject.org"
+
+    url  = 'file://' + os.path.dirname(__file__) + '/README.md'
+    sha1 = 'b2eefd95c09ba573f663a761b84811a2d7e39788'
+
+    version('1.0.0', sha1, expand=False)
+
+    variant('cuda', default=False,
+            description='Build MAGMA; enable CUDA support in libCEED and OCCA')
+    variant('mfem', default=True, description='Build MFEM and Laghos')
+    variant('nek', default=True,
+            description='Build Nek5000, GSLIB, Nekbone, and NekCEM')
+    variant('occa', default=True,
+            description='Build OCCA; enable OCCA support in libCEED')
+    variant('petsc', default=True,
+            description='Build PETSc and HPGMG')
+    variant('pumi', default=True,
+            description='Build PUMI')
+    variant('quickbuild', default=True,
+            description='Speed-up the build by disabling variants in packages')
+    # TODO: Add 'int64' variant?
+
+    # LibCEED
+    depends_on('libceed@0.2~cuda', when='@1.0.0~cuda')
+    depends_on('libceed@0.2+cuda', when='@1.0.0+cuda')
+    depends_on('libceed@0.2+occa', when='@1.0.0+occa')
+    depends_on('libceed@0.2~occa', when='@1.0.0~occa')
+
+    # OCCA
+    depends_on('occa@v1.0.0-alpha.5~cuda', when='@1.0.0+occa~cuda')
+    depends_on('occa@v1.0.0-alpha.5+cuda', when='@1.0.0+occa+cuda')
+
+    # Nek5000, GSLIB, Nekbone, and NekCEM
+    depends_on('nek5000@17.0', when='@1.0.0+nek')
+    depends_on('gslib@1.0.2', when='@1.0.0+nek')
+    depends_on('nekbone@17.0', when='@1.0.0+nek')
+    depends_on('nekcem@0b8bedd', when='@1.0.0+nek')
+
+    # PETSc, HPGMG
+    # For a +quickbuild we disable hdf5, and superlu-dist in PETSc.
+    # Ideally, these can be turned into recommendations to Spack for
+    # concretizing the PETSc spec, if Spack ever supports recommendations.
+    depends_on('petsc@3.8.3~hdf5~superlu-dist',
+               when='@1.0.0+petsc+quickbuild')
+    depends_on('petsc@3.8.3+mpi+double~int64', when='@1.0.0+petsc~mfem')
+    # The mfem petsc examples need the petsc variants +hypre, +suite-sparse,
+    # and +mumps:
+    depends_on('petsc@3.8.3+mpi+hypre+suite-sparse+mumps+double~int64',
+               when='@1.0.0+petsc+mfem')
+    depends_on('hpgmg@a0a5510df23b+fe', when='@1.0.0+petsc')
+
+    # MAGMA
+    depends_on('magma@2.3.0', when='@1.0.0+cuda')
+
+    # PUMI
+    depends_on('pumi@2.1.0', when='@1.0.0+pumi')
+
+    # MFEM, Laghos
+    depends_on('mfem@3.3.2+mpi+examples+miniapps', when='@1.0.0+mfem~petsc')
+    depends_on('mfem@3.3.2+mpi+petsc+examples+miniapps',
+               when='@1.0.0+mfem+petsc')
+    depends_on('laghos@1.0', when='@1.0.0+mfem')
+    # The next line seems to be necessary because the concretizer somehow
+    # decides that mfem requires 'hypre+internal-superlu' even though the mfem
+    # package lists simply 'hypre' as dependency. This is only an issue because
+    # petsc explicitly requires 'hypre~internal-superlu' which for the
+    # concretizer is a conflict.
+    depends_on('hypre~internal-superlu', when='@1.0.0+mfem')
+
+    # If using gcc version <= 4.8 build suite-sparse version <= 5.1.0
+    depends_on('suite-sparse@:5.1.0', when='@1.0.0%gcc@:4.8+mfem+petsc')
+
+    # Dummy install
+    def install(self, spec, prefix):
+        install('README.md', prefix)
diff --git a/var/spack/repos/builtin/packages/cereal/package.py b/var/spack/repos/builtin/packages/cereal/package.py
index 637257053e..4317303d48 100644
--- a/var/spack/repos/builtin/packages/cereal/package.py
+++ b/var/spack/repos/builtin/packages/cereal/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/ceres-solver/package.py b/var/spack/repos/builtin/packages/ceres-solver/package.py
new file mode 100644
index 0000000000..a30e6468cd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ceres-solver/package.py
@@ -0,0 +1,35 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class CeresSolver(CMakePackage):
+    """Ceres Solver is an open source C++ library for modeling and solving
+    large, complicated optimization problems. It can be used to solve
+    Non-linear Least Squares problems with bounds constraints and general
+    unconstrained optimization problems. It is a mature, feature rich, and
+    performant library that has been used in production at Google since 2010.
+    """
+
+    homepage = "http://ceres-solver.org"
+    url      = "http://ceres-solver.org/ceres-solver-1.12.0.tar.gz"
+
+    version('1.12.0', '278a7b366881cc45e258da71464114d9')
+
+    depends_on('eigen@3:')
+    depends_on('lapack')
+    depends_on('glog')
+
+    def cmake_args(self):
+        args = [
+            '-DSUITESPARSE=OFF',
+            '-DCXSPARSE=OFF',
+            '-DEIGENSPARSE=ON',
+            '-DLAPACK=ON',
+            '-DBUILD_SHARED_LIBS=ON',
+            '-DSCHUR_SPECIALIZATIONS=OFF'
+        ]
+        return args
diff --git a/var/spack/repos/builtin/packages/cfitsio/package.py b/var/spack/repos/builtin/packages/cfitsio/package.py
index 49d71cdcab..2fb871cce2 100644
--- a/var/spack/repos/builtin/packages/cfitsio/package.py
+++ b/var/spack/repos/builtin/packages/cfitsio/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,8 +12,10 @@ class Cfitsio(AutotoolsPackage):
     """
 
     homepage = 'http://heasarc.gsfc.nasa.gov/fitsio/'
-    url      = 'http://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/cfitsio3410.tar.gz'
+    url      = 'http://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/cfitsio3450.tar.gz'
 
+    version('3.450', 'f470849bb43561d9a9b1925eeb7f7f0d')
+    version('3.420', '26e5c0dfb85b8d00f536e706305caa13')
     version('3.410', '8a4a66fcdd816aae41768baa0b025552')
     version('3.370', 'abebd2d02ba5b0503c633581e3bfa116')
 
diff --git a/var/spack/repos/builtin/packages/cgal/package.py b/var/spack/repos/builtin/packages/cgal/package.py
index 8961ee48bc..785402b5e8 100644
--- a/var/spack/repos/builtin/packages/cgal/package.py
+++ b/var/spack/repos/builtin/packages/cgal/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,12 +14,14 @@ class Cgal(CMakePackage):
     molecular biology, medical imaging, computer graphics, and robotics.
     """
     homepage = 'http://www.cgal.org/'
-    url = 'https://github.com/CGAL/cgal/archive/releases/CGAL-4.7.tar.gz'
+    url      = 'https://github.com/CGAL/cgal/releases/download/releases/CGAL-4.11/CGAL-4.11.tar.xz'
 
-    version('4.9.1', 'df6517df3320bf6c9de2e1b0361738b9')
-    version('4.9', '7b628db3e5614347f776c046b7666089')
-    version('4.7', '4826714810f3b4c65cac96b90fb03b67')
-    version('4.6.3', 'e8ee2ecc8d2b09b94a121c09257b576d')
+    version('4.12', 'b12fd24dedfa889a04abfaea565a88bd')
+    version('4.11',  '0e9566046e402f8dc514caef11155864')
+    version('4.9.1', '820ef17ffa7ed87af6cc9918a961d966')
+    version('4.9',   'ee31343dbc4bf7b5b7501ec1650e9233')
+    version('4.7',   '623d91fb2ab0a35049dc6098a0f235cc')
+    version('4.6.3', '6953897544d41ffcc63ffe58b32a688f')
 
     variant('shared', default=True,
             description='Enables the build of shared libraries')
diff --git a/var/spack/repos/builtin/packages/cgm/package.py b/var/spack/repos/builtin/packages/cgm/package.py
index 8f2fa13f9a..11de8aa7df 100644
--- a/var/spack/repos/builtin/packages/cgm/package.py
+++ b/var/spack/repos/builtin/packages/cgm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/cgns/package.py b/var/spack/repos/builtin/packages/cgns/package.py
index c9d46dc8e9..e101f84c27 100644
--- a/var/spack/repos/builtin/packages/cgns/package.py
+++ b/var/spack/repos/builtin/packages/cgns/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,31 +14,53 @@ class Cgns(CMakePackage):
     homepage = "http://cgns.github.io/"
     url      = "https://github.com/CGNS/CGNS/archive/v3.3.0.tar.gz"
 
+    version('3.3.1', '65c55998270c3e125e28ec5c3742e15d')
     version('3.3.0', '64e5e8d97144c1462bee9ea6b2a81d7f')
 
     variant('hdf5', default=True, description='Enable HDF5 interface')
+    variant('fortran', default=False, description='Enable Fortran interface')
+    variant('scoping', default=True, description='Enable scoping')
+    variant('mpi', default=True, description='Enable parallel cgns')
 
-    depends_on('cmake@2.8:', type='build')
-    depends_on('hdf5', when='+hdf5')
-
-    parallel = False
+    depends_on('hdf5', when='+hdf5~mpi')
+    depends_on('hdf5+mpi', when='+hdf5+mpi')
+    depends_on('mpi', when='+mpi')
 
     def cmake_args(self):
         spec = self.spec
-        cmake_args = []
+        options = []
 
-        if self.compiler.f77 and self.compiler.fc:
-            cmake_args.append('-DCGNS_ENABLE_FORTRAN=ON')
-        else:
-            cmake_args.append('-DCGNS_ENABLE_FORTRAN=OFF')
+        options.extend([
+            '-DCGNS_ENABLE_FORTRAN:BOOL=%s' % (
+                'ON' if '+fortran' in spec else 'OFF'),
+            '-DCGNS_ENABLE_SCOPING:BOOL=%s' % (
+                'ON' if '+scoping' in spec else 'OFF'),
+            '-DCGNS_ENABLE_PARALLEL:BOOL=%s' % (
+                'ON' if '+mpi' in spec else 'OFF'),
+            '-DCGNS_ENABLE_TESTS:BOOL=OFF',
+            '-DCGNS_BUILD_CGNSTOOLS:BOOL=OFF'
+        ])
 
-        if '+hdf5' in spec:
-            cmake_args.extend([
-                '-DCGNS_ENABLE_HDF5=ON',
-                '-DHDF5_DIR=%s' % spec['hdf5'].prefix
+        if '+mpi' in spec:
+            options.extend([
+                '-DCMAKE_C_COMPILER=%s'       % spec['mpi'].mpicc,
+                '-DCMAKE_CXX_COMPILER=%s'     % spec['mpi'].mpicxx,
+                '-DCMAKE_Fortran_COMPILER=%s' % spec['mpi'].mpifc
             ])
 
+        if '+hdf5' in spec:
+            options.extend([
+                '-DCGNS_ENABLE_HDF5:BOOL=ON',
+                '-DHDF5_NEED_ZLIB:BOOL=ON',
+                '-DHDF5_INCLUDE_DIR:PATH=%s' % spec['hdf5'].prefix.include,
+                '-DHDF5_LIBRARY_DIR:PATH=%s' % spec['hdf5'].prefix.lib
+            ])
+            if '+mpi' in spec:
+                options.extend([
+                    '-DHDF5_NEED_MPI:BOOL=ON',
+                    '-DHDF5_ENABLE_PARALLEL:BOOL=ON'
+                ])
         else:
-            cmake_args.append('-DCGNS_ENABLE_HDF5=OFF')
+            options.extend(['-DCGNS_ENABLE_HDF5=OFF'])
 
-        return cmake_args
+        return options
diff --git a/var/spack/repos/builtin/packages/channelflow/package.py b/var/spack/repos/builtin/packages/channelflow/package.py
new file mode 100644
index 0000000000..1a396f0600
--- /dev/null
+++ b/var/spack/repos/builtin/packages/channelflow/package.py
@@ -0,0 +1,85 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Channelflow(CMakePackage):
+    """Channelflow is a software system for numerical analysis of the
+    incompressible fluid flow in channel geometries, written in C++.
+    """
+
+    homepage = 'https://github.com/epfl-ecps/channelflow'
+    url = 'https://github.com/epfl-ecps/channelflow.git'
+
+    version(
+        'develop',
+        git='https://github.com/epfl-ecps/channelflow.git',
+        branch='master'
+    )
+
+    variant('shared', default=True, description='Build shared libs')
+    variant('mpi', default=True, description='Enable MPI parallelism')
+    variant('hdf5', default=True, description='Enable support for HDF5 I/O')
+    variant(
+        'netcdf', default='serial', values=('none', 'serial', 'parallel'),
+        multi=False, description='Level of support for NetCDF I/O'
+    )
+    variant('python', default=False, description='Build python bindings')
+
+    depends_on('eigen')
+    depends_on('fftw')
+
+    # MPI related constraints
+    depends_on('mpi', when='+mpi')
+    depends_on('fftw+mpi', when='+mpi')
+
+    # Support for different I/O formats
+    depends_on('hdf5+cxx', when='+hdf5')
+    depends_on('netcdf', when='netcdf=serial')
+    depends_on('netcdf+mpi', when='netcdf=parallel')
+
+    # Python bindings
+    depends_on('boost+python', when='+python')
+
+    conflicts('~mpi', when='netcdf=parallel', msg='Parallel NetCDF requires MPI')
+    conflicts(
+        '+mpi', when='+python',
+        msg='Building python bindings is possible only for the serial code'
+    )
+    conflicts('~mpi', when='^mpi',
+              msg='There should be no MPI in the DAG when ~mpi is active')
+
+    def cmake_args(self):
+        spec = self.spec
+
+        on_or_off = lambda predicate: 'ON' if predicate else 'OFF'
+
+        args = [
+            '-DBUILD_SHARED_LIBS:BOOL={0}'.format(
+                on_or_off('+shared' in spec)
+            ),
+            '-DUSE_MPI:BOOL={0}'.format(on_or_off('+mpi' in spec)),
+            '-DWITH_HDF5CXX:BOOL={0}'.format(on_or_off('+hdf5' in spec)),
+            '-DWITH_PYTHON:BOOL={0}'.format(on_or_off('+python' in spec))
+        ]
+
+        netcdf_str = {
+            'none': 'OFF',
+            'serial': 'Serial',
+            'parallel': 'Parallel'
+        }
+
+        args.append('-DWITH_NETCDF:STRING={0}'.format(
+            netcdf_str[spec.variants['netcdf'].value]
+        ))
+
+        # Set an MPI compiler for parallel builds
+        if '+mpi' in spec:
+            args.append(
+                '-DCMAKE_CXX_COMPILER:PATH={0}'.format(spec['mpi'].mpicxx)
+            )
+
+        return args
diff --git a/var/spack/repos/builtin/packages/charliecloud/package.py b/var/spack/repos/builtin/packages/charliecloud/package.py
new file mode 100644
index 0000000000..c9e59fd5ec
--- /dev/null
+++ b/var/spack/repos/builtin/packages/charliecloud/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Charliecloud(MakefilePackage):
+    """Lightweight user-defined software stacks for HPC."""
+
+    homepage = "https://hpc.github.io/charliecloud"
+    url      = "https://github.com/hpc/charliecloud/archive/v0.2.4.tar.gz"
+
+    version('0.9.3', sha256='f1bf032377b8845bc9a93b8a4fad6386161e35900223c0acc61d1f3aa3a87bc7')
+    version('0.9.2', sha256='8d0e4804d412beef720a66f886a0a78bce42f3269e880ebf11f602581f8047d4')
+    version('0.9.1', sha256='8e69150a271285da71ece7a09b48251ef6593f72207c5126741d9976aa737d95')
+    version('0.9.0', sha256='7e74cb16e31fd9d502198f7509bab14d1049ec68ba90b15e277e76f805db9458')
+    version('0.2.4', 'b112de661c2c360174b42c99022c1967')
+
+    @property
+    def install_targets(self):
+        return ['install', 'PREFIX=%s' % self.prefix]
diff --git a/var/spack/repos/builtin/packages/charm/package.py b/var/spack/repos/builtin/packages/charm/package.py
deleted file mode 100644
index b5568920d9..0000000000
--- a/var/spack/repos/builtin/packages/charm/package.py
+++ /dev/null
@@ -1,182 +0,0 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-
-import os
-import platform
-import shutil
-import sys
-from spack import *
-
-
-class Charm(Package):
-    """Charm++ is a parallel programming framework in C++ supported by
-    an adaptive runtime system, which enhances user productivity and
-    allows programs to run portably from small multicore computers
-    (your laptop) to the largest supercomputers."""
-
-    homepage = "http://charmplusplus.org"
-    url      = "http://charm.cs.illinois.edu/distrib/charm-6.7.1.tar.gz"
-
-    version("6.7.1", "a8e20cf85e9c8721158f5bbd0ade48d9")
-    version("6.7.0", "35a39a7975f1954a7db2d76736158231")
-    version("6.6.1", "9554230f741e2599deaaac4d9d93d7ab")
-    version("6.6.0", "31e95901b3f7324d52107e6ad000fcc8")
-    version("6.5.1", "034d99458474a3ab96d8bede8a691a5d")
-
-    # Support OpenMPI; see
-    # <https://charm.cs.illinois.edu/redmine/issues/1206>
-    patch("mpi.patch")
-    # Ignore compiler warnings while configuring
-    patch("strictpass.patch")
-
-    # Communication mechanisms (choose exactly one)
-    # TODO: Support Blue Gene/Q PAMI, Cray GNI, Cray shmem, CUDA
-    variant(
-        'backend',
-        default='mpi',
-        values=('mpi', 'multicore', 'net', 'netlrts', 'verbs'),
-        description='Set the backend to use'
-    )
-
-    # Other options
-    # Something is off with PAPI -- there are build errors. Maybe
-    # Charm++ expects a particular version?
-    variant("papi", default=False, description="Enable PAPI integration")
-    variant("smp", default=True,
-            description=(
-                "Enable SMP parallelism (does not work with +multicore)"))
-    variant("tcp", default=False,
-            description="Use TCP as transport mechanism (requires +net)")
-    variant("shared", default=True, description="Enable shared link support")
-
-    # Note: We could add variants for AMPI, LIBS, bigemulator, msa, Tau
-
-    depends_on('mpi', when='backend=mpi')
-    depends_on("papi", when="+papi")
-
-    def install(self, spec, prefix):
-        target = "charm++"
-
-        comm = spec.variants['backend'].value
-
-        plat = sys.platform
-        if plat.startswith("linux"):
-            plat = "linux"
-        mach = platform.machine()
-
-        # Define Charm++ version names for various (plat, mach, comm)
-        # combinations. Note that not all combinations are supported.
-        versions = {
-            ("darwin", "i386", "multicore"): "multicore-darwin-x86",
-            ("darwin", "i386", "net"): "net-darwin-x86",
-            ("darwin", "x86_64", "mpi"): "mpi-darwin-x86_64",
-            ("darwin", "x86_64", "multicore"): "multicore-darwin-x86_64",
-            ("darwin", "x86_64", "net"): "net-darwin-x86_64",
-            ("darwin", "x86_64", "netlrts"): "netlrts-darwin-x86_64",
-            ("linux", "i386", "mpi"): "mpi-linux",
-            ("linux", "i386", "multicore"): "multicore-linux32",
-            ("linux", "i386", "net"): "net-linux",
-            ("linux", "i386", "netlrts"): "netlrts-linux",
-            ("linux", "x86_64", "mpi"): "mpi-linux-x86_64",
-            ("linux", "x86_64", "multicore"): "multicore-linux64",
-            ("linux", "x86_64", "net"): "net-linux-x86_64",
-            ("linux", "x86_64", "netlrts"): "netlrts-linux-x86_64",
-            ("linux", "x86_64", "verbs"): "verbs-linux-x86_64",
-        }
-        if (plat, mach, comm) not in versions:
-            raise InstallError(
-                "The communication mechanism %s is not supported "
-                "on a %s platform with a %s CPU" %
-                (comm, plat, mach))
-        version = versions[(plat, mach, comm)]
-
-        # We assume that Spack's compiler wrappers make this work. If
-        # not, then we need to query the compiler vendor from Spack
-        # here.
-        compiler = os.path.basename(self.compiler.cc)
-
-        options = [compiler]
-        if compiler == 'icc':
-            options.append('ifort')
-
-        options.extend([
-            "--with-production",   # Note: turn this into a variant
-            "-j%d" % make_jobs,
-            "--destination=%s" % prefix])
-
-        if 'backend=mpi' in spec:
-            # in intelmpi <prefix>/include and <prefix>/lib fails so --basedir
-            # cannot be used
-            options.extend([
-                '--incdir={0}'.format(incdir)
-                for incdir in spec["mpi"].headers.directories
-            ])
-            options.extend([
-                '--libdir={0}'.format(libdir)
-                for libdir in spec["mpi"].libs.directories
-            ])
-        if "+papi" in spec:
-            options.extend(["papi", "--basedir=%s" % spec["papi"].prefix])
-        if "+smp" in spec:
-            if 'backend=multicore' in spec:
-                # This is a Charm++ limitation; it would lead to a
-                # build error
-                raise InstallError("Cannot combine +smp with +multicore")
-            options.append("smp")
-        if "+tcp" in spec:
-            if 'backend=net' not in spec:
-                # This is a Charm++ limitation; it would lead to a
-                # build error
-                raise InstallError(
-                    "The +tcp variant requires "
-                    "the backend=net communication mechanism")
-            options.append("tcp")
-        if "+shared" in spec:
-            options.append("--build-shared")
-
-        # Call "make" via the build script
-        # Note: This builds Charm++ in the "tmp" subdirectory of the
-        # install directory. Maybe we could set up a symbolic link
-        # back to the build tree to prevent this? Alternatively, we
-        # could dissect the build script; the build instructions say
-        # this wouldn't be difficult.
-        build = Executable(join_path(".", "build"))
-        build(target, version, *options)
-
-        # Charm++'s install script does not copy files, it only creates
-        # symbolic links. Fix this.
-        for dirpath, dirnames, filenames in os.walk(prefix):
-            for filename in filenames:
-                filepath = join_path(dirpath, filename)
-                if os.path.islink(filepath):
-                    tmppath = filepath + ".tmp"
-                    # Skip dangling symbolic links
-                    try:
-                        shutil.copy2(filepath, tmppath)
-                        os.remove(filepath)
-                        os.rename(tmppath, filepath)
-                    except (IOError, OSError):
-                        pass
-        shutil.rmtree(join_path(prefix, "tmp"))
diff --git a/var/spack/repos/builtin/packages/charm/mpi.patch b/var/spack/repos/builtin/packages/charmpp/mpi.patch
index e909d5f876..e909d5f876 100644
--- a/var/spack/repos/builtin/packages/charm/mpi.patch
+++ b/var/spack/repos/builtin/packages/charmpp/mpi.patch
diff --git a/var/spack/repos/builtin/packages/charmpp/package.py b/var/spack/repos/builtin/packages/charmpp/package.py
new file mode 100644
index 0000000000..d192f3e156
--- /dev/null
+++ b/var/spack/repos/builtin/packages/charmpp/package.py
@@ -0,0 +1,244 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+import os
+import platform
+import shutil
+import sys
+from spack import *
+
+
+class Charmpp(Package):
+    """Charm++ is a parallel programming framework in C++ supported by
+    an adaptive runtime system, which enhances user productivity and
+    allows programs to run portably from small multicore computers
+    (your laptop) to the largest supercomputers."""
+
+    homepage = "http://charmplusplus.org"
+    url      = "http://charm.cs.illinois.edu/distrib/charm-6.8.2.tar.gz"
+    git      = "https://github.com/UIUC-PPL/charm.git"
+
+    version("develop", branch="charm")
+    version("6.8.2", "a887a34b638a5b2f7fcf7ff3c262496d")
+    version("6.8.1", "3e95ffa760909154ef16b643c9bb8193")
+    version("6.8.0", "54df066a5aefb0bbc1a263c2383c2bba")
+    version("6.7.1", "a8e20cf85e9c8721158f5bbd0ade48d9")
+    version("6.7.0", "35a39a7975f1954a7db2d76736158231")
+    version("6.6.1", "9554230f741e2599deaaac4d9d93d7ab")
+    version("6.6.0", "31e95901b3f7324d52107e6ad000fcc8")
+    version("6.5.1", "034d99458474a3ab96d8bede8a691a5d")
+
+    # Support OpenMPI; see
+    # <https://charm.cs.illinois.edu/redmine/issues/1206>
+    # Patch is no longer needed in versions 6.8.0+
+    patch("mpi.patch", when="@:6.7.1")
+
+    # Ignore compiler warnings while configuring
+    patch("strictpass.patch", when="@:6.8.2")
+
+    # Build targets
+    # "target" is reserved, so we have to use something else.
+    variant(
+        "build-target",
+        default="LIBS",
+        # AMPI also builds charm++, LIBS also builds AMPI and charm++
+        values=("charm++", "AMPI", "LIBS"),
+        description="Specify the target to build"
+    )
+
+    # Communication mechanisms (choose exactly one)
+    variant(
+        "backend",
+        default="netlrts",
+        values=("mpi", "multicore", "netlrts", "verbs", "gni",
+                "ofi", "pami", "pamilrts"),
+        description="Set the backend to use"
+    )
+
+    # Other options
+    variant("papi", default=False, description="Enable PAPI integration")
+    variant("syncft", default=False, description="Compile with Charm++ fault tolerance support")
+    variant("smp", default=True,
+            description=(
+                "Enable SMP parallelism (does not work with +multicore)"))
+    variant("tcp", default=False,
+            description="Use TCP as transport mechanism (requires +net)")
+    variant("omp", default=False, description="Support for the integrated LLVM OpenMP runtime")
+    variant("pthreads", default=False, description="Compile with pthreads Converse threads")
+    variant("cuda", default=False, description="Enable CUDA toolkit")
+
+    variant("shared", default=True, description="Enable shared link support")
+    variant("production", default=True, description="Build charm++ with all optimizations")
+    variant("tracing", default=False, description="Enable tracing modules")
+
+    # FIXME: backend=mpi also provides mpi, but spack does not support
+    # depends_on("mpi") and provides("mpi") in the same package currently.
+    for b in ['multicore', 'netlrts', 'verbs', 'gni', 'ofi', 'pami',
+              'pamilrts']:
+        provides('mpi@2', when='@6.7.1: build-target=AMPI backend={0}'.format(b))
+        provides('mpi@2', when='@6.7.1: build-target=LIBS backend={0}'.format(b))
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        spack_env.set('MPICC',  join_path(self.prefix.bin, 'ampicc'))
+        spack_env.set('MPICXX', join_path(self.prefix.bin, 'ampicxx'))
+        spack_env.set('MPIF77', join_path(self.prefix.bin, 'ampif77'))
+        spack_env.set('MPIF90', join_path(self.prefix.bin, 'ampif90'))
+
+    def setup_dependent_package(self, module, dependent_spec):
+        self.spec.mpicc = join_path(self.prefix.bin, 'ampicc')
+        self.spec.mpicxx = join_path(self.prefix.bin, 'ampicxx')
+        self.spec.mpifc = join_path(self.prefix.bin, 'ampif90')
+        self.spec.mpif77 = join_path(self.prefix.bin, 'ampif77')
+
+    depends_on("mpi", when="backend=mpi")
+    depends_on("papi", when="+papi")
+    depends_on("cuda", when="+cuda")
+
+    # Git versions of Charm++ require automake and autoconf
+    depends_on("automake", when="@develop")
+    depends_on("autoconf", when="@develop")
+
+    conflicts("~tracing", "+papi")
+
+    conflicts("backend=multicore", "+smp")
+
+    def install(self, spec, prefix):
+        target = spec.variants["build-target"].value
+
+        plat = sys.platform
+        if plat.startswith("linux"):
+            plat = "linux"
+        elif plat.startswith("win"):
+            plat = "win"
+        elif plat.startswith("cnl"):
+            plat = "cnl"
+        elif plat.startswith("cnk"):
+            plat = "cnk"
+
+        mach = platform.machine()
+        if mach.startswith("ppc"):
+            mach = "ppc"
+        elif mach.startswith("arm"):
+            mach = "arm"
+
+        comm = spec.variants['backend'].value
+
+        # Define Charm++ version names for various (plat, mach, comm)
+        # combinations. Note that not all combinations are supported.
+        versions = {
+            ("darwin",  "x86_64",   "mpi"):         "mpi-darwin-x86_64",
+            ("darwin",  "x86_64",   "multicore"):   "multicore-darwin-x86_64",
+            ("darwin",  "x86_64",   "netlrts"):     "netlrts-darwin-x86_64",
+            ("linux",   "i386",     "mpi"):         "mpi-linux",
+            ("linux",   "i386",     "multicore"):   "multicore-linux",
+            ("linux",   "i386",     "netlrts"):     "netlrts-linux",
+            ("linux",   "i386",     "uth"):         "uth-linux",
+            ("linux",   "x86_64",   "mpi"):         "mpi-linux-x86_64",
+            ("linux",   "x86_64",   "multicore"):   "multicore-linux-x86_64",
+            ("linux",   "x86_64",   "netlrts"):     "netlrts-linux-x86_64",
+            ("linux",   "x86_64",   "verbs"):       "verbs-linux-x86_64",
+            ("linux",   "x86_64",   "ofi"):         "ofi-linux-x86_64",
+            ("linux",   "x86_64",   "uth"):         "uth-linux-x86_64",
+            ("linux",   "ppc",      "mpi"):         "mpi-linux-ppc",
+            ("linux",   "ppc",      "multicore"):   "multicore-linux-ppc",
+            ("linux",   "ppc",      "netlrts"):     "netlrts-linux-ppc",
+            ("linux",   "ppc",      "pami"):        "pami-linux-ppc64le",
+            ("linux",   "ppc",      "verbs"):       "verbs-linux-ppc64le",
+            ("linux",   "arm",      "netlrts"):     "netlrts-linux-arm7",
+            ("linux",   "arm",      "multicore"):   "multicore-arm7",
+            ("win",     "x86_64",   "mpi"):         "mpi-win-x86_64",
+            ("win",     "x86_64",   "multicore"):   "multicore-win-x86_64",
+            ("win",     "x86_64",   "netlrts"):     "netlrts-win-x86_64",
+            ("cnl",     "x86_64",   "gni"):         "gni-crayxc",
+            ("cnl",     "x86_64",   "mpi"):         "mpi-crayxc",
+            ("cnk",     "x86_64",   "mpi"):         "mpi-bluegeneq",
+            ("cnk",     "x86_64",   "pami"):        "pami-bluegeneq",
+            ("cnk",     "x86_64",   "pamilrts"):    "pamilrts-bluegeneq",
+        }
+        if (plat, mach, comm) not in versions:
+            raise InstallError(
+                "The communication mechanism %s is not supported "
+                "on a %s platform with a %s CPU" %
+                (comm, plat, mach))
+        version = versions[(plat, mach, comm)]
+
+        # We assume that Spack's compiler wrappers make this work. If
+        # not, then we need to query the compiler vendor from Spack
+        # here.
+        options = [
+            os.path.basename(self.compiler.cc),
+            os.path.basename(self.compiler.fc),
+            "-j%d" % make_jobs,
+            "--destination=%s" % prefix,
+        ]
+
+        if 'backend=mpi' in spec:
+            # in intelmpi <prefix>/include and <prefix>/lib fails so --basedir
+            # cannot be used
+            options.extend([
+                '--incdir={0}'.format(incdir)
+                for incdir in spec["mpi"].headers.directories
+            ])
+            options.extend([
+                '--libdir={0}'.format(libdir)
+                for libdir in spec["mpi"].libs.directories
+            ])
+        if "+papi" in spec:
+            options.extend(["papi", "--basedir=%s" % spec["papi"].prefix])
+        if "+smp" in spec:
+            options.append("smp")
+        if "+tcp" in spec:
+            if 'backend=netlrts' not in spec:
+                # This is a Charm++ limitation; it would lead to a
+                # build error
+                raise InstallError(
+                    "The +tcp variant requires "
+                    "the backend=netlrts communication mechanism")
+            options.append("tcp")
+        if "+omp" in spec:
+            options.append("omp")
+        if "+pthreads" in spec:
+            options.append("pthreads")
+        if "+cuda" in spec:
+            options.append("cuda")
+
+        if "+shared" in spec:
+            options.append("--build-shared")
+        if "+production" in spec:
+            options.append("--with-production")
+        if "+tracing" in spec:
+            options.append("--enable-tracing")
+
+        # Call "make" via the build script
+        # Note: This builds Charm++ in the "tmp" subdirectory of the
+        # install directory. Maybe we could set up a symbolic link
+        # back to the build tree to prevent this? Alternatively, we
+        # could dissect the build script; the build instructions say
+        # this wouldn't be difficult.
+        build = Executable(join_path(".", "build"))
+        build(target, version, *options)
+
+        # Charm++'s install script does not copy files, it only creates
+        # symbolic links. Fix this.
+        for dirpath, dirnames, filenames in os.walk(prefix):
+            for filename in filenames:
+                filepath = join_path(dirpath, filename)
+                if os.path.islink(filepath):
+                    tmppath = filepath + ".tmp"
+                    # Skip dangling symbolic links
+                    try:
+                        copy(filepath, tmppath)
+                        os.remove(filepath)
+                        os.rename(tmppath, filepath)
+                    except (IOError, OSError):
+                        pass
+        shutil.rmtree(join_path(prefix, "tmp"))
+
+    @run_after('install')
+    @on_package_attributes(run_tests=True)
+    def check_build(self):
+        make('-C', join_path(self.stage.path, 'charm/tests'),
+             'test', parallel=False)
diff --git a/var/spack/repos/builtin/packages/charm/strictpass.patch b/var/spack/repos/builtin/packages/charmpp/strictpass.patch
index 44aa4fbd38..44aa4fbd38 100644
--- a/var/spack/repos/builtin/packages/charm/strictpass.patch
+++ b/var/spack/repos/builtin/packages/charmpp/strictpass.patch
diff --git a/var/spack/repos/builtin/packages/chatterbug/package.py b/var/spack/repos/builtin/packages/chatterbug/package.py
new file mode 100644
index 0000000000..abaf8e9bd9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/chatterbug/package.py
@@ -0,0 +1,46 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Chatterbug(MakefilePackage):
+    """A suite of communication-intensive proxy applications that mimic
+       commonly found communication patterns in HPC codes. These codes can be
+       used as synthetic codes for benchmarking, or for trace generation using
+       Score-P / OTF2.
+    """
+    tags = ['proxy-app']
+
+    homepage = "https://chatterbug.readthedocs.io"
+    git      = "https://github.com/LLNL/chatterbug.git"
+
+    version('develop', branch='master')
+    version('1.0', tag='v1.0')
+
+    variant('scorep', default=False, description='Build with Score-P tracing')
+
+    depends_on('mpi')
+    depends_on('scorep', when='+scorep')
+
+    @property
+    def build_targets(self):
+        targets = []
+
+        targets.append('MPICXX = {0}'.format(self.spec['mpi'].mpicxx))
+
+        return targets
+
+    def build(self, spec, prefix):
+        if "+scorep" in spec:
+            make('WITH_OTF2=YES')
+        else:
+            make()
+
+    def install(self, spec, prefix):
+        if "+scorep" in spec:
+            make('WITH_OTF2=YES', 'PREFIX=' + spec.prefix, 'install')
+        else:
+            make('PREFIX=' + spec.prefix, 'install')
diff --git a/var/spack/repos/builtin/packages/check/package.py b/var/spack/repos/builtin/packages/check/package.py
index c87a982fa5..d28c428137 100644
--- a/var/spack/repos/builtin/packages/check/package.py
+++ b/var/spack/repos/builtin/packages/check/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/chlorop/package.py b/var/spack/repos/builtin/packages/chlorop/package.py
index 2bccd6d951..c6a9fd6514 100644
--- a/var/spack/repos/builtin/packages/chlorop/package.py
+++ b/var/spack/repos/builtin/packages/chlorop/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-import distutils.dir_util
 import os
 
 
@@ -47,7 +27,7 @@ class Chlorop(Package):
 
     def install(self, spec, prefix):
         os.rename('chlorop', 'bin/chlorop')
-        distutils.dir_util.copy_tree(".", prefix)
+        install_tree('.', prefix)
 
     def setup_environment(self, spack_env, run_env):
         run_env.set('CHLOROP', self.prefix)
diff --git a/var/spack/repos/builtin/packages/chombo/package.py b/var/spack/repos/builtin/packages/chombo/package.py
index 8dd5155199..29b113b782 100644
--- a/var/spack/repos/builtin/packages/chombo/package.py
+++ b/var/spack/repos/builtin/packages/chombo/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from shutil import copyfile
 import glob
 
 
@@ -34,12 +14,13 @@ class Chombo(MakefilePackage):
        logically rectangular (i.e. Cartesian) grids."""
 
     homepage = "https://commons.lbl.gov/display/chombo"
-    url      = "http://bitbucket.org/drhansj/chombo-xsdk.git"
+    git      = "http://bitbucket.org/drhansj/chombo-xsdk.git"
+
+    tags = ['ecp', 'ecp-apps']
 
     # Use whatever path Brian V. and Terry L. agreed upon, but preserve version
-    version('3.2', git='http://bitbucket.org/drhansj/chombo-xsdk.git', commit='71d856c')
-    version('develop', git='http://bitbucket.org/drhansj/chombo-xsdk.git', tag='master')
-#    version('3.2', svn='https://anag-repo.lbl.gov/svn/Chombo/release/3.2')
+    version('3.2', commit='71d856c')
+    version('develop', tag='master')
 
     variant('mpi', default=True, description='Enable MPI parallel support')
     variant('hdf5', default=True, description='Enable HDF5 support')
@@ -70,8 +51,8 @@ class Chombo(MakefilePackage):
         # Set remaining variables in Make.defs.local
         # Make.defs.local.template.patch ensures lines for USE_TIMER,
         # USE_LAPACK and lapackincflags are present
-        copyfile('./lib/mk/Make.defs.local.template',
-                 './lib/mk/Make.defs.local')
+        copy('./lib/mk/Make.defs.local.template',
+             './lib/mk/Make.defs.local')
 
         defs_file = FileFilter('./lib/mk/Make.defs.local')
 
diff --git a/var/spack/repos/builtin/packages/cistem/package.py b/var/spack/repos/builtin/packages/cistem/package.py
new file mode 100644
index 0000000000..52b7dad557
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cistem/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Cistem(AutotoolsPackage):
+    """cisTEM is user-friendly software to process cryo-EM images of
+       macromolecular complexes and obtain high-resolution 3D reconstructions
+       from them."""
+
+    homepage = "https://cistem.org/"
+    url      = "https://cistem.org/system/tdf/upload3/cistem-1.0.0-beta-source-code.tar.gz?file=1&type=cistem_details&id=37&force=0"
+
+    version('1.0.0-beta', '479f395b30ad630df3cbba9c56eb29c2')
+
+    depends_on('wx@3.0.2')
+    depends_on('fftw')
diff --git a/var/spack/repos/builtin/packages/cityhash/package.py b/var/spack/repos/builtin/packages/cityhash/package.py
index 67ee8561a3..4712e309dc 100644
--- a/var/spack/repos/builtin/packages/cityhash/package.py
+++ b/var/spack/repos/builtin/packages/cityhash/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,12 +10,10 @@ class Cityhash(AutotoolsPackage):
     """CityHash, a family of hash functions for strings."""
 
     homepage = "https://github.com/google/cityhash"
-    url      = "https://github.com/google/cityhash"
+    git      = "https://github.com/google/cityhash.git"
 
-    version('2013-07-31', git='https://github.com/google/cityhash.git',
-            commit='8af9b8c2b889d80c22d6bc26ba0df1afb79a30db')
-    version('master', branch='master',
-            git='https://github.com/google/cityhash.git')
+    version('master', branch='master')
+    version('2013-07-31', commit='8af9b8c2b889d80c22d6bc26ba0df1afb79a30db')
 
     def configure_args(self):
         return ['--enable-sse4.2']
diff --git a/var/spack/repos/builtin/packages/clamr/package.py b/var/spack/repos/builtin/packages/clamr/package.py
index 3608c64ca2..ce3f9b236d 100644
--- a/var/spack/repos/builtin/packages/clamr/package.py
+++ b/var/spack/repos/builtin/packages/clamr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,10 +13,10 @@ class Clamr(CMakePackage):
     """
 
     homepage = "https://github.com/lanl/CLAMR"
-    url      = "https://github.com/lanl/CLAMR.git"
+    git      = "https://github.com/lanl/CLAMR.git"
     tags     = ['proxy-app']
 
-    version('master', git='https://github.com/lanl/CLAMR.git')
+    version('master')
 
     variant(
         'graphics', default='opengl',
@@ -46,6 +27,7 @@ class Clamr(CMakePackage):
         values=('single', 'mixed', 'full'),
         description='single, mixed, or full double precision values')
 
+    depends_on('cmake@3.1:')
     depends_on('mpi')
     depends_on('mpe', when='graphics=mpe')
 
diff --git a/var/spack/repos/builtin/packages/clapack/package.py b/var/spack/repos/builtin/packages/clapack/package.py
new file mode 100644
index 0000000000..70d159b336
--- /dev/null
+++ b/var/spack/repos/builtin/packages/clapack/package.py
@@ -0,0 +1,44 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Clapack(MakefilePackage):
+    """CLAPACK is a f2c'ed version of LAPACK.
+
+       The CLAPACK library was built using a Fortran to C conversion utility
+    called f2c.  The entire Fortran 77 LAPACK library is run through f2c to
+    obtain C code, and then modified to improve readability.  CLAPACK's goal
+    is to provide LAPACK for someone who does not have access to a Fortran
+    compiler."""
+
+    homepage = "http://www.netlib.org/clapack/"
+    url      = "http://www.netlib.org/clapack/clapack.tgz"
+
+    version('3.2.1', '040da31f3a7d4fbc9ac376c748d18d1f')
+
+    variant('external-blas', default=True,
+            description='Build with external BLAS (ATLAS here).')
+
+    depends_on('atlas', when='+external-blas')
+
+    def edit(self, spec, prefix):
+        copy('make.inc.example', 'make.inc')
+        if '+external-blas' in spec:
+            make_inc = FileFilter('make.inc')
+            make_inc.filter(r'^BLASLIB.*',
+                            'BLASLIB = ../../libcblaswr.a -lcblas -latlas')
+            makefile = FileFilter('Makefile')
+            makefile.filter(r'^lib.*',
+                            'lib: variants lapacklib tmglib')
+
+    def build(self, spec, prefix):
+        make('f2clib')
+        make('cblaswrap' if '+external-blas' in spec else 'blaslib')
+        make('lib')
+
+    def install(self, spec, prefix):
+        install_tree('.', prefix)
diff --git a/var/spack/repos/builtin/packages/claw/package.py b/var/spack/repos/builtin/packages/claw/package.py
new file mode 100644
index 0000000000..d905faf2bc
--- /dev/null
+++ b/var/spack/repos/builtin/packages/claw/package.py
@@ -0,0 +1,36 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Claw(CMakePackage):
+    """CLAW Compiler targets performance portability problem in climate and
+       weather application written in Fortran. From a single source code, it
+       generates architecture specific code decorated with OpenMP or OpenACC"""
+
+    homepage = 'https://claw-project.github.io/'
+    git      = 'https://github.com/claw-project/claw-compiler.git'
+    maintainers = ['clementval']
+
+    version('1.1.0', commit='16b165a443b11b025a77cad830b1280b8c9bcf01', submodules=True)
+
+    depends_on('cmake@3.0:', type='build')
+    depends_on('java@7:')
+    depends_on('ant@1.9:')
+    depends_on('libxml2')
+    depends_on('bison')
+
+    def cmake_args(self):
+        args = []
+        spec = self.spec
+
+        args.append('-DOMNI_CONF_OPTION=--with-libxml2={0}'.
+                    format(spec['libxml2'].prefix))
+
+        args.append('-DCMAKE_Fortran_COMPILER={0}'.
+                    format(self.compiler.fc))
+
+        return args
diff --git a/var/spack/repos/builtin/packages/cleaveland4/package.py b/var/spack/repos/builtin/packages/cleaveland4/package.py
index 910ef7cb12..c2b7fb0272 100644
--- a/var/spack/repos/builtin/packages/cleaveland4/package.py
+++ b/var/spack/repos/builtin/packages/cleaveland4/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/cleverleaf/package.py b/var/spack/repos/builtin/packages/cleverleaf/package.py
index 0e40d3ff4c..65e6ec5f43 100644
--- a/var/spack/repos/builtin/packages/cleverleaf/package.py
+++ b/var/spack/repos/builtin/packages/cleverleaf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,16 +12,20 @@ class Cleverleaf(CMakePackage):
        Livermore National Laboratory. The primary goal of CleverLeaf is
        to evaluate the application of AMR to the Lagrangian-Eulerian
        hydrodynamics scheme used by CloverLeaf.
-
     """
 
     homepage = "http://uk-mac.github.io/CleverLeaf/"
-    url      = "https://github.com/UK-MAC/CleverLeaf/tarball/master"
+    git      = "https://github.com/UK-MAC/CleverLeaf_ref.git"
 
-    version('develop', git='https://github.com/UK-MAC/CleverLeaf_ref.git',
-            branch='develop')
+    version('develop', branch='develop')
 
     depends_on('samrai@3.8.0:')
     depends_on('hdf5+mpi')
     depends_on('boost')
     depends_on('cmake@3.1:', type='build')
+
+    def flag_handler(self, name, flags):
+        if self.spec.satisfies('%intel') and name in ['cppflags', 'cxxflags']:
+            flags.append(self.compiler.cxx11_flag)
+
+        return (None, None, flags)
diff --git a/var/spack/repos/builtin/packages/clfft/package.py b/var/spack/repos/builtin/packages/clfft/package.py
index d626e8964a..9851439a09 100644
--- a/var/spack/repos/builtin/packages/clfft/package.py
+++ b/var/spack/repos/builtin/packages/clfft/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/clhep/package.py b/var/spack/repos/builtin/packages/clhep/package.py
index f1f1d2db96..8db6263539 100644
--- a/var/spack/repos/builtin/packages/clhep/package.py
+++ b/var/spack/repos/builtin/packages/clhep/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -33,22 +14,26 @@ class Clhep(CMakePackage):
     list_url = "https://proj-clhep.web.cern.ch/proj-clhep/"
     list_depth = 1
 
-    version('2.3.4.4', '8b8a33d0d19213b60d6c22ce5fc93761')
-    version('2.3.4.3', '6941279f70d69492fff1aa955f3f2562')
-    version('2.3.4.2', '1e7a9046c9ad0b347d6812f8031191da')
-    version('2.3.4.1', '5ae85571ff3d8b2c481c3f95ea89b751')
-    version('2.3.4.0', 'dd899d0791a823221927f97edf190348')
-    version('2.3.3.2', '8b9f8d7f4dccec6d058b3a078f66b6a3')
-    version('2.3.3.1', '456ef9d262ef4e776af984bfbe2f48c7')
-    version('2.3.3.0', '3637eaa6750606e589e52c9e155a382e')
-    version('2.3.2.2', '567b304b0fa017e1e9fbf199f456ebe9')
-    version('2.3.2.1', '064903cb5c23b54f520d04ca6230b901')
-    version('2.3.1.1', '16efca7641bc118c9d217cc96fe90bf5')
-    version('2.3.1.0', 'b084934fc26a4182a08c09c292e19161')
-    version('2.3.0.0', 'a00399a2ca867f2be902c22fc71d7e2e')
-    version('2.2.0.8', '5a23ed3af785ac100a25f6cb791846af')
-    version('2.2.0.5', '1584e8ce6ebf395821aed377df315c7c')
-    version('2.2.0.4', '71d2c7c2e39d86a0262e555148de01c1')
+    version('2.4.1.0', sha256='d14736eb5c3d21f86ce831dc1afcf03d423825b35c84deb6f8fd16773528c54d')
+    version('2.4.0.4', sha256='eb013841c57990befa1e977a11a552ab8328733c1c3b6cecfde86da40dc22113')
+    version('2.4.0.2', sha256='1e9891c5badb718c24933e7a5c6ee4d64fd4d5cf3a40c150ad18e864ec86b8a4')
+    version('2.4.0.1', sha256='4c7e2c6ac63e0237100e4ddcbfdc3d7e7dc6592f95bdbdcc0e43a6892b9fd6e0')
+    version('2.4.0.0', sha256='5e5cf284323898b4c807db6e684d65d379ade65fe0e93f7b10456890a6dee8cc')
+    version('2.3.4.6', sha256='3e53947036f8570c7a08bed670a862426dbca17328afcecd6c875d8487fef204')
+    version('2.3.4.5', sha256='1199d04626cb8bc1307e282b143018691077cc61fe2f286a382030262eda8764')
+    version('2.3.4.4', sha256='e54de15ffa5108a1913c4910845436345c89ddb83480cd03277a795fafabfb9d')
+    version('2.3.4.3', sha256='1019479265f956bd660c11cb439e1443d4fd1655e8d51accf8b1e703e4262dff')
+    version('2.3.4.2', sha256='6d1e15ccbe1ca6e71d541e78ca7e8c9f3d986ee0da5177a4b8cda00c619dc691')
+    version('2.3.3.2', sha256='4e69a5afb1b7ecc435395195140afc85bbbb9f4d3572f59451c3882f3015a7c1')
+    version('2.3.3.1', sha256='cd74bfae4773620dd0c7cc9c1696a08386931d7e47a3906aa632cc5cb44ed6bd')
+    version('2.3.3.0', sha256='0bcae1bed8d3aa4256e3a553a4f60484312f2121dcc83492a40f08a70881c8c0')
+    version('2.3.2.2', sha256='885481ae32c2f31c3b7f14a5e5d68bc56dc3df0c597be464d7ffa265b8a5a1af')
+    version('2.3.1.1', sha256='0e2b170df99176feb0aa4f20ea3b33463193c086682749790c5b9b79388d0ff4')
+    version('2.3.1.0', sha256='66272ae3100d3aec096b1298e1e24ec25b80e4dac28332b45ec3284023592963')
+    version('2.3.0.0', sha256='63e77f4f34baa5eaa0adb1ca2438734f2d6f5ca112d830650dd005a6109f2397')
+    version('2.2.0.8', sha256='f735e236b1f023ba7399269733b2e84eaed4de615081555b1ab3af25a1e92112')
+    version('2.2.0.5', sha256='92e8b5d32ae96154edd27d0c641ba048ad33cb69dd4f1cfb72fc578770a34818')
+    version('2.2.0.4', sha256='9bf7fcd9892313c8d1436bc4a4a285a016c4f8e81e1fc65bdf6783207ae57550')
 
     variant('cxx11', default=True, description="Compile using c++11 dialect.")
     variant('cxx14', default=False, description="Compile using c++14 dialect.")
diff --git a/var/spack/repos/builtin/packages/clingo/package.py b/var/spack/repos/builtin/packages/clingo/package.py
new file mode 100644
index 0000000000..942d502c52
--- /dev/null
+++ b/var/spack/repos/builtin/packages/clingo/package.py
@@ -0,0 +1,37 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Clingo(CMakePackage):
+    """Clingo: A grounder and solver for logic programs
+
+       Clingo is part of the Potassco project for Answer Set
+       Programming (ASP). ASP offers a simple and powerful modeling
+       language to describe combinatorial problems as logic
+       programs. The clingo system then takes such a logic program and
+       computes answer sets representing solutions to the given
+       problem."""
+
+    homepage = "https://potassco.org/clingo/"
+    url      = "https://github.com/potassco/clingo/archive/v5.2.2.tar.gz"
+
+    version('5.2.2', 'd46a1567f772eebad85c6300d55d2cc3')
+
+    depends_on('doxygen', type=('build'))
+    depends_on('python')
+
+    def cmake_args(self):
+        try:
+            self.compiler.cxx14_flag
+        except UnsupportedCompilerFlag:
+            InstallError('clingo requires a C++14-compliant C++ compiler')
+
+        args = ['-DCLINGO_BUILD_WITH_PYTHON=ON',
+                '-DCLING_BUILD_PY_SHARED=ON',
+                '-DPYCLINGO_USE_INSTALL_PREFIX=ON',
+                '-DCLINGO_BUILD_WITH_LUA=OFF']
+        return args
diff --git a/var/spack/repos/builtin/packages/cloc/package.py b/var/spack/repos/builtin/packages/cloc/package.py
index a5f7f1ecf5..4b5c81b5a8 100644
--- a/var/spack/repos/builtin/packages/cloc/package.py
+++ b/var/spack/repos/builtin/packages/cloc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/cloog/package.py b/var/spack/repos/builtin/packages/cloog/package.py
index b8fad45331..48322a3b22 100644
--- a/var/spack/repos/builtin/packages/cloog/package.py
+++ b/var/spack/repos/builtin/packages/cloog/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/cloverleaf/package.py b/var/spack/repos/builtin/packages/cloverleaf/package.py
index 1f23d5398c..27b6403b56 100644
--- a/var/spack/repos/builtin/packages/cloverleaf/package.py
+++ b/var/spack/repos/builtin/packages/cloverleaf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 import glob
 
diff --git a/var/spack/repos/builtin/packages/cloverleaf3d/package.py b/var/spack/repos/builtin/packages/cloverleaf3d/package.py
index 0d00922325..4879b33473 100644
--- a/var/spack/repos/builtin/packages/cloverleaf3d/package.py
+++ b/var/spack/repos/builtin/packages/cloverleaf3d/package.py
@@ -1,27 +1,8 @@
-#############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 import glob
 
diff --git a/var/spack/repos/builtin/packages/clustalo/package.py b/var/spack/repos/builtin/packages/clustalo/package.py
index 5f3911ac29..ebf6daab9a 100644
--- a/var/spack/repos/builtin/packages/clustalo/package.py
+++ b/var/spack/repos/builtin/packages/clustalo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/clustalw/package.py b/var/spack/repos/builtin/packages/clustalw/package.py
index 478fb702ce..0ebd8986c9 100644
--- a/var/spack/repos/builtin/packages/clustalw/package.py
+++ b/var/spack/repos/builtin/packages/clustalw/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/cmake/nag-response-files.patch b/var/spack/repos/builtin/packages/cmake/nag-response-files.patch
new file mode 100644
index 0000000000..07dc4a1aa1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cmake/nag-response-files.patch
@@ -0,0 +1,9 @@
+diff --git a/Modules/Compiler/NAG-Fortran.cmake b/Modules/Compiler/NAG-Fortran.cmake
+index 39aae1883..9973febc3 100644
+--- a/Modules/Compiler/NAG-Fortran.cmake
++++ b/Modules/Compiler/NAG-Fortran.cmake
+@@ -34,3 +34,4 @@ set(CMAKE_Fortran_FORMAT_FIXED_FLAG "-fixed")
+ set(CMAKE_Fortran_FORMAT_FREE_FLAG "-free")
+ set(CMAKE_Fortran_COMPILE_OPTIONS_PIC "-PIC")
+ set(CMAKE_Fortran_COMPILE_OPTIONS_PIE "-PIC")
++set(CMAKE_Fortran_RESPONSE_FILE_LINK_FLAG "-Wl,@")
diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py
index 150936d1cb..a43c9b7ffb 100644
--- a/var/spack/repos/builtin/packages/cmake/package.py
+++ b/var/spack/repos/builtin/packages/cmake/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,6 +14,20 @@ class Cmake(Package):
     list_url = 'https://cmake.org/files/'
     list_depth = 1
 
+    version('3.12.3',   'acbf13af31a741794106b76e5d22448b004a66485fc99f6d7df4d22e99da164a')
+    version('3.12.2',   '6e7c550cfa1c2e216b35903dc70d80af')
+    version('3.12.1',   '10109246a51102bfda45ff3935275fbf')
+    version('3.12.0',   'ab4aa7df9301c94cdd6f8ee4fe66458b')
+    version('3.11.4',   '72e168b3bad2f9c34dcebbad7af56ff0')
+    version('3.11.3',   '3f923154ed47128f13b08eacd207d9ee')
+    version('3.11.2',   'd2d554c05fc07cfae7846d2aa205f12a')
+    version('3.11.1',   '12a3177477e4e2c7bc514193d421dafe')
+    version('3.11.0',   'f3ebc79b5dec85b49abe75958ffa1a03')
+    version('3.10.3',   '1c38c67295ca696aeafd8c059d748b38')
+    version('3.10.2',   '732808e17fc14dc8cee50d51518c34eb')
+    version('3.10.1',   '9a726e5ec69618b172aa4b06d18c3998')
+    version('3.10.0',   'f3f8e70ca3055f3cd288f89ff233057e')
+    version('3.9.6',    '084b1c8b2efc1c1ba432dea37243c0ae')
     version('3.9.4',    '33769e001bdcd788f565bf378692e5ae')
     version('3.9.0',    '180e23b4c9b55915d271b315297f6951')
     version('3.8.2',    'b5dff61f6a7f1305271ab3f6ae261419')
@@ -78,8 +73,14 @@ class Cmake(Package):
     # https://gitlab.kitware.com/cmake/cmake/issues/16226
     patch('intel-c-gnu11.patch', when='@3.6.0:3.6.1')
 
+    # https://gitlab.kitware.com/cmake/cmake/issues/18232
+    patch('nag-response-files.patch', when='@3.7:3.12')
+
     conflicts('+qt', when='^qt@5.4.0')  # qt-5.4.0 has broken CMake modules
 
+    # https://gitlab.kitware.com/cmake/cmake/issues/18166
+    conflicts('%intel', when='@3.11.0:3.11.4')
+
     phases = ['bootstrap', 'build', 'install']
 
     def url_for_version(self, version):
diff --git a/var/spack/repos/builtin/packages/cmocka/package.py b/var/spack/repos/builtin/packages/cmocka/package.py
index 7598532476..3a09ae9100 100644
--- a/var/spack/repos/builtin/packages/cmocka/package.py
+++ b/var/spack/repos/builtin/packages/cmocka/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/cmor/package.py b/var/spack/repos/builtin/packages/cmor/package.py
index 59a0330324..54aa1ae7c6 100644
--- a/var/spack/repos/builtin/packages/cmor/package.py
+++ b/var/spack/repos/builtin/packages/cmor/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,6 +15,7 @@ class Cmor(AutotoolsPackage):
     homepage = "http://cmor.llnl.gov"
     url = "https://github.com/PCMDI/cmor/archive/3.1.2.tar.gz"
 
+    version('3.3.0', 'cfdeeddab1aedb823e26ec38723bd67e')
     version('3.2.0', 'b48105105d4261012c19cd65e89ff7a6')
     version('3.1.2', '72f7227159c901e4bcf80d2c73a8ce77')
 
@@ -43,7 +25,7 @@ class Cmor(AutotoolsPackage):
     depends_on('uuid')
     depends_on('netcdf')
     depends_on('udunits2')
-    depends_on('hdf5@:1.8')
+    depends_on('hdf5@:1.8.19')
 
     extends('python', when='+python')
     depends_on('python@:2.8', when='+python')
diff --git a/var/spack/repos/builtin/packages/cnmem/package.py b/var/spack/repos/builtin/packages/cnmem/package.py
index 7b068e1ede..cda66b37e2 100644
--- a/var/spack/repos/builtin/packages/cnmem/package.py
+++ b/var/spack/repos/builtin/packages/cnmem/package.py
@@ -1,34 +1,17 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class Cnmem(CMakePackage):
     """CNMem mempool for CUDA devices"""
+
     homepage = "https://github.com/NVIDIA/cnmem"
+    git      = "https://github.com/NVIDIA/cnmem.git"
 
-    version('git', git='https://github.com/NVIDIA/cnmem.git', branch="master")
+    version('git', branch='master')
 
     depends_on('cmake@2.8.8:', type='build')
diff --git a/var/spack/repos/builtin/packages/cnpy/package.py b/var/spack/repos/builtin/packages/cnpy/package.py
index 7c868b62b4..15bd3da174 100644
--- a/var/spack/repos/builtin/packages/cnpy/package.py
+++ b/var/spack/repos/builtin/packages/cnpy/package.py
@@ -1,34 +1,24 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
+import sys
+
 
 class Cnpy(CMakePackage):
     """cnpy: library to read/write .npy and .npz files in C/C++."""
 
     homepage = "https://github.com/rogersce/cnpy"
-    url      = "https://github.com/rogersce/cnpy"
+    git      = "https://github.com/rogersce/cnpy.git"
+
+    version('master', branch='master')
+
+    def cmake_args(self):
+        args = []
+        if sys.platform == 'darwin':
+            args.extend(['-DCMAKE_MACOSX_RPATH=ON'])
 
-    version('master', git='https://github.com/rogersce/cnpy.git', branch="master")
+        return args
diff --git a/var/spack/repos/builtin/packages/cns-nospec/package.py b/var/spack/repos/builtin/packages/cns-nospec/package.py
deleted file mode 100644
index f4b56d7596..0000000000
--- a/var/spack/repos/builtin/packages/cns-nospec/package.py
+++ /dev/null
@@ -1,109 +0,0 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-from spack import *
-import glob
-
-
-class CnsNospec(MakefilePackage):
-    """A simple, explicit, stencil-based test code for integrating
-    the compressible Navier-Stokes equations. The code uses
-    8th order finite differences in space and a 3rd order,
-    low-storage TVD RK algorithm in time."""
-
-    homepage = "https://ccse.lbl.gov/ExaCT/index.html"
-    url      = "https://ccse.lbl.gov/ExaCT/CNS_Nospec.tgz"
-    tags     = ['proxy-app']
-
-    version('master', '14ff5be62539d829b30b17281688ee3f')
-
-    variant('mpi', default=True, description='Build with MPI support')
-    variant('debug', default=False, description='Build with debugging')
-    variant('omp', default=False, description='Build with OpenMP support')
-    variant('prof', default=False, description='Build with profiling')
-
-    depends_on('mpi', when='+mpi')
-    depends_on('gmake', type='build')
-
-    build_directory = 'MiniApps/CNS_NoSpec'
-
-    def edit(self, spec, prefix):
-        def_file = FileFilter('Tools/F_mk/GMakedefs.mak')
-        def_file.filter('tdir = t/.*', 'tdir := t/$(suf)')
-        def_file.filter('hdir = t/.*', 'hdir := t/html')
-        def_file.filter('include $(BOXLIB_HOME)/Tools/F_mk/GMakeMPI.mak', '#')
-
-        if '+mpi' in spec:
-            def_file.filter('FC.*:=.*', 'FC = {0}'.format(spec['mpi'].mpifc))
-            def_file.filter('F90.*:=.*', 'F90 = {0}'.format(spec['mpi'].mpifc))
-            def_file.filter(
-                'mpi_include_dir =.*',
-                'mpi_include_dir = {0}'.format(spec['mpi'].prefix.include))
-            def_file.filter(
-                'mpi_lib_dir =.*',
-                'mpi_lib_dir = {0}'.format(spec['mpi'].prefix.lib))
-
-        with working_dir(self.build_directory):
-            makefile = FileFilter('GNUmakefile')
-            if '+mpi' in spec:
-                makefile.filter('MPI .*', 'MPI := t')
-            if '+debug' in spec:
-                makefile.filter('NDEBUG.*', '#')
-            if '+omp' in spec:
-                makefile.filter('OMP.*', 'OMP := t')
-            if '+prof' in spec:
-                makefile.filter('PROF.*', 'PROF := t')
-
-            if self.compiler.name == 'gcc':
-                makefile.filter('COMP .*', 'COMP = gfortran')
-            if self.compiler.name == 'intel':
-                makefile.filter('COMP .*', 'COMP = Intel')
-            if self.compiler.name == 'pgi':
-                makefile.filter('COMP .*', 'COMP = PGI')
-            if self.compiler.name == 'xl':
-                makefile.filter('COMP .*', 'COMP = IBM')
-            if self.compiler.name == 'cce':
-                makefile.filter('COMP .*', 'COMP = Cray')
-
-    @property
-    def build_targets(self):
-        spec = self.spec
-        if '+mpi' in spec:
-            return ['CC = {0}'.format(spec['mpi'].mpicc),
-                    'CXX = {0}'.format(spec['mpi'].mpicxx)]
-        else:
-            return []
-
-    def build(self, spec, prefix):
-        with working_dir(self.build_directory):
-            gmake()
-
-    def install(self, spec, prefix):
-        mkdirp(prefix.bin)
-        files = glob.glob(join_path(self.build_directory, '*.exe'))
-        for f in files:
-            install(f, prefix.bin)
-        install('README.txt', prefix)
-        install('license.txt', prefix)
-        install(join_path(self.build_directory, 'README'), prefix)
diff --git a/var/spack/repos/builtin/packages/cntk/package.py b/var/spack/repos/builtin/packages/cntk/package.py
index b55c547e10..efb8cb7ca3 100644
--- a/var/spack/repos/builtin/packages/cntk/package.py
+++ b/var/spack/repos/builtin/packages/cntk/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,8 +13,9 @@ class Cntk(Package):
 
     homepage = "https://www.microsoft.com/en-us/research/product/cognitive-toolkit"
     url      = "https://github.com/Microsoft/CNTK/archive/v2.0.tar.gz"
+    git      = "https://github.com/Microsoft/CNTK.git"
 
-    version('master', git='https://github.com/Microsoft/CNTK.git', branch='master')
+    version('master', branch='master')
     version('2.0', '8038780f1169ceea578e5ef4d69e4c6f')
 
     variant('opencv', default=False, description="Enable OpenCV support.")
diff --git a/var/spack/repos/builtin/packages/cntk1bitsgd/package.py b/var/spack/repos/builtin/packages/cntk1bitsgd/package.py
index 6d30792b09..c046bc34e4 100644
--- a/var/spack/repos/builtin/packages/cntk1bitsgd/package.py
+++ b/var/spack/repos/builtin/packages/cntk1bitsgd/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 from os import listdir
 
@@ -32,10 +13,10 @@ class Cntk1bitsgd(Package):
     the Computational Network Toolkit (CNTK)."""
 
     homepage = "https://github.com/CNTK-components/CNTK1bitSGD"
+    git      = "https://github.com/CNTK-components/CNTK1bitSGD.git"
 
-    version('master', git='https://github.com/CNTK-components/CNTK1bitSGD.git')
-    version('c8b77d', git='https://github.com/CNTK-components/CNTK1bitSGD.git',
-            commit='c8b77d6e325a4786547b27624890276c1483aed1')
+    version('master')
+    version('c8b77d', commit='c8b77d6e325a4786547b27624890276c1483aed1')
 
     def install(self, spec, prefix):
         mkdirp(prefix.include)
diff --git a/var/spack/repos/builtin/packages/codar-cheetah/package.py b/var/spack/repos/builtin/packages/codar-cheetah/package.py
index de39fb2a79..ba559342ba 100644
--- a/var/spack/repos/builtin/packages/codar-cheetah/package.py
+++ b/var/spack/repos/builtin/packages/codar-cheetah/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from distutils.dir_util import copy_tree
 
 
 class CodarCheetah(Package):
@@ -32,14 +12,14 @@ class CodarCheetah(Package):
     """
 
     homepage = "https://github.com/CODARcode/cheetah"
-    url = "https://github.com/CODARcode/cheetah/archive/v0.1.tar.gz"
+    url      = "https://github.com/CODARcode/cheetah/archive/v0.1.tar.gz"
+    git      = "https://github.com/CODARcode/cheetah.git"
 
+    version('develop', branch='master')
     version('0.1', '6918021f74fa7a2f1de26c0bb31a63ef')
-    version('develop', git='https://github.com/CODARcode/cheetah.git',
-            branch='master')
 
     depends_on('python@3:', type=('build', 'run'))
     depends_on('savanna')
 
     def install(self, spec, prefix):
-        copy_tree('.', prefix)
+        install_tree('.', prefix)
diff --git a/var/spack/repos/builtin/packages/codes/codes-1.0.0.patch b/var/spack/repos/builtin/packages/codes/codes-1.0.0.patch
new file mode 100644
index 0000000000..d0fbaf7ebb
--- /dev/null
+++ b/var/spack/repos/builtin/packages/codes/codes-1.0.0.patch
@@ -0,0 +1,16 @@
+diff --git a/configure.ac b/configure.ac
+index b3650e5..5ec28b4 100755
+--- a/configure.ac
++++ b/configure.ac
+@@ -222,9 +222,9 @@ AS_IF([test "x$enable_valgrind_clean" = "xyes"], [
+ 
+ 
+ dnl AC_CONFIG_FILES([src/iokernellang/codesparser.y])
+-if test "x$srcdir" != "x."; then
++AS_IF([test ! -d tests/conf], [
+     AC_CONFIG_LINKS([tests/conf:$srcdir/tests/conf])
+-fi
++])
+ 
+ AC_CONFIG_FILES([Makefile])
+ 
diff --git a/var/spack/repos/builtin/packages/codes/package.py b/var/spack/repos/builtin/packages/codes/package.py
new file mode 100644
index 0000000000..e3c5053e9a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/codes/package.py
@@ -0,0 +1,51 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Codes(AutotoolsPackage):
+    """ CO-Design of multi-layer Exascale Storage (CODES) simulation framework
+    """
+
+    homepage = "http://www.mcs.anl.gov/projects/codes"
+    git      = "https://xgitlab.cels.anl.gov/codes/codes.git"
+
+    version('develop', branch='master')
+    version('1.0.0', tag='1.0.0')
+
+    variant('dumpi', default=False, description="Enable DUMPI support")
+
+    # Build dependencies
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool', type='build')
+    depends_on('m4', type='build')
+    depends_on('pkgconfig', type='build')
+    depends_on('bison', type='build')
+    depends_on('flex', type='build')
+
+    depends_on('mpi')
+    depends_on('ross')
+    depends_on('sst-dumpi', when="+dumpi")
+
+    # add the local m4 directory to the search path
+    autoreconf_extra_args = ["-Im4"]
+    # Testing if srcdir is '.' in configure.ac does not work with spack
+    patch('codes-1.0.0.patch')
+
+    def configure_args(self):
+        spec = self.spec
+
+        config_args = [
+            "CC=%s" % spec['mpi'].mpicc,
+            "CXX=%s" % spec['mpi'].mpicxx,
+            "PKG_CONFIG_PATH=%s/pkgconfig" % spec['ross'].prefix.lib]
+
+        if "+dumpi" in spec:
+            config_args.extend([
+                '--with-dumpi=%s'.format(spec['sst-dumpi'].prefix)])
+
+        return config_args
diff --git a/var/spack/repos/builtin/packages/coevp/package.py b/var/spack/repos/builtin/packages/coevp/package.py
index 655f91062e..300e441fe0 100644
--- a/var/spack/repos/builtin/packages/coevp/package.py
+++ b/var/spack/repos/builtin/packages/coevp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -39,9 +20,9 @@ class Coevp(MakefilePackage):
     proxy application provides the adaptive sampling support."""
 
     homepage = 'https://github.com/exmatex/CoEVP'
+    git      = 'https://github.com/exmatex/CoEVP.git'
 
-    version('develop', git='https://github.com/exmatex/CoEVP.git',
-            branch='master')
+    version('develop', branch='master')
 
     variant('mpi', default=True, description='Build with MPI Support')
     variant('silo', default=False, description='Build with silo Support')
diff --git a/var/spack/repos/builtin/packages/cohmm/package.py b/var/spack/repos/builtin/packages/cohmm/package.py
index 70e87c70ff..a68e3a58e5 100644
--- a/var/spack/repos/builtin/packages/cohmm/package.py
+++ b/var/spack/repos/builtin/packages/cohmm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
 
@@ -35,13 +16,12 @@ class Cohmm(MakefilePackage):
     tags = ['proxy-app']
 
     homepage = "http://www.exmatex.org/cohmm.html"
-    url = "https://github.com/exmatex/CoHMM/archive/sad.tar.gz"
+    git      = "https://github.com/exmatex/CoHMM.git"
 
-    version('develop', git='https://github.com/exmatex/CoHMM.git',
-            branch='sad')
+    version('develop', branch='sad')
 
     variant('openmp', default=True, description='Build with OpenMP Support')
-    variant('gnuplot', default=True, description='Enable gnu plot Support')
+    variant('gnuplot', default=False, description='Enable gnu plot Support')
     depends_on('gnuplot', when='+gnuplot')
 
     def edit(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/coinhsl/package.py b/var/spack/repos/builtin/packages/coinhsl/package.py
index a97c0274d3..55c695dbc9 100644
--- a/var/spack/repos/builtin/packages/coinhsl/package.py
+++ b/var/spack/repos/builtin/packages/coinhsl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
@@ -44,4 +25,39 @@ class Coinhsl(AutotoolsPackage):
     homepage = "http://www.hsl.rl.ac.uk/ipopt/"
     url = "file://{0}/coinhsl-archive-2014.01.17.tar.gz".format(os.getcwd())
 
-    version('2014.01.17', '9eb3dd40ed034814ed8dfee75b281180c1d9d2ae')
+    # CoinHSL has a few versions that vary with respect to stability/features
+    # and licensing terms.
+
+    # Version 2015.06.23 is a full-featured "release candidate"
+    # version available via an "academic license" that can be used for
+    # personal teaching and research purposes only. For a full list of
+    # conditions, see http://www.hsl.rl.ac.uk/academic.html.
+    version('2015.06.23', sha256='3e955a2072f669b8f357ae746531b37aea921552e415dc219a5dd13577575fb3')
+
+    # Version 2014.01.17 is a full-featured "stable" version available
+    # via an "academic license" that can be used for personal teaching
+    # and research purposes only.
+    version('2014.01.17', sha256='ed49fea62692c5d2f928d4007988930da9ff9a2e944e4c559d028671d122437b')
+
+    # Version 2014.01.10 only has MA27, MA28, and MC19, and is
+    # available as a "personal license" that is free to all, and
+    # permits commercial use, but *not redistribution* (emphasis from
+    # original source).
+    version('2014.01.10', sha256='7c2be60a3913b406904c66ee83acdbd0709f229b652c4e39ee5d0876f6b2e907',
+            preferred=True)
+
+    # CoinHSL fails to build in parallel
+    parallel = False
+
+    variant('blas', default=False, description='Link to external BLAS library')
+
+    depends_on('blas', when='+blas')
+
+    def configure_args(self):
+        spec = self.spec
+        args = []
+
+        if spec.satisfies('+blas'):
+            args.append('--with-blas={0}'.format(spec['blas'].libs.ld_flags))
+
+        return args
diff --git a/var/spack/repos/builtin/packages/colm/package.py b/var/spack/repos/builtin/packages/colm/package.py
new file mode 100644
index 0000000000..bf27dabd39
--- /dev/null
+++ b/var/spack/repos/builtin/packages/colm/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Colm(AutotoolsPackage):
+    """Colm Programming Language
+    Colm is a programming language designed for the analysis and
+    transformation of computer languages. Colm is influenced primarily
+    by TXL. It is in the family of program transformation languages.
+    """
+
+    homepage = "http://www.colm.net/open-source/colm"
+    url      = "http://www.colm.net/files/colm/colm-0.12.0.tar.gz"
+
+    version('0.12.0', '079a1ed44f71d48a349d954096c8e411')
diff --git a/var/spack/repos/builtin/packages/colordiff/package.py b/var/spack/repos/builtin/packages/colordiff/package.py
new file mode 100644
index 0000000000..cd62f2347f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/colordiff/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Colordiff(Package):
+    """Colorful diff utility."""
+
+    homepage = "https://www.colordiff.org"
+    url      = "https://www.colordiff.org/colordiff-1.0.18.tar.gz"
+
+    version('1.0.18', '07658f09a44f30a3b5c1cea9c132baed')
+
+    depends_on('perl')
+
+    def install(self, spec, prefix):
+        make("INSTALL_DIR=" + prefix.bin, "ETC_DIR=" + prefix.etc,
+             "MAN_DIR=" + prefix.man, 'install', parallel=False)
diff --git a/var/spack/repos/builtin/packages/comd/package.py b/var/spack/repos/builtin/packages/comd/package.py
index ad7689beee..3c6d762473 100644
--- a/var/spack/repos/builtin/packages/comd/package.py
+++ b/var/spack/repos/builtin/packages/comd/package.py
@@ -1,30 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack import *
-import shutil
 
 
 class Comd(MakefilePackage):
@@ -37,18 +16,19 @@ class Comd(MakefilePackage):
     versions of CoMD will be released to incorporate the lessons learned from
     the co-design process."""
 
-    tags = ['proxy-app', 'ecp-proxy-app']
+    tags = ['proxy-app']
 
     homepage = "http://www.exmatex.org/comd.html"
     url      = "https://github.com/ECP-copa/CoMD/archive/v1.1.tar.gz"
+    git      = "https://github.com/ECP-copa/CoMD.git"
 
+    version('develop', branch='master')
     version('1.1', '5051310a8d2c93cccba63de40bcfaa78')
-    version('develop', git='https://github.com/ECP-copa/CoMD', branch='master')
 
     variant('mpi', default=True, description='Build with MPI support')
     variant('openmp', default=False, description='Build with OpenMP support')
     variant('precision', default=True, description='Toggle Precesion Options')
-    variant('graphs', default=True, description='Enable graph visuals')
+    variant('graphs', default=False, description='Enable graph visuals')
 
     depends_on('mpi', when='+mpi')
     depends_on('graphviz', when='+graphs')
@@ -57,7 +37,7 @@ class Comd(MakefilePackage):
 
     def edit(self, spec, prefix):
         with working_dir('src-mpi') or working_dir('src-openmp'):
-            shutil.copy('Makefile.vanilla', 'Makefile')
+            copy('Makefile.vanilla', 'Makefile')
 
     @property
     def build_targets(self):
diff --git a/var/spack/repos/builtin/packages/commons-lang/package.py b/var/spack/repos/builtin/packages/commons-lang/package.py
new file mode 100644
index 0000000000..dcb40f8869
--- /dev/null
+++ b/var/spack/repos/builtin/packages/commons-lang/package.py
@@ -0,0 +1,31 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class CommonsLang(Package):
+    """The standard Java libraries fail to provide enough methods for
+    manipulation of its core classes. Apache Commons Lang provides these
+    extra methods.
+
+    Lang provides a host of helper utilities for the java.lang API, notably
+    String manipulation methods, basic numerical methods, object reflection,
+    concurrency, creation and serialization and System properties. Additionally
+    it contains basic enhancements to java.util.Date and a series of utilities
+    dedicated to help with building methods, such as hashCode, toString and
+    equals."""
+
+    homepage = "http://commons.apache.org/proper/commons-lang/"
+    url      = "https://archive.apache.org/dist/commons/lang/binaries/commons-lang-2.6-bin.tar.gz"
+
+    version('2.6', '444075803459bffebfb5e28877861d23')
+    version('2.4', '5ff5d890e46021a2dbd77caba80f90f2')
+
+    extends('jdk')
+    depends_on('java@2:', type='run')
+
+    def install(self, spec, prefix):
+        install('commons-lang-{0}.jar'.format(self.version), prefix)
diff --git a/var/spack/repos/builtin/packages/commons-lang3/package.py b/var/spack/repos/builtin/packages/commons-lang3/package.py
new file mode 100644
index 0000000000..543b20d9f7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/commons-lang3/package.py
@@ -0,0 +1,30 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class CommonsLang3(Package):
+    """The standard Java libraries fail to provide enough methods for
+    manipulation of its core classes. Apache Commons Lang provides these
+    extra methods.
+
+    Lang provides a host of helper utilities for the java.lang API, notably
+    String manipulation methods, basic numerical methods, object reflection,
+    concurrency, creation and serialization and System properties. Additionally
+    it contains basic enhancements to java.util.Date and a series of utilities
+    dedicated to help with building methods, such as hashCode, toString and
+    equals."""
+
+    homepage = "http://commons.apache.org/proper/commons-lang/"
+    url      = "https://archive.apache.org/dist/commons/lang/binaries/commons-lang3-3.7-bin.tar.gz"
+
+    version('3.7', 'c7577443639dc6efadc80f1cbc7fced5')
+
+    extends('jdk')
+    depends_on('java@7:', type='run')
+
+    def install(self, spec, prefix):
+        install('commons-lang3-{0}.jar'.format(self.version), prefix)
diff --git a/var/spack/repos/builtin/packages/commons-logging/package.py b/var/spack/repos/builtin/packages/commons-logging/package.py
new file mode 100644
index 0000000000..41483f8c61
--- /dev/null
+++ b/var/spack/repos/builtin/packages/commons-logging/package.py
@@ -0,0 +1,32 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class CommonsLogging(Package):
+    """When writing a library it is very useful to log information. However
+    there are many logging implementations out there, and a library cannot
+    impose the use of a particular one on the overall application that the
+    library is a part of.
+
+    The Logging package is an ultra-thin bridge between different logging
+    implementations. A library that uses the commons-logging API can be used
+    with any logging implementation at runtime. Commons-logging comes with
+    support for a number of popular logging implementations, and writing
+    adapters for others is a reasonably simple task."""
+
+    homepage = "http://commons.apache.org/proper/commons-logging/"
+    url      = "http://archive.apache.org/dist/commons/logging/binaries/commons-logging-1.2-bin.tar.gz"
+
+    version('1.2',   'ac043ce7ab3374eb4ed58354a6b2c3de')
+    version('1.1.3', 'b132f9a1e875677ae6b449406cff2a78')
+    version('1.1.1', 'e5de09672af9b386c30a311654d8541a')
+
+    extends('jdk')
+    depends_on('java', type='run')
+
+    def install(self, spec, prefix):
+        install('commons-logging-{0}.jar'.format(self.version), prefix)
diff --git a/var/spack/repos/builtin/packages/compiz/package.py b/var/spack/repos/builtin/packages/compiz/package.py
index 5387483879..9ce3526b89 100644
--- a/var/spack/repos/builtin/packages/compiz/package.py
+++ b/var/spack/repos/builtin/packages/compiz/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/compositeproto/package.py b/var/spack/repos/builtin/packages/compositeproto/package.py
index b4a041e7a2..b160bbd5a5 100644
--- a/var/spack/repos/builtin/packages/compositeproto/package.py
+++ b/var/spack/repos/builtin/packages/compositeproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Compositeproto(AutotoolsPackage):
 
     version('0.4.2', '2dea7c339432b3363faf2d29c208e7b5')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/conduit/package.py b/var/spack/repos/builtin/packages/conduit/package.py
index 6793a391c3..d2820b92ec 100644
--- a/var/spack/repos/builtin/packages/conduit/package.py
+++ b/var/spack/repos/builtin/packages/conduit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 import socket
@@ -46,8 +27,11 @@ class Conduit(Package):
     coupling between packages in-core, serialization, and I/O tasks."""
 
     homepage = "http://software.llnl.gov/conduit"
-    url = "https://github.com/LLNL/conduit/releases/download/v0.3.0/conduit-v0.3.0-src-with-blt.tar.gz"
+    url      = "https://github.com/LLNL/conduit/releases/download/v0.3.0/conduit-v0.3.0-src-with-blt.tar.gz"
+    git      = "https://github.com/LLNL/conduit.git"
 
+    version('master', branch='master', submodules=True)
+    version('0.3.1', 'b98d1476199a46bde197220cd9cde042')
     version('0.3.0', '6396f1d1ca16594d7c66d4535d4f898e')
     # note: checksums on github automatic release source tars changed ~9/17
     version('0.2.1', 'ed7358af3463ba03f07eddd6a6e626ff')
@@ -55,11 +39,6 @@ class Conduit(Package):
 
     maintainers = ['cyrush']
 
-    version('master',
-            git='https://github.com/LLNL/conduit.git',
-            branch="master",
-            submodules=True)
-
     ###########################################################################
     # package variants
     ###########################################################################
@@ -79,6 +58,9 @@ class Conduit(Package):
 
     # variants for dev-tools (docs, etc)
     variant("doc", default=False, description="Build Conduit's documentation")
+    # doxygen support is wip, since doxygen has several dependencies
+    # we want folks to explicitly opt in to building doxygen
+    variant("doxygen", default=False, description="Build Conduit's Doxygen documentation")
 
     ###########################################################################
     # package dependencies
@@ -95,11 +77,9 @@ class Conduit(Package):
     #######################
     # we need a shared version of python b/c linking with static python lib
     # causes duplicate state issues when running compiled python modules.
-    depends_on("python+shared")
+    depends_on("python+shared", when="+python")
     extends("python", when="+python")
-    # TODO: blas and lapack are disabled due to build
-    # issues Cyrus experienced on OSX 10.11.6
-    depends_on("py-numpy~blas~lapack", when="+python", type=('build', 'run'))
+    depends_on("py-numpy", when="+python", type=('build', 'run'))
 
     #######################
     # I/O Packages
@@ -108,9 +88,10 @@ class Conduit(Package):
     # experienced on BGQ. When on, the static build tries
     # to link against shared libs.
     #
-    # we are not using hdf5's mpi or fortran features.
-    depends_on("hdf5~cxx~mpi~fortran", when="+hdf5+shared")
-    depends_on("hdf5~shared~cxx~mpi~fortran", when="+hdf5~shared")
+    # Use HDF5 1.8, for wider output compatibly
+    # variants reflect we are not using hdf5's mpi or fortran features.
+    depends_on("hdf5@1.8.19:1.8.999~cxx~mpi~fortran", when="+hdf5+shared")
+    depends_on("hdf5@1.8.19:1.8.999~shared~cxx~mpi~fortran", when="+hdf5~shared")
 
     # we are not using silo's fortran features
     depends_on("silo~fortran", when="+silo+shared")
@@ -125,7 +106,7 @@ class Conduit(Package):
     # Documentation related
     #######################
     depends_on("py-sphinx", when="+python+doc", type='build')
-    depends_on("doxygen", when="+doc")
+    depends_on("doxygen", when="+doc+doxygen")
 
     def url_for_version(self, version):
         """
@@ -136,11 +117,12 @@ class Conduit(Package):
             return "https://github.com/LLNL/conduit/archive/v0.2.0.tar.gz"
         elif v == "0.2.1":
             return "https://github.com/LLNL/conduit/archive/v0.2.1.tar.gz"
-        elif v == "0.3.0":
-            # conduit uses BLT (https://github.com/llnl/blt) as a submodule,
-            # since github does not automatically package source from
-            # submodules, conduit provides a custom src tarball
-            return "https://github.com/LLNL/conduit/releases/download/v0.3.0/conduit-v0.3.0-src-with-blt.tar.gz"
+        else:
+            # starting with v 0.3.0, conduit uses BLT
+            # (https://github.com/llnl/blt) as a submodule, since github does
+            # not automatically package source from submodules, conduit
+            # provides a custom src tarball
+            return "https://github.com/LLNL/conduit/releases/download/v{0}/conduit-v{1}-src-with-blt.tar.gz".format(v, v)
         return url
 
     def install(self, spec, prefix):
@@ -148,7 +130,13 @@ class Conduit(Package):
         Build and install Conduit.
         """
         with working_dir('spack-build', create=True):
-            host_cfg_fname = self.create_host_config(spec, prefix)
+            py_site_pkgs_dir = None
+            if "+python" in spec:
+                py_site_pkgs_dir = site_packages_dir
+
+            host_cfg_fname = self.create_host_config(spec,
+                                                     prefix,
+                                                     py_site_pkgs_dir)
             cmake_args = []
             # if we have a static build, we need to avoid any of
             # spack's default cmake settings related to rpaths
@@ -163,14 +151,26 @@ class Conduit(Package):
             cmake(*cmake_args)
             make()
             make("install")
+            # install copy of host config for provenance
+            install(host_cfg_fname, prefix)
 
-    def create_host_config(self, spec, prefix):
+    def create_host_config(self, spec, prefix, py_site_pkgs_dir=None):
         """
         This method creates a 'host-config' file that specifies
         all of the options used to configure and build conduit.
 
-        For more details see about 'host-config' files see:
+        For more details about 'host-config' files see:
             http://software.llnl.gov/conduit/building.html
+
+        Note:
+          The `py_site_pkgs_dir` arg exists to allow a package that
+          subclasses this package provide a specific site packages
+          dir when calling this function. `py_site_pkgs_dir` should
+          be an absolute path or `None`.
+
+          This is necessary because the spack `site_packages_dir`
+          var will not exist in the base class. For more details
+          on this issue see: https://github.com/spack/spack/issues/6261
         """
 
         #######################
@@ -209,9 +209,9 @@ class Conduit(Package):
                 raise RuntimeError(msg)
             cmake_exe = cmake_exe.path
 
-        host_cfg_fname = "%s-%s-%s.cmake" % (socket.gethostname(),
-                                             sys_type,
-                                             spec.compiler)
+        host_cfg_fname = "%s-%s-%s-conduit.cmake" % (socket.gethostname(),
+                                                     sys_type,
+                                                     spec.compiler)
 
         cfg = open(host_cfg_fname, "w")
         cfg.write("##################################\n")
@@ -256,10 +256,10 @@ class Conduit(Package):
             cfg.write("# python from spack \n")
             cfg.write(cmake_cache_entry("PYTHON_EXECUTABLE",
                       spec['python'].command.path))
-            # install module to standard style site packages dir
-            # so we can support spack activate
-            cfg.write(cmake_cache_entry("PYTHON_MODULE_INSTALL_PREFIX",
-                                        site_packages_dir))
+            # only set dest python site packages dir if passed
+            if py_site_pkgs_dir:
+                cfg.write(cmake_cache_entry("PYTHON_MODULE_INSTALL_PREFIX",
+                                            py_site_pkgs_dir))
         else:
             cfg.write(cmake_cache_entry("ENABLE_PYTHON", "OFF"))
 
@@ -270,10 +270,10 @@ class Conduit(Package):
             sphinx_build_exe = join_path(spec['py-sphinx'].prefix.bin,
                                          "sphinx-build")
             cfg.write(cmake_cache_entry("SPHINX_EXECUTABLE", sphinx_build_exe))
-
-            cfg.write("# doxygen from uberenv\n")
-            doxygen_exe = spec['doxygen'].command.path
-            cfg.write(cmake_cache_entry("DOXYGEN_EXECUTABLE", doxygen_exe))
+            if "+doxygen" in spec:
+                cfg.write("# doxygen from uberenv\n")
+                doxygen_exe = spec['doxygen'].command.path
+                cfg.write(cmake_cache_entry("DOXYGEN_EXECUTABLE", doxygen_exe))
         else:
             cfg.write(cmake_cache_entry("ENABLE_DOCS", "OFF"))
 
@@ -290,6 +290,16 @@ class Conduit(Package):
                                         spec['mpi'].mpicxx))
             cfg.write(cmake_cache_entry("MPI_Fortran_COMPILER",
                                         spec['mpi'].mpifc))
+            mpiexe_bin = join_path(spec['mpi'].prefix.bin, 'mpiexec')
+            if os.path.isfile(mpiexe_bin):
+                # starting with cmake 3.10, FindMPI expects MPIEXEC_EXECUTABLE
+                # vs the older versions which expect MPIEXEC
+                if self.spec["cmake"].satisfies('@3.10:'):
+                    cfg.write(cmake_cache_entry("MPIEXEC_EXECUTABLE",
+                                                mpiexe_bin))
+                else:
+                    cfg.write(cmake_cache_entry("MPIEXEC",
+                                                mpiexe_bin))
         else:
             cfg.write(cmake_cache_entry("ENABLE_MPI", "OFF"))
 
diff --git a/var/spack/repos/builtin/packages/constype/package.py b/var/spack/repos/builtin/packages/constype/package.py
index 731217b527..5996386854 100644
--- a/var/spack/repos/builtin/packages/constype/package.py
+++ b/var/spack/repos/builtin/packages/constype/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Constype(AutotoolsPackage):
 
     version('1.0.4', '2333b9ac9fd32e58b05afa651c4590a3')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/converge/package.py b/var/spack/repos/builtin/packages/converge/package.py
index 7a17436ed3..3d0cf54808 100644
--- a/var/spack/repos/builtin/packages/converge/package.py
+++ b/var/spack/repos/builtin/packages/converge/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import glob
 import os
 
diff --git a/var/spack/repos/builtin/packages/coreutils/package.py b/var/spack/repos/builtin/packages/coreutils/package.py
index fa4298a42a..312f6f7375 100644
--- a/var/spack/repos/builtin/packages/coreutils/package.py
+++ b/var/spack/repos/builtin/packages/coreutils/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,8 +13,9 @@ class Coreutils(AutotoolsPackage):
        operating system.
     """
     homepage = "http://www.gnu.org/software/coreutils/"
-    url      = "http://ftp.gnu.org/gnu/coreutils/coreutils-8.26.tar.xz"
+    url      = "https://ftpmirror.gnu.org/coreutils/coreutils-8.26.tar.xz"
 
+    version('8.29', '960cfe75a42c9907c71439f8eb436303')
     version('8.26', 'd5aa2072f662d4118b9f4c63b94601a6')
     version('8.23', 'abed135279f87ad6762ce57ff6d89c41')
 
diff --git a/var/spack/repos/builtin/packages/corset/package.py b/var/spack/repos/builtin/packages/corset/package.py
index 7b5ef695cb..aa9c036090 100644
--- a/var/spack/repos/builtin/packages/corset/package.py
+++ b/var/spack/repos/builtin/packages/corset/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/cosmomc/package.py b/var/spack/repos/builtin/packages/cosmomc/package.py
index c3788c53ce..e1bb2ee9bc 100644
--- a/var/spack/repos/builtin/packages/cosmomc/package.py
+++ b/var/spack/repos/builtin/packages/cosmomc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 import fnmatch
diff --git a/var/spack/repos/builtin/packages/cosp2/package.py b/var/spack/repos/builtin/packages/cosp2/package.py
index 2bd69e73d3..a702a48c5f 100644
--- a/var/spack/repos/builtin/packages/cosp2/package.py
+++ b/var/spack/repos/builtin/packages/cosp2/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-import shutil
 
 
 class Cosp2(MakefilePackage):
@@ -37,10 +17,9 @@ class Cosp2(MakefilePackage):
     tags = ['proxy-app']
 
     homepage = "http://www.exmatex.org/cosp2.html"
-    url = "https://github.com/exmatex/CoSP2/archive/master.tar.gz"
+    git      = "https://github.com/exmatex/CoSP2.git"
 
-    version('master', git='https://github.com/exmatex/CoSP2.git',
-            description='master')
+    version('master', branch='master')
 
     variant('double', default=True,
             description='Build with double precision.')
@@ -63,7 +42,7 @@ class Cosp2(MakefilePackage):
             if '+double' in spec:
                 filter_file('DOUBLE_PRECISION = O.*', 'DOUBLE_PRECISION = OFF',
                             'Makefile.vanilla')
-            shutil.copy('Makefile.vanilla', 'Makefile')
+            copy('Makefile.vanilla', 'Makefile')
 
     def install(self, spec, prefix):
         install_tree('bin/', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/cp2k/package.py b/var/spack/repos/builtin/packages/cp2k/package.py
index 53eb29f336..e810c84eb3 100644
--- a/var/spack/repos/builtin/packages/cp2k/package.py
+++ b/var/spack/repos/builtin/packages/cp2k/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
-import shutil
 import copy
 
 from spack import *
@@ -36,33 +16,39 @@ class Cp2k(Package):
     """
     homepage = 'https://www.cp2k.org'
     url = 'https://sourceforge.net/projects/cp2k/files/cp2k-3.0.tar.bz2'
+    list_url = 'https://sourceforge.net/projects/cp2k/files/'
 
+    version('5.1', 'f25cf301aec471d7059179de4dac3ee7')
     version('4.1', 'b0534b530592de15ac89828b1541185e')
     version('3.0', 'c05bc47335f68597a310b1ed75601d35')
 
     variant('mpi', default=True, description='Enable MPI support')
+    variant('smm', default='libxsmm', values=('libxsmm', 'libsmm', 'none'),
+            description='Library for small matrix multiplications')
     variant('plumed', default=False, description='Enable PLUMED support')
 
     depends_on('python', type='build')
 
     depends_on('lapack')
     depends_on('blas')
-    depends_on('fftw')
-    depends_on('libint@:1.2', when='@3.0,4.1')
+    depends_on('fftw@3:')
+    depends_on('libint@1.1.4:1.2', when='@3.0:5.999')
+    depends_on('libxsmm', when='smm=libxsmm')
+    depends_on('libxc@2.2.2:')
 
     depends_on('mpi@2:', when='+mpi')
     depends_on('scalapack', when='+mpi')
+    depends_on('elpa@2011.12:2016.13', when='+mpi')
+    depends_on('pexsi+fortran@0.9.0:0.9.999', when='+mpi@:4.999')
+    depends_on('pexsi+fortran@0.10.0:', when='+mpi@5.0:')
     depends_on('plumed+shared+mpi', when='+plumed+mpi')
     depends_on('plumed+shared~mpi', when='+plumed~mpi')
-    depends_on('pexsi+fortran', when='+mpi')
 
     # Apparently cp2k@4.1 needs an "experimental" version of libwannier.a
     # which is only available contacting the developer directly. See INSTALL
     # in the stage of cp2k@4.1
     depends_on('wannier90', when='@3.0+mpi')
-    depends_on('elpa', when='+mpi')
 
-    # TODO : add dependency on libsmm, libxsmm
     # TODO : add dependency on CUDA
 
     parallel = False
@@ -78,24 +64,31 @@ class Cp2k(Package):
         with open(makefile, 'w') as mkf:
             # Optimization flags
             optflags = {
-                'gcc': ['-O2',
-                        '-ffast-math',
-                        '-ftree-vectorize',
-                        '-funroll-loops',
-                        '-mtune=native'],
-                'intel': ['-O2',
-                          '-pc64',
-                          '-unroll']
+                'gcc': [
+                    '-O2',
+                    '-mtune=native',
+                    '-funroll-loops',
+                    '-ffast-math',
+                    '-ftree-vectorize',
+                ], 'intel': [
+                    '-O2',
+                    '-pc64',
+                    '-unroll',
+                ]
             }
 
             dflags = ['-DNDEBUG']
 
+            libxc = spec['libxc:fortran,static']
+
             cppflags = [
                 '-D__FFTW3',
                 '-D__LIBINT',
                 '-D__LIBINT_MAX_AM=6',
                 '-D__LIBDERIV_MAX_AM1=5',
-                spec['fftw'].headers.cpp_flags
+                '-D__LIBXC',
+                spec['fftw'].headers.cpp_flags,
+                libxc.headers.cpp_flags
             ]
 
             if '^mpi@3:' in spec:
@@ -109,18 +102,15 @@ class Cp2k(Package):
             cflags = copy.deepcopy(optflags[self.spec.compiler.name])
             cxxflags = copy.deepcopy(optflags[self.spec.compiler.name])
             fcflags = copy.deepcopy(optflags[self.spec.compiler.name])
-            fcflags.extend([
-                '-ffree-form',
-                '-ffree-line-length-none',
-                spec['fftw'].headers.cpp_flags
-            ])
 
             if '%intel' in spec:
                 cflags.append('-fp-model precise')
                 cxxflags.append('-fp-model precise')
                 fcflags.extend(['-fp-model source', '-heap-arrays 64'])
+            elif '%gcc' in spec:
+                fcflags.extend(['-ffree-form', '-ffree-line-length-none'])
 
-            fftw = find_libraries('libfftw3', root=spec['fftw'].prefix.lib)
+            fftw = spec['fftw'].libs
             ldflags = [fftw.search_flags]
 
             if 'superlu-dist@4.3' in spec:
@@ -160,7 +150,7 @@ class Cp2k(Package):
                 mkf.write('CPP = # {0.compiler.cc} -P\n\n'.format(self))
                 mkf.write('AR = xiar -r\n\n')
             else:
-                mkf.write('CPP = {0.compiler.cc} -E\n\n'.format(self))
+                mkf.write('CPP = # {0.compiler.cc} -E\n\n'.format(self))
                 mkf.write('AR = ar -r\n\n')
             fc = self.compiler.fc if '~mpi' in spec else self.spec['mpi'].mpifc
             mkf.write('FC = {0}\n'.format(fc))
@@ -183,18 +173,34 @@ class Cp2k(Package):
                 cppflags.extend([
                     '-D__parallel',
                     '-D__LIBPEXSI',
-                    '-D__ELPA3',
                     '-D__SCALAPACK'
                 ])
+
+                elpa = spec['elpa']
+                if spec.satisfies('@:4.999'):
+                    if elpa.satisfies('@:2014.5.999'):
+                        cppflags.append('-D__ELPA')
+                    elif elpa.satisfies('@2014.6:2015.10.999'):
+                        cppflags.append('-D__ELPA2')
+                    else:
+                        cppflags.append('-D__ELPA3')
+                else:
+                    cppflags.append('-D__ELPA={0}{1:02d}'.format(
+                        elpa.version[0], int(elpa.version[1])))
+                    fcflags.append('-I' + join_path(
+                        elpa.prefix, 'include',
+                        'elpa-{0}'.format(str(elpa.version)), 'elpa'
+                    ))
+
                 if 'wannier90' in spec:
                     cppflags.append('-D__WANNIER90')
 
                 fcflags.extend([
                     # spec['elpa:fortran'].headers.cpp_flags
                     '-I' + join_path(
-                        spec['elpa'].prefix,
+                        elpa.prefix,
                         'include',
-                        'elpa-{0}'.format(str(spec['elpa'].version)),
+                        'elpa-{0}'.format(str(elpa.version)),
                         'modules'
                     ),
                     # spec[pexsi:fortran].headers.cpp_flags
@@ -203,7 +209,7 @@ class Cp2k(Package):
                 scalapack = spec['scalapack'].libs
                 ldflags.append(scalapack.search_flags)
                 libs.extend([
-                    join_path(spec['elpa'].prefix.lib,
+                    join_path(elpa.prefix.lib,
                               'libelpa.{0}'.format(dso_suffix)),
                     join_path(spec['pexsi'].prefix.lib, 'libpexsi.a'),
                     join_path(spec['superlu-dist'].prefix.lib,
@@ -230,9 +236,36 @@ class Cp2k(Package):
             # LAPACK / BLAS
             lapack = spec['lapack'].libs
             blas = spec['blas'].libs
-
             ldflags.append((lapack + blas).search_flags)
-            libs.extend([str(x) for x in (fftw, lapack, blas)])
+
+            ldflags.append(libxc.libs.search_flags)
+
+            libs.extend([str(x) for x in (fftw, lapack, blas, libxc.libs)])
+
+            if 'smm=libsmm' in spec:
+                lib_dir = join_path('lib', cp2k_architecture, cp2k_version)
+                mkdirp(lib_dir)
+                try:
+                    copy(env['LIBSMM_PATH'], join_path(lib_dir, 'libsmm.a'))
+                except KeyError:
+                    raise KeyError('Point environment variable LIBSMM_PATH to '
+                                   'the absolute path of the libsmm.a file')
+                except IOError:
+                    raise IOError('The file LIBSMM_PATH pointed to does not '
+                                  'exist. Note that it must be absolute path.')
+                cppflags.extend([
+                    '-D__HAS_smm_dnn',
+                    '-D__HAS_smm_vec',
+                ])
+                libs.append('-lsmm')
+            elif 'smm=libxsmm' in spec:
+                cppflags.extend([
+                    '-D__LIBXSMM',
+                    spec['libxsmm'].headers.cpp_flags,
+                ])
+                libxsmm = spec['libxsmm'].libs
+                ldflags.append(libxsmm.search_flags)
+                libs.append(str(libxsmm))
 
             dflags.extend(cppflags)
             cflags.extend(cppflags)
@@ -261,4 +294,4 @@ class Cp2k(Package):
                  'VERSION={0}'.format(cp2k_version))
             env['PWD'] = pwd_backup
         exe_dir = join_path('exe', cp2k_architecture)
-        shutil.copytree(exe_dir, self.prefix.bin)
+        install_tree(exe_dir, self.prefix.bin)
diff --git a/var/spack/repos/builtin/packages/cppad/package.py b/var/spack/repos/builtin/packages/cppad/package.py
index 3b503fe1c8..aec3cc629b 100644
--- a/var/spack/repos/builtin/packages/cppad/package.py
+++ b/var/spack/repos/builtin/packages/cppad/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,10 @@ class Cppad(CMakePackage):
 
     homepage = "https://www.coin-or.org/CppAD/"
     url      = "http://www.coin-or.org/download/source/CppAD/cppad-20170114.gpl.tgz"
+    git      = "https://github.com/coin-or/CppAD.git"
 
+    version('develop', branch='master')
     version('20170114', '565a534dc813fa1289764222cd8c11ea')
-    version('develop', git='https://github.com/coin-or/CppAD.git')
 
     def cmake_args(self):
         # This package does not obey CMAKE_INSTALL_PREFIX
diff --git a/var/spack/repos/builtin/packages/cppcheck/package.py b/var/spack/repos/builtin/packages/cppcheck/package.py
index a9933920a9..ae13240537 100644
--- a/var/spack/repos/builtin/packages/cppcheck/package.py
+++ b/var/spack/repos/builtin/packages/cppcheck/package.py
@@ -1,45 +1,32 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-import os
-import shutil
 
 
-class Cppcheck(Package):
+class Cppcheck(MakefilePackage):
     """A tool for static C/C++ code analysis."""
     homepage = "http://cppcheck.sourceforge.net/"
     url      = "https://downloads.sourceforge.net/project/cppcheck/cppcheck/1.78/cppcheck-1.78.tar.bz2"
 
+    version('1.81', '0c60a1d00652044ef511bdd017689938')
     version('1.78', 'f02d0ee0a4e71023703c6c5efff6cf9d')
     version('1.72', '2bd36f91ae0191ef5273bb7f6dc0d72e')
     version('1.68', 'c015195f5d61a542f350269030150708')
 
+    variant('htmlreport', default=False, description="Install cppcheck-htmlreport")
+
+    depends_on('py-pygments', when='+htmlreport', type='run')
+
+    def build(self, spec, prefix):
+        make('CFGDIR={0}'.format(prefix.cfg))
+
     def install(self, spec, prefix):
-        # cppcheck does not have a configure script
-        make("CFGDIR=%s" % os.path.join(prefix, 'cfg'))
-        # manually install the final cppcheck binary
+        # Manually install the final cppcheck binary
         mkdirp(prefix.bin)
         install('cppcheck', prefix.bin)
-        shutil.copytree('cfg', os.path.join(prefix, 'cfg'))
+        install_tree('cfg', prefix.cfg)
+        if spec.satisfies('+htmlreport'):
+            install('htmlreport/cppcheck-htmlreport', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/cppgsl/package.py b/var/spack/repos/builtin/packages/cppgsl/package.py
new file mode 100644
index 0000000000..73fdb70590
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cppgsl/package.py
@@ -0,0 +1,32 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Cppgsl(CMakePackage):
+    """C++ Guideline Support Library"""
+
+    homepage = "https://github.com/Microsoft/GSL"
+    url      = "https://github.com/Microsoft/GSL/archive/v2.0.0.tar.gz"
+    git      = "https://github.com/Microsoft/GSL.git"
+
+    version('develop', branch='master')
+    version('2.0.0', sha256='6cce6fb16b651e62711a4f58e484931013c33979b795d1b1f7646f640cfa9c8e')
+    version('1.0.0', sha256='9694b04cd78e5b1a769868f19fdd9eea2002de3d4c3a81a1b769209364543c36')
+
+    variant('cxxstd',
+            default='14',
+            values=('14', '17'),
+            multi=False,
+            description='Use the specified C++ standard when building.')
+
+    depends_on('cmake@3.1.3:', type='build')
+
+    def cmake_args(self):
+        args = [
+            '-DGSL_CXX_STANDARD={0}'.format(self.spec.variants['cxxstd'].value)
+        ]
+        return args
diff --git a/var/spack/repos/builtin/packages/cpprestsdk/package.py b/var/spack/repos/builtin/packages/cpprestsdk/package.py
index a92b49c7a7..7b98c59b43 100644
--- a/var/spack/repos/builtin/packages/cpprestsdk/package.py
+++ b/var/spack/repos/builtin/packages/cpprestsdk/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/cppunit/package.py b/var/spack/repos/builtin/packages/cppunit/package.py
index ef6fa6ee24..c109076986 100644
--- a/var/spack/repos/builtin/packages/cppunit/package.py
+++ b/var/spack/repos/builtin/packages/cppunit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/cppzmq/package.py b/var/spack/repos/builtin/packages/cppzmq/package.py
index 689e3924de..aa038509be 100644
--- a/var/spack/repos/builtin/packages/cppzmq/package.py
+++ b/var/spack/repos/builtin/packages/cppzmq/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,11 +11,12 @@ class Cppzmq(CMakePackage):
 
     homepage = "http://www.zeromq.org"
     url      = "https://github.com/zeromq/cppzmq/archive/v4.2.2.tar.gz"
+    git      = "https://github.com/zeromq/cppzmq.git"
 
-    version('develop', branch='master',
-            git='https://github.com/zeromq/cppzmq.git')
-
+    version('develop', branch='master')
+    version('4.3.0', sha256='27d1f56406ba94ee779e639203218820975cf68174f92fbeae0f645df0fcada4')
     version('4.2.2', 'bd809b47296e77fe9f192bd9dafd5cc3')
 
     depends_on('cmake@3.0.0:', type='build')
-    depends_on('zeromq@4.2.2')
+    depends_on('zeromq@4.2.5', when='@4.3.0')
+    depends_on('zeromq@4.2.2', when='@4.2.2')
diff --git a/var/spack/repos/builtin/packages/cpu-features/package.py b/var/spack/repos/builtin/packages/cpu-features/package.py
new file mode 100644
index 0000000000..f54b964a20
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cpu-features/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class CpuFeatures(CMakePackage):
+    """A cross platform C99 library to get cpu features at runtime."""
+
+    homepage = "https://github.com/google/cpu_features"
+    git      = "https://github.com/google/cpu_features.git"
+
+    version('develop', branch='master')
+
+    depends_on('cmake@3.0.0:', type='build')
+
+    def cmake_args(self):
+        args = [
+            '-DBUILD_TESTING:BOOL=OFF'
+        ]
+        return args
diff --git a/var/spack/repos/builtin/packages/cpuinfo/package.py b/var/spack/repos/builtin/packages/cpuinfo/package.py
new file mode 100644
index 0000000000..e3bc736415
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cpuinfo/package.py
@@ -0,0 +1,16 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Cpuinfo(CMakePackage):
+    """cpuinfo is a library to detect essential
+    for performance optimization information about host CPU."""
+
+    homepage = "https://github.com/Maratyszcza/cpuinfo/"
+    git      = "https://github.com/Maratyszcza/cpuinfo.git"
+
+    version('master')
diff --git a/var/spack/repos/builtin/packages/cram/package.py b/var/spack/repos/builtin/packages/cram/package.py
index 73a8584572..3f213d3118 100644
--- a/var/spack/repos/builtin/packages/cram/package.py
+++ b/var/spack/repos/builtin/packages/cram/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/cryptopp/package.py b/var/spack/repos/builtin/packages/cryptopp/package.py
index c8fe6968a7..9ca8cf98d4 100644
--- a/var/spack/repos/builtin/packages/cryptopp/package.py
+++ b/var/spack/repos/builtin/packages/cryptopp/package.py
@@ -1,57 +1,35 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-import glob
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class Cryptopp(Package):
+class Cryptopp(MakefilePackage):
     """Crypto++ is an open-source C++ library of cryptographic schemes. The
-       library supports a number of different cryptography algorithms,
-       including authenticated encryption schemes (GCM, CCM), hash
-       functions (SHA-1, SHA2), public-key encryption (RSA, DSA), and a
-       few obsolete/historical encryption algorithms (MD5, Panama).
-
-    """
+    library supports a number of different cryptography algorithms, including
+    authenticated encryption schemes (GCM, CCM), hash functions (SHA-1, SHA2),
+    public-key encryption (RSA, DSA), and a few obsolete/historical encryption
+    algorithms (MD5, Panama)."""
 
     homepage = "http://www.cryptopp.com"
-    url      = "http://www.cryptopp.com/cryptopp563.zip"
+    url      = "http://www.cryptopp.com/cryptopp700.zip"
 
+    version('7.0.0', '8f34884b572901b6ede89bd18f1c7ef6')
+    version('6.1.0', sha256='21289d2511101a9350c87c8eb1f4982d4a266e8037b19dab79a32cc13ea108c7')
+    version('6.0.0', sha256='64ac2db96b3f1b7a23675e2be95d16c96055edffa2d5e2de6245fdb6baa92dda')
+    version('5.6.5', sha256='a75ef486fe3128008bbb201efee3dcdcffbe791120952910883b26337ec32c34')
+    version('5.6.4', sha256='be430377b05c15971d5ccb6e44b4d95470f561024ed6d701fe3da3a188c84ad7')
     version('5.6.3', '3c5b70e2ec98b7a24988734446242d07')
     version('5.6.2', '7ed022585698df48e65ce9218f6c6a67')
     version('5.6.1', '96cbeba0907562b077e26bcffb483828')
 
+    depends_on('gmake', type='build')
+
     def url_for_version(self, version):
-        url = "{0}/{1}{2}.zip"
+        url = '{0}/{1}{2}.zip'
         return url.format(self.homepage, self.name, version.joined)
 
     def install(self, spec, prefix):
-        make()
-
-        mkdirp(prefix.include)
-        for hfile in glob.glob('*.h*'):
-            install(hfile, prefix.include)
-
-        mkdirp(prefix.lib)
-        install('libcryptopp.a', prefix.lib)
+        make('install', 'PREFIX={0}'.format(prefix))
diff --git a/var/spack/repos/builtin/packages/cscope/package.py b/var/spack/repos/builtin/packages/cscope/package.py
index d7e7d29935..96f7ed1d67 100644
--- a/var/spack/repos/builtin/packages/cscope/package.py
+++ b/var/spack/repos/builtin/packages/cscope/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,6 +18,6 @@ class Cscope(AutotoolsPackage):
 
     depends_on('flex', type='build')
     depends_on('bison', type='build')
-    depends_on('pkg-config', type='build')
+    depends_on('pkgconfig', type='build')
 
     build_targets = ['CURSES_LIBS=-lncursesw']
diff --git a/var/spack/repos/builtin/packages/csdp/package.py b/var/spack/repos/builtin/packages/csdp/package.py
index a242f3b0c0..2735b14a41 100644
--- a/var/spack/repos/builtin/packages/csdp/package.py
+++ b/var/spack/repos/builtin/packages/csdp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/ctffind/package.py b/var/spack/repos/builtin/packages/ctffind/package.py
new file mode 100644
index 0000000000..3f8fb844bd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ctffind/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Ctffind(AutotoolsPackage):
+    """Fast and accurate defocus estimation from electron micrographs."""
+
+    homepage = "http://grigoriefflab.janelia.org/ctffind4"
+    url      = "http://grigoriefflab.janelia.org/sites/default/files/ctffind-4.1.8.tar.gz"
+
+    version('4.1.8', '8ae9d9abe363141a3792981b5a2fae94')
+
+    depends_on('wx')
+    depends_on('fftw@3:')
diff --git a/var/spack/repos/builtin/packages/cub/package.py b/var/spack/repos/builtin/packages/cub/package.py
index 1ca42f8e91..3db6d76eed 100644
--- a/var/spack/repos/builtin/packages/cub/package.py
+++ b/var/spack/repos/builtin/packages/cub/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/cube/package.py b/var/spack/repos/builtin/packages/cube/package.py
index 4f1f643bf2..d9da5ad7e4 100644
--- a/var/spack/repos/builtin/packages/cube/package.py
+++ b/var/spack/repos/builtin/packages/cube/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,23 +15,37 @@ class Cube(AutotoolsPackage):
     """
 
     homepage = "http://www.scalasca.org/software/cube-4.x/download.html"
-    url = "http://apps.fz-juelich.de/scalasca/releases/cube/4.2/dist/cube-4.2.3.tar.gz"
+    url      = "http://apps.fz-juelich.de/scalasca/releases/cube/4.4/dist/cubegui-4.4.2.tar.gz"
 
+    version('4.4.2', '29b6479616a524f8325f5031a883963bf965fb92569de33271a020f08650ec7b')
+    version('4.4',   '0620bae3ac357d0486ce7f5f97e448eeb2494c9a31865b679380ee08c6750e70')
     version('4.3.5', 'e5dce986e3c6381ea3a5fcb66c553adc')
     version('4.3.4', '50f73060f55311cb12c5b3cb354d59fa')
     version('4.3.3', '07e109248ed8ffc7bdcce614264a2909')
-
     version('4.2.3', '8f95b9531f5a8f8134f279c2767c9b20')
 
-    variant('gui', default=False, description='Build CUBE GUI')
+    variant('gui', default=True, description='Build Cube GUI')
+
+    patch('qt-version.patch', when='@4.3.0:4.3.999 +gui')
+
+    depends_on('cubelib', when='@4.4:')
 
+    depends_on('pkgconfig', type='build')
+    depends_on('dbus')
     depends_on('zlib')
 
-    depends_on('qt@5:', when='@4.3.0:4.3.999 +gui')
+    depends_on('qt@5:', when='@4.3.0: +gui')
     depends_on('qt@4.8:', when='@4.2.0:4.2.999 +gui')
 
+    conflicts('~gui', when='@4.4:')
+
     def url_for_version(self, version):
-        return 'http://apps.fz-juelich.de/scalasca/releases/cube/{0}/dist/cube-{1}.tar.gz'.format(version.up_to(2), version)
+        if version >= Version('4.4'):
+            url = 'http://apps.fz-juelich.de/scalasca/releases/cube/{0}/dist/cubegui-{1}.tar.gz'
+        else:
+            url = 'http://apps.fz-juelich.de/scalasca/releases/cube/{0}/dist/cube-{1}.tar.gz'
+
+        return url.format(version.up_to(2), version)
 
     def configure_args(self):
         spec = self.spec
diff --git a/var/spack/repos/builtin/packages/cube/qt-version.patch b/var/spack/repos/builtin/packages/cube/qt-version.patch
new file mode 100644
index 0000000000..33f36e76d2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cube/qt-version.patch
@@ -0,0 +1,24 @@
+diff -ruw cube-4.3.5.orig/build-backend/configure cube-4.3.5/build-backend/configure
+--- cube-4.3.5.orig/build-backend/configure	2017-05-23 13:15:46.121704000 +0200
++++ cube-4.3.5/build-backend/configure	2018-02-14 15:07:27.313842086 +0100
+@@ -5589,7 +5589,7 @@
+ else
+   echo "$as_me:$LINENO: Running $QMAKE --version:" >&5
+   $QMAKE --version >&5 2>&1
+-  qmake_version_sed='/^.*Qt.version.\([0-9]\.[0-9]\.[0-9]\).in.*$/!d;s//\1/'
++  qmake_version_sed='/^.*Qt.version.\([0-9]\.[0-9]\+\.[0-9]\+\).in.*$/!d;s//\1/'
+   at_cv_QT_VERSION=`$QMAKE --version 2>&1 | sed "$qmake_version_sed"`
+ fi
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $at_cv_QT_VERSION" >&5
+diff -ruw cube-4.3.5.orig/build-frontend/configure cube-4.3.5/build-frontend/configure
+--- cube-4.3.5.orig/build-frontend/configure	2017-05-23 13:16:00.499773000 +0200
++++ cube-4.3.5/build-frontend/configure	2018-02-14 15:07:46.349487111 +0100
+@@ -19757,7 +19757,7 @@
+ else
+   echo "$as_me:$LINENO: Running $QMAKE --version:" >&5
+   $QMAKE --version >&5 2>&1
+-  qmake_version_sed='/^.*Qt.version.\([0-9]\.[0-9]\.[0-9]\).in.*$/!d;s//\1/'
++  qmake_version_sed='/^.*Qt.version.\([0-9]\.[0-9]\+\.[0-9]\+\).in.*$/!d;s//\1/'
+   at_cv_QT_VERSION=`$QMAKE --version 2>&1 | sed "$qmake_version_sed"`
+ fi
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $at_cv_QT_VERSION" >&5
diff --git a/var/spack/repos/builtin/packages/cubelib/package.py b/var/spack/repos/builtin/packages/cubelib/package.py
new file mode 100644
index 0000000000..8ccd9f1bcd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cubelib/package.py
@@ -0,0 +1,31 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Cubelib(AutotoolsPackage):
+    """Component of CubeBundle: General purpose C++ library and tools """
+
+    homepage = "http://www.scalasca.org/software/cube-4.x/download.html"
+    url = "http://apps.fz-juelich.de/scalasca/releases/cube/4.4/dist/cubelib-4.4.tar.gz"
+
+    version('4.4.2', '843335c7d238493f1b4cb8e07555ccfe99a3fa521bf162e9d8eaa6733aa1f949')
+    version('4.4',   'c903f3c44d3228ebefd00c831966988e')
+
+    depends_on('zlib')
+
+    def url_for_version(self, version):
+        url = 'http://apps.fz-juelich.de/scalasca/releases/cube/{0}/dist/cubelib-{1}.tar.gz'
+
+        return url.format(version.up_to(2), version)
+
+    def configure_args(self):
+        configure_args = ['--enable-shared']
+
+        return configure_args
+
+    def install(self, spec, prefix):
+        make('install', parallel=False)
diff --git a/var/spack/repos/builtin/packages/cubew/package.py b/var/spack/repos/builtin/packages/cubew/package.py
new file mode 100644
index 0000000000..79c8464c62
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cubew/package.py
@@ -0,0 +1,31 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Cubew(AutotoolsPackage):
+    """Component of CubeBundle: High performance C Writer library """
+
+    homepage = "http://www.scalasca.org/software/cube-4.x/download.html"
+    url = "http://apps.fz-juelich.de/scalasca/releases/cube/4.4/dist/cubew-4.4.tar.gz"
+
+    version('4.4.1', 'c09e3f5a3533ebedee2cc7dfaacd7bac4680c14c3fa540669466583a23f04b67')
+    version('4.4',   'e9beb140719c2ad3d971e1efb99e0916')
+
+    depends_on('zlib')
+
+    def url_for_version(self, version):
+        url = 'http://apps.fz-juelich.de/scalasca/releases/cube/{0}/dist/cubew-{1}.tar.gz'
+
+        return url.format(version.up_to(2), version)
+
+    def configure_args(self):
+        configure_args = ['--enable-shared']
+
+        return configure_args
+
+    def install(self, spec, prefix):
+        make('install', parallel=True)
diff --git a/var/spack/repos/builtin/packages/cuda-memtest/package.py b/var/spack/repos/builtin/packages/cuda-memtest/package.py
index d7a4e2a04a..53a7204950 100644
--- a/var/spack/repos/builtin/packages/cuda-memtest/package.py
+++ b/var/spack/repos/builtin/packages/cuda-memtest/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,10 +16,11 @@ class CudaMemtest(CMakePackage):
     """
 
     homepage = "https://github.com/ComputationalRadiationPhysics/cuda_memtest"
-    url      = "https://github.com/ComputationalRadiationPhysics/cuda_memtest.git"
+    git      = "https://github.com/ComputationalRadiationPhysics/cuda_memtest.git"
+
+    maintainers = ['ax3l']
 
-    version('master', branch='dev',
-            git='https://github.com/ComputationalRadiationPhysics/cuda_memtest.git')
+    version('master', branch='dev')
 
     depends_on('cmake@2.8.5:', type='build')
     # depends_on('nvml', when='+nvml')
diff --git a/var/spack/repos/builtin/packages/cuda/package.py b/var/spack/repos/builtin/packages/cuda/package.py
index e54501d8fe..b807ddd966 100644
--- a/var/spack/repos/builtin/packages/cuda/package.py
+++ b/var/spack/repos/builtin/packages/cuda/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 from glob import glob
 
@@ -33,11 +14,16 @@ class Cuda(Package):
 
     Note: This package does not currently install the drivers necessary
     to run CUDA. These will need to be installed manually. See:
-    http://docs.nvidia.com/cuda/cuda-getting-started-guide-for-linux for
-    details."""
+    https://docs.nvidia.com/cuda/ for details."""
 
-    homepage = "http://www.nvidia.com/object/cuda_home_new.html"
+    homepage = "https://developer.nvidia.com/cuda-zone"
 
+    version('10.0.130', sha256='92351f0e4346694d0fcb4ea1539856c9eb82060c25654463bfd8574ec35ee39a', expand=False,
+            url="https://developer.nvidia.com/compute/cuda/10.0/Prod/local_installers/cuda_10.0.130_410.48_linux")
+    version('9.2.88', 'dd6e33e10d32a29914b7700c7b3d1ca0', expand=False,
+            url="https://developer.nvidia.com/compute/cuda/9.2/Prod/local_installers/cuda_9.2.88_396.26_linux")
+    version('9.1.85', '67a5c3933109507df6b68f80650b4b4a', expand=False,
+            url="https://developer.nvidia.com/compute/cuda/9.1/Prod/local_installers/cuda_9.1.85_387.26_linux")
     version('9.0.176', '7a00187b2ce5c5e350e68882f42dd507', expand=False,
             url="https://developer.nvidia.com/compute/cuda/9.0/Prod/local_installers/cuda_9.0.176_384.81_linux-run")
     version('8.0.61', '33e1bd980e91af4e55f3ef835c103f9b', expand=False,
@@ -50,7 +36,7 @@ class Cuda(Package):
             url="http://developer.download.nvidia.com/compute/cuda/6_5/rel/installers/cuda_6.5.14_linux_64.run")
 
     def install(self, spec, prefix):
-        runfile = glob(join_path(self.stage.path, 'cuda*run'))[0]
+        runfile = glob(join_path(self.stage.path, 'cuda*_linux*'))[0]
         chmod = which('chmod')
         chmod('+x', runfile)
         runfile = which(runfile)
@@ -59,6 +45,7 @@ class Cuda(Package):
         # compilers.  For example, on CentOS 6, you must use GCC 4.4.7 or
         # older. See:
         # http://docs.nvidia.com/cuda/cuda-installation-guide-linux/#system-requirements
+        # https://gist.github.com/ax3l/9489132
         # for details.
 
         runfile(
diff --git a/var/spack/repos/builtin/packages/cudnn/package.py b/var/spack/repos/builtin/packages/cudnn/package.py
index 53af7f9635..2524749ca2 100644
--- a/var/spack/repos/builtin/packages/cudnn/package.py
+++ b/var/spack/repos/builtin/packages/cudnn/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from distutils.dir_util import copy_tree
 
 
 class Cudnn(Package):
@@ -32,6 +12,8 @@ class Cudnn(Package):
 
     homepage = "https://developer.nvidia.com/cudnn"
 
+    version('7.3', '72666d3532850752612706601258a0b2',
+            url='https://developer.nvidia.com/compute/machine-learning/cudnn/secure/v7.3.0/prod/9.0_2018920/cudnn-9.0-linux-x64-v7.3.0.29.tgz')
     version('6.0', 'a08ca487f88774e39eb6b0ef6507451d',
             url='http://developer.download.nvidia.com/compute/redist/cudnn/v6.0/cudnn-8.0-linux-x64-v6.0.tgz')
     version('5.1', '406f4ac7f7ee8aa9e41304c143461a69',
@@ -40,4 +22,4 @@ class Cudnn(Package):
     depends_on('cuda@8:')
 
     def install(self, spec, prefix):
-        copy_tree('.', prefix)
+        install_tree('.', prefix)
diff --git a/var/spack/repos/builtin/packages/cufflinks/package.py b/var/spack/repos/builtin/packages/cufflinks/package.py
index 97197258dd..a0c039ff1f 100644
--- a/var/spack/repos/builtin/packages/cufflinks/package.py
+++ b/var/spack/repos/builtin/packages/cufflinks/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/cups/package.py b/var/spack/repos/builtin/packages/cups/package.py
index b674bd637a..f9f60f70e0 100644
--- a/var/spack/repos/builtin/packages/cups/package.py
+++ b/var/spack/repos/builtin/packages/cups/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/curl/package.py b/var/spack/repos/builtin/packages/curl/package.py
index c12e50b71c..5dabe83f80 100644
--- a/var/spack/repos/builtin/packages/curl/package.py
+++ b/var/spack/repos/builtin/packages/curl/package.py
@@ -1,28 +1,10 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
+import sys
 
 
 class Curl(AutotoolsPackage):
@@ -31,8 +13,10 @@ class Curl(AutotoolsPackage):
 
     homepage = "http://curl.haxx.se"
     # URL must remain http:// so Spack can bootstrap curl
-    url      = "http://curl.haxx.se/download/curl-7.54.0.tar.bz2"
+    url      = "http://curl.haxx.se/download/curl-7.60.0.tar.bz2"
 
+    version('7.60.0', 'bd2aabf78ded6a9aec8a54532fd6b5d7')
+    version('7.59.0', 'a2192804f7c2636a09320416afcf888e')
     version('7.56.0', 'e0caf257103e0c77cee5be7e9ac66ca4')
     version('7.54.0', '89bb7ba87384dfbf4f1a3f953da42458')
     version('7.53.1', 'fb1f03a142236840c1a77c035fa4c542')
@@ -48,15 +32,37 @@ class Curl(AutotoolsPackage):
     version('7.43.0', '11bddbb452a8b766b932f859aaeeed39')
     version('7.42.1', '296945012ce647b94083ed427c1877a8')
 
-    depends_on('openssl')
+    variant('nghttp2',    default=False, description='build nghttp2 library (requires C++11)')
+    variant('libssh2',    default=False, description='enable libssh2 support')
+    variant('libssh',     default=False, description='enable libssh support')  # , when='7.58:')
+    variant('darwinssl',  default=sys.platform == 'darwin', description="use Apple's SSL/TLS implementation")
+
+    conflicts('+libssh', when='@:7.57.99')
+    # on OSX and --with-ssh the configure steps fails with
+    # one or more libs available at link-time are not available run-time
+    # unless the libssh are installed externally (e.g. via homebrew), even
+    # though spack isn't supposed to know about such a libssh installation.
+    # C.f. https://github.com/spack/spack/issues/7777
+    conflicts('platform=darwin', when='+libssh2')
+    conflicts('platform=darwin', when='+libssh')
+    conflicts('platform=linux', when='+darwinssl')
+
+    depends_on('openssl', when='~darwinssl')
     depends_on('zlib')
-    depends_on('nghttp2')
+    depends_on('nghttp2', when='+nghttp2')
+    depends_on('libssh2', when='+libssh2')
+    depends_on('libssh', when='+libssh')
 
     def configure_args(self):
         spec = self.spec
 
-        return [
-            '--with-zlib={0}'.format(spec['zlib'].prefix),
-            '--with-ssl={0}'.format(spec['openssl'].prefix),
-            '--with-http2={0}'.format(spec['nghttp2'].prefix),
-        ]
+        args = ['--with-zlib={0}'.format(spec['zlib'].prefix)]
+        if spec.satisfies('+darwinssl'):
+            args.append('--with-darwinssl')
+        else:
+            args.append('--with-ssl={0}'.format(spec['openssl'].prefix))
+
+        args += self.with_or_without('nghttp2')
+        args += self.with_or_without('libssh2')
+        args += self.with_or_without('libssh')
+        return args
diff --git a/var/spack/repos/builtin/packages/cvs/package.py b/var/spack/repos/builtin/packages/cvs/package.py
index 58943886bf..be5c0baeda 100644
--- a/var/spack/repos/builtin/packages/cvs/package.py
+++ b/var/spack/repos/builtin/packages/cvs/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -29,7 +10,7 @@ from spack import *
 class Cvs(AutotoolsPackage):
     """CVS a very traditional source control system"""
     homepage = "http://www.nongnu.org/cvs/"
-    url      = "https://ftp.gnu.org/non-gnu/cvs/source/feature/1.12.13/cvs-1.12.13.tar.bz2"
+    url      = "https://ftpmirror.gnu.org/non-gnu/cvs/source/feature/1.12.13/cvs-1.12.13.tar.bz2"
 
     version('1.12.13', '93a8dacc6ff0e723a130835713235863f1f5ada9')
 
diff --git a/var/spack/repos/builtin/packages/czmq/package.py b/var/spack/repos/builtin/packages/czmq/package.py
index 799b577398..f567637a78 100644
--- a/var/spack/repos/builtin/packages/czmq/package.py
+++ b/var/spack/repos/builtin/packages/czmq/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,13 +11,15 @@ class Czmq(AutotoolsPackage):
     homepage = "http://czmq.zeromq.org"
     url      = "https://github.com/zeromq/czmq/archive/v4.0.2.tar.gz"
 
+    version('4.1.1', 'a2ab03cddd14399c6ba75b030a256211')
     version('4.0.2', 'a65317a3fb8238cf70e3e992e381f9cc')
     version('3.0.2', '23e9885f7ee3ce88d99d0425f52e9be1')
 
     depends_on('libtool', type='build')
     depends_on('automake', type='build')
     depends_on('autoconf', type='build')
-    depends_on('pkg-config', type='build')
+    depends_on('pkgconfig', type='build')
+    depends_on("libuuid")
     depends_on('zeromq')
 
     def configure_args(self):
diff --git a/var/spack/repos/builtin/packages/dakota/package.py b/var/spack/repos/builtin/packages/dakota/package.py
index b90fb5641a..09b34fc1b2 100644
--- a/var/spack/repos/builtin/packages/dakota/package.py
+++ b/var/spack/repos/builtin/packages/dakota/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/daligner/package.py b/var/spack/repos/builtin/packages/daligner/package.py
index 91322b5b3a..fd7fe30dd8 100644
--- a/var/spack/repos/builtin/packages/daligner/package.py
+++ b/var/spack/repos/builtin/packages/daligner/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/damageproto/package.py b/var/spack/repos/builtin/packages/damageproto/package.py
index 06d8815bb4..d439814375 100644
--- a/var/spack/repos/builtin/packages/damageproto/package.py
+++ b/var/spack/repos/builtin/packages/damageproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Damageproto(AutotoolsPackage):
 
     version('1.2.1', 'bf8c47b7f48625230cff155180f8ddce')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/damaris/package.py b/var/spack/repos/builtin/packages/damaris/package.py
new file mode 100644
index 0000000000..8bc0f7497f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/damaris/package.py
@@ -0,0 +1,64 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Damaris(CMakePackage):
+    """Damaris is a middleware for I/O and in situ analytics
+    targeting large-scale, MPI-based HPC simulations."""
+
+    homepage = "https://project.inria.fr/damaris/"
+    url = "https://gitlab.inria.fr/Damaris/damaris"
+
+    version('master', git='https://gitlab.inria.fr/Damaris/damaris.git')
+    version('1.3.1',  git='https://gitlab.inria.fr/Damaris/damaris.git', tag='v1.3.1', preferred=True)
+
+    variant('fortran',  default=True,  description='Enables Fortran support')
+    variant('hdf5',     default=False, description='Enables the HDF5 storage plugin')
+    variant('static',   default=False, description='Builds a static version of the library')
+    variant('catalyst', default=False, description='Enables the Catalyst visualization plugin')
+    variant('visit',    default=False, description='Enables the VisIt visualization plugin')
+
+    depends_on('mpi')
+    depends_on('cmake@3.12.0:', type=('build'))
+    depends_on('boost +thread+log+filesystem+date_time @1.67:')
+    depends_on('xsd')
+    depends_on('xerces-c')
+    depends_on('hdf5@1.8.20:', when='+hdf5')
+    depends_on('catalyst+python', when='+catalyst')
+    depends_on('visit+mpi', when='+visit')
+
+    def cmake_args(self):
+
+        args = []
+        if(not self.spec.variants['static'].value):
+            args.extend(['-DBUILD_SHARED_LIBS=ON'])
+
+        args.extend(['-DCMAKE_CXX_COMPILER=%s' % self.spec['mpi'].mpicxx])
+        args.extend(['-DCMAKE_C_COMPILER=%s' % self.spec['mpi'].mpicc])
+        args.extend(['-DBOOST_ROOT=%s' % self.spec['boost'].prefix])
+        args.extend(['-DXercesC_ROOT=%s' % self.spec['xerces-c'].prefix])
+        args.extend(['-DXSD_ROOT=%s' % self.spec['xsd'].prefix])
+
+        if (self.spec.variants['fortran'].value):
+            args.extend(['-DCMAKE_Fortran_COMPILER=%s'
+                         % self.spec['mpi'].mpifc])
+            args.extend(['-DENABLE_FORTRAN:BOOL=ON'])
+
+        if (self.spec.variants['hdf5'].value):
+            args.extend(['-DENABLE_HDF5:BOOL=ON'])
+            args.extend(['-DHDF5_ROOT:PATH=%s' % self.spec['hdf5'].prefix])
+
+        if (self.spec.variants['catalyst'].value):
+            args.extend(['-DENABLE_CATALYST:BOOL=ON'])
+            args.extend(['-DParaView_ROOT:PATH=%s'
+                         % self.spec['catalyst'].prefix])
+
+        if (self.spec.variants['visit'].value):
+            args.extend(['-DENABLE_VISIT:BOOL=ON'])
+            args.extend(['-DVisIt_ROOT:PATH=%s' % self.spec['visit'].prefix])
+        return args
diff --git a/var/spack/repos/builtin/packages/damselfly/package.py b/var/spack/repos/builtin/packages/damselfly/package.py
index c98ad5ca7b..6e7ecaf3de 100644
--- a/var/spack/repos/builtin/packages/damselfly/package.py
+++ b/var/spack/repos/builtin/packages/damselfly/package.py
@@ -1,36 +1,16 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class Damselfly(CMakePackage):
     """Damselfly is a model-based parallel network simulator."""
     homepage = "https://github.com/llnl/damselfly"
-    url      = "https://github.com/llnl/damselfly"
+    url      = "https://github.com/LLNL/damselfly/archive/v1.0.tar.gz"
 
-    version('1.0', '05cf7e2d8ece4408c0f2abb7ab63fd74c0d62895',
-            git='https://github.com/llnl/damselfly.git', tag='v1.0')
+    version('1.0', sha256='560e1b800c9036766396a1033c00914bd8d181b911e87140c3ac8879baf6545a')
 
     depends_on('cmake@2.6:', type='build')
diff --git a/var/spack/repos/builtin/packages/darshan-runtime/package.py b/var/spack/repos/builtin/packages/darshan-runtime/package.py
index 7be03f19c1..5aff9a0a1b 100644
--- a/var/spack/repos/builtin/packages/darshan-runtime/package.py
+++ b/var/spack/repos/builtin/packages/darshan-runtime/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
@@ -36,6 +17,7 @@ class DarshanRuntime(Package):
     homepage = "http://www.mcs.anl.gov/research/projects/darshan/"
     url = "http://ftp.mcs.anl.gov/pub/darshan/releases/darshan-3.1.0.tar.gz"
 
+    version('3.1.6', 'ce5b8f1e69d602edd4753b57258b57c1')
     version('3.1.0', '439d717323e6265b2612ed127886ae52')
     version('3.0.0', '732577fe94238936268d74d7d74ebd08')
 
diff --git a/var/spack/repos/builtin/packages/darshan-util/package.py b/var/spack/repos/builtin/packages/darshan-util/package.py
index 35d3ddb97a..af2d56be81 100644
--- a/var/spack/repos/builtin/packages/darshan-util/package.py
+++ b/var/spack/repos/builtin/packages/darshan-util/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,10 +15,13 @@ class DarshanUtil(Package):
     homepage = "http://www.mcs.anl.gov/research/projects/darshan/"
     url = "http://ftp.mcs.anl.gov/pub/darshan/releases/darshan-3.1.0.tar.gz"
 
+    version('3.1.6', 'ce5b8f1e69d602edd4753b57258b57c1')
     version('3.1.0', '439d717323e6265b2612ed127886ae52')
     version('3.0.0', '732577fe94238936268d74d7d74ebd08')
 
+    variant('bzip2', default=False, description="Enable bzip2 compression")
     depends_on('zlib')
+    depends_on('bzip2', when="+bzip2", type=("build", "link", "run"))
 
     def install(self, spec, prefix):
 
diff --git a/var/spack/repos/builtin/packages/dash/package.py b/var/spack/repos/builtin/packages/dash/package.py
index 9c79be238e..06adb572d0 100644
--- a/var/spack/repos/builtin/packages/dash/package.py
+++ b/var/spack/repos/builtin/packages/dash/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/datamash/package.py b/var/spack/repos/builtin/packages/datamash/package.py
index b72a1c21bb..ce80da9add 100644
--- a/var/spack/repos/builtin/packages/datamash/package.py
+++ b/var/spack/repos/builtin/packages/datamash/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,8 +12,9 @@ class Datamash(AutotoolsPackage):
     """
 
     homepage = "https://www.gnu.org/software/datamash/"
-    url      = "http://ftp.gnu.org/gnu/datamash/datamash-1.0.5.tar.gz"
+    url      = "https://ftpmirror.gnu.org/datamash/datamash-1.0.5.tar.gz"
 
+    version('1.3',   '47d382090e367ddb4967d640aba77b66')
     version('1.1.0', '79a6affca08107a095e97e4237fc8775')
     version('1.0.7', '9f317bab07454032ba9c068e7f17b04b')
     version('1.0.6', 'ff26fdef0f343cb695cf1853e14a1a5b')
diff --git a/var/spack/repos/builtin/packages/dataspaces/package.py b/var/spack/repos/builtin/packages/dataspaces/package.py
index 37121c2b47..552d0a0219 100644
--- a/var/spack/repos/builtin/packages/dataspaces/package.py
+++ b/var/spack/repos/builtin/packages/dataspaces/package.py
@@ -1,28 +1,11 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 ##############################################################################
+# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
+
 
 from spack import *
 import six
@@ -41,9 +24,9 @@ class Dataspaces(AutotoolsPackage):
 
     homepage = "http://www.dataspaces.org"
     url      = "http://personal.cac.rutgers.edu/TASSL/projects/data/downloads/dataspaces-1.6.2.tar.gz"
+    git      = "https://github.com/melrom/dataspaces.git"
 
-    version('develop', git='https://github.com/melrom/dataspaces.git',
-            branch='master')
+    version('develop', branch='master')
     version('1.6.2', '73caa4920b6f2c0c6d6cb87640ff04be')
 
     variant('dimes',
@@ -70,7 +53,7 @@ class Dataspaces(AutotoolsPackage):
     depends_on('libtool', type='build')
     depends_on('mpi', when='+mpi')
 
-    def autoreconf(spec, prefix, self):
+    def autoreconf(self, spec, prefix):
         bash = which('bash')
         bash('./autogen.sh')
 
diff --git a/var/spack/repos/builtin/packages/davix/package.py b/var/spack/repos/builtin/packages/davix/package.py
new file mode 100644
index 0000000000..3338cad733
--- /dev/null
+++ b/var/spack/repos/builtin/packages/davix/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Davix(CMakePackage):
+    """High-performance file management over WebDAV/HTTP."""
+
+    homepage = "https://dmc.web.cern.ch/projects/davix"
+    url      = "http://grid-deployment.web.cern.ch/grid-deployment/dms/lcgutil/tar/davix/0.6.7/davix-0.6.7.tar.gz"
+    list_url = "http://grid-deployment.web.cern.ch/grid-deployment/dms/lcgutil/tar/davix/"
+    list_depth = 1
+
+    version('0.6.8', 'e1820f4cc3fc44858ae97197a3922cce2a1130ff553b080ba19e06eb8383ddf7',
+            url='http://grid-deployment.web.cern.ch/grid-deployment/dms/lcgutil/tar/davix/0.6.8/davix-0.6.8.tar.gz')
+
+    depends_on('pkgconfig', type='build')
+    depends_on('libxml2')
+    depends_on('libuuid')
+    depends_on('openssl')
diff --git a/var/spack/repos/builtin/packages/dbcsr/package.py b/var/spack/repos/builtin/packages/dbcsr/package.py
new file mode 100644
index 0000000000..af1ba5f749
--- /dev/null
+++ b/var/spack/repos/builtin/packages/dbcsr/package.py
@@ -0,0 +1,40 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Dbcsr(CMakePackage):
+    """Distributed Block Compressed Sparse Row matrix library."""
+
+    homepage = "https://github.com/cp2k/dbcsr"
+    url      = "https://github.com/cp2k/dbcsr/archive/v1.0.0-rc.0.tar.gz"
+
+    version('develop', git='https://github.com/cp2k/dbcsr.git', branch='develop')
+
+    variant('mpi',    default=True,  description='Compile with MPI')
+    variant('openmp', default=False, description='Build with OpenMP support')
+
+    depends_on('blas')
+    depends_on('lapack')
+    depends_on('mpi', when='+mpi')
+    depends_on('py-fypp')
+
+    def cmake_args(self):
+        spec = self.spec
+        args = [
+            '-DUSE_MPI=%s' % ('ON' if '+mpi' in spec else 'OFF'),
+            '-DUSE_OPENMP=%s' % (
+                'ON' if '+openmp' in spec else 'OFF'),
+            '-DWITH_C_API=ON',
+            '-DLAPACK_FOUND=true',
+            '-DLAPACK_LIBRARIES=%s' % spec['lapack'].libs.joined(';'),
+            '-DBLAS_FOUND=true',
+            '-DBLAS_LIBRARIES=%s' % spec['blas'].libs.joined(';'),
+            '-DWITH_EXAMPLES=OFF',
+            '-DBUILD_SHARED_LIBS=ON'
+        ]
+
+        return args
diff --git a/var/spack/repos/builtin/packages/dbus/package.py b/var/spack/repos/builtin/packages/dbus/package.py
index 4d55665a4e..2b70ecab40 100644
--- a/var/spack/repos/builtin/packages/dbus/package.py
+++ b/var/spack/repos/builtin/packages/dbus/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,6 +19,7 @@ class Dbus(Package):
     homepage = "http://dbus.freedesktop.org/"
     url      = "http://dbus.freedesktop.org/releases/dbus/dbus-1.8.8.tar.gz"
 
+    version('1.12.8', '2764bf150e5aa8005b7bc0d6c388756a')
     version('1.11.2', '957a07f066f3730d2bb3ea0932f0081b')
     version('1.9.0', 'ec6895a4d5c0637b01f0d0e7689e2b36')
     version('1.8.8', 'b9f4a18ee3faa1e07c04aa1d83239c43')
@@ -45,6 +27,7 @@ class Dbus(Package):
     version('1.8.4', '4717cb8ab5b80978fcadf2b4f2f72e1b')
     version('1.8.2', 'd6f709bbec0a022a1847c7caec9d6068')
 
+    depends_on('pkgconfig', type='build')
     depends_on('expat')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/dealii-parameter-gui/package.py b/var/spack/repos/builtin/packages/dealii-parameter-gui/package.py
new file mode 100644
index 0000000000..86f4527197
--- /dev/null
+++ b/var/spack/repos/builtin/packages/dealii-parameter-gui/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class DealiiParameterGui(CMakePackage):
+    """A qt based graphical user interface for editing deal.II .prm parameter
+    files."""
+
+    homepage = "https://github.com/dealii/parameter_gui"
+    git      = "https://github.com/dealii/parameter_gui.git"
+
+    version('develop', branch='master')
+
+    depends_on('qt')
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.set('PARAMETER_GUI_DIR', self.prefix)
diff --git a/var/spack/repos/builtin/packages/dealii/boost_1.65.1_singleton.patch b/var/spack/repos/builtin/packages/dealii/boost_1.65.1_singleton.patch
new file mode 100644
index 0000000000..fffd85aa1a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/dealii/boost_1.65.1_singleton.patch
@@ -0,0 +1,43 @@
+diff --git a/boost/serialization/singleton.hpp b/boost/serialization/singleton.hpp
+index b50afed..e891d55 100644
+--- a/boost/serialization/singleton.hpp
++++ b/boost/serialization/singleton.hpp
+@@ -91,7 +91,7 @@ class BOOST_SYMBOL_VISIBLE singleton_module :
+     public boost::noncopyable
+ {
+ private:
+-    BOOST_SERIALIZATION_DECL BOOST_DLLEXPORT static bool & get_lock() BOOST_USED;
++    BOOST_DLLEXPORT static bool & get_lock() BOOST_USED;
+ public:
+     BOOST_DLLEXPORT static void lock(){
+         get_lock() = true;
+@@ -115,7 +115,7 @@ private:
+         // use a wrapper so that types T with protected constructors
+         // can be used
+         class singleton_wrapper : public T {};
+-        static singleton_wrapper t;
++        static singleton_wrapper* t = new singleton_wrapper;
+         // refer to instance, causing it to be instantiated (and
+         // initialized at startup on working compilers)
+         BOOST_ASSERT(! is_destroyed());
+@@ -125,7 +125,9 @@ private:
+         // our usage/implementation of "locking" and introduce uncertainty into
+         // the sequence of object initializaition.
+         use(& m_instance);
+-        return static_cast<T &>(t);
++        if (!t)
++            t = new singleton_wrapper;
++        return static_cast<T &>(*t);
+     }
+     static bool & get_is_destroyed(){
+         static bool is_destroyed;
+@@ -147,6 +149,9 @@ public:
+         get_is_destroyed() = false;
+     }
+     BOOST_DLLEXPORT ~singleton() {
++        if (!get_is_destroyed()) {
++            delete &(get_instance());
++        }
+         get_is_destroyed() = true;
+     }
+ };
diff --git a/var/spack/repos/builtin/packages/dealii/boost_1.68.0.patch b/var/spack/repos/builtin/packages/dealii/boost_1.68.0.patch
new file mode 100644
index 0000000000..e5b5e86f5e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/dealii/boost_1.68.0.patch
@@ -0,0 +1,135 @@
+diff --git a/boost/archive/impl/archive_serializer_map.ipp b/boost/archive/impl/archive_serializer_map.ipp
+index 7f163ec..8dabf0d 100644
+--- a/boost/archive/impl/archive_serializer_map.ipp
++++ b/boost/archive/impl/archive_serializer_map.ipp
+@@ -47,10 +47,6 @@ archive_serializer_map<Archive>::insert(const basic_serializer * bs){
+ template<class Archive>
+ BOOST_ARCHIVE_OR_WARCHIVE_DECL void
+ archive_serializer_map<Archive>::erase(const basic_serializer * bs){
+-    BOOST_ASSERT(! boost::serialization::singleton<
+-            extra_detail::map<Archive>
+-        >::is_destroyed()
+-    );
+     if(boost::serialization::singleton<
+         extra_detail::map<Archive>
+     >::is_destroyed())
+diff --git a/boost/serialization/singleton.hpp b/boost/serialization/singleton.hpp
+index 3437f38..3eac8eb 100644
+--- a/boost/serialization/singleton.hpp
++++ b/boost/serialization/singleton.hpp
+@@ -108,6 +108,29 @@ public:
+     }
+ };
+ 
++namespace detail {
++// This is the class actually instantiated and hence the real singleton.
++// So there will only be one instance of this class. This does not hold
++// for singleton<T> as a class derived from singleton<T> could be
++// instantiated multiple times.
++template<class T>
++class singleton_wrapper : public T
++{
++public:
++    singleton_wrapper(){
++        BOOST_ASSERT(!get_is_destroyed());
++    }
++    ~singleton_wrapper(){
++        get_is_destroyed() = true;
++    }
++    static bool & get_is_destroyed(){
++        // Prefer a static function member to avoid LNK1179. Note: Never reset!
++        static bool is_destroyed = false;
++        return is_destroyed;
++    }
++};
++} // detail
++
+ template <class T>
+ class singleton : public singleton_module
+ {
+@@ -116,14 +139,11 @@ private:
+     // include this to provoke instantiation at pre-execution time
+     static void use(T const *) {}
+     static T & get_instance() {
+-        // use a wrapper so that types T with protected constructors
+-        // can be used
+-        class singleton_wrapper : public T {};
+-        static singleton_wrapper t;
++        BOOST_ASSERT(!is_destroyed());
+ 
+-        // refer to instance, causing it to be instantiated (and
+-        // initialized at startup on working compilers)
+-        BOOST_ASSERT(! is_destroyed());
++        // use a wrapper so that types T with protected constructors can be used
++        // Using a static function member avoids LNK1179
++        static detail::singleton_wrapper< T > t;
+ 
+         // note that the following is absolutely essential.
+         // commenting out this statement will cause compilers to fail to
+@@ -134,10 +154,11 @@ private:
+ 
+         return static_cast<T &>(t);
+     }
+-    static bool & get_is_destroyed(){
+-        static bool is_destroyed;
+-        return is_destroyed;
+-    }
++
++protected:
++    // Do not allow instantiation of a singleton<T>. But we want to allow
++    // `class T: public singleton<T>` so we can't delete this ctor
++    BOOST_DLLEXPORT singleton(){}
+ 
+ public:
+     BOOST_DLLEXPORT static T & get_mutable_instance(){
+@@ -148,13 +169,7 @@ public:
+         return get_instance();
+     }
+     BOOST_DLLEXPORT static bool is_destroyed(){
+-        return get_is_destroyed();
+-    }
+-    BOOST_DLLEXPORT singleton(){
+-        get_is_destroyed() = false;
+-    }
+-    BOOST_DLLEXPORT ~singleton() {
+-        get_is_destroyed() = true;
++        return detail::singleton_wrapper< T >::get_is_destroyed();
+     }
+ };
+ 
+diff --git a/libs/serialization/src/extended_type_info.cpp b/libs/serialization/src/extended_type_info.cpp
+index 364fe56..13a60c3 100644
+--- a/libs/serialization/src/extended_type_info.cpp
++++ b/libs/serialization/src/extended_type_info.cpp
+@@ -125,7 +125,6 @@ BOOST_SERIALIZATION_DECL void
+ extended_type_info::key_unregister() const{
+     if(NULL == get_key())
+         return;
+-    BOOST_ASSERT(! singleton<detail::ktmap>::is_destroyed());
+     if(! singleton<detail::ktmap>::is_destroyed()){
+         detail::ktmap & x = singleton<detail::ktmap>::get_mutable_instance();
+         detail::ktmap::iterator start = x.lower_bound(this);
+diff --git a/libs/serialization/src/extended_type_info_typeid.cpp b/libs/serialization/src/extended_type_info_typeid.cpp
+index 7413d2e..af188ef 100644
+--- a/libs/serialization/src/extended_type_info_typeid.cpp
++++ b/libs/serialization/src/extended_type_info_typeid.cpp
+@@ -95,7 +95,6 @@ BOOST_SERIALIZATION_DECL void
+ extended_type_info_typeid_0::type_unregister()
+ {
+     if(NULL != m_ti){
+-        BOOST_ASSERT(! singleton<tkmap>::is_destroyed());
+         if(! singleton<tkmap>::is_destroyed()){
+             tkmap & x = singleton<tkmap>::get_mutable_instance();
+ 
+diff --git a/libs/serialization/src/void_cast.cpp b/libs/serialization/src/void_cast.cpp
+index 4051303..9009993 100644
+--- a/libs/serialization/src/void_cast.cpp
++++ b/libs/serialization/src/void_cast.cpp
+@@ -276,7 +276,6 @@ void_caster::recursive_register(bool includes_virtual_base) const {
+ 
+ BOOST_SERIALIZATION_DECL void
+ void_caster::recursive_unregister() const {
+-    BOOST_ASSERT(! void_caster_registry::is_destroyed());
+     if(void_caster_registry::is_destroyed())
+         return;
+ 
diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py
index 8f3e5d80ea..55cd7cbd00 100644
--- a/var/spack/repos/builtin/packages/dealii/package.py
+++ b/var/spack/repos/builtin/packages/dealii/package.py
@@ -1,36 +1,18 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-import os
 
 
-class Dealii(CMakePackage):
+class Dealii(CMakePackage, CudaPackage):
     """C++ software library providing well-documented tools to build finite
     element codes for a broad variety of PDEs."""
+
     homepage = "https://www.dealii.org"
-    url = "https://github.com/dealii/dealii/releases/download/v8.4.1/dealii-8.4.1.tar.gz"
+    url      = "https://github.com/dealii/dealii/releases/download/v8.4.1/dealii-8.4.1.tar.gz"
+    git      = "https://github.com/dealii/dealii.git"
 
     maintainers = ['davydden', 'jppelteret']
 
@@ -38,30 +20,34 @@ class Dealii(CMakePackage):
     # only add for immediate deps.
     transitive_rpaths = False
 
-    version('8.5.1', '39b9ebd6ab083d63cfc9044319aaa2ee')
-    version('8.5.0', 'ef999cc310b007559a6343bf5b1759bc')
-    version('8.4.2', '84c6bd3f250d3e0681b645d24cb987a7')
-    version('8.4.1', 'efbaf16f9ad59cfccad62302f36c3c1d')
-    version('8.4.0', 'ac5dbf676096ff61e092ce98c80c2b00')
-    version('8.3.0', 'fc6cdcb16309ef4bea338a4f014de6fa')
-    version('8.2.1', '71c728dbec14f371297cd405776ccf08')
-    version('8.1.0', 'aa8fadc2ce5eb674f44f997461bf668d')
-    version('develop', git='https://github.com/dealii/dealii.git', branch='master')
+    version('develop', branch='master')
+    version('9.0.1', sha256='df2f0d666f2224be07e3741c0e8e02132fd67ea4579cd16a2429f7416146ee64')
+    version('9.0.0', sha256='c918dc5c1a31d62f6eea7b524dcc81c6d00b3c378d4ed6965a708ab548944f08')
+    version('8.5.1', sha256='d33e812c21a51f7e5e3d3e6af86aec343155650b611d61c1891fbc3cabce09ae')
+    version('8.5.0', sha256='e6913ff6f184d16bc2598c1ba31f879535b72b6dff043e15aef048043ff1d779')
+    version('8.4.2', sha256='ec7c00fadc9d298d1a0d16c08fb26818868410a9622c59ba624096872f3058e4')
+    version('8.4.1', sha256='00a0e92d069cdafd216816f1aff460f7dbd48744b0d9e0da193287ebf7d6b3ad')
+    version('8.4.0', sha256='36a20e097a03f17b557e11aad1400af8c6252d25f7feca40b611d5fc16d71990')
+    version('8.3.0', sha256='4ddf72632eb501e1c814e299f32fc04fd680d6fda9daff58be4209e400e41779')
+    version('8.2.1', sha256='d75674e45fe63cd9fa294460fe45228904d51a68f744dbb99cd7b60720f3b2a0')
+    version('8.1.0', sha256='d666bbda2a17b41b80221d7029468246f2658051b8c00d9c5907cd6434c4df99')
 
     variant('mpi',      default=True,  description='Compile with MPI')
-    variant('assimp',   default=False,
+    variant('assimp',   default=True,
             description='Compile with Assimp')
     variant('arpack',   default=True,
             description='Compile with Arpack and PArpack (only with MPI)')
-    variant('adol-c',   default=False,
+    variant('adol-c',   default=True,
             description='Compile with Adol-c')
     variant('doc',      default=False,
             description='Compile with documentation')
+    variant('gmsh',     default=True,  description='Compile with GMSH')
     variant('gsl',      default=True,  description='Compile with GSL')
     variant('hdf5',     default=True,
             description='Compile with HDF5 (only with MPI)')
     variant('metis',    default=True,  description='Compile with Metis')
-    variant('nanoflann', default=False, description='Compile with Nanoflann')
+    variant('muparser', default=True,  description='Compile with muParser')
+    variant('nanoflann', default=True, description='Compile with Nanoflann')
     variant('netcdf',   default=True,
             description='Compile with Netcdf (only with MPI)')
     variant('oce',      default=True,  description='Compile with OCE')
@@ -69,13 +55,15 @@ class Dealii(CMakePackage):
             description='Compile with P4est (only with MPI)')
     variant('petsc',    default=True,
             description='Compile with Petsc (only with MPI)')
-    variant('sundials', default=False,
+    variant('scalapack', default=True,
+            description='Compile with ScaLAPACK (only with MPI)')
+    variant('sundials', default=True,
             description='Compile with Sundials')
     variant('slepc',    default=True,
             description='Compile with Slepc (only with Petsc and MPI)')
     variant('trilinos', default=True,
             description='Compile with Trilinos (only with MPI)')
-    variant('python',   default=True,
+    variant('python',   default=False,
             description='Compile with Python bindings')
     variant('int64',    default=False,
             description='Compile with 64 bit indices support')
@@ -84,83 +72,115 @@ class Dealii(CMakePackage):
     variant('build_type', default='DebugRelease',
             description='The build type to build',
             values=('Debug', 'Release', 'DebugRelease'))
-    variant('cuda', default=False,
-            description='Build with CUDA')
 
     # required dependencies, light version
-    depends_on("blas")
-    # Boost 1.58 is blacklisted, see
+    depends_on('blas')
+    # Boost 1.58 is blacklisted, require at least 1.59, see
     # https://github.com/dealii/dealii/issues/1591
-    # Require at least 1.59
-    # +python won't affect @:8.4.2
-    # FIXME: once concretizer can unite unconditional and
-    # conditional dependencies, simplify to:
-    # depends_on("boost@1.59.0+thread+system+serialization+iostreams")
-    # depends_on("boost+mpi", when='+mpi')
-    # depends_on("boost+python", when='+python')
-    depends_on("boost@1.59.0:1.63,1.66:+thread+system+serialization+iostreams",
-               when='@:8.4.2~mpi')
-    depends_on("boost@1.59.0:1.63,1.66:+thread+system+serialization+iostreams+mpi",
-               when='@:8.4.2+mpi')
-    # since @8.5.0: (and @develop) python bindings are introduced:
-    depends_on("boost@1.59.0:1.63,1.66:+thread+system+serialization+iostreams",
-               when='@8.5.0:~mpi~python')
-    depends_on("boost@1.59.0:1.63,1.66:+thread+system+serialization+iostreams+mpi",
-               when='@8.5.0:+mpi~python')
-    depends_on("boost@1.59.0:1.63,1.66:+thread+system+serialization+iostreams+python",
-               when='@8.5.0:~mpi+python')
-    depends_on("boost@1.59.0:1.63,1.66:+thread+system+serialization+iostreams+mpi+python",
-               when='@8.5.0:+mpi+python')
+    # There are issues with 1.65.1 and 1.65.0:
+    # https://github.com/dealii/dealii/issues/5262
+    # we take the patch from https://github.com/boostorg/serialization/pull/79
+    # more precisely its variation https://github.com/dealii/dealii/pull/5572#issuecomment-349742019
+    # 1.68.0 has issues with serialization https://github.com/dealii/dealii/issues/7074
+    # adopt https://github.com/boostorg/serialization/pull/105 as a fix
+    depends_on('boost@1.59.0:1.63,1.65.1,1.67.0:+thread+system+serialization+iostreams',
+               patches=[patch('boost_1.65.1_singleton.patch',
+                              level=1,
+                              when='@1.65.1'),
+                        patch('boost_1.68.0.patch',
+                              level=1,
+                              when='@1.68.0'),
+                       ],
+               when='~python')
+    depends_on('boost@1.59.0:1.63,1.65.1,1.67.0:+thread+system+serialization+iostreams+python',
+               patches=[patch('boost_1.65.1_singleton.patch',
+                              level=1,
+                              when='@1.65.1'),
+                        patch('boost_1.68.0.patch',
+                              level=1,
+                              when='@1.68.0'),
+                       ],
+               when='+python')
     # bzip2 is not needed since 9.0
-    depends_on("bzip2", when='@:8.99')
-    depends_on("lapack")
-    depends_on("muparser")
-    depends_on("suite-sparse")
-    depends_on("tbb")
-    depends_on("zlib")
+    depends_on('bzip2', when='@:8.99')
+    depends_on('lapack')
+    depends_on('suite-sparse')
+    depends_on('tbb')
+    depends_on('zlib')
 
     # optional dependencies
-    depends_on("mpi",              when="+mpi")
-    depends_on("adol-c@2.6.4:",    when='@9.0:+adol-c')
-    depends_on("arpack-ng+mpi",    when='+arpack+mpi')
-    depends_on("assimp",           when='@9.0:+assimp')
-    depends_on("doxygen+graphviz", when='+doc')
-    depends_on("graphviz",         when='+doc')
-    depends_on("gsl",              when='@8.5.0:+gsl')
-    depends_on("hdf5+mpi",         when='+hdf5+mpi')
-    depends_on("cuda@8:",          when='+cuda')
-    depends_on("cmake@3.9:",       when='+cuda')
+    depends_on('mpi',              when='+mpi')
+    depends_on('adol-c@2.6.4:',    when='@9.0:+adol-c')
+    depends_on('arpack-ng+mpi',    when='+arpack+mpi')
+    depends_on('assimp',           when='@9.0:+assimp')
+    depends_on('doxygen+graphviz', when='+doc')
+    depends_on('graphviz',         when='+doc')
+    depends_on('gmsh+tetgen+netgen+oce', when='@9.0:+gmsh', type=('build', 'run'))
+    depends_on('gsl',              when='@8.5.0:+gsl')
+    depends_on('hdf5+mpi+hl',      when='+hdf5+mpi')
+    depends_on('cuda@8:',          when='+cuda')
+    depends_on('cmake@3.9:',       when='+cuda')
+    # older version of deal.II do not build with Cmake 3.10, see
+    # https://github.com/dealii/dealii/issues/5510
+    depends_on('cmake@:3.9.99',    when='@:8.99')
     # FIXME: concretizer bug. The two lines mimic what comes from PETSc
     # but we should not need it
-    depends_on("metis@5:+int64+real64",   when='+metis+int64')
-    depends_on("metis@5:~int64+real64",   when='+metis~int64')
-    depends_on("nanoflann",        when="@9.0:+nanoflann")
-    depends_on("netcdf+mpi",       when="+netcdf+mpi")
-    depends_on("netcdf-cxx",       when='+netcdf+mpi')
-    depends_on("oce",              when='+oce')
-    depends_on("p4est",            when='+p4est+mpi')
-    depends_on("petsc+mpi~int64",  when='+petsc+mpi~int64')
-    depends_on("petsc+mpi+int64",  when='+petsc+mpi+int64')
-    depends_on("petsc@:3.6.4",     when='@:8.4.1+petsc+mpi')
+    depends_on('metis@5:+int64+real64',   when='+metis+int64')
+    depends_on('metis@5:~int64+real64',   when='+metis~int64')
+    depends_on('muparser', when='+muparser')
+    depends_on('nanoflann',        when='@9.0:+nanoflann')
+    depends_on('netcdf+mpi',       when='+netcdf+mpi')
+    depends_on('netcdf-cxx',       when='+netcdf+mpi')
+    depends_on('oce',              when='+oce')
+    depends_on('p4est',            when='+p4est+mpi')
+    depends_on('petsc+mpi~int64',  when='+petsc+mpi~int64')
+    depends_on('petsc+mpi+int64',  when='+petsc+mpi+int64')
+    depends_on('petsc@:3.6.4',     when='@:8.4.1+petsc+mpi')
     depends_on('python',           when='@8.5.0:+python')
-    depends_on("slepc",            when='+slepc+petsc+mpi')
-    depends_on("slepc@:3.6.3",     when='@:8.4.1+slepc+petsc+mpi')
-    depends_on("slepc~arpack",     when='+slepc+petsc+mpi+int64')
-    depends_on("sundials~pthread", when='@9.0:+sundials')
-    depends_on("trilinos+amesos+aztec+epetra+ifpack+ml+muelu+sacado+teuchos",       when='+trilinos+mpi~int64')
-    depends_on("trilinos+amesos+aztec+epetra+ifpack+ml+muelu+sacado+teuchos~hypre", when="+trilinos+mpi+int64")
+    depends_on('scalapack',        when='@9.0:+scalapack')
+    depends_on('slepc',            when='+slepc+petsc+mpi')
+    depends_on('slepc@:3.6.3',     when='@:8.4.1+slepc+petsc+mpi')
+    depends_on('slepc~arpack',     when='+slepc+petsc+mpi+int64')
+    depends_on('sundials~pthread', when='@9.0:+sundials')
+    # do not require +rol to make concretization of xsdk possible
+    depends_on('trilinos+amesos+aztec+epetra+ifpack+ml+muelu+sacado+teuchos',       when='+trilinos+mpi~int64~cuda')
+    depends_on('trilinos+amesos+aztec+epetra+ifpack+ml+muelu+sacado+teuchos~hypre', when='+trilinos+mpi+int64~cuda')
+    # FIXME: temporary disable Tpetra when using CUDA due to
+    # namespace "Kokkos::Impl" has no member "cuda_abort"
+    depends_on('trilinos@master+amesos+aztec+epetra+ifpack+ml+muelu+rol+sacado+teuchos~amesos2~ifpack2~intrepid2~kokkos~tpetra~zoltan2',       when='+trilinos+mpi~int64+cuda')
+    depends_on('trilinos@master+amesos+aztec+epetra+ifpack+ml+muelu+rol+sacado+teuchos~hypre~amesos2~ifpack2~intrepid2~kokkos~tpetra~zoltan2', when='+trilinos+mpi+int64+cuda')
 
     # check that the combination of variants makes sense
-    conflicts('+assimp', when='@:8.5.1')
-    conflicts('+nanoflann', when='@:8.5.1')
-    conflicts('+sundials', when='@:8.5.1')
-    conflicts('+adol-c', when='@:8.5.1')
-    conflicts('+gsl',    when='@:8.4.2')
-    conflicts('+python', when='@:8.4.2')
-    conflicts('+cuda', when='%gcc@6:')
-    for p in ['+arpack', '+hdf5', '+netcdf', '+p4est', '+petsc',
-              '+slepc', '+trilinos']:
-        conflicts(p, when='~mpi')
+    # 64-bit BLAS:
+    for p in ['openblas', 'intel-mkl', 'intel-parallel-studio+mkl']:
+        conflicts('^{0}+ilp64'.format(p), when='@:8.5.1',
+                  msg='64bit BLAS is only supported from 9.0.0')
+
+    # interfaces added in 9.0.0:
+    for p in ['assimp', 'gmsh', 'nanoflann', 'scalapack', 'sundials',
+              'adol-c']:
+        conflicts('+{0}'.format(p), when='@:8.5.1',
+                  msg='The interface to {0} is supported from version 9.0.0 '
+                      'onwards. Please explicitly disable this variant '
+                      'via ~{0}'.format(p))
+
+    conflicts('+slepc', when='~petsc',
+              msg='It is not possible to enable slepc interfaces '
+                  'without petsc.')
+
+    # interfaces added in 8.5.0:
+    for p in ['gsl', 'python']:
+        conflicts('+{0}'.format(p), when='@:8.4.2',
+                  msg='The interface to {0} is supported from version 8.5.0 '
+                      'onwards. Please explicitly disable this variant '
+                      'via ~{0}'.format(p))
+
+    # MPI requirements:
+    for p in ['arpack', 'hdf5', 'netcdf', 'p4est', 'petsc', 'scalapack',
+              'slepc', 'trilinos']:
+        conflicts('+{0}'.format(p), when='~mpi',
+                  msg='To enable {0} it is necessary to build deal.II with '
+                      'MPI support enabled.'.format(p))
 
     def cmake_args(self):
         spec = self.spec
@@ -182,13 +202,17 @@ class Dealii(CMakePackage):
             '-DLAPACK_INCLUDE_DIRS=%s;%s' % (
                 spec['lapack'].prefix.include, spec['blas'].prefix.include),
             '-DLAPACK_LIBRARIES=%s' % lapack_blas.joined(';'),
-            '-DMUPARSER_DIR=%s' % spec['muparser'].prefix,
             '-DUMFPACK_DIR=%s' % spec['suite-sparse'].prefix,
             '-DTBB_DIR=%s' % spec['tbb'].prefix,
             '-DZLIB_DIR=%s' % spec['zlib'].prefix,
             '-DDEAL_II_ALLOW_BUNDLED=OFF'
         ])
 
+        if (spec.satisfies('^openblas+ilp64') or
+            spec.satisfies('^intel-mkl+ilp64') or
+            spec.satisfies('^intel-parallel-studio+mkl+ilp64')):
+            options.append('-DLAPACK_WITH_64BIT_BLAS_INDICES=ON')
+
         if spec.satisfies('@:8.99'):
             options.extend([
                 # Cmake may still pick up system's bzip2, fix this:
@@ -215,6 +239,15 @@ class Dealii(CMakePackage):
                 '-DDEAL_II_COMPONENT_PYTHON_BINDINGS=%s' %
                 ('ON' if '+python' in spec else 'OFF')
             ])
+            if '+python' in spec:
+                python_exe = spec['python'].command.path
+                python_library = spec['python'].libs[0]
+                python_include = spec['python'].headers.directories[0]
+                options.extend([
+                    '-DPYTHON_EXECUTABLE=%s' % python_exe,
+                    '-DPYTHON_INCLUDE_DIR=%s' % python_include,
+                    '-DPYTHON_LIBRARY=%s' % python_library
+                ])
 
         # Set directory structure:
         if spec.satisfies('@:8.2.1'):
@@ -227,12 +260,25 @@ class Dealii(CMakePackage):
             ])
 
         # CUDA
-        # FIXME  -DDEAL_II_CUDA_FLAGS="-arch=sm_60"
         if '+cuda' in spec:
-            options.extend([
-                '-DDEAL_II_WITH_CUDA=ON',
-                '-DDEAL_II_WITH_CXX14=OFF'
-            ])
+            options.append(
+                '-DDEAL_II_WITH_CUDA=ON'
+            )
+            if not spec.satisfies('^cuda@9:'):
+                options.append('-DDEAL_II_WITH_CXX14=OFF')
+            cuda_arch = spec.variants['cuda_arch'].value
+            if cuda_arch is not None and cuda_arch[0] is not '':
+                if len(cuda_arch) > 1:
+                    raise InstallError(
+                        'deal.II only supports compilation for a single GPU!'
+                    )
+                flags = '-arch=sm_{0}'.format(cuda_arch[0])
+                # FIXME: there are some compiler errors in dealii
+                # with: flags = ' '.join(self.cuda_flags(cuda_arch))
+                # Stick with -arch=sm_xy for now.
+                options.append(
+                    '-DDEAL_II_CUDA_FLAGS={0}'.format(flags)
+                )
         else:
             options.extend([
                 '-DDEAL_II_WITH_CUDA=OFF',
@@ -255,8 +301,8 @@ class Dealii(CMakePackage):
         # variables:
         for library in (
                 'gsl', 'hdf5', 'p4est', 'petsc', 'slepc', 'trilinos', 'metis',
-                'sundials', 'nanoflann'):
-            if library in spec:
+                'sundials', 'nanoflann', 'assimp', 'gmsh', 'muparser'):
+            if ('+' + library) in spec:
                 options.extend([
                     '-D%s_DIR=%s' % (library.upper(), spec[library].prefix),
                     '-DDEAL_II_WITH_%s:BOOL=ON' % library.upper()
@@ -295,36 +341,12 @@ class Dealii(CMakePackage):
                 '-DDEAL_II_WITH_ARPACK=OFF'
             ])
 
-        # Assimp
-        if '+assimp' in spec:
-            options.extend([
-                '-DDEAL_II_WITH_ASSIMP=ON',
-                '-DASSIMP_DIR=%s' % spec['assimp'].prefix
-            ])
-        else:
-            options.extend([
-                '-DDEAL_II_WITH_ASSIMP=OFF'
-            ])
-
         # since Netcdf is spread among two, need to do it by hand:
         if '+netcdf' in spec and '+mpi' in spec:
-            # take care of lib64 vs lib installed lib locations:
-            if os.path.isdir(spec['netcdf-cxx'].prefix.lib):
-                netcdfcxx_lib_dir = spec['netcdf-cxx'].prefix.lib
-            else:
-                netcdfcxx_lib_dir = spec['netcdf-cxx'].prefix.lib64
-            if os.path.isdir(spec['netcdf'].prefix.lib):
-                netcdf_lib_dir = spec['netcdf'].prefix.lib
-            else:
-                netcdf_lib_dir = spec['netcdf'].prefix.lib64
-
+            netcdf = spec['netcdf-cxx'].libs + spec['netcdf'].libs
             options.extend([
                 '-DNETCDF_FOUND=true',
-                '-DNETCDF_LIBRARIES=%s;%s' % (
-                    join_path(netcdfcxx_lib_dir,
-                              'libnetcdf_c++.%s' % dso_suffix),
-                    join_path(netcdf_lib_dir,
-                              'libnetcdf.%s' % dso_suffix)),
+                '-DNETCDF_LIBRARIES=%s' % netcdf.joined(';'),
                 '-DNETCDF_INCLUDE_DIRS=%s;%s' % (
                     spec['netcdf-cxx'].prefix.include,
                     spec['netcdf'].prefix.include),
@@ -334,6 +356,20 @@ class Dealii(CMakePackage):
                 '-DDEAL_II_WITH_NETCDF=OFF'
             ])
 
+        if '+scalapack' in spec:
+            scalapack = spec['scalapack'].libs
+            options.extend([
+                '-DSCALAPACK_FOUND=true',
+                '-DSCALAPACK_INCLUDE_DIRS=%s' % (
+                    spec['scalapack'].prefix.include),
+                '-DSCALAPACK_LIBRARIES=%s' % scalapack.joined(';'),
+                '-DDEAL_II_WITH_SCALAPACK=ON'
+            ])
+        else:
+            options.extend([
+                '-DDEAL_II_WITH_SCALAPACK=OFF'
+            ])
+
         # Open Cascade
         if '+oce' in spec:
             options.extend([
diff --git a/var/spack/repos/builtin/packages/deconseq-standalone/package.py b/var/spack/repos/builtin/packages/deconseq-standalone/package.py
new file mode 100644
index 0000000000..ab6d2c3099
--- /dev/null
+++ b/var/spack/repos/builtin/packages/deconseq-standalone/package.py
@@ -0,0 +1,41 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class DeconseqStandalone(Package):
+    """The DeconSeq tool can be used to automatically detect and efficiently
+    remove sequence contaminations from genomic and metagenomic datasets."""
+
+    homepage = "http://deconseq.sourceforge.net"
+    url      = "https://sourceforge.net/projects/deconseq/files/standalone/deconseq-standalone-0.4.3.tar.gz"
+
+    version('0.4.3', 'cb3fddb90e584d89fd9c2b6b8f2e20a2')
+
+    depends_on('perl@5:')
+
+    def install(self, spec, prefix):
+
+        filter_file(r'#!/usr/bin/perl',
+                    '#!/usr/bin/env perl', 'deconseq.pl')
+        filter_file(r'#!/usr/bin/perl',
+                    '#!/usr/bin/env perl', 'splitFasta.pl')
+
+        mkdirp(prefix.bin)
+        install('bwa64', prefix.bin)
+        install('bwaMAC', prefix.bin)
+        install('deconseq.pl', prefix.bin)
+        install('splitFasta.pl', prefix.bin)
+        install('DeconSeqConfig.pm', prefix)
+
+        chmod = which('chmod')
+        chmod('+x', join_path(prefix.bin, 'bwa64'))
+        chmod('+x', join_path(prefix.bin, 'bwaMAC'))
+        chmod('+x', join_path(prefix.bin, 'deconseq.pl'))
+        chmod('+x', join_path(prefix.bin, 'splitFasta.pl'))
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PERL5LIB', prefix)
diff --git a/var/spack/repos/builtin/packages/dejagnu/package.py b/var/spack/repos/builtin/packages/dejagnu/package.py
index 7b083d00b4..f659f3174b 100644
--- a/var/spack/repos/builtin/packages/dejagnu/package.py
+++ b/var/spack/repos/builtin/packages/dejagnu/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,7 +11,7 @@ class Dejagnu(AutotoolsPackage):
     is to provide a single front end for all tests."""
 
     homepage = "https://www.gnu.org/software/dejagnu/"
-    url      = "http://mirror.team-cymru.org/gnu/dejagnu/dejagnu-1.6.tar.gz"
+    url      = "https://ftpmirror.gnu.org/dejagnu/dejagnu-1.6.tar.gz"
 
     version('1.6',   '1fdc2eb0d592c4f89d82d24dfdf02f0b')
     version('1.4.4', '053f18fd5d00873de365413cab17a666')
diff --git a/var/spack/repos/builtin/packages/delly2/package.py b/var/spack/repos/builtin/packages/delly2/package.py
index e922d2c566..d7dffea4a7 100644
--- a/var/spack/repos/builtin/packages/delly2/package.py
+++ b/var/spack/repos/builtin/packages/delly2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,10 +13,9 @@ class Delly2(MakefilePackage):
        short-read massively parallel sequencing data.."""
 
     homepage = "https://github.com/dellytools/delly"
-    url      = "https://github.com/dellytools/delly"
+    git      = "https://github.com/dellytools/delly.git"
 
-    version('2017-08-03', commit='e32a9cd55c7e3df5a6ae4a91f31a0deb354529fc',
-            git='https://github.com/dellytools/delly.git')
+    version('2017-08-03', commit='e32a9cd55c7e3df5a6ae4a91f31a0deb354529fc')
 
     depends_on('htslib')
     depends_on('boost')
diff --git a/var/spack/repos/builtin/packages/denovogear/package.py b/var/spack/repos/builtin/packages/denovogear/package.py
new file mode 100644
index 0000000000..cd7cd87813
--- /dev/null
+++ b/var/spack/repos/builtin/packages/denovogear/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Denovogear(CMakePackage):
+    """DeNovoGear is a software package to detect de novo mutations using
+    next-generation sequencing data. It supports the analysis of many
+    differential experimental designs and uses advanced statistical models
+    to reduce the false positve rate."""
+
+    homepage = "https://github.com/denovogear/denovogear"
+    url      = "https://github.com/denovogear/denovogear/archive/v1.1.1.tar.gz"
+
+    version('1.1.1', 'da30e46851c3a774653e57f98fe62e5f')
+    version('1.1.0', '7d441d56462efb7ff5d3a6f6bddfd8b9')
+
+    depends_on('cmake@3.1:', type=('build'))
+    depends_on('boost@1.47:1.60', type=('build'))
+    depends_on('htslib@1.2:', type=('build'))
+    depends_on('eigen', type=('build'))
diff --git a/var/spack/repos/builtin/packages/dftfe/package.py b/var/spack/repos/builtin/packages/dftfe/package.py
new file mode 100644
index 0000000000..bac67b1fbe
--- /dev/null
+++ b/var/spack/repos/builtin/packages/dftfe/package.py
@@ -0,0 +1,65 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+from spack import *
+
+
+class Dftfe(CMakePackage):
+    """Real-space DFT calculations using Finite Elements"""
+
+    homepage = "https://sites.google.com/umich.edu/dftfe/"
+    url      = "https://github.com/dftfeDevelopers/dftfe/archive/0.5.1.tar.gz"
+
+    maintainers = ['rmsds']
+
+    version('0.6.0', sha256='66b633a3aae2f557f241ee45b2faa41aa179e4a0bdf39c4ae2e679a2970845a1')
+    version('0.5.2', sha256='9dc4fa9f16b00be6fb1890d8af4a1cd3e4a2f06a2539df999671a09f3d26ec64')
+    version('0.5.1', sha256='e47272d3783cf675dcd8bc31da07765695164110bfebbbab29f5815531f148c1')
+    version('0.5.0', sha256='9aadb9a9b059f98f88c7756b417423dc67d02f1cdd2ed7472ba395fcfafc6dcb')
+
+    variant('scalapack', default=True, description='Use ScaLAPACK, strongly recommended for problem sizes >5000 electrons')
+    variant('build_type', default='Release',
+            description='The build type to build',
+            values=('Debug', 'Release'))
+
+    depends_on('mpi')
+    depends_on('dealii+p4est+petsc+slepc+int64+scalapack+mpi')
+    depends_on('dealii+p4est+petsc+slepc+int64+scalapack+mpi@9.0.0:', when='@0.5.1:')
+    depends_on('scalapack', when='+scalapack')
+    depends_on('alglib')
+    depends_on('libxc')
+    depends_on('spglib')
+    depends_on('libxml2')
+
+    def cmake_args(self):
+        spec = self.spec
+        args = [
+            '-DCMAKE_C_COMPILER={0}'.format(spec['mpi'].mpicc),
+            '-DCMAKE_CXX_COMPILER={0}'.format(spec['mpi'].mpicxx),
+            '-DALGLIB_DIR={0}'.format(spec['alglib'].prefix),
+            '-DLIBXC_DIR={0}'.format(spec['libxc'].prefix),
+            '-DXML_LIB_DIR={0}/lib'.format(spec['libxml2'].prefix),
+            '-DXML_INCLUDE_DIR={0}/include'.format(spec['libxml2'].prefix),
+            '-DSPGLIB_DIR={0}'.format(spec['spglib'].prefix),
+        ]
+
+        if spec.satisfies('^intel-mkl'):
+            args.append('-DWITH_INTEL_MKL=ON')
+        else:
+            args.append('-DWITH_INTEL_MKL=OFF')
+
+        if spec.satisfies('%gcc'):
+            args.append('-DCMAKE_C_FLAGS=-fpermissive')
+            args.append('-DCMAKE_CXX_FLAGS=-fpermissive')
+
+        return args
+
+    @when('@:0.5.2')
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        mkdirp(prefix.lib64)
+        install(join_path(self.build_directory, 'main'),
+                join_path(prefix.bin, 'dftfe'))
+        install(join_path(self.build_directory, 'libdftfe.so'),
+                prefix.lib64)
diff --git a/var/spack/repos/builtin/packages/dia/package.py b/var/spack/repos/builtin/packages/dia/package.py
index 59abc88b15..b0459d5faa 100644
--- a/var/spack/repos/builtin/packages/dia/package.py
+++ b/var/spack/repos/builtin/packages/dia/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,7 +14,9 @@ class Dia(Package):
     version('0.97.3',    '0e744a0f6a6c4cb6a089e4d955392c3c')
 
     depends_on('intltool', type='build')
-    depends_on('gtkplus@2.6.0:+X')
+    depends_on('gettext', type='build')
+    depends_on('pkgconfig', type='build')
+    depends_on('gtkplus@2.6.0:')
     depends_on('libxslt')
     depends_on('python')
     depends_on('swig')
diff --git a/var/spack/repos/builtin/packages/dialign-tx/package.py b/var/spack/repos/builtin/packages/dialign-tx/package.py
index 009793216f..a5daf8f088 100644
--- a/var/spack/repos/builtin/packages/dialign-tx/package.py
+++ b/var/spack/repos/builtin/packages/dialign-tx/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/diamond/package.py b/var/spack/repos/builtin/packages/diamond/package.py
new file mode 100644
index 0000000000..bf51e174ea
--- /dev/null
+++ b/var/spack/repos/builtin/packages/diamond/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Diamond(CMakePackage):
+    """DIAMOND is a sequence aligner for protein and translated DNA searches,
+    designed for high performance analysis of big sequence data."""
+
+    homepage = "https://ab.inf.uni-tuebingen.de/software/diamond"
+    url      = "https://github.com/bbuchfink/diamond/archive/v0.9.14.tar.gz"
+
+    version('0.9.21', '6f3c53520f3dad37dfa3183d61f21dd5')
+    version('0.9.20', 'd73f4955909d16456d83b30d9c294b2b')
+    version('0.9.19', '8565d2d3bfe407ee778eeabe7c6a7fde')
+    version('0.9.14', 'b9e1d0bc57f07afa05dbfbb53c31aae2')
+    version('0.8.38', 'd4719c8a7947ba9f743446ac95cfe644')
+    version('0.8.26', '0d86305ab25cc9b3bb3564188d30fff2')
+
+    depends_on('zlib')
diff --git a/var/spack/repos/builtin/packages/diffsplice/package.py b/var/spack/repos/builtin/packages/diffsplice/package.py
new file mode 100644
index 0000000000..fa6c4f2907
--- /dev/null
+++ b/var/spack/repos/builtin/packages/diffsplice/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Diffsplice(MakefilePackage):
+    """A novel tool for discovering and quantitating alternative splicing
+    variants present in an RNA-seq dataset, without relying on annotated
+    transcriptome or pre-determined splice pattern."""
+
+    homepage = "http://www.netlab.uky.edu/p/bioinfo/DiffSplice"
+    url      = "http://protocols.netlab.uky.edu/~yin/download/diffsplice/diffsplice_0.1.1.tgz"
+
+    version('0.1.2beta', 'a1df6e0b50968f2c229d5d7f97327336')
+    version('0.1.1',     'be90e6c072402d5aae0b4e2cbb8c10ac')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('diffsplice', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/diffutils/package.py b/var/spack/repos/builtin/packages/diffutils/package.py
new file mode 100644
index 0000000000..b37ca50e15
--- /dev/null
+++ b/var/spack/repos/builtin/packages/diffutils/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Diffutils(AutotoolsPackage):
+    """GNU Diffutils is a package of several programs related to finding
+    differences between files."""
+
+    homepage = "https://www.gnu.org/software/diffutils/"
+    url      = "https://ftp.gnu.org/gnu/diffutils/diffutils-3.6.tar.xz"
+
+    version('3.6', sha256='d621e8bdd4b573918c8145f7ae61817d1be9deb4c8d2328a65cea8e11d783bd6')
+
+    build_directory = 'spack-build'
diff --git a/var/spack/repos/builtin/packages/direnv/package.py b/var/spack/repos/builtin/packages/direnv/package.py
index 83ec1db935..82272e472d 100644
--- a/var/spack/repos/builtin/packages/direnv/package.py
+++ b/var/spack/repos/builtin/packages/direnv/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/discovar/package.py b/var/spack/repos/builtin/packages/discovar/package.py
index e0521d3e95..48e3509a17 100644
--- a/var/spack/repos/builtin/packages/discovar/package.py
+++ b/var/spack/repos/builtin/packages/discovar/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/discovardenovo/package.py b/var/spack/repos/builtin/packages/discovardenovo/package.py
new file mode 100644
index 0000000000..e3c86e314e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/discovardenovo/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Discovardenovo(AutotoolsPackage):
+    """DISCOVAR de novo is a large (and small) de novo genome assembler.
+       It quickly generates highly accurate and complete assemblies using the
+       same single library data as used by DISCOVAR. It currently doesn't
+       support variant calling, for that, please use DISCOVAR instead."""
+
+    homepage = "https://software.broadinstitute.org/software/discovar/blog/"
+    url      = "ftp://ftp.broadinstitute.org/pub/crd/DiscovarDeNovo/latest_source_code/discovardenovo-52488.tar.gz"
+
+    version('52488', '2b08c77b1b998d85be8048e5efb10358')
+
+    # lots of compiler errors with GCC7, works with 4.8.5
+    # and devs claim it works with 4.7 so I'm assuming 4.7-4.8'll work
+    conflicts('%gcc@5:')
+    conflicts('%gcc@:4.7.0')
+
+    depends_on('samtools')
+    depends_on('jemalloc')
diff --git a/var/spack/repos/builtin/packages/dislin/package.py b/var/spack/repos/builtin/packages/dislin/package.py
new file mode 100644
index 0000000000..ebf82b6394
--- /dev/null
+++ b/var/spack/repos/builtin/packages/dislin/package.py
@@ -0,0 +1,57 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Dislin(Package):
+    """DISLIN is a high level and easy to use graphics library for displaying
+       data as curves,  bar graphs,  pie charts,  3D-colour plots,  surfaces,
+       contours and maps."""
+
+    homepage = "http://www.mps.mpg.de/dislin"
+    url      = "ftp://ftp.gwdg.de/pub/grafik/dislin/linux/i586_64/dislin-11.0.linux.i586_64.tar.gz"
+
+    version('11.1.linux.i586_64', '34218c257efedaf706f058bdf111ce9d')
+    version('11.0.linux.i586_64', '6fb099b54f41db009cafc702eebb5bc6')
+
+    depends_on('motif')
+    depends_on('mesa')
+
+    @property
+    def libs(self):
+        query_parameters = self.spec.last_query.extra_parameters
+        query2libraries = {
+            tuple(): ['libdislin'],
+            ('d',): ['libdislin_d'],
+            ('c', ): ['libdislnc'],
+            ('cd',): ['libdislnc_d'],
+            ('cxx',): ['libdiscpp'],
+            ('java',): ['libdisjava']
+        }
+
+        key = tuple(query_parameters)
+        libraries = query2libraries[key]
+
+        return find_libraries(
+            libraries, root=self.prefix, shared=True, recursive=True
+        )
+
+    def setup_environment(self, spack_env, run_env):
+        spack_env.set('DISLIN', self.prefix)
+        run_env.set('DISLIN', self.prefix)
+        run_env.prepend_path('PATH', self.prefix)
+        run_env.prepend_path('LD_LIBRARY_PATH', self.prefix)
+        run_env.prepend_path('LD_LIBRARY_PATH', self.spec['motif'].prefix.lib)
+        run_env.prepend_path('LD_LIBRARY_PATH', self.spec['mesa'].prefix.lib)
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        run_env.prepend_path('LD_LIBRARY_PATH', self.prefix)
+
+    def install(self, spec, prefix):
+        install = Executable('./INSTALL')
+        install()
+        with working_dir('examples'):
+            install('dislin_d.h', prefix)
diff --git a/var/spack/repos/builtin/packages/diy/package.py b/var/spack/repos/builtin/packages/diy/package.py
new file mode 100644
index 0000000000..c05419682c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/diy/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Diy(CMakePackage):
+    """Data-parallel out-of-core library"""
+
+    homepage = "https://github.com/diatomic/diy"
+    url      = "https://github.com/diatomic/diy/archive/3.5.0.tar.gz"
+    git      = "https://github.com/diatomic/diy.git"
+
+    version('3.5.0', sha256='b3b5490441d521b6e9b33471c782948194bf95c7c3df3eb97bc5cf4530b91576')
+    version('master', branch='master')
+
+    def cmake_args(self):
+        args = ['-Dbuild_examples=off', '-Dbuild_tests=off']
+        return args
diff --git a/var/spack/repos/builtin/packages/dlpack/package.py b/var/spack/repos/builtin/packages/dlpack/package.py
index 69dd99b5a0..80db27a27b 100644
--- a/var/spack/repos/builtin/packages/dlpack/package.py
+++ b/var/spack/repos/builtin/packages/dlpack/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,8 +11,9 @@ class Dlpack(Package):
     in deep learning systems."""
 
     homepage = "https://github.com/sjtuhpcc/dlpack"
+    git      = "https://github.com/dmlc/dlpack.git"
 
-    version('master', git='https://github.com/dmlc/dlpack.git', branch='master')
+    version('master', branch='master')
 
     def install(self, spec, prefix):
         install_tree('include', prefix.include)
diff --git a/var/spack/repos/builtin/packages/dmd/package.py b/var/spack/repos/builtin/packages/dmd/package.py
new file mode 100644
index 0000000000..a84d65987b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/dmd/package.py
@@ -0,0 +1,77 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class Dmd(MakefilePackage):
+    """DMD is the reference compiler for the D programming language."""
+
+    homepage = "https://github.com/dlang/dmd"
+    url      = "https://github.com/dlang/dmd/archive/v2.081.1.tar.gz"
+
+    version('2.081.1', sha256='14f3aafe1c93c86646aaeb3ed7361a5fc5a24374cf25c8848c81942bfd9fae1a')
+
+    depends_on('openssl')
+    depends_on('curl')
+
+    # https://wiki.dlang.org/Building_under_Posix
+    resource(name='druntime',
+             url='https://github.com/dlang/druntime/archive/v2.081.1.tar.gz',
+             md5='49c8ba48fcb1e53d553a52d8ed7f9164',
+             placement='druntime')
+    resource(name='phobos',
+             url='https://github.com/dlang/phobos/archive/v2.081.1.tar.gz',
+             md5='ccf4787275b490eb2ddfc6713f9e9882',
+             placement='phobos')
+    resource(name='tools',
+             url='https://github.com/dlang/tools/archive/v2.081.1.tar.gz',
+             md5='a3bc7ed3d60b39712ef011bf19b3d427',
+             placement='tools')
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PATH', self.prefix.linux.bin64)
+        run_env.prepend_path('LIBRARY_PATH', self.prefix.linux.lib64)
+        run_env.prepend_path('LD_LIBRARY_PATH', self.prefix.linux.lib64)
+
+    def edit(self, spec, prefix):
+        # Move contents to dmd/
+        mkdir = which('mkdir')
+        mkdir('dmd')
+        mv = which('mv')
+        dmd_files = [f for f in os.listdir('.')
+                     if not f.startswith(('dmd',
+                                          'druntime',
+                                          'phobos',
+                                          'tools',
+                                          'spack-build'))]
+        for f in dmd_files:
+            mv(f, 'dmd')
+        # Edit
+        dmd_mak = FileFilter('dmd/posix.mak')
+        dmd_mak.filter('$(PWD)/../install', prefix, string=True)
+        dr_mak = FileFilter('druntime/posix.mak')
+        dr_mak.filter('INSTALL_DIR=.*', 'INSTALL_DIR={0}'.format(prefix))
+        pb_mak = FileFilter('phobos/posix.mak')
+        pb_mak.filter('INSTALL_DIR = .*', 'INSTALL_DIR = {0}'.format(prefix))
+        tl_mak = FileFilter('tools/posix.mak')
+        tl_mak.filter('INSTALL_DIR = .*', 'INSTALL_DIR = {0}'.format(prefix))
+
+    def build(self, spec, prefix):
+        with working_dir('dmd'):
+            make('-f', 'posix.mak', 'AUTO_BOOTSTRAP=1')
+        with working_dir('phobos'):
+            make('-f', 'posix.mak')
+
+    def install(self, spec, prefix):
+        with working_dir('dmd'):
+            make('-f', 'posix.mak', 'install', 'AUTO_BOOTSTRAP=1')
+        with working_dir('phobos'):
+            make('-f', 'posix.mak', 'install')
+        with working_dir('tools'):
+            make('-f', 'posix.mak', 'install')
+        with working_dir('druntime'):
+            make('-f', 'posix.mak', 'install')
diff --git a/var/spack/repos/builtin/packages/dmlc-core/package.py b/var/spack/repos/builtin/packages/dmlc-core/package.py
index f463acb836..93da95f932 100644
--- a/var/spack/repos/builtin/packages/dmlc-core/package.py
+++ b/var/spack/repos/builtin/packages/dmlc-core/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,11 +12,10 @@ class DmlcCore(CMakePackage):
     distributed machine learning libraries."""
 
     homepage = "https://github.com/dmlc/dmlc-core"
-    url      = "https://github.com/dmlc/dmlc-core.git"
+    git      = "https://github.com/dmlc/dmlc-core.git"
 
-    version('master', git='https://github.com/dmlc/dmlc-core.git')
-    version('20170508', git='https://github.com/dmlc/dmlc-core.git',
-    commit='a6c5701219e635fea808d264aefc5b03c3aec314')
+    version('master')
+    version('20170508', commit='a6c5701219e635fea808d264aefc5b03c3aec314')
 
     variant('openmp', default=False, description='Enable OpenMP support')
 
diff --git a/var/spack/repos/builtin/packages/dmtcp/package.py b/var/spack/repos/builtin/packages/dmtcp/package.py
new file mode 100644
index 0000000000..41665ef3f4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/dmtcp/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Dmtcp(AutotoolsPackage):
+    """DMTCP (Distributed MultiThreaded Checkpointing) transparently
+    checkpoints a single-host or distributed computation in user-space --
+    with no modifications to user code or to the O/S."""
+
+    homepage = "http://dmtcp.sourceforge.net/"
+    url      = "https://sourceforge.net/projects/dmtcp/files/2.5.2/dmtcp-2.5.2.tar.gz/download"
+
+    version('2.5.2', sha256='0e3e5e15bd401b7b6937f2b678cd7d6a252eab0a143d5740b89cc3bebb4282be')
diff --git a/var/spack/repos/builtin/packages/dmxproto/package.py b/var/spack/repos/builtin/packages/dmxproto/package.py
index b668dc9b58..ee1eb91be6 100644
--- a/var/spack/repos/builtin/packages/dmxproto/package.py
+++ b/var/spack/repos/builtin/packages/dmxproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Dmxproto(AutotoolsPackage):
 
     version('2.3.1', '7c52af95aac192e8de31bd9a588ce121')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/docbook-xml/package.py b/var/spack/repos/builtin/packages/docbook-xml/package.py
index c91473a669..62f87a6ae1 100644
--- a/var/spack/repos/builtin/packages/docbook-xml/package.py
+++ b/var/spack/repos/builtin/packages/docbook-xml/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/docbook-xsl/package.py b/var/spack/repos/builtin/packages/docbook-xsl/package.py
index 1f3d774b82..1cd1c3ae3d 100644
--- a/var/spack/repos/builtin/packages/docbook-xsl/package.py
+++ b/var/spack/repos/builtin/packages/docbook-xsl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/dos2unix/package.py b/var/spack/repos/builtin/packages/dos2unix/package.py
index 2457f9b9e6..c73f53614f 100644
--- a/var/spack/repos/builtin/packages/dos2unix/package.py
+++ b/var/spack/repos/builtin/packages/dos2unix/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/dotnet-core-sdk/package.py b/var/spack/repos/builtin/packages/dotnet-core-sdk/package.py
new file mode 100644
index 0000000000..8b1f1ad9b6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/dotnet-core-sdk/package.py
@@ -0,0 +1,34 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from os import symlink
+from spack import *
+
+
+class DotnetCoreSdk(Package):
+    """The .NET Core SDK is a powerful development environment to write
+    applications for all types of infrastructure."""
+
+    homepage = "https://www.microsoft.com/net/"
+    url      = "https://github.com/dotnet/core/"
+
+    version('2.1.300',
+            url='https://download.microsoft.com/download/8/8/5/88544F33-836A'
+                '-49A5-8B67-451C24709A8F/dotnet-sdk-2.1.300-linux-x64.tar.gz',
+            sha224='80a6bfb1db5862804e90f819c1adeebe3d624eae0d6147e5d6694333'
+                'f0458afd7d34ce73623964752971495a310ff7fcc266030ce5aef82d5de'
+                '7293d94d13770')
+
+    variant('telemetry', default=False,
+            description='allow collection of telemetry data')
+
+    def setup_environment(self, spack_env, run_env):
+        if '-telemetry' in self.spec:
+            spack_env.set('DOTNET_CLI_TELEMETRY_OPTOUT', 1)
+
+    def install(self, spec, prefix):
+        mkdirp('bin')
+        symlink('../dotnet', 'bin/dotnet')
+        install_tree(".", prefix)
diff --git a/var/spack/repos/builtin/packages/double-conversion/package.py b/var/spack/repos/builtin/packages/double-conversion/package.py
index e4f4803a24..ca132f8b03 100644
--- a/var/spack/repos/builtin/packages/double-conversion/package.py
+++ b/var/spack/repos/builtin/packages/double-conversion/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/doxygen/package.py b/var/spack/repos/builtin/packages/doxygen/package.py
index 61cfdf8a89..3fa767f50d 100644
--- a/var/spack/repos/builtin/packages/doxygen/package.py
+++ b/var/spack/repos/builtin/packages/doxygen/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,6 +16,7 @@ class Doxygen(CMakePackage):
     homepage = "http://www.stack.nl/~dimitri/doxygen/"
     url      = "http://ftp.stack.nl/pub/users/dimitri/doxygen-1.8.10.src.tar.gz"
 
+    version('1.8.14', '41d8821133e8d8104280030553e2b42b')
     version('1.8.12', '08e0f7850c4d22cb5188da226b209a96')
     version('1.8.11', 'f4697a444feaed739cfa2f0644abc19b')
     version('1.8.10', '79767ccd986f12a0f949015efb5f058f')
@@ -49,3 +31,8 @@ class Doxygen(CMakePackage):
 
     # optional dependencies
     depends_on("graphviz", when="+graphviz", type='run')
+
+    # Support C++14's std::shared_ptr. For details about this patch, see
+    # https://github.com/Sleepyowl/doxygen/commit/6c380ba91ae41c6d5c409a5163119318932ae2a3?diff=unified
+    # Also - https://github.com/doxygen/doxygen/pull/6588
+    patch('shared_ptr.patch', when='@1.8.14')
diff --git a/var/spack/repos/builtin/packages/doxygen/shared_ptr.patch b/var/spack/repos/builtin/packages/doxygen/shared_ptr.patch
new file mode 100644
index 0000000000..87581b5152
--- /dev/null
+++ b/var/spack/repos/builtin/packages/doxygen/shared_ptr.patch
@@ -0,0 +1,26 @@
+diff --git a/src/doxygen.cpp b/src/doxygen.cpp
+index 00826d6..a474129 100644
+--- a/src/doxygen.cpp
++++ b/src/doxygen.cpp
+@@ -342,6 +342,7 @@ static STLInfo g_stlinfo[] =
+   { "auto_ptr",             0,                              0,                     "T",           "ptr",         0,            0,             FALSE,              FALSE }, // deprecated
+   { "smart_ptr",            0,                              0,                     "T",           "ptr",         0,            0,             FALSE,              FALSE }, // C++11
+   { "unique_ptr",           0,                              0,                     "T",           "ptr",         0,            0,             FALSE,              FALSE }, // C++11
++  { "shared_ptr",           0,                              0,                     "T",           "ptr",         0,            0,             FALSE,              FALSE }, // C++14
+   { "weak_ptr",             0,                              0,                     "T",           "ptr",         0,            0,             FALSE,              FALSE }, // C++11
+   { "ios_base",             0,                              0,                     0,             0,             0,            0,             FALSE,              FALSE }, // C++11
+   { "error_code",           0,                              0,                     0,             0,             0,            0,             FALSE,              FALSE }, // C++11
+@@ -515,7 +516,7 @@ static void addSTLClasses(EntryNav *rootNav)
+     {
+       addSTLMember(classEntryNav,info->templType2,info->templName2);
+     }
+-    if (fullName=="std::auto_ptr" || fullName=="std::smart_ptr" ||
++    if (fullName=="std::auto_ptr" || fullName=="std::smart_ptr" || fullName=="std::shared_ptr" ||
+         fullName=="std::unique_ptr" || fullName=="std::weak_ptr")
+     {
+       Entry *memEntry = new Entry;
+@@ -11770,4 +11771,3 @@ void generateOutput()
+   delete Doxygen::symbolStorage;
+   g_successfulRun=TRUE;
+ }
+-
diff --git a/var/spack/repos/builtin/packages/dri2proto/package.py b/var/spack/repos/builtin/packages/dri2proto/package.py
index 00c4cc812d..86ee95a00f 100644
--- a/var/spack/repos/builtin/packages/dri2proto/package.py
+++ b/var/spack/repos/builtin/packages/dri2proto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Dri2proto(AutotoolsPackage):
 
     version('2.8', '19ea18f63d8ae8053c9fa84b60365b77')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/dri3proto/package.py b/var/spack/repos/builtin/packages/dri3proto/package.py
index 5f4604789d..6568e10f71 100644
--- a/var/spack/repos/builtin/packages/dri3proto/package.py
+++ b/var/spack/repos/builtin/packages/dri3proto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Dri3proto(AutotoolsPackage):
 
     version('1.0', '25e84a49a076862277ee12aebd49ff5f')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/dsdp/malloc.patch b/var/spack/repos/builtin/packages/dsdp/malloc.patch
new file mode 100644
index 0000000000..54b92628be
--- /dev/null
+++ b/var/spack/repos/builtin/packages/dsdp/malloc.patch
@@ -0,0 +1,16 @@
+malloc.h does not exist on macOS. The same functionality is
+already provided by stdlib.h, so there's no need for it.
+Patch stolen from:
+https://github.com/sjackman/homebrew-science-deprecated/blob/master/dsdp.rb
+
+diff --git a/src/sys/dsdploginfo.c b/src/sys/dsdploginfo.c
+index 9313549..cee4f93 100644
+--- a/src/sys/dsdploginfo.c
++++ b/src/sys/dsdploginfo.c
+@@ -6,7 +6,6 @@
+ #include <stdarg.h>
+ #include <sys/types.h>
+ #include <stdlib.h>
+-#include <malloc.h>
+ #include "dsdpsys.h"
+ #include "dsdpbasictypes.h"
diff --git a/var/spack/repos/builtin/packages/dsdp/package.py b/var/spack/repos/builtin/packages/dsdp/package.py
new file mode 100644
index 0000000000..d10325c664
--- /dev/null
+++ b/var/spack/repos/builtin/packages/dsdp/package.py
@@ -0,0 +1,52 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class Dsdp(MakefilePackage):
+    """The DSDP software is a free open source implementation of an
+    interior-point method for semidefinite programming. It provides primal and
+    dual solutions, exploits low-rank structure and sparsity in the data, and
+    has relatively low memory requirements for an interior-point method. It
+    allows feasible and infeasible starting points and provides approximate
+    certificates of infeasibility when no feasible solution exists."""
+
+    homepage = "http://www.mcs.anl.gov/hs/software/DSDP/"
+    url      = "http://www.mcs.anl.gov/hs/software/DSDP/DSDP5.8.tar.gz"
+
+    version('5.8', '37c15a3c6c3f13e31262f65ac4364b5e')
+
+    depends_on('blas')
+    depends_on('lapack')
+
+    patch('malloc.patch')
+
+    build_targets = ['dsdpapi']
+
+    def edit(self, spec, prefix):
+        make_include = FileFilter('make.include')
+
+        # STEP 1: Set DSDPROOT.
+        make_include.filter('^#DSDPROOT.*=.*',
+                            'DSDPROOT = {0}'.format(os.getcwd()))
+
+        # STEP 2: Set the name of the C compiler.
+        make_include.filter('^CC.*=.*', 'CC = {0}'.format(spack_cc))
+
+        # STEP 5:
+        # Location of BLAS AND LAPACK libraries.
+        # Also include the math library and other libraries needed to
+        # link the BLAS to the C files that call them.
+        lapackblas = spec['lapack'].libs + spec['blas'].libs
+        make_include.filter('^LAPACKBLAS.*=.*',
+                            'LAPACKBLAS = {0}'.format(
+                                lapackblas.link_flags + ' -lm'))
+
+    def install(self, spec, prefix):
+        # Manual installation
+        install_tree('lib', prefix.lib)
+        install_tree('include', prefix.include)
diff --git a/var/spack/repos/builtin/packages/dsrc/package.py b/var/spack/repos/builtin/packages/dsrc/package.py
new file mode 100644
index 0000000000..9846bc2b34
--- /dev/null
+++ b/var/spack/repos/builtin/packages/dsrc/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Dsrc(MakefilePackage):
+    """DNA Sequence Reads Compression is an application designed for
+    compression of data files containing reads from DNA sequencing in
+    FASTQ format."""
+
+    homepage = "http://sun.aei.polsl.pl/dsrc"
+    url      = "https://github.com/refresh-bio/DSRC/archive/v2.0.2.tar.gz"
+
+    version('2.0.2', '0a75deb6db948f9179df0756c259b870')
+
+    parallel = False
+
+    def install(self, spec, prefix):
+        install_tree('bin', prefix.bin)
+        install_tree('lib', prefix.lib)
+        install_tree('include', prefix.include)
+        install_tree('examples', prefix.examples)
diff --git a/var/spack/repos/builtin/packages/dtcmp/package.py b/var/spack/repos/builtin/packages/dtcmp/package.py
index c64fa540fa..2b93cf1ce2 100644
--- a/var/spack/repos/builtin/packages/dtcmp/package.py
+++ b/var/spack/repos/builtin/packages/dtcmp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/dyninst/package.py b/var/spack/repos/builtin/packages/dyninst/package.py
index 8a18b99940..9d9ab52669 100644
--- a/var/spack/repos/builtin/packages/dyninst/package.py
+++ b/var/spack/repos/builtin/packages/dyninst/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,29 +11,38 @@ class Dyninst(Package):
     are executing without recompiling, re-linking, or re-executing."""
 
     homepage = "https://paradyn.org"
-    url = "https://github.com/dyninst/dyninst/archive/v9.2.0.tar.gz"
-    list_url = "http://www.dyninst.org/downloads/dyninst-8.x"
+    git      = "https://github.com/dyninst/dyninst.git"
 
-    version('9.3.2', 'a2bf03b6d1d424853e80d39b13e9c229')
-    version('9.3.0', 'edde7847dc673ca69bd59412af572450')
-    version('9.2.0', 'ad023f85e8e57837ed9de073b59d6bab',
-            url="https://github.com/dyninst/dyninst/archive/v9.2.0.tar.gz")
-    version('9.1.0', '5c64b77521457199db44bec82e4988ac',
-            url="http://www.paradyn.org/release9.1.0/DyninstAPI-9.1.0.tgz")
-    version('8.2.1', 'abf60b7faabe7a2e4b54395757be39c7',
-            url="http://www.paradyn.org/release8.2/DyninstAPI-8.2.1.tgz")
-    version('8.1.2', 'bf03b33375afa66fe0efa46ce3f4b17a',
-            url="http://www.paradyn.org/release8.1.2/DyninstAPI-8.1.2.tgz")
-    version('8.1.1', 'd1a04e995b7aa70960cd1d1fac8bd6ac',
-            url="http://www.paradyn.org/release8.1/DyninstAPI-8.1.1.tgz")
+    version('develop', branch='master')
+    version('10.0.0', tag='v10.0.0')
+    version('9.3.2', tag='v9.3.2')
+    version('9.3.0', tag='v9.3.0')
+    version('9.2.0', tag='v9.2.0')
+    version('9.1.0', tag='v9.1.0')
+    version('8.2.1', tag='v8.2.1')
+    version('8.1.2', tag='v8.1.2')
+    version('8.1.1', tag='v8.1.1')
 
     variant('stat_dysect', default=False,
             description="patch for STAT's DySectAPI")
 
+    # Dyninst depends on libelf and libdwarf prior to @9.3.0
+    # Dyninst depends on elfutils and libdwarf from @9.3.0 to but
+    # not including @develop
+    # Dyninst depends on elfutils and elfutils libdw from @develop forward
+    # elf@0 is an abstaction for libelf
+    # elf@1 is an abstaction for elfutils
     depends_on("elf@0", type='link', when='@:9.2.99')
+    # The sorting algorithm puts numbered releases as newer than alphabetic
+    # releases, but spack has special logic in place to ensure that
+    # develop is considered newer than all other releases.
+    # So, develop is included in the elf@1 line below.
     depends_on("elf@1", type='link', when='@9.3.0:')
-    depends_on("libdwarf")
+    depends_on("libdwarf", when='@:9')
     depends_on("boost@1.42:")
+    depends_on('libiberty+pic')
+    depends_on("tbb@2018.6:", when='@develop')
+    depends_on("tbb@2018.6:", when='@10:')
     depends_on('cmake', type='build')
 
     patch('stat_dysect.patch', when='+stat_dysect')
@@ -67,7 +57,8 @@ class Dyninst(Package):
             return
 
         libelf = spec['elf'].prefix
-        libdwarf = spec['libdwarf'].prefix
+        if spec.satisfies('@:9'):
+            libdwarf = spec['libdwarf'].prefix
 
         with working_dir('spack-build', create=True):
             args = ['..',
@@ -77,10 +68,21 @@ class Dyninst(Package):
                     '-DLIBELF_INCLUDE_DIR=%s'   % join_path(
                         libelf.include, 'libelf'),
                     '-DLIBELF_LIBRARIES=%s'     % join_path(
-                        libelf.lib, 'libelf.so'),
-                    '-DLIBDWARF_INCLUDE_DIR=%s' % libdwarf.include,
-                    '-DLIBDWARF_LIBRARIES=%s'   % join_path(
-                        libdwarf.lib, 'libdwarf.so')]
+                        libelf.lib, "libelf." + dso_suffix)]
+            if spec.satisfies('@:9'):
+                args.append('-DLIBDWARF_INCLUDE_DIR=%s' % libdwarf.include)
+                args.append('-DLIBDWARF_LIBRARIES=%s'   % join_path(
+                    libdwarf.lib, "libdwarf." + dso_suffix))
+            # For @develop + use elfutils libdw, libelf is an abstraction
+            # we are really using elfutils here
+            if spec.satisfies('@develop') or spec.satisfies('@10:'):
+                tbb = spec['tbb'].prefix
+                args.append('-DTBB_INCLUDE_DIRS=%s' % tbb.include)
+                args.append('-DTBB_LIBRARIES=%s'    % join_path(
+                    tbb.lib, "libtbb." + dso_suffix))
+                args.append('-DLIBDWARF_INCLUDE_DIR=%s' % libelf.include)
+                args.append('-DLIBDWARF_LIBRARIES=%s'   % join_path(
+                    libelf.lib, "libdw." + dso_suffix))
             if spec.satisfies('arch=linux-redhat7-ppc64le'):
                 args.append('-Darch_ppc64_little_endian=1')
             args += std_cmake_args
diff --git a/var/spack/repos/builtin/packages/ea-utils/package.py b/var/spack/repos/builtin/packages/ea-utils/package.py
index 181248a401..acbdd641ef 100644
--- a/var/spack/repos/builtin/packages/ea-utils/package.py
+++ b/var/spack/repos/builtin/packages/ea-utils/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/easybuild/package.py b/var/spack/repos/builtin/packages/easybuild/package.py
index 4fa7eb99fb..333e308bb8 100644
--- a/var/spack/repos/builtin/packages/easybuild/package.py
+++ b/var/spack/repos/builtin/packages/easybuild/package.py
@@ -1,25 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Kenneth Hoste
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Kenneth Hoste, kenneth.hoste@gmail.com
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/ebms/package.py b/var/spack/repos/builtin/packages/ebms/package.py
index 252be1bd3d..3bef478c94 100644
--- a/var/spack/repos/builtin/packages/ebms/package.py
+++ b/var/spack/repos/builtin/packages/ebms/package.py
@@ -1,27 +1,8 @@
-#############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -37,13 +18,13 @@ class Ebms(MakefilePackage):
     """
 
     homepage = "https://github.com/ANL-CESAR/EBMS"
-    url = "https://github.com/ANL-CESAR/EBMS/archive/master.tar.gz"
+    git      = "https://github.com/ANL-CESAR/EBMS.git"
 
-    version('develop', git='https://github.com/ANL-CESAR/EBMS.git')
+    version('develop')
 
     variant('mpi', default=True, description='Build with MPI support')
 
-    depends_on('mpi', when='+mpi')
+    depends_on('mpi@2:', when='+mpi')
 
     tags = ['proxy-app']
 
diff --git a/var/spack/repos/builtin/packages/eccodes/cmake_install_rpath.patch b/var/spack/repos/builtin/packages/eccodes/cmake_install_rpath.patch
new file mode 100644
index 0000000000..7e2b250883
--- /dev/null
+++ b/var/spack/repos/builtin/packages/eccodes/cmake_install_rpath.patch
@@ -0,0 +1,11 @@
+--- a/cmake/ecbuild_append_to_rpath.cmake
++++ b/cmake/ecbuild_append_to_rpath.cmake
+@@ -31,7 +31,7 @@ function( _path_append var path )
+ 	else()
+ 		list( FIND ${var} ${path} _found )
+ 		if( _found EQUAL "-1" )
+-			set( ${var} "${${var}}:${path}" PARENT_SCOPE )
++			set( ${var} "${${var}};${path}" PARENT_SCOPE )
+ 		endif()
+ 	endif()
+ endfunction()
diff --git a/var/spack/repos/builtin/packages/eccodes/enable_only_jasper.patch b/var/spack/repos/builtin/packages/eccodes/enable_only_jasper.patch
index 9f7dc22ac5..ad09c75199 100644
--- a/var/spack/repos/builtin/packages/eccodes/enable_only_jasper.patch
+++ b/var/spack/repos/builtin/packages/eccodes/enable_only_jasper.patch
@@ -1,17 +1,25 @@
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index bf4d78b..ea2f3e9 100644
 --- a/CMakeLists.txt
 +++ b/CMakeLists.txt
-@@ -162,8 +162,6 @@ if( ENABLE_JPG )
-     set(CMAKE_PREFIX_PATH ${_CMAKE_PREFIX_PATH})    # Restore CMAKE_PREFIX_PATH
-     set(CMAKE_WARN_DEPRECATED ON)  # Remove suppression
+@@ -151,18 +151,7 @@ set( HAVE_LIBOPENJPEG 0 )
  
--    find_package( OpenJPEG )
+ if( ENABLE_JPG )
+ 
+-    # Note: This is a deprecated feature but we need it to find Jasper at ECMWF.
+-    #       ecbuild_add_extra_search_paths modifies CMAKE_PREFIX_PATH
+-    #       which can affect future package discovery if not undone by the caller.
+-    #       The current CMAKE_PREFIX_PATH is backed up as _CMAKE_PREFIX_PATH
+-    #
+-    set(CMAKE_WARN_DEPRECATED OFF) # Suppress deprecation message
+-    ecbuild_add_extra_search_paths( jasper )
+     find_package( Jasper )
+-    set(CMAKE_PREFIX_PATH ${_CMAKE_PREFIX_PATH})    # Restore CMAKE_PREFIX_PATH
+-    set(CMAKE_WARN_DEPRECATED ON)  # Remove suppression
 -
+-    find_package( OpenJPEG )
+ 
      if( JASPER_FOUND )
          list( APPEND ECCODES_TPLS Jasper )
-         set( HAVE_JPEG 1 )
-@@ -172,12 +170,6 @@ if( ENABLE_JPG )
+@@ -172,12 +161,6 @@ if( ENABLE_JPG )
          string(REGEX REPLACE "^([0-9]+)\\.[0-9]+\\.[0-9]+.*" "\\1" JASPER_VERSION_MAJOR "${JASPER_VERSION_STRING}")
      endif()
  
diff --git a/var/spack/repos/builtin/packages/eccodes/enable_only_openjpeg.patch b/var/spack/repos/builtin/packages/eccodes/enable_only_openjpeg.patch
index 7bf8b7b59f..29a6dff454 100644
--- a/var/spack/repos/builtin/packages/eccodes/enable_only_openjpeg.patch
+++ b/var/spack/repos/builtin/packages/eccodes/enable_only_openjpeg.patch
@@ -1,5 +1,3 @@
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index bf4d78b..3ae50ba 100644
 --- a/CMakeLists.txt
 +++ b/CMakeLists.txt
 @@ -151,27 +151,8 @@ set( HAVE_LIBOPENJPEG 0 )
diff --git a/var/spack/repos/builtin/packages/eccodes/package.py b/var/spack/repos/builtin/packages/eccodes/package.py
index 3843ce2ddc..55303d4ed2 100644
--- a/var/spack/repos/builtin/packages/eccodes/package.py
+++ b/var/spack/repos/builtin/packages/eccodes/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 from spack import *
 
@@ -30,9 +11,11 @@ class Eccodes(CMakePackage):
     """ecCodes is a package developed by ECMWF for processing meteorological
     data in GRIB (1/2), BUFR (3/4) and GTS header formats."""
 
-    homepage = "https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home"
-    url      = "https://software.ecmwf.int/wiki/download/attachments/45757960/eccodes-2.2.0-Source.tar.gz?api=v2"
-    list_url = "https://software.ecmwf.int/wiki/display/ECC/Releases"
+    homepage = 'https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home'
+    url = 'https://software.ecmwf.int/wiki/download/attachments/45757960/eccodes-2.2.0-Source.tar.gz?api=v2'
+    list_url = 'https://software.ecmwf.int/wiki/display/ECC/Releases'
+
+    maintainers = ['skosukhin']
 
     version('2.5.0', '5a7e92c58418d855082fa573efd352aa')
     version('2.2.0', 'b27e6f0a3eea5b92dac37372e4c45a62')
@@ -53,17 +36,28 @@ class Eccodes(CMakePackage):
             description='Enable memory based access to definitions/samples')
     variant('python', default=False,
             description='Enable the Python interface')
-    variant('fortran', default=True, description='Enable the Fortran support')
+    variant('fortran', default=False, description='Enable the Fortran support')
+    variant('examples', default=True,
+            description='Build the examples (part of the full test suite)')
+    variant('test', default=True, description='Enable the tests')
     variant('build_type', default='RelWithDebInfo',
             description='The build type to build',
             values=('Debug', 'Release', 'RelWithDebInfo', 'Production'))
 
+    # The building script tries to find an optional package valgrind when
+    # tests are enabled but the testing scripts don't use it.
+    # depends_on('valgrind', type='test', when='+test')
+
     depends_on('netcdf', when='+netcdf')
-    depends_on('openjpeg', when='jp2k=openjpeg')
+    depends_on('openjpeg@1.5.0:1.5.999,2.1.0:2.1.999', when='jp2k=openjpeg')
     depends_on('jasper', when='jp2k=jasper')
     depends_on('libpng', when='+png')
     depends_on('libaec', when='+aec')
-    depends_on('python@:2', when='+python')
+    # Can be built with Python2 or Python3.
+    depends_on('python', when='+memfs', type='build')
+    # The interface works only for Python2.
+    depends_on('python@2.6:2.999', when='+python',
+               type=('build', 'link', 'run'))
     depends_on('py-numpy', when='+python', type=('build', 'run'))
     extends('python', when='+python')
 
@@ -74,21 +68,62 @@ class Eccodes(CMakePackage):
     patch('enable_only_openjpeg.patch', when='jp2k=openjpeg')
     patch('enable_only_jasper.patch', when='jp2k=jasper')
 
+    # CMAKE_INSTALL_RPATH must be a semicolon-separated list.
+    patch('cmake_install_rpath.patch')
+
+    @run_before('cmake')
+    def check_fortran(self):
+        if '+fortran' in self.spec and self.compiler.fc is None:
+            raise InstallError(
+                'Fortran interface requires a Fortran compiler!')
+
     def cmake_args(self):
-        variants = ['+netcdf', '+png', '+aec', '+pthreads',
-                    '+openmp', '+memfs', '+python', '+fortran']
-        options = ['NETCDF', 'PNG', 'AEC', 'ECCODES_THREADS',
-                   'ECCODES_OMP_THREADS', 'MEMFS', 'PYTHON', 'FORTRAN']
+        var_opt_list = [('+pthreads', 'ECCODES_THREADS'),
+                        ('+openmp', 'ECCODES_OMP_THREADS'),
+                        ('+memfs', 'MEMFS'),
+                        ('+python', 'PYTHON'),
+                        ('+fortran', 'FORTRAN'),
+                        ('+examples', 'EXAMPLES'),
+                        ('+test', 'TESTS'),
+                        ('+test', 'EXTRA_TESTS')]
 
-        args = map(lambda var, opt:
-                   "-DENABLE_%s=%s" %
-                   (opt, 'ON' if var in self.spec else 'OFF'),
-                   variants,
-                   options)
+        args = ['-DENABLE_%s=%s' % (opt, 'ON' if var in self.spec else 'OFF')
+                for var, opt in var_opt_list]
+
+        if '+netcdf' in self.spec:
+            args.extend(['-DENABLE_NETCDF=ON',
+                         # Prevent overriding by environment variable
+                         # HDF5_ROOT.
+                         '-DHDF5_ROOT=' + self.spec['hdf5'].prefix,
+                         # Prevent possible overriding by environment variables
+                         # NETCDF_ROOT, NETCDF_DIR, and NETCDF_PATH.
+                         '-DNETCDF_PATH=' + self.spec['netcdf'].prefix])
+        else:
+            args.append('-DENABLE_NETCDF=OFF')
 
         if self.spec.variants['jp2k'].value == 'none':
             args.append('-DENABLE_JPG=OFF')
         else:
             args.append('-DENABLE_JPG=ON')
 
+        if self.spec.variants['jp2k'].value == 'openjpeg':
+            args.append('-DOPENJPEG_PATH=' + self.spec['openjpeg'].prefix)
+
+        if '+png' in self.spec:
+            args.extend(['-DENABLE_PNG=ON',
+                         '-DZLIB_ROOT=' + self.spec['zlib'].prefix])
+        else:
+            args.append('-DENABLE_PNG=OFF')
+
+        if '+aec' in self.spec:
+            args.extend(['-DENABLE_AEC=ON',
+                         # Prevent overriding by environment variables
+                         # AEC_DIR and AEC_PATH.
+                         '-DAEC_DIR=' + self.spec['libaec'].prefix])
+        else:
+            args.append('-DENABLE_AEC=OFF')
+
+        if '^python' in self.spec:
+            args.append('-DPYTHON_EXECUTABLE:FILEPATH=' + python.path)
+
         return args
diff --git a/var/spack/repos/builtin/packages/eclipse-gcj-parser/package.py b/var/spack/repos/builtin/packages/eclipse-gcj-parser/package.py
new file mode 100644
index 0000000000..52937c57d0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/eclipse-gcj-parser/package.py
@@ -0,0 +1,50 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class EclipseGcjParser(Package):
+    """GCJ requires the Eclipse Java parser, but does not ship with it.
+    This builds that parser into an executable binary, thereby
+    making GCJ work."""
+
+    homepage = "https://github.com/spack/spack/issues/8165"
+    url = "ftp://sourceware.org/pub/java/ecj-4.8.jar"
+    # Official download found at (see ecj-4.8M4.jar and ecjsrc-4.8M4.jar)
+    # http://download.eclipse.org/eclipse/downloads/drops4/S-4.8M4-201712062000/
+
+    maintainers = ['citibeth']
+
+    version('4.8', 'd7cd6a27c8801e66cbaa964a039ecfdb', expand=False)
+
+    phases = ('build', 'install')
+
+    @property
+    def gcj(self):
+        """Obtain Executable for the gcj included with this GCC,
+        even in the face of GCC binaries with version numbers
+        included in their names."""
+
+        dir, gcc = os.path.split(str(self.compiler.cc))
+        if 'gcc' not in gcc:
+            raise ValueError(
+                'Package {0} requires GCC to build'.format(self.name))
+
+        return Executable(join_path(dir, gcc.replace('gcc', 'gcj')))
+
+    def build(self, spec, prefix):
+        self.gcj(
+            '-o', 'ecj1',
+            '--main=org.eclipse.jdt.internal.compiler.batch.GCCMain',
+            'ecj-4.8.jar')
+
+    def install(self, spec, prefix):
+        mkdirp(spec.prefix.bin)
+        install('ecj1', spec.prefix.bin)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PATH', self.prefix.bin)
diff --git a/var/spack/repos/builtin/packages/ecp-proxy-apps/package.py b/var/spack/repos/builtin/packages/ecp-proxy-apps/package.py
index ee1a881aff..bd2117cd99 100644
--- a/var/spack/repos/builtin/packages/ecp-proxy-apps/package.py
+++ b/var/spack/repos/builtin/packages/ecp-proxy-apps/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 import os
 from spack import *
@@ -33,27 +14,56 @@ class EcpProxyApps(Package):
        installs the ECP proxy application suite.
     """
 
-    homepage = "https://exascaleproject.github.io/proxy-apps"
+    tags = ['proxy-app', 'ecp-proxy-app']
+    maintainers = ['bhatele']
 
+    homepage = "https://exascaleproject.github.io/proxy-apps"
     # Dummy url
     url = 'https://github.com/exascaleproject/proxy-apps/archive/v1.0.tar.gz'
 
-    tags = ['proxy-app', 'ecp-proxy-app']
+    version('2.0', sha256='5f3cb3a772224e738c1dab42fb34d40f6b313af51ab1c575fb334e573e41e09a')
+    version('1.1', '15825c318acd3726fd8e72803b1c1090')
+    version('1.0', '8b3f00f05e6cde88d8d913da4293ee62')
+
+    variant('candle', default=False,
+            description='Also build CANDLE Benchmarks')
+
+    # Added with release 2.0
+    depends_on('ember@1.0.0', when='@2.0:')
+    depends_on('miniqmc@0.4.0', when='@2.0:')
+    depends_on('minivite@1.0', when='@2.0:')
+    depends_on('picsarlite@0.1', when='@2.0:')
+    depends_on('thornado-mini@1.0', when='@2.0:')
+
+    depends_on('amg@1.1', when='@2.0:')
+    depends_on('candle-benchmarks@0.1', when='+candle @2.0:')
+    depends_on('laghos@1.1', when='@2.0:')
+    depends_on('macsio@1.1', when='@2.0:')
+    depends_on('miniamr@1.4.1', when='@2.0:')
+    depends_on('sw4lite@1.1', when='@2.0:')
+    depends_on('xsbench@18', when='@2.0:')
+
+    # Added with release 1.1
+    depends_on('examinimd@1.0', when='@1.1:')
+
+    depends_on('nekbone@17.0', when='@1.0:')
+    depends_on('swfft@1.0', when='@1.0:')
+
+    # Dependencies for versions 1.0:1.1
+    depends_on('amg@1.0', when='@1.0:1.1')
+    depends_on('candle-benchmarks@0.0', when='+candle @1.0:1.1')
+    depends_on('laghos@1.0', when='@1.0:1.1')
+    depends_on('macsio@1.0', when='@1.0:1.1')
+    depends_on('miniamr@1.4.0', when='@1.0:1.1')
+    depends_on('sw4lite@1.0', when='@1.0:1.1')
+    depends_on('xsbench@14', when='@1.0:1.1')
 
-    version('1.0', '5a26b184f506afeb7d221f15c0e8f153')
+    # Removed after release 1.1
+    depends_on('minife@2.1.0', when='@1.0:1.1')
+    depends_on('minitri@1.0', when='@1.0:1.1')
 
-    depends_on('amg@1.0', when='@1.0')
-    depends_on('candle-benchmarks@1.0', when='@1.0')
+    # Removed after release 1.0
     depends_on('comd@1.1', when='@1.0')
-    depends_on('laghos@1.0', when='@1.0')
-    depends_on('macsio@1.0', when='@1.0')
-    depends_on('miniamr@1.4.0', when='@1.0')
-    depends_on('minife@2.1.0', when='@1.0')
-    depends_on('minitri@1.0', when='@1.0')
-    depends_on('nekbone@17.0', when='@1.0')
-    depends_on('sw4lite@1.0', when='@1.0')
-    depends_on('swfft@1.0', when='@1.0')
-    depends_on('xsbench@14', when='@1.0')
 
     # Dummy install for now,  will be removed when metapackage is available
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/ed/package.py b/var/spack/repos/builtin/packages/ed/package.py
new file mode 100644
index 0000000000..c9b8b872b5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ed/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Ed(AutotoolsPackage):
+    """GNU ed is a line-oriented text editor. It is used to create,
+       display, modify and otherwise manipulate text files, both
+       interactively and via shell scripts."""
+
+    homepage = "https://www.gnu.org/software/ed"
+    url      = "https://ftpmirror.gnu.org/ed/ed-1.4.tar.gz"
+
+    version('1.4', 'da0ddc0e0b0bec2da4b13b0d0d1bce2b')
+
+    parallel = False
diff --git a/var/spack/repos/builtin/packages/editres/package.py b/var/spack/repos/builtin/packages/editres/package.py
index 1bba68d305..9501f00637 100644
--- a/var/spack/repos/builtin/packages/editres/package.py
+++ b/var/spack/repos/builtin/packages/editres/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Editres(AutotoolsPackage):
     depends_on('libxt')
     depends_on('libxmu')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/eigen/find-ptscotch.patch b/var/spack/repos/builtin/packages/eigen/find-ptscotch.patch
new file mode 100644
index 0000000000..4f6e286b72
--- /dev/null
+++ b/var/spack/repos/builtin/packages/eigen/find-ptscotch.patch
@@ -0,0 +1,27 @@
+Version 3.3.4 contained a bug that prevented it from finding scotch~mpi.
+
+diff --git a/tmp/FindPTSCOTCH.cmake b/cmake/FindPTSCOTCH.cmake
+index 1396d05..23451b1 100644
+--- a/tmp/FindPTSCOTCH.cmake
++++ b/cmake/FindPTSCOTCH.cmake
+@@ -167,11 +167,11 @@ endif()
+
+ # If found, add path to cmake variable
+ # ------------------------------------
++unset(PTSCOTCH_INCLUDE_DIRS)
+ foreach(ptscotch_hdr ${PTSCOTCH_hdrs_to_find})
+   if (PTSCOTCH_${ptscotch_hdr}_DIRS)
+     list(APPEND PTSCOTCH_INCLUDE_DIRS "${PTSCOTCH_${ptscotch_hdr}_DIRS}")
+   else ()
+-    set(PTSCOTCH_INCLUDE_DIRS "PTSCOTCH_INCLUDE_DIRS-NOTFOUND")
+     if (NOT PTSCOTCH_FIND_QUIETLY)
+       message(STATUS "Looking for ptscotch -- ${ptscotch_hdr} not found")
+     endif()
+@@ -255,7 +255,6 @@ foreach(ptscotch_lib ${PTSCOTCH_libs_to_find})
+     list(APPEND PTSCOTCH_LIBRARIES "${PTSCOTCH_${ptscotch_lib}_LIBRARY}")
+     list(APPEND PTSCOTCH_LIBRARY_DIRS "${${ptscotch_lib}_lib_path}")
+   else ()
+-    list(APPEND PTSCOTCH_LIBRARIES "${PTSCOTCH_${ptscotch_lib}_LIBRARY}")
+     if (NOT PTSCOTCH_FIND_QUIETLY)
+       message(STATUS "Looking for ptscotch -- lib ${ptscotch_lib} not found")
+     endif()
diff --git a/var/spack/repos/builtin/packages/eigen/package.py b/var/spack/repos/builtin/packages/eigen/package.py
index 9e7d8c392e..6e5582d233 100644
--- a/var/spack/repos/builtin/packages/eigen/package.py
+++ b/var/spack/repos/builtin/packages/eigen/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,8 +12,10 @@ class Eigen(CMakePackage):
     """
 
     homepage = 'http://eigen.tuxfamily.org/'
-    url      = 'https://bitbucket.org/eigen/eigen/get/3.3.3.tar.bz2'
+    url      = 'https://bitbucket.org/eigen/eigen/get/3.3.4.tar.bz2'
 
+    version('3.3.5', 'e83549a79d1b721da0f8899ab34edf95')
+    version('3.3.4', 'a7aab9f758249b86c93221ad417fbe18')
     version('3.3.3', 'b2ddade41040d9cf73b39b4b51e8775b')
     version('3.3.1', 'edb6799ef413b0868aace20d2403864c')
     version('3.2.10', 'a85bb68c82988648c3d53ba9768d7dcbcfe105f8')
@@ -58,3 +41,5 @@ class Eigen(CMakePackage):
     depends_on('suite-sparse', when='+suitesparse')
     depends_on('mpfr@2.3.0:', when='+mpfr')
     depends_on('gmp', when='+mpfr')
+
+    patch('find-ptscotch.patch', when='@3.3.4')
diff --git a/var/spack/repos/builtin/packages/elasticsearch/package.py b/var/spack/repos/builtin/packages/elasticsearch/package.py
new file mode 100644
index 0000000000..3492774c35
--- /dev/null
+++ b/var/spack/repos/builtin/packages/elasticsearch/package.py
@@ -0,0 +1,32 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Elasticsearch(Package):
+    """Elasticsearch is a search engine based on Lucene. It provides a
+    distributed, multitenant-capable full-text search engine with an HTTP web
+    interface and schema-free JSON documents.
+    """
+
+    homepage = "https://www.elastic.co/"
+    url      = "https://artifacts.elastic.co/downloads/elasticsearch/elasticsearch-6.2.4.tar.gz"
+
+    version('6.4.0', '5c23c99a52600b250a6871bf6a744e8b')
+    version('6.2.4', '692d01956fe7aee2d08ac0fbf7b7a19e')
+
+    depends_on('jdk', type='run')
+
+    def install(self, spec, prefix):
+        dirs = [
+            'bin',
+            'config',
+            'lib',
+            'modules',
+            'plugins']
+
+        for d in dirs:
+            install_tree(d, join_path(prefix, d))
diff --git a/var/spack/repos/builtin/packages/elemental/package.py b/var/spack/repos/builtin/packages/elemental/package.py
index 14e376628c..43a34fcc40 100644
--- a/var/spack/repos/builtin/packages/elemental/package.py
+++ b/var/spack/repos/builtin/packages/elemental/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 from spack import *
 from spack.spec import UnsupportedCompilerError
@@ -32,9 +13,10 @@ class Elemental(CMakePackage):
        and optimization library."""
 
     homepage = "http://libelemental.org"
-    url      = "https://github.com/elemental/Elemental/archive/v0.87.6.tar.gz"
+    url      = "https://github.com/elemental/Elemental/archive/v0.87.7.tar.gz"
+    git      = "https://github.com/elemental/Elemental.git"
 
-    version('develop', git='https://github.com/elemental/Elemental.git', branch='master')
+    version('develop', branch='master')
     version('0.87.7', '6c1e7442021c59a36049e37ea69b8075')
     version('0.87.6', '9fd29783d45b0a0e27c0df85f548abe9')
 
@@ -66,8 +48,8 @@ class Elemental(CMakePackage):
     variant('build_type', default='Release',
             description='The build type to build',
             values=('Debug', 'Release'))
-    variant('blas', default='openblas', values=('openblas', 'mkl'),
-            description='Enable the use of OpenBlas/MKL')
+    variant('blas', default='openblas', values=('openblas', 'mkl', 'accelerate', 'essl'),
+            description='Enable the use of OpenBlas/MKL/Accelerate/ESSL')
     variant('mpfr', default=False,
             description='Support GNU MPFR\'s'
             'arbitrary-precision floating-point arithmetic')
@@ -75,6 +57,7 @@ class Elemental(CMakePackage):
     # Note that #1712 forces us to enumerate the different blas variants
     depends_on('blas', when='~openmp_blas ~int64_blas')
     # Hack to forward variant to openblas package
+    depends_on('openblas', when='blas=openblas ~openmp_blas ~int64_blas')
     # Allow Elemental to build internally when using 8-byte ints
     depends_on('openblas threads=openmp', when='blas=openblas +openmp_blas ~int64_blas')
 
@@ -82,8 +65,15 @@ class Elemental(CMakePackage):
     depends_on('intel-mkl threads=openmp', when='blas=mkl +openmp_blas ~int64_blas')
     depends_on('intel-mkl@2017.1 +openmp +ilp64', when='blas=mkl +openmp_blas +int64_blas')
 
+    depends_on('veclibfort', when='blas=accelerate')
+
+    depends_on('essl ~cuda', when='blas=essl ~openmp_blas ~int64_blas')
+    depends_on('essl threads=openmp', when='blas=essl +openmp_blas ~int64_blas')
+
     # Note that this forces us to use OpenBLAS until #1712 is fixed
     depends_on('lapack', when='blas=openblas ~openmp_blas')
+    depends_on('netlib-lapack +external-blas', when='blas=essl')
+
     depends_on('metis')
     depends_on('metis +int64', when='+int64')
     depends_on('mpi')
@@ -102,7 +92,7 @@ class Elemental(CMakePackage):
     def libs(self):
         shared = True if '+shared' in self.spec else False
         return find_libraries(
-            'libEl', root=self.prefix, shared=shared, recurse=True
+            'libEl', root=self.prefix, shared=shared, recursive=True
         )
 
     def cmake_args(self):
@@ -134,14 +124,23 @@ class Elemental(CMakePackage):
             ifort = env['SPACK_F77']
             intel_bin = os.path.dirname(ifort)
             intel_root = os.path.dirname(intel_bin)
-            libfortran = LibraryList('{0}/lib/intel64/libifcoremt.{1}'
-                                     .format(intel_root, dso_suffix))
+            libfortran = find_libraries('libifcoremt',
+                                        root=intel_root, recursive=True)
         elif self.spec.satisfies('%gcc'):
             # see <stage_folder>/debian/rules as an example:
             mpif77 = Executable(spec['mpi'].mpif77)
             libfortran = LibraryList(mpif77('--print-file-name',
                                             'libgfortran.%s' % dso_suffix,
-                                            output=str))
+                                            output=str).strip())
+        elif self.spec.satisfies('%xl') or self.spec.satisfies('%xl_r'):
+            xl_fort = env['SPACK_F77']
+            xl_bin = os.path.dirname(xl_fort)
+            xl_root = os.path.dirname(xl_bin)
+            libfortran = find_libraries('libxlf90_r',
+                                        root=xl_root, recursive=True)
+        else:
+            libfortran = None
+
         if libfortran:
             args.append('-DGFORTRAN_LIB=%s' % libfortran.libraries[0])
 
diff --git a/var/spack/repos/builtin/packages/elfutils/package.py b/var/spack/repos/builtin/packages/elfutils/package.py
index 2db5d71d3a..1234f5007a 100644
--- a/var/spack/repos/builtin/packages/elfutils/package.py
+++ b/var/spack/repos/builtin/packages/elfutils/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,19 +20,58 @@ class Elfutils(AutotoolsPackage):
     list_url = "https://sourceware.org/elfutils/ftp"
     list_depth = 1
 
+    version('0.173', '35decb1ebfb90d565e4c411bee4185cc')
     version('0.170', '03599aee98c9b726c7a732a2dd0245d5')
     version('0.168', '52adfa40758d0d39e5d5c57689bf38d6')
-    version('0.163', '77ce87f259987d2e54e4d87b86cbee41', preferred=True)
+    version('0.163', '77ce87f259987d2e54e4d87b86cbee41')
+
+    # Libraries for reading compressed DWARF sections.
+    variant('bzip2', default=False,
+            description='Support bzip2 compressed sections.')
+    variant('xz', default=False,
+            description='Support xz compressed sections.')
+
+    # Native language support from libintl.
+    variant('nls', default=True,
+            description='Enable Native Language Support.')
 
-    depends_on('flex', type='build')
-    depends_on('bison', type='build')
-    depends_on('gettext')
+    depends_on('bzip2', type='link', when='+bzip2')
+    depends_on('xz',    type='link', when='+xz')
+    depends_on('zlib',  type='link')
+    depends_on('gettext', when='+nls')
+
+    conflicts('%gcc@7.2.0:', when='@0.163')
 
     provides('elf@1')
 
+    # Elfutils uses nested functions in C code, which is implemented
+    # in gcc, but not in clang. C code compiled with gcc is
+    # binary-compatible with clang, so it should be possible to build
+    # elfutils with gcc, and then link it to clang-built libraries.
+    conflicts('%clang')
+
     def configure_args(self):
-        # configure doesn't use LIBS correctly
-        gettext_lib = self.spec['gettext'].prefix.lib,
-        return [
-            'LDFLAGS=-Wl,--no-as-needed -L%s -lintl' % gettext_lib,
-            '--enable-maintainer-mode']
+        spec = self.spec
+        args = []
+
+        if '+bzip2' in spec:
+            args.append('--with-bzlib=%s' % spec['bzip2'].prefix)
+        else:
+            args.append('--without-bzlib')
+
+        if '+xz' in spec:
+            args.append('--with-lzma=%s' % spec['xz'].prefix)
+        else:
+            args.append('--without-lzma')
+
+        # zlib is required
+        args.append('--with-zlib=%s' % spec['zlib'].prefix)
+
+        if '+nls' in spec:
+            # configure doesn't use LIBS correctly
+            args.append('LDFLAGS=-Wl,--no-as-needed -L%s -lintl' %
+                        spec['gettext'].prefix.lib)
+        else:
+            args.append('--disable-nls')
+
+        return args
diff --git a/var/spack/repos/builtin/packages/elk/package.py b/var/spack/repos/builtin/packages/elk/package.py
index 6abebb4174..fad0153014 100644
--- a/var/spack/repos/builtin/packages/elk/package.py
+++ b/var/spack/repos/builtin/packages/elk/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/elpa/package.py b/var/spack/repos/builtin/packages/elpa/package.py
index 3761f26cc0..13c31a26b3 100644
--- a/var/spack/repos/builtin/packages/elpa/package.py
+++ b/var/spack/repos/builtin/packages/elpa/package.py
@@ -1,27 +1,7 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack import *
 
@@ -32,12 +12,17 @@ class Elpa(AutotoolsPackage):
     homepage = 'http://elpa.mpcdf.mpg.de/'
     url = 'http://elpa.mpcdf.mpg.de/elpa-2015.11.001.tar.gz'
 
+    version('2018.05.001.rc1', 'ccd77bd8036988ee624f43c04992bcdd')
+    version('2017.11.001', '4a437be40cc966efb07aaab84c20cd6e', preferred=True)
+    version('2017.05.003', '7c8e5e58cafab212badaf4216695700f')
+    version('2017.05.002', 'd0abc1ac1f493f93bf5e30ec8ab155dc')
     version('2016.11.001.pre', '5656fd066cf0dcd071dbcaf20a639b37')
-    version('2016.05.004', 'c0dd3a53055536fc3a2a221e78d8b376', preferred=True)
+    version('2016.05.004', 'c0dd3a53055536fc3a2a221e78d8b376')
     version('2016.05.003', '88a9f3f3bfb63e16509dd1be089dcf2c')
     version('2015.11.001', 'de0f35b7ee7c971fd0dca35c900b87e6')
 
     variant('openmp', default=False, description='Activates OpenMP support')
+    variant('optflags', default=True, description='Build with optimization flags')
 
     depends_on('mpi')
     depends_on('blas')
@@ -53,18 +38,14 @@ class Elpa(AutotoolsPackage):
     # override default implementation which returns static lib
     @property
     def libs(self):
-
         libname = 'libelpa_openmp' if '+openmp' in self.spec else 'libelpa'
-
         return find_libraries(
-            libname, root=self.prefix, shared=True, recurse=True
+            libname, root=self.prefix, shared=True, recursive=True
         )
 
     build_directory = 'spack-build'
 
     def setup_environment(self, spack_env, run_env):
-        # TODO: set optimum flags for platform+compiler combo, see
-        # https://github.com/hfp/xconfigure/tree/master/elpa
         spec = self.spec
 
         spack_env.set('CC', spec['mpi'].mpicc)
@@ -76,7 +57,20 @@ class Elpa(AutotoolsPackage):
         spack_env.set('SCALAPACK_LDFLAGS', spec['scalapack'].libs.joined())
 
     def configure_args(self):
+        # TODO: set optimum flags for platform+compiler combo, see
+        # https://github.com/hfp/xconfigure/tree/master/elpa
+        # also see:
+        # https://src.fedoraproject.org/cgit/rpms/elpa.git/
+        # https://packages.qa.debian.org/e/elpa.html
         options = []
+        # without -march=native there is configure error for 2017.05.02
+        # Could not compile test program, try with --disable-sse, or
+        # adjust the C compiler or CFLAGS
+        if '+optflags' in self.spec:
+            options.extend([
+                'FCFLAGS=-O2 -march=native -ffree-line-length-none',
+                'CFLAGS=-O2 -march=native'
+            ])
         if '+openmp' in self.spec:
-            options.append("--enable-openmp")
+            options.append('--enable-openmp')
         return options
diff --git a/var/spack/repos/builtin/packages/emacs/package.py b/var/spack/repos/builtin/packages/emacs/package.py
index 4b0d7a9689..1599782d50 100644
--- a/var/spack/repos/builtin/packages/emacs/package.py
+++ b/var/spack/repos/builtin/packages/emacs/package.py
@@ -1,36 +1,20 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
+import sys
+
 
 class Emacs(AutotoolsPackage):
     """The Emacs programmable text editor."""
 
     homepage = "https://www.gnu.org/software/emacs"
-    url      = "http://ftp.gnu.org/gnu/emacs/emacs-24.5.tar.gz"
+    url      = "https://ftpmirror.gnu.org/emacs/emacs-24.5.tar.gz"
 
+    version('26.1', '544d2ab5eb142e9ca69adb023d17bf4b')
     version('25.3', '74ddd373dc52ac05ca7a8c63b1ddbf58')
     version('25.2', '0a36d1cdbba6024d4dbbac027f87995f')
     version('25.1', '95c12e6a9afdf0dcbdd7d2efa26ca42c')
@@ -43,10 +27,12 @@ class Emacs(AutotoolsPackage):
         values=('gtk', 'athena'),
         description="Select an X toolkit (gtk, athena)"
     )
+    variant('tls', default=False, description="Build Emacs with gnutls")
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
 
     depends_on('ncurses')
+    depends_on('pcre')
     depends_on('zlib')
     depends_on('libtiff', when='+X')
     depends_on('libpng', when='+X')
@@ -54,7 +40,8 @@ class Emacs(AutotoolsPackage):
     depends_on('giflib', when='+X')
     depends_on('libx11', when='+X')
     depends_on('libxaw', when='+X toolkit=athena')
-    depends_on('gtkplus+X', when='+X toolkit=gtk')
+    depends_on('gtkplus', when='+X toolkit=gtk')
+    depends_on('gnutls', when='+tls')
 
     def configure_args(self):
         spec = self.spec
@@ -68,4 +55,14 @@ class Emacs(AutotoolsPackage):
         else:
             args = ['--without-x']
 
+        # On OS X/macOS, do not build "nextstep/Emacs.app", because
+        # doing so throws an error at build-time
+        if sys.platform == 'darwin':
+            args.append('--without-ns')
+
+        if '+tls' in spec:
+            args.append('--with-gnutls')
+        else:
+            args.append('--without-gnutls')
+
         return args
diff --git a/var/spack/repos/builtin/packages/ember/package.py b/var/spack/repos/builtin/packages/ember/package.py
new file mode 100644
index 0000000000..261dc27ba7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ember/package.py
@@ -0,0 +1,87 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Ember(MakefilePackage):
+    """
+    Ember Communication Pattern Library
+    The Ember suite provides communication patterns in a simplified setting
+    (simplified by the removal of application calculations, control flow,
+    etc.).
+    """
+
+    tags = ['proxy-app', 'ecp-proxy-app']
+
+    homepage = "http://sst-simulator.org/SSTPages/SSTElementEmber/"
+    git      = "https://github.com/sstsimulator/ember.git"
+    url      = "https://github.com/sstsimulator/ember/archive/v1.0.0.tar.gz"
+
+    version('1.0.0', sha256='5b2a6b8055b46ab3ea2c7baabaf4d280d837bb7c21eba0c9f59e092c6fc1c4a6')
+
+    depends_on('mpi')
+
+    # TODO: shmem variant disabled due to lack of shmem spackage
+    def edit(self, spec, prefix):
+        file = open('Makefile', 'w')
+
+        file.write('CC = mpicc\n')
+        file.write('CFLAGS = -O3 -std=c99\n')
+        file.write('OSHMEM_CC=cc\n')
+        file.write('OSHMEM_C_FLAGS=-O3 -g\n')
+
+        file.write('export CC CFLAGS OSHMEM_CC OSHMEM_C_FLAGS\n')
+
+        file.write('all:\n')
+        file.write('\t@$(MAKE) -C mpi/halo3d -f Makefile\n')
+        file.write('\t@$(MAKE) -C mpi/halo3d-26 -f Makefile\n')
+        file.write('\t@$(MAKE) -C mpi/incast -f Makefile\n')
+        file.write('\t@$(MAKE) -C mpi/pingpong -f Makefile\n')
+        file.write('\t@$(MAKE) -C mpi/sweep3d -f Makefile\n')
+        # file.write('\t@$(MAKE) -C shmem/hotspotinc -f Makefile\n')
+        # file.write('\t@$(MAKE) -C shmem/randominc -f Makefile\n')
+
+        file.write('.PHONY: clean\n')
+        file.write('clean:\n')
+        file.write('\t@$(MAKE) -C mpi/halo3d -f Makefile clean\n')
+        file.write('\t@$(MAKE) -C mpi/halo3d-26 -f Makefile clean\n')
+        file.write('\t@$(MAKE) -C mpi/incast -f Makefile clean\n')
+        file.write('\t@$(MAKE) -C mpi/pingpong -f Makefile clean\n')
+        file.write('\t@$(MAKE) -C mpi/sweep3d -f Makefile clean\n')
+        # file.write('\t@$(MAKE) -C shmem/hotspotinc -f Makefile clean\n')
+        # file.write('\t@$(MAKE) -C shmem/randominc -f Makefile clean\n')
+
+        file.close()
+
+    @property
+    def build_targets(self):
+        targets = []
+        cc = self.spec['mpi'].mpicc
+        cflags = '-O3 -std=c99'
+        oshmem_cc = 'cc'
+        oshmem_c_flags = '-O3 -g'
+
+        targets.append('CC = {0}'.format(cc))
+        targets.append('CFLAGS = {0}'.format(cflags))
+        targets.append('OSHMEM_CC = {0}'.format(oshmem_cc))
+        targets.append('OSHMEM_C_FLAGS = {0}'.format(oshmem_c_flags))
+
+        return targets
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.docs)
+        install('README.md', prefix.docs)
+        install('README.MPI.halo3d', prefix.docs)
+        install('README.MPI.halo3d-26', prefix.docs)
+        install('README.MPI.incast', prefix.docs)
+        install('README.MPI.sweep3d', prefix.docs)
+
+        mkdirp(prefix.bin)
+        install('mpi/halo3d/halo3d', prefix.bin)
+        install('mpi/halo3d-26/halo3d-26', prefix.bin)
+        install('mpi/incast/incast', prefix.bin)
+        install('mpi/pingpong/pingpong', prefix.bin)
+        install('mpi/sweep3d/sweep3d', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/emboss/package.py b/var/spack/repos/builtin/packages/emboss/package.py
index fe3f18a0dc..bc36c8938b 100644
--- a/var/spack/repos/builtin/packages/emboss/package.py
+++ b/var/spack/repos/builtin/packages/emboss/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,3 +19,8 @@ class Emboss(AutotoolsPackage):
     depends_on('libxpm')
     depends_on('libgd')
     depends_on('postgresql')
+
+    @run_after('configure')
+    def skip_update_checks(self):
+        # Delete $(bindir)/embossupdate to skip update checks
+        filter_file('$(bindir)/embossupdate', '', 'Makefile', string=True)
diff --git a/var/spack/repos/builtin/packages/encodings/package.py b/var/spack/repos/builtin/packages/encodings/package.py
index f356b052fc..0ea51bf7da 100644
--- a/var/spack/repos/builtin/packages/encodings/package.py
+++ b/var/spack/repos/builtin/packages/encodings/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,7 +17,7 @@ class Encodings(Package):
     depends_on('font-util')
 
     depends_on('mkfontscale', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/energyplus/package.py b/var/spack/repos/builtin/packages/energyplus/package.py
new file mode 100644
index 0000000000..48cc19cf41
--- /dev/null
+++ b/var/spack/repos/builtin/packages/energyplus/package.py
@@ -0,0 +1,37 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import glob
+import os
+
+
+class Energyplus(Package):
+    """EnergyPlus is a whole building energy simulation program that engineers,
+       architects, and researchers use to model both energy consumption for
+       heating, cooling, ventilation, lighting and plug and process loads
+       and water use in buildings"""
+
+    homepage = "https://energyplus.net"
+
+    # versions require explicit URLs as they contain hashes
+    version('8.9.0', sha256='13a5192b25815eb37b3ffd019ce3b99fd9f854935f8cc4362814f41c56e9ca98',
+            url="https://github.com/NREL/EnergyPlus/releases/download/v8.9.0-WithIDDFixes/EnergyPlus-8.9.0-eba93e8e1b-Linux-x86_64.tar.gz")
+
+    def install(self, spec, prefix):
+        # binary distribution, we just unpack to lib/energyplus
+        # and then symlink the appropriate targets
+
+        # there is only one folder with a semi-predictable name so we glob it
+        install_tree(glob.glob('EnergyPlus*')[0],
+                     join_path(prefix.lib, 'energyplus'))
+
+        mkdirp(prefix.bin)
+        os.symlink(join_path(prefix.lib, 'energyplus/energyplus'),
+                   join_path(prefix.bin, 'energyplus'))
+        os.symlink(join_path(prefix.lib, 'energyplus/EPMacro'),
+                   join_path(prefix.bin, 'EPMacro'))
+        os.symlink(join_path(prefix.lib, 'energyplus/ExpandObjects'),
+                   join_path(prefix.bin, 'ExpandObjects'))
diff --git a/var/spack/repos/builtin/packages/environment-modules/package.py b/var/spack/repos/builtin/packages/environment-modules/package.py
index ed84cea0a9..60307d3865 100644
--- a/var/spack/repos/builtin/packages/environment-modules/package.py
+++ b/var/spack/repos/builtin/packages/environment-modules/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
diff --git a/var/spack/repos/builtin/packages/eospac/flang.patch b/var/spack/repos/builtin/packages/eospac/flang.patch
new file mode 100644
index 0000000000..dcde70ff50
--- /dev/null
+++ b/var/spack/repos/builtin/packages/eospac/flang.patch
@@ -0,0 +1,62 @@
+--- a/Source/config/Makefile.-linux-gnu.detect
++++ b/Source/config/Makefile.-linux-gnu.detect
+@@ -19,7 +19,7 @@
+ # Compiler suite configurations based upon F90                 ###
+ ##################################################################
+ # Default: use the first F90 compiler found from F90_List
+-F90_List = gfortran pgfortran pgf90 lf95 f90 ifort g95 ftn pathf90
++F90_List = gfortran pgfortran pgf90 lf95 f90 ifort g95 ftn pathf90 flang
+ F90_Found_List = $(foreach compiler,$(F90_List),$(call pathsearch,$(compiler)))
+ F90 = $(firstword $(F90_Found_List))
+ F90_Key = $(strip $(firstword $(foreach compiler,$(F90_List),$(call match_r1,$(compiler),$(F90)))))
+
+--- a/Source/config/Makefile.-linux-gnu.hashes
++++ b/Source/config/Makefile.-linux-gnu.hashes
+@@ -32,6 +32,7 @@
+ $(call set,_CC,g95,        gcc                       )   # G95
+ $(call set,_CC,gfortran,   gcc                       )   # gfortran
+ $(call set,_CC,ftn,        cc        gcc             )   # Cray Computing Environment (cce)
++$(call set,_CC,flang,      clang                     )   # flang/clang
+
+ $(call set,_CXX,pgfortran, pgCC      g++             )   # PGI
+ $(call set,_CXX,pgf90,     pgCC      g++             )   # PGI
+@@ -42,6 +43,7 @@
+ $(call set,_CXX,g95,       g++                       )   # G95
+ $(call set,_CXX,gfortran,  g++                       )   # gfortran
+ $(call set,_CXX,ftn,       CC        g++             )   # Cray Computing Environment (cce)
++$(call set,_CC,flang,      clang++                   )   # flang/clang++
+
+ $(call set,_F77,pgfortran, pgfortran pgf77     pgf90 )   # PGI
+ $(call set,_F77,pgf90,     pgfortran pgf77     pgf90 )   # PGI
+@@ -52,6 +54,7 @@
+ $(call set,_F77,g95,       $(F90)                    )   # G95
+ $(call set,_F77,gfortran,  $(F90)                    )   # gfortran
+ $(call set,_F77,ftn,       $(F90)                    )   # Cray Computing Environment (cce)
++$(call set,_CC,flang,      flang                     )   # flang
+
+ ##################################################################
+ ### Define CC, CXX and  F77 according to $(F90_Key).           ###
+@@ -94,6 +97,7 @@
+ $(call set,_COMP_FLAGS,gfortran,     -I"$(INCDIR)" -Wno-c-binding-type)   # gfortran
+ $(call set,_COMP_FLAGS,ppu-gfortran, -I"$(INCDIR)"                    )   # ppu-gfortran
+ $(call set,_COMP_FLAGS,ftn,          -e m -I"$(INCDIR)" -hfp0         )   # Cray Computing Environment (cce)
++$(call set,_COMP_FLAGS,flang,        -I"$(INCDIR)"                    )   # flang
+
+ # define define_module_subdir script options
+ $(call set,_DEFINE_MODULE_SUBDIR_FLAGS,f90,)           # Absoft f90
+@@ -105,6 +109,7 @@
+ $(call set,_DEFINE_MODULE_SUBDIR_FLAGS,g95,)           # G95
+ $(call set,_DEFINE_MODULE_SUBDIR_FLAGS,gfortran,)      # gfortran
+ $(call set,_DEFINE_MODULE_SUBDIR_FLAGS,ftn,)           # Cray Computing Environment (cce)
++$(call set,_DEFINE_MODULE_SUBDIR_FLAGS,flang,)         # flang
+
+ # define define_module_subdir script patterns
+ $(call set,_DEFINE_MODULE_SUBDIR_PATTS,f90,absoft)           # Absoft f90
+@@ -116,6 +121,7 @@
+ $(call set,_DEFINE_MODULE_SUBDIR_PATTS,g95,$(F90_Key))       # G95
+ $(call set,_DEFINE_MODULE_SUBDIR_PATTS,gfortran,gcc)         # gfortran
+ $(call set,_DEFINE_MODULE_SUBDIR_PATTS,ftn,cce)              # Cray Computing Environment (cce)
++$(call set,_DEFINE_MODULE_SUBDIR_PATTS,flang,clang)          # flang/clang
+
+ # define optional modules for cross-compiling
+ X_Compile_Module_List = craype-haswell craype-mic-knl
diff --git a/var/spack/repos/builtin/packages/eospac/package.py b/var/spack/repos/builtin/packages/eospac/package.py
new file mode 100644
index 0000000000..54000d6b5f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/eospac/package.py
@@ -0,0 +1,39 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Eospac(Package):
+    """A collection of C routines that can be used to access the Sesame data
+       library.
+    """
+
+    homepage = "https://laws.lanl.gov/projects/data/eos.html"
+    list_url = "https://laws.lanl.gov/projects/data/eos/eospacReleases.php"
+
+    version('6.4.0beta.2', '9b6e48090647221d5ffe7ec5f9ea4c71',
+            url="https://laws.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.4.0beta.2_69196eadbc77506561eef711f19d2f03b4ab0ffa.tgz")
+    version('6.4.0beta.1', 'e4e4beabf946f0b8953532832002afc2',
+            url="https://laws.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.4.0beta.1_r20171213193219.tgz")
+    version('6.3.1', '549fda008c4169a69b02ec2a9de1e434', preferred=True,
+            url="https://laws.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.3.1_r20161202150449.tgz")
+
+    # This patch allows the use of spack's compile wrapper 'flang'
+    patch('flang.patch', when='@:6.4.0beta.2%clang')
+
+    def install(self, spec, prefix):
+        with working_dir('Source'):
+            make('install',
+                 'CC={0}'.format(spack_cc),
+                 'CXX={0}'.format(spack_cxx),
+                 'F77={0}'.format(spack_f77),
+                 'F90={0}'.format(spack_fc),
+                 'prefix={0}'.format(prefix),
+                 'INSTALLED_LIBRARY_DIR={0}'.format(prefix.lib),
+                 'INSTALLED_INCLUDE_DIR={0}'.format(prefix.include),
+                 'INSTALLED_EXAMPLE_DIR={0}'.format(prefix.example),
+                 'INSTALLED_BIN_DIR={0}'.format(prefix.bin))
diff --git a/var/spack/repos/builtin/packages/er/package.py b/var/spack/repos/builtin/packages/er/package.py
new file mode 100644
index 0000000000..0638b792fb
--- /dev/null
+++ b/var/spack/repos/builtin/packages/er/package.py
@@ -0,0 +1,34 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Er(CMakePackage):
+    """Encoding and redundancy on a file set"""
+
+    homepage = "https://github.com/ECP-VeloC/er"
+    url      = "https://github.com/ECP-VeloC/er/archive/v0.0.2.zip"
+    git      = "https://github.com/ecp-veloc/er.git"
+
+    tags = ['ecp']
+
+    version('master', branch='master')
+    version('0.0.3', sha256='9aa08f9fe70e42f0da27a5d90d4643b520d61f24742303bf016322823b3c4d26')
+
+    depends_on('mpi')
+    depends_on('kvtree')
+    depends_on('redset')
+    depends_on('shuffile')
+
+    def cmake_args(self):
+        args = []
+        args.append("-DMPI_C_COMPILER=%s" % self.spec['mpi'].mpicc)
+        if self.spec.satisfies('platform=cray'):
+            args.append("-DER_LINK_STATIC=ON")
+        args.append("-DWITH_KVTREE_PREFIX=%s" % self.spec['kvtree'].prefix)
+        args.append("-DWITH_REDSET_PREFIX=%s" % self.spec['redset'].prefix)
+        args.append("-DWITH_SHUFFILE_PREFIX=%s" % self.spec['shuffile'].prefix)
+        return args
diff --git a/var/spack/repos/builtin/packages/es/package.py b/var/spack/repos/builtin/packages/es/package.py
index 6a73488e8f..8b918919bb 100644
--- a/var/spack/repos/builtin/packages/es/package.py
+++ b/var/spack/repos/builtin/packages/es/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/esmf/darwin_dylib_install_name.patch b/var/spack/repos/builtin/packages/esmf/darwin_dylib_install_name.patch
new file mode 100644
index 0000000000..0f363b378c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/esmf/darwin_dylib_install_name.patch
@@ -0,0 +1,18 @@
+--- a/build/common.mk	2017-11-25 17:16:31.000000000 +1100
++++ b/build/common.mk	2017-11-25 17:26:20.000000000 +1100
+@@ -3415,11 +3415,11 @@
+ 		    mkdir tmp_$$NEXTLIB ;\
+ 		    cd tmp_$$NEXTLIB  ;\
+ 	                $(ESMF_AREXTRACT) ../$$NEXTLIB.a ;\
+-                    echo $(ESMF_SL_LIBLINKER) $(ESMF_SL_LIBOPTS) -o $(ESMF_LDIR)/$$NEXTLIB.$(ESMF_SL_SUFFIX) *.o $(ESMF_SL_LIBLIBS) ;\
+-		    $(ESMF_SL_LIBLINKER) $(ESMF_SL_LIBOPTS) -o $(ESMF_LDIR)/$$NEXTLIB.$(ESMF_SL_SUFFIX) *.o $(ESMF_SL_LIBLIBS) ;\
++		    echo $(ESMF_SL_LIBLINKER) $(ESMF_SL_LIBOPTS) -Wl,-install_name -Wl,@rpath/$$NEXTLIB.$(ESMF_SL_SUFFIX) -o $(ESMF_LDIR)/$$NEXTLIB.$(ESMF_SL_SUFFIX) *.o $(ESMF_SL_LIBLIBS) ;\
++		    $(ESMF_SL_LIBLINKER) $(ESMF_SL_LIBOPTS) -Wl,-install_name -Wl,@rpath/$$NEXTLIB.$(ESMF_SL_SUFFIX) -o $(ESMF_LDIR)/$$NEXTLIB.$(ESMF_SL_SUFFIX) *.o $(ESMF_SL_LIBLIBS) ;\
+ 		    echo Converting $$NEXTLIB.a to $$NEXTLIB\_fullylinked.$(ESMF_SL_SUFFIX) ;\
+-                    echo $(ESMF_SL_LIBLINKER) $(ESMF_SL_LIBOPTS) -o $(ESMF_LDIR)/$$NEXTLIB\_fullylinked.$(ESMF_SL_SUFFIX) *.o $(ESMF_CXXLINKOPTS) $(ESMF_CXXLINKPATHS) $(ESMF_CXXLINKRPATHS) $(ESMF_CXXLINKLIBS) ;\
+-		    $(ESMF_SL_LIBLINKER) $(ESMF_SL_LIBOPTS) -o $(ESMF_LDIR)/$$NEXTLIB\_fullylinked.$(ESMF_SL_SUFFIX) *.o $(ESMF_CXXLINKOPTS) $(ESMF_CXXLINKPATHS) $(ESMF_CXXLINKRPATHS) $(ESMF_CXXLINKLIBS) ;\
++		    echo $(ESMF_SL_LIBLINKER) $(ESMF_SL_LIBOPTS) -Wl,-install_name -Wl,@rpath/$$NEXTLIB\_fullylinked.$(ESMF_SL_SUFFIX) -o $(ESMF_LDIR)/$$NEXTLIB\_fullylinked.$(ESMF_SL_SUFFIX) *.o $(ESMF_CXXLINKOPTS) $(ESMF_CXXLINKPATHS) $(ESMF_CXXLINKRPATHS) $(ESMF_CXXLINKLIBS) ;\
++		    $(ESMF_SL_LIBLINKER) $(ESMF_SL_LIBOPTS) -Wl,-install_name -Wl,@rpath/$$NEXTLIB\_fullylinked.$(ESMF_SL_SUFFIX) -o $(ESMF_LDIR)/$$NEXTLIB\_fullylinked.$(ESMF_SL_SUFFIX) *.o $(ESMF_CXXLINKOPTS) $(ESMF_CXXLINKPATHS) $(ESMF_CXXLINKRPATHS) $(ESMF_CXXLINKLIBS) ;\
+ 		    cd .. ;\
+ 		    $(ESMF_RM) -r tmp_$$NEXTLIB ;\
+ 		fi ;\
diff --git a/var/spack/repos/builtin/packages/esmf/package.py b/var/spack/repos/builtin/packages/esmf/package.py
index 394e316751..107aaffaa2 100644
--- a/var/spack/repos/builtin/packages/esmf/package.py
+++ b/var/spack/repos/builtin/packages/esmf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
@@ -59,7 +40,7 @@ class Esmf(MakefilePackage):
     depends_on('xerces-c@3.1.0:', when='+xerces')
 
     # Testing dependencies
-    # depends_on('perl', type='test')  # TODO: Add a test deptype
+    depends_on('perl', type='test')
 
     # Make esmf build with newer gcc versions
     # https://sourceforge.net/p/esmf/esmf/ci/3706bf758012daebadef83d6575c477aeff9c89b/
@@ -69,6 +50,10 @@ class Esmf(MakefilePackage):
     # https://sourceforge.net/p/esmf/esmf/ci/34de0ccf556ba75d35c9687dae5d9f666a1b2a18/
     patch('mvapich2.patch', when='@:7.0.99')
 
+    # Allow different directories for creation and
+    # installation of dynamic libraries on OSX:
+    patch('darwin_dylib_install_name.patch', when='platform=darwin')
+
     # Make script from mvapich2.patch executable
     @run_before('build')
     @when('@:7.0.99')
@@ -104,7 +89,7 @@ class Esmf(MakefilePackage):
         # bin/binO/Linux.gfortran.64.default.default
         os.environ['ESMF_INSTALL_BINDIR'] = 'bin'
         os.environ['ESMF_INSTALL_LIBDIR'] = 'lib'
-        os.environ['ESMF_INSTALL_MODDIR'] = 'mod'
+        os.environ['ESMF_INSTALL_MODDIR'] = 'include'
 
         ############
         # Compiler #
@@ -149,11 +134,17 @@ class Esmf(MakefilePackage):
         # ESMF_COMM must be set to indicate which MPI implementation
         # is used to build the ESMF library.
         if '+mpi' in spec:
-            if '^mvapich2' in spec:
+            if 'platform=cray' in self.spec:
+                os.environ['ESMF_COMM'] = 'mpi'
+            elif '^mvapich2' in spec:
                 os.environ['ESMF_COMM'] = 'mvapich2'
             elif '^mpich' in spec:
-                # FIXME: mpich or mpich2?
+                # esmf@7.0.1 does not include configs for mpich3,
+                # so we start with the configs for mpich2:
                 os.environ['ESMF_COMM'] = 'mpich2'
+                # The mpich 3 series split apart the Fortran and C bindings,
+                # so we link the Fortran libraries when building C programs:
+                os.environ['ESMF_CXXLINKLIBS'] = '-lmpifort'
             elif '^openmpi' in spec:
                 os.environ['ESMF_COMM'] = 'openmpi'
             elif '^intel-parallel-studio+mpi' in spec:
diff --git a/var/spack/repos/builtin/packages/essl/package.py b/var/spack/repos/builtin/packages/essl/package.py
new file mode 100644
index 0000000000..565b0ec6e5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/essl/package.py
@@ -0,0 +1,65 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Essl(Package):
+    """IBM's Engineering and Scientific Subroutine Library (ESSL)."""
+
+    homepage = "https://www.ibm.com/systems/power/software/essl/"
+
+    variant('ilp64', default=False, description='64 bit integers')
+    variant(
+        'threads', default='openmp',
+        description='Multithreading support',
+        values=('openmp', 'none'),
+        multi=False
+    )
+    variant('cuda', default=False, description='CUDA acceleration')
+
+    provides('blas')
+
+    conflicts('+cuda', when='+ilp64',
+              msg='ESSL+cuda+ilp64 cannot combine CUDA acceleration'
+              ' 64 bit integers')
+
+    conflicts('+cuda', when='threads=none',
+              msg='ESSL+cuda threads=none cannot combine CUDA acceleration'
+              ' without multithreading support')
+
+    @property
+    def blas_libs(self):
+        spec = self.spec
+        prefix = self.prefix
+
+        if '+ilp64' in spec:
+            essl_lib = ['libessl6464']
+        else:
+            essl_lib = ['libessl']
+
+        if spec.satisfies('threads=openmp'):
+            # ESSL SMP support requires XL or Clang OpenMP library
+            if '%xl' in spec or '%xl_r' in spec or '%clang' in spec:
+                if '+ilp64' in spec:
+                    essl_lib = ['libesslsmp6464']
+                else:
+                    if '+cuda' in spec:
+                        essl_lib = ['libesslsmpcuda']
+                    else:
+                        essl_lib = ['libesslsmp']
+
+        essl_root = prefix.lib64
+        essl_libs = find_libraries(
+            essl_lib,
+            root=essl_root,
+            shared=True
+        )
+
+        return essl_libs
+
+    def install(self, spec, prefix):
+        raise InstallError('IBM ESSL is not installable;'
+                           ' it is vendor supplied')
diff --git a/var/spack/repos/builtin/packages/ethminer/package.py b/var/spack/repos/builtin/packages/ethminer/package.py
new file mode 100644
index 0000000000..0689d6faed
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ethminer/package.py
@@ -0,0 +1,35 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Ethminer(CMakePackage):
+    """The ethminer is an Ethereum GPU mining worker."""
+
+    homepage = "https://github.com/ethereum-mining/ethminer"
+    url = "https://github.com/ethereum-mining/ethminer/archive/v0.12.0.tar.gz"
+
+    version('0.12.0', '1c7e3df8476a146702a4050ad984ae5a')
+
+    variant('opencl', default=True, description='Enable OpenCL mining.')
+    variant('cuda', default=False, description='Enable CUDA mining.')
+    variant('stratum', default=True,
+            description='Build with Stratum protocol support.')
+
+    depends_on('python')
+    depends_on('boost')
+    depends_on('json-c')
+    depends_on('curl')
+    depends_on('zlib')
+    depends_on('cuda', when='+cuda')
+    depends_on('mesa', when='+opencl')
+
+    def cmake_args(self):
+        spec = self.spec
+        return [
+            '-DETHASHCL=%s' % ('YES' if '+opencl' in spec else 'NO'),
+            '-DETHASHCUDA=%s' % ('YES' if '+cuda' in spec else 'NO'),
+            '-DETHSTRATUM=%s' % ('YES' if '+stratum' in spec else 'NO')]
diff --git a/var/spack/repos/builtin/packages/etsf-io/package.py b/var/spack/repos/builtin/packages/etsf-io/package.py
index dc0dac415f..cade69c89c 100644
--- a/var/spack/repos/builtin/packages/etsf-io/package.py
+++ b/var/spack/repos/builtin/packages/etsf-io/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/everytrace-example/package.py b/var/spack/repos/builtin/packages/everytrace-example/package.py
index cedcd684fc..1eff5f6451 100644
--- a/var/spack/repos/builtin/packages/everytrace-example/package.py
+++ b/var/spack/repos/builtin/packages/everytrace-example/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,9 @@ class EverytraceExample(CMakePackage):
     """Get stack trace EVERY time a program exits."""
 
     homepage = "https://github.com/citibeth/everytrace-example"
-    version('develop',
-            git='https://github.com/citibeth/everytrace-example.git',
-            branch='develop')
+    git      = "https://github.com/citibeth/everytrace-example.git"
+
+    version('develop', branch='develop')
 
     depends_on('everytrace+mpi+fortran')
 
diff --git a/var/spack/repos/builtin/packages/everytrace/package.py b/var/spack/repos/builtin/packages/everytrace/package.py
index 96813672ad..8aaf928add 100644
--- a/var/spack/repos/builtin/packages/everytrace/package.py
+++ b/var/spack/repos/builtin/packages/everytrace/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,15 +10,18 @@ class Everytrace(CMakePackage):
     """Get stack trace EVERY time a program exits."""
 
     homepage = "https://github.com/citibeth/everytrace"
-    url = "https://github.com/citibeth/everytrace/tarball/0.2.0"
+    url      = "https://github.com/citibeth/everytrace/archive/0.2.2.tar.gz"
+    git      = "https://github.com/citibeth/everytrace.git"
+
+    maintainers = ['citibeth']
 
-    version('0.2.0', '2af0e5b6255064d5191accebaa70d222')
-    version('develop',
-            git='https://github.com/citibeth/everytrace.git', branch='develop')
+    version('develop', branch='develop')
+    version('0.2.2', 'dd60b8bf68cbf3dc2be305a040f2fe3e')
 
     variant('mpi', default=True, description='Enables MPI parallelism')
     variant('fortran', default=True,
             description='Enable use with Fortran programs')
+    variant('cxx', default=True, description='Enable C++ Exception-based features')
 
     depends_on('mpi', when='+mpi')
 
@@ -45,7 +29,8 @@ class Everytrace(CMakePackage):
         spec = self.spec
         return [
             '-DUSE_MPI=%s' % ('YES' if '+mpi' in spec else 'NO'),
-            '-DUSE_FORTRAN=%s' % ('YES' if '+fortran' in spec else 'NO')]
+            '-DUSE_FORTRAN=%s' % ('YES' if '+fortran' in spec else 'NO'),
+            '-DUSE_CXX=%s' % ('YES' if '+cxx' in spec else 'NO')]
 
     def setup_environment(self, spack_env, run_env):
         run_env.prepend_path('PATH', join_path(self.prefix, 'bin'))
diff --git a/var/spack/repos/builtin/packages/evieext/package.py b/var/spack/repos/builtin/packages/evieext/package.py
index a88764516e..e857c0d5d5 100644
--- a/var/spack/repos/builtin/packages/evieext/package.py
+++ b/var/spack/repos/builtin/packages/evieext/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Evieext(AutotoolsPackage):
 
     version('1.1.1', '018a7d24d0c7926d594246320bcb6a86')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/exabayes/package.py b/var/spack/repos/builtin/packages/exabayes/package.py
index 1529261397..2e951f6d75 100644
--- a/var/spack/repos/builtin/packages/exabayes/package.py
+++ b/var/spack/repos/builtin/packages/exabayes/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/examinimd/package.py b/var/spack/repos/builtin/packages/examinimd/package.py
new file mode 100644
index 0000000000..ffb31a8ff8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/examinimd/package.py
@@ -0,0 +1,67 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Examinimd(MakefilePackage):
+    """ExaMiniMD is a proxy application and research vehicle for particle codes,
+    in particular Molecular Dynamics (MD). Compared to previous MD proxy apps
+    (MiniMD, COMD), its design is significantly more modular in order to allow
+    independent investigation of different aspects. To achieve that the main
+    components such as force calculation, communication, neighbor list
+    construction and binning are derived classes whose main functionality is
+    accessed via virtual functions. This allows a developer to write a new
+    derived class and drop it into the code without touching much of the
+    rest of the application."""
+
+    tags = ['proxy-app', 'ecp-proxy-app']
+
+    homepage = "https://github.com/ECP-copa/ExaMiniMD"
+    url      = "https://github.com/ECP-copa/ExaMiniMD/archive/1.0.zip"
+    git      = "https://github.com/ECP-copa/ExaMiniMD.git"
+
+    version('develop', branch='master')
+    version('1.0', '5db7679a4b9296c0cc3b2ff3a7e8f38f')
+
+    variant('mpi', default=True, description='Build with MPI support')
+    variant('openmp', default=False, description='Build with OpenMP support')
+    variant('pthreads', default=False, description='Build with POSIX Threads support')
+    # TODO: Set up cuda variant when test machine available
+
+    conflicts('+openmp', when='+pthreads')
+
+    depends_on('kokkos')
+    depends_on('mpi', when='+mpi')
+
+    @property
+    def build_targets(self):
+        targets = []
+        # Append Kokkos
+        targets.append('KOKKOS_PATH={0}'.format(self.spec['kokkos'].prefix))
+        # Set kokkos device
+        if 'openmp' in self.spec:
+            targets.append('KOKKOS_DEVICES=OpenMP')
+        elif 'pthreads' in self.spec:
+            targets.append('KOKKOS_DEVICES=Pthread')
+        else:
+            targets.append('KOKKOS_DEVICES=Serial')
+        # Set MPI as needed
+        if '+mpi' in self.spec:
+            targets.append('MPI=1')
+            targets.append('CXX = {0}'.format(self.spec['mpi'].mpicxx))
+        else:
+            targets.append('MPI=0')
+            targets.append('CXX = {0}'.format('spack_cxx'))
+        return targets
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('src/ExaMiniMD', prefix.bin)
+        install_tree('input', prefix.input)
+        mkdirp(prefix.docs)
+        install('README.md', prefix.docs)
+        install('LICENSE', prefix.docs)
diff --git a/var/spack/repos/builtin/packages/exampm/package.py b/var/spack/repos/builtin/packages/exampm/package.py
index eba2fbc442..8ea259daae 100644
--- a/var/spack/repos/builtin/packages/exampm/package.py
+++ b/var/spack/repos/builtin/packages/exampm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,8 @@ class Exampm(CMakePackage):
     """Exascale Material Point Method (MPM) Mini-App"""
 
     homepage = "https://github.com/ECP-copa/ExaMPM"
-    url      = "https://github.com/ECP-copa/ExaMPM"
+    git      = "https://github.com/ECP-copa/ExaMPM.git"
 
-    version('develop', git='https://github.com/ECP-copa/ExaMPM',
-            branch='master')
+    version('develop', branch='master')
 
     tags = ['proxy-app']
diff --git a/var/spack/repos/builtin/packages/exasp2/package.py b/var/spack/repos/builtin/packages/exasp2/package.py
index aac5419893..511ff984a7 100644
--- a/var/spack/repos/builtin/packages/exasp2/package.py
+++ b/var/spack/repos/builtin/packages/exasp2/package.py
@@ -1,28 +1,10 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
+import glob
 
 
 class Exasp2(MakefilePackage):
@@ -42,9 +24,11 @@ class Exasp2(MakefilePackage):
     tags = ['proxy-app']
 
     homepage = "https://github.com/ECP-copa/ExaSP2"
+    url      = "https://github.com/ECP-copa/ExaSP2/tarball/v1.0"
+    git      = "https://github.com/ECP-copa/ExaSP2.git"
 
-    version('develop', git='https://github.com/ECP-copa/ExaSP2',
-            branch='master')
+    version('develop', branch='master')
+    version('1.0', 'dba545995acc73f2bd1101bcb377bff5')
 
     variant('mpi', default=True, description='Build With MPI Support')
 
@@ -78,17 +62,15 @@ class Exasp2(MakefilePackage):
         math_includes += " -I" + spec['blas'].prefix.include
         targets.append('SPACKBLASINCLUDES=' + math_includes)
         # And BML
-        bmlLibDirs = spec['bml'].libs.directories[0]
-        targets.append('BML_PATH=' + bmlLibDirs)
+        bml_lib_dirs = spec['bml'].libs.directories[0]
+        targets.append('BML_PATH=' + bml_lib_dirs)
         targets.append('--file=Makefile.vanilla')
         return targets
 
     def install(self, spec, prefix):
         mkdir(prefix.bin)
         mkdir(prefix.doc)
-        if '+mpi' in self.spec:
-            install('bin/ExaSP2-parallel', prefix.bin)
-        else:
-            install('bin/ExaSP2-serial', prefix.bin)
+        for files in glob.glob('bin/ExaSP2-*'):
+            install(files, prefix.bin)
         install('LICENSE.md', prefix.doc)
         install('README.md', prefix.doc)
diff --git a/var/spack/repos/builtin/packages/exmcutils/package.py b/var/spack/repos/builtin/packages/exmcutils/package.py
index 02010deaf3..33b1827f00 100644
--- a/var/spack/repos/builtin/packages/exmcutils/package.py
+++ b/var/spack/repos/builtin/packages/exmcutils/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -30,8 +11,8 @@ class Exmcutils(AutotoolsPackage):
     """ExM C-Utils: Generic C utility library for ADLB/X and Swift/T"""
 
     homepage = 'http://swift-lang.org/Swift-T'
-    url      = 'http://swift-lang.github.io/swift-t-downloads/exmcutils-0.5.3.tar.gz'
+    url      = 'http://swift-lang.github.io/swift-t-downloads/spack/exmcutils-0.0.0.tar.gz'
 
-    version('0.5.3', '0e3ed6cc2991c684cd8f08db45c99a39')
+    version('0.5.6', 'b12a8dc163e3369492ec7c1403fe86e4')
 
     # This package has no dependencies.
diff --git a/var/spack/repos/builtin/packages/exodusii/package.py b/var/spack/repos/builtin/packages/exodusii/package.py
index d74137533c..669929abce 100644
--- a/var/spack/repos/builtin/packages/exodusii/package.py
+++ b/var/spack/repos/builtin/packages/exodusii/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 # TODO: Add support for a C++11 enabled installation that filters out the
@@ -35,13 +16,12 @@ class Exodusii(CMakePackage):
        data transfer between codes.  An Exodus II data file is a random
        access, machine independent, binary file that is written and read
        via C, C++, or Fortran API routines.
-
     """
 
     homepage = "https://github.com/gsjaardema/seacas"
-    url      = "https://github.com/gsjaardema/seacas/archive/master.zip"
+    git      = "https://github.com/gsjaardema/seacas.git"
 
-    version('2016-08-09', git='https://github.com/gsjaardema/seacas.git', commit='2ffeb1b')
+    version('2016-08-09', commit='2ffeb1b')
 
     variant('mpi', default=True, description='Enables MPI parallelism.')
 
diff --git a/var/spack/repos/builtin/packages/exonerate/package.py b/var/spack/repos/builtin/packages/exonerate/package.py
index 2dae693b72..27b1c557c3 100644
--- a/var/spack/repos/builtin/packages/exonerate/package.py
+++ b/var/spack/repos/builtin/packages/exonerate/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,7 +14,7 @@ class Exonerate(Package):
 
     version('2.4.0', '126fbade003b80b663a1d530c56f1904')
 
-    depends_on('pkg-config', type="build")
+    depends_on('pkgconfig', type="build")
     depends_on('glib')
 
     parallel = False
diff --git a/var/spack/repos/builtin/packages/expat/package.py b/var/spack/repos/builtin/packages/expat/package.py
index a4ca544e57..2068401160 100644
--- a/var/spack/repos/builtin/packages/expat/package.py
+++ b/var/spack/repos/builtin/packages/expat/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import sys
 
@@ -29,8 +10,8 @@ import sys
 class Expat(AutotoolsPackage):
     """Expat is an XML parser library written in C."""
 
-    homepage = "http://expat.sourceforge.net/"
-    url      = "https://sourceforge.net/projects/expat/files/expat/2.2.2/expat-2.2.2.tar.bz2"
+    homepage = "https://libexpat.github.io/"
+    url      = "https://github.com/libexpat/libexpat/releases/download/R_2_2_2/expat-2.2.2.tar.bz2"
 
     # Version 2.2.2 introduced a requirement for a high quality
     # entropy source.  "Older" linux systems (aka CentOS 7) do not
@@ -44,9 +25,14 @@ class Expat(AutotoolsPackage):
             description="Use libbsd (for high quality randomness)")
     depends_on('libbsd', when="@2.2.1:+libbsd")
 
+    version('2.2.5', '789e297f547980fc9ecc036f9a070d49')
     version('2.2.2', '1ede9a41223c78528b8c5d23e69a2667')
     version('2.2.0', '2f47841c829facb346eb6e3fab5212e2')
 
+    def url_for_version(self, version):
+        url = 'https://github.com/libexpat/libexpat/releases/download/R_{0}/expat-{1}.tar.bz2'
+        return url.format(version.underscored, version.dotted)
+
     def configure_args(self):
         spec = self.spec
         args = []
diff --git a/var/spack/repos/builtin/packages/expect/package.py b/var/spack/repos/builtin/packages/expect/package.py
index 786539d025..8e17b3d5d9 100644
--- a/var/spack/repos/builtin/packages/expect/package.py
+++ b/var/spack/repos/builtin/packages/expect/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
 import os
diff --git a/var/spack/repos/builtin/packages/express/package.py b/var/spack/repos/builtin/packages/express/package.py
new file mode 100644
index 0000000000..cfb262d313
--- /dev/null
+++ b/var/spack/repos/builtin/packages/express/package.py
@@ -0,0 +1,40 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os.path
+import glob
+
+
+class Express(CMakePackage):
+    """eXpress is a streaming tool for quantifying the abundances of a set of
+       target sequences from sampled subsequences."""
+
+    homepage = "http://bio.math.berkeley.edu/eXpress/"
+    git      = "https://github.com/adarob/eXpress.git"
+
+    version('2015-11-29', commit='f845cab2c7f2d9247b35143e4aa05869cfb10e79')
+
+    depends_on('boost')
+    depends_on('bamtools')
+    depends_on('zlib')
+
+    conflicts('%gcc@6.0.0:', when='@2015-11-29')
+
+    def patch(self):
+        with working_dir('src'):
+            files = glob.iglob('*.*')
+            for file in files:
+                if os.path.isfile(file):
+                    edit = FileFilter(file)
+                    edit.filter('#include <api', '#include <%s' % self.spec[
+                                'bamtools'].prefix.include.bamtools.api)
+            edit = FileFilter('CMakeLists.txt')
+            edit.filter('\${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/'
+                        'libbamtools.a', '%s' % self.spec['bamtools'].libs)
+
+    def setup_environment(self, spack_env, run_env):
+        spack_env.prepend_path('CPATH', self.spec[
+                               'bamtools'].prefix.include.bamtools)
diff --git a/var/spack/repos/builtin/packages/extrae/package.py b/var/spack/repos/builtin/packages/extrae/package.py
index a13963655b..c79573424d 100644
--- a/var/spack/repos/builtin/packages/extrae/package.py
+++ b/var/spack/repos/builtin/packages/extrae/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 # typical working line with extrae 3.0.1
diff --git a/var/spack/repos/builtin/packages/exuberant-ctags/package.py b/var/spack/repos/builtin/packages/exuberant-ctags/package.py
index 4a4f56e270..f77678b397 100644
--- a/var/spack/repos/builtin/packages/exuberant-ctags/package.py
+++ b/var/spack/repos/builtin/packages/exuberant-ctags/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/f90cache/package.py b/var/spack/repos/builtin/packages/f90cache/package.py
index ff18433912..02f37540e8 100644
--- a/var/spack/repos/builtin/packages/f90cache/package.py
+++ b/var/spack/repos/builtin/packages/f90cache/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/fabtests/package.py b/var/spack/repos/builtin/packages/fabtests/package.py
new file mode 100644
index 0000000000..77d11e68a7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fabtests/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Fabtests(AutotoolsPackage):
+    """Fabtests provides a set of examples that uses libfabric"""
+
+    homepage = "http://libfabric.org"
+    url      = "https://github.com/ofiwg/fabtests/releases/download/v1.5.3/fabtests-1.5.3.tar.gz"
+
+    version('1.6.0', '0441aa0aeda391b1bf1eb71250a4afbc')
+    version('1.5.3', 'f60cb95843ebf62e4eaa128e08ccdc7d')
+
+    depends_on('libfabric')
diff --git a/var/spack/repos/builtin/packages/falcon/package.py b/var/spack/repos/builtin/packages/falcon/package.py
index d2ca55d443..85d130a1d2 100644
--- a/var/spack/repos/builtin/packages/falcon/package.py
+++ b/var/spack/repos/builtin/packages/falcon/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -36,11 +17,9 @@ class Falcon(PythonPackage):
     front-end written in Python for convenience."""
 
     homepage = "https://github.com/PacificBiosciences/FALCON"
-    url      = "https://github.com/PacificBiosciences/FALCON.git"
+    git      = "https://github.com/PacificBiosciences/FALCON.git"
 
-    version('2017-05-30',
-            git='https://github.com/PacificBiosciences/FALCON.git',
-            commit='86cec6157291679095ea6080b0cde6561eccc041')
+    version('2017-05-30', commit='86cec6157291679095ea6080b0cde6561eccc041')
 
     depends_on('py-setuptools', type='run')
     depends_on('py-pypeflow', type='run')
diff --git a/var/spack/repos/builtin/packages/farmhash/CMakeLists.txt b/var/spack/repos/builtin/packages/farmhash/CMakeLists.txt
deleted file mode 100644
index 0286f29ad0..0000000000
--- a/var/spack/repos/builtin/packages/farmhash/CMakeLists.txt
+++ /dev/null
@@ -1,25 +0,0 @@
-cmake_minimum_required(VERSION 2.8.3)
-
-project(farmhash)
-
-set(FARMHASH_SRCS
-    "src/farmhash.h"
-    "src/farmhash.cc"
-)
-
-set(FARMHASH_INCLUDES
-    "src/farmhash.h"
-)
-
-include_directories("${CMAKE_CURRENT_SOURCE_DIR}")
-
-add_library(farmhash ${FARMHASH_SRCS})
-add_definitions(-DFARMHASH_NO_BUILTIN_EXPECT)
-
-install(TARGETS farmhash
-  LIBRARY DESTINATION lib COMPONENT RuntimeLibraries
-  ARCHIVE DESTINATION lib COMPONENT Development)
-
-foreach(FARMHASH_INCLUDE ${FARMHASH_INCLUDES})
-  install(FILES ${FARMHASH_INCLUDE} DESTINATION include COMPONENT Development)
-endforeach()
diff --git a/var/spack/repos/builtin/packages/farmhash/package.py b/var/spack/repos/builtin/packages/farmhash/package.py
deleted file mode 100644
index 071a43c1a2..0000000000
--- a/var/spack/repos/builtin/packages/farmhash/package.py
+++ /dev/null
@@ -1,42 +0,0 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-from spack import *
-import os.path
-from shutil import copyfile
-
-
-class Farmhash(CMakePackage):
-    """
-    FarmHash provides hash functions for strings and other data.
-    """
-
-    homepage = "https://github.com/google/farmhash"
-
-    version('92e897', git='https://github.com/google/farmhash.git', 
-            commit='92e897b282426729f4724d91a637596c7e2fe28f')
-
-    def patch(self):
-        copyfile(join_path(os.path.dirname(__file__), "CMakeLists.txt"),
-                 "CMakeLists.txt")
diff --git a/var/spack/repos/builtin/packages/fast-global-file-status/package.py b/var/spack/repos/builtin/packages/fast-global-file-status/package.py
new file mode 100644
index 0000000000..79b35b54ee
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fast-global-file-status/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class FastGlobalFileStatus(AutotoolsPackage):
+    """provides a scalable mechanism to retrieve such information of a file,
+       including its degree of distribution or replication and consistency."""
+
+    homepage = "https://github.com/LLNL/FastGlobalFileStatus"
+    url = 'https://github.com/LLNL/FastGlobalFileStatus/files/2271592/fastglobalfilestatus-1.1.tar.gz'
+
+    version('1.1', 'c3d764c47a60310823947c489cd0f2df')
+
+    depends_on('mrnet')
+    depends_on('mount-point-attributes')
+    depends_on('mpi')
+
+    def configure_args(self):
+        spec = self.spec
+        args = [
+            "--with-mpa=%s"   % spec['mount-point-attributes'].prefix,
+            "--with-mrnet=%s"       % spec['mrnet'].prefix
+        ]
+        return args
diff --git a/var/spack/repos/builtin/packages/fasta/package.py b/var/spack/repos/builtin/packages/fasta/package.py
new file mode 100644
index 0000000000..6a70762320
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fasta/package.py
@@ -0,0 +1,58 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Fasta(MakefilePackage):
+    """The FASTA programs find regions of local or global similarity
+    between Protein or DNA sequences, either by searching Protein or
+    DNA databases, or by identifying local duplications within a
+    sequence. Other programs provide information on the statistical
+    significance of an alignment. Like BLAST, FASTA can be used to
+    infer functional and evolutionary relationships between sequences
+    as well as help identify members of gene families.
+    """
+
+    homepage = "https://fasta.bioch.virginia.edu/fasta_www2/fasta_list2.shtml"
+    url      = "https://github.com/wrpearson/fasta36/archive/fasta-v36.3.8g.tar.gz"
+
+    version('36.3.8g', sha256='fa5318b6f8d6a3cfdef0d29de530eb005bfd3ca05835faa6ad63663f8dce7b2e')
+
+    depends_on('zlib')
+
+    # The src tree includes a plethora of variant Makefiles and the
+    # builder is expected to choose one that's appropriate.  This'll
+    # do for a first cut.  I can't test anything else....
+    @property
+    def makefile_name(self):
+        if self.spec.satisfies('platform=darwin'):
+            name = 'Makefile.os_x86_64'
+        elif (self.spec.satisfies('platform=linux') and
+              self.spec.satisfies('target=x86_64')):
+            name = 'Makefile.linux64_sse2'
+        else:
+            tty.die('''Unsupported platform/target, must be
+Darwin (assumes 64-bit)
+Linux x86_64
+''')
+        return name
+
+    @property
+    def makefile_path(self):
+        return join_path(self.stage.source_path, 'make', self.makefile_name)
+
+    def edit(self, spec, prefix):
+        makefile = FileFilter(self.makefile_path)
+        makefile.filter('XDIR = .*', 'XDIR = {0}'.format(prefix.bin))
+
+    def build(self, spec, prefix):
+        with working_dir('src'):
+            make('-f', self.makefile_path)
+
+    def install(self, spec, prefix):
+        with working_dir('src'):
+            mkdir(prefix.bin)
+            make('-f', self.makefile_path, 'install')
diff --git a/var/spack/repos/builtin/packages/fastjar/package.py b/var/spack/repos/builtin/packages/fastjar/package.py
index 19af359e81..15c98729aa 100644
--- a/var/spack/repos/builtin/packages/fastjar/package.py
+++ b/var/spack/repos/builtin/packages/fastjar/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/fastmath/package.py b/var/spack/repos/builtin/packages/fastmath/package.py
index c91289afaa..35e245e1fd 100644
--- a/var/spack/repos/builtin/packages/fastmath/package.py
+++ b/var/spack/repos/builtin/packages/fastmath/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/fastme/package.py b/var/spack/repos/builtin/packages/fastme/package.py
index a64cd3163c..2aae0380f7 100644
--- a/var/spack/repos/builtin/packages/fastme/package.py
+++ b/var/spack/repos/builtin/packages/fastme/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/fastphase/package.py b/var/spack/repos/builtin/packages/fastphase/package.py
index 857e13b3bd..80faa0d504 100644
--- a/var/spack/repos/builtin/packages/fastphase/package.py
+++ b/var/spack/repos/builtin/packages/fastphase/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/fastq-screen/package.py b/var/spack/repos/builtin/packages/fastq-screen/package.py
index 81289a5cb1..c798fdb5a8 100644
--- a/var/spack/repos/builtin/packages/fastq-screen/package.py
+++ b/var/spack/repos/builtin/packages/fastq-screen/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/fastqc/package.py b/var/spack/repos/builtin/packages/fastqc/package.py
index 9d20805907..bcebd2b4cf 100644
--- a/var/spack/repos/builtin/packages/fastqc/package.py
+++ b/var/spack/repos/builtin/packages/fastqc/package.py
@@ -1,30 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from distutils.dir_util import copy_tree, mkpath
-from distutils.file_util import copy_file
 
 
 class Fastqc(Package):
@@ -33,6 +12,7 @@ class Fastqc(Package):
     homepage = "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/"
     url = "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip"
 
+    version('0.11.7', '8fead05fa62c5e723f0d2157a9b5fcd4')
     version('0.11.5', '3524f101c0ab0bae77c7595983170a76')
     version('0.11.4', '104ff2e0e9aebf5bee1f6b068a059b0d')
 
@@ -42,15 +22,15 @@ class Fastqc(Package):
     patch('fastqc.patch', level=0)
 
     def install(self, spec, prefix):
-        mkpath(self.prefix.bin)
-        mkpath(self.prefix.lib)
-        copy_file('fastqc', self.prefix.bin)
+        mkdir(prefix.bin)
+        mkdir(prefix.lib)
+        install('fastqc', prefix.bin)
         for j in ['cisd-jhdf5.jar', 'jbzip2-0.9.jar', 'sam-1.103.jar']:
-            copy_file(j, self.prefix.lib)
+            install(j, prefix.lib)
         for d in ['Configuration', 'net', 'org', 'Templates', 'uk']:
-            copy_tree(d, join_path(self.prefix.lib, d))
+            install_tree(d, join_path(prefix.lib, d))
         chmod = which('chmod')
-        chmod('+x', join_path(self.prefix.bin, 'fastqc'))
+        chmod('+x', prefix.bin.fastqc)
 
     # In theory the 'run' dependency on 'jdk' above should take
     # care of this for me. In practice, it does not.
@@ -58,5 +38,4 @@ class Fastqc(Package):
         """Add <prefix> to the path; the package has a script at the
            top level.
         """
-        run_env.prepend_path('PATH', join_path(self.spec['java'].prefix,
-                             'bin'))
+        run_env.prepend_path('PATH', self.spec['java'].prefix.bin)
diff --git a/var/spack/repos/builtin/packages/fastqvalidator/package.py b/var/spack/repos/builtin/packages/fastqvalidator/package.py
index d91ea6d0ba..38ccafa069 100644
--- a/var/spack/repos/builtin/packages/fastqvalidator/package.py
+++ b/var/spack/repos/builtin/packages/fastqvalidator/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,10 +10,9 @@ class Fastqvalidator(MakefilePackage):
     """The fastQValidator validates the format of fastq files."""
 
     homepage = "http://genome.sph.umich.edu/wiki/FastQValidator"
-    url      = "https://github.com/statgen/fastQValidator/archive/v0.1.1a.tar.gz"
+    git      = "https://github.com/statgen/fastQValidator.git"
 
-    version('2017-01-10', commit='6d619a34749e9d33c34ef0d3e0e87324ca77f320',
-            git='https://github.com/statgen/fastQValidator.git')
+    version('2017-01-10', commit='6d619a34749e9d33c34ef0d3e0e87324ca77f320')
 
     resource(
         name='libStatGen',
diff --git a/var/spack/repos/builtin/packages/fasttree/package.py b/var/spack/repos/builtin/packages/fasttree/package.py
new file mode 100644
index 0000000000..813b5eb0d6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fasttree/package.py
@@ -0,0 +1,31 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Fasttree(Package):
+    """FastTree infers approximately-maximum-likelihood phylogenetic
+       trees from alignments of nucleotide or protein sequences.
+       FastTree can handle alignments with up to a million of sequences
+       in a reasonable amount of time and memory."""
+
+    homepage = "http://www.microbesonline.org/fasttree"
+    url      = "http://www.microbesonline.org/fasttree/FastTree-2.1.10.c"
+
+    version('2.1.10', '1c2c6425a638ec0c61ef064cda687987', expand=False, url='http://www.microbesonline.org/fasttree/FastTree-2.1.10.c')
+
+    phases = ['build', 'install']
+
+    def build(self, spec, prefix):
+        cc = Executable(spack_cc)
+        cc('-O3', self.compiler.openmp_flag,
+           '-DOPENMP', '-finline-functions', '-funroll-loops', '-Wall',
+           '-oFastTreeMP', 'FastTree-' + format(spec.version.dotted) + '.c',
+           '-lm')
+
+    def install(self, spec, prefix):
+        mkdir(prefix.bin)
+        install('FastTreeMP', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/fastx-toolkit/package.py b/var/spack/repos/builtin/packages/fastx-toolkit/package.py
index db9a1e1d6e..c1e74163d0 100644
--- a/var/spack/repos/builtin/packages/fastx-toolkit/package.py
+++ b/var/spack/repos/builtin/packages/fastx-toolkit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/fenics/package.py b/var/spack/repos/builtin/packages/fenics/package.py
index d95c826c34..f9707895fc 100644
--- a/var/spack/repos/builtin/packages/fenics/package.py
+++ b/var/spack/repos/builtin/packages/fenics/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -77,7 +58,7 @@ class Fenics(CMakePackage):
     depends_on('boost+filesystem+program_options+system+iostreams+timer+regex+chrono')
 
     depends_on('mpi', when='+mpi')
-    depends_on('hdf5', when='+hdf5')
+    depends_on('hdf5+hl', when='+hdf5')
     depends_on('parmetis@4.0.2:^metis+real64', when='+parmetis')
     depends_on('scotch~metis', when='+scotch~mpi')
     depends_on('scotch+mpi~metis', when='+scotch+mpi')
diff --git a/var/spack/repos/builtin/packages/fermi/package.py b/var/spack/repos/builtin/packages/fermi/package.py
new file mode 100644
index 0000000000..2c4693107d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fermi/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Fermi(MakefilePackage):
+    """A WGS de novo assembler based on the FMD-index for large genomes."""
+
+    homepage = "https://github.com/lh3/fermi"
+    url      = "https://github.com/downloads/lh3/fermi/fermi-1.1.tar.bz2"
+
+    version('1.1', 'd5f006315652b6f18070b31474ca5ebb')
+
+    depends_on('zlib')
+    depends_on('perl', type='run')
+
+    def install(self, spec, prefix):
+        mkdir(prefix.bin)
+        install('fermi', prefix.bin)
+        install('run-fermi.pl', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/fermikit/package.py b/var/spack/repos/builtin/packages/fermikit/package.py
new file mode 100644
index 0000000000..0f44174fda
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fermikit/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Fermikit(MakefilePackage):
+    """De novo assembly based variant calling pipeline for Illumina short
+    reads"""
+
+    homepage = "https://github.com/lh3/fermikit"
+    git      = "https://github.com/lh3/fermikit.git"
+
+    version('2017-11-7', commit='bf9c7112221577ba110665bddca8f1987250bdc7',
+            submodules=True)
+
+    depends_on('zlib')
+
+    def install(self, spec, prefix):
+        install_tree('fermi.kit', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/fermisciencetools/package.py b/var/spack/repos/builtin/packages/fermisciencetools/package.py
new file mode 100644
index 0000000000..b2e67e7c27
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fermisciencetools/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Fermisciencetools(Package):
+    """The Fermi Science Tools consists of the basic tools necessary to
+    analyze Fermi data.
+
+    This is the binary version for Linux x86_64 with libc-2.17."""
+
+    homepage = "https://fermi.gsfc.nasa.gov/ssc/data/analysis/software/"
+    url      = "https://fermi.gsfc.nasa.gov/ssc/data/analysis/software/v11r5p3/ScienceTools-v11r5p3-fssc-20180124-x86_64-unknown-linux-gnu-libc2.17.tar.gz"
+
+    # Now we are using the binary distribution. The source distribution is also
+    # available, but there might be some logical errors in the configure codes,
+    # which leads to failing in building it from source. Hopefully someone else
+    # can figure it out and we can use the source distribution instead.
+    version('11r5p3', 'cf050ddddfe9251b6ebe8d3fd7de3c3f')
+
+    def install(self, spec, prefix):
+        install_tree('x86_64-unknown-linux-gnu-libc2.17', prefix)
diff --git a/var/spack/repos/builtin/packages/ferret/package.py b/var/spack/repos/builtin/packages/ferret/package.py
index 33a6cfcb92..7ecffc3429 100644
--- a/var/spack/repos/builtin/packages/ferret/package.py
+++ b/var/spack/repos/builtin/packages/ferret/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 import os
diff --git a/var/spack/repos/builtin/packages/ffmpeg/package.py b/var/spack/repos/builtin/packages/ffmpeg/package.py
index 1a7e3b253b..e5f8aab78f 100644
--- a/var/spack/repos/builtin/packages/ffmpeg/package.py
+++ b/var/spack/repos/builtin/packages/ffmpeg/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/fftw/package.py b/var/spack/repos/builtin/packages/fftw/package.py
index e2fc311166..d3d8795fee 100644
--- a/var/spack/repos/builtin/packages/fftw/package.py
+++ b/var/spack/repos/builtin/packages/fftw/package.py
@@ -1,29 +1,12 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
+import llnl.util.lang
+
 
 class Fftw(AutotoolsPackage):
     """FFTW is a C subroutine library for computing the discrete Fourier
@@ -37,6 +20,8 @@ class Fftw(AutotoolsPackage):
     url      = "http://www.fftw.org/fftw-3.3.4.tar.gz"
     list_url = "http://www.fftw.org/download.html"
 
+    version('3.3.8', '8aac833c943d8e90d51b697b27d4384d')
+    version('3.3.7', '0d5915d7d39b3253c1cc05030d79ac47')
     version('3.3.6-pl2', '927e481edbb32575397eb3d62535a856')
     version('3.3.5', '6cc08a3b9c7ee06fdd5b9eb02e06f569')
     version('3.3.4', '2edab8c06b24feeb3b82bbb3ebf3e7b3')
@@ -65,15 +50,62 @@ class Fftw(AutotoolsPackage):
         'pfft_patches', default=False,
         description='Add extra transpose functions for PFFT compatibility')
 
+    variant(
+        'simd',
+        default='sse2,avx,avx2',
+        values=(
+            'sse', 'sse2', 'avx', 'avx2', 'avx512',  # Intel
+            'avx-128-fma', 'kcvi',  # Intel
+            'altivec', 'vsx',  # IBM
+            'neon',  # ARM
+            'generic-simd128', 'generic-simd256'  # Generic
+        ),
+        description='Optimizations that are enabled in this build',
+        multi=True
+    )
+    variant('fma', default=False, description='Activate support for fma')
+
     depends_on('mpi', when='+mpi')
     depends_on('automake', type='build', when='+pfft_patches')
     depends_on('autoconf', type='build', when='+pfft_patches')
     depends_on('libtool', type='build', when='+pfft_patches')
+    # https://github.com/FFTW/fftw3/commit/902d0982522cdf6f0acd60f01f59203824e8e6f3
+    conflicts('%gcc@8:8.9999', when="@3.3.7")
+
+    provides('fftw-api@2', when='@2.1.5')
+    provides('fftw-api@3', when='@3:')
 
     @property
     def libs(self):
-        result = find_libraries(['libfftw3'], root=self.prefix, recurse=True)
-        return result
+
+        # Reduce repetitions of entries
+        query_parameters = list(llnl.util.lang.dedupe(
+            self.spec.last_query.extra_parameters
+        ))
+
+        # List of all the suffixes associated with float precisions
+        precisions = [
+            ('float', 'f'),
+            ('double', ''),
+            ('long_double', 'l'),
+            ('quad', 'q')
+        ]
+
+        # Retrieve the correct suffixes, or use double as a default
+        suffixes = [v for k, v in precisions if k in query_parameters] or ['']
+
+        # Construct the list of libraries that needs to be found
+        libraries = []
+        for sfx in suffixes:
+            if 'mpi' in query_parameters and '+mpi' in self.spec:
+                libraries.append('libfftw3' + sfx + '_mpi')
+
+            if 'openmp' in query_parameters and '+openmp' in self.spec:
+                libraries.append('libfftw3' + sfx + '_omp')
+
+            libraries.append('libfftw3' + sfx)
+
+        return find_libraries(libraries, root=self.prefix, recursive=True)
 
     def autoreconf(self, spec, prefix):
         if '+pfft_patches' in spec:
@@ -108,12 +140,11 @@ class Fftw(AutotoolsPackage):
             options.append('--enable-mpi')
 
         # SIMD support
-        # TODO: add support for more architectures
-        float_options = []
-        double_options = []
-        if 'x86_64' in spec.architecture and spec.satisfies('@3:'):
-            float_options.append('--enable-sse2')
-            double_options.append('--enable-sse2')
+        float_options, double_options = [], []
+        if spec.satisfies('@3:', strict=True):
+            for opts in (float_options, double_options):
+                opts += self.enable_or_disable('simd')
+                opts += self.enable_or_disable('fma')
 
         configure = Executable('../configure')
 
diff --git a/var/spack/repos/builtin/packages/figtree/package.py b/var/spack/repos/builtin/packages/figtree/package.py
new file mode 100644
index 0000000000..bb4cd8258a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/figtree/package.py
@@ -0,0 +1,38 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class Figtree(Package):
+    """FigTree is designed as a graphical viewer of phylogenetic trees and
+       as a program for producing publication-ready figures. As with most of
+       my programs, it was written for my own needs so may not be as polished
+       and feature-complete as a commercial program. In particular it is
+       designed to display summarized and annotated trees produced by BEAST."""
+
+    homepage = "https://github.com/rambaut/figtree"
+    url      = "https://github.com/rambaut/figtree/releases/download/v1.4.3/FigTree_v1.4.3.tgz"
+
+    version('1.4.3', sha256='f497d4dd3a6d220f6b62495b6f47a12ade50d87dbd8d6089f168e94d202f937b')
+
+    depends_on('java', type='run')
+
+    def patch(self):
+        # we have to change up the executable to point to the right program
+        filter_file('lib/figtree.jar',
+                    join_path(self.spec.prefix.lib, 'figtree.jar'),
+                    'bin/figtree', string=True)
+
+        # also set proper executable flags
+        os.chmod('bin/figtree', 0o775)
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install_tree('bin', prefix.bin)
+
+        mkdirp(prefix.lib)
+        install_tree('lib', prefix.lib)
diff --git a/var/spack/repos/builtin/packages/fimpute/package.py b/var/spack/repos/builtin/packages/fimpute/package.py
index 177ba05640..10e93d2a54 100644
--- a/var/spack/repos/builtin/packages/fimpute/package.py
+++ b/var/spack/repos/builtin/packages/fimpute/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/findutils/package.py b/var/spack/repos/builtin/packages/findutils/package.py
index 3abd8e2728..2f301d42ee 100644
--- a/var/spack/repos/builtin/packages/findutils/package.py
+++ b/var/spack/repos/builtin/packages/findutils/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,7 +11,7 @@ class Findutils(AutotoolsPackage):
        utilities of the GNU operating system."""
 
     homepage = "https://www.gnu.org/software/findutils/"
-    url      = "http://ftpmirror.gnu.org/findutils/findutils-4.6.0.tar.gz"
+    url      = "https://ftpmirror.gnu.org/findutils/findutils-4.6.0.tar.gz"
 
     version('4.6.0',  '9936aa8009438ce185bea2694a997fc1')
     version('4.4.2',  '351cc4adb07d54877fa15f75fb77d39f')
@@ -51,3 +32,32 @@ class Findutils(AutotoolsPackage):
     version('4.2.15', 'a881b15aa7170aea045bf35cc92d48e7')
     version('4.1.20', 'e90ce7222daadeb8616b8db461e17cbc')
     version('4.1',    '3ea8fe58ef5386da75f6c707713aa059')
+
+    depends_on('autoconf', type='build', when='@4.6.0')
+    depends_on('automake', type='build', when='@4.6.0')
+    depends_on('libtool', type='build', when='@4.6.0')
+    depends_on('m4', type='build', when='@4.6.0')
+    depends_on('texinfo', type='build', when='@4.6.0')
+
+    # findutils does not build with newer versions of glibc
+    patch('https://src.fedoraproject.org/rpms/findutils/raw/97ba2d7a18d1f9ae761b6ff0b4f1c4d33d7a8efc/f/findutils-4.6.0-gnulib-fflush.patch', sha256='84b916c0bf8c51b7e7b28417692f0ad3e7030d1f3c248ba77c42ede5c1c5d11e', when='@4.6.0')
+    patch('https://src.fedoraproject.org/rpms/findutils/raw/97ba2d7a18d1f9ae761b6ff0b4f1c4d33d7a8efc/f/findutils-4.6.0-gnulib-makedev.patch', sha256='bd9e4e5cc280f9753ae14956c4e4aa17fe7a210f55dd6c84aa60b12d106d47a2', when='@4.6.0')
+
+    build_directory = 'spack-build'
+
+    @property
+    def force_autoreconf(self):
+        # Run autoreconf due to build system patch (gnulib-makedev)
+        return self.spec.satisfies('@4.6.0')
+
+    @when('@4.6.0')
+    def patch(self):
+        # We have to patch out gettext support, otherwise autoreconf tries to
+        # call autopoint, which depends on find, which is part of findutils.
+        filter_file('^AM_GNU_GETTEXT.*',
+                    '',
+                    'configure.ac')
+
+        filter_file(r'^SUBDIRS = (.*) po (.*)',
+                    r'SUBDIRS = \1 \2',
+                    'Makefile.am')
diff --git a/var/spack/repos/builtin/packages/fio/package.py b/var/spack/repos/builtin/packages/fio/package.py
index 1119961ad0..59372e0a0c 100644
--- a/var/spack/repos/builtin/packages/fio/package.py
+++ b/var/spack/repos/builtin/packages/fio/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/fish/package.py b/var/spack/repos/builtin/packages/fish/package.py
index 922aca5eb8..0f7c0eb2e9 100644
--- a/var/spack/repos/builtin/packages/fish/package.py
+++ b/var/spack/repos/builtin/packages/fish/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,10 +11,12 @@ class Fish(AutotoolsPackage):
     the rest of the family.
     """
 
-    homepage = "http://fishshell.com/"
-    url      = "http://fishshell.com/files/2.2.0/fish-2.2.0.tar.gz"
-    list_url = "http://fishshell.com/"
+    homepage = "https://fishshell.com/"
+    url      = "https://github.com/fish-shell/fish-shell/releases/download/2.7.1/fish-2.7.1.tar.gz"
+    list_url = "https://fishshell.com/"
 
     depends_on('ncurses')
 
+    version('2.7.1', 'e42bb19c7586356905a58578190be792df960fa81de35effb1ca5a5a981f0c5a')
+    version('2.7.0', '3a76b7cae92f9f88863c35c832d2427fb66082f98e92a02203dc900b8fa87bcb')
     version('2.2.0', 'a76339fd14ce2ec229283c53e805faac48c3e99d9e3ede9d82c0554acfc7b77a')
diff --git a/var/spack/repos/builtin/packages/fixesproto/package.py b/var/spack/repos/builtin/packages/fixesproto/package.py
index b98437b9ff..ed062c1a08 100644
--- a/var/spack/repos/builtin/packages/fixesproto/package.py
+++ b/var/spack/repos/builtin/packages/fixesproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Fixesproto(AutotoolsPackage):
 
     version('5.0', '1b3115574cadd4cbea1f197faa7c1de4')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/flac/package.py b/var/spack/repos/builtin/packages/flac/package.py
index 2b95a5a6f2..5c41641855 100644
--- a/var/spack/repos/builtin/packages/flac/package.py
+++ b/var/spack/repos/builtin/packages/flac/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/flang/package.py b/var/spack/repos/builtin/packages/flang/package.py
index fb84e9841d..b058febe86 100644
--- a/var/spack/repos/builtin/packages/flang/package.py
+++ b/var/spack/repos/builtin/packages/flang/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 import os
@@ -29,22 +10,23 @@ import os
 
 class Flang(CMakePackage):
     """Flang is a Fortran compiler targeting LLVM."""
+
     homepage = "https://github.com/flang-compiler/flang"
-    url      = "https://github.com/flang-compiler/flang/flecsi/tarball/v1.0"
 
-    version('develop', git='https://github.com/flang-compiler/flang', branch='master')
+    url      = "https://github.com/flang-compiler/flang/archive/flang_20180612.tar.gz"
+    git      = "https://github.com/flang-compiler/flang.git"
 
-    depends_on(
-            "llvm+clang@4.0.1,5.0.0",
-        patches=[
-            patch('https://github.com/llvm-mirror/clang/pull/33.diff',
-                      sha256='e46d7ab305e5e95c51f4656d9b52058143cd85d859b312b3c80e93a02d54b4a5',
-                      when='@4.0.1', level=1, working_dir='tools/clang'),
-            patch('https://github.com/llvm-mirror/clang/pull/35.diff',
-                      sha256='7f39555783993f78b75c380ca5ef167c1d8b88cc75c6542f6c94e0b6acfb7c5d',
-                      when='@5.0.0', level=1, working_dir='tools/clang')
-        ]
-    )
+    version('develop', branch='master')
+    version('20180612', '62284e26214eaaff261a922c67f6878c')
+
+    depends_on('llvm@flang-develop', when='@develop')
+    depends_on('llvm@flang-20180612', when='@20180612 target=x86_64')
+
+    # LLVM version specific to OpenPOWER.
+    depends_on('llvm@flang-ppc64le-20180612', when='@20180612 target=ppc64le')
+
+    depends_on('pgmath@develop', when='@develop')
+    depends_on('pgmath@20180612', when='@20180612')
 
     def cmake_args(self):
         options = [
@@ -72,11 +54,20 @@ class Flang(CMakePackage):
         with open(flang, 'w') as out:
             out.write('#!/bin/bash\n')
             out.write(
-                '{0} -I{1} -L{2} {3}{4} -B{5} "$@"\n'.format(
-                    os.path.join(self.spec['llvm'].prefix.bin, 'flang'),
+                '{0} -I{1} -L{2} -L{3} {4}{5} {6}{7} -B{8} "$@"\n'.format(
+                    self.spec['llvm'].prefix.bin.flang,
                     self.prefix.include, self.prefix.lib,
+                    self.spec['pgmath'].prefix.lib,
                     self.compiler.fc_rpath_arg, self.prefix.lib,
-                    self.spec.prefix.bin))
+                    self.compiler.fc_rpath_arg,
+                    self.spec['pgmath'].prefix.lib, self.spec.prefix.bin))
             out.close()
         chmod = which('chmod')
         chmod('+x', flang)
+
+    def setup_environment(self, spack_env, run_env):
+        # to find llvm's libc++.so
+        spack_env.set('LD_LIBRARY_PATH', self.spec['llvm'].prefix.lib)
+        run_env.set('FC', join_path(self.spec.prefix.bin, 'flang'))
+        run_env.set('F77', join_path(self.spec.prefix.bin, 'flang'))
+        run_env.set('F90', join_path(self.spec.prefix.bin, 'flang'))
diff --git a/var/spack/repos/builtin/packages/flann/linux-gcc-cmakev3.11-plus.patch b/var/spack/repos/builtin/packages/flann/linux-gcc-cmakev3.11-plus.patch
new file mode 100644
index 0000000000..d8a7dbd0d2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/flann/linux-gcc-cmakev3.11-plus.patch
@@ -0,0 +1,24 @@
+--- a/src/cpp/CMakeLists.txt
++++ b/src/cpp/CMakeLists.txt
+@@ -29,7 +29,7 @@ if (BUILD_CUDA_LIB)
+ endif()
+ 
+ if(CMAKE_SYSTEM_NAME STREQUAL "Linux" AND CMAKE_COMPILER_IS_GNUCC)
+-    add_library(flann_cpp SHARED "")
++    add_library(flann_cpp SHARED "empty.cpp")
+     set_target_properties(flann_cpp PROPERTIES LINKER_LANGUAGE CXX)
+     target_link_libraries(flann_cpp -Wl,-whole-archive flann_cpp_s -Wl,-no-whole-archive)
+ 
+@@ -83,7 +83,7 @@ if (BUILD_C_BINDINGS)
+     set_property(TARGET flann_s PROPERTY COMPILE_DEFINITIONS FLANN_STATIC)
+ 
+     if(CMAKE_SYSTEM_NAME STREQUAL "Linux" AND CMAKE_COMPILER_IS_GNUCC)
+-        add_library(flann SHARED "")
++        add_library(flann SHARED "empty.cpp")
+         set_target_properties(flann PROPERTIES LINKER_LANGUAGE CXX)
+         target_link_libraries(flann -Wl,-whole-archive flann_s -Wl,-no-whole-archive)
+     else()
+--- /dev/null
++++ b/src/cpp/empty.cpp
+@@ -0,0 +1 @@
++/* empty */
diff --git a/var/spack/repos/builtin/packages/flann/package.py b/var/spack/repos/builtin/packages/flann/package.py
index 1ed996bd51..7aee67b66c 100644
--- a/var/spack/repos/builtin/packages/flann/package.py
+++ b/var/spack/repos/builtin/packages/flann/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -92,6 +73,12 @@ class Flann(CMakePackage):
     # Example uses hdf5.
     depends_on("hdf5", when="+examples")
 
+    depends_on('hdf5', type='test')
+    depends_on('gtest', type='test')
+
+    # See: https://github.com/mariusmuja/flann/issues/369
+    patch('linux-gcc-cmakev3.11-plus.patch', when='%gcc^cmake@3.11:')
+
     def patch(self):
         # Fix up the python setup.py call inside the install(CODE
         filter_file("setup.py install",
@@ -109,10 +96,6 @@ class Flann(CMakePackage):
                     "# install( FILES",
                     "src/python/CMakeLists.txt", string=True)
 
-    # TODO: revisit after https://github.com/spack/spack/issues/1279
-    # depends_on('hdf5', type='test')
-    # depends_on('gtest', type='test')
-
     def cmake_args(self):
         spec = self.spec
         args = []
diff --git a/var/spack/repos/builtin/packages/flash/package.py b/var/spack/repos/builtin/packages/flash/package.py
index 6c918feb1a..4b464bfb11 100644
--- a/var/spack/repos/builtin/packages/flash/package.py
+++ b/var/spack/repos/builtin/packages/flash/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/flatbuffers/package.py b/var/spack/repos/builtin/packages/flatbuffers/package.py
new file mode 100644
index 0000000000..0f90221c06
--- /dev/null
+++ b/var/spack/repos/builtin/packages/flatbuffers/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Flatbuffers(CMakePackage):
+    """Memory Efficient Serialization Library
+    """
+
+    homepage = "http://google.github.io/flatbuffers/"
+    url      = "https://github.com/google/flatbuffers/archive/v1.9.0.tar.gz"
+
+    version('1.9.0', '8be7513bf960034f6873326d09521a4b')
+    version('1.8.0', '276cab8303c4189cbe3b8a70e0515d65')
diff --git a/var/spack/repos/builtin/packages/flecsale/package.py b/var/spack/repos/builtin/packages/flecsale/package.py
index 1160ea642e..803624acd0 100644
--- a/var/spack/repos/builtin/packages/flecsale/package.py
+++ b/var/spack/repos/builtin/packages/flecsale/package.py
@@ -1,37 +1,19 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
 
 class Flecsale(CMakePackage):
     """Flecsale is an ALE code based on FleCSI"""
+
     homepage = "https://github.com/laristra/flecsale"
-    url      = "https://github.com/laristra/flecsale/tarball/v1.0"
+    git      = "https://github.com/laristra/flecsale.git"
 
-    version('develop', git='https://github.com/laristra/flecsale', branch='master', submodules=True)
+    version('develop', branch='master', submodules=True)
 
     variant('mpi', default=True,
             description='Build on top of mpi conduit for mpi inoperability')
diff --git a/var/spack/repos/builtin/packages/flecsi/package.py b/var/spack/repos/builtin/packages/flecsi/package.py
index 049b28d15d..ac10a63e49 100644
--- a/var/spack/repos/builtin/packages/flecsi/package.py
+++ b/var/spack/repos/builtin/packages/flecsi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -37,9 +18,9 @@ class Flecsi(CMakePackage):
        interfaces,and dependency closures.
     """
     homepage = "http://flecsi.lanl.gov/"
-    url      = "https://github.com/laristra/flecsi/tarball/v1.0"
+    git      = "https://github.com/laristra/flecsi.git"
 
-    version('develop', git='https://github.com/laristra/flecsi', branch='master', submodules=True)
+    version('develop', branch='master', submodules=True)
 
     variant('mpi', default=True,
             description='Build on top of mpi conduit for mpi inoperability')
@@ -47,6 +28,7 @@ class Flecsi(CMakePackage):
     depends_on("cmake@3.1:", type='build')
     depends_on("legion+shared", when='~mpi')
     depends_on("legion+shared+mpi", when='+mpi')
+    depends_on("parmetis")
 
     def cmake_args(self):
         options = ['-DENABLE_UNIT_TESTS=ON']
diff --git a/var/spack/repos/builtin/packages/flex/package.py b/var/spack/repos/builtin/packages/flex/package.py
index 8d5ffe11c3..2bbef402a6 100644
--- a/var/spack/repos/builtin/packages/flex/package.py
+++ b/var/spack/repos/builtin/packages/flex/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
@@ -33,7 +14,10 @@ class Flex(AutotoolsPackage):
     url = "https://github.com/westes/flex/releases/download/v2.6.1/flex-2.6.1.tar.gz"
 
     version('2.6.4', '2882e3179748cc9f9c23ec593d6adc8d')
-    version('2.6.3', 'a5f65570cd9107ec8a8ec88f17b31bb1')
+    # 2.6.4 fails to compile with gcc@7.2:
+    # see https://github.com/spack/spack/issues/8152 and
+    # https://github.com/spack/spack/issues/6942
+    version('2.6.3', 'a5f65570cd9107ec8a8ec88f17b31bb1', preferred=True)
     # Avoid flex '2.6.2' (major bug)
     # See issue #2554; https://github.com/westes/flex/issues/113
     version('2.6.1', '05bcd8fb629e0ae130311e8a6106fa82')
@@ -53,6 +37,10 @@ class Flex(AutotoolsPackage):
     depends_on('automake', type='build', when='@:2.6.0')
     depends_on('libtool',  type='build', when='@:2.6.0')
 
+    # Build issue for v2.6.4 when gcc@7.2.0: is used
+    # See issue #219; https://github.com/westes/flex/issues/219
+    conflicts('%gcc@7.2.0:', when='@2.6.4')
+
     def url_for_version(self, version):
         url = "https://github.com/westes/flex"
         if version >= Version('2.6.1'):
diff --git a/var/spack/repos/builtin/packages/flint/package.py b/var/spack/repos/builtin/packages/flint/package.py
index 630a57c9bd..193f071013 100644
--- a/var/spack/repos/builtin/packages/flint/package.py
+++ b/var/spack/repos/builtin/packages/flint/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,10 +11,11 @@ class Flint(Package):
 
     homepage = "http://www.flintlib.org"
     url      = "http://mirrors.mit.edu/sage/spkg/upstream/flint/flint-2.5.2.tar.gz"
+    git      = "https://github.com/wbhart/flint2.git"
 
+    version('develop', branch='trunk')
     version('2.5.2', 'cda885309362150196aed66a5e0f0383')
     version('2.4.5', '6504b9deabeafb9313e57153a1730b33')
-    version('develop', git='https://github.com/wbhart/flint2.git')
 
     # Overlap in functionality between gmp and mpir
     # All other dependencies must also be built with
diff --git a/var/spack/repos/builtin/packages/flit/package.py b/var/spack/repos/builtin/packages/flit/package.py
new file mode 100644
index 0000000000..44ab5cbbcf
--- /dev/null
+++ b/var/spack/repos/builtin/packages/flit/package.py
@@ -0,0 +1,33 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Flit(MakefilePackage):
+    """Floating-point Litmus Tests (FLiT) is a C++ test infrastructure for
+    detecting variability in floating-point code caused by variations in
+    compiler code generation, hardware and execution environments."""
+
+    homepage = "https://pruners.github.io/flit"
+    url      = "https://github.com/PRUNERS/FLiT"
+    url      = "https://github.com/PRUNERS/FLiT/archive/v2.0-alpha.1.tar.gz"
+
+    version('2.0-alpha.1', '62cf7784bcdc15b962c813b11e478159')
+    # FIXME: fix install and build to handle the old version, which is not
+    #        installable
+    # version('1.0.0',       '27763c89b044c5e3cfe62dd319a36a2b')
+    conflicts("@:1.999", msg="Only can build version 2.0 and up")
+
+    # Add dependencies
+    depends_on('python@3:', type='run')
+    depends_on('py-numpy', type='run')
+    depends_on('py-matplotlib tk=False', type='run')
+    depends_on('py-toml', type='run')
+
+    @property
+    def install_targets(self):
+        return ['install', 'PREFIX=%s' % self.prefix]
diff --git a/var/spack/repos/builtin/packages/fltk/package.py b/var/spack/repos/builtin/packages/fltk/package.py
index 62fe84bb44..7f240b37eb 100644
--- a/var/spack/repos/builtin/packages/fltk/package.py
+++ b/var/spack/repos/builtin/packages/fltk/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -42,6 +23,8 @@ class Fltk(Package):
 
     version('1.3.3', '9ccdb0d19dc104b87179bd9fd10822e3')
 
+    depends_on('libx11')
+
     patch('font.patch', when='@1.3.3')
 
     variant('shared', default=True,
diff --git a/var/spack/repos/builtin/packages/flux-core/package.py b/var/spack/repos/builtin/packages/flux-core/package.py
new file mode 100644
index 0000000000..4dea197de2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/flux-core/package.py
@@ -0,0 +1,120 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class FluxCore(AutotoolsPackage):
+    """ A next-generation resource manager (pre-alpha) """
+
+    homepage = "https://github.com/flux-framework/flux-core"
+    url      = "https://github.com/flux-framework/flux-core/releases/download/v0.8.0/flux-core-0.8.0.tar.gz"
+    git      = "https://github.com/flux-framework/flux-core.git"
+
+    version('master',  branch='master')
+    version('0.10.0', 'a84a1ed53a69c805c253bc940540cbf667a059b2008fd2a6a9bb890a985ead08e88dcbba68c01567f887357306fbfded41b93cc33edfa7809955ba5ba5870284')
+    version('0.9.0',  '70eaec1005aa49e8d8cf397570789cebedfb5d917efe963390d456ee4c473eefb15b0c81ea83f60a1fd057fe7be356bbafdebcae64b499844d194c48f6aefa05')
+    version('0.8.0',  'b0fec05acedc530bcdf75b2477ac22f39d2adddc7af8ff76496208a5e1e8185b1b4a18677871d95c3cfbf34b05f391953651200917fe029931f4e2beb79d70df')
+
+    # Avoid the infinite symlink issue
+    # This workaround is documented in PR #3543
+    build_directory = 'spack-build'
+
+    variant('docs', default=False, description='Build flux manpages')
+    variant('cuda', default=False, description='Build dependencies with support for CUDA')
+
+    depends_on("zeromq@4.0.4:")
+    depends_on("czmq")
+    depends_on("czmq@2.2:3.99", when="@0.1:0.6.99")
+    depends_on("czmq@3.0.1:", when="@0.7:,master")
+    depends_on("hwloc@1.11.1:1.99")
+    depends_on("hwloc +cuda", when='+cuda')
+    depends_on("lua", type=('build', 'run', 'link'))
+    depends_on("lua@5.1:5.1.99", when="@0.1.0:0.9.0")
+    depends_on("lua@5.1:5.2.99", when="@0.10.0:,master")
+    depends_on("lua-luaposix")
+    depends_on("munge")
+    depends_on("libuuid")
+    depends_on("python", type=('build', 'run'))
+    depends_on("python@2.7:2.99", when="@0.1.0:0.10.0")
+    depends_on("python@2.7:", when="@0.11.0:,master")
+    depends_on("py-cffi", type=('build', 'run'))
+    depends_on("py-six", type=('build', 'run'), when="@0.11.0:,master")
+    depends_on("jansson")
+    depends_on("yaml-cpp")
+    depends_on("lz4", when="@0.11.0:,master")
+
+    # versions up to 0.8.0 uses pylint to check Flux's python binding
+    # later versions provide a configure flag and disable the check by default
+    depends_on("py-pylint", when='@:0.8.0', type='build')
+
+    depends_on("asciidoc", type='build', when="+docs")
+
+    # Need autotools when building on master:
+    depends_on("autoconf", type='build', when='@master')
+    depends_on("automake", type='build', when='@master')
+    depends_on("libtool", type='build', when='@master')
+
+    def setup(self):
+        pass
+
+    @when('@master')
+    def setup(self):
+        with working_dir(self.stage.source_path):
+            # Allow git-describe to get last tag so flux-version works:
+            git = which('git')
+            git('fetch', '--unshallow')
+            git("config", "remote.origin.fetch",
+                "+refs/heads/*:refs/remotes/origin/*")
+            git('fetch', 'origin')
+
+    def autoreconf(self, spec, prefix):
+        self.setup()
+        if not os.path.exists('configure'):
+            # Bootstrap with autotools
+            bash = which('bash')
+            bash('./autogen.sh')
+
+    @property
+    def lua_version(self):
+        return self.spec['lua'].version.up_to(2)
+
+    @property
+    def lua_share_dir(self):
+        return os.path.join('share', 'lua', str(self.lua_version))
+
+    @property
+    def lua_lib_dir(self):
+        return os.path.join('lib', 'lua', str(self.lua_version))
+
+    def setup_environment(self, spack_env, run_env):
+        #  Ensure ./fluxometer.lua can be found during flux's make check
+        spack_env.append_path('LUA_PATH', './?.lua', separator=';')
+
+        run_env.prepend_path(
+            'LUA_PATH',
+            os.path.join(self.spec.prefix, self.lua_share_dir, '?.lua'),
+            separator=';')
+        run_env.prepend_path(
+            'LUA_CPATH',
+            os.path.join(self.spec.prefix, self.lua_lib_dir, '?.so'),
+            separator=';')
+        run_env.prepend_path(
+            'PYTHONPATH',
+            os.path.join(
+                self.spec.prefix.lib,
+                "python{0}".format(self.spec['python'].version.up_to(2)),
+                "site-packages"),
+        )
+        run_env.prepend_path('FLUX_MODULE_PATH', self.prefix.lib.flux.modules)
+        run_env.prepend_path('FLUX_EXEC_PATH', self.prefix.libexec.flux.cmd)
+        run_env.prepend_path('FLUX_RC_PATH', self.prefix.etc.flux)
+
+    def configure_args(self):
+        args = ['--enable-pylint=no']
+        if '+docs' not in self.spec:
+            args.append('--disable-docs')
+        return args
diff --git a/var/spack/repos/builtin/packages/flux-sched/package.py b/var/spack/repos/builtin/packages/flux-sched/package.py
new file mode 100644
index 0000000000..d3c424f716
--- /dev/null
+++ b/var/spack/repos/builtin/packages/flux-sched/package.py
@@ -0,0 +1,91 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class FluxSched(AutotoolsPackage):
+    """ A scheduler for flux-core (pre-alpha) """
+
+    homepage = "https://github.com/flux-framework/flux-sched"
+    url      = "https://github.com/flux-framework/flux-sched/releases/download/v0.5.0/flux-sched-0.5.0.tar.gz"
+    git      = "https://github.com/flux-framework/flux-sched.git"
+
+    version('master', branch='master')
+    version('0.6.0', '8aad185949038c7fb6b277e6a8282947917084ebbec5c5bf0ee3a81a0dcdbe41ba18b1df837c669ae7b48ca5f1e492a5172bffa6b9feb4dda1c6a7a85abed4e8')
+    version('0.5.0', 'a9835c9c478aa41123a4e12672500052228aaf1ea770f74cb0901dbf4a049bd7d329e99d8d3484e39cfed1f911705030b2775dcfede39bc8bea59c6afe2549b1')
+    version('0.4.0', '82732641ac4594ffe9b94ca442a99e92bf5f91bc14745af92203a887a40610dd44edda3ae07f9b6c8d63799b2968d87c8da28f1488edef1310d0d12be9bd6319')
+
+    variant('cuda', default=False, description='Build dependencies with support for CUDA')
+
+    depends_on("boost+graph", when='@0.5.0:,master')
+    depends_on("py-pyyaml", when="@0.7.0:,master")
+    depends_on("libxml2@2.9.1:", when="@0.6.0,master")
+
+    depends_on("flux-core", type=('build', 'link', 'run'))
+    depends_on("flux-core+cuda", when='+cuda')
+    depends_on("flux-core@0.8.0", when='@0.4.0')
+    depends_on("flux-core@0.9.0", when='@0.5.0')
+    depends_on("flux-core@0.10.0", when='@0.6.0')
+    depends_on("flux-core@master", when='@master')
+
+    # Need autotools when building on master:
+    depends_on("autoconf", type='build', when='@master')
+    depends_on("automake", type='build', when='@master')
+    depends_on("libtool", type='build', when='@master')
+
+    def setup(self):
+        pass
+
+    @when('@master')
+    def setup(self):
+        with working_dir(self.stage.source_path):
+            # Allow git-describe to get last tag so flux-version works:
+            git = which('git')
+            git('fetch', '--unshallow')
+            git("config", "remote.origin.fetch",
+                "+refs/heads/*:refs/remotes/origin/*")
+            git('fetch', 'origin')
+
+    def autoreconf(self, spec, prefix):
+        self.setup()
+        if not os.path.exists('configure'):
+            # Bootstrap with autotools
+            bash = which('bash')
+            bash('./autogen.sh')
+
+    def configure_args(self):
+        # flux-sched's ax_boost is sometimes weird about non-system locations
+        # explicitly setting the path guarantees success
+        return ['--with-boost={0}'.format(self.spec['boost'].prefix)]
+
+    @property
+    def lua_version(self):
+        return self.spec['lua'].version.up_to(2)
+
+    @property
+    def lua_share_dir(self):
+        return os.path.join('share', 'lua', str(self.lua_version))
+
+    @property
+    def lua_lib_dir(self):
+        return os.path.join('lib', 'lua', str(self.lua_version))
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path(
+            'LUA_PATH',
+            os.path.join(self.spec.prefix, self.lua_share_dir, '?.lua'),
+            separator=';')
+        run_env.prepend_path(
+            'LUA_CPATH',
+            os.path.join(self.spec.prefix, self.lua_lib_dir, '?.so'),
+            separator=';')
+
+        run_env.prepend_path('FLUX_MODULE_PATH', self.prefix.lib.flux.modules)
+        run_env.prepend_path('FLUX_MODULE_PATH',
+                             self.prefix.lib.flux.modules.sched)
+        run_env.prepend_path('FLUX_EXEC_PATH', self.prefix.libexec.flux.cmd)
+        run_env.prepend_path('FLUX_RC_EXTRA', self.prefix.etc.flux)
diff --git a/var/spack/repos/builtin/packages/flux/package.py b/var/spack/repos/builtin/packages/flux/package.py
deleted file mode 100644
index 6bca4c541c..0000000000
--- a/var/spack/repos/builtin/packages/flux/package.py
+++ /dev/null
@@ -1,80 +0,0 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-from spack import *
-import os
-
-
-class Flux(AutotoolsPackage):
-    """ A next-generation resource manager (pre-alpha) """
-
-    homepage = "https://github.com/flux-framework/flux-core"
-    url      = "https://github.com/flux-framework/flux-core/releases/download/v0.8.0/flux-core-0.8.0.tar.gz"
-
-    version('0.8.0', md5='9ee12974a8b2ab9a30533f69826f3bec')
-    version('master', branch='master',
-            git='https://github.com/flux-framework/flux-core')
-
-    variant('docs', default=True, description='Build flux manpages')
-
-    depends_on("zeromq@4.0.4:")
-    depends_on("czmq@2.2:")
-    depends_on("hwloc")
-    depends_on("lua@5.1:5.1.99")
-    depends_on("lua-luaposix")
-    depends_on("munge")
-    depends_on("libuuid")
-    depends_on("python")
-    depends_on("py-cffi", type=('build', 'run'))
-    depends_on("jansson")
-
-    depends_on("asciidoc", type='build', when="+docs")
-
-    # Need autotools when building on master:
-    depends_on("autoconf", type='build', when='@master')
-    depends_on("automake", type='build', when='@master')
-    depends_on("libtool", type='build', when='@master')
-
-    def setup():
-        pass
-
-    @when('@master')
-    def setup(self):
-        # Allow git-describe to get last tag so flux-version works:
-        git = which('git')
-        git('pull', '--depth=50', '--tags')
-
-    def autoreconf(self, spec, prefix):
-        self.setup()
-        if os.path.exists('autogen.sh'):
-            # Bootstrap with autotools
-            bash = which('bash')
-            bash('./autogen.sh')
-
-    def setup_environment(self, spack_env, run_env):
-        #  Ensure ./fluxometer.lua can be found during flux's make check
-        spack_env.append_path('LUA_PATH', './?.lua', separator=';')
-
-    def configure_args(self):
-        return ['--disable-docs'] if '+docs' not in self.spec else []
diff --git a/var/spack/repos/builtin/packages/fluxbox/package.py b/var/spack/repos/builtin/packages/fluxbox/package.py
new file mode 100644
index 0000000000..9d4600fe1c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fluxbox/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+#
+from spack import *
+
+
+class Fluxbox(AutotoolsPackage):
+    """Fluxbox is a windowmanager for X that was based on the Blackbox 0.61.1 code.
+
+    It is very light on resources and easy to handle but yet full of features
+    to make an easy, and extremely fast, desktop experience.
+    """
+
+    homepage = "http://fluxbox.org/"
+    url      = "http://sourceforge.net/projects/fluxbox/files/fluxbox/1.3.7/fluxbox-1.3.7.tar.gz"
+
+    version('1.3.7', 'd99d7710f9daf793e0246dae5304b595')
+
+    depends_on('pkgconfig', type='build')
+    depends_on('freetype')
+    depends_on('libxrender')
+    depends_on('libxext')
+    depends_on('expat')
+    depends_on('libx11')
diff --git a/var/spack/repos/builtin/packages/fmt/package.py b/var/spack/repos/builtin/packages/fmt/package.py
index 78b4bfd664..e969fc29ee 100644
--- a/var/spack/repos/builtin/packages/fmt/package.py
+++ b/var/spack/repos/builtin/packages/fmt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,17 +12,33 @@ class Fmt(CMakePackage):
     to C++ IOStreams."""
 
     homepage = "http://fmtlib.net/latest/index.html"
-    url      = "https://github.com/fmtlib/fmt/releases/download/4.0.0/fmt-4.0.0.zip"
+    url      = "https://github.com/fmtlib/fmt/releases/download/5.2.1/fmt-5.2.1.zip"
+
+    version('5.2.1', sha256='43894ab8fe561fc9e523a8024efc23018431fa86b95d45b06dbe6ddb29ffb6cd')
+    version('5.2.0', sha256='c016db7f825bce487a7929e1edb747b9902a2935057af6512cad3df3a080a027')
+    version('5.1.0', sha256='77ef9fea638dc846e484409fbc1ea710bb9bcea042e7b35b8805041bf7655ad5')
+    version('5.0.0', sha256='8dd58daf13e7e8adca99f8725ef3ae598f9c97efda7d6d8d4c49db5047879097')
+    version('4.1.0', sha256='9d49bf02ceb9d0eec51144b203b63b77e69d3798bb402fb82e7d0bdb06c79eeb')
+    version('4.0.0', sha256='10a9f184d4d66f135093a08396d3b0a0ebe8d97b79f8b3ddb8559f75fe4fcbc3')
+    version('3.0.2', sha256='51407b62a202b29d1a9c0eb5ecd4095d30031aea65407c42c25cb10cb5c59ad4')
+    version('3.0.1', sha256='4c9af0dc919a8ae7022b44e1a03c435e42d65c866f44667d8d920d342b098550')
+    version('3.0.0', sha256='1b050b66fa31b74f1d75a14f15e99e728ab79572f176a53b2f8ad7c201c30ceb')
+
+    depends_on('cmake@3.1.0:', type='build')
 
-    version('4.0.0', '605b5abee11b83195191234f4f414cf1')
-    version('3.0.2', 'b190a7b8f2a5e522ee70cf339a53d3b2')
-    version('3.0.1', '14505463b838befe1513b09cae112715')
-    version('3.0.0', 'c099561e70fa194bb03b3fd5de2d3fd0')
+    # Supported compilers are detailed here:
+    # http://fmtlib.net/latest/index.html#portability
+    conflicts('%gcc@:4.3.999', when='@5:')
+    conflicts('%llvm@:2.8.999', when='@5:')
 
-    depends_on('cmake@2.8.12:', type='build')
+    variant('pic', default=True, description='Enable generation of position-independent code')
 
     def cmake_args(self):
-        return [
-            '-DCMAKE_C_FLAGS={0}'.format(self.compiler.pic_flag),
-            '-DCMAKE_CXX_FLAGS={0}'.format(self.compiler.pic_flag),
-        ]
+        spec = self.spec
+        args = []
+        if '+pic' in spec:
+            args.append([
+                '-DCMAKE_C_FLAGS={0}'.format(self.compiler.pic_flag),
+                '-DCMAKE_CXX_FLAGS={0}'.format(self.compiler.pic_flag)
+            ])
+        return args
diff --git a/var/spack/repos/builtin/packages/foam-extend/package.py b/var/spack/repos/builtin/packages/foam-extend/package.py
index c6861da8d3..e36fec1efb 100644
--- a/var/spack/repos/builtin/packages/foam-extend/package.py
+++ b/var/spack/repos/builtin/packages/foam-extend/package.py
@@ -1,29 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# License
-# -------
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 # Legal Notice
 # ------------
 # OPENFOAM is a trademark owned by OpenCFD Ltd
@@ -54,14 +33,15 @@
 ##############################################################################
 import glob
 import re
-import shutil
 import os
 
 from spack import *
+from spack.util.environment import EnvironmentModifications
 from spack.pkg.builtin.openfoam_com import OpenfoamArch
 from spack.pkg.builtin.openfoam_com import add_extra_files
 from spack.pkg.builtin.openfoam_com import write_environ
 from spack.pkg.builtin.openfoam_com import rewrite_environ_files
+import llnl.util.tty as tty
 
 
 class FoamExtend(Package):
@@ -74,10 +54,10 @@ class FoamExtend(Package):
 
     homepage = "http://www.extend-project.de/"
 
-    version('4.0', git='http://git.code.sf.net/p/foam-extend/foam-extend-4.0')
-    version('3.2', git='http://git.code.sf.net/p/foam-extend/foam-extend-3.2')
-    version('3.1', git='http://git.code.sf.net/p/foam-extend/foam-extend-3.1')
-    version('3.0', git='http://git.code.sf.net/p/foam-extend/foam-extend-3.0')
+    version('4.0', git='http://git.code.sf.net/p/foam-extend/foam-extend-4.0.git')
+    version('3.2', git='http://git.code.sf.net/p/foam-extend/foam-extend-3.2.git')
+    version('3.1', git='http://git.code.sf.net/p/foam-extend/foam-extend-3.1.git')
+    version('3.0', git='http://git.code.sf.net/p/foam-extend/foam-extend-3.0.git')
 
     # variant('int64', default=False,
     #         description='Compile with 64-bit label')
@@ -140,14 +120,77 @@ class FoamExtend(Package):
     #
 
     def setup_environment(self, spack_env, run_env):
-        run_env.set('FOAM_INST_DIR', os.path.dirname(self.projectdir)),
-        run_env.set('FOAM_PROJECT_DIR', self.projectdir)
-        run_env.set('WM_PROJECT_DIR', self.projectdir)
-        for d in ['wmake', self.archbin]:  # bin already added automatically
-            run_env.prepend_path('PATH', join_path(self.projectdir, d))
+        """Add environment variables to the generated module file.
+        These environment variables come from running:
+
+        .. code-block:: console
+
+           $ . $WM_PROJECT_DIR/etc/bashrc
+        """
+
+        # NOTE: Spack runs setup_environment twice.
+        # 1) pre-build to set up the build environment
+        # 2) post-install to determine runtime environment variables
+        # The etc/bashrc is only available (with corrrect content)
+        # post-installation.
+
+        bashrc = join_path(self.projectdir, 'etc', 'bashrc')
+        minimal = True
+        if os.path.isfile(bashrc):
+            # post-install: source the installed bashrc
+            try:
+                mods = EnvironmentModifications.from_sourcing_file(
+                    bashrc,
+                    clean=True,  # Remove duplicate entries
+                    blacklist=[  # Blacklist these
+                        # Inadvertent changes
+                        # -------------------
+                        'PS1',            # Leave unaffected
+                        'MANPATH',        # Leave unaffected
+
+                        # Unneeded bits
+                        # -------------
+                        'FOAM_INST_DIR',  # Possibly incorrect
+                        'FOAM_(APP|ETC|SRC|SOLVERS|UTILITIES)',
+                        'FOAM_TEST_.*_DIR',
+                        'WM_NCOMPPROCS',
+                        # 'FOAM_TUTORIALS',  # can be useful
+
+                        # Lots of third-party cruft
+                        # -------------------------
+                        '[A-Z].*_(BIN|LIB|INCLUDE)_DIR',
+                        '[A-Z].*_SYSTEM',
+                        'WM_THIRD_PARTY_.*',
+                        '(BISON|FLEX|CMAKE|ZLIB)_DIR',
+                        '(METIS|PARMETIS|PARMGRIDGEN|SCOTCH)_DIR',
+
+                        # User-specific
+                        # -------------
+                        'FOAM_RUN',
+                        '(FOAM|WM)_.*USER_.*',
+                    ],
+                    whitelist=[  # Whitelist these
+                        'MPI_ARCH_PATH',  # Can be needed for compilation
+                        'PYTHON_BIN_DIR',
+                    ])
+
+                run_env.extend(mods)
+                minimal = False
+                tty.info('foam-extend env: {0}'.format(bashrc))
+            except Exception:
+                minimal = True
+
+        if minimal:
+            # pre-build or minimal environment
+            tty.info('foam-extend minimal env {0}'.format(self.prefix))
+            run_env.set('FOAM_INST_DIR', os.path.dirname(self.projectdir)),
+            run_env.set('FOAM_PROJECT_DIR', self.projectdir)
+            run_env.set('WM_PROJECT_DIR', self.projectdir)
+            for d in ['wmake', self.archbin]:  # bin added automatically
+                run_env.prepend_path('PATH', join_path(self.projectdir, d))
 
     def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
-        """Provide location of the OpenFOAM project.
+        """Location of the OpenFOAM project.
         This is identical to the WM_PROJECT_DIR value, but we avoid that
         variable since it would mask the normal OpenFOAM cleanup of
         previous versions.
@@ -317,7 +360,6 @@ class FoamExtend(Package):
 
     def install(self, spec, prefix):
         """Install under the projectdir"""
-        opts = str(self.foam_arch)
 
         # Fairly ugly since intermediate targets are scattered inside sources
         appdir = 'applications'
@@ -354,19 +396,22 @@ class FoamExtend(Package):
             subitem = join_path(appdir, 'Allwmake')
             install(subitem, join_path(self.projectdir, subitem))
 
-            ignored = [opts]  # Ignore intermediate targets
+            foam_arch_str = str(self.foam_arch)
+            # Ignore intermediate targets
+            ignore = lambda p: os.path.basename(p) == foam_arch_str
+
             for d in ['src', 'tutorials']:
                 install_tree(
                     d,
                     join_path(self.projectdir, d),
-                    ignore=shutil.ignore_patterns(*ignored),
+                    ignore=ignore,
                     symlinks=True)
 
             for d in ['solvers', 'utilities']:
                 install_tree(
                     join_path(appdir, d),
                     join_path(self.projectdir, appdir, d),
-                    ignore=shutil.ignore_patterns(*ignored),
+                    ignore=ignore,
                     symlinks=True)
 
         etc_dir = join_path(self.projectdir, 'etc')
diff --git a/var/spack/repos/builtin/packages/folly/package.py b/var/spack/repos/builtin/packages/folly/package.py
index 9dca4bd6cf..0a2d1f36a4 100644
--- a/var/spack/repos/builtin/packages/folly/package.py
+++ b/var/spack/repos/builtin/packages/folly/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -50,7 +31,7 @@ class Folly(AutotoolsPackage):
     depends_on('autoconf', type='build')
     depends_on('automake', type='build')
     depends_on('libtool', type='build')
-    depends_on('pkg-config', type='build')
+    depends_on('pkgconfig', type='build')
 
     # TODO: folly requires gcc 4.9+ and a version of boost compiled with
     # TODO: C++14 support (but there's no neat way to check that these
diff --git a/var/spack/repos/builtin/packages/font-adobe-100dpi/package.py b/var/spack/repos/builtin/packages/font-adobe-100dpi/package.py
index 8efdebb802..bf1817238f 100644
--- a/var/spack/repos/builtin/packages/font-adobe-100dpi/package.py
+++ b/var/spack/repos/builtin/packages/font-adobe-100dpi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontAdobe100dpi(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-adobe-75dpi/package.py b/var/spack/repos/builtin/packages/font-adobe-75dpi/package.py
index 0b73bd1b9a..6e1f8402ca 100644
--- a/var/spack/repos/builtin/packages/font-adobe-75dpi/package.py
+++ b/var/spack/repos/builtin/packages/font-adobe-75dpi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontAdobe75dpi(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-adobe-utopia-100dpi/package.py b/var/spack/repos/builtin/packages/font-adobe-utopia-100dpi/package.py
index 7a61e04de5..fe4f5eb862 100644
--- a/var/spack/repos/builtin/packages/font-adobe-utopia-100dpi/package.py
+++ b/var/spack/repos/builtin/packages/font-adobe-utopia-100dpi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontAdobeUtopia100dpi(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-adobe-utopia-75dpi/package.py b/var/spack/repos/builtin/packages/font-adobe-utopia-75dpi/package.py
index dddd546cad..9fa00f29a3 100644
--- a/var/spack/repos/builtin/packages/font-adobe-utopia-75dpi/package.py
+++ b/var/spack/repos/builtin/packages/font-adobe-utopia-75dpi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontAdobeUtopia75dpi(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-adobe-utopia-type1/package.py b/var/spack/repos/builtin/packages/font-adobe-utopia-type1/package.py
index 0d03c12822..c5e832cb29 100644
--- a/var/spack/repos/builtin/packages/font-adobe-utopia-type1/package.py
+++ b/var/spack/repos/builtin/packages/font-adobe-utopia-type1/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,7 +18,7 @@ class FontAdobeUtopiaType1(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('mkfontscale', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-alias/package.py b/var/spack/repos/builtin/packages/font-alias/package.py
index 15a14bf2cb..2819678e71 100644
--- a/var/spack/repos/builtin/packages/font-alias/package.py
+++ b/var/spack/repos/builtin/packages/font-alias/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,7 +16,7 @@ class FontAlias(Package):
 
     depends_on('font-util')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-arabic-misc/package.py b/var/spack/repos/builtin/packages/font-arabic-misc/package.py
index 20ca7a2df0..910ff1af57 100644
--- a/var/spack/repos/builtin/packages/font-arabic-misc/package.py
+++ b/var/spack/repos/builtin/packages/font-arabic-misc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontArabicMisc(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-bh-100dpi/package.py b/var/spack/repos/builtin/packages/font-bh-100dpi/package.py
index 3472783671..48ca9aa37a 100644
--- a/var/spack/repos/builtin/packages/font-bh-100dpi/package.py
+++ b/var/spack/repos/builtin/packages/font-bh-100dpi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontBh100dpi(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-bh-75dpi/package.py b/var/spack/repos/builtin/packages/font-bh-75dpi/package.py
index bb5268208c..0af3c8e1d1 100644
--- a/var/spack/repos/builtin/packages/font-bh-75dpi/package.py
+++ b/var/spack/repos/builtin/packages/font-bh-75dpi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontBh75dpi(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-bh-lucidatypewriter-100dpi/package.py b/var/spack/repos/builtin/packages/font-bh-lucidatypewriter-100dpi/package.py
index 6fe18e703b..7b001c32e3 100644
--- a/var/spack/repos/builtin/packages/font-bh-lucidatypewriter-100dpi/package.py
+++ b/var/spack/repos/builtin/packages/font-bh-lucidatypewriter-100dpi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontBhLucidatypewriter100dpi(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-bh-lucidatypewriter-75dpi/package.py b/var/spack/repos/builtin/packages/font-bh-lucidatypewriter-75dpi/package.py
index f44596b882..ce0677144f 100644
--- a/var/spack/repos/builtin/packages/font-bh-lucidatypewriter-75dpi/package.py
+++ b/var/spack/repos/builtin/packages/font-bh-lucidatypewriter-75dpi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontBhLucidatypewriter75dpi(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-bh-ttf/package.py b/var/spack/repos/builtin/packages/font-bh-ttf/package.py
index 83ad928c8b..ae662cd40c 100644
--- a/var/spack/repos/builtin/packages/font-bh-ttf/package.py
+++ b/var/spack/repos/builtin/packages/font-bh-ttf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontBhTtf(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-bh-type1/package.py b/var/spack/repos/builtin/packages/font-bh-type1/package.py
index 594efb0460..d75bb953f3 100644
--- a/var/spack/repos/builtin/packages/font-bh-type1/package.py
+++ b/var/spack/repos/builtin/packages/font-bh-type1/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontBhType1(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('mkfontscale', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-bitstream-100dpi/package.py b/var/spack/repos/builtin/packages/font-bitstream-100dpi/package.py
index a5722733da..286a2dec5b 100644
--- a/var/spack/repos/builtin/packages/font-bitstream-100dpi/package.py
+++ b/var/spack/repos/builtin/packages/font-bitstream-100dpi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontBitstream100dpi(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-bitstream-75dpi/package.py b/var/spack/repos/builtin/packages/font-bitstream-75dpi/package.py
index 8dcf9dfe2c..028121c2a9 100644
--- a/var/spack/repos/builtin/packages/font-bitstream-75dpi/package.py
+++ b/var/spack/repos/builtin/packages/font-bitstream-75dpi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontBitstream75dpi(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-bitstream-speedo/package.py b/var/spack/repos/builtin/packages/font-bitstream-speedo/package.py
index e2ae5fea3c..ca3b5a2e48 100644
--- a/var/spack/repos/builtin/packages/font-bitstream-speedo/package.py
+++ b/var/spack/repos/builtin/packages/font-bitstream-speedo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontBitstreamSpeedo(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('mkfontscale', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-bitstream-type1/package.py b/var/spack/repos/builtin/packages/font-bitstream-type1/package.py
index c6699b7521..efb427de3a 100644
--- a/var/spack/repos/builtin/packages/font-bitstream-type1/package.py
+++ b/var/spack/repos/builtin/packages/font-bitstream-type1/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontBitstreamType1(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('mkfontscale', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-cronyx-cyrillic/package.py b/var/spack/repos/builtin/packages/font-cronyx-cyrillic/package.py
index 829f28ee1e..0ac07e9669 100644
--- a/var/spack/repos/builtin/packages/font-cronyx-cyrillic/package.py
+++ b/var/spack/repos/builtin/packages/font-cronyx-cyrillic/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontCronyxCyrillic(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-cursor-misc/package.py b/var/spack/repos/builtin/packages/font-cursor-misc/package.py
index 34479c7fc6..321bd01b13 100644
--- a/var/spack/repos/builtin/packages/font-cursor-misc/package.py
+++ b/var/spack/repos/builtin/packages/font-cursor-misc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontCursorMisc(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-daewoo-misc/package.py b/var/spack/repos/builtin/packages/font-daewoo-misc/package.py
index 9c346c3b8b..737d3dfac9 100644
--- a/var/spack/repos/builtin/packages/font-daewoo-misc/package.py
+++ b/var/spack/repos/builtin/packages/font-daewoo-misc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontDaewooMisc(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-dec-misc/package.py b/var/spack/repos/builtin/packages/font-dec-misc/package.py
index 22c52a95da..e4cc9cbab8 100644
--- a/var/spack/repos/builtin/packages/font-dec-misc/package.py
+++ b/var/spack/repos/builtin/packages/font-dec-misc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontDecMisc(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-ibm-type1/package.py b/var/spack/repos/builtin/packages/font-ibm-type1/package.py
index a8d06ef092..213be77570 100644
--- a/var/spack/repos/builtin/packages/font-ibm-type1/package.py
+++ b/var/spack/repos/builtin/packages/font-ibm-type1/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontIbmType1(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('mkfontscale', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-isas-misc/package.py b/var/spack/repos/builtin/packages/font-isas-misc/package.py
index 86353f22ce..d51f7daf62 100644
--- a/var/spack/repos/builtin/packages/font-isas-misc/package.py
+++ b/var/spack/repos/builtin/packages/font-isas-misc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontIsasMisc(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-jis-misc/package.py b/var/spack/repos/builtin/packages/font-jis-misc/package.py
index 18723cc129..5165a97c8a 100644
--- a/var/spack/repos/builtin/packages/font-jis-misc/package.py
+++ b/var/spack/repos/builtin/packages/font-jis-misc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontJisMisc(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-micro-misc/package.py b/var/spack/repos/builtin/packages/font-micro-misc/package.py
index 664cc158a7..4212aac2b6 100644
--- a/var/spack/repos/builtin/packages/font-micro-misc/package.py
+++ b/var/spack/repos/builtin/packages/font-micro-misc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontMicroMisc(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-misc-cyrillic/package.py b/var/spack/repos/builtin/packages/font-misc-cyrillic/package.py
index 52d2e0ca33..24085afdee 100644
--- a/var/spack/repos/builtin/packages/font-misc-cyrillic/package.py
+++ b/var/spack/repos/builtin/packages/font-misc-cyrillic/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontMiscCyrillic(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-misc-ethiopic/package.py b/var/spack/repos/builtin/packages/font-misc-ethiopic/package.py
index ed10f2ecad..5fcc5a50d1 100644
--- a/var/spack/repos/builtin/packages/font-misc-ethiopic/package.py
+++ b/var/spack/repos/builtin/packages/font-misc-ethiopic/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontMiscEthiopic(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('mkfontscale', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-misc-meltho/package.py b/var/spack/repos/builtin/packages/font-misc-meltho/package.py
index beef19e00a..29be9bfebd 100644
--- a/var/spack/repos/builtin/packages/font-misc-meltho/package.py
+++ b/var/spack/repos/builtin/packages/font-misc-meltho/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontMiscMeltho(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('mkfontscale', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-misc-misc/package.py b/var/spack/repos/builtin/packages/font-misc-misc/package.py
index b818cd6a84..d29384eaa5 100644
--- a/var/spack/repos/builtin/packages/font-misc-misc/package.py
+++ b/var/spack/repos/builtin/packages/font-misc-misc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontMiscMisc(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-mutt-misc/package.py b/var/spack/repos/builtin/packages/font-mutt-misc/package.py
index 0f303923b0..376f6d3f22 100644
--- a/var/spack/repos/builtin/packages/font-mutt-misc/package.py
+++ b/var/spack/repos/builtin/packages/font-mutt-misc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontMuttMisc(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-schumacher-misc/package.py b/var/spack/repos/builtin/packages/font-schumacher-misc/package.py
index 66e8002877..fefe1e1c61 100644
--- a/var/spack/repos/builtin/packages/font-schumacher-misc/package.py
+++ b/var/spack/repos/builtin/packages/font-schumacher-misc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontSchumacherMisc(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-screen-cyrillic/package.py b/var/spack/repos/builtin/packages/font-screen-cyrillic/package.py
index 71c2230d1f..0eec73060d 100644
--- a/var/spack/repos/builtin/packages/font-screen-cyrillic/package.py
+++ b/var/spack/repos/builtin/packages/font-screen-cyrillic/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontScreenCyrillic(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-sony-misc/package.py b/var/spack/repos/builtin/packages/font-sony-misc/package.py
index ccea5883ac..912957ab12 100644
--- a/var/spack/repos/builtin/packages/font-sony-misc/package.py
+++ b/var/spack/repos/builtin/packages/font-sony-misc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontSonyMisc(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-sun-misc/package.py b/var/spack/repos/builtin/packages/font-sun-misc/package.py
index 26e0c935ed..8555fdb428 100644
--- a/var/spack/repos/builtin/packages/font-sun-misc/package.py
+++ b/var/spack/repos/builtin/packages/font-sun-misc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,7 +18,7 @@ class FontSunMisc(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-util/package.py b/var/spack/repos/builtin/packages/font-util/package.py
index 4f55412457..7a5e163482 100644
--- a/var/spack/repos/builtin/packages/font-util/package.py
+++ b/var/spack/repos/builtin/packages/font-util/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,5 +14,5 @@ class FontUtil(AutotoolsPackage):
 
     version('1.3.1', 'd153a9af216e4498fa171faea2c82514')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/font-winitzki-cyrillic/package.py b/var/spack/repos/builtin/packages/font-winitzki-cyrillic/package.py
index dade47b7d2..e15236a20f 100644
--- a/var/spack/repos/builtin/packages/font-winitzki-cyrillic/package.py
+++ b/var/spack/repos/builtin/packages/font-winitzki-cyrillic/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontWinitzkiCyrillic(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-xfree86-type1/package.py b/var/spack/repos/builtin/packages/font-xfree86-type1/package.py
index 2a4dfea233..5cb5de7eb8 100644
--- a/var/spack/repos/builtin/packages/font-xfree86-type1/package.py
+++ b/var/spack/repos/builtin/packages/font-xfree86-type1/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontXfree86Type1(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('mkfontscale', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/fontcacheproto/package.py b/var/spack/repos/builtin/packages/fontcacheproto/package.py
index 94e952de52..77c8e4a38a 100644
--- a/var/spack/repos/builtin/packages/fontcacheproto/package.py
+++ b/var/spack/repos/builtin/packages/fontcacheproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/fontconfig/package.py b/var/spack/repos/builtin/packages/fontconfig/package.py
index 8cfd5c0d54..0ef1a3ebc9 100644
--- a/var/spack/repos/builtin/packages/fontconfig/package.py
+++ b/var/spack/repos/builtin/packages/fontconfig/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,7 +18,7 @@ class Fontconfig(AutotoolsPackage):
     depends_on('freetype')
     depends_on('gperf', type='build', when='@2.12.2:')
     depends_on('libxml2')
-    depends_on('pkg-config', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('font-util')
 
     def configure_args(self):
diff --git a/var/spack/repos/builtin/packages/fontsproto/package.py b/var/spack/repos/builtin/packages/fontsproto/package.py
index c243f9de97..22ea479567 100644
--- a/var/spack/repos/builtin/packages/fontsproto/package.py
+++ b/var/spack/repos/builtin/packages/fontsproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,5 +14,5 @@ class Fontsproto(AutotoolsPackage):
 
     version('2.1.3', '0415f0360e33f3202af67c6c46782251')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/fonttosfnt/package.py b/var/spack/repos/builtin/packages/fonttosfnt/package.py
index 145e619c54..02928b26b8 100644
--- a/var/spack/repos/builtin/packages/fonttosfnt/package.py
+++ b/var/spack/repos/builtin/packages/fonttosfnt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Fonttosfnt(AutotoolsPackage):
     depends_on('libfontenc')
 
     depends_on('xproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/fp16/package.py b/var/spack/repos/builtin/packages/fp16/package.py
new file mode 100644
index 0000000000..e20b215ce1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fp16/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Fp16(Package):
+    """FP16 is a header-only library for
+    conversion to/from half-precision floating point formats"""
+
+    homepage = "https://github.com/Maratyszcza/FP16/"
+    git      = "https://github.com/Maratyszcza/FP16.git"
+
+    version('master')
+
+    def install(self, spec, prefix):
+        install_tree('include', prefix.include)
diff --git a/var/spack/repos/builtin/packages/fpc/package.py b/var/spack/repos/builtin/packages/fpc/package.py
index 905aae3314..ec0fca7b68 100644
--- a/var/spack/repos/builtin/packages/fpc/package.py
+++ b/var/spack/repos/builtin/packages/fpc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/fr-hit/binning.patch b/var/spack/repos/builtin/packages/fr-hit/binning.patch
new file mode 100644
index 0000000000..4ee81d5d83
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fr-hit/binning.patch
@@ -0,0 +1,7 @@
+--- a/binning-1.1.1/binning.py	2018-01-30 10:46:27.302198293 -0600
++++ b/binning-1.1.1/binning.py	2018-01-30 10:50:58.482866704 -0600
+@@ -1,3 +1,4 @@
++#!/usr/bin/env python
+ ######################################################
+ #      Taxonamy binning using FR-HIT output          #
+ ######################################################
diff --git a/var/spack/repos/builtin/packages/fr-hit/package.py b/var/spack/repos/builtin/packages/fr-hit/package.py
new file mode 100644
index 0000000000..a6dc337882
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fr-hit/package.py
@@ -0,0 +1,46 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class FrHit(Package):
+    """An efficient algorithm for fragment recruitment for next generation
+    sequences against microbial reference genomes."""
+
+    homepage = "http://weizhong-lab.ucsd.edu/frhit"
+    url      = "http://weizhong-lab.ucsd.edu/frhit/fr-hit-v0.7.1-2013-02-20.tar.gz"
+
+    version('0.7.1-2013-02-20', '3e8ea41ba09ab0c13e9973fe6f493f96')
+
+    depends_on('perl')
+    depends_on('python@2.7:')
+
+    # The patch adds the python interpreter to the beginning of the script
+    # allowing it to be run directly without passing the entire path to the
+    # script to python.
+    patch('binning.patch')
+
+    def install(self, spec, prefix):
+        make()
+
+        filter_file(
+            r'#!/bin/env perl',
+            '#!/usr/bin/env perl',
+            'frhit2pairend.pl'
+        )
+        filter_file(
+            r'#!/bin/env perl',
+            '#!/usr/bin/env perl',
+            'psl2sam.pl'
+        )
+
+        mkdirp(prefix.bin)
+        install('fr-hit', prefix.bin)
+        install('frhit2pairend.pl', prefix.bin)
+        install('psl2sam.pl', prefix.bin)
+        install('binning-1.1.1/bacteria_gitax.pkl', prefix.bin)
+        install('binning-1.1.1/binning.py', prefix.bin)
+        install('binning-1.1.1/tax.pkl', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/freebayes/package.py b/var/spack/repos/builtin/packages/freebayes/package.py
index bd5c2b06a3..a50362d453 100644
--- a/var/spack/repos/builtin/packages/freebayes/package.py
+++ b/var/spack/repos/builtin/packages/freebayes/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,9 @@ class Freebayes(MakefilePackage):
        genotyping."""
 
     homepage = "https://github.com/ekg/freebayes"
+    git      = "https://github.com/ekg/freebayes.git"
 
-    version('1.1.0', git='https://github.com/ekg/freebayes.git',
-            commit='39e5e4bcb801556141f2da36aba1df5c5c60701f',
+    version('1.1.0', commit='39e5e4bcb801556141f2da36aba1df5c5c60701f',
             submodules=True)
 
     depends_on('cmake', type='build')
diff --git a/var/spack/repos/builtin/packages/freeglut/package.py b/var/spack/repos/builtin/packages/freeglut/package.py
new file mode 100644
index 0000000000..6327a20839
--- /dev/null
+++ b/var/spack/repos/builtin/packages/freeglut/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Freeglut(CMakePackage):
+    """FreeGLUT is a free-software/open-source alternative to the OpenGL
+       Utility Toolkit (GLUT) library"""
+
+    homepage = "http://freeglut.sourceforge.net/"
+    url      = "http://prdownloads.sourceforge.net/freeglut/freeglut-3.0.0.tar.gz"
+
+    version('3.0.0', '90c3ca4dd9d51cf32276bc5344ec9754')
+
+    depends_on('gl')
+    depends_on('glu')
+    depends_on('libx11')
+    depends_on('libxrandr')
+    depends_on('libxi')
+    depends_on('xrandr')
+    depends_on('inputproto')
diff --git a/var/spack/repos/builtin/packages/freetype/package.py b/var/spack/repos/builtin/packages/freetype/package.py
index 1ad65a9750..acecc649ad 100644
--- a/var/spack/repos/builtin/packages/freetype/package.py
+++ b/var/spack/repos/builtin/packages/freetype/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,13 +15,21 @@ class Freetype(AutotoolsPackage):
     homepage = "https://www.freetype.org/index.html"
     url      = "http://download.savannah.gnu.org/releases/freetype/freetype-2.7.1.tar.gz"
 
+    version('2.9.1', 'ec391504e55498adceb30baceebd147a6e963f636eb617424bcfc47a169898ce')
     version('2.7.1', '78701bee8d249578d83bb9a2f3aa3616')
     version('2.7',   '337139e5c7c5bd645fe130608e0fa8b5')
     version('2.5.3', 'cafe9f210e45360279c730d27bf071e9')
 
     depends_on('libpng')
     depends_on('bzip2')
-    depends_on('pkg-config@0.24:', type='build')
+    depends_on('pkgconfig', type='build')
 
     def configure_args(self):
-        return ['--with-harfbuzz=no']
+        args = ['--with-harfbuzz=no']
+        if self.spec.satisfies('@2.9.1:'):
+            args.append('--enable-freetype-config')
+        return args
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        spack_env.prepend_path('CPATH', self.prefix.include.freetype2)
+        run_env.prepend_path('CPATH', self.prefix.include.freetype2)
diff --git a/var/spack/repos/builtin/packages/fseq/package.py b/var/spack/repos/builtin/packages/fseq/package.py
index 037aa4f648..5397c64d1f 100644
--- a/var/spack/repos/builtin/packages/fseq/package.py
+++ b/var/spack/repos/builtin/packages/fseq/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/fsl/package.py b/var/spack/repos/builtin/packages/fsl/package.py
index 2191be1ce3..a0675ae6cf 100644
--- a/var/spack/repos/builtin/packages/fsl/package.py
+++ b/var/spack/repos/builtin/packages/fsl/package.py
@@ -1,31 +1,11 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from spack.environment import EnvironmentModifications
+from spack.util.environment import EnvironmentModifications
 import os
-import distutils.dir_util
 
 
 class Fsl(Package):
@@ -68,7 +48,7 @@ class Fsl(Package):
         build = Executable('./build')
         build()
 
-        distutils.dir_util.copy_tree(".", prefix)
+        install_tree('.', prefix)
 
     def setup_environment(self, spack_env, run_env):
         if not self.stage.source_path:
diff --git a/var/spack/repos/builtin/packages/fslsfonts/package.py b/var/spack/repos/builtin/packages/fslsfonts/package.py
index ce5b04f0ee..1f540a5509 100644
--- a/var/spack/repos/builtin/packages/fslsfonts/package.py
+++ b/var/spack/repos/builtin/packages/fslsfonts/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Fslsfonts(AutotoolsPackage):
     depends_on('libfs')
 
     depends_on('xproto@7.0.25:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/fstobdf/package.py b/var/spack/repos/builtin/packages/fstobdf/package.py
index dd51473d41..1605edddc3 100644
--- a/var/spack/repos/builtin/packages/fstobdf/package.py
+++ b/var/spack/repos/builtin/packages/fstobdf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,5 +21,5 @@ class Fstobdf(AutotoolsPackage):
     depends_on('libfs')
 
     depends_on('xproto@7.0.25:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/ftgl/package.py b/var/spack/repos/builtin/packages/ftgl/package.py
new file mode 100644
index 0000000000..030fa441ac
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ftgl/package.py
@@ -0,0 +1,48 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import sys
+import os
+
+
+class Ftgl(AutotoolsPackage):
+    """Library to use arbitrary fonts in OpenGL applications."""
+
+    homepage = "http://ftgl.sourceforge.net/docs/html/"
+    url      = "https://sourceforge.net/projects/ftgl/files/FTGL%20Source/2.1.2/ftgl-2.1.2.tar.gz/download"
+    list_url = "https://sourceforge.net/projects/ftgl/files/FTGL%20Source/"
+    list_depth = 1
+
+    version('2.1.2', 'f81c0a7128192ba11e036186f9a968f2')
+
+    # There is an unnecessary qualifier around, which makes modern GCC sad
+    patch('remove-extra-qualifier.diff')
+
+    # Ftgl does not come with a configure script
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool', type='build')
+    depends_on('m4', type='build')
+
+    depends_on('pkgconfig', type='build')
+    depends_on('gl')
+    depends_on('glu')
+    depends_on('freetype@2.0.9:')
+
+    # Currently, "make install" will fail if the docs weren't built
+    #
+    # FIXME: Can someone with autotools experience fix the build system
+    #        so that it doesn't fail when that happens?
+    #
+    depends_on('doxygen', type='build')
+
+    @property
+    @when('@2.1.2')
+    def configure_directory(self):
+        subdir = 'unix'
+        if sys.platform == 'darwin':
+            subdir = 'mac'
+        return os.path.join(self.stage.source_path, subdir)
diff --git a/var/spack/repos/builtin/packages/ftgl/remove-extra-qualifier.diff b/var/spack/repos/builtin/packages/ftgl/remove-extra-qualifier.diff
new file mode 100644
index 0000000000..cff9a3836e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ftgl/remove-extra-qualifier.diff
@@ -0,0 +1,11 @@
+--- FTGL/include/FTTextureGlyph.h   2018-07-26 08:30:55.144488976 +0000
++++ FTGL/include/FTTextureGlyph.h   2018-07-26 08:29:42.072489186 +0000
+@@ -52,7 +52,7 @@
+          * Reset the currently active texture to zero to get into a known state before
+          * drawing a string. This is to get round possible threading issues.
+          */
+-        static void FTTextureGlyph::ResetActiveTexture(){ activeTextureID = 0;}
++        static void ResetActiveTexture(){ activeTextureID = 0;}
+         
+     private:
+         /**
diff --git a/var/spack/repos/builtin/packages/funhpc/package.py b/var/spack/repos/builtin/packages/funhpc/package.py
index 26863ae4f4..8082be7b24 100644
--- a/var/spack/repos/builtin/packages/funhpc/package.py
+++ b/var/spack/repos/builtin/packages/funhpc/package.py
@@ -1,36 +1,20 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
 
 class Funhpc(CMakePackage):
     """FunHPC: Functional HPC Programming"""
+
     homepage = "https://github.com/eschnett/FunHPC.cxx"
-    url = "https://github.com/eschnett/FunHPC.cxx/archive/version/0.1.0.tar.gz"
+    url      = "https://github.com/eschnett/FunHPC.cxx/archive/version/0.1.0.tar.gz"
+    git      = "https://github.com/eschnett/FunHPC.cxx.git"
 
+    version('develop', branch='master')
     version('1.3.0', '71a1e57c4d882cdf001f29122edf7fc6')
     version('1.2.0', 'ba2bbeea3091e999b6b85eaeb1b67a83')
     version('1.1.1', '7b9ef638b02fffe35b75517e8eeff580')
@@ -38,8 +22,6 @@ class Funhpc(CMakePackage):
     version('1.0.0', 'f34e71ccd5548b42672e692c913ba5ee')
     version('0.1.1', 'f0248710f2de88ed2a595ad40d99997c')
     version('0.1.0', '00f7dabc08ed1ab77858785ce0809f50')
-    version('develop',
-            git='https://github.com/eschnett/FunHPC.cxx', branch='master')
 
     variant('pic', default=True,
             description="Produce position-independent code")
diff --git a/var/spack/repos/builtin/packages/fyba/gcc-6.patch b/var/spack/repos/builtin/packages/fyba/gcc-6.patch
new file mode 100644
index 0000000000..33551d6546
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fyba/gcc-6.patch
@@ -0,0 +1,18 @@
+diff -Nuar a/src/FYBA/FYLU.cpp b/src/FYBA/FYLU.cpp
+--- a/src/FYBA/FYLU.cpp	2014-09-22 00:36:49.000000000 -0500
++++ b/src/FYBA/FYLU.cpp	2018-05-24 15:35:43.584181379 -0500
+@@ -4,12 +4,12 @@
+ /*  Innhold: Rutiner for utvalg                                             */

+ /* ======================================================================== */

+ 

+-#include "stdafx.h"

+-

+ #include <ctype.h>

+ #include <math.h>

+ #include <locale>

+ 

++#include "stdafx.h"

++

+ using namespace std;

+ 

+ #define U_PARA_LEN    128     /* Max lengde av parameterstreng */

diff --git a/var/spack/repos/builtin/packages/fyba/package.py b/var/spack/repos/builtin/packages/fyba/package.py
new file mode 100644
index 0000000000..e0cfc046cd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fyba/package.py
@@ -0,0 +1,33 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Fyba(AutotoolsPackage):
+    """OpenFYBA is the source code release of the FYBA library, distributed
+    by the National Mapping Authority of Norway (Statens kartverk) to read
+    and write files in the National geodata standard format SOSI."""
+
+    homepage = "https://github.com/kartverket/fyba"
+    url      = "https://github.com/kartverket/fyba/archive/4.1.1.tar.gz"
+
+    version('4.1.1', 'ab687582efdef26593796271529a10cb')
+
+    # configure: error: cannot find install-sh or install.sh
+    force_autoreconf = True
+
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool',  type='build')
+    depends_on('m4',       type='build')
+
+    # error: macro "min" passed 3 arguments, but takes just 2
+    # https://github.com/kartverket/fyba/issues/21
+    patch('gcc-6.patch')
+
+    # fatal error: 'sys/vfs.h' file not found
+    # https://github.com/kartverket/fyba/issues/12
+    patch('vfs-mount-darwin.patch', when='platform=darwin')
diff --git a/var/spack/repos/builtin/packages/fyba/vfs-mount-darwin.patch b/var/spack/repos/builtin/packages/fyba/vfs-mount-darwin.patch
new file mode 100644
index 0000000000..134db87a1c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fyba/vfs-mount-darwin.patch
@@ -0,0 +1,48 @@
+diff -Naur a/configure.ac b/configure.ac
+--- a/configure.ac	2014-09-22 00:36:49.000000000 -0500
++++ b/configure.ac	2018-05-19 12:37:15.000000000 -0500
+@@ -18,7 +18,7 @@
+ # Checks for libraries.
+ 
+ # Checks for header files.
+-AC_CHECK_HEADERS([fcntl.h float.h inttypes.h limits.h locale.h memory.h stdint.h stdlib.h string.h sys/ioctl.h sys/statvfs.h sys/time.h sys/vfs.h termios.h unistd.h])
++AC_CHECK_HEADERS([fcntl.h float.h inttypes.h limits.h locale.h memory.h stdint.h stdlib.h string.h sys/ioctl.h sys/statvfs.h sys/time.h sys/mount.h termios.h unistd.h])
+ 
+ # Checks for typedefs, structures, and compiler characteristics.
+ AC_HEADER_STDBOOL
+diff -Naur a/src/UT/DISKINFO.cpp b/src/UT/DISKINFO.cpp
+--- a/src/UT/DISKINFO.cpp	2014-09-22 00:36:49.000000000 -0500
++++ b/src/UT/DISKINFO.cpp	2018-05-19 12:38:08.000000000 -0500
+@@ -17,7 +17,7 @@
+ #     include <sys/statvfs.h>

+ #  else

+ #     include <sys/stat.h>

+-#     include <sys/vfs.h>

++#     include <sys/mount.h>

+ #  endif

+ 

+ #  include <sys/types.h>

+diff -Naur a/src/UT/INQSIZE.cpp b/src/UT/INQSIZE.cpp
+--- a/src/UT/INQSIZE.cpp	2014-09-22 00:36:49.000000000 -0500
++++ b/src/UT/INQSIZE.cpp	2018-05-19 12:37:45.000000000 -0500
+@@ -16,7 +16,7 @@
+ #  include<stdio.h>

+ #  include<sys/time.h>

+ #  include<sys/types.h>

+-#  include<sys/vfs.h>

++#  include<sys/mount.h>

+ #  include<fcntl.h>

+ #  include<sys/stat.h>

+ #  include<errno.h>

+diff -Naur a/src/UT/INQTID.cpp b/src/UT/INQTID.cpp
+--- a/src/UT/INQTID.cpp	2014-09-22 00:36:49.000000000 -0500
++++ b/src/UT/INQTID.cpp	2018-05-19 12:37:57.000000000 -0500
+@@ -15,7 +15,7 @@
+ #  include<stdio.h>

+ #  include<sys/time.h>

+ #  include<sys/types.h>

+-#  include<sys/vfs.h>

++#  include<sys/mount.h>

+ #  include<fcntl.h>

+ #  include<sys/stat.h>

+ #  include<errno.h>

diff --git a/var/spack/repos/builtin/packages/gapbs/package.py b/var/spack/repos/builtin/packages/gapbs/package.py
new file mode 100644
index 0000000000..f62cbb790f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gapbs/package.py
@@ -0,0 +1,38 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Gapbs(MakefilePackage):
+    """The GAP Benchmark Suite is intended to help graph processing research by
+    standardizing evaluations. Fewer differences between graph processing
+    evaluations will make it easier to compare different research efforts and
+    quantify improvements. The benchmark not only specifies graph kernels,
+    input graphs, and evaluation methodologies, but it also provides an
+    optimized baseline implementation (this repo). These baseline
+    implementations are representative of state-of-the-art performance, and
+    thus new contributions should outperform them to demonstrate an
+    improvement."""
+
+    homepage = "http://gap.cs.berkeley.edu/benchmark.html"
+    url      = "https://github.com/sbeamer/gapbs/archive/v1.0.tar.gz"
+
+    version('1.0', 'ac2efa793f44e58553449f42b9779f3ff2d47634')
+
+    variant('serial', default=False, description='Version with no parallelism')
+
+    def build(self, spec, prefix):
+        cxx_flags = ['-O3', self.compiler.cxx11_flag]
+
+        if '-serial' in spec:
+            cxx_flags.append(self.compiler.openmp_flag)
+
+        make('CXX_FLAGS=' + ' '.join(cxx_flags))
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        for app in ["bc", "bfs", "cc", "converter", "pr", "sssp", "tc"]:
+            install(app, prefix.bin)
diff --git a/var/spack/repos/builtin/packages/gapcloser/package.py b/var/spack/repos/builtin/packages/gapcloser/package.py
index b59b46af00..d4ff137816 100644
--- a/var/spack/repos/builtin/packages/gapcloser/package.py
+++ b/var/spack/repos/builtin/packages/gapcloser/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/gapfiller/package.py b/var/spack/repos/builtin/packages/gapfiller/package.py
index 43e6eeaac0..883874007b 100644
--- a/var/spack/repos/builtin/packages/gapfiller/package.py
+++ b/var/spack/repos/builtin/packages/gapfiller/package.py
@@ -1,29 +1,11 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
+import glob
 
 
 class Gapfiller(Package):
@@ -44,9 +26,20 @@ class Gapfiller(Package):
         return "file://{0}/39GapFiller_v{1}_linux-x86_64.tar.gz".format(
                 os.getcwd(), version.dashed)
 
-    depends_on('perl', type=('build', 'run'))
+    depends_on('perl+threads', type=('build', 'run'))
+
+    def patch(self):
+        with working_dir('.'):
+            files = glob.iglob("*.pl")
+            for file in files:
+                change = FileFilter(file)
+                change.filter('usr/bin/perl', 'usr/bin/env perl')
+                change.filter('require "getopts.pl";', 'use Getopt::Std;')
+                change.filter('&Getopts', 'getopts')
+                change.filter('\r', '')
+                set_executable(file)
 
     def install(self, spec, prefix):
-        install_tree('bowtie', prefix.bowtie)
-        install_tree('bwa', prefix.bwa)
-        install('GapFiller.pl', prefix)
+        install_tree('bowtie', prefix.bin.bowtie)
+        install_tree('bwa', prefix.bin.bwa)
+        install('GapFiller.pl', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/gasnet/package.py b/var/spack/repos/builtin/packages/gasnet/package.py
index 6b8a498671..7681af2d21 100644
--- a/var/spack/repos/builtin/packages/gasnet/package.py
+++ b/var/spack/repos/builtin/packages/gasnet/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,8 +14,9 @@ class Gasnet(AutotoolsPackage):
        Cray Chapel, and Titanium.
     """
     homepage = "http://gasnet.lbl.gov"
-    url      = "http://gasnet.lbl.gov/GASNet-1.24.0.tar.gz"
+    url      = "http://gasnet.lbl.gov/download/GASNet-1.24.0.tar.gz"
 
+    version('1.32.0', sha256='42e4774b3bbc7c142f77c41b6ce86b594f579073f46c31f47f424c7e31ee1511')
     version('1.30.0', '2ddb1d8397d62acfd389095ca8da72f6')
     version('1.28.2', '6ca0463dc2430570e40646c4d1e97b36')
     version('1.28.0', 'b44446d951d3d8954aa1570e3556ba61')
diff --git a/var/spack/repos/builtin/packages/gatk/gatk.sh b/var/spack/repos/builtin/packages/gatk/gatk.sh
new file mode 100755
index 0000000000..2bd68247a6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gatk/gatk.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+# convenience wrapper for the gatk jar file
+java -jar GenomeAnalysisTK.jar "$@"
+
diff --git a/var/spack/repos/builtin/packages/gatk/package.py b/var/spack/repos/builtin/packages/gatk/package.py
new file mode 100644
index 0000000000..32bb771530
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gatk/package.py
@@ -0,0 +1,62 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import glob
+import os.path
+import re
+
+
+class Gatk(Package):
+    """Genome Analysis Toolkit
+       Variant Discovery in High-Throughput Sequencing Data
+    """
+    homepage = "https://software.broadinstitute.org/gatk/"
+    url      = "https://github.com/broadinstitute/gatk/releases/download/4.0.4.0/gatk-4.0.4.0.zip"
+
+    version('4.0.8.1', sha256='6d47463dfd8c16ffae82fd29e4e73503e5b7cd0fcc6fea2ed50ee3760dd9acd9',
+            url='https://github.com/broadinstitute/gatk/archive/4.0.8.1.tar.gz')
+    version('4.0.4.0', '083d655883fb251e837eb2458141fc2b',
+            url="https://github.com/broadinstitute/gatk/releases/download/4.0.4.0/gatk-4.0.4.0.zip")
+    version('3.8-0', '0581308d2a25f10d11d3dfd0d6e4d28e', extension='tar.gz',
+            url="https://software.broadinstitute.org/gatk/download/auth?package=GATK")
+
+    depends_on('java@8:', type='run')
+    depends_on('python@2.6:2.8,3.6:', type='run', when='@4.0:')
+    depends_on('r@3.2:', type='run', when='@4.0:')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+
+        # Install all executable non-script files to prefix bin
+        files = [x for x in glob.glob("*")
+                 if not re.match("^.*\.sh$", x) and is_exe(x)]
+        for f in files:
+            install(f, prefix.bin)
+
+        # Skip helper script settings
+        if spec.satisfies('@:4.0'):
+            return
+
+        # Set up a helper script to call java on the jar file,
+        # explicitly codes the path for java and the jar file.
+        script_sh = join_path(os.path.dirname(__file__), "gatk.sh")
+        script = join_path(prefix.bin, "gatk")
+        install(script_sh, script)
+        set_executable(script)
+
+        # Munge the helper script to explicitly point to java and the
+        # jar file.
+        java = join_path(self.spec['java'].prefix, 'bin', 'java')
+        kwargs = {'ignore_absent': False, 'backup': False, 'string': False}
+        filter_file('^java', java, script, **kwargs)
+        filter_file('GenomeAnalysisTK.jar', join_path(prefix.bin,
+                    'GenomeAnalysisTK.jar'),
+                    script, **kwargs)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('GATK',
+                             join_path(self.prefix, 'bin',
+                                                    'GenomeAnalysisTK.jar'))
diff --git a/var/spack/repos/builtin/packages/gaussian/package.py b/var/spack/repos/builtin/packages/gaussian/package.py
index ef8c599b94..a9088d11e6 100644
--- a/var/spack/repos/builtin/packages/gaussian/package.py
+++ b/var/spack/repos/builtin/packages/gaussian/package.py
@@ -1,30 +1,10 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
-import shutil
 
 
 class Gaussian(Package):
@@ -36,7 +16,7 @@ class Gaussian(Package):
     version('09', '7d4c95b535e68e48af183920df427e4e')
 
     def install(self, spec, prefix):
-        shutil.copytree(os.getcwd(), prefix.bin)
+        install_tree('.', prefix.bin)
         patch_install_files = ['flc',
                                'linda8.2/opteron-linux/bin/flc',
                                'linda8.2/opteron-linux/bin/LindaLauncher',
diff --git a/var/spack/repos/builtin/packages/gawk/package.py b/var/spack/repos/builtin/packages/gawk/package.py
index 8f9f205ff6..61e08f3158 100644
--- a/var/spack/repos/builtin/packages/gawk/package.py
+++ b/var/spack/repos/builtin/packages/gawk/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,7 +21,7 @@ class Gawk(AutotoolsPackage):
     """
 
     homepage = "https://www.gnu.org/software/gawk/"
-    url      = "http://ftp.gnu.org/gnu/gawk/gawk-4.1.4.tar.xz"
+    url      = "https://ftpmirror.gnu.org/gawk/gawk-4.1.4.tar.xz"
 
     version('4.1.4', '4e7dbc81163e60fd4f0b52496e7542c9')
 
diff --git a/var/spack/repos/builtin/packages/gblocks/package.py b/var/spack/repos/builtin/packages/gblocks/package.py
index 7e6401bc6d..38fc44b86a 100644
--- a/var/spack/repos/builtin/packages/gblocks/package.py
+++ b/var/spack/repos/builtin/packages/gblocks/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/gcc/darwin/headers-10.13-fix.patch b/var/spack/repos/builtin/packages/gcc/darwin/headers-10.13-fix.patch
new file mode 100644
index 0000000000..3dbfde0255
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gcc/darwin/headers-10.13-fix.patch
@@ -0,0 +1,127 @@
+diff -pur fixincludes/fixincl.x gcc-5.5.0/fixincludes/fixincl.x
+--- a/fixincludes/fixincl.x	2017-01-30 17:08:42.000000000 +0100
++++ b/fixincludes/fixincl.x	2017-12-21 14:34:35.000000000 +0100
+@@ -1,12 +1,12 @@
+ /*  -*- buffer-read-only: t -*- vi: set ro:
+- * 
++ *
+  * DO NOT EDIT THIS FILE   (fixincl.x)
+- * 
+- * It has been AutoGen-ed  January  5, 2017 at 06:05:06 PM by AutoGen 5.16.2
++ *
++ * It has been AutoGen-ed  December 21, 2017 at 02:34:35 PM by AutoGen 5.18.7
+  * From the definitions    inclhack.def
+  * and the template file   fixincl
+  */
+-/* DO NOT SVN-MERGE THIS FILE, EITHER Thu Jan  5 18:05:06 CET 2017
++/* DO NOT SVN-MERGE THIS FILE, EITHER Thu Dec 21 14:34:35 CET 2017
+  *
+  * You must regenerate it.  Use the ./genfixes script.
+  *
+@@ -15,7 +15,7 @@
+  * certain ANSI-incompatible system header files which are fixed to work
+  * correctly with ANSI C and placed in a directory that GNU C will search.
+  *
+- * This file contains 240 fixup descriptions.
++ * This file contains 241 fixup descriptions.
+  *
+  * See README for more information.
+  *
+@@ -2579,6 +2579,43 @@ extern \"C\" {\n\
+ 
+ /* * * * * * * * * * * * * * * * * * * * * * * * * *
+  *
++ *  Description of Darwin_Osavailability fix
++ */
++tSCC zDarwin_OsavailabilityName[] =
++     "darwin_osavailability";
++
++/*
++ *  File name selection pattern
++ */
++tSCC zDarwin_OsavailabilityList[] =
++  "os/availability.h\0";
++/*
++ *  Machine/OS name selection pattern
++ */
++tSCC* apzDarwin_OsavailabilityMachs[] = {
++        "*-*-darwin*",
++        (const char*)NULL };
++
++/*
++ *  content selection pattern - do fix if pattern found
++ */
++tSCC zDarwin_OsavailabilitySelect0[] =
++       "#define[ \t]+__(API_[A-Z_]*)\\(\\.\\.\\.\\)";
++
++#define    DARWIN_OSAVAILABILITY_TEST_CT  1
++static tTestDesc aDarwin_OsavailabilityTests[] = {
++  { TT_EGREP,    zDarwin_OsavailabilitySelect0, (regex_t*)NULL }, };
++
++/*
++ *  Fix Command Arguments for Darwin_Osavailability
++ */
++static const char* apzDarwin_OsavailabilityPatch[] = {
++    "format",
++    "#define %1(...)",
++    (char*)NULL };
++
++/* * * * * * * * * * * * * * * * * * * * * * * * * *
++ *
+  *  Description of Darwin_9_Long_Double_Funcs_2 fix
+  */
+ tSCC zDarwin_9_Long_Double_Funcs_2Name[] =
+@@ -9818,9 +9855,9 @@ static const char* apzX11_SprintfPatch[]
+  *
+  *  List of all fixes
+  */
+-#define REGEX_COUNT          276
++#define REGEX_COUNT          277
+ #define MACH_LIST_SIZE_LIMIT 187
+-#define FIX_COUNT            240
++#define FIX_COUNT            241
+ 
+ /*
+  *  Enumerate the fixes
+@@ -9885,6 +9922,7 @@ typedef enum {
+     CTRL_QUOTES_DEF_FIXIDX,
+     CTRL_QUOTES_USE_FIXIDX,
+     CXX_UNREADY_FIXIDX,
++    DARWIN_OSAVAILABILITY_FIXIDX,
+     DARWIN_9_LONG_DOUBLE_FUNCS_2_FIXIDX,
+     DARWIN_EXTERNC_FIXIDX,
+     DARWIN_GCC4_BREAKAGE_FIXIDX,
+@@ -10364,6 +10402,11 @@ tFixDesc fixDescList[ FIX_COUNT ] = {
+      CXX_UNREADY_TEST_CT, FD_MACH_ONLY | FD_SUBROUTINE,
+      aCxx_UnreadyTests,   apzCxx_UnreadyPatch, 0 },
+ 
++  {  zDarwin_OsavailabilityName,    zDarwin_OsavailabilityList,
++     apzDarwin_OsavailabilityMachs,
++     DARWIN_OSAVAILABILITY_TEST_CT, FD_MACH_ONLY | FD_SUBROUTINE,
++     aDarwin_OsavailabilityTests,   apzDarwin_OsavailabilityPatch, 0 },
++
+   {  zDarwin_9_Long_Double_Funcs_2Name,    zDarwin_9_Long_Double_Funcs_2List,
+      apzDarwin_9_Long_Double_Funcs_2Machs,
+      DARWIN_9_LONG_DOUBLE_FUNCS_2_TEST_CT, FD_MACH_ONLY | FD_SUBROUTINE,
+diff -pur fixincludes/inclhack.def gcc-5.5.0/fixincludes/inclhack.def
+--- a/fixincludes/inclhack.def	2017-01-30 17:08:42.000000000 +0100
++++ b/fixincludes/inclhack.def	2017-12-21 14:34:28.000000000 +0100
+@@ -1337,6 +1337,18 @@ fix = {
+     test_text = "extern void* malloc( size_t );";
+ };
+ 
++fix = {
++    hackname  = darwin_osavailability;
++    mach      = "*-*-darwin*";
++    files     = os/availability.h;
++    select    = "#define[ \t]+__(API_[A-Z_]*)\\(\\.\\.\\.\\)";
++    c_fix     = format;
++    c_fix_arg = "#define %1(...)";
++
++    test_text = "#define __API_AVAILABLE(...)\n"
++		"#define API_AVAILABLE(...)\n";
++};
++
+ /*
+  *  For the AAB_darwin7_9_long_double_funcs fix to be useful,
+  *  you have to not use "" includes.
diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py
index df7060e742..a029a9e0c5 100644
--- a/var/spack/repos/builtin/packages/gcc/package.py
+++ b/var/spack/repos/builtin/packages/gcc/package.py
@@ -1,34 +1,14 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from spack.operating_systems.mac_os import macOS_version
+from spack.operating_systems.mac_os import macos_version
 from llnl.util import tty
 
 import glob
 import os
-import shutil
 import sys
 
 
@@ -37,10 +17,13 @@ class Gcc(AutotoolsPackage):
     Fortran, Ada, and Go, as well as libraries for these languages."""
 
     homepage = 'https://gcc.gnu.org'
-    url      = 'http://ftp.gnu.org/gnu/gcc/gcc-7.1.0/gcc-7.1.0.tar.bz2'
+    url      = 'https://ftpmirror.gnu.org/gcc/gcc-7.1.0/gcc-7.1.0.tar.bz2'
     list_url = 'http://ftp.gnu.org/gnu/gcc/'
     list_depth = 1
 
+    version('8.2.0', '64898a165f67e136d802a92e7633bf1b06c85266027e52127ea025bf5fc2291b5e858288aac0bdba246e6cdf7c6ec88bc8e0e7f3f6f1985f4297710cafde56ed')
+    version('8.1.0', '65f7c65818dc540b3437605026d329fc')
+    version('7.3.0', 'be2da21680f27624f3a87055c4ba5af2')
     version('7.2.0', 'ff370482573133a7fcdd96cd2f552292')
     version('7.1.0', '6bf56a2bca9dac9dbbf8e8d1036964a8')
     version('6.4.0', '11ba51a0cfb8471927f387c8895fe232')
@@ -62,12 +45,17 @@ class Gcc(AutotoolsPackage):
     version('4.6.4', 'b407a3d1480c11667f293bfb1f17d1a4')
     version('4.5.4', '27e459c2566b8209ab064570e1b378f7')
 
-    # Builds all default languages by default.
-    # Ada, Go, Jit, and Objective-C++ are not default languages.
+    # We specifically do not add 'all' variant here because:
+    # (i) Ada, Go, Jit, and Objective-C++ are not default languages.
     # In that respect, the name 'all' is rather misleading.
+    # (ii) Languages other than c,c++,fortran are prone to configure bug in GCC
+    # For example, 'java' appears to ignore custom location of zlib
+    # (iii) meaning of 'all' changes with GCC version, i.e. 'java' is not part
+    # of gcc7. Correctly specifying conflicts() and depends_on() in such a
+    # case is a PITA.
     variant('languages',
-            default='all',
-            values=('all', 'ada', 'brig', 'c', 'c++', 'fortran',
+            default='c,c++,fortran',
+            values=('ada', 'brig', 'c', 'c++', 'fortran',
                     'go', 'java', 'jit', 'lto', 'objc', 'obj-c++'),
             multi=True,
             description='Compilers and runtime libraries to build')
@@ -83,27 +71,32 @@ class Gcc(AutotoolsPackage):
 
     # https://gcc.gnu.org/install/prerequisites.html
     depends_on('gmp@4.3.2:')
-    depends_on('mpfr@2.4.2:')
+    # GCC 7.3 does not compile with newer releases on some platforms, see
+    #   https://github.com/spack/spack/issues/6902#issuecomment-433030376
+    depends_on('mpfr@2.4.2:3.1.6')
     depends_on('mpc@0.8.1:', when='@4.5:')
-    depends_on('isl@0.14', when='@5:5.9')
-    depends_on('isl@0.15:', when='@6:')
+    # Already released GCC versions do not support any newer version of ISL
+    #   GCC 5.4 https://github.com/spack/spack/issues/6902#issuecomment-433072097
+    #   GCC 7.3 https://github.com/spack/spack/issues/6902#issuecomment-433030376
+    #   GCC 9+  https://gcc.gnu.org/bugzilla/show_bug.cgi?id=86724
+    depends_on('isl@0.15', when='@5:5.9')
+    depends_on('isl@0.15:0.18', when='@6:8.9')
+    depends_on('isl@0.15:0.20', when='@9:')
     depends_on('zlib', when='@6:')
     depends_on('gnat', when='languages=ada')
     depends_on('binutils~libiberty', when='+binutils')
     depends_on('zip', type='build', when='languages=java')
-    depends_on('zip', type='build', when='@:6 languages=all')
 
     # TODO: integrate these libraries.
     # depends_on('ppl')
     # depends_on('cloog')
 
-    # TODO: Add a 'test' deptype
-    # https://github.com/spack/spack/issues/1279
-    # depends_on('dejagnu@1.4.4', type='test')
-    # depends_on('expect', type='test')
-    # depends_on('tcl', type='test')
-    # depends_on('autogen@5.5.4:', type='test')
-    # depends_on('guile@1.4.1:', type='test')
+    # https://gcc.gnu.org/install/test.html
+    depends_on('dejagnu@1.4.4', type='test')
+    depends_on('expect', type='test')
+    depends_on('tcl', type='test')
+    depends_on('autogen@5.5.4:', type='test')
+    depends_on('guile@1.4.1:', type='test')
 
     # See https://golang.org/doc/install/gccgo#Releases
     provides('golang',        when='languages=go @4.6:')
@@ -152,16 +145,30 @@ class Gcc(AutotoolsPackage):
     if sys.platform == 'darwin':
         # Fix parallel build on APFS filesystem
         # https://gcc.gnu.org/bugzilla/show_bug.cgi?id=81797
-        if macOS_version() >= Version('10.13'):
-            patch('darwin/apfs.patch', when='@7.2.0')
+        if macos_version() >= Version('10.13'):
+            patch('darwin/apfs.patch', when='@5.5.0,6.1:6.4,7.1:7.3')
+            # from homebrew via macports
+            # https://trac.macports.org/ticket/56502#no1
+            # see also: https://gcc.gnu.org/bugzilla/show_bug.cgi?id=83531
+            patch('darwin/headers-10.13-fix.patch', when='@5.5.0')
         patch('darwin/gcc-7.1.0-headerpad.patch', when='@5:')
-        patch('darwin/gcc-6.1.0-jit.patch', when='@5:')
+        patch('darwin/gcc-6.1.0-jit.patch', when='@5:7')
         patch('darwin/gcc-4.9.patch1', when='@4.9.0:4.9.3')
         patch('darwin/gcc-4.9.patch2', when='@4.9.0:4.9.3')
 
     patch('piclibs.patch', when='+piclibs')
     patch('gcc-backport.patch', when='@4.7:4.9.2,5:5.3')
 
+    # Older versions do not compile with newer versions of glibc
+    # https://gcc.gnu.org/bugzilla/show_bug.cgi?id=81712
+    patch('ucontext_t.patch', when='@4.9,5.1:5.4,6.1:6.4,7.1')
+    patch('ucontext_t-java.patch', when='@4.9,5.1:5.4,6.1:6.4 languages=java')
+    # https://gcc.gnu.org/bugzilla/show_bug.cgi?id=81066
+    patch('stack_t-4.9.patch', when='@4.9')
+    patch('stack_t.patch', when='@5.1:5.4,6.1:6.4,7.1')
+    # https://bugs.busybox.net/show_bug.cgi?id=10061
+    patch('signal.patch', when='@4.9,5.1:5.4')
+
     build_directory = 'spack-build'
 
     def url_for_version(self, version):
@@ -187,7 +194,7 @@ class Gcc(AutotoolsPackage):
                 new_dispatch_dir = join_path(prefix, 'include', 'dispatch')
                 mkdirp(new_dispatch_dir)
                 new_header = join_path(new_dispatch_dir, 'object.h')
-                shutil.copyfile('/usr/include/dispatch/object.h', new_header)
+                install('/usr/include/dispatch/object.h', new_header)
                 filter_file(r'typedef void \(\^dispatch_block_t\)\(void\)',
                             'typedef void* dispatch_block_t',
                             new_header)
@@ -290,3 +297,10 @@ class Gcc(AutotoolsPackage):
                     out.write('-rpath {0}:{1} '.format(
                               self.prefix.lib, self.prefix.lib64))
         set_install_permissions(specs_file)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.set('CC', join_path(self.spec.prefix.bin, 'gcc'))
+        run_env.set('CXX', join_path(self.spec.prefix.bin, 'g++'))
+        run_env.set('FC', join_path(self.spec.prefix.bin, 'gfortran'))
+        run_env.set('F77', join_path(self.spec.prefix.bin, 'gfortran'))
+        run_env.set('F90', join_path(self.spec.prefix.bin, 'gfortran'))
diff --git a/var/spack/repos/builtin/packages/gcc/signal.patch b/var/spack/repos/builtin/packages/gcc/signal.patch
new file mode 100644
index 0000000000..21bf9e030f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gcc/signal.patch
@@ -0,0 +1,28 @@
+From 6c709b6262e8b6441b1e94526d6d65d4ce7a7dec Mon Sep 17 00:00:00 2001
+From: doko <doko@138bc75d-0d04-0410-961f-82ee72b054a4>
+Date: Thu, 7 Sep 2017 07:18:57 +0000
+Subject: [PATCH] 2017-09-07  Matthias Klose  <doko@ubuntu.com>
+
+        * asan/asan_linux.cc: Include <signal.h>
+
+
+git-svn-id: svn+ssh://gcc.gnu.org/svn/gcc/branches/gcc-5-branch@251830 138bc75d-0d04-0410-961f-82ee72b054a4
+---
+ libsanitizer/asan/asan_linux.cc | 1 +
+ 2 files changed, 5 insertions(+)
+
+diff --git a/libsanitizer/asan/asan_linux.cc b/libsanitizer/asan/asan_linux.cc
+index c504168..59087b9 100644
+--- a/libsanitizer/asan/asan_linux.cc
++++ b/libsanitizer/asan/asan_linux.cc
+@@ -29,6 +29,7 @@
+ #include <dlfcn.h>
+ #include <fcntl.h>
+ #include <pthread.h>
++#include <signal.h>
+ #include <stdio.h>
+ #include <unistd.h>
+ #include <unwind.h>
+-- 
+2.9.3
+
diff --git a/var/spack/repos/builtin/packages/gcc/stack_t-4.9.patch b/var/spack/repos/builtin/packages/gcc/stack_t-4.9.patch
new file mode 100644
index 0000000000..b894557c8c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gcc/stack_t-4.9.patch
@@ -0,0 +1,80 @@
+From 833e00c01e96f61e24cd7ec97b93fad212dc914b Mon Sep 17 00:00:00 2001
+From: doko <doko@138bc75d-0d04-0410-961f-82ee72b054a4>
+Date: Thu, 7 Sep 2017 07:17:17 +0000
+Subject: [PATCH] 2017-09-07  Matthias Klose  <doko@ubuntu.com>
+
+        Backported from mainline
+        2017-07-14  Jakub Jelinek  <jakub@redhat.com>
+
+        PR sanitizer/81066
+        * sanitizer_common/sanitizer_linux.h: Cherry-pick upstream r307969.
+        * sanitizer_common/sanitizer_linux.cc: Likewise.
+        * sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc: Likewise.
+        * tsan/tsan_platform_linux.cc: Likewise.
+
+
+git-svn-id: svn+ssh://gcc.gnu.org/svn/gcc/branches/gcc-5-branch@251829 138bc75d-0d04-0410-961f-82ee72b054a4
+---
+ libsanitizer/sanitizer_common/sanitizer_linux.cc              |  3 +--
+ libsanitizer/sanitizer_common/sanitizer_linux.h               |  4 +---
+ .../sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc  |  2 +-
+ libsanitizer/tsan/tsan_platform_linux.cc                      |  2 +-
+ 5 files changed, 15 insertions(+), 7 deletions(-)
+
+diff --git a/libsanitizer/sanitizer_common/sanitizer_linux.cc b/libsanitizer/sanitizer_common/sanitizer_linux.cc
+index 9feb307..821b26d 100644
+--- a/libsanitizer/sanitizer_common/sanitizer_linux.cc
++++ b/libsanitizer/sanitizer_common/sanitizer_linux.cc
+@@ -514,8 +514,7 @@ uptr internal_prctl(int option, uptr arg2, uptr arg3, uptr arg4, uptr arg5) {
+ }
+ #endif
+ 
+-uptr internal_sigaltstack(const struct sigaltstack *ss,
+-                         struct sigaltstack *oss) {
++uptr internal_sigaltstack(const void *ss, void *oss) {
+   return internal_syscall(__NR_sigaltstack, (uptr)ss, (uptr)oss);
+ }
+ 
+diff --git a/libsanitizer/sanitizer_common/sanitizer_linux.h b/libsanitizer/sanitizer_common/sanitizer_linux.h
+index 086834c..3a6f4cd 100644
+--- a/libsanitizer/sanitizer_common/sanitizer_linux.h
++++ b/libsanitizer/sanitizer_common/sanitizer_linux.h
+@@ -27,8 +26,7 @@ struct linux_dirent;
+ // Syscall wrappers.
+ uptr internal_getdents(fd_t fd, struct linux_dirent *dirp, unsigned int count);
+ uptr internal_prctl(int option, uptr arg2, uptr arg3, uptr arg4, uptr arg5);
+-uptr internal_sigaltstack(const struct sigaltstack* ss,
+-                          struct sigaltstack* oss);
++uptr internal_sigaltstack(const void* ss, void* oss);
+ uptr internal_sigaction(int signum, const __sanitizer_kernel_sigaction_t *act,
+     __sanitizer_kernel_sigaction_t *oldact);
+ uptr internal_sigprocmask(int how, __sanitizer_kernel_sigset_t *set,
+diff --git a/libsanitizer/sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc b/libsanitizer/sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc
+index 5881202..c54894d 100644
+--- a/libsanitizer/sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc
++++ b/libsanitizer/sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc
+@@ -234,7 +234,7 @@ static int TracerThread(void* argument) {
+ 
+   // Alternate stack for signal handling.
+   InternalScopedBuffer<char> handler_stack_memory(kHandlerStackSize);
+-  struct sigaltstack handler_stack;
++  stack_t handler_stack;
+   internal_memset(&handler_stack, 0, sizeof(handler_stack));
+   handler_stack.ss_sp = handler_stack_memory.data();
+   handler_stack.ss_size = kHandlerStackSize;
+diff --git a/libsanitizer/tsan/tsan_platform_linux.cc b/libsanitizer/tsan/tsan_platform_linux.cc
+index 3259131..b8e9078 100644
+--- a/libsanitizer/tsan/tsan_platform_linux.cc
++++ b/libsanitizer/tsan/tsan_platform_linux.cc
+@@ -377,7 +377,7 @@ bool IsGlobalVar(uptr addr) {
+ int ExtractResolvFDs(void *state, int *fds, int nfd) {
+ #if SANITIZER_LINUX
+   int cnt = 0;
+-  __res_state *statp = (__res_state*)state;
++  struct __res_state *statp = (struct __res_state*)state;
+   for (int i = 0; i < MAXNS && cnt < nfd; i++) {
+     if (statp->_u._ext.nsaddrs[i] && statp->_u._ext.nssocks[i] != -1)
+       fds[cnt++] = statp->_u._ext.nssocks[i];
+-- 
+2.9.3
+
diff --git a/var/spack/repos/builtin/packages/gcc/stack_t.patch b/var/spack/repos/builtin/packages/gcc/stack_t.patch
new file mode 100644
index 0000000000..48a5a47ade
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gcc/stack_t.patch
@@ -0,0 +1,88 @@
+From 833e00c01e96f61e24cd7ec97b93fad212dc914b Mon Sep 17 00:00:00 2001
+From: doko <doko@138bc75d-0d04-0410-961f-82ee72b054a4>
+Date: Thu, 7 Sep 2017 07:17:17 +0000
+Subject: [PATCH] 2017-09-07  Matthias Klose  <doko@ubuntu.com>
+
+        Backported from mainline
+        2017-07-14  Jakub Jelinek  <jakub@redhat.com>
+
+        PR sanitizer/81066
+        * sanitizer_common/sanitizer_linux.h: Cherry-pick upstream r307969.
+        * sanitizer_common/sanitizer_linux.cc: Likewise.
+        * sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc: Likewise.
+        * tsan/tsan_platform_linux.cc: Likewise.
+
+
+git-svn-id: svn+ssh://gcc.gnu.org/svn/gcc/branches/gcc-5-branch@251829 138bc75d-0d04-0410-961f-82ee72b054a4
+---
+ libsanitizer/sanitizer_common/sanitizer_linux.cc              |  3 +--
+ libsanitizer/sanitizer_common/sanitizer_linux.h               |  4 +---
+ .../sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc  |  2 +-
+ libsanitizer/tsan/tsan_platform_linux.cc                      |  2 +-
+ 5 files changed, 15 insertions(+), 7 deletions(-)
+
+diff --git a/libsanitizer/sanitizer_common/sanitizer_linux.cc b/libsanitizer/sanitizer_common/sanitizer_linux.cc
+index 9feb307..821b26d 100644
+--- a/libsanitizer/sanitizer_common/sanitizer_linux.cc
++++ b/libsanitizer/sanitizer_common/sanitizer_linux.cc
+@@ -514,8 +514,7 @@ uptr internal_prctl(int option, uptr arg2, uptr arg3, uptr arg4, uptr arg5) {
+ }
+ #endif
+ 
+-uptr internal_sigaltstack(const struct sigaltstack *ss,
+-                         struct sigaltstack *oss) {
++uptr internal_sigaltstack(const void *ss, void *oss) {
+   return internal_syscall(SYSCALL(sigaltstack), (uptr)ss, (uptr)oss);
+ }
+ 
+diff --git a/libsanitizer/sanitizer_common/sanitizer_linux.h b/libsanitizer/sanitizer_common/sanitizer_linux.h
+index 086834c..3a6f4cd 100644
+--- a/libsanitizer/sanitizer_common/sanitizer_linux.h
++++ b/libsanitizer/sanitizer_common/sanitizer_linux.h
+@@ -18,7 +18,6 @@
+ #include "sanitizer_platform_limits_posix.h"
+ 
+ struct link_map;  // Opaque type returned by dlopen().
+-struct sigaltstack;
+ 
+ namespace __sanitizer {
+ // Dirent structure for getdents(). Note that this structure is different from
+@@ -27,8 +26,7 @@ struct linux_dirent;
+ 
+ // Syscall wrappers.
+ uptr internal_getdents(fd_t fd, struct linux_dirent *dirp, unsigned int count);
+-uptr internal_sigaltstack(const struct sigaltstack* ss,
+-                          struct sigaltstack* oss);
++uptr internal_sigaltstack(const void* ss, void* oss);
+ uptr internal_sigprocmask(int how, __sanitizer_sigset_t *set,
+     __sanitizer_sigset_t *oldset);
+ void internal_sigfillset(__sanitizer_sigset_t *set);
+diff --git a/libsanitizer/sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc b/libsanitizer/sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc
+index 5881202..c54894d 100644
+--- a/libsanitizer/sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc
++++ b/libsanitizer/sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc
+@@ -234,7 +234,7 @@ static int TracerThread(void* argument) {
+ 
+   // Alternate stack for signal handling.
+   InternalScopedBuffer<char> handler_stack_memory(kHandlerStackSize);
+-  struct sigaltstack handler_stack;
++  stack_t handler_stack;
+   internal_memset(&handler_stack, 0, sizeof(handler_stack));
+   handler_stack.ss_sp = handler_stack_memory.data();
+   handler_stack.ss_size = kHandlerStackSize;
+diff --git a/libsanitizer/tsan/tsan_platform_linux.cc b/libsanitizer/tsan/tsan_platform_linux.cc
+index 3259131..b8e9078 100644
+--- a/libsanitizer/tsan/tsan_platform_linux.cc
++++ b/libsanitizer/tsan/tsan_platform_linux.cc
+@@ -377,7 +377,7 @@ bool IsGlobalVar(uptr addr) {
+ int ExtractResolvFDs(void *state, int *fds, int nfd) {
+ #if SANITIZER_LINUX
+   int cnt = 0;
+-  __res_state *statp = (__res_state*)state;
++  struct __res_state *statp = (struct __res_state*)state;
+   for (int i = 0; i < MAXNS && cnt < nfd; i++) {
+     if (statp->_u._ext.nsaddrs[i] && statp->_u._ext.nssocks[i] != -1)
+       fds[cnt++] = statp->_u._ext.nssocks[i];
+-- 
+2.9.3
+
diff --git a/var/spack/repos/builtin/packages/gcc/ucontext_t-java.patch b/var/spack/repos/builtin/packages/gcc/ucontext_t-java.patch
new file mode 100644
index 0000000000..a43e0b5aa2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gcc/ucontext_t-java.patch
@@ -0,0 +1,60 @@
+From 9b9287cde20ea57578cf07efb2a96ed4cc0da36f Mon Sep 17 00:00:00 2001
+From: doko <doko@138bc75d-0d04-0410-961f-82ee72b054a4>
+Date: Thu, 7 Sep 2017 07:22:07 +0000
+Subject: [PATCH] 2017-09-07  Matthias Klose  <doko@ubuntu.com>
+
+        * include/x86_64-signal.h (HANDLE_DIVIDE_OVERFLOW): Replace
+        'struct ucontext' with ucontext_t.
+        * include/i386-signal.h (HANDLE_DIVIDE_OVERFLOW): Likewise.
+        * include/s390-signal.h (HANDLE_DIVIDE_OVERFLOW): Likewise.
+
+
+git-svn-id: svn+ssh://gcc.gnu.org/svn/gcc/branches/gcc-5-branch@251832 138bc75d-0d04-0410-961f-82ee72b054a4
+---
+ libjava/include/i386-signal.h   | 2 +-
+ libjava/include/s390-signal.h   | 2 +-
+ libjava/include/x86_64-signal.h | 2 +-
+ 4 files changed, 10 insertions(+), 3 deletions(-)
+
+diff --git a/libjava/include/i386-signal.h b/libjava/include/i386-signal.h
+index c2409b0..ef77e7e 100644
+--- a/libjava/include/i386-signal.h
++++ b/libjava/include/i386-signal.h
+@@ -29,7 +29,7 @@ static void _Jv_##_name (int, siginfo_t *,			\
+ #define HANDLE_DIVIDE_OVERFLOW						\
+ do									\
+ {									\
+-  struct ucontext *_uc = (struct ucontext *)_p;				\
++  ucontext_t *_uc = (ucontext_t *)_p;					\
+   gregset_t &_gregs = _uc->uc_mcontext.gregs;				\
+   unsigned char *_eip = (unsigned char *)_gregs[REG_EIP];		\
+ 									\
+diff --git a/libjava/include/s390-signal.h b/libjava/include/s390-signal.h
+index 4ca4c10..9261b52 100644
+--- a/libjava/include/s390-signal.h
++++ b/libjava/include/s390-signal.h
+@@ -51,7 +51,7 @@ do									\
+   struct                                                                \
+   {                                                                     \
+     unsigned long int uc_flags;                                         \
+-    struct ucontext *uc_link;                                           \
++    ucontext_t *uc_link;                                                \
+     stack_t uc_stack;                                                   \
+     mcontext_t uc_mcontext;                                             \
+     unsigned long sigmask[2];                                           \
+diff --git a/libjava/include/x86_64-signal.h b/libjava/include/x86_64-signal.h
+index 12383b5..e36c5a3 100644
+--- a/libjava/include/x86_64-signal.h
++++ b/libjava/include/x86_64-signal.h
+@@ -28,7 +28,7 @@ static void _Jv_##_name (int, siginfo_t *,			\
+ #define HANDLE_DIVIDE_OVERFLOW						\
+ do									\
+ {									\
+-  struct ucontext *_uc = (struct ucontext *)_p;				\
++  ucontext_t *_uc = (ucontext_t *)_p;					\
+   gregset_t &_gregs = _uc->uc_mcontext.gregs;				\
+   unsigned char *_rip = (unsigned char *)_gregs[REG_RIP];		\
+ 									\
+-- 
+2.9.3
+
diff --git a/var/spack/repos/builtin/packages/gcc/ucontext_t.patch b/var/spack/repos/builtin/packages/gcc/ucontext_t.patch
new file mode 100644
index 0000000000..a4f04b4715
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gcc/ucontext_t.patch
@@ -0,0 +1,189 @@
+From ecf0d1a107133c715763940c2b197aa814710e1b Mon Sep 17 00:00:00 2001
+From: jsm28 <jsm28@138bc75d-0d04-0410-961f-82ee72b054a4>
+Date: Tue, 4 Jul 2017 10:25:10 +0000
+Subject: [PATCH] Use ucontext_t not struct ucontext in linux-unwind.h files.
+
+Current glibc no longer gives the ucontext_t type the tag struct
+ucontext, to conform with POSIX namespace rules.  This requires
+various linux-unwind.h files in libgcc, that were previously using
+struct ucontext, to be fixed to use ucontext_t instead.  This is
+similar to the removal of the struct siginfo tag from siginfo_t some
+years ago.
+
+This patch changes those files to use ucontext_t instead.  As the
+standard name that should be unconditionally safe, so this is not
+restricted to architectures supported by glibc, or conditioned on the
+glibc version.
+
+Tested compilation together with current glibc with glibc's
+build-many-glibcs.py.
+
+	* config/aarch64/linux-unwind.h (aarch64_fallback_frame_state),
+	config/alpha/linux-unwind.h (alpha_fallback_frame_state),
+	config/bfin/linux-unwind.h (bfin_fallback_frame_state),
+	config/i386/linux-unwind.h (x86_64_fallback_frame_state,
+	x86_fallback_frame_state), config/m68k/linux-unwind.h (struct
+	uw_ucontext), config/nios2/linux-unwind.h (struct nios2_ucontext),
+	config/pa/linux-unwind.h (pa32_fallback_frame_state),
+	config/sh/linux-unwind.h (sh_fallback_frame_state),
+	config/tilepro/linux-unwind.h (tile_fallback_frame_state),
+	config/xtensa/linux-unwind.h (xtensa_fallback_frame_state): Use
+	ucontext_t instead of struct ucontext.
+
+
+git-svn-id: svn+ssh://gcc.gnu.org/svn/gcc/branches/gcc-5-branch@249958 138bc75d-0d04-0410-961f-82ee72b054a4
+---
+ libgcc/config/aarch64/linux-unwind.h |  2 +-
+ libgcc/config/alpha/linux-unwind.h   |  2 +-
+ libgcc/config/bfin/linux-unwind.h    |  2 +-
+ libgcc/config/i386/linux-unwind.h    |  4 ++--
+ libgcc/config/m68k/linux-unwind.h    |  2 +-
+ libgcc/config/nios2/linux-unwind.h   |  2 +-
+ libgcc/config/pa/linux-unwind.h      |  2 +-
+ libgcc/config/sh/linux-unwind.h      |  2 +-
+ libgcc/config/tilepro/linux-unwind.h |  2 +-
+ libgcc/config/xtensa/linux-unwind.h  |  2 +-
+ 11 files changed, 25 insertions(+), 11 deletions(-)
+
+diff --git a/libgcc/config/aarch64/linux-unwind.h b/libgcc/config/aarch64/linux-unwind.h
+index 86d17b1..909f68f 100644
+--- a/libgcc/config/aarch64/linux-unwind.h
++++ b/libgcc/config/aarch64/linux-unwind.h
+@@ -52,7 +52,7 @@ aarch64_fallback_frame_state (struct _Unwind_Context *context,
+   struct rt_sigframe
+   {
+     siginfo_t info;
+-    struct ucontext uc;
++    ucontext_t uc;
+   };
+ 
+   struct rt_sigframe *rt_;
+diff --git a/libgcc/config/alpha/linux-unwind.h b/libgcc/config/alpha/linux-unwind.h
+index d65474f..9a226b1 100644
+--- a/libgcc/config/alpha/linux-unwind.h
++++ b/libgcc/config/alpha/linux-unwind.h
+@@ -51,7 +51,7 @@ alpha_fallback_frame_state (struct _Unwind_Context *context,
+     {
+       struct rt_sigframe {
+ 	siginfo_t info;
+-	struct ucontext uc;
++	ucontext_t uc;
+       } *rt_ = context->cfa;
+       sc = &rt_->uc.uc_mcontext;
+     }
+diff --git a/libgcc/config/bfin/linux-unwind.h b/libgcc/config/bfin/linux-unwind.h
+index 0c270e4..7fa95d2 100644
+--- a/libgcc/config/bfin/linux-unwind.h
++++ b/libgcc/config/bfin/linux-unwind.h
+@@ -52,7 +52,7 @@ bfin_fallback_frame_state (struct _Unwind_Context *context,
+ 	void *puc;
+ 	char retcode[8];
+ 	siginfo_t info;
+-	struct ucontext uc;
++	ucontext_t uc;
+       } *rt_ = context->cfa;
+ 
+       /* The void * cast is necessary to avoid an aliasing warning.
+diff --git a/libgcc/config/i386/linux-unwind.h b/libgcc/config/i386/linux-unwind.h
+index e54bf73..d35fc45 100644
+--- a/libgcc/config/i386/linux-unwind.h
++++ b/libgcc/config/i386/linux-unwind.h
+@@ -58,7 +58,7 @@ x86_64_fallback_frame_state (struct _Unwind_Context *context,
+   if (*(unsigned char *)(pc+0) == 0x48
+       && *(unsigned long long *)(pc+1) == RT_SIGRETURN_SYSCALL)
+     {
+-      struct ucontext *uc_ = context->cfa;
++      ucontext_t *uc_ = context->cfa;
+       /* The void * cast is necessary to avoid an aliasing warning.
+          The aliasing warning is correct, but should not be a problem
+          because it does not alias anything.  */
+@@ -138,7 +138,7 @@ x86_fallback_frame_state (struct _Unwind_Context *context,
+ 	siginfo_t *pinfo;
+ 	void *puc;
+ 	siginfo_t info;
+-	struct ucontext uc;
++	ucontext_t uc;
+       } *rt_ = context->cfa;
+       /* The void * cast is necessary to avoid an aliasing warning.
+          The aliasing warning is correct, but should not be a problem
+diff --git a/libgcc/config/m68k/linux-unwind.h b/libgcc/config/m68k/linux-unwind.h
+index fb79a4d..b2f5ea4 100644
+--- a/libgcc/config/m68k/linux-unwind.h
++++ b/libgcc/config/m68k/linux-unwind.h
+@@ -33,7 +33,7 @@ see the files COPYING3 and COPYING.RUNTIME respectively.  If not, see
+ /* <sys/ucontext.h> is unfortunately broken right now.  */
+ struct uw_ucontext {
+ 	unsigned long	  uc_flags;
+-	struct ucontext  *uc_link;
++	ucontext_t	 *uc_link;
+ 	stack_t		  uc_stack;
+ 	mcontext_t	  uc_mcontext;
+ 	unsigned long	  uc_filler[80];
+diff --git a/libgcc/config/nios2/linux-unwind.h b/libgcc/config/nios2/linux-unwind.h
+index dff1c20..1d88afe 100644
+--- a/libgcc/config/nios2/linux-unwind.h
++++ b/libgcc/config/nios2/linux-unwind.h
+@@ -38,7 +38,7 @@ struct nios2_mcontext {
+ 
+ struct nios2_ucontext {
+   unsigned long uc_flags;
+-  struct ucontext *uc_link;
++  ucontext_t *uc_link;
+   stack_t uc_stack;
+   struct nios2_mcontext uc_mcontext;
+   sigset_t uc_sigmask;	/* mask last for extensibility */
+diff --git a/libgcc/config/pa/linux-unwind.h b/libgcc/config/pa/linux-unwind.h
+index 0149468..9157535 100644
+--- a/libgcc/config/pa/linux-unwind.h
++++ b/libgcc/config/pa/linux-unwind.h
+@@ -80,7 +80,7 @@ pa32_fallback_frame_state (struct _Unwind_Context *context,
+   struct sigcontext *sc;
+   struct rt_sigframe {
+     siginfo_t info;
+-    struct ucontext uc;
++    ucontext_t uc;
+   } *frame;
+ 
+   /* rt_sigreturn trampoline:
+diff --git a/libgcc/config/sh/linux-unwind.h b/libgcc/config/sh/linux-unwind.h
+index e63091f..67033f0 100644
+--- a/libgcc/config/sh/linux-unwind.h
++++ b/libgcc/config/sh/linux-unwind.h
+@@ -180,7 +180,7 @@ sh_fallback_frame_state (struct _Unwind_Context *context,
+     {
+       struct rt_sigframe {
+ 	siginfo_t info;
+-	struct ucontext uc;
++	ucontext_t uc;
+       } *rt_ = context->cfa;
+       /* The void * cast is necessary to avoid an aliasing warning.
+          The aliasing warning is correct, but should not be a problem
+diff --git a/libgcc/config/tilepro/linux-unwind.h b/libgcc/config/tilepro/linux-unwind.h
+index fd83ba7..e3c9ef0 100644
+--- a/libgcc/config/tilepro/linux-unwind.h
++++ b/libgcc/config/tilepro/linux-unwind.h
+@@ -61,7 +61,7 @@ tile_fallback_frame_state (struct _Unwind_Context *context,
+   struct rt_sigframe {
+     unsigned char save_area[C_ABI_SAVE_AREA_SIZE];
+     siginfo_t info;
+-    struct ucontext uc;
++    ucontext_t uc;
+   } *rt_;
+ 
+   /* Return if this is not a signal handler.  */
+diff --git a/libgcc/config/xtensa/linux-unwind.h b/libgcc/config/xtensa/linux-unwind.h
+index 9a67b5d..98b7ea6 100644
+--- a/libgcc/config/xtensa/linux-unwind.h
++++ b/libgcc/config/xtensa/linux-unwind.h
+@@ -67,7 +67,7 @@ xtensa_fallback_frame_state (struct _Unwind_Context *context,
+ 
+   struct rt_sigframe {
+     siginfo_t info;
+-    struct ucontext uc;
++    ucontext_t uc;
+   } *rt_;
+ 
+   /* movi a2, __NR_rt_sigreturn; syscall */
+-- 
+2.9.3
+
diff --git a/var/spack/repos/builtin/packages/gccmakedep/package.py b/var/spack/repos/builtin/packages/gccmakedep/package.py
index a8ece20f43..ae0bade1fd 100644
--- a/var/spack/repos/builtin/packages/gccmakedep/package.py
+++ b/var/spack/repos/builtin/packages/gccmakedep/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,4 +14,4 @@ class Gccmakedep(AutotoolsPackage):
 
     version('1.0.3', '127ddb6131eb4a56fdf6644a63ade788')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
diff --git a/var/spack/repos/builtin/packages/gccxml/gcc-5.patch b/var/spack/repos/builtin/packages/gccxml/gcc-5.patch
new file mode 100644
index 0000000000..4348d10184
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gccxml/gcc-5.patch
@@ -0,0 +1,57 @@
+--- a/GCC/gcc/toplev.c
++++ b/GCC/gcc/toplev.c
+@@ -537,7 +537,7 @@ read_integral_parameter (const char *p, const char *pname, const int  defval)
+    for floor_log2 and exact_log2; see toplev.h.  That construct, however,
+    conflicts with the ISO C++ One Definition Rule.   */
+
+-#if GCC_VERSION < 3004 || !defined (__cplusplus)
++#if GCC_VERSION < 3004
+
+ /* Given X, an unsigned number, return the largest int Y such that 2**Y <= X.
+    If X is 0, return -1.  */
+@@ -589,7 +589,7 @@ exact_log2 (unsigned HOST_WIDE_INT x)
+ #endif
+ }
+
+-#endif /*  GCC_VERSION < 3004 || !defined (__cplusplus)  */
++#endif /*  GCC_VERSION < 3004 */
+
+ /* Handler for fatal signals, such as SIGSEGV.  These are transformed
+    into ICE messages, which is much more user friendly.  In case the
+diff --git a/GCC/gcc/toplev.h b/GCC/gcc/toplev.h
+index c935f7e..1edd5e5 100644
+--- a/GCC/gcc/toplev.h
++++ b/GCC/gcc/toplev.h
+@@ -151,6 +151,7 @@ extern void decode_d_option     (const char *);
+ /* Return true iff flags are set as if -ffast-math.  */
+ extern bool fast_math_flags_set_p  (void);
+
++#if GCC_VERSION < 3004
+ /* Return log2, or -1 if not exact.  */
+ extern int exact_log2                  (unsigned HOST_WIDE_INT);
+
+@@ -158,7 +159,7 @@ extern int exact_log2                  (unsigned HOST_WIDE_INT);
+ extern int floor_log2                  (unsigned HOST_WIDE_INT);
+
+ /* Inline versions of the above for speed.  */
+-#if GCC_VERSION >= 3004
++#else /* GCC_VERSION >= 3004 */
+ # if HOST_BITS_PER_WIDE_INT == HOST_BITS_PER_LONG
+ #  define CLZ_HWI __builtin_clzl
+ #  define CTZ_HWI __builtin_ctzl
+@@ -170,13 +171,13 @@ extern int floor_log2                  (unsigned HOST_WIDE_INT);
+ #  define CTZ_HWI __builtin_ctz
+ # endif
+
+-extern inline int
++static inline int
+ floor_log2 (unsigned HOST_WIDE_INT x)
+ {
+   return x ? HOST_BITS_PER_WIDE_INT - 1 - (int) CLZ_HWI (x) : -1;
+ }
+
+-extern inline int
++static inline int
+ exact_log2 (unsigned HOST_WIDE_INT x)
+ {
+   return x == (x & -x) && x ? (int) CTZ_HWI (x) : -1;
diff --git a/var/spack/repos/builtin/packages/gccxml/package.py b/var/spack/repos/builtin/packages/gccxml/package.py
index d7f75f8631..99ebf75a5f 100644
--- a/var/spack/repos/builtin/packages/gccxml/package.py
+++ b/var/spack/repos/builtin/packages/gccxml/package.py
@@ -1,24 +1,8 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -27,10 +11,12 @@ class Gccxml(CMakePackage):
     the GCC C++ compiler."""
 
     homepage = "http://gccxml.github.io"
-    url      = "https://github.com/gccxml/gccxml/archive/v0.6.x.tar.gz"
+    git      = "https://github.com/gccxml/gccxml.git"
 
-    version('develop', git='https://github.com/gccxml/gccxml.git', branch='master')
-    version('latest', git='https://github.com/gccxml/gccxml.git',
-            commit='3afa8ba5be6866e603dcabe80aff79856b558e24', preferred=True)
+    version('develop', branch='master')
+    version('latest', commit='3afa8ba5be6866e603dcabe80aff79856b558e24',
+            preferred=True)
 
     patch('darwin-gcc.patch', when='%gcc platform=darwin')
+    # taken from https://github.com/gccxml/gccxml/issues/11#issuecomment-140334118
+    patch('gcc-5.patch', when='%gcc@5:')
diff --git a/var/spack/repos/builtin/packages/gconf/package.py b/var/spack/repos/builtin/packages/gconf/package.py
index 395ec2ff44..abafae9c36 100644
--- a/var/spack/repos/builtin/packages/gconf/package.py
+++ b/var/spack/repos/builtin/packages/gconf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/gcta/package.py b/var/spack/repos/builtin/packages/gcta/package.py
new file mode 100644
index 0000000000..8ff01ebe05
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gcta/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Gcta(Package):
+
+    """GCTA (Genome-wide Complex Trait Analysis) was originally designed to
+    estimate the proportion of phenotypic variance explained by all genome-wide
+    SNPs for complex traits (the GREML method), and has subsequently extended
+    for many other analyses to better understand the genetic architecture of
+    complex traits. GCTA currently supports the following analyses."""
+
+    homepage = "http://cnsgenomics.com/software/gcta/#Overview"
+    url      = "http://cnsgenomics.com/software/gcta/gcta_1.91.2beta.zip"
+
+    version('1.91.2beta_mac', 'ce0882ad35dd9474ffe40911da369274700af1ecb9916c0a355b7bad14850234')
+    version('1.91.2beta', '192efb767be1c7ca9c2dac5d2c2317a97c7a9db1f801168d19ad2a51b98d9b10', preferred=True)
+
+    conflicts('@1.91.2beta', when='platform=darwin')
+    conflicts('@1.91.2beta_mac', when='platform=linux')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('gcta64', join_path(prefix.bin, 'gcta64'))
+        set_executable(join_path(prefix.bin, 'gcta64'))
diff --git a/var/spack/repos/builtin/packages/gdal/package.py b/var/spack/repos/builtin/packages/gdal/package.py
index 044013c88d..2ca0df636f 100644
--- a/var/spack/repos/builtin/packages/gdal/package.py
+++ b/var/spack/repos/builtin/packages/gdal/package.py
@@ -1,94 +1,453 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
+import sys
 
 
-class Gdal(Package):
-    """GDAL is a translator library for raster and vector geospatial
-    data formats that is released under an X/MIT style Open Source
-    license by the Open Source Geospatial Foundation. As a library,
-    it presents a single raster abstract data model and vector
-    abstract data model to the calling application for all supported
-    formats. It also comes with a variety of useful command line
-    utilities for data translation and processing.
+class Gdal(AutotoolsPackage):
+    """GDAL (Geospatial Data Abstraction Library) is a translator library for
+    raster and vector geospatial data formats that is released under an X/MIT
+    style Open Source license by the Open Source Geospatial Foundation. As a
+    library, it presents a single raster abstract data model and vector
+    abstract data model to the calling application for all supported formats.
+    It also comes with a variety of useful command line utilities for data
+    translation and processing.
     """
 
     homepage   = "http://www.gdal.org/"
-    url        = "http://download.osgeo.org/gdal/2.1.2/gdal-2.1.2.tar.xz"
+    url        = "http://download.osgeo.org/gdal/2.3.1/gdal-2.3.1.tar.xz"
     list_url   = "http://download.osgeo.org/gdal/"
     list_depth = 1
 
-    version('2.1.2', 'ae85b78888514c75e813d658cac9478e')
-    version('2.0.2', '940208e737c87d31a90eaae43d0efd65')
-
-    extends('python')
-
-    variant('hdf5', default=False, description='Enable HDF5 support')
-    variant('hdf', default=False, description='Enable HDF4 support')
-    variant('openjpeg', default=False, description='Enable JPEG2000 support')
-    variant('geos', default=False, description='Enable GEOS support')
-    variant('kea', default=False, description='Enable KEA support')
-    variant('netcdf', default=False, description='Enable netcdf support')
-
-    depends_on('swig')
-    depends_on("hdf5", when='+hdf5')
-    depends_on("hdf", when='+hdf')
-    depends_on("openjpeg", when='+openjpeg')
-    depends_on("geos", when='+geos')
-    depends_on("kealib", when='+kea')
-    depends_on("netcdf", when='+netcdf')
-    depends_on("libtiff")
-    depends_on("libpng")
-    depends_on("zlib")
-    depends_on("proj")
-    depends_on("py-numpy", type=('build', 'run'))
-
-    parallel = False
-
-    def install(self, spec, prefix):
-        args = []
-        args.append("--prefix=%s" % prefix)
-        args.append("--with-liblzma=yes")
-        args.append("--with-zlib=%s" % spec['zlib'].prefix)
-        args.append("--with-python=%s" % spec['python'].command.path)
-        args.append("--without-libtool")
+    maintainers = ['adamjstewart']
+
+    import_modules = [
+        'osgeo', 'osgeo.gdal', 'osgeo.ogr', 'osgeo.osr',
+        'osgeo.gdal_array', 'osgeo.gdalconst'
+    ]
+
+    version('2.3.1',  sha256='9c4625c45a3ee7e49a604ef221778983dd9fd8104922a87f20b99d9bedb7725a')
+    version('2.3.0',  sha256='6f75e49aa30de140525ccb58688667efe3a2d770576feb7fbc91023b7f552aa2')
+    version('2.1.2',  sha256='b597f36bd29a2b4368998ddd32b28c8cdf3c8192237a81b99af83cc17d7fa374')
+    version('2.0.2',  sha256='90f838853cc1c07e55893483faa7e923e4b4b1659c6bc9df3538366030a7e622')
+    version('1.11.5', sha256='d4fdc3e987b9926545f0a514b4328cd733f2208442f8d03bde630fe1f7eff042')
+
+    variant('libtool',   default=True,  description='Use libtool to build the library')
+    variant('libz',      default=True,  description='Include libz support')
+    variant('libiconv',  default=False, description='Include libiconv support')
+    variant('liblzma',   default=True,  description='Include liblzma support')
+    variant('zstd',      default=False, description='Include zstd support')
+    variant('pg',        default=False, description='Include PostgreSQL support')
+    variant('cfitsio',   default=False, description='Include FITS support')
+    variant('png',       default=False, description='Include PNG support')
+    variant('jpeg',      default=True,  description='Include JPEG support')
+    variant('gif',       default=False, description='Include GIF support')
+    variant('sosi',      default=False, description='Include SOSI support')
+    variant('hdf4',      default=False, description='Include HDF4 support')
+    variant('hdf5',      default=False, description='Include HDF5 support')
+    variant('kea',       default=False, description='Include kealib')
+    variant('netcdf',    default=False, description='Include netCDF support')
+    variant('jasper',    default=False, description='Include JPEG-2000 support via JasPer library')
+    variant('openjpeg',  default=False, description='Include JPEG-2000 support via OpenJPEG 2.x library')
+    variant('xerces',    default=False, description='Use Xerces-C++ parser')
+    variant('expat',     default=False, description='Use Expat XML parser')
+    variant('odbc',      default=False, description='Include ODBC support')
+    variant('curl',      default=False, description='Include curl')
+    variant('xml2',      default=False, description='Include libxml2')
+    variant('sqlite3',   default=False, description='Use SQLite 3 library')
+    variant('pcre',      default=False, description='Include libpcre support')
+    variant('geos',      default=False, description='Include GEOS support')
+    variant('qhull',     default=False, description='Include QHull support')
+    variant('opencl',    default=False, description='Include OpenCL (GPU) support')
+    variant('poppler',   default=False, description='Include poppler (for PDF) support')
+    variant('proj',      default=True,  description='Compile with PROJ.x')
+    variant('perl',      default=False, description='Enable perl bindings')
+    variant('python',    default=False, description='Enable python bindings')
+    variant('java',      default=False, description='Include Java support')
+    variant('mdb',       default=False, description='Include MDB driver')
+    variant('armadillo', default=False, description='Include Armadillo support for faster TPS transform computation')
+    variant('cryptopp',  default=False, description='Include cryptopp support')
+    variant('crypto',    default=False, description='Include crypto (from openssl) support')
+
+    # FIXME: Allow packages to extend multiple packages
+    # See https://github.com/spack/spack/issues/987
+    # extends('perl', when='+perl')
+    extends('python', when='+python')
+
+    # GDAL depends on GNUmake on Unix platforms.
+    # https://trac.osgeo.org/gdal/wiki/BuildingOnUnix
+    depends_on('gmake', type='build')
+    depends_on('pkgconfig', type='build')
+
+    # Required dependencies
+    depends_on('libtiff@3.6.0:')  # 3.9.0+ needed to pass testsuite
+    depends_on('libgeotiff@1.2.1:')
+    depends_on('json-c', when='@2.3:')
+    depends_on('json-c@0.12.1', when='@:2.2.99')
+
+    # Optional dependencies
+    depends_on('libtool', type='build', when='+libtool')
+    depends_on('zlib', when='+libz')
+    depends_on('libiconv', when='+libiconv')
+    depends_on('xz', when='+liblzma')
+    depends_on('zstd', when='+zstd @2.3:')
+    depends_on('postgresql', when='+pg')
+    depends_on('cfitsio', when='+cfitsio')
+    depends_on('libpng', when='+png')
+    depends_on('jpeg', when='+jpeg')
+    depends_on('giflib', when='+gif')
+    depends_on('fyba', when='+sosi')
+    depends_on('hdf', when='+hdf4')
+    depends_on('hdf5', when='+hdf5')
+    depends_on('kealib', when='+kea @2:')
+    depends_on('netcdf', when='+netcdf')
+    depends_on('jasper@1.900.1', patches='uuid.patch', when='+jasper')
+    depends_on('openjpeg', when='+openjpeg')
+    depends_on('xerces-c', when='+xerces')
+    depends_on('expat', when='+expat')
+    depends_on('unixodbc', when='+odbc')
+    depends_on('curl@7.10.8:', when='+curl')
+    depends_on('libxml2', when='+xml2')
+    depends_on('sqlite@3:', when='+sqlite3')
+    depends_on('pcre', when='+pcre')
+    depends_on('geos', when='+geos')
+    depends_on('qhull', when='+qhull @2.1:')
+    depends_on('opencl', when='+opencl')
+    depends_on('poppler', when='+poppler')
+    depends_on('poppler@:0.63', when='@:2.3.0 +poppler')
+    depends_on('proj', when='+proj @2.3:')
+    depends_on('perl', type=('build', 'run'), when='+perl')
+    depends_on('python', type=('build', 'link', 'run'), when='+python')
+    # swig/python/setup.py
+    depends_on('py-setuptools', type='build', when='+python')
+    depends_on('py-numpy@1.0.0:', type=('build', 'run'), when='+python')
+    depends_on('java', type=('build', 'link', 'run'), when='+java')
+    depends_on('jackcess@1.2.0:1.2.999', type='run', when='+mdb')
+    depends_on('armadillo', when='+armadillo')
+    depends_on('cryptopp', when='+cryptopp @2.1:')
+    depends_on('openssl', when='+crypto @2.3:')
+
+    # https://trac.osgeo.org/gdal/wiki/SupportedCompilers
+    msg = 'GDAL requires C++11 support'
+    conflicts('%gcc@:4.8.0', msg=msg)
+    conflicts('%clang@:3.2', msg=msg)
+    conflicts('%intel@:12',  msg=msg)
+    conflicts('%xl@:13.0',   msg=msg)
+    conflicts('%xl_r@:13.0', msg=msg)
+
+    conflicts('+mdb', when='~java', msg='MDB driver requires Java')
+
+    def setup_environment(self, spack_env, run_env):
+        # Needed to install Python bindings to GDAL installation
+        # prefix instead of Python installation prefix.
+        # See swig/python/GNUmakefile for more details.
+        spack_env.set('PREFIX', self.prefix)
+        spack_env.set('DESTDIR', '/')
+
+    # https://trac.osgeo.org/gdal/wiki/BuildHints
+    def configure_args(self):
+        spec = self.spec
+
+        # Required dependencies
+        args = [
+            # https://trac.osgeo.org/gdal/wiki/TIFF
+            '--with-libtiff={0}'.format(spec['libtiff'].prefix),
+            '--with-geotiff={0}'.format(spec['libgeotiff'].prefix),
+            '--with-libjson-c={0}'.format(spec['json-c'].prefix),
+        ]
+
+        if spec.satisfies('@2.3:'):
+            if '+zstd' in spec:
+                args.append('--with-zstd={0}'.format(spec['zstd'].prefix))
+            else:
+                args.append('--with-zstd=no')
+
+            if '+proj' in spec:
+                args.append('--with-proj={0}'.format(spec['proj'].prefix))
+                if spec.satisfies('^proj@5.0:5.999'):
+                    args.append('--with-proj5-api=yes')
+                else:
+                    args.append('--with-proj5-api=no')
+            else:
+                args.append('--with-proj=no')
+
+            if '+crypto' in spec:
+                args.append('--with-crypto={0}'.format(spec['openssl'].prefix))
+            else:
+                args.append('--with-crypto=no')
+
+        if spec.satisfies('@2.1:'):
+            if '+qhull' in spec:
+                args.append('--with-qhull=yes')
+            else:
+                args.append('--with-qhull=no')
+
+            if '+cryptopp' in spec:
+                args.append('--with-cryptopp={0}'.format(
+                    spec['cryptopp'].prefix))
+            else:
+                args.append('--with-cryptopp=no')
+
+        if spec.satisfies('@2:'):
+            if '+kea' in spec:
+                args.append('--with-kea={0}'.format(
+                    join_path(spec['kealib'].prefix.bin, 'kea-config')))
+            else:
+                args.append('--with-kea=no')
+
+        # Optional dependencies
+        if '+libtool' in spec:
+            args.append('--with-libtool=yes')
+        else:
+            args.append('--with-libtool=no')
+
+        if '+libz' in spec:
+            args.append('--with-libz={0}'.format(spec['zlib'].prefix))
+        else:
+            args.append('--with-libz=no')
+
+        if '+libiconv' in spec:
+            args.append('--with-libiconv-prefix={0}'.format(
+                spec['libiconv'].prefix))
+        else:
+            args.append('--with-libiconv-prefix=no')
+
+        if '+liblzma' in spec:
+            args.append('--with-liblzma=yes')
+        else:
+            args.append('--with-liblzma=no')
+
+        if '+pg' in spec:
+            args.append('--with-pg={0}'.format(
+                spec['postgresql'].prefix.bin.pg_config))
+        else:
+            args.append('--with-pg=no')
+
+        if '+cfitsio' in spec:
+            args.append('--with-cfitsio={0}'.format(spec['cfitsio'].prefix))
+        else:
+            args.append('--with-cfitsio=no')
+
+        if '+png' in spec:
+            args.append('--with-png={0}'.format(spec['libpng'].prefix))
+        else:
+            args.append('--with-png=no')
+
+        if '+jpeg' in spec:
+            args.append('--with-jpeg={0}'.format(spec['jpeg'].prefix))
+        else:
+            args.append('--with-jpeg=no')
+
+        if '+gif' in spec:
+            args.append('--with-gif={0}'.format(spec['giflib'].prefix))
+        else:
+            args.append('--with-gif=no')
+
+        # https://trac.osgeo.org/gdal/wiki/SOSI
+        if '+sosi' in spec:
+            args.append('--with-sosi={0}'.format(spec['fyba'].prefix))
+        else:
+            args.append('--with-sosi=no')
+
+        # https://trac.osgeo.org/gdal/wiki/HDF
+        if '+hdf4' in spec:
+            args.append('--with-hdf4={0}'.format(spec['hdf'].prefix))
+        else:
+            args.append('--with-hdf4=no')
 
-        if '+geos' in spec:
-            args.append('--with-geos=yes')
-        if '+hdf' in spec:
-            args.append('--with-hdf4=%s' % spec['hdf'].prefix)
         if '+hdf5' in spec:
-            args.append('--with-hdf5=%s' % spec['hdf5'].prefix)
-        if '+openjpeg' in spec:
-            args.append('--with-openjpeg=%s' % spec['openjpeg'].prefix)
-        if '+kea' in spec:
-            args.append('--with-kea=yes')
+            args.append('--with-hdf5={0}'.format(spec['hdf5'].prefix))
+        else:
+            args.append('--with-hdf5=no')
+
+        # https://trac.osgeo.org/gdal/wiki/NetCDF
         if '+netcdf' in spec:
-            args.append('--with-netcdf=%s' % spec['netcdf'].prefix)
+            args.append('--with-netcdf={0}'.format(spec['netcdf'].prefix))
+        else:
+            args.append('--with-netcdf=no')
+
+        # https://trac.osgeo.org/gdal/wiki/JasPer
+        if '+jasper' in spec:
+            args.append('--with-jasper={0}'.format(spec['jasper'].prefix))
+        else:
+            args.append('--with-jasper=no')
+
+        if '+openjpeg' in spec:
+            args.append('--with-openjpeg=yes')
+        else:
+            args.append('--with-openjpeg=no')
+
+        if '+xerces' in spec:
+            args.append('--with-xerces={0}'.format(spec['xerces-c'].prefix))
+        else:
+            args.append('--with-xerces=no')
+
+        if '+expat' in spec:
+            args.append('--with-expat={0}'.format(spec['expat'].prefix))
+        else:
+            args.append('--with-expat=no')
+
+        if '+odbc' in spec:
+            args.append('--with-odbc={0}'.format(spec['unixodbc'].prefix))
+        else:
+            args.append('--with-odbc=no')
+
+        # https://trac.osgeo.org/gdal/wiki/LibCurl
+        if '+curl' in spec:
+            args.append('--with-curl={0}'.format(
+                join_path(spec['curl'].prefix.bin, 'curl-config')))
+        else:
+            args.append('--with-curl=no')
+
+        if '+xml2' in spec:
+            args.append('--with-xml2={0}'.format(
+                join_path(spec['libxml2'].prefix.bin, 'xml2-config')))
+        else:
+            args.append('--with-xml2=no')
+
+        # https://trac.osgeo.org/gdal/wiki/SQLite
+        if '+sqlite3' in spec:
+            args.append('--with-sqlite3={0}'.format(spec['sqlite'].prefix))
+        else:
+            args.append('--with-sqlite3=no')
+
+        if '+pcre' in spec:
+            args.append('--with-pcre={0}'.format(spec['pcre'].prefix))
+        else:
+            args.append('--with-pcre=no')
+
+        if '+geos' in spec:
+            args.append('--with-geos={0}'.format(
+                join_path(spec['geos'].prefix.bin, 'geos-config')))
+        else:
+            args.append('--with-geos=no')
+
+        if '+opencl' in spec:
+            args.append('--with-opencl={0}'.format(spec['opencl'].prefix))
+        else:
+            args.append('--with-opencl=no')
+
+        if '+poppler' in spec:
+            args.append('--with-poppler={0}'.format(spec['poppler'].prefix))
+        else:
+            args.append('--with-poppler=no')
+
+        if '+perl' in spec:
+            args.append('--with-perl=yes')
+        else:
+            args.append('--with-perl=no')
+
+        if '+python' in spec:
+            args.append('--with-python={0}'.format(
+                spec['python'].command.path))
+        else:
+            args.append('--with-python=no')
+
+        # https://trac.osgeo.org/gdal/wiki/GdalOgrInJava
+        if '+java' in spec:
+            args.extend([
+                '--with-java={0}'.format(spec['java'].home),
+                '--with-jvm-lib={0}'.format(
+                    spec['java'].libs.directories[0]),
+                '--with-jvm-lib-add-rpath'
+            ])
+        else:
+            args.append('--with-java=no')
+
+        # https://trac.osgeo.org/gdal/wiki/mdbtools
+        # http://www.gdal.org/drv_mdb.html
+        if '+mdb' in spec:
+            args.append('--with-mdb=yes')
+        else:
+            args.append('--with-mdb=no')
+
+        if '+armadillo' in spec:
+            args.append('--with-armadillo={0}'.format(
+                spec['armadillo'].prefix))
+        else:
+            args.append('--with-armadillo=no')
+
+        # TODO: add packages for these dependencies
+        args.extend([
+            # https://trac.osgeo.org/gdal/wiki/GRASS
+            '--with-grass=no',
+            '--with-libgrass=no',
+            '--with-pcraster=no',
+            '--with-dds=no',
+            '--with-gta=no',
+            '--with-pcidsk=no',
+            '--with-ogdi=no',
+            '--with-fme=no',
+            # https://trac.osgeo.org/gdal/wiki/FileGDB
+            '--with-fgdb=no',
+            # https://trac.osgeo.org/gdal/wiki/ECW
+            '--with-ecw=no',
+            # https://trac.osgeo.org/gdal/wiki/JP2KAK
+            '--with-kakadu=no',
+            # https://trac.osgeo.org/gdal/wiki/MrSID
+            '--with-mrsid=no',
+            '--with-jp2mrsid=no',
+            '--with-mrsid_lidar=no',
+            # https://trac.osgeo.org/gdal/wiki/MSG
+            '--with-msg=no',
+            '--with-bsb=no',
+            # https://trac.osgeo.org/gdal/wiki/Oracle
+            '--with-oci=no',
+            '--with-grib=no',
+            '--with-mysql=no',
+            # https://trac.osgeo.org/gdal/wiki/Ingres
+            '--with-ingres=no',
+            # https://trac.osgeo.org/gdal/wiki/LibKML
+            '--with-libkml=no',
+            '--with-dods-root=no',
+            '--with-spatialite=no',
+            '--with-idb=no',
+            # https://trac.osgeo.org/gdal/wiki/ArcSDE
+            '--with-sde=no',
+            # https://trac.osgeo.org/gdal/wiki/Epsilon
+            '--with-epsilon=no',
+            '--with-webp=no',
+            '--with-freexl=no',
+            '--with-pam=no',
+            '--with-podofo=no',
+            '--with-php=no',
+            '--with-rasdaman=no',
+        ])
+
+        # TODO: add packages for these dependencies (only for 2.3 and newer)
+        if spec.satisfies('@2.3:'):
+            args.extend([
+                '--with-jp2lura=no',
+                '--with-rasterlite2=no',
+                # https://trac.osgeo.org/gdal/wiki/DxfDwg
+                '--with-teigha=no',
+                '--with-sfcgal=no',
+                '--with-mrf=no',
+            ])
+
+        # TODO: add packages for these dependencies (only for 2.1 and newer)
+        if spec.satisfies('@2.1:'):
+            args.extend([
+                '--with-mongocxx=no',
+                '--with-gnm=no',
+                '--with-pdfium=no',
+            ])
+
+        return args
 
-        configure(*args)
+    @run_after('install')
+    @on_package_attributes(run_tests=True)
+    def import_module_test(self):
+        if '+python' in self.spec:
+            with working_dir('spack-test', create=True):
+                for module in self.import_modules:
+                    python('-c', 'import {0}'.format(module))
 
-        make()
-        make("install")
+    @run_after('install')
+    def darwin_fix(self):
+        # The shared library is not installed correctly on Darwin; fix this
+        if sys.platform == 'darwin':
+            fix_darwin_install_name(self.prefix.lib)
diff --git a/var/spack/repos/builtin/packages/gdal/uuid.patch b/var/spack/repos/builtin/packages/gdal/uuid.patch
new file mode 100644
index 0000000000..3990dad0cd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gdal/uuid.patch
@@ -0,0 +1,234 @@
+diff -Naur jasper-1.900.1/src/libjasper/jp2/jp2_cod.c jasper-1.900.1.uuid/src/libjasper/jp2/jp2_cod.c
+--- jasper-1.900.1/src/libjasper/jp2/jp2_cod.c	2007-01-19 15:43:05.000000000 -0600
++++ jasper-1.900.1.uuid/src/libjasper/jp2/jp2_cod.c	2007-03-06 07:49:58.000000000 -0600
+@@ -5,6 +5,11 @@
+  * All rights reserved.
+  */
+ 
++/*
++ * Modified by Andrey Kiselev <dron@ak4719.spb.edu> to properly handle UUID
++ * box.
++ */
++
+ /* __START_OF_JASPER_LICENSE__
+  * 
+  * JasPer License Version 2.0
+@@ -127,6 +132,9 @@
+ static int jp2_pclr_getdata(jp2_box_t *box, jas_stream_t *in);
+ static int jp2_pclr_putdata(jp2_box_t *box, jas_stream_t *out);
+ static void jp2_pclr_dumpdata(jp2_box_t *box, FILE *out);
++static void jp2_uuid_destroy(jp2_box_t *box);
++static int jp2_uuid_getdata(jp2_box_t *box, jas_stream_t *in);
++static int jp2_uuid_putdata(jp2_box_t *box, jas_stream_t *out);
+ 
+ /******************************************************************************\
+ * Local data.
+@@ -164,7 +172,7 @@
+ 	{JP2_BOX_XML, "XML", 0,
+ 	  {0, 0, 0, 0, 0}},
+ 	{JP2_BOX_UUID, "UUID", 0,
+-	  {0, 0, 0, 0, 0}},
++	  {0, jp2_uuid_destroy, jp2_uuid_getdata, jp2_uuid_putdata, 0}},
+ 	{JP2_BOX_UINF, "UINF", JP2_BOX_SUPER,
+ 	  {0, 0, 0, 0, 0}},
+ 	{JP2_BOX_ULST, "ULST", 0,
+@@ -271,7 +279,7 @@
+ 	} else {
+ 		box->datalen = box->len - JP2_BOX_HDRLEN(false);
+ 	}
+-	if (box->len != 0 && box->len < 8) {
++	if (box->len != 0 && box->len < JP2_BOX_HDRLEN(false)) {
+ 		goto error;
+ 	}
+ 
+@@ -876,6 +884,56 @@
+ 	}
+ }
+ 
++static void jp2_uuid_destroy(jp2_box_t *box)
++{
++	jp2_uuid_t *uuid = &box->data.uuid;
++	if (uuid->data)
++	{
++	    jas_free(uuid->data);
++	    uuid->data = NULL;
++	}
++}
++
++static int jp2_uuid_getdata(jp2_box_t *box, jas_stream_t *in)
++{
++	jp2_uuid_t *uuid = &box->data.uuid;
++	int i;
++	
++	for (i = 0; i < 16; i++)
++	{
++	    if (jp2_getuint8(in, &uuid->uuid[i]))
++		return -1;
++	}
++	
++	uuid->datalen = box->datalen - 16;
++	uuid->data = jas_malloc(uuid->datalen * sizeof(uint_fast8_t));
++	for (i = 0; i < uuid->datalen; i++)
++	{
++	    if (jp2_getuint8(in, &uuid->data[i]))
++		return -1;
++	}
++	return 0;
++}
++
++static int jp2_uuid_putdata(jp2_box_t *box, jas_stream_t *out)
++{
++	jp2_uuid_t *uuid = &box->data.uuid;
++	int i;
++	
++	for (i = 0; i < 16; i++)
++	{
++	    if (jp2_putuint8(out, uuid->uuid[i]))
++		return -1;
++	}
++	
++	for (i = 0; i < uuid->datalen; i++)
++	{
++	    if (jp2_putuint8(out, uuid->data[i]))
++		return -1;
++	}
++	return 0;
++}
++
+ static int jp2_getint(jas_stream_t *in, int s, int n, int_fast32_t *val)
+ {
+ 	int c;
+diff -Naur jasper-1.900.1/src/libjasper/jp2/jp2_cod.h jasper-1.900.1.uuid/src/libjasper/jp2/jp2_cod.h
+--- jasper-1.900.1/src/libjasper/jp2/jp2_cod.h	2007-01-19 15:43:05.000000000 -0600
++++ jasper-1.900.1.uuid/src/libjasper/jp2/jp2_cod.h	2007-03-06 07:49:58.000000000 -0600
+@@ -5,6 +5,11 @@
+  * All rights reserved.
+  */
+ 
++/*
++ * Modified by Andrey Kiselev <dron@ak4719.spb.edu> to properly handle UUID
++ * box.
++ */
++
+ /* __START_OF_JASPER_LICENSE__
+  * 
+  * JasPer License Version 2.0
+@@ -229,6 +234,12 @@
+ 	jp2_cmapent_t *ents;
+ } jp2_cmap_t;
+ 
++typedef struct {
++	uint_fast32_t datalen;
++	uint_fast8_t uuid[16];
++	uint_fast8_t *data;
++} jp2_uuid_t;
++
+ #define	JP2_CMAP_DIRECT		0
+ #define	JP2_CMAP_PALETTE	1
+ 
+@@ -257,6 +268,7 @@
+ 		jp2_pclr_t pclr;
+ 		jp2_cdef_t cdef;
+ 		jp2_cmap_t cmap;
++		jp2_uuid_t uuid;
+ 	} data;
+ 
+ } jp2_box_t;
+diff -Naur jasper-1.900.1/src/libjasper/jp2/jp2_enc.c jasper-1.900.1.uuid/src/libjasper/jp2/jp2_enc.c
+--- jasper-1.900.1/src/libjasper/jp2/jp2_enc.c	2007-01-19 15:43:05.000000000 -0600
++++ jasper-1.900.1.uuid/src/libjasper/jp2/jp2_enc.c	2007-03-06 07:49:58.000000000 -0600
+@@ -5,6 +5,11 @@
+  * All rights reserved.
+  */
+ 
++/*
++ * Modified by Andrey Kiselev <dron@ak4719.spb.edu> to properly handle UUID
++ * box.
++ */
++
+ /* __START_OF_JASPER_LICENSE__
+  * 
+  * JasPer License Version 2.0
+@@ -86,7 +91,7 @@
+ * Functions.
+ \******************************************************************************/
+ 
+-int jp2_encode(jas_image_t *image, jas_stream_t *out, char *optstr)
++int jp2_write_header(jas_image_t *image, jas_stream_t *out)
+ {
+ 	jp2_box_t *box;
+ 	jp2_ftyp_t *ftyp;
+@@ -97,8 +102,6 @@
+ 	long len;
+ 	uint_fast16_t cmptno;
+ 	jp2_colr_t *colr;
+-	char buf[4096];
+-	uint_fast32_t overhead;
+ 	jp2_cdefchan_t *cdefchanent;
+ 	jp2_cdef_t *cdef;
+ 	int i;
+@@ -326,6 +329,26 @@
+ 	jas_stream_close(tmpstream);
+ 	tmpstream = 0;
+ 
++	return 0;
++	abort();
++
++error:
++
++	if (box) {
++		jp2_box_destroy(box);
++	}
++	if (tmpstream) {
++		jas_stream_close(tmpstream);
++	}
++	return -1;
++}
++
++int jp2_write_codestream(jas_image_t *image, jas_stream_t *out, char *optstr)
++{
++	jp2_box_t *box;
++	char buf[4096];
++	uint_fast32_t overhead;
++
+ 	/*
+ 	 * Output the contiguous code stream box.
+ 	 */
+@@ -358,12 +381,34 @@
+ 	if (box) {
+ 		jp2_box_destroy(box);
+ 	}
+-	if (tmpstream) {
+-		jas_stream_close(tmpstream);
+-	}
+ 	return -1;
+ }
+ 
++int jp2_encode(jas_image_t *image, jas_stream_t *out, char *optstr)
++{
++	if (jp2_write_header(image, out) < 0)
++		return -1;
++	if (jp2_write_codestream(image, out, optstr) < 0)
++		return -1;
++
++	return 0;
++}
++
++int jp2_encode_uuid(jas_image_t *image, jas_stream_t *out,
++		    char *optstr, jp2_box_t *uuid)
++{
++	if (jp2_write_header(image, out) < 0)
++		return -1;
++	if (uuid) {
++		if (jp2_box_put(uuid, out))
++			return -1;
++	}
++	if (jp2_write_codestream(image, out, optstr) < 0)
++		return -1;
++
++	return 0;
++}
++
+ static uint_fast32_t jp2_gettypeasoc(int colorspace, int ctype)
+ {
+ 	int type;
diff --git a/var/spack/repos/builtin/packages/gdb/package.py b/var/spack/repos/builtin/packages/gdb/package.py
index dedefe5191..5d6b265961 100644
--- a/var/spack/repos/builtin/packages/gdb/package.py
+++ b/var/spack/repos/builtin/packages/gdb/package.py
@@ -1,39 +1,24 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class Gdb(Package):
+class Gdb(AutotoolsPackage):
     """GDB, the GNU Project debugger, allows you to see what is going on
     'inside' another program while it executes -- or what another
     program was doing at the moment it crashed.
     """
 
     homepage = "https://www.gnu.org/software/gdb"
-    url = "http://ftp.gnu.org/gnu/gdb/gdb-7.10.tar.gz"
+    url      = "https://ftpmirror.gnu.org/gdb/gdb-7.10.tar.gz"
 
+    version('8.2', '0783c6d86775c5aff06cccc8a3d7cad8')
+    version('8.1', '0c85ecbb43569ec43b1c9230622e84ab')
+    version('8.0.1', 'bb45869f8126a84ea2ba13a8c0e7c90e')
+    version('8.0', '9bb49d134916e73b2c01d01bf20363df')
     version('7.12.1', '06c8f40521ed65fe36ebc2be29b56942')
     version('7.11', 'f585059252836a981ea5db9a5f8ce97f')
     version('7.10.1', 'b93a2721393e5fa226375b42d567d90b')
@@ -43,17 +28,19 @@ class Gdb(Package):
     version('7.8.2', '8b0ea8b3559d3d90b3ff4952f0aeafbc')
 
     variant('python', default=True, description='Compile with Python support')
+    variant('xz', default=True, description='Compile with lzma support')
 
     # Required dependency
     depends_on('texinfo', type='build')
 
-    # Optional dependency
+    # Optional dependencies
     depends_on('python', when='+python')
-
-    def install(self, spec, prefix):
-        options = ['--prefix=%s' % prefix]
-        if '+python' in spec:
-            options.extend(['--with-python'])
-        configure(*options)
-        make()
-        make("install")
+    depends_on('xz', when='+xz')
+
+    def configure_args(self):
+        args = []
+        if '+python' in self.spec:
+            args.append('--with-python')
+            args.append('LDFLAGS={0}'.format(
+                self.spec['python'].libs.ld_flags))
+        return args
diff --git a/var/spack/repos/builtin/packages/gdbm/package.py b/var/spack/repos/builtin/packages/gdbm/package.py
index 1e4a4831b7..d041c283bf 100644
--- a/var/spack/repos/builtin/packages/gdbm/package.py
+++ b/var/spack/repos/builtin/packages/gdbm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 from spack import *
 
@@ -33,8 +14,9 @@ class Gdbm(AutotoolsPackage):
     manipulate a hashed database."""
 
     homepage = "http://www.gnu.org.ua/software/gdbm/gdbm.html"
-    url      = "http://ftp.gnu.org/gnu/gdbm/gdbm-1.13.tar.gz"
+    url      = "https://ftpmirror.gnu.org/gdbm/gdbm-1.13.tar.gz"
 
+    version('1.14.1', 'c2ddcb3897efa0f57484af2bd4f4f848')
     version('1.13',  '8929dcda2a8de3fd2367bdbf66769376')
     version('1.12',  '9ce96ff4c99e74295ea19040931c8fb9')
     version('1.11',  '72c832680cf0999caedbe5b265c8c1bd')
@@ -45,9 +27,12 @@ class Gdbm(AutotoolsPackage):
     depends_on("readline")
 
     def configure_args(self):
-        config_args = [
-            '--enable-libgdbm-compat',
-            'CC=%s' % spack_cc
-        ]
 
-        return config_args
+        # GDBM uses some non-standard GNU extensions,
+        # enabled with -D_GNU_SOURCE.  See:
+        #   https://patchwork.ozlabs.org/patch/771300/
+        #   https://stackoverflow.com/questions/5582211
+        #   https://www.gnu.org/software/automake/manual/html_node/Flag-Variables-Ordering.html
+        return [
+            '--enable-libgdbm-compat',
+            'CPPFLAGS=-D_GNU_SOURCE']
diff --git a/var/spack/repos/builtin/packages/gdk-pixbuf/package.py b/var/spack/repos/builtin/packages/gdk-pixbuf/package.py
index 63d24d64c4..9aaa91b2dd 100644
--- a/var/spack/repos/builtin/packages/gdk-pixbuf/package.py
+++ b/var/spack/repos/builtin/packages/gdk-pixbuf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class GdkPixbuf(AutotoolsPackage):
 
     version('2.31.2', '6be6bbc4f356d4b79ab4226860ab8523')
 
-    depends_on("pkg-config", type="build")
+    depends_on("pkgconfig", type="build")
     depends_on("gettext")
     depends_on("glib")
     depends_on("jpeg")
diff --git a/var/spack/repos/builtin/packages/gdl/package.py b/var/spack/repos/builtin/packages/gdl/package.py
new file mode 100644
index 0000000000..ac49f17236
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gdl/package.py
@@ -0,0 +1,110 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Gdl(CMakePackage):
+    """A free and open-source IDL/PV-WAVE compiler.
+
+    GNU Data Language (GDL) is a free/libre/open source incremental compiler
+    compatible with IDL and to some extent with PV-WAVE.
+    """
+
+    homepage = "https://github.com/gnudatalanguage/gdl"
+    url      = "https://github.com/gnudatalanguage/gdl/archive/v0.9.8.tar.gz"
+
+    version('0.9.8', '447b0362e1df5ea8af814a969e89d3ec')
+
+    variant(
+            'graphicsmagick',
+            default=False,
+            description='Enable GraphicsMagick'
+           )
+    variant('hdf4', default=False, description='Enable HDF4')
+    variant('hdf5', default=True, description='Enable HDF5')
+    variant('openmp', default=True, description='Enable OpenMP')
+    variant('proj', default=True, description='Enable LIBPROJ4')
+    variant('python', default=False, description='Enable Python')
+    variant('wx', default=False, description='Enable WxWidgets')
+    variant('x11', default=False, description='Enable X11')
+
+    extends('python', when='+python')
+
+    depends_on('graphicsmagick', when='+graphicsmagick')
+    depends_on('hdf', when='+hdf4')
+    depends_on('hdf5', when='+hdf5')
+    depends_on('libx11', when='+x11')
+    depends_on('plplot+wx', when='+wx@:5.11')
+    depends_on('plplot+wx+wxold', when='+wx@5.12:')
+    depends_on('plplot~wx', when='~wx')
+    depends_on('proj', when='+proj')
+    depends_on('py-numpy', type=('build', 'run'), when='+python')
+    depends_on('python@2.7:2.8', type=('build', 'run'), when='+python')
+    depends_on('wx', when='+wx')
+
+    depends_on('eigen')
+    depends_on('fftw')
+    depends_on('gsl')
+    depends_on('jpeg')
+    depends_on('libice')
+    depends_on('libsm')
+    depends_on('libxinerama')
+    depends_on('libxxf86vm')
+    depends_on('netcdf')
+    depends_on('pslib')
+    depends_on('readline')
+
+    def cmake_args(self):
+        args = []
+
+        # GraphicsMagick covers the same features as ImageMagick and
+        # only version 6 of ImageMagick is supported (version 7 is packaged)
+        args += ['-DMAGICK=OFF']
+
+        if '+graphicsmagick' in self.spec:
+            args += ['-DGRAPHICSMAGICK=ON']
+        else:
+            args += ['-DGRAPHICSMAGICK=OFF']
+
+        if '+hdf4' in self.spec:
+            args += ['-DHDF=ON']
+        else:
+            args += ['-DHDF=OFF']
+
+        if '+hdf5' in self.spec:
+            args += ['-DHDF5=ON']
+        else:
+            args += ['-DHDF5=OFF']
+
+        if '+openmp' in self.spec:
+            args += ['-DOPENMP=ON']
+        else:
+            args += ['-DOPENMP=OFF']
+
+        if '+proj' in self.spec:
+            args += [
+                '-DLIBPROJ4=ON',
+                '-DLIBPROJ4DIR={0}'.format(self.spec['proj'].prefix)
+            ]
+        else:
+            args += ['-DLIBPROJ4=OFF']
+
+        if '+python' in self.spec:
+            args += ['-DPYTHON=ON']
+        else:
+            args += ['-DPYTHON=OFF']
+
+        if '+wx' in self.spec:
+            args += ['-DWXWIDGETS=ON']
+        else:
+            args += ['-DWXWIDGETS=OFF']
+
+        if '+x11' in self.spec:
+            args += ['-DX11=ON']
+        else:
+            args += ['-DX11=OFF']
+
+        return args
diff --git a/var/spack/repos/builtin/packages/geant4/package.py b/var/spack/repos/builtin/packages/geant4/package.py
index 2b935673c4..0685de3cd9 100644
--- a/var/spack/repos/builtin/packages/geant4/package.py
+++ b/var/spack/repos/builtin/packages/geant4/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 import platform
@@ -36,22 +17,50 @@ class Geant4(CMakePackage):
     homepage = "http://geant4.cern.ch/"
     url = "http://geant4.cern.ch/support/source/geant4.10.01.p03.tar.gz"
 
+    version('10.04', 'b84beeb756821d0c61f7c6c93a2b83de')
+    version('10.03.p03', 'ccae9fd18e3908be78784dc207f2d73b')
+    version('10.02.p03', '2b887e66f0d41174016160707662a77b')
     version('10.02.p02', '6aae1d0fc743b0edc358c5c8fbe48657')
     version('10.02.p01', 'b81f7082a15f6a34b720b6f15c6289cfe4ddbbbdcef0dc52719f71fac95f7f1c')
     version('10.01.p03', '4fb4175cc0dabcd517443fbdccd97439')
 
-    variant('qt', default=True, description='Enable Qt support')
+    variant('qt', default=False, description='Enable Qt support')
+    variant('vecgeom', default=False, description='Enable vecgeom support')
+    variant('cxx11', default=True, description='Enable CXX11 support')
+    variant('cxx14', default=False, description='Enable CXX14 support')
+    variant('opengl', default=False, description='Optional OpenGL support')
+    variant('x11', default=False, description='Optional X11 support')
+    variant('motif', default=False, description='Optional motif support')
+    variant('threads', default=True, description='Build with multithreading')
 
     depends_on('cmake@3.5:', type='build')
 
-    depends_on("clhep@2.3.1.1~cxx11+cxx14", when="@10.02.p02")
-    depends_on("clhep@2.3.1.1~cxx11+cxx14", when="@10.02.p01")
-    depends_on("clhep@2.2.0.4~cxx11+cxx14", when="@10.01.p03")
+    conflicts('+cxx14', when='+cxx11')
+    conflicts('+cxx11', when='+cxx14')
+
+    # C++11 support
+    depends_on("clhep@2.4.0.0+cxx11~cxx14", when="@10.04+cxx11~cxx14")
+    depends_on("clhep@2.3.4.3+cxx11~cxx14", when="@10.03.p03+cxx11~cxx14")
+    depends_on("clhep@2.3.1.1+cxx11~cxx14", when="@10.02.p01+cxx11~cxx14")
+    depends_on("clhep@2.3.1.1+cxx11~cxx14", when="@10.02.p01+cxx11~cxx14")
+    depends_on("clhep@2.2.0.4+cxx11~cxx14", when="@10.01.p03+cxx11~cxx14")
+
+    # C++14 support
+    depends_on("clhep@2.4.0.0+cxx11~cxx14", when="@10.04~cxx11+cxx14")
+    depends_on("clhep@2.3.4.3+cxx11~cxx14", when="@10.03.p03~cxx11+cxx14")
+    depends_on("clhep@2.3.1.1~cxx11+cxx14", when="@10.02.p02~cxx11+cxx14")
+    depends_on("clhep@2.3.1.1~cxx11+cxx14", when="@10.02.p01~cxx11+cxx14")
+    depends_on("clhep@2.2.0.4~cxx11+cxx14", when="@10.01.p03~cxx11+cxx14")
+
     depends_on("expat")
     depends_on("zlib")
-    depends_on("vecgeom")
     depends_on("xerces-c")
-    depends_on("qt@4.8:", when="+qt")
+    depends_on("mesa", when='+opengl')
+    depends_on("libx11", when='+x11')
+    depends_on("libxmu", when='+x11')
+    depends_on("motif", when='+motif')
+    depends_on("vecgeom", when="+vecgeom")
+    depends_on("qt@4.8:4.999", when="+qt")
 
     def cmake_args(self):
         spec = self.spec
@@ -62,32 +71,38 @@ class Geant4(CMakePackage):
             '-DGEANT4_USE_G3TOG4=ON',
             '-DGEANT4_INSTALL_DATA=ON',
             '-DGEANT4_BUILD_TLS_MODEL=global-dynamic',
-            '-DGEANT4_BUILD_MULTITHREADED=ON',
-            '-DGEANT4_USE_USOLIDS=ON',
             '-DGEANT4_USE_SYSTEM_EXPAT=ON',
             '-DGEANT4_USE_SYSTEM_ZLIB=ON',
             '-DXERCESC_ROOT_DIR:STRING=%s' %
-            spec['xerces-c'].prefix,
-            '-DUSolids_DIR=%s' %
-            join_path(spec['vecgeom'].prefix, 'lib/CMake/USolids')]
+            spec['xerces-c'].prefix, ]
 
         arch = platform.system().lower()
         if arch is not 'darwin':
-            options.append('-DGEANT4_USE_OPENGL_X11=ON')
-            options.append('-DGEANT4_USE_XM=ON')
-            options.append('-DGEANT4_USE_RAYTRACER_X11=ON')
+            if "+x11" in spec and "+opengl" in spec:
+                options.append('-DGEANT4_USE_OPENGL_X11=ON')
+            if "+motif" in spec and "+opengl" in spec:
+                options.append('-DGEANT4_USE_XM=ON')
+            if "+x11" in spec:
+                options.append('-DGEANT4_USE_RAYTRACER_X11=ON')
 
         if '+cxx11' in spec:
             options.append('-DGEANT4_BUILD_CXXSTD=c++11')
-        if '+cxx14' or '+cxx1y' in spec:
+        if '+cxx14' in spec:
             options.append('-DGEANT4_BUILD_CXXSTD=c++14')
 
         if '+qt' in spec:
             options.append('-DGEANT4_USE_QT=ON')
             options.append(
                 '-DQT_QMAKE_EXECUTABLE=%s' %
-                spec['qt'].prefix + '/bin/qmake'
-            )
+                spec['qt'].prefix.bin.qmake)
+
+        if '+vecgeom' in spec:
+            options.append('-DGEANT4_USE_USOLIDS=ON')
+            options.append('-DUSolids_DIR=%s' % spec[
+                'vecgeom'].prefix.lib.CMake.USolids)
+
+        on_or_off = lambda opt: 'ON' if '+' + opt in spec else 'OFF'
+        options.append('-DGEANT4_BUILD_MULTITHREADED=' + on_or_off('threads'))
 
         return options
 
diff --git a/var/spack/repos/builtin/packages/gearshifft/package.py b/var/spack/repos/builtin/packages/gearshifft/package.py
index 8b6f5c8a31..7b71f2e2ee 100644
--- a/var/spack/repos/builtin/packages/gearshifft/package.py
+++ b/var/spack/repos/builtin/packages/gearshifft/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,14 +10,16 @@ class Gearshifft(CMakePackage):
     """Benchmark Suite for Heterogenuous FFT Implementations"""
 
     homepage = "https://github.com/mpicbg-scicomp/gearshifft"
-    url      = "https://github.com/mpicbg-scicomp/gearshifft/archive/v0.2.0.tar.gz"
+    url      = "https://github.com/mpicbg-scicomp/gearshifft/archive/v0.2.1-lw.tar.gz"
+
+    maintainers = ['ax3l']
 
     version('0.2.1-lw', 'c3208b767b24255b488a83e5d9e517ea')
 
     variant('cufft', default=True,
             description='Compile gearshifft_cufft')
-    # variant('clfft', default=True,
-    #         description='Compile gearshifft_clfft')
+    variant('clfft', default=True,
+            description='Compile gearshifft_clfft')
     variant('fftw', default=True,
             description='Compile gearshifft_fftw')
     variant('openmp', default=True,
@@ -48,8 +31,8 @@ class Gearshifft(CMakePackage):
     depends_on('cmake@2.8.0:', type='build')
     depends_on('boost@1.56.0:')
     depends_on('cuda@8.0:', when='+cufft')
-    # depends_on('opencl@1.2:', when='+clfft')
-    # depends_on('clfft@2.12.0:', when='+clfft')
+    depends_on('opencl@1.2:', when='+clfft')
+    depends_on('clfft@2.12.0:', when='+clfft')
     depends_on('fftw@3.3.4:~mpi~openmp', when='+fftw~openmp')
     depends_on('fftw@3.3.4:~mpi+openmp', when='+fftw+openmp')
 
@@ -62,13 +45,13 @@ class Gearshifft(CMakePackage):
             '-DGEARSHIFFT_CLFFT:BOOL=OFF'
         ]
         args.extend([
-            '-DGEARSHIFFT_FFTW:BOOL={0}'.format((
-                'ON' if '+fftw' in spec else 'OFF')),
-            '-DGEARSHIFFT_FFTW_OPENMP:BOOL={0}'.format((
-                'ON' if '+openmp' in spec else 'OFF')),
-            '-DGEARSHIFFT_CUFFT:BOOL={0}'.format((
-                'ON' if '+cufft' in spec else 'OFF'))
-            # '-DGEARSHIFFT_CLFFT:BOOL={0}'.format((
-            #     'ON' if '+clfft' in spec else 'OFF'))
+            '-DGEARSHIFFT_FFTW:BOOL={0}'.format(
+                'ON' if '+fftw' in spec else 'OFF'),
+            '-DGEARSHIFFT_FFTW_OPENMP:BOOL={0}'.format(
+                'ON' if '+openmp' in spec else 'OFF'),
+            '-DGEARSHIFFT_CUFFT:BOOL={0}'.format(
+                'ON' if '+cufft' in spec else 'OFF'),
+            '-DGEARSHIFFT_CLFFT:BOOL={0}'.format(
+                'ON' if '+clfft' in spec else 'OFF')
         ])
         return args
diff --git a/var/spack/repos/builtin/packages/gemmlowp/package.py b/var/spack/repos/builtin/packages/gemmlowp/package.py
index 7cd3047716..d293a9b254 100644
--- a/var/spack/repos/builtin/packages/gemmlowp/package.py
+++ b/var/spack/repos/builtin/packages/gemmlowp/package.py
@@ -1,27 +1,8 @@
-#############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,8 +10,9 @@ class Gemmlowp(Package):
     """Google low-precision matrix multiplication library"""
 
     homepage = "https://github.com/google/gemmlowp"
-    version('a6f29d9ac', git='https://github.com/google/gemmlowp.git',
-            commit='a6f29d8ac48d63293f845f2253eccbf86bc28321')
+    git      = "https://github.com/google/gemmlowp.git"
+
+    version('a6f29d9ac', commit='a6f29d8ac48d63293f845f2253eccbf86bc28321')
 
     def install(self, spec, prefix):
         header_directories = ('eight_bit_int_gemm', 'fixedpoint',
diff --git a/var/spack/repos/builtin/packages/genemark-et/package.py b/var/spack/repos/builtin/packages/genemark-et/package.py
index faf5acce6a..d38a84522a 100644
--- a/var/spack/repos/builtin/packages/genemark-et/package.py
+++ b/var/spack/repos/builtin/packages/genemark-et/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 import glob
diff --git a/var/spack/repos/builtin/packages/genomefinisher/genomefinisher.sh b/var/spack/repos/builtin/packages/genomefinisher/genomefinisher.sh
new file mode 100644
index 0000000000..b44c048751
--- /dev/null
+++ b/var/spack/repos/builtin/packages/genomefinisher/genomefinisher.sh
@@ -0,0 +1,3 @@
+#!/bin/sh
+# convenience wrapper for the GenomeFinisher jar file
+java $JAVA_ARGS $JAVA_OPTS -jar GenomeFinisher.jar "$@"
diff --git a/var/spack/repos/builtin/packages/genomefinisher/package.py b/var/spack/repos/builtin/packages/genomefinisher/package.py
new file mode 100644
index 0000000000..d9030c2a19
--- /dev/null
+++ b/var/spack/repos/builtin/packages/genomefinisher/package.py
@@ -0,0 +1,42 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class Genomefinisher(Package):
+    """GFinisher is an application tools for refinement and finalization of
+    prokaryotic genomes assemblies using the bias of GC Skew to identify
+    assembly errors and organizes the contigs/scaffolds with genomes
+    references."""
+
+    homepage = "http://gfinisher.sourceforge.net"
+    url      = "https://sourceforge.net/projects/gfinisher/files/GenomeFinisher_1.4.zip"
+
+    version('1.4', 'bd9bbca656fe15ecbe615c4732714bc7')
+
+    depends_on('java@8:', type='run')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        jar_file = 'GenomeFinisher.jar'
+        install(jar_file, prefix.bin)
+        install_tree('lib', prefix.lib)
+
+        # Set up a helper script to call java on the jar file,
+        # explicitly codes the path for java and the jar file.
+        script_sh = join_path(os.path.dirname(__file__), "genomefinisher.sh")
+        script = prefix.bin.genomefinisher
+        install(script_sh, script)
+        set_executable(script)
+
+        # Munge the helper script to explicitly point to java and the jar file
+        # jar file.
+        java = spec['jdk'].prefix.bin.java
+        kwargs = {'ignore_absent': False, 'backup': False, 'string': False}
+        filter_file('^java', java, script, **kwargs)
+        filter_file(jar_file, join_path(prefix.bin, jar_file),
+                    script, **kwargs)
diff --git a/var/spack/repos/builtin/packages/genometools/package.py b/var/spack/repos/builtin/packages/genometools/package.py
index 00f359e6d2..5d88fa0416 100644
--- a/var/spack/repos/builtin/packages/genometools/package.py
+++ b/var/spack/repos/builtin/packages/genometools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-#############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -43,3 +24,6 @@ class Genometools(MakefilePackage):
 
     def install(self, spec, prefix):
         make('install', 'prefix=%s' % prefix)
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        spack_env.set('CPATH', self.prefix.include.genometools)
diff --git a/var/spack/repos/builtin/packages/geopm/package.py b/var/spack/repos/builtin/packages/geopm/package.py
new file mode 100644
index 0000000000..37047ab1b0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/geopm/package.py
@@ -0,0 +1,77 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Geopm(AutotoolsPackage):
+    """GEOPM is an extensible power management framework targeting HPC.
+    The GEOPM package provides libgeopm, libgeopmpolicy and applications
+    geopmctl and geopmpolicy, as well as tools for postprocessing.
+    GEOPM is designed to be extended for new control algorithms and new
+    hardware power management features via its plugin infrastructure.
+
+    Note: GEOPM interfaces with hardware using Model Specific Registers (MSRs).
+    For propper usage make sure MSRs are made available directly or via the
+    msr-safe kernel module by your administrator."""
+
+    homepage = "https://geopm.github.io"
+    url      = "https://github.com/geopm/geopm/releases/download/v0.4.0/geopm-0.4.0.tar.gz"
+    git      = "https://github.com/geopm/geopm.git"
+
+    # Add additional proper versions and checksums here. "spack checksum geopm"
+    version('develop', branch='dev')
+    version('master', branch='master')
+    version('0.5.0', '61b454bc74d4606fe84818aef16c1be4')
+    version('0.4.0', 'd4cc8fffe521296dab379857d7e2064d')
+    version('0.3.0', '568fd37234396fff134f8d57b60f2b83')
+
+    # Variants reflecting most ./configure --help options
+    variant('debug', default=False, description='Enable debug.')
+    variant('coverage', default=False, description='Enable test coverage support, enables debug by default.')
+    variant('overhead', default=False, description='Enable GEOPM to calculate and display time spent in GEOPM API calls.')
+    variant('procfs', default=True, description='Enable procfs (disable for OSes not using procfs).')
+    variant('mpi', default=True, description='Enable MPI dependent components.')
+    variant('fortran', default=True, description='Build fortran interface.')
+    variant('doc', default=True, description='Create man pages with ruby-ronn.')
+    variant('openmp', default=True, description='Build with OpenMP.')
+    variant('ompt', default=False, description='Use OpenMP Tools Interface.')
+    variant('hwloc', default=True, description='Build with hwloc.')
+    variant('gnu-ld', default=False, description='Assume C compiler uses gnu-ld.')
+
+    # Added dependencies.
+    depends_on('m4', type='build')
+    depends_on('automake', type='build')
+    depends_on('autoconf', type='build')
+    depends_on('libtool', type='build')
+    depends_on('ruby-ronn', type='build', when='+doc')
+    depends_on('doxygen', type='build', when='+doc')
+    depends_on('numactl')
+    depends_on('mpi', when='+mpi')
+    # TODO: check if hwloc@specific-version still required with future openmpi
+    depends_on('hwloc@1.11.9', when='+hwloc')
+    depends_on('json-c')
+    depends_on('py-pandas', type='run')
+    depends_on('py-numpy', type='run')
+    depends_on('py-natsort', type='run')
+    depends_on('py-matplotlib', type='run')
+
+    parallel = False
+
+    def configure_args(self):
+        args = []
+        args.extend(self.enable_or_disable('debug'))
+        args.extend(self.enable_or_disable('coverage'))
+        args.extend(self.enable_or_disable('overhead'))
+        args.extend(self.enable_or_disable('procfs'))
+        args.extend(self.enable_or_disable('mpi'))
+        args.extend(self.enable_or_disable('fortran'))
+        args.extend(self.enable_or_disable('doc'))
+        args.extend(self.enable_or_disable('openmp'))
+        args.extend(self.enable_or_disable('ompt'))
+        args.extend(self.with_or_without('hwloc', activation_value='prefix'))
+        args.extend(self.with_or_without('gnu-ld'))
+
+        return args
diff --git a/var/spack/repos/builtin/packages/geos/package.py b/var/spack/repos/builtin/packages/geos/package.py
index f74e03ff57..3bd4a8f7e4 100644
--- a/var/spack/repos/builtin/packages/geos/package.py
+++ b/var/spack/repos/builtin/packages/geos/package.py
@@ -1,31 +1,12 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class Geos(Package):
+class Geos(AutotoolsPackage):
     """GEOS (Geometry Engine - Open Source) is a C++ port of the Java
        Topology Suite (JTS). As such, it aims to contain the complete
        functionality of JTS in C++. This includes all the OpenGIS
@@ -33,12 +14,14 @@ class Geos(Package):
        operators, as well as specific JTS enhanced topology functions."""
 
     homepage = "http://trac.osgeo.org/geos/"
-    url      = "http://download.osgeo.org/geos/geos-3.4.2.tar.bz2"
+    url      = "http://download.osgeo.org/geos/geos-3.6.2.tar.bz2"
 
-    # Verison 3.5.0 supports Autotools and CMake
+    version('3.6.2', 'a32142343c93d3bf151f73db3baa651f')
+    version('3.6.1', 'c97e338b3bc81f9848656e9d693ca6cc')
+    version('3.6.0', '55de5fdf075c608d2d7b9348179ee649')
+    version('3.5.1', '2e3e1ccbd42fee9ec427106b65e43dc0')
     version('3.5.0', '136842690be7f504fba46b3c539438dd')
-
-    # Versions through 3.4.2 have CMake, but only Autotools is supported
+    version('3.4.3', '77f2c2cca1e9f49bc1bece9037ac7a7a')
     version('3.4.2', 'fc5df2d926eb7e67f988a43a92683bae')
     version('3.4.1', '4c930dec44c45c49cd71f3e0931ded7e')
     version('3.4.0', 'e41318fc76b5dc764a69d43ac6b18488')
@@ -50,21 +33,39 @@ class Geos(Package):
     version('3.3.4', '1bb9f14d57ef06ffa41cb1d67acb55a1')
     version('3.3.3', '8454e653d7ecca475153cc88fd1daa26')
 
-#    # Python3 is not supported.
-#    variant('python', default=False, description='Enable Python support')
+    # Ruby bindings are fully supported
+    variant('ruby',   default=False, description='Enable Ruby support')
 
-#    extends('python', when='+python')
-#    depends_on('python', when='+python')
-#    depends_on('swig', when='+python')
+    # Since version 3.0, the Python bindings are unsupported
+    variant('python', default=False, description='Enable Python support')
 
-    def install(self, spec, prefix):
-        args = ["--prefix=%s" % prefix]
-#        if '+python' in spec:
-#            os.environ['PYTHON'] = spec['python'].command.path
-#            os.environ['SWIG'] = spec['swig'].command.path
-#
-#            args.append("--enable-python")
+    extends('ruby', when='+ruby')
+
+    # Python 3 is supposedly supported, but I couldn't get it to work
+    # https://trac.osgeo.org/geos/ticket/774
+    extends('python@:2', when='+python')
+
+    depends_on('swig', type='build', when='+ruby')
+    depends_on('swig', type='build', when='+python')
+
+    # `make check` fails with:
+    # FAIL: geos_unit
+
+    # I wasn't able to get the ruby bindings working.
+    # It resulted in "Undefined symbols for architecture x86_64".
+
+    def configure_args(self):
+        spec = self.spec
+        args = []
+
+        if '+ruby' in spec:
+            args.append('--enable-ruby')
+        else:
+            args.append('--disable-ruby')
+
+        if '+python' in spec:
+            args.append('--enable-python')
+        else:
+            args.append('--disable-python')
 
-        configure(*args)
-        make()
-        make("install")
+        return args
diff --git a/var/spack/repos/builtin/packages/gettext/package.py b/var/spack/repos/builtin/packages/gettext/package.py
index f25f3e7889..7676bb8cfb 100644
--- a/var/spack/repos/builtin/packages/gettext/package.py
+++ b/var/spack/repos/builtin/packages/gettext/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,7 +10,7 @@ class Gettext(AutotoolsPackage):
     """GNU internationalization (i18n) and localization (l10n) library."""
 
     homepage = "https://www.gnu.org/software/gettext/"
-    url      = "http://ftpmirror.gnu.org/gettext/gettext-0.19.7.tar.xz"
+    url      = "https://ftpmirror.gnu.org/gettext/gettext-0.19.7.tar.xz"
 
     version('0.19.8.1', 'df3f5690eaa30fd228537b00cb7b7590')
     version('0.19.7',   'f81e50556da41b44c1d59ac93474dca5')
@@ -84,8 +65,10 @@ class Gettext(AutotoolsPackage):
             config_args.append('--disable-curses')
 
         if '+libxml2' in spec:
-            config_args.append('--with-libxml2-prefix={0}'.format(
+            config_args.append('CPPFLAGS=-I{0}/include'.format(
                 spec['libxml2'].prefix))
+            config_args.append('LDFLAGS=-L{0} -Wl,-rpath,{0}'.format(
+                spec['libxml2'].libs.directories[0]))
         else:
             config_args.append('--with-included-libxml')
 
diff --git a/var/spack/repos/builtin/packages/gflags/package.py b/var/spack/repos/builtin/packages/gflags/package.py
index 05a168d6fa..4984af3406 100644
--- a/var/spack/repos/builtin/packages/gflags/package.py
+++ b/var/spack/repos/builtin/packages/gflags/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/ghost/package.py b/var/spack/repos/builtin/packages/ghost/package.py
new file mode 100644
index 0000000000..246f990133
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ghost/package.py
@@ -0,0 +1,65 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Ghost(CMakePackage, CudaPackage):
+    """GHOST: a General, Hybrid and Optimized Sparse Toolkit.
+       This library provides highly optimized building blocks for implementing
+       sparse iterative eigenvalue and linear solvers multi- and manycore
+       clusters and on heterogenous CPU/GPU machines. For an iterative solver
+       library using these kernels, see the phist package.
+    """
+
+    homepage = "https://www.bitbucket.org/essex/ghost/"
+    git      = "https://bitbucket.org/essex/ghost/ghost.git"
+
+    version('develop', branch='devel')
+
+    variant('shared', default=True,
+            description='Enables the build of shared libraries')
+    variant('mpi', default=True,
+            description='enable/disable MPI')
+    variant('scotch', default=False,
+            description='enable/disable matrix reordering with PT-SCOTCH')
+    variant('zoltan', default=False,
+            description='enable/disable matrix reordering with Zoltan')
+
+    # ###################### Dependencies ##########################
+
+    # Everything should be compiled position independent (-fpic)
+    depends_on('cmake@3.5:')
+    depends_on('hwloc')
+    depends_on('blas')
+    depends_on('mpi', when='+mpi')
+    depends_on('scotch', when='+scotch')
+    depends_on('zoltan', when='+zoltan')
+
+    def cmake_args(self):
+        spec = self.spec
+        # note: we require the cblas_include_dir property from the blas
+        # provider, this is implemented at least for intel-mkl and
+        # netlib-lapack
+        args = ['-DGHOST_ENABLE_MPI:BOOL=%s'
+                % ('ON' if '+mpi' in spec else 'OFF'),
+                '-DGHOST_USE_CUDA:BOOL=%s'
+                % ('ON' if '+cuda' in spec else 'OFF'),
+                '-DGHOST_USE_SCOTCH:BOOL=%s'
+                % ('ON' if '+scotch' in spec else 'OFF'),
+                '-DGHOST_USE_ZOLTAN:BOOL=%s'
+                % ('ON' if '+zoltan' in spec else 'OFF'),
+                '-DBUILD_SHARED_LIBS:BOOL=%s'
+                % ('ON' if '+shared' in spec else 'OFF'),
+                '-DCBLAS_INCLUDE_DIR:STRING=%s'
+                % format(spec['blas'].headers.directories[0]),
+                '-DBLAS_LIBRARIES=%s'
+                % spec['blas:c'].libs.joined(';')
+                ]
+        return args
+
+    def check(self):
+        make('test')
diff --git a/var/spack/repos/builtin/packages/ghostscript-fonts/package.py b/var/spack/repos/builtin/packages/ghostscript-fonts/package.py
index 9dc7e8cead..198108fd4e 100644
--- a/var/spack/repos/builtin/packages/ghostscript-fonts/package.py
+++ b/var/spack/repos/builtin/packages/ghostscript-fonts/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
 
diff --git a/var/spack/repos/builtin/packages/ghostscript/package.py b/var/spack/repos/builtin/packages/ghostscript/package.py
index 991f77199e..d5d478bf90 100644
--- a/var/spack/repos/builtin/packages/ghostscript/package.py
+++ b/var/spack/repos/builtin/packages/ghostscript/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import shutil
 
@@ -35,7 +16,7 @@ class Ghostscript(AutotoolsPackage):
     version('9.21', '5f213281761d2750fcf27476c404d17f')
     version('9.18', '33a47567d7a591c00a253caddd12a88a')
 
-    depends_on('pkg-config', type='build')
+    depends_on('pkgconfig', type='build')
 
     depends_on('freetype@2.4.2:')
     depends_on('jpeg')
@@ -43,6 +24,7 @@ class Ghostscript(AutotoolsPackage):
     depends_on('libpng')
     depends_on('libtiff')
     depends_on('zlib')
+    depends_on('libxext')
 
     def url_for_version(self, version):
         baseurl = "https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs{0}/ghostscript-{1}.tar.gz"
diff --git a/var/spack/repos/builtin/packages/giflib/bsd-head.patch b/var/spack/repos/builtin/packages/giflib/bsd-head.patch
new file mode 100644
index 0000000000..3831f2ca57
--- /dev/null
+++ b/var/spack/repos/builtin/packages/giflib/bsd-head.patch
@@ -0,0 +1,19 @@
+The BSD version of head does not accept the --bytes option,
+nor does it accept negative integers. Use dd instead for
+BSD support.
+
+--- a/tests/makefile	2014-05-16 05:46:53.000000000 -0500
++++ b/tests/makefile	2018-03-18 18:29:47.000000000 -0500
+@@ -103,10 +103,10 @@
+ 
+ giffix-rebuild:
+ 	@echo "Rebuilding giffix test."
+-	@head --bytes=-20 <$(PICS)/treescap.gif | $(UTILS)/giffix 2>/dev/null | $(UTILS)/gifbuild -d >giffixed.ico
++	@dd if=$(PICS)/treescap.gif bs=1 count=387 | $(UTILS)/giffix 2>/dev/null | $(UTILS)/gifbuild -d >giffixed.ico
+ giffix-regress:
+ 	@echo "giffix: Testing giffix behavior"
+-	@head --bytes=-20 <$(PICS)/treescap.gif | $(UTILS)/giffix 2>/dev/null | $(UTILS)/gifbuild -d | diff -u giffixed.ico -
++	@dd if=$(PICS)/treescap.gif bs=1 count=387 | $(UTILS)/giffix 2>/dev/null | $(UTILS)/gifbuild -d | diff -u giffixed.ico -
+ 
+ gifinto-regress:
+ 	@echo "gifinto: Checking behavior on short files."
diff --git a/var/spack/repos/builtin/packages/giflib/package.py b/var/spack/repos/builtin/packages/giflib/package.py
index 3ab0d8453f..a951143a12 100644
--- a/var/spack/repos/builtin/packages/giflib/package.py
+++ b/var/spack/repos/builtin/packages/giflib/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,3 +14,8 @@ class Giflib(AutotoolsPackage):
     url      = "https://downloads.sourceforge.net/project/giflib/giflib-5.1.4.tar.bz2"
 
     version('5.1.4', '2c171ced93c0e83bb09e6ccad8e3ba2b')
+
+    patch('bsd-head.patch')
+
+    def check(self):
+        make('check', parallel=False)
diff --git a/var/spack/repos/builtin/packages/git-imerge/package.py b/var/spack/repos/builtin/packages/git-imerge/package.py
new file mode 100644
index 0000000000..524a8b28ee
--- /dev/null
+++ b/var/spack/repos/builtin/packages/git-imerge/package.py
@@ -0,0 +1,43 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class GitImerge(MakefilePackage):
+    """git-imerge: Incremental merge & rebase for git
+
+       Perform a merge between two branches incrementally. If
+       conflicts are encountered, figure out exactly which pairs of
+       commits conflict, and present the user with one pairwise
+       conflict at a time for resolution.
+
+       git-imerge has two primary design goals:
+
+       * Reduce the pain of resolving merge conflicts to its
+         unavoidable minimum, by finding and presenting the smallest
+         possible conflicts: those between the changes introduced by
+         one commit from each branch.
+
+       * Allow a merge to be saved, tested, interrupted, published,
+         and collaborated on while it is in progress."""
+
+    homepage = "https://github.com/mhagger/git-imerge"
+    url      = "https://github.com/mhagger/git-imerge/archive/v1.1.0.tar.gz"
+
+    version('1.1.0', '94a44dcbe5e764d75770a24517572a76')
+    version('1.0.0', 'e5e69a22610828cc33bf2cbd31685438')
+
+    depends_on('python@2.6:')
+    depends_on('py-argparse', when='^python@2.6')
+    depends_on('git')
+
+    # Package copies a Python script and bash-completion files, so
+    # there's no need to "build" anything.
+    def build(self, spec, prefix):
+        pass
+
+    def install(self, spec, prefix):
+        make('DESTDIR={0}'.format(prefix), 'PREFIX=', 'install')
diff --git a/var/spack/repos/builtin/packages/git-lfs/package.py b/var/spack/repos/builtin/packages/git-lfs/package.py
index 7e557dd0a8..902540a603 100644
--- a/var/spack/repos/builtin/packages/git-lfs/package.py
+++ b/var/spack/repos/builtin/packages/git-lfs/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,13 +14,13 @@ class GitLfs(Package):
        Git LFS server."""
 
     homepage = "https://git-lfs.github.com"
-    git_url  = "https://github.com/github/git-lfs.git"
+    git      = "https://github.com/github/git-lfs.git"
 
-    version('2.3.0', git=git_url, tag='v2.3.0')
-    version('2.2.1', git=git_url, tag='v2.2.1')
-    version('2.0.2', git=git_url, tag='v2.0.2')
-    version('1.4.1', git=git_url, tag='v1.4.1')
-    version('1.3.1', git=git_url, tag='v1.3.1')
+    version('2.3.0', tag='v2.3.0')
+    version('2.2.1', tag='v2.2.1')
+    version('2.0.2', tag='v2.0.2')
+    version('1.4.1', tag='v1.4.1')
+    version('1.3.1', tag='v1.3.1')
 
     # TODO: Add tests by following the instructions at this location:
     # https://github.com/github/git-lfs/blob/master/CONTRIBUTING.md#building
diff --git a/var/spack/repos/builtin/packages/git/package.py b/var/spack/repos/builtin/packages/git/package.py
index 293f85974f..ba0e717fac 100644
--- a/var/spack/repos/builtin/packages/git/package.py
+++ b/var/spack/repos/builtin/packages/git/package.py
@@ -1,30 +1,10 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import sys
 from spack import *
-from distutils.dir_util import copy_tree
 
 
 class Git(AutotoolsPackage):
@@ -34,117 +14,146 @@ class Git(AutotoolsPackage):
     """
 
     homepage = "http://git-scm.com"
-    url      = "https://github.com/git/git/archive/v2.12.0.tar.gz"
+    url      = "https://mirrors.edge.kernel.org/pub/software/scm/git/git-2.12.0.tar.gz"
 
     # In order to add new versions here, add a new list entry with:
     # * version: {version}
-    # * md5: the md5sum of the v{version}.tar.gz
-    # * md5_manpages: the md5sum of the corresponding manpage from
+    # * sha256: the sha256sum of the git-{version}.tar.gz
+    # * sha256_manpages: the sha256sum of the corresponding manpage from
     #       https://www.kernel.org/pub/software/scm/git/git-manpages-{version}.tar.xz
+    # You can find the source here: https://mirrors.edge.kernel.org/pub/software/scm/git/sha256sums.asc
 
     releases = [
         {
+            'version': '2.19.1',
+            'sha256': 'ec4dc96456612c65bf6d944cee9ac640145ec7245376832b781cb03e97cbb796',
+            'sha256_manpages': 'bd27f58dc90a661e3080b97365eb7322bfa185de95634fc59d98311925a7d894'
+        },
+        {
+            'version': '2.18.0',
+            'sha256': '94faf2c0b02a7920b0b46f4961d8e9cad08e81418614102898a55f980fa3e7e4',
+            'sha256_manpages': '6cf38ab3ad43ccdcd6a73ffdcf2a016d56ab6b4b240a574b0bb96f520a04ff55'
+        },
+        {
+            'version': '2.17.1',
+            'sha256': 'ec6452f0c8d5c1f3bcceabd7070b8a8a5eea11d4e2a04955c139b5065fd7d09a',
+            'sha256_manpages': '9732053c1a618d2576c1751d0249e43702f632a571f84511331882beb360677d'
+        },
+        {
+            'version': '2.17.0',
+            'sha256': '7a0cff35dbb14b77dca6924c33ac9fe510b9de35d5267172490af548ec5ee1b8',
+            'sha256_manpages': '41b58c68e90e4c95265c75955ddd5b68f6491f4d57b2f17c6d68e60bbb07ba6a'
+        },
+        {
+            'version': '2.15.1',
+            'sha256': '85fca8781a83c96ba6db384cc1aa6a5ee1e344746bafac1cbe1f0fe6d1109c84',
+            'sha256_manpages': '472454c494c9a7f50ad38060c3eec372f617de654b20f3eb3be59fc17a683fa1',
+        },
+        {
             'version': '2.14.1',
-            'md5': 'e965a37b3d277f2e7e78f5b04de28e2a',
-            'md5_manpages': 'da2e75ea3972b9e93fb47023e3bf1401',
+            'sha256': '01925349b9683940e53a621ee48dd9d9ac3f9e59c079806b58321c2cf85a4464',
+            'sha256_manpages': '8c5810ce65d44cd333327d3a115c5b462712a2f81225d142e07bd889ad8dc0e0',
         },
         {
             'version': '2.13.0',
-            'md5': 'd0f14da0ef1d22f1ce7f7876fadcb39f',
-            'md5_manpages': 'fda8d6d5314eb5a47e315405830f9970',
+            'sha256': '9f2fa8040ebafc0c2caae4a9e2cb385c6f16c0525bcb0fbd84938bc796372e80',
+            'sha256_manpages': 'e764721796cad175a4cf9a4afe7fb4c4fc57582f6f9a6e214239498e0835355b',
         },
         {
             'version': '2.12.2',
-            'md5': 'f1a50c09ce8b5dd197f3c6c6d5ea8e75',
-            'md5_manpages': '9358777e9a67e57427b03884c82311bd',
+            'sha256': 'd9c6d787a24670d7e5100db2367c250ad9756ef8084fb153a46b82f1d186f8d8',
+            'sha256_manpages': '6e7ed503f1190734e57c9427df356b42020f125fa36ab0478777960a682adf50',
         },
         {
             'version': '2.12.1',
-            'md5': 'a05c614c80ecd41e50699f1562e1130c',
-            'md5_manpages': '8dfba0c9f51c6c23fb135d136c061c78',
+            'sha256': '65d62d10caf317fc1daf2ca9975bdb09dbff874c92d24f9529d29a7784486b43',
+            'sha256_manpages': '35e46b8acd529ea671d94035232b1795919be8f3c3a363ea9698f1fd08d7d061',
         },
         {
             'version': '2.12.0',
-            'md5': '11a440ce0ed02098adf554c797facfd3',
-            'md5_manpages': '4d11e05068231e37d7e42935e9cc43a1',
+            'sha256': '882f298daf582a07c597737eb4bbafb82c6208fe0e73c047defc12169c221a92',
+            'sha256_manpages': '1f7733a44c59f9ae8dd321d68a033499a76c82046025cc2a6792299178138d65',
         },
         {
             'version': '2.11.1',
-            'md5': '2cf960f19e56f27248816809ae896794',
-            'md5_manpages': 'ade1e458a34a89d03dda9a6de85976bd',
+            'sha256': 'a1cdd7c820f92c44abb5003b36dc8cb7201ba38e8744802399f59c97285ca043',
+            'sha256_manpages': 'ee567e7b0f95333816793714bb31c54e288cf8041f77a0092b85e62c9c2974f9',
         },
         {
             'version': '2.11.0',
-            'md5': 'c63fb83b86431af96f8e9722ebb3ca01',
-            'md5_manpages': '72718851626e5b2267877cc2194a1ac9',
+            'sha256': 'd3be9961c799562565f158ce5b836e2b90f38502d3992a115dfb653d7825fd7e',
+            'sha256_manpages': '437a0128acd707edce24e1a310ab2f09f9a09ee42de58a8e7641362012dcfe22',
         },
         {
             'version': '2.9.3',
-            'md5': 'b0edfc0f3cb046aec7ed68a4b7282a75',
-            'md5_manpages': '337165a3b2bbe4814c73075cb6854ca2',
+            'sha256': 'a252b6636b12d5ba57732c8469701544c26c2b1689933bd1b425e603cbb247c0',
+            'sha256_manpages': '8ea1a55b048fafbf0c0c6fcbca4b5b0f5e9917893221fc7345c09051d65832ce',
         },
         {
             'version': '2.9.2',
-            'md5': '3ff8a9b30fd5c99a02e6d6585ab543fc',
-            'md5_manpages': 'c4f415b4fc94cf75a1deb651ba769594',
+            'sha256': '3cb09a3917c2d8150fc1708f3019cf99a8f0feee6cd61bba3797e3b2a85be9dc',
+            'sha256_manpages': 'ac5c600153d1e4a1c6494e250cd27ca288e7667ad8d4ea2f2386f60ba1b78eec',
         },
         {
             'version': '2.9.1',
-            'md5': 'a5d806743a992300b45f734d1667ddd2',
-            'md5_manpages': '2aa797ff70c704a563c910e04c0f620a',
+            'sha256': 'c2230873bf77f93736473e6a06501bf93eed807d011107de6983dc015424b097',
+            'sha256_manpages': '324f5f173f2bd50b0102b66e474b81146ccc078d621efeb86d7f75e3c1de33e6',
         },
         {
             'version': '2.9.0',
-            'md5': 'bf33a13c2adc05bc9d654c415332bc65',
-            'md5_manpages': 'c840c968062251b768ba9852fd29054c',
+            'sha256': 'bff7560f5602fcd8e37669e0f65ef08c6edc996e4f324e4ed6bb8a84765e30bd',
+            'sha256_manpages': '35ba69a8560529aa837e395a6d6c8d42f4d29b40a3c1cc6e3dc69bb1faadb332',
         },
         {
             'version': '2.8.4',
-            'md5': '86afb10254c3803894c9863fb5896bb6',
-            'md5_manpages': '8340e772d60ccd04a5da88fa9c976dad',
+            'sha256': '626e319f8a24fc0866167ea5f6bf3e2f38f69d6cb2e59e150f13709ca3ebf301',
+            'sha256_manpages': '953a8eadaf4ae96dbad2c3ec12384c677416843917ef83d94b98367ffd55afc0',
         },
         {
             'version': '2.8.3',
-            'md5': '0e19f31f96f9364fd247b8dc737dacfd',
-            'md5_manpages': '553827e1b6c422ecc485499c1a1ae28d',
+            'sha256': '2dad50c758339d6f5235309db620e51249e0000ff34aa2f2acbcb84c2123ed09',
+            'sha256_manpages': '2dad50c758339d6f5235309db620e51249e0000ff34aa2f2acbcb84c2123ed09',
         },
         {
             'version': '2.8.2',
-            'md5': '3d55550880af98f6e35c7f1d7c5aecfe',
-            'md5_manpages': '33330463af27eb1238cbc2b4ca100b3a',
+            'sha256': 'a029c37ee2e0bb1efea5c4af827ff5afdb3356ec42fc19c1d40216d99e97e148',
+            'sha256_manpages': '82d322211aade626d1eb3bcf3b76730bfdd2fcc9c189950fb0a8bdd69c383e2f',
         },
         {
             'version': '2.8.1',
-            'md5': '1308448d95afa41a4135903f22262fc8',
-            'md5_manpages': '87bc202c6f6ae32c1c46c2dda3134ed1',
+            'sha256': 'cfc66324179b9ed62ee02833f29d39935f4ab66874125a3ab9d5bb9055c0cb67',
+            'sha256_manpages': 'df46de0c172049f935cc3736361b263c5ff289b77077c73053e63ae83fcf43f4',
         },
         {
             'version': '2.8.0',
-            'md5': 'eca687e46e9750121638f258cff8317b',
-            'md5_manpages': 'd67a7db0f363e8c3b2960cd84ad0373f',
+            'sha256': '2c6eee5506237e0886df9973fd7938a1b2611ec93d07f64ed3447493ebac90d1',
+            'sha256_manpages': '2c48902a69df3bec3b8b8f0350a65fd1b662d2f436f0e64d475ecd1c780767b6',
         },
         {
             'version': '2.7.3',
-            'md5': 'fa1c008b56618c355a32ba4a678305f6',
-            'md5_manpages': '97a525cca7fe38ff6bd7aaa4f0438896',
+            'sha256': '30d067499b61caddedaf1a407b4947244f14d10842d100f7c7c6ea1c288280cd',
+            'sha256_manpages': '84b487c9071857ab0f15f11c4a102a583d59b524831cda0dc0954bd3ab73920b',
         },
         {
             'version': '2.7.1',
-            'md5': 'bf0706b433a8dedd27a63a72f9a66060',
-            'md5_manpages': '19881ca231f73dec91fb456d74943950',
+            'sha256': 'b4ab42798b7fb038eaefabb0c32ce9dbde2919103e5e2a35adc35dd46258a66f',
+            'sha256_manpages': '0313cf4d283336088883d8416692fb6c547512233e11dbf06e5b925b7e762d61',
         },
     ]
 
     for release in releases:
-        version(release['version'], release['md5'])
+        version(release['version'], sha256=release['sha256'])
         resource(
             name='git-manpages',
-            url="https://www.kernel.org/pub/software/scm/git/git-manpages-{0}.tar.xz".format(
+            url="https://www.kernel.org/pub/software/scm/git/git-manpages-{0}.tar.gz".format(
                 release['version']),
-            md5=release['md5_manpages'],
+            sha256=release['sha256_manpages'],
             placement='git-manpages',
             when='@{0}'.format(release['version']))
 
+    variant('tcltk', default=False,
+            description='Gitk: provide Tcl/Tk in the run environment')
+
     depends_on('curl')
     depends_on('expat')
     depends_on('gettext')
@@ -159,19 +168,36 @@ class Git(AutotoolsPackage):
     depends_on('automake', type='build')
     depends_on('libtool',  type='build')
     depends_on('m4',       type='build')
+    depends_on('tk',       type=('build', 'link'), when='+tcltk')
+
+    # See the comment in setup_environment re EXTLIBS.
+    def patch(self):
+        filter_file(r'^EXTLIBS =$',
+                    '#EXTLIBS =',
+                    'Makefile')
 
     def setup_environment(self, spack_env, run_env):
-        # This is done to avoid failures when git is an external package.
+        # We use EXTLIBS rather than LDFLAGS so that git's Makefile
+        # inserts the information into the proper place in the link commands
+        # (alongside the # other libraries/paths that configure discovers).
+        # LDFLAGS is inserted *before* libgit.a, which requires libintl.
+        # EXTFLAGS is inserted *after* libgit.a.
+        # This depends on the patch method above, which keeps the Makefile
+        # from stepping on the value that we pass in via the environment.
+        #
+        # The test avoids failures when git is an external package.
         # In that case the node in the DAG gets truncated and git DOES NOT
         # have a gettext dependency.
         if 'gettext' in self.spec:
-            spack_env.append_flags('LDFLAGS', '-L{0} -lintl'.format(
+            spack_env.append_flags('EXTLIBS', '-L{0} -lintl'.format(
                 self.spec['gettext'].prefix.lib))
+            spack_env.append_flags('CFLAGS', '-I{0}'.format(
+                self.spec['gettext'].prefix.include))
 
     def configure_args(self):
         spec = self.spec
 
-        return [
+        configure_args = [
             '--with-curl={0}'.format(spec['curl'].prefix),
             '--with-expat={0}'.format(spec['expat'].prefix),
             '--with-iconv={0}'.format(spec['libiconv'].prefix),
@@ -181,15 +207,26 @@ class Git(AutotoolsPackage):
             '--with-zlib={0}'.format(spec['zlib'].prefix),
         ]
 
+        if '+tcltk' in self.spec:
+            configure_args.append('--with-tcltk={0}'.format(
+                self.spec['tk'].prefix.bin.wish))
+        else:
+            configure_args.append('--without-tcltk')
+
+        return configure_args
+
     @run_after('configure')
     def filter_rt(self):
         if sys.platform == 'darwin':
             # Don't link with -lrt; the system has no (and needs no) librt
             filter_file(r' -lrt$', '', 'Makefile')
 
+    def check(self):
+        make('test')
+
     @run_after('install')
     def install_completions(self):
-        copy_tree('contrib/completion', self.prefix.share)
+        install_tree('contrib/completion', self.prefix.share)
 
     @run_after('install')
     def install_manpages(self):
diff --git a/var/spack/repos/builtin/packages/gl2ps/package.py b/var/spack/repos/builtin/packages/gl2ps/package.py
index fbe38d4bc9..16e4453bfd 100644
--- a/var/spack/repos/builtin/packages/gl2ps/package.py
+++ b/var/spack/repos/builtin/packages/gl2ps/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/glew/package.py b/var/spack/repos/builtin/packages/glew/package.py
index 4ba7eb5894..58c5ef686e 100644
--- a/var/spack/repos/builtin/packages/glew/package.py
+++ b/var/spack/repos/builtin/packages/glew/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,6 +15,7 @@ class Glew(Package):
     version('2.0.0',  '2a2cd7c98f13854d2fcddae0d2b20411')
 
     depends_on("cmake", type='build')
+    depends_on("gl")
 
     def install(self, spec, prefix):
         options = []
diff --git a/var/spack/repos/builtin/packages/glfmultiples/package.py b/var/spack/repos/builtin/packages/glfmultiples/package.py
new file mode 100644
index 0000000000..deb5789e24
--- /dev/null
+++ b/var/spack/repos/builtin/packages/glfmultiples/package.py
@@ -0,0 +1,30 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Glfmultiples(MakefilePackage):
+    """glfMultiples is a GLF-based variant caller for next-generation
+       sequencing data. It takes a set of GLF format genotype likelihood
+       files as input and generates a VCF-format set of variant calls
+       as output. """
+
+    homepage = "https://genome.sph.umich.edu/wiki/GlfMultiples"
+    url      = "http://www.sph.umich.edu/csg/abecasis/downloads/generic-glfMultiples-2010-06-16.tar.gz"
+
+    version('2010-06-16', '64bf6bb7c76543f4c8fabce015a3cb11')
+
+    depends_on('zlib')
+
+    def edit(self, spec, prefix):
+        makefile = FileFilter('Makefile')
+        makefile.filter('CXX=.*', 'CXX = ' + env['CXX'])
+        makefile.filter('CFLAGS=.*',
+                        'CFLAGS=-O2 -I./libsrc -I./pdf ' +
+                        '-D_FILE_OFFSET_BITS=64 -D__USE_LONG_INT')
+
+    def install(self, spec, prefix):
+        make('INSTALLDIR=%s' % prefix, 'install')
diff --git a/var/spack/repos/builtin/packages/glib/old-kernels.patch b/var/spack/repos/builtin/packages/glib/old-kernels.patch
new file mode 100644
index 0000000000..4061410320
--- /dev/null
+++ b/var/spack/repos/builtin/packages/glib/old-kernels.patch
@@ -0,0 +1,16 @@
+--- a/gio/gfile.c     2018-06-11 15:28:30.527667202 -0500
++++ b/gio/gfile.c     2018-03-12 11:23:37.000000000 -0500
+@@ -3014,11 +3014,11 @@
+ 
+   /* Try a 1MiB buffer for improved throughput. If that fails, use the default
+    * pipe size. See: https://bugzilla.gnome.org/791457 */
+-  buffer_size = fcntl (buffer[1], F_SETPIPE_SZ, 1024 * 1024);
++  buffer_size = -1;
+   if (buffer_size <= 0)
+     {
+       int errsv;
+-      buffer_size = fcntl (buffer[1], F_GETPIPE_SZ);
++      buffer_size = 65536;
+       errsv = errno;
+ 
+       if (buffer_size <= 0)
diff --git a/var/spack/repos/builtin/packages/glib/package.py b/var/spack/repos/builtin/packages/glib/package.py
index 5997987fa6..ab554165a1 100644
--- a/var/spack/repos/builtin/packages/glib/package.py
+++ b/var/spack/repos/builtin/packages/glib/package.py
@@ -1,39 +1,30 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
+import os.path
+
 
 class Glib(AutotoolsPackage):
-    """The GLib package contains a low-level libraries useful for
-       providing data structure handling for C, portability wrappers
-       and interfaces for such runtime functionality as an event loop,
-       threads, dynamic loading and an object system."""
+    """GLib provides the core application building blocks for
+    libraries and applications written in C.
+
+    The GLib package contains a low-level libraries useful for
+    providing data structure handling for C, portability wrappers
+    and interfaces for such runtime functionality as an event loop,
+    threads, dynamic loading and an object system.
+    """
 
     homepage = "https://developer.gnome.org/glib/"
     url      = "https://ftp.gnome.org/pub/gnome/sources/glib/2.53/glib-2.53.1.tar.xz"
 
+    version('2.56.2', 'd64abd16813501c956c4e123ae79f47f1b58de573df9fdd3b0795f1e2c1aa789')
+    version('2.56.1', '40ef3f44f2c651c7a31aedee44259809b6f03d3d20be44545cd7d177221c0b8d')
+    version('2.56.0', 'f2b59392f2fb514bbe7791dda0c36da5')
+    version('2.55.1', '9cbb6b3c7e75ba75575588497c7707b6')
     version('2.53.1', '3362ef4da713f834ea26904caf3a75f5')
     version('2.49.7', '397ead3fcf325cb921d54e2c9e7dfd7a')
     version('2.49.4', 'e2c87c03017b0cd02c4c73274b92b148')
@@ -41,12 +32,20 @@ class Glib(AutotoolsPackage):
     version('2.42.1', '89c4119e50e767d3532158605ee9121a')
 
     variant('libmount', default=False, description='Build with libmount support')
+    variant(
+        'tracing',
+        default='',
+        values=('dtrace', 'systemtap'),
+        multi=True,
+        description='Enable tracing support'
+    )
 
-    depends_on('pkg-config@0.16:+internal_glib', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('libffi')
     depends_on('zlib')
     depends_on('gettext')
     depends_on('perl', type=('build', 'run'))
+    depends_on('python', type=('build', 'run'), when='@2.53.4:')
     depends_on('pcre+utf', when='@2.48:')
     depends_on('util-linux', when='+libmount')
 
@@ -55,6 +54,10 @@ class Glib(AutotoolsPackage):
     # Clang doesn't seem to acknowledge the pragma lines to disable the -Werror
     # around a legitimate usage.
     patch('no-Werror=format-security.patch')
+    # Patch to prevent compiler errors in kernels older than 2.6.35
+    patch('old-kernels.patch', when='@2.56.0:2.56.1 os=rhel6')
+    patch('old-kernels.patch', when='@2.56.0:2.56.1 os=centos6')
+    patch('old-kernels.patch', when='@2.56.0:2.56.1 os=scientific6')
 
     def url_for_version(self, version):
         """Handle glib's version-based custom URLs."""
@@ -62,20 +65,69 @@ class Glib(AutotoolsPackage):
         return url + '/%s/glib-%s.tar.xz' % (version.up_to(2), version)
 
     def configure_args(self):
-        spec = self.spec
         args = []
+        args.extend(self.enable_or_disable('libmount'))
+        if self.spec.satisfies('@2.53.4:'):
+            args.append('--with-python={0}'.format(
+                os.path.basename(self.spec['python'].command.path))
+            )
+        args.extend(self.enable_or_disable('tracing'))
+        return args
 
-        if '+libmount' in spec:
-            args.append('--enable-libmount')
-        else:
-            args.append('--disable-libmount')
+    @property
+    def dtrace_copy_path(self):
+        return join_path(self.stage.source_path, 'dtrace-copy')
 
-        return args
+    @run_before('configure')
+    def fix_python_path(self):
+        if not self.spec.satisfies('@2.53.4:'):
+            return
+
+        files = ['gobject/glib-genmarshal.in', 'gobject/glib-mkenums.in']
+
+        filter_file('^#!/usr/bin/env @PYTHON@',
+                    '#!/usr/bin/env python',
+                    *files)
+
+    @run_before('configure')
+    def fix_dtrace_usr_bin_path(self):
+        if 'tracing=dtrace' not in self.spec:
+            return
 
-    @run_before('install')
+        # dtrace may cause glib build to fail because it uses
+        # '/usr/bin/python' in the shebang. To work around that
+        # we copy the original script into a temporary folder, and
+        # change the shebang to '/usr/bin/env python'
+        dtrace = which('dtrace').path
+        dtrace_copy = join_path(self.dtrace_copy_path, 'dtrace')
+
+        with working_dir(self.dtrace_copy_path, create=True):
+            copy(dtrace, dtrace_copy)
+            filter_file(
+                '^#!/usr/bin/python',
+                '#!/usr/bin/env python',
+                dtrace_copy
+            )
+
+        # To have our own copy of dtrace in PATH, we need to
+        # prepend to PATH the temporary folder where it resides
+        env['PATH'] = ':'.join(
+            [self.dtrace_copy_path] + env['PATH'].split(':')
+        )
+
+    @run_after('install')
     def filter_sbang(self):
-        # Filter sbang before install so Spack's sbang hook can fix it up
-        perl = join_path(self.spec['perl'].prefix.bin, 'perl')
-        files = ['gobject/glib-mkenums']
+        # Revert sbang, so Spack's sbang hook can fix it up (we have to do
+        # this after install because otherwise the install target will try
+        # to rebuild files as filter_file updates the timestamps)
+        if self.spec.satisfies('@2.53.4:'):
+            pattern = '^#!/usr/bin/env python'
+            repl = '#!{0}'.format(self.spec['python'].command.path)
+            files = ['glib-genmarshal', 'glib-mkenums']
+        else:
+            pattern = '^#! /usr/bin/perl'
+            repl = '#!{0}'.format(self.spec['perl'].command.path)
+            files = ['glib-mkenums']
 
-        filter_file('^#! /usr/bin/perl', '#!{0}'.format(perl), *files)
+        files = [join_path(self.prefix.bin, file) for file in files]
+        filter_file(pattern, repl, *files, backup=False)
diff --git a/var/spack/repos/builtin/packages/glibmm/guint16_cast.patch b/var/spack/repos/builtin/packages/glibmm/guint16_cast.patch
new file mode 100644
index 0000000000..325eb4d21f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/glibmm/guint16_cast.patch
@@ -0,0 +1,36 @@
+diff --git a/glib/glibmm/class.cc b/glib/glibmm/class.cc
+index dc1c4a8..fc640ae 100644
+--- a/glib/glibmm/class.cc
++++ b/glib/glibmm/class.cc
+@@ -37,13 +37,13 @@ void Class::register_derived_type(GType base_type)
+ 
+   const GTypeInfo derived_info =
+   {
+-    base_query.class_size,
++    (guint16) base_query.class_size,
+     0, // base_init
+     0, // base_finalize
+     class_init_func_,
+     0, // class_finalize
+     0, // class_data
+-    base_query.instance_size,
++    (guint16) base_query.instance_size,
+     0, // n_preallocs
+     0, // instance_init
+     0, // value_table
+@@ -75,13 +75,13 @@ GType Class::clone_custom_type(const char* custom_type_name) const
+ 
+     const GTypeInfo derived_info =
+     {
+-      base_query.class_size,
++      (guint16) base_query.class_size,
+       0, // base_init
+       0, // base_finalize
+       &Class::custom_class_init_function,
+       0, // class_finalize
+       this, // class_data
+-      base_query.instance_size,
++      (guint16) base_query.instance_size,
+       0, // n_preallocs
+       0, // instance_init
+       0, // value_table
diff --git a/var/spack/repos/builtin/packages/glibmm/package.py b/var/spack/repos/builtin/packages/glibmm/package.py
new file mode 100644
index 0000000000..5fcf28ed83
--- /dev/null
+++ b/var/spack/repos/builtin/packages/glibmm/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Glibmm(AutotoolsPackage):
+    """Glibmm is a C++ wrapper for the glib library."""
+
+    homepage = "https://developer.gnome.org/glib/"
+    url      = "https://ftp.gnome.org/pub/GNOME/sources/glibmm/2.19/glibmm-2.19.3.tar.gz"
+
+    version('2.19.3', 'b50180bb93f501172a2ac4c54e83e88a')
+    version('2.16.0', '24390d2da1734205f1e572f24d4942f0')
+    version('2.4.8', 'fa8b2889cd845752446c6ce15a94bb32')
+
+    depends_on('libsigcpp')
+    depends_on('glib')
+
+    patch('guint16_cast.patch', when='@2.19.3')
+
+    def url_for_version(self, version):
+        """Handle glibmm's version-based custom URLs."""
+        url = "https://ftp.acc.umu.se/pub/GNOME/sources/glibmm"
+        ext = '.tar.gz' if version < Version('2.28.2') else '.tar.xz'
+        return url + "/%s/glibmm-%s%s" % (version.up_to(2), version, ext)
diff --git a/var/spack/repos/builtin/packages/glimmer/package.py b/var/spack/repos/builtin/packages/glimmer/package.py
new file mode 100644
index 0000000000..b93aefc08f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/glimmer/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Glimmer(MakefilePackage):
+    """Glimmer is a system for finding genes in microbial DNA, especially the
+    genomes of bacteria, archaea, and viruses."""
+
+    homepage = "https://ccb.jhu.edu/software/glimmer"
+
+    version('3.02b', '344d012ae12596de905866fe9eb7f16c')
+
+    build_directory = 'src'
+
+    def url_for_version(self, version):
+        url = "https://ccb.jhu.edu/software/glimmer/glimmer{0}.tar.gz"
+        return url.format(version.joined)
+
+    def install(self, spec, prefix):
+        install_tree('bin', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/glm/package.py b/var/spack/repos/builtin/packages/glm/package.py
index d2bf9da282..c628872feb 100644
--- a/var/spack/repos/builtin/packages/glm/package.py
+++ b/var/spack/repos/builtin/packages/glm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/global/package.py b/var/spack/repos/builtin/packages/global/package.py
index 040b7d6e71..66be9777c1 100644
--- a/var/spack/repos/builtin/packages/global/package.py
+++ b/var/spack/repos/builtin/packages/global/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
diff --git a/var/spack/repos/builtin/packages/globalarrays/ibm-xl.patch b/var/spack/repos/builtin/packages/globalarrays/ibm-xl.patch
deleted file mode 100644
index 644e3a559a..0000000000
--- a/var/spack/repos/builtin/packages/globalarrays/ibm-xl.patch
+++ /dev/null
@@ -1,250 +0,0 @@
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 2022280..dac3b7f 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -174,6 +174,15 @@ option (F2C_HIDDEN_STRING_LENGTH_AFTER_ARGS "Set F77 macros" ON)
- if (ENABLE_FORTRAN)
-   include( FortranCInterface )
-   FortranCInterface_HEADER(${CMAKE_SOURCE_DIR}/f2c_cmake.h MACRO_NAMESPACE F77_FUNC_)
-+  add_custom_command(
-+    OUTPUT ${CMAKE_CURRENT_SOURCE_DIR}/f2c_cmake.fh
-+    COMMAND ${CMAKE_COMMAND} -D INPUT:PATH="${CMAKE_CURRENT_SOURCE_DIR}/f2c_cmake.h" -D OUTPUT:PATH="${CMAKE_CURRENT_SOURCE_DIR}/f2c_cmake.fh" -P ${PROJECT_SOURCE_DIR}/tools/f2c_cmake_fh_from_h.cmake DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/f2c_cmake.h
-+    DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/f2c_cmake.h
-+  )
-+  add_custom_target(
-+    GenerateF2c_cmakeFH ALL
-+    DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/f2c_cmake.fh
-+  )
- else()
-   CONFIGURE_FILE( ${CMAKE_SOURCE_DIR}/cmake/f2c_dummy.h.in
-                 ${CMAKE_SOURCE_DIR}/f2c_cmake.h )
-@@ -336,6 +345,15 @@ if (ENABLE_FORTRAN)
-      set (F77_IARGC IARGC)
-      set (F77_FLUSH flush)
-      set (HAVE_F77_FLUSH 1)
-+  elseif (CMAKE_Fortran_COMPILER MATCHES "xlf.*")
-+     message(STATUS "Using IBM XL Fortran compiler settings")
-+     set (F90_MODULE )
-+     set (F77_GETARG GETARG)
-+     set (F77_GETARG_ARGS "i,s")
-+     set (F77_GETARG_DECLS "intrinsic GETARG")
-+     set (F77_IARGC IARGC)
-+     set (F77_FLUSH flush_)
-+     set (HAVE_F77_FLUSH 1)
-   endif()
- else()
- # need to set these variable even if only compiling C/C++
-diff --git a/cmake/config.h.in b/cmake/config.h.in
-index 3ce6a32..9ad868f 100644
---- a/cmake/config.h.in
-+++ b/cmake/config.h.in
-@@ -58,11 +58,11 @@
- 
- #cmakedefine01 F2C_HIDDEN_STRING_LENGTH_AFTER_ARGS
- 
--/*#define F77_FUNC(name,NAME) F77_FUNC_GLOBAL(name,NAME)*/
--/*#define F77_FUNC_(name,NAME) F77_FUNC_GLOBAL_(name,NAME)*/
-+#define F77_FUNC(name,NAME) F77_FUNC_GLOBAL(name,NAME)
-+#define F77_FUNC_(name,NAME) F77_FUNC_GLOBAL_(name,NAME)
- 
--#define F77_FUNC(name,NAME) name ## _
--#define F77_FUNC_(name,NAME) name ## _
-+/* #define F77_FUNC(name,NAME) name ## _ */
-+/* #define F77_FUNC_(name,NAME) name ## _ */
- 
- #define FXX_MODULE ${F90_MODULE}
- #define F77_GETARG ${F77_GETARG}
-diff --git a/tools/config_fh_from_h.cmake b/tools/config_fh_from_h.cmake
-index acdf776..fb10422 100644
---- a/tools/config_fh_from_h.cmake
-+++ b/tools/config_fh_from_h.cmake
-@@ -7,6 +7,13 @@ if (INPUT)
-     foreach (l in ${in0})
-       # Only retain lines that start with "#"
-       set(found "")
-+      string(REGEX MATCH "^#include" found "${l}")
-+      if (found)
-+        # don't include f2c_cmake.h
-+        set(out "#include \"f2c_cmake.fh\"\n")
-+       continue ()
-+      endif ()
-+      set(found "") 
-       string(REGEX MATCH "^#" found "${l}")
-       if (found)
-         set(out "${out}${l}\n")
-diff --git a/tools/f2c_cmake_fh_from_h.cmake b/tools/f2c_cmake_fh_from_h.cmake
-new file mode 100644
-index 0000000..acdf776
---- /dev/null
-+++ b/tools/f2c_cmake_fh_from_h.cmake
-@@ -0,0 +1,21 @@
-+if (INPUT)
-+  if (OUTPUT)
-+    file(READ "${INPUT}" in0)
-+# replace carriage returns with a semi-colon
-+    string (REGEX REPLACE "\n" ";" in0 "${in0}")
-+    set(out "")
-+    foreach (l in ${in0})
-+      # Only retain lines that start with "#"
-+      set(found "")
-+      string(REGEX MATCH "^#" found "${l}")
-+      if (found)
-+        set(out "${out}${l}\n")
-+      endif ()  
-+    endforeach ()
-+    file(WRITE "${OUTPUT}" "${out}")
-+  else (OUTPUT)
-+    message(ERROR "OUTPUT variable must be set")
-+  endif (OUTPUT)
-+else (INPUT)
-+  message(ERROR "INPUT variable must be set")
-+endif (INPUT)
-diff --git a/global/src/cnames.h b/global/src/cnames.h
-index efdec60..cadfd0a 100644
---- a/global/src/cnames.h
-+++ b/global/src/cnames.h
-@@ -2268,6 +2268,7 @@
- #define nga_iupdate_ghosts_ F77_FUNC_(nga_iupdate_ghosts,NGA_IUPDATE_GHOSTS)
- #define nga_supdate_ghosts_ F77_FUNC_(nga_supdate_ghosts,NGA_SUPDATE_GHOSTS)
- #define nga_zupdate_ghosts_ F77_FUNC_(nga_zupdate_ghosts,NGA_ZUPDATE_GHOSTS)
-+#define nga_update_ghosts_nb_ F77_FUNC_(nga_update_ghosts_nb, NGA_UPDATE_GHOSTS_NB)
- #define ga_update6_ghosts_  F77_FUNC_(ga_update6_ghosts, GA_UPDATE6_GHOSTS)
- #define ga_cupdate6_ghosts_ F77_FUNC_(ga_cupdate6_ghosts,GA_CUPDATE6_GHOSTS)
- #define ga_dupdate6_ghosts_ F77_FUNC_(ga_dupdate6_ghosts,GA_DUPDATE6_GHOSTS)
-diff --git a/global/testing/perform.F b/global/testing/perform.F
-index b18146d..e1b9641 100644
---- a/global/testing/perform.F
-+++ b/global/testing/perform.F
-@@ -110,7 +110,7 @@ c
-      &        ilo,ihi,jlo,jhi
-         write(6,*)'bytes  loop         get                    put',
-      &           '                 accumulate'
--        call flush(6)
-+        call F77_FLUSH(6)
-       endif
-       call ga_sync()
- c
-@@ -145,7 +145,7 @@ c
-         if (me .eq. 0) then
-           write(6,77)bytes, count, tg, 1d-6*bytes/tg,
-      &               tp, 1d-6*bytes/tp, ta, 1d-6*bytes/ta
--          call flush(6)
-+          call F77_FLUSH(6)
-         endif
-       enddo
- c
-diff --git a/global/testing/mir_perf1.F b/global/testing/mir_perf1.F
-index 074e838..3548552 100644
---- a/global/testing/mir_perf1.F
-+++ b/global/testing/mir_perf1.F
-@@ -133,7 +133,7 @@ c
-      &           '           accumulate'
-         write(6,*)' bytes    dim     sec      MB/s     sec      MB/s',
-      &           '     sec      MB/s'
--        call flush(6)
-+        call F77_FLUSH(6)
-       endif
-       call ga_sync()
- c
-@@ -174,7 +174,7 @@ c
-         if (me .eq. 0) then
-           write(6,77)bytes, chunk(loop), tg, 
-      &          1d-6*bytes/tg,tp, 1d-6*bytes/tp, ta, 1d-6*bytes/ta
--          call flush(6)
-+          call F77_FLUSH(6)
-         endif
-       enddo
- c
-@@ -388,7 +388,7 @@ c
-      &           '           accumulate'
-         write(6,*)' bytes    dim     sec      MB/s     sec      MB/s',
-      &           '     sec      MB/s'
--        call flush(6)
-+        call F77_FLUSH(6)
-       endif
-       call ga_sync()
- c
-@@ -427,7 +427,7 @@ c
-         if (me .eq. 0) then
-           write(6,77)bytes, chunk(loop), tg, 
-      &          1d-6*bytes/tg,tp, 1d-6*bytes/tp, ta, 1d-6*bytes/ta
--          call flush(6)
-+          call F77_FLUSH(6)
-         endif
-       enddo
- c
-diff --git a/global/testing/mir_perf2.F b/global/testing/mir_perf2.F
-index fb50398..3b3bed6 100644
---- a/global/testing/mir_perf2.F
-+++ b/global/testing/mir_perf2.F
-@@ -124,7 +124,7 @@ c
-      &           '           accumulate'
-         write(6,*)' bytes    dim     sec      MB/s     sec      MB/s',
-      &           '     sec      MB/s'
--        call flush(6)
-+        call F77_FLUSH(6)
-       endif
-       call ga_sync()
- c
-@@ -163,7 +163,7 @@ c
-         if (me .eq. 0) then
-           write(6,77)bytes, chunk(loop), tg, 
-      &          1d-6*bytes/tg,tp, 1d-6*bytes/tp, ta, 1d-6*bytes/ta
--          call flush(6)
-+          call F77_FLUSH(6)
-         endif
-       enddo
- c
-@@ -377,7 +377,7 @@ c
-      &           '           accumulate'
-         write(6,*)' bytes    dim     sec      MB/s     sec      MB/s',
-      &           '     sec      MB/s'
--        call flush(6)
-+        call F77_FLUSH(6)
-       endif
-       call ga_sync()
- c
-@@ -416,7 +416,7 @@ c
-         if (me .eq. 0) then
-           write(6,77)bytes, chunk(loop), tg, 
-      &          1d-6*bytes/tg,tp, 1d-6*bytes/tp, ta, 1d-6*bytes/ta
--          call flush(6)
-+          call F77_FLUSH(6)
-         endif
-       enddo
- c
-diff --git a/global/testing/perfmod.F b/global/testing/perfmod.F
-index ec3fe37..7770be7 100644
---- a/global/testing/perfmod.F
-+++ b/global/testing/perfmod.F
-@@ -119,7 +119,7 @@ c
- 
-         write(6,*)'bytes  loop         get                    put',
-      &           '                 accumulate'
--        call flush(6)
-+        call F77_FLUSH(6)
-       endif
-       call ga_sync()
- c
-@@ -157,7 +157,7 @@ c
-         if (me .eq. 0) then
-           write(6,77)bytes, count, tg, 1d-6*bytes/tg,
-      &               tp, 1d-6*bytes/tp, ta, 1d-6*bytes/ta
--          call flush(6)
-+          call F77_FLUSH(6)
-         endif
-       enddo
- c
-diff --git a/global/testing/sprsmatmult.F b/global/testing/sprsmatmult.F
-index 3fdeb3f..3682c3b 100644
---- a/global/testing/sprsmatmult.F
-+++ b/global/testing/sprsmatmult.F
-@@ -108,7 +108,7 @@ c
-         print *,'Comparing distributed multiply with serial multiply'
-         print *
- #endif
--        call flush(6)
-+        call F77_FLUSH(6)
-       endif
- c
- c***  Initialize the MA package
diff --git a/var/spack/repos/builtin/packages/globalarrays/package.py b/var/spack/repos/builtin/packages/globalarrays/package.py
index 2473be5620..a3074bccbf 100644
--- a/var/spack/repos/builtin/packages/globalarrays/package.py
+++ b/var/spack/repos/builtin/packages/globalarrays/package.py
@@ -1,66 +1,63 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at IBM.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Serban Maerean, serban@ibm.com, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class Globalarrays(CMakePackage):
-    """The Global Arrays (GA) toolkit provides a shared memory style
-    programming environment in the context of distributed array data
-    structures.
-    """
+class Globalarrays(AutotoolsPackage):
+    """Global Arrays (GA) is a Partitioned Global Address Space (PGAS)
+    programming model. It provides primitives for one-sided communication
+    (Get, Put, Accumulate) and Atomic Operations (read increment).
+    It supports blocking and non-blocking primtives, and supports location
+    consistency."""
 
     homepage = "http://hpc.pnl.gov/globalarrays/"
-    url = "https://github.com/GlobalArrays/ga"
-
-    version('master', git='https://github.com/GlobalArrays/ga', branch='master')
+    url = "https://github.com/GlobalArrays/ga/releases/download/v5.7/ga-5.7.tar.gz"
+
+    version('5.7',   'bb9a441a6b4fbb8b52b58c2d3f4cd07f')
+    version('5.6.5', '90da628dc72048deeda3f0cd095cb5b3')
+    version('5.6.4', '051901b316c9766b8ba54306bff7f6b3')
+    version('5.6.3', 'df3cf6cc8288d9f202b7fd0ea82f5491')
+    version('5.6.2', '901e4612203bac45059be524fc1abfb7')
+    version('5.6.1', '674c0ea9bf413840b1ff1e669de73fca')
+    version('5.6',   '49d7e997daed094eeb9565423879ba36')
+
+    variant('int64', default=False, description='Compile with 64 bit indices support')
+    variant('blas', default=False, description='Enable BLAS')
+    variant('lapack', default=False, description='Enable LAPACK')
+    variant('scalapack', default=False, description='Enable SCALAPACK')
+    variant('armci', values=('mpi-ts', 'mpi-pr', 'mpi3', 'openib', 'ofi'), 
+        default='mpi-ts', description='ARMCI runtime')
 
-    variant('i8', default=False, description='Build with 8 byte integers')
-
-    depends_on('blas')
-    depends_on('lapack')
     depends_on('mpi')
+    depends_on('blas', when='+blas')
+    depends_on('lapack', when='+lapack')
+    depends_on('scalapack', when='+scalapack')
+
+    conflicts('+lapack', when='~blas')
+    conflicts('+scalapack', when='~blas')
+    conflicts('+scalapack', when='~lapack')
 
-    patch('ibm-xl.patch', when='%xl')
-    patch('ibm-xl.patch', when='%xl_r')
+    def configure_args(self):
+        args = ['--with-mpi']
 
-    def cmake_args(self):
-        options = []
+        if '+blas' in self.spec:
+            if '+int64' in self.spec:
+                args.append('--with-blas8')
+            else:
+                args.append('--with-blas')
 
-        options.extend([
-            '-DENABLE_FORTRAN=ON',
-            '-DENABLE_BLAS=ON',
-        ])
+        if '+lapack' in self.spec:
+            args.append('--with-lapack')
 
-        if self.compiler.name == 'xl' or self.compiler.name == 'xl_r':
-            # use F77 compiler if IBM XL
-            options.extend([
-                '-DCMAKE_Fortran_COMPILER=%s' % self.compiler.f77,
-                '-DCMAKE_Fortran_FLAGS=-qzerosize'
-            ])
+        if '+scalapack' in self.spec:
+            if '+int64' in self.spec:
+                args.append('--with-scalapack8')
+            else:
+                args.append('--with-scalapack')
 
-        if "+i8" in self.spec:
-            options.extend(['-DENABLE_I8=ON'])
+        args.append('--with-' + self.spec.variants['armci'].value)
 
-        return options
+        return args
diff --git a/var/spack/repos/builtin/packages/globus-toolkit/package.py b/var/spack/repos/builtin/packages/globus-toolkit/package.py
index 05944b2dd5..537bcb3a3b 100644
--- a/var/spack/repos/builtin/packages/globus-toolkit/package.py
+++ b/var/spack/repos/builtin/packages/globus-toolkit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,6 +11,9 @@ class GlobusToolkit(AutotoolsPackage):
        grids"""
 
     homepage = "http://toolkit.globus.org"
-    url      = "http://toolkit.globus.org/ftppub/gt6/installers/src/globus_toolkit-6.0.1470089956.tar.gz"
+    url      = "http://toolkit.globus.org/ftppub/gt6/installers/src/globus_toolkit-6.0.1506371041.tar.gz"
+
+    version('6.0.1506371041', 'e17146f68e03b3482aaea3874d4087a5')
+    version('6.0.1493989444', '9e9298b61d045e65732e12c9727ceaa8')
 
-    version('6.0.1470089956', 'b77fe3cc5a5844df995688b0e630d077')
+    depends_on('openssl')
diff --git a/var/spack/repos/builtin/packages/glog/package.py b/var/spack/repos/builtin/packages/glog/package.py
index cc62b1250e..78c59c3b14 100644
--- a/var/spack/repos/builtin/packages/glog/package.py
+++ b/var/spack/repos/builtin/packages/glog/package.py
@@ -1,40 +1,35 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class Glog(CMakePackage):
+class Glog(Package):
     """C++ implementation of the Google logging module."""
 
     homepage = "https://github.com/google/glog"
-    url      = "https://github.com/google/glog/archive/v0.3.4.tar.gz"
+    url      = "https://github.com/google/glog/archive/v0.3.5.tar.gz"
 
+    version('0.3.5', '5df6d78b81e51b90ac0ecd7ed932b0d4')
     version('0.3.4', 'df92e05c9d02504fb96674bc776a41cb')
     version('0.3.3', 'c1f86af27bd9c73186730aa957607ed0')
 
     depends_on('gflags')
+    depends_on('cmake', when="@0.3.5:")
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix)
+        make()
+        make('install')
+
+    @when('@0.3.5:')
+    def install(self, spec, prefix):
+        cmake_args = ['-DBUILD_SHARED_LIBS=TRUE']
+        cmake_args.extend(std_cmake_args)
 
-    def cmake_args(self):
-        return ['-DBUILD_SHARED_LIBS=TRUE']
+        with working_dir('spack-build', create=True):
+            cmake('..', *cmake_args)
+            make()
+            make('install')
diff --git a/var/spack/repos/builtin/packages/gloo/package.py b/var/spack/repos/builtin/packages/gloo/package.py
new file mode 100644
index 0000000000..3fdfa1c295
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gloo/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Gloo(CMakePackage):
+    """Gloo is a collective communications library."""
+
+    homepage = "https://github.com/facebookincubator/gloo"
+    git      = "https://github.com/facebookincubator/gloo.git"
+
+    version('master')
diff --git a/var/spack/repos/builtin/packages/glpk/package.py b/var/spack/repos/builtin/packages/glpk/package.py
index 7693ba7b9a..eab6df6d1f 100644
--- a/var/spack/repos/builtin/packages/glpk/package.py
+++ b/var/spack/repos/builtin/packages/glpk/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,9 +14,10 @@ class Glpk(AutotoolsPackage):
     """
 
     homepage = "https://www.gnu.org/software/glpk"
-    url = "http://ftp.gnu.org/gnu/glpk/glpk-4.57.tar.gz"
+    url      = "https://ftpmirror.gnu.org/glpk/glpk-4.65.tar.gz"
 
-    version('4.61', '3ce3e224a8b6e75a1a0b378445830f21')    
+    version('4.65', '470a984a8b1c0e027bdb6d5859063fe8')
+    version('4.61', '3ce3e224a8b6e75a1a0b378445830f21')
     version('4.57', '237531a54f73155842f8defe51aedb0f')
 
     variant(
diff --git a/var/spack/repos/builtin/packages/glproto/package.py b/var/spack/repos/builtin/packages/glproto/package.py
index eaaabc884b..78dc23b645 100644
--- a/var/spack/repos/builtin/packages/glproto/package.py
+++ b/var/spack/repos/builtin/packages/glproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Glproto(AutotoolsPackage):
 
     version('1.4.17', 'd69554c1b51a83f2c6976a640819911b')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/glvis/package.py b/var/spack/repos/builtin/packages/glvis/package.py
new file mode 100644
index 0000000000..dca29403ea
--- /dev/null
+++ b/var/spack/repos/builtin/packages/glvis/package.py
@@ -0,0 +1,125 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Glvis(MakefilePackage):
+    """GLVis: an OpenGL tool for visualization of FEM meshes and functions"""
+
+    homepage = "http://glvis.org"
+    git      = "https://github.com/glvis/glvis.git"
+
+    maintainers = ['goxberry', 'v-dobrev', 'tzanio']
+
+    # glvis (like mfem) is downloaded from a URL shortener at request
+    # of upstream author Tzanio Kolev <tzanio@llnl.gov>.  See here:
+    # https://github.com/mfem/mfem/issues/53
+    #
+    # The following procedure should be used to verify security when a
+    # new version is added:
+    #
+    # 1. Verify that no checksums on old versions have changed.
+    #
+    # 2. Verify that the shortened URL for the new version is listed at:
+    #    http://glvis.org/download/
+    #
+    # 3. Use http://getlinkinfo.com or similar to verify that the
+    #    underling download link for the latest version comes has the
+    #    prefix: http://glvis.github.io/releases
+    #
+    # If this quick verification procedure fails, additional discussion
+    # will be required to verify the new version.
+
+    version('develop', branch='master')
+
+    version('3.4',
+            '289fbd2e09d4456e5fee6162bdc3e0b4c8c8d54625f3547ad2a69fef319279e7',
+            url='https://bit.ly/glvis-3-4',
+            extension='.tar.gz')
+
+    version('3.3',
+            'e24d7c5cb53f208b691c872fe82ea898242cfdc0fd68dd0579c739e070dcd800',
+            url='http://goo.gl/C0Oadw',
+            extension='.tar.gz')
+
+    version('3.2',
+            'c82cb110396e63b6436a770c55eb6d578441eaeaf3f9cc20436c242392e44e80',
+            url='http://goo.gl/hzupg1',
+            extension='.tar.gz')
+
+    version('3.1',
+            '793e984ddfbf825dcd13dfe1ca00eccd686cd40ad30c8789ba80ee175a1b488c',
+            url='http://goo.gl/gQZuu9',
+            extension='tar.gz')
+
+    variant('screenshots',
+            default='png',
+            values=('xwd', 'png', 'tiff'),
+            description='Backend used for screenshots')
+    variant('fonts', default=True,
+            description='Use antialiased fonts via freetype & fontconfig')
+
+    depends_on('mfem@develop', when='@develop')
+    depends_on('mfem@3.4.0', when='@3.4')
+    depends_on('mfem@3.3', when='@3.3')
+    depends_on('mfem@3.2', when='@3.2')
+    depends_on('mfem@3.1', when='@3.1')
+
+    depends_on('gl')
+    depends_on('glu')
+    depends_on('libx11')
+
+    depends_on('libpng', when='screenshots=png')
+    depends_on('libtiff', when='screenshots=tiff')
+    depends_on('freetype', when='+fonts')
+    depends_on('fontconfig', when='+fonts')
+
+    def edit(self, spec, prefix):
+
+        def yes_no(s):
+            return 'YES' if self.spec.satisfies(s) else 'NO'
+
+        mfem = spec['mfem']
+        config_mk = mfem.package.config_mk
+
+        gl_libs = spec['glu'].libs + spec['gl'].libs + spec['libx11'].libs
+        args = ['CC={0}'.format(env['CC']),
+                'PREFIX={0}'.format(prefix.bin),
+                'MFEM_DIR={0}'.format(mfem.prefix),
+                'CONFIG_MK={0}'.format(config_mk),
+                'GL_OPTS=-I{0} -I{1} -I{2}'.format(
+                    spec['libx11'].prefix.include,
+                    spec['gl'].prefix.include,
+                    spec['glu'].prefix.include),
+                'GL_LIBS={0}'.format(gl_libs.ld_flags)]
+
+        if 'screenshots=png' in spec:
+            args += [
+                'USE_LIBPNG=YES', 'USE_LIBTIFF=NO',
+                'PNG_OPTS=-DGLVIS_USE_LIBPNG -I{0}'.format(
+                    spec['libpng'].prefix.include),
+                'PNG_LIBS={0}'.format(spec['libpng'].libs.ld_flags)]
+        elif 'screenshots=tiff' in spec:
+            args += [
+                'USE_LIBPNG=NO', 'USE_LIBTIFF=YES',
+                'TIFF_OPTS=-DGLVIS_USE_LIBTIFF -I{0}'.format(
+                    spec['libtiff'].prefix.include),
+                'TIFF_LIBS={0}'.format(spec['libtiff'].libs.ld_flags)]
+        else:
+            args += ['USE_LIBPNG=NO', 'USE_LIBTIFF=NO']
+
+        args.append('USE_FREETYPE={0}'.format(yes_no('+fonts')))
+        if '+fonts' in spec:
+            args += [
+                'FT_OPTS=-DGLVIS_USE_FREETYPE -I{0} -I{1}'.format(
+                    spec['freetype'].prefix.include.freetype2,
+                    spec['fontconfig'].prefix.include),
+                'FT_LIBS={0} {1}'.format(
+                    spec['freetype'].libs.ld_flags,
+                    spec['fontconfig'].libs.ld_flags)]
+
+        self.build_targets = args
+        self.install_targets += args
diff --git a/var/spack/repos/builtin/packages/gmake/package.py b/var/spack/repos/builtin/packages/gmake/package.py
index 29042eaad6..c40b476568 100644
--- a/var/spack/repos/builtin/packages/gmake/package.py
+++ b/var/spack/repos/builtin/packages/gmake/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,17 +11,22 @@ class Gmake(AutotoolsPackage):
     other non-source files of a program from the program's source files."""
 
     homepage = "https://www.gnu.org/software/make/"
-    url      = "https://ftp.gnu.org/gnu/make/make-4.2.1.tar.gz"
+    url      = "https://ftpmirror.gnu.org/make/make-4.2.1.tar.gz"
 
     version('4.2.1', '7d0dcb6c474b258aab4d54098f2cf5a7')
     version('4.0',   'b5e558f981326d9ca1bfdb841640721a')
 
     variant('guile', default=False, description='Support GNU Guile for embedded scripting')
+    variant('nls', default=True, description='Enable Native Language Support')
 
+    depends_on('gettext', when='+nls')
     depends_on('guile', when='+guile')
 
     build_directory = 'spack-build'
 
+    patch('https://src.fedoraproject.org/rpms/make/raw/519a7c5bcbead22e6ea2d2c2341d981ef9e25c0d/f/make-4.2.1-glob-fix-2.patch', level=1, sha256='fe5b60d091c33f169740df8cb718bf4259f84528b42435194ffe0dd5b79cd125', when='@4.2.1')
+    patch('https://src.fedoraproject.org/rpms/make/raw/519a7c5bcbead22e6ea2d2c2341d981ef9e25c0d/f/make-4.2.1-glob-fix-3.patch', level=1, sha256='ca60bd9c1a1b35bc0dc58b6a4a19d5c2651f7a94a4b22b2c5ea001a1ca7a8a7f', when='@:4.2.1')
+
     def configure_args(self):
         args = []
 
@@ -49,6 +35,11 @@ class Gmake(AutotoolsPackage):
         else:
             args.append('--without-guile')
 
+        if '+nls' in self.spec:
+            args.append('--enable-nls')
+        else:
+            args.append('--disable-nls')
+
         return args
 
     @run_after('install')
diff --git a/var/spack/repos/builtin/packages/gmap-gsnap/package.py b/var/spack/repos/builtin/packages/gmap-gsnap/package.py
index 7db09fb72d..bfa53525f2 100644
--- a/var/spack/repos/builtin/packages/gmap-gsnap/package.py
+++ b/var/spack/repos/builtin/packages/gmap-gsnap/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,4 +14,42 @@ class GmapGsnap(AutotoolsPackage):
     homepage = "http://research-pub.gene.com/gmap/"
     url      = "http://research-pub.gene.com/gmap/src/gmap-gsnap-2017-06-16.tar.gz"
 
+    version('2018-07-04', sha256='a9f8c1f0810df65b2a089dc10be79611026f4c95e4681dba98fea3d55d598d24')
+    version('2018-03-25', 'f08e65c1e4d9574a3eb7f15f8ca6af16')
+    version('2018-02-12', '13152aedeef9ac66be915fc6bf6464f2')
     version('2017-06-16', 'fcc91b8bdd4bf12ae3124de0c00db0c0')
+    version('2014-12-28', '1ab07819c9e5b5b8970716165ccaa7da')
+
+    depends_on('zlib')
+    depends_on('bzip2')
+
+    variant(
+        'simd',
+        description='CPU support.',
+        values=('avx2', 'sse42', 'avx512', 'sse2'),
+        multi=True,
+        default='sse2'
+    )
+
+    def configure(self, spec, prefix):
+        configure = Executable('../configure')
+
+        for simd in spec.variants['simd'].value:
+            with working_dir(simd, create=True):
+                configure('--with-simd-level={0}'.format(simd),
+                          '--prefix={0}'.format(prefix))
+
+    def build(self, spec, prefix):
+        for simd in spec.variants['simd'].value:
+            with working_dir(simd):
+                make()
+
+    def check(self):
+        for simd in self.spec.variants['simd'].value:
+            with working_dir(simd):
+                make('check')
+
+    def install(self, spec, prefix):
+        for simd in spec.variants['simd'].value:
+            with working_dir(simd):
+                make('install')
diff --git a/var/spack/repos/builtin/packages/gmime/package.py b/var/spack/repos/builtin/packages/gmime/package.py
index d5d0e44d60..888732ee48 100644
--- a/var/spack/repos/builtin/packages/gmime/package.py
+++ b/var/spack/repos/builtin/packages/gmime/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/gmodel/package.py b/var/spack/repos/builtin/packages/gmodel/package.py
new file mode 100644
index 0000000000..65ab123158
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gmodel/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Gmodel(CMakePackage):
+    """Gmsh model generation library
+
+      Gmodel is a C++11 library that implements a minimal CAD kernel based
+      on the .geo format used by the Gmsh mesh generation code, and is
+      designed to make it easier for users to quickly construct CAD models
+      for Gmsh.
+    """
+    homepage = "https://github.com/ibaned/gmodel"
+    url      = "https://github.com/ibaned/gmodel/archive/v2.1.0.tar.gz"
+
+    version('2.1.0', '80df0c6dc413a9ffa0f0e7b65118b05b643ba3e1bfcac28fb91d2d3ad017fda0')
diff --git a/var/spack/repos/builtin/packages/gmp/package.py b/var/spack/repos/builtin/packages/gmp/package.py
index 0367a35200..c49be8f485 100644
--- a/var/spack/repos/builtin/packages/gmp/package.py
+++ b/var/spack/repos/builtin/packages/gmp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,13 +11,16 @@ class Gmp(AutotoolsPackage):
     on signed integers, rational numbers, and floating-point numbers."""
 
     homepage = "https://gmplib.org"
-    url      = "https://ftp.gnu.org/gnu/gmp/gmp-6.1.2.tar.bz2"
+    url      = "https://ftpmirror.gnu.org/gmp/gmp-6.1.2.tar.bz2"
 
     version('6.1.2',  '8ddbb26dc3bd4e2302984debba1406a5')
     version('6.1.1',  '4c175f86e11eb32d8bf9872ca3a8e11d')
     version('6.1.0',  '86ee6e54ebfc4a90b643a65e402c4048')
     version('6.0.0a', 'b7ff2d88cae7f8085bd5006096eed470')
     version('6.0.0',  '6ef5869ae735db9995619135bd856b84')
+    version('5.1.3', 'a082867cbca5e898371a97bb27b31fea')
+    # Old version needed for a binary package in ghc-bootstrap
+    version('4.3.2',  'dd60683d7057917e34630b4a787932e8')
 
     depends_on('autoconf', type='build')
     depends_on('automake', type='build')
diff --git a/var/spack/repos/builtin/packages/gmsh/package.py b/var/spack/repos/builtin/packages/gmsh/package.py
index 94794ed8a5..c56c2d415a 100644
--- a/var/spack/repos/builtin/packages/gmsh/package.py
+++ b/var/spack/repos/builtin/packages/gmsh/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,25 +19,24 @@ class Gmsh(CMakePackage):
     homepage = 'http://gmsh.info'
     url = 'http://gmsh.info/src/gmsh-2.11.0-source.tgz'
 
+    version('4.0.0', sha256='fb0c8afa37425c6f4315ab3b3124e9e102fcf270a35198423a4002796f04155f')
+    version('3.0.6',  '9700bcc440d7a6b16a49cbfcdcdc31db33efe60e1f5113774316b6fa4186987b')
     version('3.0.1',  '830b5400d9f1aeca79c3745c5c9fdaa2900cdb2fa319b664a5d26f7e615c749f')
     version('2.16.0', 'e829eaf32ea02350a385202cc749341f2a3217c464719384b18f653edd028eea')
     version('2.15.0', '992a4b580454105f719f5bc05441d3d392ab0b4b80d4ea07b61ca3bdc974070a')
     version('2.12.0', '7fbd2ec8071e79725266e72744d21e902d4fe6fa9e7c52340ad5f4be5c159d09')
-    version('2.11.0', 'f15b6e7ac9ca649c9a74440e1259d0db')
-
-    variant('shared',      default=True,
-            description='Enables the build of shared libraries')
-    variant('mpi',         default=True,
-            description='Builds MPI support for parser and solver')
-    variant('fltk',        default=False,
-            description='Enables the build of the FLTK GUI')
+    version('develop', branch='master', git='https://gitlab.onelab.info/gmsh/gmsh.git')
+
+    variant('shared',      default=True,  description='Enables the build of shared libraries')
+    variant('mpi',         default=True,  description='Builds MPI support for parser and solver')
+    variant('fltk',        default=False, description='Enables the build of the FLTK GUI')
     variant('hdf5',        default=False, description='Enables HDF5 support')
-    variant('compression', default=True,
-            description='Enables IO compression through zlib')
+    variant('compression', default=True,  description='Enables IO compression through zlib')
+    variant('netgen',      default=False, description='Build with Netgen')
     variant('oce',         default=False, description='Build with OCE')
     variant('petsc',       default=False, description='Build with PETSc')
-    variant('slepc',       default=False,
-            description='Build with SLEPc (only when PETSc is enabled)')
+    variant('slepc',       default=False, description='Build with SLEPc (only when PETSc is enabled)')
+    variant('tetgen',      default=False, description='Build with Tetgen')
 
     depends_on('blas')
     depends_on('lapack')
@@ -66,12 +46,16 @@ class Gmsh(CMakePackage):
     # Assumes OpenGL with GLU is already provided by the system:
     depends_on('fltk', when='+fltk')
     depends_on('hdf5', when='+hdf5')
+    depends_on('netgen', when='+netgen')
     depends_on('oce',  when='+oce')
     depends_on('petsc+mpi', when='+petsc+mpi')
     depends_on('petsc', when='+petsc~mpi')
     depends_on('slepc', when='+slepc+petsc')
+    depends_on('tetgen', when='+tetgen')
     depends_on('zlib',  when='+compression')
 
+    conflicts('+slepc', when='~petsc')
+
     def cmake_args(self):
         spec = self.spec
         prefix = self.prefix
@@ -102,21 +86,33 @@ class Gmsh(CMakePackage):
 
         if '+oce' in spec:
             env['CASROOT'] = self.spec['oce'].prefix
-            options.extend(['-DENABLE_OCC=ON'])
+            options.append('-DENABLE_OCC=ON')
         else:
-            options.extend(['-DENABLE_OCC=OFF'])
+            options.append('-DENABLE_OCC=OFF')
 
         if '+petsc' in spec:
             env['PETSC_DIR'] = self.spec['petsc'].prefix
-            options.extend(['-DENABLE_PETSC=ON'])
+            options.append('-DENABLE_PETSC=ON')
+        else:
+            options.append('-DENABLE_PETSC=OFF')
+
+        if '+tetgen' in spec:
+            env['TETGEN_DIR'] = self.spec['tetgen'].prefix
+            options.append('-DENABLE_TETGEN=ON')
+        else:
+            options.append('-DENABLE_TETGEN=OFF')
+
+        if '+netgen' in spec:
+            env['NETGEN_DIR'] = self.spec['netgen'].prefix
+            options.append('-DENABLE_NETGEN=ON')
         else:
-            options.extend(['-DENABLE_PETSC=OFF'])
+            options.append('-DENABLE_NETGEN=OFF')
 
         if '+slepc' in spec:
             env['SLEPC_DIR'] = self.spec['slepc'].prefix
-            options.extend(['-DENABLE_SLEPC=ON'])
+            options.append('-DENABLE_SLEPC=ON')
         else:
-            options.extend(['-DENABLE_SLEPC=OFF'])
+            options.append('-DENABLE_SLEPC=OFF')
 
         if '+shared' in spec:
             # Builds dynamic executable and installs shared library
diff --git a/var/spack/repos/builtin/packages/gnat/package.py b/var/spack/repos/builtin/packages/gnat/package.py
index 843d81d9e4..1c3ef8d5d2 100644
--- a/var/spack/repos/builtin/packages/gnat/package.py
+++ b/var/spack/repos/builtin/packages/gnat/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/gnu-prolog/package.py b/var/spack/repos/builtin/packages/gnu-prolog/package.py
index 819e57498a..b96e026e87 100644
--- a/var/spack/repos/builtin/packages/gnu-prolog/package.py
+++ b/var/spack/repos/builtin/packages/gnu-prolog/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/gnupg/package.py b/var/spack/repos/builtin/packages/gnupg/package.py
index 756f8404bc..d1d3efd014 100644
--- a/var/spack/repos/builtin/packages/gnupg/package.py
+++ b/var/spack/repos/builtin/packages/gnupg/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,8 +11,9 @@ class Gnupg(AutotoolsPackage):
        standard as defined by RFC4880 """
 
     homepage = "https://gnupg.org/index.html"
-    url = "https://gnupg.org/ftp/gcrypt/gnupg/gnupg-2.1.21.tar.bz2"
+    url = "https://gnupg.org/ftp/gcrypt/gnupg/gnupg-2.2.3.tar.bz2"
 
+    version('2.2.3', '6911c0127e4231ce52d60f26029dba68')
     version('2.1.21', '685ebf4c3a7134ba0209c96b18b2f064')
 
     depends_on('libgcrypt')
diff --git a/var/spack/repos/builtin/packages/gnuplot/package.py b/var/spack/repos/builtin/packages/gnuplot/package.py
index 1af9cbfb08..374d6cd234 100644
--- a/var/spack/repos/builtin/packages/gnuplot/package.py
+++ b/var/spack/repos/builtin/packages/gnuplot/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
@@ -45,6 +26,8 @@ class Gnuplot(AutotoolsPackage):
     # dependency of readline. Fix it with a small patch
     patch('term_include.patch')
 
+    version('5.2.5', '039db2cce62ddcfd31a6696fe576f4224b3bc3f919e66191dfe2cdb058475caa')
+    version('5.2.2', '60aedd08998160593199459dea8467fe')
     version('5.2.0', '0bd8f9af84c0ad2fa9de16772c366416')
     version('5.0.7', '8eaafddb0b12795f82ed6dd2a6ebbe80')
     version('5.0.6', '8ec46520a86a61163a701b00404faf1a')
@@ -66,7 +49,7 @@ class Gnuplot(AutotoolsPackage):
 
     # required dependencies
     depends_on('readline')
-    depends_on('pkg-config', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('libxpm')
     depends_on('libiconv')
 
diff --git a/var/spack/repos/builtin/packages/gnutls/package.py b/var/spack/repos/builtin/packages/gnutls/package.py
index 7f41eb3204..9f81cfda9a 100644
--- a/var/spack/repos/builtin/packages/gnutls/package.py
+++ b/var/spack/repos/builtin/packages/gnutls/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -49,7 +30,7 @@ class Gnutls(AutotoolsPackage):
     depends_on('zlib', when='+zlib')
     depends_on('gettext')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
 
     build_directory = 'spack-build'
 
diff --git a/var/spack/repos/builtin/packages/go-bootstrap/package.py b/var/spack/repos/builtin/packages/go-bootstrap/package.py
index 0228aa74d9..b1f94fc594 100644
--- a/var/spack/repos/builtin/packages/go-bootstrap/package.py
+++ b/var/spack/repos/builtin/packages/go-bootstrap/package.py
@@ -1,30 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-import os
-import shutil
-import glob
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 # THIS PACKAGE SHOULD NOT EXIST
@@ -36,8 +14,8 @@ from spack import *
 
 class GoBootstrap(Package):
     """Old C-bootstrapped go to bootstrap real go"""
+
     homepage = "https://golang.org"
-    url = "https://go.googlesource.com/go"
 
     extendable = True
 
@@ -46,12 +24,14 @@ class GoBootstrap(Package):
     # See: https://golang.org/doc/install/source#go14 and
     # https://github.com/golang/go/issues/17545 and
     # https://github.com/golang/go/issues/16352
+    version('1.4-bootstrap-20171003', 'dbf727a4b0e365bf88d97cbfde590016',
+            url='https://dl.google.com/go/go1.4-bootstrap-20171003.tar.gz')
     version('1.4-bootstrap-20170531', 'd2cc61cb9f829b3510ee39c0c5568014',
             url='https://storage.googleapis.com/golang/go1.4-bootstrap-20170531.tar.gz')
     version('1.4-bootstrap-20161024', '76e42c8152e8560ded880a6d1d1f53cb',
             url='https://storage.googleapis.com/golang/go1.4-bootstrap-20161024.tar.gz')
 
-    provides('golang@:1.4-bootstrap-20170531')
+    provides('golang@:1.4-bootstrap-20171003')
 
     depends_on('git', type=('build', 'link', 'run'))
 
@@ -73,15 +53,7 @@ class GoBootstrap(Package):
         with working_dir('src'):
             bash('{0}.bash'.format('all' if self.run_tests else 'make'))
 
-        try:
-            os.makedirs(prefix)
-        except OSError:
-            pass
-        for f in glob.glob('*'):
-            if os.path.isdir(f):
-                shutil.copytree(f, os.path.join(prefix, f))
-            else:
-                shutil.copy2(f, os.path.join(prefix, f))
+        install_tree('.', prefix)
 
     def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
         spack_env.set('GOROOT_BOOTSTRAP', self.spec.prefix)
diff --git a/var/spack/repos/builtin/packages/go/package.py b/var/spack/repos/builtin/packages/go/package.py
index b112ebe7d8..5fcdc57a5d 100644
--- a/var/spack/repos/builtin/packages/go/package.py
+++ b/var/spack/repos/builtin/packages/go/package.py
@@ -1,30 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
-import shutil
-import glob
 import llnl.util.tty as tty
 from spack import *
 
@@ -52,19 +31,25 @@ from spack import *
 class Go(Package):
     """The golang compiler and build environment"""
     homepage = "https://golang.org"
-    url = 'https://storage.googleapis.com/golang/go1.7.4.src.tar.gz'
+    url = 'https://dl.google.com/go/go1.10.1.src.tar.gz'
 
     extendable = True
 
-    version('1.9.2', '44105c865a1a810464df79233a05a568')
-    version('1.9.1', '27bce1ffb05f4f6bd90d90081e5d4169')
-    version('1.9',   'da2d44ea384076efec43ee1f8b7d45d2')
-    version('1.8.3', '64e9380e07bba907e26a00cf5fcbe77e')
-    version('1.8.1', '409dd21e7347dd1ea9efe64a700073cc')
-    version('1.8',   '7743960c968760437b6e39093cfe6f67')
-    version('1.7.5', '506de2d870409e9003e1440bcfeb3a65')
-    version('1.7.4', '49c1076428a5d3b5ad7ac65233fcca2f')
-    version('1.6.4', 'b023240be707b34059d2c114d3465c92')
+    version('1.11.1', '558f8c169ae215e25b81421596e8de7572bd3ba824b79add22fba6e284db1117')
+    version('1.11',   'afc1e12f5fe49a471e3aae7d906c73e9d5b1fdd36d52d72652dde8f6250152fb')
+    version('1.10.3', '567b1cc66c9704d1c019c50bef946272e911ec6baf244310f87f4e678be155f2')
+    version('1.10.2', '6264609c6b9cd8ed8e02ca84605d727ce1898d74efa79841660b2e3e985a98bd')
+    version('1.10.1', '589449ff6c3ccbff1d391d4e7ab5bb5d5643a5a41a04c99315e55c16bbf73ddc')
+    version('1.9.5',  'f1c2bb7f32bbd8fa7a19cc1608e0d06582df32ff5f0340967d83fb0017c49fbc')
+    version('1.9.2',  '44105c865a1a810464df79233a05a568')
+    version('1.9.1',  '27bce1ffb05f4f6bd90d90081e5d4169')
+    version('1.9',    'da2d44ea384076efec43ee1f8b7d45d2')
+    version('1.8.3',  '64e9380e07bba907e26a00cf5fcbe77e')
+    version('1.8.1',  '409dd21e7347dd1ea9efe64a700073cc')
+    version('1.8',    '7743960c968760437b6e39093cfe6f67')
+    version('1.7.5',  '506de2d870409e9003e1440bcfeb3a65')
+    version('1.7.4',  '49c1076428a5d3b5ad7ac65233fcca2f')
+    version('1.6.4',  'b023240be707b34059d2c114d3465c92')
 
     provides('golang')
 
@@ -97,15 +82,7 @@ class Go(Package):
         with working_dir('src'):
             bash('{0}.bash'.format('all' if self.run_tests else 'make'))
 
-        try:
-            os.makedirs(prefix)
-        except OSError:
-            pass
-        for f in glob.glob('*'):
-            if os.path.isdir(f):
-                shutil.copytree(f, os.path.join(prefix, f))
-            else:
-                shutil.copy2(f, os.path.join(prefix, f))
+        install_tree('.', prefix)
 
     def setup_environment(self, spack_env, run_env):
         spack_env.set('GOROOT_FINAL', self.spec.prefix)
@@ -119,10 +96,9 @@ class Go(Package):
 
         In most cases, extensions will only need to set GOPATH and use go::
 
-        env = os.environ
         env['GOPATH'] = self.source_path + ':' + env['GOPATH']
         go('get', '<package>', env=env)
-        shutil.copytree('bin', os.path.join(prefix, '/bin'))
+        install_tree('bin', prefix.bin)
         """
         #  Add a go command/compiler for extensions
         module.go = self.spec['go'].command
diff --git a/var/spack/repos/builtin/packages/gobject-introspection/package.py b/var/spack/repos/builtin/packages/gobject-introspection/package.py
index ec71e3cddd..7466458cd7 100644
--- a/var/spack/repos/builtin/packages/gobject-introspection/package.py
+++ b/var/spack/repos/builtin/packages/gobject-introspection/package.py
@@ -1,29 +1,10 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from spack import spack_root
+from spack.paths import spack_root
 
 
 class GobjectIntrospection(Package):
@@ -44,7 +25,7 @@ class GobjectIntrospection(Package):
     depends_on("cairo")
     depends_on("bison", type="build")
     depends_on("flex", type="build")
-    depends_on("pkg-config@0.9.0:", type="build")
+    depends_on("pkgconfig", type="build")
 
     # GobjectIntrospection does not build with sed from darwin:
     depends_on('sed', when='platform=darwin', type='build')
diff --git a/var/spack/repos/builtin/packages/googletest/package.py b/var/spack/repos/builtin/packages/googletest/package.py
index 5eab658bac..95bdff7473 100644
--- a/var/spack/repos/builtin/packages/googletest/package.py
+++ b/var/spack/repos/builtin/packages/googletest/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,6 +18,11 @@ class Googletest(CMakePackage):
     variant('gmock', default=False, description='Build with gmock')
     conflicts('+gmock', when='@:1.7.0')
 
+    variant('pthreads', default=True,
+            description='Build multithreaded version with pthreads')
+    variant('shared', default=True,
+            description='Build shared libraries (DLLs)')
+
     def cmake_args(self):
         spec = self.spec
         if '@1.8.0:' in spec:
@@ -49,6 +35,11 @@ class Googletest(CMakePackage):
         else:
             # Old style (contains only GTest)
             options = []
+
+        options.append('-Dgtest_disable_pthreads={0}'.format(
+            'ON' if '+pthreads' in spec else 'OFF'))
+        options.append('-DBUILD_SHARED_LIBS={0}'.format(
+            'ON' if '+shared' in spec else 'OFF'))
         return options
 
     @when('@:1.7.0')
@@ -61,5 +52,9 @@ class Googletest(CMakePackage):
                          prefix.include)
 
             mkdirp(prefix.lib)
-            install('libgtest.a', prefix.lib)
-            install('libgtest_main.a', prefix.lib)
+            if '+shared' in spec:
+                install('libgtest.{0}'.format(dso_suffix), prefix.lib)
+                install('libgtest_main.{0}'.format(dso_suffix), prefix.lib)
+            else:
+                install('libgtest.a', prefix.lib)
+                install('libgtest_main.a', prefix.lib)
diff --git a/var/spack/repos/builtin/packages/gotcha/package.py b/var/spack/repos/builtin/packages/gotcha/package.py
new file mode 100644
index 0000000000..e1677a4711
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gotcha/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Gotcha(CMakePackage):
+    """C software library for shared library function wrapping,
+    enables tools to intercept calls into shared libraries"""
+
+    homepage = "http://github.com/LLNL/gotcha"
+    git      = "https://github.com/LLNL/gotcha.git"
+
+    version('develop', branch='develop')
+    version('master', branch='master')
+    version('1.0.2', tag='1.0.2')
+    version('0.0.2', tag='0.0.2')
+
+    variant('test', default=False, description='Build tests for Gotcha')
+
+    def configure_args(self):
+        spec = self.spec
+        return [
+            '-DGOTCHA_ENABLE_TESTS=%s' % ('ON' if '+test' in spec else 'OFF')
+        ]
diff --git a/var/spack/repos/builtin/packages/gource/package.py b/var/spack/repos/builtin/packages/gource/package.py
index 3d9ddd1ff6..3d9fe00c80 100644
--- a/var/spack/repos/builtin/packages/gource/package.py
+++ b/var/spack/repos/builtin/packages/gource/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,7 +18,7 @@ class Gource(AutotoolsPackage):
     depends_on('autoconf',   type='build')
     depends_on('libtool',    type='build')
     depends_on('glm',        type='build')
-    depends_on('pkg-config', type='build')
+    depends_on('pkgconfig', type='build')
 
     depends_on('freetype@2.0:')
     depends_on('pcre')
diff --git a/var/spack/repos/builtin/packages/gperf/package.py b/var/spack/repos/builtin/packages/gperf/package.py
index e51f86fb4b..d3c5863c6b 100644
--- a/var/spack/repos/builtin/packages/gperf/package.py
+++ b/var/spack/repos/builtin/packages/gperf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,7 +15,7 @@ class Gperf(AutotoolsPackage):
     single string comparison only."""
 
     homepage = "https://www.gnu.org/software/gperf/"
-    url      = "http://ftp.gnu.org/pub/gnu/gperf/gperf-3.0.4.tar.gz"
+    url      = "https://ftpmirror.gnu.org/gperf/gperf-3.0.4.tar.gz"
 
     version('3.0.4', 'c1f1db32fb6598d6a93e6e88796a8632')
 
diff --git a/var/spack/repos/builtin/packages/gperftools/package.py b/var/spack/repos/builtin/packages/gperftools/package.py
index c5653f696c..df26272a71 100644
--- a/var/spack/repos/builtin/packages/gperftools/package.py
+++ b/var/spack/repos/builtin/packages/gperftools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,12 +12,11 @@ class Gperftools(AutotoolsPackage):
        heap-profiler, and cpu-profiler.
 
     """
-    homepage = "https://code.google.com/p/gperftools"
-    url      = "https://googledrive.com/host/0B6NtGsLhIcf7MWxMMF9JdTN3UVk/gperftools-2.3.tar.gz"
+    homepage = "https://github.com/gperftools/gperftools"
+    url      = "https://github.com/gperftools/gperftools/releases/download/gperftools-2.7/gperftools-2.7.tar.gz"
 
-    version('2.4', '2171cea3bbe053036fb5d5d25176a160',
-            url="https://github.com/gperftools/gperftools/releases/download/gperftools-2.4/gperftools-2.4.tar.gz")
-    version('2.3', 'f54dd119f0e46ac1f13264f8d97adf90',
-            url="https://googledrive.com/host/0B6NtGsLhIcf7MWxMMF9JdTN3UVk/gperftools-2.3.tar.gz")
+    version('2.7', '1ee8c8699a0eff6b6a203e59b43330536b22bbcbe6448f54c7091e5efb0763c9')
+    version('2.4', '982a37226eb42f40714e26b8076815d5ea677a422fb52ff8bfca3704d9c30a2d')
+    version('2.3', '093452ad45d639093c144b4ec732a3417e8ee1f3744f2b0f8d45c996223385ce')
 
-    depends_on("libunwind")
+    depends_on("unwind")
diff --git a/var/spack/repos/builtin/packages/gplates/package.py b/var/spack/repos/builtin/packages/gplates/package.py
new file mode 100644
index 0000000000..6d54c80822
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gplates/package.py
@@ -0,0 +1,58 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Gplates(CMakePackage):
+    """GPlates is desktop software for the interactive visualisation of
+    plate-tectonics. GPlates offers a novel combination of interactive
+    plate-tectonic reconstructions, geographic information system (GIS)
+    functionality and raster data visualisation. GPlates enables both the
+    visualisation and the manipulation of plate-tectonic reconstructions
+    and associated data through geological time."""
+
+    homepage = 'https://www.gplates.org'
+    url      = 'https://sourceforge.net/projects/gplates/files/gplates/2.0/gplates-2.0.0-unixsrc.tar.bz2/download'
+
+    version('2.0.0', '9e95874b35a01f4c9bff5845a1621ad5')
+
+    depends_on('cmake@2.6.2:', type='build')
+    # Qt 5 does not support (at least) the Q_WS_* constants.
+    depends_on('qt+opengl@4.4.0:4.99')
+    depends_on('qwt@6.0.1:')
+    depends_on('mesa-glu')
+    depends_on('glew')
+    # GDAL's OGRSFDriverRegistrar is not compatible anymore starting with 2.0.
+    depends_on('gdal@1.3.2:1.99')
+    depends_on('cgal@3.5:')
+    depends_on('proj@4.6.0:')
+    # Boost's Python library has a different name starting with 1.67.
+    # There were changes to Boost's optional in 1.61 that make the build fail.
+    depends_on('boost+python@1.34:1.60')
+    depends_on('python@2:2.99')
+
+    # Officially, GPlates only supports GCC 4. Moreover, it requires
+    # QtXmlPatterns, which Qt 4 only builds with GCC 4.
+    conflicts('%gcc@5:')
+
+    # When built in parallel, headers are not generated before they are used
+    # (specifically, ViewportWindowUi.h).
+    parallel = False
+
+    def url_for_version(self, version):
+        url = 'https://sourceforge.net/projects/gplates/files/gplates/{0}/gplates-{1}-unixsrc.tar.bz2/download'
+        return url.format(version.up_to(2), version)
+
+    def patch(self):
+        # GPlates overrides FindPythonLibs and finds the static library, which
+        # can not be used easily. Fall back to CMake's version, which finds
+        # the shared library instead.
+        force_remove('cmake/modules/FindPythonLibs.cmake')
+
+        # GPlates only installs its binary for the Release configuration.
+        filter_file('CONFIGURATIONS release',
+                    'CONFIGURATIONS Debug Release RelWithDebInfo MinSizeRel',
+                    'src/CMakeLists.txt')
diff --git a/var/spack/repos/builtin/packages/grackle/package.py b/var/spack/repos/builtin/packages/grackle/package.py
index 06689a3c4c..6163f72bbc 100644
--- a/var/spack/repos/builtin/packages/grackle/package.py
+++ b/var/spack/repos/builtin/packages/grackle/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os.path
-import shutil
 import inspect
 
 from spack import *
@@ -35,12 +15,16 @@ class Grackle(Package):
     generalized and trimmed down version of the chemistry network of the Enzo
     simulation code
     """
-    homepage = 'http://grackle.readthedocs.io/en/grackle-2.2/'
-    url = 'https://bitbucket.org/grackle/grackle/get/grackle-2.0.1.tar.bz2'
+    homepage = 'http://grackle.readthedocs.io/en/grackle-3.1/'
+    url = 'https://bitbucket.org/grackle/grackle/get/grackle-3.1.tar.bz2'
 
+    version('3.1', 'cee7799dc505010e2e875950561bbbe1')
+    version('3.0', 'dc85e664da7e70b65b3ef7164477a959')
     version('2.2', 'ec49ed1db5a42db21f478285150c2ba3')
     version('2.0.1', 'a9624ad13a60c592c1a0a4ea8e1ae86d')
 
+    variant('float', default=False, description='Build with float')
+
     depends_on('libtool', when='@2.2')
 
     depends_on('mpi')
@@ -74,7 +58,7 @@ class Grackle(Package):
             'clib',
             'Make.mach.{0}'.format(grackle_architecture)
         )
-        shutil.copy(template, makefile)
+        copy(template, makefile)
         for key, value in substitutions.items():
             filter_file(key, value, makefile)
 
@@ -83,6 +67,8 @@ class Grackle(Package):
             make('clean')
             make('machine-{0}'.format(grackle_architecture))
             make('opt-high')
+            if spec.satisfies("+float"):
+                make('precision-32')
             make('show-config')
             make()
             mkdirp(prefix.lib)
diff --git a/var/spack/repos/builtin/packages/gradle/package.py b/var/spack/repos/builtin/packages/gradle/package.py
index 1d4112132a..54f288e500 100644
--- a/var/spack/repos/builtin/packages/gradle/package.py
+++ b/var/spack/repos/builtin/packages/gradle/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from distutils.dir_util import copy_tree
 
 
 class Gradle(Package):
@@ -37,6 +17,7 @@ class Gradle(Package):
     homepage = "https://gradle.org"
     url      = "https://services.gradle.org/distributions/gradle-3.4-all.zip"
 
+    version('4.8.1', 'bf87b4c64bb6a43861f1964fb8a7f3bc')
     version('3.4',    '5ae23dbd730dea22eb79cd97a072f06a')
     version('3.3',    '355f61e9c5d092d49577765ab3712dc0')
     version('3.2.1',  'd44dba900ff364103e1f45c0f4b27bbe')
@@ -80,4 +61,4 @@ class Gradle(Package):
     depends_on('java')
 
     def install(self, spec, prefix):
-        copy_tree('.', prefix)
+        install_tree('.', prefix)
diff --git a/var/spack/repos/builtin/packages/grandr/package.py b/var/spack/repos/builtin/packages/grandr/package.py
index 14da4896f4..233b97b9b9 100644
--- a/var/spack/repos/builtin/packages/grandr/package.py
+++ b/var/spack/repos/builtin/packages/grandr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/graph500/package.py b/var/spack/repos/builtin/packages/graph500/package.py
new file mode 100644
index 0000000000..c689cba2ad
--- /dev/null
+++ b/var/spack/repos/builtin/packages/graph500/package.py
@@ -0,0 +1,31 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Graph500(MakefilePackage):
+    """Graph500 reference implementations."""
+
+    homepage = "https://graph500.org"
+    url      = "https://github.com/graph500/graph500/archive/graph500-3.0.0.tar.gz"
+
+    version('3.0.0', 'a2ebb4783b21e2d86387a217776395e3')
+
+    depends_on('mpi@2.0:')
+
+    build_directory = 'src'
+
+    def edit(self, spec, prefix):
+        makefile = FileFilter(join_path(self.build_directory, 'Makefile'))
+        makefile.filter(r'^MPICC\s*=.*', 'MPICC={0}'.format(spec['mpi'].mpicc))
+
+    def install(self, spec, prefix):
+        with working_dir(self.build_directory):
+            mkdir(prefix.bin)
+            install('graph500_reference_bfs', prefix.bin)
+            install('graph500_reference_bfs_sssp', prefix.bin)
+            install('graph500_custom_bfs', prefix.bin)
+            install('graph500_custom_bfs_sssp', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/graphicsmagick/package.py b/var/spack/repos/builtin/packages/graphicsmagick/package.py
new file mode 100644
index 0000000000..295ba9034b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/graphicsmagick/package.py
@@ -0,0 +1,41 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Graphicsmagick(AutotoolsPackage):
+    """GraphicsMagick is the swiss army knife of image processing.
+
+    Provides a robust and efficient collection of tools and libraries which
+    support reading, writing, and manipulating an image in over 88 major
+    formats including important formats like DPX, GIF, JPEG, JPEG-2000, PNG,
+    PDF, PNM, and TIFF.
+    """
+
+    homepage = "http://www.graphicsmagick.org/"
+    url      = "https://sourceforge.net/projects/graphicsmagick/files/graphicsmagick/1.3.29/GraphicsMagick-1.3.29.tar.xz/download"
+
+    version('1.3.29', 'ddde0dd239592db50c5378472355c03c')
+
+    depends_on('bzip2')
+    depends_on('ghostscript')
+    depends_on('ghostscript-fonts')
+    depends_on('graphviz')
+    depends_on('jasper')
+    depends_on('jpeg')
+    depends_on('lcms')
+    depends_on('libice')
+    depends_on('libpng')
+    depends_on('libsm')
+    depends_on('libtiff')
+    depends_on('libtool')
+    depends_on('libxml2')
+    depends_on('xz')
+    depends_on('zlib')
+
+    def configure_args(self):
+        args = ['--enable-shared']
+        return args
diff --git a/var/spack/repos/builtin/packages/graphlib/package.py b/var/spack/repos/builtin/packages/graphlib/package.py
index 0fa82267d8..d5b50acfe1 100644
--- a/var/spack/repos/builtin/packages/graphlib/package.py
+++ b/var/spack/repos/builtin/packages/graphlib/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/graphmap/package.py b/var/spack/repos/builtin/packages/graphmap/package.py
index 0e4a676588..25af904306 100644
--- a/var/spack/repos/builtin/packages/graphmap/package.py
+++ b/var/spack/repos/builtin/packages/graphmap/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,9 @@ class Graphmap(MakefilePackage):
     """A highly sensitive and accurate mapper for long, error-prone reads"""
 
     homepage = "https://github.com/isovic/graphmap"
-    url      = "https://github.com/isovic/graphmap/archive/v0.3.0.tar.gz"
+    git      = "https://github.com/isovic/graphmap.git"
 
-    version('0.3.0', git='https://github.com/isovic/graphmap.git', commit='eb8c75d68b03be95464318afa69b645a59f8f6b7')
+    version('0.3.0', commit='eb8c75d68b03be95464318afa69b645a59f8f6b7')
 
     def edit(self, spec, prefix):
         mkdirp(prefix.bin)
diff --git a/var/spack/repos/builtin/packages/graphviz/package.py b/var/spack/repos/builtin/packages/graphviz/package.py
index 0ec35f09e8..efb32328fa 100644
--- a/var/spack/repos/builtin/packages/graphviz/package.py
+++ b/var/spack/repos/builtin/packages/graphviz/package.py
@@ -1,38 +1,21 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
+import os
 import sys
-import shutil
 
 
 class Graphviz(AutotoolsPackage):
     """Graph Visualization Software"""
+
     homepage = 'http://www.graphviz.org'
-    url      = 'http://www.graphviz.org/pub/graphviz/stable/SOURCES/graphviz-2.38.0.tar.gz'
+    git      = 'https://gitlab.com/graphviz/graphviz.git'
 
-    version('2.38.0', '5b6a829b2ac94efcd5fa3c223ed6d3ae')
+    # This commit hash is tag='stable_release_2.40.1'
+    version('2.40.1', commit='67cd2e5121379a38e0801cc05cce5033f8a2a609')
 
     # We try to leave language bindings enabled if they don't cause
     # build issues or add dependencies.
@@ -78,9 +61,16 @@ class Graphviz(AutotoolsPackage):
             description='Build with pango+cairo support (more output formats)')
     variant('libgd', default=False,
             description='Build with libgd support (more output formats)')
-
     variant('gts', default=False,
             description='Build with GNU Triangulated Surface Library')
+    variant('expat', default=False,
+            description='Build with Expat support (enables HTML-like labels)')
+    variant('ghostscript', default=False,
+            description='Build with Ghostscript support')
+    variant('qt', default=False,
+            description='Build with Qt support')
+    variant('gtkplus', default=False,
+            description='Build with GTK+ support')
 
     parallel = False
 
@@ -96,28 +86,51 @@ class Graphviz(AutotoolsPackage):
         '+python', '+r', '+ruby', '+tcl')
 
     for b in tested_bindings + untested_bindings:
-        depends_on('swig', when=b)
+        depends_on('swig', type='build', when=b)
 
+    depends_on('java', when='+java')
+    depends_on('python@2:2.8', when='+python')
+
+    # +pangocairo
     depends_on('cairo', when='+pangocairo')
     depends_on('pango', when='+pangocairo')
+    depends_on('freetype', when='+pangocairo')
+    depends_on('glib', when='+pangocairo')
+    depends_on('fontconfig', when='+pangocairo')
+    depends_on('libpng', when='+pangocairo')
+    depends_on('zlib', when='+pangocairo')
+    # +libgd
     depends_on('libgd', when='+libgd')
+    depends_on('fontconfig', when='+libgd')
+    depends_on('freetype', when='+libgd')
+    # +gts
     depends_on('gts', when='+gts')
-    depends_on('ghostscript')
-    depends_on('freetype')
-    depends_on('expat')
-    depends_on('libtool')
-    depends_on('pkg-config', type='build')
-
-    depends_on('java', when='+java')
-    depends_on('python@2:2.8', when='+python')
-
-    def patch(self):
-        # Fix a few variable names, gs after 9.18 renamed them
-        # See http://lists.linuxfromscratch.org/pipermail/blfs-book/2015-October/056960.html
-        if self.spec.satisfies('^ghostscript@9.18:'):
-            kwargs = {'ignore_absent': False, 'backup': True, 'string': True}
-            filter_file(' e_', ' gs_error_', 'plugin/gs/gvloadimage_gs.c',
-                        **kwargs)
+    # +expat
+    depends_on('expat', when='+expat')
+    # +ghostscript
+    depends_on('ghostscript', when='+ghostscript')
+    # +qt
+    depends_on('qt', when='+qt')
+    # +gtkplus
+    depends_on('gtkplus', when='+gtkplus')
+
+    # Build dependencies
+    depends_on('pkgconfig', type='build')
+    # The following are needed when building from git
+    depends_on('automake', type='build')
+    depends_on('autoconf', type='build')
+    depends_on('bison', type='build')
+    depends_on('flex', type='build')
+    depends_on('libtool', type='build')
+
+    def autoreconf(self, spec, prefix):
+        # We need to generate 'configure' when checking out sources from git
+        # If configure exists nothing needs to be done
+        if os.path.exists(self.configure_abs_path):
+            return
+        # Else bootstrap (disabling auto-configure with NOCONFIG)
+        bash = which('bash')
+        bash('./autogen.sh', 'NOCONFIG')
 
     def configure_args(self):
         spec = self.spec
@@ -150,11 +163,17 @@ class Graphviz(AutotoolsPackage):
         else:
             options.append('--enable-swig=no')
 
-        for var in ('+pangocairo', '+libgd', '+gts'):
+        for var in ('+pangocairo', '+libgd', '+gts', '+expat', '+ghostscript',
+                    '+qt', '+gtkplus'):
+            feature = var[1:]
+            if feature == 'gtkplus':
+                # In spack terms, 'gtk+' is 'gtkplus' while
+                # the relative configure option is 'gtk'
+                feature = 'gtk'
             if var in spec:
-                options.append('--with-{0}'.format(var[1:]))
+                options.append('--with-{0}'.format(feature))
             else:
-                options.append('--without-{0}'.format(var[1:]))
+                options.append('--without-{0}'.format(feature))
 
         # On OSX fix the compiler error:
         # In file included from tkStubLib.c:15:
@@ -163,7 +182,4 @@ class Graphviz(AutotoolsPackage):
         if sys.platform == 'darwin':
             options.append('CFLAGS=-I/opt/X11/include')
 
-        # A hack to patch config.guess in the libltdl sub directory
-        shutil.copyfile('./config/config.guess', 'libltdl/config/config.guess')
-
         return options
diff --git a/var/spack/repos/builtin/packages/grass/package.py b/var/spack/repos/builtin/packages/grass/package.py
new file mode 100644
index 0000000000..a703c09327
--- /dev/null
+++ b/var/spack/repos/builtin/packages/grass/package.py
@@ -0,0 +1,185 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Grass(AutotoolsPackage):
+    """GRASS GIS (Geographic Resources Analysis Support System), is a free
+       and open source Geographic Information System (GIS) software suite
+       used for geospatial data management and analysis, image processing,
+       graphics and maps production, spatial modeling, and visualization."""
+
+    homepage = "http://grass.osgeo.org"
+    url      = "https://grass.osgeo.org/grass74/source/grass-7.4.1.tar.gz"
+
+    version('7.4.1',    'bf7add62cbeb05a3ed5ad832344ba524')
+
+    variant('cxx',       default=True,  description='Add c++ functionality')
+    variant('tiff',      default=True,  description='Add TIFF functionality')
+    variant('png',       default=True,  description='Add PNG functionality')
+    variant('postgres',  default=False, description='Add PostgreSQL functionality')
+    variant('mysql',     default=False, description='Add MySQL functionality')
+    variant('sqlite',    default=True,  description='Add SQLite functionality')
+    variant('opengl',    default=True,  description='Add OpenGL functionality')
+    variant('fftw',      default=True,  description='Add FFTW functionality')
+    variant('blas',      default=False, description='Add BLAS functionality')
+    variant('lapack',    default=False, description='Add LAPACK functionality')
+    variant('cairo',     default=True,  description='Add Cairo functionality')
+    variant('freetype',  default=True,  description='Add FreeType functionality')
+    variant('readline',  default=False, description='Add Readline functionality')
+    variant('regex',     default=True,  description='Add regex functionality')
+    variant('pthread',   default=False, description='Add POSIX threads functionality')
+    variant('openmp',    default=False, description='Add OpenMP functionality')
+    variant('opencl',    default=False, description='Add OpenCL functionality')
+    variant('bzlib',     default=False, description='Add BZIP2 functionality')
+    variant('netcdf',    default=False, description='Enable NetCDF support')
+    variant('geos',      default=False, description='Geometry Engine for v.buffer')
+
+    # required components
+    depends_on('gmake@3.8.1:', type='build')
+    depends_on('zlib')
+    depends_on('flex', type='build')
+    depends_on('bison', type='build')
+    depends_on('proj')
+    depends_on('gdal')
+    depends_on('python@2.7:2.9', type=('build', 'run'))
+    depends_on('libx11')
+
+    # optional pieces
+    depends_on('libtiff', when='+tiff')
+    depends_on('libpng', when='+png')
+    depends_on('postgresql', when='+postgres')
+    depends_on('mariadb', when='+mysql')
+    depends_on('sqlite', when='+sqlite')
+    depends_on('gl', when='+opengl')
+    depends_on('fftw', when='+fftw')
+    depends_on('blas', when='+blas')
+    depends_on('lapack', when='+lapack')
+    depends_on('cairo', when='+cairo')
+    depends_on('freetype', when='+freetype')
+    depends_on('readline', when='+readline')
+    depends_on('opencl', when='+opencl')
+    depends_on('bzip2', when='+bzlib')
+    depends_on('netcdf', when='+netcdf')
+    depends_on('geos', when='+geos')
+
+    def configure_args(self):
+        spec = self.spec
+
+        args = [
+            '--without-odbc',
+            '--without-nls',
+            '--without-opendwg',
+            '--with-x',
+            '--with-gdal={0}/bin/gdal-config'.format(
+                spec['gdal'].prefix),
+            '--with-proj-share={0}/share/proj'.format(
+                spec['proj'].prefix),
+        ]
+
+        if '+cxx' in spec:
+            args.append('--with-cxx')
+        else:
+            args.append('--without-cxx')
+
+        if '+tiff' in spec:
+            args.append('--with-tiff')
+        else:
+            args.append('--without-tiff')
+
+        if '+png' in spec:
+            args.append('--with-png')
+        else:
+            args.append('--without-png')
+
+        if '+postgres' in spec:
+            args.append('--with-postgres')
+        else:
+            args.append('--without-postgres')
+
+        if '+mysql' in spec:
+            args.append('--with-mysql')
+        else:
+            args.append('--without-mysql')
+
+        if '+sqlite' in spec:
+            args.append('--with-sqlite')
+        else:
+            args.append('--without-sqlite')
+
+        if '+opengl' in spec:
+            args.append('--with-opengl')
+        else:
+            args.append('--without-opengl')
+
+        if '+fftw' in spec:
+            args.append('--with-fftw')
+        else:
+            args.append('--without-fftw')
+
+        if '+blas' in spec:
+            args.append('--with-blas')
+        else:
+            args.append('--without-blas')
+
+        if '+lapack' in spec:
+            args.append('--with-lapack')
+        else:
+            args.append('--without-lapack')
+
+        if '+cairo' in spec:
+            args.append('--with-cairo')
+        else:
+            args.append('--without-cairo')
+
+        if '+freetype' in spec:
+            args.append('--with-freetype')
+        else:
+            args.append('--without-freetype')
+
+        if '+readline' in spec:
+            args.append('--with-readline')
+        else:
+            args.append('--without-readline')
+
+        if '+regex' in spec:
+            args.append('--with-regex')
+        else:
+            args.append('--without-regex')
+
+        if '+pthread' in spec:
+            args.append('--with-pthread')
+        else:
+            args.append('--without-pthread')
+
+        if '+openmp' in spec:
+            args.append('--with-openmp')
+        else:
+            args.append('--without-openmp')
+
+        if '+opencl' in spec:
+            args.append('--with-opencl')
+        else:
+            args.append('--without-opencl')
+
+        if '+bzlib' in spec:
+            args.append('--with-bzlib')
+        else:
+            args.append('--without-bzlib')
+
+        if '+netcdf' in spec:
+            args.append('--with-netcdf={0}/bin/nc-config'.format(
+                spec['netcdf'].prefix))
+        else:
+            args.append('--without-netcdf')
+
+        if '+geos' in spec:
+            args.append('--with-geos={0}/bin/geos-config'.format(
+                spec['geos'].prefix))
+        else:
+            args.append('--without-geos')
+
+        return args
diff --git a/var/spack/repos/builtin/packages/grib-api/cmake_install_rpath.patch b/var/spack/repos/builtin/packages/grib-api/cmake_install_rpath.patch
new file mode 100644
index 0000000000..7e2b250883
--- /dev/null
+++ b/var/spack/repos/builtin/packages/grib-api/cmake_install_rpath.patch
@@ -0,0 +1,11 @@
+--- a/cmake/ecbuild_append_to_rpath.cmake
++++ b/cmake/ecbuild_append_to_rpath.cmake
+@@ -31,7 +31,7 @@ function( _path_append var path )
+ 	else()
+ 		list( FIND ${var} ${path} _found )
+ 		if( _found EQUAL "-1" )
+-			set( ${var} "${${var}}:${path}" PARENT_SCOPE )
++			set( ${var} "${${var}};${path}" PARENT_SCOPE )
+ 		endif()
+ 	endif()
+ endfunction()
diff --git a/var/spack/repos/builtin/packages/grib-api/disable_numpy.patch b/var/spack/repos/builtin/packages/grib-api/disable_numpy.patch
new file mode 100644
index 0000000000..c056388da8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/grib-api/disable_numpy.patch
@@ -0,0 +1,12 @@
+--- a/python/CMakeLists.txt
++++ b/python/CMakeLists.txt
+@@ -6,7 +6,8 @@ if( HAVE_PYTHON )
+     #endif()
+ 
+     # check for Numpy
+-    find_package( NumPy )
++    # find_package( NumPy )
++    set(NUMPY_FOUND FALSE)
+ 
+     ###############################################################################
+     # swig python interface
diff --git a/var/spack/repos/builtin/packages/grib-api/enable_only_jasper.patch b/var/spack/repos/builtin/packages/grib-api/enable_only_jasper.patch
new file mode 100644
index 0000000000..06e9790f59
--- /dev/null
+++ b/var/spack/repos/builtin/packages/grib-api/enable_only_jasper.patch
@@ -0,0 +1,34 @@
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -106,18 +106,7 @@ set( HAVE_LIBOPENJPEG 0 )
+ 
+ if( ENABLE_JPG )
+ 
+-    # Note: This is a deprecated feature but we need it to find Jasper at ECMWF.
+-    #       ecbuild_add_extra_search_paths modifies CMAKE_PREFIX_PATH
+-    #       which can affect future package discovery if not undone by the caller.
+-    #       The current CMAKE_PREFIX_PATH is backed up as _CMAKE_PREFIX_PATH
+-    #
+-    set(CMAKE_WARN_DEPRECATED OFF) # Suppress deprecation message
+-    ecbuild_add_extra_search_paths( jasper )
+     find_package( Jasper )
+-    set(CMAKE_PREFIX_PATH ${_CMAKE_PREFIX_PATH})    # Restore CMAKE_PREFIX_PATH
+-    set(CMAKE_WARN_DEPRECATED ON)  # Remove suppression
+-
+-    find_package( OpenJPEG )
+ 
+     if( JASPER_FOUND )
+         list( APPEND GRIB_API_TPLS Jasper )
+@@ -125,12 +114,6 @@ if( ENABLE_JPG )
+         set( HAVE_LIBJASPER 1 )
+     endif()
+ 
+-    if( OPENJPEG_FOUND )
+-        list( APPEND GRIB_API_TPLS OpenJPEG )
+-        set( HAVE_JPEG 1 )
+-        set( HAVE_LIBOPENJPEG 1 )
+-    endif()
+-
+ endif()
+ 
+ 
diff --git a/var/spack/repos/builtin/packages/grib-api/enable_only_openjpeg.patch b/var/spack/repos/builtin/packages/grib-api/enable_only_openjpeg.patch
new file mode 100644
index 0000000000..a440477029
--- /dev/null
+++ b/var/spack/repos/builtin/packages/grib-api/enable_only_openjpeg.patch
@@ -0,0 +1,28 @@
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -106,25 +106,8 @@ set( HAVE_LIBOPENJPEG 0 )
+ 
+ if( ENABLE_JPG )
+ 
+-    # Note: This is a deprecated feature but we need it to find Jasper at ECMWF.
+-    #       ecbuild_add_extra_search_paths modifies CMAKE_PREFIX_PATH
+-    #       which can affect future package discovery if not undone by the caller.
+-    #       The current CMAKE_PREFIX_PATH is backed up as _CMAKE_PREFIX_PATH
+-    #
+-    set(CMAKE_WARN_DEPRECATED OFF) # Suppress deprecation message
+-    ecbuild_add_extra_search_paths( jasper )
+-    find_package( Jasper )
+-    set(CMAKE_PREFIX_PATH ${_CMAKE_PREFIX_PATH})    # Restore CMAKE_PREFIX_PATH
+-    set(CMAKE_WARN_DEPRECATED ON)  # Remove suppression
+-
+     find_package( OpenJPEG )
+ 
+-    if( JASPER_FOUND )
+-        list( APPEND GRIB_API_TPLS Jasper )
+-        set( HAVE_JPEG 1 )
+-        set( HAVE_LIBJASPER 1 )
+-    endif()
+-
+     if( OPENJPEG_FOUND )
+         list( APPEND GRIB_API_TPLS OpenJPEG )
+         set( HAVE_JPEG 1 )
diff --git a/var/spack/repos/builtin/packages/grib-api/package.py b/var/spack/repos/builtin/packages/grib-api/package.py
index 5da851c1ba..dd782a97d1 100644
--- a/var/spack/repos/builtin/packages/grib-api/package.py
+++ b/var/spack/repos/builtin/packages/grib-api/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,51 +11,122 @@ class GribApi(CMakePackage):
        C, FORTRAN and Python programs developed for encoding and decoding WMO
        FM-92 GRIB edition 1 and edition 2 messages."""
 
-    homepage = "https://software.ecmwf.int/wiki/display/GRIB/Home"
-    url      = "https://software.ecmwf.int/wiki/download/attachments/3473437/grib_api-1.17.0-Source.tar.gz"
+    homepage = 'https://software.ecmwf.int/wiki/display/GRIB/Home'
+    url = 'https://software.ecmwf.int/wiki/download/attachments/3473437/grib_api-1.17.0-Source.tar.gz?api=v2'
+    list_url = 'https://software.ecmwf.int/wiki/display/GRIB/Releases'
+
+    maintainers = ['skosukhin']
 
+    version('1.24.0', 'dcc549069cdeeaa1959732c36ab3136f')
     version('1.21.0', 'eb64c5eb72e6e90841237cba9d644016')
     version('1.17.0', 'bca7114d2c3100501a08190a146818d2')
     version('1.16.0', '8c7fdee03344e4379d400ae20976a460')
 
-    variant('netcdf', default=False, description='Enable netcdf encoding/decoding using netcdf library')
-    variant('jpeg', default=True, description='Enable jpeg 2000 for grib 2 decoding/encoding')
-    variant('png', default=False, description='Enable png for decoding/encoding')
+    variant('netcdf', default=False,
+            description='Enable netcdf encoding/decoding using netcdf library')
+    variant('jp2k', default='openjpeg', values=('openjpeg', 'jasper', 'none'),
+            description='Specify JPEG2000 decoding/encoding backend')
+    variant('png', default=False,
+            description='Enable png for decoding/encoding')
+    variant('aec', default=False,
+            description='Enable Adaptive Entropy Coding for decoding/encoding')
+    variant('pthreads', default=False,
+            description='Enable POSIX threads')
+    variant('openmp', default=False,
+            description='Enable OpenMP threads')
+    variant('python', default=False,
+            description='Enable the Python interface')
+    variant('numpy', default=False,
+            description='Enable numpy support in the Python interface')
+    variant('fortran', default=False, description='Enable the Fortran support')
+    variant('examples', default=True,
+            description='Build the examples (part of the full test suite)')
+    variant('test', default=True, description='Enable the tests')
     variant('build_type', default='RelWithDebInfo',
             description='The build type to build',
             values=('Debug', 'Release', 'RelWithDebInfo', 'Production'))
 
-    depends_on('libpng', when='+png')
+    # The building script tries to find an optional package valgrind when
+    # tests are enabled but the testing scripts don't use it.
+    # depends_on('valgrind', type='test', when='+test')
+
     depends_on('netcdf', when='+netcdf')
-    depends_on('jasper', when='+jpeg')
-    depends_on('cmake@2.8.11:', type='build')
+    depends_on('openjpeg@1.5.0:1.5.999', when='jp2k=openjpeg')
+    depends_on('jasper', when='jp2k=jasper')
+    depends_on('libpng', when='+png')
+    depends_on('libaec', when='+aec')
+    depends_on('python@2.5:2.999', when='+python',
+               type=('build', 'link', 'run'))
+    depends_on('py-numpy', when='+python+numpy', type=('build', 'run'))
+    extends('python', when='+python')
 
-    def cmake_args(self):
-        spec = self.spec
-        args = ['-DBUILD_SHARED_LIBS=BOTH']
+    conflicts('+openmp', when='+pthreads',
+              msg='Cannot enable both POSIX threads and OMP')
+    conflicts('+numpy', when='~python',
+              msg='Numpy variant is valid only when the Python interface is '
+                  'enabled')
+
+    # The following enforces linking against the specified JPEG2000 backend.
+    patch('enable_only_openjpeg.patch', when='jp2k=openjpeg')
+    patch('enable_only_jasper.patch', when='jp2k=jasper')
+
+    # Disable NumPy even if it's available.
+    patch('disable_numpy.patch', when='+python~numpy')
 
-        # We will add python support later.
-        args.append('-DENABLE_PYTHON=OFF')
+    # CMAKE_INSTALL_RPATH must be a semicolon-separated list.
+    patch('cmake_install_rpath.patch')
 
-        # Disable FORTRAN interface if we don't have it.
-        if (self.compiler.f77 is None) or (self.compiler.fc is None):
-            args.append('-DENABLE_FORTRAN=OFF')
+    @run_before('cmake')
+    def check_fortran(self):
+        if '+fortran' in self.spec and self.compiler.fc is None:
+            raise InstallError(
+                'Fortran interface requires a Fortran compiler!')
 
-        if '+netcdf' in spec:
-            args.append('-DENABLE_NETCDF=ON')
-            args.append('-DNETCDF_PATH=%s' % spec['netcdf'].prefix)
+    def cmake_args(self):
+        var_opt_list = [('+pthreads', 'GRIB_THREADS'),
+                        ('+openmp', 'GRIB_OMP_THREADS'),
+                        ('+python', 'PYTHON'),
+                        ('+fortran', 'FORTRAN'),
+                        ('+examples', 'EXAMPLES'),
+                        ('+test', 'TESTS')]
+
+        args = ['-DENABLE_%s=%s' % (opt, 'ON' if var in self.spec else 'OFF')
+                for var, opt in var_opt_list]
+
+        if '+netcdf' in self.spec:
+            args.extend(['-DENABLE_NETCDF=ON',
+                         # Prevent overriding by environment variable
+                         # HDF5_ROOT.
+                         '-DHDF5_ROOT=' + self.spec['hdf5'].prefix,
+                         # Prevent possible overriding by environment variables
+                         # NETCDF_ROOT, NETCDF_DIR, and NETCDF_PATH.
+                         '-DNETCDF_PATH=' + self.spec['netcdf'].prefix])
         else:
             args.append('-DENABLE_NETCDF=OFF')
 
-        if '+jpeg' in spec:
-            args.append('-DENABLE_JPG=ON')
-            args.append('-DJASPER_PATH=%s' % spec['jasper'].prefix)
-        else:
+        if self.spec.variants['jp2k'].value == 'none':
             args.append('-DENABLE_JPG=OFF')
+        else:
+            args.append('-DENABLE_JPG=ON')
+
+        if self.spec.variants['jp2k'].value == 'openjpeg':
+            args.append('-DOPENJPEG_PATH=' + self.spec['openjpeg'].prefix)
 
-        if '+png' in spec:
-            args.append('-DENABLE_PNG=ON')
+        if '+png' in self.spec:
+            args.extend(['-DENABLE_PNG=ON',
+                         '-DZLIB_ROOT=' + self.spec['zlib'].prefix])
         else:
             args.append('-DENABLE_PNG=OFF')
 
+        if '+aec' in self.spec:
+            args.extend(['-DENABLE_AEC=ON',
+                         # Prevent overriding by environment variables
+                         # AEC_DIR and AEC_PATH.
+                         '-DAEC_DIR=' + self.spec['libaec'].prefix])
+        else:
+            args.append('-DENABLE_AEC=OFF')
+
+        if '^python' in self.spec:
+            args.append('-DPYTHON_EXECUTABLE:FILEPATH=' + python.path)
+
         return args
diff --git a/var/spack/repos/builtin/packages/grnboost/package.py b/var/spack/repos/builtin/packages/grnboost/package.py
new file mode 100644
index 0000000000..e2e8fcaae0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/grnboost/package.py
@@ -0,0 +1,42 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Grnboost(Package):
+    """GRNBoost is a library built on top of Apache Spark that implements a
+    scalable strategy for gene regulatory network (GRN) inference.
+
+    See https://github.com/aertslab/GRNBoost/blob/master/docs/user_guide.md
+    for the user guide. The location of xgboost4j-<version>.jar and
+    GRNBoost.jar are set to $XGBOOST_JAR and $GRNBOOST_JAR. Path to
+    xgboost4j-<version>.jar is also added to CLASSPATH."""
+
+    homepage = "https://github.com/aertslab/GRNBoost"
+
+    version('2017-10-9', git='https://github.com/aertslab/GRNBoost.git',
+            commit='26c836b3dcbb85852d3c6f4b8340e8655434da02')
+
+    depends_on('sbt', type='build')
+    depends_on('java', type=('build', 'run'))
+    depends_on('xgboost+jvm-packages', type='run')
+    depends_on('spark+hadoop', type='run')
+
+    def setup_environment(self, spack_env, run_env):
+        grnboost_jar = join_path(self.prefix, 'target',
+                                 'scala-2.11', 'GRNBoost.jar')
+        xgboost_version = self.spec['xgboost'].version.string
+        xgboost_jar = join_path(self.spec['xgboost'].prefix,
+                                'xgboost4j-' + xgboost_version + '.jar')
+        run_env.set('GRNBOOST_JAR', grnboost_jar)
+        run_env.set('JAVA_HOME', self.spec['java'].prefix)
+        run_env.set('CLASSPATH', xgboost_jar)
+        run_env.set('XGBOOST_JAR', xgboost_jar)
+
+    def install(self, spec, prefix):
+        sbt = which('sbt')
+        sbt('assembly')
+        install_tree('target', prefix.target)
diff --git a/var/spack/repos/builtin/packages/groff/package.py b/var/spack/repos/builtin/packages/groff/package.py
index bc10c102be..d8854c71c6 100644
--- a/var/spack/repos/builtin/packages/groff/package.py
+++ b/var/spack/repos/builtin/packages/groff/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,7 +13,7 @@ class Groff(AutotoolsPackage):
     ASCII/UTF8 for display at the terminal."""
 
     homepage = "https://www.gnu.org/software/groff/"
-    url      = "http://ftp.gnu.org/gnu/groff/groff-1.22.3.tar.gz"
+    url      = "https://ftpmirror.gnu.org/groff/groff-1.22.3.tar.gz"
 
     # TODO: add html variant, spack doesn't have netpbm and its too
     # complicated for me to find out at this point in time.
diff --git a/var/spack/repos/builtin/packages/gromacs/package.py b/var/spack/repos/builtin/packages/gromacs/package.py
index 22f0527439..f51aa9d7d7 100644
--- a/var/spack/repos/builtin/packages/gromacs/package.py
+++ b/var/spack/repos/builtin/packages/gromacs/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,13 +20,19 @@ class Gromacs(CMakePackage):
     """
 
     homepage = 'http://www.gromacs.org'
-    url = 'http://ftp.gromacs.org/gromacs/gromacs-5.1.2.tar.gz'
+    url      = 'http://ftp.gromacs.org/gromacs/gromacs-5.1.2.tar.gz'
+    git      = 'https://github.com/gromacs/gromacs.git'
 
+    version('develop', branch='master')
+    version('2018.2', '7087462bb08393aec4ce3192fa4cd8df')
+    version('2018.1', '7ee393fa3c6b7ae351d47eae2adf980e')
+    version('2018',   '6467ffb1575b8271548a13abfba6374c')
+    version('2016.5', 'f41807e5b2911ccb547a3fd11f105d47')
     version('2016.4', '19c8b5c85f3ec62df79d2249a3c272f8')
     version('2016.3', 'e9e3a41bd123b52fbcc6b32d09f8202b')
-    version('5.1.4', 'ba2e34d59b3982603b4935d650c08040')
-    version('5.1.2', '614d0be372f1a6f1f36382b7a6fcab98')
-    version('develop', git='https://github.com/gromacs/gromacs', branch='master')
+    version('5.1.5',  '831fe741bcd9f1612155dffc919885f2')
+    version('5.1.4',  'ba2e34d59b3982603b4935d650c08040')
+    version('5.1.2',  '614d0be372f1a6f1f36382b7a6fcab98')
 
     variant('mpi', default=True, description='Activate MPI support')
     variant('shared', default=True,
@@ -64,7 +51,8 @@ class Gromacs(CMakePackage):
     depends_on('plumed+mpi', when='+plumed+mpi')
     depends_on('plumed~mpi', when='+plumed~mpi')
     depends_on('fftw')
-    depends_on('cmake@2.8.8:', type='build')
+    depends_on('cmake@2.8.8:3.9.99', type='build')
+    depends_on('cmake@3.4.3:3.9.99', type='build', when='@2018:')
     depends_on('cuda', when='+cuda')
 
     def patch(self):
diff --git a/var/spack/repos/builtin/packages/gsl/package.py b/var/spack/repos/builtin/packages/gsl/package.py
index 27be6b0d35..691c02b7e9 100644
--- a/var/spack/repos/builtin/packages/gsl/package.py
+++ b/var/spack/repos/builtin/packages/gsl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -34,8 +15,9 @@ class Gsl(AutotoolsPackage):
     over 1000 functions in total with an extensive test suite."""
 
     homepage = "http://www.gnu.org/software/gsl"
-    url      = "http://mirror.switch.ch/ftp/mirror/gnu/gsl/gsl-2.3.tar.gz"
+    url      = "https://ftpmirror.gnu.org/gsl/gsl-2.3.tar.gz"
 
+    version('2.5', sha256='0460ad7c2542caaddc6729762952d345374784100223995eb14d614861f2258d')
     version('2.4',   'dba736f15404807834dc1c7b93e83b92')
     version('2.3',   '905fcbbb97bc552d1037e34d200931a0')
     version('2.2.1', '3d90650b7cfe0a6f4b29c2d7b0f86458')
diff --git a/var/spack/repos/builtin/packages/gslib/package.py b/var/spack/repos/builtin/packages/gslib/package.py
new file mode 100644
index 0000000000..f11ed17a56
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gslib/package.py
@@ -0,0 +1,70 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Gslib(Package):
+    """Highly scalable Gather-scatter code with AMG and XXT solvers"""
+
+    homepage = "https://github.com/gslib/gslib"
+    git      = "https://github.com/gslib/gslib.git"
+
+    version('1.0.2', tag='v1.0.2')
+    version('1.0.1', tag='v1.0.1')
+    version('1.0.0', tag='v1.0.0')
+
+    variant('mpi', default=True, description='Build with MPI')
+    variant('mpiio', default=True, description='Build with MPI I/O')
+    variant('blas', default=False, description='Build with BLAS')
+
+    depends_on('mpi', when="+mpi")
+    depends_on('mpi', when="+mpiio")
+    depends_on('blas', when="+blas")
+
+    conflicts('~mpi', when='+mpiio')
+
+    def install(self, spec, prefix):
+        src_dir = 'src'
+        lib_dir = 'lib'
+        libname = 'libgs.a'
+
+        if self.version == Version('1.0.1'):
+            makefile = 'Makefile'
+        else:
+            makefile = 'src/Makefile'
+
+        cc  = self.compiler.cc
+
+        if '+mpiio' not in spec:
+            filter_file(r'MPIIO.*?=.*1', 'MPIIO = 0', makefile)
+
+        if '+mpi' in spec:
+            cc  = spec['mpi'].mpicc
+        else:
+            filter_file(r'MPI.*?=.*1', 'MPI = 0', makefile)
+            filter_file(r'MPIIO.*?=.*1', 'MPIIO = 0', makefile)
+
+        make_cmd = "CC=" + cc
+
+        if '+blas' in spec:
+            filter_file(r'BLAS.*?=.*0', 'BLAS = 1', makefile)
+            blas = spec['blas'].libs
+            ld_flags = blas.ld_flags
+            filter_file(r'\$\(LDFLAGS\)', ld_flags, makefile)
+
+        if self.version == Version('1.0.1'):
+            make(make_cmd)
+            make('install')
+            install_tree(lib_dir, prefix.lib)
+        elif self.version == Version('1.0.0'):
+            with working_dir(src_dir):
+                make(make_cmd)
+                mkdir(prefix.lib)
+                install(libname, prefix.lib)
+
+        # Should only install the headers (this will be fixed in gslib on
+        # future releases).
+        install_tree(src_dir, prefix.include)
diff --git a/var/spack/repos/builtin/packages/gtkmm/package.py b/var/spack/repos/builtin/packages/gtkmm/package.py
new file mode 100644
index 0000000000..911d1e7ebf
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gtkmm/package.py
@@ -0,0 +1,34 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Gtkmm(AutotoolsPackage):
+    """Gtkmm is the official C++ interface for the popular GUI library GTK+."""
+
+    homepage = "https://www.gtkmm.org/en/"
+    url      = "https://ftp.acc.umu.se/pub/GNOME/sources/gtkmm/2.16/gtkmm-2.16.0.tar.gz"
+
+    version('2.19.7', '2afc018e5b15cde293cd2d21db9b6a55')
+    version('2.19.6', 'fb140e82e583620defe0d70bfe7eefd7')
+    version('2.19.4', '60006a23306487938dfe0e4b17e3fa46')
+    version('2.19.2', 'dc208575a24e8d5265af2fd59c08f3d8')
+    version('2.17.11', '2326ff83439aac83721ed4694acf14e5')
+    version('2.17.1', '19358644e5e620ad738658be2cb6d739')
+    version('2.16.0', 'de178c2a6f23eda0b6a8bfb0219e2e1c')
+    version('2.4.11', 'a339958bc4ab7f74201b312bd3562d46')
+
+    depends_on('glibmm')
+    depends_on('atk')
+    depends_on('gtkplus')
+    depends_on('pangomm')
+    depends_on('cairomm')
+
+    def url_for_version(self, version):
+        """Handle glib's version-based custom URLs."""
+        url = "https://ftp.acc.umu.se/pub/GNOME/sources/gtkmm"
+        ext = '.tar.gz' if version < Version('3.1.0') else '.tar.xz'
+        return url + "/%s/gtkmm-%s%s" % (version.up_to(2), version, ext)
diff --git a/var/spack/repos/builtin/packages/gtkorvo-atl/package.py b/var/spack/repos/builtin/packages/gtkorvo-atl/package.py
index 72bcf12c1d..1dad459cb3 100644
--- a/var/spack/repos/builtin/packages/gtkorvo-atl/package.py
+++ b/var/spack/repos/builtin/packages/gtkorvo-atl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,14 +12,25 @@ class GtkorvoAtl(CMakePackage):
     """
 
     homepage = "https://github.com/GTkorvo/atl"
-    url = "https://github.com/GTkorvo/atl/archive/v2.1.tar.gz"
+    url      = "https://github.com/GTkorvo/atl/archive/v2.1.tar.gz"
+    git      = "https://github.com/GTkorvo/atl.git"
 
-    version('develop', git='https://github.com/GTkorvo/atl.git',
-            branch='master')
+    version('develop', branch='master')
+    version('2.2', 'f0e3581e4b4c6943bf4b203685630564')
     version('2.1', 'b2324ff041bccba127330a0e1b241978')
 
     depends_on('gtkorvo-cercs-env')
 
     def cmake_args(self):
-        args = ["-DENABLE_TESTING=0", "-DENABLE_BUILD_STATIC=STATIC"]
+        args = []
+        if self.spec.satisfies('@2.2:'):
+            args.append("-DBUILD_SHARED_LIBS=OFF")
+        else:
+            args.append("-DENABLE_BUILD_STATIC=STATIC")
+
+        if self.run_tests:
+            args.append('-DENABLE_TESTING=1')
+        else:
+            args.append('-DENABLE_TESTING=0')
+
         return args
diff --git a/var/spack/repos/builtin/packages/gtkorvo-cercs-env/package.py b/var/spack/repos/builtin/packages/gtkorvo-cercs-env/package.py
index 2fcfc21467..a042dd154b 100644
--- a/var/spack/repos/builtin/packages/gtkorvo-cercs-env/package.py
+++ b/var/spack/repos/builtin/packages/gtkorvo-cercs-env/package.py
@@ -1,39 +1,19 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class GtkorvoCercsEnv(CMakePackage):
-    """A utility library used by some GTkorvo packages.
-    """
+    """A utility library used by some GTkorvo packages."""
 
     homepage = "https://github.com/GTkorvo/cercs_env"
-    url = "https://github.com/GTkorvo/cercs_env/archive/v1.0.tar.gz"
+    url      = "https://github.com/GTkorvo/cercs_env/archive/v1.0.tar.gz"
+    git      = "https://github.com/GTkorvo/cercs_env.git"
 
-    version('develop', git='https://github.com/GTkorvo/cercs_env.git',
-            branch='master')
+    version('develop', branch='master')
     version('1.0', '08f0532d0c2f7bc9b53dfa7a1c40ea4d')
 
     def cmake_args(self):
diff --git a/var/spack/repos/builtin/packages/gtkorvo-dill/package.py b/var/spack/repos/builtin/packages/gtkorvo-dill/package.py
index af2c433ed6..6af9ebc9ab 100644
--- a/var/spack/repos/builtin/packages/gtkorvo-dill/package.py
+++ b/var/spack/repos/builtin/packages/gtkorvo-dill/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,12 +13,23 @@ class GtkorvoDill(CMakePackage):
     """
 
     homepage = "https://github.com/GTkorvo/dill"
-    url = "https://github.com/GTkorvo/dill/archive/v2.1.tar.gz"
+    url      = "https://github.com/GTkorvo/dill/archive/v2.1.tar.gz"
+    git      = "https://github.com/GTkorvo/dill.git"
 
-    version('develop', git='https://github.com/GTkorvo/dill.git',
-            branch='master')
+    version('develop', branch='master')
+    version('2.4', '6836673b24f395eaae044b8bb976511d')
     version('2.1', '14c835e79b66c9acd2beee01d56e6200')
 
     def cmake_args(self):
-        args = ["-DENABLE_TESTING=0", "-DBUILD_SHARED_STATIC=STATIC"]
+        args = []
+        if self.spec.satisfies('@2.4:'):
+            args.append("-DBUILD_SHARED_LIBS=OFF")
+        else:
+            args.append("-DENABLE_BUILD_STATIC=STATIC")
+
+        if self.run_tests:
+            args.append('-DENABLE_TESTING=1')
+        else:
+            args.append('-DENABLE_TESTING=0')
+
         return args
diff --git a/var/spack/repos/builtin/packages/gtkorvo-enet/package.py b/var/spack/repos/builtin/packages/gtkorvo-enet/package.py
index 2130085b93..5c9148d471 100644
--- a/var/spack/repos/builtin/packages/gtkorvo-enet/package.py
+++ b/var/spack/repos/builtin/packages/gtkorvo-enet/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,4 +16,5 @@ class GtkorvoEnet(AutotoolsPackage):
     homepage = "http://www.github.com/GTkorvo/enet"
     url = "https://github.com/GTkorvo/enet/archive/v1.3.13.tar.gz"
 
+    version('1.3.14', '05272cac1a8cb0500995eeca310e7fac')
     version('1.3.13', '3490f924a4d421e4832e45850e6ec142')
diff --git a/var/spack/repos/builtin/packages/gtkplus/package.py b/var/spack/repos/builtin/packages/gtkplus/package.py
index 033c325eb6..d7ce1c57d6 100644
--- a/var/spack/repos/builtin/packages/gtkplus/package.py
+++ b/var/spack/repos/builtin/packages/gtkplus/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,24 +11,32 @@ class Gtkplus(AutotoolsPackage):
        interfaces for applications."""
     homepage = "http://www.gtk.org"
     url = "http://ftp.gnome.org/pub/gnome/sources/gtk+/2.24/gtk+-2.24.31.tar.xz"
-
+    version('3.20.10', 'e81da1af1c5c1fee87ba439770e17272fa5c06e64572939814da406859e56b70')
+    version('2.24.32', 'b6c8a93ddda5eabe3bfee1eb39636c9a03d2a56c7b62828b359bf197943c582e')
     version('2.24.31', '68c1922732c7efc08df4656a5366dcc3afdc8791513400dac276009b40954658')
     version('2.24.25', '38af1020cb8ff3d10dda2c8807f11e92af9d2fa4045de61c62eedb7fbc7ea5b3')
 
-    variant('X', default=False, description="Enable an X toolkit")
+    depends_on('pkgconfig', type='build')
 
-    depends_on('pkg-config', type='build')
-
-    depends_on("atk")
-    depends_on("gdk-pixbuf")
-    depends_on("glib")
-    depends_on("pango")
-    depends_on("pango~X", when='~X')
-    depends_on("pango+X", when='+X')
-    depends_on('gobject-introspection', when='+X')
+    depends_on('atk')
+    depends_on('gdk-pixbuf')
+    depends_on('glib')
     depends_on('shared-mime-info')
-
-    patch('no-demos.patch')
+    # Hardcode X11 support (former +X variant),
+    # see #6940 for rationale:
+    depends_on('pango+X')
+    depends_on('gobject-introspection')
+    depends_on('libepoxy', when='@3:')
+    depends_on('libxi', when='@3:')
+    depends_on('inputproto', when='@3:')
+    depends_on('fixesproto', when='@3:')
+    depends_on('at-spi2-atk', when='@3:')
+
+    patch('no-demos.patch', when='@2:2.99')
+
+    def url_for_version(self, version):
+        url = 'http://ftp.gnome.org/pub/gnome/sources/gtk+'
+        return url + '/%s/gtk+-%s.tar.xz' % (version.up_to(2), version)
 
     def patch(self):
         # remove disable deprecated flag.
diff --git a/var/spack/repos/builtin/packages/gts/package.py b/var/spack/repos/builtin/packages/gts/package.py
index b340df34f2..d19c539f7e 100644
--- a/var/spack/repos/builtin/packages/gts/package.py
+++ b/var/spack/repos/builtin/packages/gts/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/guidance/package.py b/var/spack/repos/builtin/packages/guidance/package.py
index 6cb4e0cfc6..4246b2b49e 100644
--- a/var/spack/repos/builtin/packages/guidance/package.py
+++ b/var/spack/repos/builtin/packages/guidance/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
 
diff --git a/var/spack/repos/builtin/packages/guile/package.py b/var/spack/repos/builtin/packages/guile/package.py
index 81b61510be..1861f7da5a 100644
--- a/var/spack/repos/builtin/packages/guile/package.py
+++ b/var/spack/repos/builtin/packages/guile/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,13 +11,14 @@ class Guile(AutotoolsPackage):
     the official extension language for the GNU operating system."""
 
     homepage = "https://www.gnu.org/software/guile/"
-    url      = "https://ftp.gnu.org/gnu/guile/guile-2.2.0.tar.gz"
+    url      = "https://ftpmirror.gnu.org/guile/guile-2.2.0.tar.gz"
 
     version('2.2.0',  '0d5de8075b965f9ee5ea04399b60a3f9')
     version('2.0.14', '333b6eec83e779935a45c818f712484e')
     version('2.0.11', 'e532c68c6f17822561e3001136635ddd')
 
     variant('readline', default=True, description='Use the readline library')
+    variant('threads', default=True, description='Use the thread interface')
 
     depends_on('gmp@4.2:')
     depends_on('gettext')
@@ -45,10 +27,12 @@ class Guile(AutotoolsPackage):
     depends_on('bdw-gc@7.0:')
     depends_on('libffi')
     depends_on('readline', when='+readline')
-    depends_on('pkg-config', type='build')
+    depends_on('pkgconfig', type='build')
 
     build_directory = 'spack-build'
 
+    conflicts('+threads', when='%intel')
+
     def configure_args(self):
         spec = self.spec
 
@@ -57,8 +41,9 @@ class Guile(AutotoolsPackage):
                 spec['libunistring'].prefix),
             '--with-libltdl-prefix={0}'.format(spec['libtool'].prefix),
             '--with-libgmp-prefix={0}'.format(spec['gmp'].prefix),
-            '--with-libintl-prefix={0}'.format(spec['gettext'].prefix)
+            '--with-libintl-prefix={0}'.format(spec['gettext'].prefix),
         ]
+        config_args += self.with_or_without('threads')
 
         if '+readline' in spec:
             config_args.append('--with-libreadline-prefix={0}'.format(
diff --git a/var/spack/repos/builtin/packages/gurobi/package.py b/var/spack/repos/builtin/packages/gurobi/package.py
new file mode 100644
index 0000000000..3c9747aef4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gurobi/package.py
@@ -0,0 +1,41 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class Gurobi(Package):
+    """The Gurobi Optimizer was designed from the ground up to be the fastest,
+    most powerful solver available for your LP, QP, QCP, and MIP (MILP, MIQP,
+    and MIQCP) problems.
+
+    Note: Gurobi is licensed software. You will need to create an account on
+    the Gurobi homepage and download Gurobi Optimizer yourself. Spack will
+    search your current directory for the download file. Alternatively, add
+    this file to a mirror so that Spack can find it. For instructions on how to
+    set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html
+
+    Please set the path to licence file with the following command (for bash)
+    export GRB_LICENSE_FILE=/path/to/gurobi/license/. See section 4 in
+    $GUROBI_HOME/docs/quickstart_linux.pdf for more details."""
+
+    homepage = "http://www.gurobi.com/index"
+
+    version('7.5.2', '01f6dbb8d165838cca1664a1a14e4a85')
+
+    # Licensing
+    license_required = True
+    license_vars     = ['GRB_LICENSE_FILE']
+    license_url      = 'http://www.gurobi.com/downloads/download-center'
+
+    def url_for_version(self, version):
+        return "file://{0}/gurobi{1}_linux64.tar.gz".format(os.getcwd(), version)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.set('GUROBI_HOME', self.prefix)
+
+    def install(self, spec, prefix):
+        install_tree('linux64', prefix)
diff --git a/var/spack/repos/builtin/packages/h5hut/package.py b/var/spack/repos/builtin/packages/h5hut/package.py
index ed9ede92d6..9b34183bff 100644
--- a/var/spack/repos/builtin/packages/h5hut/package.py
+++ b/var/spack/repos/builtin/packages/h5hut/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/h5part/package.py b/var/spack/repos/builtin/packages/h5part/package.py
index f105a26831..957e9dcf89 100644
--- a/var/spack/repos/builtin/packages/h5part/package.py
+++ b/var/spack/repos/builtin/packages/h5part/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/h5utils/package.py b/var/spack/repos/builtin/packages/h5utils/package.py
index 202eb0e232..946a494cbb 100644
--- a/var/spack/repos/builtin/packages/h5utils/package.py
+++ b/var/spack/repos/builtin/packages/h5utils/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/h5z-zfp/package.py b/var/spack/repos/builtin/packages/h5z-zfp/package.py
index dff0126f01..943c874e4b 100644
--- a/var/spack/repos/builtin/packages/h5z-zfp/package.py
+++ b/var/spack/repos/builtin/packages/h5z-zfp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,14 +11,16 @@ class H5zZfp(MakefilePackage):
        HDF5 library using ZFP compression."""
 
     homepage = "http://h5z-zfp.readthedocs.io/en/latest"
-    url      = "https://github.com/LLNL/H5Z-ZFP"
+    git      = "https://github.com/LLNL/H5Z-ZFP.git"
 
-    version('develop', git='https://github.com/LLNL/H5Z-ZFP.git', tag='master')
-    version('0.7.0', git='https://github.com/LLNL/H5Z-ZFP.git', commit='58ac811')
+    version('develop', tag='master')
+    version('0.8.0', commit='af165c4')
+    version('0.7.0', commit='58ac811')
 
     variant('fortran', default=True, description='Enable Fortran support')
 
-    depends_on('hdf5')
+    depends_on('hdf5+fortran', when='+fortran')
+    depends_on('hdf5',         when='~fortran')
     depends_on('zfp bsws=8')
 
     @property
diff --git a/var/spack/repos/builtin/packages/hacckernels/package.py b/var/spack/repos/builtin/packages/hacckernels/package.py
index db48910165..d93dc42e7d 100644
--- a/var/spack/repos/builtin/packages/hacckernels/package.py
+++ b/var/spack/repos/builtin/packages/hacckernels/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,12 +14,11 @@ class Hacckernels(CMakePackage):
     cores and beyond."""
 
     homepage = "https://xgitlab.cels.anl.gov/hacc/HACCKernels"
-    url      = "https://xgitlab.cels.anl.gov/hacc/HACCKernels.git"
+    git      = "https://xgitlab.cels.anl.gov/hacc/HACCKernels.git"
 
     tags = ['proxy-app']
 
-    version('develop', git='https://xgitlab.cels.anl.gov/hacc/HACCKernels.git',
-            branch='master')
+    version('develop', branch='master')
 
     def install(self, spec, prefix):
         mkdirp(prefix.bin)
diff --git a/var/spack/repos/builtin/packages/hadoop/package.py b/var/spack/repos/builtin/packages/hadoop/package.py
index 66deb7c5d2..e581deb868 100644
--- a/var/spack/repos/builtin/packages/hadoop/package.py
+++ b/var/spack/repos/builtin/packages/hadoop/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,9 +13,10 @@ class Hadoop(Package):
     """
 
     homepage = "http://hadoop.apache.org/"
-    url      = "http://mirrors.ocf.berkeley.edu/apache/hadoop/common/hadoop-2.6.4/hadoop-2.6.4.tar.gz"
+    url      = "http://mirrors.ocf.berkeley.edu/apache/hadoop/common/hadoop-3.1.1/hadoop-3.1.1.tar.gz"
 
-    version('2.6.4', '37019f13d7dcd819727be158440b9442')
+    version('3.1.1', '0b6ab06b59ae75f433de387783f19011')
+    version('2.9.0', 'b443ead81aa2bd5086f99e62e66a8f64')
 
     depends_on('java', type='run')
 
diff --git a/var/spack/repos/builtin/packages/halc/package.py b/var/spack/repos/builtin/packages/halc/package.py
new file mode 100644
index 0000000000..7d2e76be75
--- /dev/null
+++ b/var/spack/repos/builtin/packages/halc/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Halc(MakefilePackage):
+    """HALC is software that makes error correction for long reads with
+     high throughput."""
+
+    homepage = "https://github.com/lanl001/halc"
+    url      = "https://github.com/lanl001/halc/archive/v1.1.tar.gz"
+
+    version('1.1', '4b289b366f6a5400ca481993aa68dd9c')
+
+    depends_on('blasr', type='run')
+    depends_on('lordec', type='run')
+    depends_on('dos2unix', type='build')
+    depends_on('python', type='run')
+
+    parallel = False
+
+    def install(self, spec, prefix):
+        install_tree('bin', prefix.bin)
+        install('runHALC.py', prefix.bin)
+        dos2unix = which('dos2unix')
+        dos2unix(join_path(self.prefix.bin, 'runHALC.py'))
diff --git a/var/spack/repos/builtin/packages/hapcut2/package.py b/var/spack/repos/builtin/packages/hapcut2/package.py
index 612a1c25ba..60596b4185 100644
--- a/var/spack/repos/builtin/packages/hapcut2/package.py
+++ b/var/spack/repos/builtin/packages/hapcut2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,10 +12,10 @@ class Hapcut2(MakefilePackage):
        and accuracy."""
 
     homepage = "https://github.com/vibansal/HapCUT2"
-    url      = "https://github.com/vibansal/HapCUT2"
+    git      = "https://github.com/vibansal/HapCUT2.git"
 
-    version('2017-07-10', git='https://github.com/vibansal/HapCUT2.git',
-            commit='2966b94c2c2f97813b757d4999b7a6471df1160e', submodules=True)
+    version('2017-07-10', commit='2966b94c2c2f97813b757d4999b7a6471df1160e',
+            submodules=True)
 
     def install(self, spec, prefix):
         mkdirp(prefix.bin)
diff --git a/var/spack/repos/builtin/packages/hapdip/package.py b/var/spack/repos/builtin/packages/hapdip/package.py
new file mode 100644
index 0000000000..92673b2b34
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hapdip/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Hapdip(Package):
+    """The CHM1-NA12878 benchmark for single-sample SNP/INDEL calling from
+    WGS Illumina data."""
+
+    homepage = "https://github.com/lh3/hapdip"
+    git      = "https://github.com/lh3/hapdip.git"
+
+    version('2018.02.20', commit='7c12f684471999a543fdacce972c9c86349758a3')
+
+    depends_on('k8', type='run')
+
+    def install(self, spec, prefix):
+        install_tree('.', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/haploview/package.py b/var/spack/repos/builtin/packages/haploview/package.py
index 9d1b4b3e0f..dd6acefad7 100644
--- a/var/spack/repos/builtin/packages/haploview/package.py
+++ b/var/spack/repos/builtin/packages/haploview/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os.path
 
diff --git a/var/spack/repos/builtin/packages/harfbuzz/package.py b/var/spack/repos/builtin/packages/harfbuzz/package.py
index 492a4694a8..5a6ded2e77 100644
--- a/var/spack/repos/builtin/packages/harfbuzz/package.py
+++ b/var/spack/repos/builtin/packages/harfbuzz/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,7 +14,7 @@ class Harfbuzz(AutotoolsPackage):
     version('1.4.6', '21a78b81cd20cbffdb04b59ac7edfb410e42141869f637ae1d6778e74928d293')
     version('0.9.37', 'bfe733250e34629a188d82e3b971bc1e')
 
-    depends_on("pkg-config", type="build")
+    depends_on("pkgconfig", type="build")
     depends_on("glib")
     depends_on("icu4c")
     depends_on("freetype")
diff --git a/var/spack/repos/builtin/packages/harminv/package.py b/var/spack/repos/builtin/packages/harminv/package.py
index d92405e8c7..f3aaf33bdd 100644
--- a/var/spack/repos/builtin/packages/harminv/package.py
+++ b/var/spack/repos/builtin/packages/harminv/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/hdf/package.py b/var/spack/repos/builtin/packages/hdf/package.py
index 0aefe3aa8c..3f5be4b95f 100644
--- a/var/spack/repos/builtin/packages/hdf/package.py
+++ b/var/spack/repos/builtin/packages/hdf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/hdf5-blosc/package.py b/var/spack/repos/builtin/packages/hdf5-blosc/package.py
index 704f508cb3..c79ed76c1b 100644
--- a/var/spack/repos/builtin/packages/hdf5-blosc/package.py
+++ b/var/spack/repos/builtin/packages/hdf5-blosc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 import shutil
 import sys
@@ -34,13 +15,13 @@ def _install_shlib(name, src, dst):
     if sys.platform == "darwin":
         shlib0 = name + ".0.dylib"
         shlib = name + ".dylib"
-        shutil.copyfile(join_path(src, shlib0), join_path(dst, shlib0))
+        install(join_path(src, shlib0), join_path(dst, shlib0))
         os.symlink(shlib0, join_path(dst, shlib))
     else:
         shlib000 = name + ".so.0.0.0"
         shlib0 = name + ".so.0"
         shlib = name + ".dylib"
-        shutil.copyfile(join_path(src, shlib000), join_path(dst, shlib000))
+        install(join_path(src, shlib000), join_path(dst, shlib000))
         os.symlink(shlib000, join_path(dst, shlib0))
         os.symlink(shlib0, join_path(dst, shlib))
 
@@ -48,10 +29,9 @@ def _install_shlib(name, src, dst):
 class Hdf5Blosc(Package):
     """Blosc filter for HDF5"""
     homepage = "https://github.com/Blosc/hdf5-blosc"
-    url      = "https://github.com/Blosc/hdf5-blosc"
+    git      = "https://github.com/Blosc/hdf5-blosc.git"
 
-    version('master', git='https://github.com/Blosc/hdf5-blosc',
-            branch='master')
+    version('master', branch='master')
 
     depends_on("c-blosc")
     depends_on("hdf5")
diff --git a/var/spack/repos/builtin/packages/hdf5/h5f90global-mult-obj-same-equivalence-same-common-block.patch b/var/spack/repos/builtin/packages/hdf5/h5f90global-mult-obj-same-equivalence-same-common-block.patch
new file mode 100644
index 0000000000..8bf5c142e9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hdf5/h5f90global-mult-obj-same-equivalence-same-common-block.patch
@@ -0,0 +1,16 @@
+diff --git a/fortran/src/H5f90global.F90 b/fortran/src/H5f90global.F90
+index dd2b171..629418a 100644
+--- a/fortran/src/H5f90global.F90
++++ b/fortran/src/H5f90global.F90
+@@ -142,10 +142,7 @@ MODULE H5GLOBAL
+
+   INTEGER(HID_T), DIMENSION(PREDEF_TYPES_LEN) :: predef_types
+   EQUIVALENCE (predef_types(1), H5T_NATIVE_INTEGER_KIND(1))
+-  EQUIVALENCE (predef_types(2), H5T_NATIVE_INTEGER_KIND(2))
+-  EQUIVALENCE (predef_types(3), H5T_NATIVE_INTEGER_KIND(3))
+-  EQUIVALENCE (predef_types(4), H5T_NATIVE_INTEGER_KIND(4))
+-  EQUIVALENCE (predef_types(5), H5T_NATIVE_INTEGER_KIND(5))
++  ! EQUIVALENCE predef_types(2:5) are unnecessary and violate the standard
+   EQUIVALENCE (predef_types(6), H5T_NATIVE_INTEGER)
+   EQUIVALENCE (predef_types(7), H5T_NATIVE_REAL)
+   EQUIVALENCE (predef_types(8), H5T_NATIVE_DOUBLE)
diff --git a/var/spack/repos/builtin/packages/hdf5/package.py b/var/spack/repos/builtin/packages/hdf5/package.py
index 5a15b33d98..00fd80dc54 100644
--- a/var/spack/repos/builtin/packages/hdf5/package.py
+++ b/var/spack/repos/builtin/packages/hdf5/package.py
@@ -1,31 +1,13 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-from spack import *
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import shutil
 import sys
 
+from spack import *
+
 
 class Hdf5(AutotoolsPackage):
     """HDF5 is a data model, library, and file format for storing and managing
@@ -38,6 +20,9 @@ class Hdf5(AutotoolsPackage):
     list_url = "https://support.hdfgroup.org/ftp/HDF5/releases"
     list_depth = 3
 
+    version('1.10.4', '8f60dc4dd6ab5fcd23c750d1dc5bca3d0453bdce5c8cdaf0a4a61a9d1122adb2')
+    version('1.10.3', 'b600d7c914cfa80ae127cd1a1539981213fee9994ac22ebec9e3845e951d9b39')
+    version('1.10.2', '8d4eae84e533efa57496638fd0dca8c3')
     version('1.10.1', '43a2f9466702fb1db31df98ae6677f15')
     version('1.10.0-patch1', '9180ff0ef8dc2ef3f61bd37a7404f295')
     version('1.10.0', 'bdc935337ee8282579cd6bc4270ad199')
@@ -49,6 +34,7 @@ class Hdf5(AutotoolsPackage):
     version('1.8.14', 'a482686e733514a51cde12d6fe5c5d95')
     version('1.8.13', 'c03426e9e77d7766944654280b467289')
     version('1.8.12', 'd804802feb99b87fc668a90e6fa34411')
+    version('1.8.10', '710aa9fb61a51d61a7e2c09bf0052157')
 
     variant('debug', default=False,
             description='Builds a debug version of the library')
@@ -90,6 +76,30 @@ class Hdf5(AutotoolsPackage):
     #    described in #2 we allow for such combination.
     # conflicts('+mpi+cxx')
 
+    # There are known build failures with intel@18.0.1. This issue is
+    # discussed and patch is provided at
+    # https://software.intel.com/en-us/forums/intel-fortran-compiler-for-linux-and-mac-os-x/topic/747951.
+    patch('h5f90global-mult-obj-same-equivalence-same-common-block.patch',
+          when='@1.10.1%intel@18')
+
+    # Turn line comments into block comments to conform with pre-C99 language
+    # standards. Versions of hdf5 after 1.8.10 don't require this patch,
+    # either because they conform to pre-C99 or neglect to ask for pre-C99
+    # language standards from their compiler. The hdf5 build system adds
+    # the -ansi cflag (run 'man gcc' for info on -ansi) for some versions
+    # of some compilers (see hdf5-1.8.10/config/gnu-flags). The hdf5 build
+    # system does not provide an option to disable -ansi, but since the
+    # pre-C99 code is restricted to just five lines of line comments in
+    # three src files, this patch accomplishes the simple task of patching the
+    # three src files and leaves the hdf5 build system alone.
+    patch('pre-c99-comments.patch', when='@1.8.10')
+
+    # There are build errors with GCC 8, see
+    # https://forum.hdfgroup.org/t/1-10-2-h5detect-compile-error-gcc-8-1-0-on-centos-7-2-solved/4441
+    patch('https://salsa.debian.org/debian-gis-team/hdf5/raw/bf94804af5f80f662cad80a5527535b3c6537df6/debian/patches/gcc-8.patch', sha256='57cee5ff1992b4098eda079815c36fc2da9b10e00a9056df054f2384c4fc7523', when='@1.10.2%gcc@8:')
+
+    filter_compiler_wrappers('h5cc', 'h5c++', 'h5fc', relative_root='bin')
+
     def url_for_version(self, version):
         url = "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-{0}/hdf5-{1}/src/hdf5-{1}.tar.gz"
         return url.format(version.up_to(2), version)
@@ -154,7 +164,7 @@ class Hdf5(AutotoolsPackage):
         libraries = query2libraries[key]
 
         return find_libraries(
-            libraries, root=self.prefix, shared=shared, recurse=True
+            libraries, root=self.prefix, shared=shared, recursive=True
         )
 
     @run_before('configure')
@@ -268,8 +278,8 @@ HDF5 version {version} {version}
             else:
                 cc = Executable(self.compiler.cc)
             cc(*(['-c', "check.c"] + spec['hdf5'].headers.cpp_flags.split()))
-            cc(*(['-o', "check", "check.o"] +
-                 spec['hdf5'].libs.ld_flags.split()))
+            cc(*(['-o', "check",
+                  "check.o"] + spec['hdf5'].libs.ld_flags.split()))
             try:
                 check = Executable('./check')
                 output = check(output=str)
diff --git a/var/spack/repos/builtin/packages/hdf5/pre-c99-comments.patch b/var/spack/repos/builtin/packages/hdf5/pre-c99-comments.patch
new file mode 100644
index 0000000000..97743e8fa5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hdf5/pre-c99-comments.patch
@@ -0,0 +1,43 @@
+diff --git a/test/th5s.c b/test/th5s.c
+index 462bc36..8e18fad 100644
+--- a/test/th5s.c
++++ b/test/th5s.c
+@@ -730,8 +730,8 @@ test_h5s_zero_dim(void)
+         ret = H5Pset_chunk(plist_id, SPACE1_RANK, chunk_dims);
+         CHECK(ret, FAIL, "H5Pset_chunk");
+ 
+-        // ret = H5Pset_alloc_time(plist_id, alloc_time);
+-        // CHECK(ret, FAIL, "H5Pset_alloc_time");
++        /* ret = H5Pset_alloc_time(plist_id, alloc_time); */
++        /* CHECK(ret, FAIL, "H5Pset_alloc_time"); */
+ 
+         dset1 = H5Dcreate2(fid1, BASICDATASET1, H5T_NATIVE_INT, sid_chunk, H5P_DEFAULT, plist_id, H5P_DEFAULT);
+         CHECK(dset1, FAIL, "H5Dcreate2");
+diff --git a/tools/h5dump/h5dump_ddl.c b/tools/h5dump/h5dump_ddl.c
+index ee6de5e..3ed6045 100644
+--- a/tools/h5dump/h5dump_ddl.c
++++ b/tools/h5dump/h5dump_ddl.c
+@@ -1341,8 +1341,8 @@ handle_attributes(hid_t fid, const char *attr, void UNUSED * data, int UNUSED pe
+     string_dataformat.do_escape = display_escape;
+     outputformat = &string_dataformat;
+ 
+-    //attr_name = attr + j + 1;
+-	// need to replace escape characters
++    /* attr_name = attr + j + 1; */
++	/* need to replace escape characters */
+ 	attr_name = h5tools_str_replace(attr + j + 1, "\\/", "/");
+ 
+ 
+diff --git a/tools/lib/h5tools_str.c b/tools/lib/h5tools_str.c
+index 9ce3524..3b4e5e7 100644
+--- a/tools/lib/h5tools_str.c
++++ b/tools/lib/h5tools_str.c
+@@ -632,7 +632,7 @@ h5tools_str_indent(h5tools_str_t *str, const h5tool_format_t *info,
+         h5tools_str_append(str, "%s", OPT(info->line_indent, ""));
+     }
+ 
+-//    ctx->need_prefix = 0;
++/*    ctx->need_prefix = 0; */
+ }
+ 
+ /*-------------------------------------------------------------------------
diff --git a/var/spack/repos/builtin/packages/help2man/package.py b/var/spack/repos/builtin/packages/help2man/package.py
index cc86affeaa..39ad9037f0 100644
--- a/var/spack/repos/builtin/packages/help2man/package.py
+++ b/var/spack/repos/builtin/packages/help2man/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,8 +11,9 @@ class Help2man(AutotoolsPackage):
     output of other commands."""
 
     homepage = "https://www.gnu.org/software/help2man/"
-    url      = "http://gnu.askapache.com/help2man/help2man-1.47.4.tar.xz"
+    url      = "https://ftpmirror.gnu.org/help2man/help2man-1.47.4.tar.xz"
 
     version('1.47.4', '544aca496a7d89de3e5d99e56a2f03d3')
 
     depends_on('gettext', type='build')
+    depends_on('perl', type='build')
diff --git a/var/spack/repos/builtin/packages/henson/package.py b/var/spack/repos/builtin/packages/henson/package.py
new file mode 100644
index 0000000000..b41fb080fe
--- /dev/null
+++ b/var/spack/repos/builtin/packages/henson/package.py
@@ -0,0 +1,38 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Henson(CMakePackage):
+    """Cooperative multitasking for in situ processing."""
+
+    homepage = "https://github.com/henson-insitu/henson"
+    url      = "https://github.com/henson-insitu/henson"
+    git      = "https://github.com/henson-insitu/henson.git"
+
+    version('develop', branch='master')
+
+    depends_on('mpi')
+
+    variant('python', default=False, description='Build Python bindings')
+    extends('python', when='+python')
+    variant('mpi-wrappers', default=False, description='Build MPI wrappers (PMPI)')
+
+    conflicts('^openmpi', when='+mpi-wrappers')
+
+    def cmake_args(self):
+        args = []
+        if '+python' in self.spec:
+            args += ['-Dpython=on']
+        else:
+            args += ['-Dpython=off']
+
+        if '+mpi-wrappers' in self.spec:
+            args += ['-Dmpi-wrappers=on']
+        else:
+            args += ['-Dmpi-wrappers=off']
+
+        return args
diff --git a/var/spack/repos/builtin/packages/hepmc/package.py b/var/spack/repos/builtin/packages/hepmc/package.py
index b5470225b5..16b4c707f5 100644
--- a/var/spack/repos/builtin/packages/hepmc/package.py
+++ b/var/spack/repos/builtin/packages/hepmc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -33,7 +14,8 @@ class Hepmc(CMakePackage):
     homepage = "http://hepmc.web.cern.ch/hepmc/"
     url      = "http://hepmc.web.cern.ch/hepmc/releases/hepmc2.06.09.tgz"
 
-    version('2.06.09', 'c47627ced4255b40e731b8666848b087')
+    version('3.0.0',   '2212a5e8d693fbf726c28b43ebc6377a')
+    version('2.06.09', '52518437a64f6b4284e9acc2ecad6212')
     version('2.06.08', 'a2e889114cafc4f60742029d69abd907')
     version('2.06.07', '11d7035dccb0650b331f51520c6172e7')
     version('2.06.06', '102e5503537a3ecd6ea6f466aa5bc4ae')
@@ -46,3 +28,10 @@ class Hepmc(CMakePackage):
             '-Dmomentum:STRING=GEV',
             '-Dlength:STRING=MM',
         ]
+
+    def url_for_version(self, version):
+        if version <= Version("2.06.08"):
+            url = "http://lcgapp.cern.ch/project/simu/HepMC/download/HepMC-{0}.tar.gz"
+        else:
+            url = "http://hepmc.web.cern.ch/hepmc/releases/hepmc{0}.tgz"
+        return url.format(version)
diff --git a/var/spack/repos/builtin/packages/heppdt/package.py b/var/spack/repos/builtin/packages/heppdt/package.py
index 613d8d9f8e..5933317c50 100644
--- a/var/spack/repos/builtin/packages/heppdt/package.py
+++ b/var/spack/repos/builtin/packages/heppdt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/hic-pro/package.py b/var/spack/repos/builtin/packages/hic-pro/package.py
new file mode 100644
index 0000000000..6cb89d8839
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hic-pro/package.py
@@ -0,0 +1,61 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class HicPro(MakefilePackage):
+    """HiC-Pro is a package designed to process Hi-C data,
+    from raw fastq files (paired-end Illumina data)
+    to the normalized contact maps"""
+
+    homepage = "https://github.com/nservant/HiC-Pro"
+    url      = "https://github.com/nservant/HiC-Pro/archive/v2.10.0.tar.gz"
+
+    version('2.10.0', '6ae2213dcc984b722d1a1f65fcbb21a2')
+
+    depends_on('bowtie2')
+    depends_on('samtools')
+    depends_on('python+ucs4@2.7:2.8')
+    depends_on('r')
+    depends_on('py-numpy', type=('build', 'run'))
+    depends_on('py-scipy', type=('build', 'run'))
+    depends_on('py-pysam', type=('build', 'run'))
+    depends_on('py-bx-python', type=('build', 'run'))
+    depends_on('r-rcolorbrewer', type=('build', 'run'))
+    depends_on('r-ggplot2', type=('build', 'run'))
+
+    def edit(self, spec, prefix):
+        config = FileFilter('config-install.txt')
+        config.filter('PREFIX =.*', 'PREFIX = {0}'.format(prefix))
+        config.filter('BOWTIE2 PATH =.*',
+                      'BOWTIE2_PATH = {0}'.format(spec['bowtie2'].prefix))
+        config.filter('SAMTOOLS_PATH =.*',
+                      'SAMTOOLS_PATH = {0}'.format(spec['samtools'].prefix))
+        config.filter('R_PATH =.*',
+                      'R_RPTH ={0}'.format(spec['r'].prefix))
+        config.filter('PYTHON_PATH =.*',
+                      'PYTHON_RPTH ={0}'.format(spec['python'].prefix))
+
+    def build(self, spec, preifx):
+        make('-f', './scripts/install/Makefile',
+             'CONFIG_SYS=./config-install.txt')
+        make('mapbuilder')
+        make('readstrimming')
+        make('iced')
+
+    def install(self, spec, prefix):
+        # Patch INSTALLPATH in config-system.txt
+        config = FileFilter('config-system.txt')
+        config.filter('/HiC-Pro_%s' % self.version, '')
+        # Install
+        install('config-hicpro.txt', prefix)
+        install('config-install.txt', prefix)
+        install('config-system.txt', prefix)
+        install_tree('bin', prefix.bin)
+        install_tree('annotation', prefix.annotation)
+        install_tree('doc', prefix.doc)
+        install_tree('scripts', prefix.scripts)
+        install_tree('test-op', join_path(prefix, 'test-op'))
diff --git a/var/spack/repos/builtin/packages/highfive/package.py b/var/spack/repos/builtin/packages/highfive/package.py
index ad97e716e0..cbd57f98fc 100644
--- a/var/spack/repos/builtin/packages/highfive/package.py
+++ b/var/spack/repos/builtin/packages/highfive/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -32,6 +13,7 @@ class Highfive(CMakePackage):
     homepage = "https://github.com/BlueBrain/HighFive"
     url      = "https://github.com/BlueBrain/HighFive/archive/v1.2.tar.gz"
 
+    version('1.5', '5e631c91d2ea7f3677e99d6bb6db8167')
     version('1.2', '030728d53519c7e13b5a522d34240301')
     version('1.1', '986f0bd18c5264709688a536c02d2b2a')
     version('1.0', 'e44e548560ea92afdb244c223b7655b6')
diff --git a/var/spack/repos/builtin/packages/highwayhash/package.py b/var/spack/repos/builtin/packages/highwayhash/package.py
index 3a12736aae..240faadf13 100644
--- a/var/spack/repos/builtin/packages/highwayhash/package.py
+++ b/var/spack/repos/builtin/packages/highwayhash/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 from glob import glob
 import os
@@ -34,9 +15,9 @@ class Highwayhash(MakefilePackage):
     """
 
     homepage = "https://github.com/google/highwayhash"
+    git      = "https://github.com/google/highwayhash.git"
 
-    version('dfcb97', git='https://github.com/google/highwayhash.git',
-            commit='dfcb97ca4fe9277bf9dc1802dd979b071896453b')
+    version('dfcb97', commit='dfcb97ca4fe9277bf9dc1802dd979b071896453b')
 
     build_targets = ['all', 'libhighwayhash.a']
 
diff --git a/var/spack/repos/builtin/packages/hiop/package.py b/var/spack/repos/builtin/packages/hiop/package.py
new file mode 100644
index 0000000000..cc2b07a822
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hiop/package.py
@@ -0,0 +1,55 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Hiop(CMakePackage):
+    """HiOp is an optimization solver for solving certain mathematical
+    optimization problems expressed as nonlinear programming problems.
+    HiOp is a lightweight HPC solver that leverages application's existing
+    data parallelism to parallelize the optimization iterations by using
+    specialized linear algebra kernels."""
+
+    homepage = "https://github.com/LLNL/hiop"
+    git      = "https://github.com/LLNL/hiop.git"
+
+    version('0.1', tag='v0.1')
+
+    variant('mpi', default=True,
+            description='Enable/Disable MPI')
+
+    variant('deepchecking', default=True,
+            description='Ultra safety checks - \
+            used for increased robustness and self-diagnostics')
+
+    depends_on('mpi', when='+mpi')
+    depends_on('lapack')
+    depends_on('blas')
+
+    flag_handler = build_system_flags
+
+    def cmake_args(self):
+        args = []
+        spec = self.spec
+
+        if '+mpi' in spec:
+            args.append("-DWITH_MPI=ON")
+        else:
+            args.append("-DWITH_MPI=OFF")
+
+        if '+deepchecking' in spec:
+            args.append("-DDEEP_CHECKING=ON")
+        else:
+            args.append("-DDEEP_CHECKING=OFF")
+
+        lapack_blas_libs = (
+            spec['lapack'].libs + spec['blas'].libs).joined(';')
+        args.extend([
+            '-DLAPACK_FOUND=TRUE',
+            '-DLAPACK_LIBRARIES={0}'.format(lapack_blas_libs)
+        ])
+
+        return args
diff --git a/var/spack/repos/builtin/packages/hisat2/package.py b/var/spack/repos/builtin/packages/hisat2/package.py
index 1b945c61c8..34fbf6e910 100644
--- a/var/spack/repos/builtin/packages/hisat2/package.py
+++ b/var/spack/repos/builtin/packages/hisat2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
 import os.path
diff --git a/var/spack/repos/builtin/packages/hisea/package.py b/var/spack/repos/builtin/packages/hisea/package.py
new file mode 100644
index 0000000000..f2d215242b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hisea/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Hisea(MakefilePackage):
+    """HISEA is an efficient all-vs-all long read aligner for SMRT sequencing
+       data. Its algorithm is designed to produce highest alignment sensitivity
+       among others."""
+
+    homepage = "https://doi.org/10.1186/s12859-017-1953-9"
+    url      = "https://github.com/lucian-ilie/HISEA"
+
+    version('2017.12.26', '54211bdc33b7ce52a8f1e76845935eb8',
+            url='https://github.com/lucian-ilie/HISEA/tarball/39e01e98caa0f2101da806ca59306296effe789c')
+
+    depends_on('boost')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('hisea', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/hmmer/package.py b/var/spack/repos/builtin/packages/hmmer/package.py
index 2681282b7d..2b9b045a00 100644
--- a/var/spack/repos/builtin/packages/hmmer/package.py
+++ b/var/spack/repos/builtin/packages/hmmer/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,8 +12,9 @@ class Hmmer(Package):
     probabilistic models called profile hidden Markov models (profile HMMs).
     """
     homepage = 'http://www.hmmer.org'
-    url      = 'http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2.tar.gz'
+    url      = 'http://eddylab.org/software/hmmer/hmmer-3.2.1.tar.gz'
 
+    version('3.2.1', '4e0ad5ed45462d4e36807d21e6d82b69')
     version('3.1b2', 'c8c141018bc0ccd7fc37b33f2b945d5f')
     version('3.0',   '4cf685f3bc524ba5b5cdaaa070a83588')
     version('2.4i',  'dab234c87e026ac1de942450750acd20')
@@ -45,14 +27,6 @@ class Hmmer(Package):
     depends_on('mpi', when='+mpi')
     depends_on('gsl', when='+gsl')
 
-    def url_for_version(self, version):
-        base_url = 'http://eddylab.org/software'
-
-        if version >= Version('3.0'):
-            return '{0}/hmmer3/{1}/hmmer-{1}.tar.gz'.format(base_url, version)
-        else:
-            return '{0}/hmmer/{1}/hmmer-{1}.tar.gz'.format(base_url, version)
-
     def install(self, spec, prefix):
         configure_args = [
             '--prefix={0}'.format(prefix)
diff --git a/var/spack/repos/builtin/packages/homer/package.py b/var/spack/repos/builtin/packages/homer/package.py
new file mode 100644
index 0000000000..14293169dc
--- /dev/null
+++ b/var/spack/repos/builtin/packages/homer/package.py
@@ -0,0 +1,48 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+from os import symlink
+
+
+class Homer(Package):
+    """Software for motif discovery and next generation sequencing analysis"""
+
+    homepage = "http://homer.ucsd.edu/homer"
+    url      = "http://homer.ucsd.edu/homer/data/software/homer.v4.9.zip"
+
+    version('4.9.1', sha256='ad1303b0b0400dc8a88dbeae1ee03a94631977b751a3d335326c4febf0eec3a9')
+
+    depends_on('perl', type=('build', 'run'))
+    depends_on('r-biocgenerics', type='run')
+    depends_on('r-biocparallel', type='run')
+    depends_on('r-edger', type='run')
+    depends_on('r-deseq2', type='run')
+
+    variant('data', default=False,
+            description='Download genome data packages')
+
+    def install(self, spec, prefix):
+        # initialize homer directories
+        basedir = join_path(prefix.lib, 'homer')
+        mkdirp(basedir)
+
+        install_tree('.', basedir)
+
+        # symlink bin so it is included in the PATH
+        symlink(join_path(basedir, 'bin'), prefix.bin)
+
+        # override homer base directory in configure script
+        filter_file('my $homeDir = $1;',
+                    'my $homeDir = \"{0}\";'.format(basedir),
+                    'configureHomer.pl', string=True)
+
+        # compile/prepare binaries and perl scripts with the correct paths
+        perl = which('perl')
+        perl('configureHomer.pl', '-local')
+
+        # download extra data if requested
+        if '+data' in spec:
+            perl('configureHomer.pl', '-install', '-all')
diff --git a/var/spack/repos/builtin/packages/hoomd-blue/package.py b/var/spack/repos/builtin/packages/hoomd-blue/package.py
index 547a15ae6b..4120e03410 100644
--- a/var/spack/repos/builtin/packages/hoomd-blue/package.py
+++ b/var/spack/repos/builtin/packages/hoomd-blue/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
@@ -37,20 +18,17 @@ class HoomdBlue(CMakePackage):
     and perform in situ analysis."""
 
     homepage = "http://glotzerlab.engin.umich.edu/hoomd-blue/"
-    git      = "https://bitbucket.org/glotzer/hoomd-blue"
-
-    # TODO: There is a bug in Spack that requires a url to be defined
-    # even if it isn't used. This URL can hopefully be removed someday.
-    url      = "https://bitbucket.org/glotzer/hoomd-blue/get/v2.1.6.tar.bz2"
+    git      = "https://bitbucket.org/glotzer/hoomd-blue.git"
 
-    version('develop', git=git, submodules=True)
+    version('develop', submodules=True)
 
     # Bitbucket has tarballs for each release, but they cannot be built.
     # The tarball doesn't come with the git submodules, nor does it come
     # with a .git directory, causing the build to fail. As a workaround,
     # clone a specific tag from Bitbucket instead of using the tarballs.
     # https://bitbucket.org/glotzer/hoomd-blue/issues/238
-    version('2.1.6', git=git, tag='v2.1.6', submodules=True)
+    version('2.2.2', tag='v2.2.2', submodules=True)
+    version('2.1.6', tag='v2.1.6', submodules=True)
 
     variant('mpi',  default=True,  description='Compile with MPI enabled')
     variant('cuda', default=True,  description='Compile with CUDA Toolkit')
@@ -61,26 +39,32 @@ class HoomdBlue(CMakePackage):
     # https://gcc.gnu.org/projects/cxx-status.html
     conflicts('%gcc@:4.6')
 
-    # HOOMD-blue uses hexadecimal floats, which are not technically part of
-    # the C++11 standard. GCC 6.0+ produces an error when this happens.
+    # HOOMD-blue 2.1.6 uses hexadecimal floats, which are not technically
+    # part of the C++11 standard. GCC 6.0+ produces an error when this happens.
     # https://bitbucket.org/glotzer/hoomd-blue/issues/239
     # https://bugzilla.redhat.com/show_bug.cgi?id=1321986
-    conflicts('%gcc@6.0:')
+    conflicts('%gcc@6.0:', when='@2.1.6')
+
+    # HOOMD-blue GCC 7+ is not yet supported
+    conflicts('%gcc@7.0:')
 
     extends('python')
     depends_on('python@2.7:')
     depends_on('py-numpy@1.7:', type=('build', 'run'))
-    depends_on('cmake@2.8.0:', type='build')
-    depends_on('pkg-config', type='build')
+    depends_on('cmake@2.8.0:3.9.6', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('mpi', when='+mpi')
     depends_on('cuda@7.0:', when='+cuda')
     depends_on('doxygen@1.8.5:', when='+doc', type='build')
 
     def cmake_args(self):
         spec = self.spec
+        install_dir = spec['python'].package.site_packages_dir
+        install_path = os.path.join(spec.prefix, install_dir)
 
         cmake_args = [
             '-DPYTHON_EXECUTABLE={0}'.format(spec['python'].command.path),
+            '-DCMAKE_INSTALL_PREFIX={0}'.format(install_path)
         ]
 
         # MPI support
diff --git a/var/spack/repos/builtin/packages/hpccg/package.py b/var/spack/repos/builtin/packages/hpccg/package.py
index 97fddc4f12..1a6256fe7c 100644
--- a/var/spack/repos/builtin/packages/hpccg/package.py
+++ b/var/spack/repos/builtin/packages/hpccg/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/hpctoolkit-externals/package.py b/var/spack/repos/builtin/packages/hpctoolkit-externals/package.py
index 73ee39539f..1c7c7c4622 100644
--- a/var/spack/repos/builtin/packages/hpctoolkit-externals/package.py
+++ b/var/spack/repos/builtin/packages/hpctoolkit-externals/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,10 +11,10 @@ class HpctoolkitExternals(Package):
     HpctoolkitExternals package provides all these prerequisites."""
 
     homepage = "http://hpctoolkit.org"
-    url = "https://github.com/HPCToolkit/hpctoolkit-externals"
+    git      = "https://github.com/HPCToolkit/hpctoolkit-externals.git"
 
-    version('2017.06', git=url, tag='release-2017.06')
-    version('master', git=url)
+    version('master')
+    version('2017.06', tag='release-2017.06')
 
     parallel = False
 
diff --git a/var/spack/repos/builtin/packages/hpctoolkit/package.py b/var/spack/repos/builtin/packages/hpctoolkit/package.py
index 14be6af8ef..0f4d188d4f 100644
--- a/var/spack/repos/builtin/packages/hpctoolkit/package.py
+++ b/var/spack/repos/builtin/packages/hpctoolkit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,10 +15,10 @@ class Hpctoolkit(Package):
     and attributes them to the full calling context in which they occur."""
 
     homepage = "http://hpctoolkit.org"
-    url = "https://github.com/HPCToolkit/hpctoolkit"
+    git      = "https://github.com/HPCToolkit/hpctoolkit.git"
 
-    version('2017.06', git=url, tag='release-2017.06')
-    version('master', git=url)
+    version('master')
+    version('2017.06', tag='release-2017.06')
 
     variant('mpi', default=True, description='Enable MPI supoort')
     variant('papi', default=True, description='Enable PAPI counter support')
diff --git a/var/spack/repos/builtin/packages/hpgmg/package.py b/var/spack/repos/builtin/packages/hpgmg/package.py
index db9b0ce225..e4a533a024 100644
--- a/var/spack/repos/builtin/packages/hpgmg/package.py
+++ b/var/spack/repos/builtin/packages/hpgmg/package.py
@@ -1,53 +1,38 @@
-##############################################################################
-# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class Hpgmg(Package):
-    """HPGMG implements full multigrid (FMG) algorithms using
-    finite-volume and finite-element methods.
-    Different algorithmic variants adjust the arithmetic intensity
-    and architectural properties that are tested. These FMG methods
-    converge up to discretization error in one F-cycle,
-    thus may be considered direct solvers. An F-cycle visits
-    the finest level a total of two times,
-    the first coarsening (8x smaller) 4 times,
-    the second coarsening 6 times, etc."""
+    """HPGMG implements full multigrid (FMG) algorithms using finite-volume and
+       finite-element methods.  Different algorithmic variants adjust the
+       arithmetic intensity and architectural properties that are tested. These
+       FMG methods converge up to discretization error in one F-cycle, thus may
+       be considered direct solvers. An F-cycle visits the finest level a total
+       of two times, the first coarsening (8x smaller) 4 times, the second
+       coarsening 6 times, etc.
+    """
 
     homepage = "https://bitbucket.org/hpgmg/hpgmg"
-    url      = "https://bitbucket.org/hpgmg/hpgmg/get/master.tar.gz"
-    tags     = ['proxy-app']
+    url      = "https://hpgmg.org/static/hpgmg-0.tar.gz"
+    git      = "https://bitbucket.org/hpgmg/hpgmg.git"
 
-    version('master', '4a2b139e1764c84ed7fe06334d3f8d8a')
+    tags = ['proxy-app']
+
+    version('develop', branch='master')
+    version('a0a5510df23b', 'b9c50f25e541428d4735fb07344d1d0ed9fc821bdde918d8e0defa78c0d9b4f9')
+    version('0.3',          '12a65da216fec91daea78594ae4b5a069c8f1a700f1ba21eed9f45a79a68c793')
 
     variant(
-        'fe', default=True, description='Build finite element solver')
+        'fe', default=False, description='Build finite element solver')
     variant(
         'fv', default='mpi', values=('serial', 'mpi', 'none'),
         description='Build finite volume solver with or without MPI support')
     variant('cuda', default=False, description='Build with CUDA')
+    variant('debug', default=False, description='Build in debug mode')
 
     depends_on('petsc', when='+fe')
     depends_on('mpi', when='+fe')
@@ -59,7 +44,7 @@ class Hpgmg(Package):
 
     def configure_args(self):
         args = []
-        if '+fe' in self.spec:
+        if '+fe' in self.spec and not ('@0.3' in self.spec):
             args.append('--fe')
 
         if 'fv=serial' in self.spec:
@@ -68,10 +53,24 @@ class Hpgmg(Package):
         if 'mpi' in self.spec:
             args.append('--CC={0}'.format(self.spec['mpi'].mpicc))
 
+        cflags = []
         if 'fv=none' in self.spec:
             args.append('--no-fv')
         else:
-            args.append('--CFLAGS=' + self.compiler.openmp_flag)
+            # Apple's Clang doesn't support OpenMP
+            if not (self.spec.satisfies('%clang') and self.compiler.is_apple):
+                cflags.append(self.compiler.openmp_flag)
+
+        if '+debug' in self.spec:
+            cflags.append('-g')
+        elif any(map(self.spec.satisfies, ['%gcc', '%clang', '%intel'])):
+            cflags += ['-O3', '-march=native']
+
+        args.append('--CFLAGS=' + ' '.join(cflags))
+
+        # Explicitly specify the build directory to ensure that
+        # PETSC_ARCH is not used from the environment.
+        args.append('--arch=build')
 
         return args
 
@@ -79,7 +78,7 @@ class Hpgmg(Package):
         configure(*self.configure_args())
 
     def build(self, spec, prefix):
-        make()
+        make('-C', 'build')
 
     def install(self, spec, prefix):
         install_tree('build/bin', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/hpl/package.py b/var/spack/repos/builtin/packages/hpl/package.py
index 0c484fc1f7..94fc2d5fb9 100644
--- a/var/spack/repos/builtin/packages/hpl/package.py
+++ b/var/spack/repos/builtin/packages/hpl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 import platform
diff --git a/var/spack/repos/builtin/packages/hpx/package.py b/var/spack/repos/builtin/packages/hpx/package.py
index 2c5e0c1402..9f4b3c6113 100644
--- a/var/spack/repos/builtin/packages/hpx/package.py
+++ b/var/spack/repos/builtin/packages/hpx/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/hpx5/package.py b/var/spack/repos/builtin/packages/hpx5/package.py
index dfc112fb24..d292f2c360 100644
--- a/var/spack/repos/builtin/packages/hpx5/package.py
+++ b/var/spack/repos/builtin/packages/hpx5/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -76,7 +57,7 @@ class Hpx5(AutotoolsPackage):
     depends_on("mpi", when='+photon')
     depends_on("opencl", when='+opencl')
     # depends_on("papi")
-    depends_on("pkg-config", type='build')
+    depends_on("pkgconfig", type='build')
 
     configure_directory = "hpx"
     build_directory = "spack-build"
diff --git a/var/spack/repos/builtin/packages/hsakmt/package.py b/var/spack/repos/builtin/packages/hsakmt/package.py
index 5574486066..d599dc13f5 100644
--- a/var/spack/repos/builtin/packages/hsakmt/package.py
+++ b/var/spack/repos/builtin/packages/hsakmt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/hstr/package.py b/var/spack/repos/builtin/packages/hstr/package.py
index e019e9c3af..e8ab7fadb6 100644
--- a/var/spack/repos/builtin/packages/hstr/package.py
+++ b/var/spack/repos/builtin/packages/hstr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/htop/package.py b/var/spack/repos/builtin/packages/htop/package.py
index 168c03302d..f6ae2c04b2 100644
--- a/var/spack/repos/builtin/packages/htop/package.py
+++ b/var/spack/repos/builtin/packages/htop/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,6 +14,7 @@ class Htop(AutotoolsPackage):
     list_url = "https://hisham.hm/htop/releases"
     list_depth = 1
 
+    version('2.2.0', '0d816b6beed31edc75babcfbf863ffa8')
     version('2.0.2', '7d354d904bad591a931ad57e99fea84a')
 
     depends_on('ncurses')
diff --git a/var/spack/repos/builtin/packages/htslib/package.py b/var/spack/repos/builtin/packages/htslib/package.py
index 000c68e245..c223ffc359 100644
--- a/var/spack/repos/builtin/packages/htslib/package.py
+++ b/var/spack/repos/builtin/packages/htslib/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,6 +11,9 @@ class Htslib(AutotoolsPackage):
 
     homepage = "https://github.com/samtools/htslib"
 
+    version('1.9', '2ac92c9c3eef9986345ac69a05dd4d24')
+    version('1.8', '54e9b3a04251fa59b1878f6b546b5c79')
+    version('1.7', 'd3cc7e080a9a8c4161d8f62b56d3b98d')
     version('1.6', 'd6fd14e208aca7e08cbe9072233d0af9')
     version('1.4', '2a22ff382654c033c40e4ec3ea880050')
     version('1.3.1', '16d78f90b72f29971b042e8da8be6843')
diff --git a/var/spack/repos/builtin/packages/httpie/package.py b/var/spack/repos/builtin/packages/httpie/package.py
index 2ec4c6eaad..8ac07a61e9 100644
--- a/var/spack/repos/builtin/packages/httpie/package.py
+++ b/var/spack/repos/builtin/packages/httpie/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/hub/package.py b/var/spack/repos/builtin/packages/hub/package.py
index ff38385242..3595ac6c2e 100644
--- a/var/spack/repos/builtin/packages/hub/package.py
+++ b/var/spack/repos/builtin/packages/hub/package.py
@@ -1,37 +1,20 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
 
 class Hub(Package):
     """The github git wrapper"""
+
     homepage = "https://github.com/github/hub"
-    url = "https://github.com/github/hub/archive/v2.2.3.tar.gz"
+    url      = "https://github.com/github/hub/archive/v2.2.3.tar.gz"
+    git      = "https://github.com/github/hub.git"
 
-    version('head', git='https://github.com/github/hub')
+    version('head', branch='master')
     version('2.2.3', '6675992ddd16d186eac7ba4484d57f5b')
     version('2.2.2', '7edc8f5b5d3c7c392ee191dd999596fc')
     version('2.2.1', '889a31ee9d10ae9cb333480d8dbe881f')
diff --git a/var/spack/repos/builtin/packages/hunspell/package.py b/var/spack/repos/builtin/packages/hunspell/package.py
index 2fef3d369e..ed400f3a4d 100644
--- a/var/spack/repos/builtin/packages/hunspell/package.py
+++ b/var/spack/repos/builtin/packages/hunspell/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/hwloc/package.py b/var/spack/repos/builtin/packages/hwloc/package.py
index 7961d930db..3214496a0e 100644
--- a/var/spack/repos/builtin/packages/hwloc/package.py
+++ b/var/spack/repos/builtin/packages/hwloc/package.py
@@ -1,49 +1,38 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 import sys
 
 
 class Hwloc(AutotoolsPackage):
-    """The Portable Hardware Locality (hwloc) software package
-       provides a portable abstraction (across OS, versions,
-       architectures, ...) of the hierarchical topology of modern
-       architectures, including NUMA memory nodes, sockets, shared
-       caches, cores and simultaneous multithreading. It also gathers
-       various system attributes such as cache and memory information
-       as well as the locality of I/O devices such as network
-       interfaces, InfiniBand HCAs or GPUs. It primarily aims at
-       helping applications with gathering information about modern
-       computing hardware so as to exploit it accordingly and
-       efficiently."""
+    """The Hardware Locality (hwloc) software project.
+
+    The Portable Hardware Locality (hwloc) software package
+    provides a portable abstraction (across OS, versions,
+    architectures, ...) of the hierarchical topology of modern
+    architectures, including NUMA memory nodes, sockets, shared
+    caches, cores and simultaneous multithreading. It also gathers
+    various system attributes such as cache and memory information
+    as well as the locality of I/O devices such as network
+    interfaces, InfiniBand HCAs or GPUs. It primarily aims at
+    helping applications with gathering information about modern
+    computing hardware so as to exploit it accordingly and
+    efficiently.
+    """
+
     homepage = "http://www.open-mpi.org/projects/hwloc/"
-    url      = "http://www.open-mpi.org/software/hwloc/v1.9/downloads/hwloc-1.9.tar.gz"
+    url      = "https://download.open-mpi.org/release/hwloc/v2.0/hwloc-2.0.2.tar.gz"
     list_url = "http://www.open-mpi.org/software/hwloc/"
     list_depth = 2
 
+    version('2.0.2',  '71d1211eaa4b25ac7ad80cf326784e87')
+    version('2.0.1',  '442b2482bb5b81983ed256522aadbf94')
+    version('2.0.0',  '027e6928ae0b5b64c821d0a71a61cd82')
+    version('1.11.9', '4d5f5da8b1d09731d82e865ecf3fa399')
     version('1.11.8', 'a0fa1c9109a4d8b4b6568e62cc9b6e30')
     version('1.11.7', '867a5266675e5bf1ef4ab66c459653f8')
     version('1.11.6', 'b4e95eadd2fbdb6d40bbd96be6f03c84')
@@ -58,24 +47,38 @@ class Hwloc(AutotoolsPackage):
     variant('libxml2', default=True, description="Build with libxml2")
     variant('pci', default=(sys.platform != 'darwin'),
             description="Support analyzing devices on PCI bus")
+    variant('shared', default=True, description="Build shared libraries")
+    variant(
+        'cairo',
+        default=False,
+        description='Enable the Cairo back-end of hwloc\'s lstopo command'
+    )
+
+    depends_on('pkgconfig', type='build')
 
     depends_on('cuda', when='+cuda')
     depends_on('libpciaccess', when='+pci')
     depends_on('libxml2', when='+libxml2')
-    depends_on('pkg-config', type='build')
+    depends_on('cairo', when='+cairo')
+    depends_on('numactl', when='@:1.11.9 platform=linux')
 
     def url_for_version(self, version):
         return "http://www.open-mpi.org/software/hwloc/v%s/downloads/hwloc-%s.tar.gz" % (version.up_to(2), version)
 
     def configure_args(self):
-        spec = self.spec
         args = [
-            "--enable-cuda" if '+cuda' in spec else "--disable-cuda",
-            "--enable-libxml2" if '+libxml2' in spec else "--disable-libxml2",
-            "--enable-pci" if '+pci' in spec else "--disable-pci",
             # Disable OpenCL, since hwloc might pick up an OpenCL
             # library at build time that is then not found at run time
             # (Alternatively, we could require OpenCL as dependency.)
             "--disable-opencl",
         ]
+        if '@2.0.0:' in self.spec:
+            args.append('--enable-netloc')
+
+        args.extend(self.enable_or_disable('cairo'))
+        args.extend(self.enable_or_disable('cuda'))
+        args.extend(self.enable_or_disable('libxml2'))
+        args.extend(self.enable_or_disable('pci'))
+        args.extend(self.enable_or_disable('shared'))
+
         return args
diff --git a/var/spack/repos/builtin/packages/hybpiper/package.py b/var/spack/repos/builtin/packages/hybpiper/package.py
index c3e3a22b13..fba2f13a2a 100644
--- a/var/spack/repos/builtin/packages/hybpiper/package.py
+++ b/var/spack/repos/builtin/packages/hybpiper/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
 import os
diff --git a/var/spack/repos/builtin/packages/hydra/package.py b/var/spack/repos/builtin/packages/hydra/package.py
index 428f7db386..bcf4665c5d 100644
--- a/var/spack/repos/builtin/packages/hydra/package.py
+++ b/var/spack/repos/builtin/packages/hydra/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/hydrogen/package.py b/var/spack/repos/builtin/packages/hydrogen/package.py
new file mode 100644
index 0000000000..9a65ea4fe3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hydrogen/package.py
@@ -0,0 +1,156 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import os
+import sys
+from spack import *
+
+
+class Hydrogen(CMakePackage):
+    """Hydrogen: Distributed-memory dense and sparse-direct linear algebra
+       and optimization library. Based on the Elemental library."""
+
+    homepage = "http://libelemental.org"
+    url      = "https://github.com/LLNL/Elemental/archive/0.99.tar.gz"
+    git      = "https://github.com/LLNL/Elemental.git"
+
+    version('develop', branch='hydrogen')
+    version('1.0', sha256='d8a97de3133f2c6b6bb4b80d32b4a4cc25eb25e0df4f0cec0f8cb19bf34ece98')
+    version('0.99', 'b678433ab1d498da47acf3dc5e056c23')
+
+    variant('shared', default=True,
+            description='Enables the build of shared libraries')
+    variant('hybrid', default=True,
+            description='Make use of OpenMP within MPI packing/unpacking')
+    variant('openmp_blas', default=False,
+            description='Use OpenMP for threading in the BLAS library')
+    variant('quad', default=False,
+            description='Enable quad precision')
+    variant('int64', default=False,
+            description='Use 64bit integers')
+    variant('int64_blas', default=False,
+            description='Use 64bit integers for BLAS.')
+    variant('scalapack', default=False,
+            description='Build with ScaLAPACK library')
+    variant('build_type', default='Release',
+            description='The build type to build',
+            values=('Debug', 'Release'))
+    variant('blas', default='openblas', values=('openblas', 'mkl', 'accelerate', 'essl'),
+            description='Enable the use of OpenBlas/MKL/Accelerate/ESSL')
+    variant('mpfr', default=False,
+            description='Support GNU MPFR\'s'
+            'arbitrary-precision floating-point arithmetic')
+    variant('cuda', default=False,
+            description='Builds with support for GPUs via CUDA and cuDNN')
+    variant('test', default=False,
+            description='Builds test suite')
+    variant('al', default=False,
+            description='Builds with Aluminum communication library')
+    variant('omp_taskloops', default=False,
+            description='Use OpenMP taskloops instead of parallel for loops.')
+
+    # Note that #1712 forces us to enumerate the different blas variants
+    depends_on('openblas', when='blas=openblas ~openmp_blas ~int64_blas')
+    depends_on('openblas +ilp64', when='blas=openblas ~openmp_blas +int64_blas')
+    depends_on('openblas threads=openmp', when='blas=openblas +openmp_blas ~int64_blas')
+    depends_on('openblas threads=openmp +lip64', when='blas=openblas +openmp_blas +int64_blas')
+
+    depends_on('intel-mkl', when="blas=mkl ~openmp_blas ~int64_blas")
+    depends_on('intel-mkl +ilp64', when="blas=mkl ~openmp_blas +int64_blas")
+    depends_on('intel-mkl threads=openmp', when='blas=mkl +openmp_blas ~int64_blas')
+    depends_on('intel-mkl@2017.1 +openmp +ilp64', when='blas=mkl +openmp_blas +int64_blas')
+
+    depends_on('veclibfort', when='blas=accelerate')
+    conflicts('blas=accelerate +openmp_blas')
+
+    depends_on('essl -cuda', when='blas=essl -openmp_blas ~int64_blas')
+    depends_on('essl -cuda +ilp64', when='blas=essl -openmp_blas +int64_blas')
+    depends_on('essl threads=openmp', when='blas=essl +openmp_blas ~int64_blas')
+    depends_on('essl threads=openmp +ilp64', when='blas=essl +openmp_blas +int64_blas')
+    depends_on('netlib-lapack +external-blas', when='blas=essl')
+
+    depends_on('aluminum@master', when='+al ~cuda')
+    depends_on('aluminum@master +gpu +mpi-cuda', when='+al +cuda ~nccl')
+    depends_on('aluminum@master +gpu +nccl +mpi_cuda', when='+al +cuda +nccl')
+
+    # Note that this forces us to use OpenBLAS until #1712 is fixed
+    depends_on('lapack', when='blas=openblas ~openmp_blas')
+
+    depends_on('mpi', when='~cuda')
+    depends_on('mpi +cuda', when='+cuda')
+
+    depends_on('scalapack', when='+scalapack')
+    depends_on('gmp', when='+mpfr')
+    depends_on('mpc', when='+mpfr')
+    depends_on('mpfr', when='+mpfr')
+
+    depends_on('cuda', when='+cuda')
+    depends_on('cudnn', when='+cuda')
+    depends_on('cub', when='+cuda')
+
+    conflicts('@0:0.98', msg="Hydrogen did not exist before v0.99. " +
+              "Did you mean to use Elemental instead?")
+
+    @property
+    def libs(self):
+        shared = True if '+shared' in self.spec else False
+        return find_libraries(
+            'libEl', root=self.prefix, shared=shared, recursive=True
+        )
+
+    def cmake_args(self):
+        spec = self.spec
+
+        args = [
+            '-DCMAKE_INSTALL_MESSAGE:STRING=LAZY',
+            '-DCMAKE_C_COMPILER=%s' % spec['mpi'].mpicc,
+            '-DCMAKE_CXX_COMPILER=%s' % spec['mpi'].mpicxx,
+            '-DCMAKE_Fortran_COMPILER=%s' % spec['mpi'].mpifc,
+            '-DBUILD_SHARED_LIBS:BOOL=%s'      % ('+shared' in spec),
+            '-DHydrogen_ENABLE_OPENMP:BOOL=%s'       % ('+hybrid' in spec),
+            '-DHydrogen_ENABLE_QUADMATH:BOOL=%s'     % ('+quad' in spec),
+            '-DHydrogen_USE_64BIT_INTS:BOOL=%s'      % ('+int64' in spec),
+            '-DHydrogen_USE_64BIT_BLAS_INTS:BOOL=%s' % ('+int64_blas' in spec),
+            '-DHydrogen_ENABLE_MPC:BOOL=%s'        % ('+mpfr' in spec),
+            '-DHydrogen_GENERAL_LAPACK_FALLBACK=ON',
+            '-DHydrogen_ENABLE_CUDA=%s' % ('+cuda' in spec),
+            '-DHydrogen_ENABLE_TESTING=%s' % ('+test' in spec),
+        ]
+
+        # Add support for OS X to find OpenMP
+        if (self.spec.satisfies('%clang')):
+            if (sys.platform == 'darwin'):
+                clang = self.compiler.cc
+                clang_bin = os.path.dirname(clang)
+                clang_root = os.path.dirname(clang_bin)
+                args.extend([
+                    '-DOpenMP_DIR={0}'.format(clang_root)])
+
+        if 'blas=openblas' in spec:
+            args.extend([
+                '-DHydrogen_USE_OpenBLAS:BOOL=%s' % ('blas=openblas' in spec),
+                '-DOpenBLAS_DIR:STRING={0}'.format(
+                    spec['openblas'].prefix)])
+        elif 'blas=mkl' in spec:
+            args.extend([
+                '-DHydrogen_USE_MKL:BOOL=%s' % ('blas=mkl' in spec)])
+        elif 'blas=accelerate' in spec:
+            args.extend(['-DHydrogen_USE_ACCELERATE:BOOL=TRUE'])
+        elif 'blas=essl' in spec:
+            args.extend([
+                '-DHydrogen_USE_ESSL:BOOL=%s' % ('blas=essl' in spec)])
+
+        if '+omp_taskloops' in spec:
+            args.extend([
+                '-DHydrogen_ENABLE_OMP_TASKLOOP:BOOL=%s' %
+                ('+omp_taskloops' in spec)])
+
+        if '+al' in spec:
+            args.extend([
+                '-DHydrogen_ENABLE_ALUMINUM:BOOL=%s' % ('+al' in spec),
+                '-DHYDROGEN_Aluminum_DIR={0}'.format(
+                    spec['aluminum'].prefix)])
+
+        return args
diff --git a/var/spack/repos/builtin/packages/hypre/darwin-shared-libs-for-hypre-2.13.0.patch b/var/spack/repos/builtin/packages/hypre/darwin-shared-libs-for-hypre-2.13.0.patch
new file mode 100644
index 0000000000..a793bec8fc
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hypre/darwin-shared-libs-for-hypre-2.13.0.patch
@@ -0,0 +1,578 @@
+From c8467e905debeff23b8403aab7184e128decbba3 Mon Sep 17 00:00:00 2001
+From: Geoffrey Malcolm Oxberry <goxberry@gmail.com>
+Date: Tue, 11 Sep 2018 17:46:30 -0700
+Subject: [PATCH] build system: patch to build macOS shared libs
+
+---
+ src/FEI_mv/fei-hypre/Makefile         | 4 ++--
+ src/FEI_mv/femli/Makefile             | 4 ++--
+ src/IJ_mv/Makefile                    | 4 ++--
+ src/config/configure.in               | 9 +++++++--
+ src/configure                         | 9 +++++++--
+ src/distributed_ls/Euclid/Makefile    | 4 ++--
+ src/distributed_ls/ParaSails/Makefile | 4 ++--
+ src/distributed_ls/pilut/Makefile     | 4 ++--
+ src/distributed_matrix/Makefile       | 4 ++--
+ src/krylov/Makefile                   | 4 ++--
+ src/lib/Makefile                      | 4 ++--
+ src/matrix_matrix/Makefile            | 4 ++--
+ src/multivector/Makefile              | 4 ++--
+ src/parcsr_block_mv/Makefile          | 4 ++--
+ src/parcsr_ls/Makefile                | 4 ++--
+ src/parcsr_mv/Makefile                | 4 ++--
+ src/seq_mv/Makefile                   | 4 ++--
+ src/sstruct_ls/Makefile               | 4 ++--
+ src/sstruct_mv/Makefile               | 4 ++--
+ src/struct_ls/Makefile                | 4 ++--
+ src/struct_mv/Makefile                | 4 ++--
+ src/test/Makefile                     | 8 +++++---
+ src/utilities/Makefile                | 4 ++--
+ 23 files changed, 59 insertions(+), 47 deletions(-)
+
+diff --git a/src/FEI_mv/fei-hypre/Makefile b/src/FEI_mv/fei-hypre/Makefile
+index 09cad91df..68e5b394b 100644
+--- a/src/FEI_mv/fei-hypre/Makefile
++++ b/src/FEI_mv/fei-hypre/Makefile
+@@ -159,7 +159,7 @@ OBJSC = ${FILESC:.c=.o}
+ OBJSCXX = ${FILESCXX:.cxx=.o}
+ OBJS = ${OBJSC} ${OBJSCXX}
+ 
+-SONAME = libHYPRE_FEI-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_FEI-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -211,7 +211,7 @@ libHYPRE_FEI.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_FEI.so: ${OBJS}
++libHYPRE_FEI.so libHYPRE_FEI.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/FEI_mv/femli/Makefile b/src/FEI_mv/femli/Makefile
+index eac52137f..2beea900e 100644
+--- a/src/FEI_mv/femli/Makefile
++++ b/src/FEI_mv/femli/Makefile
+@@ -128,7 +128,7 @@ OBJSC = ${FILES:.c=.o}
+ OBJSCXX = ${OBJSC:.cxx=.o}
+ OBJS = ${OBJSCXX:.f=.o}
+ 
+-SONAME = libHYPRE_mli-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_mli-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -156,7 +156,7 @@ libHYPRE_mli.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_mli.so: ${OBJS}
++libHYPRE_mli.so libHYPRE_mli.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/IJ_mv/Makefile b/src/IJ_mv/Makefile
+index ab014ff7d..4f92e717a 100644
+--- a/src/IJ_mv/Makefile
++++ b/src/IJ_mv/Makefile
+@@ -53,7 +53,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_IJ_mv-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_IJ_mv-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -84,7 +84,7 @@ libHYPRE_IJ_mv.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_IJ_mv.so: ${OBJS}
++libHYPRE_IJ_mv.so libHYPRE_IJ_mv.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/config/configure.in b/src/config/configure.in
+index de8a10255..8f2d2c90e 100644
+--- a/src/config/configure.in
++++ b/src/config/configure.in
+@@ -1383,6 +1383,8 @@ dnl *********************************************************************
+ if test "$hypre_using_shared" = "yes"
+ then
+    HYPRE_LIBSUFFIX=".so"
++   SHARED_SET_SONAME="-Wl,-soname,"
++   SHARED_OPTIONS="-Wl,-z,defs"
+    case $hypre_platform in
+       AIX* | aix* | Aix*) SHARED_COMPILE_FLAG="-qmkshrobj"
+                           SHARED_BUILD_FLAG="-G"
+@@ -1390,6 +1392,11 @@ dnl                          LINK_F77="${F77} -brtl"
+                           LINK_FC="${FC} -brtl"
+                           LINK_CC="${CC} -brtl"
+                           LINK_CXX="${CXX} -brtl" ;;
++      DARWIN* | darwin* | Darwin*) SHARED_COMPILE_FLAG="-fPIC"
++                                   SHARED_BUILD_FLAG="-dynamiclib -undefined dynamic_lookup"
++				   HYPRE_LIBSUFFIX=".dylib"
++				   SHARED_SET_SONAME="-install_name @rpath/"
++				   SHARED_OPTIONS="-undefined error" ;;
+                        *) SHARED_COMPILE_FLAG="-fPIC"
+                           SHARED_BUILD_FLAG="-shared" ;;
+    esac
+@@ -1405,8 +1412,6 @@ dnl   BUILD_F77_SHARED="${F77} ${SHARED_BUILD_FLAG}"
+       BUILD_CC_SHARED="${CC} ${SHARED_BUILD_FLAG}"
+    fi
+    BUILD_CXX_SHARED="${CXX} ${SHARED_BUILD_FLAG}"
+-   SHARED_SET_SONAME="-Wl,-soname,"
+-   SHARED_OPTIONS="-Wl,-z,defs"
+ fi
+ 
+ BUILD_PYTHON=0
+diff --git a/src/configure b/src/configure
+index fa3d0717a..763a62dc5 100755
+--- a/src/configure
++++ b/src/configure
+@@ -7676,12 +7676,19 @@ HYPRE_LIBSUFFIX=".a"
+ if test "$hypre_using_shared" = "yes"
+ then
+    HYPRE_LIBSUFFIX=".so"
++   SHARED_SET_SONAME="-Wl,-soname,"
++   SHARED_OPTIONS="-Wl,-z,defs"
+    case $hypre_platform in
+       AIX* | aix* | Aix*) SHARED_COMPILE_FLAG="-qmkshrobj"
+                           SHARED_BUILD_FLAG="-G"
+                           LINK_FC="${FC} -brtl"
+                           LINK_CC="${CC} -brtl"
+                           LINK_CXX="${CXX} -brtl" ;;
++      DARWIN* | darwin* | Darwin*) SHARED_COMPILE_FLAG="-fPIC"
++                                   SHARED_BUILD_FLAG="-dynamiclib -undefined dynamic_lookup"
++				   HYPRE_LIBSUFFIX=".dylib"
++				   SHARED_SET_SONAME="-install_name @rpath/"
++				   SHARED_OPTIONS="-undefined error" ;;
+                        *) SHARED_COMPILE_FLAG="-fPIC"
+                           SHARED_BUILD_FLAG="-shared" ;;
+    esac
+@@ -7696,8 +7703,6 @@ then
+       BUILD_CC_SHARED="${CC} ${SHARED_BUILD_FLAG}"
+    fi
+    BUILD_CXX_SHARED="${CXX} ${SHARED_BUILD_FLAG}"
+-   SHARED_SET_SONAME="-Wl,-soname,"
+-   SHARED_OPTIONS="-Wl,-z,defs"
+ fi
+ 
+ BUILD_PYTHON=0
+diff --git a/src/distributed_ls/Euclid/Makefile b/src/distributed_ls/Euclid/Makefile
+index 03d9db355..b8b71dddd 100644
+--- a/src/distributed_ls/Euclid/Makefile
++++ b/src/distributed_ls/Euclid/Makefile
+@@ -87,7 +87,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_Euclid-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_Euclid-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -114,7 +114,7 @@ libHYPRE_Euclid.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_Euclid.so: ${OBJS}
++libHYPRE_Euclid.so libHYPRE_Euclid.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/distributed_ls/ParaSails/Makefile b/src/distributed_ls/ParaSails/Makefile
+index fe881b1f3..78091ad88 100644
+--- a/src/distributed_ls/ParaSails/Makefile
++++ b/src/distributed_ls/ParaSails/Makefile
+@@ -59,7 +59,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_ParaSails-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_ParaSails-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -86,7 +86,7 @@ libHYPRE_ParaSails.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_ParaSails.so: ${OBJS}
++libHYPRE_ParaSails.so libHYPRE_ParaSails.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/distributed_ls/pilut/Makefile b/src/distributed_ls/pilut/Makefile
+index 2ed918e2c..333edbafa 100644
+--- a/src/distributed_ls/pilut/Makefile
++++ b/src/distributed_ls/pilut/Makefile
+@@ -49,7 +49,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_DistributedMatrixPilutSolver-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_DistributedMatrixPilutSolver-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -78,7 +78,7 @@ libHYPRE_DistributedMatrixPilutSolver.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_DistributedMatrixPilutSolver.so: ${OBJS}
++libHYPRE_DistributedMatrixPilutSolver.so libHYPRE_DistributedMatrixPilutSolver.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/distributed_matrix/Makefile b/src/distributed_matrix/Makefile
+index b8d42944c..d30908fa2 100644
+--- a/src/distributed_matrix/Makefile
++++ b/src/distributed_matrix/Makefile
+@@ -40,7 +40,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_DistributedMatrix-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_DistributedMatrix-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -69,7 +69,7 @@ libHYPRE_DistributedMatrix.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_DistributedMatrix.so: ${OBJS}
++libHYPRE_DistributedMatrix.so libHYPRE_DistributedMatrix.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/krylov/Makefile b/src/krylov/Makefile
+index 152d5153a..63d085431 100644
+--- a/src/krylov/Makefile
++++ b/src/krylov/Makefile
+@@ -55,7 +55,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_krylov-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_krylov-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -88,7 +88,7 @@ libHYPRE_krylov.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_krylov.so: ${OBJS}
++libHYPRE_krylov.so libHYPRE_krylov.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/lib/Makefile b/src/lib/Makefile
+index 72875e2c1..f49d16838 100644
+--- a/src/lib/Makefile
++++ b/src/lib/Makefile
+@@ -57,7 +57,7 @@ $(UTILITIESFILES)\
+ $(BLASFILES)\
+ $(LAPACKFILES)
+ 
+-SONAME = libHYPRE-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ SOLIBS = ${MPILIBDIRS} ${MPILIBS} ${LAPACKLIBDIRS} ${LAPACKLIBS}\
+  ${BLASLIBDIRS} ${BLASLIBS} ${LIBS} ${FLIBS}
+ 
+@@ -103,7 +103,7 @@ libHYPRE.a: ${FILES_HYPRE}
+ 	${AR} $@ $(UTILITIESFILES) $(BLASFILES) $(LAPACKFILES)
+ 	${RANLIB} $@
+ 
+-libHYPRE.so: ${FILES_HYPRE}
++libHYPRE.so libHYPRE.dylib: ${FILES_HYPRE}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${FILES_HYPRE} ${SOLIBS} ${SHARED_SET_SONAME}${SONAME} ${SHARED_OPTIONS} ${LDFLAGS}
+ 	ln -s ${SONAME} $@
+diff --git a/src/matrix_matrix/Makefile b/src/matrix_matrix/Makefile
+index 1da8ced0e..a611bee51 100644
+--- a/src/matrix_matrix/Makefile
++++ b/src/matrix_matrix/Makefile
+@@ -35,7 +35,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_MatrixMatrix-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_MatrixMatrix-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -64,7 +64,7 @@ libHYPRE_MatrixMatrix.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_MatrixMatrix.so: ${OBJS}
++libHYPRE_MatrixMatrix.so libHYPRE_MatrixMatrix.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/multivector/Makefile b/src/multivector/Makefile
+index 915cf5e0e..fce270f13 100644
+--- a/src/multivector/Makefile
++++ b/src/multivector/Makefile
+@@ -31,7 +31,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_multivector-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_multivector-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -60,7 +60,7 @@ libHYPRE_multivector.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_multivector.so: ${OBJS}
++libHYPRE_multivector.so libHYPRE_multivector.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/parcsr_block_mv/Makefile b/src/parcsr_block_mv/Makefile
+index 3f1e33db1..b7559d39e 100644
+--- a/src/parcsr_block_mv/Makefile
++++ b/src/parcsr_block_mv/Makefile
+@@ -59,7 +59,7 @@ DRIVER_FILES =
+ OBJS = ${FILES:.c=.o}
+ DRIVER_OBJS = ${DRIVER_FILES:.c=.o}
+ 
+-SONAME = libHYPRE_parcsr_block_mv-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_parcsr_block_mv-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -114,7 +114,7 @@ libHYPRE_parcsr_block_mv.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_parcsr_block_mv.so: ${OBJS}
++libHYPRE_parcsr_block_mv.so libHYPRE_parcsr_block_mv.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/parcsr_ls/Makefile b/src/parcsr_ls/Makefile
+index 74972be17..7670387e0 100644
+--- a/src/parcsr_ls/Makefile
++++ b/src/parcsr_ls/Makefile
+@@ -133,7 +133,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_parcsr_ls-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_parcsr_ls-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -165,7 +165,7 @@ libHYPRE_parcsr_ls.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_parcsr_ls.so: ${OBJS}
++libHYPRE_parcsr_ls.so libHYPRE_parcsr_ls.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/parcsr_mv/Makefile b/src/parcsr_mv/Makefile
+index 99b4f7ba8..ff027bb30 100644
+--- a/src/parcsr_mv/Makefile
++++ b/src/parcsr_mv/Makefile
+@@ -71,7 +71,7 @@ DRIVER_FILES =\
+ OBJS = ${FILES:.c=.o}
+ DRIVER_OBJS = ${DRIVER_FILES:.c=.o}
+ 
+-SONAME = libHYPRE_parcsr_mv-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_parcsr_mv-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -127,7 +127,7 @@ libHYPRE_parcsr_mv.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_parcsr_mv.so: ${OBJS}
++libHYPRE_parcsr_mv.so libHYPRE_parcsr_mv.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/seq_mv/Makefile b/src/seq_mv/Makefile
+index 6982fa067..b0692cd26 100644
+--- a/src/seq_mv/Makefile
++++ b/src/seq_mv/Makefile
+@@ -49,7 +49,7 @@ FILES =\
+ OBJS = ${FILES:.c=.o}
+ CUOBJS = ${FILES_NVCC:.cu=.o}
+ 
+-SONAME = libHYPRE_seq_mv-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_seq_mv-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -80,7 +80,7 @@ libHYPRE_seq_mv.a: ${OBJS} ${CUOBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_seq_mv.so: ${OBJS} ${CUOBJS}
++libHYPRE_seq_mv.so libHYPRE_seq_mv.dylib: ${OBJS} ${CUOBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/sstruct_ls/Makefile b/src/sstruct_ls/Makefile
+index 28811f8bf..463843d9a 100644
+--- a/src/sstruct_ls/Makefile
++++ b/src/sstruct_ls/Makefile
+@@ -109,7 +109,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_sstruct_ls-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_sstruct_ls-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -140,7 +140,7 @@ libHYPRE_sstruct_ls.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_sstruct_ls.so: ${OBJS}
++libHYPRE_sstruct_ls.so libHYPRE_sstruct_ls.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/sstruct_mv/Makefile b/src/sstruct_mv/Makefile
+index d9adda815..1f4dfc029 100644
+--- a/src/sstruct_mv/Makefile
++++ b/src/sstruct_mv/Makefile
+@@ -59,7 +59,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_sstruct_mv-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_sstruct_mv-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -90,7 +90,7 @@ libHYPRE_sstruct_mv.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_sstruct_mv.so: ${OBJS}
++libHYPRE_sstruct_mv.so libHYPRE_sstruct_mv.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/struct_ls/Makefile b/src/struct_ls/Makefile
+index 4653b733d..007529823 100644
+--- a/src/struct_ls/Makefile
++++ b/src/struct_ls/Makefile
+@@ -104,7 +104,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_struct_ls-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_struct_ls-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -135,7 +135,7 @@ libHYPRE_struct_ls.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_struct_ls.so: ${OBJS}
++libHYPRE_struct_ls.so libHYPRE_struct_ls.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/struct_mv/Makefile b/src/struct_mv/Makefile
+index eabf9b00f..349947a4f 100644
+--- a/src/struct_mv/Makefile
++++ b/src/struct_mv/Makefile
+@@ -66,7 +66,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_struct_mv-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_struct_mv-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -97,7 +97,7 @@ libHYPRE_struct_mv.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_struct_mv.so: ${OBJS}
++libHYPRE_struct_mv.so libHYPRE_struct_mv.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/test/Makefile b/src/test/Makefile
+index 17e8f465d..4616c6de4 100644
+--- a/src/test/Makefile
++++ b/src/test/Makefile
+@@ -40,7 +40,7 @@ F77_COMPILE_FLAGS = \
+  -I${HYPRE_BUILD_DIR}/include\
+  ${CINCLUDES}
+ 
+-MPILIBFLAGS = ${MPILIBDIRS} ${MPILIBS} ${MPIFLAGS} 
++MPILIBFLAGS = ${MPILIBDIRS} ${MPILIBS} ${MPIFLAGS}
+ LAPACKLIBFLAGS = ${LAPACKLIBDIRS} ${LAPACKLIBS}
+ BLASLIBFLAGS = ${BLASLIBDIRS} ${BLASLIBS}
+ LIBFLAGS = ${LDFLAGS} ${LIBS}
+@@ -48,6 +48,9 @@ LIBFLAGS = ${LDFLAGS} ${LIBS}
+ LFLAGS =\
+  -L${HYPRE_BUILD_DIR}/lib\
+  -lHYPRE\
++ -Wl,-rpath,${HYPRE_BUILD_DIR}/lib\
++ ${DSUPERLU_LIBS}\
++ ${SUPERLU_LIBS}\
+  ${MPILIBFLAGS}\
+  ${LAPACKLIBFLAGS}\
+  ${BLASLIBFLAGS}\
+@@ -265,7 +268,7 @@ fparcsr_mv: fparcsr_mv.f
+ 	@echo  "Building" $@ "... "
+ 	${LINK_FC} -c $@
+ 
+-fsstruct_ls: fsstruct_ls.f 
++fsstruct_ls: fsstruct_ls.f
+ 	@echo  "Building" $@ "... "
+ 	${LINK_FC} -c $@
+ 
+@@ -280,4 +283,3 @@ fstruct_ls: fstruct_ls.f
+ fstruct_mv: fstruct_mv.f
+ 	@echo  "Building" $@ "... "
+ 	${LINK_FC} -c $@
+-
+diff --git a/src/utilities/Makefile b/src/utilities/Makefile
+index 512e6d0be..c1710766a 100644
+--- a/src/utilities/Makefile
++++ b/src/utilities/Makefile
+@@ -66,7 +66,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_utilities-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_utilities-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -100,7 +100,7 @@ libHYPRE_utilities.a: ${OBJS}
+ 	${AR} $@ *.o
+ 	${RANLIB} $@
+ 
+-libHYPRE_utilities.so: ${OBJS}
++libHYPRE_utilities.so libHYPRE_utilities.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+-- 
+2.19.0
+
diff --git a/var/spack/repos/builtin/packages/hypre/darwin-shared-libs-for-hypre-2.14.0.patch b/var/spack/repos/builtin/packages/hypre/darwin-shared-libs-for-hypre-2.14.0.patch
new file mode 100644
index 0000000000..1d563f9a42
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hypre/darwin-shared-libs-for-hypre-2.14.0.patch
@@ -0,0 +1,553 @@
+From c5db8367db7873cabe2d7e60a577eb1eb158f364 Mon Sep 17 00:00:00 2001
+From: Geoffrey Malcolm Oxberry <goxberry@gmail.com>
+Date: Tue, 11 Sep 2018 17:46:30 -0700
+Subject: [PATCH] build system: patch to build macOS shared libs
+
+---
+ src/FEI_mv/fei-hypre/Makefile         | 4 ++--
+ src/FEI_mv/femli/Makefile             | 4 ++--
+ src/IJ_mv/Makefile                    | 4 ++--
+ src/config/configure.in               | 9 +++++++--
+ src/configure                         | 9 +++++++--
+ src/distributed_ls/Euclid/Makefile    | 4 ++--
+ src/distributed_ls/ParaSails/Makefile | 4 ++--
+ src/distributed_ls/pilut/Makefile     | 4 ++--
+ src/distributed_matrix/Makefile       | 4 ++--
+ src/krylov/Makefile                   | 4 ++--
+ src/lib/Makefile                      | 4 ++--
+ src/matrix_matrix/Makefile            | 4 ++--
+ src/multivector/Makefile              | 4 ++--
+ src/parcsr_block_mv/Makefile          | 4 ++--
+ src/parcsr_ls/Makefile                | 4 ++--
+ src/parcsr_mv/Makefile                | 4 ++--
+ src/seq_mv/Makefile                   | 4 ++--
+ src/sstruct_ls/Makefile               | 4 ++--
+ src/sstruct_mv/Makefile               | 4 ++--
+ src/struct_ls/Makefile                | 4 ++--
+ src/struct_mv/Makefile                | 4 ++--
+ src/test/Makefile                     | 1 +
+ src/utilities/Makefile                | 4 ++--
+ 23 files changed, 55 insertions(+), 44 deletions(-)
+
+diff --git a/src/FEI_mv/fei-hypre/Makefile b/src/FEI_mv/fei-hypre/Makefile
+index 09cad91df..68e5b394b 100644
+--- a/src/FEI_mv/fei-hypre/Makefile
++++ b/src/FEI_mv/fei-hypre/Makefile
+@@ -159,7 +159,7 @@ OBJSC = ${FILESC:.c=.o}
+ OBJSCXX = ${FILESCXX:.cxx=.o}
+ OBJS = ${OBJSC} ${OBJSCXX}
+ 
+-SONAME = libHYPRE_FEI-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_FEI-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -211,7 +211,7 @@ libHYPRE_FEI.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_FEI.so: ${OBJS}
++libHYPRE_FEI.so libHYPRE_FEI.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/FEI_mv/femli/Makefile b/src/FEI_mv/femli/Makefile
+index 07bf5dff3..499757ffa 100644
+--- a/src/FEI_mv/femli/Makefile
++++ b/src/FEI_mv/femli/Makefile
+@@ -129,7 +129,7 @@ OBJSC = ${FILES:.c=.o}
+ OBJSCXX = ${OBJSC:.cxx=.o}
+ OBJS = ${OBJSCXX:.f=.o}
+ 
+-SONAME = libHYPRE_mli-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_mli-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -157,7 +157,7 @@ libHYPRE_mli.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_mli.so: ${OBJS}
++libHYPRE_mli.so libHYPRE_mli.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/IJ_mv/Makefile b/src/IJ_mv/Makefile
+index ab014ff7d..4f92e717a 100644
+--- a/src/IJ_mv/Makefile
++++ b/src/IJ_mv/Makefile
+@@ -53,7 +53,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_IJ_mv-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_IJ_mv-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -84,7 +84,7 @@ libHYPRE_IJ_mv.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_IJ_mv.so: ${OBJS}
++libHYPRE_IJ_mv.so libHYPRE_IJ_mv.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/config/configure.in b/src/config/configure.in
+index c0a0e3091..c05e13cd2 100644
+--- a/src/config/configure.in
++++ b/src/config/configure.in
+@@ -1413,6 +1413,8 @@ dnl *********************************************************************
+ if test "$hypre_using_shared" = "yes"
+ then
+    HYPRE_LIBSUFFIX=".so"
++   SHARED_SET_SONAME="-Wl,-soname,"
++   SHARED_OPTIONS="-Wl,-z,defs"
+    case $hypre_platform in
+       AIX* | aix* | Aix*) SHARED_COMPILE_FLAG="-qmkshrobj"
+                           SHARED_BUILD_FLAG="-G"
+@@ -1420,6 +1422,11 @@ dnl                          LINK_F77="${F77} -brtl"
+                           LINK_FC="${FC} -brtl"
+                           LINK_CC="${CC} -brtl"
+                           LINK_CXX="${CXX} -brtl" ;;
++      DARWIN* | darwin* | Darwin*) SHARED_COMPILE_FLAG="-fPIC"
++                                   SHARED_BUILD_FLAG="-dynamiclib -undefined dynamic_lookup"
++				   HYPRE_LIBSUFFIX=".dylib"
++				   SHARED_SET_SONAME="-install_name @rpath/"
++				   SHARED_OPTIONS="-undefined error" ;;
+                        *) SHARED_COMPILE_FLAG="-fPIC"
+                           SHARED_BUILD_FLAG="-shared" ;;
+    esac
+@@ -1435,8 +1442,6 @@ dnl   BUILD_F77_SHARED="${F77} ${SHARED_BUILD_FLAG}"
+       BUILD_CC_SHARED="${CC} ${SHARED_BUILD_FLAG}"
+    fi
+    BUILD_CXX_SHARED="${CXX} ${SHARED_BUILD_FLAG}"
+-   SHARED_SET_SONAME="-Wl,-soname,"
+-   SHARED_OPTIONS="-Wl,-z,defs"
+ fi
+ 
+ BUILD_PYTHON=0
+diff --git a/src/configure b/src/configure
+index c4b2e42cf..2de08ceae 100755
+--- a/src/configure
++++ b/src/configure
+@@ -7876,12 +7876,19 @@ HYPRE_LIBSUFFIX=".a"
+ if test "$hypre_using_shared" = "yes"
+ then
+    HYPRE_LIBSUFFIX=".so"
++   SHARED_SET_SONAME="-Wl,-soname,"
++   SHARED_OPTIONS="-Wl,-z,defs"
+    case $hypre_platform in
+       AIX* | aix* | Aix*) SHARED_COMPILE_FLAG="-qmkshrobj"
+                           SHARED_BUILD_FLAG="-G"
+                           LINK_FC="${FC} -brtl"
+                           LINK_CC="${CC} -brtl"
+                           LINK_CXX="${CXX} -brtl" ;;
++      DARWIN* | darwin* | Darwin*) SHARED_COMPILE_FLAG="-fPIC"
++                                   SHARED_BUILD_FLAG="-dynamiclib -undefined dynamic_lookup"
++				   HYPRE_LIBSUFFIX=".dylib"
++				   SHARED_SET_SONAME="-install_name @rpath/"
++				   SHARED_OPTIONS="-undefined error" ;;
+                        *) SHARED_COMPILE_FLAG="-fPIC"
+                           SHARED_BUILD_FLAG="-shared" ;;
+    esac
+@@ -7896,8 +7903,6 @@ then
+       BUILD_CC_SHARED="${CC} ${SHARED_BUILD_FLAG}"
+    fi
+    BUILD_CXX_SHARED="${CXX} ${SHARED_BUILD_FLAG}"
+-   SHARED_SET_SONAME="-Wl,-soname,"
+-   SHARED_OPTIONS="-Wl,-z,defs"
+ fi
+ 
+ BUILD_PYTHON=0
+diff --git a/src/distributed_ls/Euclid/Makefile b/src/distributed_ls/Euclid/Makefile
+index 03d9db355..b8b71dddd 100644
+--- a/src/distributed_ls/Euclid/Makefile
++++ b/src/distributed_ls/Euclid/Makefile
+@@ -87,7 +87,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_Euclid-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_Euclid-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -114,7 +114,7 @@ libHYPRE_Euclid.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_Euclid.so: ${OBJS}
++libHYPRE_Euclid.so libHYPRE_Euclid.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/distributed_ls/ParaSails/Makefile b/src/distributed_ls/ParaSails/Makefile
+index fe881b1f3..78091ad88 100644
+--- a/src/distributed_ls/ParaSails/Makefile
++++ b/src/distributed_ls/ParaSails/Makefile
+@@ -59,7 +59,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_ParaSails-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_ParaSails-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -86,7 +86,7 @@ libHYPRE_ParaSails.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_ParaSails.so: ${OBJS}
++libHYPRE_ParaSails.so libHYPRE_ParaSails.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/distributed_ls/pilut/Makefile b/src/distributed_ls/pilut/Makefile
+index e24d4d224..67e00fb5b 100644
+--- a/src/distributed_ls/pilut/Makefile
++++ b/src/distributed_ls/pilut/Makefile
+@@ -50,7 +50,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_DistributedMatrixPilutSolver-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_DistributedMatrixPilutSolver-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -79,7 +79,7 @@ libHYPRE_DistributedMatrixPilutSolver.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_DistributedMatrixPilutSolver.so: ${OBJS}
++libHYPRE_DistributedMatrixPilutSolver.so libHYPRE_DistributedMatrixPilutSolver.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/distributed_matrix/Makefile b/src/distributed_matrix/Makefile
+index b8d42944c..d30908fa2 100644
+--- a/src/distributed_matrix/Makefile
++++ b/src/distributed_matrix/Makefile
+@@ -40,7 +40,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_DistributedMatrix-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_DistributedMatrix-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -69,7 +69,7 @@ libHYPRE_DistributedMatrix.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_DistributedMatrix.so: ${OBJS}
++libHYPRE_DistributedMatrix.so libHYPRE_DistributedMatrix.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/krylov/Makefile b/src/krylov/Makefile
+index bb3ec05cf..f4682b657 100644
+--- a/src/krylov/Makefile
++++ b/src/krylov/Makefile
+@@ -58,7 +58,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_krylov-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_krylov-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -91,7 +91,7 @@ libHYPRE_krylov.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_krylov.so: ${OBJS}
++libHYPRE_krylov.so libHYPRE_krylov.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/lib/Makefile b/src/lib/Makefile
+index 72875e2c1..f49d16838 100644
+--- a/src/lib/Makefile
++++ b/src/lib/Makefile
+@@ -57,7 +57,7 @@ $(UTILITIESFILES)\
+ $(BLASFILES)\
+ $(LAPACKFILES)
+ 
+-SONAME = libHYPRE-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ SOLIBS = ${MPILIBDIRS} ${MPILIBS} ${LAPACKLIBDIRS} ${LAPACKLIBS}\
+  ${BLASLIBDIRS} ${BLASLIBS} ${LIBS} ${FLIBS}
+ 
+@@ -103,7 +103,7 @@ libHYPRE.a: ${FILES_HYPRE}
+ 	${AR} $@ $(UTILITIESFILES) $(BLASFILES) $(LAPACKFILES)
+ 	${RANLIB} $@
+ 
+-libHYPRE.so: ${FILES_HYPRE}
++libHYPRE.so libHYPRE.dylib: ${FILES_HYPRE}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${FILES_HYPRE} ${SOLIBS} ${SHARED_SET_SONAME}${SONAME} ${SHARED_OPTIONS} ${LDFLAGS}
+ 	ln -s ${SONAME} $@
+diff --git a/src/matrix_matrix/Makefile b/src/matrix_matrix/Makefile
+index 1da8ced0e..a611bee51 100644
+--- a/src/matrix_matrix/Makefile
++++ b/src/matrix_matrix/Makefile
+@@ -35,7 +35,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_MatrixMatrix-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_MatrixMatrix-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -64,7 +64,7 @@ libHYPRE_MatrixMatrix.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_MatrixMatrix.so: ${OBJS}
++libHYPRE_MatrixMatrix.so libHYPRE_MatrixMatrix.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/multivector/Makefile b/src/multivector/Makefile
+index 915cf5e0e..fce270f13 100644
+--- a/src/multivector/Makefile
++++ b/src/multivector/Makefile
+@@ -31,7 +31,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_multivector-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_multivector-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -60,7 +60,7 @@ libHYPRE_multivector.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_multivector.so: ${OBJS}
++libHYPRE_multivector.so libHYPRE_multivector.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/parcsr_block_mv/Makefile b/src/parcsr_block_mv/Makefile
+index bac31a5ed..eba6d2589 100644
+--- a/src/parcsr_block_mv/Makefile
++++ b/src/parcsr_block_mv/Makefile
+@@ -61,7 +61,7 @@ DRIVER_FILES =
+ OBJS = ${FILES:.c=.o}
+ DRIVER_OBJS = ${DRIVER_FILES:.c=.o}
+ 
+-SONAME = libHYPRE_parcsr_block_mv-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_parcsr_block_mv-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -116,7 +116,7 @@ libHYPRE_parcsr_block_mv.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_parcsr_block_mv.so: ${OBJS}
++libHYPRE_parcsr_block_mv.so libHYPRE_parcsr_block_mv.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/parcsr_ls/Makefile b/src/parcsr_ls/Makefile
+index f25eda61f..980ccf283 100644
+--- a/src/parcsr_ls/Makefile
++++ b/src/parcsr_ls/Makefile
+@@ -139,7 +139,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_parcsr_ls-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_parcsr_ls-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -171,7 +171,7 @@ libHYPRE_parcsr_ls.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_parcsr_ls.so: ${OBJS}
++libHYPRE_parcsr_ls.so libHYPRE_parcsr_ls.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/parcsr_mv/Makefile b/src/parcsr_mv/Makefile
+index 87c697ad9..654be6dd1 100644
+--- a/src/parcsr_mv/Makefile
++++ b/src/parcsr_mv/Makefile
+@@ -73,7 +73,7 @@ DRIVER_FILES =\
+ OBJS = ${FILES:.c=.o}
+ DRIVER_OBJS = ${DRIVER_FILES:.c=.o}
+ 
+-SONAME = libHYPRE_parcsr_mv-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_parcsr_mv-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -129,7 +129,7 @@ libHYPRE_parcsr_mv.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_parcsr_mv.so: ${OBJS}
++libHYPRE_parcsr_mv.so libHYPRE_parcsr_mv.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/seq_mv/Makefile b/src/seq_mv/Makefile
+index 0f2c34d0d..da0b29a54 100644
+--- a/src/seq_mv/Makefile
++++ b/src/seq_mv/Makefile
+@@ -50,7 +50,7 @@ FILES =\
+ OBJS = ${FILES:.c=.o}
+ CUOBJS = ${FILES_NVCC:.cu=.o}
+ 
+-SONAME = libHYPRE_seq_mv-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_seq_mv-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -81,7 +81,7 @@ libHYPRE_seq_mv.a: ${OBJS} ${CUOBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_seq_mv.so: ${OBJS} ${CUOBJS}
++libHYPRE_seq_mv.so libHYPRE_seq_mv.dylib: ${OBJS} ${CUOBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/sstruct_ls/Makefile b/src/sstruct_ls/Makefile
+index b4511f4ab..0f2a0a1f3 100644
+--- a/src/sstruct_ls/Makefile
++++ b/src/sstruct_ls/Makefile
+@@ -111,7 +111,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_sstruct_ls-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_sstruct_ls-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -142,7 +142,7 @@ libHYPRE_sstruct_ls.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_sstruct_ls.so: ${OBJS}
++libHYPRE_sstruct_ls.so libHYPRE_sstruct_ls.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/sstruct_mv/Makefile b/src/sstruct_mv/Makefile
+index d9adda815..1f4dfc029 100644
+--- a/src/sstruct_mv/Makefile
++++ b/src/sstruct_mv/Makefile
+@@ -59,7 +59,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_sstruct_mv-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_sstruct_mv-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -90,7 +90,7 @@ libHYPRE_sstruct_mv.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_sstruct_mv.so: ${OBJS}
++libHYPRE_sstruct_mv.so libHYPRE_sstruct_mv.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/struct_ls/Makefile b/src/struct_ls/Makefile
+index 4653b733d..007529823 100644
+--- a/src/struct_ls/Makefile
++++ b/src/struct_ls/Makefile
+@@ -104,7 +104,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_struct_ls-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_struct_ls-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -135,7 +135,7 @@ libHYPRE_struct_ls.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_struct_ls.so: ${OBJS}
++libHYPRE_struct_ls.so libHYPRE_struct_ls.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/struct_mv/Makefile b/src/struct_mv/Makefile
+index eabf9b00f..349947a4f 100644
+--- a/src/struct_mv/Makefile
++++ b/src/struct_mv/Makefile
+@@ -66,7 +66,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_struct_mv-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_struct_mv-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -97,7 +97,7 @@ libHYPRE_struct_mv.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_struct_mv.so: ${OBJS}
++libHYPRE_struct_mv.so libHYPRE_struct_mv.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/test/Makefile b/src/test/Makefile
+index 86481720f..ec05bfcbd 100644
+--- a/src/test/Makefile
++++ b/src/test/Makefile
+@@ -52,6 +52,7 @@ LIBFLAGS = ${LDFLAGS} ${LIBS}
+ LFLAGS =\
+  -L${HYPRE_BUILD_DIR}/lib\
+  -lHYPRE\
++ -Wl,-rpath,${HYPRE_BUILD_DIR}/lib\
+  ${DSUPERLU_LIBS}\
+  ${SUPERLU_LIBS}\
+  ${MPILIBFLAGS}\
+diff --git a/src/utilities/Makefile b/src/utilities/Makefile
+index bd4a3fe67..a4993b9e4 100644
+--- a/src/utilities/Makefile
++++ b/src/utilities/Makefile
+@@ -64,7 +64,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_utilities-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_utilities-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -98,7 +98,7 @@ libHYPRE_utilities.a: ${OBJS}
+ 	${AR} $@ *.o
+ 	${RANLIB} $@
+ 
+-libHYPRE_utilities.so: ${OBJS}
++libHYPRE_utilities.so libHYPRE_utilities.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+-- 
+2.19.0
+
diff --git a/var/spack/repos/builtin/packages/hypre/package.py b/var/spack/repos/builtin/packages/hypre/package.py
index 8472d64337..c78cd16071 100644
--- a/var/spack/repos/builtin/packages/hypre/package.py
+++ b/var/spack/repos/builtin/packages/hypre/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 import sys
@@ -33,17 +14,25 @@ class Hypre(Package):
        unstructured grid problems."""
 
     homepage = "http://computation.llnl.gov/project/linear_solvers/software.php"
-    url      = "http://computation.llnl.gov/project/linear_solvers/download/hypre-2.10.0b.tar.gz"
+    url      = "https://github.com/LLNL/hypre/archive/v2.14.0.tar.gz"
+    git      = "https://github.com/LLNL/hypre.git"
 
-    version('2.12.1', 'c6fcb6d7e57cec1c7ce4a44da885068c', url='https://github.com/LLNL/hypre/archive/v2.12.1.tar.gz')
+    version('develop', branch='master')
+    version('2.15.1', '877002d49f38b6a1434955baf79eff35')
+    version('2.15.0', '4645acc49141069cae1d53de96107a08')
+    version('2.14.0', 'ecde5cc807ec45bfb647e9f28d2eaea1')
+    version('2.13.0', '4b688a5c15b6b5e3de5e045ae081b89b')
+    version('2.12.1', 'c6fcb6d7e57cec1c7ce4a44da885068c')
     version('2.11.2', 'd507943a1a3ce5681c3308e2f3a6dd34')
     version('2.11.1', '3f02ef8fd679239a6723f60b7f796519')
     version('2.10.1', 'dc048c4cabb3cd549af72591474ad674')
     version('2.10.0b', '768be38793a35bb5d055905b271f5b8e')
-    version('develop', git='https://github.com/LLNL/hypre', tag='master')
-    version('xsdk-0.2.0', git='https://github.com/LLNL/hypre', tag='xsdk-0.2.0')
+    version('xsdk-0.2.0', tag='xsdk-0.2.0')
 
-    # hypre does not know how to build shared libraries on Darwin
+    # Versions 2.13.0 and later can be patched to build shared
+    # libraries on Darwin; the patch for this capability does not
+    # apply to version 2.12.1 and earlier due to changes in the build system
+    # between versions 2.12.1 and 2.13.0.
     variant('shared', default=(sys.platform != 'darwin'),
             description="Build shared library (disables static library)")
     # SuperluDist have conflicting headers with those in Hypre
@@ -52,14 +41,32 @@ class Hypre(Package):
     variant('int64', default=False,
             description="Use 64bit integers")
     variant('mpi', default=True, description='Enable MPI support')
+    variant('debug', default=False,
+            description='Build debug instead of optimized version')
 
     # Patch to add ppc64le in config.guess
     patch('ibm-ppc64le.patch', when='@:2.11.1')
 
+    # Patch to build shared libraries on Darwin
+    patch('darwin-shared-libs-for-hypre-2.13.0.patch', when='+shared@2.13.0 platform=darwin')
+    patch('darwin-shared-libs-for-hypre-2.14.0.patch', when='+shared@2.14.0: platform=darwin')
+
     depends_on("mpi", when='+mpi')
     depends_on("blas")
     depends_on("lapack")
 
+    # Patch to build shared libraries on Darwin does not apply to
+    # versions before 2.13.0
+    conflicts("+shared@:2.12.99 platform=darwin")
+
+    def url_for_version(self, version):
+        if version >= Version('2.12.0'):
+            url = 'https://github.com/LLNL/hypre/archive/v{0}.tar.gz'
+        else:
+            url = 'http://computation.llnl.gov/project/linear_solvers/download/hypre-{0}.tar.gz'
+
+        return url.format(version)
+
     def install(self, spec, prefix):
         # Note: --with-(lapack|blas)_libs= needs space separated list of names
         lapack = spec['lapack'].libs
@@ -93,6 +100,11 @@ class Hypre(Package):
             configure_args.append("--without-mli")
             configure_args.append("--without-fei")
 
+        if '+debug' in self.spec:
+            configure_args.append("--enable-debug")
+        else:
+            configure_args.append("--disable-debug")
+
         # Hypre's source is staged under ./src so we'll have to manually
         # cd into it.
         with working_dir("src"):
@@ -108,3 +120,27 @@ class Hypre(Package):
                 sstruct('-in', 'test/sstruct.in.default', '-solver', '40',
                         '-rhsone')
             make("install")
+
+    @property
+    def headers(self):
+        """Export the main hypre header, HYPRE.h; all other headers can be found
+        in the same directory.
+        Sample usage: spec['hypre'].headers.cpp_flags
+        """
+        hdrs = find_headers('HYPRE', self.prefix.include, recursive=False)
+        return hdrs or None
+
+    @property
+    def libs(self):
+        """Export the hypre library.
+        Sample usage: spec['hypre'].libs.ld_flags
+        """
+        search_paths = [[self.prefix.lib, False], [self.prefix.lib64, False],
+                        [self.prefix, True]]
+        is_shared = '+shared' in self.spec
+        for path, recursive in search_paths:
+            libs = find_libraries('libHYPRE', root=path,
+                                  shared=is_shared, recursive=recursive)
+            if libs:
+                return libs
+        return None
diff --git a/var/spack/repos/builtin/packages/i3/package.py b/var/spack/repos/builtin/packages/i3/package.py
new file mode 100644
index 0000000000..123fdbb212
--- /dev/null
+++ b/var/spack/repos/builtin/packages/i3/package.py
@@ -0,0 +1,35 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class I3(AutotoolsPackage):
+    """i3, improved tiling wm. i3 is a tiling window manager, completely
+    written from scratch. The target platforms are GNU/Linux and BSD operating
+    systems, our code is Free and Open Source Software (FOSS) under the BSD
+    license. i3 is primarily targeted at advanced users and developers."""
+
+    homepage = "https://i3wm.org/"
+    url      = "https://github.com/i3/i3/archive/4.14.1.tar.gz"
+
+    version('4.14.1', 'bdbb6d7bb5a647c8b7b53ed10de84cc5')
+
+    depends_on('autoconf',  type='build')
+    depends_on('automake',  type='build')
+    depends_on('libtool',   type='build')
+    depends_on('m4',        type='build')
+    depends_on('pkgconfig', type='build')
+
+    depends_on('libev')
+    depends_on('startup-notification')
+    depends_on('xcb-util-cursor')
+    depends_on('xcb-util-keysyms')
+    depends_on('xcb-util-wm')
+    depends_on('xcb-util-xrm')
+    depends_on('libxkbcommon')
+    depends_on('yajl')
+    depends_on('cairo+X')
+    depends_on('pango+X')
diff --git a/var/spack/repos/builtin/packages/ibmisc/package.py b/var/spack/repos/builtin/packages/ibmisc/package.py
index 8fcf7980c8..6a78788ad5 100644
--- a/var/spack/repos/builtin/packages/ibmisc/package.py
+++ b/var/spack/repos/builtin/packages/ibmisc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/iceauth/package.py b/var/spack/repos/builtin/packages/iceauth/package.py
index a2f919be54..41f8f669a6 100644
--- a/var/spack/repos/builtin/packages/iceauth/package.py
+++ b/var/spack/repos/builtin/packages/iceauth/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Iceauth(AutotoolsPackage):
     depends_on('libice')
 
     depends_on('xproto@7.0.22:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/icedtea/package.py b/var/spack/repos/builtin/packages/icedtea/package.py
index 9bc7da3102..c8a5916c7b 100644
--- a/var/spack/repos/builtin/packages/icedtea/package.py
+++ b/var/spack/repos/builtin/packages/icedtea/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
@@ -37,12 +18,11 @@ class Icedtea(AutotoolsPackage):
 
     version('3.4.0',  'eba66765b92794495e16b83f23640872')
 
-    provides('java@8', when='@3.4.0:3.99.99')
     variant('X', default=False, description="Build with GUI support.")
     variant('shenandoah', default=False,
             description="Build with the shenandoah gc. Only for version 3+")
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('gmake', type='build')
     depends_on('cups')
     depends_on('jdk', type='build')
@@ -58,7 +38,7 @@ class Icedtea(AutotoolsPackage):
     depends_on('libxcomposite', when='~X', type='build')
     depends_on('libxau', when='~X', type='build')
     depends_on('libxdmcp', when='~X', type='build')
-    depends_on('gtkplus+X', when='~X', type='build')
+    depends_on('gtkplus', when='~X', type='build')
 
     depends_on('libx11', when='+X')
     depends_on('xproto', when='+X')
@@ -71,7 +51,7 @@ class Icedtea(AutotoolsPackage):
     depends_on('libxcomposite', when='+X')
     depends_on('libxau', when='+X')
     depends_on('libxdmcp', when='+X')
-    depends_on('gtkplus+X', when='+X')
+    depends_on('gtkplus', when='+X')
 
     depends_on('freetype@2:')
     depends_on('wget', type='build')
@@ -82,6 +62,9 @@ class Icedtea(AutotoolsPackage):
     depends_on('zlib')
     depends_on('alsa-lib')
 
+    provides('java')
+    provides('java@8', when='@3.4.0:3.99.99')
+
     force_autoreconf = True
 
     resource(name='corba', placement='corba_src',
@@ -139,6 +122,20 @@ class Icedtea(AutotoolsPackage):
              url='http://icedtea.wildebeest.org/download/drops/icedtea8/3.4.0/shenandoah.tar.xz',
              when='@3.4.0')
 
+    # FIXME:
+    # 1. `extends('java')` doesn't work, you need to use `extends('icedtea')`
+    # 2. Packages cannot extend multiple packages, see #987
+    # 3. Update `YamlFilesystemView.merge` to allow a Package to completely
+    #    override how it is symlinked into a view prefix. Then, spack activate
+    #    can symlink all *.jar files to `prefix.lib.ext`
+    extendable = True
+
+    @property
+    def home(self):
+        """For compatibility with the ``jdk`` package, so that other packages
+        can say ``spec['java'].home`` regardless of the Java provider."""
+        return self.prefix
+
     def configure_args(self):
         os.environ['POTENTIAL_CXX'] = os.environ['CXX']
         os.environ['POTENTIAL_CC'] = os.environ['CC']
@@ -175,7 +172,34 @@ class Icedtea(AutotoolsPackage):
         return args
 
     def setup_environment(self, spack_env, run_env):
-        run_env.set('JAVA_HOME', self.spec.prefix)
+        """Set JAVA_HOME."""
+
+        run_env.set('JAVA_HOME', self.home)
 
     def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
-        spack_env.set('JAVA_HOME', self.prefix)
+        """Set JAVA_HOME and CLASSPATH.
+
+        CLASSPATH contains the installation prefix for the extension and any
+        other Java extensions it depends on."""
+
+        spack_env.set('JAVA_HOME', self.home)
+
+        class_paths = []
+        for d in dependent_spec.traverse(deptype=('build', 'run', 'test')):
+            if d.package.extends(self.spec):
+                class_paths.extend(find(d.prefix, '*.jar'))
+
+        classpath = os.pathsep.join(class_paths)
+        spack_env.set('CLASSPATH', classpath)
+
+        # For runtime environment set only the path for
+        # dependent_spec and prepend it to CLASSPATH
+        if dependent_spec.package.extends(self.spec):
+            class_paths = find(dependent_spec.prefix, '*.jar')
+            classpath = os.pathsep.join(class_paths)
+            run_env.prepend_path('CLASSPATH', classpath)
+
+    def setup_dependent_package(self, module, dependent_spec):
+        """Allows spec['java'].home to work."""
+
+        self.spec.home = self.home
diff --git a/var/spack/repos/builtin/packages/icet/package.py b/var/spack/repos/builtin/packages/icet/package.py
index d8591a2411..bf1f311d0a 100644
--- a/var/spack/repos/builtin/packages/icet/package.py
+++ b/var/spack/repos/builtin/packages/icet/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,10 +11,10 @@ class Icet(CMakePackage):
        sort-last parallel rendering library."""
 
     homepage = "http://icet.sandia.gov"
-    url      = "https://gitlab.kitware.com/icet/icet/repository/archive.tar.bz2?ref=IceT-2.1.1"
+    url      = "https://gitlab.kitware.com/api/v4/projects/icet%2Ficet/repository/archive.tar.bz2?sha=IceT-2.1.1"
+    git      = "https://gitlab.kitware.com/icet/icet.git"
 
-    version('develop', branch='master',
-            git='https://gitlab.kitware.com/icet/icet.git')
+    version('develop', branch='master')
     version('2.1.1', '4f971c51105a64937460d482adca2a6c')
 
     depends_on('mpi')
diff --git a/var/spack/repos/builtin/packages/ico/package.py b/var/spack/repos/builtin/packages/ico/package.py
index 7f627f5921..1d7442ddc5 100644
--- a/var/spack/repos/builtin/packages/ico/package.py
+++ b/var/spack/repos/builtin/packages/ico/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Ico(AutotoolsPackage):
     depends_on('libx11@0.99.1:')
 
     depends_on('xproto@7.0.22:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/icu4c/package.py b/var/spack/repos/builtin/packages/icu4c/package.py
index f8dcb52805..78d63b8c3b 100644
--- a/var/spack/repos/builtin/packages/icu4c/package.py
+++ b/var/spack/repos/builtin/packages/icu4c/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,6 +16,7 @@ class Icu4c(AutotoolsPackage):
     list_url = "http://download.icu-project.org/files/icu4c"
     list_depth = 2
 
+    version('60.1', '3d164a2d1bcebd1464c6160ebb8315ef')
     version('58.2', 'fac212b32b7ec7ab007a12dff1f3aea1')
     version('57.1', '976734806026a4ef8bdd17937c8898b9')
 
@@ -45,4 +27,11 @@ class Icu4c(AutotoolsPackage):
         return url.format(version.dotted, version.underscored)
 
     def configure_args(self):
-        return ['--enable-rpath']
+        args = []
+
+        # The --enable-rpath option is only needed on MacOS, and it
+        # breaks the build for xerces-c on Linux.
+        if 'platform=darwin' in self.spec:
+            args.append('--enable-rpath')
+
+        return args
diff --git a/var/spack/repos/builtin/packages/id3lib/package.py b/var/spack/repos/builtin/packages/id3lib/package.py
index da4c513c63..23bbc99aef 100644
--- a/var/spack/repos/builtin/packages/id3lib/package.py
+++ b/var/spack/repos/builtin/packages/id3lib/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/idba/package.py b/var/spack/repos/builtin/packages/idba/package.py
index d886ac0455..a7b2a455f7 100644
--- a/var/spack/repos/builtin/packages/idba/package.py
+++ b/var/spack/repos/builtin/packages/idba/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/igraph/package.py b/var/spack/repos/builtin/packages/igraph/package.py
index 4ec2e71555..35bcb1c87e 100644
--- a/var/spack/repos/builtin/packages/igraph/package.py
+++ b/var/spack/repos/builtin/packages/igraph/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/igvtools/igvtools.sh b/var/spack/repos/builtin/packages/igvtools/igvtools.sh
new file mode 100644
index 0000000000..82023e72b3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/igvtools/igvtools.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+# convenience wrapper for the igvtools jar file
+java $JAVA_ARGS $JAVA_OPTS -jar igvtools.jar "$@"
+
diff --git a/var/spack/repos/builtin/packages/igvtools/package.py b/var/spack/repos/builtin/packages/igvtools/package.py
new file mode 100644
index 0000000000..8e57a57fb3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/igvtools/package.py
@@ -0,0 +1,40 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class Igvtools(Package):
+    """IGVTools suite of command-line utilities for preprocessing data
+    files"""
+
+    homepage = "https://software.broadinstitute.org/software/igv/home"
+    url      = "http://data.broadinstitute.org/igv/projects/downloads/2.3/igvtools_2.3.98.zip"
+
+    version('2.3.98', '17ed12a213cd9cdaeb2f2a5c56d84bc4')
+
+    depends_on('java@8:')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        jar_file = 'igvtools.jar'
+        install(jar_file, prefix.bin)
+        install_tree('genomes', prefix.genomes)
+
+        # Set up a helper script to call java on the jar file,
+        # explicitly codes the path for java and the jar file.
+        script_sh = join_path(os.path.dirname(__file__), "igvtools.sh")
+        script = prefix.bin.igvtools
+        install(script_sh, script)
+        set_executable(script)
+
+        # Munge the helper script to explicitly point to java and the
+        # jar file.
+        java = spec['jdk'].prefix.bin.java
+        kwargs = {'ignore_absent': False, 'backup': False, 'string': False}
+        filter_file('^java', java, script, **kwargs)
+        filter_file(jar_file, join_path(prefix.bin, jar_file),
+                    script, **kwargs)
diff --git a/var/spack/repos/builtin/packages/ilmbase/package.py b/var/spack/repos/builtin/packages/ilmbase/package.py
index 75e52d66c2..996e6bd104 100644
--- a/var/spack/repos/builtin/packages/ilmbase/package.py
+++ b/var/spack/repos/builtin/packages/ilmbase/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/image-magick/package.py b/var/spack/repos/builtin/packages/image-magick/package.py
index 24b92132a0..354a7fd63a 100644
--- a/var/spack/repos/builtin/packages/image-magick/package.py
+++ b/var/spack/repos/builtin/packages/image-magick/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/imake/package.py b/var/spack/repos/builtin/packages/imake/package.py
index f3da05200b..47dcefa4e9 100644
--- a/var/spack/repos/builtin/packages/imake/package.py
+++ b/var/spack/repos/builtin/packages/imake/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,4 +15,4 @@ class Imake(AutotoolsPackage):
     version('1.0.7', '186ca7b8ff0de8752f2a2d0426542363')
 
     depends_on('xproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
diff --git a/var/spack/repos/builtin/packages/imp/package.py b/var/spack/repos/builtin/packages/imp/package.py
new file mode 100644
index 0000000000..656e07e7e1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/imp/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Imp(CMakePackage):
+    """IMP, the Integrative Modeling Platform."""
+
+    homepage = "https://integrativemodeling.org"
+    url      = "https://github.com/salilab/imp/archive/2.8.0.tar.gz"
+
+    version('2.8.0', 'bc985d40dc63bb12e09d6d7403954645')
+
+    depends_on('python@2.7:')
+    depends_on('swig')
+    depends_on('boost@1.40:')
+    depends_on('hdf5')
+    depends_on('eigen')
diff --git a/var/spack/repos/builtin/packages/impute2/package.py b/var/spack/repos/builtin/packages/impute2/package.py
index 44993a306f..41c51a796d 100644
--- a/var/spack/repos/builtin/packages/impute2/package.py
+++ b/var/spack/repos/builtin/packages/impute2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/infernal/package.py b/var/spack/repos/builtin/packages/infernal/package.py
index f84722964d..59c2d7ce61 100644
--- a/var/spack/repos/builtin/packages/infernal/package.py
+++ b/var/spack/repos/builtin/packages/infernal/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/inputproto/package.py b/var/spack/repos/builtin/packages/inputproto/package.py
index f60b08cacf..31d0732aca 100644
--- a/var/spack/repos/builtin/packages/inputproto/package.py
+++ b/var/spack/repos/builtin/packages/inputproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Inputproto(AutotoolsPackage):
 
     version('2.3.2', '6450bad6f8d5ebe354b01b734d1fd7ca')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/intel-daal/package.py b/var/spack/repos/builtin/packages/intel-daal/package.py
index d528f88461..acf84f5021 100644
--- a/var/spack/repos/builtin/packages/intel-daal/package.py
+++ b/var/spack/repos/builtin/packages/intel-daal/package.py
@@ -1,31 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-import os
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack import *
-from spack.environment import EnvironmentModifications
 
 
 class IntelDaal(IntelPackage):
@@ -33,6 +11,14 @@ class IntelDaal(IntelPackage):
 
     homepage = "https://software.intel.com/en-us/daal"
 
+    version('2019.0.117', 'd42fb6c3e8b31b1288049e89df37f2e8',
+            url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13577/l_daal_2019.0.117.tgz")
+    version('2018.3.222', 'e688825c563e357b7b626ece610d6a85',
+            url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13007/l_daal_2018.3.222.tgz")
+    version('2018.2.199', 'd015ff34a87a18922736b5fba0d0b0e0',
+            url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12727/l_daal_2018.2.199.tgz")
+    version('2018.1.163', '12a9586734a03a956095440161fd741a',
+            url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12414/l_daal_2018.1.163.tgz")
     version('2018.0.128', '5779e670f67c33cc1c6cdcdca5e4636e',
             url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12072/l_daal_2018.0.128.tgz")
     version('2017.4.239', 'b47e9b92d948ee312e8a98170a1c0640',
@@ -51,36 +37,3 @@ class IntelDaal(IntelPackage):
             url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8687/l_daal_2016.2.181.tgz")
 
     provides('daal')
-
-    @property
-    def license_required(self):
-        # The Intel libraries are provided without requiring a license as of
-        # version 2017.2. Trying to specify the license will fail. See:
-        # https://software.intel.com/en-us/articles/free-ipsxe-tools-and-libraries
-        if self.version >= Version('2017.2'):
-            return False
-        else:
-            return True
-
-    def setup_environment(self, spack_env, run_env):
-        """Adds environment variables to the generated module file.
-
-        These environment variables come from running:
-
-        .. code-block:: console
-
-           $ source daal/bin/daalvars.sh intel64
-        """
-        # NOTE: Spack runs setup_environment twice, once pre-build to set up
-        # the build environment, and once post-installation to determine
-        # the environment variables needed at run-time to add to the module
-        # file. The script we need to source is only present post-installation,
-        # so check for its existence before sourcing.
-        # TODO: At some point we should split setup_environment into
-        # setup_build_environment and setup_run_environment to get around
-        # this problem.
-        daalvars = os.path.join(self.prefix.daal.bin, 'daalvars.sh')
-
-        if os.path.isfile(daalvars):
-            run_env.extend(EnvironmentModifications.from_sourcing_file(
-                daalvars, 'intel64'))
diff --git a/var/spack/repos/builtin/packages/intel-gpu-tools/package.py b/var/spack/repos/builtin/packages/intel-gpu-tools/package.py
index 5238e57e32..24b01fb0c6 100644
--- a/var/spack/repos/builtin/packages/intel-gpu-tools/package.py
+++ b/var/spack/repos/builtin/packages/intel-gpu-tools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import sys
 
@@ -49,7 +30,7 @@ class IntelGpuTools(AutotoolsPackage):
     depends_on('flex', type='build')
     depends_on('bison', type='build')
     depends_on('python@3:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     # xrandr ?
diff --git a/var/spack/repos/builtin/packages/intel-ipp/package.py b/var/spack/repos/builtin/packages/intel-ipp/package.py
index ae7a1358e1..b9bc862882 100644
--- a/var/spack/repos/builtin/packages/intel-ipp/package.py
+++ b/var/spack/repos/builtin/packages/intel-ipp/package.py
@@ -1,31 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-import os
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack import *
-from spack.environment import EnvironmentModifications
 
 
 class IntelIpp(IntelPackage):
@@ -33,6 +11,14 @@ class IntelIpp(IntelPackage):
 
     homepage = "https://software.intel.com/en-us/intel-ipp"
 
+    version('2019.0.117', 'c96be6e138d32bf9b8abc789d25db71d',
+            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13576/l_ipp_2019.0.117.tgz')
+    version('2018.3.222', '2ccc16ec002466e52f1e6e1bfe9b1149',
+            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13006/l_ipp_2018.3.222.tgz')
+    version('2018.2.199', 'f87276b485d2f6ec070c1b41ac1ed871',
+            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12726/l_ipp_2018.2.199.tgz')
+    version('2018.1.163', '183d4888f3d91f632b617fdd401f04ed',
+            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12414/l_ipp_2018.1.163.tgz')
     version('2018.0.128', 'e64190bc9041b52d9eed7e8ee91bf1de',
             url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12071/l_ipp_2018.0.128.tgz')
     version('2017.3.196', '47e53bd1a2740041f4d0be7c36b61a18',
@@ -43,40 +29,8 @@ class IntelIpp(IntelPackage):
             url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11031/l_ipp_2017.1.132.tgz")
     version('2017.0.098', 'e7be757ebe351d9f9beed7efdc7b7118',
             url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9663/l_ipp_2017.0.098.tgz")
+    # built from parallel_studio_xe_2016.3.067
     version('9.0.3.210', '0e1520dd3de7f811a6ef6ebc7aa429a3',
             url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9067/l_ipp_9.0.3.210.tgz")
 
     provides('ipp')
-
-    @property
-    def license_required(self):
-        # The Intel libraries are provided without requiring a license as of
-        # version 2017.2. Trying to specify the license will fail. See:
-        # https://software.intel.com/en-us/articles/free-ipsxe-tools-and-libraries
-        if self.version >= Version('2017.2'):
-            return False
-        else:
-            return True
-
-    def setup_environment(self, spack_env, run_env):
-        """Adds environment variables to the generated module file.
-
-        These environment variables come from running:
-
-        .. code-block:: console
-
-           $ source ipp/bin/ippvars.sh intel64
-        """
-        # NOTE: Spack runs setup_environment twice, once pre-build to set up
-        # the build environment, and once post-installation to determine
-        # the environment variables needed at run-time to add to the module
-        # file. The script we need to source is only present post-installation,
-        # so check for its existence before sourcing.
-        # TODO: At some point we should split setup_environment into
-        # setup_build_environment and setup_run_environment to get around
-        # this problem.
-        ippvars = os.path.join(self.prefix.ipp.bin, 'ippvars.sh')
-
-        if os.path.isfile(ippvars):
-            run_env.extend(EnvironmentModifications.from_sourcing_file(
-                ippvars, 'intel64'))
diff --git a/var/spack/repos/builtin/packages/intel-mkl-dnn/package.py b/var/spack/repos/builtin/packages/intel-mkl-dnn/package.py
new file mode 100644
index 0000000000..72dafd7572
--- /dev/null
+++ b/var/spack/repos/builtin/packages/intel-mkl-dnn/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class IntelMklDnn(CMakePackage):
+    """Intel(R) Math Kernel Library for Deep Neural Networks
+    (Intel(R) MKL-DNN)."""
+
+    homepage = "https://01.org/mkl-dnn"
+    url      = "https://github.com/01org/mkl-dnn/archive/v0.11.tar.gz"
+
+    version('0.11', 'a060a42753f633a146c3db699eeee666')
+    version('0.10', '3855ad02452a6906e3a9adc9cecef49c')
+    version('0.9',  'dfb89d8f9d0bce55e878df32544cb0ea')
+
+    depends_on('intel-mkl')
diff --git a/var/spack/repos/builtin/packages/intel-mkl/package.py b/var/spack/repos/builtin/packages/intel-mkl/package.py
index e2c2b8d46a..4b04e97d34 100644
--- a/var/spack/repos/builtin/packages/intel-mkl/package.py
+++ b/var/spack/repos/builtin/packages/intel-mkl/package.py
@@ -1,32 +1,11 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-import os
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import sys
 
 from spack import *
-from spack.environment import EnvironmentModifications
 
 
 class IntelMkl(IntelPackage):
@@ -34,6 +13,14 @@ class IntelMkl(IntelPackage):
 
     homepage = "https://software.intel.com/en-us/intel-mkl"
 
+    version('2019.0.117', 'd9e1b6b96fbffd4b306c7e8291f141a2',
+            url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13575/l_mkl_2019.0.117.tgz")
+    version('2018.3.222', '3e63646a4306eff95e8d0aafd53a2983',
+            url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13005/l_mkl_2018.3.222.tgz")
+    version('2018.2.199', 'fd31b656a8eb859c89495b9cc41230b4',
+            url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12725/l_mkl_2018.2.199.tgz")
+    version('2018.1.163', 'f1f7b6ddd7eb57dfe39bd4643446dc1c',
+            url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12414/l_mkl_2018.1.163.tgz")
     version('2018.0.128', '0fa23779816a0f2ee23a396fc1af9978',
             url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12070/l_mkl_2018.0.128.tgz")
     version('2017.4.239', '3066272dd0ad3da7961b3d782e1fab3b',
@@ -46,8 +33,10 @@ class IntelMkl(IntelPackage):
             url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11024/l_mkl_2017.1.132.tgz")
     version('2017.0.098', '3cdcb739ab5ab1e047eb130b9ffdd8d0',
             url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9662/l_mkl_2017.0.098.tgz")
+    # built from parallel_studio_xe_2016.3.x
     version('11.3.3.210', 'f72546df27f5ebb0941b5d21fd804e34',
             url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9068/l_mkl_11.3.3.210.tgz")
+    # built from parallel_studio_xe_2016.2.062
     version('11.3.2.181', '536dbd82896d6facc16de8f961d17d65',
             url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8711/l_mkl_11.3.2.181.tgz")
 
@@ -56,7 +45,7 @@ class IntelMkl(IntelPackage):
     variant(
         'threads', default='none',
         description='Multithreading support',
-        values=('openmp', 'none'),
+        values=('openmp', 'tbb', 'none'),
         multi=False
     )
 
@@ -64,158 +53,8 @@ class IntelMkl(IntelPackage):
     provides('lapack')
     provides('scalapack')
     provides('mkl')
+    provides('fftw-api@3', when='@2017:')
 
     if sys.platform == 'darwin':
         # there is no libmkl_gnu_thread on macOS
         conflicts('threads=openmp', when='%gcc')
-
-    @property
-    def license_required(self):
-        # The Intel libraries are provided without requiring a license as of
-        # version 2017.2. Trying to specify the license will fail. See:
-        # https://software.intel.com/en-us/articles/free-ipsxe-tools-and-libraries
-        if self.version >= Version('2017.2'):
-            return False
-        else:
-            return True
-
-    @property
-    def blas_libs(self):
-        spec = self.spec
-        prefix = self.prefix
-        shared = '+shared' in spec
-
-        if '+ilp64' in spec:
-            mkl_integer = ['libmkl_intel_ilp64']
-        else:
-            mkl_integer = ['libmkl_intel_lp64']
-
-        mkl_threading = ['libmkl_sequential']
-
-        omp_libs = LibraryList([])
-
-        if spec.satisfies('threads=openmp'):
-            if '%intel' in spec:
-                mkl_threading = ['libmkl_intel_thread']
-                omp_threading = ['libiomp5']
-
-                if sys.platform != 'darwin':
-                    omp_root = prefix.compilers_and_libraries.linux.lib.intel64
-                else:
-                    omp_root = prefix.lib
-                omp_libs = find_libraries(
-                    omp_threading, root=omp_root, shared=shared)
-            elif '%gcc' in spec:
-                mkl_threading = ['libmkl_gnu_thread']
-
-                gcc = Executable(self.compiler.cc)
-                libgomp = gcc('--print-file-name', 'libgomp.{0}'.format(
-                    dso_suffix), output=str)
-                omp_libs = LibraryList(libgomp)
-
-        # TODO: TBB threading: ['libmkl_tbb_thread', 'libtbb', 'libstdc++']
-
-        if sys.platform != 'darwin':
-            mkl_root = prefix.compilers_and_libraries.linux.mkl.lib.intel64
-        else:
-            mkl_root = prefix.mkl.lib
-
-        mkl_libs = find_libraries(
-            mkl_integer + ['libmkl_core'] + mkl_threading,
-            root=mkl_root,
-            shared=shared
-        )
-
-        # Intel MKL link line advisor recommends these system libraries
-        system_libs = find_system_libraries(
-            ['libpthread', 'libm', 'libdl'],
-            shared=shared
-        )
-
-        return mkl_libs + omp_libs + system_libs
-
-    @property
-    def lapack_libs(self):
-        return self.blas_libs
-
-    @property
-    def scalapack_libs(self):
-        libnames = ['libmkl_scalapack']
-
-        # Intel MKL does not directly depend on mpi but the scalapack
-        # interface does and the corresponding  BLACS library changes
-        # depending on the MPI implementation we are using. We need then to
-        # inspect the root package which asked for Scalapack and check which
-        # MPI it depends on.
-        root = self.spec.root
-        if sys.platform == 'darwin' and '^mpich' in root:
-            # MKL 2018 supports only MPICH on darwin
-            libnames.append('libmkl_blacs_mpich')
-        elif '^openmpi' in root:
-            libnames.append('libmkl_blacs_openmpi')
-        elif '^mpich@1' in root:
-            libnames.append('libmkl_blacs')
-        elif '^mpich@2:' in root:
-            libnames.append('libmkl_blacs_intelmpi')
-        elif '^mvapich2' in root:
-            libnames.append('libmkl_blacs_intelmpi')
-        elif '^mpt' in root:
-            libnames.append('libmkl_blacs_sgimpt')
-        elif '^intel-mpi' in root:
-            libnames.append('libmkl_blacs_intelmpi')
-        else:
-            raise InstallError('No MPI found for scalapack')
-
-        integer = 'ilp64' if '+ilp64' in self.spec else 'lp64'
-        mkl_root = self.prefix.mkl.lib if sys.platform == 'darwin' else \
-            self.prefix.compilers_and_libraries.linux.mkl.lib.intel64
-
-        shared = True if '+shared' in self.spec else False
-
-        libs = find_libraries(
-            ['{0}_{1}'.format(l, integer) for l in libnames],
-            root=mkl_root,
-            shared=shared
-        )
-
-        return libs
-
-    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
-        # set up MKLROOT for everyone using MKL package
-        if sys.platform == 'darwin':
-            mkl_lib = self.prefix.mkl.lib
-            mkl_root = self.prefix.mkl
-        else:
-            mkl_lib = self.prefix.compilers_and_libraries.linux.mkl.lib.intel64
-            mkl_root = self.prefix.compilers_and_libraries.linux.mkl
-
-        spack_env.set('MKLROOT', mkl_root)
-        spack_env.append_path('SPACK_COMPILER_EXTRA_RPATHS', mkl_lib)
-
-    def setup_environment(self, spack_env, run_env):
-        """Adds environment variables to the generated module file.
-
-        These environment variables come from running:
-
-        .. code-block:: console
-
-           $ source mkl/bin/mklvars.sh intel64
-        """
-        # NOTE: Spack runs setup_environment twice, once pre-build to set up
-        # the build environment, and once post-installation to determine
-        # the environment variables needed at run-time to add to the module
-        # file. The script we need to source is only present post-installation,
-        # so check for its existence before sourcing.
-        # TODO: At some point we should split setup_environment into
-        # setup_build_environment and setup_run_environment to get around
-        # this problem.
-        mklvars = os.path.join(self.prefix.mkl.bin, 'mklvars.sh')
-
-        if sys.platform == 'darwin':
-            if os.path.isfile(mklvars):
-                run_env.extend(EnvironmentModifications.from_sourcing_file(
-                    mklvars))
-        else:
-            if os.path.isfile(mklvars):
-                run_env.extend(EnvironmentModifications.from_sourcing_file(
-                    mklvars, 'intel64'))
diff --git a/var/spack/repos/builtin/packages/intel-mpi/package.py b/var/spack/repos/builtin/packages/intel-mpi/package.py
index 42b9872b30..c3ac5b68be 100644
--- a/var/spack/repos/builtin/packages/intel-mpi/package.py
+++ b/var/spack/repos/builtin/packages/intel-mpi/package.py
@@ -1,31 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-import os
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack import *
-from spack.environment import EnvironmentModifications
 
 
 class IntelMpi(IntelPackage):
@@ -33,6 +11,14 @@ class IntelMpi(IntelPackage):
 
     homepage = "https://software.intel.com/en-us/intel-mpi-library"
 
+    version('2019.0.117', '8572d5fa1f26a7de8edc8b64653b0955',
+            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13584/l_mpi_2019.0.117.tgz')
+    version('2018.3.222', 'df92593818fadff63c57418669c6083b',
+            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13112/l_mpi_2018.3.222.tgz')
+    version('2018.2.199', '6ffeab59c83a8842537484d53e180520',
+            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12748/l_mpi_2018.2.199.tgz')
+    version('2018.1.163', '437ce50224c5bbf98fd578a810c3e401',
+            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12414/l_mpi_2018.1.163.tgz')
     version('2018.0.128', '15b46fc6a3014595de897aa48d3a658b',
             url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12120/l_mpi_2018.0.128.tgz')
     version('2017.4.239', '460a9ef1b3599d60b4d696e3f0f2a14d',
@@ -43,95 +29,21 @@ class IntelMpi(IntelPackage):
             url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11334/l_mpi_2017.2.174.tgz')
     version('2017.1.132', 'd5e941ac2bcf7c5576f85f6bcfee4c18',
             url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11014/l_mpi_2017.1.132.tgz')
+    # built from parallel_studio_xe_2016.3.068
     version('5.1.3.223',  '4316e78533a932081b1a86368e890800',
             url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9278/l_mpi_p_5.1.3.223.tgz')
 
     provides('mpi')
 
-    @property
-    def license_required(self):
-        # The Intel libraries are provided without requiring a license as of
-        # version 2017.2. Trying to specify the license will fail. See:
-        # https://software.intel.com/en-us/articles/free-ipsxe-tools-and-libraries
-        if self.version >= Version('2017.2'):
-            return False
-        else:
-            return True
-
-    @property
-    def mpi_libs(self):
-        mpi_root = self.prefix.compilers_and_libraries.linux.mpi.lib64
-        query_parameters = self.spec.last_query.extra_parameters
-        libraries = ['libmpifort', 'libmpi']
-
-        if 'cxx' in query_parameters:
-            libraries = ['libmpicxx'] + libraries
-
-        return find_libraries(
-            libraries, root=mpi_root, shared=True, recurse=True
-        )
-
-    @property
-    def mpi_headers(self):
-        # recurse from self.prefix will find too many things for all the
-        # supported sub-architectures like 'mic'
-        mpi_root = self.prefix.compilers_and_libraries.linux.mpi.include64
-        return find_headers('mpi', root=mpi_root, recurse=False)
-
-    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
-        spack_env.set('I_MPI_CC', spack_cc)
-        spack_env.set('I_MPI_CXX', spack_cxx)
-        spack_env.set('I_MPI_F77', spack_fc)
-        spack_env.set('I_MPI_F90', spack_f77)
-        spack_env.set('I_MPI_FC', spack_fc)
-
-    def setup_dependent_package(self, module, dep_spec):
-        # Intel comes with 2 different flavors of MPI wrappers:
-        #
-        # * mpiicc, mpiicpc, and mpifort are hardcoded to wrap around
-        #   the Intel compilers.
-        # * mpicc, mpicxx, mpif90, and mpif77 allow you to set which
-        #   compilers to wrap using I_MPI_CC and friends. By default,
-        #   wraps around the GCC compilers.
-        #
-        # In theory, these should be equivalent as long as I_MPI_CC
-        # and friends are set to point to the Intel compilers, but in
-        # practice, mpicc fails to compile some applications while
-        # mpiicc works.
-        bindir = self.prefix.compilers_and_libraries.linux.mpi.intel64.bin
-
-        if self.compiler.name == 'intel':
-            self.spec.mpicc  = bindir.mpiicc
-            self.spec.mpicxx = bindir.mpiicpc
-            self.spec.mpifc  = bindir.mpiifort
-            self.spec.mpif77 = bindir.mpiifort
-        else:
-            self.spec.mpicc  = bindir.mpicc
-            self.spec.mpicxx = bindir.mpicxx
-            self.spec.mpifc  = bindir.mpif90
-            self.spec.mpif77 = bindir.mpif77
-
-    def setup_environment(self, spack_env, run_env):
-        """Adds environment variables to the generated module file.
-
-        These environment variables come from running:
-
-        .. code-block:: console
-
-           $ source compilers_and_libraries/linux/mpi/intel64/bin/mpivars.sh
-        """
-        # NOTE: Spack runs setup_environment twice, once pre-build to set up
-        # the build environment, and once post-installation to determine
-        # the environment variables needed at run-time to add to the module
-        # file. The script we need to source is only present post-installation,
-        # so check for its existence before sourcing.
-        # TODO: At some point we should split setup_environment into
-        # setup_build_environment and setup_run_environment to get around
-        # this problem.
-        mpivars = os.path.join(
-            self.prefix.compilers_and_libraries.linux.mpi.intel64.bin,
-            'mpivars.sh')
-
-        if os.path.isfile(mpivars):
-            run_env.extend(EnvironmentModifications.from_sourcing_file(
-                mpivars))
+    def setup_dependent_environment(self, *args):
+        # Handle in callback, conveying client's compilers in additional arg.
+        # CAUTION - DUP code in:
+        #   ../intel-mpi/package.py
+        #   ../intel-parallel-studio/package.py
+        self._setup_dependent_env_callback(*args, compilers_of_client={
+            'CC':   spack_cc,
+            'CXX':  spack_cxx,
+            'F77':  spack_f77,
+            'F90':  spack_fc,
+            'FC':   spack_fc,
+        })
diff --git a/var/spack/repos/builtin/packages/intel-parallel-studio/package.py b/var/spack/repos/builtin/packages/intel-parallel-studio/package.py
index 9828eaf6c0..666623f154 100644
--- a/var/spack/repos/builtin/packages/intel-parallel-studio/package.py
+++ b/var/spack/repos/builtin/packages/intel-parallel-studio/package.py
@@ -1,32 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-import glob
-import os
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack import *
-from spack.environment import EnvironmentModifications
 
 
 class IntelParallelStudio(IntelPackage):
@@ -34,66 +11,87 @@ class IntelParallelStudio(IntelPackage):
 
     homepage = "https://software.intel.com/en-us/intel-parallel-studio-xe"
 
-    version('professional.2018.0', '9a233854e9218937bc5f46f02b3c7542',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12062/parallel_studio_xe_2018_professional_edition.tgz')
-    version('cluster.2018.0',      'fa9baeb83dd2e8e4a464e3db38f28d0f',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12058/parallel_studio_xe_2018_cluster_edition.tgz')
-    version('composer.2018.0',     '31ba768fba6e7322957b03feaa3add28',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12067/parallel_studio_xe_2018_composer_edition.tgz')
-    version('professional.2017.4', '27398416078e1e4005afced3e9a6df7e',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11537/parallel_studio_xe_2017_update4.tgz')
-    version('cluster.2017.4',      '27398416078e1e4005afced3e9a6df7e',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11537/parallel_studio_xe_2017_update4.tgz')
-    version('composer.2017.4',     'd03d351809e182c481dc65e07376d9a2',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11541/parallel_studio_xe_2017_update4_composer_edition.tgz')
-    version('professional.2017.3', '691874735458d3e88fe0bcca4438b2a9',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11460/parallel_studio_xe_2017_update3.tgz')
-    version('cluster.2017.3',      '691874735458d3e88fe0bcca4438b2a9',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11460/parallel_studio_xe_2017_update3.tgz')
-    version('composer.2017.3',     '52344df122c17ddff3687f84ceb21623',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11464/parallel_studio_xe_2017_update3_composer_edition.tgz')
-    version('professional.2017.2', '70e54b33d940a1609ff1d35d3c56e3b3',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11298/parallel_studio_xe_2017_update2.tgz')
-    version('cluster.2017.2',      '70e54b33d940a1609ff1d35d3c56e3b3',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11298/parallel_studio_xe_2017_update2.tgz')
-    version('composer.2017.2',     '2891ab1ece43eb61b6ab892f07c47f01',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11302/parallel_studio_xe_2017_update2_composer_edition.tgz')
-    version('professional.2017.1', '7f75a4a7e2c563be778c377f9d35a542',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/10973/parallel_studio_xe_2017_update1.tgz')
-    version('cluster.2017.1',      '7f75a4a7e2c563be778c377f9d35a542',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/10973/parallel_studio_xe_2017_update1.tgz')
-    version('composer.2017.1',     '1f31976931ed8ec424ac7c3ef56f5e85',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/10978/parallel_studio_xe_2017_update1_composer_edition.tgz')
-    version('professional.2017.0', '34c98e3329d6ac57408b738ae1daaa01',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9651/parallel_studio_xe_2017.tgz')
-    version('cluster.2017.0',      '34c98e3329d6ac57408b738ae1daaa01',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9651/parallel_studio_xe_2017.tgz')
-    version('composer.2017.0',     'b67da0065a17a05f110ed1d15c3c6312',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9656/parallel_studio_xe_2017_composer_edition.tgz')
-    version('professional.2016.4', '16a641a06b156bb647c8a56e71f3bb33',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9781/parallel_studio_xe_2016_update4.tgz')
-    version('cluster.2016.4',      '16a641a06b156bb647c8a56e71f3bb33',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9781/parallel_studio_xe_2016_update4.tgz')
-    version('composer.2016.4',      '2bc9bfc9be9c1968a6e42efb4378f40e',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9785/parallel_studio_xe_2016_composer_edition_update4.tgz')
-    version('professional.2016.3', 'eda19bb0d0d19709197ede58f13443f3',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9061/parallel_studio_xe_2016_update3.tgz')
-    version('cluster.2016.3',      'eda19bb0d0d19709197ede58f13443f3',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9061/parallel_studio_xe_2016_update3.tgz')
-    version('composer.2016.3',     '3208eeabee951fc27579177b593cefe9',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9063/parallel_studio_xe_2016_composer_edition_update3.tgz')
-    version('professional.2016.2', '70be832f2d34c9bf596a5e99d5f2d832',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8676/parallel_studio_xe_2016_update2.tgz')
-    version('cluster.2016.2',      '70be832f2d34c9bf596a5e99d5f2d832',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8676/parallel_studio_xe_2016_update2.tgz')
-    version('composer.2016.2',     '1133fb831312eb519f7da897fec223fa',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8680/parallel_studio_xe_2016_composer_edition_update2.tgz')
-    version('professional.2015.6', 'd460f362c30017b60f85da2e51ad25bf',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8469/parallel_studio_xe_2015_update6.tgz')
-    version('cluster.2015.6',      'd460f362c30017b60f85da2e51ad25bf',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8469/parallel_studio_xe_2015_update6.tgz')
-    version('composer.2015.6',      'da9f8600c18d43d58fba0488844f79c9',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8432/l_compxe_2015.6.233.tgz')
+    # As of 2016, the product comes in three "editions" that vary by scope.
+    #
+    # In Spack, select the edition via the version number in the spec, e.g.:
+    #   intel-parallel-studio@cluster.2018
+
+    # Cluster Edition (top tier; all components included)
+    version('cluster.2019.0',      'd4c249c5438c1a55640291efcc96418d', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13589/parallel_studio_xe_2019_cluster_edition.tgz')
+    #
+    version('cluster.2018.3',      '7112837d20a100b895d9cd9ba9b6748d', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12998/parallel_studio_xe_2018_update3_cluster_edition.tgz')
+    version('cluster.2018.2',      '3b8d93a3fa10869dde024b739b96a9c4', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12717/parallel_studio_xe_2018_update2_cluster_edition.tgz')
+    version('cluster.2018.1',      '9c007011e0e3fc72747b58756fbf01cd', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12374/parallel_studio_xe_2018_update1_cluster_edition.tgz')
+    version('cluster.2018.0',      'fa9baeb83dd2e8e4a464e3db38f28d0f', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12058/parallel_studio_xe_2018_cluster_edition.tgz')
+    #
+    version('cluster.2017.7',      '158461b000b31f0ef8169b6f0277bfb5', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12856/parallel_studio_xe_2017_update7.tgz')
+    version('cluster.2017.6',      'b0bbddeec3e78a84b967c9ca70dade77', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12534/parallel_studio_xe_2017_update6.tgz')
+    version('cluster.2017.5',      'baeb8e584317fcdf1f60b8208bd4eab5', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12138/parallel_studio_xe_2017_update5.tgz')
+    version('cluster.2017.4',      '27398416078e1e4005afced3e9a6df7e', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11537/parallel_studio_xe_2017_update4.tgz')
+    version('cluster.2017.3',      '691874735458d3e88fe0bcca4438b2a9', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11460/parallel_studio_xe_2017_update3.tgz')
+    version('cluster.2017.2',      '70e54b33d940a1609ff1d35d3c56e3b3', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11298/parallel_studio_xe_2017_update2.tgz')
+    version('cluster.2017.1',      '7f75a4a7e2c563be778c377f9d35a542', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/10973/parallel_studio_xe_2017_update1.tgz')
+    version('cluster.2017.0',      '34c98e3329d6ac57408b738ae1daaa01', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9651/parallel_studio_xe_2017.tgz')
+    #
+    version('cluster.2016.4',      '16a641a06b156bb647c8a56e71f3bb33', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9781/parallel_studio_xe_2016_update4.tgz')
+    version('cluster.2016.3',      'eda19bb0d0d19709197ede58f13443f3', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9061/parallel_studio_xe_2016_update3.tgz')
+    version('cluster.2016.2',      '70be832f2d34c9bf596a5e99d5f2d832', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8676/parallel_studio_xe_2016_update2.tgz')
+    version('cluster.2016.1',      '83b260ef3fcfd4e30afbeb7eb31b6b20', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8365/parallel_studio_xe_2016_update1.tgz')
+    version('cluster.2016.0',      '00b4de9727a906a3aff468c26dd3f89c', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/7997/parallel_studio_xe_2016.tgz')
+    #
+    version('cluster.2015.6',      'd460f362c30017b60f85da2e51ad25bf', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8469/parallel_studio_xe_2015_update6.tgz')
+    version('cluster.2015.1',      '542b78c86beff9d7b01076a7be9c6ddc', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/4992/parallel_studio_xe_2015_update1.tgz')
+
+    # Professional Edition (middle tier; excluded: MPI/TAC/Cluster Checker)
+    #
+    # NB: Pre-2018 download packages for Professional are the same as for
+    # Cluster; differences manifest only in the tokens present in the license
+    # file delivered as part of the purchase.
+    version('professional.2018.3', 'e0fb828de0a5f238f775b6122cc7e2c5', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12999/parallel_studio_xe_2018_update3_professional_edition.tgz')
+    version('professional.2018.2', '91ed14aeb6157d60a0ec39929d0bc778', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12718/parallel_studio_xe_2018_update2_professional_edition.tgz')
+    version('professional.2018.1', '91669ff7afbfd07868a429a122c90357', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12375/parallel_studio_xe_2018_update1_professional_edition.tgz')
+    version('professional.2018.0', '9a233854e9218937bc5f46f02b3c7542', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12062/parallel_studio_xe_2018_professional_edition.tgz')
+    #
+    version('professional.2017.7', '158461b000b31f0ef8169b6f0277bfb5', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12856/parallel_studio_xe_2017_update7.tgz')
+    version('professional.2017.6', 'b0bbddeec3e78a84b967c9ca70dade77', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12534/parallel_studio_xe_2017_update6.tgz')
+    version('professional.2017.5', 'baeb8e584317fcdf1f60b8208bd4eab5', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12138/parallel_studio_xe_2017_update5.tgz')
+    version('professional.2017.4', '27398416078e1e4005afced3e9a6df7e', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11537/parallel_studio_xe_2017_update4.tgz')
+    version('professional.2017.3', '691874735458d3e88fe0bcca4438b2a9', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11460/parallel_studio_xe_2017_update3.tgz')
+    version('professional.2017.2', '70e54b33d940a1609ff1d35d3c56e3b3', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11298/parallel_studio_xe_2017_update2.tgz')
+    version('professional.2017.1', '7f75a4a7e2c563be778c377f9d35a542', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/10973/parallel_studio_xe_2017_update1.tgz')
+    version('professional.2017.0', '34c98e3329d6ac57408b738ae1daaa01', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9651/parallel_studio_xe_2017.tgz')
+    #
+    version('professional.2016.4', '16a641a06b156bb647c8a56e71f3bb33', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9781/parallel_studio_xe_2016_update4.tgz')
+    version('professional.2016.3', 'eda19bb0d0d19709197ede58f13443f3', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9061/parallel_studio_xe_2016_update3.tgz')
+    version('professional.2016.2', '70be832f2d34c9bf596a5e99d5f2d832', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8676/parallel_studio_xe_2016_update2.tgz')
+    version('professional.2016.1', '83b260ef3fcfd4e30afbeb7eb31b6b20', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8365/parallel_studio_xe_2016_update1.tgz')
+    version('professional.2016.0', '00b4de9727a906a3aff468c26dd3f89c', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/7997/parallel_studio_xe_2016.tgz')
+    #
+    version('professional.2015.6', 'd460f362c30017b60f85da2e51ad25bf', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8469/parallel_studio_xe_2015_update6.tgz')
+    version('professional.2015.1', '542b78c86beff9d7b01076a7be9c6ddc', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/4992/parallel_studio_xe_2015_update1.tgz')
+
+    # Composer Edition (basic tier; excluded: MPI/..., Advisor/Inspector/Vtune)
+    version('composer.2018.3',     '234223cc470717c2095456d9f048d690', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13002/parallel_studio_xe_2018_update3_composer_edition.tgz')
+    version('composer.2018.2',     '76f820f53de4c1ff998229c983cf4f53', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12722/parallel_studio_xe_2018_update2_composer_edition.tgz')
+    version('composer.2018.1',     '28cb807126d713350f4aa6f9f167448a', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12381/parallel_studio_xe_2018_update1_composer_edition.tgz')
+    version('composer.2018.0',     '31ba768fba6e7322957b03feaa3add28', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12067/parallel_studio_xe_2018_composer_edition.tgz')
+    #
+    version('composer.2017.7',     '4c02a4a29a8f2424f31baa23116a1001', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12860/parallel_studio_xe_2017_update7_composer_edition.tgz')
+    version('composer.2017.6',     'd96cce0c3feef20091efde458f581a9f', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12538/parallel_studio_xe_2017_update6_composer_edition.tgz')
+    # version('composer.2017.5',     -- TBD --
+    version('composer.2017.4',     'd03d351809e182c481dc65e07376d9a2', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11541/parallel_studio_xe_2017_update4_composer_edition.tgz')
+    version('composer.2017.3',     '52344df122c17ddff3687f84ceb21623', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11464/parallel_studio_xe_2017_update3_composer_edition.tgz')
+    version('composer.2017.2',     '2891ab1ece43eb61b6ab892f07c47f01', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11302/parallel_studio_xe_2017_update2_composer_edition.tgz')
+    version('composer.2017.1',     '1f31976931ed8ec424ac7c3ef56f5e85', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/10978/parallel_studio_xe_2017_update1_composer_edition.tgz')
+    version('composer.2017.0',     'b67da0065a17a05f110ed1d15c3c6312', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9656/parallel_studio_xe_2017_composer_edition.tgz')
+    #
+    version('composer.2016.4',     '2bc9bfc9be9c1968a6e42efb4378f40e', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9785/parallel_studio_xe_2016_composer_edition_update4.tgz')
+    version('composer.2016.3',     '3208eeabee951fc27579177b593cefe9', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9063/parallel_studio_xe_2016_composer_edition_update3.tgz')
+    version('composer.2016.2',     '1133fb831312eb519f7da897fec223fa', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8680/parallel_studio_xe_2016_composer_edition_update2.tgz')
+    #
+    # Pre-2016, the only product was "Composer XE"; dir structure is different.
+    version('composer.2015.6',     'da9f8600c18d43d58fba0488844f79c9', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8432/l_compxe_2015.6.233.tgz')
+    version('composer.2015.1',     '85beae681ae56411a8e791a7c44a5c0a', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/4933/l_compxe_2015.1.133.tgz')
 
     # Generic Variants
     variant('rpath',    default=True,
@@ -137,368 +135,46 @@ class IntelParallelStudio(IntelPackage):
     variant('vtune',     default=False,
             description='Install the Intel VTune Amplifier XE')
 
-    provides('daal', when='+daal')
-
-    provides('ipp', when='+ipp')
+    provides('daal',        when='+daal')
+    provides('ipp',         when='+ipp')
 
-    provides('mkl',       when='+mkl')
-    provides('blas',      when='+mkl')
-    provides('lapack',    when='+mkl')
-    provides('scalapack', when='+mkl')
+    provides('mkl',         when='+mkl')
+    provides('blas',        when='+mkl')
+    provides('lapack',      when='+mkl')
+    provides('scalapack',   when='+mkl')
 
-    provides('mpi', when='+mpi')
+    provides('mpi',         when='+mpi')
+    provides('tbb',         when='+tbb')
 
-    provides('tbb', when='+tbb')
+    # For TBB, static linkage is not and has never been supported by Intel:
+    # https://www.threadingbuildingblocks.org/faq/there-version-tbb-provides-statically-linked-libraries
+    conflicts('+tbb',       when='~shared')
 
-    # The following components are not available in the Composer Edition
     conflicts('+advisor',   when='@composer.0:composer.9999')
     conflicts('+clck',      when='@composer.0:composer.9999')
     conflicts('+inspector', when='@composer.0:composer.9999')
     conflicts('+itac',      when='@composer.0:composer.9999')
+    conflicts('+mpi',       when='@composer.0:composer.9999')
     conflicts('+vtune',     when='@composer.0:composer.9999')
 
-    @property
-    def blas_libs(self):
-        spec = self.spec
-        prefix = self.prefix
-        shared = '+shared' in spec
-
-        if '+ilp64' in spec:
-            mkl_integer = ['libmkl_intel_ilp64']
-        else:
-            mkl_integer = ['libmkl_intel_lp64']
-
-        mkl_threading = ['libmkl_sequential']
-
-        omp_libs = LibraryList([])
-
-        if spec.satisfies('threads=openmp'):
-            if '%intel' in spec:
-                mkl_threading = ['libmkl_intel_thread']
-                omp_threading = ['libiomp5']
-
-                omp_root = prefix.compilers_and_libraries.linux.lib.intel64
-                omp_libs = find_libraries(
-                    omp_threading, root=omp_root, shared=shared)
-            elif '%gcc' in spec:
-                mkl_threading = ['libmkl_gnu_thread']
-
-                gcc = Executable(self.compiler.cc)
-                omp_libs = gcc('--print-file-name', 'libgomp.{0}'.format(
-                    dso_suffix), output=str)
-                omp_libs = LibraryList(omp_libs)
-
-        # TODO: TBB threading: ['libmkl_tbb_thread', 'libtbb', 'libstdc++']
-
-        mkl_root = prefix.compilers_and_libraries.linux.mkl.lib.intel64
-
-        mkl_libs = find_libraries(
-            mkl_integer + ['libmkl_core'] + mkl_threading,
-            root=mkl_root,
-            shared=shared
-        )
-
-        # Intel MKL link line advisor recommends these system libraries
-        system_libs = find_system_libraries(
-            ['libpthread', 'libm', 'libdl'],
-            shared=shared
-        )
-
-        return mkl_libs + omp_libs + system_libs
-
-    @property
-    def lapack_libs(self):
-        return self.blas_libs
-
-    @property
-    def scalapack_libs(self):
-        libnames = ['libmkl_scalapack']
-        if self.spec.satisfies('^openmpi'):
-            libnames.append('libmkl_blacs_openmpi')
-        elif self.spec.satisfies('^mpich@1'):
-            libnames.append('libmkl_blacs')
-        elif self.spec.satisfies('^mpich@2:'):
-            libnames.append('libmkl_blacs_intelmpi')
-        elif self.spec.satisfies('^mvapich2'):
-            libnames.append('libmkl_blacs_intelmpi')
-        elif self.spec.satisfies('^mpt'):
-            libnames.append('libmkl_blacs_sgimpt')
-        # TODO: ^intel-parallel-studio can mean intel mpi, a compiler or a lib
-        # elif self.spec.satisfies('^intel-parallel-studio'):
-        #     libnames.append('libmkl_blacs_intelmpi')
-        else:
-            raise InstallError('No MPI found for scalapack')
-
-        integer = 'ilp64' if '+ilp64' in self.spec else 'lp64'
-        mkl_root = self.prefix.compilers_and_libraries.linux.mkl.lib.intel64
-        shared = True if '+shared' in self.spec else False
-
-        libs = find_libraries(
-            ['{0}_{1}'.format(l, integer) for l in libnames],
-            root=mkl_root,
-            shared=shared
-        )
-        return libs
-
-    @property
-    def mpi_libs(self):
-        mpi_root = self.prefix.compilers_and_libraries.linux.mpi.lib64
-        query_parameters = self.spec.last_query.extra_parameters
-        libraries = ['libmpifort', 'libmpi']
-
-        if 'cxx' in query_parameters:
-            libraries = ['libmpicxx'] + libraries
-
-        return find_libraries(
-            libraries, root=mpi_root, shared=True, recurse=True
-        )
-
-    @property
-    def mpi_headers(self):
-        # recurse from self.prefix will find too many things for all the
-        # supported sub-architectures like 'mic'
-        mpi_root = self.prefix.compilers_and_libraries.linux.mpi.include64
-        return find_headers('mpi', root=mpi_root, recurse=False)
-
-    @property
-    def components(self):
-        spec = self.spec
-        edition = self.version[0]
-
-        # Intel(R) Compilers
-        components = [
-            # Common files
-            'intel-comp-',
-            'intel-openmp',
-
-            # C/C++
-            'intel-icc',
-
-            # Fortran
-            'intel-ifort',
-
-            # Parallel Studio Documentation and Licensing Files
-            'intel-psxe',
-        ]
-
-        # Intel(R) Parallel Studio XE Suite Files and Documentation
-        if edition == 'cluster':
-            components.append('intel-icsxe')
-        elif edition == 'professional':
-            components.extend(['intel-ips', 'intel-ipsc', 'intel-ipsf'])
-        elif edition == 'composer':
-            components.extend([
-                'intel-compxe', 'intel-ccompxe', 'intel-fcompxe'
-            ])
-
-        # Intel(R) Data Analytics Acceleration Library
-        if '+daal' in spec:
-            components.append('intel-daal')
-
-        # Intel(R) Debugger for Heterogeneous Compute
-        if '+gdb' in spec:
-            components.append('intel-gdb')
-
-        # Intel(R) Integrated Performance Primitives
-        if '+ipp' in spec:
-            components.extend(['intel-ipp', 'intel-crypto-ipp'])
-
-        # Intel(R) Math Kernel Library
-        if '+mkl' in spec:
-            components.append('intel-mkl')
-
-        # Intel(R) MPI Library
-        if '+mpi' in spec:
-            components.extend(['intel-mpi', 'intel-mpirt', 'intel-imb'])
-
-        # Intel(R) Threading Building Blocks
-        if '+tbb' in spec:
-            components.append('intel-tbb')
-
-        # Intel(R) Advisor
-        if '+advisor' in spec:
-            components.append('intel-advisor')
-
-        # Intel(R) Cluster Checker
-        if '+clck' in spec:
-            components.append('intel_clck')
-
-        # Intel(R) Inspector
-        if '+inspector' in spec:
-            components.append('intel-inspector')
-
-        # Intel(R) Trace Analyzer and Collector
-        if '+itac' in spec:
-            components.extend(['intel-itac', 'intel-ta', 'intel-tc'])
-
-        # Intel(R) VTune(TM) Amplifier XE
-        if '+vtune' in spec:
-            components.append('intel-vtune-amplifier-xe')
-
-        return components
-
-    @property
-    def bin_dir(self):
-        """The relative path to the bin directory with symlinks resolved."""
-
-        bin_path = os.path.join(self.prefix.bin, 'icc')
-        absolute_path = os.path.realpath(bin_path)  # resolve symlinks
-        relative_path = os.path.relpath(absolute_path, self.prefix)
-        return os.path.dirname(relative_path)
-
-    @property
-    def lib_dir(self):
-        """The relative path to the lib directory with symlinks resolved."""
-
-        lib_path = os.path.join(self.prefix.lib, 'intel64', 'libimf.a')
-        absolute_path = os.path.realpath(lib_path)  # resolve symlinks
-        relative_path = os.path.relpath(absolute_path, self.prefix)
-        return os.path.dirname(relative_path)
-
-    @property
-    def license_files(self):
-        spec = self.spec
-        year = self.version[1]
-
-        directories = [
-            'Licenses',
-            self.bin_dir
-        ]
-
-        if '+advisor' in spec:
-            advisor_dir = 'advisor_xe/licenses'
-
-            if year >= 2017:
-                advisor_dir = 'advisor/licenses'
-
-            directories.append(advisor_dir)
-
-        if '+inspector' in spec:
-            inspector_dir = 'inspector_xe/licenses'
-
-            if year >= 2017:
-                inspector_dir = 'inspector/licenses'
-
-            directories.append(inspector_dir)
-
-        if '+itac' in spec:
-            itac_dir = 'itac_{0}'.format(year)
-
-            directories.append(itac_dir)
-
-        if '+vtune' in spec:
-            vtune_dir = 'vtune_amplifier_xe/licenses'
-
-            directories.append(vtune_dir)
-
-        return [os.path.join(dir, 'license.lic') for dir in directories]
-
-    @run_after('install')
-    def filter_compiler_wrappers(self):
-        spec = self.spec
-
-        if '+mpi' in spec:
-            if '~newdtags' in spec:
-                wrappers = [
-                    'mpif77', 'mpif90', 'mpigcc', 'mpigxx',
-                    'mpiicc', 'mpiicpc', 'mpiifort'
-                ]
-                wrapper_paths = []
-                for root, dirs, files in os.walk(spec.prefix):
-                    for name in files:
-                        if name in wrappers:
-                            wrapper_paths.append(os.path.join(spec.prefix,
-                                                              root, name))
-                for wrapper in wrapper_paths:
-                    filter_file('-Xlinker --enable-new-dtags', ' ',
-                                wrapper, string=True)
-
-    @run_after('install')
-    def rpath_configuration(self):
-        spec = self.spec
-
-        if '+rpath' in spec:
-            lib_dir = os.path.join(self.prefix, self.lib_dir)
-            for compiler in ['icc', 'icpc', 'ifort']:
-                cfgfilename = os.path.join(
-                    self.prefix, self.bin_dir, '{0}.cfg'.format(compiler))
-                with open(cfgfilename, 'w') as f:
-                    f.write('-Xlinker -rpath -Xlinker {0}\n'.format(lib_dir))
-
-    @run_after('install')
-    def fix_psxevars(self):
-        """Newer versions of Intel Parallel Studio have a bug in the
-        ``psxevars.sh`` script."""
-
-        bindir = glob.glob(join_path(
-            self.prefix, 'parallel_studio*', 'bin'))[0]
-
-        filter_file('^SCRIPTPATH=.*', 'SCRIPTPATH={0}'.format(self.prefix),
-                    os.path.join(bindir, 'psxevars.sh'),
-                    os.path.join(bindir, 'psxevars.csh'))
-
-    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
-        if '+mpi' in self.spec:
-            spack_env.set('I_MPI_CC',  spack_cc)
-            spack_env.set('I_MPI_CXX', spack_cxx)
-            spack_env.set('I_MPI_F77', spack_fc)
-            spack_env.set('I_MPI_F90', spack_f77)
-            spack_env.set('I_MPI_FC',  spack_fc)
-
-        # set up MKLROOT for everyone using MKL package
-        if '+mkl' in self.spec:
-            mkl_root = self.prefix.compilers_and_libraries.linux.mkl.lib.intel64  # noqa
-
-            spack_env.set('MKLROOT', self.prefix)
-            spack_env.append_path('SPACK_COMPILER_EXTRA_RPATHS', mkl_root)
-
-    def setup_dependent_package(self, module, dep_spec):
-        if '+mpi' in self.spec:
-            # Intel comes with 2 different flavors of MPI wrappers:
-            #
-            # * mpiicc, mpiicpc, and mpifort are hardcoded to wrap around
-            #   the Intel compilers.
-            # * mpicc, mpicxx, mpif90, and mpif77 allow you to set which
-            #   compilers to wrap using I_MPI_CC and friends. By default,
-            #   wraps around the GCC compilers.
-            #
-            # In theory, these should be equivalent as long as I_MPI_CC
-            # and friends are set to point to the Intel compilers, but in
-            # practice, mpicc fails to compile some applications while
-            # mpiicc works.
-            bindir = self.prefix.compilers_and_libraries.linux.mpi.intel64.bin
-
-            if self.compiler.name == 'intel':
-                self.spec.mpicc  = bindir.mpiicc
-                self.spec.mpicxx = bindir.mpiicpc
-                self.spec.mpifc  = bindir.mpiifort
-                self.spec.mpif77 = bindir.mpiifort
-            else:
-                self.spec.mpicc  = bindir.mpicc
-                self.spec.mpicxx = bindir.mpicxx
-                self.spec.mpifc  = bindir.mpif90
-                self.spec.mpif77 = bindir.mpif77
-
-    def setup_environment(self, spack_env, run_env):
-        """Adds environment variables to the generated module file.
-
-        These environment variables come from running:
-
-        .. code-block:: console
-
-           $ source parallel_studio_xe_2017/bin/psxevars.sh intel64
-        """
-        # NOTE: Spack runs setup_environment twice, once pre-build to set up
-        # the build environment, and once post-installation to determine
-        # the environment variables needed at run-time to add to the module
-        # file. The script we need to source is only present post-installation,
-        # so check for its existence before sourcing.
-        # TODO: At some point we should split setup_environment into
-        # setup_build_environment and setup_run_environment to get around
-        # this problem.
-        psxevars = glob.glob(join_path(
-            self.prefix, 'parallel_studio*', 'bin', 'psxevars.sh'))
-
-        if psxevars:
-            run_env.extend(EnvironmentModifications.from_sourcing_file(
-                psxevars[0], 'intel64'))
+    conflicts('+clck',      when='@professional.0:professional.9999')
+    conflicts('+itac',      when='@professional.0:professional.9999')
+    conflicts('+mpi',       when='@professional.0:professional.9999')
+
+    # The following components are not available before 2016
+    conflicts('+daal',      when='@professional.0:professional.2015.7')
+    conflicts('+daal',      when='@cluster.0:cluster.2015.7')
+    conflicts('+daal',      when='@composer.0:composer.2015.7')
+
+    def setup_dependent_environment(self, *args):
+        # Handle in callback, conveying client's compilers in additional arg.
+        # CAUTION - DUP code in:
+        #   ../intel-mpi/package.py
+        #   ../intel-parallel-studio/package.py
+        self._setup_dependent_env_callback(*args, compilers_of_client={
+            'CC':   spack_cc,
+            'CXX':  spack_cxx,
+            'F77':  spack_f77,
+            'F90':  spack_fc,
+            'FC':   spack_fc,
+        })
diff --git a/var/spack/repos/builtin/packages/intel-tbb/disable-tm.patch b/var/spack/repos/builtin/packages/intel-tbb/disable-tm.patch
new file mode 100644
index 0000000000..7ef0e93b78
--- /dev/null
+++ b/var/spack/repos/builtin/packages/intel-tbb/disable-tm.patch
@@ -0,0 +1,15 @@
+Disable transactional memory.  This is needed for some AMD or very old
+Intel systems.  See issue #6090.
+
+diff -Naurb tbb-2018_U4.orig/include/tbb/tbb_config.h tbb-2018_U4/include/tbb/tbb_config.h
+--- tbb-2018_U4.orig/include/tbb/tbb_config.h	2018-05-30 07:35:25.000000000 -0500
++++ tbb-2018_U4/include/tbb/tbb_config.h	2018-07-24 16:26:11.662673434 -0500
+@@ -98,7 +98,7 @@
+ #define __TBB_DEFINE_MIC 1
+ #endif
+ 
+-#define __TBB_TSX_AVAILABLE  ((__TBB_x86_32 || __TBB_x86_64) && !__TBB_DEFINE_MIC)
++#define __TBB_TSX_AVAILABLE  0
+ 
+ /** Presence of compiler features **/
+ 
diff --git a/var/spack/repos/builtin/packages/intel-tbb/package.py b/var/spack/repos/builtin/packages/intel-tbb/package.py
index 05185ce297..55eaa995ac 100644
--- a/var/spack/repos/builtin/packages/intel-tbb/package.py
+++ b/var/spack/repos/builtin/packages/intel-tbb/package.py
@@ -1,29 +1,12 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
+import inspect
+import platform
 
 
 class IntelTbb(Package):
@@ -34,28 +17,69 @@ class IntelTbb(Package):
     """
     homepage = "http://www.threadingbuildingblocks.org/"
 
-    # Only version-specific URL's work for TBB
-    version('2018.1', 'b2f2fa09adf44a22f4024049907f774b',
-            url='https://github.com/01org/tbb/archive/2018_U1.tar.gz')
-    version('2018.0', 'e54de69981905ad69eb9cf0226b9bf5f9a4ba065',
-            url='https://github.com/01org/tbb/archive/2018.tar.gz')
-    version('2017.8', '488f049fd107d8b1f6ba59cf4aad881172525106',
-            url='https://github.com/01org/tbb/archive/2017_U8.tar.gz')
-    version('2017.6', 'c0a722fd1ae66b40aeab25da6049086ef5f02f17',
-            url='https://github.com/01org/tbb/archive/2017_U6.tar.gz')
-    version('2017.5', '26f720729d322913912e99d1e4a36bd10625d3ca',
-            url='https://github.com/01org/tbb/archive/2017_U5.tar.gz')
-    version('2017.3', '2c451a5bcf6fc31487b98b4b29651c369874277c',
-            url='https://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb2017_20161128oss_src.tgz')
-    version('4.4.4', 'd4cee5e4ca75cab5181834877738619c56afeb71',
-            url='https://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb44_20160413oss_src.tgz')
-    version('4.4.3', '80707e277f69d9b20eeebdd7a5f5331137868ce1',
-            url='https://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb44_20160128oss_src_0.tgz')
+    # See url_for_version() below.
+    version('2019',   '2119f1db2f905dc5b423482d7689b7d6')
+    version('2018.6', '9a0f78db4f72356068b00f29f54ee6bc')
+    version('2018.5', 'ff3ae09f8c23892fbc3008c39f78288f')
+    version('2018.4', '5e2e6ba0e25624a94331c945856551c2')
+    version('2018.3', 'cd2e136598ffa5c136f077ee85a35b4c')
+    version('2018.2', '0b8dfe30917a54e40828eeb0ed7562ae')
+    version('2018.1', 'b2f2fa09adf44a22f4024049907f774b')
+    version('2018',   '7fb30d5ea2545f26ce02757d9ab05e6c')
+    version('2017.8', '7240f57f1aeea0e266a5e17ae68fdc16')
+    version('2017.7', '364f2a4b80e978f38a69cbf7c466b898')
+    version('2017.6', 'ec21254af4fc2a29574c272f501a3138')
+    version('2017.5', '85b41c64102c052e24d8a39f6193e599')
+    version('2017.4', '71526b2fef098515e212302d1455de7d')
+    version('2017.3', 'd7622eeaafeff8d271c7aa684bd82ddb')
+    version('2017.2', '9605cbea96998a10a186fc72c35cbd76')
+    version('2017.1', '6c0fe8aa7bc911a85e8e522e620511b3')
+    version('2017',   '9e7f9ea684ecf84ac74dcd3c6012cfa6')
+    version('4.4.6',  '20e15206f70c2651bfc964e451a443a0')
+    version('4.4.5',  '531a67cd98f9b4ec8ece95c5f8193a83')
+    version('4.4.4',  '61531b2e8684e06a621dcdca1a7a420e')
+    version('4.4.3',  '8e3e39e1fdfb3f7c3a5ac8ec1afe186e')
+    version('4.4.2',  'e92b110e8eb238741b00e3789b39969e')
+    version('4.4.1',  'a02c9958f02c1b5f3626874219979ae8')
+    version('4.4',    '1d512085221996eae6cec04e1a4cd3dd')
 
     provides('tbb')
 
-    # include patch for gcc rtm options
-    patch("tbb_gcc_rtm_key.patch", level=0)
+    conflicts('%gcc@6.1:', when='@:4.4.3',
+              msg='4.4.4 or later required for GCC >= 6.1.')
+
+    variant('shared', default=True,
+            description='Builds a shared version of TBB libraries')
+
+    variant('cxxstd',
+            default='default',
+            values=('default', '98', '11', '14', '17'),
+            multi=False,
+            description='Use the specified C++ standard when building.')
+
+    variant('tm', default=True,
+            description='Enable use of transactional memory on x86')
+
+    # Build and install CMake config files if we're new enough.
+    depends_on('cmake@3.0.0:', type='build', when='@2017.0:')
+
+    # Deactivate use of RTM with GCC when on an OS with an elderly assembler.
+    patch("tbb_gcc_rtm_key.patch", level=0, when='%gcc@4.8.0: os=rhel6')
+    patch("tbb_gcc_rtm_key.patch", level=0, when='%gcc@4.8.0: os=scientific6')
+    patch("tbb_gcc_rtm_key.patch", level=0, when='%gcc@4.8.0: os=centos6')
+
+    # Patch cmakeConfig.cmake.in to find the libraries where we install them.
+    patch("tbb_cmakeConfig.patch", level=0, when='@2017.0:')
+
+    # Some very old systems don't support transactional memory.
+    patch("disable-tm.patch", when='~tm')
+
+    def url_for_version(self, version):
+        url = 'https://github.com/01org/tbb/archive/{0}.tar.gz'
+        if (version[0] >= 2017) and len(version) > 1:
+            return url.format('{0}_U{1}'.format(version[0], version[1]))
+        else:
+            return url.format(version)
 
     def coerce_to_spack(self, tbb_build_subdir):
         for compiler in ["icc", "gcc", "clang"]:
@@ -75,9 +99,6 @@ class IntelTbb(Package):
                         of.write(l)
 
     def install(self, spec, prefix):
-        if spec.satisfies('%gcc@6.1:') and spec.satisfies('@:4.4.3'):
-            raise InstallError('Only TBB 4.4.4 and above build with GCC 6.1!')
-
         # We need to follow TBB's compiler selection logic to get the proper
         # build + link flags but we still need to use spack's compiler wrappers
         # to accomplish this, we do two things:
@@ -100,11 +121,24 @@ class IntelTbb(Package):
         mkdirp(prefix)
         mkdirp(prefix.lib)
 
+        make_opts = []
+
+        # Static builds of TBB are enabled by including 'big_iron.inc' file
+        # See caveats in 'big_iron.inc' for limits on using TBB statically
+        # Lore states this file must be handed to make before other options
+        if '+shared' not in self.spec:
+            make_opts.append("extra_inc=big_iron.inc")
+
+        if spec.variants['cxxstd'].value != 'default':
+            make_opts.append('stdver=c++{0}'.
+                             format(spec.variants['cxxstd'].value))
+
         #
         # tbb does not have a configure script or make install target
         # we simply call make, and try to put the pieces together
         #
-        make("compiler=%s"  % (tbb_compiler))
+        make_opts.append("compiler={0}".format(tbb_compiler))
+        make(*make_opts)
 
         # install headers to {prefix}/include
         install_tree('include', prefix.include)
@@ -123,3 +157,12 @@ class IntelTbb(Package):
             fs = glob.glob(join_path("build", "*debug", lib_name + "_debug.*"))
             for f in fs:
                 install(f, prefix.lib)
+
+        if self.spec.satisfies('@2017.0:'):
+            # Generate and install the CMake Config file.
+            cmake_args = ('-DTBB_ROOT={0}'.format(prefix),
+                          '-DTBB_OS={0}'.format(platform.system()),
+                          '-P',
+                          'tbb_config_generator.cmake')
+            with working_dir(join_path(self.stage.source_path, 'cmake')):
+                inspect.getmodule(self).cmake(*cmake_args)
diff --git a/var/spack/repos/builtin/packages/intel-tbb/tbb_cmakeConfig.patch b/var/spack/repos/builtin/packages/intel-tbb/tbb_cmakeConfig.patch
new file mode 100644
index 0000000000..a7a7ec24a2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/intel-tbb/tbb_cmakeConfig.patch
@@ -0,0 +1,11 @@
+--- cmake/templates/TBBConfig.cmake.in~	2018-03-30 10:55:05.000000000 -0500
++++ cmake/templates/TBBConfig.cmake.in	2018-05-25 10:25:52.498708945 -0500
+@@ -52,7 +52,7 @@
+ 
+ @TBB_CHOOSE_COMPILER_SUBDIR@
+ 
+-get_filename_component(_tbb_lib_path "${_tbb_root}/@TBB_SHARED_LIB_DIR@/${_tbb_arch_subdir}/${_tbb_compiler_subdir}" ABSOLUTE)
++get_filename_component(_tbb_lib_path "${_tbb_root}/@TBB_SHARED_LIB_DIR@" ABSOLUTE)
+ 
+ foreach (_tbb_component ${TBB_FIND_COMPONENTS})
+     set(_tbb_release_lib "${_tbb_lib_path}/@TBB_LIB_PREFIX@${_tbb_component}.@TBB_LIB_EXT@")
diff --git a/var/spack/repos/builtin/packages/intel-tbb/tbb_gcc_rtm_key.patch b/var/spack/repos/builtin/packages/intel-tbb/tbb_gcc_rtm_key.patch
index f1a42fb52f..29f040d4a8 100644
--- a/var/spack/repos/builtin/packages/intel-tbb/tbb_gcc_rtm_key.patch
+++ b/var/spack/repos/builtin/packages/intel-tbb/tbb_gcc_rtm_key.patch
@@ -1,23 +1,11 @@
-*** build/linux.gcc.inc.orig	2017-01-10 16:54:01.000000000 -0800
---- build/linux.gcc.inc	2017-01-10 16:54:04.000000000 -0800
-***************
-*** 49,57 ****
-  endif
-  
-  # gcc 4.8 and later support RTM intrinsics, but require command line switch to enable them
-! ifneq (,$(shell gcc -dumpversion | egrep  "^(4\.[8-9]|[5-9])"))
-!     RTM_KEY = -mrtm
-! endif
-  
-  ifeq ($(cfg), release)
-          CPLUS_FLAGS = $(ITT_NOTIFY) -g -O2 -DUSE_PTHREAD
---- 49,57 ----
-  endif
-  
-  # gcc 4.8 and later support RTM intrinsics, but require command line switch to enable them
-! #ifneq (,$(shell gcc -dumpversion | egrep  "^(4\.[8-9]|[5-9])"))
-! #    RTM_KEY = -mrtm
-! #endif
-  
-  ifeq ($(cfg), release)
-          CPLUS_FLAGS = $(ITT_NOTIFY) -g -O2 -DUSE_PTHREAD
\ No newline at end of file
+--- build/linux.gcc.inc~	2016-09-15 07:00:44.000000000 -0500
++++ build/linux.gcc.inc	2018-06-07 17:32:53.181194974 -0500
+@@ -46,7 +46,7 @@
+ 
+ # gcc 4.8 and later support RTM intrinsics, but require command line switch to enable them
+ ifneq (,$(shell gcc -dumpversion | egrep  "^(4\.[8-9]|[5-9])"))
+-    RTM_KEY = -mrtm
++    RTM_KEY = # -mrtm
+ endif
+ 
+ ifeq ($(cfg), release)
diff --git a/var/spack/repos/builtin/packages/intel-xed/package.py b/var/spack/repos/builtin/packages/intel-xed/package.py
new file mode 100644
index 0000000000..3469a531fd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/intel-xed/package.py
@@ -0,0 +1,84 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import glob
+import os
+
+
+class IntelXed(Package):
+    """The Intel X86 Encoder Decoder library for encoding and decoding x86
+    machine instructions (64- and 32-bit).  Also includes libxed-ild,
+    a lightweight library for decoding the length of an instruction."""
+
+    homepage = "https://intelxed.github.io/"
+    git      = "https://github.com/intelxed/xed.git"
+
+    version('2018.02.14', commit='44d06033b69aef2c20ab01bfb518c52cd71bb537')
+
+    resource(name='mbuild',
+             git='https://github.com/intelxed/mbuild.git',
+             commit='bb9123152a330c7fa1ff1a502950dc199c83e177',
+             destination='')
+
+    variant('debug', default=False, description='enable debug symbols')
+
+    depends_on('python@2.7:', type='build')
+
+    mycflags = []
+
+    # Save CFLAGS for use in install.
+    def flag_handler(self, name, flags):
+        if name == 'cflags':
+            self.mycflags = flags
+        return (flags, None, None)
+
+    def install(self, spec, prefix):
+        # XED needs PYTHONPATH to find the mbuild directory.
+        mbuild_dir = join_path(self.stage.source_path, 'mbuild')
+        python_path = os.getenv('PYTHONPATH', '')
+        os.environ['PYTHONPATH'] = mbuild_dir + ':' + python_path
+
+        mfile = Executable('./mfile.py')
+
+        args = ['-j', str(make_jobs),
+                '--cc=%s' % spack_cc,
+                '--no-werror']
+
+        if '+debug' in spec:
+            args.append('--debug')
+
+        # If an optimization flag (-O...) is specified in CFLAGS, use
+        # that, else set default opt level.
+        for flag in self.mycflags:
+            if len(flag) >= 2 and flag[0:2] == '-O':
+                break
+        else:
+            args.append('--opt=2')
+
+        # Build and install static libxed.a.
+        mfile('--clean')
+        mfile(*args)
+
+        mkdirp(prefix.include)
+        mkdirp(prefix.lib)
+
+        libs = glob.glob(join_path('obj', 'lib*.a'))
+        for lib in libs:
+            install(lib, prefix.lib)
+
+        # Build and install shared libxed.so.
+        mfile('--clean')
+        mfile('--shared', *args)
+
+        libs = glob.glob(join_path('obj', 'lib*.so'))
+        for lib in libs:
+            install(lib, prefix.lib)
+
+        # Install header files.
+        hdrs = glob.glob(join_path('include', 'public', 'xed', '*.h'))  \
+            + glob.glob(join_path('obj', '*.h'))
+        for hdr in hdrs:
+            install(hdr, prefix.include)
diff --git a/var/spack/repos/builtin/packages/intel/package.py b/var/spack/repos/builtin/packages/intel/package.py
index d67550caa6..69db3e21a6 100644
--- a/var/spack/repos/builtin/packages/intel/package.py
+++ b/var/spack/repos/builtin/packages/intel/package.py
@@ -1,31 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-import os
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack import *
-from spack.environment import EnvironmentModifications
 
 
 class Intel(IntelPackage):
@@ -33,78 +11,31 @@ class Intel(IntelPackage):
 
     homepage = "https://software.intel.com/en-us/intel-parallel-studio-xe"
 
-    version('18.0.0', '31ba768fba6e7322957b03feaa3add28',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12067/parallel_studio_xe_2018_composer_edition.tgz')
-    version('17.0.4', 'd03d351809e182c481dc65e07376d9a2',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11541/parallel_studio_xe_2017_update4_composer_edition.tgz')
-    version('17.0.3', '52344df122c17ddff3687f84ceb21623',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11464/parallel_studio_xe_2017_update3_composer_edition.tgz')
-    version('17.0.2', '2891ab1ece43eb61b6ab892f07c47f01',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11302/parallel_studio_xe_2017_update2_composer_edition.tgz')
-    version('17.0.1', '1f31976931ed8ec424ac7c3ef56f5e85',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/10978/parallel_studio_xe_2017_update1_composer_edition.tgz')
-    version('17.0.0', 'b67da0065a17a05f110ed1d15c3c6312',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9656/parallel_studio_xe_2017_composer_edition.tgz')
-    version('16.0.4', '2bc9bfc9be9c1968a6e42efb4378f40e',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9785/parallel_studio_xe_2016_composer_edition_update4.tgz')
-    version('16.0.3', '3208eeabee951fc27579177b593cefe9',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9063/parallel_studio_xe_2016_composer_edition_update3.tgz')
-    version('16.0.2', '1133fb831312eb519f7da897fec223fa',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8680/parallel_studio_xe_2016_composer_edition_update2.tgz')
+    # Same as in ../intel-parallel-studio/package.py, Composer Edition,
+    # but the version numbering in Spack differs.
+    version('18.0.3',              '234223cc470717c2095456d9f048d690', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13002/parallel_studio_xe_2018_update3_composer_edition.tgz')
+    version('18.0.2',              '76f820f53de4c1ff998229c983cf4f53', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12722/parallel_studio_xe_2018_update2_composer_edition.tgz')
+    version('18.0.1',              '28cb807126d713350f4aa6f9f167448a', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12381/parallel_studio_xe_2018_update1_composer_edition.tgz')
+    version('18.0.0',              '31ba768fba6e7322957b03feaa3add28', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12067/parallel_studio_xe_2018_composer_edition.tgz')
+    #
+    version('17.0.7',              '4c02a4a29a8f2424f31baa23116a1001', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12860/parallel_studio_xe_2017_update7_composer_edition.tgz')
+    version('17.0.6',              'd96cce0c3feef20091efde458f581a9f', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12538/parallel_studio_xe_2017_update6_composer_edition.tgz')
+    # version('17.0.5',              -- TBD --
+    version('17.0.4',              'd03d351809e182c481dc65e07376d9a2', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11541/parallel_studio_xe_2017_update4_composer_edition.tgz')
+    version('17.0.3',              '52344df122c17ddff3687f84ceb21623', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11464/parallel_studio_xe_2017_update3_composer_edition.tgz')
+    version('17.0.2',              '2891ab1ece43eb61b6ab892f07c47f01', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11302/parallel_studio_xe_2017_update2_composer_edition.tgz')
+    version('17.0.1',              '1f31976931ed8ec424ac7c3ef56f5e85', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/10978/parallel_studio_xe_2017_update1_composer_edition.tgz')
+    version('17.0.0',              'b67da0065a17a05f110ed1d15c3c6312', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9656/parallel_studio_xe_2017_composer_edition.tgz')
+    #
+    version('16.0.4',              '2bc9bfc9be9c1968a6e42efb4378f40e', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9785/parallel_studio_xe_2016_composer_edition_update4.tgz')
+    version('16.0.3',              '3208eeabee951fc27579177b593cefe9', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9063/parallel_studio_xe_2016_composer_edition_update3.tgz')
+    version('16.0.2',              '1133fb831312eb519f7da897fec223fa', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8680/parallel_studio_xe_2016_composer_edition_update2.tgz')
+    #
+    # Grandfathered release; different directory structure.
+    version('15.0.6',              'da9f8600c18d43d58fba0488844f79c9', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8432/l_compxe_2015.6.233.tgz')
+    version('15.0.1',              '85beae681ae56411a8e791a7c44a5c0a', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/4933/l_compxe_2015.1.133.tgz')
 
     variant('rpath', default=True, description='Add rpath to .cfg files')
 
-    components = [
-        # Common files
-        'intel-comp-',
-        'intel-openmp',
-
-        # C/C++
-        'intel-icc',
-
-        # Fortran
-        'intel-ifort',
-    ]
-
-    @property
-    def license_files(self):
-        return [
-            'Licenses/license.lic',
-            join_path('compilers_and_libraries', 'linux', 'bin',
-                      'intel64', 'license.lic')
-        ]
-
-    @run_after('install')
-    def rpath_configuration(self):
-        if '+rpath' in self.spec:
-            bin_dir = join_path(self.prefix, 'compilers_and_libraries',
-                                'linux', 'bin', 'intel64')
-            lib_dir = join_path(self.prefix, 'compilers_and_libraries',
-                                'linux', 'compiler', 'lib', 'intel64_lin')
-            for compiler in ['icc', 'icpc', 'ifort']:
-                cfgfilename = join_path(bin_dir, '{0}.cfg'.format(compiler))
-                with open(cfgfilename, 'w') as f:
-                    f.write('-Xlinker -rpath -Xlinker {0}\n'.format(lib_dir))
-
-    def setup_environment(self, spack_env, run_env):
-        """Adds environment variables to the generated module file.
-
-        These environment variables come from running:
-
-        .. code-block:: console
-
-           $ source bin/compilervars.sh intel64
-        """
-        # NOTE: Spack runs setup_environment twice, once pre-build to set up
-        # the build environment, and once post-installation to determine
-        # the environment variables needed at run-time to add to the module
-        # file. The script we need to source is only present post-installation,
-        # so check for its existence before sourcing.
-        # TODO: At some point we should split setup_environment into
-        # setup_build_environment and setup_run_environment to get around
-        # this problem.
-        compilervars = os.path.join(self.prefix.bin, 'compilervars.sh')
-
-        if os.path.isfile(compilervars):
-            run_env.extend(EnvironmentModifications.from_sourcing_file(
-                compilervars, 'intel64'))
+    # Since the current package is a subset of 'intel-parallel-studio',
+    # all remaining Spack actions are handled in the package class.
diff --git a/var/spack/repos/builtin/packages/intltool/package.py b/var/spack/repos/builtin/packages/intltool/package.py
index 0c84d3b516..dea21ab25a 100644
--- a/var/spack/repos/builtin/packages/intltool/package.py
+++ b/var/spack/repos/builtin/packages/intltool/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,6 +20,12 @@ class Intltool(AutotoolsPackage):
     depends_on('perl-xml-parser', type=('build', 'run'))
     depends_on('perl@5.8.1:',     type=('build', 'run'))
 
+    # patch for "Unescaped left brace in regex is illegal here in regex"
+    # warnings witn perl 5.22 and errors with perl 5.26 and newer
+    patch('https://launchpadlibrarian.net/216052398/intltool-perl-5.22.patch',
+          sha256='ca9d6562f29f06c64150f50369a24402b7aa01a3a0dc73dce55106f3224330a1',
+          level=0)
+
     def check(self):
         # `make check` passes but causes `make install` to fail
         pass
diff --git a/var/spack/repos/builtin/packages/ior/package.py b/var/spack/repos/builtin/packages/ior/package.py
index 96b5a455c9..eee53a9911 100644
--- a/var/spack/repos/builtin/packages/ior/package.py
+++ b/var/spack/repos/builtin/packages/ior/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/iozone/package.py b/var/spack/repos/builtin/packages/iozone/package.py
index c75595ba14..09124c2196 100644
--- a/var/spack/repos/builtin/packages/iozone/package.py
+++ b/var/spack/repos/builtin/packages/iozone/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/iperf2/package.py b/var/spack/repos/builtin/packages/iperf2/package.py
new file mode 100644
index 0000000000..3e9498ddf1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/iperf2/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Iperf2(AutotoolsPackage):
+    """This code is a continuation based from the no longer maintained iperf
+    2.0.5 code base. Iperf 2.0.5 is still widely deployed and used by many for
+    testing networks and for qualifying networking products."""
+
+    homepage = "https://sourceforge.net/projects/iperf2"
+    url      = "https://downloads.sourceforge.net/project/iperf2/iperf-2.0.12.tar.gz"
+
+    version('2.0.12', 'e501e26b9289097086ce0c44a42b10bc')
diff --git a/var/spack/repos/builtin/packages/iperf3/package.py b/var/spack/repos/builtin/packages/iperf3/package.py
new file mode 100644
index 0000000000..16cf48f157
--- /dev/null
+++ b/var/spack/repos/builtin/packages/iperf3/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Iperf3(AutotoolsPackage):
+    """The iperf series of tools perform active measurements to determine the
+    maximum achievable bandwidth on IP networks. iperf2 is a separately
+    maintained project."""
+
+    homepage = "https://software.es.net/iperf/"
+    url      = "https://github.com/esnet/iperf/archive/3.6.tar.gz"
+
+    version('3.6', '5082ffc4141abc1bac7cbd59337ff409')
diff --git a/var/spack/repos/builtin/packages/ipopt/package.py b/var/spack/repos/builtin/packages/ipopt/package.py
index a9502a3e85..64930c5ca7 100644
--- a/var/spack/repos/builtin/packages/ipopt/package.py
+++ b/var/spack/repos/builtin/packages/ipopt/package.py
@@ -1,36 +1,20 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class Ipopt(Package):
+class Ipopt(AutotoolsPackage):
     """Ipopt (Interior Point OPTimizer, pronounced eye-pea-Opt) is a
        software package for large-scale nonlinear optimization."""
     homepage = "https://projects.coin-or.org/Ipopt"
     url      = "http://www.coin-or.org/download/source/Ipopt/Ipopt-3.12.4.tgz"
 
+    version('3.12.10', 'e1a3ad09e41edbfe41948555ece0bdc78757a5ca764b6be5a9a127af2e202d2e')
+    version('3.12.9', '8ff3fe1a8560896fc5559839a87c2530cac4ed231b0806e487bfd3cf2d294ab8')
+    version('3.12.8', '62c6de314220851b8f4d6898b9ae8cf0a8f1e96b68429be1161f8550bb7ddb03')
     version('3.12.7', '2a36e4a04717a8ed7012ac7d1253ae4ffbc1a8fd')
     version('3.12.6', 'ed4072427fab786fcf6082fe7e6f6c2ed9b5e6f8')
     version('3.12.5', '3f63ddfff517235ead17af6cceb426ca858dda37')
@@ -44,17 +28,26 @@ class Ipopt(Package):
             description="Build with Coin Harwell Subroutine Libraries")
     variant('metis', default=False,
             description="Build with METIS partitioning support")
+    variant('debug', default=False,
+            description="Build debug instead of optimized version")
 
     depends_on("blas")
     depends_on("lapack")
-    depends_on("pkg-config", type='build')
+    depends_on("pkgconfig", type='build')
     depends_on("mumps+double~mpi")
     depends_on('coinhsl', when='+coinhsl')
-    depends_on('metis@4.0:4.999', when='+metis')
+    depends_on('metis@4.0:', when='+metis')
 
     patch('ipopt_ppc_build.patch', when='arch=ppc64le')
 
-    def install(self, spec, prefix):
+    flag_handler = build_system_flags
+    build_directory = 'spack-build'
+
+    # IPOPT does not build correctly in parallel on OS X
+    parallel = False
+
+    def configure_args(self):
+        spec = self.spec
         # Dependency directories
         blas_dir = spec['blas'].prefix
         lapack_dir = spec['lapack'].prefix
@@ -68,8 +61,8 @@ class Ipopt(Package):
         blas_lib = spec['blas'].libs.ld_flags
         lapack_lib = spec['lapack'].libs.ld_flags
 
-        configure_args = [
-            "--prefix=%s" % prefix,
+        args = [
+            "--prefix=%s" % self.prefix,
             "--with-mumps-incdir=%s" % mumps_dir.include,
             "--with-mumps-lib=%s" % mumps_libcmd,
             "--enable-shared",
@@ -81,18 +74,21 @@ class Ipopt(Package):
         ]
 
         if 'coinhsl' in spec:
-            configure_args.extend([
+            args.extend([
                 '--with-hsl-lib=%s' % spec['coinhsl'].libs.ld_flags,
                 '--with-hsl-incdir=%s' % spec['coinhsl'].prefix.include])
 
         if 'metis' in spec:
-            configure_args.extend([
+            args.extend([
                 '--with-metis-lib=%s' % spec['metis'].libs.ld_flags,
                 '--with-metis-incdir=%s' % spec['metis'].prefix.include])
 
-        configure(*configure_args)
+        # The IPOPT configure file states that '--enable-debug' implies
+        # '--disable-shared', but adding '--enable-shared' overrides
+        # '--disable-shared' and builds a shared library with debug symbols
+        if '+debug' in spec:
+            args.append('--enable-debug')
+        else:
+            args.append('--disable-debug')
 
-        # IPOPT does not build correctly in parallel on OS X
-        make(parallel=False)
-        make("test", parallel=False)
-        make("install", parallel=False)
+        return args
diff --git a/var/spack/repos/builtin/packages/isaac-server/package.py b/var/spack/repos/builtin/packages/isaac-server/package.py
index 3bfad09f98..f8451ad443 100644
--- a/var/spack/repos/builtin/packages/isaac-server/package.py
+++ b/var/spack/repos/builtin/packages/isaac-server/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,11 +11,14 @@ class IsaacServer(CMakePackage):
 
     homepage = "http://computationalradiationphysics.github.io/isaac/"
     url      = "https://github.com/ComputationalRadiationPhysics/isaac/archive/v1.3.0.tar.gz"
+    git      = "https://github.com/ComputationalRadiationPhysics/isaac.git"
+
+    maintainers = ['ax3l']
 
-    version('develop', branch='dev',
-            git='https://github.com/ComputationalRadiationPhysics/isaac.git')
-    version('master', branch='master',
-            git='https://github.com/ComputationalRadiationPhysics/isaac.git')
+    version('develop', branch='dev')
+    version('master', branch='master')
+    version('1.4.0', '3ad05c8fad4673366077204c5d39285f')
+    version('1.3.3', '7aeebaf0c5a77e2cb9bea066750e369b')
     version('1.3.2', 'c557daa74de52fd79e734c9758fca38b')
     version('1.3.1', '7fe075f9af68d05355eaba0e224f20ca')
     version('1.3.0', 'c8a794da9bb998ef0e75449bfece1a12')
@@ -49,7 +33,7 @@ class IsaacServer(CMakePackage):
     depends_on('libwebsockets@2.1.1:', type='link')
     # depends_on('gstreamer@1.0', when='+gstreamer')
 
-    # Until the pull request is merged: https://github.com/ComputationalRadiationPhysics/isaac/pull/70
+    # https://github.com/ComputationalRadiationPhysics/isaac/pull/70
     patch('jpeg.patch', when='@:1.3.1')
 
     root_cmakelists_dir = 'server'
diff --git a/var/spack/repos/builtin/packages/isaac/package.py b/var/spack/repos/builtin/packages/isaac/package.py
index 4c05faeb26..c8f3793fc6 100644
--- a/var/spack/repos/builtin/packages/isaac/package.py
+++ b/var/spack/repos/builtin/packages/isaac/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,11 +11,13 @@ class Isaac(CMakePackage):
 
     homepage = "http://computationalradiationphysics.github.io/isaac/"
     url      = "https://github.com/ComputationalRadiationPhysics/isaac/archive/v1.3.0.tar.gz"
+    git      = "https://github.com/ComputationalRadiationPhysics/isaac.git"
+
+    maintainers = ['ax3l']
 
-    version('develop', branch='dev',
-            git='https://github.com/ComputationalRadiationPhysics/isaac.git')
-    version('master', branch='master',
-            git='https://github.com/ComputationalRadiationPhysics/isaac.git')
+    version('develop', branch='dev')
+    version('master', branch='master')
+    version('1.4.0', '3ad05c8fad4673366077204c5d39285f')
     version('1.3.3', '7aeebaf0c5a77e2cb9bea066750e369b')
     version('1.3.2', 'c557daa74de52fd79e734c9758fca38b')
     version('1.3.1', '7fe075f9af68d05355eaba0e224f20ca')
@@ -51,7 +34,7 @@ class Isaac(CMakePackage):
     depends_on('boost@1.56.0:', type='link')
     depends_on('boost@1.65.1:', type='link', when='^cuda@9:')
     depends_on('cuda@7.0:', type='link', when='+cuda')
-    # depends_on('alpaka', when='+alpaka')
+    # depends_on('alpaka@0.3', when='+alpaka')
     depends_on('icet', type='link')
     depends_on('mpi', type='link')
 
diff --git a/var/spack/repos/builtin/packages/isl/package.py b/var/spack/repos/builtin/packages/isl/package.py
index 4c25f3ec97..cca2ba21f3 100644
--- a/var/spack/repos/builtin/packages/isl/package.py
+++ b/var/spack/repos/builtin/packages/isl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,10 +11,12 @@ class Isl(AutotoolsPackage):
     sets and relations of integer points bounded by affine constraints."""
 
     homepage = "http://isl.gforge.inria.fr"
-    url      = "http://isl.gforge.inria.fr/isl-0.18.tar.bz2"
+    url      = "http://isl.gforge.inria.fr/isl-0.19.tar.bz2"
 
-    version('0.18', '11436d6b205e516635b666090b94ab32')
-    version('0.14', 'acd347243fca5609e3df37dba47fd0bb')
+    version('0.19', sha256='d59726f34f7852a081fbd3defd1ab2136f174110fc2e0c8d10bb122173fa9ed8')
+    version('0.18', sha256='6b8b0fd7f81d0a957beb3679c81bbb34ccc7568d5682844d8924424a0dadcb1b')
+    version('0.15', sha256='8ceebbf4d9a81afa2b4449113cee4b7cb14a687d7a549a963deb5e2a41458b6b')
+    version('0.14', sha256='7e3c02ff52f8540f6a85534f54158968417fd676001651c8289c705bd0228f36')
 
     depends_on('gmp')
 
diff --git a/var/spack/repos/builtin/packages/itstool/package.py b/var/spack/repos/builtin/packages/itstool/package.py
index 00e273bb2f..b0858df2b9 100644
--- a/var/spack/repos/builtin/packages/itstool/package.py
+++ b/var/spack/repos/builtin/packages/itstool/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/itsx/package.py b/var/spack/repos/builtin/packages/itsx/package.py
index 84dc525740..6d4414db12 100644
--- a/var/spack/repos/builtin/packages/itsx/package.py
+++ b/var/spack/repos/builtin/packages/itsx/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/jackcess/package.py b/var/spack/repos/builtin/packages/jackcess/package.py
new file mode 100644
index 0000000000..d55357bccf
--- /dev/null
+++ b/var/spack/repos/builtin/packages/jackcess/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Jackcess(Package):
+    """Jackcess is a pure Java library for reading from and writing to
+    MS Access databases (currently supporting versions 2000-2016)."""
+
+    homepage = "http://jackcess.sourceforge.net/"
+    url      = "https://sourceforge.net/projects/jackcess/files/jackcess/2.1.12/jackcess-2.1.12.jar"
+
+    version('2.1.12',   '7d051d8dd93f2fe7e5e86389ea380619', expand=False)
+    version('1.2.14.3', 'ef778421c1385ac9ab4aa7edfb954caa', expand=False)
+
+    extends('jdk')
+    depends_on('java', type='run')
+    depends_on('commons-lang@2.6', when='@2.1.12', type='run')
+    depends_on('commons-lang@2.4', when='@1.2.14.3', type='run')
+    depends_on('commons-logging@1.1.3', when='@2.1.12', type='run')
+    depends_on('commons-logging@1.1.1', when='@1.2.14.3', type='run')
+
+    def install(self, spec, prefix):
+        install('jackcess-{0}.jar'.format(self.version), prefix)
diff --git a/var/spack/repos/builtin/packages/jags/package.py b/var/spack/repos/builtin/packages/jags/package.py
index 248f4019d6..0916d85f72 100644
--- a/var/spack/repos/builtin/packages/jags/package.py
+++ b/var/spack/repos/builtin/packages/jags/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,15 +11,18 @@ class Jags(AutotoolsPackage):
        Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC)
        simulation not wholly unlike BUGS"""
 
+    tags = ['mcmc', 'Gibbs sampler']
+
     homepage = "http://mcmc-jags.sourceforge.net/"
     url = "https://downloads.sourceforge.net/project/mcmc-jags/JAGS/4.x/Source/JAGS-4.2.0.tar.gz"
 
+    version('4.3.0', 'd88dff326603deee39ce7fa4234c5a43')
     version('4.2.0', '9e521b3cfb23d3290a8c6bc0b79bf426')
 
     depends_on('blas')
     depends_on('lapack')
 
     def configure_args(self):
-        args = ['--with-blas=-L%s' % self.spec['blas'].prefix.lib,
-                '--with-lapack=-L%s' % self.spec['lapack'].prefix.lib]
+        args = ['--with-blas=%s' % self.spec['blas'].libs.ld_flags,
+                '--with-lapack=%s' % self.spec['lapack'].libs.ld_flags]
         return args
diff --git a/var/spack/repos/builtin/packages/jansson/package.py b/var/spack/repos/builtin/packages/jansson/package.py
index e3e2d56cff..c929eaa865 100644
--- a/var/spack/repos/builtin/packages/jansson/package.py
+++ b/var/spack/repos/builtin/packages/jansson/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,6 +12,7 @@ class Jansson(CMakePackage):
 
     homepage = "http://www.digip.org/jansson/"
     url      = "https://github.com/akheron/jansson/archive/v2.9.tar.gz"
+    maintainers = ['ax3l']
 
     version('2.9', 'd2db25c437b359fc5a065ed938962237')
 
diff --git a/var/spack/repos/builtin/packages/jasper/package.py b/var/spack/repos/builtin/packages/jasper/package.py
index 5739f902a1..6b0fc9c866 100644
--- a/var/spack/repos/builtin/packages/jasper/package.py
+++ b/var/spack/repos/builtin/packages/jasper/package.py
@@ -1,58 +1,102 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class Jasper(AutotoolsPackage):
+class Jasper(Package):
     """Library for manipulating JPEG-2000 images"""
 
     homepage = "https://www.ece.uvic.ca/~frodo/jasper/"
-    url = "https://www.ece.uvic.ca/~frodo/jasper/software/jasper-1.900.1.zip"
+    url      = "https://www.ece.uvic.ca/~frodo/jasper/software/jasper-2.0.14.tar.gz"
+    list_url = homepage
 
-    version('1.900.1', 'a342b2b4495b3e1394e161eb5d85d754')
+    version('2.0.14',  '23561b51da8eb5d0dc85b91eff3d9a7f',
+            url="https://www.ece.uvic.ca/~frodo/jasper/software/jasper-2.0.14.tar.gz")
+    version('1.900.1', 'a342b2b4495b3e1394e161eb5d85d754',
+            url="https://www.ece.uvic.ca/~frodo/jasper/software/jasper-1.900.1.zip")
 
-    variant('shared', default=True,
-            description='Builds shared versions of the libraries')
-    variant('debug', default=False,
-            description='Builds debug versions of the libraries')
+    variant('jpeg',   default=True,  description='Enable the use of the JPEG library')
+    variant('opengl', default=False, description='Enable the use of the OpenGL and GLUT libraries')
+    variant('shared', default=True,  description='Enable the building of shared libraries')
+    variant('build_type', default='Release', description='CMake build type', values=('Debug', 'Release'))
+
+    depends_on('cmake@2.8.11:', type='build', when='@2:')
+    depends_on('jpeg', when='+jpeg')
+    depends_on('gl', when='+opengl')
+
+    # Fixes a bug where an assertion fails when certain JPEG-2000
+    # files with an alpha channel are processed.
+    # See: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=469786
+    patch('fix_alpha_channel_assert_fail.patch', when='@1.900.1')
+
+    def cmake_args(self):
+        spec = self.spec
+        args = std_cmake_args
+        args.append('-DJAS_ENABLE_DOC=false')
 
-    depends_on('jpeg')
+        if '+jpeg' in spec:
+            args.append('-DJAS_ENABLE_LIBJPEG=true')
+        else:
+            args.append('-DJAS_ENABLE_LIBJPEG=false')
 
-    # Fixes a bug (still in upstream as of v.1.900.1) where an assertion fails
-    # when certain JPEG-2000 files with an alpha channel are processed
-    # see: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=469786
-    patch('fix_alpha_channel_assert_fail.patch')
+        if '+opengl' in spec:
+            args.append('-DJAS_ENABLE_OPENGL=true')
+        else:
+            args.append('-DJAS_ENABLE_OPENGL=false')
+
+        if '+shared' in spec:
+            args.append('-DJAS_ENABLE_SHARED=true')
+        else:
+            args.append('-DJAS_ENABLE_SHARED=false')
+
+        return args
 
     def configure_args(self):
         spec = self.spec
-        args = ['--mandir={0}'.format(spec.prefix.man)]
+        args = [
+            '--prefix={0}'.format(self.prefix)
+        ]
+
+        if '+jpeg' in spec:
+            args.append('--enable-libjpeg')
+        else:
+            args.append('--disable-libjpeg')
+
+        if '+opengl' in spec:
+            args.append('--enable-opengl')
+        else:
+            args.append('--disable-opengl')
 
         if '+shared' in spec:
             args.append('--enable-shared')
+        else:
+            args.append('--disable-shared')
 
-        if '+debug' not in spec:
+        if 'build_type=Debug' in spec:
+            args.append('--enable-debug')
+        else:
             args.append('--disable-debug')
 
         return args
+
+    @when('@2:')
+    def install(self, spec, prefix):
+        with working_dir('spack-build', create=True):
+            cmake('..', *self.cmake_args())
+            make()
+            if self.run_tests:
+                make('test')
+            make('install')
+
+    @when('@:1')
+    def install(self, spec, prefix):
+        configure(*self.configure_args())
+        make()
+        if self.run_tests:
+            make('check')
+        make('install')
+        if self.run_tests:
+            make('installcheck')
diff --git a/var/spack/repos/builtin/packages/jbigkit/package.py b/var/spack/repos/builtin/packages/jbigkit/package.py
new file mode 100644
index 0000000000..66dd1b202c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/jbigkit/package.py
@@ -0,0 +1,35 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Jbigkit(MakefilePackage):
+    """JBIG-Kit is a software implementation of
+    the JBIG1 data compression standard."""
+
+    homepage = "http://www.cl.cam.ac.uk/~mgk25/jbigkit/"
+    url      = "http://www.cl.cam.ac.uk/~mgk25/jbigkit/download/jbigkit-2.1.tar.gz"
+
+    version('2.1', 'ebcf09bed9f14d7fa188d3bd57349522')
+    version('1.6', 'ce196e45f293d40ba76af3dc981ccfd7')
+
+    build_directory = 'libjbig'
+
+    def edit(self, spec, prefix):
+        makefile = FileFilter('libjbig/Makefile')
+        makefile.filter('CC = .*', 'CC = cc')
+
+    def install(self, spec, prefix):
+        with working_dir(self.build_directory):
+            mkdir(prefix.include)
+            for f in ['jbig85.h', 'jbig_ar.h', 'jbig.h']:
+                install(f, prefix.include)
+            mkdir(prefix.lib)
+            for f in ['libjbig85.a', 'libjbig.a']:
+                install(f, prefix.lib)
+            mkdir(prefix.bin)
+            for f in ['tstcodec', 'tstcodec85']:
+                install(f, prefix.bin)
diff --git a/var/spack/repos/builtin/packages/jchronoss/package.py b/var/spack/repos/builtin/packages/jchronoss/package.py
new file mode 100644
index 0000000000..dc8763b064
--- /dev/null
+++ b/var/spack/repos/builtin/packages/jchronoss/package.py
@@ -0,0 +1,44 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Jchronoss(CMakePackage):
+    """ JCHRONOSS aims to help HPC application testing process
+     to scale as much as the application does. """
+
+    homepage = "http://jchronoss.hpcframework.com"
+    url      = "http://fs.paratools.com/mpc/contrib/apps/jchronoss/JCHRONOSS-1.2.tar.gz"
+
+    version('1.2',   'f083ca453537e4f60ad17d266bbab1f1')
+    version('1.1.1', '2d78a0998efec20e7726af19fff76a72')
+    version('1.1',   'a8ba0b21b18548874b8ab2a6ca6e1081')
+    version('1.0',   '78d81e00248e21f4adea4a1ccfd6156b')
+
+    variant("realtime", default=False, description="Enable Real-Time support")
+    variant("openmp", default=False, description="Enable OpenMP constructs")
+    variant("ncurses", default=False, description="Enable ncurses-based tool")
+    variant('color', default=False, description='Enable colour-themed output')
+
+    depends_on("libxml2")
+    depends_on("libwebsockets", when="+realtime")
+    depends_on("libev", when="+realtime")
+    depends_on("ncurses", when="+ncurses")
+
+    def cmake_args(self):
+        args = ["-DSPACK_DRIVEN=ON"]
+
+        if '+color' in self.spec:
+            args.append("-DENABLE_COLOR=yes")
+        if '+openmp' in self.spec:
+            args.append("-DENABLE_OPENMP=yes")
+        if '+ncurses' in self.spec:
+            args.append("-DENABLE_PLUGIN_NCURSES=yes")
+        if '+realtime' in self.spec:
+            args.append("-DENABLE_PLUGIN_SERVER=yes")
+
+        return args
diff --git a/var/spack/repos/builtin/packages/jdk/package.py b/var/spack/repos/builtin/packages/jdk/package.py
index 9c221fa364..0204572f25 100644
--- a/var/spack/repos/builtin/packages/jdk/package.py
+++ b/var/spack/repos/builtin/packages/jdk/package.py
@@ -1,79 +1,178 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-#
-# Author: Justin Too <too1@llnl.gov>
-#
-import distutils.dir_util
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.util.prefix import Prefix
 from spack import *
 
+import llnl.util.tty as tty
+import os
+
 
 class Jdk(Package):
-    """The Java Development Kit (JDK) released by Oracle Corporation
-       in the form of a binary product aimed at Java developers."""
+    """The Java Development Kit (JDK) released by Oracle Corporation in the
+    form of a binary product aimed at Java developers. Includes a complete JRE
+    plus tools for developing, debugging, and monitoring Java applications."""
+
     homepage = "http://www.oracle.com/technetwork/java/javase/downloads/index.html"
 
+    maintainers = ['justintoo']
+
     # Oracle requires that you accept their License Agreement in order
     # to access the Java packages in download.oracle.com. In order to
     # automate this process, we need to utilize these additional curl
-    # commandline options.
-    #
-    # See http://stackoverflow.com/questions/10268583/how-to-automate-download-and-installation-of-java-jdk-on-linux
+    # command-line options. See:
+    # http://stackoverflow.com/questions/10268583/how-to-automate-download-and-installation-of-java-jdk-on-linux
     curl_options = [
         '-j',  # junk cookies
         '-H',  # specify required License Agreement cookie
-        'Cookie: oraclelicense=accept-securebackup-cookie']
+        'Cookie: oraclelicense=accept-securebackup-cookie'
+    ]
 
-    # For instructions on how to find the magic URL, see:
-    # https://gist.github.com/P7h/9741922
-    # https://linuxconfig.org/how-to-install-java-se-development-kit-on-debian-linux
-    version('8u141-b15', '8cf4c4e00744bfafc023d770cb65328c', curl_options=curl_options,
+    # To add the latest version, go to the homepage listed above,
+    # click "JDK Download", click "Accept License Agreement", right-click the
+    # Linux .tar.gz link, and select Copy Link Address. The checksum can be
+    # found in a link above. The build number can be deciphered from the URL.
+    # Alternatively, run `bin/java -version` after extracting. Replace '+'
+    # symbol in version with '_', otherwise it will be interpreted as a variant
+    version('11.0.1', sha256='e7fd856bacad04b6dbf3606094b6a81fa9930d6dbb044bbd787be7ea93abc885', curl_options=curl_options,
+            url='http://download.oracle.com/otn-pub/java/jdk/11.0.1+13/90cf5d8f270a4347a95050320eef3fb7/jdk-11.0.1_linux-x64_bin.tar.gz')
+    version('10.0.2_13', sha256='6633c20d53c50c20835364d0f3e172e0cbbce78fff81867488f22a6298fa372b', curl_options=curl_options,
+            url='http://download.oracle.com/otn-pub/java/jdk/10.0.2+13/19aef61b38124481863b1413dce1855f/jdk-10.0.2_linux-x64_bin.tar.gz')
+    version('10.0.1_10', 'ae8ed645e6af38432a56a847597ac61d4283b7536688dbab44ab536199d1e5a4', curl_options=curl_options,
+            url='http://download.oracle.com/otn-pub/java/jdk/10.0.1+10/fb4372174a714e6b8c52526dc134031e/jdk-10.0.1_linux-x64_bin.tar.gz')
+    version('1.8.0_181-b13', 'ef599e322eee42f6769991dd3e3b1a31', curl_options=curl_options, 
+            url='http://download.oracle.com/otn-pub/java/jdk/8u181-b13/96a7b8442fe848ef90c96a2fad6ed6d1/jdk-8u181-linux-x64.tar.gz')
+    version('1.8.0_172-b11', 'eda2945e8c02b84adbf78f46c37b71c1', curl_options=curl_options,
+            url='http://download.oracle.com/otn-pub/java/jdk/8u172-b11/a58eab1ec242421181065cdc37240b08/jdk-8u172-linux-x64.tar.gz')
+    version('1.8.0_141-b15', '8cf4c4e00744bfafc023d770cb65328c', curl_options=curl_options,
             url='http://download.oracle.com/otn-pub/java/jdk/8u141-b15/336fa29ff2bb4ef291e347e091f7f4a7/jdk-8u141-linux-x64.tar.gz')
-    version('8u131-b11', '75b2cb2249710d822a60f83e28860053', curl_options=curl_options,
+    version('1.8.0_131-b11', '75b2cb2249710d822a60f83e28860053', curl_options=curl_options,
             url='http://download.oracle.com/otn-pub/java/jdk/8u131-b11/d54c1d3a095b4ff2b6607d096fa80163/jdk-8u131-linux-x64.tar.gz')
-    version('8u92-b14',  '65a1cc17ea362453a6e0eb4f13be76e4', curl_options=curl_options)
-    version('8u73-b02',  '1b0120970aa8bc182606a16bf848a686', curl_options=curl_options)
-    version('8u66-b17',  '88f31f3d642c3287134297b8c10e61bf', curl_options=curl_options)
-    # The 7u80 tarball is not readily available from Oracle.  If you have
-    # the tarball, add it to your mirror as mirror/jdk/jdk-7u80.tar.gz and
-    # away you go.
-    version('7u80-b0', '6152f8a7561acf795ca4701daa10a965')
-
-    provides('java@8', when='@8u0:8u999')
-    provides('java@7', when='@7u0:7u999')
-
-    def url_for_version(self, version):
-        url = "http://download.oracle.com/otn-pub/java/jdk/{0}/jdk-{1}-linux-x64.tar.gz"
-        version = str(version)
-        minor_version = version[:version.index('-')]
-        return url.format(version, minor_version)
+    version('1.8.0_92-b14', '65a1cc17ea362453a6e0eb4f13be76e4', curl_options=curl_options)
+    version('1.8.0_73-b02', '1b0120970aa8bc182606a16bf848a686', curl_options=curl_options)
+    version('1.8.0_66-b17', '88f31f3d642c3287134297b8c10e61bf', curl_options=curl_options)
+    version('1.7.0_80-b0', '6152f8a7561acf795ca4701daa10a965', curl_options=curl_options)
+
+    provides('java')
+    provides('java@11', when='@11.0:11.999')
+    provides('java@10', when='@10.0:10.999')
+    provides('java@9',  when='@9.0:9.999')
+    provides('java@8',  when='@1.8.0:1.8.999')
+    provides('java@7',  when='@1.7.0:1.7.999')
+
+    # FIXME:
+    # 1. `extends('java')` doesn't work, you need to use `extends('jdk')`
+    # 2. Packages cannot extend multiple packages, see #987
+    # 3. Update `YamlFilesystemView.merge` to allow a Package to completely
+    #    override how it is symlinked into a view prefix. Then, spack activate
+    #    can symlink all *.jar files to `prefix.lib.ext`
+    extendable = True
+
+    @property
+    def home(self):
+        """Most of the time, ``JAVA_HOME`` is simply ``spec['java'].prefix``.
+        However, if the user is using an externally installed JDK, it may be
+        symlinked. For example, on macOS, the ``java`` executable can be found
+        in ``/usr/bin``, but ``JAVA_HOME`` is actually
+        ``/Library/Java/JavaVirtualMachines/jdk-10.0.1.jdk/Contents/Home``.
+        Users may not know the actual installation directory and add ``/usr``
+        to their ``packages.yaml`` unknowingly. Run ``java_home`` if it exists
+        to determine exactly where it is installed. Specify which version we
+        are expecting in case multiple Java versions are installed.
+        See ``man java_home`` for more details."""
+
+        prefix = self.prefix
+        java_home = prefix.libexec.java_home
+        if os.path.exists(java_home):
+            java_home = Executable(java_home)
+            version = str(self.version.up_to(2))
+            prefix = java_home('--version', version, output=str).strip()
+            prefix = Prefix(prefix)
+
+        return prefix
+
+    @property
+    def libs(self):
+        """Depending on the version number and whether the full JDK or just
+        the JRE was installed, Java libraries can be in several locations:
+
+        * ``lib/libjvm.so``
+        * ``jre/lib/libjvm.dylib``
+
+        Search recursively to find the correct library location."""
+
+        return find_libraries(['libjvm'], root=self.home, recursive=True)
+
+    @run_before('install')
+    def macos_check(self):
+        if self.spec.satisfies('platform=darwin'):
+            msg = """\
+Spack's JDK package only supports Linux. If you need to install JDK on macOS,
+manually download the .dmg from:
+
+    {0}
+
+and double-click to install. Once JDK is installed, you can tell Spack where
+to find it like so. To find the JDK installation directory, run:
+
+    $ /usr/libexec/java_home
+
+If you have multiple versions of JDK installed, you can specify a particular
+version to search for with the --version flag. To find the exact version
+number, run:
+
+    $ java -version
+
+If the version number contains a '+' symbol, replace it with '_', otherwise
+Spack will think it is a variant. Add JDK as an external package by running:
+
+    $ spack config edit packages
+
+and adding entries for each installation:
+
+    packages:
+        jdk:
+            paths:
+                jdk@10.0.1_10:    /path/to/jdk/Home
+                jdk@1.7.0_45-b18: /path/to/jdk/Home
+            buildable: False""".format(self.homepage)
+
+            tty.die(msg)
 
     def install(self, spec, prefix):
-        distutils.dir_util.copy_tree(".", prefix)
+        install_tree('.', prefix)
 
     def setup_environment(self, spack_env, run_env):
-        run_env.set('JAVA_HOME', self.spec.prefix)
+        """Set JAVA_HOME."""
+
+        run_env.set('JAVA_HOME', self.home)
 
     def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
-        spack_env.set('JAVA_HOME', self.spec.prefix)
+        """Set JAVA_HOME and CLASSPATH.
+
+        CLASSPATH contains the installation prefix for the extension and any
+        other Java extensions it depends on."""
+
+        spack_env.set('JAVA_HOME', self.home)
+
+        class_paths = []
+        for d in dependent_spec.traverse(deptype=('build', 'run', 'test')):
+            if d.package.extends(self.spec):
+                class_paths.extend(find(d.prefix, '*.jar'))
+
+        classpath = os.pathsep.join(class_paths)
+        spack_env.set('CLASSPATH', classpath)
+
+        # For runtime environment set only the path for
+        # dependent_spec and prepend it to CLASSPATH
+        if dependent_spec.package.extends(self.spec):
+            class_paths = find(dependent_spec.prefix, '*.jar')
+            classpath = os.pathsep.join(class_paths)
+            run_env.prepend_path('CLASSPATH', classpath)
+
+    def setup_dependent_package(self, module, dependent_spec):
+        """Allows spec['java'].home to work."""
+
+        self.spec.home = self.home
diff --git a/var/spack/repos/builtin/packages/jellyfish/package.py b/var/spack/repos/builtin/packages/jellyfish/package.py
index e6d65838a1..a90438d633 100644
--- a/var/spack/repos/builtin/packages/jellyfish/package.py
+++ b/var/spack/repos/builtin/packages/jellyfish/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,12 @@ class Jellyfish(AutotoolsPackage):
        DNA."""
 
     homepage = "http://www.cbcb.umd.edu/software/jellyfish/"
-    url      = "http://www.cbcb.umd.edu/software/jellyfish/jellyfish-1.1.11.tar.gz"
+    url      = "https://github.com/gmarcais/Jellyfish/releases/download/v2.2.7/jellyfish-2.2.7.tar.gz"
+    list_url = "http://www.cbcb.umd.edu/software/jellyfish/"
 
-    version('1.1.11', 'dc994ea8b0896156500ea8c648f24846')
+    version('2.2.7', 'f741192d9061f28e34cb67c86a1027ab')
+    version('1.1.11', 'dc994ea8b0896156500ea8c648f24846',
+            url='http://www.cbcb.umd.edu/software/jellyfish/jellyfish-1.1.11.tar.gz')
 
     depends_on('perl', type=('build', 'run'))
     depends_on('python', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/jemalloc/package.py b/var/spack/repos/builtin/packages/jemalloc/package.py
index 0534c72ed5..25d75d5541 100644
--- a/var/spack/repos/builtin/packages/jemalloc/package.py
+++ b/var/spack/repos/builtin/packages/jemalloc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/jmol/package.py b/var/spack/repos/builtin/packages/jmol/package.py
index 0688d63816..3ea84eb7bc 100644
--- a/var/spack/repos/builtin/packages/jmol/package.py
+++ b/var/spack/repos/builtin/packages/jmol/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from distutils.dir_util import copy_tree
 
 
 class Jmol(Package):
@@ -38,7 +18,7 @@ class Jmol(Package):
     depends_on('java', type='run')
 
     def install(self, spec, prefix):
-        copy_tree('jmol-{0}'.format(self.version), prefix)
+        install_tree('jmol-{0}'.format(self.version), prefix)
 
     def setup_environment(self, spack_env, run_env):
         run_env.prepend_path('PATH', self.prefix)
diff --git a/var/spack/repos/builtin/packages/jq/package.py b/var/spack/repos/builtin/packages/jq/package.py
index 1d7d912a91..87db91d292 100644
--- a/var/spack/repos/builtin/packages/jq/package.py
+++ b/var/spack/repos/builtin/packages/jq/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/json-c/package.py b/var/spack/repos/builtin/packages/json-c/package.py
index 5076650d69..420fe695e2 100644
--- a/var/spack/repos/builtin/packages/json-c/package.py
+++ b/var/spack/repos/builtin/packages/json-c/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,16 @@ class JsonC(AutotoolsPackage):
     homepage = "https://github.com/json-c/json-c/wiki"
     url      = "https://s3.amazonaws.com/json-c_releases/releases/json-c-0.12.1.tar.gz"
 
+    version('0.13.1', '04969ad59cc37bddd83741a08b98f350')
     version('0.12.1', '55f7853f7d8cf664554ce3fa71bf1c7d')
     version('0.11',   'aa02367d2f7a830bf1e3376f77881e98')
 
     depends_on('autoconf', type='build')
 
     parallel = False
+
+    @when('@0.12.1 %gcc@7:')
+    def patch(self):
+        filter_file('-Wextra',
+                    '-Wextra -Wno-error=implicit-fallthrough',
+                    'Makefile.in')
diff --git a/var/spack/repos/builtin/packages/json-cwx/package.py b/var/spack/repos/builtin/packages/json-cwx/package.py
index bd331acb03..2f3d928bbf 100644
--- a/var/spack/repos/builtin/packages/json-cwx/package.py
+++ b/var/spack/repos/builtin/packages/json-cwx/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/json-glib/package.py b/var/spack/repos/builtin/packages/json-glib/package.py
new file mode 100644
index 0000000000..f69aa247fc
--- /dev/null
+++ b/var/spack/repos/builtin/packages/json-glib/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class JsonGlib(AutotoolsPackage):
+    """JSON-GLib is a library for reading and parsing JSON using GLib and
+    GObject data types and API."""
+
+    homepage = "https://developer.gnome.org/json-glib"
+    url      = "https://ftp.gnome.org/pub/gnome/sources/json-glib/1.2/json-glib-1.2.8.tar.xz"
+
+    version('1.2.8', 'ff31e7d0594df44318e12facda3d086e')
+
+    depends_on('glib')
diff --git a/var/spack/repos/builtin/packages/jsoncpp/package.py b/var/spack/repos/builtin/packages/jsoncpp/package.py
index 3b486bf356..f8bf532e53 100644
--- a/var/spack/repos/builtin/packages/jsoncpp/package.py
+++ b/var/spack/repos/builtin/packages/jsoncpp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -42,8 +23,7 @@ class Jsoncpp(CMakePackage):
                     'MinSizeRel', 'Coverage'))
 
     depends_on('cmake@3.1:', type='build')
-    # TODO: Add a 'test' deptype
-    # depends_on('python', type='test')
+    depends_on('python', type='test')
 
     def cmake_args(self):
         return ['-DBUILD_SHARED_LIBS=ON']
diff --git a/var/spack/repos/builtin/packages/judy/package.py b/var/spack/repos/builtin/packages/judy/package.py
index 87b061bd33..7b17e2e163 100644
--- a/var/spack/repos/builtin/packages/judy/package.py
+++ b/var/spack/repos/builtin/packages/judy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/julia/package.py b/var/spack/repos/builtin/packages/julia/package.py
index fa6aaf3f95..c9e3a23cb2 100644
--- a/var/spack/repos/builtin/packages/julia/package.py
+++ b/var/spack/repos/builtin/packages/julia/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 import os
@@ -30,18 +11,18 @@ import sys
 
 class Julia(Package):
     """The Julia Language: A fresh approach to technical computing"""
+
     homepage = "http://julialang.org"
     url      = "https://github.com/JuliaLang/julia/releases/download/v0.4.3/julia-0.4.3-full.tar.gz"
+    git      = "https://github.com/JuliaLang/julia.git"
 
-    version('master',
-            git='https://github.com/JuliaLang/julia.git', branch='master')
-    version('release-0.5',
-            git='https://github.com/JuliaLang/julia.git', branch='release-0.5')
-    version('0.5.2', '8c3fff150a6f96cf0536fb3b4eaa5cbb', preferred=True)
+    version('master', branch='master')
+    version('0.6.2', '255d80bc8d56d5f059fe18f0798e32f6')
+    version('release-0.5', branch='release-0.5')
+    version('0.5.2', '8c3fff150a6f96cf0536fb3b4eaa5cbb')
     version('0.5.1', 'bce119b98f274e0f07ce01498c463ad5')
     version('0.5.0', 'b61385671ba74767ab452363c43131fb')
-    version('release-0.4',
-            git='https://github.com/JuliaLang/julia.git', branch='release-0.4')
+    version('release-0.4', branch='release-0.4')
     version('0.4.7', '75a7a7dd882b7840829d8f165e9b9078')
     version('0.4.6', 'd88db18c579049c23ab8ef427ccedf5d')
     version('0.4.5', '69141ff5aa6cee7c0ec8c85a34aa49a6')
@@ -66,7 +47,7 @@ class Julia(Package):
     # Build-time dependencies:
     # depends_on("awk")
     depends_on("m4", type="build")
-    # depends_on("pkg-config")
+    # depends_on("pkgconfig")
 
     # Combined build-time and run-time dependencies:
     # (Yes, these are run-time dependencies used by Julia's package manager.)
diff --git a/var/spack/repos/builtin/packages/k8/package.py b/var/spack/repos/builtin/packages/k8/package.py
new file mode 100644
index 0000000000..efdcb06af9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/k8/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import sys
+import os
+from spack import *
+
+
+class K8(Package):
+    """K8 is a Javascript shell based on Google's V8 Javascript engine."""
+
+    homepage = "https://github.com/attractivechaos/k8"
+    url      = "https://github.com/attractivechaos/k8/releases/download/v0.2.4/k8-0.2.4.tar.bz2"
+
+    version('0.2.4', 'edc5579ff18842a2a59aa92ce8bab8b4')
+
+    depends_on('zlib', type='run')
+
+    def install(self, spec, prefix):
+        if (sys.platform == 'darwin'):
+            os.rename('k8-Darwin', 'k8')
+
+        if (sys.platform != 'darwin'):
+            os.rename('k8-Linux', 'k8')
+        install_tree('.', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/kahip/package.py b/var/spack/repos/builtin/packages/kahip/package.py
index 30565a5180..29c6adae77 100644
--- a/var/spack/repos/builtin/packages/kahip/package.py
+++ b/var/spack/repos/builtin/packages/kahip/package.py
@@ -1,28 +1,8 @@
-##############################################################################
-# Copyright (c) 2017 Christian Schulz
-# Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is released as part of Spack under the LGPL license
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE file for the LLNL notice and LGPL.
-#
-# License
-# -------
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 import os
@@ -44,8 +24,9 @@ class Kahip(SConsPackage):
 
     homepage  = 'http://algo2.iti.kit.edu/documents/kahip/index.html'
     url       = 'http://algo2.iti.kit.edu/schulz/software_releases/KaHIP_2.00.tar.gz'
+    git       = 'https://github.com/schulzchristian/KaHIP.git'
 
-    version('develop', git='https://github.com/schulzchristian/KaHIP.git')
+    version('develop', branch='master')
     version('2.00', '0a66b0a604ad72cfb7e3dce00e2c9fdfac82b855')
 
     depends_on('argtable')
diff --git a/var/spack/repos/builtin/packages/kaiju/package.py b/var/spack/repos/builtin/packages/kaiju/package.py
new file mode 100644
index 0000000000..621c81969c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/kaiju/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Kaiju(MakefilePackage):
+    """Kaiju is a program for the taxonomic classification
+    of high-throughput sequencing reads."""
+
+    homepage = "https://github.com/bioinformatics-centre/kaiju"
+    url      = "https://github.com/bioinformatics-centre/kaiju/archive/v1.6.2.zip"
+
+    version('1.6.2', '0bd85368954837aa31f3de8b87ea410b')
+
+    build_directory = 'src'
+
+    depends_on('perl-io-compress', type='run')
+    depends_on('py-htseq', type='run')
+
+    def edit(self, spec, prefix):
+        # Replace ftp:// with https://
+        makedb = FileFilter('util/makeDB.sh')
+        makedb.filter('ftp://', 'https://', string=True)
+
+    def install(self, spec, prefix):
+        install_tree('bin', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/kaks-calculator/package.py b/var/spack/repos/builtin/packages/kaks-calculator/package.py
index 622e499e7f..f9244acc3b 100644
--- a/var/spack/repos/builtin/packages/kaks-calculator/package.py
+++ b/var/spack/repos/builtin/packages/kaks-calculator/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/kaldi/package.py b/var/spack/repos/builtin/packages/kaldi/package.py
index bb2481d879..6b3457f12a 100644
--- a/var/spack/repos/builtin/packages/kaldi/package.py
+++ b/var/spack/repos/builtin/packages/kaldi/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from distutils.dir_util import copy_tree
 from os.path import join
 from fnmatch import fnmatch
 import os
@@ -35,11 +15,11 @@ class Kaldi(Package):    # Does not use Autotools
     Kaldi is intended for use by speech recognition researchers."""
 
     homepage = "https://github.com/kaldi-asr/kaldi"
-    url      = "https://github.com/kaldi-asr/kaldi/archive/master.zip"
+    git      = "https://github.com/kaldi-asr/kaldi.git"
 
-    version('master', git='https://github.com/kaldi-asr/kaldi.git')
-    version('c024e8', git='https://github.com/kaldi-asr/kaldi.git',
-            commit='c024e8aa0a727bf76c91a318f76a1f8b0b59249e')
+    version('master')
+    version('2018-07-11', commit='6f2140b032b0108bc313eefdca65151289642773')
+    version('2015-10-07', commit='c024e8aa0a727bf76c91a318f76a1f8b0b59249e')
 
     variant('shared', default=True,
             description='build shared libraries')
@@ -53,18 +33,16 @@ class Kaldi(Package):    # Does not use Autotools
     depends_on('sph2pipe', type='run')
     depends_on('sctk', type='run')
     depends_on('speex', type='run')
-    depends_on('openfst@1.4.1-patch', when='@c024e8')
+    depends_on('openfst@1.4.1-patch', when='@2015-10-07')
+    depends_on('openfst@1.6.0:', when='@2018-07-11')
     depends_on('openfst')
 
-    patch('openfst-1.4.1.patch', when='@c024e8')
+    patch('openfst-1.4.1.patch', when='@2015-10-07')
 
     def install(self, spec, prefix):
         configure_args = ['--fst-root=' + spec['openfst'].prefix]
-
-        if spec.satisfies('c024e8'):
-            configure_args.append('--speex-root=' + spec['speex'].prefix)
-            configure_args.append('--fst-version=' +
-                                  str(spec['openfst'].version))
+        configure_args.append('--fst-version=' + str(spec['openfst'].version))
+        configure_args.append('--speex-root=' + spec['speex'].prefix)
 
         if '~shared' in spec:
             configure_args.append('--static')
@@ -96,13 +74,18 @@ class Kaldi(Package):    # Does not use Autotools
             make()
 
             mkdirp(prefix.bin)
-            for root, dirs, files in os.walk('bin'):
+            for root, dirs, files in os.walk('.'):
                 for name in files:
+                    if name.endswith(".so") or name.endswith(".cc") \
+                            or name.endswith(".pptx"):
+                        continue
+                    if "configure" is name:
+                        continue
                     if os.access(join(root, name), os.X_OK):
                         install(join(root, name), prefix.bin)
 
             mkdir(prefix.lib)
-            copy_tree('lib', prefix.lib)
+            install_tree('lib', prefix.lib)
 
             for root, dirs, files in os.walk('.'):
                 for name in files:
diff --git a/var/spack/repos/builtin/packages/kallisto/package.py b/var/spack/repos/builtin/packages/kallisto/package.py
index 1d0cb35a18..c537ca6ad4 100644
--- a/var/spack/repos/builtin/packages/kallisto/package.py
+++ b/var/spack/repos/builtin/packages/kallisto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/karma/package.py b/var/spack/repos/builtin/packages/karma/package.py
new file mode 100644
index 0000000000..b1a45f6919
--- /dev/null
+++ b/var/spack/repos/builtin/packages/karma/package.py
@@ -0,0 +1,39 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Karma(Package):
+    """Karma is a toolkit for interprocess communications, authentication,
+    encryption, graphics display, user interface and manipulating the Karma
+    network data structure. It contains KarmaLib (the structured libraries
+    and API) and a large number of modules (applications)
+    to perform many standard tasks. """
+
+    homepage = "https://www.atnf.csiro.au/computing/software/karma/"
+    url      = "ftp://ftp.atnf.csiro.au/pub/software/karma/karma-1.7.25-common.tar.bz2"
+
+    version('1.7.25-common', sha256='afda682d79c0923df5a6c447a32b09294da1582933abae3205c008104da54fbd')
+
+    depends_on('libx11', type=('build', 'run'))
+    depends_on('libxaw', type=('build', 'run'))
+
+    phases = ['install']
+
+    resource(
+                name='karma-linux',
+                url='ftp://ftp.atnf.csiro.au/pub/software/karma/karma-1.7.25-amd64_Linux_libc6.3.tar.bz2',
+                sha256='effc3ed61c28b966b357147d90357d03c22d743c6af6edb49a863c6eb625a441',
+                destination='./'
+               )
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('LIBRARY_PATH', self.prefix.lib)
+        run_env.prepend_path('LD_LIBRARY_PATH', self.prefix.lib)
+
+    def install(self, spec, prefix):
+        install_tree('./karma-1.7.25/amd64_Linux_libc6.3/bin', prefix.bin)
+        install_tree('./karma-1.7.25/amd64_Linux_libc6.3/lib', prefix.lib)
diff --git a/var/spack/repos/builtin/packages/kbproto/package.py b/var/spack/repos/builtin/packages/kbproto/package.py
index fa210e9101..05b6f5e665 100644
--- a/var/spack/repos/builtin/packages/kbproto/package.py
+++ b/var/spack/repos/builtin/packages/kbproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Kbproto(AutotoolsPackage):
 
     version('1.0.7', '19acc5f02ae80381e216f443134e0bbb')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/kdiff3/package.py b/var/spack/repos/builtin/packages/kdiff3/package.py
index 4d60416497..93f1e097fd 100644
--- a/var/spack/repos/builtin/packages/kdiff3/package.py
+++ b/var/spack/repos/builtin/packages/kdiff3/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/kealib/cmake.patch b/var/spack/repos/builtin/packages/kealib/cmake.patch
new file mode 100644
index 0000000000..97d7f8cc27
--- /dev/null
+++ b/var/spack/repos/builtin/packages/kealib/cmake.patch
@@ -0,0 +1,73 @@
+# HG changeset patch
+# User Sam Gillingham <gillingham.sam@gmail.com>
+# Date 1526963592 -36000
+# Node ID d103fef327d47ba31826007f9c9ab02c1f354330
+# Parent  a4e63dbb642c83516104ea82cec0e45c4caffd54
+More work on making out of tree builds work
+
+diff --git a/trunk/CMakeLists.txt b/trunk/CMakeLists.txt
+--- a/trunk/CMakeLists.txt
++++ b/trunk/CMakeLists.txt
+@@ -20,14 +20,6 @@
+   set (WINDOWS ${WIN32})
+ endif()
+ 
+-set (PROJECT_BINARY_DIR bin)
+-set (PROJECT_LIBRARY_DIR lib)
+-set (PROJECT_SOURCE_DIR src)
+-set (PROJECT_TEST_DIR tests)
+-set (PROJECT_HEADER_DIR include)
+-set (PROJECT_TOOLS_DIR tools)
+-set (PROJECT_GDAL_DIR gdal)
+-
+ # The version number.
+ set (LIBKEA_HG_VERSION 289)
+ set (LIBKEA_VERSION_MAJOR 1)
+@@ -160,8 +152,8 @@
+ 
+ ###############################################################################
+ # Setup configure file
+-configure_file ( "${PROJECT_HEADER_DIR}/kea-config.h.in" "${PROJECT_HEADER_DIR}/libkea/kea-config.h" )
+-configure_file ( "${PROJECT_TOOLS_DIR}/kea-config.in" "${PROJECT_BINARY_DIR}/kea-config" )
++configure_file ( "${PROJECT_SOURCE_DIR}/include/kea-config.h.in" "${PROJECT_BINARY_DIR}/include/libkea/kea-config.h" )
++configure_file ( "${PROJECT_SOURCE_DIR}/tools/kea-config.in" "${PROJECT_BINARY_DIR}/bin/kea-config" )
+ ###############################################################################
+ 
+ ###############################################################################
+@@ -173,11 +165,12 @@
+ ###############################################################################
+ # Build library
+ 
+-include_directories ("${PROJECT_HEADER_DIR}")
++include_directories ("${PROJECT_SOURCE_DIR}/include")
++include_directories ("${PROJECT_BINARY_DIR}/include") # for kea-config.h
+ include_directories(${HDF5_INCLUDE_DIR})
+-add_subdirectory ("${PROJECT_SOURCE_DIR}")
++add_subdirectory ("${PROJECT_SOURCE_DIR}/src")
+ if (LIBKEA_WITH_GDAL)
+-	add_subdirectory ("${PROJECT_GDAL_DIR}")
++	add_subdirectory ("${PROJECT_SOURCE_DIR}/gdal")
+ endif(LIBKEA_WITH_GDAL)
+ ###############################################################################
+ 
+@@ -191,7 +184,7 @@
+ ###############################################################################
+ # Installation
+ 
+-install (FILES "${PROJECT_BINARY_DIR}/kea-config" DESTINATION bin PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)
++install (FILES "${PROJECT_BINARY_DIR}/bin/kea-config" DESTINATION bin PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)
+ ###############################################################################
+ 
+ ###############################################################################
+diff --git a/trunk/src/CMakeLists.txt b/trunk/src/CMakeLists.txt
+--- a/trunk/src/CMakeLists.txt
++++ b/trunk/src/CMakeLists.txt
+@@ -38,7 +38,7 @@
+ ###############################################################################
+ # Testing
+ # exe needs to be in 'src' otherwise it doesn't work
+-add_executable (test1 ${PROJECT_TEST_DIR}/test1.cpp)
++add_executable (test1 ${PROJECT_SOURCE_DIR}/src/tests/test1.cpp)
+ target_link_libraries (test1 ${LIBKEA_LIB_NAME})
+ if(NOT WIN32)
+     # set rpath so the text exe finds hdf5. Really only needed
diff --git a/var/spack/repos/builtin/packages/kealib/package.py b/var/spack/repos/builtin/packages/kealib/package.py
index 3b24a08393..92ca45f5ba 100644
--- a/var/spack/repos/builtin/packages/kealib/package.py
+++ b/var/spack/repos/builtin/packages/kealib/package.py
@@ -1,32 +1,13 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class Kealib(CMakePackage):
-    """An HDF5 Based Raster File Format
+    """An HDF5 Based Raster File Format.
 
     KEALib provides an implementation of the GDAL data model.
     The format supports raster attribute tables, image pyramids,
@@ -41,18 +22,39 @@ class Kealib(CMakePackage):
 
     Development work on this project has been funded by Landcare Research.
     """
-    homepage = "http://kealib.org/"
-    url      = "https://bitbucket.org/chchrsc/kealib/get/kealib-1.4.5.tar.gz"
+    homepage = "http://www.kealib.org/"
+    url      = "https://bitbucket.org/chchrsc/kealib/get/kealib-1.4.10.tar.gz"
+    hg       = "https://bitbucket.org/chchrsc/kealib"
 
-    version('1.4.5', '112e9c42d980b2d2987a3c15d0833a5d')
+    version('develop', hg=hg)
+    version('1.4.10', '5684aeb2085a67a4270c73e79d4ab768')
+    version('1.4.9',  'a095d0b9d6de1d609ffaf242e00cc2b6')
+    version('1.4.8',  '1af2514c908f9168ff6665cc012815ad')
+    version('1.4.7',  '6139e31e50f552247ddf98f489948893')
 
-    depends_on('hdf5')
     depends_on('cmake@2.8.10:', type='build')
+    depends_on('hdf5+cxx+hl')
+
+    patch('cmake.patch', when='@1.4.7')
 
-    root_cmakelists_dir = 'trunk'
+    @property
+    def root_cmakelists_dir(self):
+        if self.version >= Version('1.4.9'):
+            return '.'
+        else:
+            return 'trunk'
 
     def cmake_args(self):
-        return [
-            '-DHDF5_INCLUDE_DIR=%s' % self.spec['hdf5'].prefix.include,
-            '-DHDF5_LIB_PATH=%s' % self.spec['hdf5'].prefix.lib,
-        ]
+        spec = self.spec
+
+        if self.version >= Version('1.4.9'):
+            return [
+                '-DHDF5_ROOT={0}'.format(spec['hdf5'].prefix)
+            ]
+        else:
+            return [
+                '-DHDF5_INCLUDE_DIR={0}'.format(
+                    spec['hdf5'].headers.directories[0]),
+                '-DHDF5_LIB_PATH={0}'.format(
+                    spec['hdf5'].libs.directories[0])
+            ]
diff --git a/var/spack/repos/builtin/packages/kentutils/package.py b/var/spack/repos/builtin/packages/kentutils/package.py
index 3fdd495a17..11680cecec 100644
--- a/var/spack/repos/builtin/packages/kentutils/package.py
+++ b/var/spack/repos/builtin/packages/kentutils/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,9 @@ class Kentutils(MakefilePackage):
     """Jim Kent command line bioinformatic utilities"""
 
     homepage = "https://github.com/ENCODE-DCC/kentUtils"
-    url      = "https://github.com/ENCODE-DCC/kentUtils"
+    git      = "https://github.com/ENCODE-DCC/kentUtils.git"
 
-    version('302.1', git='https://github.com/ENCODE-DCC/kentUtils.git', commit='d8376c5d52a161f2267346ed3dc94b5dce74c2f9')
+    version('302.1', commit='d8376c5d52a161f2267346ed3dc94b5dce74c2f9')
 
     depends_on('libpng')
     depends_on('openssl')
diff --git a/var/spack/repos/builtin/packages/kibana/package.py b/var/spack/repos/builtin/packages/kibana/package.py
new file mode 100644
index 0000000000..c47e75bd5b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/kibana/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Kibana(Package):
+    """Kibana lets you visualize your Elasticsearch data and navigate the
+    Elastic Stack"""
+
+    homepage = "https://www.elastic.co/products/kibana"
+    url      = "https://artifacts.elastic.co/downloads/kibana/kibana-6.4.0-linux-x86_64.tar.gz"
+
+    version('6.4.0', sha256='df2056105a08c206a1adf9caed09a152a53429a0f1efc1ba3ccd616092d78aee')
+
+    depends_on('jdk', type='run')
+
+    def install(self, spec, prefix):
+        install_tree('.', join_path(prefix, '.'))
diff --git a/var/spack/repos/builtin/packages/kim-api/package.py b/var/spack/repos/builtin/packages/kim-api/package.py
new file mode 100644
index 0000000000..f8141813f1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/kim-api/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class KimApi(CMakePackage):
+    """OpenKIM is an online framework for making molecular simulations
+       reliable, reproducible, and portable. Computer implementations of
+       inter-atomic models are archived in OpenKIM, verified for coding
+       integrity, and tested by computing their predictions for a variety
+       of material properties. Models conforming to the KIM application
+       programming interface (API) work seamlessly with major simulation
+       codes that have adopted the KIM API standard.
+    """
+    homepage = "https://openkim.org/"
+    git      = "https://github.com/openkim/kim-api"
+
+    version('develop', branch='master')
+    version('2.0rc1', commit="c2ab409ec0154ebd85d20a0a1a0bd2ba6ea95a9c") 
+
+    def cmake_args(self):
+        args = ['-DBUILD_MODULES=OFF']
+
+        return args
diff --git a/var/spack/repos/builtin/packages/kmergenie/package.py b/var/spack/repos/builtin/packages/kmergenie/package.py
index 7f64892d70..e3c122bdad 100644
--- a/var/spack/repos/builtin/packages/kmergenie/package.py
+++ b/var/spack/repos/builtin/packages/kmergenie/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/kokkos/package.py b/var/spack/repos/builtin/packages/kokkos/package.py
index e1ebf79eca..6de38510c4 100644
--- a/var/spack/repos/builtin/packages/kokkos/package.py
+++ b/var/spack/repos/builtin/packages/kokkos/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,13 +12,121 @@ class Kokkos(Package):
 
     homepage = "https://github.com/kokkos/kokkos"
     url      = "https://github.com/kokkos/kokkos/archive/2.03.00.tar.gz"
+    git      = "https://github.com/kokkos/kokkos.git"
 
+    version('develop', branch='develop')
+    version('2.7.00',  'b357f9374c1008754babb4495f95e392')
+    version('2.5.00',  '2db83c56587cb83b772d0c81a3228a21')
+    version('2.04.11', 'd4849cee6eb9001d61c30f1d9fe74336')
+    version('2.04.04', '2c6d1c2569b91c9fcd4117296438e65c')
+    version('2.04.00', 'd99ac790ff5f29545d8eb53de90c0a85')
+    version('2.03.13', '3874a159a517384541ea5b52f85501ba')
+    version('2.03.05', '8727d783453f719eec392e10a36b49fd')
     version('2.03.00', 'f205d659d4304747759fabfba32d43c3')
+    version('2.02.15', 'de41e38f452a50bb03363c519fe20769')
+    version('2.02.07', 'd5baeea70109249f7dca763074ffb202')
 
+    variant('serial', default=True, description="enable Serial backend (default)")
     variant('qthreads', default=False, description="enable Qthreads backend")
     variant('cuda', default=False, description="enable Cuda backend")
+    variant('openmp', default=False, description="enable OpenMP backend")
+
+    # Compilation options
+    variant('pic', default=False,
+            description="enable position independent code (-fPIC flag)")
+
+    # Kokkos options
+    variant('aggressive_vectorization', default=False,
+            description="set aggressive_vectorization Kokkos option")
+    variant('disable_profiling', default=False,
+            description="set disable_profiling Kokkos option")
+    variant('disable_dualview_modify_check', default=False,
+            description="set disable_dualview_modify_check Kokkos option")
+    variant('enable_profile_load_print', default=False,
+            description="set enable_profile_load_print Kokkos option")
+    variant('compiler_warnings', default=False,
+            description="set compiler_warnings Kokkos option")
+    variant('disable_deprecated_code', default=False,
+            description="set disable_deprecated_code Kokkos option")
+    variant('enable_eti', default=False,
+            description="set enable_eti Kokkos option")
+
+    # CUDA options
+    variant('force_uvm', default=False,
+            description="set force_uvm Kokkos CUDA option")
+    variant('use_ldg', default=False,
+            description="set use_ldg Kokkos CUDA option")
+    variant('rdc', default=False,
+            description="set rdc Kokkos CUDA option")
+    variant('enable_lambda', default=False,
+            description="set enable_lambda Kokkos CUDA option")
+
+    gpu_values = ('Kepler30', 'Kepler32', 'Kepler35', 'Kepler37',
+                  'Maxwell50', 'Maxwell52', 'Maxwell53',
+                  'Pascal60', 'Pascal61',
+                  'Volta70', 'Volta72')
+
+    cuda_options = ('force_uvm', 'use_ldg', 'rdc', 'enable_lambda')
+
+    # Host architecture variant
+    variant(
+        'host_arch',
+        default=None,
+        values=('AMDAVX', 'ARMv80', 'ARMv81', 'ARMv8-ThunderX',
+                'Power7', 'Power8', 'Power9',
+                'WSM', 'SNB', 'HSW', 'BDW', 'SKX', 'KNC', 'KNL'),
+        description='Set the host architecture to use'
+    )
 
-    depends_on('hwloc')
+    # GPU architecture variant
+    variant(
+        'gpu_arch',
+        default=None,
+        values=gpu_values,
+        description='Set the GPU architecture to use'
+    )
+
+    # Checks on Kokkos version and Kokkos options
+    conflicts('+aggressive_vectorization', when='@:2.0.99',)
+    conflicts('+disable_profiling', when='@:2.0.99',)
+    conflicts('+disable_dualview_modify_check', when='@:2.03.04',)
+    conflicts('+enable_profile_load_print', when='@:2.03.04',)
+    conflicts('+compiler_warnings', when='@:2.03.14',)
+    conflicts('+disable_deprecated_code', when='@:2.5.99',)
+    conflicts('+enable_eti', when='@:2.6.99',)
+
+    # Check that we haven't specified a gpu architecture
+    # without specifying CUDA
+    for p in gpu_values:
+        conflicts('gpu_arch={0}'.format(p), when='~cuda',
+            msg='Must specify CUDA backend to use a GPU architecture.')
+
+    # Check that we haven't specified a Kokkos CUDA option
+    # without specifying CUDA
+    conflicts('+force_uvm', when='~cuda',
+        msg='Must enable CUDA to use force_uvm.')
+    conflicts('+use_ldg', when='~cuda',
+        msg='Must enable CUDA to use use_ldg.')
+    conflicts('+rdc', when='~cuda',
+        msg='Must enable CUDA to use rdc.')
+    conflicts('+enable_lambda', when='~cuda',
+        msg='Must enable CUDA to use enable_lambda.')
+
+    # Check that we haven't asked for a GPU architecture that
+    # the revision of kokkos does not support
+    conflicts('gpu_arch=Volta70', when='@:2.5.99')
+    conflicts('gpu_arch=Volta72', when='@:2.5.99')
+
+    # conflicts on kokkos version and cuda enabled
+    # see kokkos issue #1296
+    # https://github.com/kokkos/kokkos/issues/1296
+    conflicts('+cuda', when='@2.5.00:develop',
+        msg='Kokkos build system has issue when CUDA enabled'
+        ' in version 2.5.00 through 2.7.00, and develop until '
+        'issue #1296 is resolved.')
+
+    # Specify that v1.x is required as v2.x has API changes
+    depends_on('hwloc@:1')
     depends_on('qthreads', when='+qthreads')
     depends_on('cuda', when='+cuda')
 
@@ -48,13 +137,67 @@ class Kokkos(Package):
             g_args = [
                 '--prefix=%s' % prefix,
                 '--with-hwloc=%s' % spec['hwloc'].prefix,
-                '--with-serial',
-                '--with-openmp',
             ]
-            if 'qthreads' in spec:
+            arch_args = []
+            kokkos_options_args = []
+            cuda_options_args = []
+
+            # PIC
+            if '+pic' in spec:
+                g_args.append('--cxxflags=-fPIC')
+
+            # Backends
+            if '+serial' in spec:
+                g_args.append('--with-serial')
+            if '+openmp' in spec:
+                g_args.append('--with-openmp')
+            if '+qthreads' in spec:
                 g_args.append('--with-qthreads=%s' % spec['qthreads'].prefix)
-            if 'cuda' in spec:
+            if '+cuda' in spec:
                 g_args.append('--with-cuda=%s' % spec['cuda'].prefix)
+            # Host architectures
+            host_arch = spec.variants['host_arch'].value
+            # GPU architectures
+            gpu_arch  = spec.variants['gpu_arch'].value
+            if host_arch:
+                arch_args.append(host_arch)
+            if gpu_arch:
+                arch_args.append(gpu_arch)
+            # Combined architecture flags
+            if arch_args:
+                g_args.append('--arch={0}'.format(','.join(arch_args)))
+
+            # CUDA options
+            if '+force_uvm' in spec:
+                cuda_options_args.append('force_uvm')
+            if '+use_ldg' in spec:
+                cuda_options_args.append('use_ldg')
+            if '+rdc' in spec:
+                cuda_options_args.append('rdc')
+            if '+enable_lambda' in spec:
+                cuda_options_args.append('enable_lambda')
+            if cuda_options_args:
+                g_args.append('--with-cuda-options={0}'
+                              .format(','.join(cuda_options_args)))
+
+            # Kokkos options
+            if '+aggressive_vectorization' in spec:
+                kokkos_options_args.append('aggressive_vectorization')
+            if '+disable_profiling' in spec:
+                kokkos_options_args.append('disable_profiling')
+            if '+disable_dualview_modify_check' in spec:
+                kokkos_options_args.append('disable_dualview_modify_check')
+            if '+enable_profile_load_print' in spec:
+                kokkos_options_args.append('enable_profile_load_print')
+            if '+compiler_warnings' in spec:
+                kokkos_options_args.append('compiler_warnings')
+            if '+disable_deprecated_code' in spec:
+                kokkos_options_args.append('disable_deprecated_code')
+            if '+enable_eti' in spec:
+                kokkos_options_args.append('enable_eti')
+            if kokkos_options_args:
+                g_args.append('--with-options={0}'
+                              .format(','.join(kokkos_options_args)))
 
             generate(*g_args)
             make()
diff --git a/var/spack/repos/builtin/packages/kraken/package.py b/var/spack/repos/builtin/packages/kraken/package.py
index 3994c8c138..4c32e153da 100644
--- a/var/spack/repos/builtin/packages/kraken/package.py
+++ b/var/spack/repos/builtin/packages/kraken/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
 import os
diff --git a/var/spack/repos/builtin/packages/krb5/package.py b/var/spack/repos/builtin/packages/krb5/package.py
new file mode 100644
index 0000000000..70c7b4aac4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/krb5/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Krb5(AutotoolsPackage):
+    """Network authentication protocol"""
+
+    homepage = "https://kerberos.org"
+    url      = "https://kerberos.org/dist/krb5/1.16/krb5-1.16.1.tar.gz"
+
+    version('1.16.1', '848e9b80d6aaaa798e3f3df24b83c407')
+
+    depends_on('openssl')
+
+    configure_directory = 'src'
+    build_directory = 'src'
+
+    def configure_args(self):
+        args = ['--disable-debug',
+                '--disable-dependency-tracking',
+                '--disable-silent-rules',
+                '--without-system-verto']
+        return args
diff --git a/var/spack/repos/builtin/packages/krims/package.py b/var/spack/repos/builtin/packages/krims/package.py
index f64092de6c..fe40186d21 100644
--- a/var/spack/repos/builtin/packages/krims/package.py
+++ b/var/spack/repos/builtin/packages/krims/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,15 +10,16 @@ class Krims(CMakePackage):
     """The bucket of Krimskrams every C or C++ project needs"""
 
     homepage = "http://lazyten.org/krims"
-    url = "https://github.com/lazyten/krims/archive/v0.2.1.tar.gz"
+    url      = "https://github.com/lazyten/krims/archive/v0.2.1.tar.gz"
+    git      = "https://github.com/lazyten/krims.git"
+
     maintainers = ['mfherbst']
 
     #
     # Versions
     #
+    version("develop", branch="master")
     version("0.2.1", "bf219656fd81c342a4782bad7d7beed0")
-    version("develop", git="https://github.com/lazyten/krims.git",
-            branch="master")
 
     #
     # Variants
diff --git a/var/spack/repos/builtin/packages/kripke/package.py b/var/spack/repos/builtin/packages/kripke/package.py
index d2030cbcfe..c8614d933c 100644
--- a/var/spack/repos/builtin/packages/kripke/package.py
+++ b/var/spack/repos/builtin/packages/kripke/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,8 +10,8 @@ class Kripke(CMakePackage):
     """Kripke is a simple, scalable, 3D Sn deterministic particle
        transport proxy/mini app.
     """
-    homepage = "https://codesign.llnl.gov/kripke.php"
-    url      = "https://codesign.llnl.gov/downloads/kripke-openmp-1.1.tar.gz"
+    homepage = "https://computation.llnl.gov/projects/co-design/kripke"
+    url      = "https://computation.llnl.gov/projects/co-design/download/kripke-openmp-1.1.tar.gz"
 
     tags = ['proxy-app']
     version('1.1', '7fe6f2b26ed983a6ce5495ab701f85bf')
diff --git a/var/spack/repos/builtin/packages/kvasir-mpl/package.py b/var/spack/repos/builtin/packages/kvasir-mpl/package.py
new file mode 100644
index 0000000000..7561fc17cc
--- /dev/null
+++ b/var/spack/repos/builtin/packages/kvasir-mpl/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class KvasirMpl(Package):
+    """Kvasir metaprogramming library"""
+
+    homepage = "https://github.com/kvasir-io/mpl"
+    git      = "https://github.com/kvasir-io/mpl.git"
+
+    version('develop', branch='development')
+
+    def install(self, spec, prefix):
+        install_tree('src', prefix.include)
diff --git a/var/spack/repos/builtin/packages/kvtree/package.py b/var/spack/repos/builtin/packages/kvtree/package.py
new file mode 100644
index 0000000000..8f1c64607d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/kvtree/package.py
@@ -0,0 +1,34 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Kvtree(CMakePackage):
+    """KVTree provides a fully extensible C datastructure modeled after perl
+    hashes."""
+
+    homepage = "https://github.com/ECP-VeloC/KVTree"
+    url      = "https://github.com/ECP-VeloC/KVTree/archive/v1.0.1.zip"
+    git      = "https://github.com/ecp-veloc/kvtree.git"
+
+    tags = ['ecp']
+
+    version('master', branch='master')
+    version('1.0.2', sha256='6b54f4658e5ebab747c0c2472b1505ac1905eefc8a0b2a97d8776f800ee737a3')
+
+    variant('mpi', default=True, description="Build with MPI message packing")
+    depends_on('mpi', when='+mpi')
+
+    def cmake_args(self):
+        args = []
+        if self.spec.satisfies('+mpi'):
+            args.append("-DMPI=ON")
+            args.append("-DMPI_C_COMPILER=%s" % self.spec['mpi'].mpicc)
+        else:
+            args.append("-DMPI=OFF")
+        if self.spec.satisfies('platform=cray'):
+            args.append("-DKVTREE_LINK_STATIC=ON")
+        return args
diff --git a/var/spack/repos/builtin/packages/laghos/package.py b/var/spack/repos/builtin/packages/laghos/package.py
index 0e889782e6..deab6d8f0b 100644
--- a/var/spack/repos/builtin/packages/laghos/package.py
+++ b/var/spack/repos/builtin/packages/laghos/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,15 +14,21 @@ class Laghos(MakefilePackage):
     """
     tags = ['proxy-app', 'ecp-proxy-app']
 
-    homepage = "https://codesign.llnl.gov/laghos.php"
-    git      = "https://github.com/CEED/Laghos"
+    homepage = "https://computation.llnl.gov/projects/co-design/laghos"
     url      = "https://github.com/CEED/Laghos/archive/v1.0.tar.gz"
+    git      = "https://github.com/CEED/Laghos.git"
+
+    version('develop', branch='master')
+    version('1.1', sha256='53b9bfe2af263c63eb4544ca1731dd26f40b73a0d2775a9883db51821bf23b7f')
+    version('1.0', '4c091e115883c79bed81c557ef16baff')
+
+    variant('metis', default=True, description='Enable/disable METIS support')
 
-    version('1.0', '107c2f693936723e764a4d404d33d44a')
-    version('develop', git=git, branch='master')
+    depends_on('mfem@develop+mpi+metis', when='@develop+metis')
+    depends_on('mfem@develop+mpi~metis', when='@develop~metis')
 
-    depends_on('mpi')
-    depends_on('mfem@laghos-v1.0', when='@1.0')
+    depends_on('mfem@laghos-v1.0,3.3.2:+mpi+metis', when='@1.0:+metis')
+    depends_on('mfem@laghos-v1.0,3.3.2:+mpi~metis', when='@1.0:~metis')
 
     @property
     def build_targets(self):
@@ -49,13 +36,24 @@ class Laghos(MakefilePackage):
         spec = self.spec
 
         targets.append('MFEM_DIR=%s' % spec['mfem'].prefix)
-        targets.append('CONFIG_MK=%s' % join_path(spec['mfem'].prefix,
-                       'share/mfem/config.mk'))
-        targets.append('TEST_MK=%s' % join_path(spec['mfem'].prefix,
-                       'share/mfem/test.mk'))
+        targets.append('CONFIG_MK=%s' % spec['mfem'].package.config_mk)
+        targets.append('TEST_MK=%s' % spec['mfem'].package.test_mk)
+        targets.append('CXX=%s' % spec['mpi'].mpicxx)
 
         return targets
 
+    # See lib/spack/spack/build_systems/makefile.py
+    def check(self):
+        targets = []
+        spec = self.spec
+
+        targets.append('MFEM_DIR=%s' % spec['mfem'].prefix)
+        targets.append('CONFIG_MK=%s' % spec['mfem'].package.config_mk)
+        targets.append('TEST_MK=%s' % spec['mfem'].package.test_mk)
+
+        with working_dir(self.build_directory):
+            make('test', *targets)
+
     def install(self, spec, prefix):
         mkdirp(prefix.bin)
         install('laghos', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/lammps/package.py b/var/spack/repos/builtin/packages/lammps/package.py
index 7eeea42773..5743d39189 100644
--- a/var/spack/repos/builtin/packages/lammps/package.py
+++ b/var/spack/repos/builtin/packages/lammps/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-#
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import datetime as dt
 
@@ -35,10 +16,17 @@ class Lammps(CMakePackage):
     """
     homepage = "http://lammps.sandia.gov/"
     url      = "https://github.com/lammps/lammps/archive/patch_1Sep2017.tar.gz"
+    git      = "https://github.com/lammps/lammps.git"
+
+    tags = ['ecp', 'ecp-apps']
 
+    version('develop', branch='master')
+    version('20180822', sha256='9f8942ca3f8e81377ae88ccfd075da4e27d0dd677526085e1a807777c8324074')
+    version('20180629', '6d5941863ee25ad2227ff3b7577d5e7c')
+    version('20180316', '25bad35679583e0dd8cb8753665bb84b')
+    version('20180222', '4d0513e3183bd57721814d217fdaf957')
     version('20170922', '4306071f919ec7e759bda195c26cfd9a')
     version('20170901', '767e7f07289663f033474dfe974974e7')
-    version('develop', git='https://github.com/lammps/lammps', branch='master')
 
     def url_for_version(self, version):
         vdate = dt.datetime.strptime(str(version), "%Y%m%d")
@@ -68,7 +56,9 @@ class Lammps(CMakePackage):
     depends_on('netcdf+mpi', when='+user-netcdf')
     depends_on('blas', when='+user-atc')
     depends_on('lapack', when='+user-atc')
-    depends_on('latte', when='+latte')
+    depends_on('latte@1.0.1', when='@:20180222+latte')
+    depends_on('latte@1.1.1:', when='@20180316:20180628+latte')
+    depends_on('latte@1.2.1:', when='@20180629:+latte')
     depends_on('blas', when='+latte')
     depends_on('lapack', when='+latte')
     depends_on('python', when='+python')
@@ -76,7 +66,7 @@ class Lammps(CMakePackage):
     depends_on('mpi', when='+user-h5md')
     depends_on('hdf5', when='+user-h5md')
 
-    conflicts('+body', when='+poems')
+    conflicts('+body', when='+poems@:20180628')
     conflicts('+latte', when='@:20170921')
     conflicts('+python', when='~lib')
     conflicts('+qeq', when='~manybody')
@@ -93,15 +83,25 @@ class Lammps(CMakePackage):
     def cmake_args(self):
         spec = self.spec
 
+        mpi_prefix = 'ENABLE'
+        pkg_prefix = 'ENABLE'
+        if spec.satisfies('@20180629:'):
+            mpi_prefix = 'BUILD'
+            pkg_prefix = 'PKG'
+
         args = [
             '-DBUILD_SHARED_LIBS={0}'.format(
                 'ON' if '+lib' in spec else 'OFF'),
-            '-DENABLE_MPI={0}'.format(
+            '-D{0}_MPI={1}'.format(
+                mpi_prefix,
                 'ON' if '+mpi' in spec else 'OFF')
         ]
 
+        if spec.satisfies('@20180629:+lib'):
+            args.append('-DBUILD_LIB=ON')
+
         for pkg in self.supported_packages:
-            opt = '-DENABLE_{0}'.format(pkg.upper())
+            opt = '-D{0}_{1}'.format(pkg_prefix, pkg.upper())
             if '+{0}'.format(pkg) in spec:
                 args.append('{0}=ON'.format(opt))
             else:
diff --git a/var/spack/repos/builtin/packages/last/package.py b/var/spack/repos/builtin/packages/last/package.py
index 34054313f7..9e0ac55850 100644
--- a/var/spack/repos/builtin/packages/last/package.py
+++ b/var/spack/repos/builtin/packages/last/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/lastz/package.py b/var/spack/repos/builtin/packages/lastz/package.py
new file mode 100644
index 0000000000..1b438c81b6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/lastz/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Lastz(MakefilePackage):
+    """LASTZ is a program for aligning DNA sequences, a pairwise aligner."""
+
+    homepage = "https://lastz.github.io/lastz"
+    url      = "https://github.com/lastz/lastz/archive/1.04.00.tar.gz"
+
+    version('1.04.00', sha256='a4c2c7a77430387e96dbc9f5bdc75874334c672be90f5720956c0f211abf9f5a')
+
+    def install(self, spec, prefix):
+        make('install', 'LASTZ_INSTALL={0}'.format(prefix.bin))
diff --git a/var/spack/repos/builtin/packages/latte/package.py b/var/spack/repos/builtin/packages/latte/package.py
index 7e3c9afa61..fe7b75b8a8 100644
--- a/var/spack/repos/builtin/packages/latte/package.py
+++ b/var/spack/repos/builtin/packages/latte/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -30,9 +11,15 @@ class Latte(CMakePackage):
     """Open source density functional tight binding molecular dynamics."""
 
     homepage = "https://github.com/lanl/latte"
-    url      = "https://github.com/lanl/latte/tarball/v1.0"
+    url      = "https://github.com/lanl/latte/tarball/v1.2.1"
+    git      = "https://github.com/lanl/latte.git"
+
+    tags = ['ecp', 'ecp-apps']
 
-    version('develop', git='https://github.com/lanl/latte', branch='master')
+    version('develop', branch='master')
+    version('1.2.1', '56db44afaba2a89e6ca62ac565c3c012')
+    version('1.2.0', 'b9bf8f84a0e0cf7b0e278a1bc7751b3d')
+    version('1.1.1', 'ab11867ba6235189681cf6e50a50cc50')
     version('1.0.1', 'd0b99edbcf7a19abe0a68a192d6f6234')
 
     variant('mpi', default=True,
@@ -60,4 +47,9 @@ class Latte(CMakePackage):
         if '+progress' in self.spec:
             options.append('-DPROGRESS=yes')
 
+        blas_list = ';'.join(self.spec['blas'].libs)
+        lapack_list = ';'.join(self.spec['lapack'].libs)
+        options.append('-DBLAS_LIBRARIES={0}'.format(blas_list))
+        options.append('-DLAPACK_LIBRARIES={0}'.format(lapack_list))
+
         return options
diff --git a/var/spack/repos/builtin/packages/launchmon/package.py b/var/spack/repos/builtin/packages/launchmon/package.py
index 5697a1f370..2042d0bb27 100644
--- a/var/spack/repos/builtin/packages/launchmon/package.py
+++ b/var/spack/repos/builtin/packages/launchmon/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/lazyten/package.py b/var/spack/repos/builtin/packages/lazyten/package.py
index 4827b9495e..20099f549a 100644
--- a/var/spack/repos/builtin/packages/lazyten/package.py
+++ b/var/spack/repos/builtin/packages/lazyten/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
@@ -30,15 +11,16 @@ class Lazyten(CMakePackage):
     """Lightweight linear algebra library based on lazy matrices"""
 
     homepage = "http://lazyten.org"
-    url = "https://github.com/lazyten/lazyten/archive/v0.4.1.tar.gz"
+    url      = "https://github.com/lazyten/lazyten/archive/v0.4.1.tar.gz"
+    git      = "https://github.com/lazyten/lazyten.git"
+
     maintainers = ['mfherbst']
 
     #
     # Versions
     #
+    version("develop", branch="master")
     version('0.4.1', 'd06f7996144e1bf1b0aee82c2af36e83')
-    version("develop", git="https://github.com/lazyten/lazyten.git",
-            branch="master")
 
     #
     # Variants
diff --git a/var/spack/repos/builtin/packages/lbann/package.py b/var/spack/repos/builtin/packages/lbann/package.py
index 5e65566cb2..148b097051 100644
--- a/var/spack/repos/builtin/packages/lbann/package.py
+++ b/var/spack/repos/builtin/packages/lbann/package.py
@@ -1,27 +1,10 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import os
+import sys
 from spack import *
 
 
@@ -32,39 +15,167 @@ class Lbann(CMakePackage):
 
     homepage = "http://software.llnl.gov/lbann/"
     url      = "https://github.com/LLNL/lbann/archive/v0.91.tar.gz"
+    git      = "https://github.com/LLNL/lbann.git"
 
-    version('develop', git='https://github.com/LLNL/lbann.git', branch="develop")
+    version('develop', branch='develop')
+    version('0.95', sha256='d310b986948b5ee2bedec36383a7fe79403721c8dc2663a280676b4e431f83c2')
+    version('0.94', sha256='567e99b488ebe6294933c98a212281bffd5220fc13a0a5cd8441f9a3761ceccf')
+    version('0.93', '1913a25a53d4025fa04c16f14afdaa55')
+    version('0.92', 'c0eb1595a7c74640e96f280beb497564')
     version('0.91', '83b0ec9cd0b7625d41dfb06d2abd4134')
 
     variant('gpu', default=False, description='Builds with support for GPUs via CUDA and cuDNN')
+    variant('nccl', default=False, description='Builds with support for NCCL communication lib')
     variant('opencv', default=True, description='Builds with support for image processing routines with OpenCV')
     variant('seq_init', default=False, description='Force serial initialization of weight matrices.')
-    variant('dtype', default=4, description='Size (bits) of floating point representation for weights')
+    variant('dtype', default='float',
+            description='Type for floating point representation of weights',
+            values=('float', 'double'))
     variant('build_type', default='Release',
             description='The build type to build',
             values=('Debug', 'Release'))
+    variant('al', default=True, description='Builds with support for Aluminum Library')
+    variant('conduit', default=False, description='Builds with support for Conduit Library')
+
+    # It seems that there is a need for one statement per version bounds
+    depends_on('hydrogen +openmp_blas +shared +int64', when='@:0.90,0.95: ~al')
+    depends_on('hydrogen +openmp_blas +shared +int64 +al', when='@:0.90,0.95: +al')
+
+    depends_on('hydrogen +openmp_blas +shared +int64 build_type=Debug',
+               when='build_type=Debug @:0.90,0.95: ~al')
+    depends_on('hydrogen +openmp_blas +shared +int64 build_type=Debug +al',
+               when='build_type=Debug @:0.90,0.95: +al')
+
+    depends_on('hydrogen +openmp_blas +shared +int64 +cuda',
+               when='+gpu @:0.90,0.95: ~al')
+    depends_on('hydrogen +openmp_blas +shared +int64 +cuda +al',
+               when='+gpu @:0.90,0.95: +al')
+
+    depends_on('hydrogen +openmp_blas +shared +int64 +cuda build_type=Debug',
+               when='build_type=Debug @:0.90,0.95: +gpu')
+    depends_on('hydrogen +openmp_blas +shared +int64 +cuda build_type=Debug +al',
+               when='build_type=Debug @:0.90,0.95: +gpu +al')
+
+    # Older versions depended on Elemental not Hydrogen
+    depends_on('elemental +openmp_blas +shared +int64', when='@0.91:0.94')
+    depends_on('elemental +openmp_blas +shared +int64 build_type=Debug',
+               when='build_type=Debug @0.91:0.94')
+
+    depends_on('aluminum@master', when='@:0.90,0.95: +al ~gpu')
+    depends_on('aluminum@master +gpu +mpi-cuda', when='@:0.90,0.95: +al +gpu ~nccl')
+    depends_on('aluminum@master +gpu +nccl +mpi_cuda', when='@:0.90,0.95: +al +gpu +nccl')
 
-    depends_on('elemental +openmp_blas +shared +int64')
-    depends_on('elemental +openmp_blas +shared +int64 build_type=Debug', 
-               when=('build_type=Debug'))
     depends_on('cuda', when='+gpu')
     depends_on('cudnn', when='+gpu')
     depends_on('cub', when='+gpu')
-    depends_on('mpi')
+    depends_on('mpi', when='~gpu')
+    depends_on('mpi +cuda', when='+gpu')
     depends_on('hwloc')
-    depends_on('opencv@3.2.0: +openmp +core +highgui +imgproc +jpeg +png +tiff +zlib ~eigen', when='+opencv')
+
+    # LBANN wraps OpenCV calls in OpenMP parallel loops, build without OpenMP
+    # Additionally disable video related options, they incorrectly link in a
+    # bad OpenMP library when building with clang or Intel compilers
+    depends_on('opencv@3.2.0: +core +highgui +imgproc +jpeg +png +tiff +zlib '
+               '+fast-math +powerpc +vsx ~calib3d ~cuda ~dnn ~eigen'
+               '~features2d ~flann ~gtk ~ipp ~ipp_iw ~jasper ~java ~lapack ~ml'
+               '~openmp ~opencl ~opencl_svm ~openclamdblas ~openclamdfft'
+               '~pthreads_pf ~python ~qt ~stitching ~superres ~ts ~video'
+               '~videostab ~videoio ~vtk', when='+opencv')
+
     depends_on('protobuf@3.0.2:')
     depends_on('cnpy')
+    depends_on('nccl', when='+gpu +nccl')
 
-    def cmake_args(self):
+    depends_on('conduit@master +hdf5', when='+conduit')
+
+    @property
+    def common_config_args(self):
         spec = self.spec
         # Environment variables
-        CPPFLAGS = []
-        CPPFLAGS.append('-DLBANN_SET_EL_RNG')
+        cppflags = []
+        cppflags.append('-DLBANN_SET_EL_RNG -ldl')
 
-        args = [
+        return [
             '-DCMAKE_INSTALL_MESSAGE=LAZY',
-            '-DCMAKE_CXX_FLAGS=%s' % ' '.join(CPPFLAGS),
+            '-DCMAKE_CXX_FLAGS=%s' % ' '.join(cppflags),
+            '-DLBANN_VERSION=spack',
+            '-DCNPY_DIR={0}'.format(spec['cnpy'].prefix),
+        ]
+
+    # Get any recent versions or non-numeric version
+    # Note that develop > numeric and non-develop < numeric
+    @when('@:0.90,0.94:')
+    def cmake_args(self):
+        spec = self.spec
+        args = self.common_config_args
+        args.extend([
+            '-DLBANN_WITH_TOPO_AWARE:BOOL=%s' % ('+gpu +nccl' in spec),
+            '-DLBANN_SEQUENTIAL_INITIALIZATION:BOOL=%s' %
+            ('+seq_init' in spec),
+            '-DLBANN_WITH_TBINF=OFF',
+            '-DLBANN_WITH_VTUNE=OFF',
+            '-DLBANN_DATATYPE={0}'.format(spec.variants['dtype'].value),
+            '-DLBANN_VERBOSE=0'])
+
+        if self.spec.satisfies('@:0.90') or self.spec.satisfies('@0.95:'):
+            args.extend([
+                '-DHydrogen_DIR={0}/CMake/hydrogen'.format(
+                    spec['hydrogen'].prefix)])
+        elif self.spec.satisfies('@0.94'):
+            args.extend([
+                '-DElemental_DIR={0}/CMake/elemental'.format(
+                    spec['elemental'].prefix)])
+
+        if '+al' in spec:
+            args.extend(['-DLBANN_WITH_ALUMINUM:BOOL=%s' % ('+al' in spec),
+                         '-DAluminum_DIR={0}'.format(spec['aluminum'].prefix)])
+
+        if '+conduit' in spec:
+            args.extend(['-DLBANN_CONDUIT_DIR:BOOL=%s' % ('+conduit' in spec),
+                         '-DLBANN_CONDUIT_DIR={0}'.format(
+                             spec['conduit'].prefix)])
+
+        # Add support for OpenMP
+        if (self.spec.satisfies('%clang')):
+            if (sys.platform == 'darwin'):
+                clang = self.compiler.cc
+                clang_bin = os.path.dirname(clang)
+                clang_root = os.path.dirname(clang_bin)
+                args.extend([
+                    '-DOpenMP_CXX_FLAGS=-fopenmp=libomp',
+                    '-DOpenMP_CXX_LIB_NAMES=libomp',
+                    '-DOpenMP_libomp_LIBRARY={0}/lib/libomp.dylib'.format(
+                        clang_root)])
+
+        if '+opencv' in spec:
+            args.extend(['-DOpenCV_DIR:STRING={0}'.format(
+                spec['opencv'].prefix)])
+
+        if '+gpu' in spec:
+            args.extend([
+                '-DLBANN_WITH_CUDA:BOOL=%s' % ('+gpu' in spec),
+                '-DLBANN_WITH_SOFTMAX_CUDA:BOOL=%s' % ('+gpu' in spec),
+                '-DCUDA_TOOLKIT_ROOT_DIR={0}'.format(
+                    spec['cuda'].prefix)])
+            args.extend([
+                '-DLBANN_WITH_CUDNN:BOOL=%s' % ('+gpu' in spec),
+                '-DcuDNN_DIR={0}'.format(
+                    spec['cudnn'].prefix)])
+            args.extend(['-DCUB_DIR={0}'.format(
+                spec['cub'].prefix)])
+            if '+nccl' in spec:
+                args.extend([
+                    '-DLBANN_WITH_NCCL:BOOL=%s' % ('+gpu +nccl' in spec),
+                    '-DNCCL_DIR={0}'.format(
+                        spec['nccl'].prefix)])
+
+        return args
+
+    @when('@0.91:0.93')
+    def cmake_args(self):
+        spec = self.spec
+        args = self.common_config_args
+        args.extend([
             '-DWITH_CUDA:BOOL=%s' % ('+gpu' in spec),
             '-DWITH_CUDNN:BOOL=%s' % ('+gpu' in spec),
             '-DELEMENTAL_USE_CUBLAS:BOOL=%s' % (
@@ -72,14 +183,16 @@ class Lbann(CMakePackage):
             '-DWITH_TBINF=OFF',
             '-DWITH_VTUNE=OFF',
             '-DElemental_DIR={0}'.format(spec['elemental'].prefix),
-            '-DCNPY_DIR={0}'.format(spec['cnpy'].prefix),
             '-DELEMENTAL_MATH_LIBS={0}'.format(
                 spec['elemental'].libs),
             '-DSEQ_INIT:BOOL=%s' % ('+seq_init' in spec),
-            '-DDATATYPE={0}'.format(int(spec.variants['dtype'].value)),
             '-DVERBOSE=0',
-            '-DLBANN_HOME=.',
-            '-DLBANN_VER=spack']
+            '-DLBANN_HOME=.'])
+
+        if spec.variants['dtype'].value == 'float':
+            args.extend(['-DDATATYPE=4'])
+        elif spec.variants['dtype'].value == 'double':
+            args.extend(['-DDATATYPE=8'])
 
         if '+opencv' in spec:
             args.extend(['-DOpenCV_DIR:STRING={0}'.format(
@@ -89,7 +202,7 @@ class Lbann(CMakePackage):
             args.extend(['-DcuDNN_DIR={0}'.format(
                 spec['cudnn'].prefix)])
 
-        if '+cudnn' in spec:
+        if '+cub' in spec:
             args.extend(['-DCUB_DIR={0}'.format(
                 spec['cub'].prefix)])
 
diff --git a/var/spack/repos/builtin/packages/lbxproxy/package.py b/var/spack/repos/builtin/packages/lbxproxy/package.py
index 6b5c4d0bc7..6548807b1a 100644
--- a/var/spack/repos/builtin/packages/lbxproxy/package.py
+++ b/var/spack/repos/builtin/packages/lbxproxy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -48,5 +29,5 @@ class Lbxproxy(AutotoolsPackage):
     depends_on('xtrans', type='build')
     depends_on('xproxymanagementprotocol', type='build')
     depends_on('bigreqsproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/lbzip2/package.py b/var/spack/repos/builtin/packages/lbzip2/package.py
new file mode 100644
index 0000000000..6103ce00e3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/lbzip2/package.py
@@ -0,0 +1,16 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Lbzip2(AutotoolsPackage):
+    """Multi-threaded compression utility with support for bzip2
+       compressed file format"""
+
+    homepage = "http://lbzip2.org/"
+    url      = "http://archive.lbzip2.org/lbzip2-2.5.tar.gz"
+
+    version('2.5', sha256='46c75ee93cc95eedc6005625442b2b8e59a2bef3ba80987d0491f055185650e9')
diff --git a/var/spack/repos/builtin/packages/lcals/package.py b/var/spack/repos/builtin/packages/lcals/package.py
index bd12081130..e697be8989 100644
--- a/var/spack/repos/builtin/packages/lcals/package.py
+++ b/var/spack/repos/builtin/packages/lcals/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 import platform
@@ -35,8 +16,8 @@ class Lcals(MakefilePackage):
         by Frank H. McMahon, UCRL-53745.). The suite contains facilities to
         generate timing statistics and reports."""
 
-    homepage = "https://codesign.llnl.gov/LCALS-downloads/"
-    url = "https://codesign.llnl.gov/LCALS-downloads/lcals-v1.0.2.tgz"
+    homepage = "https://computation.llnl.gov/projects/co-design/lcals"
+    url      = "https://computation.llnl.gov/projects/co-design/download/lcals-v1.0.2.tgz"
 
     tags = ['proxy-app']
 
diff --git a/var/spack/repos/builtin/packages/lcms/package.py b/var/spack/repos/builtin/packages/lcms/package.py
index 816cc3f005..e68e96bdc9 100644
--- a/var/spack/repos/builtin/packages/lcms/package.py
+++ b/var/spack/repos/builtin/packages/lcms/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,11 @@ class Lcms(AutotoolsPackage):
     """Little cms is a color management library. Implements fast
        transforms between ICC profiles. It is focused on speed, and is
        portable across several platforms (MIT license)."""
+
     homepage = "http://www.littlecms.com"
-    url      = "http://downloads.sourceforge.net/project/lcms/lcms/2.8/lcms2-2.8.tar.gz"
+    url      = "http://downloads.sourceforge.net/project/lcms/lcms/2.9/lcms2-2.9.tar.gz"
 
+    version('2.9', '8de1b7724f578d2995c8fdfa35c3ad0e')
     version('2.8', '87a5913f1a52464190bb655ad230539c')
     version('2.6', 'f4c08d38ceade4a664ebff7228910a33')
 
diff --git a/var/spack/repos/builtin/packages/ldc-bootstrap/package.py b/var/spack/repos/builtin/packages/ldc-bootstrap/package.py
index 6e3288f085..5cff31e35d 100644
--- a/var/spack/repos/builtin/packages/ldc-bootstrap/package.py
+++ b/var/spack/repos/builtin/packages/ldc-bootstrap/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/ldc/package.py b/var/spack/repos/builtin/packages/ldc/package.py
index 8dd2052fca..26a9d61ccd 100644
--- a/var/spack/repos/builtin/packages/ldc/package.py
+++ b/var/spack/repos/builtin/packages/ldc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,7 +17,7 @@ class Ldc(CMakePackage):
     """
 
     homepage = "https://dlang.org/"
-    url = "https://github.com/ldc-developers/ldc/releases/download/v0.17.4/ldc-0.17.4-src.tar.gz"
+    url      = "https://github.com/ldc-developers/ldc/releases/download/v1.3.0/ldc-1.3.0-src.tar.gz"
 
     version('1.3.0', '537d992a361b0fd0440b24a5145c9107')
 
diff --git a/var/spack/repos/builtin/packages/legion/package.py b/var/spack/repos/builtin/packages/legion/package.py
index 0ec388994f..4ae0cf533c 100644
--- a/var/spack/repos/builtin/packages/legion/package.py
+++ b/var/spack/repos/builtin/packages/legion/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -42,8 +23,11 @@ class Legion(CMakePackage):
     """
     homepage = "http://legion.stanford.edu/"
     url      = "https://github.com/StanfordLegion/legion/tarball/legion-17.02.0"
+    git      = "https://github.com/StanfordLegion/legion.git"
 
-    version('develop', git='https://github.com/StanfordLegion/legion', branch='master')
+    version('develop', branch='master')
+    version('18.05.0', 'ab5ac8cd4aa4c91e6187bf1333a031bf')
+    version('18.02.0', '14937b386100347b051a5fc514636353')
     version('17.10.0', 'ebfc974dc82a9d7f3ba53242ecae62e1')
     version('17.08.0', 'acc1ea8c564c4a382a015e0c9cf94574')
     version('17.02.0', '31ac3004e2fb0996764362d2b6f6844a')
diff --git a/var/spack/repos/builtin/packages/leveldb/package.py b/var/spack/repos/builtin/packages/leveldb/package.py
index db61668021..e06f347e23 100644
--- a/var/spack/repos/builtin/packages/leveldb/package.py
+++ b/var/spack/repos/builtin/packages/leveldb/package.py
@@ -1,32 +1,13 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import glob
 from spack import *
 
 
-class Leveldb(Package):
+class Leveldb(MakefilePackage):
     """LevelDB is a fast key-value storage library written at Google
     that provides an ordered mapping from string keys to string values."""
 
@@ -39,21 +20,14 @@ class Leveldb(Package):
     depends_on("snappy")
 
     def install(self, spec, prefix):
-        make()
-
-        mkdirp(prefix.include)
-        mkdirp(prefix.lib)
-        mkdirp(join_path(prefix.lib, 'pkgconfig'))
-
-        cp = which('cp')
+        mkdirp(prefix.lib.pkgconfig)
 
-        # cp --preserve=links libleveldb.* prefix/lib
-        args = glob.glob('out-shared/libleveldb.*') \
-            + glob.glob('out-static/libleveldb.*')
-        args.append(prefix.lib)
-        cp('--preserve=links', *args)
+        libraries  = glob.glob('out-shared/libleveldb.*')
+        libraries += glob.glob('out-static/libleveldb.*')
+        for library in libraries:
+            install(library, prefix.lib)
 
-        cp('-r', 'include/leveldb', prefix.include)
+        install_tree('include', prefix.include)
 
         with open(join_path(prefix.lib, 'pkgconfig', 'leveldb.pc'), 'w') as f:
             f.write('prefix={0}\n'.format(prefix))
diff --git a/var/spack/repos/builtin/packages/lftp/package.py b/var/spack/repos/builtin/packages/lftp/package.py
index 47b4706776..1525298538 100644
--- a/var/spack/repos/builtin/packages/lftp/package.py
+++ b/var/spack/repos/builtin/packages/lftp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,6 +15,7 @@ class Lftp(AutotoolsPackage):
 
     version('4.8.1', '419b27c016d968a0226b2e5df1454c22')
     version('4.7.7', 'ddc71b3b11a1af465e829075ae14b3ff')
+    version('4.6.4', 'f84ecfc368b7afcc56fe7d3da2457d12')
 
     depends_on('expat')
     depends_on('libiconv')
diff --git a/var/spack/repos/builtin/packages/libaec/package.py b/var/spack/repos/builtin/packages/libaec/package.py
index 814f7760c5..2a40d3f602 100644
--- a/var/spack/repos/builtin/packages/libaec/package.py
+++ b/var/spack/repos/builtin/packages/libaec/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,7 +14,7 @@ class Libaec(CMakePackage):
     """
 
     homepage = 'https://gitlab.dkrz.de/k202009/libaec'
-    url = 'https://gitlab.dkrz.de/k202009/libaec/repository/archive.tar.gz?ref=v1.0.2'
+    url = 'https://gitlab.dkrz.de/api/v4/projects/k202009%2Flibaec/repository/archive.tar.gz?sha=v1.0.2'
     list_url = 'https://gitlab.dkrz.de/k202009/libaec/tags'
 
     provides('szip')
diff --git a/var/spack/repos/builtin/packages/libaio/package.py b/var/spack/repos/builtin/packages/libaio/package.py
index 2a617c0518..56872455cd 100644
--- a/var/spack/repos/builtin/packages/libaio/package.py
+++ b/var/spack/repos/builtin/packages/libaio/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,7 +10,7 @@ class Libaio(Package):
     """This is the linux native Asynchronous I/O interface library."""
 
     homepage = "http://lse.sourceforge.net/io/aio.html"
-    url      = "https://ftp.de.debian.org/debian/pool/main/liba/libaio/libaio_0.3.110.orig.tar.gz"
+    url      = "https://debian.inf.tu-dresden.de/debian/pool/main/liba/libaio/libaio_0.3.110.orig.tar.gz"
 
     version('0.3.110', '2a35602e43778383e2f4907a4ca39ab8')
 
diff --git a/var/spack/repos/builtin/packages/libapplewm/package.py b/var/spack/repos/builtin/packages/libapplewm/package.py
index 146596081f..373b373487 100644
--- a/var/spack/repos/builtin/packages/libapplewm/package.py
+++ b/var/spack/repos/builtin/packages/libapplewm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,7 +21,7 @@ class Libapplewm(AutotoolsPackage):
 
     depends_on('xextproto', type='build')
     depends_on('applewmproto@1.4:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     # Crashes with this error message on Linux:
diff --git a/var/spack/repos/builtin/packages/libarchive/package.py b/var/spack/repos/builtin/packages/libarchive/package.py
index f06f09b391..08c743e724 100644
--- a/var/spack/repos/builtin/packages/libarchive/package.py
+++ b/var/spack/repos/builtin/packages/libarchive/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,6 +13,7 @@ class Libarchive(AutotoolsPackage):
     homepage = "http://www.libarchive.org"
     url      = "http://www.libarchive.org/downloads/libarchive-3.1.2.tar.gz"
 
+    version('3.3.2', '4583bd6b2ebf7e0e8963d90879eb1b27')
     version('3.2.1', 'afa257047d1941a565216edbf0171e72')
     version('3.1.2', 'efad5a503f66329bb9d2f4308b5de98a')
     version('3.1.1', '1f3d883daf7161a0065e42a15bbf168f')
diff --git a/var/spack/repos/builtin/packages/libassuan/package.py b/var/spack/repos/builtin/packages/libassuan/package.py
index 8a56551ff5..7f28942a53 100644
--- a/var/spack/repos/builtin/packages/libassuan/package.py
+++ b/var/spack/repos/builtin/packages/libassuan/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,8 +11,9 @@ class Libassuan(AutotoolsPackage):
        protocol."""
 
     homepage = "https://gnupg.org/software/libassuan/index.html"
-    url = "https://gnupg.org/ftp/gcrypt/libassuan/libassuan-2.4.3.tar.bz2"
+    url = "https://gnupg.org/ftp/gcrypt/libassuan/libassuan-2.4.5.tar.bz2"
 
+    version('2.4.5', '4f22bdb70d424cfb41b64fd73b7e1e45')
     version('2.4.3', '8e01a7c72d3e5d154481230668e6eb5a')
 
     depends_on('libgpg-error')
diff --git a/var/spack/repos/builtin/packages/libatomic-ops/package.py b/var/spack/repos/builtin/packages/libatomic-ops/package.py
index df12c000f3..a629eab02d 100644
--- a/var/spack/repos/builtin/packages/libatomic-ops/package.py
+++ b/var/spack/repos/builtin/packages/libatomic-ops/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libbeagle/package.py b/var/spack/repos/builtin/packages/libbeagle/package.py
index 4d064a063b..a4f9352e72 100644
--- a/var/spack/repos/builtin/packages/libbeagle/package.py
+++ b/var/spack/repos/builtin/packages/libbeagle/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,8 +21,13 @@ class Libbeagle(AutotoolsPackage):
     depends_on('m4',       type='build')
 
     depends_on('subversion', type='build')
-    depends_on('pkg-config', type='build')
+    depends_on('pkgconfig', type='build')
+    depends_on('java', type='build')
 
     def url_for_version(self, version):
         url = "https://github.com/beagle-dev/beagle-lib/archive/beagle_release_{0}.tar.gz"
         return url.format(version.underscored)
+
+    def setup_environment(self, spack_env, run_env):
+        prefix = self.prefix
+        run_env.prepend_path('BEAST_LIB', prefix.lib)
diff --git a/var/spack/repos/builtin/packages/libbeato/package.py b/var/spack/repos/builtin/packages/libbeato/package.py
new file mode 100644
index 0000000000..0cc0a19a13
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libbeato/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Libbeato(AutotoolsPackage):
+    """libbeato is a C library containing routines for various uses in Genomics,
+    and includes a copy of the freeware portion of the C library
+    from UCSC's Genome Browser Group."""
+
+    homepage = "https://github.com/CRG-Barcelona/libbeato"
+    url      = "https://github.com/CRG-Barcelona/libbeato/archive/master.tar.gz"
+
+    version('master', 'ee6f0f0f3f09c4f601fcfed3b13e7395')
diff --git a/var/spack/repos/builtin/packages/libbsd/package.py b/var/spack/repos/builtin/packages/libbsd/package.py
index f9b8a291ca..4587d29e1f 100644
--- a/var/spack/repos/builtin/packages/libbsd/package.py
+++ b/var/spack/repos/builtin/packages/libbsd/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libbson/package.py b/var/spack/repos/builtin/packages/libbson/package.py
index 39a606cf73..92f5a26f14 100644
--- a/var/spack/repos/builtin/packages/libbson/package.py
+++ b/var/spack/repos/builtin/packages/libbson/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,6 +13,10 @@ class Libbson(AutotoolsPackage):
     homepage = "https://github.com/mongodb/libbson"
     url      = "https://github.com/mongodb/libbson/releases/download/1.7.0/libbson-1.7.0.tar.gz"
 
+    maintainers = ['michaelkuhn']
+
+    version('1.9.1', 'f91f59fc5a0cbba94d4d32dad1bd0cfd')
+    version('1.8.1', '42601455cf7f450b46f62c4e6115c440')
     version('1.8.0', '8b3c64570eec721f951831958e707a5a')
     version('1.7.0', 'e196ad77dd8458ebc1166e6135030b63')
     version('1.6.3', 'b7bdb314197106fcfb4af105a582d343')
diff --git a/var/spack/repos/builtin/packages/libcanberra/package.py b/var/spack/repos/builtin/packages/libcanberra/package.py
index f7b8a78659..6c6fd99ae1 100644
--- a/var/spack/repos/builtin/packages/libcanberra/package.py
+++ b/var/spack/repos/builtin/packages/libcanberra/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -55,7 +36,7 @@ class Libcanberra(AutotoolsPackage):
 
     depends_on('libvorbis')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
 
     def configure_args(self):
         args = ['--enable-static']
diff --git a/var/spack/repos/builtin/packages/libcap/package.py b/var/spack/repos/builtin/packages/libcap/package.py
index af7c363bf0..234c1846b4 100644
--- a/var/spack/repos/builtin/packages/libcap/package.py
+++ b/var/spack/repos/builtin/packages/libcap/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libceed/occaFree-0.2.diff b/var/spack/repos/builtin/packages/libceed/occaFree-0.2.diff
new file mode 100644
index 0000000000..060710d4ad
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libceed/occaFree-0.2.diff
@@ -0,0 +1,41 @@
+diff --git a/backends/occa/ceed-occa-basis.c b/backends/occa/ceed-occa-basis.c
+index 85ec292..86a46ee 100644
+--- a/backends/occa/ceed-occa-basis.c
++++ b/backends/occa/ceed-occa-basis.c
+@@ -293,10 +293,6 @@ static int CeedBasisDestroy_Occa(CeedBasis basis) {
+   const Ceed ceed = basis->ceed;
+   CeedBasis_Occa *data = basis->data;
+   dbg("[CeedBasis][Destroy]");
+-  occaFree(data->kZero);
+-  occaFree(data->kInterp);
+-  occaFree(data->kGrad);
+-  occaFree(data->kWeight);
+   occaFree(data->qref1d);
+   occaFree(data->qweight1d);
+   occaFree(data->interp1d);
+diff --git a/backends/occa/ceed-occa-qfunction.c b/backends/occa/ceed-occa-qfunction.c
+index a2776c3..abf7de0 100644
+--- a/backends/occa/ceed-occa-qfunction.c
++++ b/backends/occa/ceed-occa-qfunction.c
+@@ -154,7 +154,6 @@ static int CeedQFunctionDestroy_Occa(CeedQFunction qf) {
+   CeedQFunction_Occa *data=qf->data;
+   free(data->oklPath);
+   dbg("[CeedQFunction][Destroy]");
+-  occaFree(data->kQFunctionApply);
+   if (data->ready) {
+     if (!data->op) occaFree(data->d_q);
+     occaFree(data->d_u);
+diff --git a/backends/occa/ceed-occa-restrict.c b/backends/occa/ceed-occa-restrict.c
+index 6b7786c..c5360dc 100644
+--- a/backends/occa/ceed-occa-restrict.c
++++ b/backends/occa/ceed-occa-restrict.c
+@@ -95,9 +95,6 @@ static int CeedElemRestrictionDestroy_Occa(CeedElemRestriction r) {
+   const Ceed ceed = r->ceed;
+   CeedElemRestriction_Occa *data = r->data;
+   dbg("[CeedElemRestriction][Destroy]");
+-  for (int i=0; i<9; i++) {
+-    occaFree(data->kRestrict[i]);
+-  }
+   ierr = CeedFree(&data); CeedChk(ierr);
+   return 0;
+ }
diff --git a/var/spack/repos/builtin/packages/libceed/package.py b/var/spack/repos/builtin/packages/libceed/package.py
new file mode 100644
index 0000000000..54bb7b495f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libceed/package.py
@@ -0,0 +1,60 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Libceed(Package):
+    """The CEED API Library: Code for Efficient Extensible Discretizations."""
+
+    homepage = "https://github.com/CEED/libCEED"
+    git      = "https://github.com/CEED/libCEED.git"
+
+    version('develop', branch='master')
+    version('0.2', tag='v0.2')
+    version('0.1', tag='v0.1')
+
+    variant('occa', default=True, description='Enable OCCA backends')
+    variant('cuda', default=False, description='Enable CUDA support')
+    variant('debug', default=False, description='Enable debug build')
+
+    depends_on('occa@v1.0.0-alpha.5,develop', when='+occa')
+    depends_on('occa@develop', when='@develop+occa')
+    depends_on('occa+cuda', when='+occa+cuda')
+    depends_on('occa~cuda', when='+occa~cuda')
+
+    # occa: do not occaFree kernels
+    # Repeated creation and freeing of kernels appears to expose a caching
+    # bug in Occa.
+    patch('occaFree-0.2.diff', when='@0.2')
+
+    phases = ['build', 'install']
+
+    def build(self, spec, prefix):
+        # Note: The occa package exports OCCA_DIR in the environment
+
+        makeopts = ['V=1']
+        makeopts += ['NDEBUG=%s' % ('' if '+debug' in spec else '1')]
+        make(*makeopts)
+
+        if self.run_tests:
+            make('prove', *makeopts, parallel=False)
+
+    def install(self, spec, prefix):
+        make('install', 'prefix=%s' % prefix, parallel=False)
+
+    @when('@0.1')
+    def install(self, spec, prefix):
+        mkdirp(prefix.include)
+        install('ceed.h', prefix.include)
+        mkdirp(prefix.lib)
+        install('libceed.%s' % dso_suffix, prefix.lib)
+        filter_file('^prefix=.*$', 'prefix=%s' % prefix, 'ceed.pc')
+        filter_file('^includedir=\$\{prefix\}$',
+                    'includedir=${prefix}/include', 'ceed.pc')
+        filter_file('^libdir=\$\{prefix\}$', 'libdir=${prefix}/lib', 'ceed.pc')
+        filter_file('Version:.*$', 'Version: 0.1', 'ceed.pc')
+        mkdirp(prefix.lib.pkgconfig)
+        install('ceed.pc', prefix.lib.pkgconfig)
diff --git a/var/spack/repos/builtin/packages/libcerf/package.py b/var/spack/repos/builtin/packages/libcerf/package.py
index f119f96832..ecf35f87f4 100644
--- a/var/spack/repos/builtin/packages/libcerf/package.py
+++ b/var/spack/repos/builtin/packages/libcerf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/libcheck/package.py b/var/spack/repos/builtin/packages/libcheck/package.py
new file mode 100644
index 0000000000..19553b8b6a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libcheck/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Libcheck(CMakePackage):
+    """A unit testing framework for C."""
+
+    homepage = "https://libcheck.github.io/check/index.html"
+    url      = "https://github.com/libcheck/check/releases/download/0.12.0/check-0.12.0.tar.gz"
+
+    version('0.12.0', '31b17c6075820a434119592941186f70')
+    version('0.11.0', '9b90522b31f5628c2e0f55dda348e558')
+    version('0.10.0', '53c5e5c77d090e103a17f3ed7fd7d8b8')
diff --git a/var/spack/repos/builtin/packages/libcint/package.py b/var/spack/repos/builtin/packages/libcint/package.py
new file mode 100644
index 0000000000..1698dbb3ce
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libcint/package.py
@@ -0,0 +1,63 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Libcint(CMakePackage):
+    """Library for analytical Gaussian integrals for quantum chemistry."""
+
+    homepage    = "https://github.com/sunqm/libcint"
+    url         = "https://github.com/sunqm/libcint/archive/v3.0.4.tar.gz"
+    maintainers = ['mfherbst']
+
+    #
+    # Versions
+    #
+    version('3.0.13', sha256='ee64f0bc7fb6073063ac3c9bbef8951feada141e197b1a5cc389c8cccf8dc360')
+    version('3.0.12', sha256='7409ef41f1465cf4c1ae9834dfc0b0585c0fdc63b55d8ee8b8a7a6d5e31f309d')
+    version('3.0.11', sha256='4c9c24d4bd4791391848f19a4be5177137aca27a8e0375574101a7a1261157cf')
+    version('3.0.10', sha256='aac6d9630dc4c62840f03262166e877d3aeaf27b6b33498fb490fa3428f12fe4')
+    version('3.0.8',  sha256='ca94772f74aaf7b8ad4d7c1b09578c9115ec909c3d8b82dacc908c351c631c35')
+    version('3.0.7',  sha256='e603cd90567c6116d4f704ea66a010b447c11052e90db1d91488adc187142ead')
+    version('3.0.6',  sha256='a7d6d46de9be044409270b27727a1d620d21b5fda6aa7291548938e1ced25404')
+    version('3.0.5',  sha256='7bde241ce83c00b89c80459e3af5734d40925d8fd9fcaaa7245f61b08192c722')
+    version('3.0.4',  sha256='0f25ef7ad282dd7a20e4decf283558e4f949243a5423ff4c0cd875276c310c47')
+
+    #
+    # Variants
+    #
+    variant('f12', default=True,
+            description="Enable explicitly correlated f12 integrals.")
+    variant('coulomb_erf', default=True,
+            description="Enable attenuated coulomb operator integrals.")
+    variant('test', default=False, description="Build test programs")
+    variant('shared', default=True,
+            description="Build the shared library")
+
+    #
+    # Dependencies and conflicts
+    #
+    depends_on('cmake@2.6:', type="build")
+    depends_on('blas')
+    depends_on('python', type=("build", "test"), when="+test")
+    depends_on('py-numpy', type=("build", "test"), when="+test")
+
+    # Libcint tests only work with a shared libcint library
+    conflicts('+test~shared')
+
+    #
+    # Settings and cmake cache
+    #
+    def cmake_args(self):
+        spec = self.spec
+        args = [
+            "-DWITH_COULOMB_ERF=" + str("+coulomb_erf" in spec),
+            "-DWITH_F12=" + str("+f12" in spec),
+            "-DBUILD_SHARED_LIBS=" + str("+shared" in spec),
+            "-DENABLE_TEST=" + str("+test" in spec),
+            "-DENABLE_EXAMPLE=OFF",  # Requires fortran compiler
+        ]
+        return args
diff --git a/var/spack/repos/builtin/packages/libcircle/package.py b/var/spack/repos/builtin/packages/libcircle/package.py
index 98778ea9a4..5bd6bf719f 100644
--- a/var/spack/repos/builtin/packages/libcircle/package.py
+++ b/var/spack/repos/builtin/packages/libcircle/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libconfig/package.py b/var/spack/repos/builtin/packages/libconfig/package.py
index e62ec6bd83..9dea0cd4c8 100644
--- a/var/spack/repos/builtin/packages/libconfig/package.py
+++ b/var/spack/repos/builtin/packages/libconfig/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,7 +10,7 @@ class Libconfig(AutotoolsPackage):
     """C/C++ Configuration File Library"""
 
     homepage = "http://www.hyperrealm.com/libconfig/"
-    url      = "https://github.com/hyperrealm/libconfig/archive/v1.6.tar.gz"
+    url      = "https://github.com/hyperrealm/libconfig/archive/v1.5.tar.gz"
 
     force_autoreconf = True
     # there is currently a build error with version 1.6, see:
diff --git a/var/spack/repos/builtin/packages/libcroco/package.py b/var/spack/repos/builtin/packages/libcroco/package.py
new file mode 100644
index 0000000000..eefc188457
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libcroco/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Libcroco(AutotoolsPackage):
+    """Libcroco is a standalone css2 parsing and manipulation library."""
+
+    homepage = "https://developer.gnome.org/libcroco"
+    url      = "http://ftp.gnome.org/pub/gnome/sources/libcroco/0.6/libcroco-0.6.12.tar.xz"
+
+    version('0.6.12', 'bc0984fce078ba2ce29f9500c6b9ddce')
+
+    depends_on('glib')
+    depends_on('libxml2')
diff --git a/var/spack/repos/builtin/packages/libctl/package.py b/var/spack/repos/builtin/packages/libctl/package.py
index fc729d6db8..ae68dc5bef 100644
--- a/var/spack/repos/builtin/packages/libctl/package.py
+++ b/var/spack/repos/builtin/packages/libctl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libdivsufsort/package.py b/var/spack/repos/builtin/packages/libdivsufsort/package.py
index 1e679eb2ec..2ac8d6f65e 100644
--- a/var/spack/repos/builtin/packages/libdivsufsort/package.py
+++ b/var/spack/repos/builtin/packages/libdivsufsort/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libdmx/package.py b/var/spack/repos/builtin/packages/libdmx/package.py
index c89323935f..9514dc9f00 100644
--- a/var/spack/repos/builtin/packages/libdmx/package.py
+++ b/var/spack/repos/builtin/packages/libdmx/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Libdmx(AutotoolsPackage):
 
     depends_on('xextproto', type='build')
     depends_on('dmxproto@2.2.99.1:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libdrm/package.py b/var/spack/repos/builtin/packages/libdrm/package.py
index 521e097dc8..ca4e26577c 100644
--- a/var/spack/repos/builtin/packages/libdrm/package.py
+++ b/var/spack/repos/builtin/packages/libdrm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import sys
 
@@ -39,7 +20,7 @@ class Libdrm(Package):
     version('2.4.59', '105ac7af1afcd742d402ca7b4eb168b6')
     version('2.4.33', '86e4e3debe7087d5404461e0032231c8')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('libpciaccess@0.10:', when=(sys.platform != 'darwin'))
     depends_on('libpthread-stubs')
 
diff --git a/var/spack/repos/builtin/packages/libdwarf/package.py b/var/spack/repos/builtin/packages/libdwarf/package.py
index 970a4502b4..a473b2c83a 100644
--- a/var/spack/repos/builtin/packages/libdwarf/package.py
+++ b/var/spack/repos/builtin/packages/libdwarf/package.py
@@ -1,28 +1,11 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
+import sys
+import os
 
 # Only build certain parts of dwarf because the other ones break.
 dwarf_dirs = ['libdwarf', 'dwarfdump2']
@@ -44,11 +27,14 @@ class Libdwarf(Package):
     url      = "http://www.prevanders.net/libdwarf-20160507.tar.gz"
     list_url = homepage
 
+    version('20180129', 'c5e90fad4640f0d713ae8b986031f959')
     version('20160507', 'ae32d6f9ece5daf05e2d4b14822ea811')
     version('20130729', '4cc5e48693f7b93b7aa0261e63c0e21d')
     version('20130207', '64b42692e947d5180e162e46c689dfbf')
     version('20130126', 'ded74a5e90edb5a12aac3c29d260c5db')
+    depends_on("elfutils@0.163", when='@20160507', type='link')
     depends_on("elf", type='link')
+    depends_on('zlib', type='link')
 
     parallel = False
 
@@ -56,49 +42,71 @@ class Libdwarf(Package):
         filter_file(r'^typedef struct Elf Elf;$', '', 'libdwarf/libdwarf.h.in')
 
     def install(self, spec, prefix):
-
-        # elfutils contains a dwarf.h that conflicts with libdwarf's
-        # TODO: we should remove this when we can modify the include order
-        hide_list = []
-        if spec.satisfies('^elfutils'):
-            dwarf_h = join_path(spec['elfutils'].prefix, 'include/dwarf.h')
-            hide_list.append(dwarf_h)
-        with hide_files(*hide_list):
-            # dwarf build does not set arguments for ar properly
-            make.add_default_arg('ARFLAGS=rcs')
-
-            # Dwarf doesn't provide an install, so we have to do it.
-            mkdirp(prefix.bin, prefix.include, prefix.lib, prefix.man.man1)
-
-            with working_dir('libdwarf'):
-                extra_config_args = []
-
-                # this is to prevent picking up system /usr/include/libelf.h
-                if spec.satisfies('^libelf'):
-                    libelf_inc_dir = join_path(spec['libelf'].prefix,
-                                               'include/libelf')
-                    extra_config_args.append('CFLAGS=-I{0}'.format(
-                                             libelf_inc_dir))
-                configure("--prefix=" + prefix, "--enable-shared",
-                          *extra_config_args)
-                make()
-
-                install('libdwarf.a',  prefix.lib)
-                install('libdwarf.so', prefix.lib)
-                install('libdwarf.h',  prefix.include)
-                install('dwarf.h',     prefix.include)
-
-            if spec.satisfies('@20130126:20130729'):
-                dwarfdump_dir = 'dwarfdump2'
-            else:
-                dwarfdump_dir = 'dwarfdump'
-            with working_dir(dwarfdump_dir):
-                configure("--prefix=" + prefix)
-
-                # This makefile has strings of copy commands that
-                # cause a race in parallel
-                make(parallel=False)
-
-                install('dwarfdump',      prefix.bin)
-                install('dwarfdump.conf', prefix.lib)
-                install('dwarfdump.1',    prefix.man.man1)
+        # dwarf build does not set arguments for ar properly
+        make.add_default_arg('ARFLAGS=rcs')
+
+        # Dwarf doesn't provide an install, so we have to do it.
+        mkdirp(prefix.bin, prefix.include, prefix.lib, prefix.man.man1)
+
+        with working_dir('libdwarf'):
+            extra_config_args = []
+
+            # this is to prevent picking up system /usr/include/libelf.h
+            if spec.satisfies('^libelf'):
+                libelf_inc_dir = join_path(spec['libelf'].prefix,
+                                           'include/libelf')
+                extra_config_args.append(
+                    'CFLAGS=-I{0} -Wl,-L{1} -Wl,-lelf'.format(
+                        libelf_inc_dir, spec['libelf'].prefix.lib))
+            configure("--prefix=" + prefix, "--enable-shared",
+                      *extra_config_args)
+            filter_file(r'^dwfzlib\s*=\s*-lz',
+                        'dwfzlib=-L{0} -lz'.format(
+                            self.spec['zlib'].prefix.lib),
+                        'Makefile')
+            make()
+
+            libdwarf_name = 'libdwarf.{0}'.format(dso_suffix)
+            libdwarf1_name = 'libdwarf.{0}'.format(dso_suffix) + ".1"
+            install('libdwarf.a',  prefix.lib)
+            install('libdwarf.so', join_path(prefix.lib, libdwarf1_name))
+            if spec.satisfies('@20160507:'):
+                with working_dir(prefix.lib):
+                    os.symlink(libdwarf1_name, libdwarf_name)
+            install('libdwarf.h',  prefix.include)
+            install('dwarf.h',     prefix.include)
+
+            # It seems like fix_darwin_install_name can't be used
+            # here directly; the install name of the library in
+            # the stage directory must be fixed in order for dyld
+            # to locate it on Darwin when spack builds dwarfdump
+            if sys.platform == 'darwin':
+                install_name_tool = which('install_name_tool')
+                install_name_tool('-id',
+                                  join_path('..', 'libdwarf',
+                                            'libdwarf.so'),
+                                  'libdwarf.so')
+
+        if spec.satisfies('@20130126:20130729'):
+            dwarfdump_dir = 'dwarfdump2'
+        else:
+            dwarfdump_dir = 'dwarfdump'
+        with working_dir(dwarfdump_dir):
+            configure("--prefix=" + prefix)
+            filter_file(r'^dwfzlib\s*=\s*-lz',
+                        'dwfzlib=-L{0} -lz'.format(
+                            self.spec['zlib'].prefix.lib),
+                        'Makefile')
+
+            # This makefile has strings of copy commands that
+            # cause a race in parallel
+            make(parallel=False)
+
+            install('dwarfdump',      prefix.bin)
+            install('dwarfdump.conf', prefix.lib)
+            install('dwarfdump.1',    prefix.man.man1)
+
+    @run_after('install')
+    def darwin_fix(self):
+        if sys.platform == 'darwin':
+            fix_darwin_install_name(self.prefix.lib)
diff --git a/var/spack/repos/builtin/packages/libedit/package.py b/var/spack/repos/builtin/packages/libedit/package.py
index 42a09fd540..b253397ee4 100644
--- a/var/spack/repos/builtin/packages/libedit/package.py
+++ b/var/spack/repos/builtin/packages/libedit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libelf/package.py b/var/spack/repos/builtin/packages/libelf/package.py
index 5d433c19d5..b843966310 100644
--- a/var/spack/repos/builtin/packages/libelf/package.py
+++ b/var/spack/repos/builtin/packages/libelf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libemos/package.py b/var/spack/repos/builtin/packages/libemos/package.py
index 8db882d4be..02d953c4ab 100644
--- a/var/spack/repos/builtin/packages/libemos/package.py
+++ b/var/spack/repos/builtin/packages/libemos/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,31 +12,37 @@ class Libemos(CMakePackage):
 
     homepage = "https://software.ecmwf.int/wiki/display/EMOS/Emoslib"
     url      = "https://software.ecmwf.int/wiki/download/attachments/3473472/libemos-4.4.2-Source.tar.gz"
+    list_url = "https://software.ecmwf.int/wiki/display/EMOS/Releases"
 
+    version('4.5.1', 'eec1ef4de841df3c68c08fa94d7939ff')
+    version('4.5.0', '0ad8962a73e3ca90a8094561adc81276')
+    version('4.4.9', '24d098cd062d443a544fe17727726285')
     version('4.4.7', '395dcf21cf06872f772fb6b73d8e67b9')
     version('4.4.2', 'f15a9aff0f40861f3f046c9088197376')
 
-    variant('eccodes', default=False,
-            description="Use eccodes instead of grib-api for GRIB decoding")
+    variant('grib', default='eccodes', values=('eccodes', 'grib-api'),
+            description='Specify GRIB backend')
     variant('build_type', default='RelWithDebInfo',
             description='The build type to build',
             values=('Debug', 'Release', 'RelWithDebInfo', 'Production'))
 
-    depends_on('eccodes', when='+eccodes')
-    depends_on('grib-api', when='~eccodes')
+    depends_on('eccodes', when='grib=eccodes')
+    depends_on('grib-api', when='grib=grib-api')
     depends_on('fftw+float+double')
     depends_on('cmake@2.8.11:', type='build')
+    depends_on('pkgconfig', type='build')
+
+    conflicts('grib=eccodes', when='@:4.4.1',
+              msg='Eccodes is supported starting version 4.4.2')
 
     def cmake_args(self):
-        spec = self.spec
         args = []
 
-        if spec.satisfies('+eccodes'):
+        if self.spec.variants['grib'].value == 'eccodes':
             args.append('-DENABLE_ECCODES=ON')
-            args.append('-DECCODES_PATH=%s' % spec['eccodes'].prefix)
         else:
-            args.append('-DENABLE_ECCODES=OFF')
-            args.append('-DGRIB_API_PATH=%s' % spec['grib-api'].prefix)
+            if self.spec.satisfies('@4.4.2:'):
+                args.append('-DENABLE_ECCODES=OFF')
 
         # To support long pathnames that spack generates
         args.append('-DCMAKE_Fortran_FLAGS=-ffree-line-length-none')
diff --git a/var/spack/repos/builtin/packages/libepoxy/package.py b/var/spack/repos/builtin/packages/libepoxy/package.py
index 9f29a701a0..a8fcb945b1 100644
--- a/var/spack/repos/builtin/packages/libepoxy/package.py
+++ b/var/spack/repos/builtin/packages/libepoxy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,6 +10,18 @@ class Libepoxy(AutotoolsPackage):
     """Epoxy is a library for handling OpenGL function pointer management for
     you."""
     homepage = "https://github.com/anholt/libepoxy"
-    url      = "https://github.com/anholt/libepoxy/releases/download/v1.3.1/libepoxy-1.3.1.tar.bz2"
+    url      = "https://github.com/anholt/libepoxy/releases/download/1.4.3/libepoxy-1.4.3.tar.xz"
+    list_url = "https://github.com/anholt/libepoxy/releases"
 
+    version('1.4.3', 'af4c3ce0fb1143bdc4e43f85695a9bed')
     version('1.3.1', '96f6620a9b005a503e7b44b0b528287d')
+
+    depends_on('pkgconfig', type='build')
+    depends_on('meson')
+    depends_on('mesa')
+
+    def configure_args(self):
+        # Disable egl, otherwise configure fails with:
+        # error: Package requirements (egl) were not met
+        # Package 'egl', required by 'virtual:world', not found
+        return ['--enable-egl=no']
diff --git a/var/spack/repos/builtin/packages/libev/package.py b/var/spack/repos/builtin/packages/libev/package.py
new file mode 100644
index 0000000000..26eec70d3e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libev/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Libev(AutotoolsPackage):
+    """A full-featured and high-performance event loop that is loosely modelled
+    after libevent, but without its limitations and bugs."""
+
+    homepage = "http://software.schmorp.de/pkg/libev.html"
+    url      = "http://dist.schmorp.de/libev/libev-4.24.tar.gz"
+    git      = "https://github.com/enki/libev.git"
+    list_url = "http://dist.schmorp.de/libev/Attic/"
+
+    version('develop', branch='master')
+    version('4.24', '94459a5a22db041dec6f98424d6efe54')
+
+    depends_on('autoconf', type='build', when='@develop')
+    depends_on('automake', type='build', when='@develop')
+    depends_on('libtool',  type='build', when='@develop')
+    depends_on('m4',       type='build', when='@develop')
diff --git a/var/spack/repos/builtin/packages/libevent/package.py b/var/spack/repos/builtin/packages/libevent/package.py
index 562bb212f9..49cda592fb 100644
--- a/var/spack/repos/builtin/packages/libevent/package.py
+++ b/var/spack/repos/builtin/packages/libevent/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libevpath/package.py b/var/spack/repos/builtin/packages/libevpath/package.py
index 64c2fb44e3..b27b8c6b70 100644
--- a/var/spack/repos/builtin/packages/libevpath/package.py
+++ b/var/spack/repos/builtin/packages/libevpath/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,17 +14,32 @@ class Libevpath(CMakePackage):
     """
 
     homepage = "https://github.com/GTkorvo/evpath"
-    url = "https://github.com/GTkorvo/evpath/archive/v4.1.1.tar.gz"
+    url      = "https://github.com/GTkorvo/evpath/archive/v4.1.1.tar.gz"
+    git      = "https://github.com/GTkorvo/evpath.git"
 
-    version('develop', git='https://github.com/GTkorvo/evpath.git',
-            branch='master')
+    version('develop', branch='master')
+    version('4.4.0', 'd8630eb358ec90ae2d188e0e6c74022a')
+    version('4.2.4', '757ce010a6b7564dc62d3c79edd861d5')
     version('4.2.1', 'f928dc0dee41668afc91634c7051ce1a')
     version('4.1.2', '1a187f55431c991ae7040e3ff041d75c')
     version('4.1.1', '65a8db820f396ff2926e3d31908d123d')
 
+    variant('enet_transport', default=False, description='Build an ENET transport for EVpath')
+
+    depends_on('gtkorvo-enet', when='@4.4.0: +enet_transport')
+    depends_on('gtkorvo-enet@1.3.13', when='@:4.2.4 +enet_transport')
     depends_on('libffs')
 
     def cmake_args(self):
-        args = ["-DENABLE_TESTING=0", "-DTARGET_CNL=1",
-                "-DBUILD_SHARED_STATIC=STATIC"]
+        args = ["-DTARGET_CNL=1"]
+        if self.spec.satisfies('@4.4.0:'):
+            args.append("-DBUILD_SHARED_LIBS=OFF")
+        else:
+            args.append("-DENABLE_BUILD_STATIC=STATIC")
+
+        if self.run_tests:
+            args.append('-DENABLE_TESTING=1')
+        else:
+            args.append('-DENABLE_TESTING=0')
+
         return args
diff --git a/var/spack/repos/builtin/packages/libfabric/package.py b/var/spack/repos/builtin/packages/libfabric/package.py
index 01e139824a..3644b6205c 100644
--- a/var/spack/repos/builtin/packages/libfabric/package.py
+++ b/var/spack/repos/builtin/packages/libfabric/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,21 +11,27 @@ class Libfabric(AutotoolsPackage):
        fabric communication services to applications."""
 
     homepage = "https://libfabric.org/"
-    url      = "https://github.com/ofiwg/libfabric/releases/download/v1.5.0/libfabric-1.5.0.tar.gz"
+    url      = "https://github.com/ofiwg/libfabric/releases/download/v1.6.1/libfabric-1.6.1.tar.gz"
+    git = "https://github.com/ofiwg/libfabric.git"
 
+    version('develop', branch='master')
+    version('1.6.1', 'ff78dc9fcbf273a119c737a4e1df46d1')
+    version('1.6.0', '91d63ab3c0b9724a4db660019f928cab')
+    version('1.5.3', '1fe07e972fe487c6a3e44c0fb68b49a2')
     version('1.5.0', 'fda3e9b31ebe184f5157288d059672d6')
+    version('1.4.2', '2009c8e0817060fb99606ddbf6c5ccf8')
 
     fabrics = ('psm',
                'psm2',
                'sockets',
                'verbs',
                'usnic',
-               'mxm',
                'gni',
                'xpmem',
                'udp',
                'rxm',
-               'rxd')
+               'rxd',
+               'mlx')
 
     variant(
        'fabrics',
@@ -54,6 +41,21 @@ class Libfabric(AutotoolsPackage):
        multi=True
     )
 
+    depends_on('rdma-core', when='fabrics=verbs')
+    depends_on('opa-psm2', when='fabrics=psm2')
+    depends_on('psm', when='fabrics=psm')
+    depends_on('ucx', when='fabrics=mlx')
+
+    depends_on('m4', when='@develop', type='build')
+    depends_on('autoconf', when='@develop', type='build')
+    depends_on('automake', when='@develop', type='build')
+    depends_on('libtool', when='@develop', type='build')
+
+    @when('@develop')
+    def autoreconf(self, spec, prefix):
+        bash = which('bash')
+        bash('./autogen.sh')
+
     def configure_args(self):
         args = []
 
diff --git a/var/spack/repos/builtin/packages/libffi/package.py b/var/spack/repos/builtin/packages/libffi/package.py
index f87060118d..b43eb91619 100644
--- a/var/spack/repos/builtin/packages/libffi/package.py
+++ b/var/spack/repos/builtin/packages/libffi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,3 +18,8 @@ class Libffi(AutotoolsPackage):
     # version('3.1', 'f5898b29bbfd70502831a212d9249d10',url =
     # "ftp://sourceware.org/pub/libffi/libffi-3.1.tar.gz") # Has a bug
     # $(lib64) instead of ${lib64} in libffi.pc
+
+    @property
+    def headers(self):
+        # The headers are probably in self.prefix.lib but we search everywhere
+        return find_headers('ffi', self.prefix, recursive=True)
diff --git a/var/spack/repos/builtin/packages/libffs/package.py b/var/spack/repos/builtin/packages/libffs/package.py
index ee7a690214..1500777652 100644
--- a/var/spack/repos/builtin/packages/libffs/package.py
+++ b/var/spack/repos/builtin/packages/libffs/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,20 +15,30 @@ class Libffs(CMakePackage):
     """
 
     homepage = "http://www.cc.gatech.edu/systems/projects/FFS"
-    url = "https://github.com/GTkorvo/ffs/archive/v1.1.tar.gz"
+    url      = "https://github.com/GTkorvo/ffs/archive/v1.1.tar.gz"
+    git      = "https://github.com/GTkorvo/ffs.git"
 
-    version('develop', git='https://github.com/GTkorvo/ffs.git',
-            branch='master')
+    version('develop', branch='master')
+    version('1.5',   'c41c5f5f448b627740deecd695b7bbf8')
     version('1.1.1', 'aa1c8ad5cf35e8cf76735e3a60891509')
-    version('1.1', '561c6b3abc53e12b3c01192e8ef2ffbc')
+    version('1.1',   '561c6b3abc53e12b3c01192e8ef2ffbc')
 
-    depends_on('flex')
-    depends_on('bison')
+    depends_on('flex', type='build', when='@:1.4')
+    depends_on('bison', type='build', when='@:1.4')
+    depends_on('gtkorvo-cercs-env', type='build', when='@:1.4')
     depends_on('gtkorvo-atl')
     depends_on('gtkorvo-dill')
-    depends_on('gtkorvo-cercs-env')
 
     def cmake_args(self):
-        args = ["-DENABLE_TESTING=0", "-DTARGET_CNL=1",
-                "-DBUILD_SHARED_STATIC=STATIC"]
+        args = ["-DTARGET_CNL=1"]
+        if self.spec.satisfies('@1.5:'):
+            args.append("-DBUILD_SHARED_LIBS=OFF")
+        else:
+            args.append("-DENABLE_BUILD_STATIC=STATIC")
+
+        if self.run_tests:
+            args.append('-DENABLE_TESTING=0')
+        else:
+            args.append('-DENABLE_TESTING=0')
+
         return args
diff --git a/var/spack/repos/builtin/packages/libfontenc/package.py b/var/spack/repos/builtin/packages/libfontenc/package.py
index c5bc0478b2..579cbf3f9d 100644
--- a/var/spack/repos/builtin/packages/libfontenc/package.py
+++ b/var/spack/repos/builtin/packages/libfontenc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Libfontenc(AutotoolsPackage):
     depends_on('zlib')
 
     depends_on('xproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libfs/package.py b/var/spack/repos/builtin/packages/libfs/package.py
index 95d5708d2f..ace282f7fb 100644
--- a/var/spack/repos/builtin/packages/libfs/package.py
+++ b/var/spack/repos/builtin/packages/libfs/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Libfs(AutotoolsPackage):
     depends_on('xproto@7.0.17:', type='build')
     depends_on('fontsproto', type='build')
     depends_on('xtrans', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libgcrypt/package.py b/var/spack/repos/builtin/packages/libgcrypt/package.py
index 053f62f9fc..dbc4bf5022 100644
--- a/var/spack/repos/builtin/packages/libgcrypt/package.py
+++ b/var/spack/repos/builtin/packages/libgcrypt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,8 +13,9 @@ class Libgcrypt(AutotoolsPackage):
        key algorithms, large integer functions, random numbers and a lot
        of supporting functions. """
     homepage = "http://www.gnu.org/software/libgcrypt/"
-    url = "https://gnupg.org/ftp/gcrypt/libgcrypt/libgcrypt-1.7.6.tar.bz2"
+    url = "https://gnupg.org/ftp/gcrypt/libgcrypt/libgcrypt-1.8.1.tar.bz2"
 
+    version('1.8.1', 'b21817f9d850064d2177285f1073ec55')
     version('1.7.6', '54e180679a7ae4d090f8689ca32b654c')
     version('1.6.2', 'b54395a93cb1e57619943c082da09d5f')
 
diff --git a/var/spack/repos/builtin/packages/libgd/package.py b/var/spack/repos/builtin/packages/libgd/package.py
index 22eb66d1c3..89178e649a 100644
--- a/var/spack/repos/builtin/packages/libgd/package.py
+++ b/var/spack/repos/builtin/packages/libgd/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -50,7 +31,7 @@ class Libgd(AutotoolsPackage):
     depends_on('libtool', type='build')
     depends_on('m4', type='build')
     depends_on('gettext', type='build')
-    depends_on('pkg-config', type='build')
+    depends_on('pkgconfig', type='build')
 
     depends_on('libiconv')
     depends_on('libpng')
diff --git a/var/spack/repos/builtin/packages/libgeotiff/package.py b/var/spack/repos/builtin/packages/libgeotiff/package.py
new file mode 100644
index 0000000000..e7a76d2eec
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libgeotiff/package.py
@@ -0,0 +1,51 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Libgeotiff(AutotoolsPackage):
+    """GeoTIFF represents an effort by over 160 different remote sensing, GIS,
+    cartographic, and surveying related companies and organizations to
+    establish a TIFF based interchange format for georeferenced raster imagery.
+    """
+
+    homepage = "https://trac.osgeo.org/geotiff/"
+    url      = "http://download.osgeo.org/geotiff/libgeotiff/libgeotiff-1.4.2.tar.gz"
+
+    version('1.4.2', '96ab80e0d4eff7820579957245d844f8')
+
+    variant('zlib', default=True, description='Include zlib support')
+    variant('jpeg', default=True, description='Include jpeg support')
+    variant('proj', default=True, description='Use PROJ.4 library')
+
+    depends_on('zlib', when='+zlib')
+    depends_on('jpeg', when='+jpeg')
+    depends_on('libtiff')
+    depends_on('proj', when='+proj')
+
+    def configure_args(self):
+        spec = self.spec
+
+        args = [
+            '--with-libtiff={0}'.format(spec['libtiff'].prefix),
+        ]
+
+        if '+zlib' in spec:
+            args.append('--with-zlib={0}'.format(spec['zlib'].prefix))
+        else:
+            args.append('--with-zlib=no')
+
+        if '+jpeg' in spec:
+            args.append('--with-jpeg={0}'.format(spec['jpeg'].prefix))
+        else:
+            args.append('--with-jpeg=no')
+
+        if '+proj' in spec:
+            args.append('--with-proj={0}'.format(spec['proj'].prefix))
+        else:
+            args.append('--with-proj=no')
+
+        return args
diff --git a/var/spack/repos/builtin/packages/libgit2/package.py b/var/spack/repos/builtin/packages/libgit2/package.py
index 9ea82790ac..dfeecb1918 100644
--- a/var/spack/repos/builtin/packages/libgit2/package.py
+++ b/var/spack/repos/builtin/packages/libgit2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,6 +16,7 @@ class Libgit2(CMakePackage):
     homepage = "https://libgit2.github.com/"
     url      = "https://github.com/libgit2/libgit2/archive/v0.24.2.tar.gz"
 
+    version('0.26.0', '6ea75a8a5745a7b2a14d3ed94486e761')
     version('0.24.2', '735661b5b73e3c120d13e2bae21e49b3')
 
     depends_on('cmake@2.8:', type='build')
diff --git a/var/spack/repos/builtin/packages/libgpg-error/package.py b/var/spack/repos/builtin/packages/libgpg-error/package.py
index ea97c9e13e..e094fbf4dc 100644
--- a/var/spack/repos/builtin/packages/libgpg-error/package.py
+++ b/var/spack/repos/builtin/packages/libgpg-error/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libgpuarray/package.py b/var/spack/repos/builtin/packages/libgpuarray/package.py
index 3bc1100c81..a9a40b8312 100644
--- a/var/spack/repos/builtin/packages/libgpuarray/package.py
+++ b/var/spack/repos/builtin/packages/libgpuarray/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,11 +14,17 @@ class Libgpuarray(CMakePackage):
     homepage = "http://deeplearning.net/software/libgpuarray/"
     url      = "https://github.com/Theano/libgpuarray/archive/v0.6.1.tar.gz"
 
+    version('0.7.5', '2534011464555c3e99d14231db965c20')
+    version('0.7.4', '19f57cd381175162048c8154f5251546')
+    version('0.7.3', 'cb44aeb8482330974abdb36b0a477e5d')
+    version('0.7.2', '0f9d7748501bc5c71bf04aae2285ac4e')
+    version('0.7.1', '7eb5bb6689ddbc386a9d498f5c0027fb')
+    version('0.7.0', 'f71b066f21ef7666f3a851e96c26f52e')
+    version('0.6.9', '7f75c39f1436c920ed9c5ffde5631fc0')
     version('0.6.2', '7f163bd5f48f399cd6e608ee3d528ee4')
     version('0.6.1', 'cfcd1b54447f9d55b05514df62c70ae2')
     version('0.6.0', '98a4ec1b4c8f225f0b89c18b899a000b')
 
     depends_on('cuda')
     depends_on('cmake@3:', type='build')
-
-    extends('python')
+    depends_on('libcheck')
diff --git a/var/spack/repos/builtin/packages/libgridxc/package.py b/var/spack/repos/builtin/packages/libgridxc/package.py
new file mode 100644
index 0000000000..a4d7d3ccdf
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libgridxc/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Libgridxc(Package):
+    """A library to compute the exchange and correlation energy and potential
+       in spherical (i.e. an atom) or periodic systems."""
+
+    homepage = "https://launchpad.net/libgridxc"
+    url      = "https://launchpad.net/libgridxc/trunk/0.7/+download/libgridxc-0.7.6.tgz"
+
+    version('0.7.6', 'a593f845d7565a168f1cf515a0a89879')
+
+    phases = ['configure', 'install']
+
+    def configure(self, spec, prefix):
+        sh = which('sh')
+        with working_dir('build', create=True):
+            sh('../src/config.sh')
+            copy('../extra/fortran.mk', 'fortran.mk')
+
+    def install(self, spec, prefix):
+        with working_dir('build'):
+            make('PREFIX=%s' % self.prefix, 'FC=fc')
diff --git a/var/spack/repos/builtin/packages/libgtextutils/package.py b/var/spack/repos/builtin/packages/libgtextutils/package.py
index be6759e91e..535bb7694e 100644
--- a/var/spack/repos/builtin/packages/libgtextutils/package.py
+++ b/var/spack/repos/builtin/packages/libgtextutils/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libharu/package.py b/var/spack/repos/builtin/packages/libharu/package.py
index 3542582df8..9193de7e96 100644
--- a/var/spack/repos/builtin/packages/libharu/package.py
+++ b/var/spack/repos/builtin/packages/libharu/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
@@ -34,11 +15,17 @@ class Libharu(AutotoolsPackage):
 
     homepage = "http://libharu.org"
     url      = "https://github.com/libharu/libharu/archive/RELEASE_2_3_0.tar.gz"
+    git      = "https://github.com/libharu/libharu.git"
 
+    version('master', branch='master')
     version('2.3.0', '4f916aa49c3069b3a10850013c507460')
     version('2.2.0', 'b65a6fc33a0bdad89bec6b7def101f01')
-    version('master', branch='master',
-            git='https://github.com/libharu/libharu.git')
+
+    depends_on('libtool', type=('build'))
+    depends_on('autoconf', type=('build'))
+    depends_on('automake', type=('build'))
+    depends_on('libpng')
+    depends_on('zlib')
 
     def autoreconf(self, spec, prefix):
         """execute their autotools wrapper script"""
@@ -46,6 +33,16 @@ class Libharu(AutotoolsPackage):
             bash = which('bash')
             bash('./buildconf.sh', '--force')
 
+    def configure_args(self):
+        """Point to spack-installed zlib and libpng"""
+        spec = self.spec
+        args = []
+
+        args.append('--with-zlib={0}'.format(spec['zlib'].prefix))
+        args.append('--with-png={0}'.format(spec['libpng'].prefix))
+
+        return args
+
     def url_for_version(self, version):
         url = 'https://github.com/libharu/libharu/archive/RELEASE_{0}.tar.gz'
         return url.format(version.underscored)
diff --git a/var/spack/repos/builtin/packages/libhio/0001-configury-fix-a-problem-with-bz2-configury.patch b/var/spack/repos/builtin/packages/libhio/0001-configury-fix-a-problem-with-bz2-configury.patch
new file mode 100644
index 0000000000..b5cf61bdc6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libhio/0001-configury-fix-a-problem-with-bz2-configury.patch
@@ -0,0 +1,38 @@
+From 3a7b7432a7354661d0a971b074c30529f5db457c Mon Sep 17 00:00:00 2001
+From: Howard Pritchard <howardp@lanl.gov>
+Date: Sat, 10 Mar 2018 13:51:41 -0800
+Subject: [PATCH] configury: fix a problem with bz2 configury
+
+turns out by default spack wants to use a non-default
+location bz2, or we have to turn it off.  either way
+the bz2 configury is wrong and needs to be fixed.
+
+Signed-off-by: Howard Pritchard <howardp@lanl.gov>
+
+diff --git a/m4/hio_check_bz2.m4 b/m4/hio_check_bz2.m4
+index 3a373ad1..b7dfdb75 100644
+--- a/m4/hio_check_bz2.m4
++++ b/m4/hio_check_bz2.m4
+@@ -1,9 +1,9 @@
+ # -*- mode: shell-script -*-
+-# Copyright 2015-2016 Los Alamos National Security, LLC. All rights
++# Copyright 2015-2018 Los Alamos National Security, LLC. All rights
+ #                     reserved.
+ 
+ AC_DEFUN([HIO_CHECK_BZ2],[
+-    AC_ARG_WITH(bz2, [AS_HELP_STRING([--with-external-bz2=PATH],
++    AC_ARG_WITH(external-bz2, [AS_HELP_STRING([--with-external_bz2=PATH],
+                                      [use external bzip2. pass yes to use default version @<:@default=no@:>@])],
+                 [], [with_external_bz2=no])
+ 
+@@ -14,6 +14,7 @@ AC_DEFUN([HIO_CHECK_BZ2],[
+             else
+                 LDFLAGS="$LDFLAGS -L$with_external_bz2/lib64"
+             fi
++            LIBS="$LIBS -lbz2"
+         fi
+ 
+         AC_CHECK_LIB([bz2],[BZ2_bzBuffToBuffCompress],[hio_have_bz2=1])
+-- 
+2.4.0.rc3.16.g0ab00b9
+
diff --git a/var/spack/repos/builtin/packages/libhio/0001-hdf5-make-docs-optional.patch b/var/spack/repos/builtin/packages/libhio/0001-hdf5-make-docs-optional.patch
new file mode 100644
index 0000000000..588edec602
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libhio/0001-hdf5-make-docs-optional.patch
@@ -0,0 +1,37 @@
+From 6aec1b94fe84f2fe3a82e3ff338fd4721c84db34 Mon Sep 17 00:00:00 2001
+From: Howard Pritchard <howardp@lanl.gov>
+Date: Mon, 12 Mar 2018 14:19:28 -0700
+Subject: [PATCH] hdf5: make docs optional
+
+With the current makefile, configuring in hdf5
+hio plugin always ends up trying to generate docs.
+Make generating hdf5/hio plugin docs optional with
+
+make docs
+
+Signed-off-by: Howard Pritchard <howardp@lanl.gov>
+
+diff --git a/hdf5-hio/Makefile.am b/hdf5-hio/Makefile.am
+index e4c93b77..1733866d 100644
+--- a/hdf5-hio/Makefile.am
++++ b/hdf5-hio/Makefile.am
+@@ -1,6 +1,6 @@
+ # -*- Makefile.am -*-
+ #
+-# Copyright (c) 2014-2016 Los Alamos National Security, LLC. All rights
++# Copyright (c) 2014-2018 Los Alamos National Security, LLC. All rights
+ #                         reserved.
+ # $COPYRIGHT$
+ #
+@@ -11,7 +11,7 @@
+ 
+ ACLOCAL_AMFLAGS=-I m4
+ 
+-SUBDIRS = src test doc
++SUBDIRS = src test
+ 
+ EXTRA_DIST =
+ DISTCLEANFILES =
+-- 
+2.4.0.rc3.16.g0ab00b9
+
diff --git a/var/spack/repos/builtin/packages/libhio/0001-spack-fix-for-spack-to-work-on-non-cray-systems.patch b/var/spack/repos/builtin/packages/libhio/0001-spack-fix-for-spack-to-work-on-non-cray-systems.patch
new file mode 100644
index 0000000000..f9b8b8e163
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libhio/0001-spack-fix-for-spack-to-work-on-non-cray-systems.patch
@@ -0,0 +1,31 @@
+From f6f806c2ea46866c9490d2d2ddc3f119666d26d4 Mon Sep 17 00:00:00 2001
+From: Howard Pritchard <hppritcha@gmail.com>
+Date: Mon, 17 Sep 2018 05:05:01 -0600
+Subject: [PATCH] spack: fix for spack to work on non-cray systems
+
+or when one wants to use Open MPI on a cray system with spack.
+The problem is that when using an MPI with spack, its going to
+use a long value for the CC and CXX variables.  This confused
+the libhio configury, resulting in it being built without mpi
+support, leading to failure of xexec to properly compile, etc.
+
+This commit fixes that problem.
+
+Signed-off-by: Howard Pritchard <hppritcha@gmail.com>
+
+diff --git a/configure.ac b/configure.ac
+index afab5553..62d35c85 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -37,7 +37,7 @@ if ( test -n "$XTOS_VERSION" || test -n "$CRAYPE_DIR" ) && (test -z $CC || test
+     if test ! -n "$LD" ; then
+         LD=ld
+     fi
+-elif test ${MPICC} = "mpicc" ; then
++elif test -n "$MPICC" ; then
+     CC=${MPICC}
+     CXX=${MPICXX}
+     hio_use_mpi=1
+-- 
+1.8.3.1
+
diff --git a/var/spack/repos/builtin/packages/libhio/package.py b/var/spack/repos/builtin/packages/libhio/package.py
index db74e7c546..64224b6528 100644
--- a/var/spack/repos/builtin/packages/libhio/package.py
+++ b/var/spack/repos/builtin/packages/libhio/package.py
@@ -1,40 +1,62 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
 from spack import *
 
 
 class Libhio(AutotoolsPackage):
-    """
-    A library for writing to hierarchical data store systems.
+    """libHIO is a flexible, high-performance parallel IO package developed
+       at LANL.  libHIO supports IO to either a conventional PFS or to Cray
+       DataWarp with management of Cray DataWarp space and stage-in and
+       stage-out from and to the PFS.
     """
 
-    homepage = "https://github.com/hpc/libhio/"
-    url      = "https://github.com/hpc/libhio/releases/download/hio.1.3.0.1/libhio-1.3.0.1.tar.gz"
+    homepage = "https://github.com/hpc/libhio"
+    url      = "https://github.com/hpc/libhio/releases/download/hio.1.4.1.0/libhio-1.4.1.0.tar.bz2"
 
-    version('1.3.0.1', 'c073541de8dd70aeb8878bd00d6d877f')
+    #
+    # We don't include older versions since they are missing features
+    # needed by current and future consumers of libhio
+    #
+    version('1.4.1.2', '38c7d33210155e5796b16d536d1b5cfe')
+    version('1.4.1.0', '6ef566fd8cf31fdcd05fab01dd3fae44')
+
+    #
+    # main users of libhio thru spack will want to use HFDF5 plugin,
+    # so make hdf5 variant a default
+    #
+    variant('hdf5', default=True, description='Enable HDF5 support')
 
     depends_on("json-c")
     depends_on("bzip2")
-    depends_on("pkg-config", type="build")
+    depends_on("pkgconfig", type="build")
+    depends_on('mpi')
+
+    #
+    # libhio depends on hdf5+mpi if hdf5 is being used since it
+    # autodetects the presence of an MPI and/or uses mpicc by default to build
+    depends_on('hdf5+mpi', when='+hdf5')
+
+    #
+    # wow, we need to patch libhio
+    #
+    patch('0001-configury-fix-a-problem-with-bz2-configury.patch', when="@1.4.1.0")
+    patch('0001-hdf5-make-docs-optional.patch', when="@1.4.1.0")
+    patch('0001-spack-fix-for-spack-to-work-on-non-cray-systems.patch', when="@1.4.1.2")
+
+    def autoreconf(self, spec, prefix):
+        autoreconf = which('autoreconf')
+        autoreconf('-ifv')
+
+    def configure_args(self):
+        spec = self.spec
+        args = []
+
+        args.append('--with-external_bz2={0}'.format(spec['bzip2'].prefix))
+        if '+hdf5' in spec:
+            args.append('--with-hdf5={0}'.format(spec['hdf5'].prefix))
+
+        return args
diff --git a/var/spack/repos/builtin/packages/libiberty/package.py b/var/spack/repos/builtin/packages/libiberty/package.py
new file mode 100644
index 0000000000..166979d30c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libiberty/package.py
@@ -0,0 +1,54 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+# Libiberty has two homes: binutils and gcc.  This package uses the
+# binutils tarfile but only builds the libiberty subdirectory.  This
+# is useful for other packages that want the demangling functions
+# without the rest of binutils.
+
+class Libiberty(AutotoolsPackage):
+    """The libiberty.a library from GNU binutils.  Libiberty provides
+    demangling and support functions for the GNU toolchain."""
+
+    homepage = "https://www.gnu.org/software/binutils/"
+    url      = "https://ftpmirror.gnu.org/binutils/binutils-2.31.1.tar.xz"
+
+    version('2.31.1', '5b7c9d4ce96f507d95c1b9a255e52418')
+    version('2.30',   'ffc476dd46c96f932875d1b2e27e929f')
+    version('2.29.1', 'acc9cd826edb9954ac7cecb81c727793')
+    version('2.28.1', 'a3bf359889e4b299fce1f4cb919dc7b6')
+
+    variant('pic', default=False,
+            description='Compile with position independent code.')
+
+    # Configure and build just libiberty.
+    configure_directory = 'libiberty'
+
+    # Set default cflags (-g -O2), add -fPIC if requested, and move to
+    # the configure line.
+    def flag_handler(self, name, flags):
+        if name != 'cflags':
+            return (flags, None, None)
+
+        if '-g' not in flags:
+            flags.append('-g')
+
+        for flag in flags:
+            if flag.startswith('-O'):
+                break
+        else:
+            flags.append('-O2')
+
+        if '+pic' in self.spec:
+            flags.append(self.compiler.pic_flag)
+
+        return (None, None, flags)
+
+    def configure_args(self):
+        args = ['--enable-install-libiberty']
+        return args
diff --git a/var/spack/repos/builtin/packages/libice/package.py b/var/spack/repos/builtin/packages/libice/package.py
index 4ffc67ed9c..501fe81677 100644
--- a/var/spack/repos/builtin/packages/libice/package.py
+++ b/var/spack/repos/builtin/packages/libice/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,5 +16,5 @@ class Libice(AutotoolsPackage):
 
     depends_on('xproto', type='build')
     depends_on('xtrans', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libiconv/package.py b/var/spack/repos/builtin/packages/libiconv/package.py
index 1e3d29a4df..b435f19f1e 100644
--- a/var/spack/repos/builtin/packages/libiconv/package.py
+++ b/var/spack/repos/builtin/packages/libiconv/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-import shutil
 
 
 class Libiconv(AutotoolsPackage):
@@ -31,7 +11,7 @@ class Libiconv(AutotoolsPackage):
     and the iconv program for character set conversion."""
 
     homepage = "https://www.gnu.org/software/libiconv/"
-    url      = "http://ftp.gnu.org/pub/gnu/libiconv/libiconv-1.15.tar.gz"
+    url      = "https://ftpmirror.gnu.org/libiconv/libiconv-1.15.tar.gz"
 
     version('1.15', 'ace8b5f2db42f7b3b3057585e80d9808')
     version('1.14', 'e34509b1623cec449dfeb73d7ce9c6c6')
@@ -40,10 +20,12 @@ class Libiconv(AutotoolsPackage):
     # of C11 any more and thus might not exist.
     patch('gets.patch', when='@1.14')
 
+    conflicts('@1.14', when='%gcc@5:')
+
     def configure_args(self):
         args = ['--enable-extra-encodings']
 
         # A hack to patch config.guess in the libcharset sub directory
-        shutil.copyfile('./build-aux/config.guess',
-                        'libcharset/build-aux/config.guess')
+        copy('./build-aux/config.guess',
+             'libcharset/build-aux/config.guess')
         return args
diff --git a/var/spack/repos/builtin/packages/libint/package.py b/var/spack/repos/builtin/packages/libint/package.py
index 8fa0906658..1ea8031dec 100644
--- a/var/spack/repos/builtin/packages/libint/package.py
+++ b/var/spack/repos/builtin/packages/libint/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -64,11 +45,10 @@ class Libint(AutotoolsPackage):
     @property
     def optflags(self):
         flags = '-O2'
-
         # Optimizations for the Intel compiler, suggested by CP2K
+        # See ../libxc/package.py for rationale and doc.
         if '%intel' in self.spec:
-            # -xSSE2 will make it usable on old architecture
-            flags += ' -xSSE2 -xAVX -axCORE-AVX2 -ipo'
+            flags += ' -xSSE4.2 -axAVX,CORE-AVX2 -ipo'
 
         return flags
 
diff --git a/var/spack/repos/builtin/packages/libjpeg-turbo/package.py b/var/spack/repos/builtin/packages/libjpeg-turbo/package.py
index 2264147362..e57b8b84d2 100644
--- a/var/spack/repos/builtin/packages/libjpeg-turbo/package.py
+++ b/var/spack/repos/builtin/packages/libjpeg-turbo/package.py
@@ -1,41 +1,24 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class LibjpegTurbo(AutotoolsPackage):
+class LibjpegTurbo(Package):
     """libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to
        accelerate baseline JPEG compression and decompression. libjpeg is a
        library that implements JPEG image encoding, decoding and
        transcoding."""
+    # https://github.com/libjpeg-turbo/libjpeg-turbo/blob/master/BUILDING.md
+    homepage = "https://libjpeg-turbo.org/"
+    url      = "https://github.com/libjpeg-turbo/libjpeg-turbo/archive/1.5.90.tar.gz"
 
-    homepage = "http://libjpeg-turbo.virtualgl.org"
-    url      = "http://downloads.sourceforge.net/libjpeg-turbo/libjpeg-turbo-1.3.1.tar.gz"
-
-    version('1.5.0', '3fc5d9b6a8bce96161659ae7a9939257')
-    version('1.3.1', '2c3a68129dac443a72815ff5bb374b05')
+    version('1.5.90', '85f7f9c377b70cbf48e61726097d4efa')
+    version('1.5.3', '5b7549d440b86c98a517355c102d155e')
+    version('1.5.0', 'eff98ac84de05eafc65ae96caa6e23e9')
+    version('1.3.1', '5e4bc19c3cb602bcab1296b9bee5124c')
 
     provides('jpeg')
 
@@ -45,3 +28,27 @@ class LibjpegTurbo(AutotoolsPackage):
     # TODO: Implement the selection between two supported assemblers.
     # depends_on("yasm", type='build')
     depends_on("nasm", type='build')
+    depends_on('autoconf', type='build', when="@1.3.1:1.5.3")
+    depends_on('automake', type='build', when="@1.3.1:1.5.3")
+    depends_on('libtool', type='build', when="@1.3.1:1.5.3")
+    depends_on('cmake', type='build', when="@1.5.90:")
+
+    @property
+    def libs(self):
+        return find_libraries("libjpeg*", root=self.prefix, recursive=True)
+
+    @when('@1.3.1:1.5.3')
+    def install(self, spec, prefix):
+        autoreconf('-ifv')
+        configure('--prefix=%s' % prefix)
+        make()
+        make('install')
+
+    @when('@1.5.90:')
+    def install(self, spec, prefix):
+        cmake_args = ['-GUnix Makefiles']
+        cmake_args.extend(std_cmake_args)
+        with working_dir('spack-build', create=True):
+            cmake('..', *cmake_args)
+            make()
+            make('install')
diff --git a/var/spack/repos/builtin/packages/libjpeg/package.py b/var/spack/repos/builtin/packages/libjpeg/package.py
index bd789200cb..908b6f6bea 100644
--- a/var/spack/repos/builtin/packages/libjpeg/package.py
+++ b/var/spack/repos/builtin/packages/libjpeg/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,9 +12,15 @@ class Libjpeg(AutotoolsPackage):
     alongside various utilities for handling JPEG data."""
 
     homepage = "http://www.ijg.org"
-    url      = "http://www.ijg.org/files/jpegsrc.v9b.tar.gz"
+    url      = "http://www.ijg.org/files/jpegsrc.v9c.tar.gz"
 
+    version('9c', '93c62597eeef81a84d988bccbda1e990')
     version('9b', '6a9996ce116ec5c52b4870dbcd6d3ddb')
     version('9a', '3353992aecaee1805ef4109aadd433e7')
 
     provides('jpeg')
+
+    def check(self):
+        # Libjpeg has both 'check' and 'test' targets that are aliases.
+        # Only need to run the tests once.
+        make('check')
diff --git a/var/spack/repos/builtin/packages/libksba/package.py b/var/spack/repos/builtin/packages/libksba/package.py
index a9f498e3d3..48be52968f 100644
--- a/var/spack/repos/builtin/packages/libksba/package.py
+++ b/var/spack/repos/builtin/packages/libksba/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/liblbxutil/package.py b/var/spack/repos/builtin/packages/liblbxutil/package.py
index 90be9b3cdd..32c49195d3 100644
--- a/var/spack/repos/builtin/packages/liblbxutil/package.py
+++ b/var/spack/repos/builtin/packages/liblbxutil/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,7 +16,7 @@ class Liblbxutil(AutotoolsPackage):
 
     depends_on('xextproto@7.0.99.1:', type='build')
     depends_on('xproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     # There is a bug in the library that causes the following messages:
diff --git a/var/spack/repos/builtin/packages/liblockfile/install_as_nonroot.patch b/var/spack/repos/builtin/packages/liblockfile/install_as_nonroot.patch
new file mode 100644
index 0000000000..66c6f994eb
--- /dev/null
+++ b/var/spack/repos/builtin/packages/liblockfile/install_as_nonroot.patch
@@ -0,0 +1,46 @@
+--- liblockfile-1.14/Makefile.in	2017-01-17 13:21:05.000000000 +0000
++++ liblockfile-1.14/Makefile.in	2018-03-28 07:20:45.054312625 +0000
+@@ -49,35 +49,33 @@ xlockfile.o:	lockfile.c
+ 		$(CC) $(CFLAGS) -c lockfile.c -o xlockfile.o
+ 
+ install_static:	static install_common
+-		install -d -m 755 -g root -p $(libdir)
++		install -d -m 755 -p $(libdir)
+ 		install -m 644 liblockfile.a $(libdir)
+ 
+ install_shared:	shared install_static install_common
+-		install -d -m 755 -g root -p $(libdir)
++		install -d -m 755 -p $(libdir)
+ 		install -m 755 liblockfile.so \
+ 			$(libdir)/liblockfile.so.$(SOVER)
+ 		ln -s liblockfile.so.$(SOVER) $(libdir)/liblockfile.so.$(MAJOR)
+ 		ln -s liblockfile.so.$(SOVER) $(libdir)/liblockfile.so
+-		if test "$(DESTDIR)" = ""; then @LDCONFIG@; fi
+ 
+ install_common:
+-		install -d -m 755 -g root -p $(includedir)
+-		install -d -m 755 -g root -p $(bindir)
+-		install -d -m 755 -g root -p $(mandir)/man1
+-		install -d -m 755 -g root -p $(mandir)/man3
++		install -d -m 755 -p $(includedir)
++		install -d -m 755 -p $(bindir)
++		install -d -m 755 -p $(mandir)/man1
++		install -d -m 755 -p $(mandir)/man3
+ 		install -m 644 lockfile.h maillock.h $(includedir)
+ 		if [ "$(MAILGROUP)" != "" ]; then\
+ 		  install -g $(MAILGROUP) -m 2755 dotlockfile $(bindir);\
+ 		else \
+-		  install -g root -m 755 dotlockfile $(bindir); \
++		  install -m 755 dotlockfile $(bindir); \
+ 		fi
+ 		install -m 644 *.1 $(mandir)/man1
+ 		install -m 644 *.3 $(mandir)/man3
+ 
+ install_nfslib:	nfslib
+-		install -d -m 755 -g root -p $(nfslockdir)
++		install -d -m 755 -p $(nfslockdir)
+ 		install -m 755 nfslock.so.$(NFSVER) $(nfslockdir)
+-		if test "$(DESTDIR)" = ""; then @LDCONFIG@; fi
+ 
+ clean:
+ 		rm -f *.a *.o *.so *.so.* dotlockfile
diff --git a/var/spack/repos/builtin/packages/liblockfile/package.py b/var/spack/repos/builtin/packages/liblockfile/package.py
new file mode 100644
index 0000000000..1598a026a2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/liblockfile/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Liblockfile(AutotoolsPackage):
+    """NFS-safe locking library"""
+
+    homepage = "https://github.com/miquels/liblockfile"
+    url      = "https://github.com/miquels/liblockfile/archive/v1.14.tar.gz"
+
+    version('1.14', '24ce9dbb34d7f508a52a91f762746ce3')
+
+    patch('install_as_nonroot.patch')
+
+    def configure_args(self):
+        args = ['--enable-shared']
+        return args
diff --git a/var/spack/repos/builtin/packages/libmatheval/guile-2.0.patch b/var/spack/repos/builtin/packages/libmatheval/guile-2.0.patch
new file mode 100644
index 0000000000..18bacb44ca
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libmatheval/guile-2.0.patch
@@ -0,0 +1,197 @@
+--- libmatheval-1.1.11-v/configure	2018-07-13 11:16:19.115719477 +0200
++++ libmatheval-1.1.11/configure	2018-07-13 11:33:07.914093005 +0200
+@@ -640,6 +640,7 @@
+ GUILE_CFLAGS
+ GUILE_TOOLS
+ GUILE_CONFIG
++GUILE_EFFECTIVE_VERSION
+ GUILE
+ AUTOM4TE
+ YFLAGS
+@@ -4831,21 +4832,6 @@
+ 
+ 
+ 
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+ # Check whether --with-gnu-ld was given.
+ if test "${with_gnu_ld+set}" = set; then :
+   withval=$with_gnu_ld; test "$withval" = no || with_gnu_ld=yes
+@@ -12267,8 +12253,9 @@
+  break
+ fi
+ done
++# start patch
+ 
+-
++CPPFLAGS="$GUILE_CFLAGS  -DSCM_ENABLE_DEPRECATED=0 $CPPFLAGS"
+ ac_fn_c_check_type "$LINENO" "scm_t_bits" "ac_cv_type_scm_t_bits" "#include <libguile.h>
+ "
+ if test "x$ac_cv_type_scm_t_bits" = xyes; then :
+@@ -12276,14 +12263,15 @@
+ $as_echo "#define HAVE_SCM_T_BITS 1" >>confdefs.h
+ 
+ fi
+-
+-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for scm_c_define_gsubr in -lguile" >&5
+-$as_echo_n "checking for scm_c_define_gsubr in -lguile... " >&6; }
+-if ${ac_cv_lib_guile_scm_c_define_gsubr+:} false; then :
++GUILE_EFFECTIVE_VERSION=2.0
++as_ac_Lib=`$as_echo "ac_cv_lib_guile-$GUILE_EFFECTIVE_VERSION''_scm_c_define_gsubr" | $as_tr_sh`
++{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for scm_c_define_gsubr in -lguile-$GUILE_EFFECTIVE_VERSION" >&5
++$as_echo_n "checking for scm_c_define_gsubr in -lguile-$GUILE_EFFECTIVE_VERSION... " >&6; }
++if eval \${$as_ac_Lib+:} false; then :
+   $as_echo_n "(cached) " >&6
+ else
+   ac_check_lib_save_LIBS=$LIBS
+-LIBS="-lguile $GUILE_LDFLAGS $LIBS"
++LIBS="-lguile-$GUILE_EFFECTIVE_VERSION $GUILE_LDFLAGS $LIBS"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ /* end confdefs.h.  */
+ 
+@@ -12303,29 +12291,31 @@
+ }
+ _ACEOF
+ if ac_fn_c_try_link "$LINENO"; then :
+-  ac_cv_lib_guile_scm_c_define_gsubr=yes
++  eval "$as_ac_Lib=yes"
+ else
+-  ac_cv_lib_guile_scm_c_define_gsubr=no
++  eval "$as_ac_Lib=no"
+ fi
+ rm -f core conftest.err conftest.$ac_objext \
+     conftest$ac_exeext conftest.$ac_ext
+ LIBS=$ac_check_lib_save_LIBS
+ fi
+-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_guile_scm_c_define_gsubr" >&5
+-$as_echo "$ac_cv_lib_guile_scm_c_define_gsubr" >&6; }
+-if test "x$ac_cv_lib_guile_scm_c_define_gsubr" = xyes; then :
++eval ac_res=\$$as_ac_Lib
++	       { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
++$as_echo "$ac_res" >&6; }
++if eval test \"x\$"$as_ac_Lib"\" = x"yes"; then :
+ 
+ $as_echo "#define HAVE_SCM_C_DEFINE_GSUBR 1" >>confdefs.h
+ 
+ fi
+ 
+-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for scm_make_gsubr in -lguile" >&5
+-$as_echo_n "checking for scm_make_gsubr in -lguile... " >&6; }
+-if ${ac_cv_lib_guile_scm_make_gsubr+:} false; then :
++as_ac_Lib=`$as_echo "ac_cv_lib_guile-$GUILE_EFFECTIVE_VERSION''_scm_make_gsubr" | $as_tr_sh`
++{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for scm_make_gsubr in -lguile-$GUILE_EFFECTIVE_VERSION" >&5
++$as_echo_n "checking for scm_make_gsubr in -lguile-$GUILE_EFFECTIVE_VERSION... " >&6; }
++if eval \${$as_ac_Lib+:} false; then :
+   $as_echo_n "(cached) " >&6
+ else
+   ac_check_lib_save_LIBS=$LIBS
+-LIBS="-lguile $GUILE_LDFLAGS $LIBS"
++LIBS="-lguile-$GUILE_EFFECTIVE_VERSION $GUILE_LDFLAGS $LIBS"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ /* end confdefs.h.  */
+ 
+@@ -12345,29 +12335,31 @@
+ }
+ _ACEOF
+ if ac_fn_c_try_link "$LINENO"; then :
+-  ac_cv_lib_guile_scm_make_gsubr=yes
++  eval "$as_ac_Lib=yes"
+ else
+-  ac_cv_lib_guile_scm_make_gsubr=no
++  eval "$as_ac_Lib=no"
+ fi
+ rm -f core conftest.err conftest.$ac_objext \
+     conftest$ac_exeext conftest.$ac_ext
+ LIBS=$ac_check_lib_save_LIBS
+ fi
+-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_guile_scm_make_gsubr" >&5
+-$as_echo "$ac_cv_lib_guile_scm_make_gsubr" >&6; }
+-if test "x$ac_cv_lib_guile_scm_make_gsubr" = xyes; then :
++eval ac_res=\$$as_ac_Lib
++	       { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
++$as_echo "$ac_res" >&6; }
++if eval test \"x\$"$as_ac_Lib"\" = x"yes"; then :
+ 
+ $as_echo "#define HAVE_SCM_MAKE_GSUBR 1" >>confdefs.h
+ 
+ fi
+ 
+-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for scm_num2dbl in -lguile" >&5
+-$as_echo_n "checking for scm_num2dbl in -lguile... " >&6; }
+-if ${ac_cv_lib_guile_scm_num2dbl+:} false; then :
++as_ac_Lib=`$as_echo "ac_cv_lib_guile-$GUILE_EFFECTIVE_VERSION''_scm_num2dbl" | $as_tr_sh`
++{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for scm_num2dbl in -lguile-$GUILE_EFFECTIVE_VERSION" >&5
++$as_echo_n "checking for scm_num2dbl in -lguile-$GUILE_EFFECTIVE_VERSION... " >&6; }
++if eval \${$as_ac_Lib+:} false; then :
+   $as_echo_n "(cached) " >&6
+ else
+   ac_check_lib_save_LIBS=$LIBS
+-LIBS="-lguile $GUILE_LDFLAGS $LIBS"
++LIBS="-lguile-$GUILE_EFFECTIVE_VERSION $GUILE_LDFLAGS $LIBS"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ /* end confdefs.h.  */
+ 
+@@ -12387,22 +12379,25 @@
+ }
+ _ACEOF
+ if ac_fn_c_try_link "$LINENO"; then :
+-  ac_cv_lib_guile_scm_num2dbl=yes
++  eval "$as_ac_Lib=yes"
+ else
+-  ac_cv_lib_guile_scm_num2dbl=no
++  eval "$as_ac_Lib=no"
+ fi
+ rm -f core conftest.err conftest.$ac_objext \
+     conftest$ac_exeext conftest.$ac_ext
+ LIBS=$ac_check_lib_save_LIBS
+ fi
+-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_guile_scm_num2dbl" >&5
+-$as_echo "$ac_cv_lib_guile_scm_num2dbl" >&6; }
+-if test "x$ac_cv_lib_guile_scm_num2dbl" = xyes; then :
++eval ac_res=\$$as_ac_Lib
++	       { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
++$as_echo "$ac_res" >&6; }
++if eval test \"x\$"$as_ac_Lib"\" = x"yes"; then :
+ 
+ $as_echo "#define HAVE_SCM_NUM2DBL 1" >>confdefs.h
+ 
+ fi
+ 
++# end patch
++# end patch
+ 
+ ac_config_files="$ac_config_files Makefile doc/Makefile lib/Makefile"
+ 
+--- libmatheval-1.1.11-v/tests/matheval.c.bak	2018-07-13 12:43:21.718862366 +0200
++++ libmatheval-1.1.11/tests/matheval.c	2018-07-13 12:46:34.162597100 +0200
+@@ -51,7 +51,7 @@
+ 
+ /* Guile interface for libmatheval library.  Procedures below are simple
+  * wrappers for corresponding libmatheval procedures. */
+-static scm_sizet evaluator_destroy_scm(SCM evaluator_smob);
++static size_t    evaluator_destroy_scm(SCM evaluator_smob);
+ static SCM      evaluator_create_scm(SCM string);
+ static SCM      evaluator_evaluate_scm(SCM evaluator_smob, SCM count,
+ 				       SCM names, SCM values);
+@@ -122,7 +122,7 @@
+ }
+ 
+ /* Wrapper for evaluator_destroy() procedure from libmatheval library. */
+-static          scm_sizet
++static          size_t
+ evaluator_destroy_scm(SCM evaluator_smob)
+ {
+ 	SCM_ASSERT((SCM_NIMP(evaluator_smob)
diff --git a/var/spack/repos/builtin/packages/libmatheval/guile-2.2.patch b/var/spack/repos/builtin/packages/libmatheval/guile-2.2.patch
new file mode 100644
index 0000000000..394f9ebdef
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libmatheval/guile-2.2.patch
@@ -0,0 +1,20 @@
+--- libmatheval-1.1.11/Makefile.in.orig	2018-07-13 17:42:03.426339145 +0200
++++ libmatheval-1.1.11/Makefile.in	2018-07-13 17:42:24.190310979 +0200
+@@ -316,7 +316,7 @@
+ MAINTAINERCLEANFILES = Makefile.in aclocal.m4 configure config.h.in	\
+ config.log config.status stamp-h.in $(AUX_DIST)
+ 
+-SUBDIRS = doc lib tests
++SUBDIRS = doc lib 
+ pkgconfigdir = $(libdir)/pkgconfig
+ pkgconfig_DATA = libmatheval.pc
+ all: config.h
+@@ -863,7 +863,7 @@
+ .PHONY: beauty dist-hook
+ 
+ beauty:
+-	-for dir in lib tests; do cd $$dir; $(MAKE) $@; cd ..; done
++	-for dir in lib ; do cd $$dir; $(MAKE) $@; cd ..; done
+ 
+ dist-hook:
+ 	for file in $(AUX_DIST); do \
diff --git a/var/spack/repos/builtin/packages/libmatheval/package.py b/var/spack/repos/builtin/packages/libmatheval/package.py
index f0992c4b42..da39d24515 100644
--- a/var/spack/repos/builtin/packages/libmatheval/package.py
+++ b/var/spack/repos/builtin/packages/libmatheval/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,9 +15,18 @@ class Libmatheval(AutotoolsPackage):
     compute symbolic derivatives and output expressions to strings."""
 
     homepage = "https://www.gnu.org/software/libmatheval/"
-    url      = "https://ftp.gnu.org/gnu/libmatheval/libmatheval-1.1.11.tar.gz"
+    url      = "https://ftpmirror.gnu.org/libmatheval/libmatheval-1.1.11.tar.gz"
 
     version('1.1.11', '595420ea60f6ddd75623847f46ca45c4')
 
     # Only needed for unit tests, but configure crashes without it
     depends_on('guile', type='build')
+
+    depends_on('flex')
+
+    # guile 2.0 provides a deprecated interface for the unit test using guile
+    patch('guile-2.0.patch', when='^guile@2.0')
+
+    # guile 2.2 does not support deprecated functions any longer
+    # the patch skips the unit tests
+    patch('guile-2.2.patch', when='^guile@2.2:')
diff --git a/var/spack/repos/builtin/packages/libmaxminddb/package.py b/var/spack/repos/builtin/packages/libmaxminddb/package.py
new file mode 100644
index 0000000000..abe154bb01
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libmaxminddb/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Libmaxminddb(AutotoolsPackage):
+    """C library for the MaxMind DB file format"""
+
+    homepage = "https://github.com/maxmind/libmaxminddb"
+    url      = "https://github.com/maxmind/libmaxminddb/releases/download/1.3.2/libmaxminddb-1.3.2.tar.gz"
+
+    version('1.3.2', '67a861965b30d045bf29a2126bcc05ed')
+
+    def configure_args(self):
+        args = ['--disable-debug',
+                '--disable-dependency-tracking',
+                '--disable-silent-rules']
+        return args
diff --git a/var/spack/repos/builtin/packages/libmesh/package.py b/var/spack/repos/builtin/packages/libmesh/package.py
index 20603a6589..d21e056b33 100644
--- a/var/spack/repos/builtin/packages/libmesh/package.py
+++ b/var/spack/repos/builtin/packages/libmesh/package.py
@@ -1,56 +1,212 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class Libmesh(Package):
+class Libmesh(AutotoolsPackage):
     """The libMesh library provides a framework for the numerical simulation of
        partial differential equations using arbitrary unstructured
        discretizations on serial and parallel platforms."""
 
     homepage = "http://libmesh.github.io/"
     url      = "https://github.com/libMesh/libmesh/releases/download/v1.0.0/libmesh-1.0.0.tar.bz2"
+    git      = "https://github.com/libMesh/libmesh.git"
 
+    version('1.3.0', sha256='a8cc2cd44f42b960989dba10fa438b04af5798c46db0b4ec3ed29591b8359786')
+    version('1.2.1', sha256='11c22c7d96874a17de6b8c74caa45d6745d40bf3610e88b2bd28fd3381f5ba70')
     version('1.0.0', 'cb464fc63ea0b71b1e69fa3f5d4f93a4')
 
+    # support for libraries that are only available through the bundled copies:
+    # TODO libMesh 1.2.1 gained the ability to specify a path to capnproto
+    variant('capnproto', default=False, description='Compile with the bundled capnproto serialization library')
+    variant('exodusii', default=False, description='Compile with the bundled ExodusII output library')
+    variant('fparser', default=False, description='Compile with the bundled fparser function parser library')
+    variant('gmv', default=False, description='Compile with the bundled gmv format IO library')
+    variant('laspack', default=False, description='Compile with the bundled laspack interative solver library')
+    variant('libhilbert', default=False, description='Compile with the bundled libHilbert partitioning library')
+    variant('metaphysicl', default=False, description='Compile with the bundled metaphysicl AD library')
+    variant('metis', default=False, description='Compile with the bundled METIS graph partitioning library')
+    variant('nanoflann', default=False, description='Compile with the bundled nanoflann graph library')
+    variant('nemesis', default=False, description='Compile with the bundled nemesis IO library')
+    variant('netcdf', default=False, description='Compile with the bundled NETCDF IO library')
+    # TODO the copy of parmetis bundled with libMesh assumes that we use the
+    # bundled copy of metis, but previous versions of this build script use an
+    # external metis installation. Be conservative and completely disable
+    # parmetis support to preserve the old behavior (and to prevent compiling
+    # with two different copies of metis).
+    #
+    # variant('parmetis', default=False,
+    #         description='Compile with the bundled PARMETIS graph library')
+    variant('qhull', default=False, description='Compile with the bundled qhull mesh generation library')
+    variant('sfc', default=False, description='Compile with the bundled sfcurves partitioning library')
+    variant('tetgen', default=False, description='Compile with the bundled tetgen mesh generation library')
+    variant('triangle', default=False, description='Compile with the bundled Triangle mesh generation library')
+
+    # support for libraries that may be externally installed:
+    variant('boost', default=False, description='Compile with components dependent on boost')
+    variant('eigen', default=False, description='support for dense linear algebra with Eigen')
+    variant('hdf5', default=False, description='Compile with support for HDF5 files')
+    variant('slepc', default=False, description='Compile with support for the SLEPc eigensolver')
+
+    # other features:
+    variant('debug', default=False, description='Compile with support for debugging')
     variant('mpi', default=True, description='Enables MPI parallelism')
+    # While it is possible to configure libMesh to use openMP with neither
+    # pthreads nor TBB, no openMP code can actually be reached without enabling
+    # pthreads as well. Hence, since enabling openMP while disabling pthreads
+    # is not useful, we include openMP in the same variant to make it clear
+    # which scheduler is ultimately used.
+    variant('threads', default='none',
+            description='Enable threading support (with a particular '
+            'scheduler, in the case of openmp and tbb)',
+            values=('none', 'pthreads', 'tbb', 'openmp'), multi=False)
 
-    depends_on('mpi', when='+mpi')
+    conflicts('+metaphysicl', when='@:1.2.999',
+              msg='The interface to metaphysicl is not available in libMesh '
+              'versions older than 1.3.0. Please explicitly disable this '
+              'variant.')
 
-    # Parallel version of libmesh needs parallel solvers
+    depends_on('boost', when='+boost')
+    # The Scotch dependency of Eigen is not used by libMesh. Since Scotch can
+    # only be used with certain versions of flex it conflicts with several
+    # versions of GCC, so explicitly disable it.
+    depends_on('eigen~scotch', when='+eigen')
+    depends_on('hdf5+mpi', when='+hdf5+mpi')
+    depends_on('mpi', when='+mpi')
+    depends_on('mpi', when='+slepc')
+    # compilation dependencies depend on perl
+    depends_on('perl')
     depends_on('petsc+mpi', when='+mpi')
+    depends_on('petsc+metis', when='+metis')
+    depends_on('slepc', when='+slepc')
+    depends_on('tbb', when='threads=tbb')
+
+    def configure_args(self):
+        options = []
+
+        # GLIBCXX debugging is not, by default, supported by other libraries,
+        # so unconditionally disable it for libmesh
+        options.append('--enable-glibcxx-debugging=no')
+
+        # All bundled dependencies are explicitly disabled, so we do not need
+        # to perform this check:
+        options.append('--disable-strict-lgpl')
+
+        # The Hinnant unique pointer implementation is incompatible with boost
+        # (and not necessary with C++11 support), so unconditionally disable
+        # it:
+        options.append('--disable-hinnant-unique-ptr')
+        # libMesh does not allow for us to specify an installation location for
+        # zlib, an undocumented dependency of gzstreams: hence we must
+        # unconditionally disable gzstreams.
+        options.append('--enable-gzstreams=no')
+        # Similarly, since we cannot specify a location for bzip2 or xz, so
+        # disable them to avoid picking up system installations:
+        options.append('--disable-bzip2')
+        options.append('--disable-xz')
+        # TODO enable GDB backtracing. Disable for now to avoid picking up the
+        # system gdb installation:
+        options.append('--without-gdb-command')
+
+        # TODO add X11 as a dependency to get tecplot working
+        options.append('--enable-tecio=no')
+        options.append('--enable-tecplot=no')
+
+        # handle the bundled libraries that are not themselves dependencies of
+        # other bundled libaries:
+        for bundled_library in ['capnproto', 'exodusii', 'fparser', 'gmv',
+                                'laspack', 'libHilbert', 'metaphysicl',
+                                'nanoflann', 'nemesis', 'parmetis', 'qhull',
+                                'sfc', 'tetgen', 'triangle']:
+            if '+' + bundled_library.lower() in self.spec:
+                options.append('--enable-' + bundled_library + "=yes")
+            else:
+                options.append('--enable-' + bundled_library + "=no")
+
+        # and the ones which are dependencies of other bundled libraries:
+        if '+exodusii' in self.spec or '+netcdf' in self.spec:
+            options.append('--enable-netcdf=yes')
+        else:
+            options.append('--enable-netcdf=no')
+
+        # handle external library dependencies:
+        if '+boost' in self.spec:
+            options.append('--with-boost=%s' % self.spec['boost'].prefix)
+        else:
+            options.append('--enable-boost=no')
+
+        if '+eigen' in self.spec:
+            options.append('--with-eigen=%s' % self.spec['eigen'].prefix)
+        else:
+            options.append('--enable-eigen=no')
+
+        if '+hdf5' in self.spec:
+            options.append('--with-hdf5=%s' % self.spec['hdf5'].prefix)
+        else:
+            options.append('--enable-hdf5=no')
+            # This is necessary with libMesh 1.2.1 to prevent a configure
+            # error:
+            if '+netcdf' not in self.spec:
+                options.append('--disable-netcdf-4')
+
+        if '+metis' in self.spec:
+            options.append('--with-metis=PETSc')
+
+        if '+petsc' in self.spec:
+            options.append('--enable-petsc=yes')
+            options.append('PETSC_DIR=%s' % self.spec['petsc'].prefix)
+        else:
+            options.append('--enable-petsc=no')
+
+        if '+slepc' in self.spec:
+            options.append('SLEPC_DIR=%s' % self.spec['slepc'].prefix)
+        else:
+            options.append('--enable-slepc=no')
+
+        # and, finally, other things:
+        if '+debug' in self.spec:
+            options.append('--with-methods=dbg')
+        else:
+            options.append('--with-methods=opt')
+
+        if '+mpi' in self.spec:
+            options.append('CC=%s' % self.spec['mpi'].mpicc)
+            options.append('CXX=%s' % self.spec['mpi'].mpicxx)
+            options.append('--with-mpi=%s' % self.spec['mpi'].prefix)
+        else:
+            options.append('--disable-mpi')
+            # libMesh will try to link with the system MPI library unless we
+            # provide explicit overrides
+            options.append('CC=%s' % self.compiler.cc)
+            options.append('CXX=%s' % self.compiler.cxx)
+
+        if 'threads=openmp' in self.spec:
+            # OpenMP cannot be used if pthreads is not available: see
+            # parallel/threads_pthread.h and parallel/threads.h
+            options.append('--enable-openmp=yes')
+            options.append('--with-thread-model=pthread')
+            options.append('--enable-pthreads=yes')
+        else:
+            options.append('--enable-openmp=no')
 
-    def install(self, spec, prefix):
-        config_args = ["--prefix=%s" % prefix]
+        if 'threads=pthreads' in self.spec:
+            options.append('--with-thread-model=pthread')
+            options.append('--enable-pthreads=yes')
+        else:
+            if 'threads=openmp' not in self.spec:
+                options.append('--enable-pthreads=no')
 
-        if '+mpi' in spec:
-            config_args.append('CC=%s' % spec['mpi'].mpicc)
-            config_args.append('CXX=%s' % spec['mpi'].mpicxx)
-            config_args.append('PETSC_DIR=%s' % spec['petsc'].prefix)
+        if 'threads=tbb' in self.spec:
+            options.append('--with-thread-model=tbb')
+            options.append('--enable-tbb=yes')
+            options.append('--with-tbb=%s' % self.spec['tbb'].prefix)
+        else:
+            options.append('--enable-tbb=no')
 
-        configure(*config_args)
+        return options
 
-        make()
-        make('install')
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        spack_env.append_flags('PERL', self.spec['perl'].command.path)
diff --git a/var/spack/repos/builtin/packages/libmng/package.py b/var/spack/repos/builtin/packages/libmng/package.py
index 95542361ef..e4e11c9594 100644
--- a/var/spack/repos/builtin/packages/libmng/package.py
+++ b/var/spack/repos/builtin/packages/libmng/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libmongoc/package.py b/var/spack/repos/builtin/packages/libmongoc/package.py
index 5050dd0336..2f1dc4d7f7 100644
--- a/var/spack/repos/builtin/packages/libmongoc/package.py
+++ b/var/spack/repos/builtin/packages/libmongoc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,6 +12,10 @@ class Libmongoc(AutotoolsPackage):
     homepage = "https://github.com/mongodb/mongo-c-driver"
     url      = "https://github.com/mongodb/mongo-c-driver/releases/download/1.7.0/mongo-c-driver-1.7.0.tar.gz"
 
+    maintainers = ['michaelkuhn']
+
+    version('1.9.1', '86f98ace1a5f073eea6875a96761b198')
+    version('1.8.1', '52d54a4107a2da20c1a1b28bc1ff9d44')
     version('1.8.0', '8c271a16ff30f6d4f5e134f699f7360f')
     version('1.7.0', '21acf3584e92631422bc91e9e3cf4f76')
     version('1.6.3', '0193610cf1d98aae7008f272a1000972')
@@ -41,12 +26,25 @@ class Libmongoc(AutotoolsPackage):
     variant('snappy', default=True, description='Enable Snappy support.')
     variant('zlib', default=True, description='Enable zlib support.')
 
+    patch('https://github.com/mongodb/mongo-c-driver/pull/466.patch', sha256='713a872217d11aba04a774785a2824d26b566543c270a1fa386114f5200fda20', when='@1.8.1')
+
+    depends_on('autoconf', type='build', when='@1.8.1')
+    depends_on('automake', type='build', when='@1.8.1')
+    depends_on('libtool', type='build', when='@1.8.1')
+    depends_on('m4', type='build', when='@1.8.1')
+    depends_on('pkgconfig', type='build')
+
     depends_on('libbson')
 
     depends_on('openssl', when='+ssl')
     depends_on('snappy', when='+snappy')
     depends_on('zlib', when='+zlib')
 
+    @property
+    def force_autoreconf(self):
+        # Run autoreconf due to build system patch
+        return self.spec.satisfies('@1.8.1')
+
     def configure_args(self):
         spec = self.spec
 
@@ -61,12 +59,15 @@ class Libmongoc(AutotoolsPackage):
             args.append('--enable-ssl=no')
 
         if spec.satisfies('@1.7.0:'):
-            # --with-{snappy,zlib}=system are currently broken and cause
-            # configure to not find the dependencies. We still want to
-            # explicitly disable them when appropriate.
+            # --with-{snappy,zlib}=system are broken for versions < 1.8.1
             if '+snappy' not in spec:
                 args.append('--with-snappy=no')
+            elif spec.satisfies('@1.8.1:'):
+                args.append('--with-snappy=system')
+
             if '+zlib' not in spec:
                 args.append('--with-zlib=no')
+            elif spec.satisfies('@1.8.1:'):
+                args.append('--with-zlib=system')
 
         return args
diff --git a/var/spack/repos/builtin/packages/libmonitor/package.py b/var/spack/repos/builtin/packages/libmonitor/package.py
index 7ec87ca453..314f195af9 100644
--- a/var/spack/repos/builtin/packages/libmonitor/package.py
+++ b/var/spack/repos/builtin/packages/libmonitor/package.py
@@ -1,38 +1,77 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class Libmonitor(AutotoolsPackage):
-    """Libmonitor is a library for process and thread control."""
+    """Libmonitor is a library providing callback functions for the
+    begin and end of processes and threads.  It provides a layer on
+    which to build process monitoring tools and profilers."""
+
     homepage = "https://github.com/HPCToolkit/libmonitor"
-    version('20130218', git='https://github.com/HPCToolkit/libmonitor.git',
-            commit='4f2311e')
+    git      = "https://github.com/HPCToolkit/libmonitor.git"
+
+    version('master', branch='master')
+    version('2018.07.18', commit='d28cc1d3c08c02013a68a022a57a6ac73db88166',
+            preferred=True)
+    version('2013.02.18', commit='4f2311e413fd90583263d6f20453bbe552ccfef3')
+
+    # Configure for Rice HPCToolkit.
+    variant('hpctoolkit', default=False,
+            description='Configure for HPCToolkit')
+
+    variant('bgq', default=False,
+            description='Configure for Blue Gene/Q')
+
+    # Configure for Krell and OpenSpeedshop.
     variant('krellpatch', default=False,
-            description="build with openspeedshop based patch.")
+            description="Build with openspeedshop based patch.")
+
+    patch('libmonitorkrell-0000.patch', when='@2013.02.18+krellpatch')
+    patch('libmonitorkrell-0001.patch', when='@2013.02.18+krellpatch')
+    patch('libmonitorkrell-0002.patch', when='@2013.02.18+krellpatch')
+
+    signals = 'SIGBUS, SIGSEGV, SIGPROF, 36, 37, 38'
+
+    # Set default cflags (-g -O2) and move to the configure line.
+    def flag_handler(self, name, flags):
+        if name != 'cflags':
+            return (flags, None, None)
+
+        if '-g' not in flags:
+            flags.append('-g')
+        for flag in flags:
+            if flag.startswith('-O'):
+                break
+        else:
+            flags.append('-O2')
+
+        return (None, None, flags)
+
+    def configure_args(self):
+        args = []
+
+        if '+hpctoolkit' in self.spec:
+            args.append('--enable-client-signals=%s' % self.signals)
+
+        # TODO: Spack has trouble finding cross-compilers; the +bgq variant
+        # manually specifies the appropriate compiler to build for BGQ (by
+        # setting that here, Spack's choice of CC is overridden).
+        # If the user manually defines an entry in compilers.yaml, the bgq
+        # variant should not be required if the user specifies the bgq
+        # architecture for the libmonitor package. See #8860
+        # TODO: users want to build this for the backend and dependents for the
+        # frontend. Spack ought to make that easy by finding the appropriate
+        # compiler for each if the root and libmonitor are designated to build
+        # on the frontend and backend, respectively. As of now though, there
+        # is an issue with compiler concretization such that spack will attempt
+        # to assign the compiler chosen for libmonitor to the root (unless the
+        # user specifies the compiler for each in addition to the arch).
+        # See #8859
+        if '+bgq' in self.spec:
+            args.append('CC=powerpc64-bgq-linux-gcc')
 
-    patch('libmonitorkrell-0000.patch', when='@20130218+krellpatch')
-    patch('libmonitorkrell-0001.patch', when='@20130218+krellpatch')
-    patch('libmonitorkrell-0002.patch', when='@20130218+krellpatch')
+        return args
diff --git a/var/spack/repos/builtin/packages/libnbc/package.py b/var/spack/repos/builtin/packages/libnbc/package.py
index 67ac5da744..daf7b95c57 100644
--- a/var/spack/repos/builtin/packages/libnbc/package.py
+++ b/var/spack/repos/builtin/packages/libnbc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libnl/package.py b/var/spack/repos/builtin/packages/libnl/package.py
new file mode 100644
index 0000000000..1eabb45108
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libnl/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Libnl(AutotoolsPackage):
+    """libnl - Netlink Protocol Library Suite"""
+
+    homepage = "https://www.infradead.org/~tgr/libnl/"
+    url      = "https://github.com/thom311/libnl/releases/download/libnl3_3_0/libnl-3.3.0.tar.gz"
+
+    version('3.3.0', 'ab3ef137cad95bdda5ff0ffa5175dfa5')
+    version('3.2.25', '03f74d0cd5037cadc8cdfa313bbd195c')
+
+    depends_on('bison', type='build')
+    depends_on('flex', type='build')
+    depends_on('m4', type='build')
+
+    conflicts('platform=darwin', msg='libnl requires FreeBSD or Linux')
diff --git a/var/spack/repos/builtin/packages/libnova/package.py b/var/spack/repos/builtin/packages/libnova/package.py
new file mode 100644
index 0000000000..63745e8dd4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libnova/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Libnova(AutotoolsPackage):
+    """"libnova is a general purpose, double precision, Celestial Mechanics,
+        Astrometry and Astrodynamics library."""
+
+    homepage = "http://libnova.sourceforge.net"
+    url      = "https://sourceforge.net/projects/libnova/files/libnova/v%200.15.0/libnova-0.15.0.tar.gz/download"
+
+    version('0.15.0', '756fdb55745cb78511f83a62c25f3be4')
+
+    depends_on('m4')
+    depends_on('autoconf')
+    depends_on('automake')
+    depends_on('libtool')
+
+    force_autoreconf = True
diff --git a/var/spack/repos/builtin/packages/libogg/package.py b/var/spack/repos/builtin/packages/libogg/package.py
index e2c38e7759..bdb5700cc9 100644
--- a/var/spack/repos/builtin/packages/libogg/package.py
+++ b/var/spack/repos/builtin/packages/libogg/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/liboldx/package.py b/var/spack/repos/builtin/packages/liboldx/package.py
index f03e0bfe88..210f12a1af 100644
--- a/var/spack/repos/builtin/packages/liboldx/package.py
+++ b/var/spack/repos/builtin/packages/liboldx/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,5 +16,5 @@ class Liboldx(AutotoolsPackage):
 
     depends_on('libx11')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libpcap/package.py b/var/spack/repos/builtin/packages/libpcap/package.py
index 02221b371e..5956353568 100644
--- a/var/spack/repos/builtin/packages/libpcap/package.py
+++ b/var/spack/repos/builtin/packages/libpcap/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,3 +13,6 @@ class Libpcap(AutotoolsPackage):
     url      = "http://www.tcpdump.org/release/libpcap-1.8.1.tar.gz"
 
     version('1.8.1', '3d48f9cd171ff12b0efd9134b52f1447')
+
+    depends_on('flex', type='build')
+    depends_on('bison', type='build')
diff --git a/var/spack/repos/builtin/packages/libpciaccess/package.py b/var/spack/repos/builtin/packages/libpciaccess/package.py
index 7c4efde8ca..ad30ebd082 100644
--- a/var/spack/repos/builtin/packages/libpciaccess/package.py
+++ b/var/spack/repos/builtin/packages/libpciaccess/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,5 +16,5 @@ class Libpciaccess(AutotoolsPackage):
     version('0.13.4', 'cc1fad87da60682af1d5fa43a5da45a4')
 
     depends_on('libtool', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libpfm4/package.py b/var/spack/repos/builtin/packages/libpfm4/package.py
index 3e30ead2dc..32d72371b9 100644
--- a/var/spack/repos/builtin/packages/libpfm4/package.py
+++ b/var/spack/repos/builtin/packages/libpfm4/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,11 +14,30 @@ class Libpfm4(MakefilePackage):
     homepage = "http://perfmon2.sourceforge.net"
     url      = "https://downloads.sourceforge.net/project/perfmon2/libpfm4/libpfm-4.8.0.tar.gz"
 
+    version('4.10.1', 'd8f66cb9bfa7e1434434e0de6409db5b')
+    version('4.9.0', '42ad4a2e5b8e1f015310db8535739c73')
     version('4.8.0', '730383896db92e12fb2cc10f2d41dd43')
 
     # Fails to build libpfm4 with intel compiler version 16 and 17
     conflicts('%intel@16:17')
 
+    # Set default optimization level (-O2) if not specified.
+    def flag_handler(self, name, flags):
+        if name == 'cflags':
+            for flag in flags:
+                if flag.startswith('-O'):
+                    break
+            else:
+                flags.append('-O2')
+
+        return (flags, None, None)
+
+    # Remove -Werror from CFLAGS.  Given the large space of platform,
+    # compiler, version, we don't want to fail the build over a stray
+    # warning.
+    def patch(self):
+        filter_file('-Werror', '', 'config.mk')
+
     @property
     def install_targets(self):
         return ['DESTDIR={0}'.format(self.prefix),
diff --git a/var/spack/repos/builtin/packages/libpipeline/package.py b/var/spack/repos/builtin/packages/libpipeline/package.py
index a242862b34..b5528d7dc3 100644
--- a/var/spack/repos/builtin/packages/libpipeline/package.py
+++ b/var/spack/repos/builtin/packages/libpipeline/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,7 +15,5 @@ class Libpipeline(AutotoolsPackage):
 
     version('1.4.2', '30cec7bcd6fee723adea6a54389f3da2')
 
-    depends_on('pkg-config', type='build')
-    # TODO: Add a 'test' deptype
-    # See https://github.com/spack/spack/issues/1279
-    # depends_on('check', type='test')
+    depends_on('pkgconfig', type='build')
+    depends_on('check', type='test')
diff --git a/var/spack/repos/builtin/packages/libpng/package.py b/var/spack/repos/builtin/packages/libpng/package.py
index a328bd44f8..e9e9d9e56f 100644
--- a/var/spack/repos/builtin/packages/libpng/package.py
+++ b/var/spack/repos/builtin/packages/libpng/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,11 +10,13 @@ class Libpng(AutotoolsPackage):
     """libpng is the official PNG reference library."""
 
     homepage = "http://www.libpng.org/pub/png/libpng.html"
-    url      = "http://download.sourceforge.net/libpng/libpng-1.6.29.tar.gz"
+    url      = "http://download.sourceforge.net/libpng/libpng-1.6.34.tar.gz"
     list_url = "https://sourceforge.net/projects/libpng/files/"
     list_depth = 2
 
+    version('1.6.34', '03fbc5134830240104e96d3cda648e71')
     version('1.6.29', '68553080685f812d1dd7a6b8215c37d8')
+    version('1.6.28', '897ccec1ebfb0922e83c2bfaa1be8748')
     version('1.6.27', '58698519e9f6126c1caeefc28dbcbd5f')
     # From http://www.libpng.org/pub/png/libpng.html (2017-01-04)
     #     Virtually all libpng versions through 1.6.26, 1.5.27,
@@ -57,7 +40,12 @@ class Libpng(AutotoolsPackage):
             # not honored, see
             #   https://sourceforge.net/p/libpng/bugs/210/#33f1
             # '--with-zlib=' + self.spec['zlib'].prefix,
-            'CFLAGS={0}'.format(self.spec['zlib'].headers.include_flags),
+            'CPPFLAGS={0}'.format(self.spec['zlib'].headers.include_flags),
             'LDFLAGS={0}'.format(self.spec['zlib'].libs.search_flags)
         ]
         return args
+
+    def check(self):
+        # Libpng has both 'check' and 'test' targets that are aliases.
+        # Only need to run the tests once.
+        make('check')
diff --git a/var/spack/repos/builtin/packages/libpsl/package.py b/var/spack/repos/builtin/packages/libpsl/package.py
index 75722c63fd..88d843bb1e 100644
--- a/var/spack/repos/builtin/packages/libpsl/package.py
+++ b/var/spack/repos/builtin/packages/libpsl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,7 +17,7 @@ class Libpsl(AutotoolsPackage):
     depends_on('icu4c')
 
     depends_on('gettext', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('python@2.7:', type='build')
 
     depends_on('valgrind~mpi~boost', type='test')
diff --git a/var/spack/repos/builtin/packages/libpthread-stubs/package.py b/var/spack/repos/builtin/packages/libpthread-stubs/package.py
index 286120d908..1cc977316b 100644
--- a/var/spack/repos/builtin/packages/libpthread-stubs/package.py
+++ b/var/spack/repos/builtin/packages/libpthread-stubs/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libquo/package.py b/var/spack/repos/builtin/packages/libquo/package.py
index 08006c4295..4677798391 100644
--- a/var/spack/repos/builtin/packages/libquo/package.py
+++ b/var/spack/repos/builtin/packages/libquo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,16 +13,24 @@ class Libquo(AutotoolsPackage):
     single- and multi-threaded libraries."""
 
     homepage = "https://github.com/lanl/libquo"
-    url      = "https://github.com/lanl/libquo/archive/v1.2.9.tar.gz"
+    url      = "http://lanl.github.io/libquo/dists/libquo-1.3.tar.gz"
+    git      = "https://github.com/lanl/libquo.git"
 
-    version('develop', git='https://github.com/lanl/libquo', branch='master')
-    version('1.3', '3ff74162837425a15ecf695ca0201e4a')
-    version('1.2.9', 'ca82ab33f13e2b89983f81e7c02e98c2')
+    version('develop', branch='master')
+    version('1.3',   '1a1fb83d2c9e99ef5d5fcd71037ef8e8')
+    version('1.2.9', '85907cfbdb8b1e57fc5fcf3bced7cfa8')
 
     depends_on('mpi')
-    depends_on('autoconf', type='build')
-    depends_on('automake', type='build')
-    depends_on('libtool', type='build')
+
+    depends_on('m4',       when='@develop', type='build')
+    depends_on('autoconf', when='@develop', type='build')
+    depends_on('automake', when='@develop', type='build')
+    depends_on('libtool',  when='@develop', type='build')
+
+    @when('@develop')
+    def autoreconf(self, spec, prefix):
+        bash = which('bash')
+        bash('./autogen')
 
     def configure_args(self):
         return [
diff --git a/var/spack/repos/builtin/packages/librom/package.py b/var/spack/repos/builtin/packages/librom/package.py
new file mode 100644
index 0000000000..e00792e777
--- /dev/null
+++ b/var/spack/repos/builtin/packages/librom/package.py
@@ -0,0 +1,57 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import glob
+
+
+class Librom(AutotoolsPackage):
+    """libROM: library for computing large-scale reduced order models"""
+
+    homepage = "https://github.com/LLNL/libROM"
+    git      = "https://github.com/LLNL/libROM.git"
+
+    version('develop', branch='master')
+
+    depends_on('lapack')
+    depends_on('mpi')
+    depends_on('zlib')
+    depends_on('libszip')
+    depends_on('hdf5')
+    depends_on('perl')
+    depends_on('graphviz')
+    depends_on('doxygen')
+    depends_on('boost')
+
+    def configure_args(self):
+        spec = self.spec
+        args = ['--with-lapack={0}'.format(spec['lapack'].prefix),
+                '--with-lapack-libs={0}'.format(spec['lapack'].libs.ld_flags),
+                '--with-zlib={0}'.format(spec['zlib'].prefix),
+                '--with-szlib={0}'.format(spec['libszip'].prefix),
+                '--with-hdf5={0}'.format(spec['hdf5'].prefix),
+                '--with-MPICC={0}'.format(spec['mpi'].mpicc),
+                '--with-mpi-include={0}'.format(spec['mpi'].prefix.include),
+                '--with-mpi-libs={0}'.format(spec['mpi'].libs.ld_flags),
+                '--with-perl={0}'.format(spec['perl'].prefix),
+                '--with-doxygen={0}'.format(spec['doxygen'].prefix)]
+        return args
+
+    # TODO(oxberry1@llnl.gov): Submit PR upstream that implements
+    # install phase in autotools
+    def install(self, spec, prefix):
+        mkdirp(self.spec.prefix.lib)
+        install('libROM.a', join_path(self.spec.prefix.lib, 'libROM.a'))
+
+        mkdirp(self.spec.prefix.include)
+        for f in glob.glob('*.h'):
+            install(f, join_path(self.spec.prefix.include, f))
+
+        mkdirp(self.spec.prefix.share)
+        install('libROM_Design_and_Theory.pdf',
+                join_path(self.spec.prefix.share,
+                          'libROM_Design_and_Theory.pdf'))
+
+        install_tree('docs', self.spec.prefix.share.docs)
diff --git a/var/spack/repos/builtin/packages/libsharp/package.py b/var/spack/repos/builtin/packages/libsharp/package.py
new file mode 100644
index 0000000000..a80eb7f58f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libsharp/package.py
@@ -0,0 +1,41 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Libsharp(AutotoolsPackage):
+    """Libsharp is a code library for spherical harmonic transforms (SHTs) and
+    spin-weighted spherical harmonic transforms, which evolved from the libpsht
+    library."""
+
+    variant('openmp', default=True, description='Build with openmp support')
+    variant('mpi', default=True, description='Build with MPI support')
+
+    homepage = "https://github.com/Libsharp/libsharp"
+    git      = "https://github.com/Libsharp/libsharp.git"
+
+    version('1.0.0', commit='cc4753ff4b0ef393f0d4ada41a175c6d1dd85d71')
+    version('2018-01-17', commit='593d4eba67d61827191c32fb94bf235cb31205e1')
+
+    depends_on('autoconf', type='build')
+    depends_on('mpi', when='+mpi')
+
+    def autoreconf(self, spec, prefix):
+        """Generate autotools configuration"""
+        bash = which('bash')
+        bash('autoconf')
+
+    def configure_args(self):
+        args = []
+        if '+openmp' not in self.spec:
+            args.append("--disable-openmp")
+        if '+mpi' not in self.spec:
+            args.append("--disable-mpi")
+        return args
+
+    def install(self, spec, prefix):
+        install_tree('auto/include', join_path(prefix, 'include'))
+        install_tree('auto/lib', join_path(prefix, 'lib'))
diff --git a/var/spack/repos/builtin/packages/libshm/package.py b/var/spack/repos/builtin/packages/libshm/package.py
new file mode 100644
index 0000000000..3e52739131
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libshm/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Libshm(Package):
+    """Libshm is a header library
+    making an easy C++11 access to a shared memory."""
+
+    homepage = "https://github.com/afeldman/libshm"
+    git      = "https://github.com/afeldman/libshm.git"
+
+    version('master')
+
+    def install(self, spec, prefix):
+        install_tree('include', prefix.include)
diff --git a/var/spack/repos/builtin/packages/libsigcpp/package.py b/var/spack/repos/builtin/packages/libsigcpp/package.py
new file mode 100644
index 0000000000..32a3674fd6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libsigcpp/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Libsigcpp(AutotoolsPackage):
+    """Libsigc++ is a C++ library for typesafe callbacks"""
+
+    homepage = "https://libsigcplusplus.github.io/libsigcplusplus/index.html"
+    url      = "https://ftp.acc.umu.se/pub/GNOME/sources/libsigc++/2.0/libsigc++-2.0.3.tar.gz"
+
+    version('2.9.3', '0e5630fd0557ee80b5e5cbbcebaa2594')
+    version('2.1.1', '5ae4d6da9a408c90e86c776673c38972')
+    version('2.0.3', '57c6887dd46ce0bd312a4823589db5d8')
+
+    def url_for_version(self, version):
+        """Handle version-based custom URLs."""
+        url = "https://ftp.acc.umu.se/pub/GNOME/sources/libsigc++"
+        ext = '.tar.gz' if version < Version('2.2.10') else '.tar.xz'
+        return url + "/%s/libsigc++-%s%s" % (version.up_to(2), version, ext)
diff --git a/var/spack/repos/builtin/packages/libsigsegv/package.py b/var/spack/repos/builtin/packages/libsigsegv/package.py
index f13710bff9..68c88a11aa 100644
--- a/var/spack/repos/builtin/packages/libsigsegv/package.py
+++ b/var/spack/repos/builtin/packages/libsigsegv/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,7 +10,7 @@ class Libsigsegv(AutotoolsPackage):
     """GNU libsigsegv is a library for handling page faults in user mode."""
 
     homepage = "https://www.gnu.org/software/libsigsegv/"
-    url      = "https://ftp.gnu.org/gnu/libsigsegv/libsigsegv-2.11.tar.gz"
+    url      = "https://ftpmirror.gnu.org/libsigsegv/libsigsegv-2.11.tar.gz"
 
     patch('patch.new_config_guess', when='@2.10')
 
diff --git a/var/spack/repos/builtin/packages/libsm/package.py b/var/spack/repos/builtin/packages/libsm/package.py
index 602f5daa56..50e0fb3fca 100644
--- a/var/spack/repos/builtin/packages/libsm/package.py
+++ b/var/spack/repos/builtin/packages/libsm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Libsm(AutotoolsPackage):
 
     depends_on('xproto', type='build')
     depends_on('xtrans', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libsodium/package.py b/var/spack/repos/builtin/packages/libsodium/package.py
index e62319e439..c7c1a2191a 100644
--- a/var/spack/repos/builtin/packages/libsodium/package.py
+++ b/var/spack/repos/builtin/packages/libsodium/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,6 +13,7 @@ class Libsodium(AutotoolsPackage):
     url      = "https://download.libsodium.org/libsodium/releases/libsodium-1.0.13.tar.gz"
     list_url = "https://download.libsodium.org/libsodium/releases/old"
 
+    version('1.0.15', '070373e73a0b10bd96f412e1732ebc42')
     version('1.0.13', 'f38aac160a4bd05f06f743863e54e499')
     version('1.0.12', 'c308e3faa724b630b86cc0aaf887a5d4')
     version('1.0.11', 'b58928d035064b2a46fb564937b83540')
diff --git a/var/spack/repos/builtin/packages/libspatialindex/package.py b/var/spack/repos/builtin/packages/libspatialindex/package.py
index 69183c8131..9f1a27c60d 100644
--- a/var/spack/repos/builtin/packages/libspatialindex/package.py
+++ b/var/spack/repos/builtin/packages/libspatialindex/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libsplash/package.py b/var/spack/repos/builtin/packages/libsplash/package.py
index b710dae58c..37a7c09b0e 100644
--- a/var/spack/repos/builtin/packages/libsplash/package.py
+++ b/var/spack/repos/builtin/packages/libsplash/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,11 +17,12 @@ class Libsplash(CMakePackage):
 
     homepage = "https://github.com/ComputationalRadiationPhysics/libSplash"
     url      = "https://github.com/ComputationalRadiationPhysics/libSplash/archive/v1.4.0.tar.gz"
+    git      = "https://github.com/ComputationalRadiationPhysics/libSplash.git"
+    maintainers = ['ax3l']
 
-    version('develop', branch='dev',
-            git='https://github.com/ComputationalRadiationPhysics/libSplash.git')
-    version('master', branch='master',
-            git='https://github.com/ComputationalRadiationPhysics/libSplash.git')
+    version('develop', branch='dev')
+    version('master', branch='master')
+    version('1.7.0', '22dea94734fe4f4c5f4e875ce70900d3')
     version('1.6.0', 'c05bce95abfe1ae4cd9d9817acf58d94')
     version('1.5.0', 'c1efec4c20334242c8a3b6bfdc0207e3')
     version('1.4.0', '2de37bcef6fafa1960391bf44b1b50e0')
@@ -50,6 +32,23 @@ class Libsplash(CMakePackage):
     variant('mpi', default=True,
             description='Enable parallel I/O (one-file aggregation) support')
 
-    depends_on('hdf5@1.8.6:')
-    depends_on('hdf5+mpi', when='+mpi')
+    depends_on('cmake@3.10.0:', type='build', when='@1.7.0:')
+    depends_on('hdf5@1.8.6: ~mpi', when='~mpi')
+    depends_on('hdf5@1.8.6: +mpi', when='+mpi')
     depends_on('mpi', when='+mpi')
+
+    patch('root_cmake_1.7.0.patch', when='@1.7.0')
+
+    def cmake_args(self):
+        spec = self.spec
+        args = []
+
+        if spec.satisfies('@1.7.0:'):
+            args += [
+                '-DSplash_USE_MPI:BOOL={0}'.format(
+                    'ON' if '+mpi' in spec else 'OFF'),
+                '-DSplash_USE_PARALLEL:BOOL={0}'.format(
+                    'ON' if '+mpi' in spec else 'OFF')
+            ]
+
+        return args
diff --git a/var/spack/repos/builtin/packages/libsplash/root_cmake_1.7.0.patch b/var/spack/repos/builtin/packages/libsplash/root_cmake_1.7.0.patch
new file mode 100644
index 0000000000..788e24925d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libsplash/root_cmake_1.7.0.patch
@@ -0,0 +1,15 @@
+diff --git CMakeLists.txt CMakeLists.txt
+index 4846ff7..5e102ce 100644
+--- libSplash-1.7.0/CMakeLists.txt
++++ libSplash-1.7.0/CMakeLists.txt
+@@ -392,7 +392,8 @@ install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/tools/splash2xdmf.py DESTINATION bin)
+ #
+ enable_testing()
+ 
+-if($ENV{USER} STREQUAL root)
++# OpenMPI root guard: https://github.com/open-mpi/ompi/issues/4451
++if("$ENV{USER}" STREQUAL "root")
+     set(MPI_ALLOW_ROOT --allow-run-as-root)
+ endif()
+ set(MPI_TEST_EXE ${MPIEXEC_EXECUTABLE} ${MPI_ALLOW_ROOT} ${MPIEXEC_NUMPROC_FLAG})
+
diff --git a/var/spack/repos/builtin/packages/libssh/package.py b/var/spack/repos/builtin/packages/libssh/package.py
new file mode 100644
index 0000000000..511e2779a0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libssh/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Libssh(CMakePackage):
+    """libssh: the SSH library"""
+
+    homepage = "https://www.libssh.org"
+    url      = "https://red.libssh.org/attachments/download/218/libssh-0.7.5.tar.xz"
+
+    version('0.7.5', 'd3fc864208bf607ad87cdee836894feb')
+
+    depends_on('openssl')
+    depends_on('zlib')
diff --git a/var/spack/repos/builtin/packages/libssh2/package.py b/var/spack/repos/builtin/packages/libssh2/package.py
index 030e7aeab5..bf56dc36b1 100644
--- a/var/spack/repos/builtin/packages/libssh2/package.py
+++ b/var/spack/repos/builtin/packages/libssh2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,6 +12,7 @@ class Libssh2(CMakePackage):
     homepage = "https://www.libssh2.org/"
     url      = "https://www.libssh2.org/download/libssh2-1.7.0.tar.gz"
 
+    version('1.8.0', '3d1147cae66e2959ea5441b183de1b1c')
     version('1.7.0', 'b01662a210e94cccf2f76094db7dac5c')
     version('1.4.3', '071004c60c5d6f90354ad1b701013a0b')  # CentOS7
 
diff --git a/var/spack/repos/builtin/packages/libsvm/package.py b/var/spack/repos/builtin/packages/libsvm/package.py
index 564775c91c..2c35ef7dce 100644
--- a/var/spack/repos/builtin/packages/libsvm/package.py
+++ b/var/spack/repos/builtin/packages/libsvm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libszip/package.py b/var/spack/repos/builtin/packages/libszip/package.py
index 2f4b570fec..feef66a655 100644
--- a/var/spack/repos/builtin/packages/libszip/package.py
+++ b/var/spack/repos/builtin/packages/libszip/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,11 +17,11 @@ class Libszip(AutotoolsPackage):
     homepage = "https://support.hdfgroup.org/doc_resource/SZIP/"
     url      = "https://support.hdfgroup.org/ftp/lib-external/szip/2.1.1/src/szip-2.1.1.tar.gz"
     list_url = "https://support.hdfgroup.org/ftp/lib-external/szip"
-    list_depth = 2
+    list_depth = 3
 
     provides('szip')
 
-    version('2.1.1', 'dd579cf0f26d44afd10a0ad7291fc282')
+    version('2.1.1', '5addbf2a5b1bf928b92c47286e921f72')
     version('2.1',   '902f831bcefb69c6b635374424acbead')
 
     def configure_args(self):
diff --git a/var/spack/repos/builtin/packages/libtermkey/package.py b/var/spack/repos/builtin/packages/libtermkey/package.py
index 6b8b6b58bd..28a6aa5552 100644
--- a/var/spack/repos/builtin/packages/libtermkey/package.py
+++ b/var/spack/repos/builtin/packages/libtermkey/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libtiff/package.py b/var/spack/repos/builtin/packages/libtiff/package.py
index a28d553429..3a2efbfb5c 100644
--- a/var/spack/repos/builtin/packages/libtiff/package.py
+++ b/var/spack/repos/builtin/packages/libtiff/package.py
@@ -1,39 +1,23 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class Libtiff(AutotoolsPackage):
-    """libtiff graphics format library"""
+    """LibTIFF - Tag Image File Format (TIFF) Library and Utilities."""
+
     homepage = "http://www.simplesystems.org/libtiff/"
-    url      = "http://download.osgeo.org/libtiff/tiff-4.0.8.tar.gz"
+    url      = "http://download.osgeo.org/libtiff/tiff-4.0.9.tar.gz"
 
+    version('4.0.9', '54bad211279cc93eb4fca31ba9bfdc79')
     version('4.0.8', '2a7d1c1318416ddf36d5f6fa4600069b')
     version('4.0.7', '77ae928d2c6b7fb46a21c3a29325157b')
     version('4.0.6', 'd1d2e940dea0b5ad435f21f03d96dd72')
     version('4.0.3', '051c1068e6a0627f461948c365290410')
+    version('3.9.7', '626102f448ba441d42e3212538ad67d2')
 
     depends_on('jpeg')
     depends_on('zlib')
diff --git a/var/spack/repos/builtin/packages/libtool/flag_space.patch b/var/spack/repos/builtin/packages/libtool/flag_space.patch
new file mode 100644
index 0000000000..4ec1fc8c98
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libtool/flag_space.patch
@@ -0,0 +1,19 @@
+diff --git a/m4/libtool.m4 b/m4/libtool.m4
+index b55a6e57..26febc87 100644
+--- a/m4/libtool.m4
++++ b/m4/libtool.m4
+@@ -7557,10 +7557,11 @@ if AC_TRY_EVAL(ac_compile); then
+     case $prev$p in
+ 
+     -L* | -R* | -l*)
+-       # Some compilers place space between "-{L,R}" and the path.
++       # Some compilers place space between "-{L,R,l}" and the path (value).
+        # Remove the space.
+-       if test x-L = "$p" ||
+-          test x-R = "$p"; then
++       if test x-L = x"$p" ||
++          test x-R = x"$p" ||
++          test x-l = x"$p"; then
+ 	 prev=$p
+ 	 continue
+        fi
diff --git a/var/spack/repos/builtin/packages/libtool/package.py b/var/spack/repos/builtin/packages/libtool/package.py
index eca530ce0c..37c6f2a876 100644
--- a/var/spack/repos/builtin/packages/libtool/package.py
+++ b/var/spack/repos/builtin/packages/libtool/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,15 +10,30 @@ class Libtool(AutotoolsPackage):
     """libtool -- library building part of autotools."""
 
     homepage = 'https://www.gnu.org/software/libtool/'
-    url = 'http://ftpmirror.gnu.org/libtool/libtool-2.4.2.tar.gz'
+    url      = 'https://ftpmirror.gnu.org/libtool/libtool-2.4.2.tar.gz'
 
+    version('develop', git='https://git.savannah.gnu.org/git/libtool.git',
+            branch='master', submodules=True)
     version('2.4.6', 'addf44b646ddb4e3919805aa88fa7c5e')
     version('2.4.2', 'd2f3b7d4627e69e13514a40e72a24d50')
 
     depends_on('m4@1.4.6:', type='build')
+    depends_on('autoconf', type='build', when='@develop')
+    depends_on('automake', type='build', when='@develop')
+    depends_on('help2man', type='build', when='@develop')
+    depends_on('xz', type='build', when='@develop')
+    depends_on('texinfo', type='build', when='@develop')
+
+    # Fix parsing of compiler output when collecting predeps and postdeps
+    # http://lists.gnu.org/archive/html/bug-libtool/2016-03/msg00003.html
+    patch('flag_space.patch', when='@develop')
 
     build_directory = 'spack-build'
 
+    @when('@develop')
+    def autoreconf(self, spec, prefix):
+        Executable('./bootstrap')()
+
     def _make_executable(self, name):
         return Executable(join_path(self.prefix.bin, name))
 
@@ -46,8 +42,25 @@ class Libtool(AutotoolsPackage):
                               join_path(self.prefix.share, 'aclocal'))
 
     def setup_dependent_package(self, module, dependent_spec):
-        # Automake is very likely to be a build dependency,
-        # so we add the tools it provides to the dependent module
-        executables = ['libtoolize', 'libtool']
+        # Automake is very likely to be a build dependency, so we add
+        # the tools it provides to the dependent module. Some build
+        # systems differentiate between BSD libtool (e.g., Darwin) and
+        # GNU libtool, so also add 'glibtool' and 'glibtoolize' to the
+        # list of executables. See Homebrew:
+        # https://github.com/Homebrew/homebrew-core/blob/master/Formula/libtool.rb
+        executables = ['libtoolize', 'libtool', 'glibtoolize', 'glibtool']
         for name in executables:
             setattr(module, name, self._make_executable(name))
+
+    @run_after('install')
+    def post_install(self):
+        # Some platforms name GNU libtool and GNU libtoolize
+        # 'glibtool' and 'glibtoolize', respectively, to differentiate
+        # them from BSD libtool and BSD libtoolize. On these BSD
+        # platforms, build systems sometimes expect to use the assumed
+        # GNU commands glibtool and glibtoolize instead of the BSD
+        # variant; this happens frequently, for instance, on Darwin
+        symlink(join_path(self.prefix.bin, 'libtool'),
+                join_path(self.prefix.bin, 'glibtool'))
+        symlink(join_path(self.prefix.bin, 'libtoolize'),
+                join_path(self.prefix.bin, 'glibtoolize'))
diff --git a/var/spack/repos/builtin/packages/libunistring/package.py b/var/spack/repos/builtin/packages/libunistring/package.py
index a4250bc8ee..5653a0eba5 100644
--- a/var/spack/repos/builtin/packages/libunistring/package.py
+++ b/var/spack/repos/builtin/packages/libunistring/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,7 +11,7 @@ class Libunistring(AutotoolsPackage):
     and for manipulating C strings according to the Unicode standard."""
 
     homepage = "https://www.gnu.org/software/libunistring/"
-    url      = "http://ftp.gnu.org/gnu/libunistring/libunistring-0.9.7.tar.xz"
+    url      = "https://ftpmirror.gnu.org/libunistring/libunistring-0.9.7.tar.xz"
 
     version('0.9.7', '82e0545363d111bfdfec2ddbfe62ffd3')
     version('0.9.6', 'cb09c398020c27edac10ca590e9e9ef3')
diff --git a/var/spack/repos/builtin/packages/libunwind/package.py b/var/spack/repos/builtin/packages/libunwind/package.py
index 9c8c0574b1..201c31af52 100644
--- a/var/spack/repos/builtin/packages/libunwind/package.py
+++ b/var/spack/repos/builtin/packages/libunwind/package.py
@@ -1,34 +1,39 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class Libunwind(AutotoolsPackage):
     """A portable and efficient C programming interface (API) to determine
        the call-chain of a program."""
+
     homepage = "http://www.nongnu.org/libunwind/"
     url      = "http://download.savannah.gnu.org/releases/libunwind/libunwind-1.1.tar.gz"
 
+    version('1.3-rc1', 'f09b670de5db6430a3de666e6aed60e3')
+    version('1.2.1', '06ba9e60d92fd6f55cd9dadb084df19e', preferred=True)
     version('1.1', 'fb4ea2f6fbbe45bf032cd36e586883ce')
+
+    variant('xz', default=False,
+            description='Support xz (lzma) compressed symbol tables.')
+
+    depends_on('xz', type='link', when='+xz')
+
+    conflicts('platform=darwin',
+              msg='Non-GNU libunwind needs ELF libraries Darwin does not have')
+
+    provides('unwind')
+
+    def configure_args(self):
+        spec = self.spec
+        args = []
+
+        if '+xz' in spec:
+            args.append('--enable-minidebuginfo')
+        else:
+            args.append('--disable-minidebuginfo')
+
+        return args
diff --git a/var/spack/repos/builtin/packages/libuuid/package.py b/var/spack/repos/builtin/packages/libuuid/package.py
index 750730b6ed..e50030468b 100644
--- a/var/spack/repos/builtin/packages/libuuid/package.py
+++ b/var/spack/repos/builtin/packages/libuuid/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libuv/package.py b/var/spack/repos/builtin/packages/libuv/package.py
index d88b2306aa..5fd2121580 100644
--- a/var/spack/repos/builtin/packages/libuv/package.py
+++ b/var/spack/repos/builtin/packages/libuv/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libvorbis/package.py b/var/spack/repos/builtin/packages/libvorbis/package.py
index 6a3561fb1a..9c526dba0f 100644
--- a/var/spack/repos/builtin/packages/libvorbis/package.py
+++ b/var/spack/repos/builtin/packages/libvorbis/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class Libvorbis(AutotoolsPackage):
 
     depends_on('libogg')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
 
     # `make check` crashes when run in parallel
     parallel = False
diff --git a/var/spack/repos/builtin/packages/libvterm/package.py b/var/spack/repos/builtin/packages/libvterm/package.py
index 5ed4d0b74e..aef6d23d27 100644
--- a/var/spack/repos/builtin/packages/libvterm/package.py
+++ b/var/spack/repos/builtin/packages/libvterm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libwebsockets/package.py b/var/spack/repos/builtin/packages/libwebsockets/package.py
index 0b02793554..94f0982ba1 100644
--- a/var/spack/repos/builtin/packages/libwebsockets/package.py
+++ b/var/spack/repos/builtin/packages/libwebsockets/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,6 +11,7 @@ class Libwebsockets(CMakePackage):
 
     homepage = "https://github.com/warmcat/libwebsockets"
     url      = "https://github.com/warmcat/libwebsockets/archive/v2.1.0.tar.gz"
+    maintainers = ['ax3l']
 
     version('2.2.1', '1f641cde2ab3687db3d553f68fe0f620')
     version('2.1.1', '674684ffb90d4a0bcf7a075eb7b90192')
diff --git a/var/spack/repos/builtin/packages/libwindowswm/package.py b/var/spack/repos/builtin/packages/libwindowswm/package.py
index ffbff1f652..26a5bdb066 100644
--- a/var/spack/repos/builtin/packages/libwindowswm/package.py
+++ b/var/spack/repos/builtin/packages/libwindowswm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -43,5 +24,5 @@ class Libwindowswm(AutotoolsPackage):
 
     depends_on('xextproto', type='build')
     depends_on('windowswmproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libx11/package.py b/var/spack/repos/builtin/packages/libx11/package.py
index 9658fab352..8f49422985 100644
--- a/var/spack/repos/builtin/packages/libx11/package.py
+++ b/var/spack/repos/builtin/packages/libx11/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -41,6 +22,15 @@ class Libx11(AutotoolsPackage):
     depends_on('xtrans', type='build')
     depends_on('kbproto', type=('build', 'link'))
     depends_on('inputproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
     depends_on('perl', type='build')
+
+    @property
+    def libs(self):
+        for dir in ['lib64', 'lib']:
+            libs = find_libraries('libX11', join_path(self.prefix, dir),
+                                  shared=True, recursive=False)
+            if libs:
+                return libs
+        return None
diff --git a/var/spack/repos/builtin/packages/libxau/package.py b/var/spack/repos/builtin/packages/libxau/package.py
index 64f9a3a526..4c5acaf985 100644
--- a/var/spack/repos/builtin/packages/libxau/package.py
+++ b/var/spack/repos/builtin/packages/libxau/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Libxau(AutotoolsPackage):
     version('1.0.8', 'a85cd601d82bc79c0daa280917572e20')
 
     depends_on('xproto', type=('build', 'link'))
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxaw/package.py b/var/spack/repos/builtin/packages/libxaw/package.py
index 7470ce2f72..327c8c6088 100644
--- a/var/spack/repos/builtin/packages/libxaw/package.py
+++ b/var/spack/repos/builtin/packages/libxaw/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -42,5 +23,5 @@ class Libxaw(AutotoolsPackage):
 
     depends_on('xproto', type='build')
     depends_on('xextproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxaw3d/package.py b/var/spack/repos/builtin/packages/libxaw3d/package.py
index 13137d622f..85b53d2bfc 100644
--- a/var/spack/repos/builtin/packages/libxaw3d/package.py
+++ b/var/spack/repos/builtin/packages/libxaw3d/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,5 +21,5 @@ class Libxaw3d(AutotoolsPackage):
     depends_on('libxext')
     depends_on('libxpm')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxc/package.py b/var/spack/repos/builtin/packages/libxc/package.py
index d92ba97e73..bdb5fcabd2 100644
--- a/var/spack/repos/builtin/packages/libxc/package.py
+++ b/var/spack/repos/builtin/packages/libxc/package.py
@@ -1,31 +1,12 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class Libxc(Package):
+class Libxc(AutotoolsPackage):
     """Libxc is a library of exchange-correlation functionals for
     density-functional theory."""
 
@@ -52,7 +33,7 @@ class Libxc(Package):
         # Libxc installs both shared and static libraries.
         # If a client ask for static explicitly then return
         # the static libraries
-        shared = False if 'static' in query_parameters else True
+        shared = ('static' not in query_parameters)
 
         # Libxc has a fortran90 interface: give clients the
         # possibility to query for it
@@ -60,34 +41,46 @@ class Libxc(Package):
             libraries = ['libxcf90'] + libraries
 
         return find_libraries(
-            libraries, root=self.prefix, shared=shared, recurse=True
+            libraries, root=self.prefix, shared=shared, recursive=True
         )
 
-    def install(self, spec, prefix):
-        # Optimizations for the Intel compiler, suggested by CP2K
+    def setup_environment(self, spack_env, run_env):
         optflags = '-O2'
         if self.compiler.name == 'intel':
-            optflags += ' -xAVX -axCORE-AVX2 -ipo'
+            # Optimizations for the Intel compiler, suggested by CP2K
+            #
+            # Note that not every lowly login node has advanced CPUs:
+            #
+            #   $ icc  -xAVX -axCORE-AVX2 -ipo hello.c
+            #   $ ./a.out
+            #   Please verify that both the operating system and the \
+            #   processor support Intel(R) AVX instructions.
+            #
+            # NB: The same flags are applied in:
+            #   - ../libint/package.py
+            #
+            # Related:
+            #   - ../fftw/package.py        variants: simd, fma
+            #   - ../c-blosc/package.py     variant:  avx2
+            #   - ../r-rcppblaze/package.py AVX* in "info" but not in code?
+            #   - ../openblas/package.py    variants: cpu_target!?!
+            #   - ../cp2k/package.py
+            #
+            # Documentation at:
+            # https://software.intel.com/en-us/cpp-compiler-18.0-developer-guide-and-reference-ax-qax
+            #
+            optflags += ' -xSSE4.2 -axAVX,CORE-AVX2 -ipo'
             if which('xiar'):
-                env['AR'] = 'xiar'
-
-        if 'CFLAGS' in env and env['CFLAGS']:
-            env['CFLAGS'] += ' ' + optflags
-        else:
-            env['CFLAGS'] = optflags
+                spack_env.set('AR', 'xiar')
 
-        if 'FCFLAGS' in env and env['FCFLAGS']:
-            env['FCFLAGS'] += ' ' + optflags
-        else:
-            env['FCFLAGS'] = optflags
+        spack_env.append_flags('CFLAGS',  optflags)
+        spack_env.append_flags('FCFLAGS', optflags)
 
-        configure('--prefix={0}'.format(prefix),
-                  '--enable-shared')
-
-        make()
+    def configure_args(self):
+        args = ['--enable-shared']
+        return args
 
+    def check(self):
         # libxc provides a testsuite, but many tests fail
         # http://www.tddft.org/pipermail/libxc/2013-February/000032.html
-        # make('check')
-
-        make('install')
+        pass
diff --git a/var/spack/repos/builtin/packages/libxcb/package.py b/var/spack/repos/builtin/packages/libxcb/package.py
index cbca3bfd39..91f6d3f648 100644
--- a/var/spack/repos/builtin/packages/libxcb/package.py
+++ b/var/spack/repos/builtin/packages/libxcb/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,20 +13,30 @@ class Libxcb(AutotoolsPackage):
     extensibility."""
 
     homepage = "https://xcb.freedesktop.org/"
-    url      = "https://xcb.freedesktop.org/dist/libxcb-1.11.tar.gz"
+    url      = "https://xcb.freedesktop.org/dist/libxcb-1.13.tar.gz"
 
-    version('1.12', '95eee7c28798e16ba5443f188b27a476')
-    version('1.11', '1698dd837d7e6e94d029dbe8b3a82deb')
+    version('1.13',   '3ba7fe0a7d60650bfb73fbf623aa57cc')
+    version('1.12',   '95eee7c28798e16ba5443f188b27a476')
     version('1.11.1', '118623c15a96b08622603a71d8789bf3')
+    version('1.11',   '1698dd837d7e6e94d029dbe8b3a82deb')
 
     depends_on('libpthread-stubs')
     depends_on('libxau@0.99.2:')
     depends_on('libxdmcp')
 
+    # libxcb 1.X requires xcb-proto >= 1.X
     depends_on('xcb-proto', type='build')
+    depends_on('xcb-proto@1.13:', when='@1.13:1.13.999', type='build')
+    depends_on('xcb-proto@1.12:', when='@1.12:1.12.999', type='build')
+    depends_on('xcb-proto@1.11:', when='@1.11:1.11.999', type='build')
+
     # TODO: uncomment once build deps can be resolved separately
-    # depends_on('python@2:2.8', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    # See #7646, #4145, #4063, and #2548 for details
+    # libxcb 1.13 added Python 3 support
+    # depends_on('python', type='build')
+    # depends_on('python@2:2.8', when='@:1.12', type='build')
+
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def patch(self):
diff --git a/var/spack/repos/builtin/packages/libxcomposite/package.py b/var/spack/repos/builtin/packages/libxcomposite/package.py
index b408a08394..d0a9a2f971 100644
--- a/var/spack/repos/builtin/packages/libxcomposite/package.py
+++ b/var/spack/repos/builtin/packages/libxcomposite/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,7 +17,7 @@ class Libxcomposite(AutotoolsPackage):
 
     depends_on('libx11')
     depends_on('libxfixes')
-
+    depends_on('fixesproto@0.4:', type='build')
     depends_on('compositeproto@0.4:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxcursor/package.py b/var/spack/repos/builtin/packages/libxcursor/package.py
index ec6b4d28f1..1160708781 100644
--- a/var/spack/repos/builtin/packages/libxcursor/package.py
+++ b/var/spack/repos/builtin/packages/libxcursor/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Libxcursor(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('fixesproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxdamage/package.py b/var/spack/repos/builtin/packages/libxdamage/package.py
index 948e266aba..bb1684c364 100644
--- a/var/spack/repos/builtin/packages/libxdamage/package.py
+++ b/var/spack/repos/builtin/packages/libxdamage/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Libxdamage(AutotoolsPackage):
     depends_on('damageproto@1.1:', type='build')
     depends_on('fixesproto', type='build')
     depends_on('xextproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxdmcp/package.py b/var/spack/repos/builtin/packages/libxdmcp/package.py
index 093aa90dd3..f3fbc87ef4 100644
--- a/var/spack/repos/builtin/packages/libxdmcp/package.py
+++ b/var/spack/repos/builtin/packages/libxdmcp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,5 +15,5 @@ class Libxdmcp(AutotoolsPackage):
     version('1.1.2', 'ab0d6a38f0344a05d698ec7d48cfa5a8')
 
     depends_on('xproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxevie/package.py b/var/spack/repos/builtin/packages/libxevie/package.py
index 0ad59c24ee..a1ceb23dbb 100644
--- a/var/spack/repos/builtin/packages/libxevie/package.py
+++ b/var/spack/repos/builtin/packages/libxevie/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Libxevie(AutotoolsPackage):
     depends_on('xproto', type='build')
     depends_on('xextproto', type='build')
     depends_on('evieext', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxext/package.py b/var/spack/repos/builtin/packages/libxext/package.py
index 2ecdad7be5..a4e7b9234c 100644
--- a/var/spack/repos/builtin/packages/libxext/package.py
+++ b/var/spack/repos/builtin/packages/libxext/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Libxext(AutotoolsPackage):
 
     depends_on('xproto@7.0.13:', type='build')
     depends_on('xextproto@7.1.99:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxfixes/package.py b/var/spack/repos/builtin/packages/libxfixes/package.py
index 5c18e389f1..cfcaa5f466 100644
--- a/var/spack/repos/builtin/packages/libxfixes/package.py
+++ b/var/spack/repos/builtin/packages/libxfixes/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Libxfixes(AutotoolsPackage):
     depends_on('xproto', type='build')
     depends_on('fixesproto@5.0:', type='build')
     depends_on('xextproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxfont/package.py b/var/spack/repos/builtin/packages/libxfont/package.py
index 4d08c4db71..1fef06a9bb 100644
--- a/var/spack/repos/builtin/packages/libxfont/package.py
+++ b/var/spack/repos/builtin/packages/libxfont/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -44,5 +25,5 @@ class Libxfont(AutotoolsPackage):
     depends_on('xtrans', type='build')
     depends_on('xproto', type='build')
     depends_on('fontsproto@2.1.3:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxfont2/package.py b/var/spack/repos/builtin/packages/libxfont2/package.py
index b2a6a793cd..ee3f0ac054 100644
--- a/var/spack/repos/builtin/packages/libxfont2/package.py
+++ b/var/spack/repos/builtin/packages/libxfont2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -44,5 +25,5 @@ class Libxfont2(AutotoolsPackage):
     depends_on('xtrans', type='build')
     depends_on('xproto', type='build')
     depends_on('fontsproto@2.1.3:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxfontcache/package.py b/var/spack/repos/builtin/packages/libxfontcache/package.py
index d113cda057..a48a671dc1 100644
--- a/var/spack/repos/builtin/packages/libxfontcache/package.py
+++ b/var/spack/repos/builtin/packages/libxfontcache/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Libxfontcache(AutotoolsPackage):
 
     depends_on('xextproto', type='build')
     depends_on('fontcacheproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxft/package.py b/var/spack/repos/builtin/packages/libxft/package.py
index 63f9236302..baa61ba7f0 100644
--- a/var/spack/repos/builtin/packages/libxft/package.py
+++ b/var/spack/repos/builtin/packages/libxft/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -42,5 +23,5 @@ class Libxft(AutotoolsPackage):
     depends_on('libx11')
     depends_on('libxrender@0.8.2:')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxi/package.py b/var/spack/repos/builtin/packages/libxi/package.py
index a16be21fba..3c474aaf4b 100644
--- a/var/spack/repos/builtin/packages/libxi/package.py
+++ b/var/spack/repos/builtin/packages/libxi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,10 +14,14 @@ class Libxi(AutotoolsPackage):
 
     version('1.7.6', 'f3828f9d7893068f6f6f10fe15b31afa')
 
+    depends_on('pkgconfig', type='build')
     depends_on('libx11@1.6:')
     depends_on('libxext@1.0.99.1:')
     depends_on('libxfixes@5:')
 
+    # transient build dependency (from libxfixes), i.e. shouldn't be needed?
+    depends_on('fixesproto@5.0:', type='build')
+
     depends_on('xproto@7.0.13:', type='build')
     depends_on('xextproto@7.0.3:', type='build')
     depends_on('inputproto@2.2.99.1:', type='build')
diff --git a/var/spack/repos/builtin/packages/libxinerama/package.py b/var/spack/repos/builtin/packages/libxinerama/package.py
index 74ec63f266..151d74eb79 100644
--- a/var/spack/repos/builtin/packages/libxinerama/package.py
+++ b/var/spack/repos/builtin/packages/libxinerama/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Libxinerama(AutotoolsPackage):
 
     depends_on('xextproto', type='build')
     depends_on('xineramaproto@1.1.99.1:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxkbcommon/package.py b/var/spack/repos/builtin/packages/libxkbcommon/package.py
new file mode 100644
index 0000000000..d864c4b786
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libxkbcommon/package.py
@@ -0,0 +1,32 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Libxkbcommon(AutotoolsPackage):
+    """xkbcommon is a library to handle keyboard descriptions, including
+    loading them from disk, parsing them and handling their state. It's mainly
+    meant for client toolkits, window systems, and other system
+    applications."""
+
+    homepage = "https://xkbcommon.org/"
+    url      = "https://github.com/xkbcommon/libxkbcommon/archive/xkbcommon-0.8.0.tar.gz"
+
+    version('0.8.0', '0d9738fb2ed2dcc6e2c6920d94e135ce')
+
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool',  type='build')
+    depends_on('m4',       type='build')
+    depends_on('bison',    type='build')
+    depends_on('xkbdata')
+
+    def configure_args(self):
+        spec = self.spec
+        args = []
+        args.append('--with-xkb-config-root={0}'
+                    .format(spec['xkbdata'].prefix))
+        return args
diff --git a/var/spack/repos/builtin/packages/libxkbfile/package.py b/var/spack/repos/builtin/packages/libxkbfile/package.py
index c345a8a362..e1730005f9 100644
--- a/var/spack/repos/builtin/packages/libxkbfile/package.py
+++ b/var/spack/repos/builtin/packages/libxkbfile/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Libxkbfile(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('kbproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxkbui/package.py b/var/spack/repos/builtin/packages/libxkbui/package.py
index eb34053918..168fb2fa3d 100644
--- a/var/spack/repos/builtin/packages/libxkbui/package.py
+++ b/var/spack/repos/builtin/packages/libxkbui/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Libxkbui(AutotoolsPackage):
     depends_on('libxt')
     depends_on('libxkbfile')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxml2/package.py b/var/spack/repos/builtin/packages/libxml2/package.py
index 87bbb965b8..eb2409ebf2 100644
--- a/var/spack/repos/builtin/packages/libxml2/package.py
+++ b/var/spack/repos/builtin/packages/libxml2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,11 @@ class Libxml2(AutotoolsPackage):
     """Libxml2 is the XML C parser and toolkit developed for the Gnome
        project (but usable outside of the Gnome platform), it is free
        software available under the MIT License."""
+
     homepage = "http://xmlsoft.org"
-    url      = "http://xmlsoft.org/sources/libxml2-2.9.2.tar.gz"
+    url      = "http://xmlsoft.org/sources/libxml2-2.9.8.tar.gz"
 
+    version('2.9.8', 'b786e353e2aa1b872d70d5d1ca0c740d')
     version('2.9.4', 'ae249165c173b1ff386ee8ad676815f5')
     version('2.9.2', '9e6a9aca9d155737868b3dc5fd82f788')
     version('2.7.8', '8127a65e8c3b08856093099b52599c86')
@@ -44,7 +27,7 @@ class Libxml2(AutotoolsPackage):
     depends_on('zlib')
     depends_on('xz')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
 
     def configure_args(self):
         spec = self.spec
@@ -60,3 +43,7 @@ class Libxml2(AutotoolsPackage):
             args.append('--without-python')
 
         return args
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        spack_env.prepend_path('CPATH', self.prefix.include.libxml2)
+        run_env.prepend_path('CPATH', self.prefix.include.libxml2)
diff --git a/var/spack/repos/builtin/packages/libxmu/package.py b/var/spack/repos/builtin/packages/libxmu/package.py
index bb3f168d6a..854946016b 100644
--- a/var/spack/repos/builtin/packages/libxmu/package.py
+++ b/var/spack/repos/builtin/packages/libxmu/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -41,5 +22,5 @@ class Libxmu(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xextproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxp/package.py b/var/spack/repos/builtin/packages/libxp/package.py
index f18d4b89c9..d5260e0039 100644
--- a/var/spack/repos/builtin/packages/libxp/package.py
+++ b/var/spack/repos/builtin/packages/libxp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Libxp(AutotoolsPackage):
 
     depends_on('xextproto', type='build')
     depends_on('printproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxpm/package.py b/var/spack/repos/builtin/packages/libxpm/package.py
index 11ede1fe88..6eb7b81af7 100644
--- a/var/spack/repos/builtin/packages/libxpm/package.py
+++ b/var/spack/repos/builtin/packages/libxpm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -42,7 +23,7 @@ class Libxpm(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def setup_environment(self, spack_env, run_env):
diff --git a/var/spack/repos/builtin/packages/libxpresent/package.py b/var/spack/repos/builtin/packages/libxpresent/package.py
index 286bf89fb8..3dbc97145e 100644
--- a/var/spack/repos/builtin/packages/libxpresent/package.py
+++ b/var/spack/repos/builtin/packages/libxpresent/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Libxpresent(AutotoolsPackage):
     depends_on('xproto', type='build')
     depends_on('presentproto@1.0:', type='build')
     depends_on('xextproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxprintapputil/package.py b/var/spack/repos/builtin/packages/libxprintapputil/package.py
index a6d2838d4d..a1207a4323 100644
--- a/var/spack/repos/builtin/packages/libxprintapputil/package.py
+++ b/var/spack/repos/builtin/packages/libxprintapputil/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Libxprintapputil(AutotoolsPackage):
     depends_on('libxau')
 
     depends_on('printproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxprintutil/package.py b/var/spack/repos/builtin/packages/libxprintutil/package.py
index 9bd765e1b6..0bbb53d62f 100644
--- a/var/spack/repos/builtin/packages/libxprintutil/package.py
+++ b/var/spack/repos/builtin/packages/libxprintutil/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Libxprintutil(AutotoolsPackage):
     depends_on('libxau')
 
     depends_on('printproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxrandr/package.py b/var/spack/repos/builtin/packages/libxrandr/package.py
index 2ee8f76acb..29167ef0a1 100644
--- a/var/spack/repos/builtin/packages/libxrandr/package.py
+++ b/var/spack/repos/builtin/packages/libxrandr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,5 +21,5 @@ class Libxrandr(AutotoolsPackage):
     depends_on('randrproto@1.5:', type='build')
     depends_on('xextproto', type='build')
     depends_on('renderproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxrender/package.py b/var/spack/repos/builtin/packages/libxrender/package.py
index 49ed107daa..ac46c46ce8 100644
--- a/var/spack/repos/builtin/packages/libxrender/package.py
+++ b/var/spack/repos/builtin/packages/libxrender/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Libxrender(AutotoolsPackage):
     depends_on('libx11@1.6:')
 
     depends_on('renderproto@0.9:', type=('build', 'link'))
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxres/package.py b/var/spack/repos/builtin/packages/libxres/package.py
index eb691f8835..f5a8758d3d 100644
--- a/var/spack/repos/builtin/packages/libxres/package.py
+++ b/var/spack/repos/builtin/packages/libxres/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Libxres(AutotoolsPackage):
 
     depends_on('xextproto', type='build')
     depends_on('resourceproto@1.0:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxscrnsaver/package.py b/var/spack/repos/builtin/packages/libxscrnsaver/package.py
index ec68e8d395..242ddbd50f 100644
--- a/var/spack/repos/builtin/packages/libxscrnsaver/package.py
+++ b/var/spack/repos/builtin/packages/libxscrnsaver/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Libxscrnsaver(AutotoolsPackage):
 
     depends_on('xextproto', type='build')
     depends_on('scrnsaverproto@1.2:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxshmfence/package.py b/var/spack/repos/builtin/packages/libxshmfence/package.py
index fea8c64fdd..c0206fa598 100644
--- a/var/spack/repos/builtin/packages/libxshmfence/package.py
+++ b/var/spack/repos/builtin/packages/libxshmfence/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,10 +14,11 @@ class Libxshmfence(AutotoolsPackage):
     using file descriptor passing."""
 
     homepage = "https://cgit.freedesktop.org/xorg/lib/libxshmfence/"
-    url      = "http://xorg.freedesktop.org/archive/individual/lib/libxshmfence-1.2.tar.gz"
+    url      = "https://www.x.org/archive/individual/lib/libxshmfence-1.3.tar.bz2"
 
-    version('1.2', 'f0b30c0fc568b22ec524859ee28556f1')
+    version('1.3', '42dda8016943dc12aff2c03a036e0937')
+    version('1.2', '66662e76899112c0f99e22f2fc775a7e')
 
     depends_on('xproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxslt/package.py b/var/spack/repos/builtin/packages/libxslt/package.py
index cbb04c0ee2..cdd361928f 100644
--- a/var/spack/repos/builtin/packages/libxslt/package.py
+++ b/var/spack/repos/builtin/packages/libxslt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libxsmm/package.py b/var/spack/repos/builtin/packages/libxsmm/package.py
index ec1fa2f0bc..0786ec051c 100644
--- a/var/spack/repos/builtin/packages/libxsmm/package.py
+++ b/var/spack/repos/builtin/packages/libxsmm/package.py
@@ -1,41 +1,25 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 from glob import glob
 
 
-class Libxsmm(Package):
+class Libxsmm(MakefilePackage):
     '''Library targeting Intel Architecture
     for small, dense or sparse matrix multiplications,
     and small convolutions.'''
 
     homepage = 'https://github.com/hfp/libxsmm'
-    url      = 'https://github.com/hfp/libxsmm/archive/1.8.1.tar.gz'
-
-    version('develop', git='https://github.com/hfp/libxsmm.git')
+    url      = 'https://github.com/hfp/libxsmm/archive/1.9.tar.gz'
+    git      = 'https://github.com/hfp/libxsmm.git'
 
+    version('develop', branch='master')
+    version('1.9',   'a001a491d9b98239bc2bfd906bd09d90')
+    version('1.8.3', '3415928340929c3a29773934de05c978')
+    version('1.8.2', '8f11ece699244c28dcb6742969a2ccd4')
     version('1.8.1', 'ece51ec767580f4542f509655daa5ec0')
     version('1.8',   '2d513afbdad99e5d04c6c4ab4c9bb25b')
     version('1.7.1', 'a938335b1c2c90616dc72c2c1a5824ab')
@@ -60,17 +44,19 @@ class Libxsmm(Package):
             description='Unoptimized with call-trace (LIBXSMM_TRACE).')
     variant('header-only', default=False,
             description='Produce header-only installation')
+    conflicts('+header-only', when='@:1.6.2',
+              msg='Header-only is available since v1.6.2!')
 
     @property
     def libs(self):
         result = find_libraries(['libxsmm', 'libxsmmf'], root=self.prefix,
-                                recurse=True)
+                                recursive=True)
         if len(result) == 0:
             result = find_libraries(['libxsmm', 'libxsmmf'], root=self.prefix,
-                                    shared=False, recurse=True)
+                                    shared=False, recursive=True)
         return result
 
-    def patch(self):
+    def edit(self, spec, prefix):
         kwargs = {'ignore_absent': False, 'backup': False, 'string': True}
         makefile = FileFilter('Makefile.inc')
 
@@ -83,26 +69,7 @@ class Libxsmm(Package):
         makefile.filter('FC = ifort',       'FC ?= ifort', **kwargs)
         makefile.filter('FC = gfortran',    'FC ?= gfortran', **kwargs)
 
-    def manual_install(self, prefix):
-        spec = self.spec
-        install_tree('include', prefix.include)
-        if '~header-only' in spec:
-            install_tree('lib', prefix.lib)
-        doc_path = prefix.share + '/libxsmm/doc'
-        mkdirp(doc_path)
-        for doc_file in glob('documentation/*.md'):
-            install(doc_file, doc_path)
-        for doc_file in glob('documentation/*.pdf'):
-            install(doc_file, doc_path)
-        install('README.md', doc_path)
-        install('LICENSE', doc_path)
-
-    def install(self, spec, prefix):
-        if '+header-only' in spec and '@1.6.2:' not in spec:
-            raise InstallError(
-                "The variant +header-only is only available " +
-                "for versions @1.6.2:")
-
+    def build(self, spec, prefix):
         # include symbols by default
         make_args = ['SYM=1']
 
@@ -118,4 +85,21 @@ class Libxsmm(Package):
             make_args += ['TRACE=1']
 
         make(*make_args)
-        self.manual_install(prefix)
+
+    def install(self, spec, prefix):
+        install_tree('include', prefix.include)
+        if '+header-only' in spec:
+            install_tree('src', prefix.src)
+        else:
+            install_tree('lib', prefix.lib)
+        mkdirp(prefix.doc)
+        for doc_file in glob(join_path('documentation', '*.md')):
+            install(doc_file, prefix.doc)
+        for doc_file in glob(join_path('documentation', '*.pdf')):
+            install(doc_file, prefix.doc)
+        if '@1.8.2:' in spec:
+            install('LICENSE.md', prefix.doc)
+        else:
+            install('README.md', prefix.doc)
+            install('LICENSE', prefix.doc)
+        install('version.txt', prefix.doc)
diff --git a/var/spack/repos/builtin/packages/libxstream/package.py b/var/spack/repos/builtin/packages/libxstream/package.py
index 00b7c0be32..df27052dbc 100644
--- a/var/spack/repos/builtin/packages/libxstream/package.py
+++ b/var/spack/repos/builtin/packages/libxstream/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libxt/package.py b/var/spack/repos/builtin/packages/libxt/package.py
index b3e2ac4e63..65746869a0 100644
--- a/var/spack/repos/builtin/packages/libxt/package.py
+++ b/var/spack/repos/builtin/packages/libxt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,11 @@ class Libxt(AutotoolsPackage):
 
     depends_on('xproto', type='build')
     depends_on('kbproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
+
+    @property
+    def libs(self):
+        return find_libraries(
+            'libXt', root=self.prefix, shared=True, recursive=True
+        )
diff --git a/var/spack/repos/builtin/packages/libxtrap/package.py b/var/spack/repos/builtin/packages/libxtrap/package.py
index 83405cf48d..9a7f3ac1ff 100644
--- a/var/spack/repos/builtin/packages/libxtrap/package.py
+++ b/var/spack/repos/builtin/packages/libxtrap/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -48,5 +29,5 @@ class Libxtrap(AutotoolsPackage):
 
     depends_on('trapproto', type='build')
     depends_on('xextproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxtst/package.py b/var/spack/repos/builtin/packages/libxtst/package.py
index 9b6b4093ba..2bd5d8cefd 100644
--- a/var/spack/repos/builtin/packages/libxtst/package.py
+++ b/var/spack/repos/builtin/packages/libxtst/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -50,5 +31,5 @@ class Libxtst(AutotoolsPackage):
     depends_on('xextproto@7.0.99.3:', type='build')
     depends_on('inputproto', type='build')
     depends_on('fixesproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxv/package.py b/var/spack/repos/builtin/packages/libxv/package.py
index e29ec91b84..773f6eee2a 100644
--- a/var/spack/repos/builtin/packages/libxv/package.py
+++ b/var/spack/repos/builtin/packages/libxv/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Libxv(AutotoolsPackage):
 
     depends_on('xextproto', type='build')
     depends_on('videoproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxvmc/package.py b/var/spack/repos/builtin/packages/libxvmc/package.py
index 42e56618a4..a3ca179a86 100644
--- a/var/spack/repos/builtin/packages/libxvmc/package.py
+++ b/var/spack/repos/builtin/packages/libxvmc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Libxvmc(AutotoolsPackage):
 
     depends_on('xextproto', type='build')
     depends_on('videoproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxxf86dga/package.py b/var/spack/repos/builtin/packages/libxxf86dga/package.py
index f92ff7fb63..45ad7a1540 100644
--- a/var/spack/repos/builtin/packages/libxxf86dga/package.py
+++ b/var/spack/repos/builtin/packages/libxxf86dga/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Libxxf86dga(AutotoolsPackage):
     depends_on('xproto', type='build')
     depends_on('xextproto', type='build')
     depends_on('xf86dgaproto@2.0.99.2:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxxf86misc/package.py b/var/spack/repos/builtin/packages/libxxf86misc/package.py
index 8b161008f8..a8abde1e66 100644
--- a/var/spack/repos/builtin/packages/libxxf86misc/package.py
+++ b/var/spack/repos/builtin/packages/libxxf86misc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Libxxf86misc(AutotoolsPackage):
     depends_on('xproto', type='build')
     depends_on('xextproto', type='build')
     depends_on('xf86miscproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxxf86vm/package.py b/var/spack/repos/builtin/packages/libxxf86vm/package.py
index 6b2cf951ed..4ec5eae3e0 100644
--- a/var/spack/repos/builtin/packages/libxxf86vm/package.py
+++ b/var/spack/repos/builtin/packages/libxxf86vm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Libxxf86vm(AutotoolsPackage):
     depends_on('xproto', type='build')
     depends_on('xextproto', type='build')
     depends_on('xf86vidmodeproto@2.2.99.1:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libyogrt/package.py b/var/spack/repos/builtin/packages/libyogrt/package.py
index f48ce80e83..5d63913911 100644
--- a/var/spack/repos/builtin/packages/libyogrt/package.py
+++ b/var/spack/repos/builtin/packages/libyogrt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libzip/package.py b/var/spack/repos/builtin/packages/libzip/package.py
index c193caae7f..c40bc283e1 100644
--- a/var/spack/repos/builtin/packages/libzip/package.py
+++ b/var/spack/repos/builtin/packages/libzip/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/lighttpd/package.py b/var/spack/repos/builtin/packages/lighttpd/package.py
new file mode 100644
index 0000000000..7824d9392b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/lighttpd/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Lighttpd(CMakePackage):
+    """a secure, fast, compliant and very flexible web-server"""
+
+    homepage = "https://www.lighttpd.net"
+    url      = "https://download.lighttpd.net/lighttpd/releases-1.4.x/lighttpd-1.4.50.tar.gz"
+
+    version('1.4.50', sha256='c9a9f175aca6db22ebebbc47de52c54a99bbd1dce8d61bb75103609a3d798235')
+    version('1.4.49', sha256='8b744baf9f29c386fff1a6d2e435491e726cb8d29cfdb1fe20ab782ee2fc2ac7')
+
+    def cmake_args(self):
+        return ["-DSBINDIR=bin"]
diff --git a/var/spack/repos/builtin/packages/likwid/package.py b/var/spack/repos/builtin/packages/likwid/package.py
index edba82da40..c7f8403f47 100644
--- a/var/spack/repos/builtin/packages/likwid/package.py
+++ b/var/spack/repos/builtin/packages/likwid/package.py
@@ -1,45 +1,29 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
+import os
 
 
 class Likwid(Package):
     """Likwid is a simple to install and use toolsuite of command line
     applications for performance oriented programmers. It works for Intel and
-    AMD processors on the Linux operating system."""
+    AMD processors on the Linux operating system. This version uses the
+    perf_event backend which reduces the feature set but allows user installs.
+    See https://github.com/RRZE-HPC/likwid/wiki/TutorialLikwidPerf#feature-limitations
+    for information."""
 
     homepage = "https://github.com/RRZE-HPC/likwid"
     url      = "https://github.com/RRZE-HPC/likwid/archive/4.1.2.tar.gz"
 
     maintainers = ['davydden']
 
-    version('4.3.0', 'f6bdf12513af95bd6eefa9c68644e724')
-    version('4.2.1', 'c408ddcf0317cdd894af4c580cd74294')
-    version('4.2.0', 'e41ff334b8f032a323d941ce32907a75')
-    version('4.1.2', 'a857ce5bd23e31d96e2963fe81cb38f0')
+    version('4.3.2', '2cf00e220dfe22c8d9b6e44f7534e11d')
+    version('4.3.1', 'ff28250f622185688bf5e2e0975368ea')
+    version('4.3.0', '7f8f6981d7d341fce2621554323f8c8b')
 
     # NOTE: There is no way to use an externally provided hwloc with Likwid.
     # The reason is that the internal hwloc is patched to contain extra
@@ -64,10 +48,11 @@ class Likwid(Package):
     @run_before('install')
     def filter_sbang(self):
         # Filter sbang before install so Spack's sbang hook can fix it up
-        perl = join_path(self.spec['perl'].prefix.bin, 'perl')
         files = ['perl/feedGnuplot'] + glob.glob('filters/*')
 
-        filter_file('^#!/usr/bin/perl', '#!{0}'.format(perl), *files)
+        filter_file('^#!/usr/bin/perl',
+                    '#!{0}'.format(self.spec['perl'].command.path),
+                    *files)
 
     def install(self, spec, prefix):
         if self.compiler.name not in self.supported_compilers:
@@ -83,8 +68,16 @@ class Likwid(Package):
                     prefix,
                     'config.mk')
 
-        filter_file('^INSTALL_CHOWN.*',
-                    'INSTALL_CHOWN = -o $(USER)',
+        # FIXME: once https://github.com/spack/spack/issues/4432 is
+        # resolved, install as root by default and remove this
+        filter_file('^ACCESSMODE .*',
+                    'ACCESSMODE = perf_event',
+                    'config.mk')
+        filter_file('^BUILDFREQ .*',
+                    'BUILDFREQ = false',
+                    'config.mk')
+        filter_file('^BUILDDAEMON .*',
+                    'BUILDDAEMON = false',
                     'config.mk')
 
         if spec.satisfies('^lua'):
@@ -104,5 +97,6 @@ class Likwid(Package):
                             spec['lua'].prefix.bin),
                         'config.mk')
 
+        env['PWD'] = os.getcwd()
         make()
         make('install')
diff --git a/var/spack/repos/builtin/packages/linkphase3/package.py b/var/spack/repos/builtin/packages/linkphase3/package.py
index 4cba38115a..2aed38c49c 100644
--- a/var/spack/repos/builtin/packages/linkphase3/package.py
+++ b/var/spack/repos/builtin/packages/linkphase3/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,10 +10,9 @@ class Linkphase3(Package):
     """Haplotype reconstruction in pedigreed populations."""
 
     homepage = "https://github.com/tdruet/LINKPHASE3"
-    url      = "https://github.com/tdruet/LINKPHASE3"
+    git      = "https://github.com/tdruet/LINKPHASE3.git"
 
-    version('2017-06-14', commit='559913593fc818bb1adb29796a548cf5bf323827',
-            git='https://github.com/tdruet/LINKPHASE3.git')
+    version('2017-06-14', commit='559913593fc818bb1adb29796a548cf5bf323827')
 
     def install(self, spec, prefix):
         fortran = Executable(self.compiler.fc)
diff --git a/var/spack/repos/builtin/packages/linux-headers/package.py b/var/spack/repos/builtin/packages/linux-headers/package.py
index 224c502121..1ad8e9687a 100644
--- a/var/spack/repos/builtin/packages/linux-headers/package.py
+++ b/var/spack/repos/builtin/packages/linux-headers/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/listres/package.py b/var/spack/repos/builtin/packages/listres/package.py
index 783b4f48d6..62a953fb61 100644
--- a/var/spack/repos/builtin/packages/listres/package.py
+++ b/var/spack/repos/builtin/packages/listres/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Listres(AutotoolsPackage):
     depends_on('libxmu')
 
     depends_on('xproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/llvm-lld/package.py b/var/spack/repos/builtin/packages/llvm-lld/package.py
deleted file mode 100644
index ff27c21f94..0000000000
--- a/var/spack/repos/builtin/packages/llvm-lld/package.py
+++ /dev/null
@@ -1,48 +0,0 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-from spack import *
-
-
-class LlvmLld(CMakePackage):
-    """lld - The LLVM Linker
-       lld is a new set of modular code for creating linker tools."""
-    homepage = "http://lld.llvm.org"
-    url      = "http://llvm.org/releases/3.4/lld-3.4.src.tar.gz"
-
-    version('3.4', '3b6a17e58c8416c869c14dd37682f78e')
-
-    depends_on('llvm')
-    depends_on('cmake@2.8:', type='build')
-
-    def cmake_args(self):
-        if 'CXXFLAGS' in env and env['CXXFLAGS']:
-            env['CXXFLAGS'] += ' ' + self.compiler.cxx11_flag
-        else:
-            env['CXXFLAGS'] = self.compiler.cxx11_flag
-
-        return [
-            '-DLLD_PATH_TO_LLVM_BUILD=%s' % self.spec['llvm'].prefix,
-            '-DLLVM_MAIN_SRC_DIR=%s' % self.spec['llvm'].prefix,
-        ]
diff --git a/var/spack/repos/builtin/packages/llvm-openmp-ompt/package.py b/var/spack/repos/builtin/packages/llvm-openmp-ompt/package.py
index 2526cd4d03..bc274649f6 100644
--- a/var/spack/repos/builtin/packages/llvm-openmp-ompt/package.py
+++ b/var/spack/repos/builtin/packages/llvm-openmp-ompt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -32,19 +13,14 @@ class LlvmOpenmpOmpt(CMakePackage):
        changes for OMPT, the OpenMP Tools interface"""
 
     homepage = "https://github.com/OpenMPToolsInterface/LLVM-openmp"
+    git      = "https://github.com/OpenMPToolsInterface/LLVM-openmp.git"
 
-    # towards_tr4 branch
-    version('towards_tr4', branch='towards_tr4',
-            git='https://github.com/OpenMPToolsInterface/LLVM-openmp.git')
-
-    version('3.9.2b2',
-            git='https://github.com/OpenMPToolsInterface/LLVM-openmp.git',
-            commit='5cdca5dd3c0c336d42a335ca7cff622e270c9d47')
+    # tr6_forwards branch
+    version('tr6_forwards', branch='tr6_forwards')
+    version('3.9.2b2', commit='5cdca5dd3c0c336d42a335ca7cff622e270c9d47')
 
     # align-to-tr-rebased branch
-    version('3.9.2b',
-            git='https://github.com/OpenMPToolsInterface/LLVM-openmp.git',
-            commit='982a08bcf3df9fb5afc04ac3bada47f19cc4e3d3')
+    version('3.9.2b', commit='982a08bcf3df9fb5afc04ac3bada47f19cc4e3d3')
 
     # variant for building llvm-openmp-ompt as a stand alone library
     variant('standalone', default=False,
@@ -79,9 +55,9 @@ class LlvmOpenmpOmpt(CMakePackage):
                      '-DCMAKE_BUILD_WITH_INSTALL_RPATH=true',
                      '-DLIBOMP_USE_DEBUGGER=false'])
 
-        # Build llvm-openmp-ompt using the toward_tr4 branch
+        # Build llvm-openmp-ompt using the tr6_forwards branch
         # This requires the version to be 5.0 (50)
-        if '@towards_tr4' in self.spec:
+        if '@tr6_forwards' in self.spec:
                 cmake_args.extend(
                     ['-DLIBOMP_OMP_VERSION=50'])
 
diff --git a/var/spack/repos/builtin/packages/llvm/package.py b/var/spack/repos/builtin/packages/llvm/package.py
index 48f767aa17..8ec8d7fc37 100644
--- a/var/spack/repos/builtin/packages/llvm/package.py
+++ b/var/spack/repos/builtin/packages/llvm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -50,6 +31,7 @@ class Llvm(CMakePackage):
     variant('clang', default=True,
             description="Build the LLVM C/C++/Objective-C compiler frontend")
     variant('lldb', default=True, description="Build the LLVM debugger")
+    variant('lld', default=True, description="Build the LLVM linker")
     variant('internal_unwind', default=True,
             description="Build the libcxxabi libunwind")
     variant('polly', default=True,
@@ -80,13 +62,15 @@ class Llvm(CMakePackage):
     depends_on('cmake@3.4.3:', type='build')
 
     # Universal dependency
-    depends_on('python@2.7:2.8')  # Seems not to support python 3.X.Y
+    depends_on('python@2.7:2.8', when='@:4.999')
+    depends_on('python')
     depends_on('py-lit', type=('build', 'run'))
 
     # lldb dependencies
     depends_on('ncurses', when='+lldb')
     depends_on('swig', when='+lldb')
     depends_on('libedit', when='+lldb')
+    depends_on('py-six', when='@5.0.0: +lldb +python')
 
     # gold support
     depends_on('binutils+gold', when='+gold')
@@ -97,6 +81,8 @@ class Llvm(CMakePackage):
 
     base_url = 'http://llvm.org/releases/%%(version)s/%(pkg)s-%%(version)s.src.tar.xz'
     llvm_url = base_url % {'pkg': 'llvm'}
+    # Flang uses its own fork of llvm.
+    flang_llvm_url = 'https://github.com/flang-compiler/llvm.git'
 
     resources = {
         'compiler-rt': {
@@ -141,6 +127,12 @@ class Llvm(CMakePackage):
             'placement': 'lldb',
             'variant': '+lldb',
         },
+        'lld': {
+            'url':  base_url % {'pkg': 'lld'},
+            'destination': 'tools',
+            'placement': 'lld',
+            'variant': '+lld',
+        },
         'polly': {
             'url':  base_url % {'pkg': 'polly'},
             'destination': 'tools',
@@ -156,7 +148,7 @@ class Llvm(CMakePackage):
     }
     releases = [
         {
-            'version': 'trunk',
+            'version': 'develop',
             'repo': 'http://llvm.org/svn/llvm-project/llvm/trunk',
             'resources': {
                 'compiler-rt': 'http://llvm.org/svn/llvm-project/compiler-rt/trunk',
@@ -167,10 +159,91 @@ class Llvm(CMakePackage):
                 'cfe': 'http://llvm.org/svn/llvm-project/cfe/trunk',
                 'clang-tools-extra': 'http://llvm.org/svn/llvm-project/clang-tools-extra/trunk',
                 'lldb': 'http://llvm.org/svn/llvm-project/lldb/trunk',
+                'lld': 'http://llvm.org/svn/llvm-project/lld/trunk',
                 'libunwind': 'http://llvm.org/svn/llvm-project/libunwind/trunk',
             }
         },
         {
+            'version': '7.0.0',
+            'md5': 'e0140354db83cdeb8668531b431398f0',
+            'resources': {
+                'compiler-rt': '3b759c47076298363f4443395e0e51c1',
+                'openmp': '8800aac08f2f9dad0ebf66e0e152bd63',
+                'polly': 'ff689bbfdca3ea812d195f60e63d8346',
+                'libcxx': '5ef835bf8c9f49611af4d5f3362d9658',
+                'libcxxabi': 'f04adafa019f4f5cce9550007da251c1',
+                'cfe': '2ac5d8d78be681e31611c5e546e11174',
+                'clang-tools-extra': 'e98b37a5911cd556775cba0868a56981',
+                'lldb': '76338963b3ccc4f9dccc923716207310',
+                'lld': '5eb148c3064acff71d8e5856163c8323',
+                'libunwind': 'e585a3e4ae6045f2561bc8a8fcd0bfbb'
+            }
+        },
+        {
+            'version': '6.0.1',
+            'md5': 'c88c98709300ce2c285391f387fecce0',
+            'resources': {
+                'compiler-rt': '99bf8bcb68ba96dda74f6aee6c55f639',
+                'openmp': '4826402ae3633c36c51ba4d0e5527d30',
+                'polly': '4e5937753d1f77e2c0feca485fc7f9da',
+                'libcxx': '2c13cd0136ab6f8060a4cde85b5f86e2',
+                'libcxxabi': '41764959176d5fcc7baee8cd22ed1705',
+                'cfe': '4e419bd4e3b55aa06d872320f754bd85',
+                'clang-tools-extra': '431cba2b652e9c227a59a6d681388160',
+                'lldb': '482eba39e78c75a83216cf2d5b7a54b4',
+                'lld': '31cc580b32be124972c40c19c0839fed',
+                'libunwind': '569eed6f508af4c4c053b1112e6f3d0b'
+            }
+        },
+        {
+            'version': '6.0.0',
+            'md5': '788a11a35fa62eb008019b37187d09d2',
+            'resources': {
+                'compiler-rt': 'ba6368e894b5528e527d86a69d8533c6',
+                'openmp': 'eb6b8d0318a950a8192933a3b500585d',
+                'polly': 'e5808a3a1ed1c23f56dd1854b86689d0',
+                'libcxx': '4ecad7dfd8ea636205d3ffef028df73a',
+                'libcxxabi': '9d06327892fc5d8acec4ef2e2821ab3d',
+                'cfe': '121b3896cb0c7765d690acc5d9495d24',
+                'clang-tools-extra': '6b1d543116dab5a3caba10091d983743',
+                'lldb': '1ec6498066e273b7261270f344b68121',
+                'lld': '7ab2612417477b03538f11cd8b5e12f8',
+                'libunwind': '022a4ee2c3bf7b6d151e0444f66aca64'
+            }
+        },
+        {
+            'version': '5.0.2',
+            'md5': 'c5e980edf7f22d66f0f7561b35c1e195',
+            'resources': {
+                'compiler-rt': '22728d702a64ffc6d073d1dda25a1eb9',
+                'openmp': 'ad214f7f46d671f9b73d75e9d54e4594',
+                'polly': '5777f1248633ebc2b81ffe6ecb8cf4b1',
+                'libcxx': '93e7942c01cdd5bce5378bc3926f97ea',
+                'libcxxabi': '855ada029899c95cd6a852f13ed0ea71',
+                'cfe': '1cd6ee1b74331fb37c27b4a2a1802c97',
+                'clang-tools-extra': 'd4d0d9637fa1e47daf3f51e743d8f138',
+                'lldb': '9d0addd1a28a4c155b8f69919e7bbff7',
+                'lld': '7b7e2371cd250aec54879ae13b441382',
+                'libunwind': '5b2a11e475fe8e7f3725792ba66da086',
+            }
+        },
+        {
+            'version': '5.0.1',
+            'md5': '3a4ec6dcbc71579eeaec7cb157fe2168',
+            'resources': {
+                'compiler-rt': '6329380d643fb5dc5f5abdd0d5eecd70',
+                'openmp': '7f9c8f6aecd97df9c18187157ed2f813',
+                'polly': '49c49fb61b0e73855fc21a60db9f5ab3',
+                'libcxx': 'a9dd49822f2c82cef9a9240d1714a67c',
+                'libcxxabi': '60972ef307539aa517c9878d45b43452',
+                'cfe': 'e4daa278d8f252585ab73d196484bf11',
+                'clang-tools-extra': 'c2bd3733c183b033b49f7a416c6dca36',
+                'lldb': 'd64078681215b5935614b6b83b2d1463',
+                'lld': 'a873c7fdaac647613d8eed2cb03d82de',
+                'libunwind': 'ccf48200065481244d3d09828d54e87f',
+            }
+        },
+        {
             'version': '5.0.0',
             'md5': '5ce9c5ad55243347ea0fdb4c16754be0',
             'resources': {
@@ -182,6 +255,7 @@ class Llvm(CMakePackage):
                 'cfe': '699c448c6d6d0edb693c87beb1cc8c6e',
                 'clang-tools-extra': '0cda05d1a61becb393eb63746963d7f5',
                 'lldb': '8de19973d044ca2cfe325d4625a5cfef',
+                'lld': 'a39cbecced3263feab9139b47118e062',
                 'libunwind': '98fb2c677068c6f36727fb1d5397bca3',
             }
         },
@@ -197,6 +271,7 @@ class Llvm(CMakePackage):
                 'cfe': 'a6c7b3e953f8b93e252af5917df7db97',
                 'clang-tools-extra': 'cfd46027a0ab7eed483dfcc803e86bd9',
                 'lldb': '908bdd777d3b527a914ba360477b8ab3',
+                'lld': '39cd3512cddcfd7d37ef12066c961660',
                 'libunwind': 'b72ec95fb784e61f15d6196414b92f5e',
             }
         },
@@ -212,6 +287,7 @@ class Llvm(CMakePackage):
                 'cfe': '756e17349fdc708c62974b883bf72d37',
                 'clang-tools-extra': '99e711337ec3e9a8bb36e8dd62b2cd6e',
                 'lldb': 'bd41ba7fcca55d2a554409bbccd34d2d',
+                'lld': 'e5784656e0f38e3578f10ff7551d3896',
                 'libunwind': '0c3534eaa11c0cae33a1dcf5f36ce287',
             }
         },
@@ -227,6 +303,7 @@ class Llvm(CMakePackage):
                 'cfe': '45713ec5c417ed9cad614cd283d786a1',
                 'clang-tools-extra': '1a01d545a064fcbc46a2f05f6880d3d7',
                 'lldb': '91399402f287d3f637db1207113deecb',
+                'lld': '6254dd138e23b098df4ef7840c11e2c8',
                 'libunwind': 'f273dd0ed638ad0601b23176a36f187b',
             }
         },
@@ -242,6 +319,7 @@ class Llvm(CMakePackage):
                 'cfe': '29e1d86bee422ab5345f5e9fb808d2dc',
                 'clang-tools-extra': 'f4f663068c77fc742113211841e94d5e',
                 'lldb': '968d053c3c3d7297983589164c6999e9',
+                'lld': 'c23c895c0d855a0dc426af686538a95e',
                 'libunwind': '3e5c87c723a456be599727a444b1c166',
             }
         },
@@ -257,6 +335,7 @@ class Llvm(CMakePackage):
                 'cfe': '4ff2f8844a786edb0220f490f7896080',
                 'clang-tools-extra': '6e49f285d0b366cc3cab782d8c92d382',
                 'lldb': '9e4787b71be8e432fffd31e13ac87623',
+                'lld': '68cd069bf99c71ebcfbe01d557c0e14d',
                 'libunwind': 'd66e2387e1d37a8a0c8fe6a0063a3bab',
             }
         },
@@ -272,6 +351,7 @@ class Llvm(CMakePackage):
                 'cfe': 'cc99e7019bb74e6459e80863606250c5',
                 'clang-tools-extra': 'c2344f50e0eea0b402f0092a80ddc036',
                 'lldb': 'a5da35ed9cc8c8817ee854e3dbfba00e',
+                'lld': 'de33b5c6c77698ee2f8d024fbffb8df1',
                 'libunwind': '162ade468607f153cca12be90b5194fa',
             }
         },
@@ -287,6 +367,7 @@ class Llvm(CMakePackage):
                 'cfe': '0acd026b5529164197563d135a8fd83e',
                 'clang-tools-extra': '5d49ff745037f061a7c86aeb6a24c3d2',
                 'lldb': 'a106d8a0d21fc84d76953822fbaf3398',
+                'lld': '6c3794e30fbe118a601fb694627f34f8',
                 'libunwind': '814bd52c9247c5d04629658fbcb3ab8c',
             }
         },
@@ -302,6 +383,7 @@ class Llvm(CMakePackage):
                 'cfe': '8f9d27335e7331cf0a4711e952f21f01',
                 'clang-tools-extra': 'd5a87dacb65d981a427a536f6964642e',
                 'lldb': 'e5931740400d1dc3e7db4c7ba2ceff68',
+                'lld': '91bd593a67293d84dad0bf11845546c2',
                 'libunwind': '9a75392eb7eb8ed5c0840007e212baf5',
             }
         },
@@ -316,6 +398,7 @@ class Llvm(CMakePackage):
                 'cfe': 'ff862793682f714bb7862325b9c06e20',
                 'clang-tools-extra': '3ebc1dc41659fcec3db1b47d81575e06',
                 'lldb': '51e5eb552f777b950bb0ff326e60d5f0',
+                'lld': '7143cc4fa88851a9f9b9a03621fbb387',
             }
         },
         {
@@ -329,12 +412,54 @@ class Llvm(CMakePackage):
                 'cfe': '93f9532f8f7e6f1d8e5c1116907051cb',
                 'clang-tools-extra': 'f13f31ed3038acadc6fa63fef812a246',
                 'lldb': 'cc5ea8a414c62c33e760517f8929a204',
+                'lld': '173be02b7ff4e5e31fbb0a591a03d7a3',
+            }
+        },
+    ]
+
+    # Flang uses its own fork of clang (renamed flang-driver).
+    flang_resources = {
+        'flang-driver': {
+            'git': 'https://github.com/flang-compiler/flang-driver.git',
+            'destination': 'tools',
+            'placement': 'clang'
+        },
+        'openmp': {
+            'git': 'https://github.com/llvm-mirror/openmp.git',
+            'destination': 'projects',
+            'placement': 'openmp'
+        }
+    }
+
+    flang_releases = [
+        {
+            'version': 'develop',
+            'branch': 'release_60',
+            'resources': {
+                'flang-driver': 'release_60',
+                'openmp': 'release_60',
             }
         },
+        {
+            'version': '20180612',
+            'commit': 'f26a3ece4ccd68a52f5aa970ec42837ee0743296',
+            'resources': {
+                'flang-driver': 'e079fa68cb35a53c88c41a1939f90b94d539e984',
+                'openmp': 'd5aa29cb3bcf51289d326b4e565613db8aff65ef'
+            }
+        },
+        {
+            'version': 'ppc64le-20180612',
+            'commit': '4158932a46eb2f06a166f22a4a52ae48c7d2949e',
+            'resources': {
+                'flang-driver': '50c1828a134d5a0f1553b355bf0946db48b0aa6d',
+                'openmp': '29b515e1e6d26b5b0d32d47d28dcdb4b8a11470d'
+            }
+        }
     ]
 
     for release in releases:
-        if release['version'] == 'trunk':
+        if release['version'] == 'develop':
             version(release['version'], svn=release['repo'])
 
             for name, repo in release['resources'].items():
@@ -356,15 +481,67 @@ class Llvm(CMakePackage):
                                          resources[name].get('variant', "")),
                          placement=resources[name].get('placement', None))
 
+    for release in flang_releases:
+        if release['version'] == 'develop':
+            version('flang-' + release['version'], git=flang_llvm_url, branch=release['branch'])
+
+            for name, branch in release['resources'].items():
+                flang_resource = flang_resources[name]
+                resource(name=name,
+                         git=flang_resource['git'],
+                         branch=branch,
+                         destination=flang_resource['destination'],
+                         placement=flang_resource['placement'],
+                         when='@flang-' + release['version'])
+
+        else:
+            version('flang-' + release['version'], git=flang_llvm_url, commit=release['commit'])
+
+            for name, commit in release['resources'].items():
+                flang_resource = flang_resources[name]
+                resource(name=name,
+                         git=flang_resource['git'],
+                         commit=commit,
+                         destination=flang_resource['destination'],
+                         placement=flang_resource['placement'],
+                         when='@flang-' + release['version'])
+
     conflicts('+clang_extra', when='~clang')
     conflicts('+lldb',        when='~clang')
 
+    # LLVM 4 and 5 does not build with GCC 8
+    conflicts('%gcc@8:',      when='@:5')
+
     # Github issue #4986
     patch('llvm_gcc7.patch', when='@4.0.0:4.0.1+lldb %gcc@7.0:')
 
+    @run_before('cmake')
+    def check_darwin_lldb_codesign_requirement(self):
+        if not self.spec.satisfies('+lldb platform=darwin'):
+            return
+        codesign = which('codesign')
+        mkdir('tmp')
+        llvm_check_file = join_path('tmp', 'llvm_check')
+        copy('/usr/bin/false', llvm_check_file)
+
+        try:
+            codesign('-f', '-s', 'lldb_codesign', '--dryrun',
+                     llvm_check_file)
+
+        except ProcessError:
+            explanation = ('The "lldb_codesign" identity must be available'
+                           ' to build LLVM with LLDB. See https://llvm.org/'
+                           'svn/llvm-project/lldb/trunk/docs/code-signing'
+                           '.txt for details on how to create this identity.')
+            raise RuntimeError(explanation)
+
     def setup_environment(self, spack_env, run_env):
         spack_env.append_flags('CXXFLAGS', self.compiler.cxx11_flag)
 
+        if '+clang' in self.spec:
+            run_env.set('CC', join_path(self.spec.prefix.bin, 'clang'))
+            run_env.set('CXX', join_path(self.spec.prefix.bin, 'clang++'))
+
     def cmake_args(self):
         spec = self.spec
 
@@ -385,11 +562,15 @@ class Llvm(CMakePackage):
                                '-DLLVM_POLLY_BUILD:Bool=OFF',
                                '-DLLVM_POLLY_LINK_INTO_TOOLS:Bool=OFF'])
 
+        if '+python' in spec and '+lldb' in spec and spec.satisfies('@5.0.0:'):
+            cmake_args.append('-DLLDB_USE_SYSTEM_SIX:Bool=TRUE')
         if '+clang' not in spec:
             cmake_args.append('-DLLVM_EXTERNAL_CLANG_BUILD:Bool=OFF')
         if '+lldb' not in spec:
             cmake_args.extend(['-DLLVM_EXTERNAL_LLDB_BUILD:Bool=OFF',
                                '-DLLVM_TOOL_LLDB_BUILD:Bool=OFF'])
+        if '+lld' not in spec:
+            cmake_args.append('-DLLVM_TOOL_LLD_BUILD:Bool=OFF')
         if '+internal_unwind' not in spec:
             cmake_args.append('-DLLVM_EXTERNAL_LIBUNWIND_BUILD:Bool=OFF')
         if '+libcxx' in spec:
@@ -408,7 +589,15 @@ class Llvm(CMakePackage):
             cmake_args.append('-DLLVM_LINK_LLVM_DYLIB:Bool=ON')
 
         if '+all_targets' not in spec:  # all is default on cmake
-            targets = ['CppBackend', 'NVPTX', 'AMDGPU']
+
+            if spec.version < Version('3.9.0'):
+                targets = ['CppBackend', 'NVPTX', 'AMDGPU']
+            else:
+                # Starting in 3.9.0 CppBackend is no longer a target (see
+                # LLVM_ALL_TARGETS in llvm's top-level CMakeLists.txt for
+                # the complete list of targets)
+                targets = ['NVPTX', 'AMDGPU']
+
             if 'x86' in spec.architecture.target.lower():
                 targets.append('X86')
             elif 'arm' in spec.architecture.target.lower():
@@ -416,7 +605,7 @@ class Llvm(CMakePackage):
             elif 'aarch64' in spec.architecture.target.lower():
                 targets.append('AArch64')
             elif 'sparc' in spec.architecture.target.lower():
-                targets.append('sparc')
+                targets.append('Sparc')
             elif ('ppc' in spec.architecture.target.lower() or
                   'power' in spec.architecture.target.lower()):
                 targets.append('PowerPC')
@@ -433,7 +622,9 @@ class Llvm(CMakePackage):
         with working_dir(self.build_directory):
             # When building shared libraries these need to be installed first
             make('install-LLVMTableGen')
-            make('install-LLVMDemangle')
+            if self.spec.version >= Version('4.0.0'):
+                # LLVMDemangle target was added in 4.0.0
+                make('install-LLVMDemangle')
             make('install-LLVMSupport')
 
     @run_after('install')
diff --git a/var/spack/repos/builtin/packages/lmdb/package.py b/var/spack/repos/builtin/packages/lmdb/package.py
index fb147403d9..2900dc6bd6 100644
--- a/var/spack/repos/builtin/packages/lmdb/package.py
+++ b/var/spack/repos/builtin/packages/lmdb/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/lmod/package.py b/var/spack/repos/builtin/packages/lmod/package.py
index 73cfcd2b88..f9ba114cf7 100644
--- a/var/spack/repos/builtin/packages/lmod/package.py
+++ b/var/spack/repos/builtin/packages/lmod/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 from glob import glob
 
@@ -38,6 +19,9 @@ class Lmod(AutotoolsPackage):
     homepage = 'https://www.tacc.utexas.edu/research-development/tacc-projects/lmod'
     url      = 'https://github.com/TACC/Lmod/archive/7.4.11.tar.gz'
 
+    version('7.8', sha256='40388380a36a00c3ce929a9f88c8fffc93deeabf87a7c3f8864a82acad38c3ba')
+    version('7.7.29', 'bd3f171995e6863505e8a958d158ced1')
+    version('7.7.13', 'e1d222fa04148707dceb08c82d7e9fa5')
     version('7.7',    '8ac594401716c6d1b40cac22bc1030ca')
     version('7.6.14', '60726c991038b6337fbb27b6a333a2d4')
     version('7.4.11', '70c55ba0ba3877b6d8df536ee7ea6d49')
@@ -52,7 +36,7 @@ class Lmod(AutotoolsPackage):
     version('6.3.7',  '0fa4d5a24c41cae03776f781aa2dedc1')
     version('6.0.1',  '91abf52fe5033bd419ffe2842ebe7af9')
 
-    depends_on('lua@5.2:')
+    depends_on('lua@5.1:')
     depends_on('lua-luaposix', type=('build', 'run'))
     depends_on('lua-luafilesystem', type=('build', 'run'))
     depends_on('tcl', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/lndir/package.py b/var/spack/repos/builtin/packages/lndir/package.py
index 071ce420d8..35a2517af0 100644
--- a/var/spack/repos/builtin/packages/lndir/package.py
+++ b/var/spack/repos/builtin/packages/lndir/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,4 +16,4 @@ class Lndir(AutotoolsPackage):
     version('1.0.3', '7173b2e4832658d319c2980a7c834205')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
diff --git a/var/spack/repos/builtin/packages/log4cplus/package.py b/var/spack/repos/builtin/packages/log4cplus/package.py
new file mode 100644
index 0000000000..d759f2f6d3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/log4cplus/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Log4cplus(CMakePackage):
+    """log4cplus is a simple to use C++ logging API
+    providing thread-safe, flexible, and arbitrarily
+    granular control over log management and configuration."""
+
+    homepage = "https://sourceforge.net/projects/log4cplus/"
+    url      = "https://download.sourceforge.net/project/log4cplus/log4cplus-stable/2.0.1/log4cplus-2.0.1.tar.bz2"
+
+    version('2.0.1', 'ec01c03241ebd31127a44d1880830d8f')
+    version('1.2.1', 'e4e6c38b065b70b5d6efc238a5106bc9')
+    version('1.2.0', 'e250f0f431c0723f8b625323e7b6465d')
diff --git a/var/spack/repos/builtin/packages/log4cxx/package.py b/var/spack/repos/builtin/packages/log4cxx/package.py
index b2bf7a4e35..a88e9cccbb 100644
--- a/var/spack/repos/builtin/packages/log4cxx/package.py
+++ b/var/spack/repos/builtin/packages/log4cxx/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,8 +14,9 @@ class Log4cxx(AutotoolsPackage):
 
     version('0.10.0', 'b30ffb8da3665178e68940ff7a61084c')
 
-    depends_on('libxml2')
     depends_on('apr-util')
+    depends_on('apr')
+    depends_on('zip')
 
     build_directory = 'spack-build'
 
@@ -44,4 +26,5 @@ class Log4cxx(AutotoolsPackage):
 
     def configure_args(self):
         args = ['--disable-static']
+
         return args
diff --git a/var/spack/repos/builtin/packages/loki/package.py b/var/spack/repos/builtin/packages/loki/package.py
new file mode 100644
index 0000000000..1f4cac66f0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/loki/package.py
@@ -0,0 +1,31 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Loki(MakefilePackage):
+    """Loki is a C++ library of designs, containing flexible implementations
+    of common design patterns and idioms."""
+
+    homepage = "http://loki-lib.sourceforge.net"
+    url      = "https://downloads.sourceforge.net/project/loki-lib/Loki/Loki%200.1.7/loki-0.1.7.tar.bz2"
+
+    version('0.1.7', '33a24bcbb99fa2ec8fcbbab65649f3f6')
+
+    variant('shared', default=True, description="Build shared libraries")
+
+    def build(self, spec, prefix):
+        if '+shared' in spec:
+            make('-C', 'src', 'build-shared')
+        else:
+            make('-C', 'src', 'build-static')
+
+    def install(self, spec, prefix):
+        make('-C', 'include', 'install', 'prefix={0}'.format(prefix))
+        if '+shared' in spec:
+            make('-C', 'src', 'install-shared', 'prefix={0}'.format(prefix))
+        else:
+            make('-C', 'src', 'install-static', 'prefix={0}'.format(prefix))
diff --git a/var/spack/repos/builtin/packages/lordec/package.py b/var/spack/repos/builtin/packages/lordec/package.py
new file mode 100644
index 0000000000..f02ec371b2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/lordec/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Lordec(MakefilePackage):
+    """LoRDEC is a program to correct sequencing errors in long reads from
+    3rd generation sequencing with high error rate, and is especially
+    intended for PacBio reads."""
+
+    homepage = "http://www.atgc-montpellier.fr/lordec/"
+    url      = "https://gite.lirmm.fr/lordec/lordec-releases/uploads/e3116a5f251e46e47f7a3b7ddb2bd7f6/lordec-src_0.8.tar.gz"
+
+    version('0.8', 'd5a57db681d1cd31c516aa780ce53f9d')
+
+    depends_on('boost')
+    depends_on('cmake@3.1.0:', type='build')
+
+    build_targets = ['clean', 'all']
+
+    def install(self, spec, prefix):
+        install_tree('.', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/lrslib/package.py b/var/spack/repos/builtin/packages/lrslib/package.py
index 586750b9bf..05b7941fd9 100644
--- a/var/spack/repos/builtin/packages/lrslib/package.py
+++ b/var/spack/repos/builtin/packages/lrslib/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/lrzip/package.py b/var/spack/repos/builtin/packages/lrzip/package.py
index 531cba2b87..bacc3a2f01 100644
--- a/var/spack/repos/builtin/packages/lrzip/package.py
+++ b/var/spack/repos/builtin/packages/lrzip/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,9 +15,10 @@ class Lrzip(Package):
     but not both."""
 
     homepage = 'http://lrzip.kolivas.org'
-    url = 'https://github.com/ckolivas/lrzip/archive/v0.630.tar.gz'
+    url      = 'https://github.com/ckolivas/lrzip/archive/v0.630.tar.gz'
+    git      = 'https://github.com/ckolivas/lrzip.git'
 
-    version('master', git='https://github.com/ckolivas/lrzip.git')
+    version('master', branch='master')
     version('0.630', '3ca7f1d1365aa105089d1fbfc6b0924a')
     version('0.621', '1f07227b39ae81a98934411e8611e341')
     version('0.616', 'd40bdb046d0807ef602e36b1e9782cc0')
diff --git a/var/spack/repos/builtin/packages/lsof/package.py b/var/spack/repos/builtin/packages/lsof/package.py
new file mode 100644
index 0000000000..b03afeb004
--- /dev/null
+++ b/var/spack/repos/builtin/packages/lsof/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Lsof(Package):
+    """Lsof displays information about files open to Unix processes."""
+
+    homepage = "https://people.freebsd.org/~abe/"
+    url      = "https://www.mirrorservice.org/sites/lsof.itap.purdue.edu/pub/tools/unix/lsof/lsof_4.89.tar.gz"
+
+    version('4.89', '8afbaff3ee308edc130bdc5df0801c8f')
+
+    def install(self, spec, prefix):
+        tar = which('tar')
+        tar('xf', 'lsof_{0}_src.tar'.format(self.version))
+
+        with working_dir('lsof_{0}_src'.format(self.version)):
+            configure = Executable('./Configure')
+            configure('-n', 'linux')
+
+            make()
+
+            mkdir(prefix.bin)
+            install('lsof', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/ltrace/package.py b/var/spack/repos/builtin/packages/ltrace/package.py
new file mode 100644
index 0000000000..3e18f659ee
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ltrace/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Ltrace(AutotoolsPackage):
+    """Ltrace intercepts and records dynamic library calls which are called
+    by an executed process and the signals received by that process. It
+    can also intercept and print the system calls executed by the program."""
+
+    homepage = "https://www.ltrace.org"
+    url      = "https://www.ltrace.org/ltrace_0.7.3.orig.tar.bz2"
+
+    version('0.7.3', 'b3dd199af8f18637f7d4ef97fdfb9d14')
+
+    conflicts('platform=darwin', msg='ltrace runs only on Linux.')
diff --git a/var/spack/repos/builtin/packages/lua-bitlib/package.py b/var/spack/repos/builtin/packages/lua-bitlib/package.py
index 014eb77e43..55a04311c2 100644
--- a/var/spack/repos/builtin/packages/lua-bitlib/package.py
+++ b/var/spack/repos/builtin/packages/lua-bitlib/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 import os
diff --git a/var/spack/repos/builtin/packages/lua-jit/package.py b/var/spack/repos/builtin/packages/lua-jit/package.py
index 2005936110..be3d28e4c8 100644
--- a/var/spack/repos/builtin/packages/lua-jit/package.py
+++ b/var/spack/repos/builtin/packages/lua-jit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/lua-lpeg/package.py b/var/spack/repos/builtin/packages/lua-lpeg/package.py
index aa9a491e4b..1d57d0bc9c 100644
--- a/var/spack/repos/builtin/packages/lua-lpeg/package.py
+++ b/var/spack/repos/builtin/packages/lua-lpeg/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/lua-luafilesystem/package.py b/var/spack/repos/builtin/packages/lua-luafilesystem/package.py
index 7194654838..1611a64b3a 100644
--- a/var/spack/repos/builtin/packages/lua-luafilesystem/package.py
+++ b/var/spack/repos/builtin/packages/lua-luafilesystem/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/lua-luaposix/package.py b/var/spack/repos/builtin/packages/lua-luaposix/package.py
index 5cc81d6e65..8d9ad7f832 100644
--- a/var/spack/repos/builtin/packages/lua-luaposix/package.py
+++ b/var/spack/repos/builtin/packages/lua-luaposix/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
 
diff --git a/var/spack/repos/builtin/packages/lua-mpack/package.py b/var/spack/repos/builtin/packages/lua-mpack/package.py
index ffdb953428..f6cca90e0d 100644
--- a/var/spack/repos/builtin/packages/lua-mpack/package.py
+++ b/var/spack/repos/builtin/packages/lua-mpack/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/lua/package.py b/var/spack/repos/builtin/packages/lua/package.py
index 46d1e5c094..ceb816a5d7 100644
--- a/var/spack/repos/builtin/packages/lua/package.py
+++ b/var/spack/repos/builtin/packages/lua/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
@@ -49,6 +30,8 @@ class Lua(Package):
 
     depends_on('ncurses')
     depends_on('readline')
+    # luarocks needs unzip for some packages (e.g. lua-luaposix)
+    depends_on('unzip', type='run')
 
     resource(
         name="luarocks",
@@ -64,28 +47,41 @@ class Lua(Package):
         else:
             target = 'linux'
         make('INSTALL_TOP=%s' % prefix,
-             'MYCFLAGS=%s' % (
-                 self.compiler.pic_flag),
              'MYLDFLAGS=-L%s -L%s' % (
                  spec['readline'].prefix.lib,
                  spec['ncurses'].prefix.lib),
              'MYLIBS=-lncursesw',
-             'CC=%s -std=gnu99' % spack_cc,
+             'CC=%s -std=gnu99 %s' % (spack_cc,
+                                      self.compiler.pic_flag),
              target)
         make('INSTALL_TOP=%s' % prefix,
-             'MYCFLAGS=%s' % (
-                 self.compiler.pic_flag),
-             'MYLDFLAGS=-L%s -L%s' % (
-                 spec['readline'].prefix.lib,
-                 spec['ncurses'].prefix.lib),
-             'MYLIBS=-lncursesw',
-             'CC=%s -std=gnu99' % spack_cc,
              'install')
 
         static_to_shared_library(join_path(prefix.lib, 'liblua.a'),
                                  arguments=['-lm'], version=self.version,
                                  compat_version=self.version.up_to(2))
 
+        # compatibility with ax_lua.m4 from autoconf-archive
+        # https://www.gnu.org/software/autoconf-archive/ax_lua.html
+        with working_dir(prefix.lib):
+            # e.g., liblua.so.5.1.5
+            src_path = 'liblua.{0}.{1}'.format(dso_suffix,
+                                               str(self.version.up_to(3)))
+
+            # For lua version 5.1.X, the symlinks should be:
+            # liblua5.1.so
+            # liblua51.so
+            # liblua-5.1.so
+            # liblua-51.so
+            version_formats = [str(self.version.up_to(2)),
+                               Version(str(self.version.up_to(2))).joined]
+            for version_str in version_formats:
+                for joiner in ['', '-']:
+                    dest_path = 'liblua{0}{1}.{2}'.format(joiner,
+                                                          version_str,
+                                                          dso_suffix)
+                    os.symlink(src_path, dest_path)
+
         with working_dir(os.path.join('luarocks', 'luarocks')):
             configure('--prefix=' + prefix, '--with-lua=' + prefix)
             make('build')
@@ -102,6 +98,7 @@ class Lua(Package):
                 deptypes=('build', 'run'), deptype_query='run'):
             if d.package.extends(self.spec):
                 lua_paths.append(os.path.join(d.prefix, self.lua_lib_dir))
+                lua_paths.append(os.path.join(d.prefix, self.lua_lib64_dir))
                 lua_paths.append(os.path.join(d.prefix, self.lua_share_dir))
 
         lua_patterns = []
@@ -112,6 +109,7 @@ class Lua(Package):
 
         # Always add this package's paths
         for p in (os.path.join(self.spec.prefix, self.lua_lib_dir),
+                  os.path.join(self.spec.prefix, self.lua_lib64_dir),
                   os.path.join(self.spec.prefix, self.lua_share_dir)):
             self.append_paths(lua_patterns, lua_cpatterns, p)
 
@@ -156,6 +154,10 @@ class Lua(Package):
         return os.path.join('lib', 'lua', str(self.version.up_to(2)))
 
     @property
+    def lua_lib64_dir(self):
+        return os.path.join('lib64', 'lua', str(self.version.up_to(2)))
+
+    @property
     def lua_share_dir(self):
         return os.path.join('share', 'lua', str(self.version.up_to(2)))
 
diff --git a/var/spack/repos/builtin/packages/luit/package.py b/var/spack/repos/builtin/packages/luit/package.py
index 47eb6be44c..4969375a19 100644
--- a/var/spack/repos/builtin/packages/luit/package.py
+++ b/var/spack/repos/builtin/packages/luit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,7 +20,7 @@ class Luit(Package):
     depends_on('libfontenc')
     depends_on('libx11')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/lulesh/package.py b/var/spack/repos/builtin/packages/lulesh/package.py
index 489a175108..614d8cf933 100644
--- a/var/spack/repos/builtin/packages/lulesh/package.py
+++ b/var/spack/repos/builtin/packages/lulesh/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,10 +12,10 @@ class Lulesh(MakefilePackage):
     code to only solve a Sedov blast problem with analytic answer
     """
     tags = ['proxy-app']
-    homepage = "https://codesign.llnl.gov/lulesh.php"
-    url      = "https://codesign.llnl.gov/lulesh/lulesh2.0.3.tgz"
+    homepage = "https://computation.llnl.gov/projects/co-design/lulesh"
+    git      = "https://github.com/LLNL/LULESH.git"
 
-    version('2.0.3', '336644a8750f71c7c6b9d2960976e7aa')
+    version('2.0.3', tag='2.0.3')
 
     variant('mpi', default=True, description='Build with MPI support')
     variant('openmp', default=True, description='Build with OpenMP support')
diff --git a/var/spack/repos/builtin/packages/lumpy-sv/package.py b/var/spack/repos/builtin/packages/lumpy-sv/package.py
new file mode 100644
index 0000000000..709f7d0f4c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/lumpy-sv/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class LumpySv(MakefilePackage):
+    """A probabilistic framework for structural variant discovery."""
+
+    homepage = "https://github.com/arq5x/lumpy-sv"
+    url      = "https://github.com/arq5x/lumpy-sv/archive/0.2.13.tar.gz"
+
+    version('0.2.13', '36929d29fc3a171d3abbe1d93f9f3b50')
+
+    depends_on('htslib')
+
+    def edit(self, spec, prefix):
+        makefile = FileFilter('Makefile')
+        makefile.filter('export CXX .*', '')
+
+    def install(self, spec, prefix):
+        install_tree('bin', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/lwgrp/package.py b/var/spack/repos/builtin/packages/lwgrp/package.py
index aa742230ac..76926714d1 100644
--- a/var/spack/repos/builtin/packages/lwgrp/package.py
+++ b/var/spack/repos/builtin/packages/lwgrp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/lwm2/package.py b/var/spack/repos/builtin/packages/lwm2/package.py
index 4858391f2a..58c6d73f94 100644
--- a/var/spack/repos/builtin/packages/lwm2/package.py
+++ b/var/spack/repos/builtin/packages/lwm2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,8 +12,9 @@ class Lwm2(AutotoolsPackage):
        measurements from a program.
     """
     homepage = "https://jay.grs.rwth-aachen.de/redmine/projects/lwm2"
+    hg       = "https://jay.grs.rwth-aachen.de/hg/lwm2"
 
-    version('torus', hg='https://jay.grs.rwth-aachen.de/hg/lwm2', revision='torus')
+    version('torus', revision='torus')
 
     depends_on("papi")
     depends_on("mpi")
diff --git a/var/spack/repos/builtin/packages/lz4/package.py b/var/spack/repos/builtin/packages/lz4/package.py
index 2c8d0977ae..fed8c3bfe2 100644
--- a/var/spack/repos/builtin/packages/lz4/package.py
+++ b/var/spack/repos/builtin/packages/lz4/package.py
@@ -1,28 +1,10 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
+import sys
 
 
 class Lz4(Package):
@@ -34,10 +16,11 @@ class Lz4(Package):
     homepage = "http://lz4.github.io/lz4/"
     url      = "https://github.com/lz4/lz4/archive/v1.7.5.tar.gz"
 
+    version('1.8.1.2', '343538e69ba752a386c669b1a28111e2')
     version('1.7.5', 'c9610c5ce97eb431dddddf0073d919b9')
     version('1.3.1', '42b09fab42331da9d3fb33bd5c560de9')
 
-    # depends_on('valgrind', type='test')
+    depends_on('valgrind', type='test')
 
     def url_for_version(self, version):
         url = "https://github.com/lz4/lz4/archive"
@@ -48,7 +31,15 @@ class Lz4(Package):
             return "{0}/r{1}.tar.gz".format(url, version.joined)
 
     def install(self, spec, prefix):
-        make()
+        if sys.platform != "darwin":
+            make('MOREFLAGS=-lrt')  # fixes make error on CentOS6
+        else:
+            make()
         if self.run_tests:
             make('test')  # requires valgrind to be installed
         make('install', 'PREFIX={0}'.format(prefix))
+
+    @run_after('install')
+    def darwin_fix(self):
+        if sys.platform == 'darwin':
+            fix_darwin_install_name(self.prefix.lib)
diff --git a/var/spack/repos/builtin/packages/lzma/package.py b/var/spack/repos/builtin/packages/lzma/package.py
index 3e256d54b0..a5abb82ff7 100644
--- a/var/spack/repos/builtin/packages/lzma/package.py
+++ b/var/spack/repos/builtin/packages/lzma/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/lzo/package.py b/var/spack/repos/builtin/packages/lzo/package.py
index ded3a32375..f5b4fe8060 100644
--- a/var/spack/repos/builtin/packages/lzo/package.py
+++ b/var/spack/repos/builtin/packages/lzo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/m4/package.py b/var/spack/repos/builtin/packages/m4/package.py
index f3cb8122f5..926758a766 100644
--- a/var/spack/repos/builtin/packages/m4/package.py
+++ b/var/spack/repos/builtin/packages/m4/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,13 +10,18 @@ class M4(AutotoolsPackage):
     """GNU M4 is an implementation of the traditional Unix macro processor."""
 
     homepage = "https://www.gnu.org/software/m4/m4.html"
-    url      = "https://ftp.gnu.org/gnu/m4/m4-1.4.18.tar.gz"
+    url      = "https://ftpmirror.gnu.org/m4/m4-1.4.18.tar.gz"
 
     version('1.4.18', 'a077779db287adf4e12a035029002d28')
     version('1.4.17', 'a5e9954b1dae036762f7b13673a2cf76')
 
     patch('gnulib-pgi.patch', when='@1.4.18')
     patch('pgi.patch', when='@1.4.17')
+    # from: https://github.com/Homebrew/homebrew-core/blob/master/Formula/m4.rb
+    # Patch credit to Jeremy Huddleston Sequoia <jeremyhu@apple.com>
+    patch('secure_snprintf.patch', when='platform_os = highsierra')
+    # https://bugzilla.redhat.com/show_bug.cgi?id=1573342
+    patch('https://src.fedoraproject.org/rpms/m4/raw/5d147168d4b93f38a4833f5dd1d650ad88af5a8a/f/m4-1.4.18-glibc-change-work-around.patch', sha256='fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8', when='@1.4.18')
 
     variant('sigsegv', default=True,
             description="Build the libsigsegv dependency")
diff --git a/var/spack/repos/builtin/packages/m4/secure_snprintf.patch b/var/spack/repos/builtin/packages/m4/secure_snprintf.patch
new file mode 100644
index 0000000000..da3ae5ba0d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/m4/secure_snprintf.patch
@@ -0,0 +1,15 @@
+With format string strictness, High Sierra also enforces that %n isn't used
+in dynamic format strings, but we should just disable its use on darwin in
+general.
+
+--- a/lib/vasnprintf.c.orig	2017-06-22 15:19:15.000000000 -0700
++++ b/lib/vasnprintf.c	2017-06-22 15:20:20.000000000 -0700
+@@ -4869,7 +4869,7 @@ VASNPRINTF (DCHAR_T *resultbuf, size_t *
+ #endif
+                   *fbp = dp->conversion;
+ #if USE_SNPRINTF
+-# if !(((__GLIBC__ > 2 || (__GLIBC__ == 2 && __GLIBC_MINOR__ >= 3)) && !defined __UCLIBC__) || ((defined _WIN32 || defined __WIN32__) && ! defined __CYGWIN__))
++# if !defined(__APPLE__) && !(((__GLIBC__ > 2 || (__GLIBC__ == 2 && __GLIBC_MINOR__ >= 3)) && !defined __UCLIBC__) || ((defined _WIN32 || defined __WIN32__) && ! defined __CYGWIN__))
+                 fbp[1] = '%';
+                 fbp[2] = 'n';
+                 fbp[3] = '\0';
diff --git a/var/spack/repos/builtin/packages/macsio/package.py b/var/spack/repos/builtin/packages/macsio/package.py
index f17cec4350..09d4f50c50 100644
--- a/var/spack/repos/builtin/packages/macsio/package.py
+++ b/var/spack/repos/builtin/packages/macsio/package.py
@@ -1,41 +1,24 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class Macsio(CMakePackage):
-    """A Multi-purpose, Application-Centric, Scalable I/O Proxy Application
-    """
+    """A Multi-purpose, Application-Centric, Scalable I/O Proxy Application."""
+
     tags = ['proxy-app', 'ecp-proxy-app']
 
-    homepage = "http://llnl.github.io/MACSio"
-    url = "https://github.com/LLNL/MACSio/archive/1.0.tar.gz"
+    homepage = "https://computation.llnl.gov/projects/co-design/macsio"
+    url      = "https://github.com/LLNL/MACSio/archive/v1.1.tar.gz"
+    git      = "https://github.com/LLNL/MACSio.git"
 
+    version('develop', branch='master')
+
+    version('1.1', sha256='a86249b0f10647c0b631773db69568388094605ec1a0af149d9e61e95e6961ec')
     version('1.0', '90e8e00ea84af2a47bee387ad331dbde')
-    version('develop', git='https://github.com/LLNL/MACSio.git',
-            branch='master')
 
     variant('mpi', default=True, description="Build MPI plugin")
     variant('silo', default=True, description="Build with SILO plugin")
@@ -52,7 +35,7 @@ class Macsio(CMakePackage):
     depends_on('json-cwx')
     depends_on('mpi', when="+mpi")
     depends_on('silo', when="+silo")
-    depends_on('hdf5', when="+hdf5")
+    depends_on('hdf5+hl', when="+hdf5")
     # depends_on('hdf5+szip', when="+szip")
     depends_on('exodusii', when="+exodus")
     # pdb is packaged with silo
@@ -114,3 +97,7 @@ class Macsio(CMakePackage):
                               .format(spec['netcdf'].prefix))
 
         return cmake_args
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('spack-build/macsio/macsio', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/mad-numdiff/package.py b/var/spack/repos/builtin/packages/mad-numdiff/package.py
index 8d687e2258..660fe03203 100644
--- a/var/spack/repos/builtin/packages/mad-numdiff/package.py
+++ b/var/spack/repos/builtin/packages/mad-numdiff/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -31,6 +12,7 @@ class MadNumdiff(CMakePackage):
 
     homepage = "https://github.com/quinoacomputing/ndiff"
     url      = "https://github.com/quinoacomputing/ndiff/tarball/20150724"
+    git      = "https://github.com/quinoacomputing/ndiff.git"
 
-    version('develop', git='https://github.com/quinoacomputing/ndiff', branch='master')
+    version('develop', branch='master')
     version('20150724', '7723c0f2499aea8fd960377c5bed28d8')
diff --git a/var/spack/repos/builtin/packages/mafft/package.py b/var/spack/repos/builtin/packages/mafft/package.py
index 2b46cf9332..f2b75416bf 100644
--- a/var/spack/repos/builtin/packages/mafft/package.py
+++ b/var/spack/repos/builtin/packages/mafft/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/magics/package.py b/var/spack/repos/builtin/packages/magics/package.py
index 540abd6c1d..bd35327480 100644
--- a/var/spack/repos/builtin/packages/magics/package.py
+++ b/var/spack/repos/builtin/packages/magics/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
 
@@ -33,48 +14,86 @@ class Magics(CMakePackage):
 
     homepage = "https://software.ecmwf.int/wiki/display/MAGP/Magics"
     url      = "https://software.ecmwf.int/wiki/download/attachments/3473464/Magics-2.29.0-Source.tar.gz"
+    list_url = "https://software.ecmwf.int/wiki/display/MAGP/Releases"
 
-    # Maintainers of Magics do not keep tarballs of minor releases. Once the
-    # next minor released is published the previous one becomes unavailable.
-    # That is why the preferred version is the latest stable one.
+    # The policy on which minor releases remain available and which get deleted
+    # after a newer version becomes available is unclear.
+    version('2.34.3', 'b4180bc4114ffd723b80728947f50c17')
+    version('2.34.1', '1ecc5cc20cb0c3f2f0b9171626f09d53')
+    version('2.33.0', '8d513fd2244f2974b3517a8b30dd51f6')
     version('2.32.0', 'e17956fffce9ea826cf994f8d275e0f5')
+    version('2.31.0', '3564dca9e1b4af096fd631906f5e6c89')
+    version('2.29.6', '56d2c31ca75162e5e86ef75d355e87f1')
     version('2.29.4', '91c561f413316fb665b3bb563f3878d1')
-    version('2.29.0', 'db20a4d3c51a2da5657c31ae3de59709', preferred=True)
+    version('2.29.0', 'db20a4d3c51a2da5657c31ae3de59709')
 
     # The patch reorders includes and adds namespaces where necessary to
     # resolve ambiguity of invocations of isnan and isinf functions. The
     # patch is not needed since the version 2.29.1
     patch('resolve_isnan_ambiguity.patch', when='@2.29.0')
 
-    variant('bufr', default=False, description='Enable BUFR support')
+    variant('grib', default='eccodes', values=('eccodes', 'grib-api'),
+            description='Specify GRIB backend')
     variant('netcdf', default=False, description='Enable NetCDF support')
-    variant('cairo', default=True, description='Enable cairo support[png/jpeg]')
+    variant('cairo', default=False,
+            description='Enable cairo support[png/jpeg]')
+    variant('python', default=False, description='Enable Python interface')
+    variant('fortran', default=False, description='Enable Fortran interface')
     variant('metview', default=False, description='Enable metview support')
     variant('qt', default=False, description='Enable metview support with qt')
-    variant('eccodes', default=False, description='Use eccodes instead of grib-api')
+    variant('bufr', default=False, description='Enable BUFR support')
+
     variant('build_type', default='RelWithDebInfo',
             description='The build type to build',
             values=('Debug', 'Release', 'RelWithDebInfo', 'Production'))
 
+    # Build dependencies
     depends_on('cmake@2.8.11:', type='build')
-    depends_on('pkg-config', type='build')
-
-    # Currently python is only necessary to run
-    # building preprocessing scripts.
-    depends_on('python', type='build')
+    depends_on('pkgconfig', type='build')
+    depends_on('python@:2', type='build')
     depends_on('perl', type='build')
     depends_on('perl-xml-parser', type='build')
-    depends_on('eccodes', when='+eccodes')
-    depends_on('grib-api', when='~eccodes')
+
+    # Non-optional dependencies
     depends_on('proj')
     depends_on('boost')
     depends_on('expat')
-    depends_on('pango', when='+cairo')
+
+    # Magics (at least up to version 2.34.3) should directly and
+    # unconditionally depend on zlib, which is not reflected neither in the
+    # installation instructions nor explicitly stated in the cmake script:
+    # zlib is pulled as a dependency of png. The dependency on png is formally
+    # optional and depends on an unofficial flag ENABLE_PNG, which is
+    # redundant, because png is used only when ENABLE_CAIRO=ON. The problem is
+    # that files that make calls to png library get compiled and linked
+    # unconditionally, which makes png a non-optional dependency (and
+    # ENABLE_PNG always has to be set to ON).
+    depends_on('zlib')
+    depends_on('libpng')
+
+    # GRIB support is non-optional, regardless of what the instruction says.
+    depends_on('eccodes', when='grib=eccodes')
+    depends_on('grib-api', when='grib=grib-api')
+
+    # Optional dependencies
     depends_on('netcdf-cxx', when='+netcdf')
-    depends_on('libemos', when='+bufr')
+    depends_on('pango', when='+cairo')
+    depends_on('libemos grib=eccodes', when='+bufr grib=eccodes')
+    depends_on('libemos grib=grib-api', when='+bufr grib=grib-api')
     depends_on('qt', when='+metview+qt')
 
-    conflicts('+eccodes', when='@:2.29.0')
+    extends('python', when='+python')
+    # Python 2 is required for running the building scripts. Since we can't
+    # have two different versions of Python at the same time, we haven't even
+    # tested if the Python interface supports Python 3.
+    depends_on('python', when='+python', type=('link', 'run'))
+    depends_on('py-numpy', when='+python', type=('build', 'run'))
+    depends_on('swig', when='+python', type='build')
+
+    conflicts('grib=eccodes', when='@:2.29.0',
+              msg='Eccodes is supported starting version 2.29.1')
+    conflicts('+python', when='@:2.28',
+              msg='Python interface is supported starting version 2.29.0')
 
     # Replace system python and perl by spack versions:
     def patch(self):
@@ -84,50 +103,51 @@ class Magics(CMakePackage):
             filter_file('#!/usr/bin/python', '#!/usr/bin/env python', pyfile)
 
     def cmake_args(self):
-        spec = self.spec
         args = [
             '-DENABLE_ODB=OFF',
-            '-DENABLE_PYTHON=OFF',
-            '-DBOOST_ROOT=%s' % spec['boost'].prefix,
-            '-DPROJ4_PATH=%s' % spec['proj'].prefix,
-            '-DENABLE_TESTS=OFF',
+            '-DENABLE_SPOT=OFF'
         ]
 
-        if '+bufr' in spec:
-            args.append('-DENABLE_BUFR=ON')
-            args.append('-DLIBEMOS_PATH=%s' % spec['libemos'].prefix)
+        if self.spec.variants['grib'].value == 'eccodes':
+            args.append('-DENABLE_ECCODES=ON')
         else:
-            args.append('-DENABLE_BUFR=OFF')
+            if self.spec.satisfies('@2.29.1:'):
+                args.append('-DENABLE_ECCODES=OFF')
 
-        if '+netcdf' in spec:
+        if '+netcdf' in self.spec:
             args.append('-DENABLE_NETCDF=ON')
-            args.append('-DNETCDF_PATH=%s' % spec['netcdf-cxx'].prefix)
         else:
             args.append('-DENABLE_NETCDF=OFF')
 
-        if '+cairo' in spec:
+        if '+cairo' in self.spec:
             args.append('-DENABLE_CAIRO=ON')
         else:
             args.append('-DENABLE_CAIRO=OFF')
 
-        if '+metview' in spec:
-            if '+qt' in spec:
+        if '+python' in self.spec:
+            args.append('-DENABLE_PYTHON=ON')
+        else:
+            if self.spec.satisfies('@2.29.0:'):
+                args.append('-DENABLE_PYTHON=OFF')
+
+        if '+fortran' in self.spec:
+            args.append('-DENABLE_FORTRAN=ON')
+        else:
+            args.append('-DENABLE_FORTRAN=OFF')
+
+        if '+bufr' in self.spec:
+            args.append('-DENABLE_BUFR=ON')
+        else:
+            args.append('-DENABLE_BUFR=OFF')
+
+        if '+metview' in self.spec:
+            if '+qt' in self.spec:
                 args.append('-DENABLE_METVIEW=ON')
-                if spec['qt'].version[0] == 5:
+                if self.spec['qt'].satisfies('@5:'):
                     args.append('-DENABLE_QT5=ON')
             else:
                 args.append('-DENABLE_METVIEW_NO_QT=ON')
         else:
             args.append('-DENABLE_METVIEW=OFF')
 
-        if '+eccodes' in spec:
-            args.append('-DENABLE_ECCODES=ON')
-            args.append('-DECCODES_PATH=%s' % spec['eccodes'].prefix)
-        else:
-            args.append('-DENABLE_ECCODES=OFF')
-            args.append('-DGRIB_API_PATH=%s' % spec['grib-api'].prefix)
-
-        if (self.compiler.f77 is None) or (self.compiler.fc is None):
-            args.append('-DENABLE_FORTRAN=OFF')
-
         return args
diff --git a/var/spack/repos/builtin/packages/magma/magma-2.3.0-gcc-4.8.patch b/var/spack/repos/builtin/packages/magma/magma-2.3.0-gcc-4.8.patch
new file mode 100644
index 0000000000..f734a5f16a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/magma/magma-2.3.0-gcc-4.8.patch
@@ -0,0 +1,24 @@
+diff -ru magma-2.3.0/testing/testings.h magma-2.3.0-patched/testing/testings.h
+--- magma-2.3.0/testing/testings.h	2017-11-14 21:34:00.000000000 -0800
++++ magma-2.3.0-patched/testing/testings.h	2018-03-23 20:41:16.459934643 -0700
+@@ -269,4 +269,20 @@
+     typename blas::traits<FloatT>::real_t* sigma,
+     FloatT* A, magma_int_t lda );
+ 
++// This overload for the case sigma = nullptr is a workaround for an issue
++// when building with gcc 4.8.5. This is not an issue with gcc 4.9.2.
++template< typename FloatT >
++void magma_generate_matrix(
++    magma_opts& opts,
++    magma_int_t m, magma_int_t n,
++    std::nullptr_t sigma,
++    FloatT* A, magma_int_t lda )
++{
++    magma_generate_matrix<FloatT>(
++        opts,
++        m, n,
++        (typename blas::traits<FloatT>::real_t*) sigma,
++        A, lda );
++}
++
+ #endif /* TESTINGS_H */
diff --git a/var/spack/repos/builtin/packages/magma/package.py b/var/spack/repos/builtin/packages/magma/package.py
index bccac28497..7a28a3bd85 100644
--- a/var/spack/repos/builtin/packages/magma/package.py
+++ b/var/spack/repos/builtin/packages/magma/package.py
@@ -1,49 +1,40 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Serban Maerean, serban@us.ibm.com, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
 from spack import *
 
 
 class Magma(CMakePackage):
-    """The MAGMA project aims to develop a dense linear algebra library
-    similar to LAPACK but for heterogeneous/hybrid architectures,
-    starting with current "Multicore+GPU" systems.
+    """The MAGMA project aims to develop a dense linear algebra library similar to
+       LAPACK but for heterogeneous/hybrid architectures, starting with current
+       "Multicore+GPU" systems.
     """
 
     homepage = "http://icl.cs.utk.edu/magma/"
     url = "http://icl.cs.utk.edu/projectsfiles/magma/downloads/magma-2.2.0.tar.gz"
 
-    version('2.2.0', '6c1ebf4cdf63eb302ff6258ff8c49217')
+    version('2.4.0', sha256='4eb839b1295405fd29c8a6f5b4ed578476010bf976af46573f80d1169f1f9a4f')
+    version('2.3.0', sha256='010a4a057d7aa1e57b9426bffc0958f3d06913c9151463737e289e67dd9ea608')
+    version('2.2.0', sha256='df5d4ace417e5bf52694eae0d91490c6bde4cde1b0da98e8d400c5c3a70d83a2')
 
     variant('fortran', default=True,
             description='Enable Fortran bindings support')
+    variant('shared', default=True,
+            description='Enable shared library')
 
+    depends_on('blas')
     depends_on('lapack')
-    depends_on('cuda@9.0:', when='%gcc@6.0:6.9.9')
-    depends_on('cuda@8.0:', when='%gcc@5.0:')
+    depends_on('cuda')
+
+    conflicts('%gcc@6:', when='^cuda@:8')
+    conflicts('%gcc@7:', when='^cuda@:9')
+
     patch('ibm-xl.patch', when='@2.2:%xl')
     patch('ibm-xl.patch', when='@2.2:%xl_r')
+    patch('magma-2.3.0-gcc-4.8.patch', when='@2.3.0%gcc@:4.8')
 
     def cmake_args(self):
         spec = self.spec
@@ -52,10 +43,17 @@ class Magma(CMakePackage):
         options.extend([
             '-DCMAKE_INSTALL_PREFIX=%s' % prefix,
             '-DCMAKE_INSTALL_NAME_DIR:PATH=%s/lib' % prefix,
-            '-DLAPACK_LIBRARIES=%s;%s' % (spec['blas'].libs,
-                                          spec['lapack'].libs)
+            '-DBLAS_LIBRARIES=%s' % spec['blas'].libs.joined(';'),
+            # As of MAGMA v2.3.0, CMakeLists.txt does not use the variable
+            # BLAS_LIBRARIES, but only LAPACK_LIBRARIES, so we need to
+            # explicitly add blas to LAPACK_LIBRARIES.
+            '-DLAPACK_LIBRARIES=%s' %
+            (spec['lapack'].libs + spec['blas'].libs).joined(';')
         ])
 
+        options += ['-DBUILD_SHARED_LIBS=%s' %
+                    ('ON' if ('+shared' in spec) else 'OFF')]
+
         if '+fortran' in spec:
             options.extend([
                 '-DUSE_FORTRAN=yes'
@@ -66,8 +64,16 @@ class Magma(CMakePackage):
                 ])
 
         if spec.satisfies('^cuda@9.0:'):
-            options.extend([
-                '-DGPU_TARGET=sm30'
-            ])
+            if '@:2.2.0' in spec:
+                options.extend(['-DGPU_TARGET=sm30'])
+            else:
+                options.extend(['-DGPU_TARGET=sm_30'])
 
         return options
+
+    @run_after('install')
+    def post_install(self):
+        install('magmablas/atomics.cuh', self.prefix.include)
+        install('control/magma_threadsetting.h', self.prefix.include)
+        install('control/pthread_barrier.h', self.prefix.include)
+        install('control/magma_internal.h', self.prefix.include)
diff --git a/var/spack/repos/builtin/packages/makedepend/package.py b/var/spack/repos/builtin/packages/makedepend/package.py
index 41edb6ed69..9dd5ea50f5 100644
--- a/var/spack/repos/builtin/packages/makedepend/package.py
+++ b/var/spack/repos/builtin/packages/makedepend/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,4 +15,4 @@ class Makedepend(AutotoolsPackage):
     version('1.0.5', 'efb2d7c7e22840947863efaedc175747')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
diff --git a/var/spack/repos/builtin/packages/mallocmc/package.py b/var/spack/repos/builtin/packages/mallocmc/package.py
index ed8ba9bdeb..d5d4faa21c 100644
--- a/var/spack/repos/builtin/packages/mallocmc/package.py
+++ b/var/spack/repos/builtin/packages/mallocmc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,11 +20,12 @@ class Mallocmc(CMakePackage):
 
     homepage = "https://github.com/ComputationalRadiationPhysics/mallocMC"
     url      = "https://github.com/ComputationalRadiationPhysics/mallocMC/archive/2.2.0crp.tar.gz"
+    git      = "https://github.com/ComputationalRadiationPhysics/mallocMC.git"
+
+    maintainers = ['ax3l']
 
-    version('develop', branch='dev',
-            git='https://github.com/ComputationalRadiationPhysics/mallocMC.git')
-    version('master', branch='master',
-            git='https://github.com/ComputationalRadiationPhysics/mallocMC.git')
+    version('develop', branch='dev')
+    version('master', branch='master')
     version('2.2.0crp', '3e5c5fc963d1a9abc829ff701504e54c')
     version('2.1.0crp', 'd2bd2644012b64a246048575e9a9051c')
     version('2.0.1crp', '1f674d5d1ae05446d9a4e4b65465dca0')
diff --git a/var/spack/repos/builtin/packages/man-db/package.py b/var/spack/repos/builtin/packages/man-db/package.py
index 7a6a03731e..634815260d 100644
--- a/var/spack/repos/builtin/packages/man-db/package.py
+++ b/var/spack/repos/builtin/packages/man-db/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/manta/package.py b/var/spack/repos/builtin/packages/manta/package.py
new file mode 100644
index 0000000000..74f717920a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/manta/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Manta(CMakePackage):
+    """Structural variant and indel caller for mapped sequencing data"""
+
+    homepage = "https://github.com/Illumina/manta"
+    url      = "https://github.com/Illumina/manta/releases/download/v1.3.2/manta-1.3.2.release_src.tar.bz2"
+
+    depends_on('boost@1.58.0:', type='build')
+    depends_on('cmake@2.8.12:', type='build')
+    depends_on('python@2.7.0:2.7.999', type=('build', 'run'))
+
+    version('1.4.0', '582d10f3bc56aecfa5c24931af3742b4')
+    version('1.3.2', '83f43fe1a12605c1e9803d1020b24bd1')
+    version('1.3.1', 'e315caff775878872ee300ed34e8adae')
+    version('1.3.0', '1243e2bb58ca7c9d69bbfbe528f492ec')
diff --git a/var/spack/repos/builtin/packages/maq/package.py b/var/spack/repos/builtin/packages/maq/package.py
new file mode 100644
index 0000000000..222b56827d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/maq/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Maq(AutotoolsPackage):
+    """Maq is a software that builds mapping assemblies from short reads
+       generated by the next-generation sequencing machines."""
+
+    homepage = "http://maq.sourceforge.net/"
+    url      = "https://downloads.sourceforge.net/project/maq/maq/0.7.1/maq-0.7.1.tar.bz2"
+    list_url = "https://sourceforge.net/projects/maq/files/maq/"
+
+    version('0.7.1', '51130f6c8257c133719adacdd1433f35')
+    version('0.5.0', '854e2bee32d5237236d4c68c0ed7c52d')
+
+    conflicts('%gcc@4.7.0:', when='@0.7.1')
diff --git a/var/spack/repos/builtin/packages/mariadb/package.py b/var/spack/repos/builtin/packages/mariadb/package.py
index 53203f585a..c2ec90f299 100644
--- a/var/spack/repos/builtin/packages/mariadb/package.py
+++ b/var/spack/repos/builtin/packages/mariadb/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/masa/package.py b/var/spack/repos/builtin/packages/masa/package.py
index e0e7c00cde..a269d0362c 100644
--- a/var/spack/repos/builtin/packages/masa/package.py
+++ b/var/spack/repos/builtin/packages/masa/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,12 +12,11 @@ class Masa(AutotoolsPackage):
        provides a suite of manufactured solutions for the software
        verification of partial differential equation solvers in multiple
        dimensions."""
+
     homepage = "https://github.com/manufactured-solutions/MASA"
-    url      = "https://github.com/manufactured-solutions/MASA.git"
+    git      = "https://github.com/manufactured-solutions/MASA.git"
 
-    version('master',
-            git='https://github.com/manufactured-solutions/MASA.git',
-            tag='master')
+    version('master', tag='master')
 
     variant('fortran', default=True,
             description='Compile with Fortran interfaces')
diff --git a/var/spack/repos/builtin/packages/masurca/package.py b/var/spack/repos/builtin/packages/masurca/package.py
new file mode 100644
index 0000000000..4aeb00e0dd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/masurca/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Masurca(Package):
+    """MaSuRCA is whole genome assembly software. It combines the efficiency
+       of the de Bruijn graph and Overlap-Layout-Consensus (OLC)
+       approaches."""
+
+    homepage = "http://www.genome.umd.edu/masurca.html"
+    url      = "ftp://ftp.genome.umd.edu/pub/MaSuRCA/latest/MaSuRCA-3.2.3.tar.gz"
+
+    version('3.2.6', 'f068f91e33fd7381de406a7a954bfe01')
+    version('3.2.3', 'd9b4419adfe6b64e42ce986253a50ff5')
+
+    depends_on('perl', type=('build', 'run'))
+    depends_on('boost')
+    depends_on('zlib')
+
+    def install(self, spec, prefix):
+        installer = Executable('./install.sh')
+        installer()
+        install_tree('.', prefix)
diff --git a/var/spack/repos/builtin/packages/matio/package.py b/var/spack/repos/builtin/packages/matio/package.py
index 8569893375..89be615244 100644
--- a/var/spack/repos/builtin/packages/matio/package.py
+++ b/var/spack/repos/builtin/packages/matio/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/matlab/package.py b/var/spack/repos/builtin/packages/matlab/package.py
index c61bbe05d6..d9f3a9476c 100644
--- a/var/spack/repos/builtin/packages/matlab/package.py
+++ b/var/spack/repos/builtin/packages/matlab/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 import subprocess
@@ -41,8 +22,8 @@ class Matlab(Package):
     mirror so that Spack can find it. For instructions on how to set up a
     mirror, see http://spack.readthedocs.io/en/latest/mirrors.html"""
 
-    homepage = "https://www.mathworks.com/products/matlab.html"
-
+    homepage = "https://www.mathworks.com/products/matlab.html" 
+    version('R2018b', sha256='8cfcddd3878d3a69371c4e838773bcabf12aaf0362cc2e1ae7e8820845635cac')
     version('R2016b', 'b0e0b688894282139fa787b5a86a5cf7')
 
     variant(
@@ -80,15 +61,15 @@ class Matlab(Package):
         }
 
         # Store values requested by the installer in a file
-        with open('spack_installer_input.txt', 'w') as inputFile:
+        with open('spack_installer_input.txt', 'w') as input_file:
             for key in config:
-                inputFile.write('{0}={1}\n'.format(key, config[key]))
+                input_file.write('{0}={1}\n'.format(key, config[key]))
 
     def install(self, spec, prefix):
         self.configure(spec, prefix)
 
         # Run silent installation script
         # Full path required
-        inputFile = join_path(self.stage.source_path,
-                              'spack_installer_input.txt')
-        subprocess.call(['./install', '-inputFile', inputFile])
+        input_file = join_path(
+            self.stage.source_path, 'spack_installer_input.txt')
+        subprocess.call(['./install', '-inputFile', input_file])
diff --git a/var/spack/repos/builtin/packages/maven/package.py b/var/spack/repos/builtin/packages/maven/package.py
index 425e5abaab..58cfe004d7 100644
--- a/var/spack/repos/builtin/packages/maven/package.py
+++ b/var/spack/repos/builtin/packages/maven/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from distutils.dir_util import copy_tree
 
 
 class Maven(Package):
@@ -39,4 +19,4 @@ class Maven(Package):
 
     def install(self, spec, prefix):
         # install pre-built distribution
-        copy_tree('.', prefix)
+        install_tree('.', prefix)
diff --git a/var/spack/repos/builtin/packages/maverick/package.py b/var/spack/repos/builtin/packages/maverick/package.py
index b898beafb7..047540cce1 100644
--- a/var/spack/repos/builtin/packages/maverick/package.py
+++ b/var/spack/repos/builtin/packages/maverick/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/mawk/package.py b/var/spack/repos/builtin/packages/mawk/package.py
index 2749736796..864e76b8f3 100644
--- a/var/spack/repos/builtin/packages/mawk/package.py
+++ b/var/spack/repos/builtin/packages/mawk/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/mbedtls/package.py b/var/spack/repos/builtin/packages/mbedtls/package.py
index 12687ea5a8..f6ea6c5dbe 100644
--- a/var/spack/repos/builtin/packages/mbedtls/package.py
+++ b/var/spack/repos/builtin/packages/mbedtls/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/mc/package.py b/var/spack/repos/builtin/packages/mc/package.py
new file mode 100644
index 0000000000..38037f1707
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mc/package.py
@@ -0,0 +1,37 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Mc(AutotoolsPackage):
+    """The GNU Midnight Commander is a visual file manager."""
+
+    homepage = "https://midnight-commander.org"
+    url      = "http://ftp.midnight-commander.org/mc-4.8.20.tar.bz2"
+
+    version('4.8.20', 'dcfc7aa613c62291a0f71f6b698d8267')
+
+    depends_on('ncurses')
+    depends_on('pkgconfig', type='build')
+    depends_on('glib@2.14:')
+    depends_on('libssh2@1.2.5:')
+
+    def setup_environment(self, spack_env, run_env):
+        # Fix compilation bug on macOS by pretending we don't have utimensat()
+        # https://github.com/MidnightCommander/mc/pull/130
+        if 'darwin' in self.spec.architecture:
+            env['ac_cv_func_utimensat'] = 'no'
+
+    def configure_args(self):
+        args = [
+            '--disable-debug',
+            '--disable-dependency-tracking',
+            '--disable-silent-rules',
+            '--without-x',
+            '--with-screen=ncurses',
+            '--enable-vfs-sftp'
+        ]
+        return args
diff --git a/var/spack/repos/builtin/packages/mcl/package.py b/var/spack/repos/builtin/packages/mcl/package.py
index 4644cc39ac..91352caac2 100644
--- a/var/spack/repos/builtin/packages/mcl/package.py
+++ b/var/spack/repos/builtin/packages/mcl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/mdtest/package.py b/var/spack/repos/builtin/packages/mdtest/package.py
index 519aed704c..56bede2f87 100644
--- a/var/spack/repos/builtin/packages/mdtest/package.py
+++ b/var/spack/repos/builtin/packages/mdtest/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,8 +12,9 @@ class Mdtest(Package):
        and directories and then reports the performance."""
 
     homepage = "https://github.com/LLNL/mdtest"
+    git      = "https://github.com/LLNL/mdtest.git"
 
-    version('1.9.3', git='https://github.com/LLNL/mdtest.git', commit='49f3f0')
+    version('1.9.3', commit='49f3f0')
 
     depends_on('mpi')
 
diff --git a/var/spack/repos/builtin/packages/med/package.py b/var/spack/repos/builtin/packages/med/package.py
new file mode 100644
index 0000000000..95d3794ced
--- /dev/null
+++ b/var/spack/repos/builtin/packages/med/package.py
@@ -0,0 +1,52 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Med(CMakePackage):
+    """The MED file format is a specialization of the HDF5 standard."""
+
+    homepage = "http://docs.salome-platform.org/latest/dev/MEDCoupling/med-file.html"
+    url = "http://files.salome-platform.org/Salome/other/med-3.2.0.tar.gz"
+
+    maintainers = ['likask']
+
+    version('3.2.0', 'eb61df92f0624feb6328f517cd756a23')
+
+    variant('api23', default=True, description='Enable API2.3')
+
+    depends_on('mpi')
+    depends_on('hdf5@:1.8.19+mpi')
+
+    # FIXME This is minimal installation.
+
+    def cmake_args(self):
+        spec = self.spec
+
+        options = []
+
+        if '+api23' in spec:
+            options.extend([
+                '-DCMAKE_CXX_FLAGS:STRING=-DMED_API_23=1',
+                '-DCMAKE_C_FLAGS:STRING=-DMED_API_23=1',
+                '-DMED_API_23=1'])
+
+        options.extend([
+            '-DMEDFILE_USE_MPI=YES'
+            '-DMEDFILE_BUILD_TESTS={0}'.format(
+                'ON' if self.run_tests else 'OFF'),
+            '-DMEDFILE_BUILD_PYTHON=OFF',
+            '-DMEDFILE_INSTALL_DOC=OFF',
+            '-DMEDFILE_BUILD_SHARED_LIBS=OFF',
+            '-DMEDFILE_BUILD_STATIC_LIBS=ON',
+            '-DCMAKE_Fortran_COMPILER='])
+
+        options.extend([
+            '-DHDF5_ROOT_DIR=%s' % spec['hdf5'].prefix,
+            '-DMPI_ROOT_DIR=%s' % spec['mpi'].prefix])
+
+        return options
diff --git a/var/spack/repos/builtin/packages/meep/package.py b/var/spack/repos/builtin/packages/meep/package.py
index 79c50a8123..3a125c8bb9 100644
--- a/var/spack/repos/builtin/packages/meep/package.py
+++ b/var/spack/repos/builtin/packages/meep/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/mefit/package.py b/var/spack/repos/builtin/packages/mefit/package.py
new file mode 100644
index 0000000000..ce21fc9261
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mefit/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Mefit(Package):
+    """This pipeline will merge overlapping paired-end reads, calculate
+    merge statistics, and filter reads for quality."""
+
+    homepage = "https://github.com/nisheth/MeFiT"
+    git      = "https://github.com/nisheth/MeFiT.git"
+
+    version('1.0', commit='0733326d8917570bbf70ff5c0f710bf66c13db09')
+
+    depends_on('py-numpy')
+    depends_on('py-htseq')
+    depends_on('jellyfish')
+    depends_on('casper %gcc@4.8.5')
+
+    def install(self, spec, prefix):
+        install_tree('.', prefix)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PATH', self.prefix)
diff --git a/var/spack/repos/builtin/packages/megahit/package.py b/var/spack/repos/builtin/packages/megahit/package.py
new file mode 100644
index 0000000000..d753c611ab
--- /dev/null
+++ b/var/spack/repos/builtin/packages/megahit/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Megahit(MakefilePackage):
+    """MEGAHIT: An ultra-fast single-node solution for
+    large and complex metagenomics assembly via succinct de Bruijn graph"""
+
+    homepage = "https://github.com/voutcn/megahit"
+    url      = "https://github.com/voutcn/megahit/archive/v1.1.3.tar.gz"
+
+    version('1.1.3', '2962a781a22c0884fa97b95f740ed2fe')
+
+    depends_on('zlib')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('megahit', prefix.bin)
+        install('megahit_asm_core', prefix.bin)
+        install('megahit_sdbg_build', prefix.bin)
+        install('megahit_toolkit', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/memaxes/package.py b/var/spack/repos/builtin/packages/memaxes/package.py
index 581454ef06..3b5e7f8733 100644
--- a/var/spack/repos/builtin/packages/memaxes/package.py
+++ b/var/spack/repos/builtin/packages/memaxes/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/meme/package.py b/var/spack/repos/builtin/packages/meme/package.py
index 224410e85e..b7b66f3b04 100644
--- a/var/spack/repos/builtin/packages/meme/package.py
+++ b/var/spack/repos/builtin/packages/meme/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,22 +14,24 @@ class Meme(AutotoolsPackage):
     homepage = "http://meme-suite.org"
     url      = "http://meme-suite.org/meme-software/4.11.4/meme_4.11.4.tar.gz"
 
+    version('4.12.0', '40d282cc33f7dedb06b24b9f34ac15c1')
     version('4.11.4', '371f513f82fa0888205748e333003897')
 
     variant('mpi', default=True, description='Enable MPI support')
+    variant('image-magick', default=False, description='Enable image-magick for png output')
 
     depends_on('zlib', type=('link'))
-    depends_on('libxml2', type=('link'))
-    depends_on('libxslt', type=('link'))
     depends_on('libgcrypt', type=('link'))
     depends_on('perl', type=('build', 'run'))
     depends_on('python@2.7:', type=('build', 'run'))
     depends_on('mpi', when='+mpi')
+    depends_on('image-magick', type=('build', 'run'), when='+image-magick')
+    depends_on('perl-xml-parser', type=('build', 'run'))
 
-    # disable mpi support
     def configure_args(self):
         spec = self.spec
-        args = []
+        # have meme build its own versions of libxml2/libxslt, see #6736
+        args = ['--enable-build-libxml2', '--enable-build-libxslt']
         if '~mpi' in spec:
             args += ['--enable-serial']
         return args
diff --git a/var/spack/repos/builtin/packages/memkind/package.py b/var/spack/repos/builtin/packages/memkind/package.py
new file mode 100644
index 0000000000..097a642f13
--- /dev/null
+++ b/var/spack/repos/builtin/packages/memkind/package.py
@@ -0,0 +1,49 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class Memkind(AutotoolsPackage):
+    """The memkind library is a user extensible heap manager built on top of
+    jemalloc which enables control of memory characteristics and a partitioning
+    of the heap between kinds of memory. The kinds of memory are defined by
+    operating system memory policies that have been applied to virtual address
+    ranges. Memory characteristics supported by memkind without user extension
+    include control of NUMA and page size features. The jemalloc non-standard
+    interface has been extended to enable specialized arenas to make requests
+    for virtual memory from the operating system through the memkind partition
+    interface. Through the other memkind interfaces the user can control and
+    extend memory partition features and allocate memory while selecting
+    enabled features."""
+
+    homepage = "https://github.com/memkind/memkind"
+    url      = "https://github.com/memkind/memkind/archive/v1.7.0.tar.gz"
+
+    version('1.7.0', 'bfbbb9226d40fd12ae1822a8be4c9207')
+
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool',  type='build')
+    depends_on('m4',       type='build')
+    depends_on('numactl')
+
+    phases = ['build_jemalloc', 'autoreconf', 'configure', 'build',
+              'install']
+
+    def patch(self):
+        with open('VERSION', 'w') as version_file:
+            version_file.write('{0}\n'.format(self.version))
+
+    def build_jemalloc(self, spec, prefix):
+        if os.path.exists('build_jemalloc.sh'):
+            bash = which('bash')
+            bash('./build_jemalloc.sh')
+
+    def autoreconf(self, spec, prefix):
+        if os.path.exists('autogen.sh'):
+            bash = which('bash')
+            bash('./autogen.sh')
diff --git a/var/spack/repos/builtin/packages/meraculous/package.py b/var/spack/repos/builtin/packages/meraculous/package.py
new file mode 100644
index 0000000000..cb9c96eff7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/meraculous/package.py
@@ -0,0 +1,33 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Meraculous(CMakePackage):
+    """Meraculous is a while genome assembler for Next Generation Sequencing
+       data geared for large genomes."""
+
+    homepage = "http://jgi.doe.gov/data-and-tools/meraculous/"
+    url      = "https://downloads.sourceforge.net/project/meraculous20/Meraculous-v2.2.4.tar.gz"
+    git      = "https://bitbucket.org/berkeleylab/genomics-meraculous2.git"
+
+    version('2.2.5.1', branch='release-2.2.5.1')
+    version('2.2.4', '349feb6cb178643a46e4b092c87bad3a')
+
+    depends_on('perl', type=('build', 'run'))
+    depends_on('boost@1.5.0:')
+    depends_on('gnuplot@3.7:')
+    depends_on('perl-log-log4perl', type=('build', 'run'))
+
+    conflicts('%gcc@6.0.0:', when='@2.2.4')
+
+    def patch(self):
+        edit = FileFilter('CMakeLists.txt')
+        edit.filter("-static-libstdc\+\+", "")
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.set('MERACULOUS_ROOT', self.prefix)
+        run_env.prepend_path('PERL5LIB', self.prefix.lib)
diff --git a/var/spack/repos/builtin/packages/mercurial/package.py b/var/spack/repos/builtin/packages/mercurial/package.py
index 4ecd3332a9..aaabdd6c01 100644
--- a/var/spack/repos/builtin/packages/mercurial/package.py
+++ b/var/spack/repos/builtin/packages/mercurial/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 from llnl.util import tty
 
@@ -39,6 +20,7 @@ class Mercurial(PythonPackage):
         'mercurial.httpclient', 'mercurial.pure'
     ]
 
+    version('4.4.1', '37974a416d1d9525e1375c92025b16d9')
     version('4.1.2', '934c99808bdc8385e074b902d59b0d93')
     version('3.9.1', '3759dd10edb8c1a6dfb8ff0ce82658ce')
     version('3.9',   'e2b355da744e94747daae3a5339d28a0')
@@ -47,7 +29,8 @@ class Mercurial(PythonPackage):
     version('3.8.2', 'c38daa0cbe264fc621dc3bb05933b0b3')
     version('3.8.1', '172a8c588adca12308c2aca16608d7f4')
 
-    depends_on('python@2.6:2.8')
+    depends_on('python@2.6:2.8', when='@:4.2.99')
+    depends_on('python@2.7:2.8,3.5:3.5.999,3.6.2:', when='@4.3:')
     depends_on('py-docutils', type='build')
     depends_on('py-pygments', type=('build', 'run'))
     depends_on('py-certifi',  type=('build', 'run'))
@@ -84,8 +67,8 @@ class Mercurial(PythonPackage):
         hgrc_filename = join_path(etc_dir, 'hgrc')
 
         # Use certifi to find the location of the CA certificate
-        certificate = python('-c', 'import certifi; print certifi.where()',
-                             output=str)
+        print_str = self.spec['python'].package.print_string('certifi.where()')
+        certificate = python('-c', 'import certifi; ' + print_str)
 
         if not certificate:
             tty.warn('CA certificate not found. You may not be able to '
diff --git a/var/spack/repos/builtin/packages/mesa-glu/package.py b/var/spack/repos/builtin/packages/mesa-glu/package.py
index b450728e75..efd45dfa39 100644
--- a/var/spack/repos/builtin/packages/mesa-glu/package.py
+++ b/var/spack/repos/builtin/packages/mesa-glu/package.py
@@ -1,28 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,3 +17,13 @@ class MesaGlu(AutotoolsPackage):
     variant('mesa', default=True,
        description='Usually depends on mesa, disable for accelerated OpenGL')
     depends_on('mesa', when='+mesa')
+
+    provides('glu@1.3')
+
+    @property
+    def libs(self):
+        for dir in ['lib64', 'lib']:
+            libs = find_libraries('libGLU', join_path(self.prefix, dir),
+                                  shared=True, recursive=False)
+            if libs:
+                return libs
diff --git a/var/spack/repos/builtin/packages/mesa/package.py b/var/spack/repos/builtin/packages/mesa/package.py
index af8c20ae52..2823a98260 100644
--- a/var/spack/repos/builtin/packages/mesa/package.py
+++ b/var/spack/repos/builtin/packages/mesa/package.py
@@ -1,27 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is released as part of spack under the LGPL license.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+import sys
 from spack import *
 
 
@@ -36,6 +18,7 @@ class Mesa(AutotoolsPackage):
     _oldurlfmt = "https://mesa.freedesktop.org/archive/older-versions/{0}.x/{1}/mesa-{1}.tar.xz"
     list_depth = 2
 
+    version('18.1.2', 'a2d4f031eb6bd6111d44d84004476918')
     version('17.2.3', 'a7dca71afbc7294cb7d505067fd44ef6')
     version('17.2.2', '1a157b5baefb5adf9f4fbb8a6632d74c')
     version('17.1.5', '6cf936fbcaadd98924298a7009e8265d')
@@ -46,6 +29,10 @@ class Mesa(AutotoolsPackage):
     version('12.0.6', '1a3d4fea0656c208db59289e4ed33b3f')
     version('12.0.3', '1113699c714042d8c4df4766be8c57d8')
 
+    provides('gl@:4.5', when='@17:')
+    provides('gl@:4.4', when='@13:')
+    provides('gl@:4.3', when='@12:')
+
     variant('swrender', default=True,
             description="Build with (gallium) software rendering.")
     variant('hwrender', default=False,
@@ -54,12 +41,13 @@ class Mesa(AutotoolsPackage):
             description="Use llvm for rendering pipes.")
 
     # General dependencies
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('flex@2.5.35:', type='build')
     depends_on('bison@2.4.1:', type='build')
-    depends_on('binutils', type='build')
+    depends_on('binutils', type='build', when=(sys.platform != 'darwin'))
     depends_on('python@2.6.4:', type='build')
     depends_on('py-mako@0.3.4:', type='build')
+    depends_on('py-argparse', type='build')
     depends_on('gettext')
     depends_on('icu4c')
     depends_on('expat')
@@ -76,6 +64,7 @@ class Mesa(AutotoolsPackage):
     depends_on('libxfixes')
     depends_on('libxv')
     depends_on('libxvmc')
+    depends_on('zlib@1.2.3:')
 
     # For DRI and hardware acceleration
     depends_on('dri2proto@2.6:', type='build', when='+hwrender')
@@ -86,6 +75,8 @@ class Mesa(AutotoolsPackage):
     depends_on('llvm@:3.9.1+link_dylib', when='@13:13.99+llvm')
     depends_on('llvm+link_dylib', when='+llvm')
     depends_on('libelf', when='+llvm')
+    depends_on('damageproto', when='+hwrender')
+    depends_on('fixesproto', when='+hwrender')
 
     def url_for_version(self, version):
         """Handle Mesa version-based custom URLs."""
@@ -190,3 +181,16 @@ class Mesa(AutotoolsPackage):
                 configure(*options)
             else:
                 raise
+
+    @property
+    def libs(self):
+        for dir in ['lib64', 'lib']:
+            libs = find_libraries('libGL', join_path(self.prefix, dir),
+                                  shared=True, recursive=False)
+            if libs:
+                return libs
+
+    @when('^python@3:')
+    def setup_environment(self, spack_env, run_env):
+        # this avoids an "import site" error in the build
+        spack_env.unset('PYTHONHOME')
diff --git a/var/spack/repos/builtin/packages/meshkit/package.py b/var/spack/repos/builtin/packages/meshkit/package.py
index 9db76fc4d8..9ed67edc96 100644
--- a/var/spack/repos/builtin/packages/meshkit/package.py
+++ b/var/spack/repos/builtin/packages/meshkit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/meson/package.py b/var/spack/repos/builtin/packages/meson/package.py
index 046d9b2dea..7ede3c996d 100644
--- a/var/spack/repos/builtin/packages/meson/package.py
+++ b/var/spack/repos/builtin/packages/meson/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/mesquite/package.py b/var/spack/repos/builtin/packages/mesquite/package.py
index b23f1294ce..2abaa589b9 100644
--- a/var/spack/repos/builtin/packages/mesquite/package.py
+++ b/var/spack/repos/builtin/packages/mesquite/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/metabat/package.py b/var/spack/repos/builtin/packages/metabat/package.py
new file mode 100644
index 0000000000..d8be2b90ec
--- /dev/null
+++ b/var/spack/repos/builtin/packages/metabat/package.py
@@ -0,0 +1,35 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Metabat(SConsPackage):
+    """MetaBAT, an efficient tool for accurately reconstructing single
+    genomes from complex microbial communities."""
+
+    homepage = "https://bitbucket.org/berkeleylab/metabat"
+    url      = "https://bitbucket.org/berkeleylab/metabat/get/v2.12.1.tar.gz"
+
+    version('2.12.1', 'c032f47a8b24e58a5a9fefe52cb6e0f8')
+
+    depends_on('boost@1.55.0:', type=('build', 'run'))
+    depends_on('perl', type='run')
+
+    def setup_environment(self, spack_env, run_env):
+        spack_env.set('BOOST_ROOT', self.spec['boost'].prefix)
+
+    def install_args(self, spec, prefix):
+        return ["PREFIX={0}".format(prefix)]
+
+    @run_after('build')
+    def fix_perl_scripts(self):
+        filter_file(r'#!/usr/bin/perl',
+                    '#!/usr/bin/env perl',
+                    'aggregateBinDepths.pl')
+
+        filter_file(r'#!/usr/bin/perl',
+                    '#!/usr/bin/env perl',
+                    'aggregateContigOverlapsByBin.pl')
diff --git a/var/spack/repos/builtin/packages/metaphysicl/package.py b/var/spack/repos/builtin/packages/metaphysicl/package.py
index 52548f7b4c..bfa0157cad 100644
--- a/var/spack/repos/builtin/packages/metaphysicl/package.py
+++ b/var/spack/repos/builtin/packages/metaphysicl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/metis/package.py b/var/spack/repos/builtin/packages/metis/package.py
index 20e601fbd8..ad03293d29 100644
--- a/var/spack/repos/builtin/packages/metis/package.py
+++ b/var/spack/repos/builtin/packages/metis/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 import glob
@@ -45,12 +26,25 @@ class Metis(Package):
     version('4.0.3', 'd3848b454532ef18dc83e4fb160d1e10')
 
     variant('shared', default=True, description='Enables the build of shared libraries.')
-    variant('debug', default=False, description='Builds the library in debug mode.')
-    variant('gdb', default=False, description='Enables gdb support.')
-
+    variant('gdb', default=False, description='Enables gdb support (version 5+).')
     variant('int64', default=False, description='Sets the bit width of METIS\'s index type to 64.')
     variant('real64', default=False, description='Sets the bit width of METIS\'s real type to 64.')
 
+    # For Metis version 5:, the build system is CMake, provide the
+    # `build_type` variant.
+    variant('build_type', default='Release',
+            description='The build type for the installation (only Debug or'
+            ' Release allowed for version 4).',
+            values=('Debug', 'Release', 'RelWithDebInfo', 'MinSizeRel'))
+
+    # Prior to version 5, the (non-cmake) build system only knows about
+    # 'build_type=Debug|Release'.
+    conflicts('@:4.999', when='build_type=RelWithDebInfo')
+    conflicts('@:4.999', when='build_type=MinSizeRel')
+    conflicts('@:4.999', when='+gdb')
+    conflicts('@:4.999', when='+int64')
+    conflicts('@:4.999', when='+real64')
+
     depends_on('cmake@2.8:', when='@5:', type='build')
 
     patch('install_gklib_defs_rename.patch', when='@5:')
@@ -87,12 +81,10 @@ class Metis(Package):
     @when('@:4')
     def install(self, spec, prefix):
         # Process library spec and options
-        if any('+{0}'.format(v) in spec for v in ['gdb', 'int64', 'real64']):
-            raise InstallError('METIS@:4 does not support the following '
-                               'variants: gdb, int64, real64.')
-
-        options = ['COPTIONS={0}'.format(self.compiler.pic_flag)]
-        if '+debug' in spec:
+        options = []
+        if '+shared' in spec:
+            options.append('COPTIONS={0}'.format(self.compiler.pic_flag))
+        if spec.variants['build_type'].value == 'Debug':
             options.append('OPTFLAGS=-g -O0')
         make(*options)
 
@@ -135,8 +127,8 @@ class Metis(Package):
 
         # Set up and run tests on installation
         ccompile('-I%s' % prefix.include, '-L%s' % prefix.lib,
-                 self.compiler.cc_rpath_arg +
-                 '%s' % (prefix.lib if '+shared' in spec else ''),
+                 (self.compiler.cc_rpath_arg + prefix.lib
+                  if '+shared' in spec else ''),
                  join_path('Programs', 'io.o'), join_path('Test', 'mtest.c'),
                  '-o', '%s/mtest' % prefix.bin, '-lmetis', '-lm')
 
@@ -185,6 +177,11 @@ class Metis(Package):
         options.append('-DGKLIB_PATH:PATH=%s/GKlib' % source_directory)
         options.append('-DCMAKE_INSTALL_NAME_DIR:PATH=%s/lib' % prefix)
 
+        # Normally this is available via the 'CMakePackage' object, but metis
+        # IS-A 'Package' (not a 'CMakePackage') to support non-cmake metis@:5.
+        build_type = spec.variants['build_type'].value
+        options.extend(['-DCMAKE_BUILD_TYPE:STRING={0}'.format(build_type)])
+
         if '+shared' in spec:
             options.append('-DSHARED:BOOL=ON')
         else:
@@ -196,9 +193,6 @@ class Metis(Package):
                     rpath_options.append(o)
             for o in rpath_options:
                 options.remove(o)
-        if '+debug' in spec:
-            options.extend(['-DDEBUG:BOOL=ON',
-                            '-DCMAKE_BUILD_TYPE:STRING=Debug'])
         if '+gdb' in spec:
             options.append('-DGDB:BOOL=ON')
 
@@ -208,11 +202,11 @@ class Metis(Package):
             make('install')
 
             # install GKlib headers, which will be needed for ParMETIS
-            GKlib_dist = join_path(prefix.include, 'GKlib')
-            mkdirp(GKlib_dist)
+            gklib_dist = join_path(prefix.include, 'GKlib')
+            mkdirp(gklib_dist)
             hfiles = glob.glob(join_path(source_directory, 'GKlib', '*.h'))
             for hfile in hfiles:
-                install(hfile, GKlib_dist)
+                install(hfile, gklib_dist)
 
         if self.run_tests:
             # FIXME: On some systems, the installed binaries for METIS cannot
diff --git a/var/spack/repos/builtin/packages/mfem/mfem-3.3-3.4-petsc-3.9.patch b/var/spack/repos/builtin/packages/mfem/mfem-3.3-3.4-petsc-3.9.patch
new file mode 100644
index 0000000000..dcf4870a25
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mfem/mfem-3.3-3.4-petsc-3.9.patch
@@ -0,0 +1,71 @@
+diff --git a/examples/petsc/rc_ex3p b/examples/petsc/rc_ex3p
+index 2cbe07ef2..c585d9b52 100644
+--- a/examples/petsc/rc_ex3p
++++ b/examples/petsc/rc_ex3p
+@@ -6,4 +6,4 @@
+ # it needs PETSc configured with MUMPS
+ 
+ -solver_pc_type cholesky
+--solver_pc_factor_mat_solver_package mumps
++-solver_pc_factor_mat_solver_type mumps
+diff --git a/examples/petsc/rc_ex3p_bddc b/examples/petsc/rc_ex3p_bddc
+index ea887bb29..2e1eba0d5 100644
+--- a/examples/petsc/rc_ex3p_bddc
++++ b/examples/petsc/rc_ex3p_bddc
+@@ -16,7 +16,7 @@
+ #-pc_bddc_adaptive_threshold 10
+ 
+ # Customization of the local solvers
+-#-pc_bddc_neumann_pc_factor_mat_solver_package mumps
+-#-pc_bddc_dirichlet_pc_factor_mat_solver_package mumps
++#-pc_bddc_neumann_pc_factor_mat_solver_type mumps
++#-pc_bddc_dirichlet_pc_factor_mat_solver_type mumps
+ #-pc_bddc_coarse_pc_type cholesky
+-#-pc_bddc_coarse_pc_factor_mat_solver_package mumps
++#-pc_bddc_coarse_pc_factor_mat_solver_type mumps
+diff --git a/examples/petsc/rc_ex4p b/examples/petsc/rc_ex4p
+index f734f35fe..64fbe9427 100644
+--- a/examples/petsc/rc_ex4p
++++ b/examples/petsc/rc_ex4p
+@@ -2,4 +2,4 @@
+ # it needs PETSc configured with MUMPS
+ 
+ -solver_pc_type cholesky
+--solver_pc_factor_mat_solver_package mumps
++-solver_pc_factor_mat_solver_type mumps
+diff --git a/examples/petsc/rc_ex4p_bddc b/examples/petsc/rc_ex4p_bddc
+index 9507ad431..e8ef99db7 100644
+--- a/examples/petsc/rc_ex4p_bddc
++++ b/examples/petsc/rc_ex4p_bddc
+@@ -13,7 +13,7 @@
+ #-pc_bddc_adaptive_threshold 10
+ 
+ # Customization of the local solvers
+-#-pc_bddc_neumann_pc_factor_mat_solver_package mumps
+-#-pc_bddc_dirichlet_pc_factor_mat_solver_package mumps
++#-pc_bddc_neumann_pc_factor_mat_solver_type mumps
++#-pc_bddc_dirichlet_pc_factor_mat_solver_type mumps
+ #-pc_bddc_coarse_pc_type cholesky
+-#-pc_bddc_coarse_pc_factor_mat_solver_package mumps
++#-pc_bddc_coarse_pc_factor_mat_solver_type mumps
+diff --git a/examples/petsc/rc_ex5p_bddc b/examples/petsc/rc_ex5p_bddc
+index b243c53c8..a4bc899c3 100644
+--- a/examples/petsc/rc_ex5p_bddc
++++ b/examples/petsc/rc_ex5p_bddc
+@@ -28,13 +28,13 @@
+ # local solvers (needs PETSc compiled with support for SuiteSparse)
+ # default solvers will fail
+ -prec_pc_bddc_neumann_pc_type lu
+--prec_pc_bddc_neumann_pc_factor_mat_solver_package umfpack
++-prec_pc_bddc_neumann_pc_factor_mat_solver_type umfpack
+ -prec_pc_bddc_dirichlet_pc_type lu
+--prec_pc_bddc_dirichlet_pc_factor_mat_solver_package umfpack
++-prec_pc_bddc_dirichlet_pc_factor_mat_solver_type umfpack
+ 
+ # coarse solver (needs PETSc compiled with support for MUMPS)
+ # default solver may fail
+--prec_pc_bddc_coarse_pc_factor_mat_solver_package mumps
++-prec_pc_bddc_coarse_pc_factor_mat_solver_type mumps
+ -prec_pc_bddc_coarse_pc_type cholesky
+ 
+ # deluxe scaling (needs PETSc compiled with support for MUMPS)
diff --git a/var/spack/repos/builtin/packages/mfem/mfem-3.4.patch b/var/spack/repos/builtin/packages/mfem/mfem-3.4.patch
new file mode 100644
index 0000000000..465e0525ea
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mfem/mfem-3.4.patch
@@ -0,0 +1,36 @@
+diff --git a/config/test.mk b/config/test.mk
+index 4821b084d..62479fc63 100644
+--- a/config/test.mk
++++ b/config/test.mk
+@@ -14,11 +14,13 @@
+ # Colors used below:
+ # green    '\033[0;32m'
+ # red      '\033[0;31m'
++# yellow   '\033[0;33m'
+ # no color '\033[0m'
+ COLOR_PRINT = if [ -t 1 ]; then \
+    printf $(1)$(2)'\033[0m'$(3); else printf $(2)$(3); fi
+ PRINT_OK = $(call COLOR_PRINT,'\033[0;32m',OK,"  ($$1 $$2)\n")
+ PRINT_FAILED = $(call COLOR_PRINT,'\033[0;31m',FAILED,"  ($$1 $$2)\n")
++PRINT_SKIP = $(call COLOR_PRINT,'\033[0;33m',SKIP,"\n")
+ 
+ # Timing support
+ define TIMECMD_detect
+diff --git a/examples/pumi/makefile b/examples/pumi/makefile
+index 2f98eeca7..5ff652aca 100644
+--- a/examples/pumi/makefile
++++ b/examples/pumi/makefile
+@@ -51,6 +51,13 @@ endif
+ MFEM_TESTS = EXAMPLES
+ include $(MFEM_TEST_MK)
+ 
++ifneq (,$(filter test%,$(MAKECMDGOALS)))
++   ifeq (,$(wildcard ../../data/pumi))
++      $(info PUMI data directory not found. The PUMI tests will be SKIPPED.)
++      mfem-test = printf "   $(3) [$(2) $(1) ... ]: "; $(PRINT_SKIP)
++   endif
++endif
++
+ # Testing: Parallel vs. serial runs
+ RUN_MPI_NP = $(MFEM_MPIEXEC) $(MFEM_MPIEXEC_NP)
+ RUN_MPI = $(RUN_MPI_NP) $(MFEM_MPI_NP)
diff --git a/var/spack/repos/builtin/packages/mfem/package.py b/var/spack/repos/builtin/packages/mfem/package.py
index 3afbd4ca2f..d6f55b6566 100644
--- a/var/spack/repos/builtin/packages/mfem/package.py
+++ b/var/spack/repos/builtin/packages/mfem/package.py
@@ -1,43 +1,33 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-import re
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
+import os
+import shutil
 
 
 class Mfem(Package):
     """Free, lightweight, scalable C++ library for finite element methods."""
 
+    tags = ['FEM', 'finite elements', 'high-order', 'AMR', 'HPC']
+
     homepage = 'http://www.mfem.org'
-    url      = 'https://github.com/mfem/mfem'
+    git      = 'https://github.com/mfem/mfem.git'
+
+    maintainers = ['goxberry', 'tzanio', 'markcmiller86', 'acfisher',
+                   'v-dobrev']
+
+    # Recommended mfem builds to test when updating this file: see the shell
+    # script 'test_builds.sh' in the same directory as this file.
 
     # mfem is downloaded from a URL shortener at request of upstream
     # author Tzanio Kolev <tzanio@llnl.gov>.  See here:
     #     https://github.com/mfem/mfem/issues/53
     #
     # The following procedure should be used to verify security when a
-    # new verison is added:
+    # new version is added:
     #
     # 1. Verify that no checksums on old versions have changed.
     #
@@ -51,13 +41,20 @@ class Mfem(Package):
     # If this quick verification procedure fails, additional discussion
     # will be required to verify the new version.
 
-    version('3.3.2', 
-            '01a762a5d0a2bc59ce4e2f59009045a4',
-            url='https://goo.gl/Kd7Jk8', extension='.tar.gz',
+    # 'develop' is a special version that is always larger (or newer) than any
+    # other version.
+    version('develop', branch='master')
+
+    version('3.4.0',
+            '4e73e4fe0482636de3c5dc983cd395839a83cb16f6f509bd88b053e8b3858e05',
+            url='https://bit.ly/mfem-3-4', extension='.tar.gz',
             preferred=True)
 
-    version('laghos-v1.0', git='https://github.com/mfem/mfem',
-            tag='laghos-v1.0')
+    version('3.3.2',
+            'b70fa3c5080b9ec514fc05f4a04ff74322b99ac4ecd6d99c229f0ed5188fc0ce',
+            url='https://goo.gl/Kd7Jk8', extension='.tar.gz')
+
+    version('laghos-v1.0', tag='laghos-v1.0')
 
     version('3.3',
             'b17bd452593aada93dc0fee748fcfbbf4f04ce3e7d77fdd0341cc9103bcacd0b',
@@ -71,8 +68,19 @@ class Mfem(Package):
             '841ea5cf58de6fae4de0f553b0e01ebaab9cd9c67fa821e8a715666ecf18fc57',
             url='http://goo.gl/xrScXn', extension='.tar.gz')
 
+    variant('static', default=True,
+        description='Build static library')
+    variant('shared', default=False,
+        description='Build shared library')
     variant('mpi', default=True,
         description='Enable MPI parallelism')
+    # Can we make the default value for 'metis' to depend on the 'mpi' value?
+    variant('metis', default=True,
+        description='Enable METIS support')
+    # TODO: The 'hypre' variant is the same as 'mpi', we may want to remove it.
+    #       For now, keep the 'hypre' variant while ignoring its setting. This
+    #       is done to preserve compatibility with other packages that refer to
+    #       it, e.g. xSDK.
     variant('hypre', default=True,
         description='Required for MPI parallelism')
     variant('openmp', default=False,
@@ -83,12 +91,17 @@ class Mfem(Package):
             ' May cause minor performance issues.'))
     variant('superlu-dist', default=False,
         description='Enable MPI parallel, sparse direct solvers')
+    # Placeholder for STRUMPACK, support added in mfem v3.3.2:
+    # variant('strumpack', default=False,
+    #     description='Enable support for STRUMPACK')
     variant('suite-sparse', default=False,
         description='Enable serial, sparse direct solvers')
     variant('petsc', default=False,
-        description='Enable PETSc solvers, preconditioners, etc..')
+        description='Enable PETSc solvers, preconditioners, etc.')
     variant('sundials', default=False,
         description='Enable Sundials time integrators')
+    variant('pumi', default=False,
+        description='Enable functionality based on PUMI')
     variant('mpfr', default=False,
         description='Enable precise, 1D quadrature rules')
     variant('lapack', default=False,
@@ -97,43 +110,87 @@ class Mfem(Package):
         description='Build debug instead of optimized version')
     variant('netcdf', default=False,
         description='Enable Cubit/Genesis reader')
+    variant('conduit', default=False,
+        description='Enable binary data I/O using Conduit')
     variant('gzstream', default=True,
         description='Support zip\'d streams for I/O')
+    variant('gnutls', default=False,
+        description='Enable secure sockets using GnuTLS')
+    variant('libunwind', default=False,
+        description='Enable backtrace on error support using Libunwind')
+    variant('timer', default='auto',
+        values=('auto', 'std', 'posix', 'mac', 'mpi'),
+        description='Timing functions to use in mfem::StopWatch')
     variant('examples', default=False,
         description='Build and install examples')
     variant('miniapps', default=False,
         description='Build and install miniapps')
 
-    conflicts('+mpi', when='~hypre')
-    conflicts('+suite-sparse', when='~lapack')
-    conflicts('+superlu-dist', when='@:3.1')
+    conflicts('+shared', when='@:3.3.2')
+    conflicts('~static~shared')
+    conflicts('~threadsafe', when='+openmp')
+
     conflicts('+netcdf', when='@:3.1')
+    conflicts('+superlu-dist', when='@:3.1')
+    conflicts('+gnutls', when='@:3.1')
+    conflicts('+gzstream', when='@:3.2')
+    conflicts('+mpfr', when='@:3.2')
+    conflicts('+petsc', when='@:3.2')
+    conflicts('+sundials', when='@:3.2')
+    conflicts('+pumi', when='@:3.3.2')
+    conflicts('timer=mac', when='@:3.3.0')
+    conflicts('timer=mpi', when='@:3.3.0')
+    conflicts('~metis+mpi', when='@:3.3.0')
+    conflicts('+metis~mpi', when='@:3.3.0')
+    conflicts('+conduit', when='@:3.3.2')
+
+    conflicts('+superlu-dist', when='~mpi')
+    conflicts('+petsc', when='~mpi')
+    conflicts('+pumi', when='~mpi')
+    conflicts('timer=mpi', when='~mpi')
+
+    conflicts('+pumi', when='+shared')
 
-    depends_on('hypre', when='+hypre')
+    depends_on('mpi', when='+mpi')
+    depends_on('hypre@2.10.0:2.13.999', when='@:3.3.999+mpi')
+    depends_on('hypre', when='@3.4:+mpi')
+
+    depends_on('metis', when='+metis')
     depends_on('blas', when='+lapack')
-    depends_on('blas', when='+suite-sparse')
     depends_on('lapack', when='+lapack')
-    depends_on('lapack', when='+suite-sparse')
-
-    depends_on('mpi', when='+mpi')
-    depends_on('metis')
-    depends_on('parmetis', when='+superlu-dist')
-    depends_on('metis@5:', when='+superlu-dist')
-    depends_on('metis@5:', when='+suite-sparse ^suite-sparse@4.5:')
 
-    depends_on('sundials@2.7:+hypre', when='+sundials')
+    depends_on('sundials@2.7.0', when='@:3.3.0+sundials~mpi')
+    depends_on('sundials@2.7.0+mpi+hypre', when='@:3.3.0+sundials+mpi')
+    depends_on('sundials@2.7.0:', when='@3.3.2:+sundials~mpi')
+    depends_on('sundials@2.7.0:+mpi+hypre', when='@3.3.2:+sundials+mpi')
+    depends_on('pumi', when='+pumi')
     depends_on('suite-sparse', when='+suite-sparse')
-    depends_on('superlu-dist', when='@3.2: +superlu-dist')
-    depends_on('petsc@3.8:', when='+petsc')
-
+    depends_on('superlu-dist', when='+superlu-dist')
+    # The PETSc tests in MFEM will fail if PETSc is not configured with
+    # SuiteSparse and MUMPS. On the other hand, if we require the variants
+    # '+suite-sparse+mumps' of PETSc, the xsdk package concretization fails.
+    depends_on('petsc@3.8:+mpi+double+hypre', when='+petsc')
+    # Recommended when building outside of xsdk:
+    # depends_on('petsc@3.8:+mpi+double+hypre+suite-sparse+mumps',
+    #            when='+petsc')
     depends_on('mpfr', when='+mpfr')
-    depends_on('netcdf', when='@3.2: +netcdf')
-    depends_on('zlib', when='@3.2: +netcdf')
-    depends_on('hdf5', when='@3.2: +netcdf')
-    depends_on('libunwind', when='+debug')
+    depends_on('netcdf', when='+netcdf')
+    depends_on('unwind', when='+libunwind')
     depends_on('zlib', when='+gzstream')
+    depends_on('gnutls', when='+gnutls')
+    depends_on('conduit@0.3.1:', when='+conduit')
+    depends_on('conduit+mpi', when='+conduit+mpi')
+
+    patch('mfem_ppc_build.patch', when='@3.2:3.3.0 arch=ppc64le')
+    patch('mfem-3.4.patch', when='@3.4.0')
+    patch('mfem-3.3-3.4-petsc-3.9.patch',
+          when='@3.3.0:3.4.0 +petsc ^petsc@3.9.0:')
 
-    patch('mfem_ppc_build.patch', when='@3.2:3.3 arch=ppc64le')
+    phases = ['configure', 'build', 'install']
+
+    def setup_environment(self, spack_env, run_env):
+        spack_env.unset('MFEM_DIR')
+        spack_env.unset('MFEM_BUILD_DIR')
 
     #
     # Note: Although MFEM does support CMake configuration, MFEM
@@ -142,144 +199,230 @@ class Mfem(Package):
     # likely to be up to date in supporting *all* of MFEM's
     # configuration options. So, don't use CMake
     #
-    def install(self, spec, prefix):
+    def configure(self, spec, prefix):
 
         def yes_no(varstr):
             return 'YES' if varstr in self.spec else 'NO'
 
-        metis5_str = 'NO'
-        if '+superlu-dist' in spec or  \
-            spec.satisfies('+suite-sparse ^suite-sparse@4.5:') or \
-                spec['metis'].satisfies('@5:'):
-                metis5_str = 'YES'
+        # We need to add rpaths explicitly to allow proper export of link flags
+        # from within MFEM.
+
+        # Similar to spec[pkg].libs.ld_flags but prepends rpath flags too.
+        def ld_flags_from_library_list(libs_list):
+            flags = ['-Wl,-rpath,%s' % dir for dir in libs_list.directories]
+            flags += [libs_list.ld_flags]
+            return ' '.join(flags)
+
+        def ld_flags_from_dirs(pkg_dirs_list, pkg_libs_list):
+            flags = ['-Wl,-rpath,%s' % dir for dir in pkg_dirs_list]
+            flags += ['-L%s' % dir for dir in pkg_dirs_list]
+            flags += ['-l%s' % lib for lib in pkg_libs_list]
+            return ' '.join(flags)
+
+        def find_optional_library(name, prefix):
+            for shared in [True, False]:
+                for path in ['lib64', 'lib']:
+                    lib = find_libraries(name, join_path(prefix, path),
+                                         shared=shared, recursive=False)
+                    if lib:
+                        return lib
+            return LibraryList([])
 
-        threadsafe_str = 'NO'
-        if '+openmp' in spec or '+threadsafe' in spec:
-            threadsafe_str = 'YES'
+        metis5_str = 'NO'
+        if ('+metis' in spec) and spec['metis'].satisfies('@5:'):
+            metis5_str = 'YES'
 
         options = [
             'PREFIX=%s' % prefix,
             'MFEM_USE_MEMALLOC=YES',
             'MFEM_DEBUG=%s' % yes_no('+debug'),
+            # NOTE: env['CXX'] is the spack c++ compiler wrapper. The real
+            # compiler is defined by env['SPACK_CXX'].
             'CXX=%s' % env['CXX'],
-            'MFEM_USE_LIBUNWIND=%s' % yes_no('+debug'),
+            'MFEM_USE_LIBUNWIND=%s' % yes_no('+libunwind'),
             'MFEM_USE_GZSTREAM=%s' % yes_no('+gzstream'),
+            'MFEM_USE_METIS=%s' % yes_no('+metis'),
             'MFEM_USE_METIS_5=%s' % metis5_str,
-            'MFEM_THREAD_SAFE=%s' % threadsafe_str,
+            'MFEM_THREAD_SAFE=%s' % yes_no('+threadsafe'),
             'MFEM_USE_MPI=%s' % yes_no('+mpi'),
             'MFEM_USE_LAPACK=%s' % yes_no('+lapack'),
             'MFEM_USE_SUPERLU=%s' % yes_no('+superlu-dist'),
             'MFEM_USE_SUITESPARSE=%s' % yes_no('+suite-sparse'),
             'MFEM_USE_SUNDIALS=%s' % yes_no('+sundials'),
             'MFEM_USE_PETSC=%s' % yes_no('+petsc'),
+            'MFEM_USE_PUMI=%s' % yes_no('+pumi'),
             'MFEM_USE_NETCDF=%s' % yes_no('+netcdf'),
             'MFEM_USE_MPFR=%s' % yes_no('+mpfr'),
-            'MFEM_USE_OPENMP=%s' % yes_no('+openmp')]
+            'MFEM_USE_GNUTLS=%s' % yes_no('+gnutls'),
+            'MFEM_USE_OPENMP=%s' % yes_no('+openmp'),
+            'MFEM_USE_CONDUIT=%s' % yes_no('+conduit')]
+
+        cxxflags = spec.compiler_flags['cxxflags']
+        if cxxflags:
+            # The cxxflags are set by the spack c++ compiler wrapper. We also
+            # set CXXFLAGS explicitly, for clarity, and to properly export the
+            # cxxflags in the variable MFEM_CXXFLAGS in config.mk.
+            options += ['CXXFLAGS=%s' % ' '.join(cxxflags)]
+
+        if '~static' in spec:
+            options += ['STATIC=NO']
+        if '+shared' in spec:
+            options += ['SHARED=YES', 'PICFLAG=%s' % self.compiler.pic_flag]
 
         if '+mpi' in spec:
             options += ['MPICXX=%s' % spec['mpi'].mpicxx]
+            hypre = spec['hypre']
+            # The hypre package always links with 'blas' and 'lapack'.
+            all_hypre_libs = hypre.libs + hypre['lapack'].libs + \
+                hypre['blas'].libs
+            options += [
+                'HYPRE_OPT=-I%s' % hypre.prefix.include,
+                'HYPRE_LIB=%s' % ld_flags_from_library_list(all_hypre_libs)]
 
-        if '+hypre' in spec:
+        if '+metis' in spec:
             options += [
-                'HYPRE_DIR=%s' % spec['hypre'].prefix,
-                'HYPRE_OPT=-I%s' % spec['hypre'].prefix.include,
-                'HYPRE_LIB=-L%s' % spec['hypre'].prefix.lib + ' -lHYPRE']
+                'METIS_OPT=-I%s' % spec['metis'].prefix.include,
+                'METIS_LIB=%s' %
+                ld_flags_from_dirs([spec['metis'].prefix.lib], ['metis'])]
 
         if '+lapack' in spec:
-            lapack_lib = (spec['lapack'].libs + spec['blas'].libs).ld_flags  # NOQA: ignore=E501
+            lapack_blas = spec['lapack'].libs + spec['blas'].libs
             options += [
-                'LAPACK_OPT=-I%s' % spec['lapack'].prefix.include,
-                'LAPACK_LIB=%s' % lapack_lib]
+                # LAPACK_OPT is not used
+                'LAPACK_LIB=%s' % ld_flags_from_library_list(lapack_blas)]
 
         if '+superlu-dist' in spec:
-            metis_lib = '-L%s -lparmetis -lmetis' % spec['parmetis'].prefix.lib
-            options += [
-                'METIS_DIR=%s' % spec['parmetis'].prefix,
-                'METIS_OPT=-I%s' % spec['parmetis'].prefix.include,
-                'METIS_LIB=%s' % metis_lib]
-            superlu_lib = '-L%s' % spec['superlu-dist'].prefix.lib
-            superlu_lib += ' -lsuperlu_dist'
+            lapack_blas = spec['lapack'].libs + spec['blas'].libs
             options += [
-                'SUPERLU_DIR=%s' % spec['superlu-dist'].prefix,
-                'SUPERLU_OPT=-I%s' % spec['superlu-dist'].prefix.include,
-                'SUPERLU_LIB=%s' % superlu_lib]
-        else:
-            metis_lib = '-L%s -lmetis' % spec['metis'].prefix.lib
-            options += [
-                'METIS_DIR=%s' % spec['metis'].prefix,
-                'METIS_OPT=-I%s' % spec['metis'].prefix.include,
-                'METIS_LIB=%s' % metis_lib]
+                'SUPERLU_OPT=-I%s -I%s' %
+                (spec['superlu-dist'].prefix.include,
+                 spec['parmetis'].prefix.include),
+                'SUPERLU_LIB=-L%s -L%s -lsuperlu_dist -lparmetis %s' %
+                (spec['superlu-dist'].prefix.lib,
+                 spec['parmetis'].prefix.lib,
+                 ld_flags_from_library_list(lapack_blas))]
 
         if '+suite-sparse' in spec:
-            ssp = spec['suite-sparse'].prefix
-            ss_lib = '-L%s' % ssp.lib
-            if '@3.2:' in spec:
-                ss_lib += ' -lklu -lbtf'
-            ss_lib += (' -lumfpack -lcholmod -lcolamd' +
-                       ' -lamd -lcamd -lccolamd -lsuitesparseconfig')
-            no_rt = spec.satisfies('platform=darwin')
-            if not no_rt:
-                ss_lib += ' -lrt'
-            ss_lib += (' ' + metis_lib + ' ' + lapack_lib)
+            ss_spec = 'suite-sparse:' + self.suitesparse_components
             options += [
-                'SUITESPARSE_DIR=%s' % ssp,
-                'SUITESPARSE_OPT=-I%s' % ssp.include,
-                'SUITESPARSE_LIB=%s' % ss_lib]
+                'SUITESPARSE_OPT=-I%s' % spec[ss_spec].prefix.include,
+                'SUITESPARSE_LIB=%s' %
+                ld_flags_from_library_list(spec[ss_spec].libs)]
 
         if '+sundials' in spec:
-            sundials_libs = (
-                '-lsundials_arkode -lsundials_cvode'
-                ' -lsundials_nvecserial -lsundials_kinsol')
-            if '+mpi' in spec:
-                sundials_libs += (
-                    ' -lsundials_nvecparhyp -lsundials_nvecparallel')
+            sun_spec = 'sundials:' + self.sundials_components
             options += [
-                'SUNDIALS_DIR=%s' % spec['sundials'].prefix,
-                'SUNDIALS_OPT=-I%s' % spec['sundials'].prefix.include,
-                'SUNDIALS_LIB=-L%s %s' % (spec['sundials'].prefix.lib,
-                                          sundials_libs)]
+                'SUNDIALS_OPT=%s' % spec[sun_spec].headers.cpp_flags,
+                'SUNDIALS_LIB=%s' %
+                ld_flags_from_library_list(spec[sun_spec].libs)]
 
         if '+petsc' in spec:
-            f = open('%s/lib/pkgconfig/PETSc.pc' % spec['petsc'].prefix, 'r')
-            for line in f:
-                if re.search('^\s*Cflags: ', line):
-                    petsc_opts = re.sub('^\s*Cflags: (.*)', '\\1', line)
-                elif re.search('^\s*Libs.*: ', line):
-                    petsc_libs = re.sub('^\s*Libs.*: (.*)', '\\1', line)
-            f.close()
+            # options += ['PETSC_DIR=%s' % spec['petsc'].prefix]
             options += [
-                'PETSC_DIR=%s' % spec['petsc'].prefix,
-                'PETSC_OPT=%s' % petsc_opts,
-                'PETSC_LIB=-L%s -lpetsc %s' %
-                (spec['petsc'].prefix.lib, petsc_libs)]
+                'PETSC_OPT=%s' % spec['petsc'].headers.cpp_flags,
+                'PETSC_LIB=%s' %
+                ld_flags_from_library_list(spec['petsc'].libs)]
+
+        if '+pumi' in spec:
+            options += ['PUMI_DIR=%s' % spec['pumi'].prefix]
 
         if '+netcdf' in spec:
-            np = spec['netcdf'].prefix
-            zp = spec['zlib'].prefix
-            h5p = spec['hdf5'].prefix
-            nlib = '-L%s -lnetcdf ' % np.lib
-            nlib += '-L%s -lhdf5_hl -lhdf5 ' % h5p.lib
-            nlib += '-L%s -lz' % zp.lib
             options += [
-                'NETCDF_DIR=%s' % np,
-                'HDF5_DIR=%s' % h5p,
-                'ZLIB_DIR=%s' % zp,
-                'NETCDF_OPT=-I%s' % np.include,
-                'NETCDF_LIB=%s' % nlib]
+                'NETCDF_OPT=-I%s' % spec['netcdf'].prefix.include,
+                'NETCDF_LIB=%s' %
+                ld_flags_from_dirs([spec['netcdf'].prefix.lib], ['netcdf'])]
+
+        if '+gzstream' in spec:
+            if "@:3.3.2" in spec:
+                options += ['ZLIB_DIR=%s' % spec['zlib'].prefix]
+            else:
+                options += [
+                    'ZLIB_OPT=-I%s' % spec['zlib'].prefix.include,
+                    'ZLIB_LIB=%s' %
+                    ld_flags_from_library_list(spec['zlib'].libs)]
 
         if '+mpfr' in spec:
-            options += ['MPFR_LIB=-L%s -lmpfr' % spec['mpfr'].prefix.lib]
+            options += [
+                'MPFR_OPT=-I%s' % spec['mpfr'].prefix.include,
+                'MPFR_LIB=%s' %
+                ld_flags_from_dirs([spec['mpfr'].prefix.lib], ['mpfr'])]
+
+        if '+gnutls' in spec:
+            options += [
+                'GNUTLS_OPT=-I%s' % spec['gnutls'].prefix.include,
+                'GNUTLS_LIB=%s' %
+                ld_flags_from_dirs([spec['gnutls'].prefix.lib], ['gnutls'])]
+
+        if '+libunwind' in spec:
+            libunwind = spec['unwind']
+            headers = find_headers('libunwind', libunwind.prefix.include)
+            headers.add_macro('-g')
+            libs = find_optional_library('libunwind', libunwind.prefix)
+            # When mfem uses libunwind, it also needs 'libdl'.
+            libs += LibraryList(find_system_libraries('libdl'))
+            options += [
+                'LIBUNWIND_OPT=%s' % headers.cpp_flags,
+                'LIBUNWIND_LIB=%s' % ld_flags_from_library_list(libs)]
 
         if '+openmp' in spec:
-            options += ['OPENMP_OPT = %s' % self.compiler.openmp_flag]
+            options += ['OPENMP_OPT=%s' % self.compiler.openmp_flag]
+
+        timer_ids = {'std': '0', 'posix': '2', 'mac': '4', 'mpi': '6'}
+        timer = spec.variants['timer'].value
+        if timer != 'auto':
+            options += ['MFEM_TIMER_TYPE=%s' % timer_ids[timer]]
+
+        if '+conduit' in spec:
+            conduit = spec['conduit']
+            headers = HeaderList(find(conduit.prefix.include, 'conduit.hpp',
+                                      recursive=True))
+            conduit_libs = ['libconduit', 'libconduit_relay',
+                            'libconduit_blueprint']
+            libs = find_libraries(conduit_libs, conduit.prefix.lib,
+                                  shared=('+shared' in conduit))
+            libs += LibraryList(find_system_libraries('libdl'))
+            if '+hdf5' in conduit:
+                hdf5 = conduit['hdf5']
+                headers += find_headers('hdf5', hdf5.prefix.include)
+                libs += hdf5.libs
+            options += [
+                'CONDUIT_OPT=%s' % headers.cpp_flags,
+                'CONDUIT_LIB=%s' % ld_flags_from_library_list(libs)]
+
+        make('config', *options, parallel=False)
+        make('info', parallel=False)
 
-        make('config', *options)
+    def build(self, spec, prefix):
         make('lib')
 
-        if self.run_tests:
-            make('check')
+    @run_after('build')
+    def check_or_test(self):
+        # Running 'make check' or 'make test' may fail if MFEM_MPIEXEC or
+        # MFEM_MPIEXEC_NP are not set appropriately.
+        if not self.run_tests:
+            # check we can build ex1 (~mpi) or ex1p (+mpi).
+            make('-C', 'examples', 'ex1p' if ('+mpi' in self.spec) else 'ex1',
+                 parallel=False)
+            # make('check', parallel=False)
+        else:
+            make('all')
+            make('test', parallel=False)
+
+    def install(self, spec, prefix):
+        make('install', parallel=False)
 
-        make('install')
+        # TODO: The way the examples and miniapps are being installed is not
+        # perfect. For example, the makefiles do not work.
+
+        install_em = ('+examples' in spec) or ('+miniapps' in spec)
+        if install_em and ('+shared' in spec):
+            make('examples/clean', 'miniapps/clean')
+            # This is a hack to get the examples and miniapps to link with the
+            # installed shared mfem library:
+            with working_dir('config'):
+                os.rename('config.mk', 'config.mk.orig')
+                copy(str(self.config_mk), 'config.mk')
+                shutil.copystat('config.mk.orig', 'config.mk')
 
         if '+examples' in spec:
             make('examples')
@@ -288,3 +431,64 @@ class Mfem(Package):
         if '+miniapps' in spec:
             make('miniapps')
             install_tree('miniapps', join_path(prefix, 'miniapps'))
+
+        if install_em:
+            install_tree('data', join_path(prefix, 'data'))
+
+    @property
+    def suitesparse_components(self):
+        """Return the SuiteSparse components needed by MFEM."""
+        ss_comps = 'umfpack,cholmod,colamd,amd,camd,ccolamd,suitesparseconfig'
+        if self.spec.satisfies('@3.2:'):
+            ss_comps = 'klu,btf,' + ss_comps
+        return ss_comps
+
+    @property
+    def sundials_components(self):
+        """Return the SUNDIALS components needed by MFEM."""
+        sun_comps = 'arkode,cvode,nvecserial,kinsol'
+        if '+mpi' in self.spec:
+            sun_comps += ',nvecparhyp,nvecparallel'
+        return sun_comps
+
+    @property
+    def headers(self):
+        """Export the main mfem header, mfem.hpp.
+        """
+        hdrs = HeaderList(find(self.prefix.include, 'mfem.hpp',
+                               recursive=False))
+        return hdrs or None
+
+    @property
+    def libs(self):
+        """Export the mfem library file.
+        """
+        libs = find_libraries('libmfem', root=self.prefix.lib,
+                              shared=('+shared' in self.spec), recursive=False)
+        return libs or None
+
+    @property
+    def config_mk(self):
+        """Export the location of the config.mk file.
+           This property can be accessed using spec['mfem'].package.config_mk
+        """
+        dirs = [self.prefix, self.prefix.share.mfem]
+        for d in dirs:
+            f = join_path(d, 'config.mk')
+            if os.access(f, os.R_OK):
+                return FileList(f)
+        return FileList(find(self.prefix, 'config.mk', recursive=True))
+
+    @property
+    def test_mk(self):
+        """Export the location of the test.mk file.
+           This property can be accessed using spec['mfem'].package.test_mk.
+           In version 3.3.2 and newer, the location of test.mk is also defined
+           inside config.mk, variable MFEM_TEST_MK.
+        """
+        dirs = [self.prefix, self.prefix.share.mfem]
+        for d in dirs:
+            f = join_path(d, 'test.mk')
+            if os.access(f, os.R_OK):
+                return FileList(f)
+        return FileList(find(self.prefix, 'test.mk', recursive=True))
diff --git a/var/spack/repos/builtin/packages/mfem/test_builds.sh b/var/spack/repos/builtin/packages/mfem/test_builds.sh
new file mode 100755
index 0000000000..125fa0055c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mfem/test_builds.sh
@@ -0,0 +1,75 @@
+#!/bin/bash
+
+builds=(
+    # preferred version:
+    'mfem'
+    'mfem~mpi~metis~gzstream'
+    'mfem+mpi+superlu-dist+suite-sparse+petsc \
+        +sundials+pumi+mpfr+netcdf+gzstream+gnutls+libunwind \
+        ^hypre~internal-superlu ^petsc+suite-sparse+mumps'
+    'mfem~mpi+suite-sparse+sundials+mpfr+netcdf \
+        +gzstream+gnutls+libunwind'
+    # develop version:
+    'mfem@develop+shared~static'
+    'mfem@develop+shared~static~mpi~metis~gzstream'
+    # TODO: Replace '^conduit~python~hdf5' with '^conduit~python' when conduit
+    # is fixed to accept '^hdf5+mpi'.
+    # NOTE: Skip PUMI since it conflicts with '+shared'.
+    'mfem@develop+shared~static+mpi \
+        +superlu-dist+suite-sparse+petsc+sundials+mpfr+netcdf+gzstream \
+        +gnutls+libunwind+conduit ^hypre~internal-superlu \
+        ^petsc+suite-sparse+mumps ^conduit~python~hdf5'
+    # TODO: The options '^netcdf~mpi ^hdf5@1.8.19~mpi' are added just to make
+    # conduit happy.
+    'mfem@develop+shared~static~mpi \
+        +suite-sparse+sundials+mpfr+netcdf+gzstream+gnutls+libunwind \
+        +conduit ^conduit~python ^netcdf~mpi ^hdf5@1.8.19~mpi'
+)
+
+builds2=(
+    # preferred version
+    'mfem+superlu-dist'
+    'mfem+suite-sparse~mpi'
+    'mfem+suite-sparse'
+    'mfem+sundials~mpi'
+    'mfem+sundials'
+    'mfem+pumi'
+    'mfem+netcdf~mpi'
+    'mfem+netcdf'
+    'mfem+mpfr'
+    'mfem+gnutls'
+    'mfem+petsc+mpi ^hypre~internal-superlu ^petsc+suite-sparse+mumps'
+    # develop version
+    'mfem@develop+superlu-dist'
+    'mfem@develop+suite-sparse~mpi'
+    'mfem@develop+suite-sparse'
+    'mfem@develop+sundials~mpi'
+    'mfem@develop+sundials'
+    'mfem@develop+pumi'
+    'mfem@develop+netcdf~mpi'
+    'mfem@develop+netcdf'
+    'mfem@develop+mpfr'
+    'mfem@develop+gnutls'
+    'mfem@develop+conduit~mpi ^conduit~python'
+    'mfem@develop+conduit ^conduit~python'
+    'mfem@develop+petsc+mpi ^hypre~internal-superlu \
+        ^petsc+suite-sparse+mumps'
+)
+
+trap 'printf "\nScript interrupted.\n"; exit 33' INT
+
+SEP='=========================================================================='
+sep='--------------------------------------------------------------------------'
+
+for bld in "${builds[@]}" "${builds2[@]}"; do
+    printf "\n%s\n" "${SEP}"
+    printf "    %s\n" "${bld}"
+    printf "%s\n" "${SEP}"
+    eval bbb="\"${bld}\""
+    spack spec -I $bbb || exit 1
+    printf "%s\n" "${sep}"
+    spack install --test=root $bbb || exit 2
+done
+
+# Uninstall all mfem builds:
+# spack uninstall --all mfem
diff --git a/var/spack/repos/builtin/packages/microbiomeutil/package.py b/var/spack/repos/builtin/packages/microbiomeutil/package.py
index 319148f71d..64952c6165 100644
--- a/var/spack/repos/builtin/packages/microbiomeutil/package.py
+++ b/var/spack/repos/builtin/packages/microbiomeutil/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/minced/package.py b/var/spack/repos/builtin/packages/minced/package.py
new file mode 100644
index 0000000000..c237ad2737
--- /dev/null
+++ b/var/spack/repos/builtin/packages/minced/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Minced(Package):
+    """MinCED is a program to find Clustered Regularly Interspaced Short
+    Palindromic Repeats (CRISPRs) in full genomes or environmental datasets
+    such as metagenomes, in which sequence size can be anywhere from 100 to
+    800 bp."""
+
+    homepage = "https://github.com/ctSkennerton/minced"
+    url      = "https://github.com/ctSkennerton/minced/archive/0.2.0.tar.gz"
+
+    version('0.2.0', '32544f5a523f10fece6a127699e11245')
+
+    depends_on('java', type=('build', 'run'))
+
+    def install(self, spec, prefix):
+        make()
+        install('minced', prefix)
+        install('minced.jar', prefix)
diff --git a/var/spack/repos/builtin/packages/mindthegap/package.py b/var/spack/repos/builtin/packages/mindthegap/package.py
new file mode 100644
index 0000000000..11dbdb8ac5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mindthegap/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Mindthegap(CMakePackage):
+    """MindTheGap is a software that performs integrated detection and
+       assembly of genomic insertion variants in NGS read datasets with
+       respect to a reference genome."""
+
+    homepage = "https://gatb.inria.fr/software/mind-the-gap/"
+    git      = "https://github.com/GATB/MindTheGap.git"
+
+    version('2.0.2', tags='v2.0.2', submodules=True)
+
+    depends_on('zlib')
diff --git a/var/spack/repos/builtin/packages/miniaero/package.py b/var/spack/repos/builtin/packages/miniaero/package.py
index da1421963f..46907a0fc8 100644
--- a/var/spack/repos/builtin/packages/miniaero/package.py
+++ b/var/spack/repos/builtin/packages/miniaero/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -32,12 +13,11 @@ class Miniaero(MakefilePackage):
     """
 
     homepage = "http://mantevo.org"
-    url      = "https://github.com/Mantevo/miniAero.git"
+    git      = "https://github.com/Mantevo/miniAero.git"
 
     tags = ['proxy-app']
 
-    version('2016-11-11', git='https://github.com/Mantevo/miniAero.git',
-            commit='f46d135479a5be19ec5d146ccaf0e581aeff4596')
+    version('2016-11-11', commit='f46d135479a5be19ec5d146ccaf0e581aeff4596')
 
     depends_on('kokkos')
 
diff --git a/var/spack/repos/builtin/packages/miniamr/package.py b/var/spack/repos/builtin/packages/miniamr/package.py
index 1740ab461c..0a0147e50e 100644
--- a/var/spack/repos/builtin/packages/miniamr/package.py
+++ b/var/spack/repos/builtin/packages/miniamr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -32,10 +13,11 @@ class Miniamr(MakefilePackage):
     """
 
     homepage = "https://mantevo.org"
-    url      = "https://github.com/Mantevo/miniAMR/archive/v1.4.tar.gz"
+    url      = "https://github.com/Mantevo/miniAMR/archive/v1.4.0.tar.gz"
 
     tags = ['proxy-app', 'ecp-proxy-app']
 
+    version('1.4.1', sha256='dd8e8d9fd0768cb4f2c5d7fe6989dfa6bb95a8461f04deaccdbb50b0dd51e97a')
     version('1.4.0', '3aab0247047a94e343709cf2e51cc46e')
 
     variant('mpi', default=True, description='Build with MPI support')
@@ -59,8 +41,8 @@ class Miniamr(MakefilePackage):
     def install(self, spec, prefix):
         # Manual installation
         mkdir(prefix.bin)
-        mkdir(prefix.doc)
+        mkdir(prefix.docs)
 
         install('ref/ma.x', prefix.bin)
         # Install Support Documents
-        install('ref/README', prefix.doc)
+        install('ref/README', prefix.docs)
diff --git a/var/spack/repos/builtin/packages/miniasm/package.py b/var/spack/repos/builtin/packages/miniasm/package.py
new file mode 100644
index 0000000000..8c32b90555
--- /dev/null
+++ b/var/spack/repos/builtin/packages/miniasm/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Miniasm(MakefilePackage):
+    """Miniasm is a very fast OLC-based de novo assembler for noisy long
+    reads."""
+
+    homepage = "http://www.example.co://github.com/lh3/miniasm"
+    git      = "https://github.com/lh3/miniasm.git"
+
+    version('2018-3-30', commit='55cf0189e2f7d5bda5868396cebe066eec0a9547')
+
+    depends_on('zlib')
+
+    def install(self, spec, prefix):
+        install_tree('.', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/miniconda2/package.py b/var/spack/repos/builtin/packages/miniconda2/package.py
index 7433b2d731..c5c5fb3f40 100644
--- a/var/spack/repos/builtin/packages/miniconda2/package.py
+++ b/var/spack/repos/builtin/packages/miniconda2/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from six.moves.urllib.parse import urlparse
 from os.path import split
 
 
@@ -33,12 +13,15 @@ class Miniconda2(Package):
     homepage = "https://conda.io/miniconda.html"
     url      = "https://repo.continuum.io/miniconda/Miniconda2-4.3.11-Linux-x86_64.sh"
 
+    version('4.5.11', sha256='0e23e8d0a1a14445f78960a66b363b464b889ee3b0e3f275b7ffb836df1cb0c6', expand=False)
+    version('4.5.4', '8a1c02f6941d8778f8afad7328265cf5', expand=False)
+    version('4.3.30', 'bd1655b4b313f7b2a1f2e15b7b925d03', expand=False)
     version('4.3.14', '8cb075cf5462480980ef2373ad9fad38', expand=False)
     version('4.3.11', 'd573980fe3b5cdf80485add2466463f5', expand=False)
 
     def install(self, spec, prefix):
-        # peel the name of the script out of the url
-        result = urlparse(self.url)
-        dir, script = split(result.path)
+        # peel the name of the script out of the pathname of the
+        # downloaded file
+        dir, script = split(self.stage.archive_file)
         bash = which('bash')
         bash(script, '-b', '-f', '-p', self.prefix)
diff --git a/var/spack/repos/builtin/packages/miniconda3/package.py b/var/spack/repos/builtin/packages/miniconda3/package.py
index faaa786b6c..cf47b424c5 100644
--- a/var/spack/repos/builtin/packages/miniconda3/package.py
+++ b/var/spack/repos/builtin/packages/miniconda3/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from six.moves.urllib.parse import urlparse
 from os.path import split
 
 
@@ -33,12 +13,15 @@ class Miniconda3(Package):
     homepage = "https://conda.io/miniconda.html"
     url      = "https://repo.continuum.io/miniconda/Miniconda3-4.3.11-Linux-x86_64.sh"
 
+    version('4.5.11', sha256='ea4594241e13a2671c5b158b3b813f0794fe58d514795fbf72a1aad24db918cf', expand=False)
+    version('4.5.4', 'a946ea1d0c4a642ddf0c3a26a18bb16d', expand=False)
+    version('4.3.30', '0b80a152332a4ce5250f3c09589c7a81', expand=False)
     version('4.3.14', 'fc6fc37479e3e3fcf3f9ba52cae98991', expand=False)
     version('4.3.11', '1924c8d9ec0abf09005aa03425e9ab1a', expand=False)
 
     def install(self, spec, prefix):
-        # peel the name of the script out of the url
-        result = urlparse(self.url)
-        dir, script = split(result.path)
+        # peel the name of the script out of the pathname of the
+        # downloaded file
+        dir, script = split(self.stage.archive_file)
         bash = which('bash')
         bash(script, '-b', '-f', '-p', self.prefix)
diff --git a/var/spack/repos/builtin/packages/minife/package.py b/var/spack/repos/builtin/packages/minife/package.py
index 0757a8c6db..00279455d3 100644
--- a/var/spack/repos/builtin/packages/minife/package.py
+++ b/var/spack/repos/builtin/packages/minife/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/minighost/package.py b/var/spack/repos/builtin/packages/minighost/package.py
index f397306645..c4cf78f5a9 100644
--- a/var/spack/repos/builtin/packages/minighost/package.py
+++ b/var/spack/repos/builtin/packages/minighost/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 import tarfile
 
@@ -54,17 +35,16 @@ class Minighost(MakefilePackage):
         if '+mpi' in self.spec:
             targets.append('PROTOCOL=-D_MG_MPI')
             targets.append('FC={0}'.format(self.spec['mpi'].mpif77))
-            targets.append('CC={0}'.format(self.spec['mpi'].mpicc))
-            targets.append(
-                'LIBS=-lm -lgfortran -lmpi_usempi -lmpi_mpifh -lmpi')
+            # CC is only used for linking, use it to pull in the right f77 libs
+            targets.append('CC={0}'.format(self.spec['mpi'].mpif77))
         else:
             targets.append('PROTOCOL=-D_MG_SERIAL')
             targets.append('FC=f77')
             targets.append('CC=cc')
-            targets.append('LIBS=-lm -lgfortran')
 
         if '%gcc' in self.spec:
             targets.append('COMPILER_SUITE=gnu')
+            targets.append('LIBS=-lm -lgfortran')
         elif '%cce' in self.spec:
             targets.append('COMPILER_SUITE=cray')
         elif '%intel' in self.spec:
diff --git a/var/spack/repos/builtin/packages/minigmg/package.py b/var/spack/repos/builtin/packages/minigmg/package.py
index 8cbd35faff..730ae4df5c 100644
--- a/var/spack/repos/builtin/packages/minigmg/package.py
+++ b/var/spack/repos/builtin/packages/minigmg/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
 
diff --git a/var/spack/repos/builtin/packages/minimap2/package.py b/var/spack/repos/builtin/packages/minimap2/package.py
index 17abaaeafa..92da1ac170 100644
--- a/var/spack/repos/builtin/packages/minimap2/package.py
+++ b/var/spack/repos/builtin/packages/minimap2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/minimd/package.py b/var/spack/repos/builtin/packages/minimd/package.py
index a9a6d90aa2..34192f64d2 100644
--- a/var/spack/repos/builtin/packages/minimd/package.py
+++ b/var/spack/repos/builtin/packages/minimd/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 import glob
 import tarfile
diff --git a/var/spack/repos/builtin/packages/miniqmc/package.py b/var/spack/repos/builtin/packages/miniqmc/package.py
new file mode 100644
index 0000000000..f243b6a8fb
--- /dev/null
+++ b/var/spack/repos/builtin/packages/miniqmc/package.py
@@ -0,0 +1,35 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Miniqmc(CMakePackage):
+    """A simplified real space QMC code for algorithm development,
+       performance portability testing, and computer science experiments
+    """
+
+    homepage = "https://github.com/QMCPACK/miniqmc"
+    url      = "https://github.com/QMCPACK/miniqmc/archive/0.2.0.tar.gz"
+
+    version('0.4.0', sha256='41ddb5de6dcc85404344c80dc7538aedf5e1f1eb0f2a67ebac069209f7dd11e4')
+    version('0.3.0', sha256='3ba494ba1055df91e157cb426d1fbe4192aa3f04b019277d9e571d057664d5a9')
+    version('0.2.0', 'b96bacaf48b8e9c0de05d04a95066bc1')
+
+    tags = ['proxy-app', 'ecp-proxy-app']
+
+    depends_on('mpi')
+    depends_on('lapack')
+
+    def cmake_args(self):
+        args = [
+            '-DCMAKE_CXX_COMPILER=%s' % self.spec['mpi'].mpicxx,
+            '-DCMAKE_C_COMPILER=%s' % self.spec['mpi'].mpicc
+        ]
+        return args
+
+    def install(self, spec, prefix):
+        install_tree(join_path('spack-build', 'bin'), prefix.bin)
+        install_tree(join_path('spack-build', 'lib'), prefix.lib)
diff --git a/var/spack/repos/builtin/packages/minisign/package.py b/var/spack/repos/builtin/packages/minisign/package.py
new file mode 100755
index 0000000000..a380fedd15
--- /dev/null
+++ b/var/spack/repos/builtin/packages/minisign/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Minisign(CMakePackage):
+    """Minisign is a dead simple tool to sign files and verify signatures."""
+
+    homepage = "https://jedisct1.github.io/minisign/"
+    url = "https://github.com/jedisct1/minisign/archive/0.7.tar.gz"
+
+    version('0.7', 'd634202555c4f499e8ef9d6848d6f4ca')
+
+    depends_on('libsodium')
diff --git a/var/spack/repos/builtin/packages/minismac2d/package.py b/var/spack/repos/builtin/packages/minismac2d/package.py
index 4e961fac94..e793337868 100644
--- a/var/spack/repos/builtin/packages/minismac2d/package.py
+++ b/var/spack/repos/builtin/packages/minismac2d/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -49,7 +30,7 @@ class Minismac2d(MakefilePackage):
             'CPP=cpp',
             'FC={0}'.format(self.spec['mpi'].mpifc),
             'LD={0}'.format(self.spec['mpi'].mpifc),
-            'MPIDIR=-I{0}/include'.format(self.spec['mpi'].prefix),
+            'MPIDIR=-I{0}'.format(self.spec['mpi'].headers.directories[0]),
             'CPPFLAGS=-P -traditional  -DD_PRECISION',
             'FFLAGS=-O3 -c -g -DD_PRECISION',
             'LDFLAGS=-O3',
diff --git a/var/spack/repos/builtin/packages/minitri/package.py b/var/spack/repos/builtin/packages/minitri/package.py
index 6451a8b86a..570d4b44a4 100644
--- a/var/spack/repos/builtin/packages/minitri/package.py
+++ b/var/spack/repos/builtin/packages/minitri/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/minivite/package.py b/var/spack/repos/builtin/packages/minivite/package.py
new file mode 100644
index 0000000000..f39a6f4f5e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/minivite/package.py
@@ -0,0 +1,46 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Minivite(MakefilePackage):
+    """miniVite is a proxy application that implements a single phase of
+       Louvain method in distributed memory for graph community detection.
+    """
+    tags = ['proxy-app', 'ecp-proxy-app']
+
+    homepage = "http://hpc.pnl.gov/people/hala/grappolo.html"
+    git      = "https://github.com/Exa-Graph/miniVite.git"
+
+    version('develop', branch='master')
+    version('1.0', tag='v1.0')
+
+    variant('openmp', default=True, description='Build with OpenMP support')
+    variant('opt', default=True, description='Optimization flags')
+
+    depends_on('mpi')
+
+    @property
+    def build_targets(self):
+        targets = []
+        cxxflags = ['-std=c++11 -g -DCHECK_NUM_EDGES -DPRINT_EXTRA_NEDGES']
+        ldflags = []
+
+        if '+openmp' in self.spec:
+            cxxflags.append(self.compiler.openmp_flag)
+            ldflags.append(self.compiler.openmp_flag)
+        if '+opt' in self.spec:
+            cxxflags.append(' -O3 ')
+
+        targets.append('CXXFLAGS={0}'.format(' '.join(cxxflags)))
+        targets.append('OPTFLAGS={0}'.format(' '.join(ldflags)))
+        targets.append('CXX={0}'.format(self.spec['mpi'].mpicxx))
+
+        return targets
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('dspl', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/minixyce/package.py b/var/spack/repos/builtin/packages/minixyce/package.py
index 6273838f7e..b014203cc5 100644
--- a/var/spack/repos/builtin/packages/minixyce/package.py
+++ b/var/spack/repos/builtin/packages/minixyce/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/minuit/LASymMatrix.h.patch b/var/spack/repos/builtin/packages/minuit/LASymMatrix.h.patch
new file mode 100644
index 0000000000..645d2ccd35
--- /dev/null
+++ b/var/spack/repos/builtin/packages/minuit/LASymMatrix.h.patch
@@ -0,0 +1,117 @@
+commit 62772d5fb0c6c7661c7acaa73d21de4205579d73
+Author: Paul Chelarescu <paulchelarescu@gmail.com>
+Date:   Fri Jun 22 15:34:20 2018 +0200
+
+    Patched LASymMatrix.h
+
+diff --git a/Minuit/LASymMatrix.h b/Minuit/LASymMatrix.h
+index 755eb11..976c0de 100644
+--- a/Minuit/LASymMatrix.h
++++ b/Minuit/LASymMatrix.h
+@@ -16,6 +16,7 @@
+ // #include <iostream>
+ 
+ #include "Minuit/StackAllocator.h"
++#include <cstring>
+ //extern StackAllocator StackAllocatorHolder::get();
+ 
+ int mndaxpy(unsigned int, double, const double*, int, double*, int);
+@@ -37,7 +38,7 @@ public:
+ 
+   LASymMatrix(unsigned int n) : theSize(n*(n+1)/2), theNRow(n), theData((double*)StackAllocatorHolder::get().allocate(sizeof(double)*n*(n+1)/2)) {
+ //     assert(theSize>0);
+-    memset(theData, 0, theSize*sizeof(double));
++    std::memset(theData, 0, theSize*sizeof(double));
+ //     std::cout<<"LASymMatrix(unsigned int n), n= "<<n<<std::endl;
+   }
+ 
+@@ -52,7 +53,7 @@ public:
+   LASymMatrix(const LASymMatrix& v) : 
+     theSize(v.size()), theNRow(v.nrow()), theData((double*)StackAllocatorHolder::get().allocate(sizeof(double)*v.size())) {
+ //     std::cout<<"LASymMatrix(const LASymMatrix& v)"<<std::endl;
+-    memcpy(theData, v.data(), theSize*sizeof(double));
++    std::memcpy(theData, v.data(), theSize*sizeof(double));
+   }
+ 
+   LASymMatrix& operator=(const LASymMatrix& v) {
+@@ -60,7 +61,7 @@ public:
+ //     std::cout<<"theSize= "<<theSize<<std::endl;
+ //     std::cout<<"v.size()= "<<v.size()<<std::endl;
+     assert(theSize == v.size());
+-    memcpy(theData, v.data(), theSize*sizeof(double));
++    std::memcpy(theData, v.data(), theSize*sizeof(double));
+     return *this;
+   }
+ 
+@@ -69,7 +70,7 @@ public:
+     theSize(v.obj().size()), theNRow(v.obj().nrow()), theData((double*)StackAllocatorHolder::get().allocate(sizeof(double)*v.obj().size())) {
+ //     std::cout<<"LASymMatrix(const ABObj<sym, LASymMatrix, T>& v)"<<std::endl;
+     //std::cout<<"allocate "<<theSize<<std::endl;    
+-    memcpy(theData, v.obj().data(), theSize*sizeof(double));
++    std::memcpy(theData, v.obj().data(), theSize*sizeof(double));
+     mndscal(theSize, double(v.f()), theData, 1);
+     //std::cout<<"theData= "<<theData[0]<<" "<<theData[1]<<std::endl;
+   } 
+@@ -105,7 +106,7 @@ public:
+ 
+   template<class T>
+   LASymMatrix(const ABObj<sym, MatrixInverse<sym, ABObj<sym, LASymMatrix, T>, T>, T>& inv) : theSize(inv.obj().obj().obj().size()), theNRow(inv.obj().obj().obj().nrow()), theData((double*)StackAllocatorHolder::get().allocate(sizeof(double)*inv.obj().obj().obj().size())) {
+-    memcpy(theData, inv.obj().obj().obj().data(), theSize*sizeof(double));
++    std::memcpy(theData, inv.obj().obj().obj().data(), theSize*sizeof(double));
+     mndscal(theSize, double(inv.obj().obj().f()), theData, 1);
+     invert(*this);
+     mndscal(theSize, double(inv.f()), theData, 1);
+@@ -236,7 +237,7 @@ public:
+       assert(theSize == v.obj().size());
+     }
+     //std::cout<<"theData= "<<theData[0]<<" "<<theData[1]<<std::endl;
+-    memcpy(theData, v.obj().data(), theSize*sizeof(double));
++    std::memcpy(theData, v.obj().data(), theSize*sizeof(double));
+     (*this) *= v.f();
+     return *this;
+   }
+@@ -251,7 +252,7 @@ public:
+       LASymMatrix tmp(something.obj());
+       tmp *= something.f();
+       assert(theSize == tmp.size());
+-      memcpy(theData, tmp.data(), theSize*sizeof(double)); 
++      std::memcpy(theData, tmp.data(), theSize*sizeof(double)); 
+     }
+     //std::cout<<"template<class A, class T> LASymMatrix& operator=(const ABObj<sym, ABObj<sym, A, T>, T>& something)"<<std::endl;
+     return *this;
+@@ -270,7 +271,7 @@ public:
+       tmp += sum.obj().b();
+       tmp *= sum.f();
+       assert(theSize == tmp.size());
+-      memcpy(theData, tmp.data(), theSize*sizeof(double));
++      std::memcpy(theData, tmp.data(), theSize*sizeof(double));
+     }
+     return *this;
+   }
+@@ -290,7 +291,7 @@ public:
+       tmp += sum.obj().a();
+       tmp *= sum.f();
+       assert(theSize == tmp.size());
+-      memcpy(theData, tmp.data(), theSize*sizeof(double));
++      std::memcpy(theData, tmp.data(), theSize*sizeof(double));
+     }
+     //std::cout<<"leaving LASymMatrix& operator=(const ABObj<sym, ABSum<ABObj<sym, LASymMatrix..."<<std::endl;
+     return *this;
+@@ -302,7 +303,7 @@ public:
+       theSize = inv.obj().obj().obj().size();
+       theNRow = inv.obj().obj().obj().nrow();
+       theData = (double*)StackAllocatorHolder::get().allocate(sizeof(double)*theSize);
+-      memcpy(theData, inv.obj().obj().obj().data(), theSize*sizeof(double));
++      std::memcpy(theData, inv.obj().obj().obj().data(), theSize*sizeof(double));
+       (*this) *= inv.obj().obj().f();
+       invert(*this);
+       (*this) *= inv.f();
+@@ -311,7 +312,7 @@ public:
+       invert(tmp);
+       tmp *= double(inv.f());
+       assert(theSize == tmp.size());
+-      memcpy(theData, tmp.data(), theSize*sizeof(double));
++      std::memcpy(theData, tmp.data(), theSize*sizeof(double));
+     }
+     return *this;
+   }
diff --git a/var/spack/repos/builtin/packages/minuit/package.py b/var/spack/repos/builtin/packages/minuit/package.py
new file mode 100644
index 0000000000..54b4644866
--- /dev/null
+++ b/var/spack/repos/builtin/packages/minuit/package.py
@@ -0,0 +1,47 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Minuit(AutotoolsPackage):
+    """MINUIT is a physics analysis tool for function minimization."""
+
+    homepage = "https://seal.web.cern.ch/seal/snapshot/work-packages/mathlibs/minuit/home.html"
+    url      = "http://www.cern.ch/mathlibs/sw/5_34_14/Minuit2/Minuit2-5.34.14.tar.gz"
+    list_url = "https://seal.web.cern.ch/seal/snapshot/work-packages/mathlibs/minuit/release/download.html"
+
+    version('5.34.14', '7fc00378a2ed1f731b719d4837d62d6a')
+    version('5.28.00', '536a1d29e5cc9bd4499d17d665021370')
+    version('5.27.02', 'b54673f2b9b62a8ff4e6937a2ed8fda5')
+    version('5.24.00', '9a915e56bee1e8986a719aa80e7b05d6')
+    version('5.22.00', '2cbc34907bfe202c7a779e9713355846')
+    version('5.21.06', 'b431ed129abb6c5020fd58d53cb8d27c')
+    version('5.20.00', '3083d31e3764de45d477d082d60f2c29')
+    version('5.18.00', 'a8764e7213fe811e56d5b6e5f3a91f5e')
+    version('5.16.00', '6ea5feca06fca365d324bcfe16db7f08')
+    version('5.14.00', 'b7452867b01c76cd115c696336c202d2')
+    version('5.12.00', '36726b8c6fcddf4f0837c900461a1d3c')
+    version('5.10.00', 'dfc7afc0add70deaca105ff549f5a786')
+    version('5.08.00', '1cc8da07c4a247c877f39acf8d76ba02')
+    version('1.7.9', '10fd518fc778317fdadbc4ef6f7ce8e4')
+    version('1.7.6', '6a9a8341557de154274caff810686364')
+    version('1.7.1', 'd202a1cf58662e9833f2967b4dc8808e')
+    version('1.6.3', '955f560d0fb17bd7f081eddd7080fad6')
+    version('1.6.0', '6992d70fc8fded50be49b6b358b58507')
+    version('1.5.2', '31a0698febe59edd70aa001c4d7a56f8')
+    version('1.5.0', 'bc502c66af071fcdc0a2ae45a8740c75')
+
+    def url_for_version(self, version):
+        if version > Version('5.0.0'):
+            url = "http://www.cern.ch/mathlibs/sw/{0}/Minuit2/Minuit2-{1}.tar.gz"
+            return url.format(version.underscored, version)
+        else:
+            url = "http://seal.web.cern.ch/seal/minuit/releases/Minuit-{0}.tar.gz"
+            return url.format(version.underscored)
+
+    patch('sprintf.cxx.patch', when='@5.08.00:5.18.00')
+    patch('sprintf.patch', when='@:1.7.9')
+    patch('LASymMatrix.h.patch', when='@:1.7.6')
diff --git a/var/spack/repos/builtin/packages/minuit/sprintf.cxx.patch b/var/spack/repos/builtin/packages/minuit/sprintf.cxx.patch
new file mode 100644
index 0000000000..f6bf81cbc3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/minuit/sprintf.cxx.patch
@@ -0,0 +1,10 @@
+--- a/src/MnUserTransformation.cxx	2008-01-17 15:05:38.000000000 +0100
++++ b/src/MnUserTransformation.cxx	2018-06-22 13:44:02.629389848 +0200
+@@ -11,6 +11,7 @@
+ #include "Minuit2/MnUserCovariance.h"
+ 
+ #include <algorithm>
++#include <cstdio>
+ 
+ namespace ROOT {
+ 
diff --git a/var/spack/repos/builtin/packages/minuit/sprintf.patch b/var/spack/repos/builtin/packages/minuit/sprintf.patch
new file mode 100644
index 0000000000..be49ed772a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/minuit/sprintf.patch
@@ -0,0 +1,10 @@
+--- a/src/MnUserTransformation.cpp	2018-06-22 11:35:34.476798087 +0200
++++ b/src/MnUserTransformation.cpp	2018-06-22 11:08:01.729725829 +0200
+@@ -2,6 +2,7 @@
+ #include "Minuit/MnUserCovariance.h"
+ 
+ #include <algorithm>
++#include <cstdio>
+ 
+ class MnParStr {
+ 
diff --git a/var/spack/repos/builtin/packages/mira/package.py b/var/spack/repos/builtin/packages/mira/package.py
new file mode 100644
index 0000000000..f842ed8860
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mira/package.py
@@ -0,0 +1,33 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Mira(AutotoolsPackage):
+    """MIRA is a multi-pass DNA sequence data assembler/mapper for whole genome
+       and EST/RNASeq projects."""
+
+    homepage = "http://sourceforge.net/projects/mira-assembler/"
+    url      = "https://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira-4.0.2.tar.bz2"
+
+    version('4.0.2', '1921b426910653a34a6dbb37346f28ea')
+
+    depends_on('boost@1.46:')
+    depends_on('expat@2.0.1:')
+    depends_on('gperftools')
+
+    conflicts('%gcc@6:', when='@:4.0.2')
+
+    def patch(self):
+        with working_dir(join_path('src', 'progs')):
+            edit = FileFilter('quirks.C')
+            edit.filter('#include <boost/filesystem.hpp>',
+                        '#include <boost/filesystem.hpp>\n#include <iostream>')
+
+    def configure_args(self):
+        args = ['--with-boost=%s' % self.spec['boost'].prefix,
+                '--with-expat=%s' % self.spec['expat'].prefix]
+        return args
diff --git a/var/spack/repos/builtin/packages/mirdeep/package.py b/var/spack/repos/builtin/packages/mirdeep/package.py
deleted file mode 100644
index 28981eade5..0000000000
--- a/var/spack/repos/builtin/packages/mirdeep/package.py
+++ /dev/null
@@ -1,67 +0,0 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-from spack import *
-import glob
-
-
-class Mirdeep(Package):
-    """miRDeep2 is a completely overhauled tool which discovers microRNA genes
-       by analyzing sequenced RNAs."""
-
-    homepage = "https://www.mdc-berlin.de/8551903/en/"
-    url      = "https://www.mdc-berlin.de/45995549/en/research/research_teams/systems_biology_of_gene_regulatory_elements/projects/miRDeep/mirdeep2_0_0_8.zip"
-
-    version('2.0.0.8', 'a707f7d7ad4a2975fb8b2e78c5bcf483')
-
-    depends_on('perl', type=('build', 'run'))
-    depends_on('perl-pdf-api2', type=('build', 'run'))
-    depends_on('bowtie')
-    depends_on('viennarna')
-    depends_on('squid')
-    depends_on('randfold')
-
-    def url_for_version(self, version):
-        url = 'https://www.mdc-berlin.de/45995549/en/research/research_teams/systems_biology_of_gene_regulatory_elements/projects/miRDeep/mirdeep{0}.zip'
-        return url.format(version.underscored)
-
-    def patch(self):
-        with working_dir('src'):
-            files = glob.iglob("*.pl")
-            for file in files:
-                change = FileFilter(file)
-                change.filter('usr/bin/perl', 'usr/bin/env perl')
-                change.filter('perl -W', 'perl')
-                change.filter("../Rfam_for_miRDeep.fa",
-                              "Rfam_for_miRDeep.fa")
-                change.filter("../install_successful",
-                              "install_successful")
-
-    def install(self, spec, prefix):
-        install_tree('src', prefix.bin)
-        install('Rfam_for_miRDeep.fa', prefix.bin)
-        # miRDeep looks for the install_sucessful file to check if you used
-        # their automated install script which we'll just be kind of hacking
-        # around
-        touch(prefix.bin.install_successful)
diff --git a/var/spack/repos/builtin/packages/mirdeep2/package.py b/var/spack/repos/builtin/packages/mirdeep2/package.py
new file mode 100644
index 0000000000..cf85705750
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mirdeep2/package.py
@@ -0,0 +1,48 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import glob
+
+
+class Mirdeep2(Package):
+    """miRDeep2 is a completely overhauled tool which discovers microRNA genes
+       by analyzing sequenced RNAs."""
+
+    homepage = "https://www.mdc-berlin.de/8551903/en/"
+    url      = "https://www.mdc-berlin.de/system/files/migrated_files/fiona/mirdeep2_0_0_8.zip"
+
+    version('0.0.8', 'a707f7d7ad4a2975fb8b2e78c5bcf483')
+
+    depends_on('perl', type=('build', 'run'))
+    depends_on('perl-pdf-api2', type=('build', 'run'))
+    depends_on('bowtie')
+    depends_on('viennarna')
+    depends_on('squid')
+    depends_on('randfold')
+
+    def url_for_version(self, version):
+        url = 'https://www.mdc-berlin.de/system/files/migrated_files/fiona/mirdeep2_{0}.zip'
+        return url.format(version.underscored)
+
+    def patch(self):
+        with working_dir('src'):
+            files = glob.iglob("*.pl")
+            for file in files:
+                change = FileFilter(file)
+                change.filter('usr/bin/perl', 'usr/bin/env perl')
+                change.filter('perl -W', 'perl')
+                change.filter("../Rfam_for_miRDeep.fa",
+                              "Rfam_for_miRDeep.fa")
+                change.filter("../install_successful",
+                              "install_successful")
+
+    def install(self, spec, prefix):
+        install_tree('src', prefix.bin)
+        install('Rfam_for_miRDeep.fa', prefix.bin)
+        # miRDeep looks for the install_sucessful file to check if you used
+        # their automated install script which we'll just be kind of hacking
+        # around
+        touch(prefix.bin.install_successful)
diff --git a/var/spack/repos/builtin/packages/mitofates/DirichletRegulator_fast.patch b/var/spack/repos/builtin/packages/mitofates/DirichletRegulator_fast.patch
new file mode 100644
index 0000000000..85e836878e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mitofates/DirichletRegulator_fast.patch
@@ -0,0 +1,13 @@
+--- a/bin/modules/DirichletRegulator_fast.pm	2014-10-23 01:59:55.000000000 -0500
++++ b/bin/modules/DirichletRegulator_fast.pm	2018-07-11 11:19:07.814358134 -0500
+@@ -10,9 +10,7 @@
+ use strict;
+ use warnings;
+ use FindBin qw($Bin);
+-use Inline (Config => 
+-	      DIRECTORY => "$Bin/modules/_Inline/",
+-            );
++use Inline;
+ use Inline 'C';
+ 
+ # Sub-routin: DirichletParser
diff --git a/var/spack/repos/builtin/packages/mitofates/package.py b/var/spack/repos/builtin/packages/mitofates/package.py
index 0ba5535b3d..beefab38e1 100644
--- a/var/spack/repos/builtin/packages/mitofates/package.py
+++ b/var/spack/repos/builtin/packages/mitofates/package.py
@@ -1,28 +1,10 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
+import glob
 
 
 class Mitofates(Package):
@@ -35,7 +17,33 @@ class Mitofates(Package):
     version('1.2', 'aaac42a8e8c7318a4abde9df3a4b72d1')
 
     depends_on('libsvm')
+    depends_on('perl', type='run')
+    depends_on('perl-inline-c', type='run')
+    depends_on('perl-perl6-slurp', type='run')
+    depends_on('perl-math-cephes', type='run')
+
+    # The DirichletRegulator_fast.pm sets the perl Inline directory
+    # to be inside the deployed source (which won't be writable by
+    # the end user of site wide deployed software.
+    # Removing that config entry will cause the inline module to auto
+    # create a directory in the user's homedir instead
+    patch('DirichletRegulator_fast.patch')
+
+    def patch(self):
+        perlscripts = FileFilter('MitoFates.pl')
+        perlscripts.filter('#!/usr/bin/perl', '#!/usr/bin/env perl')
+
+        # other perl module files probably should get this filter too
+        with working_dir(join_path(self.stage.source_path, 'bin/modules')):
+            perlmodules = glob.glob('*.pm')
+            filter_file('#!/usr/bin/perl', '#!/usr/bin/env perl', *perlmodules)
 
     def install(self, spec, prefix):
         install_tree('bin', prefix.bin)
         install('MitoFates.pl', prefix)
+        chmod = which('chmod')
+        chmod('+x', join_path(prefix, 'MitoFates.pl'))
+
+    def setup_environment(self, spack_env, run_env):
+        # We want the main MitoFates.pl script in the path
+        run_env.prepend_path('PATH', self.prefix)
diff --git a/var/spack/repos/builtin/packages/mitos/package.py b/var/spack/repos/builtin/packages/mitos/package.py
index 1cc402590b..bfefd762e9 100644
--- a/var/spack/repos/builtin/packages/mitos/package.py
+++ b/var/spack/repos/builtin/packages/mitos/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,10 +12,9 @@ class Mitos(CMakePackage):
 
     homepage = "https://github.com/llnl/Mitos"
     url      = "https://github.com/LLNL/Mitos/archive/v0.9.1.tar.gz"
+    git      = "https://github.com/llnl/Mitos.git"
 
-    version('0.9.2',
-            git='https://github.com/llnl/Mitos.git',
-            commit='8cb143a2e8c00353ff531a781a9ca0992b0aaa3d')
+    version('0.9.2', commit='8cb143a2e8c00353ff531a781a9ca0992b0aaa3d')
     version('0.9.1', 'c6cb57f3cae54f5157affd97ef7ef79e')
 
     depends_on('dyninst@8.2.1:')
diff --git a/var/spack/repos/builtin/packages/mkfontdir/package.py b/var/spack/repos/builtin/packages/mkfontdir/package.py
index f1f12b514e..1a907d79ce 100644
--- a/var/spack/repos/builtin/packages/mkfontdir/package.py
+++ b/var/spack/repos/builtin/packages/mkfontdir/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Mkfontdir(AutotoolsPackage):
 
     depends_on('mkfontscale', type='run')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/mkfontscale/package.py b/var/spack/repos/builtin/packages/mkfontscale/package.py
index 9e8945f045..b1ad4f492c 100644
--- a/var/spack/repos/builtin/packages/mkfontscale/package.py
+++ b/var/spack/repos/builtin/packages/mkfontscale/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Mkfontscale(AutotoolsPackage):
     depends_on('freetype')
 
     depends_on('xproto@7.0.25:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/mlhka/package.py b/var/spack/repos/builtin/packages/mlhka/package.py
index 85a23d5edd..303c868ba3 100644
--- a/var/spack/repos/builtin/packages/mlhka/package.py
+++ b/var/spack/repos/builtin/packages/mlhka/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,10 +11,9 @@ class Mlhka(Package):
        and divergence data."""
 
     homepage = "https://wright.eeb.utoronto.ca"
-    url      = "https://github.com/rossibarra/MLHKA"
+    git      = "https://github.com/rossibarra/MLHKA.git"
 
-    version('2.1', git='https://github.com/rossibarra/MLHKA.git',
-            commit='e735ddd39073af58da21b00b27dea203736e5467')
+    version('2.1', commit='e735ddd39073af58da21b00b27dea203736e5467')
 
     def install(self, spec, prefix):
         cxx = which('c++')
diff --git a/var/spack/repos/builtin/packages/moab/package.py b/var/spack/repos/builtin/packages/moab/package.py
index 8e84f63b2c..0f7bad2143 100644
--- a/var/spack/repos/builtin/packages/moab/package.py
+++ b/var/spack/repos/builtin/packages/moab/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -60,6 +41,7 @@ class Moab(AutotoolsPackage):
     variant('irel', default=False, description='Enable irel interface')
     variant('fbigeom', default=False, description='Enable fbigeom interface')
     variant('coupler', default=True, description='Enable mbcoupler tool')
+    variant('dagmc', default=False, description='Enable dagmc tool')
 
     variant("debug", default=False, description='enable debug symbols')
     variant('shared', default=False,
@@ -80,6 +62,7 @@ class Moab(AutotoolsPackage):
     # depends_on('vtk', when='+vtk')
 
     depends_on('blas')
+    depends_on('lapack')
     depends_on('mpi', when='+mpi')
     depends_on('hdf5', when='+hdf5')
     depends_on('hdf5+mpi', when='+hdf5+mpi')
@@ -124,6 +107,9 @@ class Moab(AutotoolsPackage):
 #       else:
 #           options.append('--without-mpi')
 
+        options.append('--with-blas=%s' % spec['blas'].libs.ld_flags)
+        options.append('--with-lapack=%s' % spec['lapack'].libs.ld_flags)
+
         if '+hdf5' in spec:
             options.append('--with-hdf5=%s' % spec['hdf5'].prefix)
         else:
@@ -158,6 +144,11 @@ class Moab(AutotoolsPackage):
         else:
             options.append('--disable-mbcoupler')
 
+        if '+dagmc' in spec:
+            options.append('--enable-dagmc')
+        else:
+            options.append('--disable-dagmc')
+
         if '+metis' in spec:
             options.append('--with-metis=%s' % spec['metis'].prefix)
         else:
diff --git a/var/spack/repos/builtin/packages/modern-wheel/package.py b/var/spack/repos/builtin/packages/modern-wheel/package.py
new file mode 100644
index 0000000000..4e3b9b8322
--- /dev/null
+++ b/var/spack/repos/builtin/packages/modern-wheel/package.py
@@ -0,0 +1,45 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import sys
+
+
+class ModernWheel(CMakePackage):
+    """C++ utility collection. Provides various facilities of common use in
+    modern codebases like dynamic linking helpers, loadable plugins facilities
+    and misc patterns."""
+
+    homepage = "https://github.com/alalazo/modern_wheel"
+    url      = "https://github.com/alalazo/modern_wheel/archive/1.2.tar.gz"
+
+    version('1.2', 'dc440099c52b6af3b8ddff6fd7730aff')
+    version('1.1', '289455239ad19497b7db55aacb299ca8')
+    version('1.0', '503dc3e7da2b422c4295e4afcba09dfb')
+
+    variant('shared', default=True,
+            description='Enables the build of shared libraries')
+    # Test implementation files cause some issues on darwin,
+    # needs to be investigated.
+    variant('test',   default=sys.platform != 'darwin',
+            description='Enables the build of unit tests')
+
+    # FindBoost shipped with CMake up to version 3.10.2 (latest one
+    # up to now) is known to be unable to detect Boost >= 1.66.0.
+    # This issue will be probably fixed in CMake >= 3.11.0:
+    # https://gitlab.kitware.com/cmake/cmake/issues/17575
+    # Until then, just assume that we cannot correctly configure
+    # ModernWheel with Boost >= 1.66.0.
+    depends_on('boost           +system +filesystem', when='@:1.1.999')
+    depends_on('boost@:1.65.999 +system +filesystem', when='@1.2:')
+
+    def cmake_args(self):
+        spec = self.spec
+        return [
+            '-DBUILD_UNIT_TEST:BOOL={0}'.format(
+                'ON' if '+test' in spec else 'OFF'),
+            '-DBUILD_SHARED_LIBS:BOOL={0}'.format(
+                'ON' if '+shared' in spec else 'OFF'),
+        ]
diff --git a/var/spack/repos/builtin/packages/mofem-cephas/package.py b/var/spack/repos/builtin/packages/mofem-cephas/package.py
new file mode 100644
index 0000000000..7ddacfb780
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mofem-cephas/package.py
@@ -0,0 +1,81 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class MofemCephas(CMakePackage):
+    """mofem-cephas core library"""
+
+    homepage = "http://mofem.eng.gla.ac.uk"
+    git      = "https://bitbucket.org/likask/mofem-cephas.git"
+
+    maintainers = ['likask']
+
+    version('develop', branch='develop', submodules=True)
+    version('0.8.7', tag='v0.8.7', submodules=True)
+
+    # This option can be only used for development of core lib
+    variant('copy_user_modules', default=True,
+        description='Copy user modules directory instead linking to source')
+    variant('adol-c', default=True, description='Compile with Adol-C')
+    variant('tetgen', default=True, description='Compile with Tetgen')
+    variant('med', default=True, description='Compile with Med')
+    variant('slepc', default=False, description='Compile with Slepc')
+
+    depends_on("mpi")
+    depends_on("boost")
+    depends_on("parmetis")
+    # Fixed version of hdf5, to remove some problems with dependent
+    # packages, f.e. MED format
+    depends_on("hdf5@:1.8.19+hl+mpi")
+    depends_on("petsc@:3.9.2+mumps+mpi")
+    depends_on('slepc', when='+slepc')
+    depends_on("moab")
+    # Upper bound set to ADOL-C until issues with memory leaks
+    # for versions 2.6: fully resolved
+    depends_on("adol-c@2.5.2~examples", when="+adol-c")
+    depends_on("tetgen", when="+tetgen")
+    depends_on("med", when='+med')
+
+    extendable = True
+
+    root_cmakelists_dir = 'mofem'
+
+    def cmake_args(self):
+        spec = self.spec
+        options = []
+
+        # obligatory options
+        options.extend([
+            '-DWITH_SPACK=YES',
+            '-DPETSC_DIR=%s' % spec['petsc'].prefix,
+            '-DPETSC_ARCH=',
+            '-DMOAB_DIR=%s' % spec['moab'].prefix,
+            '-DBOOST_DIR=%s' % spec['boost'].prefix])
+
+        # build tests
+        options.append('-DMOFEM_BUILD_TETS={0}'.format(
+            'ON' if self.run_tests else 'OFF'))
+
+        # variant packages
+        if '+adol-c' in spec:
+            options.append('-DADOL-C_DIR=%s' % spec['adol-c'].prefix)
+
+        if '+tetgen' in spec:
+            options.append('-DTETGEN_DIR=%s' % spec['tetgen'].prefix)
+
+        if '+med' in spec:
+            options.append('-DMED_DIR=%s' % spec['med'].prefix)
+
+        if '+slepc' in spec:
+            options.append('-DSLEPC_DIR=%s' % spec['slepc'].prefix)
+
+        # copy users modules, i.e. stand alone vs linked users modules
+        options.append(
+            '-DSTAND_ALLONE_USERS_MODULES=%s' %
+            ('YES' if '+copy_user_modules' in spec else 'NO'))
+        return options
diff --git a/var/spack/repos/builtin/packages/mofem-fracture-module/package.py b/var/spack/repos/builtin/packages/mofem-fracture-module/package.py
new file mode 100644
index 0000000000..f573d7def1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mofem-fracture-module/package.py
@@ -0,0 +1,87 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class MofemFractureModule(CMakePackage):
+    """mofem fracture module"""
+
+    homepage = "http://mofem.eng.gla.ac.uk"
+    git = "https://bitbucket.org/likask/mofem_um_fracture_mechanics.git"
+
+    maintainers = ['likask']
+
+    version('develop', branch='develop')
+    version('0.9.42', tag='v0.9.42')
+
+    variant('copy_user_modules', default=True,
+        description='Copy user modules directory instead linking')
+
+    extends('mofem-cephas')
+    depends_on("mofem-users-modules", type=('build', 'link', 'run'))
+
+    # The CMakeLists.txt installed with mofem-cephas package set cmake
+    # environment to install extension from extension repository. It searches
+    # for modules in user provides paths, for example in Spack source path.Also
+    # it finds all cmake exported targets installed in lib directory, which are
+    # built with dependent extensions, f.e.mofem - users - modules or others if
+    # needed.
+    @property
+    def root_cmakelists_dir(self):
+        """The relative path to the directory containing CMakeLists.txt
+
+        This path is relative to the root of the extracted tarball,
+        not to the ``build_directory``. Defaults to the current directory.
+
+        :return: directory containing CMakeLists.txt
+        """
+        spec = self.spec
+        return spec['mofem-cephas'].prefix.users_modules
+
+    def cmake_args(self):
+        spec = self.spec
+        source = self.stage.source_path
+
+        options = []
+
+        # obligatory options
+        options.extend([
+            '-DWITH_SPACK=YES',
+            '-DEXTERNAL_MODULES_BUILD=YES',
+            '-DUM_INSTALL_BREFIX=%s' % spec['mofem-users-modules'].prefix,
+            '-DEXTERNAL_MODULE_SOURCE_DIRS=%s' % source,
+            '-DSTAND_ALLONE_USERS_MODULES=%s' %
+            ('YES' if '+copy_user_modules' in spec else 'NO')])
+
+        # Set module version
+        if self.spec.version == Version('develop'):
+            options.extend([
+                '-DFM_VERSION_MAJOR=%s' % 0,
+                '-DFM_VERSION_MINOR=%s' % 0,
+                '-DFM_VERSION_BUILD=%s' % 0])
+        else:
+            options.extend([
+                '-DFM_VERSION_MAJOR=%s' % self.spec.version[0],
+                '-DFM_VERSION_MINOR=%s' % self.spec.version[1],
+                '-DFM_VERSION_BUILD=%s' % self.spec.version[2]])
+
+        # build tests
+        options.append('-DMOFEM_UM_BUILD_TETS={0}'.format(
+            'ON' if self.run_tests else 'OFF'))
+
+        return options
+
+    # This function is not needed to run code installed by extension, nor in
+    # the install process. However for users like to have access to source code
+    # to play and make with it. Having source code at hand one can compile in
+    # own build directory it in mofem-cephas view when the extension is
+    # activated.
+    @run_after('install')
+    def copy_source_code(self):
+        source = self.stage.source_path
+        prefix = self.prefix
+        install_tree(source, prefix.ext_users_modules.fracture_mechanics)
diff --git a/var/spack/repos/builtin/packages/mofem-minimal-surface-equation/package.py b/var/spack/repos/builtin/packages/mofem-minimal-surface-equation/package.py
new file mode 100644
index 0000000000..b967a45e7f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mofem-minimal-surface-equation/package.py
@@ -0,0 +1,75 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class MofemMinimalSurfaceEquation(CMakePackage):
+    """mofem minimal surface equation"""
+
+    homepage = "http://mofem.eng.gla.ac.uk"
+    git      = "https://bitbucket.org/likask/mofem_um_minimal_surface_equation.git"
+
+    maintainers = ['likask']
+
+    version('develop', branch='develop')
+    version('0.3.9', tag='v0.3.9')
+
+    variant('copy_user_modules', default=True,
+        description='Copy user modules directory instead linking')
+
+    extends('mofem-cephas')
+    depends_on("mofem-users-modules", type=('build', 'link', 'run'))
+
+    # The CMakeLists.txt installed with mofem - cephas package set cmake
+    # environment to install extension from extension repository.It searches
+    # for modules in user provides paths, for example in Spack source path.Also
+    # it finds all cmake exported targets installed in lib directory, which are
+    # built with dependent extensions, f.e.mofem - users - modules or others if
+    # needed.
+    @property
+    def root_cmakelists_dir(self):
+        """The relative path to the directory containing CMakeLists.txt
+
+        This path is relative to the root of the extracted tarball,
+        not to the ``build_directory``. Defaults to the current directory.
+
+        :return: directory containing CMakeLists.txt
+        """
+        spec = self.spec
+        return spec['mofem-cephas'].prefix.users_modules
+
+    def cmake_args(self):
+        spec = self.spec
+        source = self.stage.source_path
+
+        options = []
+
+        # obligatory options
+        options.extend([
+            '-DWITH_SPACK=YES',
+            '-DEXTERNAL_MODULES_BUILD=YES',
+            '-DUM_INSTALL_BREFIX=%s' % spec['mofem-users-modules'].prefix,
+            '-DEXTERNAL_MODULE_SOURCE_DIRS=%s' % source,
+            '-DSTAND_ALLONE_USERS_MODULES=%s' %
+            ('YES' if '+copy_user_modules' in spec else 'NO')])
+
+        # build tests
+        options.append('-DMOFEM_UM_BUILD_TETS={0}'.format(
+            'ON' if self.run_tests else 'OFF'))
+
+        return options
+
+    # This function is not needed to run code installed by extension, nor in
+    # the install process. However for users like to have access to source code
+    # to play and make with it. Having source code at hand one can compile in
+    # own build directory it in mofem-cephas view when the extension is
+    # activated.
+    @run_after('install')
+    def copy_source_code(self):
+        source = self.stage.source_path
+        prefix = self.prefix
+        install_tree(source, prefix.ext_users_modules.minimal_surface_equation)
diff --git a/var/spack/repos/builtin/packages/mofem-users-modules/package.py b/var/spack/repos/builtin/packages/mofem-users-modules/package.py
new file mode 100644
index 0000000000..8ddec392d0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mofem-users-modules/package.py
@@ -0,0 +1,66 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class MofemUsersModules(CMakePackage):
+    """MofemUsersModules creates installation environment for user-provided
+    modules and extends of mofem-cephas package. The CMakeList.txt file for
+    user modules is located in mofem-cephas/user_modules prefix.
+    MofemUsersModules itself does not contain any code (is a dummy with a
+    single dummy version). It provide sources location of users modules, i.e.
+    mofem-fracture-module. Those are kept as a stand-alone package (instead
+    of resources) as they have different versions and developers. One can
+    install the extension, f.e. spack installs extension spack install
+    mofem-fracture-module. Next, create a symlink to run the code, f.e. spack
+    view symlink um_view mofem-cephas, and activate the extension, i.e. spack
+    activate um_view mofem-minimal-surface-equation. Basic mofem
+    functionality is available when with spack install mofem-users-modules,
+    it provides simple examples for calculating elasticity problems,
+    magnetostatics, saturated and unsaturated flow and a couple more. For
+    more information how to work with Spack and MoFEM see
+    http://mofem.eng.gla.ac.uk/mofem/html/install_spack.html"""
+
+    homepage = "http://mofem.eng.gla.ac.uk"
+    url = "https://bitbucket.org/likask/mofem-joseph/downloads/users_modules_dummy"
+    version('1.0', '5a8b22c9cdcad7bbad92b1590d55edb1', expand=False)
+
+    maintainers = ['likask']
+
+    variant('copy_user_modules', default=True,
+        description='Copy user modules directory instead linking')
+
+    extends('mofem-cephas')
+
+    @property
+    def root_cmakelists_dir(self):
+        """The relative path to the directory containing CMakeLists.txt
+
+        This path is relative to the root of the extracted tarball,
+        not to the ``build_directory``. Defaults to the current directory.
+
+        :return: directory containing CMakeLists.txt
+        """
+        spec = self.spec
+        return spec['mofem-cephas'].prefix.users_modules
+
+    def cmake_args(self):
+        spec = self.spec
+
+        options = []
+
+        # obligatory options
+        options.extend([
+            '-DWITH_SPACK=YES',
+            '-DSTAND_ALLONE_USERS_MODULES=%s' %
+            ('YES' if '+copy_user_modules' in spec else 'NO')])
+
+        # build tests
+        options.append('-DMOFEM_UM_BUILD_TETS={0}'.format(
+            'ON' if self.run_tests else 'OFF'))
+
+        return options
diff --git a/var/spack/repos/builtin/packages/molcas/package.py b/var/spack/repos/builtin/packages/molcas/package.py
index 7c4958cc94..38d7c1be2d 100644
--- a/var/spack/repos/builtin/packages/molcas/package.py
+++ b/var/spack/repos/builtin/packages/molcas/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
diff --git a/var/spack/repos/builtin/packages/mono/package.py b/var/spack/repos/builtin/packages/mono/package.py
index a2f841ceb1..b3a7161b4d 100644
--- a/var/spack/repos/builtin/packages/mono/package.py
+++ b/var/spack/repos/builtin/packages/mono/package.py
@@ -1,27 +1,8 @@
-###############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -47,6 +28,7 @@ class Mono(AutotoolsPackage):
     depends_on('libiconv')
     depends_on('perl', type=('build'))
 
+    version('5.4.1.7', '28a82df5d0b7854b387d4f21d852ac70')
     version('5.4.0.167', '103c7a737632046a9e9a0b039d752ee1')
     version('5.0.1.1', '17692c7a797f95ee6f9a0987fda3d486')
     version('4.8.0.524', 'baeed5b8139a85ad7e291d402a4bcccb')
diff --git a/var/spack/repos/builtin/packages/mosh/package.py b/var/spack/repos/builtin/packages/mosh/package.py
index de15e46bde..23d9cd0f1c 100644
--- a/var/spack/repos/builtin/packages/mosh/package.py
+++ b/var/spack/repos/builtin/packages/mosh/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -44,6 +25,7 @@ class Mosh(AutotoolsPackage):
     depends_on('zlib')
     depends_on('openssl')
 
+    depends_on('pkgconfig', type='build')
     depends_on('perl', type='run')
 
     build_directory = 'spack-build'
diff --git a/var/spack/repos/builtin/packages/mothur/package.py b/var/spack/repos/builtin/packages/mothur/package.py
index e19ee30f98..ad66649025 100644
--- a/var/spack/repos/builtin/packages/mothur/package.py
+++ b/var/spack/repos/builtin/packages/mothur/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,11 +14,9 @@ class Mothur(MakefilePackage):
     homepage = "https://github.com/mothur/mothur"
     url      = "https://github.com/mothur/mothur/archive/v1.39.5.tar.gz"
 
+    version('1.40.5', 'd57847849fdb961c3f66c9b9fdf3057b')
     version('1.39.5', '1f826ea4420e6822fc0db002c5940b92')
 
-    variant('mpi', default=True, description='Enable MPI parallel support')
-
-    depends_on('mpi', when='+mpi')
     depends_on('boost')
     depends_on('readline')
 
diff --git a/var/spack/repos/builtin/packages/motif/package.py b/var/spack/repos/builtin/packages/motif/package.py
new file mode 100644
index 0000000000..fdafcc065a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/motif/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Motif(AutotoolsPackage):
+    """"
+    Motif - Graphical user interface (GUI)
+    specification and the widget toolkit
+    """
+    homepage = "http://motif.ics.com/"
+    url = "http://cfhcable.dl.sourceforge.net/project/motif/Motif 2.3.8 Source Code/motif-2.3.8.tar.gz"
+
+    version('2.3.8', '7572140bb52ba21ec2f0c85b2605e2b1')
+
+    depends_on("flex")
+    depends_on("libx11")
+    depends_on("libxt")
+    depends_on("libxext")
+    depends_on("libxft")
+    depends_on("libxcomposite")
+    depends_on("libxfixes")
+    depends_on("xbitmaps")
diff --git a/var/spack/repos/builtin/packages/motioncor2/package.py b/var/spack/repos/builtin/packages/motioncor2/package.py
index 304e369d99..91f1a493ce 100644
--- a/var/spack/repos/builtin/packages/motioncor2/package.py
+++ b/var/spack/repos/builtin/packages/motioncor2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 from glob import glob
 
@@ -36,15 +17,24 @@ class Motioncor2(Package):
     to keep up with automated data collection."""
 
     homepage = "http://msg.ucsf.edu/em/software"
-    url      = "http://msg.ucsf.edu/MotionCor2/MotionCor2-1.0.2.tar.gz"
+    url      = "http://msg.ucsf.edu/MotionCor2/MotionCor2-1.1.0.zip"
 
-    version('1.0.2',        'f2f4c5b09170ab8480ca657f14cdba2b')
-    version('1.0.1',        '73d94a80abdef9bf37bbc80fbbe76622')
-    version('1.0.0',        '490f4df8daa9f5ddb9eec3962ba3ddf5')
+    version('1.1.0',
+            '6e37e7ed63a9f0aab5d794b2604d5ba79333960bb9440a1a218630b03dbeaeac')
+    version('1.0.5',
+            '4efa55af25644bcff1ca7882419267b8c094c9cc6155b37d2c204b154c56f5a8',
+            url='http://msg.ucsf.edu/MotionCor2/MotionCor2-1.0.5.tar.gz')
+    version('1.0.4',
+            'c75738160ac18d3f27c33677e78e63313d8ec2b023b5a46173428c3fa0451a94',
+            url='http://msg.ucsf.edu/MotionCor2/MotionCor2-1.0.4.tar.gz')
 
     depends_on('cuda@8.0:8.99', type='run')
+    # libtiff.so.3 is required
+    depends_on('libtiff@3.0:3.99', type='run')
 
     def install(self, spec, prefix):
         mkdirp(prefix.bin)
         for files in glob("MotionCor2_*"):
             install(files, prefix.bin)
+        with working_dir(prefix.bin):
+            symlink('MotionCor2_{0}'.format(spec.version), 'MotionCor2')
diff --git a/var/spack/repos/builtin/packages/mount-point-attributes/package.py b/var/spack/repos/builtin/packages/mount-point-attributes/package.py
new file mode 100644
index 0000000000..1a82e18b6c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mount-point-attributes/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class MountPointAttributes(AutotoolsPackage):
+    """Library to turn expensive, non-scalable file system calls into simple
+       string comparison operations."""
+
+    homepage = "https://github.com/LLNL/MountPointAttributes"
+    url = 'https://github.com/LLNL/MountPointAttributes/files/2270601/mountpointattr-1.1.tar.gz'
+
+    version('1.1', 'c9f0e7f5a3e16b9a022e5948712ecb2a')
+
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool', type='build')
diff --git a/var/spack/repos/builtin/packages/mozjs/package.py b/var/spack/repos/builtin/packages/mozjs/package.py
index b0e98772af..08c467b763 100644
--- a/var/spack/repos/builtin/packages/mozjs/package.py
+++ b/var/spack/repos/builtin/packages/mozjs/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,7 +21,7 @@ class Mozjs(AutotoolsPackage):
             url="http://ftp.mozilla.org/pub/js/js185-1.0.0.tar.gz")
 
     depends_on('perl@5.6:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('python@2.7.3:2.8', type='build')
     depends_on('nspr', when='@:27')
     depends_on('libffi@3.0.9:')
diff --git a/var/spack/repos/builtin/packages/mpark-variant/package.py b/var/spack/repos/builtin/packages/mpark-variant/package.py
new file mode 100644
index 0000000000..ad1704d6f7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mpark-variant/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class MparkVariant(CMakePackage):
+    """C++17 `std::variant` for C++11/14/17"""
+
+    homepage = "https://mpark.github.io/variant"
+    url      = "https://github.com/mpark/variant/archive/v1.3.0.tar.gz"
+    maintainers = ['ax3l']
+
+    version('1.3.0', '368b7d6f1a07bd6ee26ff518258dc71c')
+
+    conflicts('%gcc@:4.7')
+    conflicts('%clang@:3.5')
diff --git a/var/spack/repos/builtin/packages/mpc/package.py b/var/spack/repos/builtin/packages/mpc/package.py
index 749794015a..1e1763d0df 100644
--- a/var/spack/repos/builtin/packages/mpc/package.py
+++ b/var/spack/repos/builtin/packages/mpc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,20 +10,28 @@ class Mpc(AutotoolsPackage):
     """Gnu Mpc is a C library for the arithmetic of complex numbers
        with arbitrarily high precision and correct rounding of the
        result."""
+
     homepage = "http://www.multiprecision.org"
-    url      = "https://ftp.gnu.org/gnu/mpc/mpc-1.0.2.tar.gz"
+    url      = "https://ftpmirror.gnu.org/mpc/mpc-1.1.0.tar.gz"
+    list_url = "http://www.multiprecision.org/mpc/download.html"
 
+    version('1.1.0', '4125404e41e482ec68282a2e687f6c73')
     version('1.0.3', 'd6a1d5f8ddea3abd2cc3e98f58352d26')
     version('1.0.2', '68fadff3358fb3e7976c7a398a0af4c3')
 
-    depends_on('gmp@4.3.2:')   # mpir is a drop-in replacement for this
-    depends_on('mpfr@2.4.2:')  # Could also be built against mpir
+    # Could also be built against mpir instead
+    depends_on('gmp@4.3.2:')
+    depends_on('gmp@5.0.0:', when='@1.1.0:')
+    depends_on('mpfr@2.4.2:')
+    depends_on('mpfr@3.0.0:', when='@1.1.0:')
 
     def url_for_version(self, version):
         if version < Version("1.0.1"):
-            return "http://www.multiprecision.org/mpc/download/mpc-%s.tar.gz" % version
+            url = "http://www.multiprecision.org/mpc/download/mpc-{0}.tar.gz"
         else:
-            return "https://ftp.gnu.org/gnu/mpc/mpc-%s.tar.gz" % version
+            url = "https://ftp.gnu.org/gnu/mpc/mpc-{0}.tar.gz"
+
+        return url.format(version)
 
     def configure_args(self):
         spec = self.spec
diff --git a/var/spack/repos/builtin/packages/mpe2/package.py b/var/spack/repos/builtin/packages/mpe2/package.py
index d5041d7a32..470a29d8b2 100644
--- a/var/spack/repos/builtin/packages/mpe2/package.py
+++ b/var/spack/repos/builtin/packages/mpe2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/mpest/package.py b/var/spack/repos/builtin/packages/mpest/package.py
index c5cba773dd..25e7e4f156 100644
--- a/var/spack/repos/builtin/packages/mpest/package.py
+++ b/var/spack/repos/builtin/packages/mpest/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/mpfr/package.py b/var/spack/repos/builtin/packages/mpfr/package.py
index 01006dd72a..3ddf429f52 100644
--- a/var/spack/repos/builtin/packages/mpfr/package.py
+++ b/var/spack/repos/builtin/packages/mpfr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,18 +11,33 @@ class Mpfr(AutotoolsPackage):
        floating-point computations with correct rounding."""
 
     homepage = "http://www.mpfr.org"
-    url      = "https://ftp.gnu.org/gnu/mpfr/mpfr-3.1.5.tar.bz2"
+    url      = "https://ftpmirror.gnu.org/mpfr/mpfr-4.0.1.tar.bz2"
 
+    version('4.0.1', '8c21d8ac7460493b2b9f3ef3cc610454')
+    version('4.0.0', 'ef619f3bb68039e35c4a219e06be72d0')
+    version('3.1.6', '320c28198def956aeacdb240b46b8969')
     version('3.1.5', 'b1d23a55588e3b2a13e3be66bc69fd8d')
     version('3.1.4', 'b8a2f6b0e68bef46e53da2ac439e1cf4')
     version('3.1.3', '5fdfa3cfa5c86514ee4a241a1affa138')
     version('3.1.2', 'ee2c3ac63bf0c2359bf08fc3ee094c19')
 
     # mpir is a drop-in replacement for gmp
-    depends_on('gmp@4.1.0:')  # 4.2.3 or higher is recommended
+    depends_on('gmp@4.1:')  # 4.2.3 or higher is recommended
+    depends_on('gmp@5.0:', when='@4.0.0:')  # http://www.mpfr.org/mpfr-4.0.0/
+
+    # Check the Bugs section of old release pages for patches.
+    # http://www.mpfr.org/mpfr-X.Y.Z/#bugs
+    patches = {
+        '3.1.6': '66a5d58364113a21405fc53f4a48f4e8',
+        '3.1.5': '1dc5fe65feb5607b89fe0f410d53b627',
+        '3.1.4': 'd124381573404fe83654c7d5a79aeabf',
+        '3.1.3': 'ebd1d835e0ae2fd8a9339210ccd1d0a8',
+        '3.1.2': '9f96a5c7cac1d6cd983ed9cf7d997074',
+    }
 
-    patch('vasprintf.patch', when='@3.1.5')
-    patch('strtofr.patch',   when='@3.1.5')
+    for ver, checksum in patches.items():
+        patch('http://www.mpfr.org/mpfr-{0}/allpatches'.format(ver),
+              when='@' + ver, sha256=checksum)
 
     def configure_args(self):
         args = [
diff --git a/var/spack/repos/builtin/packages/mpfr/strtofr.patch b/var/spack/repos/builtin/packages/mpfr/strtofr.patch
deleted file mode 100644
index 01878bf1b0..0000000000
--- a/var/spack/repos/builtin/packages/mpfr/strtofr.patch
+++ /dev/null
@@ -1,92 +0,0 @@
-diff -Naurd mpfr-3.1.5-a/PATCHES mpfr-3.1.5-b/PATCHES
---- mpfr-3.1.5-a/PATCHES	2016-12-19 22:11:17.022676737 +0000
-+++ mpfr-3.1.5-b/PATCHES	2016-12-19 22:11:17.094676820 +0000
-@@ -0,0 +1 @@
-+strtofr
-diff -Naurd mpfr-3.1.5-a/VERSION mpfr-3.1.5-b/VERSION
---- mpfr-3.1.5-a/VERSION	2016-12-15 08:35:46.544430346 +0000
-+++ mpfr-3.1.5-b/VERSION	2016-12-19 22:11:17.094676820 +0000
-@@ -1 +1 @@
--3.1.5-p1
-+3.1.5-p2
-diff -Naurd mpfr-3.1.5-a/src/mpfr.h mpfr-3.1.5-b/src/mpfr.h
---- mpfr-3.1.5-a/src/mpfr.h	2016-12-15 08:35:46.540430340 +0000
-+++ mpfr-3.1.5-b/src/mpfr.h	2016-12-19 22:11:17.090676815 +0000
-@@ -27,7 +27,7 @@
- #define MPFR_VERSION_MAJOR 3
- #define MPFR_VERSION_MINOR 1
- #define MPFR_VERSION_PATCHLEVEL 5
--#define MPFR_VERSION_STRING "3.1.5-p1"
-+#define MPFR_VERSION_STRING "3.1.5-p2"
- 
- /* Macros dealing with MPFR VERSION */
- #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c))
-diff -Naurd mpfr-3.1.5-a/src/strtofr.c mpfr-3.1.5-b/src/strtofr.c
---- mpfr-3.1.5-a/src/strtofr.c	2016-09-27 07:58:15.000000000 +0000
-+++ mpfr-3.1.5-b/src/strtofr.c	2016-12-19 22:11:17.066676788 +0000
-@@ -743,11 +743,14 @@
-          of the pstr_size most significant digits of pstr->mant, with
-          equality in case exact is non-zero. */
- 
--      /* test if rounding is possible, and if so exit the loop */
--      if (exact || mpfr_can_round_raw (result, ysize,
--                                       (pstr->negative) ? -1 : 1,
--                                       ysize_bits - err - 1,
--                                       MPFR_RNDN, rnd, MPFR_PREC(x)))
-+      /* test if rounding is possible, and if so exit the loop.
-+         Note: we also need to be able to determine the correct ternary value,
-+         thus we use the MPFR_PREC(x) + (rnd == MPFR_RNDN) trick.
-+         For example if result = xxx...xxx111...111 and rnd = RNDN,
-+         then we know the correct rounding is xxx...xx(x+1), but we cannot know
-+         the correct ternary value. */
-+      if (exact || mpfr_round_p (result, ysize, ysize_bits - err - 1,
-+                                 MPFR_PREC(x) + (rnd == MPFR_RNDN)))
-         break;
- 
-     next_loop:
-diff -Naurd mpfr-3.1.5-a/src/version.c mpfr-3.1.5-b/src/version.c
---- mpfr-3.1.5-a/src/version.c	2016-12-15 08:35:46.544430346 +0000
-+++ mpfr-3.1.5-b/src/version.c	2016-12-19 22:11:17.094676820 +0000
-@@ -25,5 +25,5 @@
- const char *
- mpfr_get_version (void)
- {
--  return "3.1.5-p1";
-+  return "3.1.5-p2";
- }
-diff -Naurd mpfr-3.1.5-a/tests/tstrtofr.c mpfr-3.1.5-b/tests/tstrtofr.c
---- mpfr-3.1.5-a/tests/tstrtofr.c	2016-09-27 07:58:14.000000000 +0000
-+++ mpfr-3.1.5-b/tests/tstrtofr.c	2016-12-19 22:11:17.066676788 +0000
-@@ -1191,6 +1191,24 @@
-   mpfr_clears (e, x1, x2, (mpfr_ptr) 0);
- }
- 
-+/* Note: the number is 5^47/2^9. */
-+static void
-+bug20161217 (void)
-+{
-+  mpfr_t fp, z;
-+  static const char * num = "0.1387778780781445675529539585113525390625e31";
-+  int inex;
-+
-+  mpfr_init2 (fp, 110);
-+  mpfr_init2 (z, 110);
-+  inex = mpfr_strtofr (fp, num, NULL, 10, MPFR_RNDN);
-+  MPFR_ASSERTN(inex == 0);
-+  mpfr_set_str_binary (z, "10001100001000010011110110011101101001010000001011011110010001010100010100100110111101000010001011001100001101E-9");
-+  MPFR_ASSERTN(mpfr_equal_p (fp, z));
-+  mpfr_clear (fp);
-+  mpfr_clear (z);
-+}
-+
- int
- main (int argc, char *argv[])
- {
-@@ -1205,6 +1223,7 @@
-   test20100310 ();
-   bug20120814 ();
-   bug20120829 ();
-+  bug20161217 ();
- 
-   tests_end_mpfr ();
-   return 0;
diff --git a/var/spack/repos/builtin/packages/mpfr/vasprintf.patch b/var/spack/repos/builtin/packages/mpfr/vasprintf.patch
deleted file mode 100644
index e1576d5976..0000000000
--- a/var/spack/repos/builtin/packages/mpfr/vasprintf.patch
+++ /dev/null
@@ -1,82 +0,0 @@
-diff -Naurd mpfr-3.1.5-a/PATCHES mpfr-3.1.5-b/PATCHES
---- mpfr-3.1.5-a/PATCHES	2016-12-15 08:35:46.476430238 +0000
-+++ mpfr-3.1.5-b/PATCHES	2016-12-15 08:35:46.544430346 +0000
-@@ -0,0 +1 @@
-+vasprintf
-diff -Naurd mpfr-3.1.5-a/VERSION mpfr-3.1.5-b/VERSION
---- mpfr-3.1.5-a/VERSION	2016-09-27 07:58:14.000000000 +0000
-+++ mpfr-3.1.5-b/VERSION	2016-12-15 08:35:46.544430346 +0000
-@@ -1 +1 @@
--3.1.5
-+3.1.5-p1
-diff -Naurd mpfr-3.1.5-a/src/mpfr.h mpfr-3.1.5-b/src/mpfr.h
---- mpfr-3.1.5-a/src/mpfr.h	2016-09-27 07:58:15.000000000 +0000
-+++ mpfr-3.1.5-b/src/mpfr.h	2016-12-15 08:35:46.540430340 +0000
-@@ -27,7 +27,7 @@
- #define MPFR_VERSION_MAJOR 3
- #define MPFR_VERSION_MINOR 1
- #define MPFR_VERSION_PATCHLEVEL 5
--#define MPFR_VERSION_STRING "3.1.5"
-+#define MPFR_VERSION_STRING "3.1.5-p1"
- 
- /* Macros dealing with MPFR VERSION */
- #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c))
-diff -Naurd mpfr-3.1.5-a/src/vasprintf.c mpfr-3.1.5-b/src/vasprintf.c
---- mpfr-3.1.5-a/src/vasprintf.c	2016-09-27 07:58:15.000000000 +0000
-+++ mpfr-3.1.5-b/src/vasprintf.c	2016-12-15 08:35:46.520430308 +0000
-@@ -1593,7 +1593,7 @@
-         }
-       else if (spec.spec == 'f' || spec.spec == 'F')
-         {
--          if (spec.prec == -1)
-+          if (spec.prec < 0)
-             spec.prec = 6;
-           if (regular_fg (np, p, spec, NULL) == -1)
-             goto error;
-diff -Naurd mpfr-3.1.5-a/src/version.c mpfr-3.1.5-b/src/version.c
---- mpfr-3.1.5-a/src/version.c	2016-09-27 07:58:15.000000000 +0000
-+++ mpfr-3.1.5-b/src/version.c	2016-12-15 08:35:46.544430346 +0000
-@@ -25,5 +25,5 @@
- const char *
- mpfr_get_version (void)
- {
--  return "3.1.5";
-+  return "3.1.5-p1";
- }
-diff -Naurd mpfr-3.1.5-a/tests/tsprintf.c mpfr-3.1.5-b/tests/tsprintf.c
---- mpfr-3.1.5-a/tests/tsprintf.c	2016-09-27 07:58:14.000000000 +0000
-+++ mpfr-3.1.5-b/tests/tsprintf.c	2016-12-15 08:35:46.520430308 +0000
-@@ -1251,6 +1251,25 @@
-   check_emin_aux (MPFR_EMIN_MIN);
- }
- 
-+static void
-+test20161214 (void)
-+{
-+  mpfr_t x;
-+  char buf[32];
-+  const char s[] = "0x0.fffffffffffff8p+1024";
-+  int r;
-+
-+  mpfr_init2 (x, 64);
-+  mpfr_set_str (x, s, 16, MPFR_RNDN);
-+  r = mpfr_snprintf (buf, 32, "%.*RDf", -2, x);
-+  MPFR_ASSERTN(r == 316);
-+  r = mpfr_snprintf (buf, 32, "%.*RDf", INT_MIN + 1, x);
-+  MPFR_ASSERTN(r == 316);
-+  r = mpfr_snprintf (buf, 32, "%.*RDf", INT_MIN, x);
-+  MPFR_ASSERTN(r == 316);
-+  mpfr_clear (x);
-+}
-+
- int
- main (int argc, char **argv)
- {
-@@ -1271,6 +1290,7 @@
-   mixed ();
-   check_emax ();
-   check_emin ();
-+  test20161214 ();
- 
- #if defined(HAVE_LOCALE_H) && defined(HAVE_SETLOCALE)
- #if MPFR_LCONV_DPTS
diff --git a/var/spack/repos/builtin/packages/mpibash/package.py b/var/spack/repos/builtin/packages/mpibash/package.py
index f5476328b7..f4157ca66f 100644
--- a/var/spack/repos/builtin/packages/mpibash/package.py
+++ b/var/spack/repos/builtin/packages/mpibash/package.py
@@ -1,56 +1,28 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class Mpibash(Package):
+class Mpibash(AutotoolsPackage):
     """Parallel scripting right from the Bourne-Again Shell (Bash)"""
-    homepage = "http://www.ccs3.lanl.gov/~pakin/software/mpibash-4.3.html"
 
-    version('4.3', '81348932d5da294953e15d4814c74dd1',
-            url="http://ftp.gnu.org/gnu/bash/bash-4.3.tar.gz")
+    homepage = "https://github.com/lanl/MPI-Bash"
+    url      = "https://github.com/lanl/MPI-Bash/releases/download/v1.2/mpibash-1.2.tar.gz"
 
-    # patch -p1 < ../mpibash-4.3.patch
-    patch('mpibash-4.3.patch', level=1, when='@4.3')
-
-    # above patch modifies configure.ac
-    depends_on('autoconf', type='build')
+    version('1.2', 'b81001fb234ed79c4e5bf2f7efee3529')
 
+    depends_on('bash@4.4:')
     # uses MPI_Exscan which is in MPI-1.2 and later
     depends_on('mpi@1.2:')
 
     depends_on('libcircle')
 
-    def install(self, spec, prefix):
-        # run autoconf to rebuild configure
-        autoconf = which('autoconf')
-        autoconf()
-
-        configure("--prefix=" + prefix,
-                  "CC=mpicc")
-
-        make(parallel=False)
-
-        make("install")
+    def configure_args(self):
+        args = [
+            "--with-bashdir={0}".format(self.spec['bash'].prefix.include.bash),
+            "CC={0}".format(self.spec['mpi'].mpicc)
+        ]
+        return args
diff --git a/var/spack/repos/builtin/packages/mpiblast/package.py b/var/spack/repos/builtin/packages/mpiblast/package.py
index eebb7da1fb..c358075f1e 100644
--- a/var/spack/repos/builtin/packages/mpiblast/package.py
+++ b/var/spack/repos/builtin/packages/mpiblast/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py
index 74234f46ae..aea92872f0 100644
--- a/var/spack/repos/builtin/packages/mpich/package.py
+++ b/var/spack/repos/builtin/packages/mpich/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
@@ -31,10 +12,13 @@ class Mpich(AutotoolsPackage):
     the Message Passing Interface (MPI) standard."""
 
     homepage = "http://www.mpich.org"
-    url = "http://www.mpich.org/static/downloads/3.0.4/mpich-3.0.4.tar.gz"
+    url      = "http://www.mpich.org/static/downloads/3.0.4/mpich-3.0.4.tar.gz"
+    git      = "https://github.com/pmodels/mpich.git"
     list_url = "http://www.mpich.org/static/downloads/"
     list_depth = 1
 
+    version('develop', submodules=True)
+    version('3.2.1', 'e175452f4d61646a52c73031683fc375')
     version('3.2',   'f414cfa77099cd1fa1a5ae4e22db508a')
     version('3.1.4', '2ab544607986486562e076b83937bba2')
     version('3.1.3', '93cb17f91ac758cbf9174ecb03563778')
@@ -42,7 +26,6 @@ class Mpich(AutotoolsPackage):
     version('3.1.1', '40dc408b1e03cc36d80209baaa2d32b7')
     version('3.1',   '5643dd176499bfb7d25079aaff25f2ec')
     version('3.0.4', '9c5d5d4fe1e17dd12153f40bc5b6dbc0')
-    version('develop', git='git://github.com/pmodels/mpich')
 
     variant('hydra', default=True,  description='Build the hydra process manager')
     variant('pmi',   default=True,  description='Build with PMI support')
@@ -71,10 +54,16 @@ spack package at this time.''',
     provides('mpi@:3.0', when='@3:')
     provides('mpi@:1.3', when='@1:')
 
+    filter_compiler_wrappers(
+        'mpicc', 'mpicxx', 'mpif77', 'mpif90', 'mpifort', relative_root='bin'
+    )
+
     # fix MPI_Barrier segmentation fault
     # see https://lists.mpich.org/pipermail/discuss/2016-May/004764.html
     # and https://lists.mpich.org/pipermail/discuss/2016-June/004768.html
-    patch('mpich32_clang.patch', when='@3.2%clang')
+    patch('mpich32_clang.patch', when='@3.2:3.2.0%clang')
+
+    depends_on('findutils', type='build')
 
     depends_on('libfabric', when='netmod=ofi')
 
@@ -169,34 +158,3 @@ spack package at this time.''',
         config_args.append(device_config)
 
         return config_args
-
-    @run_after('install')
-    def filter_compilers(self):
-        """Run after install to make the MPI compilers use the
-        compilers that Spack built the package with.
-
-        If this isn't done, they'll have CC, CXX, F77, and FC set
-        to Spack's generic cc, c++, f77, and f90.  We want them to
-        be bound to whatever compiler they were built with."""
-
-        mpicc = join_path(self.prefix.bin, 'mpicc')
-        mpicxx = join_path(self.prefix.bin, 'mpicxx')
-        mpif77 = join_path(self.prefix.bin, 'mpif77')
-        mpif90 = join_path(self.prefix.bin, 'mpif90')
-
-        # Substitute Spack compile wrappers for the real
-        # underlying compiler
-        kwargs = {
-            'ignore_absent': True,
-            'backup': False,
-            'string': True
-        }
-        filter_file(env['CC'],  self.compiler.cc,  mpicc,  **kwargs)
-        filter_file(env['CXX'], self.compiler.cxx, mpicxx, **kwargs)
-        filter_file(env['F77'], self.compiler.f77, mpif77, **kwargs)
-        filter_file(env['FC'],  self.compiler.fc,  mpif90, **kwargs)
-
-        # Remove this linking flag if present
-        # (it turns RPATH into RUNPATH)
-        for wrapper in (mpicc, mpicxx, mpif77, mpif90):
-            filter_file('-Wl,--enable-new-dtags', '', wrapper, **kwargs)
diff --git a/var/spack/repos/builtin/packages/mpifileutils/package.py b/var/spack/repos/builtin/packages/mpifileutils/package.py
index f1bb7e3f39..8257587f1b 100644
--- a/var/spack/repos/builtin/packages/mpifileutils/package.py
+++ b/var/spack/repos/builtin/packages/mpifileutils/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,14 +18,22 @@ class Mpifileutils(AutotoolsPackage):
 
     homepage = "https://github.com/hpc/mpifileutils"
     url      = "https://github.com/hpc/mpifileutils/releases/download/v0.6/mpifileutils-0.6.tar.gz"
+    git      = "https://github.com/hpc/mpifileutils.git"
 
+    version('develop', branch='master')
+    version('0.8', '1082600e7ac4e6b2c13d91bbec40cffb')
     version('0.7', 'c081f7f72c4521dddccdcf9e087c5a2b')
     version('0.6', '620bcc4966907481f1b1a965b28fc9bf')
 
     depends_on('mpi')
     depends_on('libcircle')
     depends_on('lwgrp')
-    depends_on('dtcmp')
+
+    # need precise version of dtcmp, since DTCMP_Segmented_exscan added
+    # in v1.0.3 but renamed in v1.1.0 and later
+    depends_on('dtcmp@1.0.3',  when='@:0.7')
+    depends_on('dtcmp@1.1.0:', when='@0.8:')
+
     depends_on('libarchive')
 
     variant('xattr', default=True,
diff --git a/var/spack/repos/builtin/packages/mpilander/package.py b/var/spack/repos/builtin/packages/mpilander/package.py
new file mode 100644
index 0000000000..6f53f4d59a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mpilander/package.py
@@ -0,0 +1,45 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Mpilander(CMakePackage):
+    """There can only be one (MPI process)!"""
+
+    homepage = "https://github.com/MPILander/MPILander"
+    git      = "https://github.com/MPILander/MPILander.git"
+
+    maintainers = ['ax3l']
+
+    version('develop', branch='master')
+
+    # variant('cuda', default=False, description='Enable CUDA support')
+    # variant(
+    #     'schedulers',
+    #     description='List of supported schedulers',
+    #     values=('alps', 'lsf', 'tm', 'slurm', 'sge', 'loadleveler'),
+    #     multi=True
+    # )
+
+    depends_on('cmake@3.9.2:', type='build')
+
+    provides('mpi@:3.1')
+
+    # compiler support
+    conflicts('%gcc@:4.7')
+    conflicts('%clang@:3.8')
+    conflicts('%intel@:16')
+
+    def cmake_args(self):
+        args = [
+            # tests and examples
+            '-DBUILD_TESTING:BOOL={0}'.format(
+                'ON' if self.run_tests else 'OFF'),
+            '-DBUILD_EXAMPLES:BOOL={0}'.format(
+                'ON' if self.run_tests else 'OFF'),
+        ]
+
+        return args
diff --git a/var/spack/repos/builtin/packages/mpileaks/package.py b/var/spack/repos/builtin/packages/mpileaks/package.py
index cbf330666a..291df5da34 100644
--- a/var/spack/repos/builtin/packages/mpileaks/package.py
+++ b/var/spack/repos/builtin/packages/mpileaks/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/mpip/package.py b/var/spack/repos/builtin/packages/mpip/package.py
index a641217622..172207885c 100644
--- a/var/spack/repos/builtin/packages/mpip/package.py
+++ b/var/spack/repos/builtin/packages/mpip/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
diff --git a/var/spack/repos/builtin/packages/mpir/package.py b/var/spack/repos/builtin/packages/mpir/package.py
index 14be170a3a..6e79df36e1 100644
--- a/var/spack/repos/builtin/packages/mpir/package.py
+++ b/var/spack/repos/builtin/packages/mpir/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,10 +11,11 @@ class Mpir(Package):
 
     homepage = "https://github.com/wbhart/mpir"
     url      = "https://github.com/wbhart/mpir/archive/mpir-2.7.0.tar.gz"
+    git      = "https://github.com/wbhart/mpir.git"
 
+    version('develop', branch='master')
     version('2.7.0', '985b5d57bd0e74c74125ee885b9c8f71')
     version('2.6.0', 'ec17d6a7e026114ceb734b2466aa0a91')
-    version('develop', git='https://github.com/wbhart/mpir.git')
 
     # This setting allows mpir to act as a drop-in replacement for gmp
     variant('gmp_compat',        default=False,
diff --git a/var/spack/repos/builtin/packages/mpix-launch-swift/package.py b/var/spack/repos/builtin/packages/mpix-launch-swift/package.py
index a56337fdd4..83d3d28799 100644
--- a/var/spack/repos/builtin/packages/mpix-launch-swift/package.py
+++ b/var/spack/repos/builtin/packages/mpix-launch-swift/package.py
@@ -1,41 +1,20 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from distutils.dir_util import copy_tree
 
 
-class MpixLaunchSwift(Package):
+class MpixLaunchSwift(MakefilePackage):
     """Library that allows a child MPI application to be launched
     inside a subset of processes in a parent MPI application.
     """
 
     homepage = "https://bitbucket.org/kshitijvmehta/mpix_launch_swift"
-    url = "https://kshitijvmehta@bitbucket.org/kshitijvmehta/mpix_launch_swift.git"
+    git      = "https://kshitijvmehta@bitbucket.org/kshitijvmehta/mpix_launch_swift.git"
 
-    version('develop', git='https://kshitijvmehta@bitbucket.org/kshitijvmehta/mpix_launch_swift.git',
-            branch='envs')
+    version('develop', branch='envs')
 
     depends_on('stc')
     depends_on('tcl')
@@ -43,5 +22,4 @@ class MpixLaunchSwift(Package):
     depends_on('swig', type='build')
 
     def install(self, spec, prefix):
-        make()
-        copy_tree('.', prefix)
+        install_tree('.', prefix)
diff --git a/var/spack/repos/builtin/packages/mrbayes/package.py b/var/spack/repos/builtin/packages/mrbayes/package.py
index 9361c3cc0e..79701d2a03 100644
--- a/var/spack/repos/builtin/packages/mrbayes/package.py
+++ b/var/spack/repos/builtin/packages/mrbayes/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,9 +13,9 @@ class Mrbayes(AutotoolsPackage):
        of model parameters."""
 
     homepage = "http://mrbayes.sourceforge.net"
-    url      = "https://downloads.sourceforge.net/project/mrbayes/mrbayes/3.2.6/mrbayes-3.2.6.tar.gz"
+    git      = "https://github.com/NBISweden/MrBayes.git"
 
-    version('3.2.6', '95f9822f24be47b976bf87540b55d1fe')
+    version('2017-11-22', commit='8a9adb11bcc538cb95d91d57568dff383f924503')
 
     variant('mpi', default=True, description='Enable MPI parallel support')
     variant('beagle', default=True, description='Enable BEAGLE library for speed benefits')
@@ -48,8 +29,6 @@ class Mrbayes(AutotoolsPackage):
     depends_on('libbeagle', when='+beagle')
     depends_on('mpi', when='+mpi')
 
-    configure_directory = 'src'
-
     def configure_args(self):
         args = []
         if '~beagle' in self.spec:
diff --git a/var/spack/repos/builtin/packages/mrnet/package.py b/var/spack/repos/builtin/packages/mrnet/package.py
index 6569934817..14e2fc8200 100644
--- a/var/spack/repos/builtin/packages/mrnet/package.py
+++ b/var/spack/repos/builtin/packages/mrnet/package.py
@@ -1,47 +1,33 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class Mrnet(AutotoolsPackage):
     """The MRNet Multi-Cast Reduction Network."""
+
     homepage = "http://paradyn.org/mrnet"
     url      = "http://ftp.cs.wisc.edu/pub/paradyn/mrnet/mrnet_5.0.1.tar.gz"
+    git      = "https://github.com/dyninst/mrnet.git"
     list_url = "http://ftp.cs.wisc.edu/paradyn/mrnet"
 
-    version('5.0.1-2', git='https://github.com/dyninst/mrnet.git',
-            commit='20b1eacfc6d680d9f6472146d2dfaa0f900cc2e9')
+    version('5.0.1-3', branch='master')
+    version('5.0.1-2', commit='20b1eacfc6d680d9f6472146d2dfaa0f900cc2e9')
     version('5.0.1', '17f65738cf1b9f9b95647ff85f69ecdd')
     version('4.1.0', '5a248298b395b329e2371bf25366115c')
     version('4.0.0', 'd00301c078cba57ef68613be32ceea2f')
 
+    variant('cti', default=False,
+            description="Build the MRNet with the CTI startup option")
     variant('lwthreads', default=False,
             description="Also build the MRNet LW threadsafe libraries")
     parallel = False
 
     depends_on("boost")
+    depends_on("cti", when='+cti')
 
     def configure_args(self):
         spec = self.spec
@@ -51,5 +37,11 @@ class Mrnet(AutotoolsPackage):
         # lwthreads variant is present
         if '+lwthreads' in spec:
             config_args.append('--enable-ltwt-threadsafe')
-
+        # Build the MRNet with CTI based start-up when
+        # the cti variant is present
+        if '+cti' in spec:
+            config_args.append('--with-startup=cray-cti')
+            cti = self.spec['cti'].prefix
+            config_args.append('--with-craycti-inc=-I%s/include' % cti)
+            config_args.append('--with-craycti-lib=-I%s/lib' % cti)
         return config_args
diff --git a/var/spack/repos/builtin/packages/mrtrix3/package.py b/var/spack/repos/builtin/packages/mrtrix3/package.py
index f5daeabf5a..fc99abfc9a 100644
--- a/var/spack/repos/builtin/packages/mrtrix3/package.py
+++ b/var/spack/repos/builtin/packages/mrtrix3/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-import distutils.dir_util
 
 
 class Mrtrix3(Package):
@@ -33,10 +13,9 @@ class Mrtrix3(Package):
        density."""
 
     homepage = "http://www.mrtrix.org/"
-    url      = "https://github.com/MRtrix3/mrtrix3"
+    git      = "https://github.com/MRtrix3/mrtrix3.git"
 
-    version('2017-09-25', commit='72aca89e3d38c9d9e0c47104d0fb5bd2cbdb536d',
-            git='https://github.com/MRtrix3/mrtrix3.git')
+    version('2017-09-25', commit='72aca89e3d38c9d9e0c47104d0fb5bd2cbdb536d')
 
     depends_on('python@2.7:', type=('build', 'run'))
     depends_on('py-numpy', type=('build', 'run'))
@@ -54,9 +33,7 @@ class Mrtrix3(Package):
         build = Executable('./build')
         configure()
         build()
-        # install_tree('.', prefix) does not work since the prefix
-        # directory already exists by this point
-        distutils.dir_util.copy_tree('.', prefix)
+        install_tree('.', prefix)
 
     def setup_environment(self, spac_env, run_env):
         run_env.prepend_path('PATH', self.prefix)
diff --git a/var/spack/repos/builtin/packages/mscgen/package.py b/var/spack/repos/builtin/packages/mscgen/package.py
new file mode 100644
index 0000000000..f926b539af
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mscgen/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Mscgen(AutotoolsPackage):
+    """Mscgen is a small program that parses Message Sequence Chart descriptions
+    and produces PNG, SVG, EPS or server side image maps (ismaps) as the
+    output."""
+
+    homepage = "http://www.mcternan.me.uk/mscgen/"
+    url      = "http://www.mcternan.me.uk/mscgen/software/mscgen-src-0.20.tar.gz"
+
+    version('0.20', '65c90fb5150d7176b65b793f0faa7377')
+
+    depends_on('flex')
+    depends_on('bison')
+    depends_on('pkgconf')
+    depends_on('libgd')
diff --git a/var/spack/repos/builtin/packages/msgpack-c/package.py b/var/spack/repos/builtin/packages/msgpack-c/package.py
index bf78e8d931..49cd4f765d 100644
--- a/var/spack/repos/builtin/packages/msgpack-c/package.py
+++ b/var/spack/repos/builtin/packages/msgpack-c/package.py
@@ -1,35 +1,27 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class MsgpackC(CMakePackage):
     """A small, fast binary interchange format convertible to/from JSON"""
     homepage = "http://www.msgpack.org"
-    url      = "https://github.com/msgpack/msgpack-c/archive/cpp-1.4.1.tar.gz"
+    url      = "https://github.com/msgpack/msgpack-c/archive/cpp-3.0.1.tar.gz"
 
+    version('3.0.1', 'a79f05f0dc5637c161805d6c0e9bfbe7')
     version('1.4.1', 'e2fd3a7419b9bc49e5017fdbefab87e0')
 
     depends_on('cmake@2.8.12:', type='build')
+    depends_on('googletest', type='test')
+
+    def cmake_args(self):
+        args = [
+            "-DCMAKE_CXX_FLAGS=-Wno-implicit-fallthrough",
+            "-DCMAKE_C_FLAGS=-Wno-implicit-fallthrough",
+            '-DMSGPACK_BUILD_TESTS:BOOL={0}'.format(
+                'ON' if self.run_tests else 'OFF')
+        ]
+        return args
diff --git a/var/spack/repos/builtin/packages/mshadow/package.py b/var/spack/repos/builtin/packages/mshadow/package.py
index cd9ecfce86..3dde91770c 100644
--- a/var/spack/repos/builtin/packages/mshadow/package.py
+++ b/var/spack/repos/builtin/packages/mshadow/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,11 +11,10 @@ class Mshadow(Package):
     in C++/CUDA."""
 
     homepage = "https://github.com/dmlc/mshadow"
-    url      = "https://github.com/dmlc/mshadow/archive/v1.1.tar.gz"
+    git      = "https://github.com/dmlc/mshadow.git"
 
-    version('master', git='https://github.com/dmlc/mshadow.git', branch='master')
-    version('20170721', git='https://github.com/dmlc/mshadow.git',
-            commit='20b54f068c1035f0319fa5e5bbfb129c450a5256')
+    version('master', branch='master')
+    version('20170721', commit='20b54f068c1035f0319fa5e5bbfb129c450a5256')
 
     def install(self, spec, prefix):
         install_tree('mshadow', prefix.include.mshadow)
diff --git a/var/spack/repos/builtin/packages/msmc/package.py b/var/spack/repos/builtin/packages/msmc/package.py
new file mode 100644
index 0000000000..7acde0f400
--- /dev/null
+++ b/var/spack/repos/builtin/packages/msmc/package.py
@@ -0,0 +1,34 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Msmc(MakefilePackage):
+    """This software implements MSMC, a method to infer population size
+       and gene flow from multiple genome sequences"""
+
+    homepage = "https://github.com/stschiff/msmc"
+    url      = "https://github.com/stschiff/msmc/archive/v1.1.0.tar.gz"
+
+    version('1.1.0', sha256='989064400fe392ca3d2ac1a253ce7edf1801b6a7eeb77bbf2ff7bf67910216c4')
+
+    depends_on('gsl', type=('build', 'run'))
+    depends_on('dmd', type='build')
+
+    def edit(self, spec, prefix):
+        filter_file('dmd',
+                    join_path(self.spec['dmd'].prefix.linux.bin64, 'dmd'),
+                    'Makefile', string=True)
+
+    def build(self, spec, prefix):
+        gsllibdir = self.spec['gsl'].prefix.lib
+        libgsl = join_path(gsllibdir, 'libgsl.a')
+        libgslcblas = join_path(gsllibdir, 'libgslcblas.a')
+        make('GSL={0} {1}'.format(libgsl, libgslcblas))
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install_tree('build', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/multitail/package.py b/var/spack/repos/builtin/packages/multitail/package.py
index 9c9ef2cca0..5857fbd751 100644
--- a/var/spack/repos/builtin/packages/multitail/package.py
+++ b/var/spack/repos/builtin/packages/multitail/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/multiverso/package.py b/var/spack/repos/builtin/packages/multiverso/package.py
index 8993ce1b4d..5d1a27e153 100644
--- a/var/spack/repos/builtin/packages/multiverso/package.py
+++ b/var/spack/repos/builtin/packages/multiverso/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,11 +12,10 @@ class Multiverso(CMakePackage):
 
     homepage = "https://github.com/Microsoft/Multiverso"
     url      = "https://github.com/Microsoft/Multiverso/archive/v0.2.tar.gz"
+    git      = "https://github.com/Microsoft/Multiverso.git"
 
-    version('master', git='https://github.com/Microsoft/Multiverso.git',
-            branch='master')
-    version('143187', git='https://github.com/Microsoft/Multiverso.git',
-            commit='143187575d1cfa410100037b8aea2e767e0af637')
+    version('master', branch='master')
+    version('143187', commit='143187575d1cfa410100037b8aea2e767e0af637')
     version('0.2', '483ca7524fea14a311389e421f2bc098')
 
     depends_on('mpi')
diff --git a/var/spack/repos/builtin/packages/mummer/package.py b/var/spack/repos/builtin/packages/mummer/package.py
index 8aabf502f9..a698f27463 100644
--- a/var/spack/repos/builtin/packages/mummer/package.py
+++ b/var/spack/repos/builtin/packages/mummer/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/mumps/examples.patch b/var/spack/repos/builtin/packages/mumps/examples.patch
new file mode 100644
index 0000000000..78003935a6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mumps/examples.patch
@@ -0,0 +1,41 @@
+--- a/examples/Makefile
++++ b/examples/Makefile
+@@ -27,32 +27,32 @@
+ LIBSMUMPS = $(libdir)/libsmumps$(PLAT)$(LIBEXT) $(LIBMUMPS_COMMON)
+ 
+ ssimpletest:  $(LIBSMUMPS)  $$@.o
+-	$(FL) -o $@ $(OPTL) ssimpletest.o  $(LIBSMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
++	$(FL) -o $@ ssimpletest.o  $(LIBSMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
+ 
+ 
+ LIBDMUMPS = $(libdir)/libdmumps$(PLAT)$(LIBEXT) $(LIBMUMPS_COMMON)
+ 
+ dsimpletest: $(LIBDMUMPS)  $$@.o 
+-	$(FL) -o $@ $(OPTL) dsimpletest.o  $(LIBDMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
++	$(FL) -o $@ dsimpletest.o  $(LIBDMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
+ 
+ 
+ LIBCMUMPS = $(libdir)/libcmumps$(PLAT)$(LIBEXT) $(LIBMUMPS_COMMON)
+ 
+ csimpletest: $(LIBCMUMPS)  $$@.o
+-	$(FL) -o $@ $(OPTL) csimpletest.o  $(LIBCMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
++	$(FL) -o $@ csimpletest.o  $(LIBCMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
+ 
+ 
+ LIBZMUMPS = $(libdir)/libzmumps$(PLAT)$(LIBEXT) $(LIBMUMPS_COMMON)
+ 
+ zsimpletest: $(LIBZMUMPS)  $$@.o
+-	$(FL) -o $@ $(OPTL) zsimpletest.o  $(LIBZMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
++	$(FL) -o $@ zsimpletest.o  $(LIBZMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
+ 
+ c_example:	$(LIBDMUMPS) $$@.o
+-	$(FL) -o $@ $(OPTL) $@.o $(LIBDMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
++	$(FL) -o $@ $@.o $(LIBDMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
+ 
+ 
+ multiple_arithmetics_example:	$(LIBSMUMPS) $(LIBDMUMPS) $(LIBCMUMPS) $(LIBZMUMPS) $$@.o
+-	$(FL) -o $@ $(OPTL) $@.o $(LIBSMUMPS) $(LIBDMUMPS) $(LIBCMUMPS) $(LIBZMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
++	$(FL) -o $@ $@.o $(LIBSMUMPS) $(LIBDMUMPS) $(LIBCMUMPS) $(LIBZMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
+ 
+ 
+ .SUFFIXES: .c .F .o
diff --git a/var/spack/repos/builtin/packages/mumps/mumps-5.0.2-spectrum-mpi-xl.patch b/var/spack/repos/builtin/packages/mumps/mumps-5.0.2-spectrum-mpi-xl.patch
deleted file mode 100644
index d2bd17cb44..0000000000
--- a/var/spack/repos/builtin/packages/mumps/mumps-5.0.2-spectrum-mpi-xl.patch
+++ /dev/null
@@ -1,75 +0,0 @@
-diff -Naur MUMPS_5.0.1/Makefile MUMPS_5.0.1-patched/MUMPS_5.0.1/Makefile
---- ./Makefile	2015-07-23 13:08:29.000000000 -0400
-+++ ./Makefile	2016-12-05 14:08:30.788638382 -0500
-@@ -62,7 +62,7 @@
- $(libdir)/libpord$(PLAT)$(LIBEXT):
- 	if [ "$(LPORDDIR)" != "" ] ; then \
- 	  cd $(LPORDDIR); \
--	  $(MAKE) CC="$(CC)" CFLAGS="$(OPTC)" AR="$(AR)" RANLIB="$(RANLIB)" OUTC="$(OUTC)" LIBEXT=$(LIBEXT); \
-+	  $(MAKE) CC="$(CC)" CFLAGS="$(OPTC)" SAR="$(SAR)" RANLIB="$(RANLIB)" OUTC="$(OUTC)" LIBEXT=$(LIBEXT); \
- 	fi;
- 	if [ "$(LPORDDIR)" != "" ] ; then \
- 	  cp $(LPORDDIR)/libpord$(LIBEXT) $@; \
-diff -Naur MUMPS_5.0.1/PORD/lib/Makefile MUMPS_5.0.1-patched/PORD/lib/MUMPS_5.0.1/Makefile
---- ./PORD/lib/Makefile	2015-07-23 13:08:29.000000000 -0400
-+++ ./PORD/lib/Makefile	2016-12-05 11:26:24.785317467 -0500
-@@ -25,7 +25,7 @@
- 	$(CC) $(COPTIONS) -c $*.c $(OUTC)$*.o
- 
- libpord$(LIBEXT):$(OBJS)
--	$(AR)$@ $(OBJS)
-+	$(SAR)$@ $(OBJS)
- 	$(RANLIB) $@
- 
- clean:
-diff -Naur MUMPS_5.0.1/examples/Makefile MUMPS_5.0.1-patched/examples/Makefile
---- ./examples/Makefile	2015-07-23 13:08:32.000000000 -0400
-+++ ./examples/Makefile	2016-12-05 14:36:10.692857906 -0500
-@@ -25,37 +25,30 @@
- 
- LIBSMUMPS = $(libdir)/libsmumps$(PLAT)$(LIBEXT) $(LIBMUMPS_COMMON)
- 
--ssimpletest:  $(LIBSMUMPS)  $$@.o
--	$(FL) -o $@ $(OPTL) ssimpletest.o  $(LIBSMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
-+ssimpletest:  $(LIBSMUMPS)  $$@.F
-+	$(FC) -o $@ $(OPTF) $(INCS) -I. -I$(topdir)/include ssimpletest.F  $(LIBSMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
- 
- 
- LIBDMUMPS = $(libdir)/libdmumps$(PLAT)$(LIBEXT) $(LIBMUMPS_COMMON)
- 
--dsimpletest: $(LIBDMUMPS)  $$@.o 
--	$(FL) -o $@ $(OPTL) dsimpletest.o  $(LIBDMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
-+dsimpletest: $(LIBDMUMPS)  $$@.F 
-+	$(FC) -o $@ $(OPTF) $(INCS) -I. -I$(topdir)/include dsimpletest.F  $(LIBDMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
- 
- 
- LIBCMUMPS = $(libdir)/libcmumps$(PLAT)$(LIBEXT) $(LIBMUMPS_COMMON)
- 
--csimpletest: $(LIBCMUMPS)  $$@.o
--	$(FL) -o $@ $(OPTL) csimpletest.o  $(LIBCMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
-+csimpletest: $(LIBCMUMPS)  $$@.F
-+	$(FC) -o $@ $(OPTF) $(INCS) -I. -I$(topdir)/include csimpletest.F  $(LIBCMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
- 
- 
- LIBZMUMPS = $(libdir)/libzmumps$(PLAT)$(LIBEXT) $(LIBMUMPS_COMMON)
- 
--zsimpletest: $(LIBZMUMPS)  $$@.o
--	$(FL) -o $@ $(OPTL) zsimpletest.o  $(LIBZMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
-+zsimpletest: $(LIBZMUMPS)  $$@.F
-+	$(FC) -o $@ $(OPTF) $(INCS) -I. -I$(topdir)/include zsimpletest.F  $(LIBZMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
- 
- 
--c_example:	$(LIBDMUMPS) $$@.o
--	$(FL) -o $@ $(OPTL) $@.o $(LIBDMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
--
--
--.SUFFIXES: .c .F .o
--.F.o:
--	$(FC) $(OPTF) $(INCS) -I. -I$(topdir)/include -c $*.F $(OUTF)$*.o
--.c.o:
--	$(CC) $(OPTC) $(INCS) $(CDEFS) -I. -I$(topdir)/include -I$(topdir)/src -c $*.c $(OUTC)$*.o
-+c_example:	$(LIBDMUMPS) $$@.c
-+	$(CC) -o $@ $(OPTC) $(INCS) -I. -I$(topdir)/include c_example.c $(LIBDMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
- 
- 
- $(libdir)/libsmumps$(PLAT)$(LIBEXT):
diff --git a/var/spack/repos/builtin/packages/mumps/mumps-5.1.1-spectrum-mpi-xl.patch b/var/spack/repos/builtin/packages/mumps/mumps-5.1.1-spectrum-mpi-xl.patch
deleted file mode 100644
index 8d9c1fb93a..0000000000
--- a/var/spack/repos/builtin/packages/mumps/mumps-5.1.1-spectrum-mpi-xl.patch
+++ /dev/null
@@ -1,79 +0,0 @@
-diff -Naur MUMPS_5.0.1/Makefile MUMPS_5.0.1-patched/MUMPS_5.0.1/Makefile
---- ./Makefile	2015-07-23 13:08:29.000000000 -0400
-+++ ./Makefile	2016-12-05 14:08:30.788638382 -0500
-@@ -62,7 +62,7 @@
- $(libdir)/libpord$(PLAT)$(LIBEXT):
- 	if [ "$(LPORDDIR)" != "" ] ; then \
- 	  cd $(LPORDDIR); \
--	  $(MAKE) CC="$(CC)" CFLAGS="$(OPTC)" AR="$(AR)" RANLIB="$(RANLIB)" OUTC="$(OUTC)" LIBEXT=$(LIBEXT); \
-+	  $(MAKE) CC="$(CC)" CFLAGS="$(OPTC)" SAR="$(SAR)" RANLIB="$(RANLIB)" OUTC="$(OUTC)" LIBEXT=$(LIBEXT); \
- 	fi;
- 	if [ "$(LPORDDIR)" != "" ] ; then \
- 	  cp $(LPORDDIR)/libpord$(LIBEXT) $@; \
-diff -Naur MUMPS_5.0.1/PORD/lib/Makefile MUMPS_5.0.1-patched/PORD/lib/MUMPS_5.0.1/Makefile
---- ./PORD/lib/Makefile	2015-07-23 13:08:29.000000000 -0400
-+++ ./PORD/lib/Makefile	2016-12-05 11:26:24.785317467 -0500
-@@ -25,7 +25,7 @@
- 	$(CC) $(COPTIONS) -c $*.c $(OUTC)$*.o
- 
- libpord$(LIBEXT):$(OBJS)
--	$(AR)$@ $(OBJS)
-+	$(SAR)$@ $(OBJS)
- 	$(RANLIB) $@
- 
- clean:
---- ./examples/Makefile	2017-06-07 15:40:49.366671322 -0400
-+++ ./examples/Makefile	2017-06-07 15:47:55.666685772 -0400
-@@ -26,40 +26,33 @@
- 
- LIBSMUMPS = $(libdir)/libsmumps$(PLAT)$(LIBEXT) $(LIBMUMPS_COMMON)
- 
--ssimpletest:  $(LIBSMUMPS)  $$@.o
--	$(FL) -o $@ $(OPTL) ssimpletest.o  $(LIBSMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
-+ssimpletest:  $(LIBSMUMPS)  $$@.F
-+	$(FC) -o $@ $(OPTF) $(INCS) -I. -I$(topdir)/include ssimpletest.F  $(LIBSMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
- 
- 
- LIBDMUMPS = $(libdir)/libdmumps$(PLAT)$(LIBEXT) $(LIBMUMPS_COMMON)
- 
--dsimpletest: $(LIBDMUMPS)  $$@.o 
--	$(FL) -o $@ $(OPTL) dsimpletest.o  $(LIBDMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
-+dsimpletest: $(LIBDMUMPS)  $$@.F
-+	$(FC) -o $@ $(OPTF) $(INCS) -I. -I$(topdir)/include dsimpletest.F  $(LIBDMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
- 
- 
- LIBCMUMPS = $(libdir)/libcmumps$(PLAT)$(LIBEXT) $(LIBMUMPS_COMMON)
- 
--csimpletest: $(LIBCMUMPS)  $$@.o
--	$(FL) -o $@ $(OPTL) csimpletest.o  $(LIBCMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
-+csimpletest: $(LIBCMUMPS)  $$@.F
-+	$(FC) -o $@ $(OPTF) $(INCS) -I. -I$(topdir)/include csimpletest.F  $(LIBCMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
- 
- 
- LIBZMUMPS = $(libdir)/libzmumps$(PLAT)$(LIBEXT) $(LIBMUMPS_COMMON)
- 
--zsimpletest: $(LIBZMUMPS)  $$@.o
--	$(FL) -o $@ $(OPTL) zsimpletest.o  $(LIBZMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
-+zsimpletest: $(LIBZMUMPS)  $$@.F
-+	$(FC) -o $@ $(OPTF) $(INCS) -I. -I$(topdir)/include zsimpletest.F  $(LIBZMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
- 
--c_example:	$(LIBDMUMPS) $$@.o
--	$(FL) -o $@ $(OPTL) $@.o $(LIBDMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
-+c_example:	$(LIBDMUMPS) $$@.c
-+	$(CC) -o $@ $(OPTC) $(INCS) -I. -I$(topdir)/include c_example.c $(LIBDMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
- 
- 
--multiple_arithmetics_example:	$(LIBSMUMPS) $(LIBDMUMPS) $(LIBCMUMPS) $(LIBZMUMPS) $$@.o
--	$(FL) -o $@ $(OPTL) $@.o $(LIBSMUMPS) $(LIBDMUMPS) $(LIBCMUMPS) $(LIBZMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
--
--
--.SUFFIXES: .c .F .o
--.F.o:
--	$(FC) $(OPTF) $(INCS) -I. -I$(topdir)/include -c $*.F $(OUTF)$*.o
--.c.o:
--	$(CC) $(OPTC) $(INCS) $(CDEFS) -I. -I$(topdir)/include -I$(topdir)/src -c $*.c $(OUTC)$*.o
-+multiple_arithmetics_example:	$(LIBSMUMPS) $(LIBDMUMPS) $(LIBCMUMPS) $(LIBZMUMPS) $$@.F
-+	$(FC) -o $@ $(OPTF) $(INCS) -I. -I$(topdir)/include multiple_arithmetics_example.F $(LIBSMUMPS) $(LIBDMUMPS) $(LIBCMUMPS) $(LIBZMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
- 
- 
- $(libdir)/libsmumps$(PLAT)$(LIBEXT):
diff --git a/var/spack/repos/builtin/packages/mumps/package.py b/var/spack/repos/builtin/packages/mumps/package.py
index cf3c4bbd1e..5ddd6606b4 100644
--- a/var/spack/repos/builtin/packages/mumps/package.py
+++ b/var/spack/repos/builtin/packages/mumps/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 import sys
@@ -69,10 +50,7 @@ class Mumps(Package):
     depends_on('scalapack', when='+mpi')
     depends_on('mpi', when='+mpi')
 
-    patch('mumps-5.0.2-spectrum-mpi-xl.patch', when='@5.0.2%xl^spectrum-mpi')
-    patch('mumps-5.0.2-spectrum-mpi-xl.patch', when='@5.0.2%xl_r^spectrum-mpi')
-    patch('mumps-5.1.1-spectrum-mpi-xl.patch', when='@5.1.1%xl^spectrum-mpi')
-    patch('mumps-5.1.1-spectrum-mpi-xl.patch', when='@5.1.1%xl_r^spectrum-mpi')
+    patch('examples.patch', when='@5.1.1%clang^spectrum-mpi')
 
     # this function is not a patch function because in case scalapack
     # is needed it uses self.spec['scalapack'].fc_link set by the
@@ -85,16 +63,26 @@ class Mumps(Package):
             raise RuntimeError(
                 'You cannot use the variants parmetis or ptscotch without mpi')
 
-        lapack_blas = (self.spec['lapack'].libs +
-                       self.spec['blas'].libs)
-        makefile_conf = ["LIBBLAS = %s" % lapack_blas.ld_flags]
+        # The makefile variables LIBBLAS, LSCOTCH, LMETIS, and SCALAP are only
+        # used to link the examples, so if building '+shared' there is no need
+        # to explicitly link with the respective libraries because we make sure
+        # the mumps shared libraries are already linked with them. See also the
+        # comment below about 'inject_libs'. This behaviour may cause problems
+        # if building '+shared' and the used libraries were build static
+        # without the PIC option.
+        shared = '+shared' in self.spec
+
+        lapack_blas = (self.spec['lapack'].libs + self.spec['blas'].libs)
+        makefile_conf = ["LIBBLAS = %s" %
+                         lapack_blas.ld_flags if not shared else '']
 
         orderings = ['-Dpord']
 
         if '+ptscotch' in self.spec or '+scotch' in self.spec:
             makefile_conf.extend([
                 "ISCOTCH = -I%s" % self.spec['scotch'].prefix.include,
-                "LSCOTCH = {0}".format(self.spec['scotch'].libs.ld_flags)
+                "LSCOTCH = {0}".format(
+                    self.spec['scotch'].libs.ld_flags if not shared else '')
             ])
 
             orderings.append('-Dscotch')
@@ -104,22 +92,37 @@ class Mumps(Package):
         if '+parmetis' in self.spec and '+metis' in self.spec:
             makefile_conf.extend([
                 "IMETIS = -I%s" % self.spec['parmetis'].prefix.include,
-                "LMETIS = -L%s -l%s -L%s -l%s" % (
+                ("LMETIS = -L%s -l%s -L%s -l%s" % (
                     self.spec['parmetis'].prefix.lib, 'parmetis',
-                    self.spec['metis'].prefix.lib, 'metis')
+                    self.spec['metis'].prefix.lib, 'metis')) if not shared
+                else 'LMETIS ='
             ])
 
             orderings.append('-Dparmetis')
         elif '+metis' in self.spec:
             makefile_conf.extend([
                 "IMETIS = -I%s" % self.spec['metis'].prefix.include,
-                "LMETIS = -L%s -l%s" % (self.spec['metis'].prefix.lib, 'metis')
+                ("LMETIS = -L%s -l%s" % (
+                    self.spec['metis'].prefix.lib, 'metis')) if not shared
+                else 'LMETIS ='
             ])
 
             orderings.append('-Dmetis')
 
         makefile_conf.append("ORDERINGSF = %s" % (' '.join(orderings)))
 
+        # Determine which compiler suite we are using
+        using_gcc = self.compiler.name == "gcc"
+        using_pgi = self.compiler.name == "pgi"
+        using_intel = self.compiler.name == "intel"
+        using_xl = self.compiler.name in ['xl', 'xl_r']
+
+        # The llvm compiler suite does not contain a Fortran compiler by
+        # default.  Its possible that a Spack user may have configured
+        # ~/.spack/<platform>/compilers.yaml for using xlf.
+        using_xlf = using_xl or \
+            (spack_f77.endswith('xlf') or spack_f77.endswith('xlf_r'))
+
         # when building shared libs need -fPIC, otherwise
         # /usr/bin/ld: graph.o: relocation R_X86_64_32 against `.rodata.str1.1'
         # can not be used when making a shared object; recompile with -fPIC
@@ -127,45 +130,47 @@ class Mumps(Package):
         # TODO: test this part, it needs a full blas, scalapack and
         # partitionning environment with 64bit integers
 
+        opt_level = '3' if using_xl else ''
+
         if '+int64' in self.spec:
-            if self.compiler.name == "xl" or self.compiler.name == "xl_r":
-                makefile_conf.extend(
-                    ['OPTF    = -O3',
-                     'OPTL    = %s -O3' % fpic,
-                     'OPTC    = %s -O3-DINTSIZE64' % fpic])
+            if using_xlf:
+                makefile_conf.append('OPTF = -O%s' % opt_level)
             else:
-                makefile_conf.extend(
-                    # the fortran compilation flags most probably are
-                    # working only for intel and gnu compilers this is
-                    # perhaps something the compiler should provide
-                    ['OPTF    = %s -O  -DALLOW_NON_INIT %s' % (fpic, '-fdefault-integer-8' if self.compiler.name == "gcc" else '-i8'),  # noqa
-                     'OPTL    = %s -O ' % fpic,
-                     'OPTC    = %s -O -DINTSIZE64' % fpic])
+                # the fortran compilation flags most probably are
+                # working only for intel and gnu compilers this is
+                # perhaps something the compiler should provide
+                makefile_conf.extend([
+                    'OPTF = %s -O  -DALLOW_NON_INIT %s' % (
+                        fpic,
+                        '-fdefault-integer-8' if using_gcc
+                                              else '-i8'),  # noqa
+                ])
+
+            makefile_conf.extend([
+                'OPTL = %s -O%s' % (fpic, opt_level),
+                'OPTC = %s -O%s -DINTSIZE64' % (fpic, opt_level)
+            ])
         else:
-            if self.compiler.name == "xl" or self.compiler.name == "xl_r":
-                makefile_conf.extend(
-                    ['OPTF    = -O3 -qfixed',
-                     'OPTL    = %s -O3' % fpic,
-                     'OPTC    = %s -O3' % fpic])
+            if using_xlf:
+                makefile_conf.append('OPTF = -O%s -qfixed' % opt_level)
             else:
-                makefile_conf.extend(
-                    ['OPTF    = %s -O  -DALLOW_NON_INIT' % fpic,
-                     'OPTL    = %s -O ' % fpic,
-                     'OPTC    = %s -O ' % fpic])
+                makefile_conf.append('OPTF = %s -O%s -DALLOW_NON_INIT' % (
+                    fpic, opt_level))
+
+            makefile_conf.extend([
+                'OPTL = %s -O%s' % (fpic, opt_level),
+                'OPTC = %s -O%s' % (fpic, opt_level)
+            ])
 
         if '+mpi' in self.spec:
-            scalapack = self.spec['scalapack'].libs
+            scalapack = self.spec['scalapack'].libs if not shared \
+                else LibraryList([])
             makefile_conf.extend(
                 ['CC = {0}'.format(self.spec['mpi'].mpicc),
                  'FC = {0}'.format(self.spec['mpi'].mpifc),
+                 'FL = {0}'.format(self.spec['mpi'].mpifc),
                  "SCALAP = %s" % scalapack.ld_flags,
                  "MUMPS_TYPE = par"])
-            if (self.spec.satisfies('%xl_r' or '%xl')) and self.spec.satisfies('^spectrum-mpi'):  # noqa
-                makefile_conf.extend(
-                    ['FL = {0}'.format(self.spec['mpi'].mpicc)])
-            else:
-                makefile_conf.extend(
-                    ['FL = {0}'.format(self.spec['mpi'].mpifc)])
         else:
             makefile_conf.extend(
                 ["CC = cc",
@@ -175,35 +180,64 @@ class Mumps(Package):
 
         # TODO: change the value to the correct one according to the
         # compiler possible values are -DAdd_, -DAdd__ and/or -DUPPER
-        if self.compiler.name == 'intel' or self.compiler.name == 'pgi':
+        if using_intel or using_pgi:
             # Intel & PGI Fortran compiler provides the main() function so
             # C examples linked with the Fortran compiler require a
             # hack defined by _DMAIN_COMP (see examples/c_example.c)
             makefile_conf.append("CDEFS   = -DAdd_ -DMAIN_COMP")
         else:
-            if self.compiler.name != "xl" and self.compiler.name != "xl_r":
-                makefile_conf.append("CDEFS   = -DAdd_")
+            if not using_xlf:
+                makefile_conf.append("CDEFS = -DAdd_")
 
         if '+shared' in self.spec:
+            # All Mumps libraries will be linked with 'inject_libs'.
+            inject_libs = []
+            if '+mpi' in self.spec:
+                inject_libs += [self.spec['scalapack'].libs.ld_flags]
+            if '+ptscotch' in self.spec or '+scotch' in self.spec:
+                inject_libs += [self.spec['scotch'].libs.ld_flags]
+            if '+parmetis' in self.spec and '+metis' in self.spec:
+                inject_libs += [
+                    "-L%s -l%s -L%s -l%s" % (
+                        self.spec['parmetis'].prefix.lib, 'parmetis',
+                        self.spec['metis'].prefix.lib, 'metis')]
+            elif '+metis' in self.spec:
+                inject_libs += [
+                    "-L%s -l%s" % (self.spec['metis'].prefix.lib, 'metis')]
+            inject_libs += [lapack_blas.ld_flags]
+            inject_libs = ' '.join(inject_libs)
+
             if sys.platform == 'darwin':
                 # Building dylibs with mpif90 causes segfaults on 10.8 and
                 # 10.10. Use gfortran. (Homebrew)
                 makefile_conf.extend([
                     'LIBEXT=.dylib',
-                    'AR=%s -dynamiclib -Wl,-install_name -Wl,%s/$(notdir $@) -undefined dynamic_lookup -o ' % (os.environ['FC'], prefix.lib),  # noqa
+                    'AR=%s -dynamiclib -Wl,-install_name -Wl,%s/$(notdir $@)'
+                    ' -undefined dynamic_lookup %s -o ' %
+                    (os.environ['FC'], prefix.lib, inject_libs),
                     'RANLIB=echo'
                 ])
             else:
+                if using_xlf:
+                    build_shared_flag = "qmkshrobj"
+                else:
+                    build_shared_flag = "shared"
+
                 makefile_conf.extend([
                     'LIBEXT=.so',
-                    'AR=$(FL) -shared -Wl,-soname -Wl,%s/$(notdir $@) -o' % prefix.lib,  # noqa
-                    'RANLIB=echo'
+                    'AR=link_cmd() { $(FL) -%s -Wl,-soname '
+                    '-Wl,%s/$(notdir $@) -o "$$@" %s; }; link_cmd ' %
+                    (build_shared_flag, prefix.lib, inject_libs),
+                    'RANLIB=ls'
                 ])
+                # When building libpord, read AR from Makefile.inc instead of
+                # going through the make command line - this prevents various
+                # problems with the substring "$$@".
+                filter_file(' AR="\$\(AR\)"', '', 'Makefile')
+                filter_file('^(INCLUDES = -I../include)',
+                            '\\1\ninclude ../../Makefile.inc',
+                            join_path('PORD', 'lib', 'Makefile'))
 
-                if self.compiler.name == 'xl' or self.compiler.name == 'xl_r':
-                    makefile_conf.extend([
-                        'SAR=/bin/xlc -shared -Wl,-soname -Wl,%s/$(notdir $@) -o' % prefix.lib  # noqa
-                    ])
         else:
             makefile_conf.extend([
                 'LIBEXT  = .a',
@@ -222,24 +256,17 @@ class Mumps(Package):
                 fh.write(makefile_inc)
 
     def install(self, spec, prefix):
-        make_libs = []
-
-        # the choice to compile ?examples is to have kind of a sanity
-        # check on the libraries generated.
-        if '+float' in spec:
-            make_libs.append('sexamples')
-            if '+complex' in spec:
-                make_libs.append('cexamples')
-
-        if '+double' in spec:
-            make_libs.append('dexamples')
-            if '+complex' in spec:
-                make_libs.append('zexamples')
-
         self.write_makefile_inc()
 
         # Build fails in parallel
-        make(*make_libs, parallel=False)
+        # That is why we split the builds of 's', 'c', 'd', and/or 'z' which
+        # can be build one after the other, each using a parallel build.
+        letters_variants = [
+            ['s', '+float'], ['c', '+complex+float'],
+            ['d', '+double'], ['z', '+complex+double']]
+        for l, v in letters_variants:
+            if v in spec:
+                make(l + 'examples')
 
         install_tree('lib', prefix.lib)
         install_tree('include', prefix.include)
@@ -253,12 +280,28 @@ class Mumps(Package):
 
         # FIXME: extend the tests to mpirun -np 2 when build with MPI
         # FIXME: use something like numdiff to compare output files
-        with working_dir('examples'):
-            if '+float' in spec:
-                os.system('./ssimpletest < input_simpletest_real')
-                if '+complex' in spec:
-                    os.system('./csimpletest < input_simpletest_real')
-            if '+double' in spec:
-                os.system('./dsimpletest < input_simpletest_real')
-                if '+complex' in spec:
-                    os.system('./zsimpletest < input_simpletest_cmplx')
+        # Note: In some cases, when 'mpi' is enabled, the examples below cannot
+        # be run without 'mpirun', so we enabled the tests only if explicitly
+        # requested with the Spack '--test' option.
+        if self.run_tests:
+            with working_dir('examples'):
+                if '+float' in spec:
+                    ssimpletest = Executable('./ssimpletest')
+                    ssimpletest(input='input_simpletest_real')
+                    if '+complex' in spec:
+                        csimpletest = Executable('./csimpletest')
+                        csimpletest(input='input_simpletest_cmplx')
+                if '+double' in spec:
+                    dsimpletest = Executable('./dsimpletest')
+                    dsimpletest(input='input_simpletest_real')
+                    if '+complex' in spec:
+                        zsimpletest = Executable('./zsimpletest')
+                        zsimpletest(input='input_simpletest_cmplx')
+
+    @property
+    def libs(self):
+        component_libs = ['*mumps*', 'pord']
+        return find_libraries(['lib' + comp for comp in component_libs],
+                              root=self.prefix.lib,
+                              shared=('+shared' in self.spec),
+                              recursive=False) or None
diff --git a/var/spack/repos/builtin/packages/munge/package.py b/var/spack/repos/builtin/packages/munge/package.py
index f53fa5953e..cca523acb0 100644
--- a/var/spack/repos/builtin/packages/munge/package.py
+++ b/var/spack/repos/builtin/packages/munge/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
diff --git a/var/spack/repos/builtin/packages/muparser/auto_ptr.patch b/var/spack/repos/builtin/packages/muparser/auto_ptr.patch
new file mode 100644
index 0000000000..7e39ea603f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/muparser/auto_ptr.patch
@@ -0,0 +1,52 @@
+diff --git a/include/muParserBase.h b/include/muParserBase.h
+index beb15bb..685f59f 100644
+--- a/include/muParserBase.h
++++ b/include/muParserBase.h
+@@ -288,7 +288,7 @@ private:
+     mutable stringbuf_type  m_vStringBuf; ///< String buffer, used for storing string function arguments

+     stringbuf_type  m_vStringVarBuf;

+ 

+-    std::auto_ptr<token_reader_type> m_pTokenReader; ///< Managed pointer to the token reader object.

++    std::unique_ptr<token_reader_type> m_pTokenReader; ///< Managed pointer to the token reader object.

+ 

+     funmap_type  m_FunDef;         ///< Map of function names and pointers.

+     funmap_type  m_PostOprtDef;    ///< Postfix operator callbacks

+diff --git a/include/muParserToken.h b/include/muParserToken.h
+index fc91d78..0cca469 100644
+--- a/include/muParserToken.h
++++ b/include/muParserToken.h
+@@ -69,7 +69,7 @@ namespace mu
+       TString m_strTok;   ///< Token string

+       TString m_strVal;   ///< Value for string variables

+       value_type m_fVal;  ///< the value 

+-      std::auto_ptr<ParserCallback> m_pCallback;

++      std::unique_ptr<ParserCallback> m_pCallback;

+ 

+   public:

+ 

+diff --git a/src/muParserTest.cpp b/src/muParserTest.cpp
+index 4006b27..8feaa2c 100644
+--- a/src/muParserTest.cpp
++++ b/src/muParserTest.cpp
+@@ -1258,7 +1258,7 @@ namespace mu
+ 

+       try

+       {

+-        std::auto_ptr<Parser> p1;

++        std::unique_ptr<Parser> p1;

+         Parser  p2, p3;   // three parser objects

+                           // they will be used for testing copy and assignment operators

+         // p1 is a pointer since i'm going to delete it in order to test if

+diff --git a/src/muParserTokenReader.cpp b/src/muParserTokenReader.cpp
+index 8da1e40..49cee68 100644
+--- a/src/muParserTokenReader.cpp
++++ b/src/muParserTokenReader.cpp
+@@ -147,7 +147,7 @@ namespace mu
+   */

+   ParserTokenReader* ParserTokenReader::Clone(ParserBase *a_pParent) const

+   {

+-    std::auto_ptr<ParserTokenReader> ptr(new ParserTokenReader(*this));

++    std::unique_ptr<ParserTokenReader> ptr(new ParserTokenReader(*this));

+     ptr->SetParent(a_pParent);

+     return ptr.release();

+   }

diff --git a/var/spack/repos/builtin/packages/muparser/package.py b/var/spack/repos/builtin/packages/muparser/package.py
index 8c65207dc5..fe16e5617e 100644
--- a/var/spack/repos/builtin/packages/muparser/package.py
+++ b/var/spack/repos/builtin/packages/muparser/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,11 +11,40 @@ class Muparser(Package):
     homepage = "http://muparser.beltoforion.de/"
     url      = "https://github.com/beltoforion/muparser/archive/v2.2.5.tar.gz"
 
+    version('2.2.6.1', '410d29b4c58d1cdc2fc9ed1c1c7f67fe')
+    # 2.2.6 presents itself as 2.2.5, don't add it to Spack
+    # version('2.2.6', 'f197b2815ca0422b2091788a78f2dc8a')
     version('2.2.5', '02dae671aa5ad955fdcbcd3fee313fb7')
 
+    # Replace std::auto_ptr by std::unique_ptr
+    # https://github.com/beltoforion/muparser/pull/46
+    patch('auto_ptr.patch',
+          when='@2.2.5')
+
+    depends_on('cmake@3.1.0:', when='@2.2.6:', type='build')
+
+    # Cmake build since 2.2.6
+    @when('@2.2.6:')
+    def install(self, spec, prefix):
+        cmake_args = [
+            '-DENABLE_SAMPLES=OFF',
+            '-DENABLE_OPENMP=OFF',
+            '-DBUILD_SHARED_LIBS=ON'
+        ]
+
+        cmake_args.extend(std_cmake_args)
+
+        with working_dir('spack-build', create=True):
+            cmake('..', *cmake_args)
+            make()
+            make('install')
+
+    @when('@2.2.5')
     def install(self, spec, prefix):
         options = ['--disable-debug',
+                   '--disable-samples',
                    '--disable-dependency-tracking',
+                   'CXXFLAGS={0}'.format(self.compiler.cxx11_flag),
                    '--prefix=%s' % prefix]
 
         configure(*options)
diff --git a/var/spack/repos/builtin/packages/muscle/package.py b/var/spack/repos/builtin/packages/muscle/package.py
index 7ba57284c6..71c835613f 100644
--- a/var/spack/repos/builtin/packages/muscle/package.py
+++ b/var/spack/repos/builtin/packages/muscle/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/muse/package.py b/var/spack/repos/builtin/packages/muse/package.py
index 3c3616854e..89a3402e9f 100644
--- a/var/spack/repos/builtin/packages/muse/package.py
+++ b/var/spack/repos/builtin/packages/muse/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/muster/package.py b/var/spack/repos/builtin/packages/muster/package.py
index d926c90d8e..88a7d06560 100644
--- a/var/spack/repos/builtin/packages/muster/package.py
+++ b/var/spack/repos/builtin/packages/muster/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/mvapich2/ad_lustre_rwcontig_open_source.patch b/var/spack/repos/builtin/packages/mvapich2/ad_lustre_rwcontig_open_source.patch
deleted file mode 100644
index ff85845cf8..0000000000
--- a/var/spack/repos/builtin/packages/mvapich2/ad_lustre_rwcontig_open_source.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/src/mpi/romio/adio/ad_lustre/ad_lustre_rwcontig.c	2013-12-10 12:05:44.806417000 -0800
-+++ b/src/mpi/romio/adio/ad_lustre/ad_lustre_rwcontig.c	2013-12-10 11:53:03.295622000 -0800
-@@ -8,7 +8,7 @@
-  *   Copyright (C) 2008 Sun Microsystems, Lustre group
-  */
- 
--#define _XOPEN_SOURCE 600
-+//#define _XOPEN_SOURCE 600
- #include <stdlib.h>
- #include <malloc.h>
- #include "ad_lustre.h"
diff --git a/var/spack/repos/builtin/packages/mvapich2/package.py b/var/spack/repos/builtin/packages/mvapich2/package.py
index 4454907b74..44b064d256 100644
--- a/var/spack/repos/builtin/packages/mvapich2/package.py
+++ b/var/spack/repos/builtin/packages/mvapich2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import sys
 
 from spack import *
@@ -41,20 +22,18 @@ class Mvapich2(AutotoolsPackage):
     url = "http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.2.tar.gz"
     list_url = "http://mvapich.cse.ohio-state.edu/downloads/"
 
-    # Newer alpha release
+    version('2.3rc2', '6fcf22fe2a16023b462ef57614daa357')
+    version('2.3rc1', '386d79ae36b2136d203826465ad8b6cc')
     version('2.3a', '87c3fbf8a755b53806fa9ecb21453445')
 
     # Prefer the latest stable release
-    version('2.2', '939b65ebe5b89a5bc822cdab0f31f96e', preferred=True)
+    version('2.3', sha256='01d5fb592454ddd9ecc17e91c8983b6aea0e7559aa38f410b111c8ef385b50dd', preferred=True)
+    version('2.2', '939b65ebe5b89a5bc822cdab0f31f96e')
     version('2.1', '0095ceecb19bbb7fb262131cb9c2cdd6')
     version('2.0', '9fbb68a4111a8b6338e476dc657388b4')
-    version('1.9', '5dc58ed08fd3142c260b70fe297e127c')
-
-    patch('ad_lustre_rwcontig_open_source.patch', when='@1.9')
 
     provides('mpi')
-    provides('mpi@:2.2', when='@1.9')  # MVAPICH2-1.9 supports MPI 2.2
-    provides('mpi@:3.0', when='@2.0:')  # MVAPICH2-2.0 supports MPI 3.0
+    provides('mpi@:3.0')
 
     variant('debug', default=False,
             description='Enable debug info and error messages at run-time')
@@ -62,6 +41,9 @@ class Mvapich2(AutotoolsPackage):
     variant('cuda', default=False,
             description='Enable CUDA extension')
 
+    variant('regcache', default=True,
+            description='Enable memory registration cache')
+
     # Accepted values are:
     #   single      - No threads (MPI_THREAD_SINGLE)
     #   funneled    - Only the main thread calls MPI (MPI_THREAD_FUNNELED)
@@ -103,16 +85,44 @@ class Mvapich2(AutotoolsPackage):
         )
     )
 
+    variant(
+        'alloca',
+        default=False,
+        description='Use alloca to allocate temporary memory if available'
+    )
+
+    variant(
+        'file_systems',
+        description='List of the ROMIO file systems to activate',
+        values=('lustre', 'gpfs', 'nfs', 'ufs'),
+        multi=True
+    )
+
+    depends_on('findutils', type='build')
     depends_on('bison', type='build')
     depends_on('libpciaccess', when=(sys.platform != 'darwin'))
     depends_on('cuda', when='+cuda')
+    depends_on('psm', when='fabrics=psm')
+    depends_on('rdma-core', when='fabrics=mrail')
+    depends_on('rdma-core', when='fabrics=nemesisib')
+    depends_on('rdma-core', when='fabrics=nemesistcpib')
+    depends_on('rdma-core', when='fabrics=nemesisibtcp')
+
+    filter_compiler_wrappers(
+        'mpicc', 'mpicxx', 'mpif77', 'mpif90', 'mpifort', relative_root='bin'
+    )
 
-    def url_for_version(self, version):
-        base_url = "http://mvapich.cse.ohio-state.edu/download"
-        if version < Version('2.0'):
-            return "%s/mvapich2/mv2/mvapich2-%s.tar.gz" % (base_url, version)
-        else:
-            return "%s/mvapich/mv2/mvapich2-%s.tar.gz"  % (base_url, version)
+    @property
+    def libs(self):
+        query_parameters = self.spec.last_query.extra_parameters
+        libraries = ['libmpi']
+
+        if 'cxx' in query_parameters:
+            libraries = ['libmpicxx'] + libraries
+
+        return find_libraries(
+            libraries, root=self.prefix, shared=True, recursive=True
+        )
 
     @property
     def process_manager_options(self):
@@ -122,20 +132,17 @@ class Mvapich2(AutotoolsPackage):
         for x in ('hydra', 'gforker', 'remshell'):
             if 'process_managers={0}'.format(x) in spec:
                 other_pms.append(x)
-        opts = ['--with-pm=%s' % ':'.join(other_pms)]
+
+        opts = []
+        if len(other_pms) > 0:
+            opts = ['--with-pm=%s' % ':'.join(other_pms)]
 
         # See: http://slurm.schedmd.com/mpi_guide.html#mvapich2
         if 'process_managers=slurm' in spec:
-            if self.version > Version('2.0'):
-                opts = [
-                    '--with-pmi=pmi2',
-                    '--with-pm=slurm'
-                ]
-            else:
-                opts = [
-                    '--with-pmi=slurm',
-                    '--with-pm=no'
-                ]
+            opts = [
+                '--with-pmi=pmi2',
+                '--with-pm=slurm'
+            ]
 
         return opts
 
@@ -144,7 +151,10 @@ class Mvapich2(AutotoolsPackage):
         opts = []
         # From here on I can suppose that only one variant has been selected
         if 'fabrics=psm' in self.spec:
-            opts = ["--with-device=ch3:psm"]
+            opts = [
+                "--with-device=ch3:psm",
+                "--with-psm={0}".format(self.spec['psm'].prefix)
+            ]
         elif 'fabrics=sock' in self.spec:
             opts = ["--with-device=ch3:sock"]
         elif 'fabrics=nemesistcpib' in self.spec:
@@ -156,12 +166,31 @@ class Mvapich2(AutotoolsPackage):
         elif 'fabrics=nemesis' in self.spec:
             opts = ["--with-device=ch3:nemesis"]
         elif 'fabrics=mrail' in self.spec:
-            opts = ["--with-device=ch3:mrail", "--with-rdma=gen2"]
+            opts = ["--with-device=ch3:mrail", "--with-rdma=gen2",
+                    "--disable-mcast"]
+        return opts
+
+    @property
+    def file_system_options(self):
+        spec = self.spec
+
+        fs = []
+        for x in ('lustre', 'gpfs', 'nfs', 'ufs'):
+            if 'file_systems={0}'.format(x) in spec:
+                fs.append(x)
+
+        opts = []
+        if len(fs) > 0:
+            opts.append('--with-file-system=%s' % '+'.join(fs))
+
         return opts
 
     def setup_environment(self, spack_env, run_env):
         spec = self.spec
-        if 'process_managers=slurm' in spec and spec.satisfies('@2.0:'):
+        # mvapich2 configure fails when F90 and F90FLAGS are set
+        spack_env.unset('F90')
+        spack_env.unset('F90FLAGS')
+        if 'process_managers=slurm' in spec:
             run_env.set('SLURM_MPI_TYPE', 'pmi2')
 
     def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
@@ -201,13 +230,16 @@ class Mvapich2(AutotoolsPackage):
         args = [
             '--enable-shared',
             '--enable-romio',
-            '-disable-silent-rules',
+            '--disable-silent-rules',
+            '--disable-new-dtags',
             '--enable-fortran=all',
             "--enable-threads={0}".format(spec.variants['threads'].value),
             "--with-ch3-rank-bits={0}".format(
                 spec.variants['ch3_rank_bits'].value),
         ]
 
+        args.extend(self.enable_or_disable('alloca'))
+
         if '+debug' in self.spec:
             args.extend([
                 '--disable-fast',
@@ -228,36 +260,12 @@ class Mvapich2(AutotoolsPackage):
         else:
             args.append('--disable-cuda')
 
+        if '+regcache' in self.spec:
+            args.append('--enable-registration-cache')
+        else:
+            args.append('--disable-registration-cache')
+
         args.extend(self.process_manager_options)
         args.extend(self.network_options)
+        args.extend(self.file_system_options)
         return args
-
-    @run_after('install')
-    def filter_compilers(self):
-        """Run after install to make the MPI compilers use the
-           compilers that Spack built the package with.
-
-           If this isn't done, they'll have CC, CXX, F77, and FC set
-           to Spack's generic cc, c++, f77, and f90.  We want them to
-           be bound to whatever compiler they were built with.
-        """
-        bin = self.prefix.bin
-        mpicc = join_path(bin, 'mpicc')
-        mpicxx = join_path(bin, 'mpicxx')
-        mpif77 = join_path(bin, 'mpif77')
-        mpif90 = join_path(bin, 'mpif90')
-        mpifort = join_path(bin, 'mpifort')
-
-        # Substitute Spack compile wrappers for the real
-        # underlying compiler
-        kwargs = {'ignore_absent': True, 'backup': False, 'string': True}
-        filter_file(env['CC'], self.compiler.cc, mpicc, **kwargs)
-        filter_file(env['CXX'], self.compiler.cxx, mpicxx, **kwargs)
-        filter_file(env['F77'], self.compiler.f77, mpif77, **kwargs)
-        filter_file(env['FC'], self.compiler.fc, mpif90, **kwargs)
-        filter_file(env['FC'], self.compiler.fc, mpifort, **kwargs)
-
-        # Remove this linking flag if present
-        # (it turns RPATH into RUNPATH)
-        for wrapper in (mpicc, mpicxx, mpif77, mpif90, mpifort):
-            filter_file('-Wl,--enable-new-dtags', '', wrapper, **kwargs)
diff --git a/var/spack/repos/builtin/packages/mxml/package.py b/var/spack/repos/builtin/packages/mxml/package.py
index c1e0a8f968..05a27c20e3 100644
--- a/var/spack/repos/builtin/packages/mxml/package.py
+++ b/var/spack/repos/builtin/packages/mxml/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/mxnet/package.py b/var/spack/repos/builtin/packages/mxnet/package.py
index 00443ec633..cc1e5861ba 100644
--- a/var/spack/repos/builtin/packages/mxnet/package.py
+++ b/var/spack/repos/builtin/packages/mxnet/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,6 +13,8 @@ class Mxnet(MakefilePackage):
     homepage = "http://mxnet.io"
     url      = "https://github.com/apache/incubator-mxnet/archive/0.10.0.post2.tar.gz"
 
+    version('1.3.0', 'c00d6fbb2947144ce36c835308e603f002c1eb90a9f4c5a62f4d398154eed4d2',
+            url='https://github.com/apache/incubator-mxnet/releases/download/1.3.0/apache-mxnet-src-1.3.0-incubating.tar.gz')
     version('0.10.0.post2',  '7819d511cf4a6efad681e6662fa966e4',
             url="https://github.com/apache/incubator-mxnet/archive/0.10.0.post2.tar.gz")
     version('0.10.0.post1',  '16d540f407cd22285555b3ab22040032',
@@ -43,6 +26,7 @@ class Mxnet(MakefilePackage):
     variant('opencv', default=True, description='Enable OpenCV support')
     variant('openmp', default=False, description='Enable OpenMP support')
     variant('profiler', default=False, description='Enable Profiler (for verification and debug only).')
+    variant('python', default=True, description='Install python bindings')
 
     depends_on('dmlc-core@20170508')
     depends_on('dmlc-core+openmp', when='+openmp')
@@ -50,29 +34,45 @@ class Mxnet(MakefilePackage):
     depends_on('mshadow@20170721')
     depends_on('ps-lite@20170328')
     depends_on('nnvm~shared@20170418')
-    depends_on('openblas')
+    depends_on('blas')
     depends_on('cudnn', when='+cuda')
     depends_on('cudnn', when='+cuda')
     depends_on('cub', when='+cuda')
     depends_on('opencv+core+imgproc+highgui+jpeg+png+tiff~eigen~ipp@3.0:', when='+opencv')
 
+    # python extensions
+    depends_on('python@2.7:', type=('build', 'run'), when='+python')
+    depends_on('py-setuptools', type='build', when='+python')
+    extends('python', when='+python')
+
     patch('makefile.patch', when='@0.10:0.11')
 
     def build(self, spec, prefix):
-        filter_file('export CC = gcc', '', 'make/config.mk', string=True)
-        filter_file('export CXX = g++', '', 'make/config.mk', string=True)
+        # copy template configuration file
+        copy('make/config.mk', 'config.mk')
+
+        # remove compiler overrides
+        filter_file('export CC = gcc', '', 'config.mk', string=True)
+        filter_file('export CXX = g++', '', 'config.mk', string=True)
+
+        # add blas prefix to include paths
+        filter_file(
+            '-I$(NNVM_PATH)/include',
+            '-I$(NNVM_PATH)/include -I%s/include' % spec['blas'].prefix,
+            'Makefile', string=True
+        )
+
+        # mxnet comes with its own version of nnvm and dmlc.
+        # building it will fail if we use the spack paths
 
         args = [
             'CC=%s' % self.compiler.cc,
             'CXX=%s' % self.compiler.cxx,
-            'DMLC_CORE=%s' % spec['dmlc-core'].prefix,
             'MSHADOW_PATH=%s' % spec['mshadow'].prefix,
             'PS_PATH=%s' % spec['ps-lite'].prefix,
-            'NNVM_PATH=%s' % spec['nnvm'].prefix,
             'USE_OPENMP=%s' % ('1' if '+openmp' in spec else '0'),
             'USE_CUDA=%s' % ('1' if '+cuda' in spec else '0'),
             'USE_CUDNN=%s' % ('1' if '+cuda' in spec else '0'),
-            'CUB_INCLUDE=%s' % spec['cub'].prefix.include,
             'USE_OPENCV=%s' % ('1' if '+opencv' in spec else '0'),
             'USE_PROFILER=%s' % ('1' if '+profiler' in spec else '0'),
         ]
@@ -86,16 +86,27 @@ class Mxnet(MakefilePackage):
                         '-lopencv_core -lopencv_imgproc -lopencv_imgcodecs',
                         'Makefile', string=True)
 
-        # TODO: Add more BLAS support
-        args.append('USE_BLAS=openblas')
+        if 'openblas' in spec:
+            args.extend(['USE_BLAS=openblas'])
+        elif 'atlas' in spec or 'cblas' in spec:
+            args.extend(['USE_BLAS=atlas'])
+        else:
+            args.extend(['USE_BLAS=blas'])
 
         if '+cuda' in spec:
             args.extend(['USE_CUDA_PATH=%s' % spec['cuda'].prefix,
-                         'CUDNN_PATH=%s' % spec['cudnn'].prefix])
+                         'CUDNN_PATH=%s' % spec['cudnn'].prefix,
+                         'CUB_INCLUDE=%s' % spec['cub'].prefix.include])
 
         make(*args)
 
     def install(self, spec, prefix):
+        # mxnet is just a shared library -- no need to install a bin tree
+
         install_tree('include', prefix.include)
         install_tree('lib', prefix.lib)
-        install_tree('bin', prefix.bin)
+
+        # install python bindings
+        if '+python' in spec:
+            python = which('python')
+            python('python/setup.py', 'install', '--prefix={0}'.format(prefix))
diff --git a/var/spack/repos/builtin/packages/nag/package.py b/var/spack/repos/builtin/packages/nag/package.py
index 226cd90353..8c72d36a40 100644
--- a/var/spack/repos/builtin/packages/nag/package.py
+++ b/var/spack/repos/builtin/packages/nag/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
@@ -30,7 +11,8 @@ class Nag(Package):
     """The NAG Fortran Compiler."""
     homepage = "http://www.nag.com/nagware/np.asp"
 
-    version('6.1', '0040d2254258223c78a6a4ab4829d7e0')
+    version('6.2', '8b119cc3296969bbd68b781f625de272')
+    version('6.1', '9b3cc0f8703c79f6231ae12359535119')
     version('6.0', '3fa1e7f7b51ef8a23e6c687cdcad9f96')
 
     # Licensing
diff --git a/var/spack/repos/builtin/packages/nalu-wind/package.py b/var/spack/repos/builtin/packages/nalu-wind/package.py
new file mode 100644
index 0000000000..0b3414ad85
--- /dev/null
+++ b/var/spack/repos/builtin/packages/nalu-wind/package.py
@@ -0,0 +1,84 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import sys
+
+
+class NaluWind(CMakePackage):
+    """Nalu-Wind: Wind energy focused variant of Nalu."""
+
+    homepage = "https://github.com/exawind/nalu-wind"
+    git      = "https://github.com/exawind/nalu-wind.git"
+
+    maintainers = ['jrood-nrel']
+
+    tags = ['ecp', 'ecp-apps']
+
+    version('master', branch='master')
+
+    variant('openfast', default=False,
+            description='Compile with OpenFAST support')
+    variant('tioga', default=False,
+            description='Compile with Tioga support')
+    variant('hypre', default=False,
+            description='Compile with Hypre support')
+    variant('shared', default=(sys.platform != 'darwin'),
+            description='Build Trilinos as shared library')
+    variant('pic', default=True,
+            description='Position independent code')
+
+    depends_on('mpi')
+    depends_on('yaml-cpp@0.5.3:')
+    depends_on('trilinos+exodus+tpetra+muelu+belos+ifpack2+amesos2+zoltan+stk+boost~superlu-dist+superlu+hdf5+zlib+pnetcdf+shards~hypre@master,develop', when='+shared')
+    # Cannot build Trilinos as a shared library with STK on Darwin
+    # https://github.com/trilinos/Trilinos/issues/2994
+    depends_on('trilinos~shared+exodus+tpetra+muelu+belos+ifpack2+amesos2+zoltan+stk+boost~superlu-dist+superlu+hdf5+zlib+pnetcdf+shards~hypre@master,develop', when='~shared')
+    depends_on('openfast+cxx', when='+openfast')
+    depends_on('tioga', when='+tioga')
+    depends_on('hypre+mpi+int64', when='+hypre')
+
+    def cmake_args(self):
+        spec = self.spec
+        options = []
+
+        options.extend([
+            '-DTrilinos_DIR:PATH=%s' % spec['trilinos'].prefix,
+            '-DYAML_DIR:PATH=%s' % spec['yaml-cpp'].prefix,
+            '-DCMAKE_C_COMPILER=%s' % spec['mpi'].mpicc,
+            '-DCMAKE_CXX_COMPILER=%s' % spec['mpi'].mpicxx,
+            '-DCMAKE_Fortran_COMPILER=%s' % spec['mpi'].mpifc,
+            '-DMPI_C_COMPILER=%s' % spec['mpi'].mpicc,
+            '-DMPI_CXX_COMPILER=%s' % spec['mpi'].mpicxx,
+            '-DMPI_Fortran_COMPILER=%s' % spec['mpi'].mpifc,
+            '-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=%s' % (
+                'ON' if '+pic' in spec else 'OFF'),
+        ])
+
+        if '+openfast' in spec:
+            options.extend([
+                '-DENABLE_OPENFAST:BOOL=ON',
+                '-DOpenFAST_DIR:PATH=%s' % spec['openfast'].prefix
+            ])
+        else:
+            options.append('-DENABLE_OPENFAST:BOOL=OFF')
+
+        if '+tioga' in spec:
+            options.extend([
+                '-DENABLE_TIOGA:BOOL=ON',
+                '-DTIOGA_DIR:PATH=%s' % spec['tioga'].prefix
+            ])
+        else:
+            options.append('-DENABLE_TIOGA:BOOL=OFF')
+
+        if '+hypre' in spec:
+            options.extend([
+                '-DENABLE_HYPRE:BOOL=ON',
+                '-DHYPRE_DIR:PATH=%s' % spec['hypre'].prefix
+            ])
+        else:
+            options.append('-DENABLE_HYPRE:BOOL=OFF')
+
+        return options
diff --git a/var/spack/repos/builtin/packages/nalu/package.py b/var/spack/repos/builtin/packages/nalu/package.py
index 36dd317009..5e009d7e01 100644
--- a/var/spack/repos/builtin/packages/nalu/package.py
+++ b/var/spack/repos/builtin/packages/nalu/package.py
@@ -1,52 +1,43 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
+import sys
 
 
 class Nalu(CMakePackage):
     """Nalu: a generalized unstructured massively parallel low Mach flow code
-       designed to support a variety of energy applications of interest (most
-       notably Wind ECP) built on the Sierra Toolkit and Trilinos solver
-       Tpetra/Epetra stack
+       designed to support a variety of energy applications of interest
+       built on the Sierra Toolkit and Trilinos solver Tpetra/Epetra stack
     """
 
     homepage = "https://github.com/NaluCFD/Nalu"
-    url      = "https://github.com/NaluCFD/Nalu.git"
+    git      = "https://github.com/NaluCFD/Nalu.git"
 
-    maintainers = ['jrood-nrel']
+    version('master', branch='master')
 
     variant('openfast', default=False,
             description='Compile with OpenFAST support')
+    variant('tioga', default=False,
+            description='Compile with Tioga support')
+    variant('hypre', default=False,
+            description='Compile with Hypre support')
+    variant('shared', default=(sys.platform != 'darwin'),
+            description='Build Trilinos as shared library')
+    variant('pic', default=True,
+            description='Position independent code')
 
-    version('master',
-            git='https://github.com/NaluCFD/Nalu.git', branch='master')
-
-    # Currently Nalu only builds static libraries; To be fixed soon
-    depends_on('yaml-cpp+pic~shared@0.5.3:')
-    depends_on('trilinos~shared+exodus+tpetra+muelu+belos+ifpack2+amesos2+zoltan+stk+boost~superlu-dist+superlu+hdf5+zlib+pnetcdf+shards@master,12.12.1:')
+    depends_on('mpi')
+    depends_on('yaml-cpp@0.5.3:')
+    depends_on('trilinos+exodus+tpetra+muelu+belos+ifpack2+amesos2+zoltan+stk+boost~superlu-dist+superlu+hdf5+zlib+pnetcdf+shards~hypre@master,develop', when='+shared')
+    # Cannot build Trilinos as a shared library with STK on Darwin
+    # https://github.com/trilinos/Trilinos/issues/2994
+    depends_on('trilinos~shared+exodus+tpetra+muelu+belos+ifpack2+amesos2+zoltan+stk+boost~superlu-dist+superlu+hdf5+zlib+pnetcdf+shards~hypre@master,develop', when='~shared')
     depends_on('openfast+cxx', when='+openfast')
+    depends_on('tioga', when='+tioga')
+    depends_on('hypre+mpi+int64', when='+hypre')
 
     def cmake_args(self):
         spec = self.spec
@@ -55,12 +46,32 @@ class Nalu(CMakePackage):
         options.extend([
             '-DTrilinos_DIR:PATH=%s' % spec['trilinos'].prefix,
             '-DYAML_DIR:PATH=%s' % spec['yaml-cpp'].prefix,
-            '-DENABLE_INSTALL:BOOL=ON'
+            '-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=%s' % (
+                'ON' if '+pic' in spec else 'OFF'),
         ])
 
         if '+openfast' in spec:
             options.extend([
+                '-DENABLE_OPENFAST:BOOL=ON',
                 '-DOpenFAST_DIR:PATH=%s' % spec['openfast'].prefix
             ])
+        else:
+            options.append('-DENABLE_OPENFAST:BOOL=OFF')
+
+        if '+tioga' in spec:
+            options.extend([
+                '-DENABLE_TIOGA:BOOL=ON',
+                '-DTIOGA_DIR:PATH=%s' % spec['tioga'].prefix
+            ])
+        else:
+            options.append('-DENABLE_TIOGA:BOOL=OFF')
+
+        if '+hypre' in spec:
+            options.extend([
+                '-DENABLE_HYPRE:BOOL=ON',
+                '-DHYPRE_DIR:PATH=%s' % spec['hypre'].prefix
+            ])
+        else:
+            options.append('-DENABLE_HYPRE:BOOL=OFF')
 
         return options
diff --git a/var/spack/repos/builtin/packages/namd/package.py b/var/spack/repos/builtin/packages/namd/package.py
index 54d165525b..a7e82fd1d0 100644
--- a/var/spack/repos/builtin/packages/namd/package.py
+++ b/var/spack/repos/builtin/packages/namd/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import platform
-import shutil
 import sys
 import os
 from spack import *
@@ -44,7 +24,7 @@ class Namd(MakefilePackage):
     variant('interface', default='none', values=('none', 'tcl', 'python'),
             description='Enables TCL and/or python interface')
 
-    depends_on('charm')
+    depends_on('charmpp')
 
     depends_on('fftw@:2.99', when="fftw=2")
     depends_on('fftw@3:', when="fftw=3")
@@ -58,8 +38,8 @@ class Namd(MakefilePackage):
 
     def _copy_arch_file(self, lib):
         config_filename = 'arch/{0}.{1}'.format(self.arch, lib)
-        shutil.copy('arch/Linux-x86_64.{0}'.format(lib),
-                    config_filename)
+        copy('arch/Linux-x86_64.{0}'.format(lib),
+             config_filename)
         if lib == 'tcl':
             filter_file(r'-ltcl8\.5',
                         '-ltcl{0}'.format(self.spec['tcl'].version.up_to(2)),
diff --git a/var/spack/repos/builtin/packages/nano/package.py b/var/spack/repos/builtin/packages/nano/package.py
index 200c47a7b3..bbb2523d5a 100644
--- a/var/spack/repos/builtin/packages/nano/package.py
+++ b/var/spack/repos/builtin/packages/nano/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/nanoflann/package.py b/var/spack/repos/builtin/packages/nanoflann/package.py
index 13c5797d69..f042e8e4b9 100644
--- a/var/spack/repos/builtin/packages/nanoflann/package.py
+++ b/var/spack/repos/builtin/packages/nanoflann/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/nanopb/package.py b/var/spack/repos/builtin/packages/nanopb/package.py
new file mode 100644
index 0000000000..1b8472f3d7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/nanopb/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Nanopb(CMakePackage):
+    """Nanopb is a small code-size Protocol Buffers implementation
+    in ansi C."""
+
+    homepage = "https://jpa.kapsi.fi/nanopb/"
+    url      = "https://github.com/nanopb/nanopb/archive/0.3.9.1.tar.gz"
+
+    version('0.3.9.1', '08d71b315819626366b0303f8658fc68')
+
+    depends_on('protobuf', type=('build'))
+    depends_on('py-protobuf', type=('build'))
diff --git a/var/spack/repos/builtin/packages/nasm/package.py b/var/spack/repos/builtin/packages/nasm/package.py
index 2979ad43f5..3604b1ec28 100644
--- a/var/spack/repos/builtin/packages/nasm/package.py
+++ b/var/spack/repos/builtin/packages/nasm/package.py
@@ -1,34 +1,23 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class Nasm(AutotoolsPackage):
     """NASM (Netwide Assembler) is an 80x86 assembler designed for
-       portability and modularity. It includes a disassembler as well."""
+    portability and modularity. It includes a disassembler as well."""
+
     homepage = "http://www.nasm.us"
-    url      = "http://www.nasm.us/pub/nasm/releasebuilds/2.11.06/nasm-2.11.06.tar.xz"
+    url      = "http://www.nasm.us/pub/nasm/releasebuilds/2.13.03/nasm-2.13.03.tar.xz"
+    list_url = "http://www.nasm.us/pub/nasm/releasebuilds"
+    list_depth = 1
 
+    version('2.13.03', 'd5ca2ad7121ccbae69dd606b1038532c')
     version('2.11.06', '2b958e9f5d200641e6fc9564977aecc5')
+
+    # Fix compilation with GCC 8
+    # https://bugzilla.nasm.us/show_bug.cgi?id=3392461
+    patch('https://src.fedoraproject.org/rpms/nasm/raw/0cc3eb244bd971df81a7f02bc12c5ec259e1a5d6/f/0001-Remove-invalid-pure_func-qualifiers.patch', level=1, sha256='ac9f315d204afa6b99ceefa1fe46d4eed2b8a23c7315d32d33c0f378d930e950', when='@2.13.03 %gcc@8:')
diff --git a/var/spack/repos/builtin/packages/nauty/package.py b/var/spack/repos/builtin/packages/nauty/package.py
index ef032ad7c9..a350ff207d 100644
--- a/var/spack/repos/builtin/packages/nauty/package.py
+++ b/var/spack/repos/builtin/packages/nauty/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 import os
 from spack import *
@@ -74,7 +55,7 @@ class Nauty(AutotoolsPackage):
     depends_on('autoconf',  type='build', when='@2.6r7')
     depends_on('automake',  type='build', when='@2.6r7')
     depends_on('libtool',  type='build', when='@2.6r7')
-    depends_on('pkg-config',  type='build')
+    depends_on('pkgconfig',  type='build')
     depends_on('help2man', type='build')
     depends_on('zlib')
     depends_on('gmp')
diff --git a/var/spack/repos/builtin/packages/ncbi-magicblast/package.py b/var/spack/repos/builtin/packages/ncbi-magicblast/package.py
new file mode 100644
index 0000000000..b0e9c3434a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ncbi-magicblast/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class NcbiMagicblast(AutotoolsPackage):
+    """Magic-BLAST is a tool for mapping large next-generation RNA or DNA
+    sequencing runs against a whole genome or transcriptome. """
+
+    homepage = "https://ncbi.github.io/magicblast/"
+    url      = "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/magicblast/1.3.0/ncbi-magicblast-1.3.0-src.tar.gz"
+
+    version('1.3.0', '2615b919c1fe1bf7dc3d816392ab4420')
+
+    depends_on('lmdb')
+    configure_directory = 'c++'
+
+    def configure_args(self):
+        return ['--without-internal']
diff --git a/var/spack/repos/builtin/packages/ncbi-rmblastn/package.py b/var/spack/repos/builtin/packages/ncbi-rmblastn/package.py
index 57b918cde8..8dd04b5586 100644
--- a/var/spack/repos/builtin/packages/ncbi-rmblastn/package.py
+++ b/var/spack/repos/builtin/packages/ncbi-rmblastn/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/ncbi-toolkit/package.py b/var/spack/repos/builtin/packages/ncbi-toolkit/package.py
new file mode 100644
index 0000000000..3f1bc0d543
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ncbi-toolkit/package.py
@@ -0,0 +1,46 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class NcbiToolkit(AutotoolsPackage):
+    """NCBI C++ Toolkit"""
+
+    homepage = "https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/"
+    url      = "ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/CURRENT/ncbi_cxx--21_0_0.tar.gz"
+
+    version('21_0_0', '14e021e08b1a78ac9cde98d0cab92098')
+
+    depends_on('boost@1.35.0:')
+    depends_on('bzip2')
+    depends_on('libjpeg')
+    depends_on('libpng')
+    depends_on('libtiff')
+    depends_on('libxml2')
+    depends_on('libxslt@1.1.14:')
+    depends_on('lzo')
+    depends_on('pcre')
+    depends_on('giflib')
+    depends_on('sqlite@3.6.6:')
+    depends_on('zlib')
+    depends_on('samtools')
+    depends_on('bamtools')
+
+    def configure_args(self):
+        return ['--without-sybase', '--without-fastcgi']
+
+    def patch(self):
+        with working_dir(join_path('src', 'util', 'image')):
+            filter_file(r'jpeg_start_compress(&cinfo, true)',
+                        'jpeg_start_compress(&cinfo, TRUE)',
+                        'image_io_jpeg.cpp', string=True)
+
+    def build(self, spec, prefix):
+        compiler_version = self.compiler.version.joined
+
+        with working_dir(join_path(
+                'GCC{0}-DebugMT64'.format(compiler_version), 'build')):
+            make('all_r')
diff --git a/var/spack/repos/builtin/packages/nccl/package.py b/var/spack/repos/builtin/packages/nccl/package.py
index e1ac486e16..5ea2b9689c 100644
--- a/var/spack/repos/builtin/packages/nccl/package.py
+++ b/var/spack/repos/builtin/packages/nccl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,6 +12,9 @@ class Nccl(MakefilePackage):
     homepage = "https://github.com/NVIDIA/nccl"
     url      = "https://github.com/NVIDIA/nccl/archive/v1.3.4-1.tar.gz"
 
+    version('2.3.5-5',
+            sha256='bac9950b4d3980c25baa8e3e4541d2dfb4d21edf32ad3b89022d04920357142f')
+    version('2.2', '5b9ce7fbdce0fde68e0f66318e6ff422')
     version('1.3.4-1', '5b9ce7fbdce0fde68e0f66318e6ff422')
     version('1.3.0-1', 'f6fb1d56913a7d212ca0c300e76f01fb')
 
@@ -42,4 +26,7 @@ class Nccl(MakefilePackage):
 
     @property
     def install_targets(self):
-        return ['PREFIX={0}'.format(self.prefix), 'install']
+        if self.version >= Version('2.3.5-5'):
+            return ['PREFIX={0}'.format(self.prefix), 'src.install']
+        else:
+            return ['PREFIX={0}'.format(self.prefix), 'install']
diff --git a/var/spack/repos/builtin/packages/nccmp/package.py b/var/spack/repos/builtin/packages/nccmp/package.py
index e710faa034..69736cc34b 100644
--- a/var/spack/repos/builtin/packages/nccmp/package.py
+++ b/var/spack/repos/builtin/packages/nccmp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/ncdu/package.py b/var/spack/repos/builtin/packages/ncdu/package.py
index a95fc5b1ca..d77478c618 100644
--- a/var/spack/repos/builtin/packages/ncdu/package.py
+++ b/var/spack/repos/builtin/packages/ncdu/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,6 +17,8 @@ class Ncdu(Package):
     homepage = "http://dev.yorhel.nl/ncdu"
     url      = "http://dev.yorhel.nl/download/ncdu-1.11.tar.gz"
 
+    version('1.13', sha256='f4d9285c38292c2de05e444d0ba271cbfe1a705eee37c2b23ea7c448ab37255a')
+    version('1.12', sha256='820e4e4747a2a2ec7a2e9f06d2f5a353516362c22496a10a9834f871b877499a')
     version('1.11', '9e44240a5356b029f05f0e70a63c4d12')
     version('1.10', '7535decc8d54eca811493e82d4bfab2d')
     version('1.9', '93258079db897d28bb8890e2db89b1fb')
diff --git a/var/spack/repos/builtin/packages/ncftp/package.py b/var/spack/repos/builtin/packages/ncftp/package.py
index 704affdad3..2b9e417aa8 100644
--- a/var/spack/repos/builtin/packages/ncftp/package.py
+++ b/var/spack/repos/builtin/packages/ncftp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/ncl/package.py b/var/spack/repos/builtin/packages/ncl/package.py
index 25b903e4c7..8a231761fd 100644
--- a/var/spack/repos/builtin/packages/ncl/package.py
+++ b/var/spack/repos/builtin/packages/ncl/package.py
@@ -1,31 +1,11 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
 import os
-import shutil
 import tempfile
 
 
@@ -37,15 +17,16 @@ class Ncl(Package):
 
     homepage = "https://www.ncl.ucar.edu"
 
-    version('6.4.0', 'a981848ddcaf1c263279648265f24766',
-            url='https://www.earthsystemgrid.org/download/fileDownload.html?logicalFileId=86b9bec2-fa01-11e6-a976-00c0f03d5b7c',
-            extension='tar.gz')
+    url = "https://github.com/NCAR/ncl/archive/6.4.0.tar.gz"
+
+    version('6.5.0', '133446f3302eddf237db56bf349e1ebf228240a7320699acc339a3d7ee414591')
+    version('6.4.0', 'd891452cda7bb25afad9b6c876c73986')
 
     patch('spack_ncl.patch')
-    # Make ncl compile with hdf5 1.10
-    patch('hdf5.patch')
-    # ymake-filter's buffer may overflow
-    patch('ymake-filter.patch')
+    # Make ncl compile with hdf5 1.10 (upstream as of 6.5.0)
+    patch('hdf5.patch', when="@6.4.0")
+    # ymake-filter's buffer may overflow (upstream as of 6.5.0)
+    patch('ymake-filter.patch', when="@6.4.0")
 
     # This installation script is implemented according to this manual:
     # http://www.ncl.ucar.edu/Download/build_from_src.shtml
@@ -106,6 +87,8 @@ class Ncl(Package):
         placement='triangle_src',
         when='+triangle')
 
+    sanity_check_is_file = ['bin/ncl']
+
     def patch(self):
         # Make configure scripts use Spack's tcsh
         files = ['Configure'] + glob.glob('config/*')
@@ -261,8 +244,8 @@ class Ncl(Package):
             triangle_src = join_path(self.stage.source_path, 'triangle_src')
             triangle_dst = join_path(self.stage.source_path, 'ni', 'src',
                                      'lib', 'hlu')
-            shutil.copy(join_path(triangle_src, 'triangle.h'), triangle_dst)
-            shutil.copy(join_path(triangle_src, 'triangle.c'), triangle_dst)
+            copy(join_path(triangle_src, 'triangle.h'), triangle_dst)
+            copy(join_path(triangle_src, 'triangle.c'), triangle_dst)
 
     @staticmethod
     def delete_files(*filenames):
diff --git a/var/spack/repos/builtin/packages/nco/package.py b/var/spack/repos/builtin/packages/nco/package.py
index 2aea5aed2c..6b46596b6e 100644
--- a/var/spack/repos/builtin/packages/nco/package.py
+++ b/var/spack/repos/builtin/packages/nco/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -60,3 +41,10 @@ class Nco(AutotoolsPackage):
     def configure_args(self):
         spec = self.spec
         return ['--{0}-doc'.format('enable' if '+doc' in spec else 'disable')]
+
+    def setup_environment(self, spack_env, run_env):
+        spec = self.spec
+        spack_env.set('NETCDF_INC', spec['netcdf'].prefix.include)
+        spack_env.set('NETCDF_LIB', spec['netcdf'].prefix.lib)
+        spack_env.set('ANTLR_ROOT', spec['antlr'].prefix)
+        spack_env.set('UDUNITS2_PATH', spec['udunits2'].prefix)
diff --git a/var/spack/repos/builtin/packages/ncurses/package.py b/var/spack/repos/builtin/packages/ncurses/package.py
index 06ffc0b650..56218a9306 100644
--- a/var/spack/repos/builtin/packages/ncurses/package.py
+++ b/var/spack/repos/builtin/packages/ncurses/package.py
@@ -1,32 +1,12 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 from glob import glob
 from os.path import exists, join
 from os import makedirs
-from shutil import copy
 
 
 class Ncurses(AutotoolsPackage):
@@ -37,15 +17,18 @@ class Ncurses(AutotoolsPackage):
     SYSV-curses enhancements over BSD curses."""
 
     homepage = "http://invisible-island.net/ncurses/ncurses.html"
-    url      = "http://ftp.gnu.org/pub/gnu/ncurses/ncurses-6.0.tar.gz"
+    url      = "https://ftpmirror.gnu.org/ncurses/ncurses-6.1.tar.gz"
 
+    version('6.1', '98c889aaf8d23910d2b92d65be2e737a')
     version('6.0', 'ee13d052e1ead260d7c28071f46eefb1')
     version('5.9', '8cb9c412e5f2d96bc6f459aa8c6282a1')
 
     variant('symlinks', default=False,
             description='Enables symlinks. Needed on AFS filesystem.')
+    variant('termlib', default=False,
+            description='Enables termlib needs for gnutls in emacs.')
 
-    depends_on('pkg-config', type='build')
+    depends_on('pkgconfig', type='build')
 
     patch('patch_gcc_5.txt', when='@6.0%gcc@5.0:')
     patch('sed_pgi.patch',   when='@:6.0')
@@ -71,6 +54,12 @@ class Ncurses(AutotoolsPackage):
         if '+symlinks' in self.spec:
             opts.append('--enable-symlinks')
 
+        if '+termlib' in self.spec:
+            opts.extend(('--with-termlib',
+                         '--enable-termcap',
+                         '--enable-getcap',
+                         '--enable-tcap-names'))
+
         prefix = '--prefix={0}'.format(prefix)
 
         configure = Executable('../configure')
@@ -100,9 +89,9 @@ class Ncurses(AutotoolsPackage):
             if not exists(path):
                 makedirs(path)
             for header in headers:
-                copy(header, path)
+                install(header, path)
 
     @property
     def libs(self):
         return find_libraries(
-            ['libncurses', 'libncursesw'], root=self.prefix, recurse=True)
+            ['libncurses', 'libncursesw'], root=self.prefix, recursive=True)
diff --git a/var/spack/repos/builtin/packages/ncview/package.py b/var/spack/repos/builtin/packages/ncview/package.py
index 5dd160e50c..f37115fe96 100644
--- a/var/spack/repos/builtin/packages/ncview/package.py
+++ b/var/spack/repos/builtin/packages/ncview/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/ndiff/package.py b/var/spack/repos/builtin/packages/ndiff/package.py
index 176a3463d3..ab997d1daa 100644
--- a/var/spack/repos/builtin/packages/ndiff/package.py
+++ b/var/spack/repos/builtin/packages/ndiff/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/nek5000/package.py b/var/spack/repos/builtin/packages/nek5000/package.py
new file mode 100644
index 0000000000..a952029a86
--- /dev/null
+++ b/var/spack/repos/builtin/packages/nek5000/package.py
@@ -0,0 +1,234 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+import numbers
+import os
+
+
+def is_integral(x):
+    """Any integer value"""
+    try:
+        return isinstance(int(x), numbers.Integral) and \
+            not isinstance(x, bool) and int(x) > 0
+    except ValueError:
+        return False
+
+
+class Nek5000(Package):
+    """A fast and scalable high-order solver for computational fluid
+       dynamics"""
+
+    homepage = "https://nek5000.mcs.anl.gov/"
+    url      = "https://github.com/Nek5000/Nek5000/releases/download/v17.0/Nek5000-v17.0.tar.gz"
+    git      = "https://github.com/Nek5000/Nek5000.git"
+
+    tags = ['cfd', 'flow', 'hpc', 'solver', 'navier-stokes',
+            'spectral-elements', 'fluid', 'ecp', 'ecp-apps']
+
+    version('develop', branch='master')
+    version('17.0', '6a13bfad2ce023897010dd88f54a0a87')
+
+    # MPI, Profiling and Visit variants
+    variant('mpi',       default=True, description='Build with MPI.')
+    variant('profiling', default=True, description='Build with profiling data.')
+    variant('visit',     default=False, description='Build with Visit.')
+
+    # TODO: add a variant 'blas' or 'external-blas' to enable the usage of
+    #       Spack installed/configured blas.
+
+    # Variant for MAXNEL, we need to read this from user
+    variant(
+        'MAXNEL',
+        default=150000,
+        description='Maximum number of elements for Nek5000 tools.',
+        values=is_integral
+    )
+
+    # Variants for Nek tools
+    variant('genbox',   default=True, description='Build genbox tool.')
+    variant('int_tp',   default=True, description='Build int_tp tool.')
+    variant('n2to3',    default=True, description='Build n2to3 tool.')
+    variant('postnek',  default=True, description='Build postnek tool.')
+    variant('reatore2', default=True, description='Build reatore2 tool.')
+    variant('genmap',   default=True, description='Build genmap tool.')
+    variant('nekmerge', default=True, description='Build nekmerge tool.')
+    variant('prenek',   default=True, description='Build prenek tool.')
+
+    # Dependencies
+    depends_on('mpi', when="+mpi")
+    depends_on('libx11', when="+prenek")
+    depends_on('libx11', when="+postnek")
+    # libxt is needed for X11/Intrinsic.h but not for linking
+    depends_on('libxt', when="+prenek")
+    depends_on('xproto', when="+prenek")
+    depends_on('libxt', when="+postnek")
+    depends_on('visit', when="+visit")
+
+    @run_before('install')
+    def fortran_check(self):
+        if not self.compiler.f77:
+            msg = 'Cannot build Nek5000 without a Fortran 77 compiler.'
+            raise RuntimeError(msg)
+
+    @run_after('install')
+    def test_install(self):
+        with working_dir('short_tests/eddy'):
+            os.system(join_path(self.prefix.bin, 'makenek') + ' eddy_uv')
+            if not os.path.isfile(join_path(os.getcwd(), 'nek5000')):
+                msg = 'Cannot build example: short_tests/eddy.'
+                raise RuntimeError(msg)
+
+    def install(self, spec, prefix):
+        tools_dir   = 'tools'
+        bin_dir     = 'bin'
+
+        # Do not use the Spack compiler wrappers.
+        # Use directly the compilers:
+        fc  = self.compiler.f77
+        cc  = self.compiler.cc
+
+        fflags = spec.compiler_flags['fflags']
+        cflags = spec.compiler_flags['cflags']
+        if ('+prenek' in spec) or ('+postnek' in spec):
+            libx11_h = find_headers('Xlib', spec['libx11'].prefix.include,
+                                    recursive=True)
+            if not libx11_h:
+                raise RuntimeError('Xlib.h not found in %s' %
+                                   spec['libx11'].prefix.include)
+            cflags += ['-I%s' % os.path.dirname(libx11_h.directories[0])]
+
+            xproto_h = find_headers('X', spec['xproto'].prefix.include,
+                                    recursive=True)
+            if not xproto_h:
+                raise RuntimeError('X.h not found in %s' %
+                                   spec['xproto'].prefix.include)
+            cflags += ['-I%s' % os.path.dirname(xproto_h.directories[0])]
+
+            libxt_h = find_headers('Intrinsic', spec['libxt'].prefix.include,
+                                   recursive=True)
+            if not libxt_h:
+                raise RuntimeError('X11/Intrinsic.h not found in %s' %
+                                   spec['libxt'].prefix.include)
+            cflags += ['-I%s' % os.path.dirname(libxt_h.directories[0])]
+        if self.compiler.name in ['xl', 'xl_r']:
+            # Use '-qextname' to add underscores.
+            # Use '-WF,-qnotrigraph' to fix an error about a string: '... ??'
+            fflags += ['-qextname', '-WF,-qnotrigraph']
+        fflags = ' '.join(fflags)
+        cflags = ' '.join(cflags)
+
+        # Build the tools, maketools copy them to Nek5000/bin by default.
+        # We will then install Nek5000/bin under prefix after that.
+        with working_dir(tools_dir):
+            # Update the maketools script to use correct compilers
+            filter_file(r'^#FC\s*=.*', 'FC="{0}"'.format(fc), 'maketools')
+            filter_file(r'^#CC\s*=.*', 'CC="{0}"'.format(cc), 'maketools')
+            if fflags:
+                filter_file(r'^#FFLAGS=.*', 'FFLAGS="{0}"'.format(fflags),
+                            'maketools')
+            if cflags:
+                filter_file(r'^#CFLAGS=.*', 'CFLAGS="{0}"'.format(cflags),
+                            'maketools')
+
+            if self.compiler.name in ['xl', 'xl_r']:
+                # Patch 'maketools' to use '-qextname' when checking for
+                # underscore becasue 'xl'/'xl_r' use this option to enable the
+                # addition of the underscore.
+                filter_file(r'^\$FC -c ', '$FC -qextname -c ', 'maketools')
+
+            libx11_lib = find_libraries('libX11', spec['libx11'].prefix.lib,
+                                        shared=True, recursive=True)
+            if not libx11_lib:
+                libx11_lib = \
+                    find_libraries('libX11', spec['libx11'].prefix.lib64,
+                                   shared=True, recursive=True)
+            if not libx11_lib:
+                raise RuntimeError('libX11 not found in %s/{lib,lib64}' %
+                                   spec['libx11'].prefix)
+            # There is no other way to set the X11 library path except brute
+            # force:
+            filter_file(r'-L\$\(X\)', libx11_lib.search_flags,
+                        join_path('prenek', 'makefile'))
+            filter_file(r'-L\$\(X\)', libx11_lib.search_flags,
+                        join_path('postnek', 'makefile'))
+
+            if self.compiler.name in ['xl', 'xl_r']:
+                # Use '-qextname' when compiling mxm.f
+                filter_file('\$\(OLAGS\)', '-qextname $(OLAGS)',
+                            join_path('postnek', 'makefile'))
+            # Define 'rename_' function that calls 'rename'
+            with open(join_path('postnek', 'xdriver.c'), 'a') as xdriver:
+                xdriver.write('\nvoid rename_(char *from, char *to)\n{\n'
+                              '   rename(from, to);\n}\n')
+
+            maxnel = self.spec.variants['MAXNEL'].value
+            filter_file(r'^#MAXNEL\s*=.*', 'MAXNEL=' + maxnel, 'maketools')
+
+            maketools = Executable('./maketools')
+
+            # Build the tools
+            if '+genbox' in spec:
+                maketools('genbox')
+            # "ERROR: int_tp does not exist!"
+            # if '+int_tp' in spec:
+            #     maketools('int_tp')
+            if '+n2to3' in spec:
+                maketools('n2to3')
+            if '+postnek' in spec:
+                maketools('postnek')
+            if '+reatore2' in spec:
+                maketools('reatore2')
+            if '+genmap' in spec:
+                maketools('genmap')
+            if '+nekmerge' in spec:
+                maketools('nekmerge')
+            if '+prenek' in spec:
+                maketools('prenek')
+
+        with working_dir(bin_dir):
+            if '+mpi' in spec:
+                fc  = spec['mpi'].mpif77
+                cc  = spec['mpi'].mpicc
+            else:
+                filter_file(r'^#MPI=0', 'MPI=0', 'makenek')
+
+            if '+profiling' not in spec:
+                filter_file(r'^#PROFILING=0', 'PROFILING=0', 'makenek')
+
+            if '+visit' in spec:
+                filter_file(r'^#VISIT=1', 'VISIT=1', 'makenek')
+                filter_file(r'^#VISIT_INSTALL=.*', 'VISIT_INSTALL=\"' +
+                            spec['visit'].prefix.bin + '\"', 'makenek')
+
+            # Update the makenek to use correct compilers and
+            # Nek5000 source.
+            filter_file(r'^#FC\s*=.*', 'FC="{0}"'.format(fc), 'makenek')
+            filter_file(r'^#CC\s*=.*', 'CC="{0}"'.format(cc), 'makenek')
+            filter_file(r'^#SOURCE_ROOT\s*=\"\$H.*',  'SOURCE_ROOT=\"' +
+                        prefix.bin.Nek5000 + '\"',  'makenek')
+            if fflags:
+                filter_file(r'^#FFLAGS=.*', 'FFLAGS="{0}"'.format(fflags),
+                            'makenek')
+            if cflags:
+                filter_file(r'^#CFLAGS=.*', 'CFLAGS="{0}"'.format(cflags),
+                            'makenek')
+
+        with working_dir('core'):
+            if self.compiler.name in ['xl', 'xl_r']:
+                # Patch 'core/makenek.inc' and 'makefile.template' to use
+                # '-qextname' when checking for underscore becasue 'xl'/'xl_r'
+                # use this option to enable the addition of the underscore.
+                filter_file(r'^\$FCcomp -c ', '$FCcomp -qextname -c ',
+                            'makenek.inc')
+                filter_file(r'\$\(FC\) -c \$\(L0\)',
+                            '$(FC) -c -qextname $(L0)', 'makefile.template')
+
+        # Install Nek5000/bin in prefix/bin
+        install_tree(bin_dir, prefix.bin)
+
+        # Copy Nek5000 source to prefix/bin
+        install_tree('../Nek5000', prefix.bin.Nek5000)
diff --git a/var/spack/repos/builtin/packages/nekbone/package.py b/var/spack/repos/builtin/packages/nekbone/package.py
index 3d419b9156..ff34fc25ac 100644
--- a/var/spack/repos/builtin/packages/nekbone/package.py
+++ b/var/spack/repos/builtin/packages/nekbone/package.py
@@ -1,27 +1,7 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack import *
 
@@ -33,32 +13,50 @@ class Nekbone(Package):
        the spectral element method."""
 
     homepage = "https://github.com/Nek5000/Nekbone"
-    url = "https://github.com/Nek5000/Nekbone/tarball/v17.0"
+    url      = "https://github.com/Nek5000/Nekbone/archive/v17.0.tar.gz"
+    git      = "https://github.com/Nek5000/Nekbone.git"
 
     tags = ['proxy-app', 'ecp-proxy-app']
 
-    version('17.0', 'cc339684547614a0725959e41839fec1')
-    version('develop', git='https://github.com/Nek5000/Nekbone.git')
+    version('develop', branch='master')
+    version('17.0', sha256='ae361cc61368a924398a28a296f675b7f0c4a9516788a7f8fa3c09d787cdf69b')
 
-    depends_on('mpi')
+    # Variants
+    variant('mpi', default=True, description='Build with MPI')
 
-    def install(self, spec, prefix):
+    # dependencies
+    depends_on('mpi', when='+mpi')
+
+    @run_before('install')
+    def fortran_check(self):
+        if not self.compiler.fc:
+            msg = 'Nekbone can not be built without a Fortran compiler.'
+            raise RuntimeError(msg)
 
-        working_dirs = ['example1', 'example2', 'example3', 'nek_comm',
-                        'nek_delay', 'nek_mgrid']
+    def install(self, spec, prefix):
         mkdir(prefix.bin)
 
-        for wdir in working_dirs:
-            with working_dir('test/' + wdir):
-                makenec = FileFilter('makenek')
-                makenec.filter('CC.*', 'CC=' + self.spec['mpi'].mpicc)
-                makenec.filter('FF77.*', 'FF77=' + self.spec['mpi'].mpif77)
-                makenek = Executable('./makenek')
-                path = join_path(prefix.bin,  wdir)
-                makenek('ex1', '../../src')
-                mkdir(path)
-                install('nekbone', path)
-                install('nekpmpi', path)
-                install('data.rea', path)
-                install('SIZE', path)
-                install('README', path)
+        fc = self.compiler.fc
+        cc = self.compiler.cc
+        if '+mpi' in spec:
+            fc = spec['mpi'].mpif77
+            cc = spec['mpi'].mpicc
+
+        # Install Nekbone in prefix.bin
+        install_tree(self.stage.source_path, prefix.bin.Nekbone)
+
+        # Install scripts in prefix.bin
+        nekpmpi = 'test/example1/nekpmpi'
+        makenek = 'test/example1/makenek'
+
+        install(makenek, prefix.bin)
+        install(nekpmpi, prefix.bin)
+
+        with working_dir(prefix.bin):
+            filter_file(r'^SOURCE_ROOT\s*=.*', 'SOURCE_ROOT=\"' +
+                        prefix.bin.Nekbone + '/src\"', 'makenek')
+            filter_file(r'^CC\s*=.*', 'CC=\"' + cc + '\"', 'makenek')
+            filter_file(r'^F77\s*=.*', 'F77=\"' + fc + '\"', 'makenek')
+
+            if '+mpi' not in spec:
+                filter_file(r'^#IFMPI=\"false\"', 'IFMPI=\"false\"', 'makenek')
diff --git a/var/spack/repos/builtin/packages/nekcem/package.py b/var/spack/repos/builtin/packages/nekcem/package.py
new file mode 100644
index 0000000000..c1b981e0c1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/nekcem/package.py
@@ -0,0 +1,111 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+import json
+
+
+class Nekcem(Package):
+    """Spectral-element solver for Maxwell's equations, drift-diffusion
+       equations, and more."""
+
+    # Links to homepage and git
+    homepage = "https://nekcem.mcs.anl.gov"
+    git      = "https://github.com/NekCEM/NekCEM.git"
+
+    # Variants
+    variant('mpi', default=True, description='Build with MPI')
+
+    # We only have a development version
+    version('develop')
+    version('0b8bedd', commit='0b8beddfdcca646bfcc866dfda1c5f893338399b')
+
+    # dependencies
+    depends_on('mpi', when='+mpi')
+    depends_on('blas')
+    depends_on('lapack')
+
+    @run_before('install')
+    def fortran_check(self):
+        if not self.compiler.fc:
+            msg = 'NekCEM can not be built without a Fortran compiler.'
+            raise RuntimeError(msg)
+
+    @run_after('install')
+    def test_install(self):
+        nekcem_test = join_path(self.prefix.bin, 'NekCEM', 'tests', '2dboxpec')
+        with working_dir(nekcem_test):
+            makenek = Executable(join_path(self.prefix.bin, 'makenek'))
+            makenek(os.path.basename(nekcem_test))
+            if not os.path.isfile('nekcem'):
+                msg = 'Cannot build example: %s' % nekcem_test
+                raise RuntimeError(msg)
+
+    def install(self, spec, prefix):
+        bin_dir = 'bin'
+        nek = 'nek'
+        configurenek = 'configurenek'
+        makenek = 'makenek'
+
+        fc = self.compiler.f77
+        cc = self.compiler.cc
+
+        fflags = spec.compiler_flags['fflags']
+        cflags = spec.compiler_flags['cflags']
+        ldflags = spec.compiler_flags['ldflags']
+
+        if '+mpi' in spec:
+            fc = spec['mpi'].mpif77
+            cc = spec['mpi'].mpicc
+
+        with working_dir(bin_dir):
+            fflags = ['-O3'] + fflags
+            cflags = ['-O3'] + cflags
+            fflags += ['-I.']
+            cflags += ['-I.', '-DGLOBAL_LONG_LONG']
+
+            if self.compiler.name == 'gcc' or self.compiler.name == 'clang':
+                # assuming 'clang' uses 'gfortran'
+                fflags += ['-fdefault-real-8', '-fdefault-double-8']
+                cflags += ['-DUNDERSCORE']
+            elif self.compiler.name == 'intel':
+                fflags += ['-r8']
+                cflags += ['-DUNDERSCORE']
+            elif self.compiler.name == 'xl' or self.compiler.name == 'xl_r':
+                fflags += ['-qrealsize=8']
+                cflags += ['-DPREFIX=jl_', '-DIBM']
+            elif self.compiler.name == 'pgi':
+                fflags += ['-r8']
+                cflags += ['-DUNDERSCORE']
+
+            if '+mpi' in spec:
+                fflags += ['-DMPI', '-DMPIIO']
+                cflags += ['-DMPI', '-DMPIIO']
+            blas_lapack = spec['lapack'].libs + spec['blas'].libs
+            pthread_lib = find_system_libraries('libpthread')
+            ldflags += (blas_lapack + pthread_lib).ld_flags.split()
+            all_arch = {
+                'spack-arch': {
+                    'FC': fc, 'FFLAGS': fflags,
+                    'CC': cc, 'CFLAGS': cflags,
+                    'LD': fc, 'LDFLAGS': ldflags
+                }
+            }
+            os.rename('arch.json', 'arch.json.orig')
+            with open('arch.json', 'w') as file:
+                file.write(json.dumps(all_arch))
+            filter_file(r'^ARCH=.*$', 'ARCH=spack-arch', 'makenek')
+            filter_file(r'^NEK=.*', 'NEK="%s"' % prefix.bin.NekCEM,
+                        'makenek')
+
+        # Install NekCEM in prefix/bin
+        install_tree('../NekCEM', prefix.bin.NekCEM)
+        # Create symlinks to makenek, nek and configurenek scripts
+        with working_dir(prefix.bin):
+            os.symlink(os.path.join('NekCEM', bin_dir, makenek), makenek)
+            os.symlink(
+                os.path.join('NekCEM', bin_dir, configurenek), configurenek)
+            os.symlink(os.path.join('NekCEM', bin_dir, nek), nek)
diff --git a/var/spack/repos/builtin/packages/nektar/package.py b/var/spack/repos/builtin/packages/nektar/package.py
new file mode 100644
index 0000000000..3e04b1c2b1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/nektar/package.py
@@ -0,0 +1,56 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Nektar(CMakePackage):
+    """Nektar++: Spectral/hp Element Framework"""
+
+    homepage = "https://www.nektar.info/"
+    url      = "https://gitlab.nektar.info/nektar/nektar/-/archive/v4.4.1/nektar-v4.4.1.tar.bz2"
+
+    version('4.4.1', '1be7d061c3cafd9a0f1eb8d281d99b89')
+
+    variant('mpi', default=True, description='Builds with mpi support')
+    variant('fftw', default=True, description='Builds with fftw support')
+    variant('arpack', default=True, description='Builds with arpack support')
+    variant('hdf5', default=True, description='Builds with hdf5 support')
+    variant('scotch', default=False,
+            description='Builds with scotch partitioning support')
+
+    depends_on('cmake@2.8.8:', type='build', when="~hdf5")
+    depends_on('cmake@3.2:', type='build', when="+hdf5")
+
+    depends_on('blas')
+    depends_on('lapack')
+    depends_on('boost@1.56.0: +iostreams')
+    depends_on('tinyxml', when='platform=darwin')
+
+    depends_on('mpi', when='+mpi')
+    depends_on('fftw@3.0: +mpi', when="+mpi+fftw")
+    depends_on('fftw@3.0: ~mpi', when="~mpi+fftw")
+    depends_on('arpack-ng +mpi', when="+arpack+mpi")
+    depends_on('arpack-ng ~mpi', when="+arpack~mpi")
+    depends_on('hdf5 +mpi +hl', when="+mpi+hdf5")
+    depends_on('scotch ~mpi ~metis', when="~mpi+scotch")
+    depends_on('scotch +mpi ~metis', when="+mpi+scotch")
+
+    conflicts("+hdf5", when="~mpi",
+              msg="Nektar's hdf5 output is for parallel builds only")
+
+    def cmake_args(self):
+        args = []
+
+        def hasfeature(feature):
+            return 'ON' if feature in self.spec else 'OFF'
+
+        args.append('-DNEKTAR_USE_MPI=%s' % hasfeature('+mpi'))
+        args.append('-DNEKTAR_USE_FFTW=%s' % hasfeature('+fftw'))
+        args.append('-DNEKTAR_USE_ARPACK=%s' % hasfeature('+arpack'))
+        args.append('-DNEKTAR_USE_HDF5=%s' % hasfeature('+hdf5'))
+        args.append('-DNEKTAR_USE_SCOTCH=%s' % hasfeature('+scotch'))
+        args.append('-DNEKTAR_USE_PETSC=OFF')
+        return args
diff --git a/var/spack/repos/builtin/packages/neovim/package.py b/var/spack/repos/builtin/packages/neovim/package.py
index 0f26daf83f..b626f34984 100644
--- a/var/spack/repos/builtin/packages/neovim/package.py
+++ b/var/spack/repos/builtin/packages/neovim/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -32,6 +13,10 @@ class Neovim(CMakePackage):
     homepage = "http://neovim.io"
     url      = "https://github.com/neovim/neovim/archive/v0.2.0.tar.gz"
 
+    version('0.3.1', '5405bced1c929ebc245c75409cd6c7ef')
+    version('0.3.0', 'e5fdb2025757c337c17449c296eddf5b')
+    version('0.2.2', '44b69f8ace88b646ec890670f1e462c4')
+    version('0.2.1', 'f4271f22d2a46fa18dace42849c56a98')
     version('0.2.0', '9af7f61f9f0b1a2891147a479d185aa2')
 
     depends_on('lua@5.1:5.2')
@@ -44,10 +29,11 @@ class Neovim(CMakePackage):
     depends_on('libvterm')
     depends_on('unibilium')
     depends_on('msgpack-c')
+    depends_on('gperf')
 
     def cmake_args(self):
-        # FIXME: Add arguments other than
-        # FIXME: CMAKE_INSTALL_PREFIX and CMAKE_BUILD_TYPE
-        # FIXME: If not needed delete this function
         args = []
+        if self.version >= Version('0.2.1'):
+            args = ['-DPREFER_LUA=ON']
+
         return args
diff --git a/var/spack/repos/builtin/packages/nest/package.py b/var/spack/repos/builtin/packages/nest/package.py
new file mode 100644
index 0000000000..a62838dc7d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/nest/package.py
@@ -0,0 +1,151 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Nest(CMakePackage):
+    """NEST is a simulator for spiking neural network models
+
+    It focuses on the dynamics, size and structure of neural systems rather
+    than on the exact morphology of individual neurons."""
+
+    homepage = "http://www.nest-simulator.org"
+    url      = "https://github.com/nest/nest-simulator/releases/download/v2.12.0/nest-2.12.0.tar.gz"
+
+    version('2.14.0', sha256='d6316d6c9153100a3220488abfa738958c4b65bf2622bd15540e4aa81e79f17f')
+    version('2.12.0', sha256='bac578f38bb0621618ee9d5f2f1febfee60cddc000ff32e51a5f5470bb3df40d')
+    version('2.10.0', sha256='2b6fc562cd6362e812d94bb742562a5a685fb1c7e08403765dbe123d59b0996c')
+    version('2.8.0',  sha256='d47325b27a5599b6ea58a3c4ef06656e7c5a4941c4e94dec6a5c2fa956209915')
+    version('2.6.0',  sha256='5fe4924bc57d0c7dd820aa371de935eedf7e813832c0eee2c976b33c9a8db4cf')
+    version('2.4.2',  sha256='8f86e58c1a12b733ffabd8b0400326e5a3494a458149ea8ebe9f19674d05b91b')
+
+    variant('python', default=True,
+            description='Build the PyNest interface')
+    variant('mpi', default=True,
+            description='Build with MPI bindings')
+    variant('openmp', default=True,
+            description='"Enable OpenMP support"')
+    variant('optimize', default=True,
+            description='Build with MPI bindings')
+    variant('modules', default=False,
+            description='Enables external module support')
+    variant('gsl',     default=True,
+            description="Enable GNU Scientific Library")
+    variant('shared',   default=True,
+            description="Build shared libraries")
+    # TODO add variants for neurosim and music when these are in spack
+
+    conflicts('~gsl', when='@:2.10.99',
+              msg='Option only introduced for non-ancient versions.')
+    conflicts('~shared', when='@:2.10.99',
+              msg='Option only introduced for non-ancient versions.')
+    conflicts('~openmp', when='@:2.10.99',
+              msg='Option only introduced for non-ancient versions.')
+
+    depends_on('python@2.6:',       when='+python', type=('build', 'run'))
+    depends_on('py-numpy',          when='+python', type=('build', 'run'))
+    depends_on('py-cython@0.19.2:', when='+python', type='build')
+    depends_on('py-nose',           when='+python', type='test')
+    depends_on('py-setuptools',     when='+python', type='build')
+
+    depends_on('mpi', when='+mpi')
+
+    depends_on('doxygen', type='build')
+
+    depends_on('gsl', when='+gsl')
+    depends_on('readline')
+    depends_on('libtool')
+    depends_on('pkgconfig', type='build')
+
+    extends('python', when='+python')
+
+    # Before 2.12.0 it was an autotools package
+    @when('@:2.10.99')
+    def cmake(self, spec, prefix):
+        pass
+
+    @when('@:2.10.99')
+    def build(self, spec, prefix):
+        pass
+
+    @when('@:2.10.99')
+    def install(self, spec, prefix):
+        configure_args = ["CXXFLAGS=-std=c++03",
+                          "--prefix=" + prefix,
+                          "--with-openmp"]
+        if '+python' in spec:
+            configure_args.append("--with-python")
+        else:
+            configure_args.append("--without-python")
+        if '+mpi' in spec:
+            configure_args.append("--with-mpi")
+        else:
+            configure_args.append("--without-mpi")
+        if '+optimize' in spec:
+            configure_args.append("--with-optimize")
+        else:
+            configure_args.append("--without-optimize")
+
+        configure(*configure_args)
+
+        make()
+        make("install")
+
+    def cmake_args(self):
+        args = []
+
+        if '+mpi' in self.spec:
+            args.append('-Dwith-mpi=ON')
+        else:
+            args.append('-Dwith-mpi=OFF')
+
+        if '+python':
+            version = self.spec['python'].version[0]
+            args.append('-Dwith-python={0}'.format(version))
+            args.append('-Dcythonize-pynest=' + self.spec['py-cython'].prefix)
+        else:
+            args.append('-Dwith-python=OFF')
+            args.append('-Dcythonize-pynest=OFF')
+
+        if '+optimize' in self.spec:
+            args.append('-Dwith-optimize=ON')
+        else:
+            args.append('-Dwith-optimize=OFF')
+
+        if '+gsl' in self.spec:
+            cmake_options.append('-Dwith-gsl=' + self.spec['gsl'].prefix)
+        else:
+            cmake_options.append('-Dwith-gsl=OFF')
+
+        if '+openmp' in self.spec:
+            cmake_options.append('-Dwith-openmp=ON')
+        else:
+            cmake_options.append('-Dwith-openmp=OFF')
+
+        if '+shared' in self.spec:
+            cmake_options.append('-Dstatic-libraries=OFF')
+        else:
+            cmake_options.append('-Dstatic-libraries=ON')
+
+        return args
+
+    @when('@:2.14.0+modules')
+    @run_after('install')
+    def install_headers(self):
+        # copy source files to installation folder for older versions
+        # (these are needed for modules to build against)
+        # see https://github.com/nest/nest-simulator/pull/844
+        path_headers = join_path(prefix, "include", "nest")
+
+        mkdirp(path_headers)
+
+        for suffix in ["h", "hpp"]:
+            for f in find_headers('*.{0}'.format(suffix),
+                                  self.stage.source_path, recursive=True):
+                install(f, path_headers)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.set("NEST_INSTALL_DIR", self.spec.prefix)
diff --git a/var/spack/repos/builtin/packages/netcdf-cxx/package.py b/var/spack/repos/builtin/packages/netcdf-cxx/package.py
index 916c8f301a..07ecd2f22a 100644
--- a/var/spack/repos/builtin/packages/netcdf-cxx/package.py
+++ b/var/spack/repos/builtin/packages/netcdf-cxx/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,3 +18,10 @@ class NetcdfCxx(AutotoolsPackage):
     version('4.2', 'd32b20c00f144ae6565d9e98d9f6204c')
 
     depends_on('netcdf')
+
+    @property
+    def libs(self):
+        shared = True
+        return find_libraries(
+            'libnetcdf_c++', root=self.prefix, shared=shared, recursive=True
+        )
diff --git a/var/spack/repos/builtin/packages/netcdf-cxx4/package.py b/var/spack/repos/builtin/packages/netcdf-cxx4/package.py
index 0e15d67bc1..8d228cc3c0 100644
--- a/var/spack/repos/builtin/packages/netcdf-cxx4/package.py
+++ b/var/spack/repos/builtin/packages/netcdf-cxx4/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,3 +21,13 @@ class NetcdfCxx4(AutotoolsPackage):
     depends_on('libtool', type='build')
 
     force_autoreconf = True
+
+    def configure_args(self):
+        return ['CPPFLAGS=-I' + self.spec['netcdf'].prefix.include]
+
+    @property
+    def libs(self):
+        shared = True
+        return find_libraries(
+            'libnetcdf_c++4', root=self.prefix, shared=shared, recursive=True
+        )
diff --git a/var/spack/repos/builtin/packages/netcdf-fortran/nag.patch b/var/spack/repos/builtin/packages/netcdf-fortran/nag.patch
new file mode 100644
index 0000000000..458c18813e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/netcdf-fortran/nag.patch
@@ -0,0 +1,31 @@
+diff --git a/configure b/configure
+index 06ac8b0..d518a1a 100755
+--- a/configure
++++ b/configure
+@@ -10657,6 +10657,8 @@ _LT_EOF
+ 	lf95*)				# Lahey Fortran 8.1
+ 	  whole_archive_flag_spec=
+ 	  tmp_sharedflag='--shared' ;;
++	nagfor*)
++	  tmp_sharedflag='-Wl,-shared' ;;
+ 	xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below)
+ 	  tmp_sharedflag='-qmkshrobj'
+ 	  tmp_addflag= ;;
+@@ -14252,6 +14254,8 @@ _LT_EOF
+ 	lf95*)				# Lahey Fortran 8.1
+ 	  whole_archive_flag_spec_F77=
+ 	  tmp_sharedflag='--shared' ;;
++	nagfor*)
++	  tmp_sharedflag='-Wl,-shared' ;;
+ 	xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below)
+ 	  tmp_sharedflag='-qmkshrobj'
+ 	  tmp_addflag= ;;
+@@ -17142,6 +17146,8 @@ _LT_EOF
+ 	lf95*)				# Lahey Fortran 8.1
+ 	  whole_archive_flag_spec_FC=
+ 	  tmp_sharedflag='--shared' ;;
++	nagfor*)
++	  tmp_sharedflag='-Wl,-shared' ;;
+ 	xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below)
+ 	  tmp_sharedflag='-qmkshrobj'
+ 	  tmp_addflag= ;;
diff --git a/var/spack/repos/builtin/packages/netcdf-fortran/package.py b/var/spack/repos/builtin/packages/netcdf-fortran/package.py
index f62db6eca0..64d4eca2a0 100644
--- a/var/spack/repos/builtin/packages/netcdf-fortran/package.py
+++ b/var/spack/repos/builtin/packages/netcdf-fortran/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,6 +17,13 @@ class NetcdfFortran(AutotoolsPackage):
 
     depends_on('netcdf')
 
+    # The default libtool.m4 is too old to handle NAG compiler properly:
+    # https://github.com/Unidata/netcdf-fortran/issues/94
+    patch('nag.patch', when='@:4.4.4%nag')
+
+    def configure_args(self):
+        return ['CPPFLAGS=-I' + self.spec['netcdf'].prefix.include]
+
     @property
     def libs(self):
         libraries = ['libnetcdff']
@@ -46,5 +34,5 @@ class NetcdfFortran(AutotoolsPackage):
         shared = 'shared' in query_parameters
 
         return find_libraries(
-            libraries, root=self.prefix, shared=shared, recurse=True
+            libraries, root=self.prefix, shared=shared, recursive=True
         )
diff --git a/var/spack/repos/builtin/packages/netcdf/package.py b/var/spack/repos/builtin/packages/netcdf/package.py
index f12e2941c8..8a806dbf95 100644
--- a/var/spack/repos/builtin/packages/netcdf/package.py
+++ b/var/spack/repos/builtin/packages/netcdf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 import numbers
@@ -45,6 +26,7 @@ class Netcdf(AutotoolsPackage):
 
     # Version 4.4.1.1 is having problems in tests
     #    https://github.com/Unidata/netcdf-c/issues/343
+    version('4.6.1', 'ee81c593efc8a6229d9bcb350b6d7849')
     version('4.4.1.1', '503a2d6b6035d116ed53b1d80c811bda')
     # netcdf@4.4.1 can crash on you (in real life and in tests).  See:
     #    https://github.com/Unidata/netcdf-c/issues/282
@@ -152,10 +134,10 @@ class Netcdf(AutotoolsPackage):
                   r'\1{0}\2'.format(max_vars))
 
     def configure_args(self):
-        CFLAGS = []
-        CPPFLAGS = []
-        LDFLAGS = []
-        LIBS = []
+        cflags = []
+        cppflags = []
+        ldflags = []
+        libs = []
 
         config_args = ['--enable-v2',
                        '--enable-utilities',
@@ -176,7 +158,7 @@ class Netcdf(AutotoolsPackage):
         if '~shared' in self.spec:
             # We don't have shared libraries but we still want it to be
             # possible to use this library in shared builds
-            CFLAGS.append(self.compiler.pic_flag)
+            cflags.append(self.compiler.pic_flag)
 
         config_args += self.enable_or_disable('dap')
         # config_args += self.enable_or_disable('cdmremote')
@@ -188,10 +170,10 @@ class Netcdf(AutotoolsPackage):
             # undefined reference to `SSL_CTX_use_certificate_chain_file
             curl = self.spec['curl']
             curl_libs = curl.libs
-            LIBS.append(curl_libs.link_flags)
-            LDFLAGS.append(curl_libs.search_flags)
+            libs.append(curl_libs.link_flags)
+            ldflags.append(curl_libs.search_flags)
             # TODO: figure out how to get correct flags via headers.cpp_flags
-            CPPFLAGS.append('-I' + curl.prefix.include)
+            cppflags.append('-I' + curl.prefix.include)
 
         if self.spec.satisfies('@4.4:'):
             if '+mpi' in self.spec:
@@ -203,16 +185,16 @@ class Netcdf(AutotoolsPackage):
         # are removed. Variables CPPFLAGS, LDFLAGS, and LD_LIBRARY_PATH must be
         # used instead.
         hdf5_hl = self.spec['hdf5:hl']
-        CPPFLAGS.append(hdf5_hl.headers.cpp_flags)
-        LDFLAGS.append(hdf5_hl.libs.search_flags)
+        cppflags.append(hdf5_hl.headers.cpp_flags)
+        ldflags.append(hdf5_hl.libs.search_flags)
 
         if '+parallel-netcdf' in self.spec:
             config_args.append('--enable-pnetcdf')
             pnetcdf = self.spec['parallel-netcdf']
-            CPPFLAGS.append(pnetcdf.headers.cpp_flags)
+            cppflags.append(pnetcdf.headers.cpp_flags)
             # TODO: change to pnetcdf.libs.search_flags once 'parallel-netcdf'
             # package gets custom implementation of 'libs'
-            LDFLAGS.append('-L' + pnetcdf.prefix.lib)
+            ldflags.append('-L' + pnetcdf.prefix.lib)
         else:
             config_args.append('--disable-pnetcdf')
 
@@ -222,26 +204,26 @@ class Netcdf(AutotoolsPackage):
         config_args += self.enable_or_disable('hdf4')
         if '+hdf4' in self.spec:
             hdf4 = self.spec['hdf']
-            CPPFLAGS.append(hdf4.headers.cpp_flags)
+            cppflags.append(hdf4.headers.cpp_flags)
             # TODO: change to hdf4.libs.search_flags once 'hdf'
             # package gets custom implementation of 'libs' property.
-            LDFLAGS.append('-L' + hdf4.prefix.lib)
+            ldflags.append('-L' + hdf4.prefix.lib)
             # TODO: change to self.spec['jpeg'].libs.link_flags once the
             # implementations of 'jpeg' virtual package get 'jpeg_libs'
             # property.
-            LIBS.append('-ljpeg')
+            libs.append('-ljpeg')
             if '+szip' in hdf4:
                 # This should also come from hdf4.libs
-                LIBS.append('-lsz')
+                libs.append('-lsz')
 
         # Fortran support
         # In version 4.2+, NetCDF-C and NetCDF-Fortran have split.
         # Use the netcdf-fortran package to install Fortran support.
 
-        config_args.append('CFLAGS=' + ' '.join(CFLAGS))
-        config_args.append('CPPFLAGS=' + ' '.join(CPPFLAGS))
-        config_args.append('LDFLAGS=' + ' '.join(LDFLAGS))
-        config_args.append('LIBS=' + ' '.join(LIBS))
+        config_args.append('CFLAGS=' + ' '.join(cflags))
+        config_args.append('CPPFLAGS=' + ' '.join(cppflags))
+        config_args.append('LDFLAGS=' + ' '.join(ldflags))
+        config_args.append('LIBS=' + ' '.join(libs))
 
         return config_args
 
diff --git a/var/spack/repos/builtin/packages/netgauge/package.py b/var/spack/repos/builtin/packages/netgauge/package.py
index f850a22c2c..69557c8cb9 100644
--- a/var/spack/repos/builtin/packages/netgauge/package.py
+++ b/var/spack/repos/builtin/packages/netgauge/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/netgen/package.py b/var/spack/repos/builtin/packages/netgen/package.py
index 9d6c4de81a..c67ed8cced 100644
--- a/var/spack/repos/builtin/packages/netgen/package.py
+++ b/var/spack/repos/builtin/packages/netgen/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -43,12 +24,13 @@ class Netgen(AutotoolsPackage):
     variant("gui", default=False, description='enable gui')
     variant("metis", default=False, description='use metis for partitioning')
 
+    depends_on('zlib')
     depends_on('mpi', when='+mpi')
     depends_on('oce+X11', when='+oce')
     depends_on('metis', when='+metis')
 
     def url_for_version(self, version):
-        url = "https://gigenet.dl.sourceforge.net/project/netgen-mesher/netgen-mesher/{0}/netgen-{1}.tar.gz"
+        url = "http://gigenet.dl.sourceforge.net/project/netgen-mesher/netgen-mesher/{0}/netgen-{1}.tar.gz"
         return url.format(version.up_to(2), version)
 
     def configure_args(self):
diff --git a/var/spack/repos/builtin/packages/netlib-lapack/ibm-xl.patch b/var/spack/repos/builtin/packages/netlib-lapack/ibm-xl.patch
index c9598a4e7c..c6fba2a028 100644
--- a/var/spack/repos/builtin/packages/netlib-lapack/ibm-xl.patch
+++ b/var/spack/repos/builtin/packages/netlib-lapack/ibm-xl.patch
@@ -1,6 +1,17 @@
-diff -Naur lapack-3.6.1/CMAKE/CheckLAPACKCompilerFlags.cmake lapack-3.6.1-patched/CMAKE/CheckLAPACKCompilerFlags.cmake
---- lapack-3.6.1/CMAKE/CheckLAPACKCompilerFlags.cmake	2017-01-27 17:14:37.414854283 -0500
-+++ lapack-3.6.1-patched/CMAKE/CheckLAPACKCompilerFlags.cmake	2017-01-27 17:14:24.754719546 -0500
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -62,7 +62,7 @@
+     set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fp-model strict")
+   endif()
+   if("${CMAKE_Fortran_COMPILER}" MATCHES "xlf")
+-    set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -qnosave -qstrict=none")
++    set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -qnosave -qstrict")
+   endif()
+ # Delete libmtsk in linking sequence for Sun/Oracle Fortran Compiler.
+ # This library is not present in the Sun package SolarisStudio12.3-linux-x86-bin
+
+--- a/CMAKE/CheckLAPACKCompilerFlags.cmake
++++ b/CMAKE/CheckLAPACKCompilerFlags.cmake
 @@ -43,12 +43,6 @@
    if( "${CMAKE_Fortran_FLAGS}" MATCHES "-qflttrap=[a-zA-Z:]:enable" )
      set( FPE_EXIT TRUE )
@@ -14,3 +25,18 @@ diff -Naur lapack-3.6.1/CMAKE/CheckLAPACKCompilerFlags.cmake lapack-3.6.1-patche
  
  # HP Fortran
  elseif( CMAKE_Fortran_COMPILER_ID STREQUAL "HP" )
+
+--- a/CBLAS/CMakeLists.txt
++++ b/CBLAS/CMakeLists.txt
+@@ -12,8 +12,8 @@
+                          SYMBOL_NAMESPACE "F77_")
+ if(NOT FortranCInterface_GLOBAL_FOUND OR NOT FortranCInterface_MODULE_FOUND)
+   message(WARNING "Reverting to pre-defined include/lapacke_mangling.h")
+-  configure_file(include/lapacke_mangling_with_flags.h.in
+-                 ${LAPACK_BINARY_DIR}/include/lapacke_mangling.h)
++  configure_file(include/cblas_mangling_with_flags.h.in
++                 ${LAPACK_BINARY_DIR}/include/cblas_mangling.h)
+ endif()
+ 
+ include_directories(include ${LAPACK_BINARY_DIR}/include)
+
diff --git a/var/spack/repos/builtin/packages/netlib-lapack/package.py b/var/spack/repos/builtin/packages/netlib-lapack/package.py
index 8166b75bf5..b5080d0ba8 100644
--- a/var/spack/repos/builtin/packages/netlib-lapack/package.py
+++ b/var/spack/repos/builtin/packages/netlib-lapack/package.py
@@ -1,31 +1,12 @@
-#############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class NetlibLapack(Package):
+class NetlibLapack(CMakePackage):
     """LAPACK version 3.X is a comprehensive FORTRAN library that does
     linear algebra operations including matrix inversions, least squared
     solutions to linear sets of equations, eigenvector analysis, singular
@@ -36,6 +17,10 @@ class NetlibLapack(Package):
     homepage = "http://www.netlib.org/lapack/"
     url = "http://www.netlib.org/lapack/lapack-3.5.0.tgz"
 
+    version('3.8.0', '96591affdbf58c450d45c1daa540dbd2',
+            url='http://www.netlib.org/lapack/lapack-3.8.0.tar.gz')
+    version('3.7.1', 'dcdeeed73de152c4643ccc5b1aeb453c')
+    version('3.7.0', '697bb8d67c7d336a0f339cc9dd0fa72f')
     version('3.6.1', '421b2cb72e15f237e144428f9c460ee0')
     version('3.6.0', 'f2f6c67134e851fe189bb3ca1fbb5101')
     version('3.5.0', 'b1d3e3e425b2e44a06760ff173104bdf')
@@ -44,23 +29,47 @@ class NetlibLapack(Package):
     version('3.4.0', '02d5706ec03ba885fc246e5fa10d8c70')
     version('3.3.1', 'd0d533ec9a5b74933c2a1e84eedc58b4')
 
-    variant('debug', default=False, description='Activates the Debug build type')
     variant('shared', default=True, description="Build shared library version")
     variant('external-blas', default=False,
             description='Build lapack with an external blas')
 
     variant('lapacke', default=True,
             description='Activates the build of the LAPACKE C interface')
+    variant('xblas', default=False,
+            description='Builds extended precision routines using XBLAS')
 
-    patch('ibm-xl.patch', when='@3:6%xl')
-    patch('ibm-xl.patch', when='@3:6%xl_r')
+    patch('ibm-xl.patch', when='@3.7: %xl')
+    patch('ibm-xl.patch', when='@3.7: %xl_r')
+
+    # https://github.com/Reference-LAPACK/lapack/issues/228
+    # TODO: update 'when' once the version of lapack
+    # containing the fix is released and added to Spack.
+    patch('undefined_declarations.patch', when='@3.8.0:')
+
+    # https://github.com/Reference-LAPACK/lapack/pull/268
+    # TODO: update 'when' once the version of lapack
+    # containing the fix is released and added to Spack.
+    patch('testing.patch', when='@3.7.0:')
 
     # virtual dependency
     provides('blas', when='~external-blas')
     provides('lapack')
 
-    depends_on('cmake', type='build')
     depends_on('blas', when='+external-blas')
+    depends_on('netlib-xblas+fortran+plain_blas', when='+xblas')
+    depends_on('python@2.7:', type='test')
+
+    # We need to run every phase twice in order to get static and shared
+    # versions of the libraries. When ~shared, we run the default
+    # implementations of the CMakePackage's phases and get only one building
+    # directory 'spack-build-static' with -DBUILD_SHARED_LIBS:BOOL=OFF (see
+    # implementations of self.build_directory and self.cmake_args() below).
+    # When +shared, we run the overridden methods for the phases, each
+    # running the default implementation twice with different values for
+    # self._building_shared. As a result, we get two building directories:
+    # 'spack-build-static' with -DBUILD_SHARED_LIBS:BOOL=OFF and
+    # 'spack-build-shared' with -DBUILD_SHARED_LIBS:BOOL=ON.
+    _building_shared = False
 
     def patch(self):
         # Fix cblas CMakeLists.txt -- has wrong case for subdirectory name.
@@ -73,61 +82,124 @@ class NetlibLapack(Package):
     @property
     def blas_libs(self):
         shared = True if '+shared' in self.spec else False
+        query_parameters = self.spec.last_query.extra_parameters
+        query2libraries = {
+            tuple(): ['libblas'],
+            ('c', 'fortran'): [
+                'libcblas',
+                'libblas',
+            ],
+            ('c',): [
+                'libcblas',
+            ],
+            ('fortran',): [
+                'libblas',
+            ]
+        }
+        key = tuple(sorted(query_parameters))
+        libraries = query2libraries[key]
         return find_libraries(
-            'libblas', root=self.prefix, shared=shared, recurse=True
+            libraries, root=self.prefix, shared=shared, recursive=True
         )
 
     @property
     def lapack_libs(self):
         shared = True if '+shared' in self.spec else False
+        query_parameters = self.spec.last_query.extra_parameters
+        query2libraries = {
+            tuple(): ['liblapack'],
+            ('c', 'fortran'): [
+                'liblapacke',
+                'liblapack',
+            ],
+            ('c',): [
+                'liblapacke',
+            ],
+            ('fortran',): [
+                'liblapack',
+            ]
+        }
+        key = tuple(sorted(query_parameters))
+        libraries = query2libraries[key]
         return find_libraries(
-            'liblapack', root=self.prefix, shared=shared, recurse=True
+            libraries, root=self.prefix, shared=shared, recursive=True
         )
 
-    def install_one(self, spec, prefix, shared):
-        cmake_args = [
-            '-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if shared else 'OFF'),
-            '-DCMAKE_BUILD_TYPE:STRING=%s' % (
-                'Debug' if '+debug' in spec else 'Release'),
-            '-DLAPACKE:BOOL=%s' % ('ON' if '+lapacke' in spec else 'OFF')]
-        if spec.satisfies('@3.6.0:'):
-            cmake_args.extend(['-DCBLAS=ON'])  # always build CBLAS
+    @property
+    def headers(self):
+        include_dir = self.spec.prefix.include
+        cblas_h = join_path(include_dir, 'cblas.h')
+        lapacke_h = join_path(include_dir, 'lapacke.h')
+        return HeaderList([cblas_h, lapacke_h])
 
-        if self.compiler.name == 'intel':
+    @property
+    def build_directory(self):
+        return join_path(self.stage.source_path,
+                         'spack-build-shared' if self._building_shared
+                         else 'spack-build-static')
+
+    def cmake_args(self):
+        args = ['-DBUILD_SHARED_LIBS:BOOL=' +
+                ('ON' if self._building_shared else 'OFF')]
+
+        if self.spec.satisfies('+lapacke'):
+            args.extend(['-DLAPACKE:BOOL=ON', '-DLAPACKE_WITH_TMG:BOOL=ON'])
+        else:
+            args.extend(['-DLAPACKE:BOOL=OFF', '-DLAPACKE_WITH_TMG:BOOL=OFF'])
+
+        if self.spec.satisfies('@3.6.0:'):
+            args.append('-DCBLAS=ON')  # always build CBLAS
+
+        if self.spec.satisfies('%intel'):
             # Intel compiler finds serious syntax issues when trying to
             # build CBLAS and LapackE
-            cmake_args.extend(['-DCBLAS=OFF'])
-            cmake_args.extend(['-DLAPACKE:BOOL=OFF'])
+            args.extend(['-DCBLAS=OFF', '-DLAPACKE:BOOL=OFF'])
 
-        if self.compiler.name == 'xl' or self.compiler.name == 'xl_r':
+        if self.spec.satisfies('%xl') or self.spec.satisfies('%xl_r'):
             # use F77 compiler if IBM XL
-            cmake_args.extend([
-                '-DCMAKE_Fortran_COMPILER=%s' % self.compiler.f77,
-                '-DCMAKE_Fortran_FLAGS=-qzerosize'
-            ])
+            args.extend(['-DCMAKE_Fortran_COMPILER=' + self.compiler.f77,
+                         '-DCMAKE_Fortran_FLAGS=' +
+                         (' '.join(self.spec.compiler_flags['fflags'])) +
+                         " -O3 -qnohot"])
 
         # deprecated routines are commonly needed by, for example, suitesparse
         # Note that OpenBLAS spack is built with deprecated routines
-        cmake_args.extend(['-DBUILD_DEPRECATED:BOOL=ON'])
+        args.append('-DBUILD_DEPRECATED:BOOL=ON')
+
+        if self.spec.satisfies('+external-blas'):
+            args.extend(['-DUSE_OPTIMIZED_BLAS:BOOL=ON',
+                         '-DBLAS_LIBRARIES:PATH=' +
+                         self.spec['blas'].libs.joined(';')])
+
+        if self.spec.satisfies('+xblas'):
+            args.extend(['-DXBLAS_INCLUDE_DIR=' +
+                         self.spec['netlib-xblas'].prefix.include,
+                         '-DXBLAS_LIBRARY=' +
+                         self.spec['netlib-xblas'].libs.joined(';')])
+
+        args.append('-DBUILD_TESTING:BOOL=' +
+                    ('ON' if self.run_tests else 'OFF'))
 
-        if '+external-blas' in spec:
-            cmake_args.extend([
-                '-DUSE_OPTIMIZED_BLAS:BOOL=ON',
-                '-DBLAS_LIBRARIES:PATH=%s' % spec['blas'].libs.joined(';')
-            ])
+        return args
 
-        cmake_args.extend(std_cmake_args)
+    # Build, install, and check both static and shared versions of the
+    # libraries when +shared
+    @when('+shared')
+    def cmake(self, spec, prefix):
+        for self._building_shared in (False, True):
+            super(NetlibLapack, self).cmake(spec, prefix)
 
-        build_dir = 'spack-build' + ('-shared' if shared else '-static')
-        with working_dir(build_dir, create=True):
-            cmake('..', *cmake_args)
-            make()
-            make("install")
+    @when('+shared')
+    def build(self, spec, prefix):
+        for self._building_shared in (False, True):
+            super(NetlibLapack, self).build(spec, prefix)
 
+    @when('+shared')
     def install(self, spec, prefix):
-        # Always build static libraries.
-        self.install_one(spec, prefix, False)
+        for self._building_shared in (False, True):
+            super(NetlibLapack, self).install(spec, prefix)
 
-        # Build shared libraries if requested.
-        if '+shared' in spec:
-            self.install_one(spec, prefix, True)
+    @when('+shared')
+    def check(self):
+        for self._building_shared in (False, True):
+            super(NetlibLapack, self).check()
diff --git a/var/spack/repos/builtin/packages/netlib-lapack/testing.patch b/var/spack/repos/builtin/packages/netlib-lapack/testing.patch
new file mode 100644
index 0000000000..fce18548c4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/netlib-lapack/testing.patch
@@ -0,0 +1,13 @@
+diff --git a/TESTING/LIN/alahd.f b/TESTING/LIN/alahd.f
+index 8f4cd58d..6a4946e0 100644
+--- a/TESTING/LIN/alahd.f
++++ b/TESTING/LIN/alahd.f
+@@ -1036,7 +1036,7 @@
+  9929 FORMAT( ' Test ratios (1-3: ', A1, 'TZRZF):' )
+  9920 FORMAT( 3X, ' 7-10: same as 3-6', 3X, ' 11-14: same as 3-6' )
+  9921 FORMAT( ' Test ratios:', / '    (1-2: ', A1, 'GELS, 3-6: ', A1,
+-     $      'GELSY, 7-10: ', A1, 'GELSS, 11-14: ', A1, 'GELSD, 15-16: '
++     $      'GELSY, 7-10: ', A1, 'GELSS, 11-14: ', A1, 'GELSD, 15-16: ',
+      $        A1, 'GETSLS)')
+  9928 FORMAT( 7X, 'where ALPHA = ( 1 + SQRT( 17 ) ) / 8' )
+  9927 FORMAT( 3X, I2, ': ABS( Largest element in L )', / 12X,
diff --git a/var/spack/repos/builtin/packages/netlib-lapack/undefined_declarations.patch b/var/spack/repos/builtin/packages/netlib-lapack/undefined_declarations.patch
new file mode 100644
index 0000000000..9dac2562f7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/netlib-lapack/undefined_declarations.patch
@@ -0,0 +1,26 @@
+diff --git a/SRC/dsytrf_aa_2stage.f b/SRC/dsytrf_aa_2stage.f
+index 2991305..f5f06cc 100644
+--- a/SRC/dsytrf_aa_2stage.f
++++ b/SRC/dsytrf_aa_2stage.f
+@@ -191,7 +191,7 @@
+       EXTERNAL           LSAME, ILAENV
+ *     ..
+ *     .. External Subroutines ..
+-      EXTERNAL           XERBLA, DCOPY, DLACGV, DLACPY,
++      EXTERNAL           XERBLA, DCOPY, DLACPY,
+      $                   DLASET, DGBTRF, DGEMM,  DGETRF, 
+      $                   DSYGST, DSWAP, DTRSM 
+ *     ..
+diff --git a/SRC/ssytrf_aa_2stage.f b/SRC/ssytrf_aa_2stage.f
+index be6809d..a929749 100644
+--- a/SRC/ssytrf_aa_2stage.f
++++ b/SRC/ssytrf_aa_2stage.f
+@@ -191,7 +191,7 @@
+       EXTERNAL           LSAME, ILAENV
+ *     ..
+ *     .. External Subroutines ..
+-      EXTERNAL           XERBLA, SCOPY, SLACGV, SLACPY,
++      EXTERNAL           XERBLA, SCOPY, SLACPY,
+      $                   SLASET, SGBTRF, SGEMM,  SGETRF, 
+      $                   SSYGST, SSWAP, STRSM 
+ *     ..
diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
index 614cbeea4b..0bc2025ba6 100644
--- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py
+++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import sys
 
@@ -59,12 +40,12 @@ class NetlibScalapack(CMakePackage):
     depends_on('cmake', when='@2.0.0:', type='build')
 
     @property
-    def scalapack_libs(self):
+    def libs(self):
         # Note that the default will be to search
         # for 'libnetlib-scalapack.<suffix>'
         shared = True if '+shared' in self.spec else False
         return find_libraries(
-            'libscalapack', root=self.prefix, shared=shared, recurse=True
+            'libscalapack', root=self.prefix, shared=shared, recursive=True
         )
 
     def cmake_args(self):
diff --git a/var/spack/repos/builtin/packages/netlib-xblas/package.py b/var/spack/repos/builtin/packages/netlib-xblas/package.py
new file mode 100644
index 0000000000..6c837f0da8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/netlib-xblas/package.py
@@ -0,0 +1,71 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class NetlibXblas(AutotoolsPackage):
+    """XBLAS is a reference implementation for extra precision BLAS.
+
+       XBLAS is a reference implementation for the dense and banded BLAS
+       routines, along with extended and mixed precision version. Extended
+       precision is only used internally; input and output arguments remain
+       the same as in the existing BLAS. Extra precisions is implemented as
+       double-double (i.e., 128-bit total, 106-bit significand). Mixed
+       precision permits some input/output arguments of different types
+       (mixing real and complex) or precisions (mixing single and
+       double). This implementation is proof of concept, and no attempt was
+       made to optimize performance; performance should be as good as
+       straightforward but careful code written by hand."""
+
+    homepage = "http://www.netlib.org/xblas"
+    url      = "http://www.netlib.org/xblas/xblas.tar.gz"
+
+    version('1.0.248', '990c680fb5e446bb86c10936e4cd7f88')
+
+    variant('fortran', default=True,
+            description='Build Fortran interfaces')
+    variant('plain_blas', default=True,
+            description='As part of XBLAS, build plain BLAS routines')
+
+    provides('blas', when='+plain_blas')
+
+    @property
+    def libs(self):
+        return find_libraries(['libxblas'], root=self.prefix,
+                              shared=False, recursive=True)
+
+    def configure_args(self):
+        args = []
+
+        if self.spec.satisfies('~fortran'):
+            args += ['--disable-fortran']
+
+        if self.spec.satisfies('~plain_blas'):
+            args += ['--disable-plain-blas']
+
+        return args
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.lib)
+        install('libxblas.a', prefix.lib)
+
+        if self.spec.satisfies('+plain_blas'):
+            # XBLAS should be a drop-in BLAS replacement
+            install('libxblas.a', join_path(prefix.lib, 'libblas.a'))
+
+        headers = ['f2c-bridge.h',
+                   'blas_dense_proto.h',
+                   'blas_enum.h',
+                   'blas_extended.h',
+                   'blas_extended_private.h',
+                   'blas_extended_proto.h',
+                   'blas_fpu.h',
+                   'blas_malloc.h']
+        mkdirp(prefix.include)
+        for h in headers:
+            install(join_path('src', h), prefix.include)
+
+        return
diff --git a/var/spack/repos/builtin/packages/nettle/package.py b/var/spack/repos/builtin/packages/nettle/package.py
index 591483b2f9..c371327901 100644
--- a/var/spack/repos/builtin/packages/nettle/package.py
+++ b/var/spack/repos/builtin/packages/nettle/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,8 +11,9 @@ class Nettle(AutotoolsPackage):
     that is designed to fit easily in many contexts."""
 
     homepage = "https://www.lysator.liu.se/~nisse/nettle/"
-    url      = "http://ftp.gnu.org/gnu/nettle/nettle-3.3.tar.gz"
+    url      = "https://ftpmirror.gnu.org/nettle/nettle-3.3.tar.gz"
 
+    version('3.4',   'dc0f13028264992f58e67b4e8915f53d')
     version('3.3',   '10f969f78a463704ae73529978148dbe')
     version('3.2',   'afb15b4764ebf1b4e6d06c62bd4d29e4')
     version('2.7.1', '003d5147911317931dd453520eb234a5')
diff --git a/var/spack/repos/builtin/packages/neuron/package.py b/var/spack/repos/builtin/packages/neuron/package.py
new file mode 100644
index 0000000000..ade0552c60
--- /dev/null
+++ b/var/spack/repos/builtin/packages/neuron/package.py
@@ -0,0 +1,202 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import os
+from spack import *
+
+
+class Neuron(Package):
+    """NEURON is a simulation environment for single and networks of neurons.
+
+    NEURON is a simulation environment for modeling individual and networks of
+    neurons. NEURON models individual neurons via the use of sections that are
+    automatically subdivided into individual compartments, instead of
+    requiring the user to manually create compartments. The primary scripting
+    language is hoc but a Python interface is also available.
+    """
+
+    homepage = "https://www.neuron.yale.edu/"
+    url      = "http://www.neuron.yale.edu/ftp/neuron/versions/v7.5/nrn-7.5.tar.gz"
+    git      = "https://github.com/nrnhines/nrn.git"
+
+    version('develop', branch='master')
+    version('7.5', 'fb72c841374dfacbb6c2168ff57bfae9')
+    version('7.4', '2c0bbee8a9e55d60fa26336f4ab7acbf')
+    version('7.3', '993e539cb8bf102ca52e9fefd644ab61')
+    version('7.2', '5486709b6366add932e3a6d141c4f7ad')
+
+    variant('mpi',           default=True,  description='Enable MPI parallelism')
+    variant('python',        default=True,  description='Enable python')
+    variant('shared',        default=False, description='Build shared libraries')
+    variant('cross-compile', default=False, description='Build for cross-compile environment')
+    variant('multisend',     default=True,  description="Enable multi-send spike exchange")
+    variant('rx3d',          default=False, description="Enable cython translated 3-d rxd")
+
+    depends_on('flex',       type='build')
+    depends_on('bison',      type='build')
+    depends_on('automake',   type='build')
+    depends_on('automake',   type='build')
+    depends_on('autoconf',   type='build')
+    depends_on('libtool',    type='build')
+    depends_on('pkgconfig',  type='build')
+
+    depends_on('mpi',         when='+mpi')
+    depends_on('python@2.6:', when='+python')
+    depends_on('ncurses',     when='~cross-compile')
+
+    conflicts('~shared', when='+python')
+
+    filter_compiler_wrappers('*/bin/nrniv_makefile')
+
+    def get_neuron_archdir(self):
+        """Determine the architecture-specific neuron base directory.
+
+        Instead of recreating the logic of the neuron's configure
+        we dynamically find the architecture-specific directory by
+        looking for a specific binary.
+        """
+        file_list = find(self.prefix, '*/bin/nrniv_makefile')
+        # check needed as when initially evaluated the prefix is empty
+        if file_list:
+            neuron_archdir = os.path.dirname(os.path.dirname(file_list[0]))
+        else:
+            neuron_archdir = self.prefix
+
+        return neuron_archdir
+
+    def patch(self):
+        # aclocal need complete include path (especially on os x)
+        pkgconf_inc = '-I %s/share/aclocal/' % (self.spec['pkgconfig'].prefix)
+        libtool_inc = '-I %s/share/aclocal/' % (self.spec['libtool'].prefix)
+        newpath = 'aclocal -I m4 %s %s' % (pkgconf_inc, libtool_inc)
+        filter_file(r'aclocal -I m4', r'%s' % newpath, "build.sh")
+
+    def get_arch_options(self, spec):
+        options = []
+
+        if spec.satisfies('+cross-compile'):
+            options.extend(['cross_compiling=yes',
+                            '--without-memacs',
+                            '--without-nmodl'])
+
+        # need to enable bg-q arch
+        if 'bgq' in self.spec.architecture:
+            options.extend(['--enable-bluegeneQ',
+                            '--host=powerpc64'])
+
+        # on os-x disable building carbon 'click' utility
+        if 'darwin' in self.spec.architecture:
+            options.append('macdarwin=no')
+
+        return options
+
+    def get_python_options(self, spec):
+        options = []
+
+        if spec.satisfies('+python'):
+            python_exec = spec['python'].command.path
+            py_inc = spec['python'].headers.directories[0]
+            py_lib = spec['python'].prefix.lib
+
+            if not os.path.isdir(py_lib):
+                py_lib = spec['python'].prefix.lib64
+
+            options.extend(['--with-nrnpython=%s' % python_exec,
+                            '--disable-pysetup',
+                            'PYINCDIR=%s' % py_inc,
+                            'PYLIBDIR=%s' % py_lib])
+
+            if spec.satisfies('~cross-compile'):
+                options.append('PYTHON_BLD=%s' % python_exec)
+
+        else:
+            options.append('--without-nrnpython')
+
+        return options
+
+    def get_compiler_options(self, spec):
+        flags = '-O2 -g'
+
+        if 'bgq' in self.spec.architecture:
+            flags = '-O3 -qtune=qp -qarch=qp -q64 -qstrict -qnohot -g'
+
+        if self.spec.satisfies('%pgi'):
+            flags += ' ' + self.compiler.pic_flag
+
+        return ['CFLAGS=%s' % flags,
+                'CXXFLAGS=%s' % flags]
+
+    def build_nmodl(self, spec, prefix):
+        # build components for front-end arch in cross compiling environment
+        options = ['--prefix=%s' % prefix,
+                   '--with-nmodl-only',
+                   '--without-x']
+
+        if 'bgq' in self.spec.architecture:
+            flags = '-qarch=ppc64'
+            options.extend(['CFLAGS=%s' % flags,
+                            'CXXFLAGS=%s' % flags])
+
+        if 'cray' in self.spec.architecture:
+            flags = '-target-cpu=x86_64 -target-network=none'
+            options.extend(['CFLAGS=%s' % flags,
+                            'CXXFLAGS=%s' % flags])
+
+        configure = Executable(join_path(self.stage.source_path, 'configure'))
+        configure(*options)
+        make()
+        make('install')
+
+    def install(self, spec, prefix):
+
+        options = ['--prefix=%s' % prefix,
+                   '--without-iv',
+                   '--without-x',
+                   '--without-readline']
+
+        if spec.satisfies('+multisend'):
+            options.append('--with-multisend')
+
+        if spec.satisfies('~rx3d'):
+            options.append('--disable-rx3d')
+
+        if spec.satisfies('+mpi'):
+            options.extend(['MPICC=%s' % spec['mpi'].mpicc,
+                            'MPICXX=%s' % spec['mpi'].mpicxx,
+                            '--with-paranrn'])
+        else:
+            options.append('--without-paranrn')
+
+        if spec.satisfies('~shared'):
+            options.extend(['--disable-shared',
+                            'linux_nrnmech=no'])
+
+        options.extend(self.get_arch_options(spec))
+        options.extend(self.get_python_options(spec))
+        options.extend(self.get_compiler_options(spec))
+
+        build = Executable('./build.sh')
+        build()
+
+        with working_dir('build', create=True):
+            if spec.satisfies('+cross-compile'):
+                self.build_nmodl(spec, prefix)
+            srcpath = self.stage.source_path
+            configure = Executable(join_path(srcpath, 'configure'))
+            configure(*options)
+            make('VERBOSE=1')
+            make('install')
+
+    def setup_environment(self, spack_env, run_env):
+        neuron_archdir = self.get_neuron_archdir()
+        run_env.prepend_path('PATH', join_path(neuron_archdir, 'bin'))
+        run_env.prepend_path(
+            'LD_LIBRARY_PATH', join_path(neuron_archdir, 'lib'))
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        neuron_archdir = self.get_neuron_archdir()
+        spack_env.prepend_path('PATH', join_path(neuron_archdir, 'bin'))
+        spack_env.prepend_path(
+            'LD_LIBRARY_PATH', join_path(neuron_archdir, 'lib'))
diff --git a/var/spack/repos/builtin/packages/nextflow/package.py b/var/spack/repos/builtin/packages/nextflow/package.py
index 715964bdc1..f1d2718010 100644
--- a/var/spack/repos/builtin/packages/nextflow/package.py
+++ b/var/spack/repos/builtin/packages/nextflow/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,6 +18,8 @@ class Nextflow(Package):
             expand=False)
     version('0.23.3', '71fb69275b6788af1c6f1165f40d362e',
             expand=False)
+    version('0.21.0', '38e5e335cb33f05ba358e1f883c8386c',
+             expand=False)
     version('0.20.1', '0e4e0e3eca1c2c97f9b4bffd944b923a',
             expand=False)
     version('0.17.3', '5df00105fb1ce6fd0ba019ae735d9617',
diff --git a/var/spack/repos/builtin/packages/nfft/package.py b/var/spack/repos/builtin/packages/nfft/package.py
index 415ddcf0eb..3e40732f39 100644
--- a/var/spack/repos/builtin/packages/nfft/package.py
+++ b/var/spack/repos/builtin/packages/nfft/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,9 +12,10 @@ class Nfft(AutotoolsPackage):
     size, and of complex data."""
 
     homepage = "https://www-user.tu-chemnitz.de/~potts/nfft"
-    url = "https://www-user.tu-chemnitz.de/~potts/nfft/download/nfft-3.3.2.tar.gz"
+    url = "https://github.com/NFFT/nfft/releases/download/3.4.1/nfft-3.4.1.tar.gz"
 
-    version('3.3.2', '550737c06f4d6ea6c156800169d8f0d9')
+    version('3.4.1', '9c2ad6cf86fe4a7bc0de8d2d92b101f4')
+    version('3.3.2', '13e48b923501ed6feb5130c3be115fc8')
 
     depends_on('fftw')
 
diff --git a/var/spack/repos/builtin/packages/nghttp2/package.py b/var/spack/repos/builtin/packages/nghttp2/package.py
index 62b936e054..53d3c6b67f 100644
--- a/var/spack/repos/builtin/packages/nghttp2/package.py
+++ b/var/spack/repos/builtin/packages/nghttp2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/nginx/package.py b/var/spack/repos/builtin/packages/nginx/package.py
index a9b5e93bfb..0db0e581c8 100644
--- a/var/spack/repos/builtin/packages/nginx/package.py
+++ b/var/spack/repos/builtin/packages/nginx/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,6 +14,7 @@ class Nginx(AutotoolsPackage):
     homepage = "https://nginx.org/en/"
     url      = "https://nginx.org/download/nginx-1.12.0.tar.gz"
 
+    version('1.13.8', 'df4be9294365782dc1349ca33ce8c4ac')
     version('1.12.0', '995eb0a140455cf0cfc497e5bd7f94b3')
 
     depends_on('openssl')
diff --git a/var/spack/repos/builtin/packages/ngmlr/package.py b/var/spack/repos/builtin/packages/ngmlr/package.py
index e1dbbe709e..1c38c9cd1a 100644
--- a/var/spack/repos/builtin/packages/ngmlr/package.py
+++ b/var/spack/repos/builtin/packages/ngmlr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/ninja-fortran/package.py b/var/spack/repos/builtin/packages/ninja-fortran/package.py
index 57903928be..5aaa5039ed 100644
--- a/var/spack/repos/builtin/packages/ninja-fortran/package.py
+++ b/var/spack/repos/builtin/packages/ninja-fortran/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/ninja/package.py b/var/spack/repos/builtin/packages/ninja/package.py
index 11c46cb81e..e6283fbff3 100644
--- a/var/spack/repos/builtin/packages/ninja/package.py
+++ b/var/spack/repos/builtin/packages/ninja/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/nlohmann-json/package.py b/var/spack/repos/builtin/packages/nlohmann-json/package.py
new file mode 100644
index 0000000000..3cfcd936a9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/nlohmann-json/package.py
@@ -0,0 +1,46 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class NlohmannJson(CMakePackage):
+    """JSON for Modern C++"""
+
+    homepage = "https://nlohmann.github.io/json/"
+    url      = "https://github.com/nlohmann/json/archive/v3.1.2.tar.gz"
+    maintainers = ['ax3l']
+
+    version('3.3.0', sha256='2fd1d207b4669a7843296c41d3b6ac5b23d00dec48dba507ba051d14564aa801')
+    version('3.2.0', sha256='2de558ff3b3b32eebfb51cf2ceb835a0fa5170e6b8712b02be9c2c07fcfe52a1')
+    version('3.1.2', sha256='e8fffa6cbdb3c15ecdff32eebf958b6c686bc188da8ad5c6489462d16f83ae54')
+    version('3.1.1', sha256='9f3549824af3ca7e9707a2503959886362801fb4926b869789d6929098a79e47')
+
+    variant('single_header', default=True,
+        description='Use amalgamated single-header')
+    variant('test', default=True,
+        description='Build the tests')
+
+    depends_on('cmake@3.8:', type='build')
+
+    # requires mature C++11 implementations
+    conflicts('%gcc@:4.7')
+    # v3.3.0 adds support for gcc 4.8
+    # https://github.com/nlohmann/json/releases/tag/v3.3.0
+    conflicts('%gcc@:4.8', when='@:3.2.9')
+    conflicts('%intel@:16')
+    conflicts('%pgi@:14')
+
+    def cmake_args(self):
+        spec = self.spec
+
+        args = [
+            '-DJSON_MultipleHeaders:BOOL={0}'.format(
+                'ON' if '~single_header' in spec else 'OFF'),
+            '-DBUILD_TESTING:BOOL={0}'.format(
+                'ON' if '+test' in spec else 'OFF')
+        ]
+
+        return args
diff --git a/var/spack/repos/builtin/packages/nlopt/package.py b/var/spack/repos/builtin/packages/nlopt/package.py
new file mode 100644
index 0000000000..c1c69cba01
--- /dev/null
+++ b/var/spack/repos/builtin/packages/nlopt/package.py
@@ -0,0 +1,62 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Nlopt(CMakePackage):
+    """NLopt is a free/open-source library for nonlinear optimization,
+    providing a common interface for a number of different free optimization
+    routines available online as well as original implementations of various
+    other algorithms."""
+
+    homepage = "https://nlopt.readthedocs.io"
+    url      = "https://github.com/stevengj/nlopt/archive/v2.5.0.tar.gz"
+    git      = "https://github.com/stevengj/nlopt.git"
+
+    version('develop', branch='master')
+    version('2.5.0', 'ada08c648bf9b52faf8729412ff6dd6d')
+
+    variant('shared', default=True, description='Enables the build of shared libraries')
+    variant('python', default=True, description='Build python wrappers')
+    variant('guile',  default=False, description='Enable Guile support')
+    variant('octave', default=False, description='Enable GNU Octave support')
+    variant('cxx',    default=False,  description='Build the C++ routines')
+
+    # Note: matlab is licenced - spack does not download automatically
+    variant("matlab", default=False, description="Build the Matlab bindings.")
+
+    depends_on('cmake@3.0:', type='build', when='@develop')
+    depends_on('python', when='+python')
+    depends_on('py-numpy', when='+python', type=('build', 'run'))
+    depends_on('swig', when='+python')
+    depends_on('guile', when='+guile')
+    depends_on('octave', when='+octave')
+    depends_on('matlab', when='+matlab')
+
+    def cmake_args(self):
+        # Add arguments other than
+        # CMAKE_INSTALL_PREFIX and CMAKE_BUILD_TYPE
+        spec = self.spec
+        args = []
+
+        # Specify on command line to alter defaults:
+        # eg: spack install nlopt@develop +guile -octave +cxx
+
+        # Spack should locate python by default - but to point to a build
+        if '+python' in spec:
+            args.append("-DPYTHON_EXECUTABLE=%s" % spec['python'].command.path)
+
+        # On is default
+        if '-shared' in spec:
+            args.append('-DBUILD_SHARED_LIBS:Bool=OFF')
+
+        if '+cxx' in spec:
+            args.append('-DNLOPT_CXX:BOOL=ON')
+
+        if '+matlab' in spec:
+            args.append("-DMatlab_ROOT_DIR=%s" % spec['matlab'].command.path)
+
+        return args
diff --git a/var/spack/repos/builtin/packages/nmap/package.py b/var/spack/repos/builtin/packages/nmap/package.py
index e4da0fbdcf..43b3aeefac 100644
--- a/var/spack/repos/builtin/packages/nmap/package.py
+++ b/var/spack/repos/builtin/packages/nmap/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,7 +12,8 @@ class Nmap(AutotoolsPackage):
        It also provides ncat an updated nc"""
 
     homepage = "https://nmap.org"
-    url      = "https://nmap.org/dist/nmap-7.31.tar.bz2"
+    url      = "https://nmap.org/dist/nmap-7.70.tar.bz2"
 
+    version('7.70', '84eb6fbe788e0d4918c2b1e39421bf79')
     version('7.31', 'f2f6660142a777862342a58cc54258ea')
     version('7.30', '8d86797d5c9e56de571f9630c0e6b5f8')
diff --git a/var/spack/repos/builtin/packages/nnvm/package.py b/var/spack/repos/builtin/packages/nnvm/package.py
index 0650df273d..542daa50af 100644
--- a/var/spack/repos/builtin/packages/nnvm/package.py
+++ b/var/spack/repos/builtin/packages/nnvm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,11 +11,10 @@ class Nnvm(CMakePackage):
     part to help build deep learning libraries."""
 
     homepage = "https://github.com/dmlc/nnvm"
-    url      = "https://github.com/dmlc/nnvm.git"
+    git      = "https://github.com/dmlc/nnvm.git"
 
-    version('master', git='https://github.com/dmlc/nnvm.git', branch='master')
-    version('20170418', git='https://github.com/dmlc/nnvm.git',
-            commit='b279286304ac954098d94a2695bca599e832effb')
+    version('master', branch='master')
+    version('20170418', commit='b279286304ac954098d94a2695bca599e832effb')
 
     variant('shared', default=True, description='Build a shared NNVM lib.')
 
diff --git a/var/spack/repos/builtin/packages/node-js/package.py b/var/spack/repos/builtin/packages/node-js/package.py
index 0b7e942400..ad19340c53 100644
--- a/var/spack/repos/builtin/packages/node-js/package.py
+++ b/var/spack/repos/builtin/packages/node-js/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import sys
 import subprocess
@@ -34,6 +15,7 @@ class NodeJs(Package):
     homepage = "https://nodejs.org/"
     url      = "https://nodejs.org/download/release/v6.3.0/node-v6.3.0.tar.gz"
 
+    version('8.9.1', '7482b2523f72000d1b6060c38945026b')
     version('7.1.0', '1db5df2cb025f9c70e83d9cf21c4266a')
     version('6.3.0', '8c14e5c89d66d4d060c91b3ba15dfd31')
     version('6.2.2', '1120e8bf191fdaee42206d031935210d')
@@ -46,7 +28,7 @@ class NodeJs(Package):
     variant('zlib', default=True,  description='Build with Spacks zlib instead of the bundled version')
 
     depends_on('libtool', type='build', when=sys.platform != 'darwin')
-    depends_on('pkg-config', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('python@2.7:2.8', type='build')
     # depends_on('bash-completion', when="+bash-completion")
     depends_on('icu4c', when='+icu4c')
diff --git a/var/spack/repos/builtin/packages/notmuch/package.py b/var/spack/repos/builtin/packages/notmuch/package.py
index 11ff488d77..9245c76d12 100644
--- a/var/spack/repos/builtin/packages/notmuch/package.py
+++ b/var/spack/repos/builtin/packages/notmuch/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/npb/package.py b/var/spack/repos/builtin/packages/npb/package.py
index 65e5294524..0840be9b8c 100644
--- a/var/spack/repos/builtin/packages/npb/package.py
+++ b/var/spack/repos/builtin/packages/npb/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import numbers
 
 from spack import *
diff --git a/var/spack/repos/builtin/packages/npm/package.py b/var/spack/repos/builtin/packages/npm/package.py
index 89a46bc19b..5f797165c3 100644
--- a/var/spack/repos/builtin/packages/npm/package.py
+++ b/var/spack/repos/builtin/packages/npm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/npth/package.py b/var/spack/repos/builtin/packages/npth/package.py
index c99c01ebb2..d99da26799 100644
--- a/var/spack/repos/builtin/packages/npth/package.py
+++ b/var/spack/repos/builtin/packages/npth/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,6 +11,7 @@ class Npth(AutotoolsPackage):
        non-preemptive threads implementation."""
 
     homepage = "https://gnupg.org/software/npth/index.html"
-    url = "https://gnupg.org/ftp/gcrypt/npth/npth-1.4.tar.bz2"
+    url = "https://gnupg.org/ftp/gcrypt/npth/npth-1.5.tar.bz2"
 
+    version('1.5', '9ba2dc4302d2f32c66737c43ed191b1b')
     version('1.4', '76cef5542e0db6a339cf960641ed86f8')
diff --git a/var/spack/repos/builtin/packages/nspr/package.py b/var/spack/repos/builtin/packages/nspr/package.py
index cddcdb16a0..5ad1d51973 100644
--- a/var/spack/repos/builtin/packages/nspr/package.py
+++ b/var/spack/repos/builtin/packages/nspr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/numactl/numactl-2.0.11-sysmacros.patch b/var/spack/repos/builtin/packages/numactl/numactl-2.0.11-sysmacros.patch
new file mode 100644
index 0000000000..3f95367573
--- /dev/null
+++ b/var/spack/repos/builtin/packages/numactl/numactl-2.0.11-sysmacros.patch
@@ -0,0 +1,41 @@
+https://bugs.gentoo.org/580098
+
+From c1644f92e340d797e490c41a9ef9961125d202b9 Mon Sep 17 00:00:00 2001
+From: Mike Frysinger <vapier@gentoo.org>
+Date: Mon, 18 Apr 2016 18:49:51 -0400
+Subject: [PATCH] include sys/sysmacros.h for major/minor
+
+These functions are not part of any official spec, and glibc has always
+kept them in sys/sysmacros.h.  As glibc moves to conform to POSIX, and
+more alternative C libraries come up, we need to include this header
+explicitly to get the prototypes.  Otherwise we fail to build like:
+
+affinity.c: In function 'affinity_file':
+affinity.c:177:7: warning: implicit declaration of function 'major' [-Wimplicit-function-declaration]
+   if (major(d) != maj || minor(d) != min)
+       ^
+affinity.c:177:26: warning: implicit declaration of function 'minor' [-Wimplicit-function-declaration]
+   if (major(d) != maj || minor(d) != min)
+                          ^
+./.libs/libnuma.so: undefined reference to 'minor'
+./.libs/libnuma.so: undefined reference to 'major'
+collect2: error: ld returned 1 exit status
+---
+ affinity.c | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/affinity.c b/affinity.c
+index 9fbd6af..984291c 100644
+--- a/affinity.c
++++ b/affinity.c
+@@ -40,6 +40,7 @@
+ #include <linux/rtnetlink.h>
+ #include <linux/netlink.h>
+ #include <sys/types.h>
++#include <sys/sysmacros.h>
+ #include <ctype.h>
+ #include <assert.h>
+ #include <regex.h>
+-- 
+2.7.4
+
diff --git a/var/spack/repos/builtin/packages/numactl/package.py b/var/spack/repos/builtin/packages/numactl/package.py
index 26df59c85a..e17a279d21 100644
--- a/var/spack/repos/builtin/packages/numactl/package.py
+++ b/var/spack/repos/builtin/packages/numactl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,6 +14,8 @@ class Numactl(AutotoolsPackage):
 
     version('2.0.11',     'b56d2367217cde390b4d8087e00773b8')
 
+    patch('numactl-2.0.11-sysmacros.patch', when="@2.0.11")
+
     depends_on('autoconf', type='build')
     depends_on('automake', type='build')
     depends_on('libtool',  type='build')
diff --git a/var/spack/repos/builtin/packages/numdiff/package.py b/var/spack/repos/builtin/packages/numdiff/package.py
index b584d1156c..8c7490482a 100644
--- a/var/spack/repos/builtin/packages/numdiff/package.py
+++ b/var/spack/repos/builtin/packages/numdiff/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/nut/package.py b/var/spack/repos/builtin/packages/nut/package.py
index 2ff9f77c9c..6450d72adf 100644
--- a/var/spack/repos/builtin/packages/nut/package.py
+++ b/var/spack/repos/builtin/packages/nut/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,20 +13,16 @@ class Nut(CMakePackage):
     and performance issues."""
 
     homepage = "https://github.com/lanl/NuT"
-    url      = "https://github.com/lanl/NuT.git"
-    tags     = ['proxy-app']
+    git      = "https://github.com/lanl/NuT.git"
+
+    tags = ['proxy-app']
 
-    version(
-        'serial', git='https://github.com/lanl/NuT.git',
-        branch='master')
-    version(
-        'openmp', git='https://github.com/lanl/NuT.git',
-        branch='openmp')
+    version('serial', branch='master')
+    version('openmp', branch='openmp')
 
+    depends_on('cmake@3.0:')
     depends_on('random123')
 
-    # serial must be built with clang
-    conflicts('%gcc', when='@serial')
     conflicts('%intel', when='@serial')
     conflicts('%pgi', when='@serial')
     conflicts('%xl', when='@serial')
@@ -59,4 +36,9 @@ class Nut(CMakePackage):
     def install(self, spec, prefix):
         install('README.md', prefix)
         mkdirp(prefix.bin)
+        mkdirp(prefix.lib)
         install('spack-build/test/nut_unittests', prefix.bin)
+        install('spack-build/apps/bh-3', prefix.bin)
+        install('spack-build/lib/libnut.a', prefix.lib)
+        install_tree('test/data', prefix.data)
+        install_tree('lib', prefix.include)
diff --git a/var/spack/repos/builtin/packages/nvptx-tools/package.py b/var/spack/repos/builtin/packages/nvptx-tools/package.py
new file mode 100644
index 0000000000..244cd6936c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/nvptx-tools/package.py
@@ -0,0 +1,31 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class NvptxTools(AutotoolsPackage):
+    """nvptx-tools: A collection of tools for use with nvptx-none GCC
+    toolchains. These tools are necessary when building a version
+    of GCC that enables offloading of OpenMP/OpenACC code to NVIDIA
+    GPUs."""
+
+    homepage = "https://github.com/MentorEmbedded/nvptx-tools"
+    git      = "https://github.com/MentorEmbedded/nvptx-tools"
+
+    version('2018-03-01', commit='5f6f343a302d620b0868edab376c00b15741e39e')
+
+    depends_on('binutils')
+    depends_on('cuda')
+
+    def configure_args(self):
+        cuda_dir = self.spec['cuda'].prefix
+
+        config_args = [
+            "--with-cuda-driver-include={0}".format(cuda_dir.include),
+            "--with-cuda-driver-lib={0}".format(cuda_dir.lib64)
+        ]
+
+        return config_args
diff --git a/var/spack/repos/builtin/packages/nwchem/package.py b/var/spack/repos/builtin/packages/nwchem/package.py
index 10262be6a8..908740ba4d 100644
--- a/var/spack/repos/builtin/packages/nwchem/package.py
+++ b/var/spack/repos/builtin/packages/nwchem/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import sys
 import os
@@ -33,6 +14,12 @@ class Nwchem(Package):
     homepage = "http://www.nwchem-sw.org"
     url      = "http://www.nwchem-sw.org/images/Nwchem-6.6.revision27746-src.2015-10-20.tar.gz"
 
+    tags = ['ecp', 'ecp-apps']
+
+    version('6.8.1', '6eccddc6db11886aa6f152626efc600c',
+            url='https://github.com/nwchemgit/nwchem/releases/download/6.8.1-release/nwchem-6.8.1-release.revision-v6.8-133-ge032219-srconly.2018-06-14.tar.bz2')
+    version('6.8', '50b18116319f4c15d1cb7eaa1b433006',
+            url='https://github.com/nwchemgit/nwchem/archive/v6.8-release.tar.gz')
     version('6.6', 'c581001c004ea5e5dfacb783385825e3',
             url='http://www.nwchem-sw.org/images/Nwchem-6.6.revision27746-src.2015-10-20.tar.gz')
 
@@ -41,7 +28,7 @@ class Nwchem(Package):
     depends_on('mpi')
     depends_on('scalapack')
 
-    depends_on('python@2.7:2.8', type=('build', 'run'))
+    depends_on('python@2.7:2.8', type=('build', 'link', 'run'))
 
     # first hash is sha256 of the patch (required for URL patches),
     # second is sha256 for the archive.
@@ -70,9 +57,9 @@ class Nwchem(Package):
         ]
     }
     # Iterate over patches
-    for condition, urls in urls_for_patches.items():
-        for url, sha256, archive_sha256 in urls:
-            patch(url, when=condition, level=0, sha256=sha256, archive_sha256=archive_sha256)
+    for __condition, __urls in urls_for_patches.items():
+        for __url, __sha256, __archive_sha256 in __urls:
+            patch(__url, when=__condition, level=0, sha256=__sha256, archive_sha256=__archive_sha256)
 
     def install(self, spec, prefix):
         scalapack = spec['scalapack'].libs
@@ -103,9 +90,9 @@ class Nwchem(Package):
         # TODO: query if blas/lapack/scalapack uses 64bit Ints
         # A flag to distinguish between 32bit and 64bit integers in linear
         # algebra (Blas, Lapack, Scalapack)
-        use32bitLinAlg = True
+        use_32_bit_lin_alg = True
 
-        if use32bitLinAlg:
+        if use_32_bit_lin_alg:
             args.extend([
                 'USE_64TO32=y',
                 'BLAS_SIZE=4',
@@ -131,7 +118,7 @@ class Nwchem(Package):
 
         with working_dir('src'):
             make('nwchem_config', *args)
-            if use32bitLinAlg:
+            if use_32_bit_lin_alg:
                 make('64_to_32', *args)
             make(*args)
 
diff --git a/var/spack/repos/builtin/packages/ocaml/package.py b/var/spack/repos/builtin/packages/ocaml/package.py
index e93d811f06..cd88782775 100644
--- a/var/spack/repos/builtin/packages/ocaml/package.py
+++ b/var/spack/repos/builtin/packages/ocaml/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,12 +13,17 @@ class Ocaml(Package):
     homepage = "http://ocaml.org/"
     url      = "http://caml.inria.fr/pub/distrib/ocaml-4.03/ocaml-4.03.0.tar.gz"
 
+    version('4.06.0', '66e5439eb63dbb8b8224cba5d1b20947')
     version('4.03.0', '43812739ea1b4641cf480f57f977c149')
 
     depends_on('ncurses')
 
+    def url_for_version(self, version):
+        url = "http://caml.inria.fr/pub/distrib/ocaml-{0}/ocaml-{1}.tar.gz"
+        return url.format(version.up_to(2), version)
+
     def install(self, spec, prefix):
         configure('-prefix', '{0}'.format(prefix))
 
         make('world.opt')
-        make('install')
+        make('install', 'PREFIX={0}'.format(prefix))
diff --git a/var/spack/repos/builtin/packages/occa/package.py b/var/spack/repos/builtin/packages/occa/package.py
new file mode 100644
index 0000000000..f9276fede9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/occa/package.py
@@ -0,0 +1,111 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Occa(Package):
+    """OCCA is an open-source (MIT license) library used to program current
+       multi-core/many-core architectures. Devices (such as CPUs, GPUs,
+       Intel's Xeon Phi, FPGAs, etc) are abstracted using an offload-model
+       for application development and programming for the devices is done
+       through a C-based (OKL) or Fortran-based kernel language (OFL).
+       OCCA gives developers the ability to target devices at run-time by
+       using run-time compilation for device kernels.
+    """
+
+    homepage = "http://libocca.org"
+    git      = 'https://github.com/libocca/occa.git'
+
+    version('develop')
+    version('v1.0.0-alpha.5', tag='v1.0.0-alpha.5')
+    version('v0.2.0', tag='v0.2.0')
+    version('v0.1.0', tag='v0.1.0')
+
+    variant('cuda',
+            default=True,
+            description='Activates support for CUDA')
+    variant('openmp',
+            default=True,
+            description='Activates support for OpenMP')
+    variant('opencl',
+            default=True,
+            description='Activates support for OpenCL')
+
+    depends_on('cuda', when='+cuda')
+
+    conflicts('%gcc@6:', when='^cuda@:8')
+    conflicts('%gcc@7:', when='^cuda@:9')
+
+    def install(self, spec, prefix):
+        # The build environment is set by the 'setup_environment' method.
+        # Copy the source to the installation directory and build OCCA there.
+        install_tree('.', prefix)
+        make('-C', prefix)
+
+        if self.run_tests:
+            make('-C', prefix, 'test', parallel=False)
+
+    def _setup_runtime_flags(self, s_env):
+        spec = self.spec
+        s_env.set('OCCA_DIR', self.prefix)
+        s_env.set('OCCA_CXX', self.compiler.cxx)
+
+        cxxflags = spec.compiler_flags['cxxflags']
+        if cxxflags:
+            # Run-time compiler flags:
+            s_env.set('OCCA_CXXFLAGS', ' '.join(cxxflags))
+
+        if '+cuda' in spec:
+            cuda_dir = spec['cuda'].prefix
+            # Run-time CUDA compiler:
+            s_env.set('OCCA_CUDA_COMPILER',
+                      join_path(cuda_dir, 'bin', 'nvcc'))
+
+    def setup_environment(self, spack_env, run_env):
+        spec = self.spec
+        # The environment variable CXX is automatically set to the Spack
+        # compiler wrapper.
+
+        # The cxxflags, if specified, will be set by the Spack compiler wrapper
+        # while the environment variable CXXFLAGS will remain undefined.
+        # We define CXXFLAGS in the environment to tell OCCA to use the user
+        # specified flags instead of its defaults. This way the compiler will
+        # get the cxxflags twice - once from the Spack compiler wrapper and
+        # second time from OCCA - however, only the second one will be seen in
+        # the verbose output, so we keep both.
+        cxxflags = spec.compiler_flags['cxxflags']
+        if cxxflags:
+            spack_env.set('CXXFLAGS', ' '.join(cxxflags))
+
+        # For the cuda, openmp, and opencl variants, set the environment
+        # variable OCCA_{CUDA,OPENMP,OPENCL}_ENABLED only if the variant is
+        # disabled. Otherwise, let OCCA autodetect what is available.
+
+        if '+cuda' in spec:
+            cuda_dir = spec['cuda'].prefix
+            cuda_libs_list = ['libcuda', 'libcudart', 'libOpenCL']
+            cuda_libs = find_libraries(cuda_libs_list,
+                                       cuda_dir,
+                                       shared=True,
+                                       recursive=True)
+            spack_env.set('OCCA_INCLUDE_PATH', cuda_dir.include)
+            spack_env.set('OCCA_LIBRARY_PATH', ':'.join(cuda_libs.directories))
+        else:
+            spack_env.set('OCCA_CUDA_ENABLED', '0')
+
+        if '~opencl' in spec:
+            spack_env.set('OCCA_OPENCL_ENABLED', '0')
+
+        # Setup run-time environment for testing.
+        spack_env.set('OCCA_VERBOSE', '1')
+        self._setup_runtime_flags(spack_env)
+        # The 'run_env' is included in the Spack generated module files.
+        self._setup_runtime_flags(run_env)
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        # Export OCCA_* variables for everyone using this package from within
+        # Spack.
+        self._setup_runtime_flags(spack_env)
diff --git a/var/spack/repos/builtin/packages/oce/package.py b/var/spack/repos/builtin/packages/oce/package.py
index 6fc6183e40..04af4466e4 100644
--- a/var/spack/repos/builtin/packages/oce/package.py
+++ b/var/spack/repos/builtin/packages/oce/package.py
@@ -1,29 +1,10 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from spack.operating_systems.mac_os import macOS_version
+from spack.operating_systems.mac_os import macos_version
 import platform
 
 
@@ -35,6 +16,7 @@ class Oce(Package):
     homepage = "https://github.com/tpaviot/oce"
     url = "https://github.com/tpaviot/oce/archive/OCE-0.18.tar.gz"
 
+    version('0.18.3', '1686393c8493bbbb2f3f242330b33cba')
     version('0.18.2', '6dfd68e459e2c62387579888a867281f')
     version('0.18.1', '2a7597f4243ee1f03245aeeb02d00956')
     version('0.18',   '226e45e77c16a4a6e127c71fefcd171410703960ae75c7ecc7eb68895446a993')
@@ -62,12 +44,12 @@ class Oce(Package):
 
     # OCE depends on xlocale.h from glibc-headers but it was removed in 2.26,
     # see https://github.com/tpaviot/oce/issues/675
-    patch('xlocale.patch', level=0, when='@0.18.1:')
+    patch('xlocale.patch', level=0, when='@0.18.1:0.18.2')
 
     # fix build with Xcode 8 "previous definition of CLOCK_REALTIME"
     # reported 27 Sep 2016 https://github.com/tpaviot/oce/issues/643
     if (platform.system() == "Darwin") and (
-       macOS_version() == Version('10.12')):
+       macos_version() == Version('10.12')):
         patch('sierra.patch', when='@0.17.2:0.18.0')
 
     def install(self, spec, prefix):
@@ -98,7 +80,7 @@ class Oce(Package):
             ])
 
         if platform.system() == 'Darwin' and (
-           macOS_version() >= Version('10.12')):
+           macos_version() >= Version('10.12')):
             # use @rpath on Sierra due to limit of dynamic loader
             options.append('-DCMAKE_MACOSX_RPATH=ON')
         else:
diff --git a/var/spack/repos/builtin/packages/oclint/bundle.patch b/var/spack/repos/builtin/packages/oclint/bundle.patch
new file mode 100644
index 0000000000..f40e72bfae
--- /dev/null
+++ b/var/spack/repos/builtin/packages/oclint/bundle.patch
@@ -0,0 +1,16 @@
+--- oclint-scripts/bundle	2017-09-29 10:27:37.000000000 -0700
++++ oclint-scripts/bundle	2018-01-26 03:49:31.000000000 -0800
+@@ -92,7 +92,7 @@
+ 
+ def install_cpp_headers():
+     if environment.is_darwin():
+-        install_dir = path.build.clang_install_dir
++        install_dir = (path.build.clang_install_dir if not args.llvm_root else args.llvm_root)
+         clang_cpp_headers_dir = os.path.join(install_dir, 'include', 'c++')
+         oclint_cpp_headers_dir = os.path.join(bundle_include_dir, 'c++')
+         path.mkdir_p(bundle_include_dir)
+@@ -141,4 +141,3 @@
+ 
+ if args.archive:
+     archive(args.release)
+-
diff --git a/var/spack/repos/builtin/packages/oclint/package.py b/var/spack/repos/builtin/packages/oclint/package.py
new file mode 100644
index 0000000000..a0810739be
--- /dev/null
+++ b/var/spack/repos/builtin/packages/oclint/package.py
@@ -0,0 +1,64 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Oclint(Package):
+    """OClint: a static analysis tool for C, C++, and Objective-C code
+
+       OCLint is a static code analysis tool for improving quality and
+       reducing defects by inspecting C, C++ and Objective-C code and
+       looking for potential problems"""
+
+    homepage = "http://oclint.org/"
+    url      = "https://github.com/oclint/oclint/archive/v0.13.tar.gz"
+
+    version('0.13', '1d0e605eb7815ac15e6a2a82327d2dd8')
+
+    depends_on('python', type=('build'))
+    depends_on('py-argparse', type=('build'))
+    depends_on('git', type=('build'))
+    depends_on('subversion', type=('build'))
+    depends_on('cmake', type=('build'))
+    depends_on('ninja', type=('build'))
+    depends_on('llvm@5.0.0:')
+
+    # Needed to fix a bug in oclint-scripts/bundle script, which
+    # attempts to install c++ headers in the wrong location
+    # contributed upstream as
+    # https://github.com/oclint/oclint/pull/492
+    patch('bundle.patch', level=0)
+
+    def install(self, spec, prefix):
+        # Build from source via directions from
+        # http://docs.oclint.org/en/stable/intro/build.html,
+        cd('oclint-scripts')
+
+        # ...but instead of using oclint-scripts/make, execute the
+        # commands in oclint-scripts/makeWithSystemLLVM so that
+        # oclint links to spack-installed LLVM
+        build_script = Executable(join_path('.', 'build'))
+        bundle_script = Executable(join_path('.', 'bundle'))
+
+        # Add the '-no-analytics' argument to the build script because
+        # 1) it doesn't detect properly a spack install of OpenSSL,
+        #    and throws an error due to missing OpenSSL headers
+        # 2) the bespoke build system is a pain to patch as it is
+        # 3) many sites don't allow software that communicates analytics data
+        build_script('-release',
+                     '-clean',
+                     '-llvm-root={0}'.format(spec['llvm'].prefix),
+                     '-use-system-compiler',
+                     '-no-analytics',
+                     'all')
+        bundle_script('-release', '-llvm-root={0}'.format(spec['llvm'].prefix))
+
+        # Copy install tree into the correct locations using the
+        # directory layout described in
+        cd(join_path('..', 'build'))
+        install_tree(join_path('oclint-release', 'include'), prefix.include)
+        install_tree(join_path('oclint-release', 'lib'), prefix.lib)
+        install_tree(join_path('oclint-release', 'bin'), prefix.bin)
diff --git a/var/spack/repos/builtin/packages/oclock/package.py b/var/spack/repos/builtin/packages/oclock/package.py
index 2d3a40457f..0108623080 100644
--- a/var/spack/repos/builtin/packages/oclock/package.py
+++ b/var/spack/repos/builtin/packages/oclock/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,5 +21,5 @@ class Oclock(AutotoolsPackage):
     depends_on('libxt')
     depends_on('libxkbfile')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/octave-optim/package.py b/var/spack/repos/builtin/packages/octave-optim/package.py
new file mode 100644
index 0000000000..5bcb323bbe
--- /dev/null
+++ b/var/spack/repos/builtin/packages/octave-optim/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class OctaveOptim(OctavePackage):
+    """Non-linear optimization toolkit for Octave."""
+
+    homepage = "https://octave.sourceforge.io/optim/"
+    url      = "https://downloads.sourceforge.net/octave/optim-1.5.2.tar.gz"
+
+    version('1.5.2', 'd3d77982869ea7c1807b13b24e044d44')
+
+    depends_on('octave-struct@1.0.12:')
+    extends('octave@3.6.0:')
diff --git a/var/spack/repos/builtin/packages/octave-splines/package.py b/var/spack/repos/builtin/packages/octave-splines/package.py
index c9a5f7b01d..857fc48d9c 100644
--- a/var/spack/repos/builtin/packages/octave-splines/package.py
+++ b/var/spack/repos/builtin/packages/octave-splines/package.py
@@ -1,44 +1,16 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class OctaveSplines(Package):
+class OctaveSplines(OctavePackage):
     """Additional spline functions."""
 
     homepage = "http://octave.sourceforge.net/splines/index.html"
     url      = "http://downloads.sourceforge.net/octave/splines-1.3.1.tar.gz"
 
     version('1.3.1', 'f9665d780c37aa6a6e17d1f424c49bdeedb89d1192319a4e39c08784122d18f9')
-
     extends('octave@3.6.0:')
-
-    def install(self, spec, prefix):
-        octave('--quiet',
-               '--norc',
-               '--built-in-docstrings-file=/dev/null',
-               '--texi-macros-file=/dev/null',
-               '--eval', 'pkg prefix %s; pkg install %s' %
-               (prefix, self.stage.archive_file))
diff --git a/var/spack/repos/builtin/packages/octave-struct/package.py b/var/spack/repos/builtin/packages/octave-struct/package.py
new file mode 100644
index 0000000000..2f08729106
--- /dev/null
+++ b/var/spack/repos/builtin/packages/octave-struct/package.py
@@ -0,0 +1,16 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class OctaveStruct(OctavePackage):
+    """Additional structure manipulation functions for Octave."""
+
+    homepage = "https://octave.sourceforge.io/struct/"
+    url      = "https://downloads.sourceforge.net/octave/struct-1.0.14.tar.gz"
+
+    version('1.0.14', '3589d5eb8000f18426e2178587eb82f4')
+    extends('octave@2.9.7:')
diff --git a/var/spack/repos/builtin/packages/octave/package.py b/var/spack/repos/builtin/packages/octave/package.py
index 79dc74b518..62f8ea7783 100644
--- a/var/spack/repos/builtin/packages/octave/package.py
+++ b/var/spack/repos/builtin/packages/octave/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import sys
 
@@ -34,10 +15,13 @@ class Octave(AutotoolsPackage):
     Matlab. It may also be used as a batch-oriented language."""
 
     homepage = "https://www.gnu.org/software/octave/"
-    url      = "https://ftp.gnu.org/gnu/octave/octave-4.0.0.tar.gz"
+    url      = "https://ftpmirror.gnu.org/octave/octave-4.0.0.tar.gz"
 
     extendable = True
 
+    version('4.4.1', '09fbd0f212f4ef21e53f1d9c41cf30ce3d7f9450fb44911601e21ed64c67ae97')
+    version('4.4.0', '72f846379fcec7e813d46adcbacd069d72c4f4d8f6003bcd92c3513aafcd6e96')
+    version('4.2.2', '77b84395d8e7728a1ab223058fe5e92dc38c03bc13f7358e6533aab36f76726e')
     version('4.2.1', '80c28f6398576b50faca0e602defb9598d6f7308b0903724442c2a35a605333b')
     version('4.2.0', '443ba73782f3531c94bcf016f2f0362a58e186ddb8269af7dcce973562795567')
     version('4.0.2', 'c2a5cacc6e4c52f924739cdf22c2c687')
@@ -76,7 +60,7 @@ class Octave(AutotoolsPackage):
     # Octave does not configure with sed from darwin:
     depends_on('sed', when=sys.platform == 'darwin', type='build')
     depends_on('pcre')
-    depends_on('pkg-config', type='build')
+    depends_on('pkgconfig', type='build')
 
     # Strongly recommended dependencies
     depends_on('readline',     when='+readline')
@@ -99,7 +83,7 @@ class Octave(AutotoolsPackage):
     depends_on('qhull',        when='+qhull')
     depends_on('qrupdate',     when='+qrupdate')
     # depends_on('qscintilla',  when='+qscintilla) # TODO: add package
-    depends_on('qt',           when='+qt')
+    depends_on('qt+opengl',    when='+qt')
     depends_on('suite-sparse', when='+suitesparse')
     depends_on('zlib',         when='+zlib')
 
@@ -186,9 +170,9 @@ class Octave(AutotoolsPackage):
 
         if '+jdk' in spec:
             config_args.extend([
-                "--with-java-homedir=%s"    % spec['java'].prefix,
-                "--with-java-includedir=%s" % spec['java'].prefix.include,
-                "--with-java-libdir=%s"     % spec['java'].prefix.lib
+                "--with-java-homedir=%s"    % spec['java'].home,
+                "--with-java-includedir=%s" % spec['java'].home.include,
+                "--with-java-libdir=%s"     % spec['java'].libs.directories[0]
             ])
         else:
             config_args.append("--disable-java")
diff --git a/var/spack/repos/builtin/packages/octopus/package.py b/var/spack/repos/builtin/packages/octopus/package.py
index c450cf6020..315beb57b5 100644
--- a/var/spack/repos/builtin/packages/octopus/package.py
+++ b/var/spack/repos/builtin/packages/octopus/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,12 +13,13 @@ class Octopus(Package):
     homepage = "http://www.tddft.org/programs/octopus/"
     url      = "http://www.tddft.org/programs/octopus/down.php?file=6.0/octopus-6.0.tar.gz"
 
+    version('7.3', '87e51fa4a3a999706ea4ea5e9136996f')
     version('6.0', '5d1168c2a8d7fd9cb9492eaebaa7182e')
     version('5.0.1', '2b6392ab67b843f9d4ca7413fc07e822')
 
     variant('scalapack', default=False,
             description='Compile with Scalapack')
-    variant('metis', default=True,
+    variant('metis', default=False,
             description='Compile with METIS')
     variant('parmetis', default=False,
             description='Compile with ParMETIS')
@@ -47,11 +29,11 @@ class Octopus(Package):
             description='Compile with ARPACK')
 
     depends_on('blas')
-    depends_on('gsl')
+    depends_on('gsl@1.9:')
     depends_on('lapack')
     depends_on('libxc')
     depends_on('mpi')
-    depends_on('fftw+mpi')
+    depends_on('fftw@3:+mpi+openmp')
     depends_on('metis@5:', when='+metis')
     depends_on('parmetis', when='+parmetis')
     depends_on('scalapack', when='+scalapack')
@@ -59,7 +41,7 @@ class Octopus(Package):
     depends_on('arpack-ng', when='+arpack')
 
     # optional dependencies:
-    # TODO: parmetis, etsf-io, sparskit,
+    # TODO: etsf-io, sparskit,
     # feast, libfm, pfft, isf, pnfft
 
     def install(self, spec, prefix):
@@ -75,7 +57,7 @@ class Octopus(Package):
             'CC=%s' % spec['mpi'].mpicc,
             'FC=%s' % spec['mpi'].mpifc,
             '--enable-mpi',
-            '--with-fft-lib=-L%s -lfftw3' % spec['fftw'].prefix.lib,
+            '--with-fftw-prefix==%s' % spec['fftw'].prefix,
         ])
         if '+metis' in spec:
             args.extend([
diff --git a/var/spack/repos/builtin/packages/of-adios-write/package.py b/var/spack/repos/builtin/packages/of-adios-write/package.py
index 0c56f0286c..98a293c1d9 100644
--- a/var/spack/repos/builtin/packages/of-adios-write/package.py
+++ b/var/spack/repos/builtin/packages/of-adios-write/package.py
@@ -1,28 +1,8 @@
-##############################################################################
-# Copyright (c) 2017 Mark Olesen, OpenCFD Ltd.
-#
-# This file was authored by Mark Olesen <mark.olesen@esi-group.com>
-# and is released as part of spack under the LGPL license.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for the LLNL notice and LGPL.
-#
-# License
-# -------
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 # Legal Notice
 # ------------
 # OPENFOAM is a trademark owned by OpenCFD Ltd
@@ -56,11 +36,11 @@ class OfAdiosWrite(Package):
     # Currently only via git, but with some branches corresponding to main
     # OpenFOAM releases.
     homepage = "https://develop.openfoam.com/Community/feature-adiosWrite/"
-    gitrepo  = "https://develop.openfoam.com/Community/feature-adiosWrite.git"
+    git      = "https://develop.openfoam.com/Community/feature-adiosWrite.git"
 
-    version('develop', branch='develop', git=gitrepo)
-    version('1706', branch='v1706', git=gitrepo)
-    version('1612', branch='v1612', git=gitrepo)
+    version('develop', branch='develop')
+    version('1706', branch='v1706')
+    version('1612', branch='v1612')
 
     variant('source', default=True, description='Install library source')
 
diff --git a/var/spack/repos/builtin/packages/of-precice/package.py b/var/spack/repos/builtin/packages/of-precice/package.py
new file mode 100644
index 0000000000..31cd530002
--- /dev/null
+++ b/var/spack/repos/builtin/packages/of-precice/package.py
@@ -0,0 +1,86 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import os
+
+import llnl.util.tty as tty
+
+from spack import *
+from spack.pkg.builtin.openfoam_com import add_extra_files
+
+
+class OfPrecice(Package):
+    """preCICE adapter for OpenFOAM"""
+
+    homepage = 'https://www.precice.org'
+    git      = 'https://github.com/precice/openfoam-adapter.git'
+
+    # Currently develop only
+    version('develop', branch='master')
+
+    depends_on('openfoam+source')
+    depends_on('precice')
+    depends_on('yaml-cpp')
+
+    # General patches
+    common = ['change-userdir.sh', 'spack-derived-Allwmake']
+    assets = []
+
+    build_script  = './spack-derived-Allwmake'
+    build_userdir = 'spack-userdir'  # Build user APPBIN, LIBBIN into here
+
+    phases = ['configure', 'build', 'install']
+
+    #
+    # - End of definitions / setup -
+    #
+
+    def patch(self):
+        """Copy additional files or other patching."""
+        add_extra_files(self, self.common, self.assets)
+        # Emit openfoam version immediately, if we resolved the wrong version
+        # it takes a very long time to rebuild!
+        tty.info('Build for ' + self.spec['openfoam'].format('$_$@$%@+$+'))
+
+    def configure(self, spec, prefix):
+        """Generate spack-config.sh file."""
+        # Local tweaks
+        # This is ugly, but otherwise it only looks for src/precice,
+        # not the installed include files
+        config = join_path(self.stage.source_path, 'spack-config.sh')
+        with open(config, 'w') as out:
+            out.write(
+                """# Local tweaks for building
+CPLUS_INCLUDE_PATH="{precice_dir}/include/precice${{CPLUS_INCLUDE_PATH:+:}}$CPLUS_INCLUDE_PATH"  ## noqa: E501
+export CPLUS_INCLUDE_PATH
+# Local build (for user appbin, libbin)
+. ./change-userdir.sh $PWD/{user_dir}
+#
+"""
+                .format(
+                    precice_dir=spec['precice'].prefix,
+                    user_dir=self.build_userdir))
+
+    def build(self, spec, prefix):
+        """Build with Allwmake script, wrapped to source environment first."""
+        args = []
+        if self.parallel:  # Parallel build? - pass via environment
+            os.environ['WM_NCOMPPROCS'] = str(make_jobs)
+        builder = Executable(self.build_script)
+        builder(*args)
+
+    def install(self, spec, prefix):
+        """Install under the prefix directory"""
+
+        for f in ['README.md', 'LICENSE']:
+            if os.path.isfile(f):
+                install(f, join_path(self.prefix, f))
+
+        install_tree('tutorials', join_path(self.prefix, 'tutorials'))
+
+        # Place directly under 'lib' (no bin)
+        install_tree(
+            join_path(self.build_userdir, 'lib'),
+            join_path(self.prefix, 'lib'))
diff --git a/var/spack/repos/builtin/packages/omega-h/package.py b/var/spack/repos/builtin/packages/omega-h/package.py
new file mode 100644
index 0000000000..18f5563cb4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/omega-h/package.py
@@ -0,0 +1,91 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class OmegaH(CMakePackage):
+    """Omega_h is a C++11 library providing data structures and algorithms
+    for adaptive discretizations. Its specialty is anisotropic triangle and
+    tetrahedral mesh adaptation. It runs efficiently on most modern HPC
+    hardware including GPUs.
+    """
+
+    homepage = "https://github.com/ibaned/omega_h"
+    url      = "https://github.com/ibaned/omega_h/archive/v9.13.4.tar.gz"
+    git      = "https://github.com/ibaned/omega_h.git"
+
+    version('develop', branch='master')
+    version('9.19.1', sha256='60ef65c2957ce03ef9d1b995d842fb65c32c5659d064de002c071effe66b1b1f')
+    version('9.19.0', sha256='4a1606c4e7287a1b67359cf6ef1c2d7e24b7dc379065566a1d2e0b0330c0abbd')
+    version('9.15.0', sha256='342a506a0ff22f6cac759862efdcf34e360110f7901eb9b4c5de8afe38741522')
+    version('9.14.0', sha256='035d0f47142f965a57818d1cb6c5c00b5ae6b5a0178b67b0bc9177fa99ba083d')
+    version('9.13.14', sha256='f617dfd024c9cc323e56800ca23df3386bfa37e1b9bd378847d1f5d32d2b8e5d')
+    version('9.13.13', sha256='753702edf4bda9ae57ea21f09ca071e341604a468d8c86468c9aebba049f581c')
+
+    variant('shared', default=True, description='Build shared libraries')
+    variant('mpi', default=True, description='Activates MPI support')
+    variant('zlib', default=True, description='Activates ZLib support')
+    variant('trilinos', default=False, description='Use Teuchos and Kokkos')
+    variant('build_type', default='')
+    variant('throw', default=False, description='Errors throw exceptions instead of abort')
+    variant('examples', default=False, description='Compile examples')
+    variant('optimize', default=True, description='Compile C++ with optimization')
+    variant('symbols', default=True, description='Compile C++ with debug symbols')
+    variant('warnings', default=False, description='Compile C++ with warnings')
+
+    depends_on('gmsh', when='+examples', type='build')
+    depends_on('mpi', when='+mpi')
+    depends_on('trilinos +kokkos +teuchos', when='+trilinos')
+    depends_on('zlib', when='+zlib')
+
+    # https://gcc.gnu.org/bugzilla/show_bug.cgi?id=86610
+    conflicts('%gcc@8:')
+
+    def _bob_options(self):
+        cmake_var_prefix = 'Omega_h_CXX_'
+        for variant in ['optimize', 'symbols', 'warnings']:
+            cmake_var = cmake_var_prefix + variant.upper()
+            if '+' + variant in self.spec:
+                yield '-D' + cmake_var + ':BOOL=ON'
+            else:
+                yield '-D' + cmake_var + ':BOOL=FALSE'
+
+    def cmake_args(self):
+        args = ['-DUSE_XSDK_DEFAULTS:BOOL=OFF']
+        if '+shared' in self.spec:
+            args.append('-DBUILD_SHARED_LIBS:BOOL=ON')
+        else:
+            args.append('-DBUILD_SHARED_LIBS:BOOL=OFF')
+        if '+mpi' in self.spec:
+            args.append('-DOmega_h_USE_MPI:BOOL=ON')
+            args.append('-DCMAKE_CXX_COMPILER:FILEPATH={0}'.format(
+                self.spec['mpi'].mpicxx))
+        else:
+            args.append('-DOmega_h_USE_MPI:BOOL=OFF')
+        if '+trilinos' in self.spec:
+            args.append('-DOmega_h_USE_Trilinos:BOOL=ON')
+        if '+zlib' in self.spec:
+            args.append('-DOmega_h_USE_ZLIB:BOOL=ON')
+            args.append('-DZLIB_ROOT:PATH={0}'.format(
+                self.spec['zlib'].prefix))
+        else:
+            args.append('-DOmega_h_USE_ZLIB:BOOL=OFF')
+        if '+examples' in self.spec:
+            args.append('-DOmega_h_EXAMPLES:BOOL=ON')
+        else:
+            args.append('-DOmega_h_EXAMPLES:BOOL=OFF')
+        if '+throw' in self.spec:
+            args.append('-DOmega_h_THROW:BOOL=ON')
+        else:
+            args.append('-DOmega_h_THROW:BOOL=OFF')
+        args += list(self._bob_options())
+        return args
+
+    def flag_handler(self, name, flags):
+        flags = list(flags)
+        if name == 'cxxflags':
+            flags.append(self.compiler.cxx11_flag)
+        return (None, None, flags)
diff --git a/var/spack/repos/builtin/packages/ompss/package.py b/var/spack/repos/builtin/packages/ompss/package.py
index f3cea1597d..e9f4f4a757 100644
--- a/var/spack/repos/builtin/packages/ompss/package.py
+++ b/var/spack/repos/builtin/packages/ompss/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 import glob
diff --git a/var/spack/repos/builtin/packages/ompt-openmp/package.py b/var/spack/repos/builtin/packages/ompt-openmp/package.py
index 803f70c7c2..50641146c1 100644
--- a/var/spack/repos/builtin/packages/ompt-openmp/package.py
+++ b/var/spack/repos/builtin/packages/ompt-openmp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/oniguruma/package.py b/var/spack/repos/builtin/packages/oniguruma/package.py
index 28fb33590c..7dda866f16 100644
--- a/var/spack/repos/builtin/packages/oniguruma/package.py
+++ b/var/spack/repos/builtin/packages/oniguruma/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/ont-albacore/package.py b/var/spack/repos/builtin/packages/ont-albacore/package.py
index 882b6f6925..79da108daf 100644
--- a/var/spack/repos/builtin/packages/ont-albacore/package.py
+++ b/var/spack/repos/builtin/packages/ont-albacore/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,8 +14,10 @@ class OntAlbacore(Package):
     kits and Flow Cells."""
 
     homepage = "https://nanoporetech.com"
-    url = "https://mirror.oxfordnanoportal.com/software/analysis/ont_albacore-1.2.4-cp35-cp35m-manylinux1_x86_64.whl"
+    url = "https://mirror.oxfordnanoportal.com/software/analysis/ont_albacore-2.3.1-cp35-cp35m-manylinux1_x86_64.whl"
 
+    version('2.3.1', '0e85ad176e691252344c4c4b673c4b68', expand=False)
+    version('2.1.2', '1e60cfb95628829f2a61a85247f1b6af', expand=False)
     version('1.2.4', '559640bec4693af12e4d923e8d77adf6', expand=False)
     version('1.1.0', 'fab4502ea1bad99d813aa2629e03e83d', expand=False)
     extends('python')
diff --git a/var/spack/repos/builtin/packages/opa-psm2/package.py b/var/spack/repos/builtin/packages/opa-psm2/package.py
new file mode 100644
index 0000000000..c10130ba55
--- /dev/null
+++ b/var/spack/repos/builtin/packages/opa-psm2/package.py
@@ -0,0 +1,35 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class OpaPsm2(MakefilePackage):
+    """ Intel Omni-Path Performance Scaled Messaging 2 (PSM2) library"""
+
+    homepage = "http://github.com/01org/opa-psm2"
+    url      = "https://github.com/01org/opa-psm2/archive/PSM2_10.3-8.tar.gz"
+
+    version('10.3-37',  '9bfca04f29b937b3856f893e1f8b1b60')
+    version('10.3-17',  'e7263eb449939cb87612e2c7623ca21c')
+    version('10.3-10',  '59d36b49eb126f980f3272a9d66a8e98')
+    version('10.3-8',   '07bc5cb2a6bf1189a29cbea836843db2')
+    version('10.2-260', '71df31b5776be64ff243417ac88eec66')
+    version('10.2-235', '23539f725a597bf2d35aac47a793a37b')
+    version('10.2-175', 'c542b8641ad573f08f61d0a6a70f4013')
+
+    depends_on('numactl')
+
+    def setup_environment(self, spack_env, run_env):
+        spack_env.set('DESTDIR', self.prefix)
+        run_env.prepend_path('CPATH',
+                             join_path(self.prefix, 'usr', 'include'))
+        run_env.prepend_path('LIBRARY_PATH',
+                             join_path(self.prefix, 'usr', 'lib64'))
+        run_env.prepend_path('LD_LIBRARY_PATH',
+                             join_path(self.prefix, 'usr', 'lib64'))
+
+    def install(self, spec, prefix):
+        make('--environment-overrides', 'install')
diff --git a/var/spack/repos/builtin/packages/opam/package.py b/var/spack/repos/builtin/packages/opam/package.py
new file mode 100644
index 0000000000..0ff0af9157
--- /dev/null
+++ b/var/spack/repos/builtin/packages/opam/package.py
@@ -0,0 +1,34 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Opam(AutotoolsPackage):
+    """OPAM: OCaml Package Manager
+
+       OPAM is a source-based package manager for OCaml. It supports
+       multiple simultaneous compiler installations, flexible package
+       constraints, and a Git-friendly development workflow."""
+
+    homepage = "https://opam.ocaml.org/"
+    url      = "https://github.com/ocaml/opam/releases/download/1.2.2/opam-full-1.2.2.tar.gz"
+
+    version('1.2.2', '7d348c2898795e9f325fb80eaaf5eae8')
+    version('1.2.1', '04e8823a099ab631943952e4c2ab18fc')
+
+    depends_on('ocaml')  # Not a strict dependency, but recommended
+
+    parallel = False
+
+    def setup_environment(self, spack_env, run_env):
+        # Environment variable setting taken from
+        # https://github.com/Homebrew/homebrew-core/blob/master/Formula/opam.rb
+        spack_env.set('OCAMLPARAM', 'safe-string=0,_')  # OCaml 4.06.0 compat
+
+    def build(self, spec, prefix):
+        make('lib-ext')
+        make()
+        make('man')
diff --git a/var/spack/repos/builtin/packages/opari2/package.py b/var/spack/repos/builtin/packages/opari2/package.py
index 9b0a4e9c47..e48d64be5e 100644
--- a/var/spack/repos/builtin/packages/opari2/package.py
+++ b/var/spack/repos/builtin/packages/opari2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,6 +20,8 @@ class Opari2(AutotoolsPackage):
     homepage = "http://www.vi-hps.org/projects/score-p"
     url      = "http://www.vi-hps.org/upload/packages/opari2/opari2-1.1.2.tar.gz"
 
+    version('2.0.4', 'f69e324792f66780b473daf2b3c81f58ee8188adc72b6fe0dacf43d4c1a0a131')
+    version('2.0.3', 'f34674718ffdb098a48732a1eb9c1aa2')
     version('2.0.1', '74af78f1f27b8caaa4271e0b97fb0fba')
     version('2.0',   '72350dbdb6139f2e68a5055a4f0ba16c')
     version('1.1.4', '245d3d11147a06de77909b0805f530c0')
diff --git a/var/spack/repos/builtin/packages/openbabel/package.py b/var/spack/repos/builtin/packages/openbabel/package.py
index b88693d531..c7d6a68ec3 100644
--- a/var/spack/repos/builtin/packages/openbabel/package.py
+++ b/var/spack/repos/builtin/packages/openbabel/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -42,7 +23,7 @@ class Openbabel(CMakePackage):
 
     depends_on('python', type=('build', 'run'), when='+python')
     depends_on('cmake@2.4.8:', type='build')
-    depends_on('pkg-config',   type='build')
+    depends_on('pkgconfig',   type='build')
     depends_on('cairo')       # required to support PNG depiction
     depends_on('eigen@3.0:')  # required if using the language bindings
     depends_on('libxml2')     # required to read/write CML files, XML formats
diff --git a/var/spack/repos/builtin/packages/openblas/openblas-0.3.2-cmake.patch b/var/spack/repos/builtin/packages/openblas/openblas-0.3.2-cmake.patch
new file mode 100644
index 0000000000..50df19805f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/openblas/openblas-0.3.2-cmake.patch
@@ -0,0 +1,43 @@
+From 8ebf541e97e7c0573cde6a51353a47e3c509ca00 Mon Sep 17 00:00:00 2001
+From: Scott Thornton <wsttiger@gmail.com>
+Date: Mon, 30 Jul 2018 15:18:29 -0500
+Subject: [PATCH 1/2] Set EXPORT_NAME to match OpenBLASConfig.cmake
+
+---
+ CMakeLists.txt | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 97f8adeda..4dc18da99 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -169,6 +169,7 @@ endif()
+ # Set output for libopenblas
+ set_target_properties( ${OpenBLAS_LIBNAME} PROPERTIES RUNTIME_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/lib)
+ set_target_properties( ${OpenBLAS_LIBNAME} PROPERTIES LIBRARY_OUTPUT_NAME_DEBUG "${OpenBLAS_LIBNAME}_d")
++set_target_properties( ${OpenBLAS_LIBNAME} PROPERTIES EXPORT_NAME "OpenBLAS")
+ 
+ foreach (OUTPUTCONFIG ${CMAKE_CONFIGURATION_TYPES})
+   string( TOUPPER ${OUTPUTCONFIG} OUTPUTCONFIG )
+
+From 2a9a9389ef6c3da56fda859c9586becc41a2e780 Mon Sep 17 00:00:00 2001
+From: Scott Thornton <wsttiger@gmail.com>
+Date: Thu, 2 Aug 2018 14:58:52 -0500
+Subject: [PATCH 2/2] Added target_include_directories()
+
+---
+ CMakeLists.txt | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 4dc18da99..20ce02e87 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -150,6 +150,7 @@ endif()
+ 
+ # add objects to the openblas lib
+ add_library(${OpenBLAS_LIBNAME} ${LA_SOURCES} ${LAPACKE_SOURCES} ${RELA_SOURCES} ${TARGET_OBJS} ${OpenBLAS_DEF_FILE})
++target_include_directories(${OpenBLAS_LIBNAME} INTERFACE $<INSTALL_INTERFACE:include>)
+ 
+ # Android needs to explicitly link against libm
+ if(ANDROID)
diff --git a/var/spack/repos/builtin/packages/openblas/openblas_icc_fortran2.patch b/var/spack/repos/builtin/packages/openblas/openblas_icc_fortran2.patch
new file mode 100644
index 0000000000..64785d4f45
--- /dev/null
+++ b/var/spack/repos/builtin/packages/openblas/openblas_icc_fortran2.patch
@@ -0,0 +1,14 @@
+diff --git a/f_check b/f_check
+index 79febfb..c9da6ed 100644
+--- a/f_check
++++ b/f_check
+@@ -359,9 +359,6 @@ print MAKEFILE "NOFORTRAN=1\n" if $nofortran == 1;
+ 
+ print CONFFILE "#define BUNDERSCORE\t$bu\n" if $bu ne "";
+ print CONFFILE "#define NEEDBUNDERSCORE\t1\n" if $bu ne "";
+-print CONFFILE "#define NEED2UNDERSCORES\t1\n" if $need2bu ne "";
+-
+-print MAKEFILE "NEED2UNDERSCORES=1\n" if $need2bu ne "";
+ 
+ if (($linker_l ne "") || ($linker_a ne "")) {
+     print MAKEFILE "FEXTRALIB=$linker_L $linker_l $linker_a\n";
diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py
index f85d0e2a02..ffa02c23e6 100644
--- a/var/spack/repos/builtin/packages/openblas/package.py
+++ b/var/spack/repos/builtin/packages/openblas/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 
 from spack import *
@@ -31,16 +12,22 @@ import spack.architecture
 
 class Openblas(MakefilePackage):
     """OpenBLAS: An optimized BLAS library"""
-    homepage = 'http://www.openblas.net'
-    url = 'http://github.com/xianyi/OpenBLAS/archive/v0.2.19.tar.gz'
 
+    homepage = 'http://www.openblas.net'
+    url      = 'http://github.com/xianyi/OpenBLAS/archive/v0.2.19.tar.gz'
+    git      = 'https://github.com/xianyi/OpenBLAS.git'
+
+    version('develop', branch='develop')
+    version('0.3.3', sha256='49d88f4494ae780e3d7fa51769c00d982d7cdb73e696054ac3baa81d42f13bab')
+    version('0.3.2', sha256='e8ba64f6b103c511ae13736100347deb7121ba9b41ba82052b1a018a65c0cb15')
+    version('0.3.1', sha256='1f5e956f35f3acdd3c74516e955d797a320c2e0135e31d838cbdb3ea94d0eb33')
+    version('0.3.0',  '42cde2c1059a8a12227f1e6551c8dbd2')
     version('0.2.20', '48637eb29f5b492b91459175dcc574b1')
     version('0.2.19', '28c998054fd377279741c6f0b9ea7941')
     version('0.2.18', '805e7f660877d588ea7e3792cda2ee65')
     version('0.2.17', '664a12807f2a2a7cda4781e3ab2ae0e1')
     version('0.2.16', 'fef46ab92463bdbb1479dcec594ef6dc')
     version('0.2.15', 'b1190f3d3471685f17cfd1ec1d252ac9')
-    version('develop', git='https://github.com/xianyi/OpenBLAS.git', branch='develop')
 
     variant(
         'shared',
@@ -61,6 +48,12 @@ class Openblas(MakefilePackage):
         multi=False
     )
 
+    variant(
+        'virtual_machine',
+        default=False,
+        description="Adding options to build openblas on Linux virtual machine"
+    )
+
     # virtual dependency
     provides('blas')
     provides('lapack')
@@ -70,8 +63,9 @@ class Openblas(MakefilePackage):
     #  https://github.com/xianyi/OpenBLAS/pull/915
     #  UPD: the patch has been merged starting version 0.2.20
     patch('openblas_icc.patch', when='@:0.2.19%intel')
-    patch('openblas_icc_openmp.patch', when='%intel@16.0:')
+    patch('openblas_icc_openmp.patch', when='@:0.2.20%intel@16.0:')
     patch('openblas_icc_fortran.patch', when='%intel@16.0:')
+    patch('openblas_icc_fortran2.patch', when='%intel@18.0:')
 
     # Fixes compilation error on POWER8 with GCC 7
     # https://github.com/xianyi/OpenBLAS/pull/1098
@@ -81,6 +75,18 @@ class Openblas(MakefilePackage):
     # https://github.com/xianyi/OpenBLAS/pull/982
     patch('openblas0.2.19.diff', when='@0.2.19')
 
+    # Fix CMake export symbol error
+    # https://github.com/xianyi/OpenBLAS/pull/1703
+    patch('openblas-0.3.2-cmake.patch', when='@0.3.1:0.3.2')
+
+    # Disable experimental TLS code that lead to many threading issues
+    # https://github.com/xianyi/OpenBLAS/issues/1735#issuecomment-422954465
+    # https://github.com/xianyi/OpenBLAS/issues/1761#issuecomment-421039174
+    # https://github.com/xianyi/OpenBLAS/pull/1765
+    patch('https://github.com/xianyi/OpenBLAS/commit/4d183e5567346f80f2ef97eb98f8601c47f8cb56.patch',
+          sha256='714aea33692304a50bd0ccde42590c176c82ded4a8ac7f06e573dc8071929c33',
+          when='@0.3.3')
+
     parallel = False
 
     conflicts('%intel@16', when='@0.2.15:0.2.19')
@@ -90,10 +96,11 @@ class Openblas(MakefilePackage):
         # As of 06/2016 there is no mechanism to specify that packages which
         # depends on Blas/Lapack need C or/and Fortran symbols. For now
         # require both.
-        if self.compiler.f77 is None:
+        if self.compiler.fc is None:
             raise InstallError(
                 'OpenBLAS requires both C and Fortran compilers!'
             )
+
         # Add support for OpenMP
         if (self.spec.satisfies('threads=openmp') and
             self.spec.satisfies('%clang')):
@@ -108,7 +115,7 @@ class Openblas(MakefilePackage):
 
     @property
     def make_defs(self):
-        # Configure fails to pick up fortran from FC=/abs/path/to/f77, but
+        # Configure fails to pick up fortran from FC=/abs/path/to/fc, but
         # works fine with FC=/abs/path/to/gfortran.
         # When mixing compilers make sure that
         # $SPACK_ROOT/lib/spack/env/<compiler> have symlinks with reasonable
@@ -116,9 +123,16 @@ class Openblas(MakefilePackage):
 
         make_defs = [
             'CC={0}'.format(spack_cc),
-            'FC={0}'.format(spack_f77),
+            'FC={0}'.format(spack_fc),
             'MAKE_NO_J=1'
         ]
+
+        if self.spec.variants['virtual_machine'].value:
+            make_defs += [
+                'DYNAMIC_ARCH=1',
+                'NO_AVX2=1'
+            ]
+
         if self.spec.variants['cpu_target'].value:
             make_defs += [
                 'TARGET={0}'.format(self.spec.variants['cpu_target'].value)
diff --git a/var/spack/repos/builtin/packages/opencoarrays/CMakeLists.patch b/var/spack/repos/builtin/packages/opencoarrays/CMakeLists.patch
new file mode 100644
index 0000000000..7ce5a60479
--- /dev/null
+++ b/var/spack/repos/builtin/packages/opencoarrays/CMakeLists.patch
@@ -0,0 +1,27 @@
+diff --git a/src/mpi/CMakeLists.txt b/src/mpi/CMakeLists.txt
+index 590d646..3f2bded 100644
+--- a/src/mpi/CMakeLists.txt
++++ b/src/mpi/CMakeLists.txt
+@@ -8,22 +8,6 @@ if (NOT MPI_C_FOUND)
+   include_directories(BEFORE ${MPI_C_INCLUDE_PATH} ${MPI_Fortran_INCLUDE_PATH})
+    endif()
+
+    -#----------------------------------
+    -# Determine if we're using Open MPI
+    -#----------------------------------
+    -cmake_host_system_information(RESULT N_CPU QUERY NUMBER_OF_LOGICAL_CORES)
+    -set(N_CPU ${N_CPU} PARENT_SCOPE)
+    -cmake_host_system_information(RESULT HOST_NAME QUERY HOSTNAME)
+    -set(HOSTNAME ${HOSTNAME} PARENT_SCOPE)
+    -execute_process(COMMAND ${MPIEXEC} --version
+    -  OUTPUT_VARIABLE mpi_version_out)
+    -if (mpi_version_out MATCHES "[Oo]pen[ -][Mm][Pp][Ii]")
+    -  message( STATUS "OpenMPI detected")
+    -  set ( openmpi true PARENT_SCOPE)
+    -  # Write out a host file because OMPI's mpiexec is dumb
+    -  file(WRITE ${CMAKE_BINARY_DIR}/hostfile "${HOST_NAME} slots=${N_CPU}\n")
+    -endif ()
+    -
+     if("${CMAKE_Fortran_COMPILER_ID}" STREQUAL "GNU")
+           set(gfortran_compiler true)
+            elseif("${CMAKE_Fortran_COMPILER_ID}" STREQUAL "Cray")
diff --git a/var/spack/repos/builtin/packages/opencoarrays/package.py b/var/spack/repos/builtin/packages/opencoarrays/package.py
index cba5651fc7..e3da9753ae 100644
--- a/var/spack/repos/builtin/packages/opencoarrays/package.py
+++ b/var/spack/repos/builtin/packages/opencoarrays/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,8 +15,9 @@ class Opencoarrays(CMakePackage):
     """
 
     homepage = "http://www.opencoarrays.org/"
-    url      = "https://github.com/sourceryinstitute/OpenCoarrays/releases/download/1.8.4/OpenCoarrays-1.8.4.tar.gz"
+    url      = "https://github.com/sourceryinstitute/OpenCoarrays/releases/download/2.2.0/OpenCoarrays-2.2.0.tar.gz"
 
+    version('2.2.0', '9311547a85a21853111f1e8555ceab4593731c6fd9edb64cfb9588805f9d1a0d')
     version('1.8.10', '9ba1670647db4d986634abf743abfd6a')
     version('1.8.4', '7c9eaffc3a0b5748d0d840e52ec9d4ad')
     version('1.8.0', 'ca78d1507b2a118c75128c6c2e093e27')
@@ -48,6 +30,9 @@ class Opencoarrays(CMakePackage):
                     'MinSizeRel', 'CodeCoverage'))
 
     depends_on('mpi')
+    # This patch removes a bunch of checks for the version of MPI available on
+    # the system. They make the Crays hang.
+    patch('CMakeLists.patch', when='platform=cray')
 
     def cmake_args(self):
         args = []
diff --git a/var/spack/repos/builtin/packages/opencv/dnn_cuda.patch b/var/spack/repos/builtin/packages/opencv/dnn_cuda.patch
new file mode 100644
index 0000000000..66ab59ba26
--- /dev/null
+++ b/var/spack/repos/builtin/packages/opencv/dnn_cuda.patch
@@ -0,0 +1,44 @@
+--- opencv-3.4.1/modules/dnn/src/layers/mvn_layer.cpp.orig	2018-06-14 10:46:28.025703093 +0200
++++ opencv-3.4.1/modules/dnn/src/layers/mvn_layer.cpp	2018-06-14 10:40:56.266069123 +0200
+@@ -43,7 +43,7 @@
+ #include "../precomp.hpp"
+ #include "layers_common.hpp"
+ #include <opencv2/dnn/shape_utils.hpp>
+-#include "math_functions.hpp"
++#include "../ocl4dnn/include/math_functions.hpp"
+ #include "opencl_kernels_dnn.hpp"
+ 
+ namespace cv
+--- opencv-3.4.1/modules/dnn/src/ocl4dnn/src/math_functions.cpp.orig	2018-06-14 10:45:23.565162940 +0200
++++ opencv-3.4.1/modules/dnn/src/ocl4dnn/src/math_functions.cpp	2018-06-14 10:44:48.513412965 +0200
+@@ -42,7 +42,7 @@
+ 
+ #include "../../precomp.hpp"
+ #include "common.hpp"
+-#include "math_functions.hpp"
++#include "../include/math_functions.hpp"
+ #include <vector>
+ #include "opencl_kernels_dnn.hpp"
+ 
+--- opencv-3.4.1/modules/dnn/src/ocl4dnn/src/ocl4dnn_conv_spatial.cpp.orig	2018-06-14 10:42:11.319534007 +0200
++++ opencv-3.4.1/modules/dnn/src/ocl4dnn/src/ocl4dnn_conv_spatial.cpp	2018-06-14 10:42:52.988236879 +0200
+@@ -52,7 +52,7 @@
+ #include "common.hpp"
+ #include "ocl4dnn.hpp"
+ #include "opencl_kernels_dnn.hpp"
+-#include "math_functions.hpp"
++#include "../include/math_functions.hpp"
+ #include "default_kernel_config.hpp"
+ 
+ #if defined WIN32 || defined _WIN32
+--- opencv-3.4.1/modules/dnn/src/ocl4dnn/src/ocl4dnn_inner_product.cpp.orig	2018-06-14 10:45:41.245036822 +0200
++++ opencv-3.4.1/modules/dnn/src/ocl4dnn/src/ocl4dnn_inner_product.cpp	2018-06-14 10:45:55.543934818 +0200
+@@ -43,7 +43,7 @@
+ #include "../../precomp.hpp"
+ #include "common.hpp"
+ #include "ocl4dnn.hpp"
+-#include "math_functions.hpp"
++#include "../include/math_functions.hpp"
+ 
+ #ifdef HAVE_OPENCL
+ namespace cv { namespace dnn { namespace ocl4dnn {
diff --git a/var/spack/repos/builtin/packages/opencv/package.py b/var/spack/repos/builtin/packages/opencv/package.py
index e76f763ffb..96a643f3a4 100644
--- a/var/spack/repos/builtin/packages/opencv/package.py
+++ b/var/spack/repos/builtin/packages/opencv/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,12 +21,17 @@ class Opencv(CMakePackage):
     """
 
     homepage = 'http://opencv.org/'
-    url = 'https://github.com/Itseez/opencv/archive/3.1.0.tar.gz'
+    url      = 'https://github.com/Itseez/opencv/archive/3.1.0.tar.gz'
+    git      = 'https://github.com/opencv/opencv.git'
 
-    version('master', git="https://github.com/opencv/opencv.git", branch="master")
+    version('master', branch='master')
+    version('3.4.3',    '712896f5815938c014c199dde142d508')
+    version('3.4.1',    'a0b7a47899e67b3490ea31edc4f6e8e6')
+    version('3.4.0',    '170732dc760e5f7ddeccbe53ba5d16a6')
+    version('3.3.1',    'b1ed9aea030bb5bd9df28524d97de84c')
     version('3.3.0',    '98a4e4c6f23ec725e808a891dc11eec4')
-    version('3.2.0',    'a43b65488124ba33dde195fea9041b70')
-    version('3.1.0',    '70e1dd07f0aa06606f1bc0e3fa15abd3')
+    version('3.2.0',    '1ea44a1d98c126ad40079d8eb914a72e')
+    version('3.1.0',    'a0669e22172dfc3225835b180744c9f0')
     version('2.4.13.2', 'fe52791ce523681a67036def4c25261b')
     version('2.4.13.1', 'f6d354500d5013e60dc0fc44b07a63d1')
     version('2.4.13',   '8feb45a71adad89b8017a777477c3eff')
@@ -53,29 +39,59 @@ class Opencv(CMakePackage):
     version('2.4.12.2', 'bc0c60c2ea1cf4078deef99569912fc7')
     version('2.4.12.1', '7192f51434710904b5e3594872b897c3')
 
+    # Standard variants
     variant('shared', default=True,
             description='Enables the build of shared libraries')
+    variant('lapack', default=True, description='Include Lapack library support')
+    variant('powerpc', default=False, description='Enable PowerPC for GCC')
+    variant('vsx', default=False, description='Enable POWER8 and above VSX (64-bit little-endian)')
+    variant('fast-math', default=False,
+            description='Enable -ffast-math (not recommended for GCC 4.6.x)')
+
+    # OpenCV modules
+    variant('calib3d', default=True, description='calib3d module')
+    variant('core', default=True, description='Include opencv_core module into the OpenCV build')
+    variant('dnn', default=True, description='Build DNN support')
+    variant('features2d', default=True, description='features2d module')
+    variant('flann', default=True, description='flann module')
+    variant('highgui', default=True, description='Include opencv_highgui module into the OpenCV build')
+    variant('imgproc', default=True, description='Include opencv_imgproc module into the OpenCV build')
+    variant('java', default=True,
+            description='Activates support for Java')
+    variant('ml', default=True, description='Build ML support')
+    variant('python', default=True,
+            description='Enables the build of Python extensions')
+    variant('stitching', default=True, description='stitching module')
+    variant('superres', default=True, description='superres module')
+    variant('ts', default=True, description='Include opencv_ts module into the OpenCV build')
+    variant('video', default=True, description='video module')
+    variant('videostab', default=True, description='videostab module')
+    variant('videoio', default=True, description='videoio module')
 
+    # Optional 3rd party components
+    variant('cuda', default=True, description='Activates support for CUDA')
     variant('eigen', default=True, description='Activates support for eigen')
     variant('ipp', default=True, description='Activates support for IPP')
+    variant('ipp_iw', default=True, description='Build IPP IW from source')
     variant('jasper', default=True, description='Activates support for JasPer')
-    variant('cuda', default=False, description='Activates support for CUDA')
-    variant('gtk', default=False, description='Activates support for GTK')
-    variant('vtk', default=False, description='Activates support for VTK')
+    variant('jpeg', default=True, description='Include JPEG support')
+    variant('opencl', default=True, description='Include OpenCL Runtime support')
+    variant('opencl_svm', default=True, description='Include OpenCL Shared Virtual Memory support')
+    variant('openclamdfft', default=True, description='Include OpenCL AMD OpenCL FFT library support')
+    variant('openclamdblas', default=True, description='Include OpenCL AMD OpenCL BLAS library support')
+    variant('openmp', default=True, description='Activates support for OpenMP threads')
+    variant('pthreads_pf', default=True, description='Use pthreads-based parallel_for')
+    variant('png', default=True, description='Include PNG support')
     variant('qt', default=False, description='Activates support for QT')
-    variant('python', default=False,
-            description='Enables the build of Python extensions')
-    variant('java', default=False,
-            description='Activates support for Java')
-    variant('openmp', default=False, description='Activates support for OpenMP threads')
-    variant('core', default=True, description='Include opencv_core module into the OpenCV build')
-    variant('highgui', default=False, description='Include opencv_highgui module into the OpenCV build')
-    variant('imgproc', default=False, description='Include opencv_imgproc module into the OpenCV build')
-    variant('jpeg', default=False, description='Include JPEG support')
-    variant('png', default=False, description='Include PNG support')
-    variant('tiff', default=False, description='Include TIFF support')
-    variant('zlib', default=False, description='Build zlib from source')
-    variant('dnn', default=False, description='Build DNN support')
+    variant('gtk', default=True, description='Activates support for GTK')
+    variant('tiff', default=True, description='Include TIFF support')
+    variant('vtk', default=True, description='Activates support for VTK')
+    variant('zlib', default=True, description='Build zlib from source')
+
+    # Patch to fix conflict between CUDA and OpenCV (reproduced with 3.3.0
+    # and 3.4.1) header file that have the same name.Problem is fixed in
+    # the current development branch of OpenCV. See #8461 for more information.
+    patch('dnn_cuda.patch', when='@3.3.0:3.4.1+cuda+dnn')
 
     depends_on('eigen~mpfr', when='+eigen', type='build')
 
@@ -93,94 +109,147 @@ class Opencv(CMakePackage):
     depends_on('py-numpy', when='+python', type=('build', 'run'))
     depends_on('protobuf@3.1.0', when='@3.3.0: +dnn')
 
+    depends_on('ffmpeg', when='+videoio')
+    depends_on('mpi', when='+videoio')
+
     extends('python', when='+python')
 
     def cmake_args(self):
         spec = self.spec
 
+        # Standard variants
         args = [
             '-DBUILD_SHARED_LIBS:BOOL={0}'.format((
                 'ON' if '+shared' in spec else 'OFF')),
             '-DENABLE_PRECOMPILED_HEADERS:BOOL=OFF',
-            '-DWITH_IPP:BOOL={0}'.format((
-                'ON' if '+ipp' in spec else 'OFF')),
-            '-DWITH_CUDA:BOOL={0}'.format((
-                'ON' if '+cuda' in spec else 'OFF')),
-            '-DWITH_QT:BOOL={0}'.format((
-                'ON' if '+qt' in spec else 'OFF')),
-            '-DWITH_VTK:BOOL={0}'.format((
-                'ON' if '+vtk' in spec else 'OFF')),
-            '-DBUILD_opencv_java:BOOL={0}'.format((
-                'ON' if '+java' in spec else 'OFF')),
+            '-DWITH_LAPACK={0}'.format((
+                'ON' if '+lapack' in spec else 'OFF')),
+            '-DENABLE_POWERPC={0}'.format((
+                'ON' if '+powerpc' in spec else 'OFF')),
+            '-DENABLE_VSX={0}'.format((
+                'ON' if '+vsx' in spec else 'OFF')),
+            '-DENABLE_FAST_MATH={0}'.format((
+                'ON' if '+fast-math' in spec else 'OFF')),
+        ]
+
+        # modules
+        args.extend([
+            '-DBUILD_opencv_calib3d={0}'.format((
+                'ON' if '+calib3d' in spec else 'OFF')),
             '-DBUILD_opencv_core:BOOL={0}'.format((
                 'ON' if '+core' in spec else 'OFF')),
+            '-DBUILD_opencv_dnn:BOOL={0}'.format((
+                'ON' if '+dnn' in spec else 'OFF')),
+            '-DBUILD_opencv_features2d={0}'.format((
+                'ON' if '+features2d' in spec else 'OFF')),
+            '-DBUILD_opencv_flann={0}'.format((
+                'ON' if '+flann' in spec else 'OFF')),
             '-DBUILD_opencv_highgui:BOOL={0}'.format((
                 'ON' if '+highgui' in spec else 'OFF')),
             '-DBUILD_opencv_imgproc:BOOL={0}'.format((
                 'ON' if '+imgproc' in spec else 'OFF')),
+            '-DBUILD_opencv_java:BOOL={0}'.format((
+                'ON' if '+java' in spec else 'OFF')),
+            '-DBUILD_opencv_ml={0}'.format((
+                'ON' if '+ml' in spec else 'OFF')),
+            '-DBUILD_opencv_stitching={0}'.format((
+                'ON' if '+stitching' in spec else 'OFF')),
+            '-DBUILD_opencv_superres={0}'.format((
+                'ON' if '+superres' in spec else 'OFF')),
+            '-DBUILD_opencv_ts={0}'.format((
+                'ON' if '+ts' in spec else 'OFF')),
+            '-DBUILD_opencv_video={0}'.format((
+                'ON' if '+video' in spec else 'OFF')),
+            '-DBUILD_opencv_videostab={0}'.format((
+                'ON' if '+videostab' in spec else 'OFF')),
+            '-DBUILD_opencv_videoio={0}'.format((
+                'ON' if '+videoio' in spec else 'OFF')),
+        ])
+
+        # 3rd party components
+        args.extend([
+            '-DBUILD_IPP_IW:BOOL={0}'.format((
+                'ON' if '+ipp_iw' in spec else 'OFF')),
+            '-DWITH_CUDA:BOOL={0}'.format((
+                'ON' if '+cuda' in spec else 'OFF')),
+            '-DWITH_EIGEN:BOOL={0}'.format((
+                'ON' if '+eigen' in spec else 'OFF')),
+            '-DWITH_IPP:BOOL={0}'.format((
+                'ON' if '+ipp' in spec else 'OFF')),
+            '-DWITH_JASPER:BOOL={0}'.format((
+                'ON' if '+jasper' in spec else 'OFF')),
             '-DWITH_JPEG:BOOL={0}'.format((
                 'ON' if '+jpeg' in spec else 'OFF')),
+            '-DWITH_OPENCL:BOOL={0}'.format((
+                'ON' if '+opencl' in spec else 'OFF')),
+            '-DWITH_OPENCL_SVM:BOOL={0}'.format((
+                'ON' if '+opencl_svm' in spec else 'OFF')),
+            '-DWITH_OPENCLAMDFFT:BOOL={0}'.format((
+                'ON' if '+openclamdfft' in spec else 'OFF')),
+            '-DWITH_OPENCLAMDBLAS:BOOL={0}'.format((
+                'ON' if '+openclamdblas' in spec else 'OFF')),
+            '-DWITH_OPENMP:BOOL={0}'.format((
+                'ON' if '+openmp' in spec else 'OFF')),
+            '-DWITH_PTHREADS_PF:BOOL={0}'.format((
+                'ON' if '+pthreads_pf' in spec else 'OFF')),
             '-DWITH_PNG:BOOL={0}'.format((
                 'ON' if '+png' in spec else 'OFF')),
+            '-DWITH_QT:BOOL={0}'.format((
+                'ON' if '+qt' in spec else 'OFF')),
             '-DWITH_TIFF:BOOL={0}'.format((
                 'ON' if '+tiff' in spec else 'OFF')),
-            '-DWITH_ZLIB:BOOL={0}'.format((
-                'ON' if '+zlib' in spec else 'OFF')),
-            '-DWITH_OPENMP:BOOL={0}'.format((
-                'ON' if '+openmp' in spec else 'OFF')),
-            '-DBUILD_opencv_dnn:BOOL={0}'.format((
-                'ON' if '+dnn' in spec else 'OFF')),
-        ]
+            '-DWITH_VTK:BOOL={0}'.format((
+                'ON' if '+vtk' in spec else 'OFF')),
+        ])
 
         # Media I/O
         if '+zlib' in spec:
             zlib = spec['zlib']
             args.extend([
                 '-DZLIB_LIBRARY_{0}:FILEPATH={1}'.format((
-                    'DEBUG' if '+debug' in spec else 'RELEASE'),
-                    join_path(zlib.prefix.lib,
-                              'libz.{0}'.format(dso_suffix))),
-                '-DZLIB_INCLUDE_DIR:PATH={0}'.format(zlib.prefix.include)
+                    'DEBUG' if 'build_type=Debug' in spec else 'RELEASE'),
+                    zlib.libs[0]),
+                '-DZLIB_INCLUDE_DIR:PATH={0}'.format(
+                    zlib.headers.directories[0])
             ])
 
         if '+png' in spec:
             libpng = spec['libpng']
             args.extend([
                 '-DPNG_LIBRARY_{0}:FILEPATH={1}'.format((
-                    'DEBUG' if '+debug' in spec else 'RELEASE'),
-                    join_path(libpng.prefix.lib,
-                              'libpng.{0}'.format(dso_suffix))),
-                '-DPNG_INCLUDE_DIR:PATH={0}'.format(libpng.prefix.include)
+                    'DEBUG' if 'build_type=Debug' in spec else 'RELEASE'),
+                    libpng.libs[0]),
+                '-DPNG_INCLUDE_DIR:PATH={0}'.format(
+                    libpng.headers.directories[0])
             ])
 
         if '+jpeg' in spec:
             libjpeg = spec['jpeg']
             args.extend([
                 '-DBUILD_JPEG:BOOL=OFF',
-                '-DJPEG_LIBRARY:FILEPATH={0}'.format(
-                    join_path(libjpeg.prefix.lib,
-                              'libjpeg.{0}'.format(dso_suffix))),
-                '-DJPEG_INCLUDE_DIR:PATH={0}'.format(libjpeg.prefix.include)
+                '-DJPEG_LIBRARY:FILEPATH={0}'.format(libjpeg.libs[0]),
+                '-DJPEG_INCLUDE_DIR:PATH={0}'.format(
+                    libjpeg.headers.directories[0])
             ])
 
         if '+tiff' in spec:
             libtiff = spec['libtiff']
             args.extend([
                 '-DTIFF_LIBRARY_{0}:FILEPATH={1}'.format((
-                    'DEBUG' if '+debug' in spec else 'RELEASE'),
-                    join_path(libtiff.prefix.lib,
-                              'libtiff.{0}'.format(dso_suffix))),
-                '-DTIFF_INCLUDE_DIR:PATH={0}'.format(libtiff.prefix.include)
+                    'DEBUG' if 'build_type=Debug' in spec else 'RELEASE'),
+                    libtiff.libs[0]),
+                '-DTIFF_INCLUDE_DIR:PATH={0}'.format(
+                    libtiff.headers.directories[0])
             ])
 
         if '+jasper' in spec:
             jasper = spec['jasper']
             args.extend([
                 '-DJASPER_LIBRARY_{0}:FILEPATH={1}'.format((
-                    'DEBUG' if '+debug' in spec else 'RELEASE'),
-                    join_path(jasper.prefix.lib,
-                              'libjasper.{0}'.format(dso_suffix))),
-                '-DJASPER_INCLUDE_DIR:PATH={0}'.format(jasper.prefix.include)
+                    'DEBUG' if 'build_type=Debug' in spec else 'RELEASE'),
+                    jasper.libs[0]),
+                '-DJASPER_INCLUDE_DIR:PATH={0}'.format(
+                    jasper.headers.directories[0])
             ])
 
         # GUI
@@ -229,3 +298,10 @@ class Opencv(CMakePackage):
             ])
 
         return args
+
+    @property
+    def libs(self):
+        shared = "+shared" in self.spec
+        return find_libraries(
+            "libopencv_*", root=self.prefix, shared=shared, recursive=True
+        )
diff --git a/var/spack/repos/builtin/packages/openexr/package.py b/var/spack/repos/builtin/packages/openexr/package.py
index ad463bc792..6cb17ee9ce 100644
--- a/var/spack/repos/builtin/packages/openexr/package.py
+++ b/var/spack/repos/builtin/packages/openexr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -43,7 +24,7 @@ class Openexr(Package):
     variant('debug', default=False,
             description='Builds a debug version of the libraries')
 
-    depends_on('pkg-config', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('ilmbase')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/openfast/package.py b/var/spack/repos/builtin/packages/openfast/package.py
index 74d1881de9..14824588db 100644
--- a/var/spack/repos/builtin/packages/openfast/package.py
+++ b/var/spack/repos/builtin/packages/openfast/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,18 +10,14 @@ class Openfast(CMakePackage):
     """Wind turbine simulation package from NREL"""
 
     homepage = "http://openfast.readthedocs.io/en/latest/"
-    url      = "https://github.com/OpenFAST/openfast.git"
+    git      = "https://github.com/OpenFAST/openfast.git"
 
     maintainers = ['jrood-nrel']
 
-    version('develop',
-            git='https://github.com/OpenFAST/openfast.git',
-            branch='dev')
-    version('master',
-            git='https://github.com/OpenFAST/openfast.git',
-            branch='master')
+    version('develop', branch='dev')
+    version('master', branch='master')
 
-    variant('shared', default=False,
+    variant('shared', default=True,
             description="Build shared libraries")
     variant('double-precision', default=True,
             description="Treat REAL as double precision")
@@ -48,6 +25,8 @@ class Openfast(CMakePackage):
             description="Enable dynamic library loading interface")
     variant('cxx', default=False,
             description="Enable C++ bindings")
+    variant('pic', default=True,
+            description="Position independent code")
 
     # Dependencies for OpenFAST Fortran
     depends_on('blas')
@@ -56,7 +35,7 @@ class Openfast(CMakePackage):
     # Additional dependencies when compiling C++ library
     depends_on('mpi', when='+cxx')
     depends_on('yaml-cpp', when='+cxx')
-    depends_on('hdf5+mpi+cxx', when='+cxx')
+    depends_on('hdf5+mpi+cxx+hl', when='+cxx')
     depends_on('zlib', when='+cxx')
     depends_on('libxml2', when='+cxx')
 
@@ -77,10 +56,22 @@ class Openfast(CMakePackage):
                 'ON' if '+dll-interface' in spec else 'OFF'),
             '-DBUILD_FAST_CPP_API:BOOL=%s' % (
                 'ON' if '+cxx' in spec else 'OFF'),
+            '-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=%s' % (
+                'ON' if '+pic' in spec else 'OFF'),
+        ])
+
+        # Make sure we use Spack's blas/lapack:
+        blas_libs = spec['lapack'].libs + spec['blas'].libs
+        options.extend([
+            '-DBLAS_LIBRARIES=%s' % blas_libs.joined(';'),
+            '-DLAPACK_LIBRARIES=%s' % blas_libs.joined(';')
         ])
 
         if '+cxx' in spec:
             options.extend([
+                '-DMPI_CXX_COMPILER:PATH=%s' % spec['mpi'].mpicxx,
+                '-DMPI_C_COMPILER:PATH=%s' % spec['mpi'].mpicc,
+                '-DMPI_Fortran_COMPILER:PATH=%s' % spec['mpi'].mpifc,
                 '-DHDF5_ROOT:PATH=%s' % spec['hdf5'].prefix,
                 '-DYAML_ROOT:PATH=%s' % spec['yaml-cpp'].prefix,
             ])
diff --git a/var/spack/repos/builtin/packages/openfoam-com/1612-bin.patch b/var/spack/repos/builtin/packages/openfoam-com/1612-bin.patch
deleted file mode 100644
index b9e87a7ec8..0000000000
--- a/var/spack/repos/builtin/packages/openfoam-com/1612-bin.patch
+++ /dev/null
@@ -1,503 +0,0 @@
---- OpenFOAM-v1612+.orig/bin/foamEtcFile	2016-12-23 15:22:59.000000000 +0100
-+++ OpenFOAM-v1612+/bin/foamEtcFile	2017-03-23 10:08:37.296887070 +0100
-@@ -4,7 +4,7 @@
- # \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
- #  \\    /   O peration     |
- #   \\  /    A nd           | Copyright (C) 2011-2016 OpenFOAM Foundation
--#    \\/     M anipulation  |
-+#    \\/     M anipulation  | Copyright (C) 2017 OpenCFD Ltd.
- #-------------------------------------------------------------------------------
- # License
- #     This file is part of OpenFOAM.
-@@ -26,7 +26,7 @@
- #     foamEtcFile
- #
- # Description
--#     Locate user/group/shipped file with semantics similar to the
-+#     Locate user/group/other files with semantics similar to the
- #     ~OpenFOAM/fileName expansion.
- #
- #     The -mode option can be used to allow chaining from
-@@ -34,40 +34,53 @@
- #
- #     For example, within the user ~/.OpenFOAM/<VER>/prefs.sh:
- #     \code
--#        foamPrefs=`$WM_PROJECT_DIR/bin/foamEtcFile -m go prefs.sh` \
--#            && _foamSource $foamPrefs
-+#        eval $(foamEtcFile -sh -mode=go prefs.sh)
- #     \endcode
- #
-+# Environment
-+#     - WM_PROJECT:         (unset defaults to OpenFOAM)
-+#     - WM_PROJECT_SITE:    (unset defaults to PREFIX/site)
-+#     - WM_PROJECT_VERSION: (unset defaults to detect from path)
-+#
- # Note
--#     This script must exist in $FOAM_INST_DIR/OpenFOAM-<VERSION>/bin/
--#     or $FOAM_INST_DIR/openfoam<VERSION>/bin/ (for the debian version)
-+#     This script must exist in one of these locations:
-+#     - $WM_PROJECT_INST_DIR/OpenFOAM-<VERSION>/bin
-+#     - $WM_PROJECT_INST_DIR/openfoam-<VERSION>/bin
-+#     - $WM_PROJECT_INST_DIR/OpenFOAM+<VERSION>/bin
-+#     - $WM_PROJECT_INST_DIR/openfoam+<VERSION>/bin
-+#     - $WM_PROJECT_INST_DIR/openfoam<VERSION>/bin  (debian version)
- #
- #-------------------------------------------------------------------------------
-+unset optQuiet optSilent
- usage() {
-     [ "${optQuiet:-$optSilent}" = true ] && exit 1
--
-     exec 1>&2
-     while [ "$#" -ge 1 ]; do echo "$1"; shift; done
-     cat<<USAGE
- 
--Usage: ${0##*/} [OPTION] fileName
--       ${0##*/} [OPTION] -list
-+Usage: foamEtcFile [OPTION] fileName
-+       foamEtcFile [OPTION] [-list|-list-test] [fileName]
- options:
--  -all              return all files (otherwise stop after the first match)
--  -list             list the directories to be searched
--  -mode <mode>      any combination of u(user), g(group), o(other)
--  -prefix <dir>     specify an alternative installation prefix
--  -quiet            suppress all normal output
--  -silent           suppress all stderr output
--  -version <ver>    specify an alternative OpenFOAM version
--                    in the form Maj.Min.Rev (eg, 1.7.0)
--  -help             print the usage
-+  -a, -all          Return all files (otherwise stop after the first match)
-+  -l, -list         List directories or files to be checked
-+  -list-test        List (existing) directories or files to be checked
-+  -mode=MODE        Any combination of u(user), g(group), o(other)
-+  -prefix=DIR       Specify an alternative installation prefix
-+  -version=VER      Specify alternative OpenFOAM version (eg, 3.0, 1612, ...)
-+  -csh | -sh        Produce output suitable for a csh or sh 'eval'
-+  -csh-verbose | -sh-verbose
-+                    As per -csh | -sh, with additional verbosity
-+  -q, -quiet        Suppress all normal output
-+  -s, -silent       Suppress stderr, except -csh-verbose, -sh-verbose output
-+  -help             Print the usage
- 
--  Locate user/group/shipped file with semantics similar to the
-+  Locate user/group/other file with semantics similar to the
-   ~OpenFOAM/fileName expansion.
- 
--  The options can also be specified as a single character
--  (eg, '-q' instead of '-quiet'), but must not be grouped.
-+  Single character options must not be grouped. Equivalent options:
-+      -mode=MODE,   -mode MODE,   -m MODE
-+      -prefix=DIR,  -prefix DIR,  -p DIR
-+      -version=VER, -version VER, -v VER
- 
-   Exit status
-       0  when the file is found. Print resolved path to stdout.
-@@ -78,61 +91,117 @@
-     exit 1
- }
- 
--#-------------------------------------------------------------------------------
-+# Report error and exit
-+die()
-+{
-+    [ "${optQuiet:-$optSilent}" = true ] && exit 1
-+    exec 1>&2
-+    echo
-+    echo "Error encountered:"
-+    while [ "$#" -ge 1 ]; do echo "    $1"; shift; done
-+    echo
-+    echo "See 'foamEtcFile -help' for usage"
-+    echo
-+    exit 1
-+}
- 
--# the bin dir:
--binDir="${0%/*}"
-+#-------------------------------------------------------------------------------
-+binDir="${0%/*}"                # The bin dir
-+projectDir="${binDir%/bin}"     # The project dir
-+prefixDir="${projectDir%/*}"    # The prefix dir (same as $WM_PROJECT_INST_DIR)
- 
--# the project dir:
-+# Could not resolve projectDir, prefixDir? (eg, called as ./bin/foamEtcFile)
-+if [ "$prefixDir" = "$projectDir" ]
-+then
-+    binDir="$(cd $binDir && pwd -L)"
- projectDir="${binDir%/bin}"
--
--# the prefix dir (same as $FOAM_INST_DIR):
- prefixDir="${projectDir%/*}"
-+fi
-+projectDirName="${projectDir##*/}"      # The project directory name
- 
--# the name used for the project directory
--projectDirName="${projectDir##*/}"
-+projectName="${WM_PROJECT:-OpenFOAM}"   # The project name
-+projectVersion="$WM_PROJECT_VERSION"    # Empty? - will be treated later
- 
--# version number used for debian packaging
--unset versionNum
- 
-+#-------------------------------------------------------------------------------
-+
-+# Guess project version or simply get the stem part of the projectDirName.
-+# Handle standard and debian naming conventions.
- #
--# handle standard and debian naming convention
-+# - projectVersion: update unless already set
- #
--case "$projectDirName" in
--OpenFOAM-*)         # standard naming convention OpenFOAM-<VERSION>
--    version="${projectDirName##OpenFOAM-}"
--    ;;
-+# Helper variables:
-+# - dirBase (for reassembling name) == projectDirName without the version
-+# - versionNum (debian packaging)
-+unset dirBase versionNum
-+guessVersion()
-+{
-+    local version
- 
--openfoam[0-9]* | openfoam-dev)     # debian naming convention 'openfoam<VERSION>'
--    versionNum="${projectDirName##openfoam}"
--    case "$versionNum" in
--    ??)         # convert 2 digit version number to decimal delineated
--        version=$(echo "$versionNum" | sed -e 's@\(.\)\(.\)@\1.\2@')
--        ;;
--    ???)        # convert 3 digit version number to decimal delineated
--        version=$(echo "$versionNum" | sed -e 's@\(.\)\(.\)\(.\)@\1.\2.\3@')
--        ;;
--    ????)       # convert 4 digit version number to decimal delineated
--        version=$(echo "$versionNum" | sed -e 's@\(.\)\(.\)\(.\)\(.\)@\1.\2.\3.\4@')
--        ;;
--    *)          # failback - use current environment setting
--        version="$WM_PROJECT_VERSION"
-+    case "$projectDirName" in
-+    (OpenFOAM-* | openfoam-*)
-+        # Standard naming: OpenFOAM-<VERSION> or openfoam-<VERSION>
-+        dirBase="${projectDirName%%-*}-"
-+        version="${projectDirName#*-}"
-+        version="${version%%*-}" # Extra safety, eg openfoam-version-packager
-+        ;;
-+
-+    (OpenFOAM+* | openfoam+*)
-+        # Alternative naming: OpenFOAM+<VERSION> or openfoam+<VERSION>
-+        dirBase="${projectDirName%%+*}+"
-+        version="${projectDirName#*+}"
-+        version="${version%%*-}" # Extra safety, eg openfoam-version-packager
-+        ;;
-+
-+    (openfoam[0-9]*)
-+        # Debian naming: openfoam<VERSION>
-+        dirBase="openfoam"
-+        version="${projectDirName#openfoam}"
-+        versionNum="$version"
-+
-+        # Convert digits version number to decimal delineated
-+        case "${#versionNum}" in (2|3|4)
-+            version=$(echo "$versionNum" | sed -e 's@\([0-9]\)@\1.@g')
-+            version="${version%.}"
-         ;;
-     esac
-+
-+        # Ignore special treatment if no decimals were inserted.
-+        [ "${#version}" -gt "${#versionNum}" ] || unset versionNum
-     ;;
- 
--*)
--    echo "Error : unknown/unsupported naming convention"
--    exit 1
-+    (*)
-+        die "unknown/unsupported naming convention for '$projectDirName'"
-     ;;
- esac
- 
-+    # Set projectVersion if required
-+    : ${projectVersion:=$version}
-+}
-+
-+
-+# Set projectVersion and update versionNum, projectDirName accordingly
-+setVersion()
-+{
-+    projectVersion="$1"
-+
-+    # Need dirBase when reassembling projectDirName
-+    [ -n "$dirBase" ] || guessVersion
-+
-+    # Debian: update x.y.z -> xyz version
-+    if [ -n "$versionNum" ]
-+    then
-+        versionNum=$(echo "$projectVersion" | sed -e 's@\.@@g')
-+    fi
-+
-+    projectDirName="$dirBase${versionNum:-$projectVersion}"
-+}
-+
- 
--# default mode is 'ugo'
--mode=ugo
--unset optAll optList optQuiet optSilent
-+optMode=ugo         # Default mode is always 'ugo'
-+unset optAll optList optShell optVersion
- 
--# parse options
-+# Parse options
- while [ "$#" -gt 0 ]
- do
-     case "$1" in
-@@ -141,27 +210,45 @@
-         ;;
-     -a | -all)
-         optAll=true
-+        unset optShell
-         ;;
-     -l | -list)
-         optList=true
-+        unset optShell
-+        ;;
-+    -list-test)
-+        optList='test'
-+        unset optShell
-+        ;;
-+    -csh | -sh | -csh-verbose | -sh-verbose)
-+        optShell="${1#-}"
-+        unset optAll
-+        ;;
-+    -mode=[ugo]*)
-+        optMode="${1#*=}"
-+        ;;
-+    -prefix=/*)
-+        prefixDir="${1#*=}"
-+        prefixDir="${prefixDir%/}"
-+        ;;
-+    -version=*)
-+        optVersion="${1#*=}"
-         ;;
-     -m | -mode)
--        [ "$#" -ge 2 ] || usage "'$1' option requires an argument"
--        mode="$2"
--
--        # sanity check:
--        case "$mode" in
--        *u* | *g* | *o* )
-+        optMode="$2"
-+        shift
-+        # Sanity check. Handles missing argument too.
-+        case "$optMode" in
-+        ([ugo]*)
-            ;;
--        *)
--           usage "'$1' option with invalid mode '$mode'"
-+        (*)
-+            die "invalid mode '$optMode'"
-            ;;
-         esac
--        shift
-         ;;
-     -p | -prefix)
--        [ "$#" -ge 2 ] || usage "'$1' option requires an argument"
--        prefixDir="$2"
-+        [ "$#" -ge 2 ] || die "'$1' option requires an argument"
-+        prefixDir="${2%/}"
-         shift
-         ;;
-     -q | -quiet)
-@@ -171,13 +258,8 @@
-         optSilent=true
-         ;;
-     -v | -version)
--        [ "$#" -ge 2 ] || usage "'$1' option requires an argument"
--        version="$2"
--        # convert x.y.z -> xyz version (if installation looked like debian)
--        if [ -n "$versionNum" ]
--        then
--            versionNum=$(echo "$version" | sed -e 's@\.@@g')
--        fi
-+        [ "$#" -ge 2 ] || die "'$1' option requires an argument"
-+        optVersion="$2"
-         shift
-         ;;
-     --)
-@@ -185,7 +267,7 @@
-         break
-         ;;
-     -*)
--        usage "unknown option: '$*'"
-+        die "unknown option: '$1'"
-         ;;
-     *)
-         break
-@@ -195,11 +277,28 @@
- done
- 
- 
--# debugging:
--# echo "Installed locations:"
--# for i in projectDir prefixDir projectDirName version versionNum
-+#-------------------------------------------------------------------------------
-+
-+if [ -n "$optVersion" ]
-+then
-+    setVersion $optVersion
-+elif [ -z "$projectVersion" ]
-+then
-+    guessVersion
-+fi
-+
-+# Updates:
-+# - projectDir  for changes via -prefix or -version
-+# - projectSite for changes via -prefix
-+projectDir="$prefixDir/$projectDirName"
-+projectSite="${WM_PROJECT_SITE:-$prefixDir/site}"
-+
-+
-+# Debugging:
-+# echo "Installed locations:" 1>&2
-+# for i in projectDir prefixDir projectDirName projectVersion
- # do
--#     eval echo "$i=\$$i"
-+#     eval echo "$i=\$$i" 1>&2
- # done
- 
- 
-@@ -210,30 +309,18 @@
- 
- # Define the various places to be searched:
- unset dirList
--case "$mode" in
--*u*)  # user
--    userDir="$HOME/.${WM_PROJECT:-OpenFOAM}"
--    dirList="$dirList $userDir/$version $userDir"
-+case "$optMode" in (*u*) # (U)ser
-+    dirList="$dirList $HOME/.$projectName/$projectVersion $HOME/.$projectName"
-     ;;
- esac
- 
--case "$mode" in
--*g*)  # group (site)
--    siteDir="${WM_PROJECT_SITE:-$prefixDir/site}"
--    dirList="$dirList $siteDir/$version $siteDir"
-+case "$optMode" in (*g*) # (G)roup == site
-+    dirList="$dirList $projectSite/$projectVersion $projectSite"
-     ;;
- esac
- 
--case "$mode" in
--*o*)  # other (shipped)
--    if [ -n "$versionNum" ]
--    then
--        # debian packaging
--        dirList="$dirList $prefixDir/openfoam$versionNum/etc"
--    else
--        # standard packaging
--        dirList="$dirList $prefixDir/${WM_PROJECT:-OpenFOAM}-$version/etc"
--    fi
-+case "$optMode" in (*o*) # (O)ther == shipped
-+    dirList="$dirList $projectDir/etc"
-     ;;
- esac
- set -- $dirList
-@@ -244,50 +331,87 @@
- #
- 
- exitCode=0
--if [ "$optList" = true ]
-+if [ -n "$optList" ]
- then
- 
--    # list directories, or potential file locations
--    [ "$nArgs" -le 1 ] || usage
-+    # List directories, or potential file locations
-+    [ "$nArgs" -le 1 ] || \
-+    die "-list expects 0 or 1 filename, but $nArgs provided"
-+
-+    # A silly combination, but -quiet does have precedence
-+    [ -n "$optQuiet" ] && exit 0
- 
--    # a silly combination, but -quiet does have precedence
--    [ "$optQuiet" = true ] && exit 0
-+    # Test for directory or file too?
-+    if [ "$optList" = "test" ]
-+    then
-+        exitCode=2  # Fallback to a general error (file not found)
- 
-+        if [ "$nArgs" -eq 1 ]
-+        then
-     for dir
-     do
--        if [ "$nArgs" -eq 1 ]
-+                resolved="$dir/$fileName"
-+                if [ -f "$resolved" ]
-         then
--            echo "$dir/$fileName"
-+                    echo "$resolved"
-+                    exitCode=0  # OK
-+                fi
-+            done
-         else
-+            for dir
-+            do
-+                if [ -d "$dir" ]
-+                then
-             echo "$dir"
-+                    exitCode=0  # OK
-         fi
-     done
-+        fi
-+    else
-+        for dir
-+        do
-+            echo "$dir${fileName:+/}$fileName"
-+        done
-+    fi
- 
- else
- 
--    [ "$nArgs" -eq 1 ] || usage
-+    [ "$nArgs" -eq 1 ] || die "One filename expected - $nArgs provided"
- 
--    # general error, eg file not found
--    exitCode=2
-+    exitCode=2  # Fallback to a general error (file not found)
- 
-     for dir
-     do
-         if [ -f "$dir/$fileName" ]
-         then
-             exitCode=0
--            if [ "$optQuiet" = true ]
--            then
-+            [ -n "$optQuiet" ] && break
-+
-+            case "$optShell" in
-+            (*verbose)
-+                echo "Using: $dir/$fileName" 1>&2
-+                ;;
-+            esac
-+
-+            case "$optShell" in
-+            csh*)
-+                echo "source $dir/$fileName"
-                 break
--            else
-+                ;;
-+            sh*)
-+                echo ". $dir/$fileName"
-+                break
-+                ;;
-+            *)
-                 echo "$dir/$fileName"
--                [ "$optAll" = true ] || break
--            fi
-+                [ -n "$optAll" ] || break
-+                ;;
-+            esac
-         fi
-     done
- 
- fi
- 
--
- exit $exitCode
- 
- #------------------------------------------------------------------------------
diff --git a/var/spack/repos/builtin/packages/openfoam-com/1612-build.patch b/var/spack/repos/builtin/packages/openfoam-com/1612-build.patch
deleted file mode 100644
index 26e2d8f085..0000000000
--- a/var/spack/repos/builtin/packages/openfoam-com/1612-build.patch
+++ /dev/null
@@ -1,17 +0,0 @@
---- OpenFOAM-v1612+.orig/Allwmake	2016-12-23 15:22:59.000000000 +0100
-+++ OpenFOAM-v1612+/Allwmake	2017-03-29 09:08:15.503865203 +0200
-@@ -17,6 +17,14 @@
-     exit 1
- }
- 
-+#------------------------------------------------------------------------------
-+echo "========================================"
-+date "+%Y-%m-%d %H:%M:%S %z" 2>/dev/null || echo "date is unknown"
-+echo "Starting ${WM_PROJECT_DIR##*/} ${0##*}"
-+echo "  $WM_COMPILER $WM_COMPILER_TYPE compiler"
-+echo "  ${WM_OPTIONS}, with ${WM_MPLIB} ${FOAM_MPI}"
-+echo
-+
- # Compile wmake support applications
- (cd wmake/src && make)
- 
diff --git a/var/spack/repos/builtin/packages/openfoam-com/1612-etc.patch b/var/spack/repos/builtin/packages/openfoam-com/1612-etc.patch
deleted file mode 100644
index dd8146e953..0000000000
--- a/var/spack/repos/builtin/packages/openfoam-com/1612-etc.patch
+++ /dev/null
@@ -1,41 +0,0 @@
---- OpenFOAM-v1612+.orig/etc/bashrc	2016-12-23 15:22:59.000000000 +0100
-+++ OpenFOAM-v1612+/etc/bashrc	2017-03-22 16:05:05.751237072 +0100
-@@ -42,7 +42,8 @@
- #
- # Please set to the appropriate path if the default is not correct.
- #
--[ $BASH_SOURCE ] && FOAM_INST_DIR=$(\cd ${BASH_SOURCE%/*/*/*} && \pwd -P) || \
-+rc="${BASH_SOURCE:-${ZSH_NAME:+$0}}"
-+[ -n "$rc" ] && FOAM_INST_DIR=$(\cd $(dirname $rc)/../.. && \pwd -L) || \
- FOAM_INST_DIR=$HOME/$WM_PROJECT
- # FOAM_INST_DIR=~$WM_PROJECT
- # FOAM_INST_DIR=/opt/$WM_PROJECT
-@@ -135,8 +136,10 @@
- # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- . $WM_PROJECT_DIR/etc/config.sh/functions
- 
--# Add in preset user or site preferences:
--_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile prefs.sh`
-+# Override definitions via prefs, with 'other' first so the sys-admin
-+# can provide base values independent of WM_PROJECT_SITE
-+_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile -mode o  prefs.sh`
-+_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile -mode ug prefs.sh`
- 
- # Evaluate command-line parameters and record settings for later
- # these can be used to set/unset values, or specify alternative pref files
-diff -uw OpenFOAM-v1612+.orig/etc/cshrc OpenFOAM-v1612+/etc/cshrc
---- OpenFOAM-v1612+.orig/etc/cshrc	2016-12-23 15:22:59.000000000 +0100
-+++ OpenFOAM-v1612+/etc/cshrc	2017-03-22 16:04:51.839291067 +0100
-@@ -148,8 +148,10 @@
- # Source files, possibly with some verbosity
- alias _foamSource 'if ($?FOAM_VERBOSE && $?prompt) echo "Sourcing: \!*"; if (\!* != "") source \!*'
- 
--# Add in preset user or site preferences:
--_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile prefs.csh`
-+# Override definitions via prefs, with 'other' first so the sys-admin
-+# can provide base values independent of WM_PROJECT_SITE
-+_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile -mode o  prefs.csh`
-+_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile -mode ug prefs.csh`
- 
- # Evaluate command-line parameters and record settings for later
- # these can be used to set/unset values, or specify alternative pref files
diff --git a/var/spack/repos/builtin/packages/openfoam-com/1612-mgridgen-lib.patch b/var/spack/repos/builtin/packages/openfoam-com/1612-mgridgen-lib.patch
deleted file mode 100644
index 8dc0b995ff..0000000000
--- a/var/spack/repos/builtin/packages/openfoam-com/1612-mgridgen-lib.patch
+++ /dev/null
@@ -1,41 +0,0 @@
---- OpenFOAM-v1612+.orig/src/fvAgglomerationMethods/Allwmake	2017-01-02 09:56:17.578558265 +0100
-+++ OpenFOAM-v1612+/src/fvAgglomerationMethods/Allwmake	2017-04-18 18:58:38.236795902 +0200
-@@ -4,9 +4,13 @@
- # Parse arguments for library compilation
- . $WM_PROJECT_DIR/wmake/scripts/AllwmakeParseArguments
- 
--export ParMGridGen=$WM_THIRD_PARTY_DIR/ParMGridGen-1.0
-+unset MGRIDGEN_ARCH_PATH
-+if settings=$($WM_PROJECT_DIR/bin/foamEtcFile config.sh/mgridgen)
-+then
-+    . $settings
-+fi
- 
--if [ -e "$FOAM_LIBBIN/libMGridGen.so" ]
-+if [ -e "$MGRIDGEN_ARCH_PATH/include/mgridgen.h" ]
- then
-     wmake $targetType MGridGenGamgAgglomeration
- fi
---- OpenFOAM-v1612+.orig/src/fvAgglomerationMethods/MGridGenGamgAgglomeration/Make/options	2017-01-02 09:56:17.578558265 +0100
-+++ OpenFOAM-v1612+/src/fvAgglomerationMethods/MGridGenGamgAgglomeration/Make/options	2017-04-18 18:59:16.860662811 +0200
-@@ -1,15 +1,9 @@
--/* Needs ParMGridGen environment variable set. (see Allwmake script) */
--
--TYPE_REAL=
--#if defined(WM_SP)
--TYPE_REAL=-DTYPE_REAL
--#endif
--
- EXE_INC = \
-     -I$(LIB_SRC)/finiteVolume/lnInclude \
--    -I$(ParMGridGen)/MGridGen/Lib/lnInclude \
--    -I$(ParMGridGen)/MGridGen/IMlib/lnInclude \
--    $(TYPE_REAL)
-+    -I$(MGRIDGEN_ARCH_PATH)/include
- 
- LIB_LIBS = \
--    -L$(FOAM_EXT_LIBBIN) -lMGridGen
-+    -L$(FOAM_EXT_LIBBIN) \
-+    -L$(MGRIDGEN_ARCH_PATH)/lib \
-+    -L$(MGRIDGEN_ARCH_PATH)/lib$(WM_COMPILER_LIB_ARCH) \
-+    -lmgrid
diff --git a/var/spack/repos/builtin/packages/openfoam-com/1612-mpi.patch b/var/spack/repos/builtin/packages/openfoam-com/1612-mpi.patch
deleted file mode 100644
index b3663b0a49..0000000000
--- a/var/spack/repos/builtin/packages/openfoam-com/1612-mpi.patch
+++ /dev/null
@@ -1,36 +0,0 @@
---- OpenFOAM-v1612+.orig/etc/config.sh/mpi	2016-12-23 15:22:59.000000000 +0100
-+++ OpenFOAM-v1612+/etc/config.sh/mpi	2017-03-29 13:55:57.507980699 +0200
-@@ -75,8 +75,15 @@
-     _foamAddMan     $MPI_ARCH_PATH/share/man
-     ;;
- 
-+USERMPI)
-+    # Use an arbitrary, user-specified mpi implementation
-+    export FOAM_MPI=mpi-user
-+    _foamSource `$WM_PROJECT_DIR/bin/foamEtcFile config.sh/mpi-user`
-+    ;;
-+
- SYSTEMMPI)
-     export FOAM_MPI=mpi-system
-+    _foamSource `$WM_PROJECT_DIR/bin/foamEtcFile config.sh/mpi-system`
- 
-     if [ -z "$MPI_ROOT" ]
-     then
---- OpenFOAM-v1612+.orig/etc/config.csh/mpi	2016-12-23 15:22:59.000000000 +0100
-+++ OpenFOAM-v1612+/etc/config.csh/mpi	2017-03-29 13:56:36.347835938 +0200
-@@ -71,8 +71,15 @@
-     _foamAddMan     $MPI_ARCH_PATH/share/man
-     breaksw
- 
-+case USERMPI:
-+    # Use an arbitrary, user-specified mpi implementation
-+    setenv FOAM_MPI mpi-user
-+    _foamSource `$WM_PROJECT_DIR/bin/foamEtcFile config.csh/mpi-user`
-+    breaksw
-+
- case SYSTEMMPI:
-     setenv FOAM_MPI mpi-system
-+    _foamSource `$WM_PROJECT_DIR/bin/foamEtcFile config.csh/mpi-system`
- 
-     if ( ! ($?MPI_ROOT) ) then
-         echo
diff --git a/var/spack/repos/builtin/packages/openfoam-com/1612-scotch-metis-lib.patch b/var/spack/repos/builtin/packages/openfoam-com/1612-scotch-metis-lib.patch
deleted file mode 100644
index b7530e6320..0000000000
--- a/var/spack/repos/builtin/packages/openfoam-com/1612-scotch-metis-lib.patch
+++ /dev/null
@@ -1,48 +0,0 @@
---- OpenFOAM-v1612+.orig/src/parallel/decompose/Allwmake	2017-03-21 16:34:44.599021283 +0100
-+++ OpenFOAM-v1612+/src/parallel/decompose/Allwmake	2017-03-21 16:28:57.243969660 +0100
-@@ -36,6 +36,7 @@
- 
-     # Library
-     [ -r $FOAM_EXT_LIBBIN/libmetis.so ] || \
-+    [ -r $METIS_ARCH_PATH/lib/libmetis.so ] || \
-     [ -r $METIS_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH/libmetis.so ] || \
-     [ "${METIS_ARCH_PATH##*-}" = system ] || {
-         echo "$warning (missing library)"
-@@ -90,6 +91,7 @@
- 
-     # Library
-     [ -r $FOAM_EXT_LIBBIN/libscotch.so ] || \
-+    [ -r $SCOTCH_ARCH_PATH/lib/libscotch.so ] || \
-     [ -r $SCOTCH_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH/libscotch.so ] || \
-     [ "${SCOTCH_ARCH_PATH##*-}" = system ] || {
-         echo "$warning (missing library)"
---- OpenFOAM-v1612+.orig/src/parallel/decompose/metisDecomp/Make/options	2017-03-21 16:34:25.383075328 +0100
-+++ OpenFOAM-v1612+/src/parallel/decompose/metisDecomp/Make/options	2017-03-21 16:30:15.727758338 +0100
-@@ -8,6 +8,7 @@
-  * to support central, non-thirdparty installations
-  */
- LIB_LIBS = \
-+    -L$(METIS_ARCH_PATH)/lib \
-     -L$(METIS_ARCH_PATH)/lib$(WM_COMPILER_LIB_ARCH) \
-     -L$(FOAM_EXT_LIBBIN) \
-     -lmetis
---- OpenFOAM-v1612+.orig/src/parallel/decompose/ptscotchDecomp/Make/options	2017-03-21 16:34:34.607049385 +0100
-+++ OpenFOAM-v1612+/src/parallel/decompose/ptscotchDecomp/Make/options	2017-03-21 16:30:00.479799399 +0100
-@@ -16,6 +16,7 @@
-  * to support central, non-thirdparty installations
-  */
- LIB_LIBS = \
-+    -L$(SCOTCH_ARCH_PATH)/lib \
-     -L$(SCOTCH_ARCH_PATH)/lib$(WM_COMPILER_LIB_ARCH) \
-     -L$(FOAM_EXT_LIBBIN) \
-     -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) \
---- OpenFOAM-v1612+.orig/src/parallel/decompose/scotchDecomp/Make/options	2017-03-21 16:34:39.159036582 +0100
-+++ OpenFOAM-v1612+/src/parallel/decompose/scotchDecomp/Make/options	2017-03-21 16:29:46.719836452 +0100
-@@ -16,6 +16,7 @@
-  * to support central, non-thirdparty installations
-  */
- LIB_LIBS = \
-+    -L$(SCOTCH_ARCH_PATH)/lib \
-     -L$(SCOTCH_ARCH_PATH)/lib$(WM_COMPILER_LIB_ARCH) \
-     -L$(FOAM_EXT_LIBBIN) \
-     -lscotch \
diff --git a/var/spack/repos/builtin/packages/openfoam-com/1612-site.patch b/var/spack/repos/builtin/packages/openfoam-com/1612-site.patch
deleted file mode 100644
index d988c2f9b8..0000000000
--- a/var/spack/repos/builtin/packages/openfoam-com/1612-site.patch
+++ /dev/null
@@ -1,42 +0,0 @@
-diff -uw OpenFOAM-v1612+.orig/etc/config.sh/settings OpenFOAM-v1612+/etc/config.sh/settings
---- OpenFOAM-v1612+.orig/etc/config.sh/settings	2016-12-23 15:22:59.000000000 +0100
-+++ OpenFOAM-v1612+/etc/config.sh/settings	2017-03-23 12:22:52.002101020 +0100
-@@ -141,7 +141,7 @@
- #------------------------------------------------------------------------------
- 
- # Location of the jobControl directory
--export FOAM_JOB_DIR=$WM_PROJECT_INST_DIR/jobControl
-+export FOAM_JOB_DIR=$HOME/.OpenFOAM/jobControl  #SPACK: non-central location
- 
- # wmake configuration
- export WM_DIR=$WM_PROJECT_DIR/wmake
-@@ -157,7 +157,7 @@
- export FOAM_EXT_LIBBIN=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/lib
- 
- # Site-specific directory
--siteDir="${WM_PROJECT_SITE:-$WM_PROJECT_INST_DIR/site}"
-+siteDir="${WM_PROJECT_SITE:-$WM_PROJECT_DIR/site}"  #SPACK: not in parent directory
- 
- # Shared site executables/libraries
- # Similar naming convention as ~OpenFOAM expansion
-diff -uw OpenFOAM-v1612+.orig/etc/config.csh/settings OpenFOAM-v1612+/etc/config.csh/settings
---- OpenFOAM-v1612+.orig/etc/config.csh/settings	2016-12-23 15:22:59.000000000 +0100
-+++ OpenFOAM-v1612+/etc/config.csh/settings	2017-03-23 12:23:52.737891912 +0100
-@@ -137,7 +137,7 @@
- #------------------------------------------------------------------------------
- 
- # Location of the jobControl directory
--setenv FOAM_JOB_DIR $WM_PROJECT_INST_DIR/jobControl
-+setenv FOAM_JOB_DIR=$HOME/.OpenFOAM/jobControl  #SPACK: non-central location
- 
- # wmake configuration
- setenv WM_DIR $WM_PROJECT_DIR/wmake
-@@ -156,7 +156,7 @@
- if ( $?WM_PROJECT_SITE ) then
-     set siteDir=$WM_PROJECT_SITE
- else
--    set siteDir=$WM_PROJECT_INST_DIR/site
-+    set siteDir=$WM_PROJECT_DIR/site  #SPACK: not in parent directory
- endif
- 
- # Shared site executables/libraries
diff --git a/var/spack/repos/builtin/packages/openfoam-com/1612-spack-patches.patch b/var/spack/repos/builtin/packages/openfoam-com/1612-spack-patches.patch
new file mode 100644
index 0000000000..00679c4c1d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/openfoam-com/1612-spack-patches.patch
@@ -0,0 +1,876 @@
+#############################################################################
+# This patch for OpenFOAM-1612 comprises the following changes:
+#
+# bin/foamEtcFile
+# - Adjust to cope with spack naming (eg, openfoam-com-1612-abcxzy).
+#   Lets us avoid a needless directory layer.
+#
+# etc/bashrc
+# - improved robustness when sourcing.
+# - source top-level prefs.sh first (for sysadmin changes)
+#
+# etc/config.*/settings
+# - write job control information to the user directory
+# - site/ directory under the OpenFOAM project dir, not its parent dir
+#
+# etc/config.*/mpi
+# - added USERMPI as place for spack mpi information
+#
+# mgridgen, zoltan:
+# - make location configurable
+#
+# metis, scotch:
+# - also check lib path (not just lib64)
+#
+# All issues patched here are addressed in OpenFOAM-1706 and later.
+#
+# <Mark.Olesen@esi-group.com>   ESI-OpenCFD   www.openfoam.com
+#
+#############################################################################
+--- OpenFOAM-v1612+.orig/bin/foamEtcFile	2016-12-23 15:22:59.000000000 +0100
++++ OpenFOAM-plus/bin/foamEtcFile	2017-12-18 17:48:35.043291205 +0100
+@@ -4,164 +4,235 @@
+ # \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+ #  \\    /   O peration     |
+ #   \\  /    A nd           | Copyright (C) 2011-2016 OpenFOAM Foundation
+-#    \\/     M anipulation  |
++#    \\/     M anipulation  | Copyright (C) 2017 OpenCFD Ltd.
+ #-------------------------------------------------------------------------------
+ # License
+-#     This file is part of OpenFOAM.
+-#
+-#     OpenFOAM is free software: you can redistribute it and/or modify it
+-#     under the terms of the GNU General Public License as published by
+-#     the Free Software Foundation, either version 3 of the License, or
+-#     (at your option) any later version.
+-#
+-#     OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
+-#     ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+-#     FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
+-#     for more details.
+-#
+-#     You should have received a copy of the GNU General Public License
+-#     along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
++#     This file is part of OpenFOAM, licensed under GNU General Public License
++#     <http://www.gnu.org/licenses/>.
+ #
+ # Script
+ #     foamEtcFile
+ #
+ # Description
+-#     Locate user/group/shipped file with semantics similar to the
+-#     ~OpenFOAM/fileName expansion.
++#     Locate user/group/other file as per '#includeEtc'.
++#
++#     The -mode option can be used to allow chaining from personal settings
++#     to site-wide settings.
+ #
+-#     The -mode option can be used to allow chaining from
+-#     personal settings to site-wide settings.
++#     For example, within the user ~/.OpenFOAM/<VER>/config.sh/compiler:
++#     \code
++#        eval $(foamEtcFile -sh -mode=go config.sh/compiler)
++#     \endcode
+ #
+-#     For example, within the user ~/.OpenFOAM/<VER>/prefs.sh:
++#     The -mode option is similarly used within etc/{bashrc,cshrc} to ensure
++#     that system prefs are respected:
+ #     \code
+-#        foamPrefs=`$WM_PROJECT_DIR/bin/foamEtcFile -m go prefs.sh` \
+-#            && _foamSource $foamPrefs
++#        eval $(foamEtcFile -sh -mode=o  prefs.sh)
++#        eval $(foamEtcFile -sh -mode=ug prefs.sh)
+ #     \endcode
+ #
++# Environment
++#     - WM_PROJECT:         (unset defaults to OpenFOAM)
++#     - WM_PROJECT_SITE:    (unset defaults to PREFIX/site)
++#     - WM_PROJECT_VERSION: (unset defaults to detect from path)
++#
+ # Note
+-#     This script must exist in $FOAM_INST_DIR/OpenFOAM-<VERSION>/bin/
+-#     or $FOAM_INST_DIR/openfoam<VERSION>/bin/ (for the debian version)
++#     This script must exist in one of these locations:
++#     - $WM_PROJECT_INST_DIR/OpenFOAM-<VERSION>/bin
++#     - $WM_PROJECT_INST_DIR/openfoam-<VERSION>/bin
++#     - $WM_PROJECT_INST_DIR/openfoam<VERSION>/bin  (debian version)
+ #
+ #-------------------------------------------------------------------------------
+-usage() {
+-    [ "${optQuiet:-$optSilent}" = true ] && exit 1
+-
+-    exec 1>&2
+-    while [ "$#" -ge 1 ]; do echo "$1"; shift; done
++printHelp() {
+     cat<<USAGE
+ 
+-Usage: ${0##*/} [OPTION] fileName
+-       ${0##*/} [OPTION] -list
++Usage: foamEtcFile [OPTION] fileName
++       foamEtcFile [OPTION] [-list|-list-test] [fileName]
++
+ options:
+-  -all              return all files (otherwise stop after the first match)
+-  -list             list the directories to be searched
+-  -mode <mode>      any combination of u(user), g(group), o(other)
+-  -prefix <dir>     specify an alternative installation prefix
+-  -quiet            suppress all normal output
+-  -silent           suppress all stderr output
+-  -version <ver>    specify an alternative OpenFOAM version
+-                    in the form Maj.Min.Rev (eg, 1.7.0)
+-  -help             print the usage
+-
+-  Locate user/group/shipped file with semantics similar to the
+-  ~OpenFOAM/fileName expansion.
+-
+-  The options can also be specified as a single character
+-  (eg, '-q' instead of '-quiet'), but must not be grouped.
+-
+-  Exit status
+-      0  when the file is found. Print resolved path to stdout.
+-      1  for miscellaneous errors.
+-      2  when the file is not found.
++  -all (-a)         Return all files (otherwise stop after the first match)
++  -list (-l)        List directories or files to be checked
++  -list-test        List (existing) directories or files to be checked
++  -mode=MODE        Any combination of u(user), g(group), o(other)
++  -prefix=DIR       Specify an alternative installation prefix
++  -version=VER      Specify alternative OpenFOAM version (eg, 3.0, 1612, ...)
++  -csh              Produce output suitable for a csh or sh 'eval'
++  -csh-verbose      As per -csh with additional verbosity
++  -sh               Produce output suitable for a csh or sh 'eval'
++  -sh-verbose       As per -sh  with additional verbosity
++  -quiet (-q)       Suppress all normal output
++  -silent (-s)      Suppress stderr, except -csh-verbose, -sh-verbose output
++  -help             Print the usage
++
++Locate user/group/other file as per '#includeEtc'
++
++Do not group single character options.
++Equivalent options:
++  |  -mode=MODE     |  -mode MODE     | -m MODE
++  |  -prefix=DIR    |  -prefix DIR    | -p DIR
++  |  -version=VER   |  -version VER   | -v VER
++
++Exit status
++    0  when the file is found. Print resolved path to stdout.
++    1  for miscellaneous errors.
++    2  when the file is not found.
+ 
+ USAGE
+-    exit 1
++    exit 0  # A clean exit
+ }
+ 
+-#-------------------------------------------------------------------------------
+ 
+-# the bin dir:
+-binDir="${0%/*}"
++unset optQuiet optSilent
++# Report error and exit
++die()
++{
++    [ "${optQuiet:-$optSilent}" = true ] && exit 1
++    exec 1>&2
++    echo
++    echo "Error encountered:"
++    while [ "$#" -ge 1 ]; do echo "    $1"; shift; done
++    echo
++    echo "See 'foamEtcFile -help' for usage"
++    echo
++    exit 1
++}
+ 
+-# the project dir:
+-projectDir="${binDir%/bin}"
++#-------------------------------------------------------------------------------
++binDir="${0%/*}"                # The bin dir
++projectDir="${binDir%/bin}"     # The project dir
++prefixDir="${projectDir%/*}"    # The prefix dir (same as $WM_PROJECT_INST_DIR)
+ 
+-# the prefix dir (same as $FOAM_INST_DIR):
+-prefixDir="${projectDir%/*}"
++# Could not resolve projectDir, prefixDir? (eg, called as ./bin/foamEtcFile)
++if [ "$prefixDir" = "$projectDir" ]
++then
++    binDir="$(cd $binDir && pwd -L)"
++    projectDir="${binDir%/bin}"
++    prefixDir="${projectDir%/*}"
++fi
++projectDirName="${projectDir##*/}"      # The project directory name
+ 
+-# the name used for the project directory
+-projectDirName="${projectDir##*/}"
++projectVersion="$WM_PROJECT_VERSION"    # Empty? - will be treated later
++userDir="$HOME/.OpenFOAM"               # Hard-coded as per foamVersion.H
+ 
+-# version number used for debian packaging
+-unset versionNum
++#-------------------------------------------------------------------------------
+ 
++# Guess project version or simply get the stem part of the projectDirName.
++# Handle standard and debian naming conventions.
+ #
+-# handle standard and debian naming convention
++# - projectVersion: update unless already set
+ #
+-case "$projectDirName" in
+-OpenFOAM-*)         # standard naming convention OpenFOAM-<VERSION>
+-    version="${projectDirName##OpenFOAM-}"
+-    ;;
++# Helper variables:
++# - dirBase (for reassembling name) == projectDirName without the version
++# - versionNum (debian packaging)
++unset dirBase versionNum
++guessVersion()
++{
++    local version
++
++    case "$projectDirName" in
++    (OpenFOAM-* | openfoam-*)
++        # Standard naming: OpenFOAM-<VERSION> or openfoam-<VERSION>
++        dirBase="${projectDirName%%-*}-"
++        version="${projectDirName#*-}"
++        version="${version%%*-}" # Extra safety, eg openfoam-version-packager
++        ;;
++
++    (openfoam[0-9]*)
++        # Debian naming: openfoam<VERSION>
++        dirBase="openfoam"
++        version="${projectDirName#openfoam}"
++        versionNum="$version"
++
++        # Convert digits version number to decimal delineated
++        case "${#versionNum}" in (2|3|4)
++            version=$(echo "$versionNum" | sed -e 's@\([0-9]\)@\1.@g')
++            version="${version%.}"
++            ;;
++        esac
+ 
+-openfoam[0-9]* | openfoam-dev)     # debian naming convention 'openfoam<VERSION>'
+-    versionNum="${projectDirName##openfoam}"
+-    case "$versionNum" in
+-    ??)         # convert 2 digit version number to decimal delineated
+-        version=$(echo "$versionNum" | sed -e 's@\(.\)\(.\)@\1.\2@')
+-        ;;
+-    ???)        # convert 3 digit version number to decimal delineated
+-        version=$(echo "$versionNum" | sed -e 's@\(.\)\(.\)\(.\)@\1.\2.\3@')
++        # Ignore special treatment if no decimals were inserted.
++        [ "${#version}" -gt "${#versionNum}" ] || unset versionNum
+         ;;
+-    ????)       # convert 4 digit version number to decimal delineated
+-        version=$(echo "$versionNum" | sed -e 's@\(.\)\(.\)\(.\)\(.\)@\1.\2.\3.\4@')
+-        ;;
+-    *)          # failback - use current environment setting
+-        version="$WM_PROJECT_VERSION"
++
++    (*)
++        die "unknown/unsupported naming convention for '$projectDirName'"
+         ;;
+     esac
+-    ;;
+ 
+-*)
+-    echo "Error : unknown/unsupported naming convention"
+-    exit 1
+-    ;;
+-esac
++    # Set projectVersion if required
++    : ${projectVersion:=$version}
++}
+ 
+ 
+-# default mode is 'ugo'
+-mode=ugo
+-unset optAll optList optQuiet optSilent
++# Set projectVersion and update versionNum, projectDirName accordingly
++setVersion()
++{
++    projectVersion="$1"
+ 
+-# parse options
++    # Need dirBase when reassembling projectDirName
++    [ -n "$dirBase" ] || guessVersion
++
++    # Debian: update x.y.z -> xyz version
++    if [ -n "$versionNum" ]
++    then
++        versionNum=$(echo "$projectVersion" | sed -e 's@\.@@g')
++    fi
++
++    projectDirName="$dirBase${versionNum:-$projectVersion}"
++}
++
++
++optMode=ugo         # Default mode is always 'ugo'
++unset optAll optList optShell optVersion
++
++# Parse options
+ while [ "$#" -gt 0 ]
+ do
+     case "$1" in
+-    -h | -help)
+-        usage
++    -h | -help*)
++        printHelp
+         ;;
+     -a | -all)
+         optAll=true
++        unset optShell
+         ;;
+     -l | -list)
+         optList=true
++        unset optShell
++        ;;
++    -list-test)
++        optList='test'
++        unset optShell
++        ;;
++    -csh | -sh | -csh-verbose | -sh-verbose)
++        optShell="${1#-}"
++        unset optAll
++        ;;
++    -mode=[ugo]*)
++        optMode="${1#*=}"
++        ;;
++    -prefix=/*)
++        prefixDir="${1#*=}"
++        prefixDir="${prefixDir%/}"
++        ;;
++    -version=*)
++        optVersion="${1#*=}"
+         ;;
+     -m | -mode)
+-        [ "$#" -ge 2 ] || usage "'$1' option requires an argument"
+-        mode="$2"
+-
+-        # sanity check:
+-        case "$mode" in
+-        *u* | *g* | *o* )
+-           ;;
+-        *)
+-           usage "'$1' option with invalid mode '$mode'"
+-           ;;
+-        esac
++        optMode="$2"
+         shift
++        # Sanity check. Handles missing argument too.
++        case "$optMode" in
++        ([ugo]*)
++            ;;
++        (*)
++            die "invalid mode '$optMode'"
++            ;;
++        esac
+         ;;
+     -p | -prefix)
+-        [ "$#" -ge 2 ] || usage "'$1' option requires an argument"
+-        prefixDir="$2"
++        [ "$#" -ge 2 ] || die "'$1' option requires an argument"
++        prefixDir="${2%/}"
+         shift
+         ;;
+     -q | -quiet)
+@@ -171,13 +242,8 @@
+         optSilent=true
+         ;;
+     -v | -version)
+-        [ "$#" -ge 2 ] || usage "'$1' option requires an argument"
+-        version="$2"
+-        # convert x.y.z -> xyz version (if installation looked like debian)
+-        if [ -n "$versionNum" ]
+-        then
+-            versionNum=$(echo "$version" | sed -e 's@\.@@g')
+-        fi
++        [ "$#" -ge 2 ] || die "'$1' option requires an argument"
++        optVersion="$2"
+         shift
+         ;;
+     --)
+@@ -185,7 +251,7 @@
+         break
+         ;;
+     -*)
+-        usage "unknown option: '$*'"
++        die "unknown option: '$1'"
+         ;;
+     *)
+         break
+@@ -195,11 +261,28 @@
+ done
+ 
+ 
+-# debugging:
+-# echo "Installed locations:"
+-# for i in projectDir prefixDir projectDirName version versionNum
++#-------------------------------------------------------------------------------
++
++if [ -n "$optVersion" ]
++then
++    setVersion $optVersion
++elif [ -z "$projectVersion" ]
++then
++    guessVersion
++fi
++
++# Updates:
++# - projectDir  for changes via -prefix or -version
++# - groupDir    for changes via -prefix
++projectDir="$prefixDir/$projectDirName"
++groupDir="${WM_PROJECT_SITE:-$prefixDir/site}"
++
++
++# Debugging:
++# echo "Installed locations:" 1>&2
++# for i in projectDir prefixDir projectDirName projectVersion
+ # do
+-#     eval echo "$i=\$$i"
++#     eval echo "$i=\$$i" 1>&2
+ # done
+ 
+ 
+@@ -210,30 +293,18 @@
+ 
+ # Define the various places to be searched:
+ unset dirList
+-case "$mode" in
+-*u*)  # user
+-    userDir="$HOME/.${WM_PROJECT:-OpenFOAM}"
+-    dirList="$dirList $userDir/$version $userDir"
++case "$optMode" in (*u*) # (U)ser
++    dirList="$dirList $userDir/$projectVersion $userDir"
+     ;;
+ esac
+ 
+-case "$mode" in
+-*g*)  # group (site)
+-    siteDir="${WM_PROJECT_SITE:-$prefixDir/site}"
+-    dirList="$dirList $siteDir/$version $siteDir"
++case "$optMode" in (*g*) # (G)roup == site
++    dirList="$dirList $groupDir/$projectVersion $groupDir"
+     ;;
+ esac
+ 
+-case "$mode" in
+-*o*)  # other (shipped)
+-    if [ -n "$versionNum" ]
+-    then
+-        # debian packaging
+-        dirList="$dirList $prefixDir/openfoam$versionNum/etc"
+-    else
+-        # standard packaging
+-        dirList="$dirList $prefixDir/${WM_PROJECT:-OpenFOAM}-$version/etc"
+-    fi
++case "$optMode" in (*o*) # (O)ther == shipped
++    dirList="$dirList $projectDir/etc"
+     ;;
+ esac
+ set -- $dirList
+@@ -244,50 +315,87 @@
+ #
+ 
+ exitCode=0
+-if [ "$optList" = true ]
++if [ -n "$optList" ]
+ then
+ 
+-    # list directories, or potential file locations
+-    [ "$nArgs" -le 1 ] || usage
++    # List directories, or potential file locations
++    [ "$nArgs" -le 1 ] || \
++    die "-list expects 0 or 1 filename, but $nArgs provided"
+ 
+-    # a silly combination, but -quiet does have precedence
+-    [ "$optQuiet" = true ] && exit 0
++    # A silly combination, but -quiet does have precedence
++    [ -n "$optQuiet" ] && exit 0
++
++    # Test for directory or file too?
++    if [ "$optList" = "test" ]
++    then
++        exitCode=2  # Fallback to a general error (file not found)
+ 
+-    for dir
+-    do
+         if [ "$nArgs" -eq 1 ]
+         then
+-            echo "$dir/$fileName"
++            for dir
++            do
++                resolved="$dir/$fileName"
++                if [ -f "$resolved" ]
++                then
++                    echo "$resolved"
++                    exitCode=0  # OK
++                fi
++            done
+         else
+-            echo "$dir"
++            for dir
++            do
++                if [ -d "$dir" ]
++                then
++                    echo "$dir"
++                    exitCode=0  # OK
++                fi
++            done
+         fi
+-    done
++    else
++        for dir
++        do
++            echo "$dir${fileName:+/}$fileName"
++        done
++    fi
+ 
+ else
+ 
+-    [ "$nArgs" -eq 1 ] || usage
++    [ "$nArgs" -eq 1 ] || die "One filename expected - $nArgs provided"
+ 
+-    # general error, eg file not found
+-    exitCode=2
++    exitCode=2  # Fallback to a general error (file not found)
+ 
+     for dir
+     do
+         if [ -f "$dir/$fileName" ]
+         then
+             exitCode=0
+-            if [ "$optQuiet" = true ]
+-            then
++            [ -n "$optQuiet" ] && break
++
++            case "$optShell" in
++            (*verbose)
++                echo "Using: $dir/$fileName" 1>&2
++                ;;
++            esac
++
++            case "$optShell" in
++            csh*)
++                echo "source $dir/$fileName"
+                 break
+-            else
++                ;;
++            sh*)
++                echo ". $dir/$fileName"
++                break
++                ;;
++            *)
+                 echo "$dir/$fileName"
+-                [ "$optAll" = true ] || break
+-            fi
++                [ -n "$optAll" ] || break
++                ;;
++            esac
+         fi
+     done
+ 
+ fi
+ 
+-
+ exit $exitCode
+ 
+ #------------------------------------------------------------------------------
+--- OpenFOAM-v1612+.orig/etc/bashrc	2016-12-23 15:22:59.000000000 +0100
++++ OpenFOAM-v1612+/etc/bashrc	2017-03-22 16:05:05.751237072 +0100
+@@ -42,7 +42,8 @@
+ #
+ # Please set to the appropriate path if the default is not correct.
+ #
+-[ $BASH_SOURCE ] && FOAM_INST_DIR=$(\cd ${BASH_SOURCE%/*/*/*} && \pwd -P) || \
++rc="${BASH_SOURCE:-${ZSH_NAME:+$0}}"
++[ -n "$rc" ] && FOAM_INST_DIR=$(\cd $(dirname $rc)/../.. && \pwd -L) || \
+ FOAM_INST_DIR=$HOME/$WM_PROJECT
+ # FOAM_INST_DIR=~$WM_PROJECT
+ # FOAM_INST_DIR=/opt/$WM_PROJECT
+@@ -135,8 +136,10 @@
+ # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ . $WM_PROJECT_DIR/etc/config.sh/functions
+ 
+-# Add in preset user or site preferences:
+-_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile prefs.sh`
++# Override definitions via prefs, with 'other' first so the sys-admin
++# can provide base values independent of WM_PROJECT_SITE
++_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile -mode o  prefs.sh`
++_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile -mode ug prefs.sh`
+ 
+ # Evaluate command-line parameters and record settings for later
+ # these can be used to set/unset values, or specify alternative pref files
+diff -uw OpenFOAM-v1612+.orig/etc/cshrc OpenFOAM-v1612+/etc/cshrc
+--- OpenFOAM-v1612+.orig/etc/cshrc	2016-12-23 15:22:59.000000000 +0100
++++ OpenFOAM-v1612+/etc/cshrc	2017-03-22 16:04:51.839291067 +0100
+@@ -148,8 +148,10 @@
+ # Source files, possibly with some verbosity
+ alias _foamSource 'if ($?FOAM_VERBOSE && $?prompt) echo "Sourcing: \!*"; if (\!* != "") source \!*'
+ 
+-# Add in preset user or site preferences:
+-_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile prefs.csh`
++# Override definitions via prefs, with 'other' first so the sys-admin
++# can provide base values independent of WM_PROJECT_SITE
++_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile -mode o  prefs.csh`
++_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile -mode ug prefs.csh`
+ 
+ # Evaluate command-line parameters and record settings for later
+ # these can be used to set/unset values, or specify alternative pref files
+--- OpenFOAM-v1612+.orig/etc/config.sh/settings	2016-12-23 15:22:59.000000000 +0100
++++ OpenFOAM-v1612+/etc/config.sh/settings	2017-12-21 20:40:50.109036445 +0100
+@@ -141,7 +141,7 @@
+ #------------------------------------------------------------------------------
+ 
+ # Location of the jobControl directory
+-export FOAM_JOB_DIR=$WM_PROJECT_INST_DIR/jobControl
++export FOAM_JOB_DIR="$HOME/.OpenFOAM/jobControl"
+ 
+ # wmake configuration
+ export WM_DIR=$WM_PROJECT_DIR/wmake
+@@ -198,8 +198,12 @@
+ unset siteDir
+ 
+ _foamAddPath $FOAM_USER_APPBIN:$FOAM_SITE_APPBIN:$FOAM_APPBIN
+-# Make sure to pick up dummy versions of external libraries last
+-_foamAddLib  $FOAM_USER_LIBBIN:$FOAM_SITE_LIBBIN:$FOAM_LIBBIN:$FOAM_EXT_LIBBIN:$FOAM_LIBBIN/dummy
++_foamAddLib  $FOAM_LIBBIN/dummy     # Dummy versions of external libraries last
++if [ -n "$FOAM_EXT_LIBBIN" ]        # External libraries (allowed to be unset)
++then
++    _foamAddLib $FOAM_EXT_LIBBIN
++fi
++_foamAddLib  $FOAM_USER_LIBBIN:$FOAM_SITE_LIBBIN:$FOAM_LIBBIN
+ 
+ # Compiler settings
+ # ~~~~~~~~~~~~~~~~~
+--- OpenFOAM-v1612+.orig/etc/config.csh/settings	2016-12-23 15:22:59.000000000 +0100
++++ OpenFOAM-v1612+/etc/config.csh/settings	2017-12-21 20:37:24.301773802 +0100
+@@ -137,7 +137,7 @@
+ #------------------------------------------------------------------------------
+ 
+ # Location of the jobControl directory
+-setenv FOAM_JOB_DIR $WM_PROJECT_INST_DIR/jobControl
++setenv FOAM_JOB_DIR "$HOME/.OpenFOAM/jobControl"
+ 
+ # wmake configuration
+ setenv WM_DIR $WM_PROJECT_DIR/wmake
+@@ -196,8 +196,11 @@
+ unset siteDir
+ 
+ _foamAddPath ${FOAM_USER_APPBIN}:${FOAM_SITE_APPBIN}:${FOAM_APPBIN}
+-# Make sure to pick up dummy versions of external libraries last
+-_foamAddLib  ${FOAM_USER_LIBBIN}:${FOAM_SITE_LIBBIN}:${FOAM_LIBBIN}:${FOAM_EXT_LIBBIN}:${FOAM_LIBBIN}/dummy
++_foamAddLib  $FOAM_LIBBIN/dummy     # Dummy versions of external libraries last
++if ( $?FOAM_EXT_LIBBIN ) then       # External libraries (allowed to be unset)
++    _foamAddLib $FOAM_EXT_LIBBIN
++endif
++_foamAddLib  ${FOAM_USER_LIBBIN}:${FOAM_SITE_LIBBIN}:${FOAM_LIBBIN}
+ 
+ # Compiler settings
+ # ~~~~~~~~~~~~~~~~~
+--- OpenFOAM-v1612+.orig/etc/config.sh/mpi	2016-12-23 15:22:59.000000000 +0100
++++ OpenFOAM-v1612+/etc/config.sh/mpi	2017-03-29 13:55:57.507980699 +0200
+@@ -75,8 +75,15 @@
+     _foamAddMan     $MPI_ARCH_PATH/share/man
+     ;;
+ 
++USERMPI)
++    # Use an arbitrary, user-specified mpi implementation
++    export FOAM_MPI=mpi-user
++    _foamSource `$WM_PROJECT_DIR/bin/foamEtcFile config.sh/mpi-user`
++    ;;
++
+ SYSTEMMPI)
+     export FOAM_MPI=mpi-system
++    _foamSource `$WM_PROJECT_DIR/bin/foamEtcFile config.sh/mpi-system`
+ 
+     if [ -z "$MPI_ROOT" ]
+     then
+--- OpenFOAM-v1612+.orig/etc/config.csh/mpi	2016-12-23 15:22:59.000000000 +0100
++++ OpenFOAM-v1612+/etc/config.csh/mpi	2017-03-29 13:56:36.347835938 +0200
+@@ -71,8 +71,15 @@
+     _foamAddMan     $MPI_ARCH_PATH/share/man
+     breaksw
+ 
++case USERMPI:
++    # Use an arbitrary, user-specified mpi implementation
++    setenv FOAM_MPI mpi-user
++    _foamSource `$WM_PROJECT_DIR/bin/foamEtcFile config.csh/mpi-user`
++    breaksw
++
+ case SYSTEMMPI:
+     setenv FOAM_MPI mpi-system
++    _foamSource `$WM_PROJECT_DIR/bin/foamEtcFile config.csh/mpi-system`
+ 
+     if ( ! ($?MPI_ROOT) ) then
+         echo
+--- OpenFOAM-v1612+.orig/src/fvAgglomerationMethods/Allwmake	2017-01-02 09:56:17.578558265 +0100
++++ OpenFOAM-v1612+/src/fvAgglomerationMethods/Allwmake	2017-04-18 18:58:38.236795902 +0200
+@@ -4,9 +4,13 @@
+ # Parse arguments for library compilation
+ . $WM_PROJECT_DIR/wmake/scripts/AllwmakeParseArguments
+ 
+-export ParMGridGen=$WM_THIRD_PARTY_DIR/ParMGridGen-1.0
++unset MGRIDGEN_ARCH_PATH
++if settings=$($WM_PROJECT_DIR/bin/foamEtcFile config.sh/mgridgen)
++then
++    . $settings
++fi
+ 
+-if [ -e "$FOAM_LIBBIN/libMGridGen.so" ]
++if [ -e "$MGRIDGEN_ARCH_PATH/include/mgridgen.h" ]
+ then
+     wmake $targetType MGridGenGamgAgglomeration
+ fi
+--- OpenFOAM-v1612+.orig/src/fvAgglomerationMethods/MGridGenGamgAgglomeration/Make/options	2017-01-02 09:56:17.578558265 +0100
++++ OpenFOAM-v1612+/src/fvAgglomerationMethods/MGridGenGamgAgglomeration/Make/options	2017-04-18 18:59:16.860662811 +0200
+@@ -1,15 +1,9 @@
+-/* Needs ParMGridGen environment variable set. (see Allwmake script) */
+-
+-TYPE_REAL=
+-#if defined(WM_SP)
+-TYPE_REAL=-DTYPE_REAL
+-#endif
+-
+ EXE_INC = \
+     -I$(LIB_SRC)/finiteVolume/lnInclude \
+-    -I$(ParMGridGen)/MGridGen/Lib/lnInclude \
+-    -I$(ParMGridGen)/MGridGen/IMlib/lnInclude \
+-    $(TYPE_REAL)
++    -I$(MGRIDGEN_ARCH_PATH)/include
+ 
+ LIB_LIBS = \
+-    -L$(FOAM_EXT_LIBBIN) -lMGridGen
++    -L$(FOAM_EXT_LIBBIN) \
++    -L$(MGRIDGEN_ARCH_PATH)/lib \
++    -L$(MGRIDGEN_ARCH_PATH)/lib$(WM_COMPILER_LIB_ARCH) \
++    -lmgrid
+--- OpenFOAM-v1612+.orig/src/parallel/decompose/Allwmake	2017-03-21 16:34:44.599021283 +0100
++++ OpenFOAM-v1612+/src/parallel/decompose/Allwmake	2017-03-21 16:28:57.243969660 +0100
+@@ -36,6 +36,7 @@
+ 
+     # Library
+     [ -r $FOAM_EXT_LIBBIN/libmetis.so ] || \
++    [ -r $METIS_ARCH_PATH/lib/libmetis.so ] || \
+     [ -r $METIS_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH/libmetis.so ] || \
+     [ "${METIS_ARCH_PATH##*-}" = system ] || {
+         echo "$warning (missing library)"
+@@ -90,6 +91,7 @@
+ 
+     # Library
+     [ -r $FOAM_EXT_LIBBIN/libscotch.so ] || \
++    [ -r $SCOTCH_ARCH_PATH/lib/libscotch.so ] || \
+     [ -r $SCOTCH_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH/libscotch.so ] || \
+     [ "${SCOTCH_ARCH_PATH##*-}" = system ] || {
+         echo "$warning (missing library)"
+--- OpenFOAM-v1612+.orig/src/parallel/decompose/metisDecomp/Make/options	2017-03-21 16:34:25.383075328 +0100
++++ OpenFOAM-v1612+/src/parallel/decompose/metisDecomp/Make/options	2017-03-21 16:30:15.727758338 +0100
+@@ -8,6 +8,7 @@
+  * to support central, non-thirdparty installations
+  */
+ LIB_LIBS = \
++    -L$(METIS_ARCH_PATH)/lib \
+     -L$(METIS_ARCH_PATH)/lib$(WM_COMPILER_LIB_ARCH) \
+     -L$(FOAM_EXT_LIBBIN) \
+     -lmetis
+--- OpenFOAM-v1612+.orig/src/parallel/decompose/ptscotchDecomp/Make/options	2017-03-21 16:34:34.607049385 +0100
++++ OpenFOAM-v1612+/src/parallel/decompose/ptscotchDecomp/Make/options	2017-03-21 16:30:00.479799399 +0100
+@@ -16,6 +16,7 @@
+  * to support central, non-thirdparty installations
+  */
+ LIB_LIBS = \
++    -L$(SCOTCH_ARCH_PATH)/lib \
+     -L$(SCOTCH_ARCH_PATH)/lib$(WM_COMPILER_LIB_ARCH) \
+     -L$(FOAM_EXT_LIBBIN) \
+     -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) \
+--- OpenFOAM-v1612+.orig/src/parallel/decompose/scotchDecomp/Make/options	2017-03-21 16:34:39.159036582 +0100
++++ OpenFOAM-v1612+/src/parallel/decompose/scotchDecomp/Make/options	2017-03-21 16:29:46.719836452 +0100
+@@ -16,6 +16,7 @@
+  * to support central, non-thirdparty installations
+  */
+ LIB_LIBS = \
++    -L$(SCOTCH_ARCH_PATH)/lib \
+     -L$(SCOTCH_ARCH_PATH)/lib$(WM_COMPILER_LIB_ARCH) \
+     -L$(FOAM_EXT_LIBBIN) \
+     -lscotch \
+--- OpenFOAM-v1612+.orig/applications/utilities/mesh/manipulation/renumberMesh/Allwmake	2016-12-23 15:22:59.000000000 +0100
++++ OpenFOAM-v1612+/applications/utilities/mesh/manipulation/renumberMesh/Allwmake	2017-03-28 11:13:35.222727218 +0200
+@@ -4,20 +4,35 @@
+ # Parse arguments for compilation (at least for error catching)
+ . $WM_PROJECT_DIR/wmake/scripts/AllwmakeParseArguments
+ 
+-export COMPILE_FLAGS=''
+-export LINK_FLAGS=''
++unset COMP_FLAGS LINK_FLAGS
+ 
+ if [ -f "${FOAM_LIBBIN}/libSloanRenumber.so" ]
+ then
+-    echo "Found libSloanRenumber.so  --  enabling Sloan renumbering support."
++    echo "    found libSloanRenumber  --  enabling sloan renumbering support."
+     export LINK_FLAGS="${LINK_FLAGS} -lSloanRenumber"
+ fi
+ 
+-if [ -f "${ZOLTAN_ARCH_PATH}/lib/libzoltan.a" -a -f "${FOAM_LIBBIN}/libzoltanRenumber.so" ]
++if [ -f "${FOAM_LIBBIN}/libzoltanRenumber.so" ]
+ then
+-    echo "Found libzoltanRenumber.so  --  enabling zoltan renumbering support."
+-    export COMPILE_FLAGS="-DFOAM_USE_ZOLTAN"
+-    export LINK_FLAGS="${LINK_FLAGS} -lzoltanRenumber -L${ZOLTAN_ARCH_PATH}/lib -lzoltan"
++    if [ -z "$ZOLTAN_ARCH_PATH" ]
++    then
++        # Optional: get ZOLTAN_ARCH_PATH
++        if settings=$($WM_PROJECT_DIR/bin/foamEtcFile config.sh/zoltan)
++        then
++            . $settings
++        fi
++    fi
++
++    for libdir in lib "lib${WM_COMPILER_LIB_ARCH}"
++    do
++        if [ -f "$ZOLTAN_ARCH_PATH/$libdir/libzoltan.a" ]
++        then
++            echo "    found libzoltanRenumber  --  enabling zoltan renumbering support."
++            export COMP_FLAGS="-DFOAM_USE_ZOLTAN"
++            export LINK_FLAGS="${LINK_FLAGS} -lzoltanRenumber -L$ZOLTAN_ARCH_PATH/$libdir -lzoltan"
++            break
++        fi
++    done
+ fi
+ 
+ wmake $targetType
+--- OpenFOAM-v1612+.orig/src/renumber/Allwmake	2016-12-23 15:22:59.000000000 +0100
++++ OpenFOAM-v1612+/src/renumber/Allwmake	2017-03-28 11:10:22.195543610 +0200
+@@ -5,14 +5,11 @@
+ targetType=libso
+ . $WM_PROJECT_DIR/wmake/scripts/AllwmakeParseArguments
+ 
+-## Get ZOLTAN_ARCH_PATH
+-#if settings=$($WM_PROJECT_DIR/bin/foamEtcFile config.sh/zoltan)
+-#then
+-#    . $settings
+-#    echo "using ZOLTAN_ARCH_PATH=$ZOLTAN_ARCH_PATH"
+-#else
+-#    echo "Error: no config.sh/zoltan settings"
+-#fi
++# Optional: get ZOLTAN_ARCH_PATH
++if settings=$($WM_PROJECT_DIR/bin/foamEtcFile config.sh/zoltan)
++then
++    . $settings
++fi
+ 
+ wmake $targetType renumberMethods
+ 
+--- OpenFOAM-v1612+.orig/src/renumber/zoltanRenumber/Make/options	2016-12-23 15:22:59.000000000 +0100
++++ OpenFOAM-v1612+/src/renumber/zoltanRenumber/Make/options	2017-03-28 11:50:46.484343848 +0200
+@@ -4,10 +4,13 @@
+ EXE_INC = \
+     /* -DFULLDEBUG -g -O0 */ \
+     $(PFLAGS) $(PINC) \
++    ${c++LESSWARN} \
+     -I$(FOAM_SRC)/renumber/renumberMethods/lnInclude \
+     -I$(ZOLTAN_ARCH_PATH)/include/ \
+     -I$(LIB_SRC)/meshTools/lnInclude
+ 
+ LIB_LIBS = \
+-    /* -L$(ZOLTAN_ARCH_PATH)/lib -lzoltan */ \
++    -L$(ZOLTAN_ARCH_PATH)/lib \
++    -L$(ZOLTAN_ARCH_PATH)/lib$(WM_COMPILER_LIB_ARCH) \
++    -lzoltan \
+     -lmeshTools
diff --git a/var/spack/repos/builtin/packages/openfoam-com/1612-zoltan-lib.patch b/var/spack/repos/builtin/packages/openfoam-com/1612-zoltan-lib.patch
deleted file mode 100644
index 712e6a7dfd..0000000000
--- a/var/spack/repos/builtin/packages/openfoam-com/1612-zoltan-lib.patch
+++ /dev/null
@@ -1,84 +0,0 @@
---- OpenFOAM-v1612+.orig/applications/utilities/mesh/manipulation/renumberMesh/Allwmake	2016-12-23 15:22:59.000000000 +0100
-+++ OpenFOAM-v1612+/applications/utilities/mesh/manipulation/renumberMesh/Allwmake	2017-03-28 11:13:35.222727218 +0200
-@@ -4,20 +4,35 @@
- # Parse arguments for compilation (at least for error catching)
- . $WM_PROJECT_DIR/wmake/scripts/AllwmakeParseArguments
- 
--export COMPILE_FLAGS=''
--export LINK_FLAGS=''
-+unset COMP_FLAGS LINK_FLAGS
- 
- if [ -f "${FOAM_LIBBIN}/libSloanRenumber.so" ]
- then
--    echo "Found libSloanRenumber.so  --  enabling Sloan renumbering support."
-+    echo "    found libSloanRenumber  --  enabling sloan renumbering support."
-     export LINK_FLAGS="${LINK_FLAGS} -lSloanRenumber"
- fi
- 
--if [ -f "${ZOLTAN_ARCH_PATH}/lib/libzoltan.a" -a -f "${FOAM_LIBBIN}/libzoltanRenumber.so" ]
-+if [ -f "${FOAM_LIBBIN}/libzoltanRenumber.so" ]
- then
--    echo "Found libzoltanRenumber.so  --  enabling zoltan renumbering support."
--    export COMPILE_FLAGS="-DFOAM_USE_ZOLTAN"
--    export LINK_FLAGS="${LINK_FLAGS} -lzoltanRenumber -L${ZOLTAN_ARCH_PATH}/lib -lzoltan"
-+    if [ -z "$ZOLTAN_ARCH_PATH" ]
-+    then
-+        # Optional: get ZOLTAN_ARCH_PATH
-+        if settings=$($WM_PROJECT_DIR/bin/foamEtcFile config.sh/zoltan)
-+        then
-+            . $settings
-+        fi
-+    fi
-+
-+    for libdir in lib "lib${WM_COMPILER_LIB_ARCH}"
-+    do
-+        if [ -f "$ZOLTAN_ARCH_PATH/$libdir/libzoltan.a" ]
-+        then
-+            echo "    found libzoltanRenumber  --  enabling zoltan renumbering support."
-+            export COMP_FLAGS="-DFOAM_USE_ZOLTAN"
-+            export LINK_FLAGS="${LINK_FLAGS} -lzoltanRenumber -L$ZOLTAN_ARCH_PATH/$libdir -lzoltan"
-+            break
-+        fi
-+    done
- fi
- 
- wmake $targetType
---- OpenFOAM-v1612+.orig/src/renumber/Allwmake	2016-12-23 15:22:59.000000000 +0100
-+++ OpenFOAM-v1612+/src/renumber/Allwmake	2017-03-28 11:10:22.195543610 +0200
-@@ -5,14 +5,11 @@
- targetType=libso
- . $WM_PROJECT_DIR/wmake/scripts/AllwmakeParseArguments
- 
--## Get ZOLTAN_ARCH_PATH
--#if settings=$($WM_PROJECT_DIR/bin/foamEtcFile config.sh/zoltan)
--#then
--#    . $settings
--#    echo "using ZOLTAN_ARCH_PATH=$ZOLTAN_ARCH_PATH"
--#else
--#    echo "Error: no config.sh/zoltan settings"
--#fi
-+# Optional: get ZOLTAN_ARCH_PATH
-+if settings=$($WM_PROJECT_DIR/bin/foamEtcFile config.sh/zoltan)
-+then
-+    . $settings
-+fi
- 
- wmake $targetType renumberMethods
- 
---- OpenFOAM-v1612+.orig/src/renumber/zoltanRenumber/Make/options	2016-12-23 15:22:59.000000000 +0100
-+++ OpenFOAM-v1612+/src/renumber/zoltanRenumber/Make/options	2017-03-28 11:50:46.484343848 +0200
-@@ -4,10 +4,13 @@
- EXE_INC = \
-     /* -DFULLDEBUG -g -O0 */ \
-     $(PFLAGS) $(PINC) \
-+    ${c++LESSWARN} \
-     -I$(FOAM_SRC)/renumber/renumberMethods/lnInclude \
-     -I$(ZOLTAN_ARCH_PATH)/include/ \
-     -I$(LIB_SRC)/meshTools/lnInclude
- 
- LIB_LIBS = \
--    /* -L$(ZOLTAN_ARCH_PATH)/lib -lzoltan */ \
-+    -L$(ZOLTAN_ARCH_PATH)/lib \
-+    -L$(ZOLTAN_ARCH_PATH)/lib$(WM_COMPILER_LIB_ARCH) \
-+    -lzoltan \
-     -lmeshTools
diff --git a/var/spack/repos/builtin/packages/openfoam-com/1806-have-kahip.patch b/var/spack/repos/builtin/packages/openfoam-com/1806-have-kahip.patch
new file mode 100644
index 0000000000..3e10a44145
--- /dev/null
+++ b/var/spack/repos/builtin/packages/openfoam-com/1806-have-kahip.patch
@@ -0,0 +1,17 @@
+--- OpenFOAM-v1806/wmake/scripts/have_kahip-ORIG	2018-06-28 16:39:32.000000000 +0200
++++ OpenFOAM-v1806/wmake/scripts/have_kahip	2018-08-11 13:37:18.250219013 +0200
+@@ -83,10 +83,10 @@
+         # FOAM_EXT_LIBBIN is allowed to be unset
+         library=$(findFirstFile \
+             $FOAM_EXT_LIBBIN/$library \
+-            $METIS_ARCH_PATH/lib/$static \
+-            $METIS_ARCH_PATH/lib/$library \
+-            $METIS_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH/$static \
+-            $METIS_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH/$library \
++            $KAHIP_ARCH_PATH/lib/$static \
++            $KAHIP_ARCH_PATH/lib/$library \
++            $KAHIP_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH/$static \
++            $KAHIP_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH/$library \
+         )
+     elif isSystem "$KAHIP_ARCH_PATH"
+     then
diff --git a/var/spack/repos/builtin/packages/openfoam-com/common/spack-Allwmake b/var/spack/repos/builtin/packages/openfoam-com/common/spack-Allwmake
index cff22daf10..6c53c2fd70 100755
--- a/var/spack/repos/builtin/packages/openfoam-com/common/spack-Allwmake
+++ b/var/spack/repos/builtin/packages/openfoam-com/common/spack-Allwmake
@@ -5,7 +5,15 @@ export FOAM_INST_DIR=$(cd .. && pwd -L)
 mkdir -p $FOAM_APPBIN $FOAM_LIBBIN 2>/dev/null  # Allow interrupt
 echo "Build openfoam with SPACK ($@)"
 echo WM_PROJECT_DIR = $WM_PROJECT_DIR
-./Allwmake $@                                   # Pass arguments
+
+# Prefer spack-specific Allwmake if it exists
+if [ -f Allwmake-spack ]
+then
+    ./Allwmake-spack $@   # Pass arguments
+else
+    ./Allwmake $@         # Pass arguments
+fi
+
 
 # Link non-dummy MPI_FOAM type to parent-dir, where rpath can find it
 if [ "${FOAM_MPI:=dummy}" != dummy -a -d "$FOAM_LIBBIN/$FOAM_MPI" ]
diff --git a/var/spack/repos/builtin/packages/openfoam-com/common/spack-derived-Allwmake b/var/spack/repos/builtin/packages/openfoam-com/common/spack-derived-Allwmake
index 407ad734e8..02741f1d13 100755
--- a/var/spack/repos/builtin/packages/openfoam-com/common/spack-derived-Allwmake
+++ b/var/spack/repos/builtin/packages/openfoam-com/common/spack-derived-Allwmake
@@ -1,6 +1,7 @@
 #!/bin/bash
 # The openfoam providers must export 'FOAM_PROJECT_DIR'
-# The package is expected to supply an appropriate Allwmake file.
+# The derived package is expected to supply an appropriate
+# <Allwmake> or <Allwmake-spack> file.
 
 [ -d "$FOAM_PROJECT_DIR" -a -f "$FOAM_PROJECT_DIR/etc/bashrc" ] || {
     echo "Error: no PROJECT=$FOAM_PROJECT_DIR" 1>&2
@@ -22,5 +23,12 @@ echo "  $WM_COMPILER $WM_COMPILER_TYPE compiler"
 echo "  $WM_OPTIONS - with $WM_MPLIB $FOAM_MPI"
 echo
 
-./Allwmake $@  # Pass arguments
+# Prefer spack-specific Allwmake if it exists
+if [ -f Allwmake-spack ]
+then
+    ./Allwmake-spack $@   # Pass arguments
+else
+    ./Allwmake $@         # Pass arguments
+fi
+
 # -----------------------------------------------------------------------------
diff --git a/var/spack/repos/builtin/packages/openfoam-com/openfoam-site.patch b/var/spack/repos/builtin/packages/openfoam-com/openfoam-site.patch
deleted file mode 100644
index a1f5d8a08a..0000000000
--- a/var/spack/repos/builtin/packages/openfoam-com/openfoam-site.patch
+++ /dev/null
@@ -1,35 +0,0 @@
-diff -uw OpenFOAM-plus.orig/etc/config.sh/settings OpenFOAM-plus/etc/config.sh/settings
---- OpenFOAM-plus.orig/etc/config.sh/settings	2017-04-04 17:34:29.875873400 +0200
-+++ OpenFOAM-plus/etc/config.sh/settings	2017-04-04 17:38:40.174992466 +0200
-@@ -154,10 +154,10 @@
- export FOAM_LIBBIN=$WM_PROJECT_DIR/platforms/$WM_OPTIONS/lib
- 
- # External (ThirdParty) libraries
--export FOAM_EXT_LIBBIN=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/lib
-+unset FOAM_EXT_LIBBIN  #SPACK: none
- 
- # Site-specific directory
--siteDir="${WM_PROJECT_SITE:-$WM_PROJECT_INST_DIR/site}"
-+siteDir="${WM_PROJECT_SITE:-$WM_PROJECT_DIR/site}"  #SPACK: not in parent directory
- 
- # Shared site executables/libraries
- # Similar naming convention as ~OpenFOAM expansion
-diff -uw OpenFOAM-plus.orig/etc/config.csh/settings OpenFOAM-plus/etc/config.csh/settings
---- OpenFOAM-plus.orig/etc/config.csh/settings	2017-04-04 17:34:28.255879107 +0200
-+++ OpenFOAM-plus/etc/config.csh/settings	2017-04-04 17:39:22.214844670 +0200
-@@ -151,13 +151,13 @@
- setenv FOAM_LIBBIN $WM_PROJECT_DIR/platforms/$WM_OPTIONS/lib
- 
- # External (ThirdParty) libraries
--setenv FOAM_EXT_LIBBIN $WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/lib
-+unsetenv FOAM_EXT_LIBBIN  #SPACK: none
- 
- # Site-specific directory
- if ( $?WM_PROJECT_SITE ) then
-     set siteDir=$WM_PROJECT_SITE
- else
--    set siteDir=$WM_PROJECT_INST_DIR/site
-+    set siteDir=$WM_PROJECT_DIR/site  #SPACK: not in parent directory
- endif
- 
- # Shared site executables/libraries
diff --git a/var/spack/repos/builtin/packages/openfoam-com/package.py b/var/spack/repos/builtin/packages/openfoam-com/package.py
index d184365720..cdb6ae1dac 100644
--- a/var/spack/repos/builtin/packages/openfoam-com/package.py
+++ b/var/spack/repos/builtin/packages/openfoam-com/package.py
@@ -1,28 +1,8 @@
-##############################################################################
-# Copyright (c) 2017 Mark Olesen, OpenCFD Ltd.
-#
-# This file was authored by Mark Olesen <mark.olesen@esi-group.com>
-# and is released as part of spack under the LGPL license.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for the LLNL notice and LGPL.
-#
-# License
-# -------
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 # Legal Notice
 # ------------
 # OPENFOAM is a trademark owned by OpenCFD Ltd
@@ -60,10 +40,10 @@
 ##############################################################################
 import glob
 import re
-import shutil
 import os
 
 from spack import *
+from spack.util.environment import EnvironmentModifications
 import llnl.util.tty as tty
 
 
@@ -73,8 +53,8 @@ __all__ = [
     'write_environ',
     'rewrite_environ_files',
     'mplib_content',
-    'foamAddPath',
-    'foamAddLib',
+    'foam_add_path',
+    'foam_add_lib',
     'OpenfoamArch',
 ]
 
@@ -150,8 +130,9 @@ def _write_environ_file(output, environ, formatter):
     Also descends into sub-dict and sub-list, but drops the key.
     """
     with open(output, 'w') as outfile:
-        outfile.write('# SPACK settings\n\n')
+        outfile.write('# spack generated\n')
         _write_environ_entries(outfile, environ, formatter)
+        outfile.write('# spack\n')
 
 
 def write_environ(environ, **kwargs):
@@ -163,12 +144,12 @@ def write_environ(environ, **kwargs):
          posix[=None]    If set, the name of the POSIX file to rewrite.
          cshell[=None]   If set, the name of the C-shell file to rewrite.
     """
-    posix = kwargs.get('posix', None)
-    if posix:
-        _write_environ_file(posix, environ, format_export)
-    cshell = kwargs.get('cshell', None)
-    if cshell:
-        _write_environ_file(cshell, environ, format_setenv)
+    rcfile = kwargs.get('posix', None)
+    if rcfile:
+        _write_environ_file(rcfile, environ, format_export)
+    rcfile = kwargs.get('cshell', None)
+    if rcfile:
+        _write_environ_file(rcfile, environ, format_setenv)
 
 
 def rewrite_environ_files(environ, **kwargs):
@@ -177,30 +158,37 @@ def rewrite_environ_files(environ, **kwargs):
          posix[=None]    If set, the name of the POSIX file to rewrite.
          cshell[=None]   If set, the name of the C-shell file to rewrite.
     """
-    posix = kwargs.get('posix', None)
-    if posix and os.path.isfile(posix):
+    rcfile = kwargs.get('posix', None)
+    if rcfile and os.path.isfile(rcfile):
         for k, v in environ.items():
-            filter_file(
-                r'^(\s*export\s+%s)=.*$' % k,
-                r'\1=%s' % v,
-                posix,
-                backup=False)
-    cshell = kwargs.get('cshell', None)
-    if cshell and os.path.isfile(cshell):
+            regex = r'^(\s*export\s+{0})=.*$'.format(k)
+            if not v:
+                replace = r'unset {0}  #SPACK: unset'.format(k)
+            elif v.startswith('#'):
+                replace = r'unset {0}  {1}'.format(k, v)
+            else:
+                replace = r'\1={0}'.format(v)
+            filter_file(regex, replace, rcfile, backup=False)
+
+    rcfile = kwargs.get('cshell', None)
+    if rcfile and os.path.isfile(rcfile):
         for k, v in environ.items():
-            filter_file(
-                r'^(\s*setenv\s+%s)\s+.*$' % k,
-                r'\1 %s' % v,
-                cshell,
-                backup=False)
+            regex = r'^(\s*setenv\s+{0})\s+.*$'.format(k)
+            if not v:
+                replace = r'unsetenv {0}  #SPACK: unset'.format(k)
+            elif v.startswith('#'):
+                replace = r'unsetenv {0}  {1}'.format(k, v)
+            else:
+                replace = r'\1 {0}'.format(v)
+            filter_file(regex, replace, rcfile, backup=False)
 
 
-def foamAddPath(*args):
+def foam_add_path(*args):
     """A string with args prepended to 'PATH'"""
     return '"' + ':'.join(args) + ':${PATH}"'
 
 
-def foamAddLib(*args):
+def foam_add_lib(*args):
     """A string with args prepended to 'LD_LIBRARY_PATH'"""
     return '"' + ':'.join(args) + ':${LD_LIBRARY_PATH}"'
 
@@ -220,8 +208,8 @@ def pkglib(package, pre=None):
 
 
 def mplib_content(spec, pre=None):
-    """The mpi settings to have wmake
-    use spack information with minimum modifications to OpenFOAM.
+    """The mpi settings (from spack) for the OpenFOAM wmake includes, which
+    allows later reuse within OpenFOAM.
 
     Optional parameter 'pre' to provide alternative prefix
     """
@@ -229,6 +217,11 @@ def mplib_content(spec, pre=None):
     bin = mpi_spec.prefix.bin
     inc = mpi_spec.prefix.include
     lib = pkglib(mpi_spec)
+
+    libname = 'mpi'
+    if 'mpich' in mpi_spec.name:
+        libname = 'mpich'
+
     if pre:
         bin = join_path(pre, os.path.basename(bin))
         inc = join_path(pre, os.path.basename(inc))
@@ -242,9 +235,9 @@ def mplib_content(spec, pre=None):
         'include': inc,
         'bindir':  bin,
         'libdir':  lib,
-        'FLAGS':  '-DOMPI_SKIP_MPICXX -DMPICH_IGNORE_CXX_SEEK',
+        'FLAGS':  '-DOMPI_SKIP_MPICXX -DMPICH_SKIP_MPICXX',
         'PINC':   '-I{0}'.format(inc),
-        'PLIBS':  '-L{0} -lmpi'.format(lib),
+        'PLIBS':  '-L{0} -l{1}'.format(lib, libname),
     }
     return info
 
@@ -260,57 +253,70 @@ class OpenfoamCom(Package):
     in 2004.
     """
 
+    maintainers = ['olesenm']
     homepage = "http://www.openfoam.com/"
-    baseurl  = "https://sourceforge.net/projects/openfoamplus/files/"
-    gitrepo  = "https://develop.openfoam.com/Development/OpenFOAM-plus.git"
+    url      = "https://sourceforge.net/projects/openfoamplus/files/v1706/OpenFOAM-v1706.tgz"
+    git      = "https://develop.openfoam.com/Development/OpenFOAM-plus.git"
+    list_url = "https://sourceforge.net/projects/openfoamplus/files/"
+    list_depth = 2
 
-    version('1706', '630d30770f7b54d6809efbf94b7d7c8f',
-            url=baseurl + 'v1706/OpenFOAM-v1706.tgz')
-    version('1612', 'ca02c491369150ab127cbb88ec60fbdf',
-            url=baseurl + 'v1612+/OpenFOAM-v1612+.tgz')
-    version('develop', branch='develop', git=gitrepo)  # Needs credentials
+    version('develop', branch='develop', submodules='True')  # Needs credentials
+    version('1806', 'bb244a3bde7048a03edfccffc46c763f')
+    version('1712', '6ad92df051f4d52c7d0ec34f4b8eb3bc')
+    version('1706', '630d30770f7b54d6809efbf94b7d7c8f')
+    version('1612', 'ca02c491369150ab127cbb88ec60fbdf')
 
-    variant('int64', default=False,
-            description='Compile with 64-bit label')
     variant('float32', default=False,
-            description='Compile with 32-bit scalar (single-precision)')
+            description='Use single-precision')
+    variant('int64', default=False,
+            description='With 64-bit labels')
     variant('knl', default=False,
             description='Use KNL compiler settings')
-    variant('scotch', default=True,
-            description='With scotch/ptscotch for decomposition')
+    variant('kahip', default=True,
+            description='With kahip decomposition')
     variant('metis', default=False,
-            description='With metis for decomposition')
+            description='With metis decomposition')
+    variant('scotch', default=True,
+            description='With scotch/ptscotch decomposition')
     variant('zoltan', default=False,
             description='With zoltan renumbering')
     # TODO?# variant('scalasca', default=False,
     # TODO?#         description='With scalasca profiling')
     variant('mgridgen', default=False, description='With mgridgen support')
-    variant('paraview', default=True,
+    variant('paraview', default=False,
             description='Build paraview plugins and runtime post-processing')
+    variant('vtk', default=False,
+            description='With VTK runTimePostProcessing')
     variant('source', default=True,
             description='Install library/application sources and tutorials')
 
     provides('openfoam')
     depends_on('mpi')
 
-    # After 1712 require openmpi+thread_multiple for collated output
-    conflicts('^openmpi~thread_multiple', when='@1712:')
+    # After 1712, could suggest openmpi+thread_multiple for collated output
+    # but particular mixes of mpi versions and InfiniBand may not work so well
+    # conflicts('^openmpi~thread_multiple', when='@1712:')
 
     depends_on('zlib')
     depends_on('fftw')
     depends_on('boost')
     depends_on('cgal')
-    depends_on('flex',  type='build')
+    # The flex restriction is ONLY to deal with a spec resolution clash
+    # introduced by the restriction within scotch!
+    depends_on('flex@:2.6.1,2.6.4:', type='build')
     depends_on('cmake', type='build')
 
     # Require scotch with ptscotch - corresponds to standard OpenFOAM setup
     depends_on('scotch~metis+mpi~int64', when='+scotch~int64')
     depends_on('scotch~metis+mpi+int64', when='+scotch+int64')
+    depends_on('kahip',        when='+kahip')
     depends_on('metis@5:',     when='+metis')
     depends_on('metis+int64',  when='+metis+int64')
     # mgridgen is statically linked
     depends_on('parmgridgen',  when='+mgridgen', type='build')
     depends_on('zoltan',       when='+zoltan')
+    depends_on('vtk',          when='+vtk')
+
     # TODO?# depends_on('scalasca',     when='+scalasca')
 
     # For OpenFOAM plugins and run-time post-processing this should just be
@@ -328,19 +334,8 @@ class OpenfoamCom(Package):
     assets = []
 
     # Version-specific patches
-    patch('1612-bin.patch', when='@1612')
-    patch('1612-build.patch', when='@1612')
-    patch('1612-etc.patch', when='@1612')
-    patch('1612-site.patch', when='@1612')
-    patch('1612-mpi.patch', when='@1612')
-    patch('1612-mgridgen-lib.patch', when='@1612')
-    patch('1612-scotch-metis-lib.patch', when='@1612')
-    patch('1612-zoltan-lib.patch', when='@1612')
-
-    # This patch is reasonably version-invariant
-    # 1) default site directly under WM_PROJECT_DIR
-    # 2) no FOAM_EXT_LIBBIN required
-    patch('openfoam-site.patch', when='@1706:')
+    patch('1612-spack-patches.patch', when='@1612')
+    patch('1806-have-kahip.patch', when='@1806')
 
     # Some user config settings
     # default: 'compile-option': 'RpathOpt',
@@ -366,14 +361,82 @@ class OpenfoamCom(Package):
     # - End of definitions / setup -
     #
 
+    def url_for_version(self, version):
+        # Prior to 'v1706' and additional '+' in the naming
+        fmt = self.list_url
+        if version <= Version('1612'):
+            fmt += 'v{0}+/OpenFOAM-v{0}+.tgz'
+        else:
+            fmt += 'v{0}/OpenFOAM-v{0}.tgz'
+        return fmt.format(version, version)
+
     def setup_environment(self, spack_env, run_env):
-        run_env.set('FOAM_PROJECT_DIR', self.projectdir)
-        run_env.set('WM_PROJECT_DIR', self.projectdir)
-        for d in ['wmake', self.archbin]:  # bin already added automatically
-            run_env.prepend_path('PATH', join_path(self.projectdir, d))
+        """Add environment variables to the generated module file.
+        These environment variables come from running:
+
+        .. code-block:: console
+
+           $ . $WM_PROJECT_DIR/etc/bashrc
+        """
+
+        # NOTE: Spack runs setup_environment twice.
+        # 1) pre-build to set up the build environment
+        # 2) post-install to determine runtime environment variables
+        # The etc/bashrc is only available (with corrrect content)
+        # post-installation.
+
+        bashrc = join_path(self.projectdir, 'etc', 'bashrc')
+        minimal = True
+        if os.path.isfile(bashrc):
+            # post-install: source the installed bashrc
+            try:
+                mods = EnvironmentModifications.from_sourcing_file(
+                    bashrc,
+                    clean=True,  # Remove duplicate entries
+                    blacklist=[  # Blacklist these
+                        # Inadvertent changes
+                        # -------------------
+                        'PS1',            # Leave unaffected
+                        'MANPATH',        # Leave unaffected
+
+                        # Unneeded bits
+                        # -------------
+                        'FOAM_SETTINGS',  # Do not use with modules
+                        'FOAM_INST_DIR',  # Old
+                        'FOAM_(APP|ETC|SRC|SOLVERS|UTILITIES)',
+                        # 'FOAM_TUTORIALS',  # can be useful
+                        'WM_OSTYPE',      # Purely optional value
+
+                        # Third-party cruft - only used for orig compilation
+                        # -----------------
+                        '[A-Z].*_ARCH_PATH',
+                        '(KAHIP|METIS|SCOTCH)_VERSION',
+
+                        # User-specific
+                        # -------------
+                        'FOAM_RUN',
+                        '(FOAM|WM)_.*USER_.*',
+                    ],
+                    whitelist=[  # Whitelist these
+                        'MPI_ARCH_PATH',  # Can be needed for compilation
+                    ])
+
+                run_env.extend(mods)
+                minimal = False
+                tty.info('OpenFOAM bashrc env: {0}'.format(bashrc))
+            except Exception:
+                minimal = True
+
+        if minimal:
+            # pre-build or minimal environment
+            tty.info('OpenFOAM minimal env {0}'.format(self.prefix))
+            run_env.set('FOAM_PROJECT_DIR', self.projectdir)
+            run_env.set('WM_PROJECT_DIR', self.projectdir)
+            for d in ['wmake', self.archbin]:  # bin added automatically
+                run_env.prepend_path('PATH', join_path(self.projectdir, d))
 
     def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
-        """Provide location of the OpenFOAM project.
+        """Location of the OpenFOAM project directory.
         This is identical to the WM_PROJECT_DIR value, but we avoid that
         variable since it would mask the normal OpenFOAM cleanup of
         previous versions.
@@ -407,18 +470,38 @@ class OpenfoamCom(Package):
         add_extra_files(self, self.common, self.assets)
 
         # Avoid WM_PROJECT_INST_DIR for ThirdParty, site or jobControl.
-        # Use openfoam-site.patch to handle jobControl, site.
         #
         # Filtering: bashrc,cshrc (using a patch is less flexible)
         edits = {
             'WM_THIRD_PARTY_DIR':
-            r'$WM_PROJECT_DIR/ThirdParty #SPACK: No separate third-party',
+            r'$WM_PROJECT_DIR/ThirdParty  #SPACK: No separate third-party',
         }
-        rewrite_environ_files(  # Adjust etc/bashrc and etc/cshrc
+        rewrite_environ_files(  # etc/{bashrc,cshrc}
             edits,
             posix=join_path('etc', 'bashrc'),
             cshell=join_path('etc', 'cshrc'))
 
+        # Filtering: settings
+        edits = {
+            'FOAM_EXT_LIBBIN': '#SPACK: No separate third-party',  # ie, unset
+        }
+        rewrite_environ_files(  # etc/config.{csh,sh}/settings
+            edits,
+            posix=join_path('etc', 'config.sh', 'settings'),
+            cshell=join_path('etc', 'config.csh', 'settings'))
+
+        # The following filtering is non-vital. It simply prevents 'site' dirs
+        # from the the wrong level (likely non-existent anyhow) from being
+        # added to PATH, LD_LIBRARY_PATH.
+        for rcdir in ['config.sh', 'config.csh']:
+            rcfile = join_path('etc', rcdir, 'settings')
+            if os.path.isfile(rcfile):
+                filter_file(
+                    'WM_PROJECT_INST_DIR/',
+                    'WM_PROJECT_DIR/',
+                    rcfile,
+                    backup=False)
+
     def configure(self, spec, prefix):
         """Make adjustments to the OpenFOAM configuration files in their various
         locations: etc/bashrc, etc/config.sh/FEATURE and customizations that
@@ -428,7 +511,7 @@ class OpenfoamCom(Package):
         # Filtering bashrc, cshrc
         edits = {}
         edits.update(self.foam_arch.foam_dict())
-        rewrite_environ_files(  # Adjust etc/bashrc and etc/cshrc
+        rewrite_environ_files(  # etc/{bashrc,cshrc}
             edits,
             posix=join_path('etc', 'bashrc'),
             cshell=join_path('etc', 'cshrc'))
@@ -450,26 +533,29 @@ class OpenfoamCom(Package):
                 ('BOOST_ARCH_PATH', spec['boost'].prefix),
                 ('CGAL_ARCH_PATH',  spec['cgal'].prefix),
                 ('LD_LIBRARY_PATH',
-                 foamAddLib(
+                 foam_add_lib(
                      pkglib(spec['boost'], '${BOOST_ARCH_PATH}'),
                      pkglib(spec['cgal'], '${CGAL_ARCH_PATH}'))),
             ],
             'FFTW': [
                 ('FFTW_ARCH_PATH', spec['fftw'].prefix),  # Absolute
                 ('LD_LIBRARY_PATH',
-                 foamAddLib(
+                 foam_add_lib(
                      pkglib(spec['fftw'], '${BOOST_ARCH_PATH}'))),
             ],
             # User-defined MPI
             'mpi-user': [
                 ('MPI_ARCH_PATH', spec['mpi'].prefix),  # Absolute
-                ('LD_LIBRARY_PATH', foamAddLib(user_mpi['libdir'])),
-                ('PATH', foamAddPath(user_mpi['bindir'])),
+                ('LD_LIBRARY_PATH', foam_add_lib(user_mpi['libdir'])),
+                ('PATH', foam_add_path(user_mpi['bindir'])),
             ],
             'scotch': {},
+            'kahip': {},
             'metis': {},
+            'ensight': {},     # Disable settings
             'paraview': [],
             'gperftools': [],  # Currently unused
+            'vtk': [],
         }
 
         if '+scotch' in spec:
@@ -479,18 +565,30 @@ class OpenfoamCom(Package):
                 'SCOTCH_VERSION': 'scotch-{0}'.format(spec['scotch'].version),
             }
 
+        if '+kahip' in spec:
+            self.etc_config['kahip'] = {
+                'KAHIP_ARCH_PATH': spec['kahip'].prefix,
+            }
+
         if '+metis' in spec:
             self.etc_config['metis'] = {
                 'METIS_ARCH_PATH': spec['metis'].prefix,
             }
 
         if '+paraview' in spec:
-            pvMajor = 'paraview-{0}'.format(spec['paraview'].version.up_to(2))
+            pvmajor = 'paraview-{0}'.format(spec['paraview'].version.up_to(2))
             self.etc_config['paraview'] = [
                 ('ParaView_DIR', spec['paraview'].prefix),
-                ('ParaView_INCLUDE_DIR', '${ParaView_DIR}/include/' + pvMajor),
-                ('PV_PLUGIN_PATH', '$FOAM_LIBBIN/' + pvMajor),
-                ('PATH', foamAddPath('${ParaView_DIR}/bin')),
+                ('ParaView_INCLUDE_DIR', '${ParaView_DIR}/include/' + pvmajor),
+                ('PV_PLUGIN_PATH', '$FOAM_LIBBIN/' + pvmajor),
+                ('PATH', foam_add_path('${ParaView_DIR}/bin')),
+            ]
+
+        if '+vtk' in spec:
+            self.etc_config['vtk'] = [
+                ('VTK_DIR', spec['vtk'].prefix),
+                ('LD_LIBRARY_PATH',
+                 foam_add_lib(pkglib(spec['vtk'], '${VTK_DIR}'))),
             ]
 
         # Optional
@@ -574,12 +672,13 @@ class OpenfoamCom(Package):
             dirs.extend(['doc'])
 
         # Install platforms (and doc) skipping intermediate targets
-        ignored = ['src', 'applications', 'html', 'Guides']
+        relative_ignore_paths = ['src', 'applications', 'html', 'Guides']
+        ignore = lambda p: p in relative_ignore_paths
         for d in dirs:
             install_tree(
                 d,
                 join_path(self.projectdir, d),
-                ignore=shutil.ignore_patterns(*ignored),
+                ignore=ignore,
                 symlinks=True)
 
         etc_dir = join_path(self.projectdir, 'etc')
@@ -613,12 +712,6 @@ class OpenfoamCom(Package):
             ]:
                 os.symlink(f, os.path.basename(f))
 
-    def openfoam_run_environment(self, projdir):
-        # This seems to bomb out with an ImportError 'site'!
-        # mods = EnvironmentModifications.from_sourcing_files(
-        #    join_path(projdir, 'etc/bashrc'))
-        pass
-
 
 # -----------------------------------------------------------------------------
 
@@ -673,6 +766,8 @@ class OpenfoamArch(object):
                 platform += 'ia64'
             elif target == 'armv7l':
                 platform += 'ARM7'
+            elif target == 'aarch64':
+                platform += 'ARM64'
             elif target == 'ppc64':
                 platform += 'PPC64'
             elif target == 'ppc64le':
diff --git a/var/spack/repos/builtin/packages/openfoam-org/240-etc.patch b/var/spack/repos/builtin/packages/openfoam-org/240-etc.patch
new file mode 100644
index 0000000000..cc0c19c78d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/openfoam-org/240-etc.patch
@@ -0,0 +1,88 @@
+--- OpenFOAM-2.4.x.orig/etc/bashrc	2016-10-16 16:11:45.000000000 +0200
++++ OpenFOAM-2.4.x/etc/bashrc	2017-03-24 12:41:25.233267894 +0100
+@@ -55,6 +55,8 @@
+ # overridden from the prefs.sh file or from command-line specification
+ #
+ #- note the location for later use (eg, in job scripts)
++rc="${BASH_SOURCE:-${ZSH_NAME:+$0}}"
++[ -n "$rc" ] && FOAM_INST_DIR=$(\cd $(dirname $rc)/../.. && \pwd -L) || \
+ : ${FOAM_INST_DIR:=$foamInstall}; export FOAM_INST_DIR
+ 
+ #- Compiler location:
+--- OpenFOAM-2.4.x.orig/applications/utilities/mesh/conversion/ansysToFoam/ansysToFoam.L	2018-04-05 14:18:12.112228183 +0100
++++ OpenFOAM-2.4.x/applications/utilities/mesh/conversion/ansysToFoam/ansysToFoam.L	2018-04-05 14:19:20.795393577 +0100
+@@ -77,7 +77,7 @@
+ // Dummy yywrap to keep yylex happy at compile time.
+ // It is called by yylex but is not used as the mechanism to change file.
+ // See <<EOF>>
+-#if YY_FLEX_SUBMINOR_VERSION < 34
++#if YY_FLEX_MINOR_VERSION < 6 && YY_FLEX_SUBMINOR_VERSION < 34
+ extern "C" int yywrap()
+ #else
+ int yyFlexLexer::yywrap()
+--- OpenFOAM-2.4.x.orig/src/thermophysicalModels/reactionThermo/chemistryReaders/chemkinReader/chemkinLexer.L	2018-04-05 14:18:19.137347383 +0100
++++ OpenFOAM-2.4.x/src/thermophysicalModels/reactionThermo/chemistryReaders/chemkinReader/chemkinLexer.L	2018-04-05 14:19:27.556508297 +0100
+@@ -54,7 +54,7 @@
+ // It is called by yylex but is not used as the mechanism to change file.
+ // See <<EOF>>
+ //! \cond dummy
+-#if YY_FLEX_SUBMINOR_VERSION < 34
++#if YY_FLEX_MINOR_VERSION < 6 && YY_FLEX_SUBMINOR_VERSION < 34
+ extern "C" int yywrap()
+ #else
+ int yyFlexLexer::yywrap()
+--- OpenFOAM-2.4.x.orig/applications/utilities/mesh/conversion/gambitToFoam/gambitToFoam.L	2018-04-05 14:18:45.689797916 +0100
++++ OpenFOAM-2.4.x/applications/utilities/mesh/conversion/gambitToFoam/gambitToFoam.L	2018-04-05 14:19:43.195773659 +0100
+@@ -80,7 +80,7 @@
+ // Dummy yywrap to keep yylex happy at compile time.
+ // It is called by yylex but is not used as the mechanism to change file.
+ // See <<EOF>>
+-#if YY_FLEX_SUBMINOR_VERSION < 34
++#if YY_FLEX_MINOR_VERSION < 6 && YY_FLEX_SUBMINOR_VERSION < 34
+ extern "C" int yywrap()
+ #else
+ int yyFlexLexer::yywrap()
+--- OpenFOAM-2.4.x.orig/src/triSurface/triSurface/interfaces/STL/readSTLASCII.L	2018-04-05 14:18:50.432878396 +0100
++++ OpenFOAM-2.4.x/src/triSurface/triSurface/interfaces/STL/readSTLASCII.L	2018-04-05 14:19:46.299826328 +0100
+@@ -55,7 +55,7 @@
+ // It is called by yylex but is not used as the mechanism to change file.
+ // See <<EOF>>
+ //! \cond dummy
+-#if YY_FLEX_SUBMINOR_VERSION < 34
++#if YY_FLEX_MINOR_VERSION < 6 && YY_FLEX_SUBMINOR_VERSION < 34
+ extern "C" int yywrap()
+ #else
+ int yyFlexLexer::yywrap()
+--- OpenFOAM-2.4.x.orig/src/surfMesh/surfaceFormats/stl/STLsurfaceFormatASCII.L	2018-04-05 14:18:57.064990927 +0100
++++ OpenFOAM-2.4.x/src/surfMesh/surfaceFormats/stl/STLsurfaceFormatASCII.L	2018-04-05 14:19:49.258876536 +0100
+@@ -50,7 +50,7 @@
+ // It is called by yylex but is not used as the mechanism to change file.
+ // See <<EOF>>
+ //! \cond dummy
+-#if YY_FLEX_SUBMINOR_VERSION < 34
++#if YY_FLEX_MINOR_VERSION < 6 && YY_FLEX_SUBMINOR_VERSION < 34
+ extern "C" int yywrap()
+ #else
+ int yyFlexLexer::yywrap()
+--- OpenFOAM-2.4.x.orig/applications/utilities/mesh/conversion/fluent3DMeshToFoam/fluent3DMeshToFoam.L	2018-04-05 14:18:27.152483381 +0100
++++ OpenFOAM-2.4.x/applications/utilities/mesh/conversion/fluent3DMeshToFoam/fluent3DMeshToFoam.L	2018-04-05 14:19:32.180586757 +0100
+@@ -123,7 +123,7 @@
+ // Dummy yywrap to keep yylex happy at compile time.
+ // It is called by yylex but is not used as the mechanism to change file.
+ // See <<EOF>>
+-#if YY_FLEX_SUBMINOR_VERSION < 34
++#if YY_FLEX_MINOR_VERSION < 6 && YY_FLEX_SUBMINOR_VERSION < 34
+ extern "C" int yywrap()
+ #else
+ int yyFlexLexer::yywrap()
+--- OpenFOAM-2.4.x.orig/applications/utilities/mesh/conversion/fluentMeshToFoam/fluentMeshToFoam.L.	2018-04-05 14:18:35.049617377 +0100
++++ OpenFOAM-2.4.x/applications/utilities/mesh/conversion/fluentMeshToFoam/fluentMeshToFoam.L	2018-04-05 14:19:38.493693876 +0100
+@@ -100,7 +100,7 @@
+ // Dummy yywrap to keep yylex happy at compile time.
+ // It is called by yylex but is not used as the mechanism to change file.
+ // See <<EOF>>
+-#if YY_FLEX_SUBMINOR_VERSION < 34
++#if YY_FLEX_MINOR_VERSION < 6 && YY_FLEX_SUBMINOR_VERSION < 34
+ extern "C" int yywrap()
+ #else
+ int yyFlexLexer::yywrap()int yyFlexLexer::yywrap()
diff --git a/var/spack/repos/builtin/packages/openfoam-org/50-etc.patch b/var/spack/repos/builtin/packages/openfoam-org/50-etc.patch
new file mode 100644
index 0000000000..ee28dfcd1b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/openfoam-org/50-etc.patch
@@ -0,0 +1,24 @@
+--- OpenFOAM-5.x.org/etc/bashrc	2017-07-25 18:43:40.000000000 +0200
++++ OpenFOAM-5.x/etc/bashrc	2017-12-11 13:36:09.479818186 +0100
+@@ -42,15 +42,17 @@
+ #
+ # Please set to the appropriate path if the default is not correct.
+ #
+-[ ${BASH_SOURCE:-$0} ] && \
+-export FOAM_INST_DIR=$(cd $(dirname ${BASH_SOURCE:-$0})/../.. && pwd -P) || \
+-export FOAM_INST_DIR=$HOME/$WM_PROJECT
+-# export FOAM_INST_DIR=~$WM_PROJECT
++rc="${BASH_SOURCE:-${ZSH_NAME:+$0}}"
++[ -n "$rc" ] && FOAM_INST_DIR=$(\cd $(dirname $rc)/../.. && \pwd -P) || \
++FOAM_INST_DIR=$HOME/$WM_PROJECT
+ # export FOAM_INST_DIR=/opt/$WM_PROJECT
+ # export FOAM_INST_DIR=/usr/local/$WM_PROJECT
+ #
+ # END OF (NORMAL) USER EDITABLE PART
+ ################################################################################
++: # Extra safety - if the user commented out all fallback values
++export FOAM_INST_DIR
++unset rc
+ 
+ # The default environment variables below can be overridden in a prefs.sh file
+ # located in ~/.OpenFOAM/$WM_PROJECT_VERSION, ~/.OpenFOAM,
diff --git a/var/spack/repos/builtin/packages/openfoam-org/assets/bin/foamEtcFile b/var/spack/repos/builtin/packages/openfoam-org/assets/bin/foamEtcFile
index 294cc26505..195b91bdbe 100755
--- a/var/spack/repos/builtin/packages/openfoam-org/assets/bin/foamEtcFile
+++ b/var/spack/repos/builtin/packages/openfoam-org/assets/bin/foamEtcFile
@@ -4,37 +4,31 @@
 # \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
 #  \\    /   O peration     |
 #   \\  /    A nd           | Copyright (C) 2011-2016 OpenFOAM Foundation
-#    \\/     M anipulation  | Copyright (C) 2017 OpenCFD Ltd.
+#    \\/     M anipulation  | Copyright (C) 2017-2018 OpenCFD Ltd.
 #-------------------------------------------------------------------------------
 # License
-#     This file is part of OpenFOAM.
-#
-#     OpenFOAM is free software: you can redistribute it and/or modify it
-#     under the terms of the GNU General Public License as published by
-#     the Free Software Foundation, either version 3 of the License, or
-#     (at your option) any later version.
-#
-#     OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
-#     ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
-#     FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
-#     for more details.
-#
-#     You should have received a copy of the GNU General Public License
-#     along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
+#     This file is part of OpenFOAM, licensed under GNU General Public License
+#     <http://www.gnu.org/licenses/>.
 #
 # Script
 #     foamEtcFile
 #
 # Description
-#     Locate user/group/other files with semantics similar to the
-#     ~OpenFOAM/fileName expansion.
+#     Locate user/group/other file as per '#includeEtc'.
+#
+#     The -mode option can be used to allow chaining from personal settings
+#     to site-wide settings.
 #
-#     The -mode option can be used to allow chaining from
-#     personal settings to site-wide settings.
+#     For example, within the user ~/.OpenFOAM/<VER>/config.sh/compiler:
+#     \code
+#        eval $(foamEtcFile -sh -mode=go config.sh/compiler)
+#     \endcode
 #
-#     For example, within the user ~/.OpenFOAM/<VER>/prefs.sh:
+#     The -mode option is similarly used within etc/{bashrc,cshrc} to ensure
+#     that system prefs are respected:
 #     \code
-#        eval $(foamEtcFile -sh -mode=go prefs.sh)
+#        eval $(foamEtcFile -sh -mode=o  prefs.sh)
+#        eval $(foamEtcFile -sh -mode=ug prefs.sh)
 #     \endcode
 #
 # Environment
@@ -46,42 +40,40 @@
 #     This script must exist in one of these locations:
 #     - $WM_PROJECT_INST_DIR/OpenFOAM-<VERSION>/bin
 #     - $WM_PROJECT_INST_DIR/openfoam-<VERSION>/bin
-#     - $WM_PROJECT_INST_DIR/OpenFOAM+<VERSION>/bin
-#     - $WM_PROJECT_INST_DIR/openfoam+<VERSION>/bin
 #     - $WM_PROJECT_INST_DIR/openfoam<VERSION>/bin  (debian version)
 #
 #-------------------------------------------------------------------------------
-unset optQuiet optSilent
-usage() {
-    [ "${optQuiet:-$optSilent}" = true ] && exit 1
-    exec 1>&2
-    while [ "$#" -ge 1 ]; do echo "$1"; shift; done
+printHelp() {
     cat<<USAGE
 
-Usage: foamEtcFile [OPTION] fileName
+Usage: foamEtcFile [OPTION] fileName [-- args]
        foamEtcFile [OPTION] [-list|-list-test] [fileName]
 
 options:
-  -a, -all          Return all files (otherwise stop after the first match)
-  -l, -list         List directories or files to be checked
+  -all (-a)         Return all files (otherwise stop after the first match)
+  -list (-l)        List directories or files to be checked
   -list-test        List (existing) directories or files to be checked
   -mode=MODE        Any combination of u(user), g(group), o(other)
   -prefix=DIR       Specify an alternative installation prefix
   -version=VER      Specify alternative OpenFOAM version (eg, 3.0, 1612, ...)
-  -csh | -sh        Produce output suitable for a csh or sh 'eval'
-  -csh-verbose | -sh-verbose
-                    As per -csh | -sh, with additional verbosity
-  -q, -quiet        Suppress all normal output
-  -s, -silent       Suppress stderr, except -csh-verbose, -sh-verbose output
+  -csh              Produce 'source FILE' output for a csh eval
+  -sh               Produce '. FILE' output for a sh eval
+  -csh-verbose      As per -csh, with additional verbosity
+  -sh-verbose       As per -sh,  with additional verbosity
+  -config           Add config directory prefix for shell type:
+                        with -csh* for a config.csh/ prefix
+                        with -sh*  for a config.sh/ prefix
+  -quiet (-q)       Suppress all normal output
+  -silent (-s)      Suppress stderr, except -csh-verbose, -sh-verbose output
   -help             Print the usage
 
-Locate user/group/other file with semantics similar to the
-~OpenFOAM/fileName expansion.
+Locate user/group/other file as per '#includeEtc'
 
-Single character options must not be grouped. Equivalent options:
-    -mode=MODE,   -mode MODE,   -m MODE
-    -prefix=DIR,  -prefix DIR,  -p DIR
-    -version=VER, -version VER, -v VER
+Do not group single character options.
+Equivalent options:
+  |  -mode=MODE     |  -mode MODE     | -m MODE
+  |  -prefix=DIR    |  -prefix DIR    | -p DIR
+  |  -version=VER   |  -version VER   | -v VER
 
 Exit status
     0  when the file is found. Print resolved path to stdout.
@@ -89,9 +81,10 @@ Exit status
     2  when the file is not found.
 
 USAGE
-    exit 1
+    exit 0  # A clean exit
 }
 
+unset optQuiet optSilent
 # Report error and exit
 die()
 {
@@ -146,13 +139,6 @@ guessVersion()
         version="${version%%*-}" # Extra safety, eg openfoam-version-packager
         ;;
 
-    (OpenFOAM+* | openfoam+*)
-        # Alternative naming: OpenFOAM+<VERSION> or openfoam+<VERSION>
-        dirBase="${projectDirName%%+*}+"
-        version="${projectDirName#*+}"
-        version="${version%%*-}" # Extra safety, eg openfoam-version-packager
-        ;;
-
     (openfoam[0-9]*)
         # Debian naming: openfoam<VERSION>
         dirBase="openfoam"
@@ -199,30 +185,36 @@ setVersion()
 
 
 optMode=ugo         # Default mode is always 'ugo'
-unset optAll optList optShell optVersion
+unset shellOutput verboseOutput
+unset optAll optConfig optList optVersion
 
 # Parse options
 while [ "$#" -gt 0 ]
 do
     case "$1" in
-    -h | -help)
-        usage
+    -h | -help*)
+        printHelp
         ;;
     -a | -all)
         optAll=true
-        unset optShell
+        unset shellOutput verboseOutput
         ;;
     -l | -list)
         optList=true
-        unset optShell
         ;;
     -list-test)
         optList='test'
-        unset optShell
         ;;
-    -csh | -sh | -csh-verbose | -sh-verbose)
-        optShell="${1#-}"
-        unset optAll
+    -csh | -sh)
+        shellOutput="${1#-}"
+        unset verboseOutput
+        ;;
+    -csh-verbose | -sh-verbose)
+        shellOutput="${1#-}"
+        verboseOutput="source "         # Report: "source FILE"
+        ;;
+    -config)
+        optConfig=true
         ;;
     -mode=[ugo]*)
         optMode="${1#*=}"
@@ -276,9 +268,33 @@ do
     shift
 done
 
-
 #-------------------------------------------------------------------------------
 
+# Split arguments into filename (for searching) and trailing bits for shell eval
+# Silently remove leading ~OpenFOAM/ (as per Foam::findEtcFile)
+nArgs=$#
+fileName="${1#~OpenFOAM/}"
+unset evalArgs
+
+if [ "$nArgs" -eq 1 ]
+then
+    if [ "$1" = "--" ]
+    then
+        nArgs=0
+        unset fileName
+    fi
+elif [ "$nArgs" -ge 2 ]
+then
+    if [ "$2" = "--" ]
+    then
+        nArgs=1
+        shift 2
+        evalArgs="$@"
+    fi
+fi
+
+
+# Get version information
 if [ -n "$optVersion" ]
 then
     setVersion $optVersion
@@ -301,12 +317,6 @@ groupDir="${WM_PROJECT_SITE:-$prefixDir/site}"
 #     eval echo "$i=\$$i" 1>&2
 # done
 
-
-# Save the essential bits of information
-# silently remove leading ~OpenFOAM/ (used in Foam::findEtcFile)
-nArgs=$#
-fileName="${1#~OpenFOAM/}"
-
 # Define the various places to be searched:
 unset dirList
 case "$optMode" in (*u*) # (U)ser
@@ -325,27 +335,61 @@ case "$optMode" in (*o*) # (O)ther == shipped
 esac
 set -- $dirList
 
+[ "$#" -ge 1 ] || die "No directories to scan. Programming error?"
+exitCode=2  # Fallback is a FileNotFound error
+
+
+#
+# Preliminaries
+#
+
+# Special handling of config.sh/ , config.csh/ directories
+if [ -n "$optConfig" -a -n "$shellOutput" -a -n "$fileName" ]
+then
+    case "$shellOutput" in
+    csh*)
+        optConfig="config.csh/"
+        ;;
+    sh*)
+        optConfig="config.sh/"
+        ;;
+    *)
+        unset optConfig
+        ;;
+    esac
+
+    if [ -n "$optConfig" ]
+    then
+        case "$fileName" in
+        /* | config.csh* | config.sh*)
+            # Does not need or cannot add a prefix
+            unset optConfig
+            ;;
+        *)
+            fileName="$optConfig$fileName"
+            ;;
+        esac
+    fi
+fi
+
 
 #
 # The main routine
 #
 
-exitCode=0
 if [ -n "$optList" ]
 then
 
     # List directories, or potential file locations
     [ "$nArgs" -le 1 ] || \
-    die "-list expects 0 or 1 filename, but $nArgs provided"
+        die "-list options expect 0 or 1 filename, but $nArgs provided"
 
-    # A silly combination, but -quiet does have precedence
+    # A silly combination, but -quiet has absolute precedence
     [ -n "$optQuiet" ] && exit 0
 
     # Test for directory or file too?
     if [ "$optList" = "test" ]
     then
-        exitCode=2  # Fallback to a general error (file not found)
-
         if [ "$nArgs" -eq 1 ]
         then
             for dir
@@ -368,6 +412,7 @@ then
             done
         fi
     else
+        exitCode=0  # OK, already verified that $# != 0
         for dir
         do
             echo "$dir${fileName:+/}$fileName"
@@ -378,35 +423,44 @@ else
 
     [ "$nArgs" -eq 1 ] || die "One filename expected - $nArgs provided"
 
-    exitCode=2  # Fallback to a general error (file not found)
+    # Output for sourcing files ("source" for csh, "." for POSIX shell)
+    # Only allow sourcing a single file (disallow combination with -all)
+    case "$shellOutput" in
+    csh*)
+        shellOutput="source "   # eg, "source FILE"
+        ;;
+    sh*)
+        shellOutput=". "        # eg, ". FILE"
+        ;;
+    esac
+
+    # Anti-pattern: -all disables shell commands
+    if [ -n "$optAll" ]
+    then
+        unset shellOutput verboseOutput
+    fi
 
     for dir
     do
-        if [ -f "$dir/$fileName" ]
+        resolved="$dir/$fileName"
+        if [ -f "$resolved" ]
         then
-            exitCode=0
-            [ -n "$optQuiet" ] && break
-
-            case "$optShell" in
-            (*verbose)
-                echo "Using: $dir/$fileName" 1>&2
-                ;;
-            esac
-
-            case "$optShell" in
-            csh*)
-                echo "source $dir/$fileName"
-                break
-                ;;
-            sh*)
-                echo ". $dir/$fileName"
+            exitCode=0  # OK
+            if [ -n "$optQuiet" ]
+            then
                 break
-                ;;
-            *)
-                echo "$dir/$fileName"
-                [ -n "$optAll" ] || break
-                ;;
-            esac
+            elif [ -n "$verboseOutput" ]
+            then
+                echo "$verboseOutput$resolved" 1>&2
+            fi
+
+            if [ -n "$shellOutput" ]
+            then
+                echo "$shellOutput$resolved $evalArgs"
+            else
+                echo "$resolved"
+            fi
+            [ -n "$optAll" ] || break
         fi
     done
 
diff --git a/var/spack/repos/builtin/packages/openfoam-org/package.py b/var/spack/repos/builtin/packages/openfoam-org/package.py
index c176adcbe5..8857257878 100644
--- a/var/spack/repos/builtin/packages/openfoam-org/package.py
+++ b/var/spack/repos/builtin/packages/openfoam-org/package.py
@@ -1,28 +1,8 @@
-##############################################################################
-# Copyright (c) 2017 Mark Olesen, OpenCFD Ltd.
-#
-# This file was authored by Mark Olesen <mark.olesen@esi-group.com>
-# and is released as part of spack under the LGPL license.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for the LLNL notice and LGPL.
-#
-# License
-# -------
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 # Legal Notice
 # ------------
 # OPENFOAM is a trademark owned by OpenCFD Ltd
@@ -55,7 +35,6 @@
 ##############################################################################
 import glob
 import re
-import shutil
 import os
 
 import llnl.util.tty as tty
@@ -80,10 +59,15 @@ class OpenfoamOrg(Package):
     homepage = "http://www.openfoam.org/"
     baseurl  = "https://github.com/OpenFOAM"
     url      = "https://github.com/OpenFOAM/OpenFOAM-4.x/archive/version-4.1.tar.gz"
+    git      = "https://github.com/OpenFOAM/OpenFOAM-dev.git"
 
-    version('4.1', '318a446c4ae6366c7296b61184acd37c',
+    version('develop', branch='master')
+    version('5.0', 'cd8c5bdd3ff39c34f61747c8e55f59d1',
+            url=baseurl + '/OpenFOAM-5.x/archive/version-5.0.tar.gz')
+    version('4.1', 'afd7d8e66e7db0ffaf519b14f1a8e1d4',
             url=baseurl + '/OpenFOAM-4.x/archive/version-4.1.tar.gz')
-    version('develop', git='https://github.com/OpenFOAM/OpenFOAM-dev.git')
+    version('2.4.0', 'ad7d8b7b0753655b2b6fd9e92eefa92a',
+            url=baseurl + '/OpenFOAM-2.4.x/archive/version-2.4.0.tar.gz')
 
     variant('int64', default=False,
             description='Compile with 64-bit label')
@@ -107,15 +91,10 @@ class OpenfoamOrg(Package):
     assets = ['bin/foamEtcFile']
 
     # Version-specific patches
+    patch('50-etc.patch', when='@5.0:')
     patch('41-etc.patch', when='@4.1')
-    patch('41-site.patch', when='@4.1')
-
-    # Some user config settings
-    config = {
-        'mplib': 'SYSTEMMPI',   # Use system mpi for spack
-        # Add links into bin/, lib/ (eg, for other applications)
-        'link': False
-    }
+    patch('41-site.patch', when='@4.1:')
+    patch('240-etc.patch', when='@2.4.0')
 
     # The openfoam architecture, compiler information etc
     _foam_arch = None
@@ -133,14 +112,34 @@ class OpenfoamOrg(Package):
     # - End of definitions / setup -
     #
 
+    # Some user config settings
+    @property
+    def config(self):
+        settings = {
+            # Use system mpi for spack
+            'mplib': 'SYSTEMMPI',
+
+            # Add links into bin/, lib/ (eg, for other applications)
+            'link': False,
+        }
+        # OpenFOAM v2.4 and earlier lacks WM_LABEL_OPTION
+        if self.spec.satisfies('@:2.4'):
+            settings['label-size'] = False
+        return settings
+
     def setup_environment(self, spack_env, run_env):
+        # This should be similar to the openfoam-com package,
+        # but sourcing the etc/bashrc here seems to exit with an error.
+        # ... this needs to be examined in more detail.
+        #
+        # Minimal environment only.
         run_env.set('FOAM_PROJECT_DIR', self.projectdir)
         run_env.set('WM_PROJECT_DIR', self.projectdir)
         for d in ['wmake', self.archbin]:  # bin already added automatically
             run_env.prepend_path('PATH', join_path(self.projectdir, d))
 
     def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
-        """Provide location of the OpenFOAM project.
+        """Location of the OpenFOAM project directory.
         This is identical to the WM_PROJECT_DIR value, but we avoid that
         variable since it would mask the normal OpenFOAM cleanup of
         previous versions.
@@ -199,8 +198,8 @@ class OpenfoamOrg(Package):
         edits = {
             'WM_THIRD_PARTY_DIR':
             r'$WM_PROJECT_DIR/ThirdParty #SPACK: No separate third-party',
-            'WM_VERSION': self.version,    # consistency
-            'FOAMY_HEX_MESH': '',          # This is horrible (unset variable?)
+            'WM_VERSION': str(self.version),  # consistency
+            'FOAMY_HEX_MESH': '',  # This is horrible (unset variable?)
         }
         rewrite_environ_files(  # Adjust etc/bashrc and etc/cshrc
             edits,
@@ -258,10 +257,18 @@ class OpenfoamOrg(Package):
 
         # Adjust components to use SPACK variants
         for component, subdict in self.etc_config.items():
-            write_environ(
-                subdict,
-                posix=join_path('etc', 'config.sh',  component),
-                cshell=join_path('etc', 'config.csh', component))
+            # Versions up to 3.0 used an etc/config/component.sh naming
+            # convention instead of etc/config.sh/component
+            if spec.satisfies('@:3.0'):
+                write_environ(
+                    subdict,
+                    posix=join_path('etc', 'config',  component) + '.sh',
+                    cshell=join_path('etc', 'config', component) + '.csh')
+            else:
+                write_environ(
+                    subdict,
+                    posix=join_path('etc', 'config.sh',  component),
+                    cshell=join_path('etc', 'config.csh', component))
 
     def build(self, spec, prefix):
         """Build using the OpenFOAM Allwmake script, with a wrapper to source
@@ -317,12 +324,13 @@ class OpenfoamOrg(Package):
             dirs.extend(['doc'])
 
         # Install platforms (and doc) skipping intermediate targets
-        ignored = ['src', 'applications', 'html', 'Guides']
+        relative_ignore_paths = ['src', 'applications', 'html', 'Guides']
+        ignore = lambda p: p in relative_ignore_paths
         for d in dirs:
             install_tree(
                 d,
                 join_path(self.projectdir, d),
-                ignore=shutil.ignore_patterns(*ignored),
+                ignore=ignore,
                 symlinks=True)
 
         etc_dir = join_path(self.projectdir, 'etc')
diff --git a/var/spack/repos/builtin/packages/openfst/package.py b/var/spack/repos/builtin/packages/openfst/package.py
index 29b5eca02d..4187ddd258 100644
--- a/var/spack/repos/builtin/packages/openfst/package.py
+++ b/var/spack/repos/builtin/packages/openfst/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -50,7 +31,18 @@ class Openfst(AutotoolsPackage):
     conflicts('%intel@16:')
     conflicts('%gcc@6:')
 
+    variant('far', default=False, description="Enable FAR support")
+
     # Patch openfst-1.4.1 for kaldi@c024e8
     # See https://github.com/kaldi-asr/kaldi/blob/c024e8aa0a727bf76c91a318f76a1f8b0b59249e/tools/Makefile#L82-L88
     patch('openfst-1.4.1.patch', when='@1.4.1-patch')
     patch('openfst_gcc41up.patch', when='@1.4.1-patch')
+
+    def configure_args(self):
+        args = []
+        spec = self.spec
+        if '+far' in spec:
+            args.append('--enable-far')
+        else:
+            args.append('--disable-far')
+        return args
diff --git a/var/spack/repos/builtin/packages/opengl/package.py b/var/spack/repos/builtin/packages/opengl/package.py
new file mode 100644
index 0000000000..577e22dbf1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/opengl/package.py
@@ -0,0 +1,70 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Opengl(Package):
+    """Placeholder for external OpenGL libraries from hardware vendors"""
+
+    homepage = "https://www.opengl.org/"
+
+    provides('gl@:4.5', when='@4.5:')
+    provides('gl@:4.4', when='@4.4:')
+    provides('gl@:4.3', when='@4.3:')
+    provides('gl@:4.2', when='@4.2:')
+    provides('gl@:4.1', when='@4.1:')
+    provides('gl@:3.3', when='@3.3:')
+
+    # Override the fetcher method to throw a useful error message;
+    # fixes GitHub issue (#7061) in which this package threw a
+    # generic, uninformative error during the `fetch` step,
+    @property
+    def fetcher(self):
+        msg = """This package is intended to be a placeholder for
+        system-provided OpenGL libraries from hardware vendors.  Please
+        download and install OpenGL drivers/libraries for your graphics
+        hardware separately, and then set that up as an external package.
+        An example of a working packages.yaml:
+
+        packages:
+          opengl:
+            paths:
+              opengl@4.5.0: /opt/opengl
+            buildable: False
+
+        In that case, /opt/opengl/ should contain these two folders:
+
+        include/GL/       (opengl headers, including "gl.h")
+        lib               (opengl libraries, including "libGL.so")
+
+        On Apple Darwin (e.g., OS X, macOS) systems, this package is
+        normally installed as part of the XCode Command Line Tools in
+        /usr/X11R6, so a working packages.yaml would be
+
+        packages:
+          opengl:
+            paths:
+              opengl@4.1: /usr/X11R6
+            buildable: False
+
+        In that case, /usr/X11R6 should contain
+
+        include/GL/      (OpenGL headers, including "gl.h")
+        lib              (OpenGL libraries, including "libGL.dylib")
+
+        On OS X/macOS, note that the version of OpenGL provided
+        depends on your hardware. Look at
+        https://support.apple.com/en-us/HT202823 to see what version
+        of OpenGL your Mac uses."""
+        raise InstallError(msg)
+
+    @property
+    def libs(self):
+        for dir in ['lib64', 'lib']:
+            libs = find_libraries('libGL', join_path(self.prefix, dir),
+                                  shared=True, recursive=False)
+            if libs:
+                return libs
diff --git a/var/spack/repos/builtin/packages/openglu/package.py b/var/spack/repos/builtin/packages/openglu/package.py
new file mode 100644
index 0000000000..c6468c95b4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/openglu/package.py
@@ -0,0 +1,66 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Openglu(Package):
+    """Placeholder for external OpenGL utility library (GLU) from hardware
+       vendors"""
+
+    homepage = "https://www.opengl.org/resources/libraries"
+
+    provides('glu@:1.3', when='@1.3:')
+    provides('glu@:1.2', when='@1.2:')
+    provides('glu@:1.1', when='@1.1:')
+    provides('glu@:1.0', when='@1.0:')
+
+    # Override the fetcher method to throw a useful error message;
+    # fixes an issue similar to Github issue (#7061), in which the
+    # opengl package threw a generic, uninformative error message
+    # during the `fetch` step
+    @property
+    def fetcher(self):
+        msg = """This package is intended to be a placeholder for
+        system-provided OpenGL utility (GLU) libraries from hardware vendors.
+        Please download and install the GLU drivers/libraries for your
+        graphics hardware separately, and then set that up as an external
+        package.  An example of a working packages.yaml:
+
+        packages:
+          openglu:
+            paths:
+              openglu@1.3: /opt/opengl
+            buildable: False
+
+        In that case, /opt/opengl/ should contain these two folders:
+
+        include/GL/       (opengl headers, including "glu.h")
+        lib               (opengl libraries, including "libGLU.so")
+
+        On Apple Darwin (OS X, macOS) systems, this package is
+        normally installed as part of the XCode Command Line Tools in
+        /usr/X11R6, so a working packages.yaml would be
+
+        packages:
+          openglu:
+            paths:
+              openglu@1.3: /usr/X11R6
+            buildable: False
+
+        In that case, /usr/X11R6 should contain
+
+        include/GL       (GLU headers, including "glu.h")
+        lib              (GLU libraries, including "libGLU.dylib")"""
+
+        raise InstallError(msg)
+
+    @property
+    def libs(self):
+        for dir in ['lib64', 'lib']:
+            libs = find_libraries('libGLU', join_path(self.prefix, dir),
+                                  shared=True, recursive=False)
+            if libs:
+                return libs
diff --git a/var/spack/repos/builtin/packages/openjpeg/macos.patch b/var/spack/repos/builtin/packages/openjpeg/macos.patch
new file mode 100644
index 0000000000..f736b92b47
--- /dev/null
+++ b/var/spack/repos/builtin/packages/openjpeg/macos.patch
@@ -0,0 +1,13 @@
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -151,6 +151,10 @@ IF(NOT OPENJPEG_INSTALL_PACKAGE_DIR)
+   SET(OPENJPEG_INSTALL_PACKAGE_DIR "${OPENJPEG_INSTALL_LIB_DIR}/${OPENJPEG_INSTALL_SUBDIR}")
+ ENDIF(NOT OPENJPEG_INSTALL_PACKAGE_DIR)
+ 
++IF(APPLE)
++    LIST(APPEND OPENJPEG_LIBRARY_PROPERTIES INSTALL_NAME_DIR "${CMAKE_INSTALL_PREFIX}/${OPENJPEG_INSTALL_LIB_DIR}")
++ENDIF()
++
+ #-----------------------------------------------------------------------------
+ # Big endian test:
+ INCLUDE (${CMAKE_ROOT}/Modules/TestBigEndian.cmake)
diff --git a/var/spack/repos/builtin/packages/openjpeg/package.py b/var/spack/repos/builtin/packages/openjpeg/package.py
index 1998885502..34b300371b 100644
--- a/var/spack/repos/builtin/packages/openjpeg/package.py
+++ b/var/spack/repos/builtin/packages/openjpeg/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,11 +16,35 @@ class Openjpeg(CMakePackage):
     ITU-T as a JPEG 2000 Reference Software.
     """
 
-    homepage = "https://github.com/uclouvain/openjpeg"
-    url = "https://github.com/uclouvain/openjpeg/archive/version.2.1.tar.gz"
+    homepage = 'https://github.com/uclouvain/openjpeg'
+    url = 'https://github.com/uclouvain/openjpeg/archive/v2.3.0.tar.gz'
+    list_url = 'https://github.com/uclouvain/openjpeg/releases'
 
-    version('2.1',   '3e1c451c087f8462955426da38aa3b3d')
+    version('2.3.0', '6a1f8aaa1fe55d2088e3a9c942e0f698')
+    version('2.2.0', '269bb0b175476f3addcc0d03bd9a97b6')
+    version('2.1.2', '40a7bfdcc66280b3c1402a0eb1a27624')
+    version('2.1.1', '0cc4b2aee0a9b6e9e21b7abcd201a3ec')
+    version('2.1.0', '3e1c451c087f8462955426da38aa3b3d')
     version('2.0.1', '105876ed43ff7dbb2f90b41b5a43cfa5')
-    version('2.0',   'cdf266530fee8af87454f15feb619609')
+    version('2.0.0', 'cdf266530fee8af87454f15feb619609')
     version('1.5.2', '545f98923430369a6b046ef3632ef95c')
     version('1.5.1', 'd774e4b5a0db5f0f171c4fc0aabfa14e')
+
+    # The problem with install name of the library on MacOs was fixed starting
+    # version 2.1.1: https://github.com/uclouvain/openjpeg/commit/b9a247b559e62e55f5561624cf4a19aee3c8afdc
+    # The solution works for the older versions (at least starting 1.5.1) too.
+    patch('macos.patch', when='@:2.1.0 platform=darwin')
+
+    def url_for_version(self, version):
+        if version >= Version('2.1.1'):
+            return super(Openjpeg, self).url_for_version(version)
+
+        # Before version 2.2.0, release tarballs of the versions like x.y.0
+        # did not have the ".0" in their names:
+        if version[2] == 0:
+            version = version.up_to(2)
+
+        url_fmt = \
+            'https://github.com/uclouvain/openjpeg/archive/version.{0}.tar.gz'
+
+        return url_fmt.format(version)
diff --git a/var/spack/repos/builtin/packages/openmc/package.py b/var/spack/repos/builtin/packages/openmc/package.py
index b48928c02c..8d3175c029 100644
--- a/var/spack/repos/builtin/packages/openmc/package.py
+++ b/var/spack/repos/builtin/packages/openmc/package.py
@@ -1,91 +1,29 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
 
-class Openmc(MakefilePackage):
+class Openmc(CMakePackage):
     """The OpenMC project aims to provide a fully-featured Monte Carlo particle
        transport code based on modern methods. It is a constructive solid
        geometry, continuous-energy transport code that uses ACE format cross
        sections. The project started under the Computational Reactor Physics
        Group at MIT."""
 
-    homepage = "https://github.com/ANL-CESAR/"
-    url = "https://github.com/ANL-CESAR/openmc.git"
-
-    tags = ['proxy-app']
-
-    version('develop', git='https://github.com/ANL-CESAR/openmc.git')
-
-    build_directory = 'src'
-
-    parallel = False
-
-    @property
-    def build_targets(self):
-
-        targets = []
+    homepage = "http://openmc.readthedocs.io/"
+    url = "https://github.com/openmc-dev/openmc/tarball/v0.10.0"
+    git = "https://github.com/openmc-dev/openmc.git"
 
-        if self.compiler.name == 'gcc':
-            targets.append('COMPILER=gnu')
-            targets.append('MACHINE=UNKNOWN')
-        if self.compiler.name == 'intel':
-            targets.append('COMPILER=intel')
-        if self.compiler.name == 'pgi':
-            targets.append('COMPILER=pgi')
-        if self.compiler.name == 'xl':
-            targets.append('COMPILER=ibm')
-        if self.compiler.name == 'cce':
-            targets.append('COMPILER=cray')
+    version('0.10.0', 'abb57bd1b226eb96909dafeec31369b0')
+    version('develop')
 
-        return targets
+    depends_on("hdf5+hl")
 
-    def install(self, spec, prefix):
-        with working_dir('src'):
-            pth_st_cmp = join_path(prefix.bin, 'statepoint_cmp')
-            pth_st_histogram = join_path(prefix.bin, 'statepoint_histogram')
-            pth_st_meshpoint = join_path(prefix.bin, 'statepoint_meshpoint')
-            pth_openmc = join_path(prefix, 'share/man/man1/openmc.1')
-            pth_copyright = join_path(prefix, 'share/doc/openmc/copyright')
-            mkdir(prefix.bin)
-            mkdirp(pth_st_cmp)
-            mkdirp(pth_st_histogram)
-            mkdirp(pth_st_meshpoint)
-            mkdirp(pth_openmc)
-            mkdirp(pth_copyright)
+    def cmake_args(self):
+        options = ['-DHDF5_ROOT:PATH=%s' % self.spec['hdf5'].prefix]
 
-            install('openmc', prefix.bin)
-            install('utils/statepoint_cmp.py', pth_st_cmp)
-            install('utils/statepoint_histogram.py',
-                    pth_st_histogram)
-            install('utils/statepoint_meshplot.py',
-                    pth_st_meshpoint)
-        install('man/man1/openmc.1', pth_openmc)
-        install('LICENSE', pth_copyright)
-        install_tree('docs/', prefix.docs)
-        install_tree('examples/', prefix.examples)
-        install_tree('data/', prefix.data)
-        install_tree('tests/', prefix.tests)
+        return options
diff --git a/var/spack/repos/builtin/packages/openmpi/btl_vader.patch b/var/spack/repos/builtin/packages/openmpi/btl_vader.patch
new file mode 100644
index 0000000000..005537d732
--- /dev/null
+++ b/var/spack/repos/builtin/packages/openmpi/btl_vader.patch
@@ -0,0 +1,24 @@
+diff --git a/opal/mca/btl/vader/btl_vader_fbox.h b/opal/mca/btl/vader/btl_vader_fbox.h
+index 17239ce8ef..ee5c913551 100644
+--- a/opal/mca/btl/vader/btl_vader_fbox.h
++++ b/opal/mca/btl/vader/btl_vader_fbox.h
+@@ -138,9 +138,6 @@ static inline bool mca_btl_vader_fbox_sendi (mca_btl_base_endpoint_t *ep, unsign
+         memcpy (data + header_size, payload, payload_size);
+     }
+ 
+-    /* write out part of the header now. the tag will be written when the data is available */
+-    mca_btl_vader_fbox_set_header (MCA_BTL_VADER_FBOX_HDR(dst), tag, ep->fbox_out.seq++, data_size);
+-
+     end += size;
+ 
+     if (OPAL_UNLIKELY(fbox_size == end)) {
+@@ -152,6 +149,9 @@ static inline bool mca_btl_vader_fbox_sendi (mca_btl_base_endpoint_t *ep, unsign
+         MCA_BTL_VADER_FBOX_HDR(ep->fbox_out.buffer + end)->ival = 0;
+     }
+ 
++    /* write out part of the header now. the tag will be written when the data is available */
++    mca_btl_vader_fbox_set_header (MCA_BTL_VADER_FBOX_HDR(dst), tag, ep->fbox_out.seq++, data_size);
++
+     /* align the buffer */
+     ep->fbox_out.end = ((uint32_t) hbs << 31) | end;
+     opal_atomic_wmb ();
diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py
index 5563198649..40ac79a2e8 100644
--- a/var/spack/repos/builtin/packages/openmpi/package.py
+++ b/var/spack/repos/builtin/packages/openmpi/package.py
@@ -1,29 +1,11 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 import os
+import sys
 
 from spack import *
 
@@ -65,27 +47,39 @@ def _mxm_dir():
 
 
 class Openmpi(AutotoolsPackage):
-    """The Open MPI Project is an open source Message Passing Interface
-       implementation that is developed and maintained by a consortium
-       of academic, research, and industry partners. Open MPI is
-       therefore able to combine the expertise, technologies, and
-       resources from all across the High Performance Computing
-       community in order to build the best MPI library available.
-       Open MPI offers advantages for system and software vendors,
-       application developers and computer science researchers.
+    """An open source Message Passing Interface implementation.
+
+    The Open MPI Project is an open source Message Passing Interface
+    implementation that is developed and maintained by a consortium
+    of academic, research, and industry partners. Open MPI is
+    therefore able to combine the expertise, technologies, and
+    resources from all across the High Performance Computing
+    community in order to build the best MPI library available.
+    Open MPI offers advantages for system and software vendors,
+    application developers and computer science researchers.
     """
 
     homepage = "http://www.open-mpi.org"
-    url = "https://www.open-mpi.org/software/ompi/v3.0/downloads/openmpi-3.0.0.tar.bz2"
+    url = "https://www.open-mpi.org/software/ompi/v3.1/downloads/openmpi-3.1.2.tar.bz2"
     list_url = "http://www.open-mpi.org/software/ompi/"
 
     # Current
-    version('3.0.0', '757d51719efec08f9f1a7f32d58b3305')  # libmpi.so.40.00.0
+    version('3.1.3', sha256='8be04307c00f51401d3fb9d837321781ea7c79f2a5a4a2e5d4eaedc874087ab6')
+    version('3.1.2', '210df69fafd964158527e7f37e333239')  # libmpi.so.40.10.2
+    version('3.1.1', '493f1db2f75afaab1c8ecba78d2f5aab')  # libmpi.so.40.10.1
+    version('3.1.0', '0895e268ca27735d7654bf64cee6c256')  # libmpi.so.40.10.0
 
     # Still supported
+    version('3.0.2', '098fa89646f5b4438d9d8534bc960cd6')  # libmpi.so.40.00.2
+    version('3.0.1', '565f5060e080b0871a64b295c3d4426a')  # libmpi.so.40.00.1
+    version('3.0.0', '757d51719efec08f9f1a7f32d58b3305')  # libmpi.so.40.00.0
+    version('2.1.5', '6019c8b67d4975d833801e72ba290918')  # libmpi.so.20.10.3 
+    version('2.1.4', '003b356a24a5b7bd1705a23ddc69d9a0')  # libmpi.so.20.10.3
+    version('2.1.3', '46079b6f898a412240a0bf523e6cd24b')  # libmpi.so.20.10.2
     version('2.1.2', 'ff2e55cc529802e7b0738cf87acd3ee4')  # libmpi.so.20.10.2
     version('2.1.1', 'ae542f5cf013943ffbbeb93df883731b')  # libmpi.so.20.10.1
     version('2.1.0', '4838a5973115c44e14442c01d3f21d52')  # libmpi.so.20.10.0
+    version('2.0.4', '7e3c71563787a67dce9acc4d639ef3f8')  # libmpi.so.20.0.4
     version('2.0.3', '6c09e56ac2230c4f9abd8ba029f03edd')  # libmpi.so.20.0.3
     version('2.0.2', 'ecd99aa436a1ca69ce936a96d6a3fa48')  # libmpi.so.20.0.2
     version('2.0.1', '6f78155bd7203039d2448390f3b51c96')  # libmpi.so.20.0.1
@@ -173,11 +167,21 @@ class Openmpi(AutotoolsPackage):
     patch('configure.patch', when="@1.10.1")
     patch('fix_multidef_pmi_class.patch', when="@2.0.0:2.0.1")
 
+    # Vader Bug: https://github.com/open-mpi/ompi/issues/5375
+    # Haven't release fix for 2.1.x
+    patch('btl_vader.patch', when='@2.1.3:2.1.5')
+
+    # Fixed in 3.0.3 and 3.1.3
+    patch('btl_vader.patch', when='@3.0.1:3.0.2')
+    patch('btl_vader.patch', when='@3.1.0:3.1.2')
+
+    fabrics = ('psm', 'psm2', 'verbs', 'mxm', 'ucx', 'libfabric')
+
     variant(
         'fabrics',
         default=None if _verbs_dir() is None else 'verbs',
-        description='List of fabrics that are enabled',
-        values=('psm', 'psm2', 'pmi', 'verbs', 'mxm'),
+        description="List of fabrics that are enabled",
+        values=fabrics,
         multi=True
     )
 
@@ -195,27 +199,74 @@ class Openmpi(AutotoolsPackage):
     variant('thread_multiple', default=False,
             description='Enable MPI_THREAD_MULTIPLE support')
     variant('cuda', default=False, description='Enable CUDA support')
+    variant('pmi', default=False, description='Enable PMI support')
+    variant('cxx_exceptions', default=True, description='Enable C++ Exception support')
+    # Adding support to build a debug version of OpenMPI that activates
+    # Memchecker, as described here:
+    #
+    # https://www.open-mpi.org/faq/?category=debugging#memchecker_what
+    #
+    # This option degrades run-time support, and thus is disabled by default
+    variant(
+        'memchecker',
+        default=False,
+        description='Memchecker support for debugging [degrades performance]'
+    )
+
+    variant(
+        'legacylaunchers',
+        default=False,
+        description='Do not remove mpirun/mpiexec when building with slurm'
+    )
 
     provides('mpi')
     provides('mpi@:2.2', when='@1.6.5')
     provides('mpi@:3.0', when='@1.7.5:')
     provides('mpi@:3.1', when='@2.0.0:')
 
+    if sys.platform != 'darwin':
+        depends_on('numactl')
+
     depends_on('hwloc')
+    # ompi@:3.0.0 doesn't support newer hwloc releases:
+    # "configure: error: OMPI does not currently support hwloc v2 API"
+    # Future ompi releases may support it, needs to be verified.
+    # See #7483 for context.
+    depends_on('hwloc@:1.999')
+
     depends_on('hwloc +cuda', when='+cuda')
     depends_on('java', when='+java')
     depends_on('sqlite', when='+sqlite3@:1.11')
+    depends_on('zlib', when='@3.0.0:')
+    depends_on('valgrind~mpi', when='+memchecker')
+    depends_on('ucx', when='fabrics=ucx')
+    depends_on('libfabric', when='fabrics=libfabric')
+    depends_on('slurm', when='schedulers=slurm')
+    depends_on('binutils+libiberty', when='fabrics=mxm')
 
     conflicts('+cuda', when='@:1.6')  # CUDA support was added in 1.7
     conflicts('fabrics=psm2', when='@:1.8')  # PSM2 support was added in 1.10.0
-    conflicts('fabrics=pmi', when='@:1.5.4')  # PMI support was added in 1.5.5
     conflicts('fabrics=mxm', when='@:1.5.3')  # MXM support was added in 1.5.4
+    conflicts('+pmi', when='@:1.5.4')  # PMI support was added in 1.5.5
+    conflicts('schedulers=slurm ~pmi', when='@1.5.4:',
+              msg='+pmi is required for openmpi(>=1.5.5) to work with SLURM.')
+
+    filter_compiler_wrappers('openmpi/*-wrapper-data*', relative_root='share')
+    conflicts('fabrics=libfabric', when='@:1.8')  # libfabric support was added in 1.10.0
+    # It may be worth considering making libfabric an exclusive fabrics choice
 
     def url_for_version(self, version):
         url = "http://www.open-mpi.org/software/ompi/v{0}/downloads/openmpi-{1}.tar.bz2"
         return url.format(version.up_to(2), version)
 
     @property
+    def headers(self):
+        hdrs = HeaderList(find(self.prefix.include, 'mpi.h', recursive=False))
+        if not hdrs:
+            hdrs = HeaderList(find(self.prefix, 'mpi.h', recursive=True))
+        return hdrs or None
+
+    @property
     def libs(self):
         query_parameters = self.spec.last_query.extra_parameters
         libraries = ['libmpi']
@@ -224,7 +275,7 @@ class Openmpi(AutotoolsPackage):
             libraries = ['libmpi_cxx'] + libraries
 
         return find_libraries(
-            libraries, root=self.prefix, shared=True, recurse=True
+            libraries, root=self.prefix, shared=True, recursive=True
         )
 
     def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
@@ -290,16 +341,45 @@ class Openmpi(AutotoolsPackage):
         spec = self.spec
         config_args = [
             '--enable-shared',
-            '--enable-static'
         ]
-        if self.spec.satisfies('@2.0:'):
+
+        # Add extra_rpaths dirs from compilers.yaml into link wrapper
+        rpaths = [self.compiler.cc_rpath_arg + path
+                  for path in self.compiler.extra_rpaths]
+        config_args.extend([
+            '--with-wrapper-ldflags={0}'.format(' '.join(rpaths))
+        ])
+
+        # According to this comment on github:
+        #
+        # https://github.com/open-mpi/ompi/issues/4338#issuecomment-383982008
+        #
+        # adding --enable-static silently disables slurm support via pmi/pmi2
+        if spec.satisfies('schedulers=slurm'):
+            config_args.append('--with-pmi={0}'.format(spec['slurm'].prefix))
+        else:
+            config_args.append('--enable-static')
+            config_args.extend(self.with_or_without('pmi'))
+
+        if spec.satisfies('@2.0:'):
             # for Open-MPI 2.0:, C++ bindings are disabled by default.
             config_args.extend(['--enable-mpi-cxx'])
 
-        # Fabrics and schedulers
+        if spec.satisfies('@3.0.0:', strict=True):
+            config_args.append('--with-zlib={0}'.format(spec['zlib'].prefix))
+
+        # Fabrics
         config_args.extend(self.with_or_without('fabrics'))
+        # Schedulers
         config_args.extend(self.with_or_without('schedulers'))
 
+        config_args.extend(self.enable_or_disable('memchecker'))
+        if spec.satisfies('+memchecker', strict=True):
+            config_args.extend([
+                '--enable-debug',
+                '--with-valgrind={0}'.format(spec['valgrind'].prefix),
+            ])
+
         # Hwloc support
         if spec.satisfies('@1.5.2:'):
             config_args.append('--with-hwloc={0}'.format(spec['hwloc'].prefix))
@@ -310,7 +390,7 @@ class Openmpi(AutotoolsPackage):
                 config_args.extend([
                     '--enable-java',
                     '--enable-mpi-java',
-                    '--with-jdk-dir={0}'.format(spec['java'].prefix)
+                    '--with-jdk-dir={0}'.format(spec['java'].home)
                 ])
             else:
                 config_args.extend([
@@ -331,7 +411,7 @@ class Openmpi(AutotoolsPackage):
                 config_args.append('--enable-contrib-no-build=vt')
 
         # Multithreading support
-        if spec.satisfies('@1.5.4:'):
+        if spec.satisfies('@1.5.4:2.999'):
             if '+thread_multiple' in spec:
                 config_args.append('--enable-mpi-thread-multiple')
             else:
@@ -364,45 +444,23 @@ class Openmpi(AutotoolsPackage):
             else:
                 config_args.append('--without-cuda')
 
+        if '+cxx_exceptions' in spec:
+            config_args.append('--enable-cxx-exceptions')
+        else:
+            config_args.append('--disable-cxx-exceptions')
         return config_args
 
     @run_after('install')
-    def filter_compilers(self):
-        """Run after install to make the MPI compilers use the
-        compilers that Spack built the package with.
-
-        If this isn't done, they'll have CC, CXX and FC set
-        to Spack's generic cc, c++ and f90.  We want them to
-        be bound to whatever compiler they were built with.
-        """
-        kwargs = {'ignore_absent': True, 'backup': False, 'string': False}
-        wrapper_basepath = join_path(self.prefix, 'share', 'openmpi')
-
-        wrappers = [
-            ('mpicc-vt-wrapper-data.txt', self.compiler.cc),
-            ('mpicc-wrapper-data.txt', self.compiler.cc),
-            ('ortecc-wrapper-data.txt', self.compiler.cc),
-            ('shmemcc-wrapper-data.txt', self.compiler.cc),
-            ('mpic++-vt-wrapper-data.txt', self.compiler.cxx),
-            ('mpic++-wrapper-data.txt', self.compiler.cxx),
-            ('ortec++-wrapper-data.txt', self.compiler.cxx),
-            ('mpifort-vt-wrapper-data.txt', self.compiler.fc),
-            ('mpifort-wrapper-data.txt', self.compiler.fc),
-            ('shmemfort-wrapper-data.txt', self.compiler.fc),
-            ('mpif90-vt-wrapper-data.txt', self.compiler.fc),
-            ('mpif90-wrapper-data.txt', self.compiler.fc),
-            ('mpif77-vt-wrapper-data.txt',  self.compiler.f77),
-            ('mpif77-wrapper-data.txt',  self.compiler.f77)
-        ]
-
-        for wrapper_name, compiler in wrappers:
-            wrapper = join_path(wrapper_basepath, wrapper_name)
-            if not os.path.islink(wrapper):
-                # Substitute Spack compile wrappers for the real
-                # underlying compiler
-                match = 'compiler=.*'
-                substitute = 'compiler={compiler}'.format(compiler=compiler)
-                filter_file(match, substitute, wrapper, **kwargs)
-                # Remove this linking flag if present
-                # (it turns RPATH into RUNPATH)
-                filter_file('-Wl,--enable-new-dtags', '', wrapper, **kwargs)
+    def delete_mpirun_mpiexec(self):
+        # The preferred way to run an application when Slurm is the
+        # scheduler is to let Slurm manage process spawning via PMI.
+        #
+        # Deleting the links to orterun avoids users running their
+        # applications via mpirun or mpiexec, and leaves srun as the
+        # only sensible choice (orterun is still present, but normal
+        # users don't know about that).
+        if '@1.6: ~legacylaunchers schedulers=slurm' in self.spec:
+            os.remove(self.prefix.bin.mpirun)
+            os.remove(self.prefix.bin.mpiexec)
+            os.remove(self.prefix.bin.shmemrun)
+            os.remove(self.prefix.bin.oshrun)
diff --git a/var/spack/repos/builtin/packages/opennurbs/package.py b/var/spack/repos/builtin/packages/opennurbs/package.py
new file mode 100644
index 0000000000..388633f841
--- /dev/null
+++ b/var/spack/repos/builtin/packages/opennurbs/package.py
@@ -0,0 +1,54 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import glob
+
+
+class Opennurbs(Package):
+    """OpenNURBS is an open-source NURBS-based geometric modeling library
+    and toolset, with meshing and display / output functions.
+    """
+
+    homepage = "https://github.com/OpenNURBS/OpenNURBS"
+    git      = "https://github.com/OpenNURBS/OpenNURBS.git"
+
+    maintainers = ['jrood-nrel']
+
+    version('develop', branch='develop')
+
+    version('percept', '59163fd085a24c7a4c2170c70bb60fea',
+            url='https://github.com/PerceptTools/percept/raw/master/build-cmake/opennurbs-percept.tar.gz')
+
+    variant('shared', default=True,
+            description="Build shared libraries")
+
+    # CMake installation method
+    def install(self, spec, prefix):
+        cmake_args = [
+            '-DBUILD_SHARED_LIBS:BOOL=%s' % (
+                'ON' if '+shared' in spec else 'OFF')
+        ]
+
+        cmake_args.extend(std_cmake_args)
+
+        with working_dir('spack-build', create=True):
+            cmake('..', *cmake_args)
+            make()
+            make('install')
+
+    # Pre-cmake installation method
+    @when('@percept')
+    def install(self, spec, prefix):
+        make(parallel=False)
+
+        # Install manually
+        mkdir(prefix.lib)
+        mkdir(prefix.include)
+        install('libopenNURBS.a', prefix.lib)
+        install_tree('zlib', join_path(prefix.include, 'zlib'))
+        headers = glob.glob(join_path('.', '*.h'))
+        for h in headers:
+            install(h, prefix.include)
diff --git a/var/spack/repos/builtin/packages/openpmd-api/package.py b/var/spack/repos/builtin/packages/openpmd-api/package.py
new file mode 100644
index 0000000000..93082d3b85
--- /dev/null
+++ b/var/spack/repos/builtin/packages/openpmd-api/package.py
@@ -0,0 +1,85 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class OpenpmdApi(CMakePackage):
+    """API for easy reading and writing of openPMD files"""
+
+    homepage = "http://www.openPMD.org"
+    git      = "https://github.com/openPMD/openPMD-api.git"
+
+    maintainers = ['ax3l']
+
+    version('develop', branch='dev')
+
+    variant('mpi', default=True,
+            description='Enable parallel I/O')
+    variant('hdf5', default=True,
+            description='Enable HDF5 support')
+    variant('adios1', default=False,
+            description='Enable ADIOS1 support')
+    variant('adios2', default=False,
+            description='Enable ADIOS2 support')
+    # variant('json', default=True,
+    #         description='Enable JSON support')
+    variant('python', default=True,
+            description='Enable Python bindings')
+
+    depends_on('cmake@3.10.0:', type='build')
+    depends_on('mpark-variant@1.3.0:')
+    depends_on('catch@2.3.0: ~single_header', type='test')
+    depends_on('mpi@2.3:', when='+mpi')  # might become MPI 3.0+
+    depends_on('hdf5@1.8.13:', when='+hdf5')
+    depends_on('hdf5@1.8.13: ~mpi', when='~mpi +hdf5')
+    depends_on('hdf5@1.8.13: +mpi', when='+mpi +hdf5')
+    depends_on('adios@1.10.0:', when='+adios1')
+    depends_on('adios@1.10.0: ~mpi', when='~mpi +adios1')
+    depends_on('adios@1.10.0: +mpi', when='+mpi +adios1')
+    depends_on('adios2@2.1.0:', when='+adios2')
+    depends_on('adios2@2.1.0: ~mpi', when='~mpi +adios2')
+    depends_on('adios2@2.1.0: +mpi', when='+mpi +adios2')
+    # ideally we want 2.3.0+ for full C++11 CT function signature support
+    depends_on('py-pybind11@2.2.3:', when='+python')
+    depends_on('py-numpy@1.15.1:', when='+python', type=['test', 'run'])
+
+    extends('python', when='+python')
+
+    def cmake_args(self):
+        spec = self.spec
+
+        args = [
+            # variants
+            '-DopenPMD_USE_MPI:BOOL={0}'.format(
+                'ON' if '+mpi' in spec else 'OFF'),
+            '-DopenPMD_USE_HDF5:BOOL={0}'.format(
+                'ON' if '+hdf5' in spec else 'OFF'),
+            '-DopenPMD_USE_ADIOS1:BOOL={0}'.format(
+                'ON' if '+adios1' in spec else 'OFF'),
+            '-DopenPMD_USE_ADIOS2:BOOL={0}'.format(
+                'ON' if '+adios2' in spec else 'OFF'),
+            # '-DopenPMD_USE_JSON:BOOL={0}'.format(
+            #     'ON' if '+json' in spec else 'OFF'),
+            '-DopenPMD_USE_PYTHON:BOOL={0}'.format(
+                'ON' if '+python' in spec else 'OFF'),
+            # tests and examples
+            '-DBUILD_TESTING:BOOL={0}'.format(
+                'ON' if self.run_tests else 'OFF'),
+            '-DBUILD_EXAMPLES:BOOL={0}'.format(
+                'ON' if self.run_tests else 'OFF'),
+        ]
+
+        if spec.satisfies('+python'):
+            args.append('-DopenPMD_USE_INTERNAL_PYBIND11:BOOL=OFF')
+            args.append('-DPYTHON_EXECUTABLE:FILEPATH={0}'.format(
+                        self.spec['python'].command.path))
+
+        # switch internally shipped third-party libraries for spack
+        args.append('-DopenPMD_USE_INTERNAL_VARIANT:BOOL=OFF')
+        if self.run_tests:
+            args.append('-DopenPMD_USE_INTERNAL_CATCH:BOOL=OFF')
+
+        return args
diff --git a/var/spack/repos/builtin/packages/openscenegraph/package.py b/var/spack/repos/builtin/packages/openscenegraph/package.py
index 915848fc23..d8adf24bf7 100644
--- a/var/spack/repos/builtin/packages/openscenegraph/package.py
+++ b/var/spack/repos/builtin/packages/openscenegraph/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/openslide/package.py b/var/spack/repos/builtin/packages/openslide/package.py
new file mode 100644
index 0000000000..2018a7e33b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/openslide/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Openslide(AutotoolsPackage):
+    """OpenSlide reads whole slide image files."""
+
+    homepage = "http://openslide.org/"
+    url      = "https://github.com/openslide/openslide/releases/download/v3.4.1/openslide-3.4.1.tar.xz"
+
+    version('3.4.1', 'ad9fa84775ed6b505d6f50bf6420c6bf')
+
+    depends_on('openjpeg')
+    depends_on('jpeg')
+    depends_on('libtiff')
+    depends_on('libxml2')
+    depends_on('sqlite@3.6:')
diff --git a/var/spack/repos/builtin/packages/openspeedshop-utils/package.py b/var/spack/repos/builtin/packages/openspeedshop-utils/package.py
new file mode 100644
index 0000000000..c70013562c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/openspeedshop-utils/package.py
@@ -0,0 +1,304 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+import spack
+import spack.store
+
+import os
+import os.path
+
+
+class OpenspeedshopUtils(CMakePackage):
+    """OpenSpeedShop is a community effort by The Krell Institute with
+       current direct funding from DOEs NNSA.  It builds on top of a
+       broad list of community infrastructures, most notably Dyninst
+       and MRNet from UW, libmonitor from Rice, and PAPI from UTK.
+       OpenSpeedShop is an open source multi platform Linux performance
+       tool which is targeted to support performance analysis of
+       applications running on both single node and large scale IA64,
+       IA32, EM64T, AMD64, PPC, ARM, Power8, Intel Phi, Blue Gene and
+       Cray platforms.  OpenSpeedShop development is hosted by the Krell
+       Institute. The infrastructure and base components of OpenSpeedShop
+       are released as open source code primarily under LGPL.
+       openspeedshop-utils is a package that does not have the
+       qt3 gui.  It was created to avoid a conflict between
+       openspeedshop and cbtf-argonavis-gui based on the fact
+       that spack will not allow a qt3 and qt4/qt5 dependency in a packages
+       dependency tree.
+    """
+
+    homepage = "http://www.openspeedshop.org"
+    git      = "https://github.com/OpenSpeedShop/openspeedshop.git"
+
+    version('develop', branch='master')
+    version('2.4.0', branch='2.4.0')
+    version('2.3.1.5', branch='2.3.1.5')
+    version('2.3.1.4', branch='2.3.1.4')
+    version('2.3.1.3', branch='2.3.1.3')
+
+    variant('runtime', default=False,
+            description="build only the runtime libraries and collectors.")
+    variant('cti', default=False,
+            description="Build MRNet with the CTI startup option")
+    variant('crayfe', default=False,
+            description="build only the FE tool using the runtime_dir \
+                         to point to target build.")
+    variant('cuda', default=False,
+            description="build with cuda packages included.")
+
+    variant('build_type', default='None', values=('None'),
+            description='CMake build type')
+
+    # MPI variants
+    variant('openmpi', default=False,
+            description="Build mpi collector for openmpi \
+                         MPI when variant is enabled.")
+    variant('mpt', default=False,
+            description="Build mpi collector for SGI \
+                         MPT MPI when variant is enabled.")
+    variant('mvapich2', default=False,
+            description="Build mpi collector for mvapich2\
+                         MPI when variant is enabled.")
+    variant('mvapich', default=False,
+            description="Build mpi collector for mvapich\
+                         MPI when variant is enabled.")
+    variant('mpich2', default=False,
+            description="Build mpi collector for mpich2\
+                         MPI when variant is enabled.")
+    variant('mpich', default=False,
+            description="Build mpi collector for mpich\
+                         MPI when variant is enabled.")
+
+    depends_on("cmake@3.0.2:", type='build')
+
+    # Dependencies for openspeedshop that are common to all
+    # the variants of the OpenSpeedShop build
+    depends_on("libtool", type='build')
+    depends_on("bison", type='build')
+    depends_on("flex@2.6.1", type='build')
+
+    # For binutils
+    depends_on("binutils", type='build')
+
+    depends_on("elf", type="link")
+    depends_on("libdwarf")
+
+    depends_on("sqlite")
+
+    # For boost
+    depends_on("boost@1.66.0:")
+
+    depends_on("dyninst@develop", when='@develop')
+    depends_on("dyninst@10:", when='@2.3.1.3:9999')
+
+    depends_on("python", when='@develop', type=('build', 'run'))
+    depends_on("python@2.7.14:2.7.15", when='@2.3.1.3:9999', type=('build', 'run'))
+
+    depends_on("libxml2")
+
+    # Dependencies for the openspeedshop cbtf packages.
+    depends_on("cbtf@develop", when='@develop', type=('build', 'link', 'run'))
+    depends_on("cbtf@1.9.1.0:9999", when='@2.3.1.3:9999', type=('build', 'link', 'run'))
+
+    depends_on("cbtf-krell@develop", when='@develop', type=('build', 'link', 'run'))
+    depends_on("cbtf-krell@1.9.1.0:9999", when='@2.3.1.3:9999', type=('build', 'link', 'run'))
+
+    depends_on('cbtf-krell@develop+crayfe', when='@develop+crayfe', type=('build', 'link', 'run'))
+    depends_on('cbtf-krell@1.9.1.0:9999+crayfe', when='@2.3.1.3:9999+crayfe', type=('build', 'link', 'run'))
+
+    depends_on('cbtf-krell@develop+cti', when='@develop+cti', type=('build', 'link', 'run'))
+    depends_on('cbtf-krell@1.9.1.0:9999+cti', when='@2.3.1.3:9999+cti', type=('build', 'link', 'run'))
+
+    depends_on('cbtf-krell@develop+mpich', when='@develop+mpich', type=('build', 'link', 'run'))
+    depends_on('cbtf-krell@1.9.1.0:9999+mpich', when='@2.3.1.3:9999+mpich', type=('build', 'link', 'run'))
+
+    depends_on('cbtf-krell@develop+mpich2', when='@develop+mpich2', type=('build', 'link', 'run'))
+    depends_on('cbtf-krell@1.9.1.0:9999+mpich2', when='@2.3.1.3:9999+mpich2', type=('build', 'link', 'run'))
+
+    depends_on('cbtf-krell@develop+mpt', when='@develop+mpt', type=('build', 'link', 'run'))
+    depends_on('cbtf-krell@1.9.1.0:9999+mpt', when='@2.3.1.3:9999+mpt', type=('build', 'link', 'run'))
+
+    depends_on('cbtf-krell@develop+mvapich', when='@develop+mvapich', type=('build', 'link', 'run'))
+    depends_on('cbtf-krell@1.9.1.0:9999+mvapich', when='@2.3.1.3:9999+mvapich', type=('build', 'link', 'run'))
+
+    depends_on('cbtf-krell@develop+mvapich2', when='@develop+mvapich2', type=('build', 'link', 'run'))
+    depends_on('cbtf-krell@1.9.1.0:9999+mvapich2', when='@2.3.1.3:9999+mvapich2', type=('build', 'link', 'run'))
+
+    depends_on('cbtf-krell@develop+openmpi', when='@develop+openmpi', type=('build', 'link', 'run'))
+    depends_on('cbtf-krell@1.9.1.0:9999+openmpi', when='@2.3.1.3:9999+openmpi', type=('build', 'link', 'run'))
+
+    depends_on("cbtf-argonavis@develop", when='@develop+cuda', type=('build', 'link', 'run'))
+    depends_on("cbtf-argonavis@1.9.1.0:9999", when='@2.3.1.3:9999+cuda', type=('build', 'link', 'run'))
+
+    # For MRNet
+    depends_on("mrnet@5.0.1-3:+cti", when='@develop+cti', type=('build', 'link', 'run'))
+    depends_on("mrnet@5.0.1-3:+lwthreads", when='@develop', type=('build', 'link', 'run'))
+
+    depends_on("mrnet@5.0.1-3:+cti", when='@2.3.1.3:9999+cti', type=('build', 'link', 'run'))
+    depends_on("mrnet@5.0.1-3:+lwthreads", when='@2.3.1.3:9999', type=('build', 'link', 'run'))
+
+    parallel = False
+
+    build_directory = 'build_openspeedshop'
+
+    def set_cray_login_node_cmake_options(self, spec, cmake_options):
+        # Appends to cmake_options the options that will enable the appropriate
+        # Cray login node libraries
+
+        cray_login_node_options = []
+        rt_platform = "cray"
+
+        # How do we get the compute node (CNL) cbtf package install
+        # directory path?
+        # spec['cbtf'].prefix is the login node value for this build, as
+        # we only get here when building the login node components and
+        # that is all that is known to spack.
+        be_ck = spack.store.db.query_one('cbtf-krell arch=cray-CNL-haswell')
+
+        # Equivalent to install-tool cmake arg:
+        # '-DCBTF_KRELL_CN_RUNTIME_DIR=%s'
+        #               % <base dir>/cbtf_v2.3.1.release/compute)
+        cray_login_node_options.append('-DCBTF_KRELL_CN_RUNTIME_DIR=%s'
+                                       % be_ck.prefix)
+        cray_login_node_options.append('-DRUNTIME_PLATFORM=%s'
+                                       % rt_platform)
+
+        cmake_options.extend(cray_login_node_options)
+
+    def cmake_args(self):
+        # Appends base options to cmake_args
+        spec = self.spec
+
+        compile_flags = "-O2 -g"
+
+        cmake_args = []
+
+        # Indicate building cbtf vers (transfer rawdata files)
+        instrumentor_setting = "cbtf"
+
+        if spec.satisfies('+runtime'):
+            self.set_defaultbase_cmake_options(spec, cmake_args)
+
+            cmake_args.extend(
+                ['-DCMAKE_CXX_FLAGS=%s'  % compile_flags,
+                 '-DCMAKE_C_FLAGS=%s'    % compile_flags,
+                 '-DINSTRUMENTOR=%s' % instrumentor_setting,
+                 '-DCBTF_DIR=%s' % spec['cbtf'].prefix,
+                 '-DCBTF_KRELL_DIR=%s' % spec['cbtf-krell'].prefix,
+                 '-DMRNET_DIR=%s' % spec['mrnet'].prefix])
+
+        else:
+
+            # Appends base options to cmake_args
+            self.set_defaultbase_cmake_options(spec, cmake_args)
+            cmake_args.extend(
+                ['-DCMAKE_CXX_FLAGS=%s' % compile_flags,
+                 '-DCMAKE_C_FLAGS=%s' % compile_flags,
+                 '-DINSTRUMENTOR=%s' % instrumentor_setting,
+                 '-DSQLITE3_DIR=%s' % spec['sqlite'].prefix,
+                 '-DCBTF_DIR=%s' % spec['cbtf'].prefix,
+                 '-DCBTF_KRELL_DIR=%s' % spec['cbtf-krell'].prefix,
+                 '-DMRNET_DIR=%s' % spec['mrnet'].prefix])
+
+            if spec.satisfies('+crayfe'):
+                # We need to build target/compute node
+                # components/libraries first then pass
+                # those libraries to the openspeedshop
+                # login node build
+                self.set_cray_login_node_cmake_options(spec, cmake_args)
+
+        cmake_args.extend(['-DBUILD_QT3_GUI=FALSE'])
+
+        return cmake_args
+
+    def set_defaultbase_cmake_options(self, spec, cmake_options):
+        # Appends to cmake_options the options that will enable
+        # the appropriate base level options to the openspeedshop
+        # cmake build.
+        python_exe = spec['python'].command.path
+        python_library = spec['python'].libs[0]
+        python_include = spec['python'].headers.directories[0]
+
+        base_options = []
+
+        base_options.append('-DBINUTILS_DIR=%s' % spec['binutils'].prefix)
+        base_options.append('-DLIBELF_DIR=%s' % spec['elf'].prefix)
+        base_options.append('-DLIBDWARF_DIR=%s' % spec['libdwarf'].prefix)
+        base_options.append('-DPYTHON_EXECUTABLE=%s' % python_exe)
+        base_options.append('-DPYTHON_INCLUDE_DIR=%s' % python_include)
+        base_options.append('-DPYTHON_LIBRARY=%s' % python_library)
+        base_options.append('-DBoost_NO_SYSTEM_PATHS=TRUE')
+        base_options.append('-DBoost_NO_BOOST_CMAKE=TRUE')
+        base_options.append('-DBOOST_ROOT=%s' % spec['boost'].prefix)
+        base_options.append('-DBoost_DIR=%s' % spec['boost'].prefix)
+        base_options.append('-DBOOST_LIBRARYDIR=%s' % spec['boost'].prefix.lib)
+        base_options.append('-DDYNINST_DIR=%s' % spec['dyninst'].prefix)
+
+        cmake_options.extend(base_options)
+
+    def set_mpi_cmake_options(self, spec, cmake_options):
+        # Appends to cmake_options the options that will enable
+        # the appropriate MPI implementations
+
+        mpi_options = []
+
+        # openmpi
+        if spec.satisfies('+openmpi'):
+            mpi_options.append('-DOPENMPI_DIR=%s' % spec['openmpi'].prefix)
+        # mpich
+        if spec.satisfies('+mpich'):
+            mpi_options.append('-DMPICH_DIR=%s' % spec['mpich'].prefix)
+        # mpich2
+        if spec.satisfies('+mpich2'):
+            mpi_options.append('-DMPICH2_DIR=%s' % spec['mpich2'].prefix)
+        # mvapich
+        if spec.satisfies('+mvapich'):
+            mpi_options.append('-DMVAPICH_DIR=%s' % spec['mvapich'].prefix)
+        # mvapich2
+        if spec.satisfies('+mvapich2'):
+            mpi_options.append('-DMVAPICH2_DIR=%s' % spec['mvapich2'].prefix)
+        # mpt
+        if spec.satisfies('+mpt'):
+            mpi_options.append('-DMPT_DIR=%s' % spec['mpt'].prefix)
+
+        cmake_options.extend(mpi_options)
+
+    def setup_environment(self, spack_env, run_env):
+        """Set up the compile and runtime environments for a package."""
+
+        # Find Dyninst library path, this is needed to
+        # set the DYNINSTAPI_RT_LIB library which is
+        # required for OpenSpeedShop to find loop level
+        # performance information
+        dyninst_libdir = find_libraries('libdyninstAPI_RT',
+                                        root=self.spec['dyninst'].prefix,
+                                        shared=True, recursive=True)
+
+        # Set Dyninst RT library path to support OSS loop resolution code
+        run_env.set('DYNINSTAPI_RT_LIB', dyninst_libdir)
+
+        # Find openspeedshop library path
+        oss_libdir = find_libraries(
+            'libopenss-framework',
+            root=self.spec['openspeedshop-utils'].prefix,
+            shared=True, recursive=True)
+        run_env.prepend_path('LD_LIBRARY_PATH',
+                             os.path.dirname(oss_libdir.joined()))
+
+        run_env.set('OPENSS_RAWDATA_DIR', '.')
+
+        cbtf_mc = '/sbin/cbtf_mrnet_commnode'
+        cbtf_lmb = '/sbin/cbtf_libcbtf_mrnet_backend'
+        run_env.set('XPLAT_RSH', 'ssh')
+        run_env.set('MRNET_COMM_PATH',
+                    join_path(self.spec['cbtf-krell'].prefix + cbtf_mc))
+        run_env.set('CBTF_MRNET_BACKEND_PATH',
+                    join_path(self.spec['cbtf-krell'].prefix + cbtf_lmb))
+        run_env.prepend_path('PATH', self.spec['mrnet'].prefix.bin)
+        run_env.prepend_path('PATH', self.spec['cbtf-krell'].prefix.bin)
+        run_env.prepend_path('PATH', self.spec['cbtf-krell'].prefix.sbin)
+        run_env.prepend_path('PATH', self.spec['python'].prefix.bin)
diff --git a/var/spack/repos/builtin/packages/openspeedshop/package.py b/var/spack/repos/builtin/packages/openspeedshop/package.py
index 36e9fb06e4..0d8957f0ac 100644
--- a/var/spack/repos/builtin/packages/openspeedshop/package.py
+++ b/var/spack/repos/builtin/packages/openspeedshop/package.py
@@ -1,48 +1,11 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-##############################################################################
-# Copyright (c) 2015-2017 Krell Institute. All Rights Reserved.
-#
-# This program is free software; you can redistribute it and/or modify it
-# under the terms of the GNU General Public License as published by the Free
-# Software Foundation; either version 2 of the License, or (at your option)
-# any later version.
-#
-# This program is distributed in the hope that it will be useful, but WITHOUT
-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
-# FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for
-# more details.
-#
-# You should have received a copy of the GNU General Public License along with
-# this program; if not, write to the Free Software Foundation, Inc., 59 Temple
-# Place, Suite 330, Boston, MA  02111-1307  USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack import *
-import os
-import os.path
+
+import spack.store
 
 
 class Openspeedshop(CMakePackage):
@@ -60,19 +23,19 @@ class Openspeedshop(CMakePackage):
     """
 
     homepage = "http://www.openspeedshop.org"
-    url = "https://github.com/OpenSpeedShop"
+    git      = "https://github.com/OpenSpeedShop/openspeedshop.git"
 
-    # Use when the git repository is available
-    version('2.3', branch='master',
-            git='https://github.com/OpenSpeedShop/openspeedshop.git')
+    version('develop', branch='master')
+    version('2.4.0', branch='2.4.0')
+    version('2.3.1.5', branch='2.3.1.5')
+    version('2.3.1.4', branch='2.3.1.4')
+    version('2.3.1.3', branch='2.3.1.3')
 
-    variant('offline', default=False,
-            description="build with offline instrumentor enabled.")
-    variant('cbtf', default=True,
-            description="build with cbtf instrumentor enabled.")
     variant('runtime', default=False,
             description="build only the runtime libraries and collectors.")
-    variant('frontend', default=False,
+    variant('cti', default=False,
+            description="Build MRNet with the CTI startup option")
+    variant('crayfe', default=False,
             description="build only the FE tool using the runtime_dir \
                          to point to target build.")
     variant('cuda', default=False,
@@ -106,238 +69,256 @@ class Openspeedshop(CMakePackage):
                          MPI when variant is enabled.")
 
     depends_on("cmake@3.0.2:", type='build')
+
     # Dependencies for openspeedshop that are common to all
     # the variants of the OpenSpeedShop build
     depends_on("libtool", type='build')
     depends_on("bison", type='build')
-    depends_on("flex", type='build')
-    depends_on("binutils", type='build')
+    depends_on("flex@2.6.1", type='build')
+
+    # For binutils
+    depends_on("binutils")
+
     depends_on("elf", type="link")
     depends_on("libdwarf")
+
     depends_on("sqlite")
-    depends_on("boost@1.50.0:1.59.0")
-    depends_on("dyninst@9.3.2")
-    depends_on("libxml2+python")
+
+    # For boost
+    depends_on("boost@1.66.0:")
+
+    depends_on("dyninst@develop", when='@develop')
+    depends_on("dyninst@10:", when='@2.3.1.3:9999')
+
+    depends_on("python", when='@develop', type=('build', 'run'))
+    depends_on("python@2.7.14:2.7.15", when='@2.3.1.3:9999', type=('build', 'run'))
+
+    depends_on("libxml2")
+
     depends_on("qt@3.3.8b+krellpatch", when='gui=qt3')
-    # Actively working on adding this gui package
-    # depends_on("cbtf-argonavis-gui", when='gui=qt4')
-
-    # Dependencies only for the openspeedshop offline package.
-    depends_on("libunwind", when='+offline')
-    depends_on("papi", when='+offline')
-    depends_on("libmonitor+krellpatch", when='+offline')
-    depends_on("openmpi", when='+offline+openmpi')
-    depends_on("mpich", when='+offline+mpich')
-    depends_on("mpich2", when='+offline+mpich2')
-    depends_on("mvapich2", when='+offline+mvapich2')
-    depends_on("mvapich", when='+offline+mvapich')
-    depends_on("mpt", when='+offline+mpt')
-
-    # Dependencies only for the openspeedshop cbtf package.
-    depends_on("cbtf", when='+cbtf')
-    depends_on('cbtf-krell', when='+cbtf')
-    depends_on('cbtf-krell+mpich', when='+cbtf+mpich')
-    depends_on('cbtf-krell+mpich2', when='+cbtf+mpich2')
-    depends_on('cbtf-krell+mpt', when='+cbtf+mpt')
-    depends_on('cbtf-krell+mvapich', when='+cbtf+mvapich')
-    depends_on('cbtf-krell+mvapich2', when='+cbtf+mvapich2')
-    depends_on('cbtf-krell+openmpi', when='+cbtf+openmpi')
-    depends_on("cbtf-argonavis", when='+cbtf+cuda')
-    depends_on("mrnet@5.0.1:+lwthreads", when='+cbtf')
+
+    # Dependencies for the openspeedshop cbtf packages.
+    depends_on("cbtf@develop", when='@develop', type=('build', 'link', 'run'))
+    depends_on("cbtf@1.9.1.0:9999", when='@2.3.1.3:9999', type=('build', 'link', 'run'))
+
+    depends_on("cbtf-krell@develop", when='@develop', type=('build', 'link', 'run'))
+    depends_on("cbtf-krell@1.9.1.0:9999", when='@2.3.1.3:9999', type=('build', 'link', 'run'))
+
+    depends_on('cbtf-krell@develop+crayfe', when='@develop+crayfe', type=('build', 'link', 'run'))
+    depends_on('cbtf-krell@1.9.1.0:9999+crayfe', when='@2.3.1.3:9999+crayfe', type=('build', 'link', 'run'))
+
+    depends_on('cbtf-krell@develop+cti', when='@develop+cti', type=('build', 'link', 'run'))
+    depends_on('cbtf-krell@1.9.1.0:9999+cti', when='@2.3.1.3:9999+cti', type=('build', 'link', 'run'))
+
+    depends_on('cbtf-krell@develop+mpich', when='@develop+mpich', type=('build', 'link', 'run'))
+    depends_on('cbtf-krell@1.9.1.0:9999+mpich', when='@2.3.1.3:9999+mpich', type=('build', 'link', 'run'))
+
+    depends_on('cbtf-krell@develop+mpich2', when='@develop+mpich2', type=('build', 'link', 'run'))
+    depends_on('cbtf-krell@1.9.1.0:9999+mpich2', when='@2.3.1.3:9999+mpich2', type=('build', 'link', 'run'))
+
+    depends_on('cbtf-krell@develop+mpt', when='@develop+mpt', type=('build', 'link', 'run'))
+    depends_on('cbtf-krell@1.9.1.0:9999+mpt', when='@2.3.1.3:9999+mpt', type=('build', 'link', 'run'))
+
+    depends_on('cbtf-krell@develop+mvapich', when='@develop+mvapich', type=('build', 'link', 'run'))
+    depends_on('cbtf-krell@1.9.1.0:9999+mvapich', when='@2.3.1.3:9999+mvapich', type=('build', 'link', 'run'))
+
+    depends_on('cbtf-krell@develop+mvapich2', when='@develop+mvapich2', type=('build', 'link', 'run'))
+    depends_on('cbtf-krell@1.9.1.0:9999+mvapich2', when='@2.3.1.3:9999+mvapich2', type=('build', 'link', 'run'))
+
+    depends_on('cbtf-krell@develop+openmpi', when='@develop+openmpi', type=('build', 'link', 'run'))
+    depends_on('cbtf-krell@1.9.1.0:9999+openmpi', when='@2.3.1.3:9999+openmpi', type=('build', 'link', 'run'))
+
+    depends_on("cbtf-argonavis@develop", when='@develop+cuda', type=('build', 'link', 'run'))
+    depends_on("cbtf-argonavis@1.9.1.0:9999", when='@2.3.1.3:9999+cuda', type=('build', 'link', 'run'))
+
+    # For MRNet
+    depends_on("mrnet@5.0.1-3:+cti", when='@develop+cti', type=('build', 'link', 'run'))
+    depends_on("mrnet@5.0.1-3:+lwthreads", when='@develop', type=('build', 'link', 'run'))
+
+    depends_on("mrnet@5.0.1-3:+cti", when='@2.3.1.3:9999+cti', type=('build', 'link', 'run'))
+    depends_on("mrnet@5.0.1-3:+lwthreads", when='@2.3.1.3:9999', type=('build', 'link', 'run'))
 
     parallel = False
 
     build_directory = 'build_openspeedshop'
 
-    def cmake_args(self):
-        spec = self.spec
-        compile_flags = "-O2 -g"
+    def set_cray_login_node_cmake_options(self, spec, cmake_options):
+        # Appends to cmake_options the options that will enable the appropriate
+        # Cray login node libraries
 
-        if '+offline' in spec:
-            # Indicate building offline vers (writes rawdata files)
-            instrumentor_setting = "offline"
-            if '+runtime' in spec:
-                cmake_args = [
-                    '-DCMAKE_CXX_FLAGS=%s'  % compile_flags,
-                    '-DCMAKE_C_FLAGS=%s'    % compile_flags,
-                    '-DINSTRUMENTOR=%s'     % instrumentor_setting,
-                    '-DLIBMONITOR_DIR=%s'   % spec['libmonitor'].prefix,
-                    '-DLIBUNWIND_DIR=%s'    % spec['libunwind'].prefix,
-                    '-DPAPI_DIR=%s'         % spec['papi'].prefix]
+        cray_login_node_options = []
+        rt_platform = "cray"
 
-                # Add any MPI implementations coming from variant settings
-                self.set_mpi_cmakeOptions(spec, cmake_args)
+        # How do we get the compute node (CNL) cbtf package install
+        # directory path?
+        # spec['cbtf'].prefix is the login node value for this build, as
+        # we only get here when building the login node components and
+        # that is all that is known to spack.
+        store = spack.store
+        be_ck = store.db.query_one('cbtf-krell arch=cray-CNL-haswell')
 
-            else:
-                cmake_args = []
+        # Equivalent to install-tool cmake arg:
+        # '-DCBTF_KRELL_CN_RUNTIME_DIR=%s'
+        #               % <base dir>/cbtf_v2.3.1.release/compute)
+        cray_login_node_options.append('-DCBTF_KRELL_CN_RUNTIME_DIR=%s'
+                                       % be_ck.prefix)
+        cray_login_node_options.append('-DRUNTIME_PLATFORM=%s'
+                                       % rt_platform)
 
-                # Appends base options to cmake_args
-                self.set_defaultbase_cmakeOptions(spec, cmake_args)
+        cmake_options.extend(cray_login_node_options)
 
-                cmake_args.extend(
-                    ['-DCMAKE_CXX_FLAGS=%s'  % compile_flags,
-                     '-DCMAKE_C_FLAGS=%s'    % compile_flags,
-                     '-DINSTRUMENTOR=%s' % instrumentor_setting,
-                     '-DLIBMONITOR_DIR=%s' % spec['libmonitor'].prefix,
-                     '-DLIBUNWIND_DIR=%s' % spec['libunwind'].prefix,
-                     '-DPAPI_DIR=%s' % spec['papi'].prefix,
-                     '-DSQLITE3_DIR=%s' % spec['sqlite'].prefix,
-                     '-DQTLIB_DIR=%s' % spec['qt'].prefix])
-
-                # Add any MPI implementations coming from variant settings
-                self.set_mpi_cmakeOptions(spec, cmake_args)
-
-        elif '+cbtf' in spec:
-            # Indicate building cbtf vers (transfer rawdata files)
-            instrumentor_setting = "cbtf"
-
-            if '+runtime' in spec:
-                # Appends base options to cmake_args
-                self.set_defaultbase_cmakeOptions(spec, cmake_args)
+    def cmake_args(self):
+
+        spec = self.spec
 
+        compile_flags = "-O2 -g"
+
+        cmake_args = []
+
+        # Indicate building cbtf vers (transfer rawdata files)
+        instrumentor_setting = "cbtf"
+
+        if spec.satisfies('+runtime'):
+            # Appends base options to cmake_args
+            self.set_defaultbase_cmake_options(spec, cmake_args)
+            cmake_args.extend(
+                ['-DCMAKE_CXX_FLAGS=%s'  % compile_flags,
+                 '-DCMAKE_C_FLAGS=%s'    % compile_flags,
+                 '-DINSTRUMENTOR=%s' % instrumentor_setting,
+                 '-DCBTF_DIR=%s' % spec['cbtf'].prefix,
+                 '-DCBTF_KRELL_DIR=%s' % spec['cbtf-krell'].prefix,
+                 '-DMRNET_DIR=%s' % spec['mrnet'].prefix])
+
+        else:
+
+            # Appends base options to cmake_args
+            self.set_defaultbase_cmake_options(spec, cmake_args)
+            guitype = self.spec.variants['gui'].value
+            cmake_args.extend(
+                ['-DCMAKE_CXX_FLAGS=%s' % compile_flags,
+                 '-DCMAKE_C_FLAGS=%s' % compile_flags,
+                 '-DINSTRUMENTOR=%s' % instrumentor_setting,
+                 '-DSQLITE3_DIR=%s' % spec['sqlite'].prefix,
+                 '-DCBTF_DIR=%s' % spec['cbtf'].prefix,
+                 '-DCBTF_KRELL_DIR=%s' % spec['cbtf-krell'].prefix,
+                 '-DMRNET_DIR=%s' % spec['mrnet'].prefix])
+
+            if guitype == 'none':
+                cmake_args.extend(
+                    ['-DBUILD_QT3_GUI=FALSE'])
+            elif guitype == 'qt4':
                 cmake_args.extend(
-                    ['-DCMAKE_CXX_FLAGS=%s'  % compile_flags,
-                     '-DCMAKE_C_FLAGS=%s'    % compile_flags,
-                     '-DINSTRUMENTOR=%s' % instrumentor_setting,
-                     '-DCBTF_DIR=%s' % spec['cbtf'].prefix,
-                     '-DCBTF_KRELL_DIR=%s' % spec['cbtf-krell'].prefix,
-                     '-DMRNET_DIR=%s' % spec['mrnet'].prefix])
-
-            else:
-                cmake_args = []
-
-                # Appends base options to cmake_args
-                self.set_defaultbase_cmakeOptions(spec, cmake_args)
-                guitype = self.spec.variants['gui'].value
+                    ['-DBUILD_QT3_GUI=FALSE'])
+            elif guitype == 'qt3':
                 cmake_args.extend(
-                    ['-DCMAKE_CXX_FLAGS=%s' % compile_flags,
-                     '-DCMAKE_C_FLAGS=%s' % compile_flags,
-                     '-DINSTRUMENTOR=%s' % instrumentor_setting,
-                     '-DSQLITE3_DIR=%s' % spec['sqlite'].prefix,
-                     '-DCBTF_DIR=%s' % spec['cbtf'].prefix,
-                     '-DCBTF_KRELL_DIR=%s' % spec['cbtf-krell'].prefix,
-                     '-DMRNET_DIR=%s' % spec['mrnet'].prefix])
-
-                if guitype == 'none':
-                    cmake_args.extend(
-                        ['-DBUILD_QT3_GUI=FALSE'])
-                elif guitype == 'qt4':
-                    cmake_args.extend(
-                        ['-DBUILD_QT3_GUI=FALSE'])
-                elif guitype == 'qt3':
-                    cmake_args.extend(
-                        ['-DQTLIB_DIR=%s'
-                            % spec['qt'].prefix])
+                    ['-DQTLIB_DIR=%s'
+                        % spec['qt'].prefix])
+
+            if spec.satisfies('+crayfe'):
+                # We need to build target/compute node
+                # components/libraries first then pass
+                # those libraries to the openspeedshop
+                # login node build
+                self.set_cray_login_node_cmake_options(spec, cmake_args)
 
         return cmake_args
 
-    def set_defaultbase_cmakeOptions(self, spec, cmakeOptions):
-        # Appends to cmakeOptions the options that will enable
+    def set_defaultbase_cmake_options(self, spec, cmake_options):
+        # Appends to cmake_options the options that will enable
         # the appropriate base level options to the openspeedshop
         # cmake build.
         python_exe = spec['python'].command.path
         python_library = spec['python'].libs[0]
         python_include = spec['python'].headers.directories[0]
 
-        BaseOptions = []
-
-        BaseOptions.append('-DBINUTILS_DIR=%s' % spec['binutils'].prefix)
-        BaseOptions.append('-DLIBELF_DIR=%s' % spec['elf'].prefix)
-        BaseOptions.append('-DLIBDWARF_DIR=%s' % spec['libdwarf'].prefix)
-        BaseOptions.append('-DPYTHON_EXECUTABLE=%s' % python_exe)
-        BaseOptions.append('-DPYTHON_INCLUDE_DIR=%s' % python_include)
-        BaseOptions.append('-DPYTHON_LIBRARY=%s' % python_library)
-        BaseOptions.append('-DBoost_NO_SYSTEM_PATHS=TRUE')
-        BaseOptions.append('-DBoost_NO_BOOST_CMAKE=TRUE')
-        BaseOptions.append('-DBOOST_ROOT=%s' % spec['boost'].prefix)
-        BaseOptions.append('-DBoost_DIR=%s' % spec['boost'].prefix)
-        BaseOptions.append('-DBOOST_LIBRARYDIR=%s' % spec['boost'].prefix.lib)
-        BaseOptions.append('-DDYNINST_DIR=%s' % spec['dyninst'].prefix)
-
-        cmakeOptions.extend(BaseOptions)
-
-    def set_mpi_cmakeOptions(self, spec, cmakeOptions):
-        # Appends to cmakeOptions the options that will enable
+        base_options = []
+
+        base_options.append('-DBINUTILS_DIR=%s' % spec['binutils'].prefix)
+        base_options.append('-DLIBELF_DIR=%s' % spec['elf'].prefix)
+        base_options.append('-DLIBDWARF_DIR=%s' % spec['libdwarf'].prefix)
+        base_options.append('-DPYTHON_EXECUTABLE=%s' % python_exe)
+        base_options.append('-DPYTHON_INCLUDE_DIR=%s' % python_include)
+        base_options.append('-DPYTHON_LIBRARY=%s' % python_library)
+        base_options.append('-DBoost_NO_SYSTEM_PATHS=TRUE')
+        base_options.append('-DBoost_NO_BOOST_CMAKE=TRUE')
+        base_options.append('-DBOOST_ROOT=%s' % spec['boost'].prefix)
+        base_options.append('-DBoost_DIR=%s' % spec['boost'].prefix)
+        base_options.append('-DBOOST_LIBRARYDIR=%s' % spec['boost'].prefix.lib)
+        base_options.append('-DDYNINST_DIR=%s' % spec['dyninst'].prefix)
+
+        cmake_options.extend(base_options)
+
+    def set_mpi_cmake_options(self, spec, cmake_options):
+        # Appends to cmake_options the options that will enable
         # the appropriate MPI implementations
 
-        MPIOptions = []
+        mpi_options = []
 
         # openmpi
-        if '+openmpi' in spec:
-            MPIOptions.append('-DOPENMPI_DIR=%s' % spec['openmpi'].prefix)
+        if spec.satisfies('+openmpi'):
+            mpi_options.append('-DOPENMPI_DIR=%s' % spec['openmpi'].prefix)
         # mpich
-        if '+mpich' in spec:
-            MPIOptions.append('-DMPICH_DIR=%s' % spec['mpich'].prefix)
+        if spec.satisfies('+mpich'):
+            mpi_options.append('-DMPICH_DIR=%s' % spec['mpich'].prefix)
         # mpich2
-        if '+mpich2' in spec:
-            MPIOptions.append('-DMPICH2_DIR=%s' % spec['mpich2'].prefix)
+        if spec.satisfies('+mpich2'):
+            mpi_options.append('-DMPICH2_DIR=%s' % spec['mpich2'].prefix)
         # mvapich
-        if '+mvapich' in spec:
-            MPIOptions.append('-DMVAPICH_DIR=%s' % spec['mvapich'].prefix)
+        if spec.satisfies('+mvapich'):
+            mpi_options.append('-DMVAPICH_DIR=%s' % spec['mvapich'].prefix)
         # mvapich2
-        if '+mvapich2' in spec:
-            MPIOptions.append('-DMVAPICH2_DIR=%s' % spec['mvapich2'].prefix)
+        if spec.satisfies('+mvapich2'):
+            mpi_options.append('-DMVAPICH2_DIR=%s' % spec['mvapich2'].prefix)
         # mpt
-        if '+mpt' in spec:
-            MPIOptions.append('-DMPT_DIR=%s' % spec['mpt'].prefix)
+        if spec.satisfies('+mpt'):
+            mpi_options.append('-DMPT_DIR=%s' % spec['mpt'].prefix)
 
-        cmakeOptions.extend(MPIOptions)
+        cmake_options.extend(mpi_options)
 
     def setup_environment(self, spack_env, run_env):
         """Set up the compile and runtime environments for a package."""
 
-        # Common settings to both offline and cbtf versions
-        # of OpenSpeedShop
-        run_env.prepend_path('PATH', self.prefix.bin)
-
         # Find Dyninst library path, this is needed to
         # set the DYNINSTAPI_RT_LIB library which is
         # required for OpenSpeedShop to find loop level
         # performance information
         dyninst_libdir = find_libraries('libdyninstAPI_RT',
                                         root=self.spec['dyninst'].prefix,
-                                        shared=True, recurse=True)
+                                        shared=True, recursive=True)
 
         # Set Dyninst RT library path to support OSS loop resolution code
         run_env.set('DYNINSTAPI_RT_LIB', dyninst_libdir)
 
-        # Find openspeedshop library path
-        oss_libdir = find_libraries('libopenss-framework',
-                                    root=self.spec['openspeedshop'].prefix,
-                                    shared=True, recurse=True)
-        run_env.prepend_path('LD_LIBRARY_PATH',
-                             os.path.dirname(oss_libdir.joined()))
-
-        # Settings specific to the version, checking here
-        # for the cbtf instrumentor
-        if '+cbtf' in self.spec:
-            cbtf_mc = '/sbin/cbtf_mrnet_commnode'
-            cbtf_lmb = '/sbin/cbtf_libcbtf_mrnet_backend'
-            run_env.set('XPLAT_RSH', 'ssh')
-            run_env.set('MRNET_COMM_PATH',
-                        join_path(self.spec['cbtf-krell'].prefix + cbtf_mc))
-
-            run_env.set('CBTF_MRNET_BACKEND_PATH',
-                        join_path(self.spec['cbtf-krell'].prefix + cbtf_lmb))
-
-            run_env.prepend_path('PATH', self.spec['mrnet'].prefix.bin)
-            run_env.prepend_path('PATH', self.spec['cbtf-krell'].prefix.bin)
-            run_env.prepend_path('PATH', self.spec['cbtf-krell'].prefix.sbin)
-
-        elif '+offline' in self.spec:
-            # Had to use this form of syntax self.prefix.lib and
-            # self.prefix.lib64 returned None all the time
-            run_env.set('OPENSS_RAWDATA_DIR', '.')
-            run_env.set('OPENSS_PLUGIN_PATH',
-                        join_path(oss_libdir + '/openspeedshop'))
-            run_env.prepend_path('PATH', self.spec['papi'].prefix.bin)
-            run_env.prepend_path('PATH', self.spec['libdwarf'].prefix.bin)
-
-            if '+mpich' in self.spec:
-                run_env.set('OPENSS_MPI_IMPLEMENTATION', 'mpich')
-            if '+mpich2' in self.spec:
-                run_env.set('OPENSS_MPI_IMPLEMENTATION', 'mpich2')
-            if '+mvapich2' in self.spec:
-                run_env.set('OPENSS_MPI_IMPLEMENTATION', 'mvapich2')
-            if '+openmpi' in self.spec:
-                run_env.set('OPENSS_MPI_IMPLEMENTATION', 'openmpi')
+        run_env.set('OPENSS_RAWDATA_DIR', '.')
+        cbtf_mc = '/sbin/cbtf_mrnet_commnode'
+        cbtf_lmb = '/sbin/cbtf_libcbtf_mrnet_backend'
+        run_env.set('XPLAT_RSH', 'ssh')
+        run_env.set('MRNET_COMM_PATH',
+                    join_path(self.spec['cbtf-krell'].prefix + cbtf_mc))
+
+        # Set CBTF_MPI_IMPLEMENTATON to the appropriate mpi implementation
+        # This is needed by O|SS and CBTF tools to deploy the correct
+        # mpi runtimes for ossmpi, ossmpit, ossmpip, and cbtfsummary
+        # Users may have to set the CBTF_MPI_IMPLEMENTATION variable
+        # manually if multiple mpi's are specified in the build
+        if self.spec.satisfies('+mpich'):
+            run_env.set('CBTF_MPI_IMPLEMENTATION', "mpich")
+
+        if self.spec.satisfies('+mvapich'):
+            run_env.set('CBTF_MPI_IMPLEMENTATION', "mvapich")
+
+        if self.spec.satisfies('+mvapich2'):
+            run_env.set('CBTF_MPI_IMPLEMENTATION', "mvapich2")
+
+        if self.spec.satisfies('+mpt'):
+            run_env.set('CBTF_MPI_IMPLEMENTATION', "mpt")
+
+        if self.spec.satisfies('+openmpi'):
+            run_env.set('CBTF_MPI_IMPLEMENTATION', "openmpi")
+
+        run_env.set('CBTF_MRNET_BACKEND_PATH',
+                    join_path(self.spec['cbtf-krell'].prefix + cbtf_lmb))
+        run_env.prepend_path('PATH', self.spec['mrnet'].prefix.bin)
+        run_env.prepend_path('PATH', self.spec['cbtf-krell'].prefix.bin)
+        run_env.prepend_path('PATH', self.spec['cbtf-krell'].prefix.sbin)
+        run_env.prepend_path('PATH', self.spec['python'].prefix.bin)
diff --git a/var/spack/repos/builtin/packages/openssh/package.py b/var/spack/repos/builtin/packages/openssh/package.py
index aab102efbd..45540989b7 100644
--- a/var/spack/repos/builtin/packages/openssh/package.py
+++ b/var/spack/repos/builtin/packages/openssh/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,8 +16,9 @@ class Openssh(AutotoolsPackage):
     """
 
     homepage = "https://www.openssh.com/"
-    url      = "https://mirrors.sonic.net/pub/OpenBSD/OpenSSH/portable/openssh-7.5p1.tar.gz"
+    url      = "https://mirrors.sonic.net/pub/OpenBSD/OpenSSH/portable/openssh-7.6p1.tar.gz"
 
+    version('7.6p1',   '06a88699018e5fef13d4655abfed1f63')
     version('7.5p1',   '652fdc7d8392f112bef11cacf7e69e23')
     version('7.4p1',   'b2db2a83caf66a208bb78d6d287cdaa3')
     version('7.3p1',   'dfadd9f035d38ce5d58a3bf130b86d08')
diff --git a/var/spack/repos/builtin/packages/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py
index 72f35ac4d5..41f73d3d53 100644
--- a/var/spack/repos/builtin/packages/openssl/package.py
+++ b/var/spack/repos/builtin/packages/openssl/package.py
@@ -1,32 +1,15 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import llnl.util.tty as tty
 
 from spack import *
 import spack.architecture
 
+import os
+
 
 class Openssl(Package):
     """OpenSSL is an open source project that provides a robust,
@@ -36,16 +19,20 @@ class Openssl(Package):
     homepage = "http://www.openssl.org"
 
     # URL must remain http:// so Spack can bootstrap curl
-    url = "http://www.openssl.org/source/openssl-1.0.1h.tar.gz"
+    url = "http://www.openssl.org/source/openssl-1.0.2m.tar.gz"
     list_url = "https://www.openssl.org/source/old/"
     list_depth = 1
 
+    version('1.1.0g', 'ba5f1b8b835b88cadbce9b35ed9531a6')
     version('1.1.0e', '51c42d152122e474754aea96f66928c6')
     version('1.1.0d', '711ce3cd5f53a99c0e12a7d5804f0f63')
     version('1.1.0c', '601e8191f72b18192a937ecf1a800f3f')
     # Note: Version 1.0.2 is the "long-term support" version that will
     # remain supported until 2019.
-    version('1.0.2k', 'f965fc0bf01bf882b31314b61391ae65', preferred=True)
+    version('1.0.2o', '44279b8557c3247cbe324e2322ecd114', preferred=True)
+    version('1.0.2n', '13bdc1b1d1ff39b6fd42a255e74676a4')
+    version('1.0.2m', '10e9e37f492094b9ef296f68f24a7666')
+    version('1.0.2k', 'f965fc0bf01bf882b31314b61391ae65')
     version('1.0.2j', '96322138f0b69e61b7212bc53d5e912b')
     version('1.0.2i', '678374e63f8df456a697d3e5e5a931fb')
     version('1.0.2h', '9392e65072ce4b614c1392eefc1f23d0')
@@ -58,15 +45,18 @@ class Openssl(Package):
     version('1.0.1r', '1abd905e079542ccae948af37e393d28')
     version('1.0.1h', '8d6d684a9430d5cc98a62a5d8fbda8cf')
 
+    variant('systemcerts', default=True, description='Use system certificates')
+
     depends_on('zlib')
 
-    # TODO: 'make test' requires Perl module Test::More version 0.96
-    # TODO: uncomment when test dependency types are supported.
-    # TODO: This is commented in the meantime to avoid dependnecy bloat.
-    # depends_on('perl@5.14.0:', type='build', when='+tests')
+    depends_on('perl@5.14.0:', type=('build', 'test'))
 
     parallel = False
 
+    @property
+    def libs(self):
+        return find_libraries(['libssl', 'libcrypto'], root=self.prefix.lib)
+
     def handle_fetch_error(self, error):
         tty.warn("Fetching OpenSSL failed. This may indicate that OpenSSL has "
                  "been updated, and the version in your instance of Spack is "
@@ -104,7 +94,37 @@ class Openssl(Package):
         filter_file(r'-arch x86_64', '', 'Makefile')
 
         make()
-        # TODO: add this back when we have a 'test' dependency type. See above.
-        # if self.run_tests:
-        #     make('test')            # 'VERBOSE=1'
+        if self.run_tests:
+            make('test')            # 'VERBOSE=1'
         make('install')
+
+    @run_after('install')
+    def link_system_certs(self):
+        if '+systemcerts' not in self.spec:
+            return
+
+        system_dirs = [
+            # CentOS, Fedora, RHEL
+            '/etc/pki/tls',
+            # Ubuntu
+            '/usr/lib/ssl'
+        ]
+
+        pkg_dir = join_path(self.prefix, 'etc', 'openssl')
+
+        for directory in system_dirs:
+            sys_cert = join_path(directory, 'cert.pem')
+            pkg_cert = join_path(pkg_dir, 'cert.pem')
+            # If a bundle exists, use it. This is the preferred way on Fedora,
+            # where the certs directory does not work.
+            if os.path.exists(sys_cert) and not os.path.exists(pkg_cert):
+                os.symlink(sys_cert, pkg_cert)
+
+            sys_certs = join_path(directory, 'certs')
+            pkg_certs = join_path(pkg_dir, 'certs')
+            # If the certs directory exists, symlink it into the package.
+            # We symlink the whole directory instead of all files because
+            # the directory contents might change without Spack noticing.
+            if os.path.isdir(sys_certs) and not os.path.islink(pkg_certs):
+                os.rmdir(pkg_certs)
+                os.symlink(sys_certs, pkg_certs)
diff --git a/var/spack/repos/builtin/packages/opium/package.py b/var/spack/repos/builtin/packages/opium/package.py
index 5ce1d8b332..c0f907c80a 100644
--- a/var/spack/repos/builtin/packages/opium/package.py
+++ b/var/spack/repos/builtin/packages/opium/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/optional-lite/package.py b/var/spack/repos/builtin/packages/optional-lite/package.py
new file mode 100644
index 0000000000..bddb490354
--- /dev/null
+++ b/var/spack/repos/builtin/packages/optional-lite/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+from shutil import copytree
+
+
+class OptionalLite(Package):
+    """
+    A single-file header-only version of a C++17-like optional, a nullable
+    object for C++98, C++11 and later.
+    """
+
+    homepage = "https://github.com/martinmoene/optional-lite"
+    url      = "https://github.com/martinmoene/optional-lite/archive/v3.0.0.tar.gz"
+
+    version('3.0.0', sha256='36ae58512c478610647978811f0f4dbe105880372bd7ed39417314d50a27254e')
+    version('2.3.0', sha256='8fe46216147234b172c6a5b182726834afc44dfdca1e976a264d6f96eb183916')
+    version('2.2.0', sha256='9ce1bb021de42f804f8d17ed30b79fc98296122bec8db60492104978cd282fa2')
+    version('2.0.0', sha256='e8d803cbc7be241df41a9ab267b525b7941df09747cd5a7deb55f863bd8a4e8d')
+    version('1.0.3', sha256='7a2fb0fe20d61d091f6730237add9bab58bc0df1288cb96f3e8a61b859539067')
+
+    def install(self, spec, prefix):
+        copytree('include', prefix.include)
diff --git a/var/spack/repos/builtin/packages/opus/package.py b/var/spack/repos/builtin/packages/opus/package.py
index 03d434926d..0300847923 100644
--- a/var/spack/repos/builtin/packages/opus/package.py
+++ b/var/spack/repos/builtin/packages/opus/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/orca/package.py b/var/spack/repos/builtin/packages/orca/package.py
new file mode 100644
index 0000000000..c137589e42
--- /dev/null
+++ b/var/spack/repos/builtin/packages/orca/package.py
@@ -0,0 +1,46 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class Orca(Package):
+    """An ab initio, DFT and semiempirical SCF-MO package
+
+       Note: Orca is licensed software. You will need to create an account
+       on the Orca homepage and download Orca yourself. Spack will search
+       your current directory for the download file. Alternatively, add this
+       file to a mirror so that Spack can find it. For instructions on how to
+       set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html"""
+
+    homepage = "https://cec.mpg.de"
+    url      = "file://{0}/orca_4_0_1_2_linux_x86-64_openmpi202.tar.zst".format(os.getcwd())
+
+    version('4.0.1.2', sha256='cea442aa99ec0d7ffde65014932196b62343f7a6191b4bfc438bfb38c03942f7',
+            expand=False)
+
+    depends_on('zstd', type='build')
+    depends_on('openmpi@2.0.0:2.1.5', type='run')
+
+    def url_for_version(self, version):
+        out = "file://{0}/orca_{1}_linux_x86-64_openmpi202.tar.zst"
+        return out.format(os.getcwd(), version.underscored)
+
+    def install(self, spec, prefix):
+        # we have to extract the archive ourself
+        # fortunately it's just full of a bunch of binaries
+
+        vername = os.path.basename(self.stage.archive_file).split('.')[0]
+
+        zstd = which('zstd')
+        zstd('-d', self.stage.archive_file, '-o', vername + '.tar')
+
+        tar = which('tar')
+        tar('-xvf', vername + '.tar')
+
+        # there are READMEs in there but they don't hurt anyone
+        mkdirp(prefix.bin)
+        install_tree(vername, prefix.bin)
diff --git a/var/spack/repos/builtin/packages/orfm/package.py b/var/spack/repos/builtin/packages/orfm/package.py
index 4b59bca7b6..092a0cb319 100644
--- a/var/spack/repos/builtin/packages/orfm/package.py
+++ b/var/spack/repos/builtin/packages/orfm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,3 +16,5 @@ class Orfm(AutotoolsPackage):
     url      = "https://github.com/wwood/OrfM/releases/download/v0.7.1/orfm-0.7.1.tar.gz"
 
     version('0.7.1', 'fcf18283a028cea2af90663a76a73a2a')
+
+    depends_on('zlib', type='link')
diff --git a/var/spack/repos/builtin/packages/orthofinder/package.py b/var/spack/repos/builtin/packages/orthofinder/package.py
new file mode 100644
index 0000000000..f89eddf6c8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/orthofinder/package.py
@@ -0,0 +1,34 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Orthofinder(Package):
+    """OrthoFinder is a fast, accurate and comprehensive analysis tool for
+    comparative genomics.
+
+    It finds orthologues and orthogroups infers rooted  gene trees for all
+    orthogroups and infers a rooted species tree for the species being
+    analysed. OrthoFinder also provides comprehensive statistics for
+    comparative genomic analyses. OrthoFinder is simple to use and all you
+    need to run it is a set of protein sequence files (one per species)
+    in FASTA format."""
+
+    homepage = "https://github.com/davidemms/OrthoFinder"
+    url      = "https://github.com/davidemms/OrthoFinder/releases/download/2.2.0/OrthoFinder-2.2.0.tar.gz"
+
+    version('2.2.0', '4ff585e1eb148fc694a219296fbdd431')
+
+    depends_on('blast-plus', type='run')
+    depends_on('mcl', type='run')
+    depends_on('fastme', type='run')
+    depends_on('py-dlcpar', type='run')
+
+    def install(self, spec, prefix):
+        install_tree('.', prefix.bin)
+
+        chmod = which('chmod')
+        chmod('+x', join_path(prefix.bin, 'orthofinder'))
diff --git a/var/spack/repos/builtin/packages/orthomcl/package.py b/var/spack/repos/builtin/packages/orthomcl/package.py
index 98bef74726..41badd0f3b 100644
--- a/var/spack/repos/builtin/packages/orthomcl/package.py
+++ b/var/spack/repos/builtin/packages/orthomcl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/osu-micro-benchmarks/package.py b/var/spack/repos/builtin/packages/osu-micro-benchmarks/package.py
index 8e5c7be65a..0797824c3b 100644
--- a/var/spack/repos/builtin/packages/osu-micro-benchmarks/package.py
+++ b/var/spack/repos/builtin/packages/osu-micro-benchmarks/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import sys
 
@@ -36,6 +17,7 @@ class OsuMicroBenchmarks(AutotoolsPackage):
     homepage = "http://mvapich.cse.ohio-state.edu/benchmarks/"
     url      = "http://mvapich.cse.ohio-state.edu/download/mvapich/osu-micro-benchmarks-5.3.tar.gz"
 
+    version('5.4', '7e7551879b944d71b7cc60d476d5403b')
     version('5.3', '42e22b931d451e8bec31a7424e4adfc2')
 
     variant('cuda', default=False, description="Enable CUDA support")
diff --git a/var/spack/repos/builtin/packages/otf/package.py b/var/spack/repos/builtin/packages/otf/package.py
index 4df0a12bdf..ee94aa20c4 100644
--- a/var/spack/repos/builtin/packages/otf/package.py
+++ b/var/spack/repos/builtin/packages/otf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/otf2/package.py b/var/spack/repos/builtin/packages/otf2/package.py
index ee08a44328..5999a816fa 100644
--- a/var/spack/repos/builtin/packages/otf2/package.py
+++ b/var/spack/repos/builtin/packages/otf2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -34,6 +15,7 @@ class Otf2(AutotoolsPackage):
     homepage = "http://www.vi-hps.org/projects/score-p"
     url      = "http://www.vi-hps.org/upload/packages/otf2/otf2-1.4.tar.gz"
 
+    version('2.1.1', 'e51ad0d8ca374d25f47426746ca629e7')
     version('2.1',   'e2994e53d9b7c2cbd0c4f564d638751e')
     version('2.0',   '5b546188b25bc1c4e285e06dddf75dfc')
     version('1.5.1', '16a9df46e0da78e374f5d12c8cdc1109')
diff --git a/var/spack/repos/builtin/packages/p4est/package.py b/var/spack/repos/builtin/packages/p4est/package.py
index 56c1ffbc93..ea26ee54f9 100644
--- a/var/spack/repos/builtin/packages/p4est/package.py
+++ b/var/spack/repos/builtin/packages/p4est/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,6 +17,8 @@ class P4est(AutotoolsPackage):
     version('2.0', 'c522c5b69896aab39aa5a81399372a19a6b03fc6200d2d5d677d9a22fe31029a')
     version('1.1', '37ba7f4410958cfb38a2140339dbf64f')
 
+    variant('openmp', default=False, description='Enable OpenMP')
+
     # build dependencies
     depends_on('automake', type='build')
     depends_on('autoconf', type='build')
@@ -45,8 +28,20 @@ class P4est(AutotoolsPackage):
     depends_on('mpi')
     depends_on('zlib')
 
+    # from sc upstream, correct the default libraries
+    patch('https://github.com/cburstedde/libsc/commit/b506aab224b988fec210cc212469f2c4f58b2d04.patch',
+          sha256='e9418b1a9347a409be241cd185519b31950e42a7f55b6fb80ce53097657098ee',
+          working_dir='sc')
+    patch('https://github.com/cburstedde/libsc/commit/b45a51a7ef97883a3d4dcbd05cb2c77890a76f75.patch',
+          sha256='8fb829e34e3a1e28afdd6e56e0bdc1d377af569b7ccb9e9d8da0eeb5829ed27e',
+          working_dir='sc')
+
+    def autoreconf(self, spec, prefix):
+        bootstrap = Executable('./bootstrap')
+        bootstrap()
+
     def configure_args(self):
-        return [
+        args = [
             '--enable-mpi',
             '--enable-shared',
             '--disable-vtk-binary',
@@ -58,3 +53,14 @@ class P4est(AutotoolsPackage):
             'FC=%s'  % self.spec['mpi'].mpifc,
             'F77=%s' % self.spec['mpi'].mpif77
         ]
+
+        if '+openmp' in self.spec:
+            try:
+                args.append(
+                    '--enable-openmp={0}'.format(self.compiler.openmp_flag))
+            except UnsupportedCompilerFlag:
+                args.append('--enable-openmp')
+        else:
+            args.append('--disable-openmp')
+
+        return args
diff --git a/var/spack/repos/builtin/packages/p7zip/package.py b/var/spack/repos/builtin/packages/p7zip/package.py
index 90b7479d80..72665ddc4b 100644
--- a/var/spack/repos/builtin/packages/p7zip/package.py
+++ b/var/spack/repos/builtin/packages/p7zip/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/pacbio-daligner/package.py b/var/spack/repos/builtin/packages/pacbio-daligner/package.py
index e568c7170e..9703eedc93 100644
--- a/var/spack/repos/builtin/packages/pacbio-daligner/package.py
+++ b/var/spack/repos/builtin/packages/pacbio-daligner/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,11 +11,9 @@ class PacbioDaligner(MakefilePackage):
        required for some pacbio utilities."""
 
     homepage = "https://github.com/PacificBiosciences/DALIGNER"
-    url      = "https://github.com/PacificBiosciences/DALIGNER"
+    git      = "https://github.com/PacificBiosciences/DALIGNER.git"
 
-    version('2017-08-05',
-            git='https://github.com/PacificBiosciences/DALIGNER.git',
-            commit='0fe5240d2cc6b55bf9e04465b700b76110749c9d')
+    version('2017-08-05', commit='0fe5240d2cc6b55bf9e04465b700b76110749c9d')
 
     depends_on('gmake', type='build')
     depends_on('pacbio-dazz-db')
diff --git a/var/spack/repos/builtin/packages/pacbio-damasker/package.py b/var/spack/repos/builtin/packages/pacbio-damasker/package.py
index cc32df052b..92ed8fad12 100644
--- a/var/spack/repos/builtin/packages/pacbio-damasker/package.py
+++ b/var/spack/repos/builtin/packages/pacbio-damasker/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,11 +11,9 @@ class PacbioDamasker(MakefilePackage):
        required for some pacbio utilities."""
 
     homepage = "https://github.com/PacificBiosciences/DAMASKER"
-    url      = "https://github.com/PacificBiosciences/DAMASKER"
+    git      = "https://github.com/PacificBiosciences/DAMASKER.git"
 
-    version('2017-02-11',
-            git='https://github.com/PacificBiosciences/DAMASKER.git',
-            commit='144244b77d52cb785cb1b3b8ae3ab6f3f0c63264')
+    version('2017-02-11', commit='144244b77d52cb785cb1b3b8ae3ab6f3f0c63264')
 
     depends_on('gmake', type='build')
 
diff --git a/var/spack/repos/builtin/packages/pacbio-dazz-db/package.py b/var/spack/repos/builtin/packages/pacbio-dazz-db/package.py
index 595ab4cd15..8d79eb9e3c 100644
--- a/var/spack/repos/builtin/packages/pacbio-dazz-db/package.py
+++ b/var/spack/repos/builtin/packages/pacbio-dazz-db/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -31,11 +12,9 @@ class PacbioDazzDb(MakefilePackage):
        required for some pacbio utilities."""
 
     homepage = "https://github.com/PacificBiosciences/DAZZ_DB"
-    url      = "https://github.com/PacificBiosciences/DAZZ_DB"
+    git      = "https://github.com/PacificBiosciences/DAZZ_DB.git"
 
-    version('2017-04-10',
-            git='https://github.com/PacificBiosciences/DAZZ_DB.git',
-            commit='f29d27d51f460563481cd227d17f4bdc5e288365')
+    version('2017-04-10', commit='f29d27d51f460563481cd227d17f4bdc5e288365')
 
     depends_on('gmake', type='build')
 
diff --git a/var/spack/repos/builtin/packages/pacbio-dextractor/package.py b/var/spack/repos/builtin/packages/pacbio-dextractor/package.py
index 75bc553733..43630ecc5e 100644
--- a/var/spack/repos/builtin/packages/pacbio-dextractor/package.py
+++ b/var/spack/repos/builtin/packages/pacbio-dextractor/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,11 +11,9 @@ class PacbioDextractor(MakefilePackage):
        fork required by some pacbio utilities."""
 
     homepage = "https://github.com/PacificBiosciences/DEXTRACTOR"
-    url      = "https://github.com/PacificBiosciences/DEXTRACTOR"
+    git      = "https://github.com/PacificBiosciences/DEXTRACTOR.git"
 
-    version('2016-08-09',
-            git='https://github.com/PacificBiosciences/DEXTRACTOR.git',
-            commit='89726800346d0bed15d98dcc577f4c7733aab4b1')
+    version('2016-08-09', commit='89726800346d0bed15d98dcc577f4c7733aab4b1')
 
     depends_on('hdf5')
     depends_on('gmake', type='build')
diff --git a/var/spack/repos/builtin/packages/packmol/package.py b/var/spack/repos/builtin/packages/packmol/package.py
new file mode 100644
index 0000000000..873e354f13
--- /dev/null
+++ b/var/spack/repos/builtin/packages/packmol/package.py
@@ -0,0 +1,16 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Packmol(CMakePackage):
+    """Packmol creates an initial point for molecular dynamics simulations
+    by packing molecules in defined regions of space."""
+
+    homepage = "http://m3g.iqm.unicamp.br/packmol/home.shtml"
+    url      = "https://github.com/mcubeg/packmol/archive/18.169.tar.gz"
+
+    version('18.169', sha256='8acf2cbc742a609e763eb00cae55aecd09af2edb4cc4e931706e2f06ac380de9')
diff --git a/var/spack/repos/builtin/packages/pacvim/package.py b/var/spack/repos/builtin/packages/pacvim/package.py
new file mode 100644
index 0000000000..1a2fa45637
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pacvim/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Pacvim(MakefilePackage):
+    """Pacvim is a command-line-based game based off of Pacman.
+       The main purpose of this software is to familiarize individuals
+       with Vim."""
+
+    homepage = "https://github.com/jmoon018/PacVim"
+    url      = "https://github.com/jmoon018/PacVim/archive/v1.1.1.tar.gz"
+
+    version('1.1.1', sha256='c869c5450fbafdfe8ba8a8a9bba3718775926f276f0552052dcfa090d21acb28')
+
+    depends_on('ncurses')
+
+    def edit(self, stage, prefix):
+        makefile = FileFilter('Makefile')
+
+        makefile.filter(r'PREFIX = /usr/local',
+                        'PREFIX={0}'.format(self.prefix))
diff --git a/var/spack/repos/builtin/packages/pagit/package.py b/var/spack/repos/builtin/packages/pagit/package.py
index 7c40da934b..b45154befd 100644
--- a/var/spack/repos/builtin/packages/pagit/package.py
+++ b/var/spack/repos/builtin/packages/pagit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/pagmo/package.py b/var/spack/repos/builtin/packages/pagmo/package.py
index 0d30d847f0..4367500442 100644
--- a/var/spack/repos/builtin/packages/pagmo/package.py
+++ b/var/spack/repos/builtin/packages/pagmo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/paml/package.py b/var/spack/repos/builtin/packages/paml/package.py
index 81d9e7c25b..9805e6bccd 100644
--- a/var/spack/repos/builtin/packages/paml/package.py
+++ b/var/spack/repos/builtin/packages/paml/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,9 @@ class Paml(MakefilePackage):
        protein sewuences using maximum likelihood."""
 
     homepage = "http://abacus.gene.ucl.ac.uk/software/paml.html"
-    url      = "http://abacus.gene.ucl.ac.uk/software/paml4.9e.tgz"
+    url      = "http://abacus.gene.ucl.ac.uk/software/paml4.9h.tgz"
 
-    version('4.9e', 'ac5a062bfea1f4eaac79008434030acf')
+    version('4.9h', sha256='623bf6cf4a018a4e7b4dbba189c41d6c0c25fdca3a0ae24703b82965c772edb3')
 
     build_directory = 'src'
 
diff --git a/var/spack/repos/builtin/packages/panda/package.py b/var/spack/repos/builtin/packages/panda/package.py
index 30323fa65a..72bac89f33 100644
--- a/var/spack/repos/builtin/packages/panda/package.py
+++ b/var/spack/repos/builtin/packages/panda/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/pandaseq/package.py b/var/spack/repos/builtin/packages/pandaseq/package.py
new file mode 100644
index 0000000000..877a55dd6b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pandaseq/package.py
@@ -0,0 +1,30 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Pandaseq(AutotoolsPackage):
+    """PANDASEQ is a program to align Illumina reads, optionally with PCR
+    primers embedded in the sequence, and reconstruct an overlapping
+    sequence."""
+
+    homepage = "https://github.com/neufeld/pandaseq"
+    url      = "https://github.com/neufeld/pandaseq/archive/v2.11.tar.gz"
+
+    version('2.11', 'a8ae0e938bac592fc07dfa668147d80b')
+    version('2.10', '5b5b04c9b693a999f10a9c9bd643f068')
+
+    depends_on('autoconf',    type='build')
+    depends_on('automake',    type='build')
+    depends_on('libtool',     type=('build', 'link'))
+    depends_on('m4',          type='build')
+    depends_on('zlib',        type='build')
+    depends_on('pkgconfig',   type='build')
+    depends_on('bzip2',       type='link')
+
+    def autoreconf(self, spec, prefix):
+        bash = which('bash')
+        bash('./autogen.sh')
diff --git a/var/spack/repos/builtin/packages/pango/package.py b/var/spack/repos/builtin/packages/pango/package.py
index 26ba05df6a..ced2c63065 100644
--- a/var/spack/repos/builtin/packages/pango/package.py
+++ b/var/spack/repos/builtin/packages/pango/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,13 +16,14 @@ class Pango(AutotoolsPackage):
     list_url = "http://ftp.gnome.org/pub/gnome/sources/pango/"
     list_depth = 1
 
+    version('1.41.0', '1f76ef95953dc58ee5d6a53e5f1cb6db913f3e0eb489713ee9266695cae580ba')
     version('1.40.3', 'abba8b5ce728520c3a0f1535eab19eac3c14aeef7faa5aded90017ceac2711d3')
     version('1.40.1', 'e27af54172c72b3ac6be53c9a4c67053e16c905e02addcf3a603ceb2005c1a40')
     version('1.36.8', '18dbb51b8ae12bae0ab7a958e7cf3317c9acfc8a1e1103ec2f147164a0fc2d07')
 
     variant('X', default=False, description="Enable an X toolkit")
 
-    depends_on("pkg-config", type="build")
+    depends_on("pkgconfig", type="build")
     depends_on("harfbuzz")
     depends_on("cairo")
     depends_on("cairo~X", when='~X')
@@ -50,6 +32,10 @@ class Pango(AutotoolsPackage):
     depends_on("glib")
     depends_on('gobject-introspection')
 
+    def url_for_version(self, version):
+        url = "http://ftp.gnome.org/pub/GNOME/sources/pango/{0}/pango-{1}.tar.xz"
+        return url.format(version.up_to(2), version)
+
     def configure_args(self):
         args = []
         if self.spec.satisfies('+X'):
diff --git a/var/spack/repos/builtin/packages/pangomm/package.py b/var/spack/repos/builtin/packages/pangomm/package.py
new file mode 100644
index 0000000000..e4275eef8d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pangomm/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Pangomm(AutotoolsPackage):
+    """Pangomm is a C++ interface to Pango."""
+
+    homepage = "http://www.pango.org/"
+    url      = "https://ftp.gnome.org/pub/GNOME/sources/pangomm/2.14/pangomm-2.14.1.tar.gz"
+
+    version('2.14.1', '607a404291d9eeb895f1df3d08f531d7')
+    version('2.14.0', '897d8c56cec4a9c297a426eb0fc2af91')
+
+    depends_on('pango')
+    depends_on('glibmm')
+    depends_on('cairomm')
+
+    def url_for_version(self, version):
+        """Handle version-based custom URLs."""
+        url = "https://ftp.acc.umu.se/pub/GNOME/sources/pangomm"
+        ext = '.tar.gz' if version < Version('2.28.3') else '.tar.xz'
+        return url + "/%s/pangomm-%s%s" % (version.up_to(2), version, ext)
diff --git a/var/spack/repos/builtin/packages/papi/package.py b/var/spack/repos/builtin/packages/papi/package.py
index 4809295bb6..57de47f4d9 100644
--- a/var/spack/repos/builtin/packages/papi/package.py
+++ b/var/spack/repos/builtin/packages/papi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
 import os
@@ -41,12 +22,17 @@ class Papi(Package):
     homepage = "http://icl.cs.utk.edu/papi/index.html"
 
     url      = "http://icl.cs.utk.edu/projects/papi/downloads/papi-5.4.1.tar.gz"
+    version('5.6.0', 'fdd075860b2bc4b8de8b8b5c3abf594a')
     version('5.5.1', '86a8a6f3d0f34cd83251da3514aae15d')
     version('5.5.0', '5e1244a04ca031d4cc29b46ce3dd05b5')
     version('5.4.3', '3211b5a5bb389fe692370f5cf4cc2412')
     version('5.4.1', '9134a99219c79767a11463a76b0b01a2')
     version('5.3.0', '367961dd0ab426e5ae367c2713924ffb')
 
+    # Does not build with newer versions of gcc, see
+    # https://bitbucket.org/icl/papi/issues/46/cannot-compile-on-arch-linux
+    patch('https://bitbucket.org/icl/papi/commits/53de184a162b8a7edff48fed01a15980664e15b1/raw', sha256='64c57b3ad4026255238cc495df6abfacc41de391a0af497c27d0ac819444a1f8', when='@5.4.0:5.6.99%gcc@8')
+
     def install(self, spec, prefix):
         with working_dir("src"):
 
diff --git a/var/spack/repos/builtin/packages/papyrus/package.py b/var/spack/repos/builtin/packages/papyrus/package.py
new file mode 100644
index 0000000000..c3a1f8e52c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/papyrus/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Papyrus(CMakePackage):
+    """Parallel Aggregate Persistent Storage"""
+
+    homepage = "https://code.ornl.gov/eck/papyrus"
+    url      = "https://code.ornl.gov/eck/papyrus/repository/archive.tar.bz2?ref=v1.0.0"
+    git      = "https://code.ornl.gov/eck/papyrus.git"
+
+    version('develop', branch='master')
+    version('1.0.0', 'fe0fca073c3604110f0507f375d71e64')
+
+    depends_on('mpi')
diff --git a/var/spack/repos/builtin/packages/paradiseo/package.py b/var/spack/repos/builtin/packages/paradiseo/package.py
index 036d7cdb4f..c559f6cf59 100644
--- a/var/spack/repos/builtin/packages/paradiseo/package.py
+++ b/var/spack/repos/builtin/packages/paradiseo/package.py
@@ -1,46 +1,27 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class Paradiseo(CMakePackage):
     """A C++ white-box object-oriented framework dedicated to the reusable
        design of metaheuristics."""
+
     homepage = "http://paradiseo.gforge.inria.fr/"
+    git      = "https://gforge.inria.fr/git/paradiseo/paradiseo.git"
 
     # Installing from the development version is a better option at this
     # point than using the very old supplied packages
-    version('head', git='https://gforge.inria.fr/git/paradiseo/paradiseo.git')
+    version('head')
 
     # This is a version that the package formula author has tested
     # successfully.  However, the clone is very large (~1Gb git
     # history). The history in the head version has been trimmed
     # significantly.
-    version(
-        'dev-safe', git='https://gforge.inria.fr/git/paradiseo/paradiseo.git',
-        commit='dbb8fbe9a786efd4d1c26408ac1883442e7643a6')
+    version('dev-safe', commit='dbb8fbe9a786efd4d1c26408ac1883442e7643a6')
 
     variant('mpi',      default=True,
             description='Compile with parallel and distributed '
diff --git a/var/spack/repos/builtin/packages/parallel-netcdf/package.py b/var/spack/repos/builtin/packages/parallel-netcdf/package.py
index 4d49ae6f8b..c1bde21108 100644
--- a/var/spack/repos/builtin/packages/parallel-netcdf/package.py
+++ b/var/spack/repos/builtin/packages/parallel-netcdf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -53,6 +34,10 @@ class ParallelNetcdf(AutotoolsPackage):
         spec = self.spec
 
         args = ['--with-mpi={0}'.format(spec['mpi'].prefix)]
+        args.append('MPICC={0}'.format(spec['mpi'].mpicc))
+        args.append('MPICXX={0}'.format(spec['mpi'].mpicxx))
+        args.append('MPIF77={0}'.format(spec['mpi'].mpifc))
+        args.append('MPIF90={0}'.format(spec['mpi'].mpifc))
         args.append('SEQ_CC={0}'.format(spack_cc))
 
         if '+pic' in spec:
@@ -69,3 +54,7 @@ class ParallelNetcdf(AutotoolsPackage):
             args.append('--disable-fortran')
 
         return args
+
+    def install(self, spec, prefix):
+        # Installation fails in parallel
+        make('install', parallel=False)
diff --git a/var/spack/repos/builtin/packages/parallel/package.py b/var/spack/repos/builtin/packages/parallel/package.py
index 407eb4af09..dbc7c8085e 100644
--- a/var/spack/repos/builtin/packages/parallel/package.py
+++ b/var/spack/repos/builtin/packages/parallel/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,7 +13,7 @@ class Parallel(AutotoolsPackage):
     """
 
     homepage = "http://www.gnu.org/software/parallel/"
-    url      = "http://ftp.gnu.org/gnu/parallel/parallel-20170122.tar.bz2"
+    url      = "https://ftpmirror.gnu.org/parallel/parallel-20170122.tar.bz2"
 
     version('20170322', '4fe1b8d2e3974d26c77f0b514988214d')
     version('20170122', 'c9f0ec01463dc75dbbf292fd8be5f1eb')
diff --git a/var/spack/repos/builtin/packages/paraver/package.py b/var/spack/repos/builtin/packages/paraver/package.py
index 3a015d4b63..5945e06d69 100644
--- a/var/spack/repos/builtin/packages/paraver/package.py
+++ b/var/spack/repos/builtin/packages/paraver/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
diff --git a/var/spack/repos/builtin/packages/paraview/package.py b/var/spack/repos/builtin/packages/paraview/package.py
index 8bf43b6132..32fdf3746a 100644
--- a/var/spack/repos/builtin/packages/paraview/package.py
+++ b/var/spack/repos/builtin/packages/paraview/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
@@ -34,6 +15,9 @@ class Paraview(CMakePackage):
     url      = "http://www.paraview.org/files/v5.3/ParaView-v5.3.0.tar.gz"
     _urlfmt  = 'http://www.paraview.org/files/v{0}/ParaView-v{1}{2}.tar.gz'
 
+    version('5.5.2', '7eb93c31a1e5deb7098c3b4275e53a4a')
+    version('5.5.1', 'a7d92a45837b67c3371006cc45163277')
+    version('5.5.0', 'a8f2f41edadffdcc89b37fdc9aa7f005')
     version('5.4.1', '4030c70477ec5a85aa72d6fc86a30753')
     version('5.4.0', 'b92847605bac9036414b644f33cb7163')
     version('5.3.0', '68fbbbe733aa607ec13d1db1ab5eba71')
@@ -49,21 +33,27 @@ class Paraview(CMakePackage):
     variant('osmesa', default=False, description='Enable OSMesa support')
     variant('qt', default=False, description='Enable Qt (gui) support')
     variant('opengl2', default=True, description='Enable OpenGL2 backend')
+    variant('examples', default=False, description="Build examples")
+    variant('hdf5', default=False, description="Use external HDF5")
 
     depends_on('python@2:2.8', when='+python')
     depends_on('py-numpy', when='+python', type='run')
     depends_on('py-matplotlib', when='+python', type='run')
     depends_on('mpi', when='+mpi')
-    depends_on('qt', when='@5.3.0:+qt')
+    depends_on('qt+opengl', when='@5.3.0:+qt+opengl2')
+    depends_on('qt~opengl', when='@5.3.0:+qt~opengl2')
     depends_on('qt@:4', when='@:5.2.0+qt')
 
     depends_on('mesa+swrender', when='+osmesa')
+    depends_on('libxt', when='+qt')
     conflicts('+qt', when='+osmesa')
 
     depends_on('bzip2')
     depends_on('freetype')
     # depends_on('hdf5+mpi', when='+mpi')
     # depends_on('hdf5~mpi', when='~mpi')
+    depends_on('hdf5+hl+mpi', when='+hdf5+mpi')
+    depends_on('hdf5+hl~mpi', when='+hdf5~mpi')
     depends_on('jpeg')
     depends_on('libpng')
     depends_on('libtiff')
@@ -90,6 +80,15 @@ class Paraview(CMakePackage):
         else:
             return self._urlfmt.format(version.up_to(2), version, '')
 
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        if os.path.isdir(self.prefix.lib64):
+            lib_dir = self.prefix.lib64
+        else:
+            lib_dir = self.prefix.lib
+        paraview_version = 'paraview-%s' % self.spec.version.up_to(2)
+        spack_env.set('PARAVIEW_VTK_DIR',
+                      join_path(lib_dir, 'cmake', paraview_version))
+
     def setup_environment(self, spack_env, run_env):
         if os.path.isdir(self.prefix.lib64):
             lib_dir = self.prefix.lib64
@@ -100,6 +99,15 @@ class Paraview(CMakePackage):
                              paraview_version))
         run_env.prepend_path('LD_LIBRARY_PATH', join_path(lib_dir,
                              paraview_version))
+        run_env.set('PARAVIEW_VTK_DIR',
+                    join_path(lib_dir, 'cmake', paraview_version))
+        if '+python' in self.spec:
+            run_env.prepend_path('PYTHONPATH', join_path(lib_dir,
+                                 paraview_version))
+            run_env.prepend_path('PYTHONPATH', join_path(lib_dir,
+                                 paraview_version, 'site-packages'))
+            run_env.prepend_path('PYTHONPATH', join_path(lib_dir,
+                                 paraview_version, 'site-packages', 'vtk'))
 
     def cmake_args(self):
         """Populate cmake arguments for ParaView."""
@@ -125,8 +133,9 @@ class Paraview(CMakePackage):
             '-DVTK_RENDERING_BACKEND:STRING=%s' % rendering,
             '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES:BOOL=%s' % includes,
             '-DBUILD_TESTING:BOOL=OFF',
+            '-DBUILD_EXAMPLES:BOOL=%s' % variant_bool('+examples'),
             '-DVTK_USE_SYSTEM_FREETYPE:BOOL=ON',
-            '-DVTK_USE_SYSTEM_HDF5:BOOL=OFF',
+            '-DVTK_USE_SYSTEM_HDF5:BOOL=%s' % variant_bool('+hdf5'),
             '-DVTK_USE_SYSTEM_JPEG:BOOL=ON',
             '-DVTK_USE_SYSTEM_LIBXML2:BOOL=ON',
             '-DVTK_USE_SYSTEM_NETCDF:BOOL=OFF',
@@ -150,7 +159,10 @@ class Paraview(CMakePackage):
         if '+mpi' in spec:
             cmake_args.extend([
                 '-DPARAVIEW_USE_MPI:BOOL=ON',
-                '-DMPIEXEC:FILEPATH=%s/bin/mpiexec' % spec['mpi'].prefix
+                '-DMPIEXEC:FILEPATH=%s/bin/mpiexec' % spec['mpi'].prefix,
+                '-DMPI_CXX_COMPILER:PATH=%s' % spec['mpi'].mpicxx,
+                '-DMPI_C_COMPILER:PATH=%s' % spec['mpi'].mpicc,
+                '-DMPI_Fortran_COMPILER:PATH=%s' % spec['mpi'].mpifc
             ])
 
         if 'darwin' in spec.architecture:
diff --git a/var/spack/repos/builtin/packages/parmetis/package.py b/var/spack/repos/builtin/packages/parmetis/package.py
index 565c06686c..dad8a7cb1e 100644
--- a/var/spack/repos/builtin/packages/parmetis/package.py
+++ b/var/spack/repos/builtin/packages/parmetis/package.py
@@ -1,33 +1,14 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 import sys
 
 
-class Parmetis(Package):
+class Parmetis(CMakePackage):
     """ParMETIS is an MPI-based parallel library that implements a variety of
        algorithms for partitioning unstructured graphs, meshes, and for
        computing fill-reducing orderings of sparse matrices."""
@@ -40,7 +21,6 @@ class Parmetis(Package):
     version('4.0.2', '0912a953da5bb9b5e5e10542298ffdce')
 
     variant('shared', default=True, description='Enables the build of shared libraries.')
-    variant('debug', default=False, description='Builds the library in debug mode.')
     variant('gdb', default=False, description='Enables gdb support.')
 
     depends_on('cmake@2.8:', type='build')
@@ -68,11 +48,10 @@ class Parmetis(Package):
         url += '/parmetis-{0}.tar.gz'.format(version)
         return url
 
-    def install(self, spec, prefix):
-        source_directory = self.stage.source_path
-        build_directory = join_path(source_directory, 'build')
+    def cmake_args(self):
+        spec = self.spec
 
-        options = std_cmake_args[:]
+        options = []
         options.extend([
             '-DGKLIB_PATH:PATH=%s/GKlib' % spec['metis'].prefix.include,
             '-DMETIS_PATH:PATH=%s' % spec['metis'].prefix,
@@ -92,17 +71,13 @@ class Parmetis(Package):
             for o in rpath_options:
                 options.remove(o)
 
-        if '+debug' in spec:
-            options.extend(['-DDEBUG:BOOL=ON',
-                            '-DCMAKE_BUILD_TYPE:STRING=Debug'])
         if '+gdb' in spec:
             options.append('-DGDB:BOOL=ON')
 
-        with working_dir(build_directory, create=True):
-            cmake(source_directory, *options)
-            make()
-            make('install')
+        return options
 
-            # The shared library is not installed correctly on Darwin; fix this
-            if (sys.platform == 'darwin') and ('+shared' in spec):
-                fix_darwin_install_name(prefix.lib)
+    @run_after('install')
+    def darwin_fix(self):
+        # The shared library is not installed correctly on Darwin; fix this
+        if (sys.platform == 'darwin') and ('+shared' in self.spec):
+            fix_darwin_install_name(prefix.lib)
diff --git a/var/spack/repos/builtin/packages/parmgridgen/package.py b/var/spack/repos/builtin/packages/parmgridgen/package.py
index bbacf519fa..58960caaf2 100644
--- a/var/spack/repos/builtin/packages/parmgridgen/package.py
+++ b/var/spack/repos/builtin/packages/parmgridgen/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/parquet/package.py b/var/spack/repos/builtin/packages/parquet/package.py
new file mode 100644
index 0000000000..ce683895f6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/parquet/package.py
@@ -0,0 +1,41 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Parquet(CMakePackage):
+    """C++ bindings for the Apache Parquet columnar data format.
+    """
+
+    homepage = "https://github.com/apache/parquet-cpp"
+    url = "https://github.com/apache/parquet-cpp/archive/apache-parquet-cpp-1.4.0.tar.gz"
+
+    version('1.4.0', '3a3659e65052ef5a76fb88e4922283b9')
+
+    depends_on('arrow')
+    depends_on('boost')
+    depends_on('cmake@3.2.0:', type='build')
+    depends_on('pkgconfig', type='build')
+    depends_on('thrift+pic')
+
+    variant('pic', default=True,
+            description='Build position independent code')
+    variant('build_type', default='Release',
+            description='CMake build type',
+            values=('Debug', 'FastDebug', 'Release'))
+
+    def cmake_args(self):
+        args = ['-DPARQUET_USE_SSE=OFF', '-DPARQUET_BUILD_TESTS=OFF']
+        for dep in ('arrow', 'thrift'):
+            args.append("-D{0}_HOME={1}".format(dep.upper(),
+                                                self.spec[dep].prefix))
+        return args
+
+    def flag_handler(self, name, flags):
+        flags = list(flags)
+        if '+pic' in self.spec and name in ('cflags', 'cxxflags'):
+            flags.append(self.compiler.pic_flag)
+        return (None, None, flags)
diff --git a/var/spack/repos/builtin/packages/parsimonator/package.py b/var/spack/repos/builtin/packages/parsimonator/package.py
index 462f81e6cf..70ac718ae9 100644
--- a/var/spack/repos/builtin/packages/parsimonator/package.py
+++ b/var/spack/repos/builtin/packages/parsimonator/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,9 @@ class Parsimonator(MakefilePackage):
        starting trees under parsimony for RAxML"""
 
     homepage = "http://www.exelixis-lab.org/"
-    url      = "https://github.com/stamatak/Parsimonator-1.0.2"
+    git      = "https://github.com/stamatak/Parsimonator-1.0.2.git"
 
-    version('1.0.2', git='https://github.com/stamatak/Parsimonator-1.0.2.git', commit='78368c6ab1e9adc7e9c6ec9256dd7ff2a5bb1b0a')
+    version('1.0.2', commit='78368c6ab1e9adc7e9c6ec9256dd7ff2a5bb1b0a')
 
     variant('sse', default=True, description='Enable SSE in order to substantially speed up execution')
     variant('avx', default=False, description='Enable AVX in order to substantially speed up execution')
diff --git a/var/spack/repos/builtin/packages/parsplice/package.py b/var/spack/repos/builtin/packages/parsplice/package.py
index 24b950548f..e07a704eb8 100644
--- a/var/spack/repos/builtin/packages/parsplice/package.py
+++ b/var/spack/repos/builtin/packages/parsplice/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -30,10 +11,13 @@ class Parsplice(CMakePackage):
     """ParSplice code implements the Parallel Trajectory Splicing algorithm"""
 
     homepage = "https://gitlab.com/exaalt/parsplice"
-    url      = "https://gitlab.com/exaalt/parsplice/repository/archive.tar.gz?ref=v1.1"
+    url      = "https://gitlab.com/api/v4/projects/exaalt%2Fparsplice/repository/archive.tar.gz?sha=v1.1"
+    git      = "https://gitlab.com/exaalt/parsplice.git"
+
+    tags = ['ecp', 'ecp-apps']
 
+    version('develop', branch='master')
     version('1.1', '3a72340d49d731a076e8942f2ae2f4e9')
-    version('develop', git='https://gitlab.com/exaalt/parsplice', branch='master')
 
     depends_on("cmake@3.1:", type='build')
     depends_on("berkeley-db")
diff --git a/var/spack/repos/builtin/packages/partitionfinder/package.py b/var/spack/repos/builtin/packages/partitionfinder/package.py
index 3089eca783..6c36c33c5c 100644
--- a/var/spack/repos/builtin/packages/partitionfinder/package.py
+++ b/var/spack/repos/builtin/packages/partitionfinder/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/patch/package.py b/var/spack/repos/builtin/packages/patch/package.py
index 6c69b7994f..78868feacf 100644
--- a/var/spack/repos/builtin/packages/patch/package.py
+++ b/var/spack/repos/builtin/packages/patch/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,8 +13,9 @@ class Patch(AutotoolsPackage):
     """
 
     homepage = "http://savannah.gnu.org/projects/patch/"
-    url      = "http://ftp.gnu.org/gnu/patch/patch-2.7.5.tar.xz"
+    url      = "https://ftpmirror.gnu.org/patch/patch-2.7.6.tar.xz"
 
+    version('2.7.6', '78ad9937e4caadcba1526ef1853730d5')
     version('2.7.5', 'e3da7940431633fb65a01b91d3b7a27a')
 
     build_directory = 'spack-build'
diff --git a/var/spack/repos/builtin/packages/patchelf/package.py b/var/spack/repos/builtin/packages/patchelf/package.py
index 273d10486c..793991cb3e 100644
--- a/var/spack/repos/builtin/packages/patchelf/package.py
+++ b/var/spack/repos/builtin/packages/patchelf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/pathfinder/package.py b/var/spack/repos/builtin/packages/pathfinder/package.py
index 79bba915d0..ec17859780 100644
--- a/var/spack/repos/builtin/packages/pathfinder/package.py
+++ b/var/spack/repos/builtin/packages/pathfinder/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/pax-utils/package.py b/var/spack/repos/builtin/packages/pax-utils/package.py
index 0230419ac0..58a77568b7 100644
--- a/var/spack/repos/builtin/packages/pax-utils/package.py
+++ b/var/spack/repos/builtin/packages/pax-utils/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/pbbam/package.py b/var/spack/repos/builtin/packages/pbbam/package.py
new file mode 100644
index 0000000000..67e2e8c585
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pbbam/package.py
@@ -0,0 +1,43 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Pbbam(CMakePackage):
+    """The pbbam software package provides components to create, query,
+    & edit PacBio BAM files and associated indices.
+    These components include a core C++ library,
+    bindings for additional languages, and command-line utilities."""
+
+    homepage = "https://github.com/PacificBiosciences/pbbam"
+    url      = "https://github.com/PacificBiosciences/pbbam/archive/0.18.0.tar.gz"
+
+    version('0.18.0', 'abbb687b1e7ea08916c26da828e11384')
+
+    depends_on('zlib')
+    depends_on('boost@1.55.0:')
+    depends_on('htslib@1.3.1:')
+    depends_on('doxygen+graphviz')
+
+    conflicts('%gcc@:5.2.0')
+
+    def cmake_args(self):
+        options = []
+        if self.run_tests:
+            options.append('-DPacBioBAM_build_tests:BOOL=ON')
+        else:
+            options.append('-DPacBioBAM_build_tests:BOOL=OFF')
+
+        return options
+
+    def install(self, spec, prefix):
+        install_tree('spack-build/bin', prefix.bin)
+        install_tree('spack-build/lib', prefix.lib)
+        install_tree('include/pbbam', prefix.include.pbbam)
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        spack_env.set('PacBioBAM_LIBRARIES', self.prefix.lib)
+        spack_env.set('PacBioBAM_INCLUDE_DIRS', self.prefix.include)
diff --git a/var/spack/repos/builtin/packages/pbmpi/package.py b/var/spack/repos/builtin/packages/pbmpi/package.py
index a8bbece03d..f0432453ed 100644
--- a/var/spack/repos/builtin/packages/pbmpi/package.py
+++ b/var/spack/repos/builtin/packages/pbmpi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,9 @@ class Pbmpi(MakefilePackage):
     """
 
     homepage = "http://megasun.bch.umontreal.ca/People/lartillot/www/index.htm"
-    url      = "https://github.com/bayesiancook/pbmpi"
+    git      = "https://github.com/bayesiancook/pbmpi.git"
 
-    version('partition', git='https://github.com/bayesiancook/pbmpi.git', branch='partition')
+    version('partition', branch='partition')
 
     depends_on('mpi')
     depends_on('libfabric')
diff --git a/var/spack/repos/builtin/packages/pcma/package.py b/var/spack/repos/builtin/packages/pcma/package.py
index d4f998d104..7d4f084402 100644
--- a/var/spack/repos/builtin/packages/pcma/package.py
+++ b/var/spack/repos/builtin/packages/pcma/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/pcre/package.py b/var/spack/repos/builtin/packages/pcre/package.py
index 213a49f731..32d61f10af 100644
--- a/var/spack/repos/builtin/packages/pcre/package.py
+++ b/var/spack/repos/builtin/packages/pcre/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,8 +12,10 @@ class Pcre(AutotoolsPackage):
     pattern matching using the same syntax and semantics as Perl 5."""
 
     homepage = "http://www.pcre.org"
-    url      = "https://ftp.pcre.org/pub/pcre/pcre-8.40.tar.bz2"
+    url      = "https://ftp.pcre.org/pub/pcre/pcre-8.42.tar.bz2"
 
+    version('8.42', '085b6aa253e0f91cae70b3cdbe8c1ac2')
+    version('8.41', 'c160d22723b1670447341b08c58981c1')
     version('8.40', '41a842bf7dcecd6634219336e2167d1d')
     version('8.39', 'e3fca7650a0556a2647821679d81f585')
     version('8.38', '00aabbfe56d5a48b270f999b508c5ad2')
diff --git a/var/spack/repos/builtin/packages/pcre2/package.py b/var/spack/repos/builtin/packages/pcre2/package.py
index 531a175ef7..855696dbf3 100644
--- a/var/spack/repos/builtin/packages/pcre2/package.py
+++ b/var/spack/repos/builtin/packages/pcre2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,7 +10,9 @@ class Pcre2(AutotoolsPackage):
     """The PCRE2 package contains Perl Compatible Regular Expression
        libraries. These are useful for implementing regular expression
        pattern matching using the same syntax and semantics as Perl 5."""
+
     homepage = "http://www.pcre.org"""
-    url      = "https://ftp.pcre.org/pub/pcre/pcre2-10.20.tar.bz2"
+    url      = "https://ftp.pcre.org/pub/pcre/pcre2-10.31.tar.bz2"
 
+    version('10.31', 'e0b91c891a3c49050f7fd15de33d0ba4')
     version('10.20', 'dcd027c57ecfdc8a6c3af9d0acf5e3f7')
diff --git a/var/spack/repos/builtin/packages/pdf2svg/package.py b/var/spack/repos/builtin/packages/pdf2svg/package.py
new file mode 100644
index 0000000000..7253d498c2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pdf2svg/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Pdf2svg(AutotoolsPackage):
+    """A simple PDF to SVG converter using the Poppler and Cairo libraries."""
+
+    homepage = "http://www.cityinthesky.co.uk/opensource/pdf2svg"
+    url      = "https://github.com/dawbarton/pdf2svg/archive/v0.2.3.tar.gz"
+
+    version('0.2.3', 'd398b3b1c1979f554596238a44f12123')
+    version('0.2.2', 'f7e0d2213f9e1422cee9421e18f72553')
+
+    depends_on('cairo', type='run')
+    depends_on('poppler', type='run')
diff --git a/var/spack/repos/builtin/packages/pdftk/package.py b/var/spack/repos/builtin/packages/pdftk/package.py
new file mode 100644
index 0000000000..10179873c7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pdftk/package.py
@@ -0,0 +1,83 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class Pdftk(MakefilePackage):
+    """PDFtk Server is a command-line tool for working with PDFs. It is
+    commonly used for client-side scripting or server-side processing
+    of PDFs."""
+
+    homepage = "https://www.pdflabs.com/tools/pdftk-server"
+    url      = "https://www.pdflabs.com/tools/pdftk-the-pdf-toolkit/pdftk-2.02-src.zip"
+    # Alternative download locations:
+    # https://sources.debian.org/src/pdftk/
+    # http://archive.ubuntu.com/ubuntu/pool/universe/p/pdftk/pdftk_2.02.orig.tar.gz
+
+    maintainers = ['citibeth']
+
+    version('2.02', '6534365fd6727724f288a556ede33faa')
+
+    depends_on('eclipse-gcj-parser', type='build')
+
+    # Only takes effect in phases not overridden here
+    build_directory = 'pdftk'
+
+    # https://www.pdflabs.com/docs/install-pdftk-on-redhat-or-centos/
+    def edit(self, spec, prefix):
+
+        # ------ Fix install directory in main Makefile
+        makefile = FileFilter(join_path('pdftk', 'Makefile.Base'))
+        makefile.filter('/usr/local/bin', spec.prefix.bin)
+
+        # ------ Create new config file
+        compiler = self.compiler
+        gcc_base = os.path.split(os.path.split(compiler.cxx)[0])[0]
+        gcc_version = compiler.version
+
+        cppflags = (
+            '-DPATH_DELIM=0x2f',
+            '-DASK_ABOUT_WARNINGS=false',
+            '-DUNBLOCK_SIGNALS',
+            '-fdollars-in-identifiers')
+        cxxflags = ('-Wall', '-Wextra', '-Weffc++', '-O2')
+        gcjflags = ('-Wall', '-Wextra', '-O2')
+        vars = [
+            ('VERSUFF', '-%s' % gcc_version),
+            ('CXX', compiler.cxx),
+            ('GCJ', spec['eclipse-gcj-parser'].package.gcj),
+            ('GCJH', join_path(gcc_base, 'bin', 'gcjh')),
+            ('GJAR', join_path(gcc_base, 'bin', 'gjar')),
+            ('LIBGCJ', join_path(
+                gcc_base, 'share', 'java',
+                'libgcj-{0}.jar'.format(gcc_version))),
+            ('AR', 'ar'),
+            ('RM', 'rm'),
+            ('ARFLAGS', 'rs'),
+            ('RMFLAGS', '-vf'),
+            ('CPPFLAGS', ' '.join(cppflags)),
+            ('CXXFLAGS', ' '.join(cxxflags)),
+            ('GCJFLAGS', ' '.join(gcjflags)),
+            ('GCJHFLAGS', '-force'),
+            ('LDLIBS', '-lgcj')
+        ]
+        with open(join_path('pdftk', 'Makefile.Spack'), 'w') as mk:
+            for var, val in vars:
+                mk.write("export {0}={1}\n".format(var, str(val)))
+            mk.write('include Makefile.Base\n')
+
+    def build(self, spec, prefix):
+        compiler = self.compiler
+        gcc_base = os.path.split(os.path.split(compiler.cxx)[0])[0]
+        env['PATH'] = join_path(gcc_base, 'bin') + ':' + env['PATH']
+        with working_dir(self.build_directory):
+            make('-f', 'Makefile.Spack', parallel=False)
+
+    def install(self, spec, prefix):
+        mkdirp(self.spec.prefix.bin)
+        with working_dir(self.build_directory):
+            make('-f', 'Makefile.Spack', 'install', parallel=False)
diff --git a/var/spack/repos/builtin/packages/pdsh/package.py b/var/spack/repos/builtin/packages/pdsh/package.py
index 708dea108c..353ea081a1 100644
--- a/var/spack/repos/builtin/packages/pdsh/package.py
+++ b/var/spack/repos/builtin/packages/pdsh/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/pdt/package.py b/var/spack/repos/builtin/packages/pdt/package.py
index ef8592e44d..503957a6c7 100644
--- a/var/spack/repos/builtin/packages/pdt/package.py
+++ b/var/spack/repos/builtin/packages/pdt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 from spack import *
 
@@ -38,6 +19,9 @@ class Pdt(AutotoolsPackage):
     homepage = "https://www.cs.uoregon.edu/research/pdt/home.php"
     url      = "http://www.cs.uoregon.edu/research/paracomp/pdtoolkit/Download/pdtoolkit-3.22.1.tar.gz"
 
+    version('3.25', '2cad41fcabf4c79cab8780d3b87f7bb4')
+    version('3.24', 'b8fa5189e5602276ce225ba497b617e4')
+    version('3.23', 'd61e7a631a27b00e58def52950230a2c')
     version('3.22.1', 'b56b9b3e621161c7fd9e4908b944840d')
     version('3.22',   '982d667617802962a1f7fe6c4c31184f')
     version('3.21',   '3092ca0d8833b69992c17e63ae66c263')
diff --git a/var/spack/repos/builtin/packages/pegtl/package.py b/var/spack/repos/builtin/packages/pegtl/package.py
index c297854797..b04d65fba2 100644
--- a/var/spack/repos/builtin/packages/pegtl/package.py
+++ b/var/spack/repos/builtin/packages/pegtl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -34,8 +15,9 @@ class Pegtl(CMakePackage):
     """
 
     homepage = "https://github.com/taocpp/PEGTL"
-    url      = "https://github.com/taocpp/PEGTL/tarball/1.3.1"
+    url      = "https://github.com/taocpp/PEGTL/tarball/2.1.4"
+    git      = "https://github.com/taocpp/PEGTL.git"
 
-    version('develop', git='https://github.com/taocpp/PEGTL', branch='master')
+    version('develop', branch='master')
     version('2.1.4', 'e5288b6968e6e910287fce93dc5557bf')
     version('2.0.0', 'c772828e7188459338a920c21f9896db')
diff --git a/var/spack/repos/builtin/packages/pennant/package.py b/var/spack/repos/builtin/packages/pennant/package.py
index e318cd991d..f8b6c22815 100644
--- a/var/spack/repos/builtin/packages/pennant/package.py
+++ b/var/spack/repos/builtin/packages/pennant/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/percept/fix_cmakelists.patch b/var/spack/repos/builtin/packages/percept/fix_cmakelists.patch
new file mode 100644
index 0000000000..a3ce6b1d95
--- /dev/null
+++ b/var/spack/repos/builtin/packages/percept/fix_cmakelists.patch
@@ -0,0 +1,54 @@
+--- percept.orig/CMakeLists.txt	2017-12-08 09:16:41.572819000 -0700
++++ percept/CMakeLists.txt	2017-12-08 09:17:25.028818000 -0700
+@@ -97,13 +97,6 @@
+     SET (INSTALL_PERCEPT TRUE)
+ ENDIF()
+ 
+-IF (INSTALL_PERCEPT)
+-  set(BINARY_INSTALL_DIR bin)
+-  set(INCLUDE_INSTALL_DIR include)
+-  set(LIB_INSTALL_DIR lib)
+-  INCLUDE(CMakePackageConfigHelpers)
+-ENDIF ()
+-
+ MESSAGE("Setting and checking of compilers:")
+ SET(CMAKE_CXX_COMPILER ${Trilinos_CXX_COMPILER} )
+ SET(CMAKE_C_COMPILER ${Trilinos_C_COMPILER} )
+@@ -269,6 +262,8 @@
+ FILE (GLOB ADAPT_SOURCE src/adapt/main/*.cpp)
+ MESSAGE("-- ADAPT_SOURCE = ${ADAPT_SOURCE}")
+ 
++file(GLOB TRANSFER_SOURCE src/percept/mesh_transfer/*.cpp)
++
+ FILE (GLOB PERCEPT_UTEST_SOURCE test/unit_tests/*.cpp)
+ MESSAGE("-- PERCEPT_UTEST_SOURCE = ${PERCEPT_UTEST_SOURCE}")
+ 
+@@ -330,8 +325,11 @@
+   TARGET_LINK_LIBRARIES(${percept_lib_name} ${Trilinos_LIBRARIES} ${YAML_LIBRARY} ${OPENNURBS_LIBRARY} ${BOOST_LIBRARIES})
+ #  TARGET_LINK_LIBRARIES(${percept_lib_name} ${GTEST_LIBRARY})
+ 
++  add_executable(mesh_transfer ${TRANSFER_SOURCE})
++  target_link_libraries(mesh_transfer ${percept_lib_name})
++
+   SET_PROPERTY(
+-    TARGET ${percept_lib_name} ${adapt_ex_name} ${percept_utest_name} ${percept_rtest_name}
++    TARGET ${percept_lib_name} mesh_transfer ${adapt_ex_name} ${percept_utest_name} ${percept_rtest_name}
+     PROPERTY COMPILE_DEFINITIONS STK_PERCEPT_LITE=0 STK_PERCEPT_HAS_GEOMETRY STK_PERCEPT_USE_INTREPID
+   )
+ 
+@@ -342,5 +340,15 @@
+ 
+ ENDIF()
+ 
++IF (INSTALL_PERCEPT)
++  install(TARGETS ${percept_ex_name} ${adapt_ex_name}
++          ${percept_htest_name} ${percept_rtest_name} ${percept_utest_name}
++          mesh_transfer percept
++          RUNTIME DESTINATION bin
++          ARCHIVE DESTINATION lib
++          LIBRARY DESTINATION lib)
++  #install(DIRECTORY include/ DESTINATION include)
++  include(CMakePackageConfigHelpers)
++ENDIF ()
+ 
+ MESSAGE("\nAnd CMake says...:")
diff --git a/var/spack/repos/builtin/packages/percept/fix_header.patch b/var/spack/repos/builtin/packages/percept/fix_header.patch
new file mode 100644
index 0000000000..feca6d022c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/percept/fix_header.patch
@@ -0,0 +1,19 @@
+--- percept.orig/src/percept/MeshType.hpp	2017-12-08 09:16:42.080818000 -0700
++++ percept/src/percept/MeshType.hpp	2017-12-08 09:17:25.568819000 -0700
+@@ -11,6 +11,7 @@
+ #include <percept/Percept.hpp>
+ 
+ #include <array>
++#include <memory>
+ #include <stk_mesh/base/Field.hpp>
+ #include <stk_mesh/base/Entity.hpp>
+ #include <stk_mesh/base/Bucket.hpp>
+@@ -62,7 +63,7 @@
+       typedef Kokkos::LayoutRight   SecondaryDataLayout;
+ #endif
+ 
+-	#elif KOKKOS_HAVE_OPENMP
++	#elif defined(KOKKOS_HAVE_OPENMP)
+   	  typedef Kokkos::OpenMP     ExecSpace;
+   	  typedef Kokkos::OpenMP     MemSpace;
+   	  typedef Kokkos::LayoutLeft DataLayout;
diff --git a/var/spack/repos/builtin/packages/percept/package.py b/var/spack/repos/builtin/packages/percept/package.py
new file mode 100644
index 0000000000..40a1d04fc9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/percept/package.py
@@ -0,0 +1,55 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Percept(CMakePackage):
+    """Parallel mesh refinement and adaptivity tools for the finite
+    element method.
+    """
+
+    homepage = "https://github.com/PerceptTools/percept"
+    git      = "https://github.com/PerceptTools/percept.git"
+
+    # This package file was created at percept
+    # commit dc1c8ec0175213146ac139946beca185a84c22e8
+    version('develop', branch='master')
+
+    depends_on('googletest~shared')
+    depends_on('opennurbs@percept')
+    depends_on('boost+graph+mpi')
+    depends_on('yaml-cpp+pic~shared@0.5.3:')
+    # Percept was initially tested against Trilinos 12.12.1
+    depends_on('trilinos~shared+exodus+tpetra+epetra+muelu+belos+ifpack2+amesos2+zoltan+stk+boost~superlu-dist+superlu+hdf5+zlib+pnetcdf+aztec+sacado~openmp+shards+intrepid+cgns@master,12.12.1:')
+
+    patch('fix_cmakelists.patch')
+    patch('fix_header.patch')
+
+    def cmake_args(self):
+        spec = self.spec
+        options = []
+
+        options.extend([
+            '-DSTK_PERCEPT_LITE:BOOL=OFF',
+            '-DSTK_ADAPT_HAVE_YAML_CPP:BOOL=ON',
+            '-DTrilinos_DIR:PATH=%s' %
+            spec['trilinos'].prefix,
+            '-DYAML_DIR:PATH=%s' %
+            spec['yaml-cpp'].prefix,
+            '-DBOOST_DIR:PATH=%s' %
+            spec['boost'].prefix,
+            '-DOPENNURBS_DIR:PATH=%s' %
+            spec['opennurbs'].prefix,
+            '-DOPENNURBS_INCLUDE_DIR:PATH=%s' %
+            spec['opennurbs'].prefix.include,
+            '-DOPENNURBS_LIBRARY_DIR:PATH=%s' %
+            spec['opennurbs'].prefix.lib,
+            '-DPERCEPT_TPLS_INSTALL_DIR:PATH=%s' %
+            spec['googletest'].prefix,
+            '-DENABLE_INSTALL:BOOL=ON'
+        ])
+
+        return options
diff --git a/var/spack/repos/builtin/packages/perl-algorithm-diff/package.py b/var/spack/repos/builtin/packages/perl-algorithm-diff/package.py
index 79f4076da5..707651baea 100644
--- a/var/spack/repos/builtin/packages/perl-algorithm-diff/package.py
+++ b/var/spack/repos/builtin/packages/perl-algorithm-diff/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-app-cmd/package.py b/var/spack/repos/builtin/packages/perl-app-cmd/package.py
new file mode 100644
index 0000000000..3240f053c0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-app-cmd/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlAppCmd(PerlPackage):
+    """Write command line apps with less suffering"""
+
+    homepage = "http://search.cpan.org/~rjbs/App-Cmd/lib/App/Cmd.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/App-Cmd-0.331.tar.gz"
+
+    version('0.331', 'b43c07d7b4d4e2a6baf32aa92cd00b93')
diff --git a/var/spack/repos/builtin/packages/perl-array-utils/package.py b/var/spack/repos/builtin/packages/perl-array-utils/package.py
new file mode 100644
index 0000000000..157cf5c77e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-array-utils/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlArrayUtils(PerlPackage):
+    """Small utils for array manipulation"""
+
+    homepage = "http://search.cpan.org/~zmij/Array-Utils/Utils.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/Z/ZM/ZMIJ/Array/Array-Utils-0.5.tar.gz"
+
+    version('0.5', 'ac15e6dce2c7c9d1855ecab9eb00aee6')
diff --git a/var/spack/repos/builtin/packages/perl-b-hooks-endofscope/package.py b/var/spack/repos/builtin/packages/perl-b-hooks-endofscope/package.py
index eecd0b69cc..39a48c4ea9 100644
--- a/var/spack/repos/builtin/packages/perl-b-hooks-endofscope/package.py
+++ b/var/spack/repos/builtin/packages/perl-b-hooks-endofscope/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-bio-perl/package.py b/var/spack/repos/builtin/packages/perl-bio-perl/package.py
index afbef8001c..6f16117b40 100644
--- a/var/spack/repos/builtin/packages/perl-bio-perl/package.py
+++ b/var/spack/repos/builtin/packages/perl-bio-perl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import inspect
 
diff --git a/var/spack/repos/builtin/packages/perl-bit-vector/package.py b/var/spack/repos/builtin/packages/perl-bit-vector/package.py
new file mode 100644
index 0000000000..1e4360a6c7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-bit-vector/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlBitVector(PerlPackage):
+    """Efficient bit vector, set of integers and "big int" math library"""
+
+    homepage = "http://search.cpan.org/~stbey/Bit-Vector-7.4/Vector.pod"
+    url      = "http://search.cpan.org/CPAN/authors/id/S/ST/STBEY/Bit-Vector-7.4.tar.gz"
+
+    version('7.4', 'bf67f144e5be5327ed79d4c69e6e0086')
+
+    depends_on('perl-carp-clan', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-cairo/package.py b/var/spack/repos/builtin/packages/perl-cairo/package.py
new file mode 100644
index 0000000000..bda7297118
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-cairo/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlCairo(PerlPackage):
+    """Perl interface to the cairo 2d vector graphics library"""
+
+    homepage = "http://search.cpan.org/~xaoc/Cairo/lib/Cairo.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/X/XA/XAOC/Cairo-1.106.tar.gz"
+
+    version('1.106', '47ca0ae0f5b9bc4c16a27627ff48bd8b')
+
+    depends_on('cairo')
+    depends_on('perl-extutils-depends')
+    depends_on('perl-extutils-pkgconfig')
diff --git a/var/spack/repos/builtin/packages/perl-capture-tiny/package.py b/var/spack/repos/builtin/packages/perl-capture-tiny/package.py
index 952ff2999c..6b60946ca5 100644
--- a/var/spack/repos/builtin/packages/perl-capture-tiny/package.py
+++ b/var/spack/repos/builtin/packages/perl-capture-tiny/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-carp-clan/package.py b/var/spack/repos/builtin/packages/perl-carp-clan/package.py
new file mode 100644
index 0000000000..d55ac04be5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-carp-clan/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlCarpClan(PerlPackage):
+    """Report errors from perspective of caller of a "clan" of modules"""
+
+    homepage = "http://search.cpan.org/~kentnl/Carp-Clan-6.06/lib/Carp/Clan.pod"
+    url      = "http://search.cpan.org/CPAN/authors/id/K/KE/KENTNL/Carp-Clan-6.06.tar.gz"
+
+    version('6.06', 'c562a35c48f43665fab735cdc7fe3cb2')
+
+    depends_on('perl-test-exception', type=('build', 'run'))
+    depends_on('perl-sub-uplevel', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-cgi/package.py b/var/spack/repos/builtin/packages/perl-cgi/package.py
new file mode 100644
index 0000000000..4d0294293f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-cgi/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlCgi(PerlPackage):
+    """CGI - Handle Common Gateway Interface requests and responses
+
+       CGI was included in the Perl distribution from 5.4 to 5.20 but
+       has since been removed."""
+
+    homepage = "https://metacpan.org/pod/CGI"
+    url      = "https://cpan.metacpan.org/authors/id/L/LE/LEEJO/CGI-4.40.tar.gz"
+
+    version('4.40', sha256='10efff3061b3c31a33b3cc59f955aef9c88d57d12dbac46389758cef92f24f56')
+    version('4.39', sha256='7e73417072445f24e03d63802ed3a9e368c9b103ddc96e2a9bcb6a251215fb76')
+    version('4.38', sha256='8c58f4a529bb92a914b22b7e64c5e31185c9854a4070a6dfad44fe5cc248e7d4')
+    version('4.37', sha256='7a14eee5df640f7141848f653cf48d99bfc9b5c68e18167338ee01b91cdfb883')
+
+    depends_on('perl-html-parser', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-class-data-inheritable/package.py b/var/spack/repos/builtin/packages/perl-class-data-inheritable/package.py
index 2fd349b077..951d254395 100644
--- a/var/spack/repos/builtin/packages/perl-class-data-inheritable/package.py
+++ b/var/spack/repos/builtin/packages/perl-class-data-inheritable/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-class-inspector/package.py b/var/spack/repos/builtin/packages/perl-class-inspector/package.py
new file mode 100644
index 0000000000..7bbd3cbbe3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-class-inspector/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlClassInspector(PerlPackage):
+    """Get information about a class and its structure"""
+
+    homepage = "http://search.cpan.org/~plicease/Class-Inspector-1.32/lib/Class/Inspector.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/P/PL/PLICEASE/Class-Inspector-1.32.tar.gz"
+
+    version('1.32', 'db471d6ecf47fa054726553319b7c34f')
diff --git a/var/spack/repos/builtin/packages/perl-class-load-xs/package.py b/var/spack/repos/builtin/packages/perl-class-load-xs/package.py
index 11130afd97..a6a21821e8 100644
--- a/var/spack/repos/builtin/packages/perl-class-load-xs/package.py
+++ b/var/spack/repos/builtin/packages/perl-class-load-xs/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-class-load/package.py b/var/spack/repos/builtin/packages/perl-class-load/package.py
index 0d10f82813..2c5b91ebf9 100644
--- a/var/spack/repos/builtin/packages/perl-class-load/package.py
+++ b/var/spack/repos/builtin/packages/perl-class-load/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-compress-raw-bzip2/package.py b/var/spack/repos/builtin/packages/perl-compress-raw-bzip2/package.py
new file mode 100644
index 0000000000..fe7e47f2f4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-compress-raw-bzip2/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlCompressRawBzip2(PerlPackage):
+    """A low-Level Interface to bzip2 compression library."""
+
+    homepage = "http://search.cpan.org/~pmqs/Compress-Raw-Bzip2-2.081/lib/Compress/Raw/Bzip2.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/P/PM/PMQS/Compress-Raw-Bzip2-2.081.tar.gz"
+
+    version('2.081', '25fa9c9cc4fd3250b65b91694f9eac2e')
+
+    depends_on('bzip2')
+    depends_on('perl-extutils-makemaker', type='build')
diff --git a/var/spack/repos/builtin/packages/perl-compress-raw-zlib/package.py b/var/spack/repos/builtin/packages/perl-compress-raw-zlib/package.py
new file mode 100644
index 0000000000..215554ef97
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-compress-raw-zlib/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlCompressRawZlib(PerlPackage):
+    "A low-Level Interface to zlib compression library"
+
+    homepage = "http://search.cpan.org/~pmqs/Compress-Raw-Zlib-2.081/lib/Compress/Raw/Zlib.pm"
+    url      = "https://cpan.metacpan.org/authors/id/P/PM/PMQS/Compress-Raw-Zlib-2.081.tar.gz"
+
+    version('2.081', 'a22d23bb4f8ce92a41ace1dff29f2bd1')
+
+    depends_on('zlib')
+    depends_on('perl-extutils-makemaker', type='build')
diff --git a/var/spack/repos/builtin/packages/perl-contextual-return/package.py b/var/spack/repos/builtin/packages/perl-contextual-return/package.py
new file mode 100644
index 0000000000..752e807eab
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-contextual-return/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlContextualReturn(PerlPackage):
+    """Create context-sensitive return values"""
+
+    homepage = "http://search.cpan.org/~dconway/Contextual-Return/lib/Contextual/Return.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/D/DC/DCONWAY/Contextual-Return-0.004014.tar.gz"
+
+    version('0.004014', '5cb31f1637c17af6a8e5b852d820af79')
+
+    depends_on('perl-want')
diff --git a/var/spack/repos/builtin/packages/perl-cpan-meta-check/package.py b/var/spack/repos/builtin/packages/perl-cpan-meta-check/package.py
index 7fe16bb2a0..b1743bcd2a 100644
--- a/var/spack/repos/builtin/packages/perl-cpan-meta-check/package.py
+++ b/var/spack/repos/builtin/packages/perl-cpan-meta-check/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-data-optlist/package.py b/var/spack/repos/builtin/packages/perl-data-optlist/package.py
index 4eaeaca1a4..acc3b0cc94 100644
--- a/var/spack/repos/builtin/packages/perl-data-optlist/package.py
+++ b/var/spack/repos/builtin/packages/perl-data-optlist/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-data-stag/package.py b/var/spack/repos/builtin/packages/perl-data-stag/package.py
index fd1bff285f..0af9e0f25f 100644
--- a/var/spack/repos/builtin/packages/perl-data-stag/package.py
+++ b/var/spack/repos/builtin/packages/perl-data-stag/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-dbd-mysql/package.py b/var/spack/repos/builtin/packages/perl-dbd-mysql/package.py
new file mode 100644
index 0000000000..81f6134814
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-dbd-mysql/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlDbdMysql(PerlPackage):
+    """MySQL driver for the Perl5 Database Interface (DBI)"""
+
+    homepage = "http://search.cpan.org/~michielb/DBD-mysql-4.043/lib/DBD/mysql.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/M/MI/MICHIELB/DBD-mysql-4.043.tar.gz"
+
+    version('4.043', '4a00dd7f1c057931147c65dfc4901c36')
+
+    depends_on('perl-test-deep', type=('build', 'run'))
+    depends_on('perl-dbi', type=('build', 'run'))
+    depends_on('mariadb@:10.1.23')
diff --git a/var/spack/repos/builtin/packages/perl-dbd-sqlite/package.py b/var/spack/repos/builtin/packages/perl-dbd-sqlite/package.py
new file mode 100644
index 0000000000..6c8bd95ad7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-dbd-sqlite/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlDbdSqlite(PerlPackage):
+    """DBD::SQLite - Self-contained RDBMS in a DBI Driver"""
+
+    homepage = "https://metacpan.org/pod/DBD::SQLite"
+    url      = "https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI/DBD-SQLite-1.58.tar.gz"
+
+    version('1.59_01', sha256='b6f331e4054688572c2010e72c355f7ba3f30d86051e50d9925d34d9df1001e2')
+    version('1.58',    sha256='7120dd99d0338dea2802fda8bfe3fbf10077d5af559f6c67ae35e9270d1a1d3b')
+    version('1.57_01', sha256='fa7fb111fa8bfc257c3208f8980ac802a9cac4531ab98afc1988b88929672184')
+    version('1.56',    sha256='c5f831a67a94f9bb2fb3c44051f309fc7994b2725d1896c018ad5d4cd865e991')
+
+    depends_on('perl-dbi', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-dbfile/package.py b/var/spack/repos/builtin/packages/perl-dbfile/package.py
index 3a5d8fea94..e1c5ba0df7 100644
--- a/var/spack/repos/builtin/packages/perl-dbfile/package.py
+++ b/var/spack/repos/builtin/packages/perl-dbfile/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-dbi/package.py b/var/spack/repos/builtin/packages/perl-dbi/package.py
index a6e5e76cc5..694aee138a 100644
--- a/var/spack/repos/builtin/packages/perl-dbi/package.py
+++ b/var/spack/repos/builtin/packages/perl-dbi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-devel-cycle/package.py b/var/spack/repos/builtin/packages/perl-devel-cycle/package.py
index ad4c575025..061b71350c 100644
--- a/var/spack/repos/builtin/packages/perl-devel-cycle/package.py
+++ b/var/spack/repos/builtin/packages/perl-devel-cycle/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-devel-globaldestruction/package.py b/var/spack/repos/builtin/packages/perl-devel-globaldestruction/package.py
index aca5245611..297a770dd1 100644
--- a/var/spack/repos/builtin/packages/perl-devel-globaldestruction/package.py
+++ b/var/spack/repos/builtin/packages/perl-devel-globaldestruction/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-devel-overloadinfo/package.py b/var/spack/repos/builtin/packages/perl-devel-overloadinfo/package.py
index 60a80aed90..3499660c94 100644
--- a/var/spack/repos/builtin/packages/perl-devel-overloadinfo/package.py
+++ b/var/spack/repos/builtin/packages/perl-devel-overloadinfo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,6 +12,7 @@ class PerlDevelOverloadinfo(PerlPackage):
     homepage = "http://search.cpan.org/~ilmari/Devel-OverloadInfo-0.004/lib/Devel/OverloadInfo.pm"
     url      = "http://search.cpan.org/CPAN/authors/id/I/IL/ILMARI/Devel-OverloadInfo-0.004.tar.gz"
 
+    version('0.005', '607b65dfe9fdb47df780f3b22dcb7917')
     version('0.004', '97a27e31858b073daba54121d57be705')
 
     depends_on('perl-mro-compat', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-devel-stacktrace/package.py b/var/spack/repos/builtin/packages/perl-devel-stacktrace/package.py
index d6b7b8f484..2e366a2c1a 100644
--- a/var/spack/repos/builtin/packages/perl-devel-stacktrace/package.py
+++ b/var/spack/repos/builtin/packages/perl-devel-stacktrace/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-digest-md5/package.py b/var/spack/repos/builtin/packages/perl-digest-md5/package.py
new file mode 100644
index 0000000000..5466bd2078
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-digest-md5/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlDigestMd5(PerlPackage):
+    """Perl interface to the MD5 Algorithm"""
+
+    homepage = "http://search.cpan.org/dist/Digest-MD5/MD5.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/Digest-MD5-2.55.tar.gz"
+
+    version('2.55', '601519b826ca14c233f13a4578b967ef')
diff --git a/var/spack/repos/builtin/packages/perl-dist-checkconflicts/package.py b/var/spack/repos/builtin/packages/perl-dist-checkconflicts/package.py
index f09ebd4a31..f545b9845e 100644
--- a/var/spack/repos/builtin/packages/perl-dist-checkconflicts/package.py
+++ b/var/spack/repos/builtin/packages/perl-dist-checkconflicts/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-encode-locale/package.py b/var/spack/repos/builtin/packages/perl-encode-locale/package.py
new file mode 100644
index 0000000000..f052970435
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-encode-locale/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlEncodeLocale(PerlPackage):
+    """Determine the locale encoding"""
+
+    homepage = "http://search.cpan.org/~gaas/Encode-Locale-1.05/lib/Encode/Locale.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/Encode-Locale-1.05.tar.gz"
+
+    version('1.05', 'fcfdb8e4ee34bcf62aed429b4a23db27')
diff --git a/var/spack/repos/builtin/packages/perl-eval-closure/package.py b/var/spack/repos/builtin/packages/perl-eval-closure/package.py
index d79d119140..5134ddaea6 100644
--- a/var/spack/repos/builtin/packages/perl-eval-closure/package.py
+++ b/var/spack/repos/builtin/packages/perl-eval-closure/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-exception-class/package.py b/var/spack/repos/builtin/packages/perl-exception-class/package.py
index 715830432d..2877352b3e 100644
--- a/var/spack/repos/builtin/packages/perl-exception-class/package.py
+++ b/var/spack/repos/builtin/packages/perl-exception-class/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-exporter-tiny/package.py b/var/spack/repos/builtin/packages/perl-exporter-tiny/package.py
new file mode 100644
index 0000000000..cea49dbba3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-exporter-tiny/package.py
@@ -0,0 +1,16 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlExporterTiny(PerlPackage):
+    """An exporter with the features of Sub::Exporter but only core
+    dependencies"""
+
+    homepage = "http://search.cpan.org/~tobyink/Exporter-Tiny/lib/Exporter/Tiny.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/T/TO/TOBYINK/Exporter-Tiny-1.000000.tar.gz"
+
+    version('1.000000', '0d413747bdcf880f9ec62de8801ccf5e')
diff --git a/var/spack/repos/builtin/packages/perl-extutils-depends/package.py b/var/spack/repos/builtin/packages/perl-extutils-depends/package.py
new file mode 100644
index 0000000000..d837ca9386
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-extutils-depends/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlExtutilsDepends(PerlPackage):
+    """Easily build XS extensions that depend on XS extensions"""
+
+    homepage = "http://search.cpan.org/~xaoc/ExtUtils-Depends/lib/ExtUtils/Depends.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/X/XA/XAOC/ExtUtils-Depends-0.405.tar.gz"
+
+    version('0.405', 'caefbca2f173d0cea3f5ac26b6c08a2c')
diff --git a/var/spack/repos/builtin/packages/perl-extutils-makemaker/package.py b/var/spack/repos/builtin/packages/perl-extutils-makemaker/package.py
index c346cead50..248056bc18 100644
--- a/var/spack/repos/builtin/packages/perl-extutils-makemaker/package.py
+++ b/var/spack/repos/builtin/packages/perl-extutils-makemaker/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-extutils-pkgconfig/package.py b/var/spack/repos/builtin/packages/perl-extutils-pkgconfig/package.py
index 547d2d2866..1d1e4427cc 100644
--- a/var/spack/repos/builtin/packages/perl-extutils-pkgconfig/package.py
+++ b/var/spack/repos/builtin/packages/perl-extutils-pkgconfig/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,3 +13,5 @@ class PerlExtutilsPkgconfig(PerlPackage):
     url      = "http://search.cpan.org/CPAN/authors/id/X/XA/XAOC/ExtUtils-PkgConfig-1.16.tar.gz"
 
     version('1.16', 'b86318f2b6ac6af3ee985299e1e38fe5')
+
+    depends_on('pkgconfig', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-file-copy-recursive/package.py b/var/spack/repos/builtin/packages/perl-file-copy-recursive/package.py
new file mode 100644
index 0000000000..4a39f17318
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-file-copy-recursive/package.py
@@ -0,0 +1,16 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlFileCopyRecursive(PerlPackage):
+    """Perl extension for recursively copying files and directories"""
+
+    homepage = "http://search.cpan.org/~dmuey/File-Copy-Recursive-0.38/Recursive.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/D/DM/DMUEY/File-Copy-Recursive-0.38.tar.gz"
+
+    version('0.40', '659c634f248885c4b3876b15baf56c79')
+    version('0.38', 'e76dc75ab456510d67c6c3a95183f72f')
diff --git a/var/spack/repos/builtin/packages/perl-file-listing/package.py b/var/spack/repos/builtin/packages/perl-file-listing/package.py
new file mode 100644
index 0000000000..7907b8df1f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-file-listing/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlFileListing(PerlPackage):
+    """Parse directory listing"""
+
+    homepage = "http://search.cpan.org/~gaas/File-Listing-6.04/lib/File/Listing.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/File-Listing-6.04.tar.gz"
+
+    version('6.04', '83f636b477741f3a014585bb9cc079a6')
+
+    depends_on('perl-http-date', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-file-pushd/package.py b/var/spack/repos/builtin/packages/perl-file-pushd/package.py
index fea45e0f9e..5cea0aed7b 100644
--- a/var/spack/repos/builtin/packages/perl-file-pushd/package.py
+++ b/var/spack/repos/builtin/packages/perl-file-pushd/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-file-sharedir-install/package.py b/var/spack/repos/builtin/packages/perl-file-sharedir-install/package.py
new file mode 100644
index 0000000000..294342c1ec
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-file-sharedir-install/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlFileSharedirInstall(PerlPackage):
+    """Install shared files"""
+
+    homepage = "http://search.cpan.org/~ether/File-ShareDir-Install-0.11/lib/File/ShareDir/Install.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/File-ShareDir-Install-0.11.tar.gz"
+
+    version('0.11', '61107e6ce6eee42bf29525b1a4d029e0')
+
+    depends_on('perl-module-build', type='build')
diff --git a/var/spack/repos/builtin/packages/perl-file-slurp-tiny/package.py b/var/spack/repos/builtin/packages/perl-file-slurp-tiny/package.py
new file mode 100644
index 0000000000..dd37eb5cb8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-file-slurp-tiny/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlFileSlurpTiny(PerlPackage):
+    """A simple, sane and efficient file slurper"""
+
+    homepage = "http://search.cpan.org/~leont/File-Slurp-Tiny-0.004/lib/File/Slurp/Tiny.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/L/LE/LEONT/File-Slurp-Tiny-0.004.tar.gz"
+
+    version('0.004', '7575b81543281ea57cdb7e5eb3f73264')
diff --git a/var/spack/repos/builtin/packages/perl-file-slurper/package.py b/var/spack/repos/builtin/packages/perl-file-slurper/package.py
new file mode 100644
index 0000000000..45a5fac76a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-file-slurper/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlFileSlurper(PerlPackage):
+    """A simple, sane and efficient module to slurp a file"""
+
+    homepage = "http://search.cpan.org/~leont/File-Slurper/lib/File/Slurper.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/L/LE/LEONT/File-Slurper-0.011.tar.gz"
+
+    version('0.011', 'e0482d3d5a0522e39132ba54af9f1ce3')
diff --git a/var/spack/repos/builtin/packages/perl-file-which/package.py b/var/spack/repos/builtin/packages/perl-file-which/package.py
new file mode 100644
index 0000000000..bda5f58262
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-file-which/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlFileWhich(PerlPackage):
+    """Perl implementation of the which utility as an API"""
+
+    homepage = "http://cpansearch.perl.org/src/PLICEASE/File-Which-1.22/lib/File/Which.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/P/PL/PLICEASE/File-Which-1.22.tar.gz"
+
+    version('1.22', 'face60fafd220dc83fa581ef6f96d480')
diff --git a/var/spack/repos/builtin/packages/perl-font-ttf/package.py b/var/spack/repos/builtin/packages/perl-font-ttf/package.py
index 81ddbf20b5..aa40f10abf 100644
--- a/var/spack/repos/builtin/packages/perl-font-ttf/package.py
+++ b/var/spack/repos/builtin/packages/perl-font-ttf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-gd-graph/package.py b/var/spack/repos/builtin/packages/perl-gd-graph/package.py
index 9e68fb208a..15b8a765ce 100644
--- a/var/spack/repos/builtin/packages/perl-gd-graph/package.py
+++ b/var/spack/repos/builtin/packages/perl-gd-graph/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,7 +10,7 @@ class PerlGdGraph(PerlPackage):
     """Graph Plotting Module for Perl 5"""
 
     homepage = "http://search.cpan.org/~bwarfield/GDGraph/Graph.pm"
-    url      = "http://search.cpan.org/CPAN/authors/id/B/BW/BWARFIELD/GDGraph-1.44.tar.gz"
+    url      = "http://search.cpan.org/CPAN/authors/id/B/BW/BWARFIELD/GDGraph-1.4308.tar.gz"
 
     version('1.4308', 'fcdd34d5e09ae917b5d264887734b3b1')
 
diff --git a/var/spack/repos/builtin/packages/perl-gd-text/package.py b/var/spack/repos/builtin/packages/perl-gd-text/package.py
index a0a512352a..71c4d053e0 100644
--- a/var/spack/repos/builtin/packages/perl-gd-text/package.py
+++ b/var/spack/repos/builtin/packages/perl-gd-text/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-gd/package.py b/var/spack/repos/builtin/packages/perl-gd/package.py
index 77e5c01aee..8b2367d439 100644
--- a/var/spack/repos/builtin/packages/perl-gd/package.py
+++ b/var/spack/repos/builtin/packages/perl-gd/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-gdgraph-histogram/package.py b/var/spack/repos/builtin/packages/perl-gdgraph-histogram/package.py
new file mode 100644
index 0000000000..ec632bceb9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-gdgraph-histogram/package.py
@@ -0,0 +1,16 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlGdgraphHistogram(PerlPackage):
+    """GD::Graph::histogram extends the GD::Graph module to create histograms.
+       The module allow creation of count or percentage histograms."""
+
+    homepage = "https://metacpan.org/pod/GD::Graph::histogram"
+    url      = "https://cpan.metacpan.org/authors/id/W/WH/WHIZDOG/GDGraph-histogram-1.1.tar.gz"
+
+    version('1.1', sha256='20f752d0e6deb59b29aa2ec3496b5883476d00280b6e83f5b47c33fac4097f8a')
diff --git a/var/spack/repos/builtin/packages/perl-graph-readwrite/package.py b/var/spack/repos/builtin/packages/perl-graph-readwrite/package.py
new file mode 100644
index 0000000000..cb4ffe7251
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-graph-readwrite/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlGraphReadwrite(PerlPackage):
+    """Write out directed graph in Dot format"""
+
+    homepage = "http://search.cpan.org/~neilb/Graph-ReadWrite/lib/Graph/Writer/Dot.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/N/NE/NEILB/Graph-ReadWrite-2.09.tar.gz"
+
+    version('2.09', '5cd9191eadd2fe8fe8bb431575434f67')
diff --git a/var/spack/repos/builtin/packages/perl-graph/package.py b/var/spack/repos/builtin/packages/perl-graph/package.py
new file mode 100644
index 0000000000..0bb59195c7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-graph/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlGraph(PerlPackage):
+    """Graph data structures and algorithms"""
+
+    homepage = "http://search.cpan.org/~jhi/Graph/lib/Graph.pod"
+    url      = "http://search.cpan.org/CPAN/authors/id/J/JH/JHI/Graph-0.9704.tar.gz"
+
+    version('0.9704', '1ab4e49420e56eeb1bc81d842aa8f3af')
+
+    depends_on('perl@5.6.0:')
diff --git a/var/spack/repos/builtin/packages/perl-html-parser/package.py b/var/spack/repos/builtin/packages/perl-html-parser/package.py
new file mode 100644
index 0000000000..bdf2418437
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-html-parser/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlHtmlParser(PerlPackage):
+    """HTML parser class"""
+
+    homepage = "http://search.cpan.org/~gaas/HTML-Parser-3.72/Parser.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/HTML-Parser-3.72.tar.gz"
+
+    version('3.72', 'eb7505e5f626913350df9dd4a03d54a8')
+
+    depends_on('perl-html-tagset', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-html-tagset/package.py b/var/spack/repos/builtin/packages/perl-html-tagset/package.py
new file mode 100644
index 0000000000..ef838d9369
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-html-tagset/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlHtmlTagset(PerlPackage):
+    """Data tables useful in parsing HTML"""
+
+    homepage = "http://search.cpan.org/~petdance/HTML-Tagset-3.20/Tagset.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/P/PE/PETDANCE/HTML-Tagset-3.20.tar.gz"
+
+    version('3.20', 'd2bfa18fe1904df7f683e96611e87437')
diff --git a/var/spack/repos/builtin/packages/perl-http-cookies/package.py b/var/spack/repos/builtin/packages/perl-http-cookies/package.py
new file mode 100644
index 0000000000..41d5857f6b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-http-cookies/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlHttpCookies(PerlPackage):
+    """HTTP cookie jars"""
+
+    homepage = "http://search.cpan.org/~oalders/HTTP-Cookies-6.04/lib/HTTP/Cookies.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/O/OA/OALDERS/HTTP-Cookies-6.04.tar.gz"
+
+    version('6.04', '7bf1e277bd5c886bc18d21eb8423b65f')
+
+    depends_on('perl-uri', type=('build', 'run'))
+    depends_on('perl-http-message', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-http-daemon/package.py b/var/spack/repos/builtin/packages/perl-http-daemon/package.py
new file mode 100644
index 0000000000..7d07ad3637
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-http-daemon/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlHttpDaemon(PerlPackage):
+    """A simple http server class"""
+
+    homepage = "http://search.cpan.org/~gaas/HTTP-Daemon-6.01/lib/HTTP/Daemon.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/HTTP-Daemon-6.01.tar.gz"
+
+    version('6.01', 'ed0ae02d25d7f1e89456d4d69732adc2')
+
+    depends_on('perl-lwp-mediatypes', type=('build', 'run'))
+    depends_on('perl-http-message', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-http-date/package.py b/var/spack/repos/builtin/packages/perl-http-date/package.py
new file mode 100644
index 0000000000..a8a0f53b8a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-http-date/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlHttpDate(PerlPackage):
+    """Date conversion routines"""
+
+    homepage = "http://search.cpan.org/~gaas/HTTP-Date-6.02/lib/HTTP/Date.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/HTTP-Date-6.02.tar.gz"
+
+    version('6.02', '52b7a0d5982d61be1edb217751d7daba')
diff --git a/var/spack/repos/builtin/packages/perl-http-message/package.py b/var/spack/repos/builtin/packages/perl-http-message/package.py
new file mode 100644
index 0000000000..4068241c75
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-http-message/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlHttpMessage(PerlPackage):
+    """HTTP style message (base class)"""
+
+    homepage = "http://search.cpan.org/~oalders/HTTP-Message-6.13/lib/HTTP/Status.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/O/OA/OALDERS/HTTP-Message-6.13.tar.gz"
+
+    version('6.13', '4c1b7c6ee114c1cff69379ec9651d9ac')
+
+    depends_on('perl-lwp-mediatypes', type=('build', 'run'))
+    depends_on('perl-encode-locale', type=('build', 'run'))
+    depends_on('perl-io-html', type=('build', 'run'))
+    depends_on('perl-try-tiny', type=('build', 'run'))
+    depends_on('perl-uri', type=('build', 'run'))
+    depends_on('perl-http-date', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-http-negotiate/package.py b/var/spack/repos/builtin/packages/perl-http-negotiate/package.py
new file mode 100644
index 0000000000..cca1ddc47a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-http-negotiate/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlHttpNegotiate(PerlPackage):
+    """Choose a variant to serve"""
+
+    homepage = "http://search.cpan.org/~gaas/HTTP-Negotiate-6.01/lib/HTTP/Negotiate.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/HTTP-Negotiate-6.01.tar.gz"
+
+    version('6.01', '1236195250e264d7436e7bb02031671b')
+
+    depends_on('perl-http-message', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-inline-c/package.py b/var/spack/repos/builtin/packages/perl-inline-c/package.py
new file mode 100644
index 0000000000..c5af6af4b7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-inline-c/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlInlineC(PerlPackage):
+    """C Language Support for Inline"""
+
+    homepage = "http://search.cpan.org/~tinita/Inline-C-0.78/lib/Inline/C.pod"
+    url      = "http://search.cpan.org/CPAN/authors/id/T/TI/TINITA/Inline-C-0.78.tar.gz"
+
+    version('0.78', '710a454b5337b1cbf3f2ae5c8c45b413')
+
+    depends_on('perl-yaml-libyaml', type=('build', 'run'))
+    depends_on('perl-parse-recdescent', type=('build', 'run'))
+    depends_on('perl-inline', type=('build', 'run'))
+    depends_on('perl-pegex', type=('build', 'run'))
+    depends_on('perl-file-copy-recursive', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-inline/package.py b/var/spack/repos/builtin/packages/perl-inline/package.py
new file mode 100644
index 0000000000..00ee8c3d9c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-inline/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlInline(PerlPackage):
+    """Write Perl Subroutines in Other Programming Languages"""
+
+    homepage = "http://search.cpan.org/~ingy/Inline-0.80/lib/Inline.pod"
+    url      = "http://search.cpan.org/CPAN/authors/id/I/IN/INGY/Inline-0.80.tar.gz"
+
+    version('0.80', '510bbac46e727bcaf240b7feac2646c9')
+
+    depends_on('perl-test-warn', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-intervaltree/package.py b/var/spack/repos/builtin/packages/perl-intervaltree/package.py
index 1a3a31f9d7..76b7c4b469 100644
--- a/var/spack/repos/builtin/packages/perl-intervaltree/package.py
+++ b/var/spack/repos/builtin/packages/perl-intervaltree/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-io-compress/package.py b/var/spack/repos/builtin/packages/perl-io-compress/package.py
new file mode 100644
index 0000000000..ed8af2cbbf
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-io-compress/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlIoCompress(PerlPackage):
+    """A perl library for uncompressing gzip, zip, bzip2
+    or lzop file/buffer."""
+
+    homepage = "http://search.cpan.org/~pmqs/IO-Compress-2.070/lib/IO/Uncompress/AnyUncompress.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/P/PM/PMQS/IO-Compress-2.081.tar.gz"
+
+    version('2.081', '379932c1b9428b873ed7ad3c1db15872')
+
+    depends_on('perl-compress-raw-zlib', type='run')
+    depends_on('perl-compress-raw-bzip2', type='run')
diff --git a/var/spack/repos/builtin/packages/perl-io-html/package.py b/var/spack/repos/builtin/packages/perl-io-html/package.py
new file mode 100644
index 0000000000..4fed8539bb
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-io-html/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlIoHtml(PerlPackage):
+    """Open an HTML file with automatic charset detection."""
+
+    homepage = "http://search.cpan.org/~cjm/IO-HTML-1.001/lib/IO/HTML.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/C/CJ/CJM/IO-HTML-1.001.tar.gz"
+
+    version('1.001', '3f8958718844dc96b9f6946f21d70d22')
diff --git a/var/spack/repos/builtin/packages/perl-io-sessiondata/package.py b/var/spack/repos/builtin/packages/perl-io-sessiondata/package.py
new file mode 100644
index 0000000000..426a0afed5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-io-sessiondata/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlIoSessiondata(PerlPackage):
+    """A wrapper around a single IO::Socket object"""
+
+    homepage = "http://search.cpan.org/~phred/IO-SessionData-1.03/"
+    url      = "http://search.cpan.org/CPAN/authors/id/P/PH/PHRED/IO-SessionData-1.03.tar.gz"
+
+    version('1.03', '790f9e05465c774cf9a6299500463104')
diff --git a/var/spack/repos/builtin/packages/perl-io-socket-ssl/package.py b/var/spack/repos/builtin/packages/perl-io-socket-ssl/package.py
new file mode 100644
index 0000000000..25df82bf0d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-io-socket-ssl/package.py
@@ -0,0 +1,32 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import inspect
+
+
+class PerlIoSocketSsl(PerlPackage):
+    """SSL sockets with IO::Socket interface"""
+
+    homepage = "http://search.cpan.org/~sullr/IO-Socket-SSL-2.052/lib/IO/Socket/SSL.pod"
+    url      = "http://search.cpan.org/CPAN/authors/id/S/SU/SULLR/IO-Socket-SSL-2.052.tar.gz"
+
+    version('2.052', '26c9bcdfb4ba8763ef89264f21326a48')
+
+    depends_on('perl-net-ssleay', type=('build', 'run'))
+
+    def configure(self, spec, prefix):
+        self.build_method = 'Makefile.PL'
+        self.build_executable = inspect.getmodule(self).make
+        # Should I do external tests?
+        config_answers = ['n\n']
+        config_answers_filename = 'spack-config.in'
+
+        with open(config_answers_filename, 'w') as f:
+            f.writelines(config_answers)
+
+        with open(config_answers_filename, 'r') as f:
+            inspect.getmodule(self).perl('Makefile.PL', 'INSTALL_BASE={0}'.
+                                         format(prefix), input=f)
diff --git a/var/spack/repos/builtin/packages/perl-io-string/package.py b/var/spack/repos/builtin/packages/perl-io-string/package.py
index ec08ac3078..2ce98e7627 100644
--- a/var/spack/repos/builtin/packages/perl-io-string/package.py
+++ b/var/spack/repos/builtin/packages/perl-io-string/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-json/package.py b/var/spack/repos/builtin/packages/perl-json/package.py
new file mode 100644
index 0000000000..2c0b41dcad
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-json/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlJson(PerlPackage):
+    """JSON (JavaScript Object Notation) encoder/decoder"""
+
+    homepage = "http://search.cpan.org/~ishigaki/JSON/lib/JSON.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/I/IS/ISHIGAKI/JSON-2.97001.tar.gz"
+
+    version('2.97001', '693d6ff167496362f8ec6c3c5b8ba5ee')
diff --git a/var/spack/repos/builtin/packages/perl-libwww-perl/package.py b/var/spack/repos/builtin/packages/perl-libwww-perl/package.py
new file mode 100644
index 0000000000..93344cc710
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-libwww-perl/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlLibwwwPerl(PerlPackage):
+    """The libwww-perl collection is a set of Perl modules which provides
+    a simple and consistent application programming interface to the
+    World-Wide Web. The main focus of the library is to provide classes and
+    functions that allow you to write WWW clients."""
+
+    homepage = "https://github.com/libwww-perl/libwww-perl"
+    url      = "http://search.cpan.org/CPAN/authors/id/O/OA/OALDERS/libwww-perl-6.33.tar.gz"
+
+    version('6.33', '2e15c1c789ac9036c99d094e47e3da23')
diff --git a/var/spack/repos/builtin/packages/perl-list-moreutils/package.py b/var/spack/repos/builtin/packages/perl-list-moreutils/package.py
new file mode 100644
index 0000000000..6a23032fd1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-list-moreutils/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlListMoreutils(PerlPackage):
+    """Provide the stuff missing in List::Util"""
+
+    homepage = "http://search.cpan.org/~rehsack/List-MoreUtils/lib/List/MoreUtils.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/R/RE/REHSACK/List-MoreUtils-0.428.tar.gz"
+
+    version('0.428', '493032a211cdff1fcf45f59ebd680407')
diff --git a/var/spack/repos/builtin/packages/perl-log-log4perl/package.py b/var/spack/repos/builtin/packages/perl-log-log4perl/package.py
new file mode 100644
index 0000000000..dabb293e13
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-log-log4perl/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlLogLog4perl(PerlPackage):
+    """Log4j implementation for Perl"""
+
+    homepage = "http://search.cpan.org/~mschilli/Log-Log4perl-1.44/lib/Log/Log4perl.pm"
+    url      = "https://github.com/mschilli/log4perl/archive/rel_146.tar.gz"
+
+    version('146', '500abbd978ed326cfe5367dc4f9f3be2')
diff --git a/var/spack/repos/builtin/packages/perl-lwp-mediatypes/package.py b/var/spack/repos/builtin/packages/perl-lwp-mediatypes/package.py
new file mode 100644
index 0000000000..6955add7fe
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-lwp-mediatypes/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlLwpMediatypes(PerlPackage):
+    """Guess media type for a file or a URL"""
+
+    homepage = "http://search.cpan.org/~gaas/LWP-MediaTypes-6.02/lib/LWP/MediaTypes.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/LWP-MediaTypes-6.02.tar.gz"
+
+    version('6.02', '8c5f25fb64b974d22aff424476ba13c9')
diff --git a/var/spack/repos/builtin/packages/perl-lwp-protocol-https/package.py b/var/spack/repos/builtin/packages/perl-lwp-protocol-https/package.py
new file mode 100644
index 0000000000..200bd7700c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-lwp-protocol-https/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlLwpProtocolHttps(PerlPackage):
+    """ Provide https support for LWP::UserAgent"""
+
+    homepage = "http://search.cpan.org/~gaas/LWP-Protocol-https-6.04/lib/LWP/Protocol/https.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/LWP-Protocol-https-6.04.tar.gz"
+
+    version('6.04', '1b422a7d3b5fed1eb4d748fdc9fd79a4')
+
+    depends_on('perl-test-requiresinternet', type=('build', 'run'))
+    depends_on('perl-io-socket-ssl', type=('build', 'run'))
+    depends_on('perl-net-http', type=('build', 'run'))
+    depends_on('perl-mozilla-ca', type=('build', 'run'))
+    depends_on('perl-lwp', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-lwp/package.py b/var/spack/repos/builtin/packages/perl-lwp/package.py
new file mode 100644
index 0000000000..7d00186250
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-lwp/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlLwp(PerlPackage):
+    """The World-Wide Web library for Perl"""
+
+    homepage = "http://search.cpan.org/~oalders/libwww-perl-6.29/lib/LWP.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/O/OA/OALDERS/libwww-perl-6.29.tar.gz"
+
+    version('6.29', 'efec8d563ffd3652333356aa722c2b56')
+
+    depends_on('perl-test-requiresinternet', type=('build', 'run'))
+    depends_on('perl-http-message', type=('build', 'run'))
+    depends_on('perl-file-listing', type=('build', 'run'))
+    depends_on('perl-http-daemon', type=('build', 'run'))
+    depends_on('perl-html-parser', type=('build', 'run'))
+    depends_on('perl-http-cookies', type=('build', 'run'))
+    depends_on('perl-www-robotrules', type=('build', 'run'))
+    depends_on('perl-test-fatal', type=('build', 'run'))
+    depends_on('perl-http-negotiate', type=('build', 'run'))
+    depends_on('perl-net-http', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-math-cdf/package.py b/var/spack/repos/builtin/packages/perl-math-cdf/package.py
index 094b08dd1d..509b916868 100644
--- a/var/spack/repos/builtin/packages/perl-math-cdf/package.py
+++ b/var/spack/repos/builtin/packages/perl-math-cdf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-math-cephes/package.py b/var/spack/repos/builtin/packages/perl-math-cephes/package.py
new file mode 100644
index 0000000000..4b5899271e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-math-cephes/package.py
@@ -0,0 +1,16 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlMathCephes(PerlPackage):
+    """This module provides an interface to over 150 functions of the
+       cephes math library of Stephen Moshier."""
+
+    homepage = "http://search.cpan.org/~shlomif/Math-Cephes/lib/Math/Cephes.pod"
+    url      = "http://search.cpan.org/CPAN/authors/id/S/SH/SHLOMIF/Math-Cephes-0.5305.tar.gz"
+
+    version('0.5305', '30922dd213783aaaf91a47626f6a1853')
diff --git a/var/spack/repos/builtin/packages/perl-math-matrixreal/package.py b/var/spack/repos/builtin/packages/perl-math-matrixreal/package.py
new file mode 100644
index 0000000000..54d57d564e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-math-matrixreal/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlMathMatrixreal(PerlPackage):
+    """Implements the data type "matrix of real numbers" (and consequently
+    also "vector of real numbers")."""
+
+    homepage = "http://search.cpan.org/~leto/Math-MatrixReal/lib/Math/MatrixReal.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/L/LE/LETO/Math-MatrixReal-2.13.tar.gz"
+
+    version('2.13', 'cf9d6ff71f2df075559ea752104ca199')
+
+    depends_on('perl-module-build', type='build')
diff --git a/var/spack/repos/builtin/packages/perl-module-build/package.py b/var/spack/repos/builtin/packages/perl-module-build/package.py
index 53bc80a062..cfe492c9e0 100644
--- a/var/spack/repos/builtin/packages/perl-module-build/package.py
+++ b/var/spack/repos/builtin/packages/perl-module-build/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 from spack import *
 
@@ -36,6 +17,7 @@ class PerlModuleBuild(PerlPackage):
     """
 
     homepage = "http://search.cpan.org/perldoc/Module::Build"
-    url      = "http://search.cpan.org/CPAN/authors/id/L/LE/LEONT/Module-Build-0.4220.tar.gz"
+    url      = "http://search.cpan.org/CPAN/authors/id/L/LE/LEONT/Module-Build-0.4224.tar.gz"
 
+    version('0.4224', sha256='a6ca15d78244a7b50fdbf27f85c85f4035aa799ce7dd018a0d98b358ef7bc782')
     version('0.4220', '9df204e188462a4410d496f316c2c531')
diff --git a/var/spack/repos/builtin/packages/perl-module-implementation/package.py b/var/spack/repos/builtin/packages/perl-module-implementation/package.py
new file mode 100644
index 0000000000..ca8c2be284
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-module-implementation/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlModuleImplementation(PerlPackage):
+    """Loads one of several alternate underlying implementations for a
+    module"""
+
+    homepage = "http://search.cpan.org/~drolsky/Module-Implementation/lib/Module/Implementation.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/D/DR/DROLSKY/Module-Implementation-0.09.tar.gz"
+
+    version('0.09', '52e3fe0ca6b1eff0488d59b7aacc0667')
+
+    depends_on('perl-module-runtime', type=('build', 'run'))
+    depends_on('perl-test-fatal', type=('build', 'run'))
+    depends_on('perl-test-requires', type=('build', 'run'))
+    depends_on('perl-try-tiny', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-module-runtime-conflicts/package.py b/var/spack/repos/builtin/packages/perl-module-runtime-conflicts/package.py
index 1b499ce7f9..d3e8c6757f 100644
--- a/var/spack/repos/builtin/packages/perl-module-runtime-conflicts/package.py
+++ b/var/spack/repos/builtin/packages/perl-module-runtime-conflicts/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-module-runtime/package.py b/var/spack/repos/builtin/packages/perl-module-runtime/package.py
new file mode 100644
index 0000000000..b694f2eeed
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-module-runtime/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlModuleRuntime(PerlPackage):
+    """Runtime module handling"""
+
+    homepage = "http://search.cpan.org/~zefram/Module-Runtime/lib/Module/Runtime.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/Z/ZE/ZEFRAM/Module-Runtime-0.016.tar.gz"
+
+    version('0.016', 'd3d47222fa2e3dfcb4526f6cc8437b20')
+
+    depends_on('perl-module-build', type='build')
diff --git a/var/spack/repos/builtin/packages/perl-moose/package.py b/var/spack/repos/builtin/packages/perl-moose/package.py
index 2a0261599f..25c5402691 100644
--- a/var/spack/repos/builtin/packages/perl-moose/package.py
+++ b/var/spack/repos/builtin/packages/perl-moose/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,6 +12,9 @@ class PerlMoose(PerlPackage):
     homepage = "http://search.cpan.org/~ether/Moose-2.2006/lib/Moose.pm"
     url      = "http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/Moose-2.2006.tar.gz"
 
+    version('2.2010', '636238ac384818ee1e92eff6b9ecc50a')
+    version('2.2009', '5527b1a5abc29b5c57fc488447e76ccd')
+    version('2.2007', 'de487ae226003f7e7f22c0fd8f0074e6')
     version('2.2006', '929c6b3877a6054ef617cf7ef1e220b5')
 
     depends_on('perl-cpan-meta-check', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-mozilla-ca/package.py b/var/spack/repos/builtin/packages/perl-mozilla-ca/package.py
new file mode 100644
index 0000000000..6ab7f85ade
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-mozilla-ca/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlMozillaCa(PerlPackage):
+    """Mozilla's CA cert bundle in PEM format"""
+
+    homepage = "http://search.cpan.org/~abh/Mozilla-CA-20160104/lib/Mozilla/CA.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/A/AB/ABH/Mozilla-CA-20160104.tar.gz"
+
+    version('20160104', '1b91edb15953a8188f011ab5ff433300')
diff --git a/var/spack/repos/builtin/packages/perl-mro-compat/package.py b/var/spack/repos/builtin/packages/perl-mro-compat/package.py
index 81b6f19ffa..be1b7ec3a5 100644
--- a/var/spack/repos/builtin/packages/perl-mro-compat/package.py
+++ b/var/spack/repos/builtin/packages/perl-mro-compat/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-namespace-clean/package.py b/var/spack/repos/builtin/packages/perl-namespace-clean/package.py
index 8dc2492430..fec8be732e 100644
--- a/var/spack/repos/builtin/packages/perl-namespace-clean/package.py
+++ b/var/spack/repos/builtin/packages/perl-namespace-clean/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-net-http/package.py b/var/spack/repos/builtin/packages/perl-net-http/package.py
new file mode 100644
index 0000000000..272ce07bb0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-net-http/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlNetHttp(PerlPackage):
+    """Low-level HTTP connection (client)"""
+
+    homepage = "http://search.cpan.org/~oalders/Net-HTTP-6.17/lib/Net/HTTP.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/O/OA/OALDERS/Net-HTTP-6.17.tar.gz"
+
+    version('6.17', '068fa02fd3c8a5b63316025b5a24844c')
+
+    depends_on('perl-uri', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-net-scp-expect/package.py b/var/spack/repos/builtin/packages/perl-net-scp-expect/package.py
new file mode 100644
index 0000000000..5969f63a4b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-net-scp-expect/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlNetScpExpect(PerlPackage):
+    """Wrapper for scp that allows passwords via Expect."""
+
+    homepage = "http://search.cpan.org/~rybskej/Net-SCP-Expect/Expect.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/R/RY/RYBSKEJ/Net-SCP-Expect-0.16.tar.gz"
+
+    version('0.16', 'a3d8f5e6a34ba3df8527aea098f64a58')
diff --git a/var/spack/repos/builtin/packages/perl-net-ssleay/package.py b/var/spack/repos/builtin/packages/perl-net-ssleay/package.py
new file mode 100644
index 0000000000..5f84ceebfb
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-net-ssleay/package.py
@@ -0,0 +1,33 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import inspect
+
+
+class PerlNetSsleay(PerlPackage):
+    """Perl extension for using OpenSSL"""
+
+    homepage = "http://search.cpan.org/~mikem/Net-SSLeay-1.82/lib/Net/SSLeay.pod"
+    url      = "http://search.cpan.org/CPAN/authors/id/M/MI/MIKEM/Net-SSLeay-1.82.tar.gz"
+
+    version('1.82', '2170469d929d5173bacffd0cb2d7fafa')
+
+    depends_on('openssl')
+
+    def configure(self, spec, prefix):
+        self.build_method = 'Makefile.PL'
+        self.build_executable = inspect.getmodule(self).make
+        # Do you want to run external tests?
+        config_answers = ['\n']
+        config_answers_filename = 'spack-config.in'
+
+        with open(config_answers_filename, 'w') as f:
+            f.writelines(config_answers)
+
+        with open(config_answers_filename, 'r') as f:
+            inspect.getmodule(self).perl('Makefile.PL', 'INSTALL_BASE={0}'.
+                                         format(prefix), 'OPENSSL_PREFIX=%s' %
+                                         self.spec['openssl'].prefix, input=f)
diff --git a/var/spack/repos/builtin/packages/perl-package-deprecationmanager/package.py b/var/spack/repos/builtin/packages/perl-package-deprecationmanager/package.py
index 89e1690fdd..ba07697509 100644
--- a/var/spack/repos/builtin/packages/perl-package-deprecationmanager/package.py
+++ b/var/spack/repos/builtin/packages/perl-package-deprecationmanager/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-package-stash-xs/package.py b/var/spack/repos/builtin/packages/perl-package-stash-xs/package.py
index 7d627ffb65..9dd65c9fb3 100644
--- a/var/spack/repos/builtin/packages/perl-package-stash-xs/package.py
+++ b/var/spack/repos/builtin/packages/perl-package-stash-xs/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-package-stash/package.py b/var/spack/repos/builtin/packages/perl-package-stash/package.py
index abc8a5ccfe..9f772e5196 100644
--- a/var/spack/repos/builtin/packages/perl-package-stash/package.py
+++ b/var/spack/repos/builtin/packages/perl-package-stash/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-padwalker/package.py b/var/spack/repos/builtin/packages/perl-padwalker/package.py
index 0ffef9cf18..f9e028e35d 100644
--- a/var/spack/repos/builtin/packages/perl-padwalker/package.py
+++ b/var/spack/repos/builtin/packages/perl-padwalker/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-parallel-forkmanager/package.py b/var/spack/repos/builtin/packages/perl-parallel-forkmanager/package.py
new file mode 100644
index 0000000000..46cb34f99f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-parallel-forkmanager/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlParallelForkmanager(PerlPackage):
+    """A simple parallel processing fork manager"""
+
+    homepage = "http://search.cpan.org/~yanick/Parallel-ForkManager/lib/Parallel/ForkManager.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/Y/YA/YANICK/Parallel-ForkManager-1.19.tar.gz"
+
+    version('1.19', '0e7137dd4b6948e1633b3b9ebe3b87e1')
diff --git a/var/spack/repos/builtin/packages/perl-params-util/package.py b/var/spack/repos/builtin/packages/perl-params-util/package.py
index 834601512b..503b276a6c 100644
--- a/var/spack/repos/builtin/packages/perl-params-util/package.py
+++ b/var/spack/repos/builtin/packages/perl-params-util/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-parse-recdescent/package.py b/var/spack/repos/builtin/packages/perl-parse-recdescent/package.py
new file mode 100644
index 0000000000..a9623c453a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-parse-recdescent/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlParseRecdescent(PerlPackage):
+    """Generate Recursive-Descent Parsers"""
+
+    homepage = "http://search.cpan.org/~jtbraun/Parse-RecDescent-1.967015/lib/Parse/RecDescent.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/J/JT/JTBRAUN/Parse-RecDescent-1.967015.tar.gz"
+
+    version('1.967015', '7a36d45d62a9b68603edcdbd276006cc')
+
+    depends_on('perl-module-build', type='build')
diff --git a/var/spack/repos/builtin/packages/perl-pdf-api2/package.py b/var/spack/repos/builtin/packages/perl-pdf-api2/package.py
index 216971529c..6322e13558 100644
--- a/var/spack/repos/builtin/packages/perl-pdf-api2/package.py
+++ b/var/spack/repos/builtin/packages/perl-pdf-api2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-pegex/package.py b/var/spack/repos/builtin/packages/perl-pegex/package.py
new file mode 100644
index 0000000000..62015d2682
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-pegex/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlPegex(PerlPackage):
+    """Acmeist PEG Parser Framework"""
+
+    homepage = "http://search.cpan.org/~ingy/Pegex-0.64/lib/Pegex.pod"
+    url      = "http://search.cpan.org/CPAN/authors/id/I/IN/INGY/Pegex-0.64.tar.gz"
+
+    version('0.64', 'db86d4f1ddc36c4c7860ce060e77976f')
+
+    depends_on('perl-file-sharedir-install', type=('build', 'run'))
+    depends_on('perl-yaml-libyaml', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-perl4-corelibs/package.py b/var/spack/repos/builtin/packages/perl-perl4-corelibs/package.py
new file mode 100644
index 0000000000..cd4f4d1d4e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-perl4-corelibs/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlPerl4Corelibs(PerlPackage):
+    """Perl4::CoreLibs - libraries historically supplied with Perl 4"""
+
+    # doesn't look like a homepage but it is
+    homepage = "https://metacpan.org/pod/release/ZEFRAM/Perl4-CoreLibs-0.003/lib/Perl4/CoreLibs.pm"
+    url      = "https://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM/Perl4-CoreLibs-0.003.tar.gz"
+
+    version('0.004', sha256='78887e3365f8935ab00d528832e9b7a426fb684ffc5c03c20e67a217ca4ac64a')
+    version('0.003', sha256='55c9b2b032944406dbaa2fd97aa3692a1ebce558effc457b4e800dabfaad9ade')
+    version('0.002', sha256='c68272e8b0e37268d9fbb93f5ef5708e12e0a13bbb5a6123af3f493ea8852521')
+    version('0.001', sha256='f7479f63e8b0cc344752a59f66fd084a14ee87bcc2a1f67c1a413afab8d0ad37')
+    version('0.000', sha256='d8f2310ad0b0f48c8fc258a75042ebeedf47bcefb231be427761dba77e734875')
+
+    depends_on('perl-module-build', type='build')
diff --git a/var/spack/repos/builtin/packages/perl-perl6-slurp/package.py b/var/spack/repos/builtin/packages/perl-perl6-slurp/package.py
new file mode 100644
index 0000000000..69721a7d04
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-perl6-slurp/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlPerl6Slurp(PerlPackage):
+    """Perl6::Slurp - Implements the Perl 6 'slurp' built-in"""
+
+    homepage = "http://search.cpan.org/~dconway/Perl6-Slurp-0.051005/lib/Perl6/Slurp.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/D/DC/DCONWAY/Perl6-Slurp-0.051005.tar.gz"
+
+    version('0.051005', '6095c8df495c7983f36996ed78c5ead7')
+
+    depends_on('perl@5.8:5.999', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-perlio-gzip/package.py b/var/spack/repos/builtin/packages/perl-perlio-gzip/package.py
new file mode 100644
index 0000000000..44996865bc
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-perlio-gzip/package.py
@@ -0,0 +1,16 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlPerlioGzip(PerlPackage):
+    """Perl extension to provide a PerlIO layer to gzip/gunzip"""
+
+    homepage = "http://search.cpan.org/~nwclark/PerlIO-gzip/gzip.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/N/NW/NWCLARK/PerlIO-gzip-0.19.tar.gz"
+
+    version('0.20', '0393eae5d0b23df6cf40ed44af7d711c')
+    version('0.19', 'dbcfc1450f6b593b65048b8ced061c98')
diff --git a/var/spack/repos/builtin/packages/perl-perlio-utf8-strict/package.py b/var/spack/repos/builtin/packages/perl-perlio-utf8-strict/package.py
new file mode 100644
index 0000000000..5bd83c8fdc
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-perlio-utf8-strict/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlPerlioUtf8Strict(PerlPackage):
+    """This module provides a fast and correct UTF-8 PerlIO layer."""
+
+    homepage = "http://search.cpan.org/~leont/PerlIO-utf8_strict/lib/PerlIO/utf8_strict.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/L/LE/LEONT/PerlIO-utf8_strict-0.002.tar.gz"
+
+    version('0.002', '2e5b13efe6dfd7748e44e47f6dedb1da')
diff --git a/var/spack/repos/builtin/packages/perl-scalar-util-numeric/package.py b/var/spack/repos/builtin/packages/perl-scalar-util-numeric/package.py
new file mode 100644
index 0000000000..dbc3e96388
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-scalar-util-numeric/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlScalarUtilNumeric(PerlPackage):
+    """This module exports a number of wrappers around perl's builtin grok_number
+       function, which returns the numeric type of its argument, or 0 if it
+       isn't numeric."""
+
+    homepage = "https://metacpan.org/pod/Scalar::Util::Numeric"
+    url      = "https://cpan.metacpan.org/authors/id/C/CH/CHOCOLATE/Scalar-Util-Numeric-0.40.tar.gz"
+
+    version('0.40', sha256='d7501b6d410703db5b1c1942fbfc41af8964a35525d7f766058acf5ca2cc4440')
diff --git a/var/spack/repos/builtin/packages/perl-soap-lite/package.py b/var/spack/repos/builtin/packages/perl-soap-lite/package.py
new file mode 100644
index 0000000000..f6e357a65b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-soap-lite/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlSoapLite(PerlPackage):
+    """Perl's Web Services Toolkit"""
+
+    homepage = "http://search.cpan.org/~phred/SOAP-Lite-1.20/lib/SOAP/Lite.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/P/PH/PHRED/SOAP-Lite-1.22.tar.gz"
+
+    version('1.22', '86c31341311498a08c6309e62168f655')
+
+    depends_on('perl-io-sessiondata', type=('build', 'run'))
+    depends_on('perl-lwp-protocol-https', type=('build', 'run'))
+    depends_on('perl-task-weaken', type=('build', 'run'))
+    depends_on('perl-xml-parser-lite', type=('build', 'run'))
+    depends_on('perl-xml-parser', type=('build', 'run'))
+    depends_on('perl-test-warn', type=('build', 'run'))
+    depends_on('perl-class-inspector', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-star-fusion/package.py b/var/spack/repos/builtin/packages/perl-star-fusion/package.py
index 5985bd7fd3..4c137739d5 100644
--- a/var/spack/repos/builtin/packages/perl-star-fusion/package.py
+++ b/var/spack/repos/builtin/packages/perl-star-fusion/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 from glob import glob
 
@@ -34,9 +15,9 @@ class PerlStarFusion(Package):
     and spanning reads to a reference annotation set."""
 
     homepage = "https://github.com/STAR-Fusion/STAR-Fusion"
-    url      = "https://github.com/STAR-Fusion/STAR-Fusion.git"
+    git      = "https://github.com/STAR-Fusion/STAR-Fusion.git"
 
-    version('master', git='https://github.com/STAR-Fusion/STAR-Fusion.git', commit='a16a0a8')
+    version('master', commit='8c5a541')
 
     extends('perl')
 
diff --git a/var/spack/repos/builtin/packages/perl-statistics-descriptive/package.py b/var/spack/repos/builtin/packages/perl-statistics-descriptive/package.py
new file mode 100644
index 0000000000..e35bca37c0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-statistics-descriptive/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlStatisticsDescriptive(PerlPackage):
+    """Module of basic descriptive statistical functions."""
+
+    homepage = "http://search.cpan.org/~shlomif/Statistics-Descriptive-3.0612/lib/Statistics/Descriptive.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/S/SH/SHLOMIF/Statistics-Descriptive-3.0612.tar.gz"
+
+    version('3.0612', 'e38cfbc1e3962d099b62a14a57a175f1')
diff --git a/var/spack/repos/builtin/packages/perl-statistics-pca/package.py b/var/spack/repos/builtin/packages/perl-statistics-pca/package.py
new file mode 100644
index 0000000000..cd2e6844a6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-statistics-pca/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlStatisticsPca(PerlPackage):
+    """A simple Perl implementation of Principal Component Analysis."""
+
+    homepage = "http://search.cpan.org/~dsth/Statistics-PCA/lib/Statistics/PCA.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/D/DS/DSTH/Statistics-PCA-0.0.1.tar.gz"
+
+    version('0.0.1', '6e0e05fe13f6becea525b973a0c29001')
+
+    depends_on('perl-module-build', type='build')
+    depends_on('perl-contextual-return', type=('build', 'run'))
+    depends_on('perl-text-simpletable', type=('build', 'run'))
+    depends_on('perl-math-matrixreal', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-sub-exporter-progressive/package.py b/var/spack/repos/builtin/packages/perl-sub-exporter-progressive/package.py
index a6642fce2c..88930215ef 100644
--- a/var/spack/repos/builtin/packages/perl-sub-exporter-progressive/package.py
+++ b/var/spack/repos/builtin/packages/perl-sub-exporter-progressive/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-sub-exporter/package.py b/var/spack/repos/builtin/packages/perl-sub-exporter/package.py
index 0b13cb870e..184af5ccda 100644
--- a/var/spack/repos/builtin/packages/perl-sub-exporter/package.py
+++ b/var/spack/repos/builtin/packages/perl-sub-exporter/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-sub-identify/package.py b/var/spack/repos/builtin/packages/perl-sub-identify/package.py
index e173ebfeae..6970774946 100644
--- a/var/spack/repos/builtin/packages/perl-sub-identify/package.py
+++ b/var/spack/repos/builtin/packages/perl-sub-identify/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-sub-install/package.py b/var/spack/repos/builtin/packages/perl-sub-install/package.py
index 8354eb5be7..ee0088d3c0 100644
--- a/var/spack/repos/builtin/packages/perl-sub-install/package.py
+++ b/var/spack/repos/builtin/packages/perl-sub-install/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-sub-name/package.py b/var/spack/repos/builtin/packages/perl-sub-name/package.py
index 74df14dbd1..82d4606fff 100644
--- a/var/spack/repos/builtin/packages/perl-sub-name/package.py
+++ b/var/spack/repos/builtin/packages/perl-sub-name/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-sub-uplevel/package.py b/var/spack/repos/builtin/packages/perl-sub-uplevel/package.py
index 049c844e1d..46f4b4f68b 100644
--- a/var/spack/repos/builtin/packages/perl-sub-uplevel/package.py
+++ b/var/spack/repos/builtin/packages/perl-sub-uplevel/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-svg/package.py b/var/spack/repos/builtin/packages/perl-svg/package.py
new file mode 100644
index 0000000000..6152c8395e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-svg/package.py
@@ -0,0 +1,16 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlSvg(PerlPackage):
+    """Perl extension for generating Scalable Vector Graphics (SVG) documents.
+    """
+
+    homepage = "http://search.cpan.org/~manwar/SVG-2.78/lib/SVG.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/M/MA/MANWAR/SVG-2.78.tar.gz"
+
+    version('2.78', 'b247c216ab11fae24533d0ce556e2e75')
diff --git a/var/spack/repos/builtin/packages/perl-swissknife/package.py b/var/spack/repos/builtin/packages/perl-swissknife/package.py
new file mode 100644
index 0000000000..6f0a105b4c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-swissknife/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlSwissknife(PerlPackage):
+    """An object-oriented Perl library to handle Swiss-Prot entries"""
+
+    homepage = "http://swissknife.sourceforge.net"
+    url      = "https://downloads.sourceforge.net/project/swissknife/swissknife/1.75/Swissknife_1.75.tar.gz"
+
+    version('1.75', '09d008cb1d1d211ae4eb9f087c213edf')
+
+    depends_on('perl-module-build', type='build')
diff --git a/var/spack/repos/builtin/packages/perl-task-weaken/package.py b/var/spack/repos/builtin/packages/perl-task-weaken/package.py
new file mode 100644
index 0000000000..810ce1dae8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-task-weaken/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlTaskWeaken(PerlPackage):
+    """Ensure that a platform has weaken support"""
+
+    homepage = "http://search.cpan.org/~adamk/Task-Weaken-1.04/lib/Task/Weaken.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/A/AD/ADAMK/Task-Weaken-1.04.tar.gz"
+
+    version('1.04', 'affd0c395515bb95d29968404d7fe6de')
diff --git a/var/spack/repos/builtin/packages/perl-term-readkey/package.py b/var/spack/repos/builtin/packages/perl-term-readkey/package.py
index b25e34c04d..fa812f1bf5 100644
--- a/var/spack/repos/builtin/packages/perl-term-readkey/package.py
+++ b/var/spack/repos/builtin/packages/perl-term-readkey/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-test-cleannamespaces/package.py b/var/spack/repos/builtin/packages/perl-test-cleannamespaces/package.py
index 86e8bfae4a..a80ec687ab 100644
--- a/var/spack/repos/builtin/packages/perl-test-cleannamespaces/package.py
+++ b/var/spack/repos/builtin/packages/perl-test-cleannamespaces/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-test-deep/package.py b/var/spack/repos/builtin/packages/perl-test-deep/package.py
index d1a6d248f5..94b6edc5cb 100644
--- a/var/spack/repos/builtin/packages/perl-test-deep/package.py
+++ b/var/spack/repos/builtin/packages/perl-test-deep/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-test-differences/package.py b/var/spack/repos/builtin/packages/perl-test-differences/package.py
index b37442fc28..10a738737c 100644
--- a/var/spack/repos/builtin/packages/perl-test-differences/package.py
+++ b/var/spack/repos/builtin/packages/perl-test-differences/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-test-exception/package.py b/var/spack/repos/builtin/packages/perl-test-exception/package.py
index 32b902221e..05ffa21c9e 100644
--- a/var/spack/repos/builtin/packages/perl-test-exception/package.py
+++ b/var/spack/repos/builtin/packages/perl-test-exception/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-test-fatal/package.py b/var/spack/repos/builtin/packages/perl-test-fatal/package.py
index 314fee9df6..6e7833f291 100644
--- a/var/spack/repos/builtin/packages/perl-test-fatal/package.py
+++ b/var/spack/repos/builtin/packages/perl-test-fatal/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-test-memory-cycle/package.py b/var/spack/repos/builtin/packages/perl-test-memory-cycle/package.py
index b9132952b2..e8c42e3839 100644
--- a/var/spack/repos/builtin/packages/perl-test-memory-cycle/package.py
+++ b/var/spack/repos/builtin/packages/perl-test-memory-cycle/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-test-most/package.py b/var/spack/repos/builtin/packages/perl-test-most/package.py
index a6a3650c42..90aa5cf79c 100644
--- a/var/spack/repos/builtin/packages/perl-test-most/package.py
+++ b/var/spack/repos/builtin/packages/perl-test-most/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-test-needs/package.py b/var/spack/repos/builtin/packages/perl-test-needs/package.py
index 9006067309..8d07133156 100644
--- a/var/spack/repos/builtin/packages/perl-test-needs/package.py
+++ b/var/spack/repos/builtin/packages/perl-test-needs/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-test-requires/package.py b/var/spack/repos/builtin/packages/perl-test-requires/package.py
index 79bfb211a0..bd4c395c68 100644
--- a/var/spack/repos/builtin/packages/perl-test-requires/package.py
+++ b/var/spack/repos/builtin/packages/perl-test-requires/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-test-requiresinternet/package.py b/var/spack/repos/builtin/packages/perl-test-requiresinternet/package.py
new file mode 100644
index 0000000000..e8f412a74f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-test-requiresinternet/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlTestRequiresinternet(PerlPackage):
+    """Easily test network connectivity"""
+
+    homepage = "http://search.cpan.org/~mallen/Test-RequiresInternet-0.05/lib/Test/RequiresInternet.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/M/MA/MALLEN/Test-RequiresInternet-0.05.tar.gz"
+
+    version('0.05', '0ba9f1cff4cf90ed2618c2eddfd525d8')
diff --git a/var/spack/repos/builtin/packages/perl-test-warn/package.py b/var/spack/repos/builtin/packages/perl-test-warn/package.py
index e1e9a873a6..d72aea1349 100644
--- a/var/spack/repos/builtin/packages/perl-test-warn/package.py
+++ b/var/spack/repos/builtin/packages/perl-test-warn/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-test-warnings/package.py b/var/spack/repos/builtin/packages/perl-test-warnings/package.py
index dc3640fe33..5d36d5d20f 100644
--- a/var/spack/repos/builtin/packages/perl-test-warnings/package.py
+++ b/var/spack/repos/builtin/packages/perl-test-warnings/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-text-csv/package.py b/var/spack/repos/builtin/packages/perl-text-csv/package.py
new file mode 100644
index 0000000000..4f57470fb4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-text-csv/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlTextCsv(PerlPackage):
+    """Comma-separated values manipulator (using XS or PurePerl)"""
+
+    homepage = "http://search.cpan.org/~ishigaki/Text-CSV/lib/Text/CSV.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/I/IS/ISHIGAKI/Text-CSV-1.95.tar.gz"
+
+    version('1.95', '1e076b4b1f8ba6a5003bf93f3c437a9e')
diff --git a/var/spack/repos/builtin/packages/perl-text-diff/package.py b/var/spack/repos/builtin/packages/perl-text-diff/package.py
index 4c61b3cbb1..2213365571 100644
--- a/var/spack/repos/builtin/packages/perl-text-diff/package.py
+++ b/var/spack/repos/builtin/packages/perl-text-diff/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-text-simpletable/package.py b/var/spack/repos/builtin/packages/perl-text-simpletable/package.py
new file mode 100644
index 0000000000..175d707fc8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-text-simpletable/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlTextSimpletable(PerlPackage):
+    """Simple Eyecandy ASCII Tables"""
+
+    homepage = "http://search.cpan.org/~mramberg/Text-SimpleTable/lib/Text/SimpleTable.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/M/MR/MRAMBERG/Text-SimpleTable-2.04.tar.gz"
+
+    version('2.04', '550136523c8da37b616988f9a5f58d59')
diff --git a/var/spack/repos/builtin/packages/perl-text-soundex/package.py b/var/spack/repos/builtin/packages/perl-text-soundex/package.py
new file mode 100644
index 0000000000..69ca76f262
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-text-soundex/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlTextSoundex(PerlPackage):
+    """Soundex is a phonetic algorithm for indexing names by sound, as
+       pronounced in English. The goal is for names with the same
+       pronunciation to be encoded to the same representation so
+       that they can be matched despite minor differences in spelling"""
+
+    homepage = "http://search.cpan.org/~rjbs/Text-Soundex-3.05/Soundex.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/Text-Soundex-3.05.tar.gz"
+
+    version('3.05', 'cb40ded7a5d27aa3a411d274d6ec18ae')
diff --git a/var/spack/repos/builtin/packages/perl-text-unidecode/package.py b/var/spack/repos/builtin/packages/perl-text-unidecode/package.py
new file mode 100644
index 0000000000..792f8e8e74
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-text-unidecode/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlTextUnidecode(PerlPackage):
+    """plain ASCII transliterations of Unicode text"""
+
+    homepage = "http://search.cpan.org/~sburke/Text-Unidecode/lib/Text/Unidecode.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/S/SB/SBURKE/Text-Unidecode-1.30.tar.gz"
+
+    version('1.30', '31cca8505bd74ed9d8036cdc84c808ca')
diff --git a/var/spack/repos/builtin/packages/perl-time-hires/package.py b/var/spack/repos/builtin/packages/perl-time-hires/package.py
new file mode 100644
index 0000000000..5250614010
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-time-hires/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlTimeHires(PerlPackage):
+    """High resolution alarm, sleep, gettimeofday, interval timers"""
+
+    homepage = "http://search.cpan.org/~jhi/Time-HiRes-1.9746/HiRes.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/J/JH/JHI/Time-HiRes-1.9746.tar.gz"
+
+    version('1.9746', '728dc2c2715313a056792191d7d0726c')
diff --git a/var/spack/repos/builtin/packages/perl-time-piece/package.py b/var/spack/repos/builtin/packages/perl-time-piece/package.py
new file mode 100644
index 0000000000..fe24c198ac
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-time-piece/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlTimePiece(PerlPackage):
+    """Object Oriented time objects"""
+
+    homepage = "http://search.cpan.org/~esaym/Time-Piece/Piece.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/E/ES/ESAYM/Time-Piece-1.3203.tar.gz"
+
+    version('1.3203', '515c1306f123a00116a95335cf543501')
diff --git a/var/spack/repos/builtin/packages/perl-try-tiny/package.py b/var/spack/repos/builtin/packages/perl-try-tiny/package.py
new file mode 100644
index 0000000000..a985b7e7fb
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-try-tiny/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlTryTiny(PerlPackage):
+    """Minimal try/catch with proper preservation of $@"""
+
+    homepage = "http://search.cpan.org/~ether/Try-Tiny-0.28/lib/Try/Tiny.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/Try-Tiny-0.28.tar.gz"
+
+    version('0.28', 'e2f8af601a62981aab30df15a6f47475')
diff --git a/var/spack/repos/builtin/packages/perl-uri-escape/package.py b/var/spack/repos/builtin/packages/perl-uri-escape/package.py
index 29f96003e3..64d7ba40fc 100644
--- a/var/spack/repos/builtin/packages/perl-uri-escape/package.py
+++ b/var/spack/repos/builtin/packages/perl-uri-escape/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-uri/package.py b/var/spack/repos/builtin/packages/perl-uri/package.py
new file mode 100644
index 0000000000..af5fb9a980
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-uri/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlUri(PerlPackage):
+    """Uniform Resource Identifiers (absolute and relative)"""
+
+    homepage = "http://search.cpan.org/~ether/URI-1.72/lib/URI.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/URI-1.72.tar.gz"
+
+    version('1.72', 'cd56d81ed429efaa97e7f3ff08851b48')
+
+    depends_on('perl-test-needs', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-version/package.py b/var/spack/repos/builtin/packages/perl-version/package.py
new file mode 100644
index 0000000000..e9a40018c8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-version/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlVersion(PerlPackage):
+    """Parse and manipulate Perl version strings"""
+
+    homepage = "http://search.cpan.org/~bdfoy/Perl-Version-1.013/lib/Perl/Version.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/B/BD/BDFOY/Perl-Version-1.013_03.tar.gz"
+
+    version('1.013_03', 'b2c94c8b33ccfa1635c760fcfa1c5358')
+
+    depends_on('perl-file-slurp-tiny', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-want/package.py b/var/spack/repos/builtin/packages/perl-want/package.py
new file mode 100644
index 0000000000..acd9e31da2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-want/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlWant(PerlPackage):
+    """A generalisation of wantarray."""
+
+    homepage = "search.cpan.org/~robin/Want/Want.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/R/RO/ROBIN/Want-0.29.tar.gz"
+
+    version('0.29', '33b2dae5db59781b9a0434fa1db04aab')
diff --git a/var/spack/repos/builtin/packages/perl-www-robotrules/package.py b/var/spack/repos/builtin/packages/perl-www-robotrules/package.py
new file mode 100644
index 0000000000..5f54470821
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-www-robotrules/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlWwwRobotrules(PerlPackage):
+    """Database of robots.txt-derived permissions"""
+
+    homepage = "http://deps.cpantesters.org/?module=WWW%3A%3ARobotRules;perl=latest"
+    url      = "http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/WWW-RobotRules-6.02.tar.gz"
+
+    version('6.02', 'b7186e8b8b3701e70c22abf430742403')
+
+    depends_on('perl-uri', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-xml-parser-lite/package.py b/var/spack/repos/builtin/packages/perl-xml-parser-lite/package.py
new file mode 100644
index 0000000000..f4b7773e21
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-xml-parser-lite/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlXmlParserLite(PerlPackage):
+    """Lightweight pure-perl XML Parser (based on regexps)"""
+
+    homepage = "http://search.cpan.org/~phred/XML-Parser-Lite-0.721/lib/XML/Parser/Lite.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/P/PH/PHRED/XML-Parser-Lite-0.721.tar.gz"
+
+    version('0.721', 'ad8a87b9bf413aa540c7cb724d650808')
+
+    depends_on('perl-test-requires', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-xml-parser/package.py b/var/spack/repos/builtin/packages/perl-xml-parser/package.py
index baa337319d..9b04cdd1b3 100644
--- a/var/spack/repos/builtin/packages/perl-xml-parser/package.py
+++ b/var/spack/repos/builtin/packages/perl-xml-parser/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/perl-xml-simple/package.py b/var/spack/repos/builtin/packages/perl-xml-simple/package.py
new file mode 100644
index 0000000000..fa7aed9723
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-xml-simple/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlXmlSimple(PerlPackage):
+    """An API for simple XML files"""
+
+    homepage = "http://search.cpan.org/~grantm/XML-Simple/lib/XML/Simple.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/G/GR/GRANTM/XML-Simple-2.24.tar.gz"
+
+    version('2.24', '1cd2e8e3421160c42277523d5b2f4dd2')
+
+    depends_on('perl-xml-parser', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-yaml-libyaml/package.py b/var/spack/repos/builtin/packages/perl-yaml-libyaml/package.py
new file mode 100644
index 0000000000..6893e7ac81
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-yaml-libyaml/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlYamlLibyaml(PerlPackage):
+    """Perl YAML Serialization using XS and libyaml  """
+
+    homepage = "http://search.cpan.org/~tinita/YAML-LibYAML/"
+    url      = "http://search.cpan.org/CPAN/authors/id/T/TI/TINITA/YAML-LibYAML-0.67.tar.gz"
+
+    version('0.67', '5a787150db680e3ab3f753f2e54640ab')
diff --git a/var/spack/repos/builtin/packages/perl/package.py b/var/spack/repos/builtin/packages/perl/package.py
index fbf788d106..fd0c4aef17 100644
--- a/var/spack/repos/builtin/packages/perl/package.py
+++ b/var/spack/repos/builtin/packages/perl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 # Author: Milton Woods <milton.woods@bom.gov.au>
 # Date: March 22, 2017
@@ -30,12 +11,13 @@
 # Author: Justin Too <justin@doubleotoo.com>
 # Date: September 6, 2015
 #
-from spack import *
 import os
 from contextlib import contextmanager
-import spack
+
 from llnl.util.lang import match_predicate
 
+from spack import *
+
 
 class Perl(Package):  # Perl doesn't use Autotools, it should subclass Package
     """Perl 5 is a highly capable, feature-rich programming language with over
@@ -45,19 +27,23 @@ class Perl(Package):  # Perl doesn't use Autotools, it should subclass Package
     # URL must remain http:// so Spack can bootstrap curl
     url = "http://www.cpan.org/src/5.0/perl-5.24.1.tar.gz"
 
-    # Development releases
+    # see http://www.cpan.org/src/README.html for
+    # explanation of version numbering scheme
+
+    # Development releases (odd numbers)
     version('5.25.11', '37a398682c36cd85992b34b5c1c25dc1')
 
-    # Maintenance releases (recommended)
-    version('5.24.1', '765ef511b5b87a164e2531403ee16b3c', preferred=True)
-    version('5.22.3', 'aa4f236dc2fc6f88b871436b8d0fda95')
+    # Maintenance releases (even numbers, recommended)
+    version('5.28.0', sha256='7e929f64d4cb0e9d1159d4a59fc89394e27fa1f7004d0836ca0d514685406ea8')
+    version('5.26.2', 'dc0fea097f3992a8cd53f8ac0810d523', preferred=True)
+    version('5.24.1', '765ef511b5b87a164e2531403ee16b3c')
 
-    # Misc releases that people need
+    # End of life releases
+    version('5.22.4', '31a71821682e02378fcdadeed85688b8')
+    version('5.22.3', 'aa4f236dc2fc6f88b871436b8d0fda95')
     version('5.22.2', '5767e2a10dd62a46d7b57f74a90d952b')
     version('5.22.1', '19295bbb775a3c36123161b9bf4892f1')
     version('5.22.0', 'e32cb6a8dda0084f2a43dac76318d68d')
-
-    # End of life releases
     version('5.20.3', 'd647d0ea5a7a8194c34759ab9f2610cd')
     version('5.18.4', '1f9334ff730adc05acd3dd7130d295db')
     version('5.16.3', 'eb5c40f2575df6c155bc99e3fe0a9d82')
@@ -71,6 +57,10 @@ class Perl(Package):  # Perl doesn't use Autotools, it should subclass Package
     # https://rt.perl.org/Public/Bug/Display.html?id=126468
     patch('protect-quotes-in-ccflags.patch', when='@5.22.0')
 
+    # Fix build on Fedora 28
+    # https://bugzilla.redhat.com/show_bug.cgi?id=1536752
+    patch('https://src.fedoraproject.org/rpms/perl/raw/004cea3a67df42e92ffdf4e9ac36d47a3c6a05a4/f/perl-5.26.1-guard_old_libcrypt_fix.patch', level=1, sha256='0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac', when='@:5.26.2')
+
     # Installing cpanm alongside the core makes it safe and simple for
     # people/projects to install their own sets of perl modules.  Not
     # having it in core increases the "energy of activation" for doing
@@ -81,6 +71,9 @@ class Perl(Package):  # Perl doesn't use Autotools, it should subclass Package
     variant('shared', default=True,
             description='Build a shared libperl.so library')
 
+    variant('threads', default=True,
+            description='Build perl with threads support')
+
     resource(
         name="cpanm",
         url="http://search.cpan.org/CPAN/authors/id/M/MI/MIYAGAWA/App-cpanminus-1.7042.tar.gz",
@@ -91,6 +84,18 @@ class Perl(Package):  # Perl doesn't use Autotools, it should subclass Package
 
     phases = ['configure', 'build', 'install']
 
+    # On a lustre filesystem, patch may fail when files
+    # aren't writeable so make pp.c user writeable
+    # before patching. This should probably walk the
+    # source and make everything writeable in the future.
+    def do_stage(self, mirror_only=False):
+        # Do Spack's regular stage
+        super(Perl, self).do_stage(mirror_only)
+        # Add write permissions on file to be patched
+        filename = join_path(self.stage.source_path, 'pp.c')
+        perm = os.stat(filename).st_mode
+        os.chmod(filename, perm | 0o200)
+
     def configure_args(self):
         spec = self.spec
         prefix = self.prefix
@@ -128,6 +133,9 @@ class Perl(Package):  # Perl doesn't use Autotools, it should subclass Package
         if '+shared' in spec:
             config_args.append('-Duseshrplib')
 
+        if '+threads' in spec:
+            config_args.append('-Dusethreads')
+
         return config_args
 
     def configure(self, spec, prefix):
@@ -252,27 +260,23 @@ class Perl(Package):  # Perl doesn't use Autotools, it should subclass Package
 
         return match_predicate(ignore_arg, patterns)
 
-    def activate(self, ext_pkg, **args):
+    def activate(self, ext_pkg, view, **args):
         ignore = self.perl_ignore(ext_pkg, args)
         args.update(ignore=ignore)
 
-        super(Perl, self).activate(ext_pkg, **args)
-
-        extensions_layout = args.get("extensions_layout",
-                                     spack.store.extensions)
+        super(Perl, self).activate(ext_pkg, view, **args)
 
+        extensions_layout = view.extensions_layout
         exts = extensions_layout.extension_map(self.spec)
         exts[ext_pkg.name] = ext_pkg.spec
 
-    def deactivate(self, ext_pkg, **args):
+    def deactivate(self, ext_pkg, view, **args):
         ignore = self.perl_ignore(ext_pkg, args)
         args.update(ignore=ignore)
 
-        super(Perl, self).deactivate(ext_pkg, **args)
-
-        extensions_layout = args.get("extensions_layout",
-                                     spack.store.extensions)
+        super(Perl, self).deactivate(ext_pkg, view, **args)
 
+        extensions_layout = view.extensions_layout
         exts = extensions_layout.extension_map(self.spec)
         # Make deactivate idempotent
         if ext_pkg.name in exts:
diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py
index 838369f4e4..8be5d8cce5 100644
--- a/var/spack/repos/builtin/packages/petsc/package.py
+++ b/var/spack/repos/builtin/packages/petsc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 import os
 import sys
@@ -35,13 +16,24 @@ class Petsc(Package):
     """
 
     homepage = "http://www.mcs.anl.gov/petsc/index.html"
-    url = "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.5.3.tar.gz"
+    url      = "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.5.3.tar.gz"
+    git      = "https://bitbucket.org/petsc/petsc.git"
 
-    maintainers = ['balay', 'barrysmith']
+    maintainers = ['balay', 'barrysmith', 'jedbrown']
 
-    version('develop', git='https://bitbucket.org/petsc/petsc.git', tag='master')
-    version('xsdk-0.2.0', git='https://bitbucket.org/petsc/petsc.git', tag='xsdk-0.2.0')
+    version('develop', branch='master')
+    version('xsdk-0.2.0', tag='xsdk-0.2.0')
 
+    version('3.10.2', '63ed950653ae9b8d19daea47e24c0338')
+    version('3.10.1', '2d0d5a9bd8112a4147a2a23f7f62a906')
+    version('3.10.0', '0240c2ce8c54e47b3531a743ee844d41')
+    version('3.9.4', 'c98eb67573efb2f91c6f239368259e44')
+    version('3.9.3', '7b71d705f66f9961cb0e2da3f9da79a1')
+    version('3.9.2', '8bedc0cd8c8603d54bfd99a6e8f77b3d')
+    version('3.9.1', 'd3a229a188dbeef9b3f29b9a63622fad')
+    version('3.9.0', '34b8a81814ca050a96d58e53a2f0ac7a')
+    version('3.8.4', 'd7767fe2919536aa393eb22841899306')
+    version('3.8.3', '322cbcf2a0f7b7bad562643b05d66f11')
     version('3.8.2', '00666e1c4cbfa8dd6eebf91ff8180f79')
     version('3.8.1', '3ed75c1147800fc156fe1f1e515a68a7')
     version('3.8.0', '02680f1f78a0d4c5a9de80a366793eb8')
@@ -69,7 +61,6 @@ class Petsc(Package):
             description='Activates support for metis and parmetis')
     variant('hdf5',    default=True,
             description='Activates support for HDF5 (only parallel)')
-    variant('boost',   default=True,  description='Activates support for Boost')
     variant('hypre',   default=True,
             description='Activates support for Hypre (only parallel)')
     # Mumps is disabled by default, because it depends on Scalapack
@@ -83,6 +74,11 @@ class Petsc(Package):
             description='Activates support for Trilinos (only parallel)')
     variant('int64', default=False,
             description='Compile with 64bit indices')
+    variant('clanguage', default='C', values=('C', 'C++'),
+            description='Specify C (recommended) or C++ to compile PETSc',
+            multi=False)
+    variant('suite-sparse', default=False,
+            description='Activates support for SuiteSparse')
 
     # 3.8.0 has a build issue with MKL - so list this conflict explicitly
     conflicts('^intel-mkl', when='@3.8.0')
@@ -93,6 +89,7 @@ class Petsc(Package):
     if sys.platform == "darwin":
         patch('macos-clang-8.1.0.diff',
               when='@3.7.5%clang@8.1.0:')
+    patch('pkg-config-3.7.6-3.8.4.diff', when='@3.7.6:3.8.4')
 
     # Virtual dependencies
     # Git repository needs sowing to build Fortran interface
@@ -108,11 +105,13 @@ class Petsc(Package):
     depends_on('python@2.6:2.8', type='build')
 
     # Other dependencies
-    depends_on('boost', when='@:3.5+boost')
-    depends_on('metis@5:~int64+real64', when='+metis~int64+double')
-    depends_on('metis@5:+int64', when='+metis+int64~double')
-    depends_on('metis@5:~int64+real64', when='+metis~int64+double')
-    depends_on('metis@5:+int64', when='+metis+int64~double')
+    depends_on('metis@5:~int64+real64', when='@:3.7.99+metis~int64+double')
+    depends_on('metis@5:~int64', when='@:3.7.99+metis~int64~double')
+    depends_on('metis@5:+int64+real64', when='@:3.7.99+metis+int64+double')
+    depends_on('metis@5:+int64', when='@:3.7.99+metis+int64~double')
+    # petsc-3.8+ uses default (float) metis with any (petsc) precision
+    depends_on('metis@5:~int64', when='@3.8:+metis~int64')
+    depends_on('metis@5:+int64', when='@3.8:+metis+int64')
 
     depends_on('hdf5+mpi+hl', when='+hdf5+mpi')
     depends_on('zlib', when='+hdf5')
@@ -121,18 +120,22 @@ class Petsc(Package):
     # Also PETSc prefer to build it without internal superlu, likely due to
     # conflict in headers see
     # https://bitbucket.org/petsc/petsc/src/90564b43f6b05485163c147b464b5d6d28cde3ef/config/BuildSystem/config/packages/hypre.py
-    depends_on('hypre~internal-superlu~int64', when='+hypre+mpi~complex~int64')
+    depends_on('hypre@:2.13.99~internal-superlu~int64', when='@:3.8.99+hypre+mpi~complex~int64')
+    depends_on('hypre@:2.13.99~internal-superlu+int64', when='@:3.8.99+hypre+mpi~complex+int64')
+    depends_on('hypre@2.14:~internal-superlu~int64', when='@3.9:+hypre+mpi~complex~int64')
+    depends_on('hypre@2.14:~internal-superlu+int64', when='@3.9+hypre+mpi~complex+int64')
     depends_on('hypre@xsdk-0.2.0~internal-superlu+int64', when='@xsdk-0.2.0+hypre+mpi~complex+int64')
     depends_on('hypre@xsdk-0.2.0~internal-superlu~int64', when='@xsdk-0.2.0+hypre+mpi~complex~int64')
     depends_on('hypre@develop~internal-superlu+int64', when='@develop+hypre+mpi~complex+int64')
     depends_on('hypre@develop~internal-superlu~int64', when='@develop+hypre+mpi~complex~int64')
-    depends_on('hypre~internal-superlu+int64', when='+hypre+mpi~complex+int64')
     depends_on('superlu-dist@:4.3~int64', when='@3.4.4:3.6.4+superlu-dist+mpi~int64')
     depends_on('superlu-dist@:4.3+int64', when='@3.4.4:3.6.4+superlu-dist+mpi+int64')
     depends_on('superlu-dist@5.0.0:~int64', when='@3.7:3.7.99+superlu-dist+mpi~int64')
     depends_on('superlu-dist@5.0.0:+int64', when='@3.7:3.7.99+superlu-dist+mpi+int64')
-    depends_on('superlu-dist@5.2:5.2.99~int64', when='@3.8:3.8.99+superlu-dist+mpi~int64')
-    depends_on('superlu-dist@5.2:5.2.99+int64', when='@3.8:3.8.99+superlu-dist+mpi+int64')
+    depends_on('superlu-dist@5.2:5.2.99~int64', when='@3.8:3.9.99+superlu-dist+mpi~int64')
+    depends_on('superlu-dist@5.2:5.2.99+int64', when='@3.8:3.9.99+superlu-dist+mpi+int64')
+    depends_on('superlu-dist@5.4:5.4.99~int64', when='@3.10:3.10.99+superlu-dist+mpi~int64')
+    depends_on('superlu-dist@5.4:5.4.99+int64', when='@3.10:3.10.99+superlu-dist+mpi+int64')
     depends_on('superlu-dist@xsdk-0.2.0~int64', when='@xsdk-0.2.0+superlu-dist+mpi~int64')
     depends_on('superlu-dist@xsdk-0.2.0+int64', when='@xsdk-0.2.0+superlu-dist+mpi+int64')
     depends_on('superlu-dist@develop~int64', when='@develop+superlu-dist+mpi~int64')
@@ -142,6 +145,7 @@ class Petsc(Package):
     depends_on('trilinos@12.6.2:', when='@3.7.0:+trilinos+mpi')
     depends_on('trilinos@xsdk-0.2.0', when='@xsdk-0.2.0+trilinos+mpi')
     depends_on('trilinos@develop', when='@xdevelop+trilinos+mpi')
+    depends_on('suite-sparse', when='+suite-sparse')
 
     def mpi_dependent_options(self):
         if '~mpi' in self.spec:
@@ -169,8 +173,12 @@ class Petsc(Package):
             compiler_opts = [
                 '--with-cc=%s' % self.spec['mpi'].mpicc,
                 '--with-cxx=%s' % self.spec['mpi'].mpicxx,
-                '--with-fc=%s' % self.spec['mpi'].mpifc
+                '--with-fc=%s' % self.spec['mpi'].mpifc,
             ]
+            if self.spec.satisfies('%intel'):
+                # mpiifort needs some help to automatically link
+                # all necessary run-time libraries
+                compiler_opts.append('--FC_LINKER_FLAGS=-lintlc')
         return compiler_opts
 
     def install(self, spec, prefix):
@@ -178,7 +186,13 @@ class Petsc(Package):
                    '--with-x=0',
                    '--download-c2html=0',
                    '--download-sowing=0',
-                   '--download-hwloc=0']
+                   '--download-hwloc=0',
+                   'CFLAGS=%s' % ' '.join(spec.compiler_flags['cflags']),
+                   'FFLAGS=%s' % ' '.join(spec.compiler_flags['fflags']),
+                   'CXXFLAGS=%s' % ' '.join(spec.compiler_flags['cxxflags']),
+                   'COPTFLAGS=',
+                   'FOPTFLAGS=',
+                   'CXXOPTFLAGS=']
         options.extend(self.mpi_dependent_options())
         options.extend([
             '--with-precision=%s' % (
@@ -198,9 +212,17 @@ class Petsc(Package):
 
         if 'trilinos' in spec:
             options.append('--with-cxx-dialect=C++11')
+            if spec.satisfies('^trilinos+boost'):
+                options.append('--with-boost=1')
+
+        if self.spec.satisfies('clanguage=C++'):
+            options.append('--with-clanguage=C++')
+        else:
+            options.append('--with-clanguage=C')
 
-        # Help PETSc pick up Scalapack from MKL:
-        if 'scalapack' in spec:
+        # PETSc depends on scalapack when '+mumps+mpi~int64' (see depends())
+        # help PETSc pick up Scalapack from MKL
+        if spec.satisfies('+mumps+mpi~int64'):
             scalapack = spec['scalapack'].libs
             options.extend([
                 '--with-scalapack-lib=%s' % scalapack.joined(),
@@ -212,8 +234,8 @@ class Petsc(Package):
             ])
 
         # Activates library support if needed
-        for library in ('metis', 'boost', 'hdf5', 'hypre', 'parmetis',
-                        'mumps', 'trilinos', 'zlib'):
+        for library in ('metis', 'hdf5', 'hypre', 'parmetis',
+                        'mumps', 'trilinos'):
             options.append(
                 '--with-{library}={value}'.format(
                     library=library, value=('1' if library in spec else '0'))
@@ -238,8 +260,31 @@ class Petsc(Package):
             options.append(
                 '--with-superlu_dist=0'
             )
+        # SuiteSparse: configuring using '--with-suitesparse-dir=...' has some
+        # issues, so specify directly the include path and the libraries.
+        if '+suite-sparse' in spec:
+            ss_spec = 'suite-sparse:umfpack,klu,cholmod,btf,ccolamd,colamd,' \
+                'camd,amd,suitesparseconfig'
+            options.extend([
+                '--with-suitesparse-include=%s' % spec[ss_spec].prefix.include,
+                '--with-suitesparse-lib=%s' % spec[ss_spec].libs.ld_flags,
+                '--with-suitesparse=1'
+            ])
+        else:
+            options.append('--with-suitesparse=0')
+
+        # zlib: configuring using '--with-zlib-dir=...' has some issues with
+        # SuiteSparse so specify directly the include path and the libraries.
+        if 'zlib' in spec:
+            options.extend([
+                '--with-zlib-include=%s' % spec['zlib'].prefix.include,
+                '--with-zlib-lib=%s'     % spec['zlib'].libs.ld_flags,
+                '--with-zlib=1'
+            ])
+        else:
+            options.append('--with-zlib=0')
 
-        configure('--prefix=%s' % prefix, *options)
+        python('configure', '--prefix=%s' % prefix, *options)
 
         # PETSc has its own way of doing parallel make.
         make('MAKE_NP=%s' % make_jobs, parallel=False)
@@ -253,6 +298,18 @@ class Petsc(Package):
                 cc('ex50.c', '-I%s' % prefix.include, '-L%s' % prefix.lib,
                    '-lpetsc', '-lm', '-o', 'ex50')
                 run = Executable(join_path(spec['mpi'].prefix.bin, 'mpirun'))
+                # For Spectrum MPI, if -np is omitted, the default behavior is
+                # to assign one process per process slot, where the default
+                # process slot allocation is one per core. On systems with
+                # many cores, the number of processes can exceed the size of
+                # the grid specified when the testcase is run and the test case
+                # fails. Specify a small number of processes to prevent
+                # failure.
+                # For more information about Spectrum MPI invocation, see URL
+                # https://www.ibm.com/support/knowledgecenter/en/SSZTET_10.1.0/smpi02/smpi02_mpirun_options.html
+                if ('spectrum-mpi' in spec):
+                    run.add_default_arg('-np')
+                    run.add_default_arg('4')
                 run('ex50', '-da_grid_x', '4', '-da_grid_y', '4')
                 if 'superlu-dist' in spec:
                     run('ex50',
@@ -288,3 +345,10 @@ class Petsc(Package):
         # Set up PETSC_DIR for everyone using PETSc package
         spack_env.set('PETSC_DIR', self.prefix)
         spack_env.unset('PETSC_ARCH')
+
+    @property
+    def headers(self):
+        return find_headers('petsc', self.prefix.include, recursive=False) \
+            or None  # return None to indicate failure
+
+    # For the 'libs' property - use the default handler.
diff --git a/var/spack/repos/builtin/packages/petsc/pkg-config-3.7.6-3.8.4.diff b/var/spack/repos/builtin/packages/petsc/pkg-config-3.7.6-3.8.4.diff
new file mode 100644
index 0000000000..a0c960dcae
--- /dev/null
+++ b/var/spack/repos/builtin/packages/petsc/pkg-config-3.7.6-3.8.4.diff
@@ -0,0 +1,29 @@
+diff --git c/config/PETSc/Configure.py w/config/PETSc/Configure.py
+index ca65368e54..995afd0799 100644
+--- c/config/PETSc/Configure.py
++++ w/config/PETSc/Configure.py
+@@ -174,19 +174,19 @@ class Configure(config.base.Configure):
+ 
+     self.setCompilers.pushLanguage('C')
+     fd.write('ccompiler='+self.setCompilers.getCompiler()+'\n')
+-    fd.write('cflags_extra="'+self.setCompilers.getCompilerFlags().strip()+'"\n')
+-    fd.write('cflags_dep="'+self.compilers.dependenciesGenerationFlag.get('C','')+'"\n')
+-    fd.write('ldflag_rpath="'+self.setCompilers.CSharedLinkerFlag+'"\n')
++    fd.write('cflags_extra='+self.setCompilers.getCompilerFlags().strip()+'\n')
++    fd.write('cflags_dep='+self.compilers.dependenciesGenerationFlag.get('C','')+'\n')
++    fd.write('ldflag_rpath='+self.setCompilers.CSharedLinkerFlag+'\n')
+     self.setCompilers.popLanguage()
+     if hasattr(self.compilers, 'C++'):
+       self.setCompilers.pushLanguage('C++')
+       fd.write('cxxcompiler='+self.setCompilers.getCompiler()+'\n')
+-      fd.write('cxxflags_extra="'+self.setCompilers.getCompilerFlags().strip()+'"\n')
++      fd.write('cxxflags_extra='+self.setCompilers.getCompilerFlags().strip()+'\n')
+       self.setCompilers.popLanguage()
+     if hasattr(self.compilers, 'FC'):
+       self.setCompilers.pushLanguage('FC')
+       fd.write('fcompiler='+self.setCompilers.getCompiler()+'\n')
+-      fd.write('fflags_extra="'+self.setCompilers.getCompilerFlags().strip()+'"\n')
++      fd.write('fflags_extra='+self.setCompilers.getCompilerFlags().strip()+'\n')
+       self.setCompilers.popLanguage()
+ 
+     fd.write('\n')
diff --git a/var/spack/repos/builtin/packages/petsc/xlc-test-3.10.1.diff b/var/spack/repos/builtin/packages/petsc/xlc-test-3.10.1.diff
new file mode 100644
index 0000000000..7009ea450d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/petsc/xlc-test-3.10.1.diff
@@ -0,0 +1,19 @@
+--- a/gmakefile.test
++++ b/gmakefile.test
+@@ -127,11 +127,14 @@
+ endif
+ 	-@$(GFORTRAN_DEP_CLEANUP)
+ 
++#add xlf2003 flags
++XLF2003FLAGS = "-qxlf2003=polymorphic:bozlitargs:stopexcept:volatile:autorealloc"
++
+ $(TESTDIR)/%.o : $(EXAMPLESDIR)/%.F90 | $$(@D)/.DIR
+ ifeq ($(FC_MODULE_OUTPUT_FLAG),)
+ 	$(call quiet,FCMOD) $(MODDIR) && $(FC) -c $(FC_FLAGS) $(FFLAGS) $(FCPPFLAGS) $(FC_DEPFLAGS) -I$(dir $<) $(abspath $<) -o $(abspath $@)
+ else
+-	$(PETSC_COMPILE.F) -I$(dir $<) $(abspath $<) -o $@ $(FC_MODULE_OUTPUT_FLAG)$(MODDIR) $(FC_MODULE_FLAG)$(MODDIR)
++	$(PETSC_COMPILE.F) ${XLF2003FLAGS} -I$(dir $<) $(abspath $<) -o $@ $(FC_MODULE_OUTPUT_FLAG)$(MODDIR) $(FC_MODULE_FLAG)$(MODDIR)
+ endif
+ 	-@$(GFORTRAN_DEP_CLEANUP)
+ 
+
diff --git a/var/spack/repos/builtin/packages/pexsi/package.py b/var/spack/repos/builtin/packages/pexsi/package.py
index 63819923af..fa93fac715 100644
--- a/var/spack/repos/builtin/packages/pexsi/package.py
+++ b/var/spack/repos/builtin/packages/pexsi/package.py
@@ -1,31 +1,11 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 import inspect
 import os.path
-import shutil
 
 from spack import *
 
@@ -54,7 +34,7 @@ class Pexsi(MakefilePackage):
     depends_on('parmetis')
     depends_on('superlu-dist@3.3:3.999', when='@:0.9.0')
     depends_on('superlu-dist@4.3:4.999', when='@0.9.2')
-    depends_on('superlu-dist@5.1.2:', when='@0.10.2:')
+    depends_on('superlu-dist@5.1.2:5.3.999', when='@0.10.2:')
 
     variant(
         'fortran', default=False, description='Builds the Fortran interface'
@@ -64,27 +44,32 @@ class Pexsi(MakefilePackage):
 
     def edit(self, spec, prefix):
 
-        substitutions = {
-            '@MPICC': self.spec['mpi'].mpicc,
-            '@MPICXX': self.spec['mpi'].mpicxx,
-            '@MPIFC': self.spec['mpi'].mpifc,
-            '@MPICXX_LIB': self.spec['mpi:cxx'].libs.joined(),
-            '@RANLIB': 'ranlib',
-            '@PEXSI_STAGE': self.stage.source_path,
-            '@SUPERLU_PREFIX': self.spec['superlu-dist'].prefix,
-            '@METIS_PREFIX': self.spec['metis'].prefix,
-            '@PARMETIS_PREFIX': self.spec['parmetis'].prefix,
-            '@LAPACK_PREFIX': self.spec['lapack'].prefix,
-            '@BLAS_PREFIX': self.spec['blas'].prefix,
-            '@LAPACK_LIBS': self.spec['lapack'].libs.joined(),
-            '@BLAS_LIBS': self.spec['blas'].libs.joined(),
+        substitutions = [
+            ('@MPICC', self.spec['mpi'].mpicc),
+            ('@MPICXX_LIB', self.spec['mpi:cxx'].libs.joined()),
+            ('@MPICXX', self.spec['mpi'].mpicxx),
+            ('@MPIFC', self.spec['mpi'].mpifc),
+            ('@RANLIB', 'ranlib'),
+            ('@PEXSI_STAGE', self.stage.source_path),
+            ('@SUPERLU_PREFIX', self.spec['superlu-dist'].prefix),
+            ('@METIS_PREFIX', self.spec['metis'].prefix),
+            ('@PARMETIS_PREFIX', self.spec['parmetis'].prefix),
+            ('@LAPACK_PREFIX', self.spec['lapack'].prefix),
+            ('@BLAS_PREFIX', self.spec['blas'].prefix),
+            ('@LAPACK_LIBS', self.spec['lapack'].libs.joined()),
+            ('@BLAS_LIBS', self.spec['blas'].libs.joined()),
             # FIXME : what to do with compiler provided libraries ?
-            '@STDCXX_LIB': ' '.join(self.compiler.stdcxx_libs),
-            '@FLDFLAGS': ''
-        }
+            ('@STDCXX_LIB', ' '.join(self.compiler.stdcxx_libs))
+        ]
 
         if '@0.9.2' in self.spec:
-            substitutions['@FLDFLAGS'] = '-Wl,--allow-multiple-definition'
+            substitutions.append(
+                ('@FLDFLAGS', '-Wl,--allow-multiple-definition')
+            )
+        else:
+            substitutions.append(
+                ('@FLDFLAGS', '')
+            )
 
         template = join_path(
             os.path.dirname(inspect.getmodule(self).__file__),
@@ -94,8 +79,8 @@ class Pexsi(MakefilePackage):
             self.stage.source_path,
             'make.inc'
         )
-        shutil.copy(template, makefile)
-        for key, value in substitutions.items():
+        copy(template, makefile)
+        for key, value in substitutions:
             filter_file(key, value, makefile)
 
     def build(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/pfft/package.py b/var/spack/repos/builtin/packages/pfft/package.py
index 93f0222a48..4121d90caa 100644
--- a/var/spack/repos/builtin/packages/pfft/package.py
+++ b/var/spack/repos/builtin/packages/pfft/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/pflotran/package.py b/var/spack/repos/builtin/packages/pflotran/package.py
index e04e33a1db..73f95f75f7 100644
--- a/var/spack/repos/builtin/packages/pflotran/package.py
+++ b/var/spack/repos/builtin/packages/pflotran/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -32,13 +13,18 @@ class Pflotran(AutotoolsPackage):
     """
 
     homepage = "http://www.pflotran.org"
+    git      = "https://bitbucket.org/pflotran/pflotran.git"
 
-    version('develop', git='https://bitbucket.org/pflotran/pflotran')
-    version('xsdk-0.2.0', git='https://bitbucket.org/pflotran/pflotran', tag='master')
+    version('develop')
+    version('xsdk-0.2.0', tag='master')
+    version('xsdk-0.3.0', branch='release/xsdk-0.3.0')
 
     depends_on('mpi')
     depends_on('hdf5@1.8.12:+mpi+fortran')
     depends_on('petsc@develop+hdf5+metis', when='@develop')
-    depends_on('petsc@xsdk-0.2.0+hdf5+metis', when='@xsdk-0.2.0')    
+    depends_on('petsc@xsdk-0.2.0+hdf5+metis', when='@xsdk-0.2.0')
+    depends_on('petsc@3.8.0:+hdf5+metis', when='@xsdk-0.3.0')
 
-    parallel = False
+    @property
+    def parallel(self):
+        return self.spec.satisfies('@develop')
diff --git a/var/spack/repos/builtin/packages/pfunit/package.py b/var/spack/repos/builtin/packages/pfunit/package.py
new file mode 100644
index 0000000000..e9faaaebbf
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pfunit/package.py
@@ -0,0 +1,81 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+#
+from spack import *
+import glob
+
+
+class Pfunit(CMakePackage):
+    """pFUnit is a unit testing framework enabling JUnit-like testing of
+    serial and MPI-parallel software written in Fortran."""
+
+    homepage = "http://pfunit.sourceforge.net/"
+    url      = "https://github.com/Goddard-Fortran-Ecosystem/pFUnit/archive/3.2.9.tar.gz"
+
+    maintainers = ['citibeth']
+
+    version('3.2.9', 'e13d8362284b13b7c863e2fe769a9d5c')
+
+    variant('shared', default=True,
+            description='Build shared library in addition to static')
+    variant('mpi', default=False, description='Enable MPI')
+    variant('openmp', default=False, description='Enable OpenMP')
+    variant('docs', default=False, description='Build docs')
+
+    depends_on('python@2.7:', type=('build', 'run'))  # python3 too!
+    depends_on('mpi', when='+mpi')
+
+    def patch(self):
+        # The package tries to put .mod files in directory ./mod;
+        # spack needs to put them in a standard location:
+        for file in glob.glob('*/CMakeLists.txt'):
+            filter_file(r'.*/mod($|[^\w].*)', '', file)
+
+    def cmake_args(self):
+        spec = self.spec
+        args = [
+            '-DPYTHON_EXECUTABLE=%s' % spec['python'].command,
+            '-DBUILD_SHARED=%s' % ('YES' if '+shared' in spec else 'NO'),
+            '-DCMAKE_Fortran_MODULE_DIRECTORY=%s' % spec.prefix.include,
+            '-DBUILD_DOCS=%s' % ('YES' if '+docs' in spec else 'NO'),
+            '-DOPENMP=%s' % ('YES' if '+openmp' in spec else 'NO')]
+
+        if spec.satisfies('+mpi'):
+            args.extend(['-DMPI=YES', '-DMPI_USE_MPIEXEC=YES',
+                         '-DMPI_Fortran_COMPILER=%s' % spec['mpi'].mpifc])
+        else:
+            args.append('-DMPI=NO')
+        return args
+
+    def check(self):
+        """Searches the CMake-generated Makefile for the target ``test``
+        and runs it if found.
+        """
+        args = ['tests']
+        if self.spec.satisfies('+mpi'):
+            args.append('MPI=YES')
+        if self.spec.satisfies('+openmp'):
+            args.append('OPENMP=YES')
+        with working_dir(self.build_directory):
+            make(*args)
+
+    def compiler_vendor(self):
+        vendors = {'%gcc': 'GNU', '%clang': 'GNU', '%intel': 'Intel',
+                   '%pgi': 'PGI', '%nag': 'NAG'}
+        for key, value in vendors.items():
+            if self.spec.satisfies(key):
+                return value
+        raise InstallError('Unsupported compiler.')
+
+    def setup_environment(self, spack_env, run_env):
+        spack_env.set('PFUNIT', self.spec.prefix)
+        run_env.set('PFUNIT', self.spec.prefix)
+        spack_env.set('F90_VENDOR', self.compiler_vendor())
+        run_env.set('F90_VENDOR', self.compiler_vendor())
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        spack_env.set('PFUNIT', self.spec.prefix)
+        spack_env.set('F90_VENDOR', self.compiler_vendor())
diff --git a/var/spack/repos/builtin/packages/pgdspider/package.py b/var/spack/repos/builtin/packages/pgdspider/package.py
index 39a518113f..5a4dab9516 100644
--- a/var/spack/repos/builtin/packages/pgdspider/package.py
+++ b/var/spack/repos/builtin/packages/pgdspider/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os.path
 
diff --git a/var/spack/repos/builtin/packages/pgi/package.py b/var/spack/repos/builtin/packages/pgi/package.py
index 63592d6cc6..47242e4ecd 100644
--- a/var/spack/repos/builtin/packages/pgi/package.py
+++ b/var/spack/repos/builtin/packages/pgi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 from spack.util.prefix import Prefix
 import os
@@ -39,6 +20,8 @@ class Pgi(Package):
 
     homepage = "http://www.pgroup.com/"
 
+    version('18.4',  'b55461f9f0986acbd51902c51c2074b9')
+    version('17.10', '85ad6506e7ada610ab11ddb35d697efa')
     version('17.4',  'a311d2756ddda657860bad8e5725597b')
     version('17.3',  '6eefc42f85e756cbaba76467ed640902')
     version('16.10', '9bb6bfb7b1052f9e6a45829ba7a24e47')
diff --git a/var/spack/repos/builtin/packages/pgmath/package.py b/var/spack/repos/builtin/packages/pgmath/package.py
new file mode 100644
index 0000000000..7b4f98be5e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pgmath/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Pgmath(CMakePackage):
+    """Flang's math library"""
+
+    homepage = "https://github.com/flang-compiler/flang"
+    url      = "https://github.com/flang-compiler/flang/archive/flang_20180612.tar.gz"
+    git      = "https://github.com/flang-compiler/flang.git"
+
+    version('develop', branch='master')
+    version('20180612', '62284e26214eaaff261a922c67f6878c')
+
+    conflicts("%gcc@:7.1.9999")
+
+    root_cmakelists_dir = 'runtime/libpgmath'
diff --git a/var/spack/repos/builtin/packages/phantompeakqualtools/package.py b/var/spack/repos/builtin/packages/phantompeakqualtools/package.py
new file mode 100644
index 0000000000..118d7032c9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/phantompeakqualtools/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Phantompeakqualtools(RPackage):
+    """This package computes informative enrichment and quality measures for
+       ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data."""
+
+    homepage = "https://github.com/kundajelab/phantompeakqualtools"
+    url      = "https://github.com/kundajelab/phantompeakqualtools/archive/1.2.tar.gz"
+
+    version('1.2', 'e94943a42132b9ff2886f006ab34c121')
+
+    depends_on('awk')
+    depends_on('samtools')
+    depends_on('r', type=('build', 'run'))
+    depends_on('r-phantompeakqualtools', type=('build', 'run'))
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('run_spp.R', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/phast/package.py b/var/spack/repos/builtin/packages/phast/package.py
new file mode 100644
index 0000000000..503246614c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/phast/package.py
@@ -0,0 +1,39 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Phast(MakefilePackage):
+    """PHAST is a freely available software package for comparative and
+       evolutionary genomics."""
+
+    homepage = "http://compgen.cshl.edu/phast/index.php"
+    url      = "https://github.com/CshlSiepelLab/phast/archive/v1.4.tar.gz"
+
+    version('1.4', '2bc0412ba58ea1f08ba5e12fad43b4c7')
+
+    # phast cannot build with clapack using external blas
+    depends_on('clapack~external-blas')
+
+    build_directory = 'src'
+
+    @property
+    def build_targets(self):
+        targets = ['CLAPACKPATH={0}'.format(self.spec['clapack'].prefix)]
+        return targets
+
+    def edit(self, spec, prefix):
+        with working_dir(self.build_directory):
+            filter_file(r'\$\{PWD\}',
+                        '$(dir $(realpath $(firstword $(MAKEFILE_LIST))))',
+                        'make-include.mk')
+            filter_file(r'\$\{PWD\}',
+                        '$(dir $(realpath $(firstword $(MAKEFILE_LIST))))',
+                        'Makefile')
+
+    def install(self, spec, prefix):
+        install_tree('bin', prefix.bin)
+        install_tree('lib', prefix.lib)
diff --git a/var/spack/repos/builtin/packages/phasta/package.py b/var/spack/repos/builtin/packages/phasta/package.py
index a73c90848b..2243281b5a 100644
--- a/var/spack/repos/builtin/packages/phasta/package.py
+++ b/var/spack/repos/builtin/packages/phasta/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,12 +11,10 @@ class Phasta(CMakePackage):
        (PHASTA) of compressible and incompressible Navier Stokes equations."""
 
     homepage = "https://www.scorec.rpi.edu/software.php"
-    url      = "https://github.com/PHASTA/phasta.git"
+    git      = "https://github.com/PHASTA/phasta.git"
 
-    version('0.0.1', git='https://github.com/PHASTA/phasta.git',
-        commit='11f431f2d1a53a529dab4b0f079ab8aab7ca1109')
-    version('develop', git='https://github.com/PHASTA/phasta.git',
-        branch='master')
+    version('develop', branch='master')
+    version('0.0.1', commit='11f431f2d1a53a529dab4b0f079ab8aab7ca1109')
 
     depends_on('mpi')
 
diff --git a/var/spack/repos/builtin/packages/phist/package.py b/var/spack/repos/builtin/packages/phist/package.py
new file mode 100644
index 0000000000..aa593157b5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/phist/package.py
@@ -0,0 +1,144 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Phist(CMakePackage):
+    """The Pipelined, Hybrid-parallel Iterative Solver Toolkit provides
+    implementations of and interfaces to block iterative solvers for sparse
+    linear and eigenvalue problems. In contrast to other libraries we support
+    multiple backends (e.g. Trilinos, PETSc and our own optimized kernels),
+    and interfaces in multiple languages such as C, C++, Fortran 2003 and
+    Python. PHIST has a clear focus on portability and hardware performance:
+    in particular support row-major storage of block vectors and using GPUs
+    (via the ghost library or Trilinos/Tpetra).
+    """
+
+    homepage = "https://bitbucket.org/essex/phist/"
+    url      = "https://bitbucket.org/essex/phist/get/phist-1.4.3.tar.gz"
+    git      = "https://bitbucket.org/essex/phist/phist.git"
+
+    version('develop', branch='devel')
+    version('master', branch='master')
+    version('1.7.3', sha256='ab2d853c9ba13bcd3069fcc61c359cb412466a2e4b22ebbd2f5263cffa685126')
+    version('1.7.2', sha256='29b504d78b5efd57b87d2ca6e20bc8a32b1ba55b40f5a5b7189cc0d28e43bcc0')
+    version('1.6.1', sha256='4ed4869f24f920a494aeae0f7d1d94fe9efce55ebe0d298a5948c9603e07994d')
+    version('1.6.0', '751f855230d6227b972b5ab7bce2c65f')
+    version('1.4.3', 'af3300378d4282366d148e38c3a3199a')
+
+    variant(name='kernel_lib', default='builtin',
+            description='select the kernel library (backend) for phist',
+            values=['builtin',
+                    'epetra',
+                    'tpetra',
+                    'petsc',
+                    'eigen',
+                    'ghost'])
+
+    variant(name='outlev', default='2', values=['0', '1', '2', '3', '4', '5'],
+            description='verbosity. 0: errors 1: +warnings 2: +info '
+                        '3: +verbose 4: +extreme 5; +debug')
+
+    variant('shared',  default=True,
+            description='Enables the build of shared libraries')
+
+    variant('mpi', default=True,
+            description='enable/disable MPI (note that the kernel library may '
+            'not support this choice)')
+
+    variant('openmp', default=True,
+            description='enable/disable OpenMP')
+
+    variant('parmetis', default=False,
+            description='enable/disable ParMETIS partitioning (only actually '
+                        'used with kernel_lib=builtin)')
+
+    variant('scamac', default=True,
+            description='enable/disable building the "SCAlable MAtrix '
+                        'Collection" matrix generators.')
+
+    variant('trilinos', default=False,
+            description='enable/disable Trilinos third-party libraries. '
+                        'For all kernel_libs, we can use Belos and Anasazi '
+                        'iterative solvers. For the Trilinos backends '
+                        '(kernel_lib=epetra|tpetra) we can use preconditioner '
+                        'packages such as Ifpack, Ifpack2 and ML.')
+
+    variant('fortran', default=True,
+            description='generate Fortran 2003 bindings (requires Python3 and '
+                        'a Fortran compiler)')
+
+    # ###################### Dependencies ##########################
+
+    depends_on('cmake@3.8:', type='build')
+    depends_on('blas')
+    depends_on('lapack')
+    # Python 3 or later is required for generating the Fortran 2003 bindings
+    # since version 1.7, you can get rid of the dependency by switching off
+    # the feature (e.g. use the '~fortran' variant)
+    depends_on('python@3:', when='@1.7: +fortran', type='build')
+    depends_on('mpi', when='+mpi')
+    depends_on('trilinos+anasazi+belos+teuchos', when='+trilinos')
+    depends_on('trilinos@12:+tpetra', when='kernel_lib=tpetra')
+    # Epetra backend also works with older Trilinos versions
+    depends_on('trilinos+epetra', when='kernel_lib=epetra')
+    depends_on('petsc', when='kernel_lib=petsc')
+    depends_on('eigen', when='kernel_lib=eigen')
+    depends_on('ghost', when='kernel_lib=ghost')
+
+    depends_on('trilinos', when='+trilinos')
+    depends_on('parmetis ^metis+int64', when='+parmetis')
+
+    # Fortran 2003 bindings were included in version 1.7, previously they
+    # required a separate package
+    conflicts('+fortran', when='@:1.6.99')
+
+    def cmake_args(self):
+        spec = self.spec
+
+        kernel_lib = spec.variants['kernel_lib'].value
+        outlev = spec.variants['outlev'].value
+
+        lapacke_libs = (spec['lapack:c'].libs + spec['blas:c'].libs +
+                        find_system_libraries(['libm'])).joined(';')
+        lapacke_include_dir = spec['lapack:c'].headers.directories[0]
+
+        args = ['-DPHIST_KERNEL_LIB=%s' % kernel_lib,
+                '-DPHIST_OUTLEV=%s' % outlev,
+                '-DTPL_LAPACKE_LIBRARIES=%s' % lapacke_libs,
+                '-DTPL_LAPACKE_INCLUDE_DIRS=%s' % lapacke_include_dir,
+                '-DPHIST_ENABLE_MPI:BOOL=%s'
+                % ('ON' if '+mpi' in spec else 'OFF'),
+                '-DPHIST_ENABLE_OPENMP=%s'
+                % ('ON' if '+openmp' in spec else 'OFF'),
+                '-DBUILD_SHARED_LIBS:BOOL=%s'
+                % ('ON' if '+shared' in spec else 'OFF'),
+                '-DPHIST_ENABLE_SCAMAC:BOOL=%s'
+                % ('ON' if '+scamac' in spec else 'OFF'),
+                '-DPHIST_USE_TRILINOS_TPLS:BOOL=%s'
+                % ('ON' if '+trilinos' in spec else 'OFF'),
+                '-DPHIST_USE_SOLVER_TPLS:BOOL=%s'
+                % ('ON' if '+trilinos' in spec else 'OFF'),
+                '-DPHIST_USE_PRECON_TPLS:BOOL=%s'
+                % ('ON' if '+trilinos' in spec else 'OFF'),
+                '-DXSDK_ENABLE_Fortran:BOOL=%s'
+                % ('ON' if '+fortran' in spec else 'OFF'),
+                ]
+
+        return args
+
+    @run_after('build')
+    @on_package_attributes(run_tests=True)
+    def check(self):
+        with working_dir(self.build_directory):
+            make("check")
+
+    @run_after('install')
+    @on_package_attributes(run_tests=True)
+    def test_install(self):
+        with working_dir(self.build_directory):
+            make("test_install")
diff --git a/var/spack/repos/builtin/packages/phylip/package.py b/var/spack/repos/builtin/packages/phylip/package.py
index 1ebe04f4ca..8869f75390 100644
--- a/var/spack/repos/builtin/packages/phylip/package.py
+++ b/var/spack/repos/builtin/packages/phylip/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,8 +11,9 @@ class Phylip(Package):
        inferring phylogenies (evolutionary trees)."""
 
     homepage = "http://evolution.genetics.washington.edu/phylip/"
-    url      = "http://evolution.gs.washington.edu/phylip/download/phylip-3.696.tar.gz"
+    url      = "http://evolution.gs.washington.edu/phylip/download/phylip-3.697.tar.gz"
 
+    version('3.697', '0e83d17fb4d668213603c86bc21d9012')
     version('3.696', 'dbe5abc26f6089ead3dba41c2db526ee')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/phyluce/package.py b/var/spack/repos/builtin/packages/phyluce/package.py
new file mode 100644
index 0000000000..3a28108ace
--- /dev/null
+++ b/var/spack/repos/builtin/packages/phyluce/package.py
@@ -0,0 +1,44 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Phyluce(PythonPackage):
+    """phyluce (phy-loo-chee) is a software package that was initially
+       developed for analyzing data collected from ultraconserved
+       elements in organismal genomes"""
+
+    homepage = "https://github.com/faircloth-lab/phyluce"
+    url      = "https://github.com/faircloth-lab/phyluce/archive/v1.6.7.tar.gz"
+
+    version('1.6.7', sha256='98c213ab1610506722ad1440ffc93f9cbc78d8b3aaf3d9a47837e1231452cdb6')
+
+    extends('python')
+    depends_on('python@2.7:', type=('build', 'run'))
+    depends_on('py-setuptools', type=('build', 'run'))
+    depends_on('py-biopython', type='run')
+
+    # runtime binary dependencies
+    depends_on('abyss', type='run')
+    depends_on('bcftools', type='run')
+    depends_on('bwa', type='run')
+    depends_on('gatk', type='run')
+    depends_on('gblocks', type='run')
+    depends_on('lastz', type='run')
+    depends_on('mafft', type='run')
+    depends_on('muscle', type='run')
+    depends_on('picard', type='run')
+    depends_on('raxml+pthreads+sse', type='run')
+    depends_on('samtools', type='run')
+    depends_on('seqtk', type='run')
+    depends_on('spades', type='run')
+    depends_on('trimal', type='run')
+    depends_on('trinity', type='run')
+    depends_on('velvet', type='run')
+
+    def install(self, spec, prefix):
+        python = which('python')
+        python('setup.py', 'install', '--prefix={0}'.format(prefix))
diff --git a/var/spack/repos/builtin/packages/picard/package.py b/var/spack/repos/builtin/packages/picard/package.py
index 744479a7f3..86c6cd6e90 100644
--- a/var/spack/repos/builtin/packages/picard/package.py
+++ b/var/spack/repos/builtin/packages/picard/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from shutil import copyfile
 import glob
 import os.path
 import re
@@ -36,13 +16,25 @@ class Picard(Package):
 
     homepage = "http://broadinstitute.github.io/picard/"
     url      = "https://github.com/broadinstitute/picard/releases/download/2.9.2/picard.jar"
+    _urlfmt  = "https://github.com/broadinstitute/picard/releases/download/{0}/picard.jar"
+    _oldurlfmt = 'https://github.com/broadinstitute/picard/releases/download/{0}/picard-tools-{0}.zip'
 
     # They started distributing a single jar file at v2.6.0, prior to
     # that it was a .zip file with multiple .jar and .so files
-    version('2.9.2', '0449279a6a89830917e8bcef3a976ef7', expand=False,
-            url="https://github.com/broadinstitute/picard/releases/download/2.9.2/picard.jar")
-    version('1.140', '308f95516d94c1f3273a4e7e2b315ec2',
-            url='https://github.com/broadinstitute/picard/releases/download/1.140/picard-tools-1.140.zip')
+    version('2.18.3', '181b1b0731fd35f0d8bd44677d8787e9', expand=False)
+    version('2.18.0', '20045ff141e4a67512365f0b6bbd8229', expand=False)
+    version('2.17.0', '72cc527f1e4ca6a799ae0117af60b54e', expand=False)
+    version('2.16.0', 'fed8928b03bb36e355656f349e579083', expand=False)
+    version('2.15.0', '3f5751630b1a3449edda47a0712a64e4', expand=False)
+    version('2.13.2', '3d7b33fd1f43ad2129e6ec7883af56f5', expand=False)
+    version('2.10.0', '96f3c11b1c9be9fc8088bc1b7b9f7538', expand=False)
+    version('2.9.4', '5ce72af4d5efd02fba7084dcfbb3c7b3', expand=False)
+    version('2.9.3', '3a33c231bcf3a61870c3d44b3b183924', expand=False)
+    version('2.9.2', '0449279a6a89830917e8bcef3a976ef7', expand=False)
+    version('2.9.0', 'b711d492f16dfe0084d33e684dca2202', expand=False)
+    version('2.8.3', '4a181f55d378cd61d0b127a40dfd5016', expand=False)
+    version('2.6.0', '91f35f22977d9692ce2718270077dc50', expand=False)
+    version('1.140', '308f95516d94c1f3273a4e7e2b315ec2')
 
     depends_on('java@8:', type='run')
 
@@ -57,13 +49,13 @@ class Picard(Package):
         # Set up a helper script to call java on the jar file,
         # explicitly codes the path for java and the jar file.
         script_sh = join_path(os.path.dirname(__file__), "picard.sh")
-        script = join_path(prefix.bin, "picard")
-        copyfile(script_sh, script)
+        script = prefix.bin.picard
+        install(script_sh, script)
         set_executable(script)
 
         # Munge the helper script to explicitly point to java and the
         # jar file.
-        java = join_path(self.spec['java'].prefix, 'bin', 'java')
+        java = self.spec['java'].prefix.bin.java
         kwargs = {'ignore_absent': False, 'backup': False, 'string': False}
         filter_file('^java', java, script, **kwargs)
         filter_file('picard.jar', join_path(prefix.bin, 'picard.jar'),
@@ -73,3 +65,9 @@ class Picard(Package):
         """The Picard docs suggest setting this as a convenience."""
         run_env.prepend_path('PICARD',
                              join_path(self.prefix, 'bin', 'picard.jar'))
+
+    def url_for_version(self, version):
+        if version < Version('2.6.0'):
+            return self._oldurlfmt.format(version)
+        else:
+            return self._urlfmt.format(version)
diff --git a/var/spack/repos/builtin/packages/picsar/package.py b/var/spack/repos/builtin/packages/picsar/package.py
new file mode 100644
index 0000000000..234b5ee856
--- /dev/null
+++ b/var/spack/repos/builtin/packages/picsar/package.py
@@ -0,0 +1,75 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Picsar(MakefilePackage):
+    """PICSAR is a high performance library of optimized versions of the key
+       functionalities of the PIC loop.
+    """
+
+    homepage = "https://picsar.net"
+    git      = "https://bitbucket.org/berkeleylab/picsar.git"
+
+    version('develop', branch='master')
+
+    variant('prod', default=True, description='Production mode (without FFTW)')
+    variant('prod_spectral', default=False,
+            description='Production mode with spectral solver and FFTW')
+    variant('debug', default=False, description='Debug mode')
+    variant('vtune', default=False, description='Vtune profiling')
+    variant('sde', default=False, description='sde profiling')
+    variant('map', default=False, description='Allinea Map profiling')
+    variant('library', default=False, 
+            description='Create static and dynamic library')
+
+    depends_on('mpi')
+    depends_on('fftw@3.0: +mpi', when='+prod_spectral')
+
+    parallel = False
+
+    @property
+    def build_targets(self):
+        targets = []
+        targets.append('FC={0}'.format(self.spec['mpi'].mpifc))
+        targets.append('CC={0}'.format(self.spec['mpi'].mpicc))
+
+        comp = 'user'
+        vendors = {'%gcc': 'gnu', '%intel': 'intel'}
+        for key, value in vendors.items():
+            if self.spec.satisfies(key):
+                comp = value
+        targets.append('COMP={0}'.format(comp))
+        if comp is 'user':
+            targets.append('FARGS={0}{1}'.format('-g -O3 ',
+                           self.compiler.openmp_flag))
+
+        if '+prod' in self.spec:
+            mode = 'prod'
+        elif '+prod_spectral' in self.spec:
+            mode = 'prod_spectral'
+        elif '+debug' in self.spec:
+            mode = 'debug'
+        elif '+vtune' in self.spec:
+            mode = 'vtune'
+        elif '+sde' in self.spec:
+            mode = 'sde'
+        elif '+map' in self.spec:
+            mode = 'map'
+        elif '+library' in self.spec:
+            mode = 'library'
+        targets.append('MODE = {0}'.format(mode))
+
+        targets.append('SYS = default')
+
+        return targets
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.docs)
+        install('README.md', prefix.docs)
+
+        mkdirp(prefix.bin)
+        install('fortran_bin/picsar', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/picsarlite/package.py b/var/spack/repos/builtin/packages/picsarlite/package.py
new file mode 100644
index 0000000000..5a5b5b58b2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/picsarlite/package.py
@@ -0,0 +1,80 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Picsarlite(MakefilePackage):
+    """PICSARlite is a self-contained proxy that adequately portrays the
+       computational loads and dataflow of more complex PIC codes.
+    """
+
+    tags = ['proxy-app', 'ecp-proxy-app']
+
+    homepage = "https://picsar.net"
+    git      = "https://bitbucket.org/berkeleylab/picsar.git"
+
+    version('develop', branch='PICSARlite')
+    version('0.1', tag='PICSARlite-0.1')
+
+    variant('prod', default=True, description='Production mode (without FFTW)')
+    variant('prod_spectral', default=False,
+            description='Production mode with spectral solver and FFTW')
+    variant('debug', default=False, description='Debug mode')
+    variant('vtune', default=False, description='Vtune profiling')
+    variant('sde', default=False, description='sde profiling')
+    variant('map', default=False, description='Allinea Map profiling')
+    variant('library', default=False, 
+            description='Create static and dynamic library')
+
+    depends_on('mpi')
+    depends_on('fftw@3.0: +mpi', when='+prod_spectral')
+
+    @property
+    def build_targets(self):
+        targets = []
+        targets.append('FC={0}'.format(self.spec['mpi'].mpifc))
+        targets.append('CC={0}'.format(self.spec['mpi'].mpicc))
+
+        comp = 'user'
+        vendors = {'%gcc': 'gnu', '%intel': 'intel'}
+        for key, value in vendors.items():
+            if self.spec.satisfies(key):
+                comp = value
+        targets.append('COMP={0}'.format(comp))
+        if comp is 'user':
+            targets.append('FARGS={0}{1}'.format('-g -O3 ',
+                           self.compiler.openmp_flag))
+
+        if '+prod' in self.spec:
+            mode = 'prod'
+        elif '+prod_spectral' in self.spec:
+            mode = 'prod_spectral'
+        elif '+debug' in self.spec:
+            mode = 'debug'
+        elif '+vtune' in self.spec:
+            mode = 'vtune'
+        elif '+sde' in self.spec:
+            mode = 'sde'
+        elif '+map' in self.spec:
+            mode = 'map'
+        elif '+library' in self.spec:
+            mode = 'library'
+        targets.append('MODE = {0}'.format(mode))
+
+        targets.append('SYS = default')
+
+        return targets
+
+    def build(self, spec, prefix):
+        with working_dir('PICSARlite'):
+            make(parallel=False)
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.docs)
+        install('PICSARlite/README.md', prefix.docs)
+
+        mkdirp(prefix.bin)
+        install('PICSARlite/bin/picsar', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/pidx/package.py b/var/spack/repos/builtin/packages/pidx/package.py
index bc3977d733..9aaf021de5 100644
--- a/var/spack/repos/builtin/packages/pidx/package.py
+++ b/var/spack/repos/builtin/packages/pidx/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,9 +14,9 @@ class Pidx(CMakePackage):
     """
 
     homepage = "http://www.cedmav.com/pidx"
+    git      = "https://github.com/sci-visus/PIDX.git"
 
-    version('1.0', git='https://github.com/sci-visus/PIDX.git',
-            commit='6afa1cf71d1c41263296dc049c8fabaf73c296da')
+    version('1.0', commit='6afa1cf71d1c41263296dc049c8fabaf73c296da')
 
     depends_on('cmake@2.8.4:', type='build')
     depends_on('mpi')
diff --git a/var/spack/repos/builtin/packages/pigz/package.py b/var/spack/repos/builtin/packages/pigz/package.py
index fe933c4f54..4b8eae6936 100644
--- a/var/spack/repos/builtin/packages/pigz/package.py
+++ b/var/spack/repos/builtin/packages/pigz/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,10 @@ class Pigz(MakefilePackage):
        multi-core machines."""
 
     homepage = "http://zlib.net/pigz/"
-    url      = "http://zlib.net/pigz/pigz-2.3.4.tar.gz"
+    url      = "https://github.com/madler/pigz/archive/v2.3.4.tar.gz"
 
-    version('2.3.4', '08e6b2e682bbf65ccf12c8966d633fc6')
+    version('2.4', '3c8a601db141d3013ef9fe5f2daaf73f')
+    version('2.3.4', 'c109057050b15edf3eb9bb4d0805235e')
 
     depends_on('zlib')
 
diff --git a/var/spack/repos/builtin/packages/pilon/package.py b/var/spack/repos/builtin/packages/pilon/package.py
new file mode 100644
index 0000000000..afcdfd4a44
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pilon/package.py
@@ -0,0 +1,40 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os.path
+
+
+class Pilon(Package):
+    """Pilon is an automated genome assembly improvement and variant
+    detection tool."""
+
+    homepage = "https://github.com/broadinstitute/pilon"
+    url      = "https://github.com/broadinstitute/pilon/releases/download/v1.22/pilon-1.22.jar"
+
+    version('1.22', '3c45568dc1b878a9a0316410ec62ab04', expand=False)
+    version('1.13', '9e96b4cf4ea595b1996c7e9ca76498b5', expand=False)
+
+    depends_on('java@1.7:', type='run')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        jar_file = 'pilon-{0}.jar'.format(self.version.dotted)
+        install(jar_file, prefix.bin)
+
+        # Set up a helper script to call java on the jar file,
+        # explicitly codes the path for java and the jar file.
+        script_sh = join_path(os.path.dirname(__file__), "pilon.sh")
+        script = prefix.bin.pilon
+        install(script_sh, script)
+        set_executable(script)
+
+        # Munge the helper script to explicitly point to java and the
+        # jar file.
+        java = self.spec['java'].prefix.bin.java
+        kwargs = {'ignore_absent': False, 'backup': False, 'string': False}
+        filter_file('^java', java, script, **kwargs)
+        filter_file('pilon-{0}.jar', join_path(prefix.bin, jar_file),
+                    script, **kwargs)
diff --git a/var/spack/repos/builtin/packages/pilon/pilon.sh b/var/spack/repos/builtin/packages/pilon/pilon.sh
new file mode 100644
index 0000000000..41a31b3407
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pilon/pilon.sh
@@ -0,0 +1,3 @@
+#!/bin/sh
+# convenience wrapper for the pilon jar file
+java -jar pilon.jar "$@"
diff --git a/var/spack/repos/builtin/packages/pindel/package.py b/var/spack/repos/builtin/packages/pindel/package.py
new file mode 100644
index 0000000000..7755fdd8aa
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pindel/package.py
@@ -0,0 +1,51 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Pindel(MakefilePackage):
+    """Pindel can detect breakpoints from next-gen sequence data."""
+
+    homepage = "http://gmt.genome.wustl.edu/packages/pindel/"
+    url      = "https://github.com/genome/pindel/archive/v0.2.5.tar.gz"
+
+    version('0.2.5b8', 'e6de2ffb38ba1cb89351cdccabe78cde')
+    version('0.2.5b6', 'dc2febb18c203f0ef1ba02b7b882e94b')
+    version('0.2.5b5', '73e964bc19de9ab9e6e8a316353e3184')
+    version('0.2.5b4', 'b4aefd538d9f62578f46440c4bce497e')
+    version('0.2.5b1', 'a8e53e8919aa29093db13fad5ede93a5')
+    version('0.2.5a7', '5fb2bac6108547b5d60c38fc66abdfc4')
+    version('0.2.5',   'd4568cbb83ec25ef9f9f6f058b30053e')
+
+    depends_on('htslib@1.7:')
+    #
+    # This Makefile2 stuff is due to the original installer,
+    # The author wants to run make twice, the first
+    # time generates a Makefile.local then returns "false"
+    # User is then suppose to run make again and the
+    # package will compile. This is an attempt to
+    # stay as close to the original installer as possible
+    #
+
+    def edit(self, spec, prefix):
+        copy('Makefile', 'Makefile2')
+        myedit = FileFilter('Makefile2')
+        myedit.filter('-include Makefile.local', '#removed include')
+        myedit.filter('@false', '#removed autofailure')
+
+    def build(self, spec, prefix):
+        make("Makefile.local", "-f",
+             "Makefile2",
+             "HTSLIB=%s" % spec['htslib'].prefix)
+        make("HTSLIB=%s" % spec['htslib'].prefix)
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('src/pindel', prefix.bin)
+        install('src/pindel2vcf', prefix.bin)
+        install('src/sam2pindel', prefix.bin)
+        install('src/pindel2vcf4tcga', prefix.bin)
+        install_tree('demo', prefix.doc)
diff --git a/var/spack/repos/builtin/packages/piranha/package.py b/var/spack/repos/builtin/packages/piranha/package.py
index 9f4b26d050..8488e826a4 100644
--- a/var/spack/repos/builtin/packages/piranha/package.py
+++ b/var/spack/repos/builtin/packages/piranha/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,9 +13,10 @@ class Piranha(CMakePackage):
 
     homepage = "https://bluescarni.github.io/piranha/sphinx/"
     url      = "https://github.com/bluescarni/piranha/archive/v0.5.tar.gz"
+    git      = "https://github.com/bluescarni/piranha.git"
 
+    version('develop', branch='master')
     version('0.5', '99546bae2be115737b6316751eb0b84d')
-    version('develop', git='https://github.com/bluescarni/piranha.git')
 
     variant('python',   default=True,
             description='Build the Python bindings')
diff --git a/var/spack/repos/builtin/packages/pism/package.py b/var/spack/repos/builtin/packages/pism/package.py
new file mode 100644
index 0000000000..6eedcbced3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pism/package.py
@@ -0,0 +1,147 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Pism(CMakePackage):
+    """Parallel Ice Sheet Model"""
+
+    homepage = "http://pism-docs.org/wiki/doku.php:="
+    url      = "https://github.com/pism/pism/archive/v0.7.3.tar.gz"
+    git      = "https://github.com/pism/pism.git"
+
+    maintainers = ['citibeth']
+
+    version('develop', branch='dev')
+    version('0.7.3', '7cfb034100d99d5c313c4ac06b7f17b6')
+    version('0.7.x', branch='stable0.7')
+    version('icebin', branch='efischer/dev')
+
+    variant('extra', default=False,
+            description='Build extra executables (testing/verification)')
+    variant('shared', default=True,
+            description='Build shared Pism libraries')
+    variant('python', default=False,
+            description='Build python bindings')
+    variant('icebin', default=False,
+            description='Build classes needed by IceBin')
+    variant('proj', default=True,
+            description='Use Proj.4 to compute cell areas, '
+            'longitudes, and latitudes.')
+    variant('parallel-netcdf4', default=False,
+            description='Enables parallel NetCDF-4 I/O.')
+    variant('parallel-netcdf3', default=False,
+            description='Enables parallel NetCDF-3 I/O using PnetCDF.')
+    variant('parallel-hdf5', default=False,
+            description='Enables parallel HDF5 I/O.')
+    # variant('tao', default=False,
+    #         description='Use TAO in inverse solvers.')
+
+    description = 'Build PISM documentation (requires LaTeX and Doxygen)'
+    variant('doc', default=False, description=description)
+
+    variant('examples', default=False,
+            description='Install examples directory')
+
+    description = 'Report errors through Everytrace (requires Everytrace)'
+    variant('everytrace', default=False, description=description)
+
+    # CMake build options not transferred to Spack variants
+    # (except from CMakeLists.txt)
+    #
+    # option (Pism_TEST_USING_VALGRIND "Add extra regression tests
+    #         using valgrind" OFF)
+    # mark_as_advanced (Pism_TEST_USING_VALGRIND)
+    #
+    # option (Pism_ADD_FPIC "Add -fPIC to C++ compiler flags
+    #         (CMAKE_CXX_FLAGS). Try turning it off if it does not work." ON)
+    # option (Pism_LINK_STATICALLY
+    #         "Set CMake flags to try to ensure that everything is
+    #         linked statically")
+    # option (Pism_LOOK_FOR_LIBRARIES
+    #         "Specifies whether PISM should look for libraries. (Disable
+    #         this on Crays.)" ON)
+    # option (Pism_USE_TR1
+    #        "Use the std::tr1 namespace to access shared pointer
+    #        definitions. Disable to get shared pointers from the std
+    #        namespace (might be needed with some compilers)." ON)
+    # option (Pism_USE_TAO "Use TAO in inverse solvers." OFF)
+
+    depends_on('fftw')
+    depends_on('gsl')
+    depends_on('mpi')
+    depends_on('netcdf')    # Only the C interface is used, no netcdf-cxx4
+    depends_on('petsc')
+    depends_on('udunits2')
+    depends_on('proj')
+    depends_on('everytrace', when='+everytrace')
+
+    extends('python', when='+python')
+    depends_on('python@2.7:2.8', when='+python')
+    depends_on('py-matplotlib', when='+python')
+    depends_on('py-numpy', when='+python')
+
+    def cmake_args(self):
+        spec = self.spec
+
+        return [
+            '-DCMAKE_C_COMPILER=%s' % spec['mpi'].mpicc,
+            '-DCMAKE_CXX_COMPILER=%s' % spec['mpi'].mpicxx,
+            # Fortran not needed for PISM...
+            # '-DCMAKE_Fortran_COMPILER=%s' % spec['mpi'].mpifc,
+            '-DPism_BUILD_EXTRA_EXECS=%s' %
+            ('YES' if '+extra' in spec else 'NO'),
+            '-DBUILD_SHARED_LIBS=%s' %
+            ('YES' if '+shared' in spec else 'NO'),
+            '-DPism_BUILD_PYTHON_BINDINGS=%s' %
+            ('YES' if '+python' in spec else 'NO'),
+            '-DPism_BUILD_ICEBIN=%s' %
+            ('YES' if '+icebin' in spec else 'NO'),
+            '-DPism_USE_PROJ4=%s' %
+            ('YES' if '+proj' in spec else 'NO'),
+            '-DPism_USE_PARALLEL_NETCDF4=%s' %
+            ('YES' if '+parallel-netcdf4' in spec else 'NO'),
+            '-DPism_USE_PNETCDF=%s' %
+            ('YES' if '+parallel-netcdf3' in spec else 'NO'),
+            '-DPism_USE_PARALLEL_HDF5=%s' %
+            ('YES' if '+parallel-hdf5' in spec else 'NO'),
+            '-DPism_BUILD_PDFS=%s' %
+            ('YES' if '+doc' in spec else 'NO'),
+            '-DPism_INSTALL_EXAMPLES=%s' %
+            ('YES' if '+examples' in spec else 'NO'),
+            '-DPism_USE_EVERYTRACE=%s' %
+            ('YES' if '+everytrace' in spec else 'NO')]
+
+    def setup_environment(self, spack_env, env):
+        env.set('PISM_PREFIX', self.prefix)
+        env.set('PISM_BIN', self.prefix.bin)
+
+
+# From email correspondence with Constantine Khroulev:
+#
+# > Do you have handy a table of which versions of PETSc are required
+# > for which versions of PISM?
+#
+# We don't. The installation manual [1] specifies the minimum PETSc
+# version for the latest "stable" release (currently PETSc 3.3). The
+# stable PISM version should support all PETSc versions starting from the
+# one specified in the manual and up to the latest PETSc release.
+#
+# The current development PISM version should be built with the latest
+# PETSc release at the time (the "maint" branch of PETSc).
+#
+# Thanks to Git it is relatively easy to find this info, though:
+#
+# | PISM version | PETSc version |
+# |--------------+---------------|
+# |          0.7 | 3.3 and later |
+# |          0.6 | 3.3           |
+# |       new_bc | 3.4.4         |
+# |          0.5 | 3.2           |
+# |          0.4 | 3.1           |
+# |          0.3 | 2.3.3 to 3.1  |
+# |          0.2 | 2.3.3 to 3.0  |
+# |          0.1 | 2.3.3-p2      |
diff --git a/var/spack/repos/builtin/packages/pixman/clang.patch b/var/spack/repos/builtin/packages/pixman/clang.patch
new file mode 100644
index 0000000000..9de9c1be60
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pixman/clang.patch
@@ -0,0 +1,28 @@
+--- pixman-0.34.0/test/utils-prng.c.bak	2018-02-01 00:34:15.757691302 +0100
++++ pixman-0.34.0/test/utils-prng.c	2018-02-01 00:36:38.285690995 +0100
+@@ -199,12 +199,24 @@
+         }
+         else
+         {
++
++#ifndef __has_builtin
++#define __has_builtin(x) 0
++#endif
++
+ #ifdef HAVE_GCC_VECTOR_EXTENSIONS
++# if !defined(__clang__) || __has_builtin(__builtin_shuffle)
+             const uint8x16 bswap_shufflemask =
+             {
+                 3, 2, 1, 0, 7, 6, 5, 4, 11, 10, 9, 8, 15, 14, 13, 12
+             };
+             randdata.vb = __builtin_shuffle (randdata.vb, bswap_shufflemask);
++# elif __has_builtin(__builtin_shufflevector)
++            randdata.vb = __builtin_shufflevector(randdata.vb, randdata.vb, 3, 2, 1, 0, 7, 6, 5, 4, 11, 10, 9, 8, 15, 14, 13, 12);
++# else
++#  error "GCC_VECTOR_EXTENSION is defined, but neither __builtin_shuffle nor __builtin_shufflevector is supported!"
++# endif
++
+             store_rand_128_data (buf, &randdata, aligned);
+             buf += 16;
+ #else
+
diff --git a/var/spack/repos/builtin/packages/pixman/package.py b/var/spack/repos/builtin/packages/pixman/package.py
index 4191550803..d3e8661dd2 100644
--- a/var/spack/repos/builtin/packages/pixman/package.py
+++ b/var/spack/repos/builtin/packages/pixman/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import sys
 
@@ -37,9 +18,35 @@ class Pixman(AutotoolsPackage):
     version('0.34.0', 'e80ebae4da01e77f68744319f01d52a3')
     version('0.32.6', '3a30859719a41bd0f5cccffbfefdd4c2')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('libpng')
 
+    # As discussed here:
+    # https://bugs.freedesktop.org/show_bug.cgi?id=104886
+    # __builtin_shuffle was removed in clang 5.0.
+    # From version 9.1 apple-clang is based on clang 5.0.
+    # Patch is obtained from above link.
+    patch('clang.patch', when='%clang@9.1.0-apple:')
+
+    @run_before('build')
+    def patch_config_h_for_intel(self):
+        config_h = join_path(self.stage.source_path, 'config.h')
+
+        # Intel disguises itself as GNU, but doesn't implement
+        # the same builtin functions. This causes in this case
+        # a positive detection of GCC vector extensions, which
+        # is bound to fail at compile time because Intel has no
+        # __builtin_shuffle. See also:
+        #
+        # https://software.intel.com/en-us/forums/intel-c-compiler/topic/758013
+        #
+        if '%intel' in self.spec:
+            filter_file(
+                '#define HAVE_GCC_VECTOR_EXTENSIONS /\*\*/',
+                '/* #undef HAVE_GCC_VECTOR_EXTENSIONS */',
+                config_h
+            )
+
     def configure_args(self):
         args = [
             '--enable-libpng',
diff --git a/var/spack/repos/builtin/packages/pkg-config/package.py b/var/spack/repos/builtin/packages/pkg-config/package.py
index 22a8833a11..a27df03b40 100644
--- a/var/spack/repos/builtin/packages/pkg-config/package.py
+++ b/var/spack/repos/builtin/packages/pkg-config/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,6 +17,8 @@ class PkgConfig(AutotoolsPackage):
     version('0.29.1', 'f739a28cae4e0ca291f82d1d41ef107d')
     version('0.28',   'aa3c86e67551adc3ac865160e34a2a0d')
 
+    provides('pkgconfig')
+
     variant('internal_glib', default=True,
             description='Builds with internal glib')
 
@@ -45,17 +28,9 @@ class PkgConfig(AutotoolsPackage):
     parallel = False
 
     def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
-        """spack built pkg-config on cray's requires adding /usr/local/
-        and /usr/lib64/  to PKG_CONFIG_PATH in order to access cray '.pc'
-        files.
-        Adds the ACLOCAL path for autotools."""
+        """Adds the ACLOCAL path for autotools."""
         spack_env.append_path('ACLOCAL_PATH',
                               join_path(self.prefix.share, 'aclocal'))
-        if 'platform=cray' in self.spec:
-            spack_env.append_path('PKG_CONFIG_PATH',
-                                  '/usr/lib64/pkgconfig')
-            spack_env.append_path('PKG_CONFIG_PATH',
-                                  '/usr/local/lib64/pkgconfig')
 
     def configure_args(self):
         config_args = ['--enable-shared']
diff --git a/var/spack/repos/builtin/packages/pkgconf/package.py b/var/spack/repos/builtin/packages/pkgconf/package.py
index 7b4b570945..742713c0ff 100644
--- a/var/spack/repos/builtin/packages/pkgconf/package.py
+++ b/var/spack/repos/builtin/packages/pkgconf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,9 +13,22 @@ class Pkgconf(AutotoolsPackage):
     maintaining compatibility."""
 
     homepage = "http://pkgconf.org/"
-    url      = "https://distfiles.dereferenced.org/pkgconf/pkgconf-1.3.8.tar.xz"
+    url      = "http://distfiles.alpinelinux.org/distfiles/pkgconf-1.4.2.tar.xz"
+
+    version('1.4.2',  '678d242b4eef1754bba6a58642af10bb')
+    version('1.4.0',  'c509c0dad5a70aa4bc3210557b7eafce')
+    version('1.3.10', '9b63707bf6f8da6efb3868101d7525fe')
+    version('1.3.8',  '484ba3360d983ce07416843d5bc916a8')
+
+    provides('pkgconfig')
+
+    # TODO: Add a package for the kyua testing framework
+    # depends_on('kyua', type='test')
 
-    version('1.3.8', '484ba3360d983ce07416843d5bc916a8')
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        """Adds the ACLOCAL path for autotools."""
+        spack_env.append_path('ACLOCAL_PATH',
+                              join_path(self.prefix.share, 'aclocal'))
 
     @run_after('install')
     def link_pkg_config(self):
diff --git a/var/spack/repos/builtin/packages/planck-likelihood/package.py b/var/spack/repos/builtin/packages/planck-likelihood/package.py
index a92fc328db..0b04aec89f 100644
--- a/var/spack/repos/builtin/packages/planck-likelihood/package.py
+++ b/var/spack/repos/builtin/packages/planck-likelihood/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -141,8 +122,8 @@ class PlanckLikelihood(Package):
     @on_package_attributes(run_tests=True)
     def check_install(self):
         prefix = self.prefix
-        clik_example_C = Executable(join_path(prefix.bin, 'clik_example_C'))
+        clik_example_c = Executable(join_path(prefix.bin, 'clik_example_C'))
         with working_dir('spack-check', create=True):
-            clik_example_C(join_path(prefix, 'share', 'clik',
+            clik_example_c(join_path(prefix, 'share', 'clik',
                                      'plc_2.0', 'hi_l', 'plik',
                                      'plik_dx11dr2_HM_v18_TT.clik'))
diff --git a/var/spack/repos/builtin/packages/plasma/package.py b/var/spack/repos/builtin/packages/plasma/package.py
index 46b662d63d..54ef75c207 100644
--- a/var/spack/repos/builtin/packages/plasma/package.py
+++ b/var/spack/repos/builtin/packages/plasma/package.py
@@ -1,17 +1,12 @@
-##############################################################################
-# Copyright (c) 2017, Innovative Computing Laboratory
-# Produced at the Innovative Computing Laboratory.
-#
-# Created by Piotr Luszczek, luszczek@icl.utk.edu, All rights reserved.
-#
-# For details, see https://github.com/spack/spack
-#
-##############################################################################
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class Plasma(MakefilePackage):
+class Plasma(CMakePackage):
     """Parallel Linear Algebra Software for Multicore Architectures, PLASMA is
     a software package for solving problems in dense linear algebra using
     multicore processors and Xeon Phi coprocessors. PLASMA provides
@@ -21,24 +16,38 @@ class Plasma(MakefilePackage):
     problems, and singular value problems."""
 
     homepage = "https://bitbucket.org/icl/plasma/"
-    url      = "https://bitbucket.org/icl/plasma/downloads/plasma-17.1.tar.gz"
+    url = "https://bitbucket.org/icl/plasma/downloads/plasma-18.10.0.tar.gz"
+    hg = "https://luszczek@bitbucket.org/icl/plasma"
 
-    version("17.1", "64b410b76023a41b3f07a5f0dca554e1")
+    version("develop", hg=hg)
+    version("18.10.0", sha256="93dceae93f57a2fbd79b85d2fbf7907d1d32e158b8d1d93892d9ff3df9963210")
+    version("18.9.0", sha256="753eae28ea48986a2cc7b8204d6eef646584541e59d42c3c94fa9879116b0774")
+    version("17.1",
+            sha256="d4b89f7c3d240a69dfe986284a14471eec4830b9e352ae902ea8861f15573dee",
+            url="https://bitbucket.org/icl/plasma/downloads/plasma-17.1.tar.gz")
 
-    version("develop", hg="https://luszczek@bitbucket.org/icl/plasma")
+    variant("shared", default=True,
+            description="Build shared library (disables static library)")
 
     depends_on("blas")
     depends_on("lapack")
 
     conflicts("atlas")  # does not have LAPACKE interface
-    conflicts("netlib-lapack@:2.999")  # missing LAPACKE features
+
+    # missing LAPACKE features and/or CBLAS headers
+    conflicts("netlib-lapack@:3.5.999")
+
     # clashes with OpenBLAS declarations and has a problem compiling on its own
     conflicts("cblas")
+
     conflicts("openblas-with-lapack")  # incomplete LAPACK implementation
     conflicts("veclibfort")
 
-    # only GCC 7+ and higher have sufficient support for OpenMP 4+ tasks+deps
-    conflicts("%gcc@:6.999")
+    # only GCC 4.9+ and higher have sufficient support for OpenMP 4+ tasks+deps
+    conflicts("%gcc@:4.8.99", when='@:17.1')
+    # only GCC 6.0+ and higher have for OpenMP 4+ Clause "priority"
+    conflicts("%gcc@:5.99", when='@17.2:')
+
     conflicts("%cce")
     conflicts("%clang")
     conflicts("%intel")
@@ -49,14 +58,52 @@ class Plasma(MakefilePackage):
 
     patch("remove_absolute_mkl_include.patch", when="@17.1")
 
+    @when("@18.9.0:")
+    def cmake_args(self):
+        options = list()
+
+        options.extend([
+            "-DCMAKE_INSTALL_PREFIX=%s" % prefix,
+            "-DCMAKE_INSTALL_NAME_DIR:PATH=%s/lib" % prefix,
+            "-DBLAS_LIBRARIES=%s" % self.spec["blas"].libs.joined(";"),
+            "-DLAPACK_LIBRARIES=%s" % self.spec["lapack"].libs.joined(";")
+        ])
+
+        options += [
+            "-DBUILD_SHARED_LIBS=%s" %
+            ('ON' if ('+shared' in self.spec) else 'OFF')
+        ]
+
+        return options
+
+    # Before 18.9.0 it was an Makefile package
+    @when("@:17.1")
+    def cmake(self, spec, prefix):
+        pass
+
+    # Before 18.9.0 it was an Makefile package
+    @when("@:17.1")
+    def build(self, spec, prefix):
+        pass
+
+    # Before 18.9.0 it was an Makefile package
+    @when("@:17.1")
+    def install(self, spec, prefix):
+        self.edit(spec, prefix)
+        make()
+        make("install")
+
+    @when("@:17.1")
     def edit(self, spec, prefix):
         # copy "make.inc.mkl-gcc" provided by default into "make.inc"
         open("make.inc", "w").write(open("make.inc.mkl-gcc").read())
 
         make_inc = FileFilter("make.inc")
 
-        if not spec.satisfies("^mkl"):
+        if not spec.satisfies("^intel-mkl"):
             make_inc.filter("-DPLASMA_WITH_MKL", "")  # not using MKL
+            make_inc.filter("LIBS *= *.*", "LIBS = " +
+                            self.spec["blas"].libs.ld_flags + " -lm")
 
         header_flags = ""
         # accumulate CPP flags for headers: <cblas.h> and <lapacke.h>
@@ -73,18 +120,3 @@ class Plasma(MakefilePackage):
 
         # make sure CC variable comes from build environment
         make_inc.filter("CC *[?]*= * .*cc", "")
-
-    @property
-    def build_targets(self):
-        targets = list()
-
-        # use $CC set by Spack
-        targets.append("CC = {0}".format(self.compiler.cc))
-
-        if self.spec.satisfies("^mkl"):
-            targets.append("MKLROOT = {0}/mkl".format(env["MKLROOT"]))
-
-        # pass BLAS library flags
-        targets.append("LIBS = {0}".format(self.spec["blas"].libs.ld_flags))
-
-        return targets
diff --git a/var/spack/repos/builtin/packages/platypus/package.py b/var/spack/repos/builtin/packages/platypus/package.py
new file mode 100644
index 0000000000..7ef22abc74
--- /dev/null
+++ b/var/spack/repos/builtin/packages/platypus/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Platypus(Package):
+    """A Haplotype-Based Variant Caller For Next Generation Sequence Data"""
+
+    homepage = "http://www.well.ox.ac.uk/platypus"
+    url      = "http://www.well.ox.ac.uk/bioinformatics/Software/Platypus-latest.tgz"
+
+    version('0.8.1', 'edf3fb5bf080241ddb75a413c8529d57')
+
+    depends_on('python@2.6:', type=('build', 'run'))
+    depends_on('py-cython', type='build')
+    depends_on('htslib')
+
+    def install(self, spec, prefix):
+        build_platypus = Executable('./buildPlatypus.sh')
+        build_platypus()
+        install_tree('.', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/plink/package.py b/var/spack/repos/builtin/packages/plink/package.py
index b6df013978..2f571e25e4 100644
--- a/var/spack/repos/builtin/packages/plink/package.py
+++ b/var/spack/repos/builtin/packages/plink/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,10 +13,22 @@ class Plink(Package):
 
     homepage = "https://www.cog-genomics.org/plink/1.9/"
 
-    version('1.9', 'a2325881594856c0f1b7523290d1e04f',
-            url='https://www.cog-genomics.org/static/bin/plink170815/plink_linux_x86_64.zip')
+    version('1.9-beta5', '737545504ae19348a44a05fa69b75c28',
+            url='https://github.com/chrchang/plink-ng/archive/b15c19f.tar.gz')
+    version('1.07', 'fd0bafeda42151b20534e4f97b0d97df',
+            url='http://zzz.bwh.harvard.edu/plink/dist/plink-1.07-x86_64.zip',
+            preferred=True)
+
+    depends_on('atlas', when='@1.9-beta5')
+    depends_on('netlib-lapack', when='@1.9-beta5')
 
     def install(self, spec, prefix):
         mkdirp(prefix.bin)
-        install('plink', prefix.bin)
-        install('prettify', prefix.bin)
+        if spec.version == Version('1.07'):
+            install('plink', prefix.bin)
+            install('gPLINK.jar', prefix.bin)
+        if spec.version == Version('1.9-beta5'):
+            with working_dir('1.9'):
+                first_compile = Executable('./plink_first_compile')
+                first_compile()
+                install('plink', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/plplot/package.py b/var/spack/repos/builtin/packages/plplot/package.py
new file mode 100644
index 0000000000..5e0d23b930
--- /dev/null
+++ b/var/spack/repos/builtin/packages/plplot/package.py
@@ -0,0 +1,104 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Plplot(CMakePackage):
+    """PLplot is a cross-platform package for creating scientific plots."""
+
+    homepage = "http://plplot.sourceforge.net/"
+    url      = "https://sourceforge.net/projects/plplot/files/plplot/5.13.0%20Source/plplot-5.13.0.tar.gz/download"
+
+    version('5.13.0', 'bfefeae7fb9a23377c6dc37b44a7da8a')
+    version('5.12.0', '998a05be218e5de8f2faf988b8dbdc51')
+    version('5.11.0', '632c9e13b09f4e2b2517b3567bc3cece')
+
+    variant('java', default=False, description='Enable Java binding')
+    variant('lua', default=False, description='Enable Lua binding')
+    variant('pango', default=False, description='Enable Pango')
+    variant('python', default=False, description='Enable Python binding')
+    variant('qt', default=False, description='Enable QT binding')
+    variant('tcl', default=True, description='Enable TCL binding')
+    variant('wx', default=False, description='Enable WxWidgets')
+    variant('wxold', default=False, description='Use WxWidgets old interface')
+
+    conflicts('~wx', when='+wxold')
+    conflicts('+wxold', when='@:5.11')
+
+    depends_on('java', when='+java')
+    depends_on('lua', when='+lua')
+    depends_on('pango', when='+pango')
+    depends_on('py-numpy', type=('build', 'run'), when='+python')
+    depends_on('python@2.7:2.8', type=('build', 'run'), when='+python')
+    depends_on('qt', when='+qt')
+    depends_on('tcl', when='+tcl')
+    depends_on('wx', when='+wx')
+
+    depends_on('freetype')
+    depends_on('gtkplus')
+    depends_on('libx11')
+    depends_on('qhull')
+    depends_on('swig')
+
+    def cmake_args(self):
+        args = []
+        # needs 'tk with wish'
+        args += ['-DENABLE_tk=OFF']
+
+        if '+java' in self.spec:
+            args += ['-DENABLE_java=ON']
+        else:
+            args += ['-DENABLE_java=OFF']
+
+        if '+lua' in self.spec:
+            args += ['-DENABLE_lua=ON']
+        else:
+            args += ['-DENABLE_lua=OFF']
+
+        if '+python' in self.spec:
+            args += ['-DENABLE_python=ON']
+        else:
+            args += ['-DENABLE_python=OFF']
+
+        if '+qt' in self.spec:
+            args += ['-DENABLE_qt=ON']
+        else:
+            args += ['-DENABLE_qt=OFF']
+
+        if '+tcl' in self.spec:
+            args += ['-DENABLE_tcl=ON']
+            # could also be addressed by creating the links within tcl
+            # as is done for the tclsh executable
+            args += [
+                '-DTCL_INCLUDE_PATH={0}/include'.format(
+                    self.spec['tcl'].prefix.include
+                ),
+                '-DTCL_LIBRARY={0}'.format(
+                    LibraryList(find_libraries(
+                        'libtcl*',
+                        self.spec['tcl'].prefix.lib,
+                        shared=True,
+                    )),
+                ),
+                '-DTCL_STUB_LIBRARY={0}'.format(
+                    LibraryList(find_libraries(
+                        'libtclstub*',
+                        self.spec['tcl'].prefix.lib,
+                        shared=False,
+                    )),
+                )
+            ]
+        else:
+            args += ['-DENABLE_tcl=OFF']
+
+        if '+wx' in self.spec:
+            args += ['-DENABLE_wxwidgets=ON']
+            if '+wxold' in self.spec:
+                args += ['-DOLD_WXWIDGETS=ON']
+        else:
+            args += ['-DENABLE_wxwidgets=OFF']
+
+        return args
diff --git a/var/spack/repos/builtin/packages/plumed/package.py b/var/spack/repos/builtin/packages/plumed/package.py
index cac4f4254f..35cad3d0b7 100644
--- a/var/spack/repos/builtin/packages/plumed/package.py
+++ b/var/spack/repos/builtin/packages/plumed/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import collections
 
 from spack import *
@@ -43,6 +24,9 @@ class Plumed(AutotoolsPackage):
     homepage = 'http://www.plumed.org/'
     url = 'https://github.com/plumed/plumed2/archive/v2.2.3.tar.gz'
 
+    version('2.4.2', '0f66f24b4c763ae8b2f39574113e9935')
+    version('2.4.1', '6558e1fd02fc46e847ab6a3fb5ed5411')
+    version('2.3.5', '3cc5f025cb6f5d963f3c778f15c77d44')
     version('2.3.3', '9f5729e406e79a06a16976fcb020e024')
     version('2.3.0', 'a9b5728f115dca8f0519111f1f5a6fa5')
     version('2.2.4', 'afb00da25a3fbd47acf377e53342059d')
@@ -66,6 +50,9 @@ class Plumed(AutotoolsPackage):
     depends_on('zlib')
     depends_on('blas')
     depends_on('lapack')
+    # For libmatheval support through the 'function' module
+    # which is enabled by default (or when optional_modules=all)
+    depends_on('libmatheval')
 
     depends_on('mpi', when='+mpi')
     depends_on('gsl', when='+gsl')
diff --git a/var/spack/repos/builtin/packages/pmgr-collective/package.py b/var/spack/repos/builtin/packages/pmgr-collective/package.py
index c96e777e5b..ff08d784b1 100644
--- a/var/spack/repos/builtin/packages/pmgr-collective/package.py
+++ b/var/spack/repos/builtin/packages/pmgr-collective/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/pmix/package.py b/var/spack/repos/builtin/packages/pmix/package.py
index 0763dfbaed..0f09c4df66 100644
--- a/var/spack/repos/builtin/packages/pmix/package.py
+++ b/var/spack/repos/builtin/packages/pmix/package.py
@@ -1,29 +1,11 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
+import spack.architecture
 
 
 class Pmix(AutotoolsPackage):
@@ -48,8 +30,16 @@ class Pmix(AutotoolsPackage):
     homepage = "https://pmix.github.io/pmix"
     url      = "https://github.com/pmix/pmix/releases/download/v2.0.1/pmix-2.0.1.tar.bz2"
 
+    version('3.0.2',    sha256='df68f35a3ed9517eeade80b13855cebad8fde2772b36a3f6be87559b6d430670')
+    version('3.0.1',    sha256='b81055d2c0d61ef5a451b63debc39c820bcd530490e2e4dcb4cdbacb618c157c')
+    version('3.0.0',    sha256='ee8f68107c24b706237a53333d832445315ae37de6773c5413d7fda415a6e2ee')
+    version('2.1.4',    sha256='eb72d292e76e200f02cf162a477eecea2559ef3ac2edf50ee95b3fe3983d033e')
+    version('2.1.3',    sha256='281283133498e7e5999ed5c6557542c22408bc9eb51ecbcf7696160616782a41')
+    version('2.1.2',    sha256='94bb9c801c51a6caa1b8cef2b85ecf67703a5dfa4d79262e6668c37c744bb643')
     version('2.0.1',    'ba3193b485843516e6b4e8641e443b1e')
     version('2.0.0',    '3e047c2ea0ba8ee9925ed92b205fd92e')
+    version('1.2.5',    'c3d20cd9d365a813dc367afdf0f41c37')
+    version('1.2.4',    '242a812e206e7c5948f1f5c9688eb2a7')
     version('1.2.3',    '102b1cc650018b62348b45d572b158e9')
     version('1.2.2',    'd85c8fd437bd88f984549425ad369e9f')
     version('1.2.1',    'f090f524681c52001ea2db3b0285596f')
@@ -58,6 +48,7 @@ class Pmix(AutotoolsPackage):
     depends_on('libevent')
 
     def configure_args(self):
+
         spec = self.spec
         config_args = [
             '--enable-shared',
@@ -68,4 +59,11 @@ class Pmix(AutotoolsPackage):
         config_args.append(
             '--with-libevent={0}'.format(spec['libevent'].prefix))
 
+        # Versions < 2.1.1 have a bug in the test code that *sometimes*
+        # causes problems on strict alignment architectures such as
+        # aarch64.  Work-around is to just not build the test code.
+        if 'aarch64' in spack.architecture.sys_type() and \
+           self.spec.version < Version('2.1.1'):
+            config_args.append('--without-tests-examples')
+
         return config_args
diff --git a/var/spack/repos/builtin/packages/pnfft/package.py b/var/spack/repos/builtin/packages/pnfft/package.py
index fbb6b636b1..d34104669d 100644
--- a/var/spack/repos/builtin/packages/pnfft/package.py
+++ b/var/spack/repos/builtin/packages/pnfft/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,6 +16,7 @@ class Pnfft(AutotoolsPackage):
     version('1.0.7-alpha', '5caa7f214eed99de2281043ca2367e9e')
 
     depends_on('pfft')
+    depends_on('gsl')
 
     def configure(self, spec, prefix):
         options = ['--prefix={0}'.format(prefix)]
diff --git a/var/spack/repos/builtin/packages/pngwriter/package.py b/var/spack/repos/builtin/packages/pngwriter/package.py
index 896b660ac6..76f4553826 100644
--- a/var/spack/repos/builtin/packages/pngwriter/package.py
+++ b/var/spack/repos/builtin/packages/pngwriter/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,14 +18,25 @@ class Pngwriter(CMakePackage):
 
     homepage = "http://pngwriter.sourceforge.net/"
     url      = "https://github.com/pngwriter/pngwriter/archive/0.5.6.tar.gz"
+    git      = "https://github.com/pngwriter/pngwriter.git"
 
-    version('develop', branch='dev',
-            git='https://github.com/pngwriter/pngwriter.git')
-    version('master', branch='master',
-            git='https://github.com/pngwriter/pngwriter.git')
+    maintainers = ['ax3l']
+
+    version('develop', branch='dev')
+    version('master', branch='master')
+    version('0.7.0', 'a68aa0889f120f5bb07848afce278a95')
     version('0.6.0', '0a19bc55c5f6379fea7343752fd3ffae')
     version('0.5.6', 'c13bd1fdc0e331a246e6127b5f262136')
 
     depends_on('libpng')
     depends_on('zlib')
     depends_on('freetype')
+
+    def cmake_args(self):
+        spec = self.spec
+        args = []
+
+        if spec.satisfies('@0.7.0:'):
+            args += ['-DPNGwriter_USE_FREETYPE:BOOL=ON']
+
+        return args
diff --git a/var/spack/repos/builtin/packages/pnmpi/package.py b/var/spack/repos/builtin/packages/pnmpi/package.py
new file mode 100644
index 0000000000..0d483724ba
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pnmpi/package.py
@@ -0,0 +1,48 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Pnmpi(CMakePackage):
+    """PnMPI is a dynamic MPI tool infrastructure that builds on top of
+       the standardized PMPI interface. """
+
+    homepage = "https://github.com/LLNL/PnMPI"
+    url      = "https://github.com/LLNL/PnMPI/releases/download/v1.7/PnMPI-v1.7-full.tar.gz"
+
+    version('1.7', '8040c1558c0deaa3d964c35d1760f3a8')
+
+    variant('fortran', default=False,
+            description='Configure PnMPI with Fortran support')
+    variant('tests', default=False,
+            description='Build test cases and enable "test" makefile target')
+
+    depends_on('cmake', type='build')
+    depends_on('argp-standalone', when='platform=darwin')
+    depends_on('binutils')
+    depends_on('help2man')
+    depends_on('doxygen')
+    depends_on('mpi')
+
+    @run_before('cmake')
+    def check_fortran(self):
+        is_no_fortran_compiler = not self.compiler.f77 and not self.compiler.fc
+        if self.spec.satisfies('+fortran'):
+            if is_no_fortran_compiler:
+                raise InstallError('pnmpi+fortran requires Fortran compiler '
+                                   'but no Fortran compiler found!')
+
+    def cmake_args(self):
+        args = []
+        spec = self.spec
+        on_off = {True: 'ON', False: 'OFF'}
+
+        has_fortran = spec.satisfies('+fortran')
+        has_tests = spec.satisfies('+tests')
+
+        args.append('-DENABLE_FORTRAN:BOOL={0}'.format(on_off[has_fortran]))
+        args.append('-DENABLE_TESTING:BOOL={0}'.format(on_off[has_tests]))
+        return args
diff --git a/var/spack/repos/builtin/packages/poamsa/package.py b/var/spack/repos/builtin/packages/poamsa/package.py
index dba8a03546..e109e39423 100644
--- a/var/spack/repos/builtin/packages/poamsa/package.py
+++ b/var/spack/repos/builtin/packages/poamsa/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/pocl/package.py b/var/spack/repos/builtin/packages/pocl/package.py
index ec4ef09bbe..c020dd9cf6 100644
--- a/var/spack/repos/builtin/packages/pocl/package.py
+++ b/var/spack/repos/builtin/packages/pocl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 
 from spack import *
@@ -35,16 +16,17 @@ class Pocl(CMakePackage):
     GPUs/accelerators."""
 
     homepage = "http://portablecl.org"
-    url = "http://portablecl.org/downloads/pocl-0.13.tar.gz"
+    url      = "https://github.com/pocl/pocl/archive/v1.1.tar.gz"
+    git      = "https://github.com/pocl/pocl.git"
 
-    version("master", git="https://github.com/pocl/pocl.git")
-    version('0.14', '1d35f09299e76b9e3918c42826555194')
-    # version("0.14-rc",
-    #         git="https://github.com/pocl/pocl.git", branch="release_0_14")
-    version("0.13", "344480864d4269f2f63f1509395898bd")
-    version("0.12", "e197ba3aa01a35f40581c48e053330dd")
-    version("0.11", "9be0640cde2983062c47393d9e8e8fe7")
-    version("0.10", "0096be4f595c7b5cbfa42430c8b3af6a")
+    version("master", branch="master")
+    version('1.1', sha256='1e8dd0693a88c84937754df947b202871a40545b1b0a97ebefa370b0281c3c53')
+    version('1.0', sha256='94bd86a2f9847c03e6c3bf8dca12af3734f8b272ffeacbc3fa8fcca58844b1d4')
+    version('0.14', sha256='2127bf925a91fbbe3daf2f1bac0da5c8aceb16e2a9434977a3057eade974106a')
+    version('0.13', sha256='a17f37d8f26819c0c8efc6de2b57f67a0c8a81514fc9cd5005434e49d67499f9')
+    version('0.12', sha256='5160d7a59721e6a7d0fc85868381c0afceaa7c07b9956c9be1e3b51e80c29f76')
+    version('0.11', sha256='24bb801fb87d104b66faaa95d1890776fdeabb37ad1b12fb977281737c7f29bb')
+    version('0.10', sha256='e9c38f774a77e61f66d850b705a5ba42d49356c40e75733db4c4811e091e5088')
 
     # This is Github's pocl/pocl#373
     patch("uint.patch", when="@:0.13")
@@ -57,20 +39,22 @@ class Pocl(CMakePackage):
 
     depends_on("cmake @2.8.12:", type="build")
     depends_on("hwloc")
-    depends_on("libtool", type=("build", "run"))
+    depends_on("hwloc@:1.99.99", when="@:1.1.99")
+    depends_on("libtool", type=("build", "link", "run"))
+    depends_on("pkgconfig", type="build")
+
     # We don't request LLVM's shared libraries because these are not
     # enabled by default, and also because they fail to build for us
     # (see #1616)
-    depends_on("llvm +clang")
-    depends_on("pkg-config", type="build")
-
     # These are the supported LLVM versions
-    depends_on("llvm @3.7:3.9", when="@master")
-    depends_on("llvm @3.7:4.0", when="@0.14")
-    depends_on("llvm @3.7:3.8", when="@0.13")
-    depends_on("llvm @3.2:3.7", when="@0.12")
-    depends_on("llvm @3.2:3.6", when="@0.11")
-    depends_on("llvm @3.2:3.5", when="@0.10")
+    depends_on("llvm +clang @6.0:7.0", when="@master")
+    depends_on("llvm +clang @5.0:6.0", when="@1.1")
+    depends_on("llvm +clang @4.0:5.0", when="@1.0")
+    depends_on("llvm +clang @3.7:4.0", when="@0.14")
+    depends_on("llvm +clang @3.7:3.8", when="@0.13")
+    depends_on("llvm +clang @3.2:3.7", when="@0.12")
+    depends_on("llvm +clang @3.2:3.6", when="@0.11")
+    depends_on("llvm +clang @3.2:3.5", when="@0.10")
 
     variant("distro", default=False,
             description=("Support several CPU architectures, "
@@ -79,6 +63,14 @@ class Pocl(CMakePackage):
     variant("icd", default=False,
             description="Support a system-wide ICD loader")
 
+    def url_for_version(self, version):
+        if version >= Version('1.0'):
+            url = "https://github.com/pocl/pocl/archive/v{0}.tar.gz"
+        else:
+            url = "http://portablecl.org/downloads/pocl-{0}.tar.gz"
+
+        return url.format(version.up_to(2))
+
     def cmake_args(self):
         spec = self.spec
         args = ["-DINSTALL_OPENCL_HEADERS=ON"]
@@ -91,8 +83,7 @@ class Pocl(CMakePackage):
 
     @run_after('install')
     def symlink_opencl(self):
-        with working_dir(self.build_directory):
-            os.symlink("OpenCL", join_path(self.prefix.include, "CL"))
+        os.symlink("CL", self.prefix.include.OpenCL)
 
     @run_after('install')
     @on_package_attributes(run_tests=True)
diff --git a/var/spack/repos/builtin/packages/polymake/package.py b/var/spack/repos/builtin/packages/polymake/package.py
index 0fbfe52640..62e7013e5a 100644
--- a/var/spack/repos/builtin/packages/polymake/package.py
+++ b/var/spack/repos/builtin/packages/polymake/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/poppler-data/package.py b/var/spack/repos/builtin/packages/poppler-data/package.py
new file mode 100644
index 0000000000..3bb5ba3e34
--- /dev/null
+++ b/var/spack/repos/builtin/packages/poppler-data/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PopplerData(CMakePackage):
+    """This package consists of encoding files for use with poppler. The
+    encoding files are optional and poppler will automatically read them if
+    they are present.  When installed, the encoding files enables poppler to
+    correctly render CJK and Cyrrilic properly.  While poppler is licensed
+    under the GPL, these encoding files have different license, and thus
+    distributed separately."""
+
+    homepage = "https://poppler.freedesktop.org/"
+    url      = "https://poppler.freedesktop.org/poppler-data-0.4.9.tar.gz"
+
+    version('0.4.9', '35cc7beba00aa174631466f06732be40')
+
+    depends_on('cmake@2.6:', type='build')
diff --git a/var/spack/repos/builtin/packages/poppler/package.py b/var/spack/repos/builtin/packages/poppler/package.py
new file mode 100644
index 0000000000..653dd2e96d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/poppler/package.py
@@ -0,0 +1,135 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Poppler(CMakePackage):
+    """Poppler is a PDF rendering library based on the xpdf-3.0 code base."""
+
+    homepage = "https://poppler.freedesktop.org"
+    url      = "https://poppler.freedesktop.org/poppler-0.65.0.tar.xz"
+    list_url = "https://poppler.freedesktop.org/releases.html"
+
+    version('0.65.0', 'b9a0af02e43deb26265f130343e90d78')
+    version('0.64.0', 'f7f687ebb60004f8ad61994575018044')
+
+    variant('cms',      default=False, description='Use color management system')
+    variant('glib',     default=False, description='Compile poppler glib wrapper')
+    variant('gobject',  default=False, description='Generate GObject introspection')
+    variant('libcurl',  default=False, description='Build libcurl based HTTP support')
+    variant('openjpeg', default=False, description='Use libopenjpeg for JPX streams')
+    variant('qt5',      default=False, description='Compile poppler qt5 wrapper')
+    variant('zlib',     default=False, description='Build with zlib')
+    variant('cairo',    default=False, description='Search for Cairo package')
+    variant('iconv',    default=False, description='Search for Iconv package')
+    variant('jpeg',     default=False, description='Search for JPEG package')
+    variant('png',      default=False, description='Search for PNG package')
+    variant('tiff',     default=False, description='Search for TIFF package')
+
+    depends_on('cmake@3.1.0:', type='build')
+    depends_on('pkgconfig', type='build')
+    depends_on('poppler-data', type=('build', 'run'))
+    depends_on('fontconfig')
+    depends_on('freetype')
+
+    depends_on('lcms', when='+cms')
+    depends_on('glib', when='+glib')
+    depends_on('gobject-introspection', when='+gobject')
+    depends_on('curl', when='+libcurl')
+    depends_on('openjpeg', when='+openjpeg')
+    depends_on('qt@5.0:5.999', when='+qt5')
+    depends_on('zlib', when='+zlib')
+    depends_on('cairo', when='+cairo')
+    depends_on('libiconv', when='+iconv')
+    depends_on('jpeg', when='+jpeg')
+    depends_on('libpng', when='+png')
+    depends_on('libtiff', when='+tiff')
+
+    # Only needed to run `make test`
+    resource(
+        name='test',
+        git='https://anongit.freedesktop.org/git/poppler/test.git',
+        placement='testdata'
+    )
+
+    def cmake_args(self):
+        spec = self.spec
+
+        args = [
+            '-DTESTDATADIR={0}'.format(
+                join_path(self.stage.source_path, 'testdata')),
+            # TODO: Add packages for these missing dependencies
+            '-DENABLE_SPLASH=OFF',
+            '-DWITH_NSS3=OFF',
+        ]
+
+        if '+cms' in spec:
+            args.append('-DENABLE_CMS=lcms2')
+        else:
+            args.append('-DENABLE_CMS=none')
+
+        if '+glib' in spec:
+            args.append('-DENABLE_GLIB=ON')
+        else:
+            args.append('-DENABLE_GLIB=OFF')
+
+        if '+gobject' in spec:
+            args.append('-DENABLE_GOBJECT_INTROSPECTION=ON')
+        else:
+            args.append('-DENABLE_GOBJECT_INTROSPECTION=OFF')
+
+        if '+libcurl' in spec:
+            args.append('-DENABLE_LIBCURL=ON')
+        else:
+            args.append('-DENABLE_LIBCURL=OFF')
+
+        if '+openjpeg' in spec:
+            args.append('-DENABLE_LIBOPENJPEG=openjpeg2')
+        else:
+            args.append('-DENABLE_LIBOPENJPEG=none')
+
+        if '+qt5' in spec:
+            args.append('-DENABLE_QT5=ON')
+        else:
+            args.append('-DENABLE_QT5=OFF')
+
+        if '+zlib' in spec:
+            args.append('-DENABLE_ZLIB=ON')
+        else:
+            args.append('-DENABLE_ZLIB=OFF')
+
+        if '+cairo' in spec:
+            args.append('-DWITH_Cairo=ON')
+        else:
+            args.append('-DWITH_Cairo=OFF')
+
+        if '+iconv' in spec:
+            args.append('-DWITH_Iconv=ON')
+        else:
+            args.append('-DWITH_Iconv=OFF')
+
+        if '+jpeg' in spec:
+            args.extend([
+                '-DENABLE_DCTDECODER=libjpeg',
+                '-DWITH_JPEG=ON'
+            ])
+        else:
+            args.extend([
+                '-DENABLE_DCTDECODER=none',
+                '-DWITH_JPEG=OFF'
+            ])
+
+        if '+png' in spec:
+            args.append('-DWITH_PNG=ON')
+        else:
+            args.append('-DWITH_PNG=OFF')
+
+        if '+tiff' in spec:
+            args.append('-DWITH_TIFF=ON')
+        else:
+            args.append('-DWITH_TIFF=OFF')
+
+        return args
diff --git a/var/spack/repos/builtin/packages/porta/package.py b/var/spack/repos/builtin/packages/porta/package.py
index e54187188f..e43374933d 100644
--- a/var/spack/repos/builtin/packages/porta/package.py
+++ b/var/spack/repos/builtin/packages/porta/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/portage/package.py b/var/spack/repos/builtin/packages/portage/package.py
index b70139c3ed..f423551243 100644
--- a/var/spack/repos/builtin/packages/portage/package.py
+++ b/var/spack/repos/builtin/packages/portage/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -32,12 +13,12 @@ class Portage(CMakePackage):
        remapping library for transfer of field data between meshes.
     """
     homepage = "http://portage.lanl.gov/"
-    url      = "https://github.com/laristra/portage/tarball/v1.0"
+    git      = "https://github.com/laristra/portage.git"
 
     # tarballs don't have submodules, so use git tags
-    version('1.1.1', git='https://github.com/laristra/portage', tag='v1.1.1', submodules=True)
-    version('1.1.0', git='https://github.com/laristra/portage', tag='v1.1.0', submodules=True)
-    version('develop', git='https://github.com/laristra/portage', branch='master', submodules=True)
+    version('develop', branch='master', submodules=True)
+    version('1.1.1', tag='v1.1.1', submodules=True)
+    version('1.1.0', tag='v1.1.0', submodules=True)
 
     variant('mpi', default=True, description='Support MPI')
 
diff --git a/var/spack/repos/builtin/packages/portcullis/package.py b/var/spack/repos/builtin/packages/portcullis/package.py
new file mode 100644
index 0000000000..6a3c334ce5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/portcullis/package.py
@@ -0,0 +1,54 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Portcullis(AutotoolsPackage):
+    """PORTable CULLing of Invalid Splice junctions"""
+
+    homepage = "https://github.com/maplesond/portcullis"
+    url      = "https://github.com/maplesond/portcullis/archive/Release-1.1.2.tar.gz"
+
+    version('1.1.2', '5c581a7f827ffeecfe68107b7fe27ed60108325fd2f86a79d93f61b328687749')
+
+    depends_on('autoconf@2.53:', type='build')
+    depends_on('automake@1.11:', type='build')
+    depends_on('libtool@2.4.2:',  type='build')
+    depends_on('m4', type='build')
+
+    depends_on('zlib', type='build')
+    depends_on('samtools', type='build')
+
+    depends_on('python@3.4:', type=('build', 'run'))
+    depends_on('py-setuptools', type=('build', 'run'))
+    depends_on('py-pandas', type=('build', 'run'))
+
+    # later versions of py-sphinx don't get detected by the configure script
+    depends_on('py-sphinx@1.3:1.4')
+
+    def patch(self):
+        # remove static linking to libstdc++
+        filter_file(
+            'AM_LDFLAGS="-static-libstdc++"',
+            'AM_LDFLAGS=""',
+            'configure.ac', string=True
+        )
+
+        # prevent install scripts from ruining our PYTHONPATH
+        filter_file(
+            'export PYTHONPATH=$(DESTDIR)$(pythondir)',
+            'export PYTHONPATH="$(PYTHONPATH):$(DESTDIR)$(pythondir)"',
+            'scripts/Makefile.am', string=True
+        )
+
+    def build(self, spec, prefix):
+        # build manpages
+        make('man')
+
+        # run boost build script
+        sh = which('sh')
+        sh('build_boost.sh')
diff --git a/var/spack/repos/builtin/packages/postgresql/package.py b/var/spack/repos/builtin/packages/postgresql/package.py
index 1323405b1f..ee33e5c55f 100644
--- a/var/spack/repos/builtin/packages/postgresql/package.py
+++ b/var/spack/repos/builtin/packages/postgresql/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,6 +15,8 @@ class Postgresql(AutotoolsPackage):
     homepage = "http://www.postgresql.org/"
     url      = "http://ftp.postgresql.org/pub/source/v9.3.4/postgresql-9.3.4.tar.bz2"
 
+    version('10.3', '506498796a314c549388cafb3d5c717a')
+    version('10.2', 'e97c3cc72bdf661441f29069299b260a')
     version('9.3.4', 'd0a41f54c377b2d2fab4a003b0dac762')
     version('9.5.3', '3f0c388566c688c82b01a0edf1e6b7a0')
 
diff --git a/var/spack/repos/builtin/packages/ppl/package.py b/var/spack/repos/builtin/packages/ppl/package.py
index 0a5636d457..d2f4eafb7b 100644
--- a/var/spack/repos/builtin/packages/ppl/package.py
+++ b/var/spack/repos/builtin/packages/ppl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/pplacer/package.py b/var/spack/repos/builtin/packages/pplacer/package.py
new file mode 100644
index 0000000000..bfcd2f2d7f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pplacer/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Pplacer(Package):
+    """Pplacer places query sequences on a fixed reference phylogenetic tree
+       to maximize phylogenetic likelihood or posterior probability according
+       to a reference alignment. Pplacer is designed to be fast, to give
+       useful information about uncertainty, and to offer advanced
+       visualization and downstream analysis.
+    """
+
+    homepage = "http://matsen.fhcrc.org/pplacer/"
+    url      = "https://github.com/matsen/pplacer/releases/download/v1.1.alpha19/pplacer-linux-v1.1.alpha19.zip"
+
+    version('1.1.alpha19', 'e6b78604882d41d4bf13592c7edebfa2')
+
+    def install(self, spec, prefix):
+        install_tree('scripts', prefix.bin)
+        force_remove(join_path(prefix.bin, 'setup.py'))
+        install('guppy', prefix.bin)
+        install('pplacer', prefix.bin)
+        install('rppr', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/prank/package.py b/var/spack/repos/builtin/packages/prank/package.py
index 740cb63b85..1dc78db621 100644
--- a/var/spack/repos/builtin/packages/prank/package.py
+++ b/var/spack/repos/builtin/packages/prank/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,11 +12,13 @@ class Prank(Package):
     homepage = "http://wasabiapp.org/software/prank/"
     url      = "http://wasabiapp.org/download/prank/prank.source.150803.tgz"
 
+    version('170427', 'a5cda14dc4e5efe1f14b84eb7a7caabd')
     version('150803', '71ac2659e91c385c96473712c0a23e8a')
 
     depends_on('mafft')
     depends_on('exonerate')
     depends_on('bpp-suite')      # for bppancestor
+    conflicts('%gcc@7.2.0', when='@:150803')
 
     def install(self, spec, prefix):
         with working_dir('src'):
diff --git a/var/spack/repos/builtin/packages/precice/package.py b/var/spack/repos/builtin/packages/precice/package.py
new file mode 100644
index 0000000000..74f78d67aa
--- /dev/null
+++ b/var/spack/repos/builtin/packages/precice/package.py
@@ -0,0 +1,59 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Precice(CMakePackage):
+    """preCICE (Precise Code Interaction Coupling Environment) is a
+    coupling library for partitioned multi-physics simulations.
+    Partitioned means that preCICE couples existing programs (solvers)
+    capable of simulating a subpart of the complete physics involved in
+    a simulation."""
+
+    homepage = 'https://www.precice.org'
+    git      = 'https://github.com/precice/precice.git'
+
+    # Skip version 1.1.1 entirely, the cmake was lacking install.
+    version('develop', branch='develop')
+
+    variant('mpi', default=True, description='Enable MPI support')
+    variant('petsc', default=False, description='Enable PETSc support')
+    variant('python', default=False, description='Enable Python support')
+    variant('shared', default=True, description='Build shared libraries')
+
+    # Not yet
+#    variant(
+#        'float', default=False,
+#        description='Use single precision for field data exchange')
+#    variant(
+#        'int64',
+#        default=False, description='Use 64-bit integers for indices')
+
+    depends_on('cmake@3.5:', type='build')
+    depends_on('boost@1.60.0:')
+    depends_on('eigen@3.2:')
+    # Implicit via eigen, don't over-constrain: depends_on('libxml2')
+    depends_on('mpi', when='+mpi')
+    depends_on('petsc', when='+petsc')
+    depends_on('python@2.7', when='+python', type=('build', 'run'))
+
+    def cmake_args(self):
+        """Populate cmake arguments for precice."""
+        spec = self.spec
+
+        def variant_bool(feature, on='ON', off='OFF'):
+            """Ternary for spec variant to ON/OFF string"""
+            if feature in spec:
+                return on
+            return off
+
+        cmake_args = [
+            '-DMPI:BOOL=%s' % variant_bool('+mpi'),
+            '-DPETSC:BOOL=%s' % variant_bool('+petsc'),
+            '-DPYTHON:BOOL=%s' % variant_bool('+python'),
+            '-DBUILD_SHARED_LIBS:BOOL=%s' % variant_bool('+shared'),
+        ]
+        return cmake_args
diff --git a/var/spack/repos/builtin/packages/presentproto/package.py b/var/spack/repos/builtin/packages/presentproto/package.py
index e31490a07c..991db65217 100644
--- a/var/spack/repos/builtin/packages/presentproto/package.py
+++ b/var/spack/repos/builtin/packages/presentproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,5 +14,5 @@ class Presentproto(AutotoolsPackage):
 
     version('1.0', '57eaf4bb58e86476ec89cfb42d675961')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/preseq/package.py b/var/spack/repos/builtin/packages/preseq/package.py
index 136bbb62b9..cbd72ce317 100644
--- a/var/spack/repos/builtin/packages/preseq/package.py
+++ b/var/spack/repos/builtin/packages/preseq/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/price/package.py b/var/spack/repos/builtin/packages/price/package.py
index ee47d600b8..8f6f1a1ef6 100644
--- a/var/spack/repos/builtin/packages/price/package.py
+++ b/var/spack/repos/builtin/packages/price/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/primer3/package.py b/var/spack/repos/builtin/packages/primer3/package.py
index 5a747d8dec..cdf17a5677 100644
--- a/var/spack/repos/builtin/packages/primer3/package.py
+++ b/var/spack/repos/builtin/packages/primer3/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/prinseq-lite/package.py b/var/spack/repos/builtin/packages/prinseq-lite/package.py
new file mode 100644
index 0000000000..764a390343
--- /dev/null
+++ b/var/spack/repos/builtin/packages/prinseq-lite/package.py
@@ -0,0 +1,41 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PrinseqLite(Package):
+    """PRINSEQ will help you to preprocess your genomic or metagenomic
+    sequence data in FASTA or FASTQ format."""
+
+    homepage = "http://prinseq.sourceforge.net"
+    url      = "https://sourceforge.net/projects/prinseq/files/standalone/prinseq-lite-0.20.4.tar.gz"
+
+    version('0.20.4', '3be1a572073ebbbecfeba42a42853ff5')
+
+    variant('nopca', default=True, description="Graphs version without PCA")
+
+    depends_on('perl', type='run')
+    depends_on('perl-cairo', type='run')
+    depends_on('perl-digest-md5', type='run')
+    depends_on('perl-json', type='run')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+
+        filter_file(r'#!/usr/bin/perl',
+                    '#!/usr/bin/env perl',
+                    'prinseq-graphs-noPCA.pl')
+
+        filter_file(r'#!/usr/bin/perl',
+                    '#!/usr/bin/env perl',
+                    'prinseq-lite.pl')
+
+        install('prinseq-graphs-noPCA.pl', prefix.bin)
+        install('prinseq-lite.pl', prefix.bin)
+
+        chmod = which('chmod')
+        chmod('+x', join_path(self.prefix.bin, 'prinseq-graphs-noPCA.pl'))
+        chmod('+x', join_path(self.prefix.bin, 'prinseq-lite.pl'))
diff --git a/var/spack/repos/builtin/packages/printproto/package.py b/var/spack/repos/builtin/packages/printproto/package.py
index c3d0e28e8f..8eb55fabeb 100644
--- a/var/spack/repos/builtin/packages/printproto/package.py
+++ b/var/spack/repos/builtin/packages/printproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,5 +15,5 @@ class Printproto(AutotoolsPackage):
 
     version('1.0.5', '5afeb3a7de8a14b417239a14ea724268')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/prng/package.py b/var/spack/repos/builtin/packages/prng/package.py
new file mode 100644
index 0000000000..3db827fd03
--- /dev/null
+++ b/var/spack/repos/builtin/packages/prng/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Prng(AutotoolsPackage):
+    """Pseudo-Random Number Generator library."""
+
+    homepage = "http://statmath.wu.ac.at/prng/"
+    url      = "http://statmath.wu.ac.at/prng/prng-3.0.2.tar.gz"
+
+    version('3.0.2', '80cb0870f2d18618bd2772f9e1dc1a70')
+
+    depends_on('automake', type='build')
+    depends_on('autoconf', type='build')
+    depends_on('libtool', type='build')
+    depends_on('m4', type='build')
+
+    patch('prng-3.0.2-shared.patch', when="@3.0.2")
+    patch('prng-3.0.2-fix-c99-inline-semantics.patch', when="@3.0.2")
+
+    # Force the autoreconf step
+    force_autoreconf = True
diff --git a/var/spack/repos/builtin/packages/prng/prng-3.0.2-fix-c99-inline-semantics.patch b/var/spack/repos/builtin/packages/prng/prng-3.0.2-fix-c99-inline-semantics.patch
new file mode 100644
index 0000000000..c84a288d47
--- /dev/null
+++ b/var/spack/repos/builtin/packages/prng/prng-3.0.2-fix-c99-inline-semantics.patch
@@ -0,0 +1,146 @@
+Use portable 'static inline' semantics that work in GNU89 and C99
+See also: http://www.greenend.org.uk/rjk/tech/inline.html
+
+--- a/src/dicg.c
++++ b/src/dicg.c
+@@ -441,7 +441,7 @@
+  * Algorithm by Karin Schaber and Otmar Lendl.
+  *
+  */                                                  
+-inline prng_num prng_dicg_multiply(int k,prng_num c, prng_num d)
++prng_num prng_dicg_multiply(int k,prng_num c, prng_num d)
+ {
+   int i;
+   struct mtable *t;
+--- a/src/external.c
++++ b/src/external.c
+@@ -139,7 +139,7 @@
+  *      gen:  Pointer to a struct prng.
+  *
+  */
+-inline prng_num prng_tt800_get_next_int(struct prng *gen)
++prng_num prng_tt800_get_next_int(struct prng *gen)
+ {
+ unsigned int y;
+ struct tt800_state *g;
+--- a/src/icg.c
++++ b/src/icg.c
+@@ -110,7 +110,7 @@
+  *      gen:  Pointer to a struct prng.
+  *
+  */
+-inline prng_num prng_icg_get_next_int(struct prng *gen)
++prng_num prng_icg_get_next_int(struct prng *gen)
+ {
+   s_prng_num inv, current, prod;
+   
+--- a/src/lcg.c
++++ b/src/lcg.c
+@@ -111,7 +111,7 @@
+  *      gen:  Pointer to a struct prng.
+  *
+  */
+-inline prng_num prng_lcg_get_next_int(struct prng *gen)
++prng_num prng_lcg_get_next_int(struct prng *gen)
+ {
+   s_prng_num ax, current;
+ 
+--- a/src/meicg.c
++++ b/src/meicg.c
+@@ -106,7 +106,7 @@
+  *      gen:  Pointer to a struct prng.
+  *
+  */
+-inline prng_num prng_meicg_get_next_int(struct prng *gen)
++prng_num prng_meicg_get_next_int(struct prng *gen)
+ {
+   s_prng_num an, sum, inv, n;
+ 
+--- a/src/mt19937.c
++++ b/src/mt19937.c
+@@ -172,7 +172,7 @@
+  *      gen:  Pointer to a struct prng.
+  *
+  */
+-inline prng_num prng_mt19937_get_next_int(struct prng *gen)
++prng_num prng_mt19937_get_next_int(struct prng *gen)
+ {
+ #define MT  gen->data.mt19937_data.mt
+ #define MTI gen->data.mt19937_data.mti
+--- a/src/prng.h
++++ b/src/prng.h
+@@ -406,7 +406,7 @@
+ /* INLINE fnk def. for mult_mod, I don't know if this works for non-GCC */
+ 
+ #ifdef __GNUC__
+-extern __inline__ prng_num mult_mod(prng_num s,struct mult_mod_struct *mm)
++static inline prng_num mult_mod(prng_num s,struct mult_mod_struct *mm)
+ {
+ s_prng_num s_tmp;
+ 
+--- a/src/qcg.c
++++ b/src/qcg.c
+@@ -107,7 +107,7 @@
+  *      gen:  Pointer to a struct prng.
+  *
+  */
+-inline prng_num prng_qcg_get_next_int(struct prng *gen)
++prng_num prng_qcg_get_next_int(struct prng *gen)
+ {
+   s_prng_num current, sum, square, q_term, l_term;
+ 
+--- a/src/support.c
++++ b/src/support.c
+@@ -449,52 +449,6 @@
+ 		}
+ }
+ 
+-#ifndef __cplusplus
+-/* 
+- * Modular Multiplication. Uses the precalculated values from mult_mod_setup.
+- *
+- *
+- * Input: 
+- *	s	An prng_num. 
+- *	mm	pointer to a struct mult_mod_struct initialized 
+- *		by mult_mod_setup.
+- *
+- * Output:
+- *      (mm->a*s) mod mm->p
+- *
+- */
+-prng_num mult_mod(prng_num s,struct mult_mod_struct *mm)
+-{
+-s_prng_num s_tmp;
+-
+-switch(mm->algorithm)
+-	{
+-	case PRNG_MM_ZERO:	return(0);
+-			break;
+-	case PRNG_MM_ONE:	return(s);
+-			break;
+-	case PRNG_MM_SIMPLE: return((s * mm->a) % mm->p );
+-			break;
+-	case PRNG_MM_SCHRAGE:
+-			s_tmp = mm->a * ( s % mm->q ) - 
+-				mm->r * ( s / mm->q );
+-			if (s_tmp < 0) s_tmp += mm->p;
+-			return(s_tmp);
+-			break;
+-	case PRNG_MM_DECOMP: return(mult_mod_generic(s,mm->a,mm->p)); 
+-			break;
+-#ifdef HAVE_LONGLONG
+-	case PRNG_MM_LL:	return(mult_mod_ll(s,mm->a,mm->p));
+-			break;
+-#endif
+-	case PRNG_MM_POW2:	return((s*mm->a) & mm->mask);
+-			break;
+-	}
+-/* not reached */
+-return(0);
+-}
+-#endif
+-
+ 
+ /* 
+  * Modular Multiplication: Decomposition method (from L'Ecuyer & Cote)
diff --git a/var/spack/repos/builtin/packages/prng/prng-3.0.2-shared.patch b/var/spack/repos/builtin/packages/prng/prng-3.0.2-shared.patch
new file mode 100644
index 0000000000..cee8de060f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/prng/prng-3.0.2-shared.patch
@@ -0,0 +1,52 @@
+--- a/configure.ac
++++ b/configure.ac
+@@ -23,6 +23,7 @@
+ AC_PROG_RANLIB
+ AC_PROG_INSTALL
+ AC_PROG_LN_S
++AC_PROG_LIBTOOL
+ 
+ dnl Checks for typedefs, structures, and compiler characteristics.
+ AC_C_CONST
+@@ -39,10 +40,7 @@
+ dnl Checks for library functions.
+ AC_CHECK_FUNCS(strtoul)
+ 
+-dnl Set flags for compiler
+-if test X"$GCC" = Xyes ; then
+-	AC_SUBST(AM_CFLAGS,"-Wall -fomit-frame-pointer")
+-fi
++AC_CHECK_LIB([m], [pow])
+ 
+ AC_CONFIG_FILES([\
+         Makefile \
+--- a/examples/Makefile.am
++++ b/examples/Makefile.am
+@@ -1,11 +1,11 @@
+ ## Process this file with automake to produce Makefile.in
+ # $Id$
+ 
+-LDADD = $(top_builddir)/src/libprng.a -lm
++LDADD = $(top_builddir)/src/libprng.la -lm
+ 
+ INCLUDES = -I$(top_srcdir)/src
+ 
+-noinst_PROGRAMS = pairs tuples
++check_PROGRAMS = pairs tuples
+ 
+ # clean backup files
+ CLEANFILES = *~
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -3,9 +3,9 @@
+ 
+ INCLUDES = 
+ 
+-lib_LIBRARIES = libprng.a
++lib_LTLIBRARIES = libprng.la
+ 
+-libprng_a_SOURCES = \
++libprng_la_SOURCES = \
+  prng.c \
+  dicg.c \
+  eicg.c \
diff --git a/var/spack/repos/builtin/packages/probconsrna/package.py b/var/spack/repos/builtin/packages/probconsrna/package.py
index 56abd8b59e..31ef7e8b28 100644
--- a/var/spack/repos/builtin/packages/probconsrna/package.py
+++ b/var/spack/repos/builtin/packages/probconsrna/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/prodigal/package.py b/var/spack/repos/builtin/packages/prodigal/package.py
new file mode 100644
index 0000000000..75ce486f50
--- /dev/null
+++ b/var/spack/repos/builtin/packages/prodigal/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Prodigal(MakefilePackage):
+    """Fast, reliable protein-coding gene prediction for prokaryotic
+    genomes."""
+
+    homepage = "https://github.com/hyattpd/Prodigal"
+    url      = "https://github.com/hyattpd/Prodigal/archive/v2.6.3.tar.gz"
+
+    version('2.6.3', '5181809fdb740e9a675cfdbb6c038466')
+
+    def install(self, spec, prefix):
+        make('INSTALLDIR={0}'.format(self.prefix), 'install')
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PATH', prefix)
diff --git a/var/spack/repos/builtin/packages/proj/package.py b/var/spack/repos/builtin/packages/proj/package.py
index efddcb876c..fe20f4e58a 100644
--- a/var/spack/repos/builtin/packages/proj/package.py
+++ b/var/spack/repos/builtin/packages/proj/package.py
@@ -1,37 +1,37 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class Proj(AutotoolsPackage):
-    """Cartographic Projections"""
-    homepage = "https://github.com/OSGeo/proj.4/wiki"
-    url      = "http://download.osgeo.org/proj/proj-4.9.2.tar.gz"
+    """PROJ is a generic coordinate transformation software, that transforms
+    geospatial coordinates from one coordinate reference system (CRS) to
+    another. This includes cartographic projections as well as geodetic
+    transformations."""
+
+    homepage = "https://proj4.org/"
+    url      = "http://download.osgeo.org/proj/proj-5.0.1.tar.gz"
 
+    version('5.0.1', '15c8d7d6a8cb945c7878d0ff322a232c')
     version('4.9.2', '9843131676e31bbd903d60ae7dc76cf9')
     version('4.9.1', '3cbb2a964fd19a496f5f4265a717d31c')
     version('4.8.0', 'd815838c92a29179298c126effbb1537')
     version('4.7.0', '927d34623b52e0209ba2bfcca18fe8cd')
     version('4.6.1', '7dbaab8431ad50c25669fd3fb28dc493')
+
+    # https://github.com/OSGeo/proj.4#distribution-files-and-format
+    # https://github.com/OSGeo/proj-datumgrid
+    resource(
+        name='proj-datumgrid',
+        url='https://download.osgeo.org/proj/proj-datumgrid-1.7.tar.gz',
+        md5='6799bd8ac411b8a78724e34850c206c4',
+        placement='nad'
+    )
+
+    def configure_args(self):
+        return [
+            'PROJ_LIB={0}'.format(join_path(self.stage.source_path, 'nad'))
+        ]
diff --git a/var/spack/repos/builtin/packages/protobuf/intel_inline.patch b/var/spack/repos/builtin/packages/protobuf/intel_inline.patch
new file mode 100644
index 0000000000..61f1334293
--- /dev/null
+++ b/var/spack/repos/builtin/packages/protobuf/intel_inline.patch
@@ -0,0 +1,25 @@
+diff -Naur src_a/google/protobuf/stubs/port.h src_b/google/protobuf/stubs/port.h
+--- a/src/google/protobuf/stubs/port.h	2017-08-24 18:17:47.149533997 -0700
++++ b/src/google/protobuf/stubs/port.h	2017-08-24 22:13:12.907241538 -0700
+@@ -167,7 +167,9 @@
+ //   is not right for you.
+ 
+ #ifndef GOOGLE_ATTRIBUTE_ALWAYS_INLINE
+-#if defined(__GNUC__) && (__GNUC__ > 3 ||(__GNUC__ == 3 && __GNUC_MINOR__ >= 1))
++#if defined(__INTEL_COMPILER) && (__INTEL_COMPILER > 1700)
++#define GOOGLE_ATTRIBUTE_ALWAYS_INLINE __attribute__ ((always_inline))
++#elif defined(__GNUC__) && (__GNUC__ > 3 ||(__GNUC__ == 3 && __GNUC_MINOR__ >= 1))
+ // For functions we want to force inline.
+ // Introduced in gcc 3.1.
+ #define GOOGLE_ATTRIBUTE_ALWAYS_INLINE __attribute__ ((always_inline))
+@@ -178,7 +180,9 @@
+ #endif
+ 
+ #ifndef GOOGLE_ATTRIBUTE_NOINLINE
+-#if defined(__GNUC__) && (__GNUC__ > 3 ||(__GNUC__ == 3 && __GNUC_MINOR__ >= 1))
++#if defined(__INTEL_COMPILER) && (__INTEL_COMPILER > 1700)
++#define GOOGLE_ATTRIBUTE_NOINLINE
++#elif defined(__GNUC__) && (__GNUC__ > 3 ||(__GNUC__ == 3 && __GNUC_MINOR__ >= 1))
+ // For functions we want to force not inline.
+ // Introduced in gcc 3.1.
+ #define GOOGLE_ATTRIBUTE_NOINLINE __attribute__ ((noinline))
diff --git a/var/spack/repos/builtin/packages/protobuf/package.py b/var/spack/repos/builtin/packages/protobuf/package.py
index 038c208864..62486aeb58 100644
--- a/var/spack/repos/builtin/packages/protobuf/package.py
+++ b/var/spack/repos/builtin/packages/protobuf/package.py
@@ -1,27 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import sys
 from spack import *
 import spack.util.web
 
@@ -33,6 +15,12 @@ class Protobuf(CMakePackage):
     url      = "https://github.com/google/protobuf/archive/v3.2.0.tar.gz"
     root_cmakelists_dir = "cmake"
 
+    version('3.5.2', 'ff6742018c172c66ecc627029ad54280')
+    version('3.5.1.1', '5005003ae6b94773c4bbca87a644b131')
+    version('3.5.1',   '710f1a75983092c9b45ecef207236104')
+    version('3.5.0.1', 'b3ed2401acf167207277b254fd7f9638')
+    version('3.5.0',   'd95db321e1a9901fffc51ed8994afd36')
+    version('3.4.1',   '31b19dcfd6567095fdb66a8c07347222')
     version('3.4.0', '1d077a7d4db3d75681f5c333f2de9b1a')
     version('3.3.0', 'f0f712e98de3db0c65c0c417f5e7aca8')
     version('3.2.0', 'efaa08ae635664fb5e7f31421a41a995')
@@ -41,6 +29,9 @@ class Protobuf(CMakePackage):
     # does not build with CMake:
     # version('2.5.0', '9c21577a03adc1879aba5b52d06e25cf')
 
+    variant('shared', default=True,
+            description='Enables the build of shared libraries')
+
     depends_on('zlib')
 
     conflicts('%gcc@:4.6')  # Requires c++11
@@ -48,6 +39,8 @@ class Protobuf(CMakePackage):
     # first fixed in 3.4.0: https://github.com/google/protobuf/pull/3406
     patch('pkgconfig.patch', when='@:3.3.2')
 
+    patch('intel_inline.patch', when='@3.2.0: %intel')
+
     def fetch_remote_versions(self):
         """Ignore additional source artifacts uploaded with releases,
            only keep known versions
@@ -60,7 +53,10 @@ class Protobuf(CMakePackage):
 
     def cmake_args(self):
         args = [
+            '-DBUILD_SHARED_LIBS=%s' % int('+shared' in self.spec),
             '-Dprotobuf_BUILD_TESTS:BOOL=OFF',
             '-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON'
         ]
+        if sys.platform == 'darwin':
+            args.extend(['-DCMAKE_MACOSX_RPATH=ON'])
         return args
diff --git a/var/spack/repos/builtin/packages/proxymngr/package.py b/var/spack/repos/builtin/packages/proxymngr/package.py
index cc38d6ae55..6f6e118e22 100644
--- a/var/spack/repos/builtin/packages/proxymngr/package.py
+++ b/var/spack/repos/builtin/packages/proxymngr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -42,5 +23,5 @@ class Proxymngr(AutotoolsPackage):
 
     depends_on('xproto@7.0.17:', type='build')
     depends_on('xproxymanagementprotocol', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/pruners-ninja/package.py b/var/spack/repos/builtin/packages/pruners-ninja/package.py
index c8e93ad997..0c86c9e2bc 100644
--- a/var/spack/repos/builtin/packages/pruners-ninja/package.py
+++ b/var/spack/repos/builtin/packages/pruners-ninja/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/ps-lite/package.py b/var/spack/repos/builtin/packages/ps-lite/package.py
index b78315c060..887e126814 100644
--- a/var/spack/repos/builtin/packages/ps-lite/package.py
+++ b/var/spack/repos/builtin/packages/ps-lite/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,11 +11,10 @@ class PsLite(CMakePackage):
     of the parameter server framework."""
 
     homepage = "https://github.com/dmlc/ps-lite"
-    url      = "https://github.com/dmlc/ps-lite.git"
+    git      = "https://github.com/dmlc/ps-lite.git"
 
-    version('master', git='https://github.com/dmlc/ps-lite.git', branch='master')
-    version('20170328', git='https://github.com/dmlc/ps-lite.git',
-            commit='acdb698fa3bb80929ef83bb37c705f025e119b82')
+    version('master', branch='master')
+    version('20170328', commit='acdb698fa3bb80929ef83bb37c705f025e119b82')
 
     depends_on('protobuf@3:')
     depends_on('zeromq')
diff --git a/var/spack/repos/builtin/packages/psi4/package.py b/var/spack/repos/builtin/packages/psi4/package.py
index f322e6c1ca..eb3e7863fe 100644
--- a/var/spack/repos/builtin/packages/psi4/package.py
+++ b/var/spack/repos/builtin/packages/psi4/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
diff --git a/var/spack/repos/builtin/packages/pslib/package.py b/var/spack/repos/builtin/packages/pslib/package.py
new file mode 100644
index 0000000000..c15a7f8b83
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pslib/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Pslib(AutotoolsPackage):
+    """C-library to create PostScript files on the fly."""
+
+    homepage = "http://pslib.sourceforge.net/"
+    url      = "https://kent.dl.sourceforge.net/project/pslib/pslib/0.4.5/pslib-0.4.5.tar.gz"
+
+    version('0.4.5', '03f39393628a6d758799b9f845047e27')
+
+    depends_on('jpeg')
+    depends_on('libpng')
diff --git a/var/spack/repos/builtin/packages/psm/package.py b/var/spack/repos/builtin/packages/psm/package.py
new file mode 100644
index 0000000000..ba661394f1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/psm/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Psm(MakefilePackage):
+    """Intel Performance scaled messaging library"""
+
+    homepage = "https://github.com/intel/psm"
+    url      = "https://github.com/intel/psm/archive/v3.3.tar.gz"
+    git      = "https://github.com/intel/psm.git"
+
+    version('3.3', '031eb27688c932867d55054e76d00875', preferred=True)
+    version('2017-04-28', commit='604758e')
+
+    conflicts('%gcc@6:', when='@3.3')
+
+    depends_on('libuuid')
+
+    def edit(self, spec, prefix):
+        makefile = FileFilter('Makefile')
+        makefile.filter('{DESTDIR}/usr/', '{LOCAL_PREFIX}/')
+
+    def install(self, spec, prefix):
+        make('LOCAL_PREFIX=%s' % prefix, 'install')
diff --git a/var/spack/repos/builtin/packages/psmc/package.py b/var/spack/repos/builtin/packages/psmc/package.py
new file mode 100644
index 0000000000..019d664e39
--- /dev/null
+++ b/var/spack/repos/builtin/packages/psmc/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Psmc(MakefilePackage):
+    """mplementation of the Pairwise Sequentially Markovian Coalescent
+    (PSMC) model"""
+
+    homepage = "https://github.com/lh3/psmc"
+    git      = "https://github.com/lh3/psmc.git"
+
+    version('2016-1-21', commit='e5f7df5d00bb75ec603ae0beff62c0d7e37640b9')
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PATH', prefix.bin.utils)
+
+    def build(self, spec, prefix):
+        make()
+        with working_dir('utils'):
+            make()
+
+    def install(self, spec, prefix):
+        install_tree(self.build_directory, prefix.bin)
diff --git a/var/spack/repos/builtin/packages/pstreams/package.py b/var/spack/repos/builtin/packages/pstreams/package.py
index 2bf7fa63c9..8c4ebc5377 100644
--- a/var/spack/repos/builtin/packages/pstreams/package.py
+++ b/var/spack/repos/builtin/packages/pstreams/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/pugixml/package.py b/var/spack/repos/builtin/packages/pugixml/package.py
index 5cab25c3b3..9418cae3e2 100644
--- a/var/spack/repos/builtin/packages/pugixml/package.py
+++ b/var/spack/repos/builtin/packages/pugixml/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/pumi/package.py b/var/spack/repos/builtin/packages/pumi/package.py
index f4f65a33d3..02cef568e4 100644
--- a/var/spack/repos/builtin/packages/pumi/package.py
+++ b/var/spack/repos/builtin/packages/pumi/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-import sys
 
 
 class Pumi(CMakePackage):
@@ -37,19 +17,23 @@ class Pumi(CMakePackage):
        and dynamic load balancing."""
 
     homepage = "https://www.scorec.rpi.edu/pumi"
-    url      = "https://github.com/SCOREC/core.git"
-
-    version('0.0.1', git='https://github.com/SCOREC/core.git',
-        commit='0c315e82b3f2478dc18bdd6cfa89f1cddb85cd6a')
-    version('develop', git='https://github.com/SCOREC/core.git',
-        branch='master')
-
-    if sys.platform == 'darwin':
-        patch('phiotimer.cc.darwin.patch', level=0)  # !clock_gettime
+    git      = "https://github.com/SCOREC/core.git"
+
+    # We will use the scorec/core master branch as the 'nightly' version
+    # of pumi in spack.  The master branch is more stable than the
+    # scorec/core develop branch and we perfer not to expose spack users
+    # to the added instability. The spack version string is 'develop' since
+    # it compares greater than a numbered version (e.g., 2.1.0). The spack
+    # version string 'master' compares less than a numbered version.
+    version('develop', branch='master')
+    version('2.2.0', commit='8c7e6f13943893b2bc1ece15003e4869a0e9634f')  # tag 2.2.0
+    version('2.1.0', commit='840fbf6ec49a63aeaa3945f11ddb224f6055ac9f')
 
     variant('zoltan', default=False, description='Enable Zoltan Features')
+    variant('fortran', default=False, description='Enable FORTRAN interface')
 
     depends_on('mpi')
+    depends_on('cmake@3:', type='build')
     depends_on('zoltan', when='+zoltan')
 
     def cmake_args(self):
@@ -60,6 +44,9 @@ class Pumi(CMakePackage):
             '-DENABLE_ZOLTAN=%s' % ('ON' if '+zoltan' in spec else 'OFF'),
             '-DCMAKE_C_COMPILER=%s' % spec['mpi'].mpicc,
             '-DCMAKE_CXX_COMPILER=%s' % spec['mpi'].mpicxx,
+            '-DCMAKE_Fortran_COMPILER=%s' % spec['mpi'].mpifc,
+            '-DPUMI_FORTRAN_INTERFACE=%s' %
+            ('ON' if '+fortran' in spec else 'OFF')
         ]
 
         return args
diff --git a/var/spack/repos/builtin/packages/pumi/phiotimer.cc.darwin.patch b/var/spack/repos/builtin/packages/pumi/phiotimer.cc.darwin.patch
deleted file mode 100644
index 52c6e63fca..0000000000
--- a/var/spack/repos/builtin/packages/pumi/phiotimer.cc.darwin.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-*** ./phasta/phiotimer.cc	2017-05-03 12:26:25.000000000 -0700
---- ./phasta/phiotimer.cc.patched	2017-05-03 12:26:11.000000000 -0700
-***************
-*** 56,63 ****
-  }
-  #else
-  void phastaio_time(phastaioTime* t) {
-!   int err;
-!   err = clock_gettime(CLOCK_MONOTONIC,t);
-    PCU_ALWAYS_ASSERT(!err);
-  }
-  /*return elapsed time in micro seconds*/
---- 56,63 ----
-  }
-  #else
-  void phastaio_time(phastaioTime* t) {
-!   int err=0;
-!   /*err = clock_gettime(CLOCK_MONOTONIC,t);*/
-    PCU_ALWAYS_ASSERT(!err);
-  }
-  /*return elapsed time in micro seconds*/
diff --git a/var/spack/repos/builtin/packages/pv/package.py b/var/spack/repos/builtin/packages/pv/package.py
new file mode 100644
index 0000000000..8a1e63a735
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pv/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Pv(AutotoolsPackage):
+    """ Pipe Viewer - is a terminal-based tool for monitoring the progress
+        of data through a pipeline
+    """
+
+    homepage = "http://www.ivarch.com/programs/pv.shtml"
+    url      = "http://www.ivarch.com/programs/sources/pv-1.6.6.tar.bz2"
+
+    version('1.6.6', 'ff3564fddcc2b9bd4a9c1d143aba4b4c')
diff --git a/var/spack/repos/builtin/packages/pvm/package.py b/var/spack/repos/builtin/packages/pvm/package.py
index de4848413d..4cb797f52d 100644
--- a/var/spack/repos/builtin/packages/pvm/package.py
+++ b/var/spack/repos/builtin/packages/pvm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import subprocess
 
diff --git a/var/spack/repos/builtin/packages/pxz/package.py b/var/spack/repos/builtin/packages/pxz/package.py
new file mode 100644
index 0000000000..8cfced300b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pxz/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Pxz(MakefilePackage):
+    """Pxz is a parallel LZMA compressor using liblzma."""
+
+    homepage = "https://jnovy.fedorapeople.org/pxz/pxz.html"
+    url      = "http://jnovy.fedorapeople.org/pxz/pxz-4.999.9beta.20091201git.tar.xz"
+    git      = "https://github.com/jnovy/pxz.git"
+
+    version('develop', branch='master')
+    version('4.999.9beta.20091201git', '4ae3926185978f5c95c9414dc4634451')
+
+    depends_on('lzma')
+
+    conflicts('platform=darwin', msg='Pxz runs only on Linux.')
+
+    def install(self, spec, prefix):
+        make('install', "DESTDIR=%s" % prefix,
+             "BINDIR=/bin", "MANDIR=/share/man")
diff --git a/var/spack/repos/builtin/packages/py-3to2/package.py b/var/spack/repos/builtin/packages/py-3to2/package.py
index 1a1a6f8805..12a3a9fef3 100644
--- a/var/spack/repos/builtin/packages/py-3to2/package.py
+++ b/var/spack/repos/builtin/packages/py-3to2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-4suite-xml/package.py b/var/spack/repos/builtin/packages/py-4suite-xml/package.py
index e0fa713fd8..872d5e75d0 100644
--- a/var/spack/repos/builtin/packages/py-4suite-xml/package.py
+++ b/var/spack/repos/builtin/packages/py-4suite-xml/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-abipy/package.py b/var/spack/repos/builtin/packages/py-abipy/package.py
index dc07aaebd2..1ab1b316ef 100644
--- a/var/spack/repos/builtin/packages/py-abipy/package.py
+++ b/var/spack/repos/builtin/packages/py-abipy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-adios/package.py b/var/spack/repos/builtin/packages/py-adios/package.py
new file mode 100644
index 0000000000..ff59a71afb
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-adios/package.py
@@ -0,0 +1,60 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyAdios(PythonPackage):
+    """NumPy bindings of ADIOS1"""
+
+    homepage = "https://www.olcf.ornl.gov/center-projects/adios/"
+    url      = "https://github.com/ornladios/ADIOS/archive/v1.12.0.tar.gz"
+    git      = "https://github.com/ornladios/ADIOS.git"
+
+    maintainers = ['ax3l']
+
+    version('develop', branch='master')
+    version('1.13.0', '68af36b821debbdf4748b20320a990ce')
+    version('1.12.0', '84a1c71b6698009224f6f748c5257fc9')
+    version('1.11.1', '5639bfc235e50bf17ba9dafb14ea4185')
+    version('1.11.0', '5eead5b2ccf962f5e6d5f254d29d5238')
+    version('1.10.0', 'eff450a4c0130479417cfd63186957f3')
+    version('1.9.0', '310ff02388bbaa2b1c1710ee970b5678')
+
+    variant('mpi', default=True,
+            description='Enable MPI support')
+
+    for v in ['1.9.0', '1.10.0', '1.11.0', '1.11.1', '1.12.0', '1.13.0',
+              'develop']:
+        depends_on('adios@{0} ~mpi'.format(v),
+                   when='@{0} ~mpi'.format(v),
+                   type=['build', 'link', 'run'])
+        depends_on('adios@{0} +mpi'.format(v),
+                   when='@{0} +mpi'.format(v),
+                   type=['build', 'link', 'run'])
+
+    depends_on('py-numpy', type=['build', 'run'])
+    depends_on('mpi', when='+mpi')
+    depends_on('py-mpi4py', type=['run'], when='+mpi')
+    depends_on('py-cython', type=['build'])
+
+    phases = ['build_clib', 'install']
+    build_directory = 'wrappers/numpy'
+
+    def setup_file(self):
+        """Returns the name of the setup file to use."""
+        if '+mpi' in self.spec:
+            return 'setup_mpi.py'
+        else:
+            return 'setup.py'
+
+    def build_clib(self, spec, prefix):
+        # calls: make [MPI=y] python
+        args = ''
+        if '+mpi' in self.spec:
+            args = 'MPI=y '
+        args += 'python'
+        with working_dir(self.build_directory):
+            make(args)
diff --git a/var/spack/repos/builtin/packages/py-affine/package.py b/var/spack/repos/builtin/packages/py-affine/package.py
new file mode 100644
index 0000000000..f421d60ae5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-affine/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyAffine(PythonPackage):
+    """Matrices describing affine transformation of the plane."""
+
+    homepage = "https://github.com/sgillies/affine"
+    url      = "https://github.com/sgillies/affine/archive/2.1.0.zip"
+
+    depends_on('py-setuptools', type='build')
+
+    version('2.1.0', '99cf61c3ef484f93da9dc062dfbce4b5')
diff --git a/var/spack/repos/builtin/packages/py-alabaster/package.py b/var/spack/repos/builtin/packages/py-alabaster/package.py
index 2f718ca9e8..f4268171b6 100644
--- a/var/spack/repos/builtin/packages/py-alabaster/package.py
+++ b/var/spack/repos/builtin/packages/py-alabaster/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-apache-libcloud/package.py b/var/spack/repos/builtin/packages/py-apache-libcloud/package.py
index c46987f2ce..157c15d592 100644
--- a/var/spack/repos/builtin/packages/py-apache-libcloud/package.py
+++ b/var/spack/repos/builtin/packages/py-apache-libcloud/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-apipkg/package.py b/var/spack/repos/builtin/packages/py-apipkg/package.py
index ee0f979b63..c2425c334e 100644
--- a/var/spack/repos/builtin/packages/py-apipkg/package.py
+++ b/var/spack/repos/builtin/packages/py-apipkg/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-appdirs/package.py b/var/spack/repos/builtin/packages/py-appdirs/package.py
index 4fd412bb39..998b71d6ba 100644
--- a/var/spack/repos/builtin/packages/py-appdirs/package.py
+++ b/var/spack/repos/builtin/packages/py-appdirs/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-appnope/package.py b/var/spack/repos/builtin/packages/py-appnope/package.py
index 98d3e44032..e17db899f8 100644
--- a/var/spack/repos/builtin/packages/py-appnope/package.py
+++ b/var/spack/repos/builtin/packages/py-appnope/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-apscheduler/package.py b/var/spack/repos/builtin/packages/py-apscheduler/package.py
index 47404f9944..ae5424f81c 100644
--- a/var/spack/repos/builtin/packages/py-apscheduler/package.py
+++ b/var/spack/repos/builtin/packages/py-apscheduler/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-argcomplete/package.py b/var/spack/repos/builtin/packages/py-argcomplete/package.py
index 9c08f46b19..057ee6c16c 100644
--- a/var/spack/repos/builtin/packages/py-argcomplete/package.py
+++ b/var/spack/repos/builtin/packages/py-argcomplete/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-argparse/package.py b/var/spack/repos/builtin/packages/py-argparse/package.py
index c89e30fdb2..14071cc026 100644
--- a/var/spack/repos/builtin/packages/py-argparse/package.py
+++ b/var/spack/repos/builtin/packages/py-argparse/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-ase/package.py b/var/spack/repos/builtin/packages/py-ase/package.py
index 0030615861..2a58740045 100644
--- a/var/spack/repos/builtin/packages/py-ase/package.py
+++ b/var/spack/repos/builtin/packages/py-ase/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,6 +14,7 @@ class PyAse(PythonPackage):
     homepage = "https://wiki.fysik.dtu.dk/ase/"
     url      = "https://pypi.io/packages/source/a/ase/ase-3.13.0.tar.gz"
 
+    version('3.15.0', '65a0143753517c2df157e53bd29a18e3')
     version('3.13.0', 'e946a0addc5b61e5e2e75857e0f99b89')
 
     depends_on('python@2.6:')
diff --git a/var/spack/repos/builtin/packages/py-asn1crypto/package.py b/var/spack/repos/builtin/packages/py-asn1crypto/package.py
index 1e1e408b4a..ed12054d7e 100644
--- a/var/spack/repos/builtin/packages/py-asn1crypto/package.py
+++ b/var/spack/repos/builtin/packages/py-asn1crypto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/py-astroid/package.py b/var/spack/repos/builtin/packages/py-astroid/package.py
index 63be8ae470..ea55f30939 100644
--- a/var/spack/repos/builtin/packages/py-astroid/package.py
+++ b/var/spack/repos/builtin/packages/py-astroid/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,12 +10,17 @@ class PyAstroid(PythonPackage):
     homepage = "https://www.astroid.org/"
     url      = "https://github.com/PyCQA/astroid/archive/astroid-1.4.5.tar.gz"
 
+    # version('1.5.3', '6f65e4ea8290ec032320460905afb828') # has broken unit tests
     version('1.4.5', '7adfc55809908297ef430efe4ea20ac3')
     version('1.4.4', '8ae6f63f6a2b260bb7f647dafccbc796')
     version('1.4.3', '4647159de7d4d0c4b1de23ecbfb8e246')
     version('1.4.2', '677f7965840f375af51b0e86403bee6a')
     version('1.4.1', 'ed70bfed5e4b25be4292e7fe72da2c02')
 
-    depends_on('py-logilab-common', type=('build', 'run'))
-    depends_on('py-setuptools', type='build')
-    depends_on('py-six', type=('build', 'run'))
+    depends_on('py-lazy-object-proxy')
+    depends_on('py-six')
+    depends_on('py-wrapt')
+    depends_on('py-enum34@1.1.3:', when='^python@:3.3.99')
+    depends_on('py-singledispatch', when='^python@:3.3.99')
+    depends_on('py-backports-functools-lru-cache', when='^python@:3.2.99')
+    depends_on('py-setuptools@17.1:')
diff --git a/var/spack/repos/builtin/packages/py-astropy/package.py b/var/spack/repos/builtin/packages/py-astropy/package.py
index e40fee11c6..1009b2e15b 100644
--- a/var/spack/repos/builtin/packages/py-astropy/package.py
+++ b/var/spack/repos/builtin/packages/py-astropy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -50,6 +31,7 @@ class PyAstropy(PythonPackage):
     depends_on('py-pytz', type=('build', 'run'))
     depends_on('py-scikit-image', type=('build', 'run'))
     depends_on('py-pandas', type=('build', 'run'))
+    depends_on('py-markupsafe', type=('build', 'run'))
 
     # System dependencies
     depends_on('cfitsio')
diff --git a/var/spack/repos/builtin/packages/py-atomicwrites/package.py b/var/spack/repos/builtin/packages/py-atomicwrites/package.py
new file mode 100644
index 0000000000..6cd224087e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-atomicwrites/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyAtomicwrites(PythonPackage):
+    """Atomic file writes."""
+
+    homepage = "https://github.com/untitaker/python-atomicwrites"
+    url      = "https://pypi.io/packages/source/a/atomicwrites/atomicwrites-1.1.5.tar.gz"
+
+    import_modules = ['atomicwrites']
+
+    version('1.1.5', sha256='240831ea22da9ab882b551b31d4225591e5e447a68c5e188db5b89ca1d487585')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-attrs/package.py b/var/spack/repos/builtin/packages/py-attrs/package.py
index 04daf75da4..eb63525b86 100644
--- a/var/spack/repos/builtin/packages/py-attrs/package.py
+++ b/var/spack/repos/builtin/packages/py-attrs/package.py
@@ -1,36 +1,27 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class PyAttrs(PythonPackage):
-    """Python Attributes Without Boilerplate"""
+    """Classes Without Boilerplate"""
 
     homepage = "http://attrs.org/"
-    url = "https://pypi.io/packages/source/a/attrs/attrs-16.3.0.tar.gz"
+    url      = "https://pypi.io/packages/source/a/attrs/attrs-18.1.0.tar.gz"
+
+    import_modules = ['attr']
 
+    version('18.1.0', '3f3f3e0750dab74cfa1dc8b0fd7a5f86')
     version('16.3.0', '4ec003c49360853cf935113d1ae56151')
 
-    depends_on('py-setuptools',         type='build')
+    depends_on('py-setuptools', type='build')
+
+    depends_on('py-coverage', type='test')
+    depends_on('py-hypothesis', type='test')
+    depends_on('py-pympler', type='test')
+    depends_on('py-pytest', type='test')
+    depends_on('py-six', type='test')
+    depends_on('py-zope-interface', type='test')
diff --git a/var/spack/repos/builtin/packages/py-autopep8/package.py b/var/spack/repos/builtin/packages/py-autopep8/package.py
index 3dff029a8a..c882e2506f 100644
--- a/var/spack/repos/builtin/packages/py-autopep8/package.py
+++ b/var/spack/repos/builtin/packages/py-autopep8/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,12 +13,14 @@ class PyAutopep8(PythonPackage):
     homepage = "https://github.com/hhatto/autopep8"
     url      = "https://pypi.io/packages/source/a/autopep8/autopep8-1.2.4.tar.gz"
 
+    version('1.3.3', '8951f43748406015b663a54ab05d891a')
     version('1.2.4', 'fcea19c0c5e505b425e2a78afb771f5c')
     version('1.2.2', '3d97f9c89d14a0975bffd32a2c61c36c')
 
     extends('python', ignore='bin/pep8')
     depends_on('python@2.6:2.8,3.2:')
 
-    depends_on('py-pycodestyle@1.5.7:1.7.0', type=('build', 'run'))
+    depends_on('py-pycodestyle@1.5.7:1.7.0', type=('build', 'run'), when='@:1.2.4')
+    depends_on('py-pycodestyle@2.3.0:', type=('build', 'run'), when='@1.3:')
 
     depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-avro-json-serializer/package.py b/var/spack/repos/builtin/packages/py-avro-json-serializer/package.py
new file mode 100644
index 0000000000..52f98286e5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-avro-json-serializer/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyAvroJsonSerializer(PythonPackage):
+    """Serializes data into a JSON format using AVRO schema."""
+
+    homepage = "https://github.com/linkedin/python-avro-json-serializer"
+    url      = "https://github.com/linkedin/python-avro-json-serializer/archive/0.4.tar.gz"
+
+    version('0.4',  'ee32f415e03820653cf8477bf5bfc779')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-simplejson', type=('build', 'run'))
+    depends_on('py-avro', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-avro/package.py b/var/spack/repos/builtin/packages/py-avro/package.py
new file mode 100644
index 0000000000..13e8670b56
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-avro/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyAvro(PythonPackage):
+    """Avro is a serialization and RPC framework."""
+
+    homepage = "http://avro.apache.org/docs/current/"
+    url      = "https://pypi.io/packages/source/a/avro/avro-1.8.2.tar.gz"
+
+    version('1.8.2', '44ec007d432a2f3c35f87eee01f1e9ec')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-babel/package.py b/var/spack/repos/builtin/packages/py-babel/package.py
index 8b20318c20..e502b2e7c2 100644
--- a/var/spack/repos/builtin/packages/py-babel/package.py
+++ b/var/spack/repos/builtin/packages/py-babel/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-backcall/package.py b/var/spack/repos/builtin/packages/py-backcall/package.py
new file mode 100644
index 0000000000..f255945211
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-backcall/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyBackcall(PythonPackage):
+    """Specifications for callback functions passed in to an API"""
+
+    homepage = "https://github.com/takluyver/backcall"
+    url = "https://pypi.io/packages/source/b/backcall/backcall-0.1.0.tar.gz"
+
+    version('0.1.0', '87ce0c7839808e6a3427d57df6a792e7')
diff --git a/var/spack/repos/builtin/packages/py-backports-abc/package.py b/var/spack/repos/builtin/packages/py-backports-abc/package.py
index 69cd6165b5..a287daaa83 100644
--- a/var/spack/repos/builtin/packages/py-backports-abc/package.py
+++ b/var/spack/repos/builtin/packages/py-backports-abc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-backports-functools-lru-cache/package.py b/var/spack/repos/builtin/packages/py-backports-functools-lru-cache/package.py
new file mode 100644
index 0000000000..f573a05594
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-backports-functools-lru-cache/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyBackportsFunctoolsLruCache(PythonPackage):
+    """Backport of functools.lru_cache from Python 3.3"""
+
+    homepage = "https://github.com/jaraco/backports.functools_lru_cache"
+    url = "https://pypi.io/packages/source/b/backports.functools_lru_cache/backports.functools_lru_cache-1.4.tar.gz"
+
+    py_namespace = 'backports'
+
+    version('1.5', '20f53f54cd3f04b3346ce75a54959754')
+    version('1.4', 'b954e7d5e2ca0f0f66ad2ed12ba800e5')
+    version('1.0.1', 'c789ef439d189330b99872746a6d9e85',
+            url="https://pypi.io/packages/source/b/backports.functools_lru_cache/backports.functools_lru_cache-1.0.1.zip")
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-setuptools-scm@1.15.0:', type='build')
+    depends_on('python@2.6.0:3.3.99',        type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-backports-shutil-get-terminal-size/package.py b/var/spack/repos/builtin/packages/py-backports-shutil-get-terminal-size/package.py
index daa019daef..40c9d88c26 100644
--- a/var/spack/repos/builtin/packages/py-backports-shutil-get-terminal-size/package.py
+++ b/var/spack/repos/builtin/packages/py-backports-shutil-get-terminal-size/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,6 +13,8 @@ class PyBackportsShutilGetTerminalSize(PythonPackage):
     homepage = "https://pypi.python.org/pypi/backports.shutil_get_terminal_size"
     url      = "https://pypi.io/packages/source/b/backports.shutil_get_terminal_size/backports.shutil_get_terminal_size-1.0.0.tar.gz"
 
+    py_namespace = 'backports'
+
     version('1.0.0', '03267762480bd86b50580dc19dff3c66')
 
     # newer setuptools version mess with "namespace" packages in an
diff --git a/var/spack/repos/builtin/packages/py-backports-ssl-match-hostname/package.py b/var/spack/repos/builtin/packages/py-backports-ssl-match-hostname/package.py
index 88edc5b571..a1e3871b54 100644
--- a/var/spack/repos/builtin/packages/py-backports-ssl-match-hostname/package.py
+++ b/var/spack/repos/builtin/packages/py-backports-ssl-match-hostname/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,4 +12,6 @@ class PyBackportsSslMatchHostname(PythonPackage):
     homepage = "https://pypi.python.org/pypi/backports.ssl_match_hostname"
     url      = "https://pypi.io/packages/source/b/backports.ssl_match_hostname/backports.ssl_match_hostname-3.5.0.1.tar.gz"
 
+    py_namespace = 'backports'
+
     version('3.5.0.1', 'c03fc5e2c7b3da46b81acf5cbacfe1e6')
diff --git a/var/spack/repos/builtin/packages/py-basemap/package.py b/var/spack/repos/builtin/packages/py-basemap/package.py
index 4e127f9626..1b531c1cf3 100644
--- a/var/spack/repos/builtin/packages/py-basemap/package.py
+++ b/var/spack/repos/builtin/packages/py-basemap/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,7 +18,7 @@ class PyBasemap(PythonPackage):
     # Per Github issue #3813, setuptools is required at runtime in order
     # to make mpl_toolkits a namespace package that can span multiple
     # directories (i.e., matplotlib and basemap)
-    depends_on('py-setuptools', type=('build', 'run'))
+    depends_on('py-setuptools', type=('run'))
     depends_on('py-numpy', type=('build', 'run'))
     depends_on('py-matplotlib', type=('build', 'run'))
     depends_on('pil', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-bcbio-gff/package.py b/var/spack/repos/builtin/packages/py-bcbio-gff/package.py
new file mode 100644
index 0000000000..4bdd1a27a5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-bcbio-gff/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyBcbioGff(PythonPackage):
+    """Read and write Generic Feature Format (GFF) with Biopython
+    integration."""
+
+    homepage = "https://pypi.python.org/pypi/bcbio-gff/0.6.2"
+    url      = "https://pypi.io/packages/source/b/bcbio-gff/bcbio-gff-0.6.2.tar.gz"
+
+    version('0.6.2', 'd5aae8b125cdad4291f15bec20cfb0ef')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-six',        type=('build', 'run'))
+    depends_on('py-biopython',  type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-beautifulsoup4/package.py b/var/spack/repos/builtin/packages/py-beautifulsoup4/package.py
index 4874f1cba5..8fd8ea3d0c 100644
--- a/var/spack/repos/builtin/packages/py-beautifulsoup4/package.py
+++ b/var/spack/repos/builtin/packages/py-beautifulsoup4/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-binwalk/package.py b/var/spack/repos/builtin/packages/py-binwalk/package.py
index 25f9eb5dd0..01bc360580 100644
--- a/var/spack/repos/builtin/packages/py-binwalk/package.py
+++ b/var/spack/repos/builtin/packages/py-binwalk/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/py-biom-format/package.py b/var/spack/repos/builtin/packages/py-biom-format/package.py
index 1323ddee3b..cc317aeb96 100644
--- a/var/spack/repos/builtin/packages/py-biom-format/package.py
+++ b/var/spack/repos/builtin/packages/py-biom-format/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,7 +18,7 @@ class PyBiomFormat(PythonPackage):
 
     variant('h5py', default=True, description='For use with BIOM 2.0+ files')
 
-    depends_on('py-setuptools', type='build')
+    depends_on('py-setuptools', type=('build', 'run'))
     depends_on('py-cython', type='build')
     depends_on('py-h5py', type=('build', 'run'), when='+h5py')
     depends_on('py-click', type=('build', 'run'))
@@ -46,3 +27,4 @@ class PyBiomFormat(PythonPackage):
     depends_on('py-scipy@0.13.0:', type=('build', 'run'))
     depends_on('py-pandas@0.19.2:', type=('build', 'run'))
     depends_on('py-six@1.10.0:', type=('build', 'run'))
+    depends_on('py-pyqi', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-biopython/package.py b/var/spack/repos/builtin/packages/py-biopython/package.py
index 4fcfeaf81d..a833fd8b66 100644
--- a/var/spack/repos/builtin/packages/py-biopython/package.py
+++ b/var/spack/repos/builtin/packages/py-biopython/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,7 +15,7 @@ class PyBiopython(PythonPackage):
     homepage = "http://biopython.org/wiki/Main_Page"
     url      = "http://biopython.org/DIST/biopython-1.65.tar.gz"
 
+    version('1.70', 'feff7a3e2777e43f9b13039b344e06ff')
     version('1.65', '143e7861ade85c0a8b5e2bbdd1da1f67')
 
-    depends_on('py-mx', type=('build', 'run'))
     depends_on('py-numpy', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-bitarray/package.py b/var/spack/repos/builtin/packages/py-bitarray/package.py
new file mode 100644
index 0000000000..3f653892a3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-bitarray/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyBitarray(PythonPackage):
+    """Efficient array of booleans - C extension"""
+
+    homepage = "https://pypi.python.org/pypi/bitarray"
+    url      = "https://pypi.io/packages/source/b/bitarray/bitarray-0.8.1.tar.gz"
+
+    version('0.8.1', '3825184f54f4d93508a28031b4c65d3b')
+
+    depends_on('python')
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-bitstring/package.py b/var/spack/repos/builtin/packages/py-bitstring/package.py
new file mode 100644
index 0000000000..ac8e8da41b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-bitstring/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyBitstring(PythonPackage):
+    """Simple construction, analysis and modification of binary data."""
+
+    homepage = "http://pythonhosted.org/bitstring"
+    url      = "https://pypi.io/packages/source/b/bitstring/bitstring-3.1.5.zip"
+
+    version('3.1.5', '70689a282f66625d0c7c3579a13e66db')
diff --git a/var/spack/repos/builtin/packages/py-bleach/package.py b/var/spack/repos/builtin/packages/py-bleach/package.py
index aa7866c3c3..728ac4ff9e 100644
--- a/var/spack/repos/builtin/packages/py-bleach/package.py
+++ b/var/spack/repos/builtin/packages/py-bleach/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-blessings/package.py b/var/spack/repos/builtin/packages/py-blessings/package.py
index 9f5b57c469..932426cf0b 100644
--- a/var/spack/repos/builtin/packages/py-blessings/package.py
+++ b/var/spack/repos/builtin/packages/py-blessings/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-bokeh/package.py b/var/spack/repos/builtin/packages/py-bokeh/package.py
index 00850c51aa..c06ad86625 100644
--- a/var/spack/repos/builtin/packages/py-bokeh/package.py
+++ b/var/spack/repos/builtin/packages/py-bokeh/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-boltons/package.py b/var/spack/repos/builtin/packages/py-boltons/package.py
index 54355ad7f1..be60d629a9 100644
--- a/var/spack/repos/builtin/packages/py-boltons/package.py
+++ b/var/spack/repos/builtin/packages/py-boltons/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-bottleneck/package.py b/var/spack/repos/builtin/packages/py-bottleneck/package.py
index 4fe32139b6..1a4ccddc3e 100644
--- a/var/spack/repos/builtin/packages/py-bottleneck/package.py
+++ b/var/spack/repos/builtin/packages/py-bottleneck/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,6 +11,7 @@ class PyBottleneck(PythonPackage):
     homepage = "https://pypi.python.org/pypi/Bottleneck/1.0.0"
     url      = "https://pypi.io/packages/source/B/Bottleneck/Bottleneck-1.0.0.tar.gz"
 
+    version('1.2.1', sha256='6efcde5f830aed64feafca0359b51db0e184c72af8ba6675b4a99f263922eb36')
     version('1.0.0', '380fa6f275bd24f27e7cf0e0d752f5d2')
 
     depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-breakseq2/package.py b/var/spack/repos/builtin/packages/py-breakseq2/package.py
new file mode 100644
index 0000000000..91d519e795
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-breakseq2/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyBreakseq2(PythonPackage):
+    """nucleotide-resolution analysis of structural variants"""
+
+    homepage = "http://bioinform.github.io/breakseq2/"
+    url      = "https://github.com/bioinform/breakseq2/archive/2.2.tar.gz"
+
+    version('2.2', '6fd5a103c2781717b0b1d0efcbdc17e7')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-biopython@1.65', type=('build', 'run'))
+    depends_on('py-cython', type='build')
+    depends_on('py-pysam@0.7.7', type=('build', 'run'))
+    depends_on('bwa', type='run')
+    depends_on('samtools', type='run')
diff --git a/var/spack/repos/builtin/packages/py-brian/package.py b/var/spack/repos/builtin/packages/py-brian/package.py
index 68ed005b4a..49b5d9ed1d 100644
--- a/var/spack/repos/builtin/packages/py-brian/package.py
+++ b/var/spack/repos/builtin/packages/py-brian/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-brian2/package.py b/var/spack/repos/builtin/packages/py-brian2/package.py
index bf28c5cda2..9e374e293a 100644
--- a/var/spack/repos/builtin/packages/py-brian2/package.py
+++ b/var/spack/repos/builtin/packages/py-brian2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,7 +15,7 @@ class PyBrian2(PythonPackage):
     version('2.0.1', 'df5990e9a71f7344887bc02f54dfd0f0')
     version('2.0rc3', '3100c5e4eb9eb83a06ff0413a7d43152')
 
-    variant('docs', default=False, description='Build the documentation')
+    variant('doc', default=False, description='Build the documentation')
 
     # depends on py-setuptools@6: for windows, if spack targets windows,
     # this will need to be added here
@@ -44,7 +25,5 @@ class PyBrian2(PythonPackage):
     depends_on('py-pyparsing',      type=('build', 'run'))
     depends_on('py-jinja2@2.7:',    type=('build', 'run'))
     depends_on('py-cpuinfo@0.1.6:', type=('build', 'run'))
-
-    # TODO: Add a 'test' deptype
-    # depends_on('py-nosetests@1.0:', type='test')
     depends_on('py-sphinx@1.4.2:',  type=('build', 'run'), when='+docs')
+    depends_on('py-nosetests@1.0:', type='test')
\ No newline at end of file
diff --git a/var/spack/repos/builtin/packages/py-bsddb3/package.py b/var/spack/repos/builtin/packages/py-bsddb3/package.py
index 91b8d72665..81d9d2e203 100644
--- a/var/spack/repos/builtin/packages/py-bsddb3/package.py
+++ b/var/spack/repos/builtin/packages/py-bsddb3/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,10 +12,14 @@ class PyBsddb3(PythonPackage):
        Sequence and Transaction objects, and each of these is exposed
        as a Python type in the bsddb3.db module."""
 
-    homepage = "://pypi.python.org/pypi/bsddb3/6.2.5"
-    url      = "https://pypi.python.org/packages/ba/a7/131dfd4e3a5002ef30e20bee679d5e6bcb2fcc6af21bd5079dc1707a132c/bsddb3-6.2.5.tar.gz#md5=610267c189964c905a931990e1ba438c"
+    homepage = "https://pypi.python.org/pypi/bsddb3/6.2.5"
+    url      = "https://pypi.io/packages/source/b/bsddb3/bsddb3-6.2.5.tar.gz"
 
     version('6.2.5', '610267c189964c905a931990e1ba438c')
 
     depends_on('python@2.6:')
-    depends_on('py-setuptools')
+    depends_on('py-setuptools', type='build')
+    depends_on('berkeley-db')
+
+    # For testing... see here for an example that uses BerkeleyDB
+    # http://code.activestate.com/recipes/189060-using-berkeley-db-database/
diff --git a/var/spack/repos/builtin/packages/py-bx-python/package.py b/var/spack/repos/builtin/packages/py-bx-python/package.py
new file mode 100644
index 0000000000..b562ad0308
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-bx-python/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyBxPython(PythonPackage):
+    """The bx-python project is a python library and associated set of scripts
+    to allow for rapid implementation of genome scale analyses."""
+
+    homepage = "https://github.com/bxlab/bx-python"
+    url      = "https://github.com/bxlab/bx-python/archive/v0.7.4.tar.gz"
+
+    version('0.7.4', 'a47b8cc55c104ac97440c6cc62be8697')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-numpy',      type=('build', 'run'))
+    depends_on('py-six',        type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-cartopy/package.py b/var/spack/repos/builtin/packages/py-cartopy/package.py
new file mode 100644
index 0000000000..f347652f26
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-cartopy/package.py
@@ -0,0 +1,44 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyCartopy(PythonPackage):
+    """Cartopy - a cartographic python library with matplotlib support."""
+
+    homepage = "http://scitools.org.uk/cartopy/"
+    url      = "https://github.com/SciTools/cartopy/archive/v0.16.0.tar.gz"
+
+    version('0.16.0', 'f9e2e528d7758da7c64f824548a53f32')
+
+    depends_on('py-setuptools@0.7.2:', type='build')
+    depends_on('py-cython@0.15.1:',    type='build')
+    depends_on('py-numpy@1.10.0:',  type=('build', 'run'))
+    depends_on('py-shapely@1.5.6:', type=('build', 'run'))
+    depends_on('py-pyshp@1.1.4:',   type=('build', 'run'))
+    depends_on('py-six@1.3.0:',     type=('build', 'run'))
+    depends_on('geos@3.3.3:')
+    depends_on('proj@4.9.0:')
+
+    # optional dependecies
+    depends_on('py-matplotlib@1.5.1:', type=('build', 'run'))
+    depends_on('gdal@1.10.0:+python',  type=('build', 'run'))
+    depends_on('py-pillow@1.7.8:',     type=('build', 'run'))
+    depends_on('py-pyepsg@0.2.0:',     type=('build', 'run'))
+    depends_on('py-scipy@0.10:',       type=('build', 'run'))
+    depends_on('py-owslib@0.8.11:',    type=('build', 'run'))
+
+    # testing dependencies
+    depends_on('py-mock@1.0.1',    type='test')
+    depends_on('py-pytest@3.0.0:', type='test')
+
+    phases = ['build_ext', 'install']
+
+    def build_ext_args(self, spec, prefix):
+        args = ['-I{0}'.format(spec['proj'].prefix.include),
+                '-L{0}'.format(spec['proj'].prefix.lib)
+                ]
+        return args
diff --git a/var/spack/repos/builtin/packages/py-cclib/package.py b/var/spack/repos/builtin/packages/py-cclib/package.py
index 7d47dcf3fb..32d55b0269 100644
--- a/var/spack/repos/builtin/packages/py-cclib/package.py
+++ b/var/spack/repos/builtin/packages/py-cclib/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-cdat-lite/package.py b/var/spack/repos/builtin/packages/py-cdat-lite/package.py
index a7bf68d50f..33ce8dce3e 100644
--- a/var/spack/repos/builtin/packages/py-cdat-lite/package.py
+++ b/var/spack/repos/builtin/packages/py-cdat-lite/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/py-cdo/package.py b/var/spack/repos/builtin/packages/py-cdo/package.py
index c5b6d39982..f2628d5e7f 100644
--- a/var/spack/repos/builtin/packages/py-cdo/package.py
+++ b/var/spack/repos/builtin/packages/py-cdo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-certifi/package.py b/var/spack/repos/builtin/packages/py-certifi/package.py
index 8a5df53a27..c13112d182 100644
--- a/var/spack/repos/builtin/packages/py-certifi/package.py
+++ b/var/spack/repos/builtin/packages/py-certifi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-cffi/package.py b/var/spack/repos/builtin/packages/py-cffi/package.py
index d75c9a4f38..2b32e8d60f 100644
--- a/var/spack/repos/builtin/packages/py-cffi/package.py
+++ b/var/spack/repos/builtin/packages/py-cffi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import sys
 
@@ -33,6 +14,7 @@ class PyCffi(PythonPackage):
 
     import_modules = ['cffi']
 
+    version('1.11.5', 'ac8492f4ad952360737413e82d661908')
     version('1.10.0', '2b5fa41182ed0edaf929a789e602a070')
     version('1.1.2',  'ca6e6c45b45caa87aee9adc7c796eaea')
 
diff --git a/var/spack/repos/builtin/packages/py-chardet/package.py b/var/spack/repos/builtin/packages/py-chardet/package.py
index c62bd1bef3..ab4b79982d 100644
--- a/var/spack/repos/builtin/packages/py-chardet/package.py
+++ b/var/spack/repos/builtin/packages/py-chardet/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-checkm-genome/package.py b/var/spack/repos/builtin/packages/py-checkm-genome/package.py
new file mode 100644
index 0000000000..fa4fe7c3f0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-checkm-genome/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyCheckmGenome(PythonPackage):
+    """Assess the quality of microbial genomes recovered from isolates, single
+    cells, and metagenomes"""
+
+    homepage = "https://ecogenomics.github.io/CheckM"
+    url      = "https://pypi.io/packages/source/c/checkm-genome/checkm-genome-1.0.11.tar.gz"
+
+    version('1.0.11', '3058546ec324e2420cf72f0d2576114b')
+
+    depends_on('hmmer@3.1b1:')
+    depends_on('prodigal@2.6.1:')
+    depends_on('py-numpy@1.8.0:',        type=('build', 'run'))
+    depends_on('py-scipy@0.9.0:',        type=('build', 'run'))
+    depends_on('py-matplotlib@1.3.1:',   type=('build', 'run'))
+    depends_on('py-pysam@0.8.3:',        type=('build', 'run'))
+    depends_on('py-dendropy@4.0.0:',     type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-cheetah/package.py b/var/spack/repos/builtin/packages/py-cheetah/package.py
new file mode 100644
index 0000000000..da75917d12
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-cheetah/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyCheetah(PythonPackage):
+    """Cheetah is a template engine and code generation tool."""
+
+    homepage = "https://pypi.python.org/pypi/Cheetah/2.4.4"
+    url      = "https://pypi.io/packages/source/C/Cheetah/Cheetah-2.3.0.tar.gz"
+
+    version('2.3.0', 'e28ffef7f5c1660d66196639f162d9ce')
diff --git a/var/spack/repos/builtin/packages/py-click/package.py b/var/spack/repos/builtin/packages/py-click/package.py
index dd2b1b3e5e..5bebd2d2ae 100644
--- a/var/spack/repos/builtin/packages/py-click/package.py
+++ b/var/spack/repos/builtin/packages/py-click/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-cligj/package.py b/var/spack/repos/builtin/packages/py-cligj/package.py
new file mode 100644
index 0000000000..fed854065c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-cligj/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyCligj(PythonPackage):
+    """Click-based argument and option decorators for Python GIS command
+    line programs"""
+
+    homepage = "https://github.com/mapbox/cligj"
+    url      = "https://github.com/mapbox/cligj/archive/0.4.0.zip"
+
+    version('0.4.0', 'fe5376068b84c5ed01e2d3adf553e226')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-click', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-cloudpickle/package.py b/var/spack/repos/builtin/packages/py-cloudpickle/package.py
new file mode 100644
index 0000000000..de87e1c8bf
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-cloudpickle/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyCloudpickle(PythonPackage):
+    """Extended pickling support for Python objects."""
+
+    homepage = "https://github.com/cloudpipe/cloudpickle"
+    url      = "https://pypi.io/packages/source/c/cloudpickle/cloudpickle-0.5.2.tar.gz"
+
+    import_modules = ['cloudpickle']
+
+    version('0.5.2', 'd0f6fc27882f865f2eb185fb0a32c84b')
+
+    depends_on('py-setuptools', type='build')
+
+    def test(self):
+        # PyPI tarball does not come with unit tests
+        pass
diff --git a/var/spack/repos/builtin/packages/py-cogent/package.py b/var/spack/repos/builtin/packages/py-cogent/package.py
new file mode 100644
index 0000000000..00111650a3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-cogent/package.py
@@ -0,0 +1,34 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyCogent(PythonPackage):
+    """A toolkit for statistical analysis of biological sequences."""
+
+    homepage = "http://pycogent.org"
+    url      = "https://pypi.io/packages/source/c/cogent/cogent-1.9.tar.gz"
+
+    version('1.9', sha256='57d8c58e0273ffe4f2b907874f9b49dadfd0600f5507b7666369f4e44d56ce14')
+    version('1.5.3', url="https://pypi.io/packages/source/c/cogent/cogent-1.5.3.tgz", 
+        sha256='1215ac219070b7b2207b0b47b4388510f3e30ccd88160aa9f02f25d24bcbcd95')
+
+    variant('matplotlib', default=False, description="graphs related to codon usage")
+    variant('mpi', default=False, description='MPI required for parallel computation.')
+    variant('mysql', default=False, description='Required for the Ensembl querying code.')
+
+    depends_on('py-setuptools', type=('build'), when='@1.9')
+    depends_on('python@2.6:2.999', type=('build', 'run'))
+    depends_on('py-numpy@1.3:', type=('build', 'run'))
+    depends_on('zlib')
+    depends_on('py-matplotlib', when='+matplotlib', type=('build', 'run'))
+    depends_on('py-mpi4py', when='+mpi', type=('build', 'run'))
+    depends_on('py-sqlalchemy', when='+mysql', type=('build', 'run'))
+    depends_on('py-pymysql', when='+mysql', type=('build', 'run'))
+    depends_on('py-cython@0.17.1:', type='build')
+
+    def setup_environment(self, spack_env, run_env):
+        spack_env.set('DONT_USE_PYREX', '1')
diff --git a/var/spack/repos/builtin/packages/py-colorama/package.py b/var/spack/repos/builtin/packages/py-colorama/package.py
index d9e2678e6e..154ff3f449 100644
--- a/var/spack/repos/builtin/packages/py-colorama/package.py
+++ b/var/spack/repos/builtin/packages/py-colorama/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-colormath/package.py b/var/spack/repos/builtin/packages/py-colormath/package.py
index 374dcd3c8e..234b60abbd 100644
--- a/var/spack/repos/builtin/packages/py-colormath/package.py
+++ b/var/spack/repos/builtin/packages/py-colormath/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,8 +12,10 @@ class PyColormath(PythonPackage):
     homepage = "https://pypi.python.org/pypi/colormath/2.1.1"
     url      = "https://pypi.io/packages/source/c/colormath/colormath-2.1.1.tar.gz"
 
+    version('3.0.0', '3d4605af344527da0e4f9f504fad7ddbebda35322c566a6c72e28edb1ff31217')
     version('2.1.1', '10a0fb17e3c24363d0e1a3f2dccaa33b')
 
     depends_on('py-setuptools', type='build')
     depends_on('py-numpy', type=('build', 'run'))
     depends_on('py-networkx', type=('build', 'run'))
+    depends_on('py-networkx@2.0:', type=('build', 'run'), when='@3.0.0:')
diff --git a/var/spack/repos/builtin/packages/py-configparser/package.py b/var/spack/repos/builtin/packages/py-configparser/package.py
index 2d463b3ef3..6652dc449e 100644
--- a/var/spack/repos/builtin/packages/py-configparser/package.py
+++ b/var/spack/repos/builtin/packages/py-configparser/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-counter/package.py b/var/spack/repos/builtin/packages/py-counter/package.py
index 37f1d62203..8bea3d5f9d 100644
--- a/var/spack/repos/builtin/packages/py-counter/package.py
+++ b/var/spack/repos/builtin/packages/py-counter/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-coverage/package.py b/var/spack/repos/builtin/packages/py-coverage/package.py
index 6912c7e898..fe95770ccf 100644
--- a/var/spack/repos/builtin/packages/py-coverage/package.py
+++ b/var/spack/repos/builtin/packages/py-coverage/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-cpuinfo/package.py b/var/spack/repos/builtin/packages/py-cpuinfo/package.py
index ae75451311..8cc74a09b9 100644
--- a/var/spack/repos/builtin/packages/py-cpuinfo/package.py
+++ b/var/spack/repos/builtin/packages/py-cpuinfo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-crispresso/package.py b/var/spack/repos/builtin/packages/py-crispresso/package.py
new file mode 100644
index 0000000000..c2b0ec85ae
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-crispresso/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyCrispresso(PythonPackage):
+    """Software pipeline for the analysis of CRISPR-Cas9 genome editing
+    outcomes from deep sequencing data."""
+
+    homepage = "https://github.com/lucapinello/CRISPResso"
+    url      = "https://pypi.io/packages/source/C/CRISPResso/CRISPResso-1.0.8.tar.gz"
+
+    version('1.0.8', '2f9b52fe62cf49012a9525845f4aea45')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('python@2.7.0:2.7.999', type=('build', 'run'))
+    depends_on('py-biopython@1.6.5:', type=('build', 'run'))
+    depends_on('py-matplotlib@1.3.1:', type=('build', 'run'))
+    depends_on('py-numpy@1.9:', type=('build', 'run'))
+    depends_on('py-pandas@0.15:', type=('build', 'run'))
+    depends_on('py-seaborn@0.7.1:', type=('build', 'run'))
+    depends_on('emboss@6:', type=('build', 'run'))
+    depends_on('flash', type=('build', 'run'))
+    depends_on('java', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-cryptography/package.py b/var/spack/repos/builtin/packages/py-cryptography/package.py
index 9ecf7015fc..d03bf4fb43 100644
--- a/var/spack/repos/builtin/packages/py-cryptography/package.py
+++ b/var/spack/repos/builtin/packages/py-cryptography/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/py-csvkit/package.py b/var/spack/repos/builtin/packages/py-csvkit/package.py
index 05682652c0..93248613b1 100644
--- a/var/spack/repos/builtin/packages/py-csvkit/package.py
+++ b/var/spack/repos/builtin/packages/py-csvkit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-current/package.py b/var/spack/repos/builtin/packages/py-current/package.py
index f4cd082492..08093894e0 100644
--- a/var/spack/repos/builtin/packages/py-current/package.py
+++ b/var/spack/repos/builtin/packages/py-current/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-cutadapt/package.py b/var/spack/repos/builtin/packages/py-cutadapt/package.py
index 5f029375e7..84bca9c3ad 100644
--- a/var/spack/repos/builtin/packages/py-cutadapt/package.py
+++ b/var/spack/repos/builtin/packages/py-cutadapt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class PyCutadapt(PythonPackage):
     version('1.13', '2d2d14e0c20ad53d7d84b57bc3e63b4c')
 
     depends_on('python@2.6:', type=('build', 'run'))
-    depends_on('py-setuptools',        type=('build'))
+    depends_on('py-setuptools', type=('build', 'run'))
     depends_on('py-xopen@0.1.1:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-cvxopt/package.py b/var/spack/repos/builtin/packages/py-cvxopt/package.py
new file mode 100644
index 0000000000..7da5f6bed6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-cvxopt/package.py
@@ -0,0 +1,124 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyCvxopt(PythonPackage):
+    """CVXOPT is a free software package for convex optimization based on the
+    Python programming language."""
+
+    homepage = "http://cvxopt.org/"
+    url      = "https://pypi.io/packages/source/c/cvxopt/cvxopt-1.1.9.tar.gz"
+
+    import_modules = ['cvxopt']
+
+    version('1.1.9', 'a56e7b23d76c2b5aaf3bea2a7c245ea7')
+
+    variant('gsl',   default=False, description='Use GSL random number generators for constructing random matrices')
+    variant('fftw',  default=False, description='Install the cvxopt.fftw interface to FFTW')
+    variant('glpk',  default=False, description='Enable support for the linear programming solver GLPK')
+    # variant('mosek', default=False, description='Enable support for the linear, second-order cone, and quadratic programming solvers in MOSEK')  # noqa: flake8
+    variant('dsdp',  default=False, description='Enable support for the semidefinite programming solver DSDP')
+
+    # Required dependencies
+    depends_on('python@2.7:')
+    depends_on('py-setuptools', type='build')
+    depends_on('blas')
+    depends_on('lapack')
+    depends_on('suite-sparse')
+
+    # Optional dependencies
+    depends_on('gsl',       when='+gsl')
+    depends_on('fftw',      when='+fftw')
+    depends_on('glpk',      when='+glpk')
+    # depends_on('mosek@8:',  when='+mosek')
+    depends_on('dsdp@5.8:', when='+dsdp')
+
+    def setup_environment(self, spack_env, run_env):
+        spec = self.spec
+
+        # BLAS/LAPACK Libraries
+
+        # Default names of BLAS and LAPACK libraries
+        spack_env.set('CVXOPT_BLAS_LIB', ';'.join(spec['blas'].libs.names))
+        spack_env.set('CVXOPT_LAPACK_LIB', ';'.join(spec['lapack'].libs.names))
+
+        # Directory containing BLAS and LAPACK libraries
+        spack_env.set('CVXOPT_BLAS_LIB_DIR', spec['blas'].libs.directories[0])
+
+        # SuiteSparse Libraries
+
+        # Directory containing SuiteSparse libraries
+        spack_env.set('CVXOPT_SUITESPARSE_LIB_DIR',
+                      spec['suite-sparse'].libs.directories[0])
+
+        # Directory containing SuiteSparse header files
+        spack_env.set('CVXOPT_SUITESPARSE_INC_DIR',
+                      spec['suite-sparse'].headers.directories[0])
+
+        # GSL Libraries
+
+        if '+gsl' in spec:
+            spack_env.set('CVXOPT_BUILD_GSL', 1)
+
+            # Directory containing libgsl
+            spack_env.set('CVXOPT_GSL_LIB_DIR',
+                          spec['gsl'].libs.directories[0])
+
+            # Directory containing the GSL header files
+            spack_env.set('CVXOPT_GSL_INC_DIR',
+                          spec['gsl'].headers.directories[0])
+        else:
+            spack_env.set('CVXOPT_BUILD_GSL', 0)
+
+        # FFTW Libraries
+
+        if '+fftw' in spec:
+            spack_env.set('CVXOPT_BUILD_FFTW', 1)
+
+            # Directory containing libfftw3
+            spack_env.set('CVXOPT_FFTW_LIB_DIR',
+                          spec['fftw'].libs.directories[0])
+
+            # Directory containing fftw.h
+            spack_env.set('CVXOPT_FFTW_INC_DIR',
+                          spec['fftw'].headers.directories[0])
+        else:
+            spack_env.set('CVXOPT_BUILD_FFTW', 0)
+
+        # GLPK Libraries
+
+        if '+glpk' in spec:
+            spack_env.set('CVXOPT_BUILD_GLPK', 1)
+
+            # Directory containing libglpk
+            spack_env.set('CVXOPT_GLPK_LIB_DIR',
+                          spec['glpk'].libs.directories[0])
+
+            # Directory containing glpk.h
+            spack_env.set('CVXOPT_GLPK_INC_DIR',
+                          spec['glpk'].headers.directories[0])
+        else:
+            spack_env.set('CVXOPT_BUILD_GLPK', 0)
+
+        # DSDP Libraries
+
+        if '+dsdp' in spec:
+            spack_env.set('CVXOPT_BUILD_DSDP', 1)
+
+            # Directory containing libdsdp
+            spack_env.set('CVXOPT_DSDP_LIB_DIR',
+                          spec['dsdp'].libs.directories[0])
+
+            # Directory containing dsdp5.h
+            spack_env.set('CVXOPT_DSDP_INC_DIR',
+                          spec['dsdp'].headers.directories[0])
+
+    @run_after('install')
+    @on_package_attributes(run_tests=True)
+    def install_test(self):
+        """Test that the installation was successful."""
+        python('-m', 'unittest', 'discover', '-s', 'tests')
diff --git a/var/spack/repos/builtin/packages/py-cycler/package.py b/var/spack/repos/builtin/packages/py-cycler/package.py
index de0be6903f..2e2c52811e 100644
--- a/var/spack/repos/builtin/packages/py-cycler/package.py
+++ b/var/spack/repos/builtin/packages/py-cycler/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-cython/package.py b/var/spack/repos/builtin/packages/py-cython/package.py
index 33b980d87b..610a6aa3b7 100644
--- a/var/spack/repos/builtin/packages/py-cython/package.py
+++ b/var/spack/repos/builtin/packages/py-cython/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,11 +11,17 @@ class PyCython(PythonPackage):
     homepage = "https://pypi.python.org/pypi/cython"
     url      = "https://pypi.io/packages/source/c/cython/Cython-0.25.2.tar.gz"
 
+    version('0.28.3', '586f0eb70ba1fcc34334e9e10c5e68c0')
+    version('0.28.1', 'c549effadb52d90bdcb1affc1e5dbb97')
     version('0.25.2', '642c81285e1bb833b14ab3f439964086')
-
     version('0.23.5', '66b62989a67c55af016c916da36e7514')
     version('0.23.4', '157df1f69bcec6b56fd97e0f2e057f6e')
 
     # These versions contain illegal Python3 code...
     version('0.22', '1ae25add4ef7b63ee9b4af697300d6b6')
     version('0.21.2', 'd21adb870c75680dc857cd05d41046a4')
+
+    @property
+    def command(self):
+        """Returns the Cython command"""
+        return Executable(self.prefix.bin.cython)
diff --git a/var/spack/repos/builtin/packages/py-dask/package.py b/var/spack/repos/builtin/packages/py-dask/package.py
index 7534e7ae7e..72f4667b61 100644
--- a/var/spack/repos/builtin/packages/py-dask/package.py
+++ b/var/spack/repos/builtin/packages/py-dask/package.py
@@ -1,35 +1,63 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class PyDask(PythonPackage):
-    """Minimal task scheduling abstraction"""
+    """Dask is a flexible parallel computing library for analytics."""
+
     homepage = "https://github.com/dask/dask/"
-    url      = "https://pypi.io/packages/source/d/dask/dask-0.8.1.tar.gz"
+    url      = "https://pypi.io/packages/source/d/dask/dask-0.17.4.tar.gz"
+
+    version('0.17.4', '4a7b9c5d7ddf52639b1c6b9e8a68d146')
+    version('0.8.1',  '5dd8e3a3823b3bc62c9a6d192e2cb5b4')
+
+    variant('array',       default=True, description='Install requirements for dask.array')
+    variant('bag',         default=True, description='Install requirements for dask.bag')
+    variant('dataframe',   default=True, description='Install requirements for dask.dataframe')
+    variant('delayed',     default=True, description='Install requirements for dask.delayed')
+
+    depends_on('py-setuptools',         type='build')
+    depends_on('py-pytest@3.1.0:',      type='test')
+    depends_on('py-requests',           type='test')
+
+    # Requirements for dask.array
+    depends_on('py-numpy@1.11.0:',      type=('build', 'run'), when='+array')
+    depends_on('py-toolz@0.7.3:',       type=('build', 'run'), when='+array')
+
+    # Requirements for dask.bag
+    depends_on('py-cloudpickle@0.2.1:', type=('build', 'run'), when='+bag')
+    depends_on('py-toolz@0.7.3:',       type=('build', 'run'), when='+bag')
+    depends_on('py-partd@0.3.8:',       type=('build', 'run'), when='+bag')
+
+    # Requirements for dask.dataframe
+    depends_on('py-numpy@1.11.0:',      type=('build', 'run'), when='+dataframe')
+    depends_on('py-pandas@0.19.0:',     type=('build', 'run'), when='+dataframe')
+    depends_on('py-toolz@0.7.3:',       type=('build', 'run'), when='+dataframe')
+    depends_on('py-partd@0.3.8:',       type=('build', 'run'), when='+dataframe')
+    depends_on('py-cloudpickle@0.2.1:', type=('build', 'run'), when='+dataframe')
+
+    # Requirements for dask.delayed
+    depends_on('py-toolz@0.7.3:',       type=('build', 'run'), when='+delayed')
+
+    @property
+    def import_modules(self):
+        modules = [
+            'dask', 'dask.bytes', 'dask.diagnostics', 'dask.store'
+        ]
+
+        if '+array' in self.spec:
+            modules.append('dask.array')
+
+        if '+bag' in self.spec:
+            modules.append('dask.bag')
 
-    version('0.8.1', '5dd8e3a3823b3bc62c9a6d192e2cb5b4')
+        if '+dataframe' in self.spec:
+            modules.extend([
+                'dask.dataframe', 'dask.dataframe.io', 'dask.dataframe.tseries'
+            ])
 
-    depends_on('py-setuptools', type='build')
+        return modules
diff --git a/var/spack/repos/builtin/packages/py-dateutil/package.py b/var/spack/repos/builtin/packages/py-dateutil/package.py
index f2b8b29429..34922f3c40 100644
--- a/var/spack/repos/builtin/packages/py-dateutil/package.py
+++ b/var/spack/repos/builtin/packages/py-dateutil/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-dbf/package.py b/var/spack/repos/builtin/packages/py-dbf/package.py
index 2dfc9cd3ec..071472321d 100644
--- a/var/spack/repos/builtin/packages/py-dbf/package.py
+++ b/var/spack/repos/builtin/packages/py-dbf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-decorator/package.py b/var/spack/repos/builtin/packages/py-decorator/package.py
index b33bcbc6ee..0ebe02a893 100644
--- a/var/spack/repos/builtin/packages/py-decorator/package.py
+++ b/var/spack/repos/builtin/packages/py-decorator/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,6 +13,7 @@ class PyDecorator(PythonPackage):
     homepage = "https://github.com/micheles/decorator"
     url      = "https://pypi.io/packages/source/d/decorator/decorator-4.0.9.tar.gz"
 
+    version('4.3.0', sha256='c39efa13fbdeb4506c476c9b3babf6a718da943dab7811c206005a4a956c080c')
     version('4.0.9', 'f12c5651ccd707e12a0abaa4f76cd69a')
 
     depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-deeptools/package.py b/var/spack/repos/builtin/packages/py-deeptools/package.py
index 68f77628ea..270da83b93 100644
--- a/var/spack/repos/builtin/packages/py-deeptools/package.py
+++ b/var/spack/repos/builtin/packages/py-deeptools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-dendropy/package.py b/var/spack/repos/builtin/packages/py-dendropy/package.py
new file mode 100644
index 0000000000..4434d1eb40
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-dendropy/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyDendropy(PythonPackage):
+    """DendroPy is a Python library for phylogenetic computing. It provides
+    classes and functions for the simulation, processing, and manipulation of
+    phylogenetic trees and character matrices, and supports the reading and
+    writing of phylogenetic data in a range of formats, such as NEXUS, NEWICK,
+    NeXML, Phylip, FASTA, etc."""
+
+    homepage = "https://www.dendropy.org"
+    url      = "https://pypi.io/packages/source/d/dendropy/DendroPy-4.3.0.tar.gz"
+
+    version('4.3.0',  '56c37eb7db69686c8ef3467562f4e7c5')
+    version('3.12.0', '6971ac9a8508b4198fd357fab0affc84')
+
+    depends_on('python@2.7:,3.4:')
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-dev/__init__.py.patch b/var/spack/repos/builtin/packages/py-dev/__init__.py.patch
deleted file mode 100644
index 1c783b82c8..0000000000
--- a/var/spack/repos/builtin/packages/py-dev/__init__.py.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- a/dev/__init__.py	2017-03-24 13:46:56.211385166 +0000
-+++ b/dev/__init__.py	2017-03-24 13:47:01.535332256 +0000
-@@ -1,6 +1,6 @@
- """
- 
--🚧 About
-+About
- --------
- 
- dev is a collection of Python developer tools presented as a
diff --git a/var/spack/repos/builtin/packages/py-dev/package.py b/var/spack/repos/builtin/packages/py-dev/package.py
deleted file mode 100644
index 49b0e9b2c3..0000000000
--- a/var/spack/repos/builtin/packages/py-dev/package.py
+++ /dev/null
@@ -1,38 +0,0 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-from spack import *
-
-
-class PyDev(PythonPackage):
-    """libraries and tools for Python development"""
-
-    homepage = "https://pypi.python.org/pypi/dev"
-    url      = "https://pypi.io/packages/source/d/dev/dev-0.4.0.tar.gz"
-
-    version('0.4.0', '00449cf0b347c32da9c840adcb4cf24b')
-
-    patch('__init__.py.patch')
-
-    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-dill/package.py b/var/spack/repos/builtin/packages/py-dill/package.py
index f5be93cdd7..c2980db0f4 100644
--- a/var/spack/repos/builtin/packages/py-dill/package.py
+++ b/var/spack/repos/builtin/packages/py-dill/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-discover/package.py b/var/spack/repos/builtin/packages/py-discover/package.py
new file mode 100644
index 0000000000..ee9231c23d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-discover/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyDiscover(PythonPackage):
+    """Test discovery for unittest."""
+
+    homepage = "https://pypi.python.org/pypi/discover"
+    url      = "https://pypi.io/packages/source/d/discover/discover-0.4.0.tar.gz"
+
+    version('0.4.0', '30bb643af4f5ea47fff572b5c346207d')
diff --git a/var/spack/repos/builtin/packages/py-dlcpar/package.py b/var/spack/repos/builtin/packages/py-dlcpar/package.py
index 22e1ccd5a6..d71c0e7bc8 100644
--- a/var/spack/repos/builtin/packages/py-dlcpar/package.py
+++ b/var/spack/repos/builtin/packages/py-dlcpar/package.py
@@ -1,32 +1,14 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class PyDlcpar(PythonPackage):
-    """FIXME: Put a proper description of your package here."""
+    """DLCpar is a reconciliation method for inferring gene duplications,
+    losses, and coalescence (accounting for incomplete lineage sorting)."""
 
     homepage = "https://www.cs.hmc.edu/~yjw/software/dlcpar/"
     url      = "https://www.cs.hmc.edu/~yjw/software/dlcpar/pub/sw/dlcpar-1.0.tar.gz"
diff --git a/var/spack/repos/builtin/packages/py-docopt/package.py b/var/spack/repos/builtin/packages/py-docopt/package.py
new file mode 100644
index 0000000000..25b4c85653
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-docopt/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyDocopt(PythonPackage):
+    """Command-line interface description language."""
+
+    homepage = "http://docopt.org/"
+    url      = "https://pypi.io/packages/source/d/docopt/docopt-0.6.2.tar.gz"
+
+    import_modules = ['docopt']
+
+    version('0.6.2', '4bc74561b37fad5d3e7d037f82a4c3b1')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-docutils/package.py b/var/spack/repos/builtin/packages/py-docutils/package.py
index 25881c9e77..732440a2a6 100644
--- a/var/spack/repos/builtin/packages/py-docutils/package.py
+++ b/var/spack/repos/builtin/packages/py-docutils/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-doxypy/package.py b/var/spack/repos/builtin/packages/py-doxypy/package.py
index eb81b080c0..d1530b40fa 100644
--- a/var/spack/repos/builtin/packages/py-doxypy/package.py
+++ b/var/spack/repos/builtin/packages/py-doxypy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,3 +13,5 @@ class PyDoxypy(PythonPackage):
     url      = "https://pypi.io/packages/source/d/doxypy/doxypy-0.3.tar.gz"
 
     version('0.3', '3b52289e0962d31b92af8be0eef8cbb2')
+
+    depends_on('python@:2.8')
diff --git a/var/spack/repos/builtin/packages/py-doxypypy/package.py b/var/spack/repos/builtin/packages/py-doxypypy/package.py
index 243909dffc..55f4e846f9 100644
--- a/var/spack/repos/builtin/packages/py-doxypypy/package.py
+++ b/var/spack/repos/builtin/packages/py-doxypypy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-dryscrape/package.py b/var/spack/repos/builtin/packages/py-dryscrape/package.py
index 675b8f87e5..2036804d88 100644
--- a/var/spack/repos/builtin/packages/py-dryscrape/package.py
+++ b/var/spack/repos/builtin/packages/py-dryscrape/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,9 +12,9 @@ class PyDryscrape(PythonPackage):
 
     homepage = "https://github.com/niklasb/dryscrape"
     url      = "https://pypi.io/packages/source/d/dryscrape/dryscrape-1.0.tar.gz"
+    git      = "https://github.com/niklasb/dryscrape.git"
 
-    version('develop', git="https://github.com/niklasb/dryscrape",
-            branch="master")
+    version('develop', branch='master')
     version('1.0', '267e380a8efaf9cd8fd94de1639d3198')
 
     depends_on('py-lxml', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-dxchange/package.py b/var/spack/repos/builtin/packages/py-dxchange/package.py
index 6c04f119ae..d70bbd3ec3 100644
--- a/var/spack/repos/builtin/packages/py-dxchange/package.py
+++ b/var/spack/repos/builtin/packages/py-dxchange/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/py-dxfile/package.py b/var/spack/repos/builtin/packages/py-dxfile/package.py
index f131b51f85..f5ca0d5764 100644
--- a/var/spack/repos/builtin/packages/py-dxfile/package.py
+++ b/var/spack/repos/builtin/packages/py-dxfile/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-easybuild-easyblocks/package.py b/var/spack/repos/builtin/packages/py-easybuild-easyblocks/package.py
index 1a116c5a15..7e8d92ae4c 100644
--- a/var/spack/repos/builtin/packages/py-easybuild-easyblocks/package.py
+++ b/var/spack/repos/builtin/packages/py-easybuild-easyblocks/package.py
@@ -1,25 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Kenneth Hoste
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Kenneth Hoste, kenneth.hoste@gmail.com
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-easybuild-easyconfigs/package.py b/var/spack/repos/builtin/packages/py-easybuild-easyconfigs/package.py
index 2acb09213b..6ab9fa9409 100644
--- a/var/spack/repos/builtin/packages/py-easybuild-easyconfigs/package.py
+++ b/var/spack/repos/builtin/packages/py-easybuild-easyconfigs/package.py
@@ -1,25 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Kenneth Hoste
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Kenneth Hoste, kenneth.hoste@gmail.com
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-easybuild-framework/package.py b/var/spack/repos/builtin/packages/py-easybuild-framework/package.py
index 61e4ee1c70..04dbe5e068 100644
--- a/var/spack/repos/builtin/packages/py-easybuild-framework/package.py
+++ b/var/spack/repos/builtin/packages/py-easybuild-framework/package.py
@@ -1,25 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Kenneth Hoste
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Kenneth Hoste, kenneth.hoste@gmail.com
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-edffile/package.py b/var/spack/repos/builtin/packages/py-edffile/package.py
index 460840e708..69e2927e6b 100644
--- a/var/spack/repos/builtin/packages/py-edffile/package.py
+++ b/var/spack/repos/builtin/packages/py-edffile/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,12 +10,11 @@ class PyEdffile(PythonPackage):
     """Generic class for Edf files manipulation."""
 
     homepage = "https://github.com/vasole/pymca/blob/master/PyMca5/PyMcaIO/EdfFile.py"
-    url      = "https://github.com/conda-forge/edffile-feedstock.git"
+    git      = "https://github.com/conda-forge/edffile-feedstock.git"
 
     import_modules = ['EdfFile']
 
-    version('5.0.0', git='https://github.com/conda-forge/edffile-feedstock.git',
-            commit='be5ab4199db9f8209c59e31874934b8536b52301')
+    version('5.0.0', commit='be5ab4199db9f8209c59e31874934b8536b52301')
 
     depends_on('py-setuptools', type='build')
     depends_on('py-numpy', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-editdistance/package.py b/var/spack/repos/builtin/packages/py-editdistance/package.py
new file mode 100644
index 0000000000..c3f79c1782
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-editdistance/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyEditdistance(PythonPackage):
+    """Fast implementation of the edit distance (Levenshtein distance)."""
+
+    homepage = "https://github.com/aflc/editdistance"
+    url      = "https://pypi.io/packages/source/e/editdistance/editdistance-0.4.tar.gz"
+
+    version('0.4', '27434720ca0930a9b6974b182b6237bc')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-elasticsearch/package.py b/var/spack/repos/builtin/packages/py-elasticsearch/package.py
index 8b324b29e2..287d2b84a1 100644
--- a/var/spack/repos/builtin/packages/py-elasticsearch/package.py
+++ b/var/spack/repos/builtin/packages/py-elasticsearch/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-elephant/package.py b/var/spack/repos/builtin/packages/py-elephant/package.py
index 3cc36b8769..c54797b073 100644
--- a/var/spack/repos/builtin/packages/py-elephant/package.py
+++ b/var/spack/repos/builtin/packages/py-elephant/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,9 +13,10 @@ class PyElephant(PythonPackage):
     homepage = "http://neuralensemble.org/elephant"
     url      = "https://pypi.io/packages/source/e/elephant/elephant-0.3.0.tar.gz"
 
+    version('0.4.1', '0e6214c96cae6ce777e4b3cf29bbdaa9')
     version('0.3.0', '84e69e6628fd617af469780c30d2da6c')
 
-    variant('docs', default=False, description='Build the documentation')
+    variant('doc', default=False, description='Build the documentation')
     variant('pandas', default=True, description='Build with pandas')
 
     depends_on('py-setuptools',         type='build')
@@ -45,4 +27,4 @@ class PyElephant(PythonPackage):
     depends_on('py-pandas@0.14.1:',     type=('build', 'run'), when='+pandas')
     depends_on('py-numpydoc@0.5:',      type=('build', 'run'), when='+docs')
     depends_on('py-sphinx@1.2.2:',      type=('build', 'run'), when='+docs')
-    # depends_on('py-nose@1.3.3:',        type=('build', 'run')) # tests
+    depends_on('py-nose@1.3.3:',        type='test')
diff --git a/var/spack/repos/builtin/packages/py-emcee/package.py b/var/spack/repos/builtin/packages/py-emcee/package.py
index 1fc6d0ac27..6077af7b01 100644
--- a/var/spack/repos/builtin/packages/py-emcee/package.py
+++ b/var/spack/repos/builtin/packages/py-emcee/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-entrypoints/package.py b/var/spack/repos/builtin/packages/py-entrypoints/package.py
index 335c04267c..6e43570832 100644
--- a/var/spack/repos/builtin/packages/py-entrypoints/package.py
+++ b/var/spack/repos/builtin/packages/py-entrypoints/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-enum34/package.py b/var/spack/repos/builtin/packages/py-enum34/package.py
index 35808b0094..eb28715f24 100644
--- a/var/spack/repos/builtin/packages/py-enum34/package.py
+++ b/var/spack/repos/builtin/packages/py-enum34/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,6 +15,7 @@ class PyEnum34(PythonPackage):
     version('1.1.6', '5f13a0841a61f7fc295c514490d120d0')
 
     depends_on('python')
+    conflicts('python@3.4:')
 
     # This dependency breaks concretization
     # See https://github.com/spack/spack/issues/2793
diff --git a/var/spack/repos/builtin/packages/py-epydoc/package.py b/var/spack/repos/builtin/packages/py-epydoc/package.py
index e6eed4c94c..03fabe3d49 100644
--- a/var/spack/repos/builtin/packages/py-epydoc/package.py
+++ b/var/spack/repos/builtin/packages/py-epydoc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-espresso/2244.patch b/var/spack/repos/builtin/packages/py-espresso/2244.patch
new file mode 100644
index 0000000000..9a6b95a573
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-espresso/2244.patch
@@ -0,0 +1,25 @@
+From 8c1b77e48f2984f7a11434959e37d08514521595 Mon Sep 17 00:00:00 2001
+From: Christoph Junghans <junghans@votca.org>
+Date: Sun, 9 Sep 2018 07:04:09 -0600
+Subject: [PATCH] cmake: workaround for cmake bug#18349
+
+---
+ CMakeLists.txt | 5 ++++-
+ 1 file changed, 4 insertions(+), 1 deletion(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 8f384f423b..f84095b5f4 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -286,7 +286,10 @@ endif(WITH_VALGRIND_INSTRUMENTATION)
+ #######################################################################
+ 
+ find_package(MPI REQUIRED)
+-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${MPI_COMPILE_FLAGS}")
++# Workaround for https://gitlab.kitware.com/cmake/cmake/issues/18349
++foreach(_MPI_FLAG ${MPI_COMPILE_FLAGS})
++  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${_MPI_FLAG}")
++endforeach()
+ set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${MPI_LINK_FLAGS}")
+ include_directories(SYSTEM ${MPI_INCLUDE_PATH})
+ list(APPEND LIBRARIES ${MPI_LIBRARIES})
diff --git a/var/spack/repos/builtin/packages/py-espresso/package.py b/var/spack/repos/builtin/packages/py-espresso/package.py
index 768fae16ee..235b622cac 100644
--- a/var/spack/repos/builtin/packages/py-espresso/package.py
+++ b/var/spack/repos/builtin/packages/py-espresso/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -38,15 +19,20 @@ class PyEspresso(CMakePackage):
        particle couplings to the LB fluid.
     """
     homepage = "http://espressomd.org/"
-    url      = "https://github.com/espressomd/espresso/tarball/v4.0"
+    git      = "https://github.com/espressomd/espresso.git"
+    url      = "https://github.com/espressomd/espresso/releases/download/4.0.0/espresso-4.0.0.tar.gz"
+
+    version('develop', branch='python')
+    version('4.0.0', sha256='8e128847447eebd843de24be9b4ad14aa19c028ae48879a5a4535a9683836e6b')
 
-    version('develop', git='https://github.com/espressomd/espresso.git', branch='python')
+    # espressomd/espresso#2244 merge upstream
+    patch('2244.patch', when="@4.0.0")
 
     depends_on("cmake@3.0:", type='build')
     depends_on("mpi")
     depends_on("boost+serialization+filesystem+system+python+mpi")
     extends("python")
-    depends_on("python")
-    depends_on("py-cython@0.23:")
-    depends_on("py-numpy")
+    depends_on("py-cython@0.23:", type="build")
+    depends_on("py-numpy", type=("build", "run"))
     depends_on("fftw")
+    depends_on("hdf5+hl+mpi")
diff --git a/var/spack/repos/builtin/packages/py-espressopp/package.py b/var/spack/repos/builtin/packages/py-espressopp/package.py
index 53d1cc4f50..c9ffea486b 100644
--- a/var/spack/repos/builtin/packages/py-espressopp/package.py
+++ b/var/spack/repos/builtin/packages/py-espressopp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -34,11 +15,12 @@ class PyEspressopp(CMakePackage):
     """
     homepage = "https://espressopp.github.io"
     url      = "https://github.com/espressopp/espressopp/tarball/v1.9.4.1"
+    git      = "https://github.com/espressopp/espressopp.git"
 
-    version('develop', git='https://github.com/espressopp/espressopp.git', branch='master')
-    version('1.9.5', '13a93c30b07132b5e5fa0d828aa17d79')
+    version('develop', branch='master')
+    version('1.9.5',   '13a93c30b07132b5e5fa0d828aa17d79')
     version('1.9.4.1', '0da74a6d4e1bfa6a2a24fca354245a4f')
-    version('1.9.4', 'f2a27993a83547ad014335006eea74ea')
+    version('1.9.4',   'f2a27993a83547ad014335006eea74ea')
 
     variant('ug', default=False, description='Build user guide')
     variant('pdf', default=False, description='Build user guide in pdf format')
diff --git a/var/spack/repos/builtin/packages/py-et-xmlfile/package.py b/var/spack/repos/builtin/packages/py-et-xmlfile/package.py
index bbe649f042..ffd88933fa 100644
--- a/var/spack/repos/builtin/packages/py-et-xmlfile/package.py
+++ b/var/spack/repos/builtin/packages/py-et-xmlfile/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-eventlet/package.py b/var/spack/repos/builtin/packages/py-eventlet/package.py
new file mode 100644
index 0000000000..af69911130
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-eventlet/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyEventlet(PythonPackage):
+    """Concurrent networking library for Python"""
+
+    homepage = "https://github.com/eventlet/eventlet"
+    url      = "https://github.com/eventlet/eventlet/releases/download/v0.22.0/eventlet-0.22.0.tar.gz"
+
+    version('0.22.0', 'a1199cecd44d7ce2ea624ac6c21db877')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-greenlet@0.3:')
+    depends_on('py-enum34', type=('build', 'run'), when='^python@:3.3.99')
diff --git a/var/spack/repos/builtin/packages/py-execnet/package.py b/var/spack/repos/builtin/packages/py-execnet/package.py
index c2b3d38b6b..c14e8823a0 100644
--- a/var/spack/repos/builtin/packages/py-execnet/package.py
+++ b/var/spack/repos/builtin/packages/py-execnet/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,4 +17,5 @@ class PyExecnet(PythonPackage):
     version('1.4.1', '0ff84b6c79d0dafb7e2971629c4d127a')
 
     depends_on('py-setuptools',  type='build')
+    depends_on('py-setuptools-scm',  type='build')
     depends_on('py-apipkg@1.4:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-fastaindex/package.py b/var/spack/repos/builtin/packages/py-fastaindex/package.py
index e22ff80326..1ddd16d4e8 100644
--- a/var/spack/repos/builtin/packages/py-fastaindex/package.py
+++ b/var/spack/repos/builtin/packages/py-fastaindex/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-fasteners/package.py b/var/spack/repos/builtin/packages/py-fasteners/package.py
index 54a21ceae4..557e3505bc 100644
--- a/var/spack/repos/builtin/packages/py-fasteners/package.py
+++ b/var/spack/repos/builtin/packages/py-fasteners/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-faststructure/package.py b/var/spack/repos/builtin/packages/py-faststructure/package.py
index ddbf1b5d8c..8d0d7833be 100644
--- a/var/spack/repos/builtin/packages/py-faststructure/package.py
+++ b/var/spack/repos/builtin/packages/py-faststructure/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-filelock/package.py b/var/spack/repos/builtin/packages/py-filelock/package.py
new file mode 100644
index 0000000000..a67d1d7be8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-filelock/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyFilelock(PythonPackage):
+    """This package contains a single module, which implements a platform
+    independent file lock in Python, which provides a simple way of
+    inter-process communication"""
+
+    homepage = "https://github.com/benediktschmitt/py-filelock"
+    url = "https://github.com/benediktschmitt/py-filelock/archive/v3.0.4.tar.gz"
+
+    version('3.0.4',  '3cafce82375c3b635f2c872acaf3a00b')
+    version('3.0.3',  'e4bd69f15ebcc6d5a3d684cea3694840')
+    version('3.0.1',  'cbf41ad3d89c89e2b752bc85b501dff6')
+    version('3.0.0',  '29d199e8998ac324d0d7cab7aa814943')
+    version('2.0.13', 'cdd0c4f3e905fbab76d1202ce8e8b454')
+    version('2.0.12', 'fffda24b6cfd459ea5d2d5c335e949e2')
+    version('2.0.11', '9e8cbbe18494d12647050bb32a7e624d')
+    version('2.0.10', '1791e72bb19e503fdd0f365fb8ce2a4d')
+    version('2.0.9',  'b0269e7f77a090cc0d5fc9cf5fbe6ac2')
+    version('2.0.8',  '939ec6d4e2ecdc353a1f27fc452d8e8c')
diff --git a/var/spack/repos/builtin/packages/py-fiscalyear/package.py b/var/spack/repos/builtin/packages/py-fiscalyear/package.py
index e86e2a397d..0f3081653c 100644
--- a/var/spack/repos/builtin/packages/py-fiscalyear/package.py
+++ b/var/spack/repos/builtin/packages/py-fiscalyear/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,16 +14,16 @@ class PyFiscalyear(PythonPackage):
 
     homepage = "https://github.com/adamjstewart/fiscalyear"
     url      = "https://pypi.io/packages/source/f/fiscalyear/fiscalyear-0.1.0.tar.gz"
+    git      = "https://github.com/adamjstewart/fiscalyear.git"
 
+    maintainers = ['adamjstewart']
     import_modules = ['fiscalyear']
 
-    version('master', branch='master',
-            git='https://github.com/adamjstewart/fiscalyear.git')
+    version('master', branch='master')
     version('0.1.0', '30e36b259f3e72e4929abbf259335742')
 
     depends_on('python@2.5:')
     depends_on('py-setuptools', type='build')
 
-    # TODO: Add a 'test' deptype
-    # depends_on('py-pytest', type='test')
-    # depends_on('py-pytest-runner', type='test')
+    depends_on('py-pytest', type='test')
+    depends_on('py-pytest-runner', type='test')
diff --git a/var/spack/repos/builtin/packages/py-flake8-polyfill/package.py b/var/spack/repos/builtin/packages/py-flake8-polyfill/package.py
new file mode 100644
index 0000000000..2a23489694
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-flake8-polyfill/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyFlake8Polyfill(PythonPackage):
+    """flake8-polyfill is a package that provides some compatibility helpers
+       for Flake8 plugins that intend to support Flake8 2.x and 3.x
+       simultaneously.
+    """
+    homepage = "https://pypi.org/project/flake8-polyfill/"
+    url      = "https://files.pythonhosted.org/packages/e6/67/1c26634a770db5c442e361311bee73cb3a177adb2eb3f7af8953cfd9f553/flake8-polyfill-1.0.2.tar.gz"
+
+    version('1.0.2', 'e44b087597f6da52ec6393a709e7108b2905317d0c0b744cdca6208e670d8eda')
+
+    extends('python', ignore='bin/(flake8|pyflakes|pycodestyle)')
+    depends_on('py-flake8', type='run')
diff --git a/var/spack/repos/builtin/packages/py-flake8/package.py b/var/spack/repos/builtin/packages/py-flake8/package.py
index c4926ae64f..75a8e999f4 100644
--- a/var/spack/repos/builtin/packages/py-flake8/package.py
+++ b/var/spack/repos/builtin/packages/py-flake8/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,6 +13,7 @@ class PyFlake8(PythonPackage):
     homepage = "https://github.com/PyCQA/flake8"
     url      = "https://github.com/PyCQA/flake8/archive/3.0.4.tar.gz"
 
+    version('3.5.0', '4e312803bbd8e4a1e566ffac887ae647')
     version('3.0.4', 'cf2a7d8c92070f7b62253404ffb54df7')
     version('2.5.4', '366dd1de6c300254c830b81e66979f06')
 
@@ -40,18 +22,24 @@ class PyFlake8(PythonPackage):
 
     # Most Python packages only require py-setuptools as a build dependency.
     # However, py-flake8 requires py-setuptools during runtime as well.
-    depends_on('py-setuptools', type=('build', 'run'))
+    depends_on('py-setuptools@30:', type=('build', 'run'))
 
+    # pyflakes >= 1.5.0, < 1.7.0
+    depends_on('py-pyflakes@1.5.0:1.6.999', when='@3.5.0', type=('build', 'run'))
     # pyflakes >= 0.8.1, != 1.2.0, != 1.2.1, != 1.2.2, < 1.3.0
     depends_on('py-pyflakes@0.8.1:1.1.0,1.2.3:1.2.3', when='@3.0.4', type=('build', 'run'))
     # pyflakes >= 0.8.1, < 1.1
     depends_on('py-pyflakes@0.8.1:1.0.0', when='@2.5.4', type=('build', 'run'))
 
+    # pycodestyle >= 2.3.0, < 2.4.0
+    depends_on('py-pycodestyle@2.3.0:2.3.999', when='@3.5.0', type=('build', 'run'))
     # pycodestyle >= 2.0.0, < 2.1.0
     depends_on('py-pycodestyle@2.0.0:2.0.999', when='@3.0.4', type=('build', 'run'))
     # pep8 >= 1.5.7, != 1.6.0, != 1.6.1, != 1.6.2
     depends_on('py-pycodestyle@1.5.7,1.7.0:', when='@2.5.4', type=('build', 'run'))
 
+    # mccabe >= 0.6.0, < 0.7.0
+    depends_on('py-mccabe@0.6.0:0.6.999', when='@3.5.0', type=('build', 'run'))
     # mccabe >= 0.5.0, < 0.6.0
     depends_on('py-mccabe@0.5.0:0.5.999', when='@3.0.4', type=('build', 'run'))
     # mccabe >= 0.2.1, < 0.5
@@ -62,10 +50,14 @@ class PyFlake8(PythonPackage):
     # depends_on('py-configparser', when='^python@:3.3', type=('build', 'run'))
     # depends_on('py-enum34', when='^python@:3.1', type=('build', 'run'))
     depends_on('py-configparser', type=('build', 'run'))
-    depends_on('py-enum34', type=('build', 'run'))
 
-    # TODO: Add test dependencies
-    # depends_on('py-nose', type='test')
+    # py-enum34 provides enum module from Python 3.4 for Python
+    # versions 2.4, 2.5, 2.6, 2.7, 3.1, 3.2, and 3.3; use built-in enum
+    # module for Python versions 3.4 and later
+    depends_on('py-enum34', when='^python@2.4:2.7.999,3.1:3.3.999',
+               type=('build', 'run'))
+
+    depends_on('py-nose', type='test')
 
     def patch(self):
         """Filter pytest-runner requirement out of setup.py."""
diff --git a/var/spack/repos/builtin/packages/py-flask-compress/package.py b/var/spack/repos/builtin/packages/py-flask-compress/package.py
new file mode 100644
index 0000000000..56565a20e7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-flask-compress/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyFlaskCompress(PythonPackage):
+    """Flask-Compress allows you to easily compress your Flask application's
+    responses with gzip."""
+
+    homepage = "https://github.com/libwilliam/flask-compress"
+    url      = "https://pypi.io/packages/source/F/Flask-Compress/Flask-Compress-1.4.0.tar.gz"
+
+    version('1.4.0', 'd997f73e4ed5793ec526c135aa765e15')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-flask@0.9:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-flask-socketio/package.py b/var/spack/repos/builtin/packages/py-flask-socketio/package.py
new file mode 100644
index 0000000000..5b016f1d5f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-flask-socketio/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyFlaskSocketio(PythonPackage):
+    """Flask-SocketIO gives Flask applications access to low latency
+    bi-directional communications between the clients and the server.
+    The client-side application can use any of the SocketIO official clients
+    libraries in Javascript, C++, Java and Swift, or any compatible client to
+    establish a permanent connection to the server.
+    """
+
+    homepage = "https://flask-socketio.readthedocs.io"
+    url      = "https://pypi.io/packages/source/F/Flask-SocketIO/Flask-SocketIO-2.9.6.tar.gz"
+
+    version('2.9.6', 'bca83faf38355bd91911f2f140f9b50f')
+
+    depends_on('py-setuptools',             type='build')
+    depends_on('py-flask@0.9:',             type=('build', 'run'))
+    depends_on('py-python-socketio@1.6.1:', type=('build', 'run'))
+    depends_on('py-werkzeug',               type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-flask/package.py b/var/spack/repos/builtin/packages/py-flask/package.py
index fb59c93a4e..50f45b2788 100644
--- a/var/spack/repos/builtin/packages/py-flask/package.py
+++ b/var/spack/repos/builtin/packages/py-flask/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,6 +12,7 @@ class PyFlask(PythonPackage):
     homepage = "http://github.com/pallets/flask"
     url      = "https://pypi.io/packages/source/F/Flask/Flask-0.11.1.tar.gz"
 
+    version('0.12.2', '97278dfdafda98ba7902e890b0289177')
     version('0.12.1', '76e9fee5c3afcf4634b9baf96c578207')
     version('0.11.1', 'd2af95d8fe79cf7da099f062dd122a08')
 
diff --git a/var/spack/repos/builtin/packages/py-flexx/package.py b/var/spack/repos/builtin/packages/py-flexx/package.py
index 30485eafa7..bf949e62bd 100644
--- a/var/spack/repos/builtin/packages/py-flexx/package.py
+++ b/var/spack/repos/builtin/packages/py-flexx/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-fn/package.py b/var/spack/repos/builtin/packages/py-fn/package.py
new file mode 100644
index 0000000000..adf6a474dc
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-fn/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyFn(PythonPackage):
+    """Functional programming in Python: implementation of missing features
+    to enjoy FP."""
+
+    homepage = "https://github.com/fnpy/fn.py"
+    url      = "https://github.com/fnpy/fn.py/archive/v0.5.2.tar.gz"
+
+    version('0.5.2', '48c168fe335e31fc6152ea0944741be2')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-fparser/package.py b/var/spack/repos/builtin/packages/py-fparser/package.py
new file mode 100644
index 0000000000..a1eccda121
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-fparser/package.py
@@ -0,0 +1,36 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+#
+from spack import *
+
+
+class PyFparser(PythonPackage):
+    """Parser for Fortran 77..2003 code."""
+
+    homepage = "https://github.com/stfc/fparser"
+    url      = "https://github.com/stfc/fparser/archive/0.0.5.tar.gz"
+    git      = "https://github.com/stfc/fparser.git"
+
+    version('develop', branch='master')
+    version('0.0.6', '15553fde76b4685fa8edb0a5472b1b53d308c3b8')
+    version('0.0.5', '14630afdb8c8bd025e5504c5ab19d133aa8cf8c7')
+
+    depends_on('py-setuptools', type='build')
+
+    depends_on('py-numpy', type=('build', 'run'), when='@:0.0.5')
+    depends_on('py-nose', type='build')
+    depends_on('py-six', type='build', when='@0.0.6:')
+
+    depends_on('py-pytest', type='test')
+
+    @run_after('install')
+    @on_package_attributes(run_tests=True)
+    def check_build(self):
+        # Ensure that pytest.ini exists inside the source tree,
+        # otherwise an external pytest.ini can cause havoc:
+        touch('pytest.ini')
+        with working_dir('src'):
+            Executable('py.test')()
diff --git a/var/spack/repos/builtin/packages/py-funcsigs/package.py b/var/spack/repos/builtin/packages/py-funcsigs/package.py
index d2d8ff2de5..c39c95ac8b 100644
--- a/var/spack/repos/builtin/packages/py-funcsigs/package.py
+++ b/var/spack/repos/builtin/packages/py-funcsigs/package.py
@@ -1,35 +1,21 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class PyFuncsigs(PythonPackage):
     """Python function signatures from PEP362 for Python 2.6, 2.7 and 3.2."""
+
     homepage = "https://pypi.python.org/pypi/funcsigs"
-    url      = "https://pypi.io/packages/source/f/funcsigs/funcsigs-0.4.tar.gz"
+    url      = "https://pypi.io/packages/source/f/funcsigs/funcsigs-1.0.2.tar.gz"
+
+    import_modules = ['funcsigs']
 
-    version('0.4', 'fb1d031f284233e09701f6db1281c2a5')
+    version('1.0.2', '7e583285b1fb8a76305d6d68f4ccc14e')
+    version('0.4',   'fb1d031f284233e09701f6db1281c2a5')
 
-    depends_on('py-setuptools', type='build')
+    depends_on('py-setuptools@17.1:', type='build')
+    depends_on('py-unittest2', type='test')
diff --git a/var/spack/repos/builtin/packages/py-functools32/package.py b/var/spack/repos/builtin/packages/py-functools32/package.py
index aebf170e46..e33afafdfe 100644
--- a/var/spack/repos/builtin/packages/py-functools32/package.py
+++ b/var/spack/repos/builtin/packages/py-functools32/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-future/package.py b/var/spack/repos/builtin/packages/py-future/package.py
index 1ebce3c7d1..862abd8e64 100644
--- a/var/spack/repos/builtin/packages/py-future/package.py
+++ b/var/spack/repos/builtin/packages/py-future/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-futures/package.py b/var/spack/repos/builtin/packages/py-futures/package.py
index c3370cbeaa..8db11089f5 100644
--- a/var/spack/repos/builtin/packages/py-futures/package.py
+++ b/var/spack/repos/builtin/packages/py-futures/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-fypp/package.py b/var/spack/repos/builtin/packages/py-fypp/package.py
new file mode 100644
index 0000000000..e2a92453d9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-fypp/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyFypp(PythonPackage):
+    """Python powered Fortran preprocessor."""
+
+    homepage = "https://github.com/aradi/fypp"
+    url      = "https://github.com/aradi/fypp/archive/2.1.1.zip"
+
+    version('2.1.1', sha256='3744ad17045e91466bbb75a33ce0cab0f65bc2c377127067a932cdf15655e049')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-gdbgui/package.py b/var/spack/repos/builtin/packages/py-gdbgui/package.py
new file mode 100644
index 0000000000..3f32218ef4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-gdbgui/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyGdbgui(PythonPackage):
+    """gdbgui is a modern, free, browser-based frontend to gdb"""
+
+    homepage = "https://gdbgui.com"
+    url      = "https://pypi.io/packages/source/g/gdbgui/gdbgui-0.11.2.1.tar.gz"
+
+    version('0.11.2.1', 'c15dd3f60fe372b2e93f705c7ee75f51')
+
+    depends_on('py-setuptools',             type=('build', 'run'))
+    depends_on('py-flask@0.12.2:',          type=('build', 'run'))
+    depends_on('py-flask-compress@1.4.0:',  type=('build', 'run'))
+    depends_on('py-flask-socketio@2.9.3:',  type=('build', 'run'))
+    depends_on('py-gevent@1.2.2:',          type=('build', 'run'))
+    depends_on('py-pygdbmi@0.8.2.0:',       type=('build', 'run'))
+    depends_on('py-pygments@2.2.0:',        type=('build', 'run'))
+    depends_on('gdb',                       type='run')
diff --git a/var/spack/repos/builtin/packages/py-genders/package.py b/var/spack/repos/builtin/packages/py-genders/package.py
index 248e4764cc..c3a210361d 100644
--- a/var/spack/repos/builtin/packages/py-genders/package.py
+++ b/var/spack/repos/builtin/packages/py-genders/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-genshi/package.py b/var/spack/repos/builtin/packages/py-genshi/package.py
index a9296ab6ed..0b2405d6e4 100644
--- a/var/spack/repos/builtin/packages/py-genshi/package.py
+++ b/var/spack/repos/builtin/packages/py-genshi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-gevent/package.py b/var/spack/repos/builtin/packages/py-gevent/package.py
new file mode 100644
index 0000000000..a69a3e5bf8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-gevent/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyGevent(PythonPackage):
+    """gevent is a coroutine-based Python networking library."""
+
+    homepage = "http://www.gevent.org"
+    url      = "https://pypi.io/packages/source/g/gevent/gevent-1.3a2.tar.gz"
+
+    version('1.3a2', '8d73a7b0ceb0ca791b22e6f7b7061e9e')
+
+    depends_on('py-setuptools@24.2:',   type='build')
+    depends_on('py-cython@0.27:',       type='build')
+    depends_on('py-cffi@1.4.0:',        type=('build', 'run'))
+    depends_on('py-greenlet@0.4.13:',   type=('build', 'run'))
+    depends_on('python@2.7:2.8,3.4:',   type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-git-review/package.py b/var/spack/repos/builtin/packages/py-git-review/package.py
index 596f8016aa..60291f5b1a 100644
--- a/var/spack/repos/builtin/packages/py-git-review/package.py
+++ b/var/spack/repos/builtin/packages/py-git-review/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,6 +12,7 @@ class PyGitReview(PythonPackage):
     homepage = "http://docs.openstack.org/infra/git-review"
     url = "https://pypi.io/packages/source/g/git-review/git-review-1.25.0.tar.gz"
 
+    version('1.26.0', 'dec20e8a259c03fe19c9dd2362c4ec3f')
     version('1.25.0', '0a061d0e23ee9b93c6212a3fe68fb7ab')
     version('1.24',   '145116fe58a3487c3ad1bf55538fd741')
     version('1.23',   'b0023ad8c037ab710da81412194c6a3a')
@@ -46,4 +28,4 @@ class PyGitReview(PythonPackage):
     depends_on('tk',               type=('run'))
 
     def setup_environment(self, spack_env, run_env):
-        run_env.set('PBR_VERSION', self.spec.version)
+        run_env.set('PBR_VERSION', str(self.spec.version))
diff --git a/var/spack/repos/builtin/packages/py-git2/package.py b/var/spack/repos/builtin/packages/py-git2/package.py
index 9e601aa3a2..ce6be1164e 100644
--- a/var/spack/repos/builtin/packages/py-git2/package.py
+++ b/var/spack/repos/builtin/packages/py-git2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-gnuplot/package.py b/var/spack/repos/builtin/packages/py-gnuplot/package.py
index e6972d280f..782c3cbe32 100644
--- a/var/spack/repos/builtin/packages/py-gnuplot/package.py
+++ b/var/spack/repos/builtin/packages/py-gnuplot/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-goatools/package.py b/var/spack/repos/builtin/packages/py-goatools/package.py
new file mode 100644
index 0000000000..4e97681f78
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-goatools/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyGoatools(PythonPackage):
+    """Python scripts to find enrichment of GO terms"""
+
+    homepage = "https://github.com/tanghaibao/goatools"
+    url      = "https://pypi.io/packages/source/g/goatools/goatools-0.7.11.tar.gz"
+
+    version('0.7.11', 'f2ab989ec9c4acdd80504b263c3b3188')
+
+    depends_on('py-nose',        type=('build', 'run'))
+    depends_on('py-numpy',       type=('build', 'run'))
+    depends_on('py-pandas',      type=('build', 'run'))
+    depends_on('py-pydot',       type=('build', 'run'))
+    depends_on('py-pyparsing',   type=('build', 'run'))
+    depends_on('py-pytest',      type=('build', 'run'))
+    depends_on('py-scipy',       type=('build', 'run'))
+    depends_on('py-statsmodels', type=('build', 'run'))
+    depends_on('py-xlrd',        type=('build', 'run'))
+    depends_on('py-xlsxwriter',  type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-gpaw/package.py b/var/spack/repos/builtin/packages/py-gpaw/package.py
new file mode 100644
index 0000000000..6761ca97e2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-gpaw/package.py
@@ -0,0 +1,88 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyGpaw(PythonPackage):
+    """GPAW is a density-functional theory (DFT) Python code based on the
+    projector-augmented wave (PAW) method and the atomic simulation environment
+    (ASE)."""
+
+    homepage = "https://wiki.fysik.dtu.dk/gpaw/index.html"
+    url      = "https://pypi.io/packages/source/g/gpaw/gpaw-1.3.0.tar.gz"
+
+    version('1.3.0', '82e8c80e637696248db00b5713cdffd1')
+
+    variant('mpi', default=True, description='Build with MPI support')
+    variant('scalapack', default=False,
+            description='Build with ScaLAPACK support')
+    variant('fftw', default=True, description='Build with FFTW support')
+
+    depends_on('mpi', when='+mpi', type=('build', 'link', 'run'))
+    depends_on('python@2.6:')
+    depends_on('py-ase@3.13.0:', type=('build', 'run'))
+    depends_on('py-numpy +blas +lapack', type=('build', 'run'))
+    depends_on('py-scipy', type=('build', 'run'))
+    depends_on('libxc')
+    depends_on('blas')
+    depends_on('lapack')
+    depends_on('fftw+mpi', when='+fftw +mpi')
+    depends_on('fftw~mpi', when='+fftw ~mpi')
+    depends_on('scalapack', when='+scalapack')
+
+    def patch(self):
+        spec = self.spec
+        # For build notes see https://wiki.fysik.dtu.dk/gpaw/install.html
+
+        libxc = spec['libxc']
+        blas = spec['blas']
+        lapack = spec['lapack']
+
+        libs = blas.libs + lapack.libs + libxc.libs
+        include_dirs = [
+            blas.prefix.include,
+            lapack.prefix.include,
+            libxc.prefix.include
+        ]
+        if '+mpi' in spec:
+            libs += spec['mpi'].libs
+            mpi_include_dirs = repr([spec['mpi'].prefix.include])
+            mpi_library_dirs = repr(list(spec['mpi'].libs.directories))
+            include_dirs.append(spec['mpi'].prefix.include)
+        if '+scalapack' in spec:
+            libs += spec['scalapack'].libs
+            include_dirs.append(spec['scalapack'].prefix.include)
+            scalapack_macros = repr([
+                ('GPAW_NO_UNDERSCORE_CBLACS', '1'),
+                ('GPAW_NO_UNDERSCORE_CSCALAPACK', '1')
+            ])
+        if '+fftw' in spec:
+            libs += spec['fftw'].libs
+            include_dirs.append(spec['fftw'].prefix.include)
+
+        lib_dirs = list(libs.directories)
+        libs = list(libs.names)
+        rpath_str = ':'.join(self.rpath)
+
+        with open('customize.py', 'w') as f:
+            f.write("libraries = {0}\n".format(repr(libs)))
+            f.write("include_dirs = {0}\n".format(repr(include_dirs)))
+            f.write("library_dirs = {0}\n".format(repr(lib_dirs)))
+            f.write(
+                "extra_link_args += ['-Wl,-rpath={0}']\n".format(rpath_str)
+            )
+            if '+mpi' in spec:
+                f.write("define_macros += [('PARALLEL', '1')]\n")
+                f.write("compiler='{0}'\n".format(spec['mpi'].mpicc))
+                f.write("mpicompiler = '{0}'\n".format(spec['mpi'].mpicc))
+                f.write("mpi_include_dirs = {0}\n".format(mpi_include_dirs))
+                f.write("mpi_library_dirs = {0}\n".format(mpi_library_dirs))
+            else:
+                f.write("compiler='{0}'\n".format(self.compiler.cc))
+                f.write("mpicompiler = None\n")
+            if '+scalapack' in spec:
+                f.write("scalapack = True\n")
+                f.write("define_macros += {0}\n".format(scalapack_macros))
diff --git a/var/spack/repos/builtin/packages/py-greenlet/package.py b/var/spack/repos/builtin/packages/py-greenlet/package.py
new file mode 100644
index 0000000000..7e62859eea
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-greenlet/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyGreenlet(PythonPackage):
+    """Lightweight in-process concurrent programming"""
+
+    homepage = "https://github.com/python-greenlet/greenlet"
+    url      = "https://pypi.io/packages/source/g/greenlet/greenlet-0.4.13.tar.gz"
+
+    version('0.4.13', '6e0b9dd5385f81d478451ec8ed1d62b3')
diff --git a/var/spack/repos/builtin/packages/py-griddataformats/package.py b/var/spack/repos/builtin/packages/py-griddataformats/package.py
index 0880d860eb..70b71323b2 100644
--- a/var/spack/repos/builtin/packages/py-griddataformats/package.py
+++ b/var/spack/repos/builtin/packages/py-griddataformats/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-guidata/package.py b/var/spack/repos/builtin/packages/py-guidata/package.py
index cf0e8447ff..328e8d36a7 100644
--- a/var/spack/repos/builtin/packages/py-guidata/package.py
+++ b/var/spack/repos/builtin/packages/py-guidata/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-guiqwt/package.py b/var/spack/repos/builtin/packages/py-guiqwt/package.py
index f135b24c57..98716625cd 100644
--- a/var/spack/repos/builtin/packages/py-guiqwt/package.py
+++ b/var/spack/repos/builtin/packages/py-guiqwt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-h5py/package.py b/var/spack/repos/builtin/packages/py-h5py/package.py
index 94dd8d6986..7a6b61c269 100644
--- a/var/spack/repos/builtin/packages/py-h5py/package.py
+++ b/var/spack/repos/builtin/packages/py-h5py/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,14 @@ class PyH5py(PythonPackage):
     """The h5py package provides both a high- and low-level interface to the
     HDF5 library from Python."""
 
-    homepage = "https://pypi.python.org/pypi/h5py"
-    url      = "https://pypi.io/packages/source/h/h5py/h5py-2.4.0.tar.gz"
+    homepage = "http://www.h5py.org/"
+    url      = "https://pypi.io/packages/source/h/h5py/h5py-2.8.0.tar.gz"
+
+    import_modules = ['h5py', 'h5py._hl']
 
+    version('2.8.0', 'ece4f358e69fc8a416f95953b91bc373')
+    version('2.7.1', 'da630aebe3ab9fa218ac405a218e95e0')
+    version('2.7.0', 'f62937f40f68d3b128b3941be239dd93')
     version('2.6.0', 'ec476211bd1de3f5ac150544189b0bf4')
     version('2.5.0', '6e4301b5ad5da0d51b0a1e5ac19e3b74')
     version('2.4.0', '80c9a94ae31f84885cc2ebe1323d6758')
@@ -39,20 +25,22 @@ class PyH5py(PythonPackage):
     variant('mpi', default=True, description='Build with MPI support')
 
     # Build dependencies
-    depends_on('py-cython@0.19:', type='build')
+    depends_on('py-cython@0.23:', type='build')
     depends_on('py-pkgconfig', type='build')
     depends_on('py-setuptools', type='build')
-    depends_on('hdf5@1.8.4:')
-    depends_on('hdf5+mpi', when='+mpi')
-    depends_on('mpi', when='+mpi')
-    depends_on('py-mpi4py', when='+mpi', type=('build', 'run'))
 
     # Build and runtime dependencies
-    depends_on('py-numpy@1.6.1:', type=('build', 'run'))
-
-    # Runtime dependencies
+    depends_on('py-numpy@1.7:', type=('build', 'run'))
     depends_on('py-six', type=('build', 'run'))
 
+    # Link dependencies
+    depends_on('hdf5@1.8.4:+hl')
+
+    # MPI dependencies
+    depends_on('hdf5+mpi', when='+mpi')
+    depends_on('mpi', when='+mpi')
+    depends_on('py-mpi4py', when='+mpi', type=('build', 'run'))
+
     phases = ['configure', 'install']
 
     def configure(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/py-hdfs/package.py b/var/spack/repos/builtin/packages/py-hdfs/package.py
new file mode 100644
index 0000000000..f983ec48a2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-hdfs/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyHdfs(PythonPackage):
+    """API and command line interface for HDFS"""
+    homepage = "https://hdfscli.readthedocs.io/en/latest/"
+    url      = "https://pypi.org/packages/source/h/hdfs/hdfs-2.1.0.tar.gz"
+
+    version('2.1.0', sha256='a40fe99ccb03b5c3247b33a4110eb21b57405dd7c3f1b775e362e66c19b44bc6')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-docopt', type=('build', 'run'))
+    depends_on('py-requests@2.7.0:', type=('build', 'run'))
+    depends_on('py-six@1.9.0:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-hepdata-validator/package.py b/var/spack/repos/builtin/packages/py-hepdata-validator/package.py
new file mode 100644
index 0000000000..71b79c5dc2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-hepdata-validator/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyHepdataValidator(PythonPackage):
+    """Validation schema and code for HEPdata submissions."""
+
+    homepage = "https://github.com/hepdata/hepdata-validator"
+    url = "https://pypi.io/packages/source/h/hepdata_validator/hepdata_validator-0.1.16.tar.gz"
+
+    version('0.1.16', '62e80db7425a4a48050af29e05295e0d')
+    version('0.1.15', 'e29aa75780b9963997e79f572ca0209f')
+    version('0.1.14', '386a2440f23fda7d877764d120bf61fb')
+    version('0.1.8', '5bf388a507a857afbe0deba0857125c7')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-jsonschema', type=('build', 'run'))
+    depends_on('py-pyyaml', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-html2text/package.py b/var/spack/repos/builtin/packages/py-html2text/package.py
index 118b86e2c9..b7509e6e72 100644
--- a/var/spack/repos/builtin/packages/py-html2text/package.py
+++ b/var/spack/repos/builtin/packages/py-html2text/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-html5lib/package.py b/var/spack/repos/builtin/packages/py-html5lib/package.py
index 927614002a..f80d0bea34 100644
--- a/var/spack/repos/builtin/packages/py-html5lib/package.py
+++ b/var/spack/repos/builtin/packages/py-html5lib/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-htseq/package.py b/var/spack/repos/builtin/packages/py-htseq/package.py
new file mode 100644
index 0000000000..0e24981d1a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-htseq/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyHtseq(PythonPackage):
+    """HTSeq is a Python package that provides infrastructure to process
+    data from high-throughput sequencing assays."""
+
+    homepage = "http://htseq.readthedocs.io/en/release_0.9.1/overview.html"
+    url      = "https://github.com/simon-anders/htseq/archive/release_0.9.1.tar.gz"
+
+    version('0.9.1', '269e7de5d39fc31f609cccd4a4740e61')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-numpy', type=('build', 'run'))
+    depends_on('py-pysam', type=('build', 'run'))
+    depends_on('py-matplotlib', type=('build', 'run'))
+    depends_on('py-cython', type=('build', 'run'))
+    depends_on('swig', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-httpbin/package.py b/var/spack/repos/builtin/packages/py-httpbin/package.py
index f8411112ad..f4a2048b4e 100644
--- a/var/spack/repos/builtin/packages/py-httpbin/package.py
+++ b/var/spack/repos/builtin/packages/py-httpbin/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-hypothesis/package.py b/var/spack/repos/builtin/packages/py-hypothesis/package.py
index ffa4e0a54e..3c9abda75c 100644
--- a/var/spack/repos/builtin/packages/py-hypothesis/package.py
+++ b/var/spack/repos/builtin/packages/py-hypothesis/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-idna/package.py b/var/spack/repos/builtin/packages/py-idna/package.py
index 74e6c0fd5d..7e37aa6441 100644
--- a/var/spack/repos/builtin/packages/py-idna/package.py
+++ b/var/spack/repos/builtin/packages/py-idna/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/py-igraph/package.py b/var/spack/repos/builtin/packages/py-igraph/package.py
index 11f7c4a990..03fe3a8a8a 100644
--- a/var/spack/repos/builtin/packages/py-igraph/package.py
+++ b/var/spack/repos/builtin/packages/py-igraph/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-illumina-utils/package.py b/var/spack/repos/builtin/packages/py-illumina-utils/package.py
new file mode 100644
index 0000000000..b970e69797
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-illumina-utils/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyIlluminaUtils(PythonPackage):
+    """A library and collection of scripts to work with Illumina paired-end
+    data (for CASAVA 1.8+)."""
+
+    homepage = "https://github.com/meren/illumina-utils"
+    url      = "https://pypi.io/packages/source/i/illumina-utils/illumina-utils-2.2.tar.gz"
+
+    version('2.3', 'c0af71723e52ab2b14660d2138620e39')
+    version('2.2', '9e19cf112ccc38a903fc41f431804d21')
+
+    depends_on('python@3:', type=('build', 'run'))
+    depends_on('py-pip', type='build')
+    depends_on('py-setuptools', type='build')
+    depends_on('py-matplotlib', type=('build', 'run'))
+    depends_on('py-numpy', type=('build', 'run'))
+    depends_on('py-python-levenshtein', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-imageio/package.py b/var/spack/repos/builtin/packages/py-imageio/package.py
new file mode 100644
index 0000000000..bff47aa4ee
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-imageio/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyImageio(PythonPackage):
+    """ Imageio is a Python library that provides an easy interface
+    to read and write a wide range of image data, including animated
+    images, video, volumetric data, and scientific formats. It is
+    cross-platform, runs on Python 2.7 and 3.4+, and is easy to install."""
+
+    homepage = "http://imageio.github.io/"
+    url      = "https://pypi.io/packages/source/i/imageio/imageio-2.3.0.tar.gz"
+
+    version('2.3.0', '4722c4e1c366748abcb18729881cffb8')
+
+    # TODO: Add variants for plugins, and optional dependencies
+
+    # Fix for python 2 if needed.
+    depends_on('py-numpy',            type=('build', 'run'))
+    depends_on('py-pillow',           type=('build', 'run'))
+    depends_on('python@2.7:2.8,3.4:', type=('build', 'run'))
+    depends_on('py-setuptools',       type='build')
+    depends_on('ffmpeg',              type='run')
diff --git a/var/spack/repos/builtin/packages/py-imagesize/package.py b/var/spack/repos/builtin/packages/py-imagesize/package.py
index f9aa0334ae..c1fc830a60 100644
--- a/var/spack/repos/builtin/packages/py-imagesize/package.py
+++ b/var/spack/repos/builtin/packages/py-imagesize/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-iminuit/package.py b/var/spack/repos/builtin/packages/py-iminuit/package.py
index cbeafa683c..01dcd9f37d 100644
--- a/var/spack/repos/builtin/packages/py-iminuit/package.py
+++ b/var/spack/repos/builtin/packages/py-iminuit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-importlib/package.py b/var/spack/repos/builtin/packages/py-importlib/package.py
index 27221dc99a..90bd1dd9df 100644
--- a/var/spack/repos/builtin/packages/py-importlib/package.py
+++ b/var/spack/repos/builtin/packages/py-importlib/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-ipaddress/package.py b/var/spack/repos/builtin/packages/py-ipaddress/package.py
index 3a84366225..287a4850ba 100644
--- a/var/spack/repos/builtin/packages/py-ipaddress/package.py
+++ b/var/spack/repos/builtin/packages/py-ipaddress/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/py-ipdb/package.py b/var/spack/repos/builtin/packages/py-ipdb/package.py
index 047a8ce2a7..f60e3b58af 100644
--- a/var/spack/repos/builtin/packages/py-ipdb/package.py
+++ b/var/spack/repos/builtin/packages/py-ipdb/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-ipykernel/package.py b/var/spack/repos/builtin/packages/py-ipykernel/package.py
index d703f94a25..804bfe88d4 100644
--- a/var/spack/repos/builtin/packages/py-ipykernel/package.py
+++ b/var/spack/repos/builtin/packages/py-ipykernel/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-ipython-genutils/package.py b/var/spack/repos/builtin/packages/py-ipython-genutils/package.py
index e0e0865238..e09aca3606 100644
--- a/var/spack/repos/builtin/packages/py-ipython-genutils/package.py
+++ b/var/spack/repos/builtin/packages/py-ipython-genutils/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-ipython/package.py b/var/spack/repos/builtin/packages/py-ipython/package.py
index 7f4aafa7a6..d6373ab393 100644
--- a/var/spack/repos/builtin/packages/py-ipython/package.py
+++ b/var/spack/repos/builtin/packages/py-ipython/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import sys
 import platform
diff --git a/var/spack/repos/builtin/packages/py-ipywidgets/package.py b/var/spack/repos/builtin/packages/py-ipywidgets/package.py
index b7c67b241c..58ce772216 100644
--- a/var/spack/repos/builtin/packages/py-ipywidgets/package.py
+++ b/var/spack/repos/builtin/packages/py-ipywidgets/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-isort/package.py b/var/spack/repos/builtin/packages/py-isort/package.py
new file mode 100644
index 0000000000..b3b9dfdd6d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-isort/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyIsort(PythonPackage):
+    """A Python utility / library to sort Python imports."""
+
+    homepage = "https://github.com/timothycrosley/isort"
+    url      = "https://pypi.io/packages/source/i/isort/isort-4.2.15.tar.gz"
+
+    version('4.2.15', '34915a2ce60e6fe3dbcbf5982deef9b4')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-itsdangerous/package.py b/var/spack/repos/builtin/packages/py-itsdangerous/package.py
index 7bb7671571..9ee5505f93 100644
--- a/var/spack/repos/builtin/packages/py-itsdangerous/package.py
+++ b/var/spack/repos/builtin/packages/py-itsdangerous/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-jdcal/package.py b/var/spack/repos/builtin/packages/py-jdcal/package.py
index 8b22cd191c..7274df377f 100644
--- a/var/spack/repos/builtin/packages/py-jdcal/package.py
+++ b/var/spack/repos/builtin/packages/py-jdcal/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-jedi/package.py b/var/spack/repos/builtin/packages/py-jedi/package.py
index fcf4043afa..3bb5b51ed9 100644
--- a/var/spack/repos/builtin/packages/py-jedi/package.py
+++ b/var/spack/repos/builtin/packages/py-jedi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-jinja2/package.py b/var/spack/repos/builtin/packages/py-jinja2/package.py
index 1df8c7366f..454ec2691c 100644
--- a/var/spack/repos/builtin/packages/py-jinja2/package.py
+++ b/var/spack/repos/builtin/packages/py-jinja2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-joblib/package.py b/var/spack/repos/builtin/packages/py-joblib/package.py
index 7792a34539..3f0e8c86af 100644
--- a/var/spack/repos/builtin/packages/py-joblib/package.py
+++ b/var/spack/repos/builtin/packages/py-joblib/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-jprops/package.py b/var/spack/repos/builtin/packages/py-jprops/package.py
new file mode 100644
index 0000000000..ed0cafdc2d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-jprops/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyJprops(PythonPackage):
+    """Java properties file parser for Python"""
+
+    homepage = "https://github.com/mgood/jprops/"
+    url      = "https://pypi.org/packages/source/j/jprops/jprops-2.0.2.tar.gz"
+
+    version('2.0.2', sha256='d297231833b6cd0a3f982a48fe148a7f9817f2895661743d166b267e4d3d5b2c')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-jpype/package.py b/var/spack/repos/builtin/packages/py-jpype/package.py
index 204da5d79e..ba72b9ac91 100644
--- a/var/spack/repos/builtin/packages/py-jpype/package.py
+++ b/var/spack/repos/builtin/packages/py-jpype/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-jsonschema/package.py b/var/spack/repos/builtin/packages/py-jsonschema/package.py
index 3c7178a4ab..dacd9cad01 100644
--- a/var/spack/repos/builtin/packages/py-jsonschema/package.py
+++ b/var/spack/repos/builtin/packages/py-jsonschema/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-junit-xml/package.py b/var/spack/repos/builtin/packages/py-junit-xml/package.py
index d256797086..f1e76c409e 100644
--- a/var/spack/repos/builtin/packages/py-junit-xml/package.py
+++ b/var/spack/repos/builtin/packages/py-junit-xml/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-jupyter-client/package.py b/var/spack/repos/builtin/packages/py-jupyter-client/package.py
index b291fcf448..23d22e2e00 100644
--- a/var/spack/repos/builtin/packages/py-jupyter-client/package.py
+++ b/var/spack/repos/builtin/packages/py-jupyter-client/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-jupyter-console/package.py b/var/spack/repos/builtin/packages/py-jupyter-console/package.py
index 7a3098b0e8..6b041bf996 100644
--- a/var/spack/repos/builtin/packages/py-jupyter-console/package.py
+++ b/var/spack/repos/builtin/packages/py-jupyter-console/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-jupyter-core/package.py b/var/spack/repos/builtin/packages/py-jupyter-core/package.py
index a07aa3fda9..f9e7af9a70 100644
--- a/var/spack/repos/builtin/packages/py-jupyter-core/package.py
+++ b/var/spack/repos/builtin/packages/py-jupyter-core/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-jupyter-notebook/package.py b/var/spack/repos/builtin/packages/py-jupyter-notebook/package.py
index 39f65d9ac7..c3cc182200 100644
--- a/var/spack/repos/builtin/packages/py-jupyter-notebook/package.py
+++ b/var/spack/repos/builtin/packages/py-jupyter-notebook/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-keras/package.py b/var/spack/repos/builtin/packages/py-keras/package.py
index d995111ca9..24ee491907 100644
--- a/var/spack/repos/builtin/packages/py-keras/package.py
+++ b/var/spack/repos/builtin/packages/py-keras/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-kiwisolver/package.py b/var/spack/repos/builtin/packages/py-kiwisolver/package.py
new file mode 100644
index 0000000000..09acd58afc
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-kiwisolver/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyKiwisolver(PythonPackage):
+    """A fast implementation of the Cassowary constraint solver"""
+
+    homepage = "https://github.com/nucleic/kiwi"
+    url      = "https://pypi.io/packages/source/k/kiwisolver/kiwisolver-1.0.1.tar.gz"
+
+    version('1.0.1', 'e2a1718b837e2cd001f7c06934616fcd')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-lark-parser/package.py b/var/spack/repos/builtin/packages/py-lark-parser/package.py
new file mode 100644
index 0000000000..08dce8163c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-lark-parser/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyLarkParser(PythonPackage):
+    """Lark is a modern general-purpose parsing library for Python."""
+
+    homepage = "https://github.com/lark-parser/lark/"
+    url      = "https://pypi.io/packages/source/l/lark-parser/lark-parser-0.6.2.tar.gz"
+
+    version('0.6.2', '675058937a7f41e661bcf2b3bfdb7ceb')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-latexcodec/package.py b/var/spack/repos/builtin/packages/py-latexcodec/package.py
index a768eaebf4..6870a4c686 100644
--- a/var/spack/repos/builtin/packages/py-latexcodec/package.py
+++ b/var/spack/repos/builtin/packages/py-latexcodec/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-lazy-object-proxy/package.py b/var/spack/repos/builtin/packages/py-lazy-object-proxy/package.py
new file mode 100644
index 0000000000..c2b420d70f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-lazy-object-proxy/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyLazyObjectProxy(PythonPackage):
+    """A fast and thorough lazy object proxy."""
+
+    homepage = "https://github.com/ionelmc/python-lazy-object-proxy"
+    url      = "https://pypi.io/packages/source/l/lazy-object-proxy/lazy-object-proxy-1.3.1.tar.gz"
+
+    version('1.3.1', 'e128152b76eb5b9ba759504936139fd0')
+
+    conflicts('^python@3.0:3.2.99')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-lazy-property/package.py b/var/spack/repos/builtin/packages/py-lazy-property/package.py
new file mode 100644
index 0000000000..8e6b0d13c9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-lazy-property/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyLazyProperty(PythonPackage):
+    """A package for making properties lazy"""
+
+    homepage = "https://github.com/jackmaney/lazy-property"
+    url      = "https://github.com/jackmaney/lazy-property/archive/0.0.1.tar.gz"
+
+    version('0.0.1', '7e046c2441abe1bd272d5360827237b3')
+    version('0.0.0', 'fda622b7f1c46ee72ad25f5e88c928f5')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-lazy/package.py b/var/spack/repos/builtin/packages/py-lazy/package.py
index d976001296..a58bc887df 100644
--- a/var/spack/repos/builtin/packages/py-lazy/package.py
+++ b/var/spack/repos/builtin/packages/py-lazy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-lazyarray/package.py b/var/spack/repos/builtin/packages/py-lazyarray/package.py
index 5b5828182f..0b60b82154 100644
--- a/var/spack/repos/builtin/packages/py-lazyarray/package.py
+++ b/var/spack/repos/builtin/packages/py-lazyarray/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-libconf/package.py b/var/spack/repos/builtin/packages/py-libconf/package.py
index 9a9d0d1059..bd7db99d99 100644
--- a/var/spack/repos/builtin/packages/py-libconf/package.py
+++ b/var/spack/repos/builtin/packages/py-libconf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-libensemble/package.py b/var/spack/repos/builtin/packages/py-libensemble/package.py
new file mode 100644
index 0000000000..bb06ab3b3b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-libensemble/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class PyLibensemble(PythonPackage):
+    """Library for managing ensemble-like collections of computations."""
+
+    homepage = "https://libensemble.readthedocs.io"
+    url      = "https://pypi.io/packages/source/l/libensemble/libensemble-0.3.0.tar.gz"
+    git      = "https://github.com/Libensemble/libensemble.git"
+
+    version('develop', branch='master')
+    version('0.3.0', sha256='c8efdf45d0da0ef6299ee778cea1c285c95972af70d3a729ee6dc855e66f9294')
+    version('0.2.0', 'ee96047594a3f5a1533f24d3b1f365f9')
+    version('0.1.0', '0c3d45dd139429de1a5273e5bd8e46ec')
+
+    depends_on('python@2.7:2.8,3.3:')
+    depends_on('py-setuptools', type='build')
+    depends_on('mpi')
+    depends_on('py-mpi4py@2.0:', type=('build', 'run'))
+    depends_on('py-numpy', type=('build', 'run'))
+    depends_on('py-scipy', type=('build', 'run'))
+    depends_on('py-petsc4py@3.5:', type=('build', 'run'))
+    depends_on('nlopt', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-line-profiler/package.py b/var/spack/repos/builtin/packages/py-line-profiler/package.py
index 809d9e751f..2079945405 100644
--- a/var/spack/repos/builtin/packages/py-line-profiler/package.py
+++ b/var/spack/repos/builtin/packages/py-line-profiler/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-linecache2/package.py b/var/spack/repos/builtin/packages/py-linecache2/package.py
new file mode 100644
index 0000000000..1d0595d464
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-linecache2/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyLinecache2(PythonPackage):
+    """Backports of the linecache module"""
+
+    homepage = "https://github.com/testing-cabal/linecache2"
+    url      = "https://pypi.io/packages/source/l/linecache2/linecache2-1.0.0.tar.gz"
+
+    version('1.0.0', '7b25d0289ec36bff1f9e63c4329ce65c')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-pbr', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-lit/package.py b/var/spack/repos/builtin/packages/py-lit/package.py
index aa7d58bc45..0712ccc1c2 100644
--- a/var/spack/repos/builtin/packages/py-lit/package.py
+++ b/var/spack/repos/builtin/packages/py-lit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-llvmlite/package.py b/var/spack/repos/builtin/packages/py-llvmlite/package.py
new file mode 100644
index 0000000000..9a597f7a29
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-llvmlite/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyLlvmlite(PythonPackage):
+    """A lightweight LLVM python binding for writing JIT compilers"""
+
+    homepage = "http://llvmlite.readthedocs.io/en/latest/index.html"
+    url = "https://pypi.io/packages/source/l/llvmlite/llvmlite-0.23.0.tar.gz"
+
+    version('0.23.0', '6fc856576a11dbeef71de862f7c419de')
+    version('0.20.0', 'f2aa60d0981842b7930ba001b03679ab')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('python@2.6:2.8,3.4:', type=('build', 'run'))
+    depends_on('py-enum34', type=('build', 'run'), when='^python@:3.3.99')
+    depends_on('llvm@6.0:6.99', when='@0.23.0:')
+    depends_on('llvm@4.0:4.99', when='@0.17.0:0.20.99')
+    depends_on('binutils', type='build')
diff --git a/var/spack/repos/builtin/packages/py-lmfit/package.py b/var/spack/repos/builtin/packages/py-lmfit/package.py
index f02440c98d..7247c55cdb 100644
--- a/var/spack/repos/builtin/packages/py-lmfit/package.py
+++ b/var/spack/repos/builtin/packages/py-lmfit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-localcider/package.py b/var/spack/repos/builtin/packages/py-localcider/package.py
new file mode 100644
index 0000000000..51fc5c50e0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-localcider/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyLocalcider(PythonPackage):
+    """Tools for calculating sequence properties of disordered proteins"""
+
+    homepage = "http://pappulab.github.io/localCIDER"
+    url      = "https://pypi.io/packages/source/l/localcider/localcider-0.1.14.tar.gz"
+
+    version('0.1.14', 'cd3c992595c5cb280374de3750663cfa')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-numpy',        type=('build', 'run'))
+    depends_on('py-matplotlib',   type=('build', 'run'))
+    depends_on('py-scipy',        type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-locket/package.py b/var/spack/repos/builtin/packages/py-locket/package.py
new file mode 100644
index 0000000000..addc225fbb
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-locket/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyLocket(PythonPackage):
+    """File-based locks for Python for Linux and Windows."""
+
+    homepage = "http://github.com/mwilliamson/locket.py"
+    url      = "https://pypi.io/packages/source/l/locket/locket-0.2.0.tar.gz"
+
+    import_modules = ['locket']
+
+    version('0.2.0', 'fe870949c513d8f7079ba352463833ca')
diff --git a/var/spack/repos/builtin/packages/py-lockfile/package.py b/var/spack/repos/builtin/packages/py-lockfile/package.py
index c3aec05f45..deb8c08e0d 100644
--- a/var/spack/repos/builtin/packages/py-lockfile/package.py
+++ b/var/spack/repos/builtin/packages/py-lockfile/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-logilab-common/package.py b/var/spack/repos/builtin/packages/py-logilab-common/package.py
index 35e5d9aa88..20c1649c7a 100644
--- a/var/spack/repos/builtin/packages/py-logilab-common/package.py
+++ b/var/spack/repos/builtin/packages/py-logilab-common/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-lrudict/package.py b/var/spack/repos/builtin/packages/py-lrudict/package.py
new file mode 100644
index 0000000000..48a94c04e4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-lrudict/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class PyLrudict(PythonPackage):
+    """ A fast LRU cache"""
+
+    homepage = "https://github.com/amitdev/lru-dict"
+    url      = "https://pypi.io/packages/source/l/lru-dict/lru-dict-1.1.6.tar.gz"
+
+    version('1.1.6', 'b33f54f1257ab541f4df4bacc7509f5a')
+
+    depends_on('python@2.7:')
+    depends_on('py-setuptools', type=('build'))
diff --git a/var/spack/repos/builtin/packages/py-lxml/package.py b/var/spack/repos/builtin/packages/py-lxml/package.py
index 10e2435562..63d2024e24 100644
--- a/var/spack/repos/builtin/packages/py-lxml/package.py
+++ b/var/spack/repos/builtin/packages/py-lxml/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-lzstring/package.py b/var/spack/repos/builtin/packages/py-lzstring/package.py
index 8ab7658339..0302eab94d 100644
--- a/var/spack/repos/builtin/packages/py-lzstring/package.py
+++ b/var/spack/repos/builtin/packages/py-lzstring/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-macholib/package.py b/var/spack/repos/builtin/packages/py-macholib/package.py
index d6755f20ba..5a82411b16 100644
--- a/var/spack/repos/builtin/packages/py-macholib/package.py
+++ b/var/spack/repos/builtin/packages/py-macholib/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-machotools/package.py b/var/spack/repos/builtin/packages/py-machotools/package.py
index d51fa17469..3ad4ca45e5 100644
--- a/var/spack/repos/builtin/packages/py-machotools/package.py
+++ b/var/spack/repos/builtin/packages/py-machotools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-macs2/package.py b/var/spack/repos/builtin/packages/py-macs2/package.py
index 9d66440373..6f0d78e33b 100644
--- a/var/spack/repos/builtin/packages/py-macs2/package.py
+++ b/var/spack/repos/builtin/packages/py-macs2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/py-maestrowf/package.py b/var/spack/repos/builtin/packages/py-maestrowf/package.py
new file mode 100644
index 0000000000..06857ed21d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-maestrowf/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyMaestrowf(PythonPackage):
+    """A general purpose workflow conductor for running multi-step
+       simulation studies."""
+
+    homepage = "https://github.com/LLNL/maestrowf/"
+    url      = "https://github.com/LLNL/maestrowf/archive/v1.1.2.tar.gz"
+
+    version('1.1.2', 'a9e05d82910cd2dd077321fb9b0c8dcd')
+    version('1.1.1', 'd38bbf634de4f29fd01d1864ba2f70e0')
+    version('1.1.0', '3c20bf36fbb85d14c3bfdb865944a409')
+    version('1.0.1', '6838fc8bdc7ca0c1adbb6a0333f005b4')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-pyyaml',     type=('build', 'run'))
+    depends_on('py-six',        type=('build', 'run'))
+    depends_on('py-enum34',     type=('build', 'run'))
+    depends_on('py-tabulate',   type=('build', 'run'), when='@1.1.0:')
+    depends_on('py-filelock',   type=('build', 'run'), when='@1.1.0:')
diff --git a/var/spack/repos/builtin/packages/py-mako/package.py b/var/spack/repos/builtin/packages/py-mako/package.py
index b6100d43bf..7bb89b2d39 100644
--- a/var/spack/repos/builtin/packages/py-mako/package.py
+++ b/var/spack/repos/builtin/packages/py-mako/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,6 +17,6 @@ class PyMako(PythonPackage):
     version('1.0.1', '9f0aafd177b039ef67b90ea350497a54')
 
     depends_on('py-setuptools', type='build')
-    # depends_on('py-mock',   type='test')  # TODO: Add test deptype
-    # depends_on('py-pytest', type='test')  # TODO: Add test deptype
+    depends_on('py-mock',   type='test')
+    depends_on('py-pytest', type='test')
     depends_on('py-markupsafe@0.9.2:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-mappy/package.py b/var/spack/repos/builtin/packages/py-mappy/package.py
index 27ca1cbb11..23f975dd8a 100644
--- a/var/spack/repos/builtin/packages/py-mappy/package.py
+++ b/var/spack/repos/builtin/packages/py-mappy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-markdown/package.py b/var/spack/repos/builtin/packages/py-markdown/package.py
index d6356d8a52..80f395dbc8 100644
--- a/var/spack/repos/builtin/packages/py-markdown/package.py
+++ b/var/spack/repos/builtin/packages/py-markdown/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -34,18 +15,20 @@ class PyMarkdown(PythonPackage):
     """
 
     homepage = "https://pythonhosted.org/Markdown/"
-    url      = "https://github.com/waylan/Python-Markdown/archive/2.6.7-final.tar.gz"
+    url      = "https://pypi.io/packages/source/m/markdown/Markdown-2.6.11.tar.gz"
 
-    version('2.6.7', 'fd27044042e197ad99249b3d60215d97')
-    version('2.6.6', '2b47a0ff7eb19ef34453fe198a0cccc4')
-    version('2.6.5', 'e4b6b65b2d6bcac07176fb209bc55614')
-    version('2.6.4', '5fb3cd9945eb534e71af597f8ee3622b')
-    version('2.6.3', 'ec7a50ce9fd4a5fd0b24555d47e9d7d1')
-    version('2.6.2', '6ce86913e9bf5bb34d9ee394ac71f044')
-    version('2.6.1', '0ae69693c5adb27caf0160941d7dcbdf')
-    version('2.6', '9acdde43d99847d0c4ef03ea56b1d2c5')
-    version('2.5.2', 'ed2a662d22799186c1ef85d173d38b8a')
-    version('2.5.1', 'be6f6ba65a8fb843d2aaf1fcdd68c755')
-    version('2.5', '8393ceab9c6e33357fb8a7be063a4849')
+    version('2.6.11', sha256='a856869c7ff079ad84a3e19cd87a64998350c2b94e9e08e44270faef33400f81')
+    version('2.6.7', sha256='daebf24846efa7ff269cfde8c41a48bb2303920c7b2c7c5e04fa82e6282d05c0')
+    version('2.6.6', sha256='9a292bb40d6d29abac8024887bcfc1159d7a32dc1d6f1f6e8d6d8e293666c504')
+    version('2.6.5', sha256='8d94cf6273606f76753fcb1324623792b3738c7612c2b180c85cc5e88642e560')
+    version('2.6.4', sha256='e436eee7aaf2a230ca3315034dd39e8a0fc27036708acaa3dd70625ec62a94ce')
+    version('2.6.3', sha256='ad75fc03c45492eba3bc63645e1e6465f65523a05fff0abf36910f810465a9af')
+    version('2.6.2', sha256='ee17d0d7dc091e645dd48302a2e21301cc68f188505c2069d8635f94554170bf')
+    version('2.6.1', sha256='b5879b87e8e5c125c92ab8c8f3babce78ad4e840446eed73c5b6e2984648d2b1')
+    version('2.6', sha256='e1c8a489bb7c7154bc5a8c14f0fd1fc356ee36c8b9988f9fd8febff22dd435da')
+    version('2.5.2', sha256='284e97e56db9ada03ede9c0ed2870ca6590ce7869f3119104d53510debf1533d')
+    version('2.5.1', sha256='8f81ed12c18608a502828acb7d318f362c42f4eca97d01e93cadfc52c1e40b73')
+    version('2.5', sha256='6ba74a1e7141c9603750d80711b639a7577bffb785708e6260090239ee5bc76d')
 
     depends_on('python@2.7:2.8,3.2:3.4')
+    depends_on('py-setuptools', type='build', when='@2.6.11:')
diff --git a/var/spack/repos/builtin/packages/py-markupsafe/package.py b/var/spack/repos/builtin/packages/py-markupsafe/package.py
index dc1bf781a0..1d681f2987 100644
--- a/var/spack/repos/builtin/packages/py-markupsafe/package.py
+++ b/var/spack/repos/builtin/packages/py-markupsafe/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-matplotlib/freetype-include-path.patch b/var/spack/repos/builtin/packages/py-matplotlib/freetype-include-path.patch
new file mode 100644
index 0000000000..7007c88d0d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-matplotlib/freetype-include-path.patch
@@ -0,0 +1,16 @@
+diff --git a/setupext.py b/setupext.py
+index 6d363012eb4..00ef3fe5a3d 100644
+--- a/setupext.py
++++ b/setupext.py
+@@ -162,8 +162,10 @@ def get_include_dirs():
+     """
+     include_dirs = [os.path.join(d, 'include') for d in get_base_dirs()]
+     if sys.platform != 'win32':
+-        # gcc includes this dir automatically, so also look for headers in
++        # gcc includes these dirs automatically, so also look for headers in
+         # these dirs
++        include_dirs.extend(
++            os.environ.get('CPATH', '').split(os.pathsep))
+         include_dirs.extend(
+             os.environ.get('CPLUS_INCLUDE_PATH', '').split(os.pathsep))
+     return include_dirs
diff --git a/var/spack/repos/builtin/packages/py-matplotlib/package.py b/var/spack/repos/builtin/packages/py-matplotlib/package.py
index cd9abd2bc1..b63a52d9ba 100644
--- a/var/spack/repos/builtin/packages/py-matplotlib/package.py
+++ b/var/spack/repos/builtin/packages/py-matplotlib/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
@@ -34,6 +15,9 @@ class PyMatplotlib(PythonPackage):
     homepage = "https://pypi.python.org/pypi/matplotlib"
     url      = "https://pypi.io/packages/source/m/matplotlib/matplotlib-2.0.2.tar.gz"
 
+    version('3.0.0', '39c7f44c8fa0f24cbf684137371ce4ae')
+    version('2.2.3', '403b0bddd751d71187416f20d4cff100')
+    version('2.2.2', 'dd1e49e041309a7fd4e32be8bf17c3b6')
     version('2.0.2', '061111784278bde89b5d4987014be4ca')
     version('2.0.0', '7aa54b06327f0e1c4f3877fc2f7d6b17')
     version('1.5.3', 'ba993b06113040fee6628d74b80af0fd')
@@ -65,8 +49,10 @@ class PyMatplotlib(PythonPackage):
     # directories (i.e., matplotlib and basemap)
     depends_on('py-setuptools', type=('build', 'run'))
 
+    depends_on('python@3.5:', when='@3:')
     depends_on('libpng@1.2:')
     depends_on('freetype@2.3:')
+    patch('freetype-include-path.patch', when='@2.2.2:2.9.9')  # Patch to pick up correct freetype headers
 
     depends_on('py-numpy@1.6:', type=('build', 'run'))
     depends_on('py-dateutil@1.1:', type=('build', 'run'))
@@ -75,6 +61,7 @@ class PyMatplotlib(PythonPackage):
     depends_on('py-cycler@0.9:', type=('build', 'run'))
     depends_on('py-subprocess32', type=('build', 'run'), when='^python@:2.7')
     depends_on('py-functools32', type=('build', 'run'), when='^python@2.7')
+    depends_on('py-kiwisolver', type=('build', 'run'), when='@2.2.0:')
 
     # ------ Optional GUI frameworks
     depends_on('tk@8.3:', when='+tk')  # not 8.6.0 or 8.6.1
@@ -86,16 +73,15 @@ class PyMatplotlib(PythonPackage):
     depends_on('image-magick', when='+animation')
 
     # --------- Optional dependencies
-    depends_on('pkg-config', type='build')    # why not...
+    depends_on('pkgconfig', type='build')    # why not...
     depends_on('pil', when='+image', type=('build', 'run'))
     depends_on('py-ipython', when='+ipython', type=('build', 'run'))
     depends_on('ghostscript', when='+latex', type='run')
     depends_on('texlive', when='+latex', type='run')
 
     # Testing dependencies
-    # TODO: Add a 'test' deptype
-    # depends_on('py-nose', type='test')
-    # depends_on('py-mock', type='test')
+    depends_on('py-nose', type='test')
+    depends_on('py-mock', type='test')
 
     # Required libraries that ship with matplotlib
     # depends_on('agg@2.4:')
diff --git a/var/spack/repos/builtin/packages/py-mccabe/package.py b/var/spack/repos/builtin/packages/py-mccabe/package.py
index 9a8e39f4c4..13dfddc0c4 100644
--- a/var/spack/repos/builtin/packages/py-mccabe/package.py
+++ b/var/spack/repos/builtin/packages/py-mccabe/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,6 +12,9 @@ class PyMccabe(PythonPackage):
     homepage = "https://github.com/PyCQA/mccabe"
     url      = "https://github.com/PyCQA/mccabe/archive/0.5.2.tar.gz"
 
+    version('0.6.1', '0360af86f0bce7a839bd3cba517edf9c')
+    version('0.6.0', '38f46ff70b5d2c02155f8fd4d96fb791')
+    version('0.5.3', 'a75f57079ce10556fd3c63a5f6b4d706')
     version('0.5.2', '3cdf2d7faa1464b18905fe9a7063a632')
     version('0.5.1', '864b364829156701bec797712be8ece0')
     version('0.5.0', '71c0ce5e5c4676753525154f6c5d3af8')
@@ -44,9 +28,7 @@ class PyMccabe(PythonPackage):
     depends_on('python@2.7:2.8,3.3:')
 
     depends_on('py-setuptools', type='build')
-
-    # TODO: Add test dependencies
-    # depends_on('py-pytest', type='test')
+    depends_on('py-pytest', type='test')
 
     def patch(self):
         """Filter pytest-runner requirement out of setup.py."""
diff --git a/var/spack/repos/builtin/packages/py-mdanalysis/package.py b/var/spack/repos/builtin/packages/py-mdanalysis/package.py
index 437f2445a7..15f40f1861 100644
--- a/var/spack/repos/builtin/packages/py-mdanalysis/package.py
+++ b/var/spack/repos/builtin/packages/py-mdanalysis/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-meep/package.py b/var/spack/repos/builtin/packages/py-meep/package.py
index a2252c3b00..0b257a64c6 100644
--- a/var/spack/repos/builtin/packages/py-meep/package.py
+++ b/var/spack/repos/builtin/packages/py-meep/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-memory-profiler/package.py b/var/spack/repos/builtin/packages/py-memory-profiler/package.py
index 7bd6b70ca1..92ccc763dc 100644
--- a/var/spack/repos/builtin/packages/py-memory-profiler/package.py
+++ b/var/spack/repos/builtin/packages/py-memory-profiler/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-methylcode/package.py b/var/spack/repos/builtin/packages/py-methylcode/package.py
index 00171890f5..b416b27f62 100644
--- a/var/spack/repos/builtin/packages/py-methylcode/package.py
+++ b/var/spack/repos/builtin/packages/py-methylcode/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-mg-rast-tools/package.py b/var/spack/repos/builtin/packages/py-mg-rast-tools/package.py
new file mode 100644
index 0000000000..0d2c084142
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-mg-rast-tools/package.py
@@ -0,0 +1,32 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyMgRastTools(PythonPackage):
+    """Repository of scripts and libraries for using the MG-RAST API and
+    MG-RAST data."""
+
+    homepage = "https://github.com/MG-RAST/MG-RAST-Tools"
+    git      = "https://github.com/MG-RAST/MG-RAST-Tools.git"
+
+    version('2018.04.17', commit='a40c6e6539ad0bc1c08e1b03dfc0a9759755a326')
+
+    depends_on('perl', type=('build', 'run'))
+    depends_on('py-setuptools@28.0:', type='build')
+    depends_on('py-prettytable@0.7:', type=('build', 'run'))
+    depends_on('py-poster@0.8.1:', type=('build', 'run'))
+    depends_on('py-requests', type=('build', 'run'))
+    depends_on('py-requests-toolbelt@0.8:', type=('build', 'run'))
+    depends_on('py-scipy', type=('build', 'run'))
+    depends_on('py-numpy', type=('build', 'run'))
+    depends_on('r-matr', type=('build', 'run'))
+    depends_on('shocklibs@0.1.30:')
+    depends_on('perl-list-moreutils', type=('build', 'run'))
+    depends_on('perl-exporter-tiny', type=('build', 'run'))
+    depends_on('perl-libwww-perl', type=('build', 'run'))
+    depends_on('perl-http-message', type=('build', 'run'))
+    depends_on('perl-json', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-misopy/package.py b/var/spack/repos/builtin/packages/py-misopy/package.py
index 6c274dbfbc..832c8ca605 100644
--- a/var/spack/repos/builtin/packages/py-misopy/package.py
+++ b/var/spack/repos/builtin/packages/py-misopy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-mistune/package.py b/var/spack/repos/builtin/packages/py-mistune/package.py
index 22b7c5e790..71378fb539 100644
--- a/var/spack/repos/builtin/packages/py-mistune/package.py
+++ b/var/spack/repos/builtin/packages/py-mistune/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-mock/package.py b/var/spack/repos/builtin/packages/py-mock/package.py
index 5600072e63..861ca10f9c 100644
--- a/var/spack/repos/builtin/packages/py-mock/package.py
+++ b/var/spack/repos/builtin/packages/py-mock/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,9 @@ class PyMock(PythonPackage):
     version('2.0.0', '0febfafd14330c9dcaa40de2d82d40ad')
     version('1.3.0', '73ee8a4afb3ff4da1b4afa287f39fdeb')
 
-    depends_on('py-pbr', type=('build', 'run'))
+    depends_on('py-pbr@0.11:', type=('build', 'run'))
+    depends_on('py-six@1.7:',  type=('build', 'run'))
+    depends_on('py-six@1.9:',  type=('build', 'run'), when='@2.0.0:')
+    # requirements.txt references @1:, but 0.4 is newest available..
+    depends_on('py-funcsigs',  type=('build', 'run'), when='^python@:3.2.99')
     depends_on('py-setuptools@17.1:', type='build')
diff --git a/var/spack/repos/builtin/packages/py-moltemplate/package.py b/var/spack/repos/builtin/packages/py-moltemplate/package.py
new file mode 100644
index 0000000000..00993fb4de
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-moltemplate/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyMoltemplate(PythonPackage):
+    """Moltemplate is a general cross-platform text-based molecule builder for
+    LAMMPS."""
+
+    homepage = "http://moltemplate.org"
+    url      = "https://github.com/jewettaij/moltemplate/archive/v2.5.8.tar.gz"
+
+    version('2.5.8', '9e127a254a206222e8a31684780f8dba')
+
+    depends_on('python@2.7:',   type=('build', 'run'))
+    depends_on('py-setuptools', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-mongo/package.py b/var/spack/repos/builtin/packages/py-mongo/package.py
index aa24299d2b..ae364c1a3f 100644
--- a/var/spack/repos/builtin/packages/py-mongo/package.py
+++ b/var/spack/repos/builtin/packages/py-mongo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,10 +10,11 @@ class PyMongo(PythonPackage):
     """Python driver for MongoDB <http://www.mongodb.org>"""
 
     homepage = "http://github.com/mongodb/mongo-python-driver"
-    url      = "https://pypi.io/packages/source/p/pymongo/pymongo-3.3.0.tar.gz"
+    url      = "https://pypi.io/packages/source/p/pymongo/pymongo-3.6.0.tar.gz"
 
+    version('3.6.0', '2f64fa7691c77535b72050704cc12afb')
     version('3.3.0', '42cd12a5014fb7d3e1987ca04f5c651f')
 
     depends_on('python@2.6:2.8,3.3:')
 
-    depends_on('setuptools', type='build')
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-monotonic/package.py b/var/spack/repos/builtin/packages/py-monotonic/package.py
index 3f8ba05a03..1d32f68c53 100644
--- a/var/spack/repos/builtin/packages/py-monotonic/package.py
+++ b/var/spack/repos/builtin/packages/py-monotonic/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-monty/package.py b/var/spack/repos/builtin/packages/py-monty/package.py
index 8b35fb6e19..abe10c6ee7 100644
--- a/var/spack/repos/builtin/packages/py-monty/package.py
+++ b/var/spack/repos/builtin/packages/py-monty/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-more-itertools/package.py b/var/spack/repos/builtin/packages/py-more-itertools/package.py
new file mode 100644
index 0000000000..eda31ded25
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-more-itertools/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyMoreItertools(PythonPackage):
+    """Additions to the standard Python itertools package."""
+
+    homepage = "https://github.com/erikrose/more-itertools"
+    url      = "https://pypi.io/packages/source/m/more-itertools/more-itertools-4.3.0.tar.gz"
+
+    import_modules = ['more_itertools', 'more_itertools.tests']
+
+    version('4.3.0', '42157ef9b677bdf6d3609ed6eadcbd4a')
+    version('4.1.0', '246f46686d95879fbad37855c115dc52')
+    version('2.2',   'b8d328a33f966bf40bb829bcf8da35ce')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-six@1.0.0:1.999', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-mpi4py/package.py b/var/spack/repos/builtin/packages/py-mpi4py/package.py
index 7193800506..aad9998201 100644
--- a/var/spack/repos/builtin/packages/py-mpi4py/package.py
+++ b/var/spack/repos/builtin/packages/py-mpi4py/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,16 +11,17 @@ class PyMpi4py(PythonPackage):
        Interface (MPI) standard. It is implemented on top of the
        MPI-1/MPI-2 specification and exposes an API which grounds on the
        standard MPI-2 C++ bindings.
-
     """
     homepage = "https://pypi.python.org/pypi/mpi4py"
-    url      = "https://pypi.io/packages/source/m/mpi4py/mpi4py-1.3.1.tar.gz"
+    url      = "https://pypi.io/packages/source/m/mpi4py/mpi4py-3.0.0.tar.gz"
+    git      = "https://github.com/mpi4py/mpi4py.git"
 
-    version('develop', git='https://github.com/mpi4py/mpi4py.git', branch='master')
+    version('develop', branch='master')
+    version('3.0.0', 'bfe19f20cef5e92f6e49e50fb627ee70')
     version('2.0.0', '4f7d8126d7367c239fd67615680990e3')
     version('1.3.1', 'dbe9d22bdc8ed965c23a7ceb6f32fc3c')
 
     depends_on('python@2.7:2.8,3.3:')
     depends_on('py-setuptools', type='build')
     depends_on('mpi')
-    depends_on('py-cython', when='@2.0.1:', type='build')
+    depends_on('py-cython', when='@develop', type='build')
diff --git a/var/spack/repos/builtin/packages/py-mpmath/package.py b/var/spack/repos/builtin/packages/py-mpmath/package.py
index d3250b43e5..b7bb79b0b1 100644
--- a/var/spack/repos/builtin/packages/py-mpmath/package.py
+++ b/var/spack/repos/builtin/packages/py-mpmath/package.py
@@ -1,33 +1,15 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class PyMpmath(PythonPackage):
     """A Python library for arbitrary-precision floating-point arithmetic."""
     homepage = "http://mpmath.org"
-    url      = "https://pypi.io/packages/source/m/mpmath/mpmath-all-0.19.tar.gz"
+    url      = "https://pypi.io/packages/source/m/mpmath/mpmath-1.0.0.tar.gz"
 
-    version('0.19', 'd1b7e19dd6830d0d7b5e1bc93d46c02c')
+    version('1.0.0', '998f10cb231af62743212ca80693f1b5')
+    version('0.19', 'af5cc956b2673b33a25c3e57299bae7b')
diff --git a/var/spack/repos/builtin/packages/py-multiprocess/package.py b/var/spack/repos/builtin/packages/py-multiprocess/package.py
index 307433e759..e9c6bbc0b5 100644
--- a/var/spack/repos/builtin/packages/py-multiprocess/package.py
+++ b/var/spack/repos/builtin/packages/py-multiprocess/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-multiqc/package.py b/var/spack/repos/builtin/packages/py-multiqc/package.py
index f2b9377b1e..62547b8873 100644
--- a/var/spack/repos/builtin/packages/py-multiqc/package.py
+++ b/var/spack/repos/builtin/packages/py-multiqc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,6 +14,8 @@ class PyMultiqc(PythonPackage):
     homepage = "https://multiqc.info"
     url      = "https://pypi.io/packages/source/m/multiqc/multiqc-1.0.tar.gz"
 
+    version('1.5', 'c9fc5f54a75b1d0c3e119e0db7f5fe72')
+    version('1.3', '78fef8a89c0bd40d559b10c1f736bbcd')
     version('1.0', '0b7310b3f75595e5be8099fbed2d2515')
 
     depends_on('python@2.7:')
@@ -41,8 +24,11 @@ class PyMultiqc(PythonPackage):
     depends_on('py-jinja2@2.9:', type=('build', 'run'))
     depends_on('py-lzstring', type=('build', 'run'))
     depends_on('py-future@0.14.1:', type=('build', 'run'))
-    depends_on('py-spectra', type=('build', 'run'))
+    depends_on('py-spectra@0.0.10:', type=('build', 'run'))
     depends_on('py-matplotlib', type=('build', 'run'))
     depends_on('py-numpy', type=('build', 'run'))
     depends_on('py-pyyaml', type=('build', 'run'))
     depends_on('py-simplejson', type=('build', 'run'))
+    depends_on('py-requests', type=('build', 'run'), when='@1.5:')
+    depends_on('py-enum34', type=('build', 'run'), when='@1.5:')
+    depends_on('py-markdown', type=('build', 'run'), when='@1.5:')
diff --git a/var/spack/repos/builtin/packages/py-mx/package.py b/var/spack/repos/builtin/packages/py-mx/package.py
index 1902b33c4f..fe4ff8fff1 100644
--- a/var/spack/repos/builtin/packages/py-mx/package.py
+++ b/var/spack/repos/builtin/packages/py-mx/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-mxnet/package.py b/var/spack/repos/builtin/packages/py-mxnet/package.py
index 5b7cca85ef..9d11ce9e20 100644
--- a/var/spack/repos/builtin/packages/py-mxnet/package.py
+++ b/var/spack/repos/builtin/packages/py-mxnet/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-myhdl/package.py b/var/spack/repos/builtin/packages/py-myhdl/package.py
index 69bf8d04b6..38f03691e0 100644
--- a/var/spack/repos/builtin/packages/py-myhdl/package.py
+++ b/var/spack/repos/builtin/packages/py-myhdl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/py-mysqldb1/package.py b/var/spack/repos/builtin/packages/py-mysqldb1/package.py
index b3d17c543a..989ddc6679 100644
--- a/var/spack/repos/builtin/packages/py-mysqldb1/package.py
+++ b/var/spack/repos/builtin/packages/py-mysqldb1/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-natsort/package.py b/var/spack/repos/builtin/packages/py-natsort/package.py
new file mode 100644
index 0000000000..958f0c1d5f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-natsort/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyNatsort(PythonPackage):
+    """Simple yet flexible natural sorting in Python."""
+
+    homepage = "https://pypi.org/project/natsort/"
+    url = "https://github.com/SethMMorton/natsort/archive/5.2.0.zip"
+
+    version('5.2.0', '2ed2826550eef1f9ea3dd04f08b5da8b')
+    version('5.1.1', '0525d4897fc98f40df5cc5a4a05f3c82')
+    version('5.1.0', '518688548936d548775fb00afba999fb')
+    version('5.0.3', '11147d75693995a946656927df7617d0')
+    version('5.0.2', '1eb11a69086a5fb21d03f8189f1afed3')
+    version('5.0.1', 'ca21c728bb3dd5dcfb010fa50b9c5e3c')
+    version('5.0.0', 'fc7800fea50dcccbf8b116e1dff2ebf8')
+    version('4.0.4', '7478ba31ec7fe554fcbfda41bb01f5ef')
+    version('4.0.3', '2dc4fb1eb6ebfe4c9d95a12c2406df33')
+    version('4.0.1', '659cf6ce95951003de0c85fc80b9f135')
+
+    depends_on('py-setuptools', type=('build'))
diff --git a/var/spack/repos/builtin/packages/py-nbconvert/package.py b/var/spack/repos/builtin/packages/py-nbconvert/package.py
index ea93c618c7..e6dc35441f 100644
--- a/var/spack/repos/builtin/packages/py-nbconvert/package.py
+++ b/var/spack/repos/builtin/packages/py-nbconvert/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/py-nbformat/package.py b/var/spack/repos/builtin/packages/py-nbformat/package.py
index 5f7ca27008..48f20262f2 100644
--- a/var/spack/repos/builtin/packages/py-nbformat/package.py
+++ b/var/spack/repos/builtin/packages/py-nbformat/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-neo/package.py b/var/spack/repos/builtin/packages/py-neo/package.py
index 03a060dec4..b1ea797753 100644
--- a/var/spack/repos/builtin/packages/py-neo/package.py
+++ b/var/spack/repos/builtin/packages/py-neo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,6 +14,7 @@ class PyNeo(PythonPackage):
     homepage = "http://neuralensemble.org/neo"
     url      = "https://pypi.io/packages/source/n/neo/neo-0.4.1.tar.gz"
 
+    version('0.5.2', 'e2b55b112ae245f24cc8ad63cfef986c')
     version('0.4.1', 'f706df3a1bce835cb490b812ac198a6e')
 
     depends_on('py-setuptools',        type='build')
diff --git a/var/spack/repos/builtin/packages/py-nestle/package.py b/var/spack/repos/builtin/packages/py-nestle/package.py
index ff64b08716..2796de3333 100644
--- a/var/spack/repos/builtin/packages/py-nestle/package.py
+++ b/var/spack/repos/builtin/packages/py-nestle/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-netcdf4/package.py b/var/spack/repos/builtin/packages/py-netcdf4/package.py
index 73e0d38586..5099183816 100644
--- a/var/spack/repos/builtin/packages/py-netcdf4/package.py
+++ b/var/spack/repos/builtin/packages/py-netcdf4/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-netifaces/package.py b/var/spack/repos/builtin/packages/py-netifaces/package.py
index fcdbf80092..3120e2b13f 100644
--- a/var/spack/repos/builtin/packages/py-netifaces/package.py
+++ b/var/spack/repos/builtin/packages/py-netifaces/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-networkx/package.py b/var/spack/repos/builtin/packages/py-networkx/package.py
index 528fe59a01..b499ca9c4e 100644
--- a/var/spack/repos/builtin/packages/py-networkx/package.py
+++ b/var/spack/repos/builtin/packages/py-networkx/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,8 +12,11 @@ class PyNetworkx(PythonPackage):
     homepage = "http://networkx.github.io/"
     url      = "https://pypi.io/packages/source/n/networkx/networkx-1.11.tar.gz"
 
-    version('1.11', '6ef584a879e9163013e9a762e1cf7cd1')
-    version('1.10', 'eb7a065e37250a4cc009919dacfe7a9d')
+    version('2.1', sha256='64272ca418972b70a196cb15d9c85a5a6041f09a2f32e0d30c0255f25d458bb1',
+            url='https://pypi.io/packages/source/n/networkx/networkx-2.1.zip')
+    version('1.11', md5='6ef584a879e9163013e9a762e1cf7cd1')
+    version('1.10', md5='eb7a065e37250a4cc009919dacfe7a9d')
 
     depends_on('py-decorator', type=('build', 'run'))
+    depends_on('py-decorator@4.1.0:', type=('build', 'run'), when='@2.1:')
     depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-nose/package.py b/var/spack/repos/builtin/packages/py-nose/package.py
index 566808b711..636d1d2195 100644
--- a/var/spack/repos/builtin/packages/py-nose/package.py
+++ b/var/spack/repos/builtin/packages/py-nose/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-nosexcover/package.py b/var/spack/repos/builtin/packages/py-nosexcover/package.py
index 7625a39d99..45da661a20 100644
--- a/var/spack/repos/builtin/packages/py-nosexcover/package.py
+++ b/var/spack/repos/builtin/packages/py-nosexcover/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-numba/package.py b/var/spack/repos/builtin/packages/py-numba/package.py
new file mode 100644
index 0000000000..550ac571a8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-numba/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyNumba(PythonPackage):
+    """NumPy aware dynamic Python compiler using LLVM"""
+
+    homepage = "https://numba.pydata.org/"
+    url      = "https://pypi.io/packages/source/n/numba/numba-0.35.0.tar.gz"
+
+    version('0.35.0', '4f447383406f54aaf18ffaba3a0e79e8')
+
+    depends_on('py-numpy@1.10:',    type=('build', 'run'))
+    depends_on('py-llvmlite@0.20:', type=('build', 'run'))
+    depends_on('py-argparse',       type=('build', 'run'))
+    depends_on('py-funcsigs',       type=('build', 'run'), when='^python@:3.3.99')
+    depends_on('py-singledispatch', type=('build', 'run'), when='^python@:3.3.99')
+
+    # Version 6.0.0 of llvm had a hidden symbol which breaks numba at runtime.
+    # See https://reviews.llvm.org/D44140
+    conflicts('^llvm@6.0.0')
diff --git a/var/spack/repos/builtin/packages/py-numexpr/package.py b/var/spack/repos/builtin/packages/py-numexpr/package.py
index 6db50bf00d..9695afb50c 100644
--- a/var/spack/repos/builtin/packages/py-numexpr/package.py
+++ b/var/spack/repos/builtin/packages/py-numexpr/package.py
@@ -1,35 +1,17 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class PyNumexpr(PythonPackage):
     """Fast numerical expression evaluator for NumPy"""
     homepage = "https://pypi.python.org/pypi/numexpr"
-    url      = "https://pypi.io/packages/source/n/numexpr/numexpr-2.6.1.tar.gz"
+    url      = "https://pypi.io/packages/source/n/numexpr/numexpr-2.6.5.tar.gz"
 
+    version('2.6.5', 'c9b5859c11bd6da092f6c8a84a472e77')
     version('2.6.1', '6365245705b446426df9543ad218dd8e')
     version('2.5',   '84f66cced45ba3e30dcf77a937763aaa')
     version('2.4.6', '17ac6fafc9ea1ce3eb970b9abccb4fbd')
diff --git a/var/spack/repos/builtin/packages/py-numexpr3/package.py b/var/spack/repos/builtin/packages/py-numexpr3/package.py
new file mode 100644
index 0000000000..9b5f1e7dd5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-numexpr3/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyNumexpr3(PythonPackage):
+    """Numexpr3 is a fast numerical expression evaluator for NumPy. With it,
+    expressions that operate on arrays (like "3*a+4*b") are accelerated and
+    use less memory than doing the same calculation in Python.
+    In addition, its multi-threaded capabilities can make use of all your
+    cores, which may accelerate computations, most specially if they are not
+    memory-bounded (e.g. those using transcendental functions).
+    Compared to NumExpr 2.6, functions have been re-written in a fashion such
+    that gcc can auto-vectorize them with SIMD instruction sets such as
+    SSE2 or AVX2, if your processor supports them. Use of a newer version of
+    gcc such as 5.4 is strongly recommended."""
+    homepage = "https://github.com/pydata/numexpr/tree/numexpr-3.0"
+    url = "https://pypi.io/packages/source/n/numexpr3/numexpr3-3.0.1a1.tar.gz"
+
+    version('3.0.1.a1', '9fa8dc59b149aa1956fc755f982a78ad')
+    # TODO: Add CMake build system for better control of passing flags related
+    # to CPU ISA.
+
+    depends_on('python@2.6:2.8,3.3:', type=('build', 'run'))
+    depends_on('py-numpy@1.7:', type=('build', 'run'))
+    depends_on('py-setuptools@18.2:', type='build')
diff --git a/var/spack/repos/builtin/packages/py-numpy/package.py b/var/spack/repos/builtin/packages/py-numpy/package.py
index f5126e36a0..39fb4f0c4c 100644
--- a/var/spack/repos/builtin/packages/py-numpy/package.py
+++ b/var/spack/repos/builtin/packages/py-numpy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import platform
 
@@ -34,7 +15,7 @@ class PyNumpy(PythonPackage):
     number capabilities"""
 
     homepage = "http://www.numpy.org/"
-    url      = "https://pypi.io/packages/source/n/numpy/numpy-1.13.1.zip"
+    url      = "https://pypi.io/packages/source/n/numpy/numpy-1.15.1.zip"
 
     install_time_test_callbacks = ['install_test', 'import_module_test']
 
@@ -45,9 +26,13 @@ class PyNumpy(PythonPackage):
         'numpy.distutils.command', 'numpy.distutils.fcompiler'
     ]
 
-    # FIXME: numpy._build_utils and numpy.core.code_generators failed to import
-    # FIXME: Is this expected?
-
+    version('1.15.2', sha256='27a0d018f608a3fe34ac5e2b876f4c23c47e38295c47dd0775cc294cd2614bc1')
+    version('1.15.1', '898004d5be091fde59ae353e3008fe9b')
+    version('1.14.3', '97416212c0a172db4bc6b905e9c4634b')
+    version('1.14.2', '080f01a19707cf467393e426382c7619')
+    version('1.14.1', 'b8324ef90ac9064cd0eac46b8b388674')
+    version('1.14.0', 'c12d4bf380ac925fcdc8a59ada6c3298')
+    version('1.13.3', '300a6f0528122128ac07c6deb5c95917')
     version('1.13.1', '2c3c0f4edf720c3a7b525dacc825b9ae')
     version('1.13.0', 'fd044f0b8079abeaf5e6d2e93b2c1d03')
     version('1.12.1', 'c75b072a984028ac746a6a332c209a91')
@@ -62,25 +47,21 @@ class PyNumpy(PythonPackage):
     variant('blas',   default=True, description='Build with BLAS support')
     variant('lapack', default=True, description='Build with LAPACK support')
 
-    depends_on('python@2.7:2.8,3.4:')
+    depends_on('python@2.7:2.8,3.4:', type=('build', 'run'))
     depends_on('py-setuptools', type='build')
     depends_on('blas',   when='+blas')
     depends_on('lapack', when='+lapack')
 
-    # Tests require:
-    # TODO: Add a 'test' deptype
-    # depends_on('py-nose@1.0.0:', type='test')
+    depends_on('py-nose@1.0.0:', when='@:1.14', type='test')
+    depends_on('py-pytest', when='@1.15:', type='test')
 
     def setup_dependent_package(self, module, dependent_spec):
         python_version = self.spec['python'].version.up_to(2)
-        arch = '{0}-{1}'.format(platform.system().lower(), platform.machine())
 
         self.spec.include = join_path(
             self.prefix.lib,
             'python{0}'.format(python_version),
             'site-packages',
-            'numpy-{0}-py{1}-{2}.egg'.format(
-                self.spec.version, python_version, arch),
             'numpy/core/include')
 
     def patch(self):
@@ -145,12 +126,27 @@ class PyNumpy(PythonPackage):
     def build_args(self, spec, prefix):
         args = []
 
-        # From NumPy 1.10.0 on it's possible to do a parallel build
+        # From NumPy 1.10.0 on it's possible to do a parallel build.
         if self.version >= Version('1.10.0'):
-            args = ['-j', str(make_jobs)]
+            # But Parallel build in Python 3.5+ is broken.  See:
+            # https://github.com/spack/spack/issues/7927
+            # https://github.com/scipy/scipy/issues/7112
+            if spec['python'].version < Version('3.5'):
+                args = ['-j', str(make_jobs)]
 
         return args
 
+    def setup_environment(self, spack_env, run_env):
+        python_version = self.spec['python'].version.up_to(2)
+
+        include_path = join_path(
+            self.prefix.lib,
+            'python{0}'.format(python_version),
+            'site-packages',
+            'numpy/core/include')
+
+        run_env.prepend_path('CPATH', include_path)
+
     def test(self):
         # `setup.py test` is not supported.  Use one of the following
         # instead:
@@ -167,5 +163,5 @@ class PyNumpy(PythonPackage):
         # ImportError: Error importing numpy: you should not try to import
         #       numpy from its source directory; please exit the numpy
         #       source tree, and relaunch your python interpreter from there.
-        with working_dir('..'):
+        with working_dir('spack-test', create=True):
             python('-c', 'import numpy; numpy.test("full", verbose=2)')
diff --git a/var/spack/repos/builtin/packages/py-numpydoc/package.py b/var/spack/repos/builtin/packages/py-numpydoc/package.py
index f0ecfbc411..48512b1943 100644
--- a/var/spack/repos/builtin/packages/py-numpydoc/package.py
+++ b/var/spack/repos/builtin/packages/py-numpydoc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-olefile/package.py b/var/spack/repos/builtin/packages/py-olefile/package.py
index 0925f67d96..3430f4360a 100644
--- a/var/spack/repos/builtin/packages/py-olefile/package.py
+++ b/var/spack/repos/builtin/packages/py-olefile/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-ont-fast5-api/package.py b/var/spack/repos/builtin/packages/py-ont-fast5-api/package.py
index d2e868c7c5..e31eeccefc 100644
--- a/var/spack/repos/builtin/packages/py-ont-fast5-api/package.py
+++ b/var/spack/repos/builtin/packages/py-ont-fast5-api/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-openpmd-validator/package.py b/var/spack/repos/builtin/packages/py-openpmd-validator/package.py
new file mode 100644
index 0000000000..64c33b8614
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-openpmd-validator/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyOpenpmdValidator(PythonPackage):
+    """Validator and Example Scripts for the openPMD markup.
+
+    openPMD is an open standard for particle-mesh data files."""
+
+    homepage = "http://www.openPMD.org"
+    url      = "https://github.com/openPMD/openPMD-validator/archive/1.0.0.2.tar.gz"
+    maintainers = ['ax3l']
+
+    version('1.0.0.2', '2b71b786288c1e7a2134bd6818ad1999')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-numpy@1.6.1:', type=('build', 'run'))
+    depends_on('py-dateutil@2.3.0:', type=('build', 'run'))
+    depends_on('py-h5py@2.0.0:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-openpyxl/package.py b/var/spack/repos/builtin/packages/py-openpyxl/package.py
index 6f28526b8e..b61118426e 100644
--- a/var/spack/repos/builtin/packages/py-openpyxl/package.py
+++ b/var/spack/repos/builtin/packages/py-openpyxl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-openslide-python/package.py b/var/spack/repos/builtin/packages/py-openslide-python/package.py
new file mode 100644
index 0000000000..5fcefccc7d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-openslide-python/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyOpenslidePython(PythonPackage):
+    """OpenSlide Python is a Python interface to the OpenSlide library."""
+
+    homepage = "https://github.com/openslide/openslide-python"
+    url      = "https://github.com/openslide/openslide-python/archive/v1.1.1.tar.gz"
+
+    version('1.1.1', '8c207e48069887b63ea1c7bc9eb7dfc0')
+
+    import_modules = ['openslide']
+
+    depends_on('openslide@3.4.0:')
+    depends_on('python@2.6:2.8,3.3:')
+    depends_on('py-setuptools', type='build')
+    depends_on('py-pillow+jpeg+jpeg2000+tiff', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-opentuner/package.py b/var/spack/repos/builtin/packages/py-opentuner/package.py
new file mode 100644
index 0000000000..77071a7c0d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-opentuner/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyOpentuner(PythonPackage):
+    """An extensible framework for program autotuning."""
+
+    homepage = "http://opentuner.org/"
+    git      = "https://github.com/jansel/opentuner.git"
+
+    version('0.8.0', commit='4cb9135')
+
+    # No support for Python 3 yet
+    depends_on('python@2.7:2.8', type=('build', 'run'))
+
+    depends_on('py-argparse@1.2.1:', type=('build', 'run'))
+    depends_on('py-fn@0.2.12:', type=('build', 'run'))
+    depends_on('py-numpy@1.8.0:', type=('build', 'run'))
+    depends_on('py-pysqlite@2.6.3:', type=('build', 'run'))
+    depends_on('py-setuptools', type='build')
+    depends_on('py-sqlalchemy@0.8.2:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-ordereddict/package.py b/var/spack/repos/builtin/packages/py-ordereddict/package.py
index 16587ba978..6167607cc7 100644
--- a/var/spack/repos/builtin/packages/py-ordereddict/package.py
+++ b/var/spack/repos/builtin/packages/py-ordereddict/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-oset/package.py b/var/spack/repos/builtin/packages/py-oset/package.py
index 10a5007932..808f785eb4 100644
--- a/var/spack/repos/builtin/packages/py-oset/package.py
+++ b/var/spack/repos/builtin/packages/py-oset/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-owslib/package.py b/var/spack/repos/builtin/packages/py-owslib/package.py
new file mode 100644
index 0000000000..dfb2372d8f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-owslib/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyOwslib(PythonPackage):
+    """OWSLib is a Python package for client programming with Open Geospatial
+    Consortium (OGC) web service (hence OWS) interface standards, and their
+    related content models."""
+
+    homepage = "http://http://geopython.github.io/OWSLib/#installation"
+    url      = "https://pypi.io/packages/source/O/OWSLib/OWSLib-0.16.0.tar.gz"
+
+    version('0.16.0', '7ff9c9edde95eadeb27ea8d8fbd1a2cf')
+
+    depends_on('py-setuptools',     type='build')
+    depends_on('py-dateutil@1.5:',  type=('build', 'run'))
+    depends_on('py-pytz',           type=('build', 'run'))
+    depends_on('py-requests@1.0:',  type=('build', 'run'))
+    depends_on('py-proj',           type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-packaging/package.py b/var/spack/repos/builtin/packages/py-packaging/package.py
index 0ee13a5cdf..71253f1689 100644
--- a/var/spack/repos/builtin/packages/py-packaging/package.py
+++ b/var/spack/repos/builtin/packages/py-packaging/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,10 +10,11 @@ class PyPackaging(PythonPackage):
     """Core utilities for Python packages."""
 
     homepage = "https://github.com/pypa/packaging"
-    url      = "https://pypi.io/packages/source/p/packaging/packaging-16.8.tar.gz"
+    url      = "https://pypi.io/packages/source/p/packaging/packaging-17.1.tar.gz"
 
     import_modules = ['packaging']
 
+    version('17.1', '8baf8241d1b6b0a5fae9b00f359976a8')
     version('16.8', '53895cdca04ecff80b54128e475b5d3b')
 
     # Not needed for the installation, but used at runtime
diff --git a/var/spack/repos/builtin/packages/py-palettable/package.py b/var/spack/repos/builtin/packages/py-palettable/package.py
index 65b7a9a27b..9bef932156 100644
--- a/var/spack/repos/builtin/packages/py-palettable/package.py
+++ b/var/spack/repos/builtin/packages/py-palettable/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pandas/package.py b/var/spack/repos/builtin/packages/py-pandas/package.py
index b6d8403502..3267ec1cd6 100644
--- a/var/spack/repos/builtin/packages/py-pandas/package.py
+++ b/var/spack/repos/builtin/packages/py-pandas/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,6 +19,9 @@ class PyPandas(PythonPackage):
     homepage = "http://pandas.pydata.org/"
     url = "https://pypi.io/packages/source/p/pandas/pandas-0.19.0.tar.gz"
 
+    version('0.23.4', sha256='5b24ca47acf69222e82530e89111dd9d14f9b970ab2cd3a1c2c78f0c4fbba4f4')
+    version('0.21.1', '42ae7f81b81a86c3f91f663b66c525f7')
+    version('0.19.2', '26df3ef7cd5686fa284321f4f48b38cd')
     version('0.19.0', 'bc9bb7188e510b5d44fbdd249698a2c3')
     version('0.18.0', 'f143762cd7a59815e348adf4308d2cf6')
     version('0.16.1', 'fac4f25748f9610a3e00e765474bdea8')
diff --git a/var/spack/repos/builtin/packages/py-paramiko/package.py b/var/spack/repos/builtin/packages/py-paramiko/package.py
index 90784be649..e0650560f0 100644
--- a/var/spack/repos/builtin/packages/py-paramiko/package.py
+++ b/var/spack/repos/builtin/packages/py-paramiko/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/py-partd/package.py b/var/spack/repos/builtin/packages/py-partd/package.py
new file mode 100644
index 0000000000..425b5566d7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-partd/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPartd(PythonPackage):
+    """Key-value byte store with appendable values."""
+
+    homepage = "http://github.com/dask/partd/"
+    url      = "https://pypi.io/packages/source/p/partd/partd-0.3.8.tar.gz"
+
+    import_modules = ['partd']
+
+    version('0.3.8', '554d0e6511c0df4c907f034858be847f')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-locket', type=('build', 'run'))
+    depends_on('py-toolz', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-pathlib2/package.py b/var/spack/repos/builtin/packages/py-pathlib2/package.py
index f5cf9cf381..e8dfd995aa 100644
--- a/var/spack/repos/builtin/packages/py-pathlib2/package.py
+++ b/var/spack/repos/builtin/packages/py-pathlib2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,13 @@ class PyPathlib2(PythonPackage):
     """Backport of pathlib from python 3.4"""
 
     homepage = "https://pypi.python.org/pypi/pathlib2"
-    url      = "https://pypi.io/packages/source/p/pathlib2/pathlib2-2.1.0.tar.gz"
+    url      = "https://pypi.io/packages/source/p/pathlib2/pathlib2-2.3.2.tar.gz"
+
+    import_modules = ['pathlib2']
 
+    version('2.3.2', 'fd76fb5d0baa798bfe12fb7965da97f8')
     version('2.1.0', '38e4f58b4d69dfcb9edb49a54a8b28d2')
 
     depends_on('py-setuptools', type='build')
-    depends_on('python@:3.3')
+    depends_on('py-six', type=('build', 'run'))
+    depends_on('py-scandir', when='^python@:3.4', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-pathos/package.py b/var/spack/repos/builtin/packages/py-pathos/package.py
index 1ebbae5cf2..5c713c3e0b 100644
--- a/var/spack/repos/builtin/packages/py-pathos/package.py
+++ b/var/spack/repos/builtin/packages/py-pathos/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pathspec/package.py b/var/spack/repos/builtin/packages/py-pathspec/package.py
index 8857ee40f5..8320b653f0 100644
--- a/var/spack/repos/builtin/packages/py-pathspec/package.py
+++ b/var/spack/repos/builtin/packages/py-pathspec/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-patsy/package.py b/var/spack/repos/builtin/packages/py-patsy/package.py
index 1b60b76cd7..44882fed93 100644
--- a/var/spack/repos/builtin/packages/py-patsy/package.py
+++ b/var/spack/repos/builtin/packages/py-patsy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -41,5 +22,4 @@ class PyPatsy(PythonPackage):
     depends_on('py-scipy',       type=('build', 'run'), when="+splines")
     depends_on('py-six',         type=('build', 'run'))
 
-    # TODO: Add a 'test' deptype
-    # depends_on('py-nose', type='test')
+    depends_on('py-nose', type='test')
diff --git a/var/spack/repos/builtin/packages/py-pbr/package.py b/var/spack/repos/builtin/packages/py-pbr/package.py
index 4ada322c89..edb79072c3 100644
--- a/var/spack/repos/builtin/packages/py-pbr/package.py
+++ b/var/spack/repos/builtin/packages/py-pbr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,6 +12,8 @@ class PyPbr(PythonPackage):
     homepage = "https://pypi.python.org/pypi/pbr"
     url      = "https://pypi.io/packages/source/p/pbr/pbr-1.10.0.tar.gz"
 
+    version('3.1.1', '4e82c2e07af544c56a5b71c801525b00')
+    version('2.0.0', 'dfc1c3788eff06acfaade6f1655fa490')
     version('1.10.0', '8e4968c587268f030e38329feb9c8f17')
     version('1.8.1', 'c8f9285e1a4ca6f9654c529b158baa3a')
 
diff --git a/var/spack/repos/builtin/packages/py-pep8-naming/package.py b/var/spack/repos/builtin/packages/py-pep8-naming/package.py
new file mode 100644
index 0000000000..796e18a18f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pep8-naming/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPep8Naming(PythonPackage):
+    """Check PEP-8 naming conventions, plugin for flake8."""
+
+    homepage = "https://pypi.org/project/pep8-naming/"
+    url      = "https://files.pythonhosted.org/packages/3e/4a/125425d6b1e017f48dfc9c961f4bb9510168db7a090618906c750184ed03/pep8-naming-0.7.0.tar.gz"
+
+    extends('python', ignore='bin/(flake8|pyflakes|pycodestyle)')
+    version('0.7.0', '624258e0dd06ef32a9daf3c36cc925ff7314da7233209c5b01f7e5cdd3c34826')
+
+    depends_on('py-flake8-polyfill', type='run')
diff --git a/var/spack/repos/builtin/packages/py-perf/package.py b/var/spack/repos/builtin/packages/py-perf/package.py
new file mode 100644
index 0000000000..4925611f02
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-perf/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPerf(PythonPackage):
+    """The Python perf module is a toolkit to write, run and
+    analyze benchmarks.
+    """
+
+    homepage = "https://pypi.python.org/pypi/perf"
+    url = "https://github.com/vstinner/perf/archive/1.5.1.tar.gz"
+
+    version('1.5.1', 'e3dc532fdbaf44f2d921556164bd74e5')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-six', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-performance/package.py b/var/spack/repos/builtin/packages/py-performance/package.py
new file mode 100644
index 0000000000..445c365025
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-performance/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPerformance(PythonPackage):
+    """The performance project is intended to be an authoritative source
+    of benchmarks for all Python implementations.
+
+    The focus is on real-world benchmarks, rather than synthetic benchmarks,
+    using whole applications when possible.
+    """
+
+    homepage = 'http://pyperformance.readthedocs.io/'
+    url = 'https://github.com/python/performance/archive/0.6.1.tar.gz'
+
+    version('0.6.1', '95477b584a284582b66c922a5335b427')
+    version('0.6.0', 'b93661e07668fa0b461236dca164eedf')
+
+    depends_on('py-setuptools', type=('build', 'run'))
+    depends_on('py-six', type=('build', 'run'))
+    depends_on('py-perf', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-periodictable/package.py b/var/spack/repos/builtin/packages/py-periodictable/package.py
index 6b6cd2ecf5..0d51387392 100644
--- a/var/spack/repos/builtin/packages/py-periodictable/package.py
+++ b/var/spack/repos/builtin/packages/py-periodictable/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-petsc4py/package.py b/var/spack/repos/builtin/packages/py-petsc4py/package.py
index 383c11fd94..4e4d00f139 100644
--- a/var/spack/repos/builtin/packages/py-petsc4py/package.py
+++ b/var/spack/repos/builtin/packages/py-petsc4py/package.py
@@ -1,38 +1,24 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class PyPetsc4py(PythonPackage):
     """This package provides Python bindings for the PETSc package.
     """
+
     homepage = "https://pypi.python.org/pypi/petsc4py"
-    url      = "https://pypi.io/packages/source/p/petsc4py/petsc4py-3.7.0.tar.gz"
+    url      = "https://pypi.io/packages/source/p/petsc4py/petsc4py-3.8.1.tar.gz"
 
+    version('3.8.1', '5157220c2b81765c581d2b17c03259f8')
+    version('3.8.0', '02029be4bdec904854f0e0692005fb06')
     version('3.7.0', '816a20040a6a477bd637f397c9fb5b6d')
 
+    depends_on('python@2.6:2.8,3.3:', type=('build', 'run'))
     depends_on('py-setuptools', type='build')
+    depends_on('py-numpy', type=('build', 'run'))
     depends_on('py-mpi4py', type=('build', 'run'))
     depends_on('petsc+mpi')
diff --git a/var/spack/repos/builtin/packages/py-pexpect/package.py b/var/spack/repos/builtin/packages/py-pexpect/package.py
index 8900698f00..85ed20ac81 100644
--- a/var/spack/repos/builtin/packages/py-pexpect/package.py
+++ b/var/spack/repos/builtin/packages/py-pexpect/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-phonopy/package.py b/var/spack/repos/builtin/packages/py-phonopy/package.py
index fd45d7db28..0e939406a6 100644
--- a/var/spack/repos/builtin/packages/py-phonopy/package.py
+++ b/var/spack/repos/builtin/packages/py-phonopy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pickleshare/package.py b/var/spack/repos/builtin/packages/py-pickleshare/package.py
index da8bdccb5e..c2b61fb28d 100644
--- a/var/spack/repos/builtin/packages/py-pickleshare/package.py
+++ b/var/spack/repos/builtin/packages/py-pickleshare/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-picrust/package.py b/var/spack/repos/builtin/packages/py-picrust/package.py
new file mode 100644
index 0000000000..347f199441
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-picrust/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPicrust(PythonPackage):
+    """bioinformatics software package designed to predict metagenome
+        functional content from marker gene surveys and full genomes."""
+
+    homepage = "http://picrust.github.io/picrust/index.html"
+    url      = "https://github.com/picrust/picrust/releases/download/v1.1.3/picrust-1.1.3.tar.gz"
+
+    version('1.1.3', sha256='7538c8544899b8855deb73a2d7a4ccac4808ff294e161530a8c8762d472d8906')
+
+    depends_on('python@2.7:2.999', type=('build', 'run'))
+    depends_on('py-cogent@1.5.3', type=('build', 'run'))
+    depends_on('py-biom-format@2.1.4:2.1.999', type=('build', 'run'))
+    depends_on('py-setuptools', type='build')
+    depends_on('py-future@0.16.0', type=('build', 'run'))
+    depends_on('py-numpy@1.5.1:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-pil/package.py b/var/spack/repos/builtin/packages/py-pil/package.py
index 332a7e91ee..4bbecf9a47 100644
--- a/var/spack/repos/builtin/packages/py-pil/package.py
+++ b/var/spack/repos/builtin/packages/py-pil/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pillow/package.py b/var/spack/repos/builtin/packages/py-pillow/package.py
index 3b54ee32ae..2bce199940 100644
--- a/var/spack/repos/builtin/packages/py-pillow/package.py
+++ b/var/spack/repos/builtin/packages/py-pillow/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import sys
 
@@ -33,17 +14,10 @@ class PyPillow(PythonPackage):
     capabilities."""
 
     homepage = "https://python-pillow.org/"
-    url = "https://pypi.io/packages/source/P/Pillow/Pillow-3.0.0.tar.gz"
-
-    # TODO: This version should be deleted once the next release comes out.
-    # TODO: It fixes a bug that prevented us from linking to Tk/Tcl.
-    # TODO: Tk/Tcl support is necessary for tkinter bitmap and photo images.
-    # TODO: If you require this support, run the following command:
-    # TODO:     `spack install py-pillow@3.3.0.dev0 ^python+tk`
-    version('3.3.0.dev0', git='https://github.com/python-pillow/Pillow.git',
-            commit='30eced62868141a6c859a4370efd40b9434a7c3f')
+    url = "https://pypi.io/packages/source/P/Pillow/Pillow-5.1.0.tar.gz"
 
-    version('3.2.0', '7cfd093c11205d9e2ebe3c51dfcad510', preferred=True)
+    version('5.1.0', '308f9c13b376abce96ab6ebd6c889cc4')
+    version('3.2.0', '7cfd093c11205d9e2ebe3c51dfcad510')
     version('3.0.0', 'fc8ac44e93da09678eac7e30c9b7377d')
 
     provides('pil')
@@ -54,8 +28,7 @@ class PyPillow(PythonPackage):
     variant('tiff', default=False, description='Access to TIFF files')
     variant('freetype', default=False, description='Font related services')
     variant('lcms', default=False, description='Color management')
-    variant('jpeg2000', default=False,
-            description='Provide JPEG 2000 functionality')
+    variant('jpeg2000', default=False, description='Provide JPEG 2000 functionality')
 
     # Spack does not (yet) support these modes of building
     # variant('webp', default=False, description='Provide the WebP format')
@@ -94,8 +67,8 @@ class PyPillow(PythonPackage):
 
         if '+jpeg' in spec:
             setup.filter('JPEG_ROOT = None',
-                         'JPEG_ROOT = ("{0}", "{1}")'.format(
-                             spec['jpeg'].prefix.lib,
+                         'JPEG_ROOT=("{0}","{1}")'.format(
+                             spec['jpeg'].libs.directories[0],
                              spec['jpeg'].prefix.include))
         if '+zlib' in spec:
             setup.filter('ZLIB_ROOT = None',
diff --git a/var/spack/repos/builtin/packages/py-pip/package.py b/var/spack/repos/builtin/packages/py-pip/package.py
index d0da3dd153..def321c229 100644
--- a/var/spack/repos/builtin/packages/py-pip/package.py
+++ b/var/spack/repos/builtin/packages/py-pip/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,6 +12,7 @@ class PyPip(PythonPackage):
     homepage = "https://pypi.python.org/pypi/pip"
     url      = "https://pypi.io/packages/source/p/pip/pip-9.0.1.tar.gz"
 
+    version('10.0.1', '83a177756e2c801d0b3a6f7b0d4f3f7e')
     version('9.0.1', '35f01da33009719497f01a4ba69d63c9')
 
     depends_on('python@2.6:2.8,3.3:')
diff --git a/var/spack/repos/builtin/packages/py-pipits/package.py b/var/spack/repos/builtin/packages/py-pipits/package.py
index e24f4718db..beef939772 100644
--- a/var/spack/repos/builtin/packages/py-pipits/package.py
+++ b/var/spack/repos/builtin/packages/py-pipits/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pkgconfig/package.py b/var/spack/repos/builtin/packages/py-pkgconfig/package.py
index eb3be23871..ccab4d8cad 100644
--- a/var/spack/repos/builtin/packages/py-pkgconfig/package.py
+++ b/var/spack/repos/builtin/packages/py-pkgconfig/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,7 +17,6 @@ class PyPkgconfig(PythonPackage):
     depends_on('python@2.6:')
     depends_on('py-setuptools', type='build')
 
-    depends_on('pkg-config', type=('build', 'run'))
+    depends_on('pkgconfig', type=('build', 'run'))
 
-    # TODO: Add a 'test' deptype
-    # depends_on('py-nose@1.0:', type='test')
+    depends_on('py-nose@1.0:', type=('build', 'test'))
diff --git a/var/spack/repos/builtin/packages/py-plotly/package.py b/var/spack/repos/builtin/packages/py-plotly/package.py
new file mode 100644
index 0000000000..6ad7a68a7e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-plotly/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPlotly(PythonPackage):
+    """An interactive, browser-based graphing library for Python"""
+
+    homepage = "https://plot.ly/python/"
+    url      = "https://github.com/plotly/plotly.py/archive/v2.2.0.tar.gz"
+
+    version('2.2.0', '835802cdc6743439ff993447dfe47a0e')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-requests@2.3.0', type=('build', 'run'))
+    depends_on('py-six@1.8.0', type=('build', 'run'))
+    depends_on('py-pytz@2014.9', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-pluggy/package.py b/var/spack/repos/builtin/packages/py-pluggy/package.py
new file mode 100644
index 0000000000..62e50a6710
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pluggy/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPluggy(PythonPackage):
+    """Plugin and hook calling mechanisms for python."""
+
+    homepage = "https://github.com/pytest-dev/pluggy"
+    url      = "https://pypi.io/packages/source/p/pluggy/pluggy-0.7.1.tar.gz"
+
+    import_modules = ['pluggy']
+
+    version('0.7.1', 'cd5cc1003143f86dd6e2a865a20f8837')
+    version('0.6.0', 'ffdde7c3a5ba9a440404570366ffb6d5')
+
+    depends_on('python@2.7:2.8,3.4:', type=('build', 'run'))
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-setuptools-scm', type='build')
diff --git a/var/spack/repos/builtin/packages/py-ply/package.py b/var/spack/repos/builtin/packages/py-ply/package.py
index f1ccd85c3f..38d81ee10d 100644
--- a/var/spack/repos/builtin/packages/py-ply/package.py
+++ b/var/spack/repos/builtin/packages/py-ply/package.py
@@ -1,33 +1,15 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class PyPly(PythonPackage):
     """PLY is nothing more than a straightforward lex/yacc implementation."""
     homepage = "http://www.dabeaz.com/ply"
-    url      = "http://www.dabeaz.com/ply/ply-3.8.tar.gz"
+    url      = "https://github.com/dabeaz/ply/archive/3.11.tar.gz"
 
-    version('3.8', '94726411496c52c87c2b9429b12d5c50')
+    version('3.11', '6465f602e656455affcd7c5734c638f8')
+    version('3.8', '94726411496c52c87c2b9429b12d5c50', url='http://www.dabeaz.com/ply/ply-3.8.tar.gz')
diff --git a/var/spack/repos/builtin/packages/py-pmw/package.py b/var/spack/repos/builtin/packages/py-pmw/package.py
index b22499d137..f2f775ced7 100644
--- a/var/spack/repos/builtin/packages/py-pmw/package.py
+++ b/var/spack/repos/builtin/packages/py-pmw/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-poster/package.py b/var/spack/repos/builtin/packages/py-poster/package.py
new file mode 100644
index 0000000000..dc1a569dc6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-poster/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPoster(PythonPackage):
+    """Streaming HTTP uploads and multipart/form-data encoding."""
+
+    homepage = "https://pypi.org/project/poster/"
+    url      = "https://atlee.ca/software/poster/dist/0.8.1/poster-0.8.1.tar.gz"
+
+    version('0.8.1', '2db12704538781fbaa7e63f1505d6fc8')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-pox/package.py b/var/spack/repos/builtin/packages/py-pox/package.py
index a4fe508ab2..cf4471c461 100644
--- a/var/spack/repos/builtin/packages/py-pox/package.py
+++ b/var/spack/repos/builtin/packages/py-pox/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-ppft/package.py b/var/spack/repos/builtin/packages/py-ppft/package.py
index ca14fbb6b0..eff3559e35 100644
--- a/var/spack/repos/builtin/packages/py-ppft/package.py
+++ b/var/spack/repos/builtin/packages/py-ppft/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-prettytable/package.py b/var/spack/repos/builtin/packages/py-prettytable/package.py
index 5f8378ca7c..1ebc32887d 100644
--- a/var/spack/repos/builtin/packages/py-prettytable/package.py
+++ b/var/spack/repos/builtin/packages/py-prettytable/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-progress/package.py b/var/spack/repos/builtin/packages/py-progress/package.py
new file mode 100644
index 0000000000..bf5697e4d9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-progress/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyProgress(PythonPackage):
+    """Easy progress reporting for Python"""
+
+    homepage = "https://github.com/verigak/progress/"
+    url      = "https://pypi.org/packages/source/p/progress/progress-1.4.tar.gz"
+
+    version('1.4', sha256='5e2f9da88ed8236a76fffbee3ceefd259589cf42dfbc2cec2877102189fae58a')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-proj/package.py b/var/spack/repos/builtin/packages/py-proj/package.py
index cea4f0c3ea..554b404742 100644
--- a/var/spack/repos/builtin/packages/py-proj/package.py
+++ b/var/spack/repos/builtin/packages/py-proj/package.py
@@ -1,39 +1,21 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class PyProj(PythonPackage):
     """Python interface to the PROJ.4 Library."""
+
     homepage = "http://jswhit.github.io/pyproj/"
     url      = "https://github.com/jswhit/pyproj/tarball/v1.9.5.1rel"
+    git      = "https://www.github.com/jswhit/pyproj.git"
 
     # This is not a tagged release of pyproj.
     # The changes in this "version" fix some bugs, especially with Python3 use.
-    version('1.9.5.1.1', git='https://www.github.com/jswhit/pyproj.git',
-            commit='0be612cc9f972e38b50a90c946a9b353e2ab140f')
+    version('1.9.5.1.1', commit='0be612cc9f972e38b50a90c946a9b353e2ab140f')
     version('1.9.5.1', 'a4b80d7170fc82aee363d7f980279835')
 
     depends_on('py-cython', type='build')
diff --git a/var/spack/repos/builtin/packages/py-projectq/package.py b/var/spack/repos/builtin/packages/py-projectq/package.py
new file mode 100644
index 0000000000..d322bbb4e1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-projectq/package.py
@@ -0,0 +1,39 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyProjectq(PythonPackage):
+    """
+    ProjectQ is an open-source software framework for quantum computing started
+    at ETH Zurich. It allows users to implement their quantum programs in
+    Python using a powerful and intuitive syntax. ProjectQ can then translate
+    these programs to any type of back-end, be it a simulator run on a
+    classical computer of an actual quantum chip.
+    """
+
+    # Homepage and git repository
+    homepage = "https://projectq.ch"
+    git      = "https://github.com/projectq-framework/projectq.git"
+
+    # Provided python modules
+    import_modules = ['projectq', 'projectq.backends', 'projectq.cengines',
+                      'projectq.libs', 'projectq.meta', 'projectq.ops',
+                      'projectq.setups', 'projectq.types']
+
+    # Versions
+    version('develop', branch='develop')
+    version('0.3.6', commit='fa484fe037a3a1772127bbd00fe4628ddba34611')
+
+    # Dependencies
+    depends_on('py-setuptools', type=('build'))
+    depends_on('py-numpy', type=('build', 'run'))
+    depends_on('py-scipy', type=('build', 'run'))
+    depends_on('py-future', type=('build', 'run'))
+    depends_on('py-pytest@3.1.0:', type=('test'))
+    depends_on('py-requests', type=('build', 'run'))
+    # conflict with pybind11@2.2.0 -> see requirements.txt
+    depends_on('py-pybind11@1.7:2.1,2.2.1:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-prompt-toolkit/package.py b/var/spack/repos/builtin/packages/py-prompt-toolkit/package.py
index f9b07f30d1..99e32ed782 100644
--- a/var/spack/repos/builtin/packages/py-prompt-toolkit/package.py
+++ b/var/spack/repos/builtin/packages/py-prompt-toolkit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-protobuf/package.py b/var/spack/repos/builtin/packages/py-protobuf/package.py
index fd3e4a6f09..1b8e99ddfd 100644
--- a/var/spack/repos/builtin/packages/py-protobuf/package.py
+++ b/var/spack/repos/builtin/packages/py-protobuf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,6 +17,12 @@ class PyProtobuf(PythonPackage):
     homepage = 'https://developers.google.com/protocol-buffers/'
     url      = 'https://pypi.io/packages/source/p/protobuf/protobuf-3.0.0b2.tar.gz'
 
+    variant('cpp', default=False,
+            description='Enable the cpp implementation')
+
+    version('3.5.2.post1', '3b60685732bd0cbdc802dfcb6071efbcf5d927ce3127c13c33ea1a8efae3aa76')
+    version('3.5.2', '09879a295fd7234e523b62066223b128c5a8a88f682e3aff62fb115e4a0d8be0')
+    version('3.5.1', '95b78959572de7d7fafa3acb718ed71f482932ddddddbd29ba8319c10639d863')
     version('3.0.0b2', 'f0d3bd2394345a9af4a277cd0302ae83')
     version('2.6.1', '6bf843912193f70073db7f22e2ea55e2')
     version('2.5.0', '338813f3629d59e9579fed9035ecd457')
@@ -43,3 +30,13 @@ class PyProtobuf(PythonPackage):
     version('2.3.0', 'bb020c962f252fe81bfda8fb433bafdd')
 
     depends_on('py-setuptools', type='build')
+    depends_on('protobuf', when='+cpp')
+
+    @when('+cpp')
+    def build_args(self, spec, prefix):
+        return ['--cpp_implementation']
+
+    @when('+cpp')
+    def install_args(self, spec, prefix):
+        args = super(PyProtobuf, self).install_args(spec, prefix)
+        return args + ['--cpp_implementation']
diff --git a/var/spack/repos/builtin/packages/py-psutil/package.py b/var/spack/repos/builtin/packages/py-psutil/package.py
index 60c3368966..2888c109bd 100644
--- a/var/spack/repos/builtin/packages/py-psutil/package.py
+++ b/var/spack/repos/builtin/packages/py-psutil/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,8 +12,9 @@ class PyPsutil(PythonPackage):
     in Python."""
 
     homepage = "https://pypi.python.org/pypi/psutil"
-    url      = "https://pypi.io/packages/source/p/psutil/psutil-5.0.1.tar.gz"
+    url      = "https://pypi.io/packages/source/p/psutil/psutil-5.4.5.tar.gz"
 
+    version('5.4.5', '7d3d7954782bba4a400e106e66f10656')
     version('5.0.1', '153dc8be94badc4072016ceeac7808dc')
 
     depends_on('python@2.6:')
diff --git a/var/spack/repos/builtin/packages/py-psyclone/package.py b/var/spack/repos/builtin/packages/py-psyclone/package.py
new file mode 100644
index 0000000000..218dedf9bf
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-psyclone/package.py
@@ -0,0 +1,43 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+#
+from spack import *
+
+
+class PyPsyclone(PythonPackage):
+    """Code generation for the PSyKAl framework from the GungHo project,
+       as used by the LFRic model at the UK Met Office."""
+
+    homepage = "https://github.com/stfc/PSyclone"
+    url      = "https://github.com/stfc/PSyclone/archive/1.5.1.tar.gz"
+    git      = "https://github.com/stfc/PSyclone.git"
+
+    version('develop', branch='master')
+    version('1.5.1', commit='eba7a097175b02f75dec70616cf267b7b3170d78')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-pyparsing', type=('build', 'run'))
+
+    # Test cases fail without compatible versions of py-fparser:
+    depends_on('py-fparser@0.0.5', type=('build', 'run'), when='@1.5.1')
+    depends_on('py-fparser', type=('build', 'run'), when='@1.5.2:')
+
+    # Dependencies only required for tests:
+    depends_on('py-numpy',  type='test')
+    depends_on('py-nose',   type='test')
+    depends_on('py-pytest', type='test')
+
+    @run_after('install')
+    @on_package_attributes(run_tests=True)
+    def check_build(self):
+        # Limit py.test to search inside the build tree:
+        touch('pytest.ini')
+        with working_dir('src'):
+            Executable('py.test')()
+
+    def setup_environment(self, spack_env, run_env):
+        # Allow testing with installed executables:
+        spack_env.prepend_path('PATH', self.prefix.bin)
diff --git a/var/spack/repos/builtin/packages/py-ptyprocess/package.py b/var/spack/repos/builtin/packages/py-ptyprocess/package.py
index f97ff6e048..cef35e3115 100644
--- a/var/spack/repos/builtin/packages/py-ptyprocess/package.py
+++ b/var/spack/repos/builtin/packages/py-ptyprocess/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pudb/package.py b/var/spack/repos/builtin/packages/py-pudb/package.py
index bbc89251fe..f37904194f 100644
--- a/var/spack/repos/builtin/packages/py-pudb/package.py
+++ b/var/spack/repos/builtin/packages/py-pudb/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/py-py/package.py b/var/spack/repos/builtin/packages/py-py/package.py
index 9706a2659d..51efc6ceae 100644
--- a/var/spack/repos/builtin/packages/py-py/package.py
+++ b/var/spack/repos/builtin/packages/py-py/package.py
@@ -1,41 +1,32 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class PyPy(PythonPackage):
-    """library with cross-python path, ini-parsing, io, code, log facilities"""
+    """Library with cross-python path, ini-parsing, io, code, log facilities"""
 
     homepage = "http://pylib.readthedocs.io/en/latest/"
-    url      = "https://pypi.io/packages/source/p/py/py-1.4.33.tar.gz"
+    url      = "https://pypi.io/packages/source/p/py/py-1.5.4.tar.gz"
 
     import_modules = [
-        'py', 'py._code', 'py._io', 'py._log', 'py._path', 'py._process',
+        'py', 'py._process', 'py._vendored_packages', 'py._path',
+        'py._log', 'py._code', 'py._io'
     ]
 
+    version('1.5.4',  '7502d66fa68ea4ae5b61c511cd177d6a')
+    version('1.5.3',  '667d37a148ad9fb81266492903f2d880')
     version('1.4.33', '15d7107cbb8b86593bf9afa16e56da65')
     version('1.4.31', '5d2c63c56dc3f2115ec35c066ecd582b')
 
+    depends_on('python@2.7:2.8,3.4:', type=('build', 'run'))
+
     depends_on('py-setuptools', type='build')
+    depends_on('py-setuptools-scm', type='build')
+
+    def test(self):
+        # Tests require pytest, creating a circular dependency
+        pass
diff --git a/var/spack/repos/builtin/packages/py-py2bit/package.py b/var/spack/repos/builtin/packages/py-py2bit/package.py
index 26d1f42a7b..2bb90a37a7 100644
--- a/var/spack/repos/builtin/packages/py-py2bit/package.py
+++ b/var/spack/repos/builtin/packages/py-py2bit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-py2cairo/package.py b/var/spack/repos/builtin/packages/py-py2cairo/package.py
index 30e363885d..13975addd2 100644
--- a/var/spack/repos/builtin/packages/py-py2cairo/package.py
+++ b/var/spack/repos/builtin/packages/py-py2cairo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,10 +19,9 @@ class PyPy2cairo(WafPackage):
     depends_on('python', type=('build', 'run'))
     depends_on('cairo@1.10.0:')
     depends_on('pixman')
-    depends_on('pkg-config', type='build')
+    depends_on('pkgconfig', type='build')
 
-    # TODO: Add a 'test' deptype
-    # depends_on('py-pytest', type='test')
+    depends_on('py-pytest', type='test')
 
     def installtest(self):
         with working_dir('test'):
diff --git a/var/spack/repos/builtin/packages/py-py2neo/package.py b/var/spack/repos/builtin/packages/py-py2neo/package.py
index 27bb043116..9ecc72d3ce 100644
--- a/var/spack/repos/builtin/packages/py-py2neo/package.py
+++ b/var/spack/repos/builtin/packages/py-py2neo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-py4j/package.py b/var/spack/repos/builtin/packages/py-py4j/package.py
index 0c7e41a1d7..c369fd3d98 100644
--- a/var/spack/repos/builtin/packages/py-py4j/package.py
+++ b/var/spack/repos/builtin/packages/py-py4j/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,10 @@ class PyPy4j(PythonPackage):
     objects."""
 
     homepage = "https://www.py4j.org/"
-    url = "https://pypi.io/packages/source/p/py4j/py4j-0.10.4.tar.gz"
+    url = "https://pypi.io/packages/source/p/py4j/py4j-0.10.4.zip"
 
-    version('0.10.4', 'de1ce072fb8d5bff8aba537b1700ace4')
-    version('0.10.3', '6c86aebb4f1cdd4bf192b16c8a8fe8e4')
+    version('0.10.6', sha256='d3e7ac7c2171c290eba87e70aa5095b7eb6d6ad34789c007c88d550d9f575083')
+    version('0.10.4', sha256='406fbfdbcbbb398739f61fafd25724670a405a668eb08c1721d832eadce06aae')
+    version('0.10.3', sha256='f4570108ad014dd52a65c2288418e31cb8227b5ecc39ad7fc7fe98314f7a26f2')
 
     depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-pyani/package.py b/var/spack/repos/builtin/packages/py-pyani/package.py
new file mode 100644
index 0000000000..b17125eddb
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pyani/package.py
@@ -0,0 +1,36 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPyani(PythonPackage):
+    """pyani is a Python3 module that provides support for calculating
+    average nucleotide identity (ANI) and related measures for whole genome
+    comparisons, and rendering relevant graphical summary output. Where
+    available, it takes advantage of multicore systems, and can integrate
+    with SGE/OGE-type job schedulers for the sequence comparisons."""
+
+    homepage = "http://widdowquinn.github.io/pyani"
+    url      = "https://pypi.io/packages/source/p/pyani/pyani-0.2.7.tar.gz"
+
+    version('0.2.7', '239ba630d375a81c35b7c60fb9bec6fa')
+    version('0.2.6', 'd5524b9a3c62c36063ed474ea95785c9')
+
+    depends_on('python@3.5:')
+    depends_on('py-setuptools', type='build')
+    depends_on('py-matplotlib', type=('build', 'run'))
+    depends_on('py-seaborn',    type=('build', 'run'))
+
+    # Required for ANI analysis
+    depends_on('py-biopython',  type=('build', 'run'))
+    depends_on('py-pandas',     type=('build', 'run'))
+    depends_on('py-scipy',      type=('build', 'run'))
+
+    # Required for ANIb analysis
+    depends_on('blast-plus~python', type='run')
+
+    # Required for ANIm analysis
+    depends_on('mummer', type='run')
diff --git a/var/spack/repos/builtin/packages/py-pyarrow/package.py b/var/spack/repos/builtin/packages/py-pyarrow/package.py
new file mode 100644
index 0000000000..650e209034
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pyarrow/package.py
@@ -0,0 +1,37 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPyarrow(PythonPackage):
+    """A cross-language development platform for in-memory data.
+
+    This package contains the Python bindings.
+    """
+
+    homepage = "http://arrow.apache.org"
+    url      = "https://pypi.org/packages/source/p/pyarrow/pyarrow-0.9.0.tar.gz"
+
+    version('0.11.0', sha256='07a6fd71c5d7440f2c42383dd2c5daa12d7f0a012f1e88288ed08a247032aead')
+    version('0.9.0', sha256='7db8ce2f0eff5a00d6da918ce9f9cfec265e13f8a119b4adb1595e5b19fd6242')
+
+    variant('parquet', default=False, description="Build with Parquet support")
+
+    depends_on('cmake@3.0.0:', type='build')
+    depends_on('pkg-config', type='build')
+    depends_on('py-setuptools', type='build')
+    depends_on('py-cython', type='build')
+
+    depends_on('arrow+python')
+    depends_on('arrow+parquet+python', when='+parquet')
+
+    phases = ['build_ext', 'install']
+
+    def build_ext_args(self, spec, prefix):
+        args = []
+        if spec.satisfies('+parquet'):
+            args.append('--with-parquet')
+        return args
diff --git a/var/spack/repos/builtin/packages/py-pyasn1/package.py b/var/spack/repos/builtin/packages/py-pyasn1/package.py
index 3a7fc949c5..e2bdf80d26 100644
--- a/var/spack/repos/builtin/packages/py-pyasn1/package.py
+++ b/var/spack/repos/builtin/packages/py-pyasn1/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/py-pybigwig/package.py b/var/spack/repos/builtin/packages/py-pybigwig/package.py
index 5c88d111f5..b0b33b76d4 100644
--- a/var/spack/repos/builtin/packages/py-pybigwig/package.py
+++ b/var/spack/repos/builtin/packages/py-pybigwig/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pybind11/package.py b/var/spack/repos/builtin/packages/py-pybind11/package.py
index aaa54370bf..b6e3118118 100644
--- a/var/spack/repos/builtin/packages/py-pybind11/package.py
+++ b/var/spack/repos/builtin/packages/py-pybind11/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,17 +17,41 @@ class PyPybind11(CMakePackage):
 
     homepage = "https://pybind11.readthedocs.io"
     url      = "https://github.com/pybind/pybind11/archive/v2.1.0.tar.gz"
+    git      = "https://github.com/pybind/pybind11.git"
 
+    version('develop', branch='master')
+    version('2.2.4', 'b69e83658513215b8d1443544d0549b7d231b9f201f6fc787a2b2218b408181e')
+    version('2.2.3', '55b637945bbf47d99d2c906bf0c13f49')
+    version('2.2.2', 'fc174e1bbfe7ec069af7eea86ec37b5c')
+    version('2.2.1', 'bab1d46bbc465af5af3a4129b12bfa3b')
     version('2.2.0', '978b26aea1c6bfc4f88518ef33771af2')
     version('2.1.1', '5518988698df937ccee53fb6ba91d12a')
     version('2.1.0', '3cf07043d677d200720c928569635e12')
 
-    depends_on('py-pytest', type=('build'))
+    depends_on('py-pytest', type='test')
+    depends_on('py-setuptools', type='build')
 
     extends('python')
 
+    # compiler support
+    conflicts('%gcc@:4.7')
+    conflicts('%clang@:3.2')
+    conflicts('%intel@:16')
+
     def cmake_args(self):
         args = []
         args.append('-DPYTHON_EXECUTABLE:FILEPATH=%s'
                     % self.spec['python'].command.path)
+        args += [
+            '-DPYBIND11_TEST:BOOL={0}'.format(
+                'ON' if self.run_tests else 'OFF')
+        ]
         return args
+
+    def setup_environment(self, spack_env, run_env):
+        spack_env.set('PYBIND11_USE_CMAKE', 1)
+
+    def install(self, spec, prefix):
+        super(PyPybind11, self).install(spec, prefix)
+        setup_py('install', '--single-version-externally-managed', '--root=/',
+                 '--prefix={0}'.format(prefix))
diff --git a/var/spack/repos/builtin/packages/py-pybtex-docutils/package.py b/var/spack/repos/builtin/packages/py-pybtex-docutils/package.py
index 45371400a3..fa46889631 100644
--- a/var/spack/repos/builtin/packages/py-pybtex-docutils/package.py
+++ b/var/spack/repos/builtin/packages/py-pybtex-docutils/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pybtex/package.py b/var/spack/repos/builtin/packages/py-pybtex/package.py
index 606c047232..fd0bac735a 100644
--- a/var/spack/repos/builtin/packages/py-pybtex/package.py
+++ b/var/spack/repos/builtin/packages/py-pybtex/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/py-pycairo/package.py b/var/spack/repos/builtin/packages/py-pycairo/package.py
new file mode 100644
index 0000000000..607981a060
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pycairo/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class PyPycairo(PythonPackage):
+    """Pycairo is a set of Python bindings for the cairo graphics library."""
+
+    homepage = "https://www.cairographics.org/pycairo/"
+    url      = "https://github.com/pygobject/pycairo/releases/download/v1.17.1/pycairo-1.17.1.tar.gz"
+    url      = "https://files.pythonhosted.org/packages/68/76/340ff847897296b2c8174dfa5a5ec3406e3ed783a2abac918cf326abad86/pycairo-1.17.1.tar.gz"
+
+    version('1.17.1', '34c1ee106655b450c4bd57e29371a4a7')
+
+    depends_on('cairo@1.2.0:')
+    depends_on('pkgconfig', type='build')
+    depends_on('py-setuptools', type='build')
+
+    @run_after('install')
+    def post_install(self):
+        src = self.prefix.lib + '/pkgconfig/py3cairo.pc'
+        dst = self.prefix.lib + '/pkgconfig/pycairo.pc'
+        if os.path.exists(src) and not os.path.exists(dst):
+            copy(src, dst)
diff --git a/var/spack/repos/builtin/packages/py-pychecker/package.py b/var/spack/repos/builtin/packages/py-pychecker/package.py
index 2f85fa88ac..49f4b39f86 100644
--- a/var/spack/repos/builtin/packages/py-pychecker/package.py
+++ b/var/spack/repos/builtin/packages/py-pychecker/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pycodestyle/package.py b/var/spack/repos/builtin/packages/py-pycodestyle/package.py
index 3bae7c4296..10f97547c5 100644
--- a/var/spack/repos/builtin/packages/py-pycodestyle/package.py
+++ b/var/spack/repos/builtin/packages/py-pycodestyle/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,6 +13,10 @@ class PyPycodestyle(PythonPackage):
     homepage = "https://github.com/PyCQA/pycodestyle"
     url      = "https://github.com/PyCQA/pycodestyle/archive/2.0.0.tar.gz"
 
+    version('2.3.1', '4185319f6137833eec9057dbf3293629')
+    version('2.3.0', '1b2019b3c39c20becadbb7fdec6dcb5a')
+    version('2.2.0', '6e21aab2e038c3dd38dca585011a6f38')
+    version('2.1.0', '1e606c687a6cf01d51305417d0e97824')
     version('2.0.0', '5c3e90001f538bf3b7896d60e92eb6f6')
     version('1.7.0', '31070a3a6391928893cbf5fa523eb8d9')
     version('1.6.2', '8df18246d82ddd3d19ffe7518f983955')
diff --git a/var/spack/repos/builtin/packages/py-pycparser/package.py b/var/spack/repos/builtin/packages/py-pycparser/package.py
index 256130b1b7..3fa5a0acb3 100644
--- a/var/spack/repos/builtin/packages/py-pycparser/package.py
+++ b/var/spack/repos/builtin/packages/py-pycparser/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,6 +13,7 @@ class PyPycparser(PythonPackage):
 
     import_modules = ['pycparser', 'pycparser.ply']
 
+    version('2.18', '72370da54358202a60130e223d488136')
     version('2.17', 'ca98dcb50bc1276f230118f6af5a40c7')
     version('2.13', 'e4fe1a2d341b22e25da0d22f034ef32f')
 
diff --git a/var/spack/repos/builtin/packages/py-pycrypto/package.py b/var/spack/repos/builtin/packages/py-pycrypto/package.py
index 948a4f7cbd..9bacd5b4ba 100644
--- a/var/spack/repos/builtin/packages/py-pycrypto/package.py
+++ b/var/spack/repos/builtin/packages/py-pycrypto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/py-pycurl/package.py b/var/spack/repos/builtin/packages/py-pycurl/package.py
index c111430b9e..85074d6341 100644
--- a/var/spack/repos/builtin/packages/py-pycurl/package.py
+++ b/var/spack/repos/builtin/packages/py-pycurl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pydatalog/package.py b/var/spack/repos/builtin/packages/py-pydatalog/package.py
index 9bd5c898a2..cbcedc385f 100644
--- a/var/spack/repos/builtin/packages/py-pydatalog/package.py
+++ b/var/spack/repos/builtin/packages/py-pydatalog/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pydispatcher/package.py b/var/spack/repos/builtin/packages/py-pydispatcher/package.py
index 9e329ab70c..89efd4f463 100644
--- a/var/spack/repos/builtin/packages/py-pydispatcher/package.py
+++ b/var/spack/repos/builtin/packages/py-pydispatcher/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pydot/package.py b/var/spack/repos/builtin/packages/py-pydot/package.py
index c6067c00a1..ed941e9513 100644
--- a/var/spack/repos/builtin/packages/py-pydot/package.py
+++ b/var/spack/repos/builtin/packages/py-pydot/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pyelftools/package.py b/var/spack/repos/builtin/packages/py-pyelftools/package.py
index a7d52ee946..632ee37917 100644
--- a/var/spack/repos/builtin/packages/py-pyelftools/package.py
+++ b/var/spack/repos/builtin/packages/py-pyelftools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pyepsg/package.py b/var/spack/repos/builtin/packages/py-pyepsg/package.py
new file mode 100644
index 0000000000..4771e56d4b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pyepsg/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPyepsg(PythonPackage):
+    """Provides simple access to http://epsg.io/."""
+
+    homepage = "https://pyepsg.readthedocs.io/en/latest/"
+    url      = "https://pypi.io/packages/source/p/pyepsg/pyepsg-0.3.2.tar.gz"
+
+    version('0.3.2', 'b0644187068a9b58378a5c58ad55b991')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-requests',   type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-pyfasta/package.py b/var/spack/repos/builtin/packages/py-pyfasta/package.py
index 40a5fcf46e..ba0a69838a 100644
--- a/var/spack/repos/builtin/packages/py-pyfasta/package.py
+++ b/var/spack/repos/builtin/packages/py-pyfasta/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,7 +11,7 @@ class PyPyfasta(PythonPackage):
        access to fasta sequence files"""
 
     homepage = "https://pypi.python.org/pypi/pyfasta/"
-    url      = "https://pypi.python.org/packages/be/3f/794fbcdaaa2113f0a1d16a962463896c1a6bdab77bd63f33a8f16aae6cdc/pyfasta-0.5.2.tar.gz"
+    url      = "https://pypi.io/packages/source/p/pyfasta/pyfasta-0.5.2.tar.gz"
 
     version('0.5.2', 'bf61ab997dca329675c3eb2ee7cdfcf2')
 
diff --git a/var/spack/repos/builtin/packages/py-pyfftw/package.py b/var/spack/repos/builtin/packages/py-pyfftw/package.py
index 4dd9fe1600..78a76f9a5d 100644
--- a/var/spack/repos/builtin/packages/py-pyfftw/package.py
+++ b/var/spack/repos/builtin/packages/py-pyfftw/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pyflakes/package.py b/var/spack/repos/builtin/packages/py-pyflakes/package.py
index 6f962ae4df..08c1229b7e 100644
--- a/var/spack/repos/builtin/packages/py-pyflakes/package.py
+++ b/var/spack/repos/builtin/packages/py-pyflakes/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,6 +12,9 @@ class PyPyflakes(PythonPackage):
     homepage = "https://github.com/PyCQA/pyflakes"
     url      = "https://github.com/PyCQA/pyflakes/archive/1.3.0.tar.gz"
 
+    version('1.6.0', '68eff61e54964e6389f8fb1d2122fc5b')
+    version('1.5.0', '1dee2ca8a0520061aac5a82f3b539fa0')
+    version('1.4.0', 'ed832ef1cbd59463e5f0f6340254f603')
     version('1.3.0', 'a76173deb7a84fe860c0b60e2fbcdfe2')
     version('1.2.3', '2ac2e148a5c46b6bb06c4785be76f7cc')
     version('1.2.2', 'fe759b9381a6500e67a2ddbbeb5161a4')
diff --git a/var/spack/repos/builtin/packages/py-pygdbmi/package.py b/var/spack/repos/builtin/packages/py-pygdbmi/package.py
new file mode 100644
index 0000000000..f8198015f8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pygdbmi/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPygdbmi(PythonPackage):
+    """Parse gdb machine interface output with Python"""
+
+    homepage = "https://github.com/cs01/pygdbmi"
+    url      = "https://pypi.io/packages/source/p/pygdbmi/pygdbmi-0.8.2.0.tar.gz"
+
+    version('0.8.2.0', 'e74d3d02fa5eef1223b5dedb13f9bbad')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-pygments/package.py b/var/spack/repos/builtin/packages/py-pygments/package.py
index 8c6ee04db8..1909a2da11 100644
--- a/var/spack/repos/builtin/packages/py-pygments/package.py
+++ b/var/spack/repos/builtin/packages/py-pygments/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pygobject/package.py b/var/spack/repos/builtin/packages/py-pygobject/package.py
index 6c81418fce..1dd08a30d0 100644
--- a/var/spack/repos/builtin/packages/py-pygobject/package.py
+++ b/var/spack/repos/builtin/packages/py-pygobject/package.py
@@ -1,47 +1,32 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class PyPygobject(AutotoolsPackage):
+class PyPygobject(PythonPackage):
     """bindings for the GLib, and GObject,
        to be used in Python."""
 
     homepage = "https://pypi.python.org/pypi/pygobject"
 
-    url      = "http://ftp.gnome.org/pub/GNOME/sources/pygobject/2.28/pygobject-2.28.6.tar.bz2"
-
-    version('2.28.6', 'a43d783228dd32899e6908352b8308f3')
-    version('2.28.3', 'aa64900b274c4661a5c32e52922977f9')
+    version('3.28.3', '3bac63c86bb963aa401f97859464aa90')
+    version('2.28.6', '9415cb7f2b3a847f2310ccea258b101e')
+    version('2.28.3', 'aa64900b274c4661a5c32e52922977f9',
+            url='http://ftp.gnome.org/pub/GNOME/sources/pygobject/2.28/pygobject-2.28.3.tar.bz2')
 
     extends('python')
 
+    depends_on('py-setuptools', type=('build'))
     depends_on("libffi")
     depends_on('glib')
-    depends_on('py-py2cairo', type=('build', 'run'))
+    depends_on('python@2:2.99', when='@2:2.99', type=('build', 'run'))
+    depends_on('py-pycairo', type=('build', 'run'), when='@3:')
+    depends_on('py-py2cairo', type=('build', 'run'), when='@2:2.99')
     depends_on('gobject-introspection')
+    depends_on('gtkplus', when='@3:')
 
     patch('pygobject-2.28.6-introspection-1.patch', when='@2.28.3:2.28.6')
 
@@ -49,5 +34,22 @@ class PyPygobject(AutotoolsPackage):
     # for https://bugzilla.gnome.org/show_bug.cgi?id=668522
     patch('pygobject-2.28.6-gio-types-2.32.patch', when='@2.28.6')
 
+    def url_for_version(self, version):
+        url = 'http://ftp.gnome.org/pub/GNOME/sources/pygobject'
+        return url + '/%s/pygobject-%s.tar.xz' % (version.up_to(2), version)
+
+    # pygobject version 2 requires an autotools build
+    @when('@2:2.99')
+    def build(self, spec, prefix):
+        configure('--prefix=%s' % spec.prefix)
+
+    @when('@2:2.99')
     def install(self, spec, prefix):
         make('install', parallel=False)
+
+    @when('^python@3:')
+    def patch(self):
+        filter_file(
+            r'Pycairo_IMPORT',
+            r'//Pycairo_IMPORT',
+            'gi/pygi-foreign-cairo.c')
diff --git a/var/spack/repos/builtin/packages/py-pygpu/package.py b/var/spack/repos/builtin/packages/py-pygpu/package.py
new file mode 100644
index 0000000000..f5838c740b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pygpu/package.py
@@ -0,0 +1,33 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPygpu(PythonPackage):
+    """Python packge for the libgpuarray C library."""
+
+    homepage = "http://deeplearning.net/software/libgpuarray/"
+    url      = "https://github.com/Theano/libgpuarray/archive/v0.6.1.tar.gz"
+
+    version('0.7.5', '2534011464555c3e99d14231db965c20')
+    version('0.7.4', '19f57cd381175162048c8154f5251546')
+    version('0.7.3', 'cb44aeb8482330974abdb36b0a477e5d')
+    version('0.7.2', '0f9d7748501bc5c71bf04aae2285ac4e')
+    version('0.7.1', '7eb5bb6689ddbc386a9d498f5c0027fb')
+    version('0.7.0', 'f71b066f21ef7666f3a851e96c26f52e')
+    version('0.6.9', '7f75c39f1436c920ed9c5ffde5631fc0')
+    version('0.6.2', '7f163bd5f48f399cd6e608ee3d528ee4')
+    version('0.6.1', 'cfcd1b54447f9d55b05514df62c70ae2')
+    version('0.6.0', '98a4ec1b4c8f225f0b89c18b899a000b')
+
+    depends_on('libgpuarray')
+    # not just build-time, requires pkg_resources
+    depends_on('py-setuptools', type=('build', 'run'))
+    depends_on('py-cython@0.25:', type=('build', 'run'))
+    depends_on('py-nose', type=('build', 'run'))
+    depends_on('py-numpy', type=('build', 'run'))
+    depends_on('py-mako', type=('build', 'run'))
+    depends_on('libcheck')
diff --git a/var/spack/repos/builtin/packages/py-pygtk/package.py b/var/spack/repos/builtin/packages/py-pygtk/package.py
index 5a05a3a402..28b2cacd27 100644
--- a/var/spack/repos/builtin/packages/py-pygtk/package.py
+++ b/var/spack/repos/builtin/packages/py-pygtk/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,11 +15,18 @@ class PyPygtk(AutotoolsPackage):
     version('2.24.0', 'd27c7f245a9e027f6b6cd9acb7468e36')
 
     extends('python')
+
+    depends_on('pkgconfig', type=('build'))
     depends_on("libffi")
+    # atk@2.28.1 depends on meson which requires python 3
+    depends_on('atk@:2.20.0')
+    # PyGTK requires python 2
+    # Use py-pygobject@3: for GTK bindings for python 3
+    depends_on('python@2:2.99', type=('build', 'run'))
     depends_on('cairo')
     depends_on('glib')
     # for GTK 3.X use pygobject 3.X instead of pygtk
-    depends_on('gtkplus+X@2.24:2.99')
+    depends_on('gtkplus@2.24:2.99')
     depends_on('py-pygobject@2.28:2.99', type=('build', 'run'))
     depends_on('py-py2cairo', type=('build', 'run'))
 
diff --git a/var/spack/repos/builtin/packages/py-pylint/package.py b/var/spack/repos/builtin/packages/py-pylint/package.py
index fb6cb2946e..404767e909 100644
--- a/var/spack/repos/builtin/packages/py-pylint/package.py
+++ b/var/spack/repos/builtin/packages/py-pylint/package.py
@@ -1,44 +1,32 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class PyPylint(PythonPackage):
     """array processing for numbers, strings, records, and objects."""
+
     homepage = "https://pypi.python.org/pypi/pylint"
-    url      = "https://pypi.io/packages/source/p/pylint/pylint-1.7.2.tar.gz"
+    url      = "https://pypi.io/packages/source/p/pylint/pylint-1.6.5.tar.gz"
 
-    version('1.7.2', '27ee752cdcfacb05bf4940947e6b35c6')
+    # version('1.7.2', '27ee752cdcfacb05bf4940947e6b35c6') # see dependencies
+    version('1.6.5', '31da2185bf59142479e4fa16d8a9e347')
     version('1.4.3', '5924c1c7ca5ca23647812f5971d0ea44')
     version('1.4.1', 'df7c679bdcce5019389038847e4de622')
 
     extends('python', ignore=r'bin/pytest')
-    depends_on('py-six', type=('build', 'run'))
     depends_on('py-astroid', type=('build', 'run'))
-    depends_on('py-logilab-common', type=('build', 'run'))
-    depends_on('py-setuptools', type='build')
-
-    # TODO: Add a 'test' deptype
-    # depends_on('py-nose', type='test')
+    # note there is no working version of astroid for this
+    depends_on('py-astroid@1.5.1:', type=('build', 'run'), when='@1.7:')
+    depends_on('py-six', type=('build', 'run'))
+    depends_on('py-isort@4.2.5:')
+    depends_on('py-mccabe')
+    depends_on('py-editdistance')
+    depends_on('py-setuptools@17.1:', type='build')
+    # depends_on('py-setuptools-scm@1.15.0:', type='build')
+    depends_on('py-configparser', when='^python@:2.8')
+    depends_on('py-backports-functools-lru-cache', when='^python@:2.8')
+    depends_on('py-singledispatch', when='^python@:3.3.99')
diff --git a/var/spack/repos/builtin/packages/py-pymatgen/package.py b/var/spack/repos/builtin/packages/py-pymatgen/package.py
index 78343e74ff..65c4337083 100644
--- a/var/spack/repos/builtin/packages/py-pymatgen/package.py
+++ b/var/spack/repos/builtin/packages/py-pymatgen/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pyminifier/package.py b/var/spack/repos/builtin/packages/py-pyminifier/package.py
index b4bc9e859b..4da150f949 100644
--- a/var/spack/repos/builtin/packages/py-pyminifier/package.py
+++ b/var/spack/repos/builtin/packages/py-pyminifier/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pymol/package.py b/var/spack/repos/builtin/packages/py-pymol/package.py
new file mode 100644
index 0000000000..1a23247499
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pymol/package.py
@@ -0,0 +1,32 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPymol(PythonPackage):
+    """PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D
+       visualization of proteins, small molecules, density, surfaces, and
+       trajectories. It also includes molecular editing, ray tracing, and
+       movies. Open Source PyMOL is free to everyone!"""
+
+    homepage = "https://pymol.org"
+    url      = "https://sourceforge.net/projects/pymol/files/pymol/2/pymol-v2.1.0.tar.bz2"
+
+    version('2.1.0', 'ef2ab2ce11d65785ca3258b4e6982dfb')
+
+    depends_on('python+tk', type=('build', 'run'))
+    depends_on('tcl')
+    depends_on('tk')
+    depends_on('py-pmw')
+    depends_on('gl')
+    depends_on('glu')
+    depends_on('glew')
+    depends_on('libpng')
+    depends_on('freetype')
+    depends_on('libxml2')
+    depends_on('msgpack-c')
+    depends_on('py-pyqt', type=('build', 'run'))
+    depends_on('freeglut')
diff --git a/var/spack/repos/builtin/packages/py-pympler/package.py b/var/spack/repos/builtin/packages/py-pympler/package.py
index 25766d10c4..7498f9e32e 100644
--- a/var/spack/repos/builtin/packages/py-pympler/package.py
+++ b/var/spack/repos/builtin/packages/py-pympler/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pymysql/package.py b/var/spack/repos/builtin/packages/py-pymysql/package.py
new file mode 100644
index 0000000000..22346c4dd0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pymysql/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPymysql(PythonPackage):
+    """Pure-Python MySQL client library"""
+
+    homepage = "https://github.com/PyMySQL/PyMySQL/"
+    url      = "https://pypi.io/packages/source/p/pymysql/PyMySQL-0.9.2.tar.gz"
+
+    version('0.9.2', sha256='9ec760cbb251c158c19d6c88c17ca00a8632bac713890e465b2be01fdc30713f')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-cryptography', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-pynn/package.py b/var/spack/repos/builtin/packages/py-pynn/package.py
index 23e9ab13a4..a91adb259c 100644
--- a/var/spack/repos/builtin/packages/py-pynn/package.py
+++ b/var/spack/repos/builtin/packages/py-pynn/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,10 +13,11 @@ class PyPynn(PythonPackage):
 
     homepage = "http://neuralensemble.org/PyNN/"
     url      = "https://pypi.io/packages/source/P/PyNN/PyNN-0.8.3.tar.gz"
+    git      = "https://github.com/NeuralEnsemble/PyNN.git"
 
+    version('0.9.1', '3b8a6c63dc59d7ac751029f84dcaf7e6')
     version('0.8.3', '28c63f898093806a57198e9271ed7b82')
-    version('0.8beta', git='https://github.com/NeuralEnsemble/PyNN.git',
-        commit='ffb0cb1661f2b0f2778db8f71865978fe7a7a6a4')
+    version('0.8beta', commit='ffb0cb1661f2b0f2778db8f71865978fe7a7a6a4')
     version('0.8.1', '7fb165ed5af35a115cb9c60991645ae6')
     version('0.7.5', 'd8280544e4c9b34b40fd372b16342841')
 
@@ -45,7 +27,8 @@ class PyPynn(PythonPackage):
     depends_on('py-numpy@1.5:',         type=('build', 'run'))
     depends_on('py-quantities@0.10:',   type=('build', 'run'))
     depends_on('py-lazyarray@0.2.9:',   type=('build', 'run'))
-    depends_on('py-neo@0.3:',           type=('build', 'run'))
 
-    # TODO: Add a 'test' deptype
-    # depends_on('py-mock@1.0:', type='test')
+    depends_on('py-neo@0.3:0.4.1',      type=('build', 'run'), when="@:0.8.3")
+    depends_on('py-neo@0.5.0:',         type=('build', 'run'), when="@0.9.0:")
+
+    depends_on('py-mock@1.0:', type='test')
diff --git a/var/spack/repos/builtin/packages/py-pypar/package.py b/var/spack/repos/builtin/packages/py-pypar/package.py
index ee1aa2735d..28fcada1fc 100644
--- a/var/spack/repos/builtin/packages/py-pypar/package.py
+++ b/var/spack/repos/builtin/packages/py-pypar/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pyparsing/package.py b/var/spack/repos/builtin/packages/py-pyparsing/package.py
index 0be88e638d..48626a37e4 100644
--- a/var/spack/repos/builtin/packages/py-pyparsing/package.py
+++ b/var/spack/repos/builtin/packages/py-pyparsing/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pypeflow/package.py b/var/spack/repos/builtin/packages/py-pypeflow/package.py
index 8eb353432c..d4abb9f330 100644
--- a/var/spack/repos/builtin/packages/py-pypeflow/package.py
+++ b/var/spack/repos/builtin/packages/py-pypeflow/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,11 +11,9 @@ class PyPypeflow(PythonPackage):
     library written in Python."""
 
     homepage = "https://github.com/PacificBiosciences/pypeFLOW"
-    url      = "https://github.com/PacificBiosciences/pypeFLOW"
+    git      = "https://github.com/PacificBiosciences/pypeFLOW.git"
 
-    version('2017-05-04',
-            git='https://github.com/PacificBiosciences/pypeFLOW.git',
-            commit='f23a1b290876bbdf130611000934ae4247158073')
+    version('2017-05-04', commit='f23a1b290876bbdf130611000934ae4247158073')
 
     depends_on('py-setuptools', type='build')
     depends_on('py-networkx@1.7:1.11', type=['build', 'run'])
diff --git a/var/spack/repos/builtin/packages/py-pyprof2html/package.py b/var/spack/repos/builtin/packages/py-pyprof2html/package.py
index efaa525267..275b52aa07 100644
--- a/var/spack/repos/builtin/packages/py-pyprof2html/package.py
+++ b/var/spack/repos/builtin/packages/py-pyprof2html/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pyqi/package.py b/var/spack/repos/builtin/packages/py-pyqi/package.py
new file mode 100644
index 0000000000..21fecdec19
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pyqi/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPyqi(PythonPackage):
+    """pyqi (canonically pronounced pie chee) is a Python framework designed
+       to support wrapping general commands in multiple types of interfaces,
+       including at the command line, HTML, and API levels."""
+
+    homepage = "https://pyqi.readthedocs.io"
+    url      = "https://pypi.io/packages/source/p/pyqi/pyqi-0.3.2.tar.gz"
+
+    version('0.3.2', '9507c06eeb22a816d963c860ad8e92ae')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-pyqt/package.py b/var/spack/repos/builtin/packages/py-pyqt/package.py
index 401cf8ded6..ce700d18bd 100644
--- a/var/spack/repos/builtin/packages/py-pyqt/package.py
+++ b/var/spack/repos/builtin/packages/py-pyqt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pyrad/package.py b/var/spack/repos/builtin/packages/py-pyrad/package.py
index 0b56dd3631..de0a082930 100644
--- a/var/spack/repos/builtin/packages/py-pyrad/package.py
+++ b/var/spack/repos/builtin/packages/py-pyrad/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pysam/package.py b/var/spack/repos/builtin/packages/py-pysam/package.py
index 7c3cccd21a..513a41f778 100644
--- a/var/spack/repos/builtin/packages/py-pysam/package.py
+++ b/var/spack/repos/builtin/packages/py-pysam/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,10 +11,18 @@ class PyPysam(PythonPackage):
        sets."""
 
     homepage = "https://pypi.python.org/pypi/pysam"
-    url      = "https://pypi.io/packages/source/p/pysam/pysam-0.11.2.2.tar.gz"
+    url      = "https://github.com/pysam-developers/pysam/archive/v0.14.1.tar.gz"
 
+    version('0.14.1', 'ad88fa5bbcc0fdf4a936734691d9c9d1')
+    version('0.13', 'a9b502dd1a7e6403e35e6972211688a2')
     version('0.11.2.2', '56230cd5f55b503845915b76c22d620a')
+    version('0.7.7', 'eaf9f37cbccc5e2708754d045909c1a0')
 
     depends_on('py-setuptools', type='build')
     depends_on('py-cython@0.21:', type='build')
+    depends_on('curl')
     depends_on('bcftools')
+    depends_on('htslib')
+    depends_on('samtools')
+
+    depends_on('htslib@:1.6', when='@:0.13')
diff --git a/var/spack/repos/builtin/packages/py-pyscaf/package.py b/var/spack/repos/builtin/packages/py-pyscaf/package.py
index a32a1aee55..508de86ad9 100644
--- a/var/spack/repos/builtin/packages/py-pyscaf/package.py
+++ b/var/spack/repos/builtin/packages/py-pyscaf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pyserial/package.py b/var/spack/repos/builtin/packages/py-pyserial/package.py
index 0ddc2c51de..cb747c2e27 100644
--- a/var/spack/repos/builtin/packages/py-pyserial/package.py
+++ b/var/spack/repos/builtin/packages/py-pyserial/package.py
@@ -1,31 +1,12 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class PyPyserial(Package):
+class PyPyserial(PythonPackage):
     """Python Serial Port Extension"""
 
     homepage = "https://github.com/pyserial/pyserial"
diff --git a/var/spack/repos/builtin/packages/py-pyshp/package.py b/var/spack/repos/builtin/packages/py-pyshp/package.py
new file mode 100644
index 0000000000..f416310fba
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pyshp/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPyshp(PythonPackage):
+    """The Python Shapefile Library (pyshp) reads and writes ESRI Shapefiles in
+    pure Python."""
+
+    homepage = "https://github.com/GeospatialPython/pyshp"
+    url      = "https://pypi.io/packages/source/p/pyshp/pyshp-1.2.12.tar.gz"
+
+    version('1.2.12', '63d33d151ac308f1db71ea0f22c30d8b')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-pyside/package.py b/var/spack/repos/builtin/packages/py-pyside/package.py
index e799b4cb72..dc728bff77 100644
--- a/var/spack/repos/builtin/packages/py-pyside/package.py
+++ b/var/spack/repos/builtin/packages/py-pyside/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
@@ -31,7 +12,21 @@ class PyPyside(PythonPackage):
     homepage = "https://pypi.python.org/pypi/pyside"
     url      = "https://pypi.io/packages/source/P/PySide/PySide-1.2.2.tar.gz"
 
+    # More recent versions of PySide2 (for Qt5) have been taken under
+    # the offical Qt umbrella.  For more information, see:
+    # http://wiki.qt.io/Qt_for_Python_Development_Getting_Started
+
+    # Version 1.2.4 claims to not work with Python 3.5, mostly
+    # because it hasn't been tested.  Otherwise, it's the same as v1.2.3
+    # https://github.com/PySide/pyside-setup/issues/58
+    # Meanwhile, developers have moved onto pyside2 (for Qt5),
+    # and show little interest in certifying PySide 1.2.4 for Python.
     version('1.2.4', '3cb7174c13bd45e3e8f77638926cb8c0')  # rpath problems
+
+    # This is not available from pypi
+    # version('1.2.3', 'fa5d5438b045ede36104bba25a6ccc10')
+
+    # v1.2.2 does not work with Python3
     version('1.2.2', 'c45bc400c8a86d6b35f34c29e379e44d', preferred=True)
 
     depends_on('cmake', type='build')
diff --git a/var/spack/repos/builtin/packages/py-pysocks/package.py b/var/spack/repos/builtin/packages/py-pysocks/package.py
index db734dd927..83661d93b0 100644
--- a/var/spack/repos/builtin/packages/py-pysocks/package.py
+++ b/var/spack/repos/builtin/packages/py-pysocks/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pyspark/package.py b/var/spack/repos/builtin/packages/py-pyspark/package.py
new file mode 100644
index 0000000000..126de2af41
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pyspark/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPyspark(PythonPackage):
+    """Python bindings for Apache Spark"""
+
+    homepage = "http://spark.apache.org"
+    url      = "https://pypi.org/packages/source/p/pyspark/pyspark-2.3.0.tar.gz"
+
+    version('2.3.0', sha256='0b3536910e154c36a94239f0ba0a201f476aadc72006409e5787198ffd01986e')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-py4j', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-pysqlite/package.py b/var/spack/repos/builtin/packages/py-pysqlite/package.py
new file mode 100644
index 0000000000..0f69acc3bf
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pysqlite/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPysqlite(PythonPackage):
+    """Python DB-API module for SQLite 3."""
+
+    homepage = "https://github.com/ghaering/pysqlite"
+    url      = "https://pypi.io/packages/source/p/pysqlite/pysqlite-2.8.3.tar.gz"
+
+    version('2.8.3', '033f17b8644577715aee55e8832ac9fc')
+
+    depends_on('python@2.7.0:2.7.999', type=('build', 'run'))
+    depends_on('sqlite', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-pytables/package.py b/var/spack/repos/builtin/packages/py-pytables/package.py
index 5e782341d9..96033237b0 100644
--- a/var/spack/repos/builtin/packages/py-pytables/package.py
+++ b/var/spack/repos/builtin/packages/py-pytables/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pytest-cov/package.py b/var/spack/repos/builtin/packages/py-pytest-cov/package.py
index 3621b54d0d..949696d3f4 100644
--- a/var/spack/repos/builtin/packages/py-pytest-cov/package.py
+++ b/var/spack/repos/builtin/packages/py-pytest-cov/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pytest-flake8/package.py b/var/spack/repos/builtin/packages/py-pytest-flake8/package.py
index 4b2ec5e014..06066572ec 100644
--- a/var/spack/repos/builtin/packages/py-pytest-flake8/package.py
+++ b/var/spack/repos/builtin/packages/py-pytest-flake8/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pytest-httpbin/package.py b/var/spack/repos/builtin/packages/py-pytest-httpbin/package.py
index f27f121d8e..0782f761d4 100644
--- a/var/spack/repos/builtin/packages/py-pytest-httpbin/package.py
+++ b/var/spack/repos/builtin/packages/py-pytest-httpbin/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pytest-mock/package.py b/var/spack/repos/builtin/packages/py-pytest-mock/package.py
index 968816f6f4..d574f6ae84 100644
--- a/var/spack/repos/builtin/packages/py-pytest-mock/package.py
+++ b/var/spack/repos/builtin/packages/py-pytest-mock/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pytest-runner/package.py b/var/spack/repos/builtin/packages/py-pytest-runner/package.py
index 771902afd9..037ec724ae 100644
--- a/var/spack/repos/builtin/packages/py-pytest-runner/package.py
+++ b/var/spack/repos/builtin/packages/py-pytest-runner/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,3 +17,4 @@ class PyPytestRunner(PythonPackage):
     version('2.11.1', 'bdb73eb18eca2727944a2dcf963c5a81')
 
     depends_on('py-setuptools', type='build')
+    depends_on('py-setuptools-scm@1.15:', type='build')
diff --git a/var/spack/repos/builtin/packages/py-pytest-xdist/package.py b/var/spack/repos/builtin/packages/py-pytest-xdist/package.py
index 968601ab29..ad3c77c7ef 100644
--- a/var/spack/repos/builtin/packages/py-pytest-xdist/package.py
+++ b/var/spack/repos/builtin/packages/py-pytest-xdist/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pytest/package.py b/var/spack/repos/builtin/packages/py-pytest/package.py
index 098a9de79c..7e6c6f555c 100644
--- a/var/spack/repos/builtin/packages/py-pytest/package.py
+++ b/var/spack/repos/builtin/packages/py-pytest/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,23 +10,31 @@ class PyPytest(PythonPackage):
     """pytest: simple powerful testing with Python."""
 
     homepage = "http://pytest.org/"
-    url      = "https://pypi.io/packages/source/p/pytest/pytest-3.0.7.tar.gz"
+    url      = "https://pypi.io/packages/source/p/pytest/pytest-3.7.2.tar.gz"
 
     import_modules = [
         '_pytest', '_pytest.assertion', '_pytest._code',
-        '_pytest.vendored_packages', 'pytest'
+        '_pytest.mark', 'pytest'
     ]
 
+    version('3.7.2', 'd12d0d556a21fd8633e105f1a8d5a0f9')
+    version('3.7.1', '2704e16bb2c11af494167f80a7cd37c4')
+    version('3.5.1', 'ffd870ee3ca561695d2f916f0f0f3c0b')
     version('3.0.7', '89c60546507dc7eb6e9e40a6e9f720bd')
     version('3.0.2', '61dc36e65a6f6c11c53b1388e043a9f5')
 
+    depends_on('python@2.7:2.8,3.4:', type=('build', 'run'))
+
     # Most Python packages only require setuptools as a build dependency.
     # However, pytest requires setuptools during runtime as well.
     depends_on('py-setuptools', type=('build', 'run'))
-    depends_on('py-py@1.4.29:', type=('build', 'run'))
-    depends_on('py-hypothesis@3.5.2:', type=('build', 'run'))
-
-    # TODO: Add a 'test' deptype
-    # depends_on('py-nose', type='test')
-    # depends_on('py-mock', type='test')
-    # depends_on('py-requests', type='test')
+    depends_on('py-setuptools-scm', type='build')
+    depends_on('py-py@1.5.0:', type=('build', 'run'))
+    depends_on('py-six@1.10.0:', type=('build', 'run'))
+    depends_on('py-attrs@17.4.0:', type=('build', 'run'))
+    depends_on('py-more-itertools@4.0.0:', type=('build', 'run'))
+    depends_on('py-atomicwrites@1.0:', type=('build', 'run'))
+    depends_on('py-pluggy@0.7:', when='@3.7:', type=('build', 'run'))
+    depends_on('py-pluggy@0.5:0.6', when='@:3.6', type=('build', 'run'))
+    depends_on('py-funcsigs', when='^python@:2', type=('build', 'run'))
+    depends_on('py-pathlib2@2.2.0:', when='^python@:3.5', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-python-daemon/package.py b/var/spack/repos/builtin/packages/py-python-daemon/package.py
index ff47d32504..8fd6e38464 100644
--- a/var/spack/repos/builtin/packages/py-python-daemon/package.py
+++ b/var/spack/repos/builtin/packages/py-python-daemon/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-python-engineio/package.py b/var/spack/repos/builtin/packages/py-python-engineio/package.py
new file mode 100644
index 0000000000..27735cb1ad
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-python-engineio/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPythonEngineio(PythonPackage):
+    """Engine.IO is the implementation of transport-based
+    cross-browser/cross-device bi-directional communication
+    layer for Socket.IO."""
+
+    homepage = "http://python-engineio.readthedocs.io/en/latest/"
+    url      = "https://github.com/miguelgrinberg/python-engineio/archive/v2.0.2.tar.gz"
+
+    version('2.0.2', 'b91c6fa900905f9a96b86c3e141e2754')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-six@1.9.0:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-python-gitlab/package.py b/var/spack/repos/builtin/packages/py-python-gitlab/package.py
index ff769b421e..d27d250d99 100644
--- a/var/spack/repos/builtin/packages/py-python-gitlab/package.py
+++ b/var/spack/repos/builtin/packages/py-python-gitlab/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-python-levenshtein/package.py b/var/spack/repos/builtin/packages/py-python-levenshtein/package.py
new file mode 100644
index 0000000000..a19247c6fe
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-python-levenshtein/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPythonLevenshtein(PythonPackage):
+    """Python extension for computing string edit distances and
+    similarities."""
+
+    homepage = "https://github.com/ztane/python-Levenshtein"
+    url      = "https://pypi.io/packages/source/p/python-Levenshtein/python-Levenshtein-0.12.0.tar.gz"
+
+    version('0.12.0', 'e8cde197d6d304bbdc3adae66fec99fb')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-python-socketio/package.py b/var/spack/repos/builtin/packages/py-python-socketio/package.py
new file mode 100644
index 0000000000..169c960f9c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-python-socketio/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPythonSocketio(PythonPackage):
+    """Python implementation of the Socket.IO realtime server."""
+
+    homepage = "https://github.com/miguelgrinberg/python-socketio"
+    url      = "https://pypi.io/packages/source/p/python-socketio/python-socketio-1.8.4.tar.gz"
+
+    version('1.8.4', '9de73990f6c32c701278c01b0fa1a0c3')
+
+    variant('eventlet', default=True,
+            description="Pulls in optional eventlet dependency, required"
+                        " for using the zmq implementation.")
+
+    depends_on('py-setuptools',                 type='build')
+    depends_on('py-six@1.9.0:',                 type=("build", "run"))
+    depends_on('py-python-engineio@1.2.1:',     type=("build", "run"))
+    depends_on('py-eventlet', when='+eventlet', type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/py-pythonqwt/package.py b/var/spack/repos/builtin/packages/py-pythonqwt/package.py
index 9f4c09b537..62551cfc9c 100644
--- a/var/spack/repos/builtin/packages/py-pythonqwt/package.py
+++ b/var/spack/repos/builtin/packages/py-pythonqwt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,7 +14,7 @@ class PyPythonqwt(PythonPackage):
 
     version('0.5.5', 'a60c7da9fbca667337d14aca094b6fda')
 
-    variant('docs', default=False, description="Build documentation.")
+    variant('doc', default=False, description="Build documentation.")
 
     depends_on('py-setuptools', type='build')
     depends_on('py-numpy@1.3:',   type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-pytorch/package.py b/var/spack/repos/builtin/packages/py-pytorch/package.py
new file mode 100644
index 0000000000..d5df52c16f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pytorch/package.py
@@ -0,0 +1,72 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPytorch(PythonPackage):
+    """Tensors and Dynamic neural networks in Python
+    with strong GPU acceleration."""
+
+    homepage = "http://pytorch.org/"
+    git      = "https://github.com/pytorch/pytorch.git"
+
+    version('0.4.0', tag='v0.4.0', submodules=True)
+    version('0.3.1', tag='v0.3.1', submodules=True)
+
+    variant('cuda', default='False', description='Add GPU support')
+    variant('cudnn', default='False', description='Add cuDNN support')
+    variant('nccl', default='False', description='Add NCCL support')
+    variant('mkldnn', default='False', description='Add Intel MKL DNN support')
+    variant('magma', default='False', description='Add MAGMA support')
+
+    conflicts('+cudnn', when='~cuda')
+    conflicts('+nccl', when='~cuda')
+    conflicts('+magma', when='~cuda')
+    conflicts('+mkldnn', when='@:0.3.2')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-cffi', type='build')
+    depends_on('py-numpy', type=('run', 'build'))
+    depends_on('blas')
+    depends_on('lapack')
+    depends_on('py-pyyaml', type=('run', 'build'))
+    depends_on('py-typing', when='@0.3.2:', type=('run', 'build'))
+    depends_on('intel-mkl', when='+mkl')
+    depends_on('cuda', when='+cuda', type=('build', 'link', 'run'))
+    depends_on('cudnn', when='+cuda+cudnn')
+    depends_on('nccl', when='+cuda+nccl')
+    depends_on('magma+shared', when='+cuda+magma')
+
+    def setup_environment(self, build_env, run_env):
+        build_env.set('MAX_JOBS', make_jobs)
+
+        if '+cuda' in self.spec:
+            build_env.set('CUDA_HOME', self.spec['cuda'].prefix)
+        else:
+            build_env.set('NO_CUDA', 'TRUE')
+
+        if '+cudnn' in self.spec:
+            build_env.set('CUDNN_LIB_DIR',
+                          self.spec['cudnn'].prefix.lib)
+            build_env.set('CUDNN_INCLUDE_DIR',
+                          self.spec['cudnn'].prefix.include)
+        else:
+            build_env.set('NO_CUDNN', 'TRUE')
+
+        if '+nccl' in self.spec:
+            build_env.set('NCCL_ROOT_DIR', self.spec['nccl'].prefix)
+        else:
+            build_env.set('NO_SYSTEM_NCCL', 'TRUE')
+
+        if '+mkldnn' in self.spec:
+            build_env.set('MKLDNN_HOME', self.spec['intel-mkl'].prefix)
+        else:
+            build_env.set('NO_MKLDNN', 'TRUE')
+
+        build_env.set('NO_NNPACK', 'TRUE')
+
+        build_env.set('PYTORCH_BUILD_VERSION', str(self.version))
+        build_env.set('PYTORCH_BUILD_NUMBER', 0)
diff --git a/var/spack/repos/builtin/packages/py-pytz/package.py b/var/spack/repos/builtin/packages/py-pytz/package.py
index d946e767e9..de453868ae 100644
--- a/var/spack/repos/builtin/packages/py-pytz/package.py
+++ b/var/spack/repos/builtin/packages/py-pytz/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,6 +19,7 @@ class PyPytz(PythonPackage):
     version('2016.10',  'cc9f16ba436efabdcef3c4d32ae4919c')
     version('2016.6.1', 'b6c28a3b968bc1d8badfb61b93874e03')
     version('2014.10',  'eb1cb941a20c5b751352c52486aa1dd7')
+    version('2014.9',   'd42bda2f4c1e873e02fbd1e4acfd1b8c')
     version('2015.4',   '417a47b1c432d90333e42084a605d3d8')
     version('2016.3',   'abae92c3301b27bd8a9f56b14f52cb29')
 
diff --git a/var/spack/repos/builtin/packages/py-pyutilib/package.py b/var/spack/repos/builtin/packages/py-pyutilib/package.py
new file mode 100644
index 0000000000..62024068f1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pyutilib/package.py
@@ -0,0 +1,32 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class PyPyutilib(PythonPackage):
+    """The PyUtilib project supports a collection of Python utilities,
+    including a well-developed component architecture and extensions to the
+    PyUnit testing framework. PyUtilib has been developed to support several
+    Python-centric projects, especially Pyomo. PyUtilib is available under the
+    BSD License."""
+
+    homepage = "https://github.com/PyUtilib/pyutilib"
+    url      = "https://github.com/PyUtilib/pyutilib/archive/5.5.1.tar.gz"
+
+    version('5.6.2', '60c6ea5083e512211984347ffeca19d2')
+    version('5.6.1', 'ddc7e896304b6fabe4d21eb5fdec386e')
+    version('5.6',   '5bfcdbf118264f1a1b8c6cac9dea8bca')
+    version('5.5.1', 'c4990cbced152d879812d109aaa857ff')
+    version('5.5',   '7940563bf951332cf836f418d67b2134')
+    version('5.4.1', 'b34b5798757e4ab73868b7655c5c8f8a')
+    version('5.4',   '9410e5a76885412310b03074d2f97e55')
+    version('5.3.5', '85e41e65f24f6711261229bcde6eb825')
+    version('5.3.4', '4fe1a8387c027f64b62ca99424275368')
+    version('5.3.3', '27a713ca8d49714244646e1ce38778b9')
+
+    depends_on('py-nose', type=('build', 'run'))
+    depends_on('py-six', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-pywavelets/package.py b/var/spack/repos/builtin/packages/py-pywavelets/package.py
index c542a23c1c..dd561b17f4 100644
--- a/var/spack/repos/builtin/packages/py-pywavelets/package.py
+++ b/var/spack/repos/builtin/packages/py-pywavelets/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/py-pyyaml/package.py b/var/spack/repos/builtin/packages/py-pyyaml/package.py
index 05ac4d2ac5..3651c6820d 100644
--- a/var/spack/repos/builtin/packages/py-pyyaml/package.py
+++ b/var/spack/repos/builtin/packages/py-pyyaml/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,4 +11,5 @@ class PyPyyaml(PythonPackage):
     homepage = "http://pyyaml.org/wiki/PyYAML"
     url      = "http://pyyaml.org/download/pyyaml/PyYAML-3.11.tar.gz"
 
+    version('3.12', '4c129761b661d181ebf7ff4eb2d79950')
     version('3.11', 'f50e08ef0fe55178479d3a618efe21db')
diff --git a/var/spack/repos/builtin/packages/py-qtawesome/package.py b/var/spack/repos/builtin/packages/py-qtawesome/package.py
index b5c08a3c60..3d9cd5f77c 100644
--- a/var/spack/repos/builtin/packages/py-qtawesome/package.py
+++ b/var/spack/repos/builtin/packages/py-qtawesome/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-qtconsole/package.py b/var/spack/repos/builtin/packages/py-qtconsole/package.py
index 07acca339b..37b05f9a1b 100644
--- a/var/spack/repos/builtin/packages/py-qtconsole/package.py
+++ b/var/spack/repos/builtin/packages/py-qtconsole/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,9 +14,8 @@ class PyQtconsole(PythonPackage):
 
     version('4.2.1', 'c08ebebc7a60629ebadf685361ca0798')
 
-    variant('docs', default=False, description='Build documentation')
+    variant('doc', default=False, description='Build documentation')
 
-    depends_on('py-setuptools',          type='build')
     depends_on('py-ipykernel@4.1:',      type=('build', 'run'))
     depends_on('py-jupyter-client@4.1:', type=('build', 'run'))
     depends_on('py-jupyter-core',        type=('build', 'run'))
@@ -43,5 +23,4 @@ class PyQtconsole(PythonPackage):
     depends_on('py-traitlets',           type=('build', 'run'))
     depends_on('py-sphinx@1.3:',         type=('build', 'run'), when='+docs')
 
-    # TODO: Add a 'test' deptype
-    # depends_on('py-mock', type='test', when='^python@2.7:2.8')
+    depends_on('py-mock', type='test', when='^python@2.7:2.8')
diff --git a/var/spack/repos/builtin/packages/py-qtpy/package.py b/var/spack/repos/builtin/packages/py-qtpy/package.py
index 020894d0e7..aef6a1deb1 100644
--- a/var/spack/repos/builtin/packages/py-qtpy/package.py
+++ b/var/spack/repos/builtin/packages/py-qtpy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-quantities/package.py b/var/spack/repos/builtin/packages/py-quantities/package.py
index d75aced6f9..c0afca77a7 100644
--- a/var/spack/repos/builtin/packages/py-quantities/package.py
+++ b/var/spack/repos/builtin/packages/py-quantities/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-quast/package.py b/var/spack/repos/builtin/packages/py-quast/package.py
new file mode 100644
index 0000000000..41e966b24b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-quast/package.py
@@ -0,0 +1,30 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyQuast(PythonPackage):
+    """Quality Assessment Tool for Genome Assemblies"""
+
+    homepage = "http://cab.spbu.ru/software/quast"
+    url      = "https://github.com/ablab/quast/archive/quast_4.6.1.tar.gz"
+
+    version('4.6.3', '16d77acb2e0f6436b58d9df7b732fb76')
+    version('4.6.1', '37ccd34e0040c17aa6f990353a92475c')
+    version('4.6.0', 'c04d62c50ec4d9caa9d7388950b8d144')
+
+    depends_on('boost@1.56.0')
+    depends_on('perl@5.6.0:')
+    depends_on('python@2.5:,3.3:')
+    depends_on('py-setuptools',    type='build')
+    depends_on('py-matplotlib',    type=('build', 'run'))
+    depends_on('java',             type=('build', 'run'))
+    depends_on('perl-time-hires',  type=('build', 'run'))
+    depends_on('gnuplot',          type=('build', 'run'))
+    depends_on('mummer',           type=('build', 'run'))
+    depends_on('bedtools2',        type=('build', 'run'))
+    depends_on('bwa',              type=('build', 'run'))
+    depends_on('glimmer',          type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-radical-utils/package.py b/var/spack/repos/builtin/packages/py-radical-utils/package.py
index 85a4832e3e..1a04087ea0 100644
--- a/var/spack/repos/builtin/packages/py-radical-utils/package.py
+++ b/var/spack/repos/builtin/packages/py-radical-utils/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-ranger/package.py b/var/spack/repos/builtin/packages/py-ranger/package.py
index 19f20c6d33..7a923fc638 100644
--- a/var/spack/repos/builtin/packages/py-ranger/package.py
+++ b/var/spack/repos/builtin/packages/py-ranger/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/py-rasterio/package.py b/var/spack/repos/builtin/packages/py-rasterio/package.py
new file mode 100644
index 0000000000..567befd2a0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-rasterio/package.py
@@ -0,0 +1,41 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyRasterio(PythonPackage):
+    """Rasterio reads and writes geospatial raster data.
+    Geographic information systems use GeoTIFF and other formats to
+    organize and store gridded, or raster, datasets. Rasterio reads
+    and writes these formats and provides a Python API based on N-D
+    arrays."""
+
+    homepage = "https://github.com/mapbox/rasterio"
+    url      = "https://github.com/mapbox/rasterio/archive/1.0a12.zip"
+
+    version('1.0a12', 'e078ca02b3513b65a9be5bb3f528b4da')
+
+    variant('aws', default=False,
+        description='Enable testing with Amazon Web Services')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-cython', type='build')
+
+    # Only use py-enum34 with Python2
+    # depends_on('py-enum34', type='run', when='^python@:2.7')
+
+    depends_on('py-attrs', type=('build', 'run'))
+    depends_on('py-numpy', type=('build', 'run'))
+    depends_on('py-cligj', type=('build', 'run'))
+    depends_on('py-click', type=('build', 'run'))
+    depends_on('py-affine', type=('build', 'run'))
+    depends_on('py-snuggs', type=('build', 'run'))
+    depends_on('gdal')
+    depends_on('jpeg')
+
+    # (Commented out for now: py-boto3 is not yet a Spack package)
+    # Some (optional) tests use py-boto3 for Amazon Web Services
+    # depends_on('py-boto3', type=('build', 'run'), when='+aws')
diff --git a/var/spack/repos/builtin/packages/py-readme-renderer/package.py b/var/spack/repos/builtin/packages/py-readme-renderer/package.py
index 20691a12ec..becbc0e1d4 100644
--- a/var/spack/repos/builtin/packages/py-readme-renderer/package.py
+++ b/var/spack/repos/builtin/packages/py-readme-renderer/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-regex/package.py b/var/spack/repos/builtin/packages/py-regex/package.py
index 14c40c50cc..e2aeb296bf 100644
--- a/var/spack/repos/builtin/packages/py-regex/package.py
+++ b/var/spack/repos/builtin/packages/py-regex/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-reportlab/package.py b/var/spack/repos/builtin/packages/py-reportlab/package.py
new file mode 100644
index 0000000000..e8a1867947
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-reportlab/package.py
@@ -0,0 +1,16 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyReportlab(PythonPackage):
+    """The ReportLab Toolkit. An Open Source Python library for generating
+    PDFs and graphics."""
+
+    homepage = "https://pypi.python.org/pypi/reportlab"
+    url      = "https://pypi.io/packages/source/r/reportlab/reportlab-3.4.0.tar.gz"
+
+    version('3.4.0', '3f2522cf3b69cd84426c216619bbff53')
diff --git a/var/spack/repos/builtin/packages/py-requests-toolbelt/package.py b/var/spack/repos/builtin/packages/py-requests-toolbelt/package.py
new file mode 100644
index 0000000000..f19e9fe1d1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-requests-toolbelt/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyRequestsToolbelt(PythonPackage):
+    """A toolbelt of useful classes and functions to be used with
+    python-requests"""
+
+    homepage = "https://toolbelt.readthedocs.org/"
+    url      = "https://github.com/requests/toolbelt/archive/0.8.0.tar.gz"
+
+    version('0.8.0', 'de9bf7fbcc6ae341a5c4fd9f8912bcac')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-requests@2.0.1:3.0.0', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-requests/package.py b/var/spack/repos/builtin/packages/py-requests/package.py
index 329c07758c..b5ba4b0d37 100644
--- a/var/spack/repos/builtin/packages/py-requests/package.py
+++ b/var/spack/repos/builtin/packages/py-requests/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -45,11 +26,11 @@ class PyRequests(PythonPackage):
     version('2.14.2', '4c3c169ed67466088a2a6947784fe444')
     version('2.13.0', '921ec6b48f2ddafc8bb6160957baf444')
     version('2.11.1', 'ad5f9c47b5c5dfdb28363ad7546b0763')
+    version('2.3.0',  '7449ffdc8ec9ac37bbcd286003c80f00')
 
     depends_on('py-setuptools', type='build')
 
-    # TODO: Add a 'test' deptype
-    # depends_on('py-pytest@2.8.0:',        type='test')
-    # depends_on('py-pytest-cov',           type='test')
-    # depends_on('py-pytest-httpbin@0.0.7', type='test')
-    # depends_on('py-pytest-mock',          type='test')
+    depends_on('py-pytest@2.8.0:',        type='test')
+    depends_on('py-pytest-cov',           type='test')
+    depends_on('py-pytest-httpbin@0.0.7', type='test')
+    depends_on('py-pytest-mock',          type='test')
diff --git a/var/spack/repos/builtin/packages/py-restview/package.py b/var/spack/repos/builtin/packages/py-restview/package.py
index bd63d64bf5..2f9c735bab 100644
--- a/var/spack/repos/builtin/packages/py-restview/package.py
+++ b/var/spack/repos/builtin/packages/py-restview/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-rope/package.py b/var/spack/repos/builtin/packages/py-rope/package.py
index 5f0d27db23..879264707f 100644
--- a/var/spack/repos/builtin/packages/py-rope/package.py
+++ b/var/spack/repos/builtin/packages/py-rope/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-rpy2/package.py b/var/spack/repos/builtin/packages/py-rpy2/package.py
index c607360f0a..9ae4464ea1 100644
--- a/var/spack/repos/builtin/packages/py-rpy2/package.py
+++ b/var/spack/repos/builtin/packages/py-rpy2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,14 +16,25 @@ class PyRpy2(PythonPackage):
     homepage = "https://pypi.python.org/pypi/rpy2"
     url = "https://pypi.io/packages/source/r/rpy2/rpy2-2.5.4.tar.gz"
 
-    version('2.5.4', '115a20ac30883f096da2bdfcab55196d')
+    version('2.9.4', '7df2562cdf43a0ccdd1e44ee1c16614f')
+    version('2.8.6', '85046aa58ba586622f67271fbca05933')
     version('2.5.6', 'a36e758b633ce6aec6a5f450bfee980f')
+    version('2.5.4', '115a20ac30883f096da2bdfcab55196d')
 
     # FIXME: Missing dependencies:
     # ld: cannot find -licuuc
     # ld: cannot find -licui18
 
-    depends_on('py-six', type=('build', 'run'))
+    # All versions
     depends_on('py-setuptools', type='build')
+    depends_on('r',             type=('build', 'run'))
+
+    # @2.9.0:
+    depends_on('r@3.3:',    when='@2.9.0:', type=('build', 'run'))
+    depends_on('python@3:', when='@2.9.0:', type=('build', 'run'))
+    depends_on('py-jinja2', when='@2.9.0:', type=('build', 'run'))
+    depends_on('py-six',    when='@2.9.0:', type=('build', 'run'))
 
-    depends_on('r')
+    # @:2.8.6
+    depends_on('r@2.8:', when='@:2.8.6', type=('build', 'run'))
+    depends_on('py-singledispatch', when='^python@:2',   type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-rsa/package.py b/var/spack/repos/builtin/packages/py-rsa/package.py
index 6cde68a33f..287d39279a 100644
--- a/var/spack/repos/builtin/packages/py-rsa/package.py
+++ b/var/spack/repos/builtin/packages/py-rsa/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-rseqc/package.py b/var/spack/repos/builtin/packages/py-rseqc/package.py
new file mode 100644
index 0000000000..15563be2a0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-rseqc/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyRseqc(PythonPackage):
+    """RSeQC package provides a number of useful modules that can
+    comprehensively evaluate high throughput sequence data especially RNA-seq
+    data."""
+
+    homepage = "http://rseqc.sourceforge.net"
+    url      = "https://pypi.io/packages/source/R/RSeQC/RSeQC-2.6.4.tar.gz"
+
+    version('2.6.4', '935779c452ffc84f3b8b9fb3d485c782')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-bx-python',  type=('build', 'run'))
+    depends_on('py-numpy',      type=('build', 'run'))
+    depends_on('py-pysam',      type=('build', 'run'))
+    depends_on('r',             type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-rtree/package.py b/var/spack/repos/builtin/packages/py-rtree/package.py
index 70eb46575c..e1be4c6aee 100644
--- a/var/spack/repos/builtin/packages/py-rtree/package.py
+++ b/var/spack/repos/builtin/packages/py-rtree/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-saga-python/package.py b/var/spack/repos/builtin/packages/py-saga-python/package.py
index 4eb83b1dc1..2890c16889 100644
--- a/var/spack/repos/builtin/packages/py-saga-python/package.py
+++ b/var/spack/repos/builtin/packages/py-saga-python/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-scandir/package.py b/var/spack/repos/builtin/packages/py-scandir/package.py
new file mode 100644
index 0000000000..09aa29a662
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-scandir/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyScandir(PythonPackage):
+    """scandir, a better directory iterator and faster os.walk()."""
+
+    homepage = "https://github.com/benhoyt/scandir"
+    url      = "https://pypi.io/packages/source/s/scandir/scandir-1.9.0.tar.gz"
+
+    import_modules = ['scandir']
+
+    version('1.9.0', '506c4cc5f38c00b301642a9cb0433910')
+    version('1.6',   '0180ddb97c96cbb2d4f25d2ae11c64ac')
+
+    depends_on('py-setuptools', type=('build'))
diff --git a/var/spack/repos/builtin/packages/py-scientificpython/package.py b/var/spack/repos/builtin/packages/py-scientificpython/package.py
index 45fedc825b..4926de0054 100644
--- a/var/spack/repos/builtin/packages/py-scientificpython/package.py
+++ b/var/spack/repos/builtin/packages/py-scientificpython/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-scikit-image/package.py b/var/spack/repos/builtin/packages/py-scikit-image/package.py
index 40cbf740fe..f9a270f96d 100644
--- a/var/spack/repos/builtin/packages/py-scikit-image/package.py
+++ b/var/spack/repos/builtin/packages/py-scikit-image/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -43,3 +24,4 @@ class PyScikitImage(PythonPackage):
     depends_on('py-scipy', type=('build', 'run'))
     depends_on('py-matplotlib', type=('build', 'run'))
     depends_on('py-setuptools', type='build')
+    depends_on('py-cython@0.23.4:', type='build')
diff --git a/var/spack/repos/builtin/packages/py-scikit-learn/package.py b/var/spack/repos/builtin/packages/py-scikit-learn/package.py
index 81f5de2737..9a5df494f2 100644
--- a/var/spack/repos/builtin/packages/py-scikit-learn/package.py
+++ b/var/spack/repos/builtin/packages/py-scikit-learn/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,6 +12,8 @@ class PyScikitLearn(PythonPackage):
     homepage = "https://pypi.python.org/pypi/scikit-learn"
     url      = "https://pypi.io/packages/source/s/scikit-learn/scikit-learn-0.18.1.tar.gz"
 
+    version('0.20.0', sha256='97d1d971f8ec257011e64b7d655df68081dd3097322690afa1a71a1d755f8c18')
+    version('0.19.1', 'b67143988c108862735a96cf2b1e827a')
     version('0.18.1', '6b0ff1eaa5010043895dd63d1e3c60c9')
     version('0.15.2', 'd9822ad0238e17b382a3c756ea94fe0d')
     version('0.16.1', '363ddda501e3b6b61726aa40b8dbdb7e')
diff --git a/var/spack/repos/builtin/packages/py-scipy/package.py b/var/spack/repos/builtin/packages/py-scipy/package.py
index 3aced0bf4a..8b04bda75d 100644
--- a/var/spack/repos/builtin/packages/py-scipy/package.py
+++ b/var/spack/repos/builtin/packages/py-scipy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -49,9 +30,9 @@ class PyScipy(PythonPackage):
         'scipy.special._precompute'
     ]
 
-    # See https://github.com/spack/spack/issues/2737
-    version('0.19.1', '6b4d91b62f1926282b127194a06b72b3',
-            url="https://pypi.io/packages/source/s/scipy/scipy-0.19.1.tar.gz")
+    version('1.1.0', 'aa6bcc85276b6f25e17bcfc4dede8718')
+    version('1.0.0', '53fa34bd3733a9a4216842b6000f7316')
+    version('0.19.1', '6b4d91b62f1926282b127194a06b72b3')
     version('0.19.0', '91b8396231eec780222a57703d3ec550',
             url="https://pypi.io/packages/source/s/scipy/scipy-0.19.0.zip")
     version('0.18.1', '5fb5fb7ccb113ab3a039702b6c2f3327')
@@ -61,6 +42,7 @@ class PyScipy(PythonPackage):
 
     depends_on('python@2.6:2.8,3.2:')
     depends_on('py-setuptools', type='build')
+    depends_on('py-nose', type='test')
     depends_on('py-numpy@1.7.1:+blas+lapack', type=('build', 'run'))
 
     # NOTE: scipy picks up Blas/Lapack from numpy, see
@@ -68,17 +50,14 @@ class PyScipy(PythonPackage):
     depends_on('blas')
     depends_on('lapack')
 
-    # Tests require:
-    # TODO: Add a 'test' deptype
-    # depends_on('py-nose', type='test')
-
     def build_args(self, spec, prefix):
         args = []
 
         # Build in parallel
-        # Known problems with Python 3
+        # Known problems with Python 3.5+
+        # https://github.com/spack/spack/issues/7927
         # https://github.com/scipy/scipy/issues/7112
-        if not spec.satisfies('^python@3:'):
+        if not spec.satisfies('^python@3.5:'):
             args.extend(['-j', str(make_jobs)])
 
         return args
@@ -99,5 +78,5 @@ class PyScipy(PythonPackage):
         # ImportError: Error importing scipy: you should not try to import
         #       scipy from its source directory; please exit the scipy
         #       source tree, and relaunch your python interpreter from there.
-        with working_dir('..'):
+        with working_dir('spack-test', create=True):
             python('-c', 'import scipy; scipy.test("full", verbose=2)')
diff --git a/var/spack/repos/builtin/packages/py-seaborn/package.py b/var/spack/repos/builtin/packages/py-seaborn/package.py
index d0bd755343..129de71574 100644
--- a/var/spack/repos/builtin/packages/py-seaborn/package.py
+++ b/var/spack/repos/builtin/packages/py-seaborn/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,6 +17,7 @@ class PySeaborn(PythonPackage):
     homepage = "http://seaborn.pydata.org/"
     url      = "https://pypi.io/packages/source/s/seaborn/seaborn-0.7.1.tar.gz"
 
+    version('0.9.0', '76c83f794ca320fb6b23a7c6192d5e185a5fcf4758966a0c0a54baee46d41e2f')
     version('0.7.1', 'ef07e29e0f8a1f2726abe506c1a36e93')
 
     depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-setuptools-git/package.py b/var/spack/repos/builtin/packages/py-setuptools-git/package.py
new file mode 100644
index 0000000000..23569c4534
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-setuptools-git/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PySetuptoolsGit(PythonPackage):
+    """Setuptools revision control system plugin for Git"""
+
+    homepage = "https://pypi.python.org/pypi/setuptools-git"
+    url      = "https://pypi.io/packages/source/s/setuptools-git/setuptools-git-1.2.tar.gz"
+
+    version('1.2', '40b2ef7687a384ea144503c2e5bc67e2')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('git')
diff --git a/var/spack/repos/builtin/packages/py-setuptools-scm/package.py b/var/spack/repos/builtin/packages/py-setuptools-scm/package.py
new file mode 100644
index 0000000000..dd2321fbd0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-setuptools-scm/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PySetuptoolsScm(PythonPackage):
+    """The blessed package to manage your versions by scm tags."""
+
+    homepage = "https://github.com/pypa/setuptools_scm"
+    url      = "https://pypi.io/packages/source/s/setuptools_scm/setuptools_scm-3.1.0.tar.gz"
+
+    import_modules = ['setuptools_scm']
+
+    version('3.1.0',  '52a8dee23c9e5f7d7d18094563db516c')
+    version('1.15.6', 'f17493d53f0d842bb0152f214775640b')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('python@2.7:2.8,3.4:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-setuptools/package.py b/var/spack/repos/builtin/packages/py-setuptools/package.py
index de7b47367b..c37d62414b 100644
--- a/var/spack/repos/builtin/packages/py-setuptools/package.py
+++ b/var/spack/repos/builtin/packages/py-setuptools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,17 +10,24 @@ class PySetuptools(PythonPackage):
     """A Python utility that aids in the process of downloading, building,
        upgrading, installing, and uninstalling Python packages."""
 
-    homepage = "https://pypi.python.org/pypi/setuptools"
-    url      = "https://pypi.io/packages/source/s/setuptools/setuptools-25.2.0.tar.gz"
+    homepage = "https://github.com/pypa/setuptools"
+    url      = "https://pypi.io/packages/source/s/setuptools/setuptools-40.2.0.zip"
 
-    import_modules = ['pkg_resources', 'setuptools', 'setuptools.command']
+    import_modules = [
+        'setuptools', 'pkg_resources', 'setuptools._vendor',
+        'setuptools.command', 'setuptools.extern',
+        'setuptools._vendor.packaging', 'pkg_resources._vendor',
+        'pkg_resources.extern', 'pkg_resources._vendor.packaging',
+        'easy_install'
+    ]
 
-    version('35.0.2', 'c368b4970d3ad3eab5afe4ef4dbe2437',
-            url="https://pypi.io/packages/source/s/setuptools/setuptools-35.0.2.zip")
-    version('34.4.1', '5f9b07aeaafd29eac2548fc0b89a4934',
-            url="https://pypi.io/packages/source/s/setuptools/setuptools-34.4.1.zip")
-    version('34.2.0', '41b630da4ea6cfa5894d9eb3142922be',
-            url="https://pypi.io/packages/source/s/setuptools/setuptools-34.2.0.zip")
+    version('40.4.3', sha256='acbc5740dd63f243f46c2b4b8e2c7fd92259c2ddb55a4115b16418a2ed371b15')
+    version('40.2.0', '592efabea3a65d8e97a025ed52f69b12')
+    version('39.2.0', 'dd4e3fa83a21bf7bf9c51026dc8a4e59')
+    version('39.0.1', '75310b72ca0ab4e673bf7679f69d7a62')
+    version('35.0.2', 'c368b4970d3ad3eab5afe4ef4dbe2437')
+    version('34.4.1', '5f9b07aeaafd29eac2548fc0b89a4934')
+    version('34.2.0', '41b630da4ea6cfa5894d9eb3142922be')
     version('25.2.0', 'a0dbb65889c46214c691f6c516cf959c')
     version('20.7.0', '5d12b39bf3e75e80fdce54e44b255615')
     version('20.6.7', '45d6110f3ec14924e44c33411db64fe6')
@@ -49,11 +37,29 @@ class PySetuptools(PythonPackage):
     version('16.0',   '0ace0b96233516fc5f7c857d086aa3ad')
     version('11.3.1', '01f69212e019a2420c1693fb43593930')
 
-    depends_on('python@2.6:2.8,3.3:')
+    depends_on('python@2.7:2.8,3.4:', type=('build', 'run'))
 
     # Previously, setuptools vendored all of its dependencies to allow
     # easy bootstrapping. As of version 34.0.0, this is no longer done
-    # and the dependencies need to be installed externally.
-    depends_on('py-packaging@16.8:', when='@34.0.0:', type=('build', 'run'))
-    depends_on('py-six@1.6.0:',      when='@34.0.0:', type=('build', 'run'))
-    depends_on('py-appdirs@1.4.0:',  when='@34.0.0:', type=('build', 'run'))
+    # and the dependencies need to be installed externally. As of version
+    # 36.0.0, setuptools now vendors its dependencies again. See
+    # https://github.com/pypa/setuptools/issues/980 for the reason they
+    # reverted back to vendoring again.
+    depends_on('py-packaging@16.8:', when='@34:35', type=('build', 'run'))
+    depends_on('py-six@1.6.0:',      when='@34:35', type=('build', 'run'))
+    depends_on('py-appdirs@1.4.0:',  when='@34:35', type=('build', 'run'))
+
+    def url_for_version(self, version):
+        url = 'https://pypi.io/packages/source/s/setuptools/setuptools-{0}'
+        url = url.format(version)
+
+        if version > Version('32.1.2'):
+            url += '.zip'
+        else:
+            url += '.tar.gz'
+
+        return url
+
+    def test(self):
+        # Unit tests require pytest, creating a circular dependency
+        pass
diff --git a/var/spack/repos/builtin/packages/py-sfepy/package.py b/var/spack/repos/builtin/packages/py-sfepy/package.py
new file mode 100644
index 0000000000..efd3305bf4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-sfepy/package.py
@@ -0,0 +1,31 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PySfepy(PythonPackage):
+    """SfePy (http://sfepy.org) is a software for solving systems of coupled
+    partial differential equations (PDEs) by the finite element method in 1D,
+    2D and 3D. It can be viewed both as black-box PDE solver, and as a Python
+    package which can be used for building custom applications.
+    """
+
+    homepage = "http://sfepy.org"
+    url      = "https://github.com/sfepy/sfepy/archive/release_2017.3.tar.gz"
+
+    version('2017.3', '65ab606a9fe80fccf17a7eb5ab8fd025')
+
+    variant('petsc', default=False, description='Enable PETSc support')
+
+    depends_on('py-numpy', type=('build', 'run'))
+    depends_on('py-setuptools', type='build')
+    depends_on('py-six', type='run')
+    depends_on('py-scipy', type='run')
+    depends_on('py-matplotlib', type='run')
+    depends_on('py-sympy', type='run')
+    depends_on('hdf5+hl', type='run')
+    depends_on('py-pytables', type='run')
+    depends_on('py-petsc4py', type='run', when='+petsc')
diff --git a/var/spack/repos/builtin/packages/py-sh/package.py b/var/spack/repos/builtin/packages/py-sh/package.py
index 8dc74c0740..4fd4ecb8bf 100644
--- a/var/spack/repos/builtin/packages/py-sh/package.py
+++ b/var/spack/repos/builtin/packages/py-sh/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-shapely/package.py b/var/spack/repos/builtin/packages/py-shapely/package.py
new file mode 100644
index 0000000000..ba82ef2229
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-shapely/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyShapely(PythonPackage):
+    """Manipulation and analysis of geometric objects in the Cartesian plane.
+    """
+
+    homepage = "https://github.com/Toblerity/Shapely"
+    url      = "https://pypi.io/packages/source/S/Shapely/Shapely-1.6.4.tar.gz"
+
+    version('1.6.4', '7581ef2d0fb346f9ed157f3efc75f6a4')
+
+    depends_on('python@2.6.0:2.8,3.4.0:', type=('build', 'run'))
+    depends_on('py-setuptools',     type='build')
+    depends_on('py-cython@0.19:',   type='build')
+    depends_on('py-numpy@1.4.1:',   type=('build', 'run'))
+    depends_on('geos@3.3:')
+
+    def setup_environment(self, spack_env, run_env):
+        spack_env.set('GEOS_CONFIG', self.spec['geos'].prefix)
+        spack_env.prepend_path('LD_LIBRARY_PATH', self.spec['geos'].prefix.lib)
diff --git a/var/spack/repos/builtin/packages/py-shiboken/package.py b/var/spack/repos/builtin/packages/py-shiboken/package.py
index cf04385c62..02197e7571 100644
--- a/var/spack/repos/builtin/packages/py-shiboken/package.py
+++ b/var/spack/repos/builtin/packages/py-shiboken/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
diff --git a/var/spack/repos/builtin/packages/py-simplegeneric/package.py b/var/spack/repos/builtin/packages/py-simplegeneric/package.py
index a704436281..5fc961ccc0 100644
--- a/var/spack/repos/builtin/packages/py-simplegeneric/package.py
+++ b/var/spack/repos/builtin/packages/py-simplegeneric/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-simplejson/package.py b/var/spack/repos/builtin/packages/py-simplejson/package.py
index 6894d62044..1b7ad7e071 100644
--- a/var/spack/repos/builtin/packages/py-simplejson/package.py
+++ b/var/spack/repos/builtin/packages/py-simplejson/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-singledispatch/package.py b/var/spack/repos/builtin/packages/py-singledispatch/package.py
index 6007fda635..ca9ed4513c 100644
--- a/var/spack/repos/builtin/packages/py-singledispatch/package.py
+++ b/var/spack/repos/builtin/packages/py-singledispatch/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-sip/package.py b/var/spack/repos/builtin/packages/py-sip/package.py
index 4c4a5af463..afa4aeee9b 100644
--- a/var/spack/repos/builtin/packages/py-sip/package.py
+++ b/var/spack/repos/builtin/packages/py-sip/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
diff --git a/var/spack/repos/builtin/packages/py-six/package.py b/var/spack/repos/builtin/packages/py-six/package.py
index 2f0bda16c6..acbc674d7b 100644
--- a/var/spack/repos/builtin/packages/py-six/package.py
+++ b/var/spack/repos/builtin/packages/py-six/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,12 +10,14 @@ class PySix(PythonPackage):
     """Python 2 and 3 compatibility utilities."""
 
     homepage = "https://pypi.python.org/pypi/six"
-    url      = "https://pypi.io/packages/source/s/six/six-1.10.0.tar.gz"
+    url      = "https://pypi.io/packages/source/s/six/six-1.11.0.tar.gz"
 
     import_modules = ['six']
 
+    version('1.11.0', 'd12789f9baf7e9fb2524c0c64f1773f8')
     version('1.10.0', '34eed507548117b2ab523ab14b2f8b55')
     version('1.9.0',  '476881ef4012262dfc8adc645ee786c4')
+    version('1.8.0',  '1626eb24cc889110c38f7e786ec69885')
 
     extends('python', ignore=r'bin/pytest')
 
diff --git a/var/spack/repos/builtin/packages/py-slepc4py/package.py b/var/spack/repos/builtin/packages/py-slepc4py/package.py
index f9603abd9b..279f805052 100644
--- a/var/spack/repos/builtin/packages/py-slepc4py/package.py
+++ b/var/spack/repos/builtin/packages/py-slepc4py/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-slurm-pipeline/package.py b/var/spack/repos/builtin/packages/py-slurm-pipeline/package.py
new file mode 100644
index 0000000000..ffece8a2ac
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-slurm-pipeline/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PySlurmPipeline(PythonPackage):
+    """A Python class for scheduling SLURM jobs"""
+
+    homepage = "https://github.com/acorg/slurm-pipeline"
+    url      = "https://pypi.io/packages/source/s/slurm-pipeline/slurm-pipeline-1.1.13.tar.gz"
+
+    version('2.0.9',  '7f97d2410db441081b79ac5c3395b8d0')
+    version('1.1.13', 'd1f8c78a64718ec5e2e40ba1b6816017')
+
+    depends_on('py-setuptools', type='build')
+    # using open range although requirements*.txt give explicit versions
+    # test dependencies are omitted, see #7681
+    depends_on('py-six@1.10.0:', type=('build', 'run'))
+    # six only required for python 2, change when ^-dependencies work, cf #2793
+    # depends_on('py-six@1.10.0:', type=('build', 'run'), when='^python@:2.8')
diff --git a/var/spack/repos/builtin/packages/py-sncosmo/package.py b/var/spack/repos/builtin/packages/py-sncosmo/package.py
index 87c1f44fad..d44724d41c 100644
--- a/var/spack/repos/builtin/packages/py-sncosmo/package.py
+++ b/var/spack/repos/builtin/packages/py-sncosmo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-snowballstemmer/package.py b/var/spack/repos/builtin/packages/py-snowballstemmer/package.py
index 5122d4600a..19e3d99afe 100644
--- a/var/spack/repos/builtin/packages/py-snowballstemmer/package.py
+++ b/var/spack/repos/builtin/packages/py-snowballstemmer/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-snuggs/package.py b/var/spack/repos/builtin/packages/py-snuggs/package.py
new file mode 100644
index 0000000000..7224d9e7bf
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-snuggs/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PySnuggs(PythonPackage):
+    """Snuggs are s-expressions for Numpy"""
+
+    homepage = "https://github.com/mapbox/snuggs"""
+    url      = "https://github.com/mapbox/snuggs/archive/1.4.1.zip"
+
+    version('1.4.1', 'bfc4058c32faa4ef76ab7946755557cc')
+
+    depends_on('py-numpy', type=('build', 'run'))
+    depends_on('py-click', type=('build', 'run'))
+    depends_on('py-pyparsing', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-spectra/package.py b/var/spack/repos/builtin/packages/py-spectra/package.py
index 9584b659f8..37891536d9 100644
--- a/var/spack/repos/builtin/packages/py-spectra/package.py
+++ b/var/spack/repos/builtin/packages/py-spectra/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,7 +12,9 @@ class PySpectra(PythonPackage):
     homepage = "https://pypi.python.org/pypi/spectra/0.0.8"
     url      = "https://pypi.io/packages/source/s/spectra/spectra-0.0.8.tar.gz"
 
+    version('0.0.11', sha256='8eb362a5187cb63cee13cd01186799c0c791a3ad3bec57b279132e12521762b8')
     version('0.0.8', '83020b29e584389f24c7720f38f0136c')
 
     depends_on('py-setuptools', type='build')
     depends_on('py-colormath', type=('build', 'run'))
+    depends_on('py-colormath@3.0.0:', type=('build', 'run'), when='@0.0.11:')
diff --git a/var/spack/repos/builtin/packages/py-spefile/package.py b/var/spack/repos/builtin/packages/py-spefile/package.py
index dbb8937dc8..c6b4adba1f 100644
--- a/var/spack/repos/builtin/packages/py-spefile/package.py
+++ b/var/spack/repos/builtin/packages/py-spefile/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,12 +11,11 @@ class PySpefile(PythonPackage):
        analysis of x-ray scattering experiments"""
 
     homepage = "https://github.com/conda-forge/spefile-feedstock"
-    url      = "https://github.com/conda-forge/spefile-feedstock.git"
+    git      = "https://github.com/conda-forge/spefile-feedstock.git"
 
     import_modules = ['spefile']
 
-    version('1.6', git='https://github.com/conda-forge/spefile-feedstock.git',
-            commit='24394e066da8dee5e7608f556ca0203c9db217f9')
+    version('1.6', commit='24394e066da8dee5e7608f556ca0203c9db217f9')
 
     depends_on('py-setuptools', type='build')
     depends_on('py-numpy', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-spglib/package.py b/var/spack/repos/builtin/packages/py-spglib/package.py
index 604aa0faf2..271ca68e82 100644
--- a/var/spack/repos/builtin/packages/py-spglib/package.py
+++ b/var/spack/repos/builtin/packages/py-spglib/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-sphinx-bootstrap-theme/package.py b/var/spack/repos/builtin/packages/py-sphinx-bootstrap-theme/package.py
index faaa9811df..878b18195c 100644
--- a/var/spack/repos/builtin/packages/py-sphinx-bootstrap-theme/package.py
+++ b/var/spack/repos/builtin/packages/py-sphinx-bootstrap-theme/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-sphinx-rtd-theme/package.py b/var/spack/repos/builtin/packages/py-sphinx-rtd-theme/package.py
index bd922fadf7..bb799915aa 100644
--- a/var/spack/repos/builtin/packages/py-sphinx-rtd-theme/package.py
+++ b/var/spack/repos/builtin/packages/py-sphinx-rtd-theme/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-sphinx/package.py b/var/spack/repos/builtin/packages/py-sphinx/package.py
index d99ee12f0e..3f0268732f 100644
--- a/var/spack/repos/builtin/packages/py-sphinx/package.py
+++ b/var/spack/repos/builtin/packages/py-sphinx/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,6 +21,7 @@ class PySphinx(PythonPackage):
         'sphinx.environment.collectors', 'sphinx.environment.adapters'
     ]
 
+    version('1.7.4', '95f3b83f521314600e5b09e99cf32c46')
     version('1.6.3', 'c5ad61f4e0974375ca2c2b58ef8d5411')
     version('1.6.1', '26cb1cdca7aa4afc8c925d926b6268e7')
     version('1.5.5', 'f9581b3556df9722143c47290273bcf8')
@@ -51,6 +33,9 @@ class PySphinx(PythonPackage):
     # Sphinx requires at least Python 2.7 or 3.4 to run
     depends_on('python@2.7:2.8,3.4:', type=('build', 'run'))
 
+    # See here for upstream list of dependencies:
+    # https://github.com/sphinx-doc/sphinx/blob/master/setup.py
+
     # Most Python packages only require py-setuptools as a build dependency.
     # However, py-sphinx requires py-setuptools during runtime as well.
     depends_on('py-setuptools',               type=('build', 'run'))
@@ -65,6 +50,8 @@ class PySphinx(PythonPackage):
     depends_on('py-imagesize', when='@1.4:',  type=('build', 'run'))
     depends_on('py-requests@2.0.0:',          type=('build', 'run'))
     depends_on('py-sphinx-rtd-theme@0.1:',    type=('build', 'run'))  # optional as of 1.4
+    # See: https://github.com/sphinx-doc/sphinx/commit/854a227501a7582510eba41a208d25816f754e0c
+    depends_on('py-packaging', type=('build', 'run'), when='@1.7.4:')
 
     # Sphinx v1.6+ no longer includes websupport by default:
     # http://www.sphinx-doc.org/en/stable/changes.html
@@ -78,8 +65,7 @@ class PySphinx(PythonPackage):
     #            type=('build', 'run'))
     depends_on('py-typing', when='@1.6:', type=('build', 'run'))
 
-    # TODO: Add a 'test' deptype
-    # depends_on('py-pytest',     type='test')
-    # depends_on('py-mock',       type='test')
-    # depends_on('py-simplejson', type='test')
-    # depends_on('py-html5lib',   type='test')
+    depends_on('py-pytest',     type='test')
+    depends_on('py-mock',       type='test')
+    depends_on('py-simplejson', type='test')
+    depends_on('py-html5lib',   type='test')
diff --git a/var/spack/repos/builtin/packages/py-sphinxcontrib-bibtex/package.py b/var/spack/repos/builtin/packages/py-sphinxcontrib-bibtex/package.py
index e643a8d933..b0dc62142b 100644
--- a/var/spack/repos/builtin/packages/py-sphinxcontrib-bibtex/package.py
+++ b/var/spack/repos/builtin/packages/py-sphinxcontrib-bibtex/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-sphinxcontrib-programoutput/package.py b/var/spack/repos/builtin/packages/py-sphinxcontrib-programoutput/package.py
index d9dbafb3e3..bc8cd15609 100644
--- a/var/spack/repos/builtin/packages/py-sphinxcontrib-programoutput/package.py
+++ b/var/spack/repos/builtin/packages/py-sphinxcontrib-programoutput/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-sphinxcontrib-websupport/package.py b/var/spack/repos/builtin/packages/py-sphinxcontrib-websupport/package.py
index b75f894c1d..f823a0fadb 100644
--- a/var/spack/repos/builtin/packages/py-sphinxcontrib-websupport/package.py
+++ b/var/spack/repos/builtin/packages/py-sphinxcontrib-websupport/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -42,6 +23,5 @@ class PySphinxcontribWebsupport(PythonPackage):
 
     depends_on('py-setuptools', type='build')
 
-    # TODO: Add a 'test' deptype
-    # depends_on('py-pytest', type='test')
-    # depends_on('py-mock',   type='test')
+    depends_on('py-pytest', type='test')
+    depends_on('py-mock',   type='test')
diff --git a/var/spack/repos/builtin/packages/py-spyder/package.py b/var/spack/repos/builtin/packages/py-spyder/package.py
index 58bc3f9fce..57ce28a28a 100644
--- a/var/spack/repos/builtin/packages/py-spyder/package.py
+++ b/var/spack/repos/builtin/packages/py-spyder/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,7 +15,7 @@ class PySpyder(PythonPackage):
     version('3.1.3', '4b9b7c8c3e6dc00001e6e98473473c36')
     version('2.3.9', 'dd01e07a77123c128ff79ba57b97c1d7')
 
-    depends_on('py-setuptools',       type='build')
+    depends_on('python@2.7.0:2.8.0,3.3.0:', type=('build', 'run'))
     depends_on('py-rope@0.9.4:',      type=('build', 'run'), when='^python@:3')
     # depends_on('py-rope_py3k',    type=('build', 'run'), when='^python@3:')
     depends_on('py-jedi@0.9.0',       type=('build', 'run'))
@@ -44,12 +25,21 @@ class PySpyder(PythonPackage):
     depends_on('py-qtconsole@4.2.0:', type=('build', 'run'))
     depends_on('py-nbconvert',        type=('build', 'run'))
     depends_on('py-sphinx',           type=('build', 'run'))
-    depends_on('py-pycodestyle',      type=('build', 'run'))
+    # The pycodestyle dependency is split in two, because internally it
+    # changes its name from pep8 to pycodestyle, and spyder does not cope
+    # with this change until @3.2.0
+    # https://github.com/PyCQA/pycodestyle/issues/466
+    # https://github.com/spyder-ide/spyder/blob/master/CHANGELOG.md#version-32-2017-07-24
+    depends_on('py-pycodestyle@:1.7.1', when='@:3.1.99', type=('build', 'run'))
+    depends_on('py-pycodestyle@2.1.0:', when='@3.2.0:',  type=('build', 'run'))
     depends_on('py-pylint',           type=('build', 'run'))
     depends_on('py-psutil',           type=('build', 'run'))
     depends_on('py-qtawesome@0.4.1:', type=('build', 'run'))
     depends_on('py-qtpy@1.1.0:',      type=('build', 'run'))
-    depends_on('py-zmq',              type=('build', 'run'))
-    depends_on('py-chardet@2:',       type=('build', 'run'))
+    # technically this is a transitive dependency in order for py-pyqt
+    # to pick up webkit, but this is the easier solution (see #9207)
+    depends_on('qt+webkit',           type=('build', 'run'))
     depends_on('py-pickleshare',      type=('build', 'run'))
+    depends_on('py-zmq',              type=('build', 'run'))
+    depends_on('py-chardet@2.0.0:',   type=('build', 'run'))
     depends_on('py-numpydoc',         type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-spykeutils/package.py b/var/spack/repos/builtin/packages/py-spykeutils/package.py
index cdccc3be67..466ec83895 100644
--- a/var/spack/repos/builtin/packages/py-spykeutils/package.py
+++ b/var/spack/repos/builtin/packages/py-spykeutils/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-sqlalchemy/package.py b/var/spack/repos/builtin/packages/py-sqlalchemy/package.py
index 8f60538c77..16ce8b76c9 100644
--- a/var/spack/repos/builtin/packages/py-sqlalchemy/package.py
+++ b/var/spack/repos/builtin/packages/py-sqlalchemy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-statsmodels/package.py b/var/spack/repos/builtin/packages/py-statsmodels/package.py
index 641dc197af..b206410d39 100644
--- a/var/spack/repos/builtin/packages/py-statsmodels/package.py
+++ b/var/spack/repos/builtin/packages/py-statsmodels/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-stevedore/package.py b/var/spack/repos/builtin/packages/py-stevedore/package.py
new file mode 100644
index 0000000000..5cd8c5ec43
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-stevedore/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyStevedore(PythonPackage):
+    """Manage Dynamic Plugins for Python Applications."""
+
+    homepage = "https://docs.openstack.org/stevedore/latest/"
+    url      = "https://pypi.io/packages/source/s/stevedore/stevedore-1.28.0.tar.gz"
+
+    version('1.28.0', 'b736a71431a2ff5831bbff4a6ccec0c1')
+
+    depends_on('python@2.6:')
+
+    depends_on('py-six@1.10.0:', type=('build', 'run'))
+    depends_on('py-pbr@2.0.0:2.1.0', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-storm/package.py b/var/spack/repos/builtin/packages/py-storm/package.py
index 8552413694..2274a5d3ea 100644
--- a/var/spack/repos/builtin/packages/py-storm/package.py
+++ b/var/spack/repos/builtin/packages/py-storm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-subprocess32/package.py b/var/spack/repos/builtin/packages/py-subprocess32/package.py
index 66c6e3b86d..831f0ae428 100644
--- a/var/spack/repos/builtin/packages/py-subprocess32/package.py
+++ b/var/spack/repos/builtin/packages/py-subprocess32/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-symengine/package.py b/var/spack/repos/builtin/packages/py-symengine/package.py
index 6de1c159c3..021604a88b 100644
--- a/var/spack/repos/builtin/packages/py-symengine/package.py
+++ b/var/spack/repos/builtin/packages/py-symengine/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,10 +10,11 @@ class PySymengine(PythonPackage):
     """Python wrappers for SymEngine, a symbolic manipulation library."""
 
     homepage = "https://github.com/symengine/symengine.py"
-    url = "https://github.com/symengine/symengine.py/archive/v0.2.0.tar.gz"
+    url      = "https://github.com/symengine/symengine.py/archive/v0.2.0.tar.gz"
+    git      = "https://github.com/symengine/symengine.py.git"
 
+    version('develop', branch='master')
     version('0.2.0', 'e1d114fa12be4c8c7e9f24007e07718c')
-    version('develop', git='https://github.com/symengine/symengine.py.git')
 
     # Build dependencies
     depends_on('python@2.7:2.8,3.3:')
diff --git a/var/spack/repos/builtin/packages/py-symfit/package.py b/var/spack/repos/builtin/packages/py-symfit/package.py
index 6ecf2ebee6..a876ef689d 100644
--- a/var/spack/repos/builtin/packages/py-symfit/package.py
+++ b/var/spack/repos/builtin/packages/py-symfit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-sympy/package.py b/var/spack/repos/builtin/packages/py-sympy/package.py
index 2a6758bbf6..f9289f9b0f 100644
--- a/var/spack/repos/builtin/packages/py-sympy/package.py
+++ b/var/spack/repos/builtin/packages/py-sympy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,7 +11,8 @@ class PySympy(PythonPackage):
     homepage = "https://pypi.python.org/pypi/sympy"
     url      = "https://pypi.io/packages/source/s/sympy/sympy-0.7.6.tar.gz"
 
-    version('0.7.6', '3d04753974306d8a13830008e17babca')
+    version('1.1.1', 'c410a9c2346878716d16ec873d72e72a')
     version('1.0', '43e797de799f00f9e8fd2307dba9fab1')
+    version('0.7.6', '3d04753974306d8a13830008e17babca')
 
     depends_on('py-mpmath', when='@1.0:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-tabulate/package.py b/var/spack/repos/builtin/packages/py-tabulate/package.py
index 7083d69506..6a3058a769 100644
--- a/var/spack/repos/builtin/packages/py-tabulate/package.py
+++ b/var/spack/repos/builtin/packages/py-tabulate/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-tappy/package.py b/var/spack/repos/builtin/packages/py-tappy/package.py
index 3600e56fc8..ae2c5b360b 100644
--- a/var/spack/repos/builtin/packages/py-tappy/package.py
+++ b/var/spack/repos/builtin/packages/py-tappy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-terminado/package.py b/var/spack/repos/builtin/packages/py-terminado/package.py
index 0cf4e582f2..f77097c4d8 100644
--- a/var/spack/repos/builtin/packages/py-terminado/package.py
+++ b/var/spack/repos/builtin/packages/py-terminado/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-testinfra/package.py b/var/spack/repos/builtin/packages/py-testinfra/package.py
new file mode 100644
index 0000000000..e866245794
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-testinfra/package.py
@@ -0,0 +1,30 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyTestinfra(PythonPackage):
+    """With Testinfra you can write unit tests in Python to test actual state
+    of your servers configured by management tools like Salt, Ansible, Puppet,
+    Chef and so on."""
+
+    homepage = "https://testinfra.readthedocs.io"
+    url      = "https://pypi.python.org/packages/source/t/testinfra/testinfra-1.11.1.tar.gz"
+
+    version('1.13.0', '1e0a135c784207f8609e7730901f1291')
+    version('1.12.0', '9784c01d7af3d624c6ec3cd25cce2011')
+    version('1.11.1', 'c64ce6b16661d647c62c9508de419f5f')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-importlib', when='^python@2.6.0:2.6.999', type=('build', 'run'))
+    depends_on('py-pytest@:3.0.1,3.0.3:', type=('build', 'run'))
+    depends_on('py-six@1.4:', type=('build', 'run'))
+
+    # Required for testing remote systems
+    depends_on('py-paramiko', type=('build', 'run'))
+
+    # Required for parallel execution
+    depends_on('py-pytest-xdist', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-tetoolkit/package.py b/var/spack/repos/builtin/packages/py-tetoolkit/package.py
new file mode 100644
index 0000000000..c43950c518
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-tetoolkit/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyTetoolkit(PythonPackage):
+    """TEToolkit is a software package that utilizes both unambiguously
+       (uniquely) and ambiguously (multi-) mapped reads to perform
+       differential enrichment analyses from high throughput sequencing
+       experiments."""
+
+    homepage = "http://hammelllab.labsites.cshl.edu/software"
+    url      = "https://pypi.io/packages/source/T/TEToolkit/TEToolkit-1.5.1.tar.gz"
+
+    version('1.5.1', '05745b2d5109911e95593e423446a831')
+
+    depends_on('py-setuptools')
+    depends_on('python@2.7:', type=('build', 'run'))
+    depends_on('py-pysam', type=('build', 'run'))
+    depends_on('r-deseq', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-theano/package.py b/var/spack/repos/builtin/packages/py-theano/package.py
index 4fe8920dd5..a808fa896b 100644
--- a/var/spack/repos/builtin/packages/py-theano/package.py
+++ b/var/spack/repos/builtin/packages/py-theano/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,10 +11,13 @@ class PyTheano(PythonPackage):
     and GPUs."""
 
     homepage = "http://deeplearning.net/software/theano/"
-    url = "https://pypi.io/packages/source/T/Theano/Theano-0.8.2.tar.gz"
+    url      = "https://pypi.io/packages/source/T/Theano/Theano-0.8.2.tar.gz"
+    git      = "https://github.com/Theano/Theano.git"
 
+    version('master', branch='master')
+    version('1.0.2', 'fcae24dfa76babe15f5f3c556d67c9f2')
+    version('1.0.1', 'a38b36c0fdc3126c574163db0a253e69')
     version('0.8.2', 'f2d0dfe7df141115201077cd933b2c52')
-    version('master', git='https://github.com/Theano/Theano.git', branch='master')
 
     variant('gpu', default=False,
             description='Builds with support for GPUs via CUDA and cuDNN')
@@ -48,8 +32,9 @@ class PyTheano(PythonPackage):
     depends_on('blas')
 
     depends_on('cuda', when='+gpu')
+    depends_on('cudnn', when='+gpu')
+    depends_on('py-pygpu', when='+gpu', type=('build', 'run'))
     depends_on('libgpuarray', when='+gpu')
 
-    # TODO: Add a 'test' deptype
-    # depends_on('py-nose@1.3.0:', type='test')
-    # depends_on('py-nose-parameterized@0.5.0:', type='test')
+    depends_on('py-nose@1.3.0:', type='test')
+    depends_on('py-nose-parameterized@0.5.0:', type='test')
diff --git a/var/spack/repos/builtin/packages/py-tifffile/package.py b/var/spack/repos/builtin/packages/py-tifffile/package.py
index b0dfb7ed1d..d8f863ef15 100644
--- a/var/spack/repos/builtin/packages/py-tifffile/package.py
+++ b/var/spack/repos/builtin/packages/py-tifffile/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-toml/package.py b/var/spack/repos/builtin/packages/py-toml/package.py
new file mode 100644
index 0000000000..22c8c3065a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-toml/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyToml(PythonPackage):
+    """A Python library for parsing and creating TOML configuration files.
+    For more information on the TOML standard, see
+    https://github.com/toml-lang/toml.git"""
+
+    homepage = "https://github.com/uiri/toml.git"
+    url      = "https://github.com/uiri/toml/archive/0.9.3.tar.gz"
+
+    version('0.9.3', '58e3023a17509dcf4f50581bfc70ff23')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('python@2.6:2.8,3.3:', type=('build', 'run'))
+
+    phases = ['build', 'check', 'install']
diff --git a/var/spack/repos/builtin/packages/py-tomopy/package.py b/var/spack/repos/builtin/packages/py-tomopy/package.py
index acba1ddcac..1b5d8f2e79 100644
--- a/var/spack/repos/builtin/packages/py-tomopy/package.py
+++ b/var/spack/repos/builtin/packages/py-tomopy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/py-toolz/package.py b/var/spack/repos/builtin/packages/py-toolz/package.py
new file mode 100644
index 0000000000..671a5dbfee
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-toolz/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyToolz(PythonPackage):
+    """A set of utility functions for iterators, functions, and dictionaries"""
+
+    homepage = "http://github.com/pytoolz/toolz/"
+    url      = "https://pypi.io/packages/source/t/toolz/toolz-0.9.0.tar.gz"
+
+    import_modules = ['toolz', 'tlz', 'toolz.curried', 'toolz.sandbox']
+
+    version('0.9.0', '6fd07249389dd0b3bfe71d4282314328')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-tornado/package.py b/var/spack/repos/builtin/packages/py-tornado/package.py
index ce1c88a2bb..c480b27470 100644
--- a/var/spack/repos/builtin/packages/py-tornado/package.py
+++ b/var/spack/repos/builtin/packages/py-tornado/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-tqdm/package.py b/var/spack/repos/builtin/packages/py-tqdm/package.py
index 1d1b2486c3..b9c3d69562 100644
--- a/var/spack/repos/builtin/packages/py-tqdm/package.py
+++ b/var/spack/repos/builtin/packages/py-tqdm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-traceback2/package.py b/var/spack/repos/builtin/packages/py-traceback2/package.py
new file mode 100644
index 0000000000..86f61b17c5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-traceback2/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyTraceback2(PythonPackage):
+    """Backports of the traceback module"""
+
+    homepage = "https://github.com/testing-cabal/traceback2"
+    url      = "https://pypi.io/packages/source/t/traceback2/traceback2-1.4.0.tar.gz"
+
+    version('1.4.0', '9e9723f4d70bfc6308fa992dd193c400')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-linecache2', type=('build', 'run'))
+    depends_on('py-pbr', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-traitlets/package.py b/var/spack/repos/builtin/packages/py-traitlets/package.py
index db90d28a66..b8d7b418e1 100644
--- a/var/spack/repos/builtin/packages/py-traitlets/package.py
+++ b/var/spack/repos/builtin/packages/py-traitlets/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-tuiview/package.py b/var/spack/repos/builtin/packages/py-tuiview/package.py
index 1223666d90..f9baeef8b8 100644
--- a/var/spack/repos/builtin/packages/py-tuiview/package.py
+++ b/var/spack/repos/builtin/packages/py-tuiview/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-twisted/package.py b/var/spack/repos/builtin/packages/py-twisted/package.py
index e596adec97..7b03f54f8f 100644
--- a/var/spack/repos/builtin/packages/py-twisted/package.py
+++ b/var/spack/repos/builtin/packages/py-twisted/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-typing/package.py b/var/spack/repos/builtin/packages/py-typing/package.py
index 656eabe6f6..c1f593f07a 100644
--- a/var/spack/repos/builtin/packages/py-typing/package.py
+++ b/var/spack/repos/builtin/packages/py-typing/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-tzlocal/package.py b/var/spack/repos/builtin/packages/py-tzlocal/package.py
index fad9c19f3b..90f31cb205 100644
--- a/var/spack/repos/builtin/packages/py-tzlocal/package.py
+++ b/var/spack/repos/builtin/packages/py-tzlocal/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-udunits/package.py b/var/spack/repos/builtin/packages/py-udunits/package.py
new file mode 100644
index 0000000000..eddfd4cc08
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-udunits/package.py
@@ -0,0 +1,50 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class PyUdunits(PythonPackage):
+    """The MetOffice cf_units Python interface to the UDUNITS-2 Library."""
+    homepage = "https://github.com/SciTools/cf_units"
+    url      = "https://github.com/SciTools/cf_units/archive/v1.1.3.tar.gz"
+
+    version('1.1.3', '61ea2239c87b4c1d5d30147800a9e750')
+
+    maintainers = ['citibeth']
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-six', type=('build', 'run'))
+    depends_on('py-netcdf4', type=('build', 'run'))
+    depends_on('udunits2')
+
+    # See: https://github.com/SciTools/cf_units/blob/master/cf_units/etc/site.cfg.template
+    # udunits2_path = /path/to/libudunits2.so
+    # udunits2_xml_path = /path/to/udunits2.xml
+    site_cfg_template = """[System]
+udunits2_path = %s
+udunits2_xml_path = %s
+"""
+
+    @run_after('install')
+    def configure_template(self):
+        spec = self.spec
+
+        cfg_templates = find(spec.prefix, ['site.cfg.template'])
+        if len(cfg_templates) != 1:
+            tty.die(
+                'Found %d instances of site.cfg.template, wanted 1' %
+                len(cfg_templates))
+        cfg_template = cfg_templates[0]
+
+        cfg = os.path.join(os.path.split(cfg_template)[0], 'site.cfg')
+
+        udunits2_xml_path = os.path.join(
+            spec['udunits2'].prefix, 'share', 'udunits', 'udunits2.xml')
+
+        with open(cfg, 'w') as fout:
+            fout.write(self.site_cfg_template %
+                       (spec['udunits2'].libs, udunits2_xml_path))
diff --git a/var/spack/repos/builtin/packages/py-umi-tools/package.py b/var/spack/repos/builtin/packages/py-umi-tools/package.py
new file mode 100644
index 0000000000..d837ba6be6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-umi-tools/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyUmiTools(PythonPackage):
+    """Tools for handling Unique Molecular Identifiers in NGS data sets"""
+
+    homepage = "https://github.com/CGATOxford/UMI-tools"
+    url      = "https://github.com/CGATOxford/UMI-tools/archive/0.5.3.tar.gz"
+
+    version('0.5.3', '08bdebe30f84867d352ff5e1a2fe4d94')
+
+    depends_on('python@2.7:')
+    depends_on('py-setuptools@1.1:',   type='build')
+    depends_on('py-numpy@1.7:',        type=('build', 'run'))
+    depends_on('py-pandas@0.12:',      type=('build', 'run'))
+    depends_on('py-pysam@0.8.4:',      type=('build', 'run'))
+    depends_on('py-future',            type=('build', 'run'))
+    depends_on('py-six',               type=('build', 'run'))
+    depends_on('py-regex',             type=('build', 'run'))
+    depends_on('py-scipy',             type=('build', 'run'))
+    depends_on('py-matplotlib',        type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-unittest2/package.py b/var/spack/repos/builtin/packages/py-unittest2/package.py
index bdac19d855..635ba1ceda 100644
--- a/var/spack/repos/builtin/packages/py-unittest2/package.py
+++ b/var/spack/repos/builtin/packages/py-unittest2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,3 +17,6 @@ class PyUnittest2(PythonPackage):
 
     depends_on('py-setuptools', type='build')
     depends_on('py-enum34', when='^python@:3.3', type=('build', 'run'))
+    depends_on('py-traceback2', type=('build', 'run'))
+    depends_on('py-six', type=('build', 'run'))
+    depends_on('py-argparse', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-unittest2py3k/package.py b/var/spack/repos/builtin/packages/py-unittest2py3k/package.py
index 1c30595d97..932d665b2f 100644
--- a/var/spack/repos/builtin/packages/py-unittest2py3k/package.py
+++ b/var/spack/repos/builtin/packages/py-unittest2py3k/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-urllib3/package.py b/var/spack/repos/builtin/packages/py-urllib3/package.py
index 000c6ef1e6..224ee6197d 100644
--- a/var/spack/repos/builtin/packages/py-urllib3/package.py
+++ b/var/spack/repos/builtin/packages/py-urllib3/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-urwid/package.py b/var/spack/repos/builtin/packages/py-urwid/package.py
index 46895ac2ee..c5f106809a 100644
--- a/var/spack/repos/builtin/packages/py-urwid/package.py
+++ b/var/spack/repos/builtin/packages/py-urwid/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-vcversioner/package.py b/var/spack/repos/builtin/packages/py-vcversioner/package.py
index fa4e2565b8..8c863ae58f 100644
--- a/var/spack/repos/builtin/packages/py-vcversioner/package.py
+++ b/var/spack/repos/builtin/packages/py-vcversioner/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-virtualenv-clone/package.py b/var/spack/repos/builtin/packages/py-virtualenv-clone/package.py
new file mode 100644
index 0000000000..ecc7abfe4f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-virtualenv-clone/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyVirtualenvClone(PythonPackage):
+    """A script for cloning a non-relocatable virtualenv."""
+
+    homepage = "https://github.com/edwardgeorge/virtualenv-clone"
+    url      = "https://pypi.io/packages/source/v/virtualenv-clone/virtualenv-clone-0.2.6.tar.gz"
+
+    version('0.2.6', 'fb03cd8c7a2be75937a13756d14068fc')
+
+    depends_on('python@2.6:')
+    # not just build-time, requires pkg_resources
+    depends_on('py-setuptools', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-virtualenv/package.py b/var/spack/repos/builtin/packages/py-virtualenv/package.py
index a91117e616..a4108b51ee 100644
--- a/var/spack/repos/builtin/packages/py-virtualenv/package.py
+++ b/var/spack/repos/builtin/packages/py-virtualenv/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,6 +12,7 @@ class PyVirtualenv(PythonPackage):
     homepage = "https://virtualenv.pypa.io/"
     url      = "https://pypi.io/packages/source/v/virtualenv/virtualenv-15.1.0.tar.gz"
 
+    version('16.0.0', '4feb74ee26255dd7e62e36ce96bcc4c6')
     version('15.1.0', '44e19f4134906fe2d75124427dc9b716')
     version('15.0.1', '28d76a0d9cbd5dc42046dd14e76a6ecc')
     version('13.0.1', '1ffc011bde6667f0e37ecd976f4934db')
diff --git a/var/spack/repos/builtin/packages/py-virtualenvwrapper/package.py b/var/spack/repos/builtin/packages/py-virtualenvwrapper/package.py
new file mode 100644
index 0000000000..009358344a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-virtualenvwrapper/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyVirtualenvwrapper(PythonPackage):
+    """virtualenvwrapper is a set of extensions to Ian Bicking's
+    virtualenv tool. The extensions include wrappers for creating and
+    deleting virtual environments and otherwise managing your development
+    workflow, making it easier to work on more than one project at a time
+    without introducing conflicts in their dependencies."""
+
+    homepage = "https://bitbucket.org/virtualenvwrapper/virtualenvwrapper.git"
+    url      = "https://pypi.io/packages/source/v/virtualenvwrapper/virtualenvwrapper-4.8.2.tar.gz"
+
+    version('4.8.2', '8e3af0e0d42733f15c5e36df484a952e')
+
+    depends_on('python@2.6:')
+    depends_on('py-virtualenv', type=('build', 'run'))
+    depends_on('py-virtualenv-clone', type=('build', 'run'))
+    depends_on('py-stevedore', type=('build', 'run'))
+    # not just build-time, requires pkg_resources
+    depends_on('py-setuptools', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-vsc-base/package.py b/var/spack/repos/builtin/packages/py-vsc-base/package.py
index 2cd0ff4b46..f2ca078d60 100644
--- a/var/spack/repos/builtin/packages/py-vsc-base/package.py
+++ b/var/spack/repos/builtin/packages/py-vsc-base/package.py
@@ -1,26 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Kenneth Hoste
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-vsc-install/package.py b/var/spack/repos/builtin/packages/py-vsc-install/package.py
index 09e9c885cf..9b74392146 100644
--- a/var/spack/repos/builtin/packages/py-vsc-install/package.py
+++ b/var/spack/repos/builtin/packages/py-vsc-install/package.py
@@ -1,25 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Kenneth Hoste
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Kenneth Hoste, kenneth.hoste@gmail.com
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-wcsaxes/package.py b/var/spack/repos/builtin/packages/py-wcsaxes/package.py
index 16fa376dc7..c3109c498a 100644
--- a/var/spack/repos/builtin/packages/py-wcsaxes/package.py
+++ b/var/spack/repos/builtin/packages/py-wcsaxes/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-wcwidth/package.py b/var/spack/repos/builtin/packages/py-wcwidth/package.py
index ca4b7740b5..4bb68362a7 100644
--- a/var/spack/repos/builtin/packages/py-wcwidth/package.py
+++ b/var/spack/repos/builtin/packages/py-wcwidth/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-webkit-server/package.py b/var/spack/repos/builtin/packages/py-webkit-server/package.py
index 66850b9682..db1e45e088 100644
--- a/var/spack/repos/builtin/packages/py-webkit-server/package.py
+++ b/var/spack/repos/builtin/packages/py-webkit-server/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,6 +11,7 @@ class PyWebkitServer(PythonPackage):
 
     homepage = "https://github.com/niklasb/webkit-server"
     url      = "https://pypi.io/packages/source/w/webkit-server/webkit-server-1.0.tar.gz"
+    git      = "https://github.com/niklasb/webkit-server.git"
 
-    version('develop', git="https://github.com/niklasb/webkit-server", branch="master")
+    version('develop', branch='master')
     version('1.0', '8463245c2b4f0264d934c0ae20bd4654')
diff --git a/var/spack/repos/builtin/packages/py-weblogo/package.py b/var/spack/repos/builtin/packages/py-weblogo/package.py
new file mode 100644
index 0000000000..1b27ac5686
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-weblogo/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyWeblogo(PythonPackage):
+    """WebLogo is a web based application designed to make the generation of
+    sequence logos as easy and painless as possible."""
+
+    homepage = "http://weblogo.threeplusone.com"
+    url      = "https://pypi.io/packages/source/w/weblogo/weblogo-3.6.0.tar.gz"
+
+    version('3.6.0', 'd0764f218057543fa664d2ae17d37b6d')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('ghostscript', type=('build', 'run'))
+    depends_on('pdf2svg', type=('build', 'run'))
+    depends_on('py-numpy', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-werkzeug/package.py b/var/spack/repos/builtin/packages/py-werkzeug/package.py
index 30573a7ff2..f2941f80fc 100644
--- a/var/spack/repos/builtin/packages/py-werkzeug/package.py
+++ b/var/spack/repos/builtin/packages/py-werkzeug/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-wheel/package.py b/var/spack/repos/builtin/packages/py-wheel/package.py
index f0a15f0886..03e91849ad 100644
--- a/var/spack/repos/builtin/packages/py-wheel/package.py
+++ b/var/spack/repos/builtin/packages/py-wheel/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-widgetsnbextension/package.py b/var/spack/repos/builtin/packages/py-widgetsnbextension/package.py
index 206f940b57..32cfc4581a 100644
--- a/var/spack/repos/builtin/packages/py-widgetsnbextension/package.py
+++ b/var/spack/repos/builtin/packages/py-widgetsnbextension/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-wrapt/package.py b/var/spack/repos/builtin/packages/py-wrapt/package.py
index 5b81eef2e1..a73a0ee70a 100644
--- a/var/spack/repos/builtin/packages/py-wrapt/package.py
+++ b/var/spack/repos/builtin/packages/py-wrapt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-xarray/package.py b/var/spack/repos/builtin/packages/py-xarray/package.py
index 27017a9227..ade407dbb9 100644
--- a/var/spack/repos/builtin/packages/py-xarray/package.py
+++ b/var/spack/repos/builtin/packages/py-xarray/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-xattr/package.py b/var/spack/repos/builtin/packages/py-xattr/package.py
new file mode 100644
index 0000000000..c6ee55760f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-xattr/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyXattr(PythonPackage):
+    """A python interface to access extended file attributes,
+        sans libattr dependency"""
+
+    homepage = "http://pyxattr.k1024.org/"
+    git      = "https://github.com/fwang2/pyxattr.git"
+
+    version('develop', branch='dev')
+
+    depends_on('python@2.7:')
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-xdot/package.py b/var/spack/repos/builtin/packages/py-xdot/package.py
new file mode 100644
index 0000000000..f840919294
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-xdot/package.py
@@ -0,0 +1,62 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyXdot(PythonPackage):
+    """xdot.py is an interactive viewer for graphs written in Graphviz's
+    dot language."""
+
+    homepage = "https://github.com/jrfonseca/xdot.py"
+    url      = "https://github.com/jrfonseca/xdot.py/archive/0.9.tar.gz"
+    git      = "https://github.com/jrfonseca/xdot.py.git"
+
+    version('master', branch="master")
+    version('1.0', '4e60c42d009a8802db6c1b4dab519863')
+    version('0.9', '19c78311d73b0f9ea059a6febf42eeea')
+
+    # setuptools is required at runtime to avoid:
+    # No module named 'pkg_resources'
+    depends_on('py-setuptools', type=('build', 'run'))
+    depends_on('python@3:', type=('build', 'run'))
+    depends_on('py-pygobject', type=('build', 'run'))
+    depends_on('py-pycairo', type=('build', 'run'))
+    depends_on('pango', type=('build', 'run'))
+    depends_on('atk', type=('build', 'run'))
+    depends_on('gdk-pixbuf', type=('build', 'run'))
+    depends_on('gtkplus', type=('build', 'run'))
+
+    @run_after('install')
+    def post_install(self):
+        spec = self.spec
+        repo_paths = '%s:%s:%s:%s' % (
+            join_path(spec['pango'].prefix.lib, 'girepository-1.0'),
+            join_path(spec['atk'].prefix.lib, 'girepository-1.0'),
+            join_path(spec['gdk-pixbuf'].prefix.lib, 'girepository-1.0'),
+            join_path(spec['gtkplus'].prefix.lib, 'girepository-1.0'))
+        dst = join_path(spec.prefix, spec['python'].package.site_packages_dir,
+                        'xdot/__init__.py')
+        filter_file("import sys",
+                    "import sys\nimport os\nos.environ['GI_TYPELIB_PATH']" +
+                    " = '%s'" % repo_paths, dst)
+        # regenerate the byte-compiled __init__.py
+        python3 = spec['python'].command
+        python3('-m', 'compileall', dst)
+
+    def setup_environment(self, spack_env, run_env):
+        spec = self.spec
+        run_env.prepend_path('GI_TYPELIB_PATH',
+                             join_path(spec['pango'].prefix.lib,
+                                       'girepository-1.0'))
+        run_env.prepend_path('GI_TYPELIB_PATH',
+                             join_path(spec['atk'].prefix.lib,
+                                       'girepository-1.0'))
+        run_env.prepend_path('GI_TYPELIB_PATH',
+                             join_path(spec['gdk-pixbuf'].prefix.lib,
+                                       'girepository-1.0'))
+        run_env.prepend_path('GI_TYPELIB_PATH',
+                             join_path(spec['gtkplus'].prefix.lib,
+                                       'girepository-1.0'))
diff --git a/var/spack/repos/builtin/packages/py-xlrd/package.py b/var/spack/repos/builtin/packages/py-xlrd/package.py
index 3fc22a7865..9117728b98 100644
--- a/var/spack/repos/builtin/packages/py-xlrd/package.py
+++ b/var/spack/repos/builtin/packages/py-xlrd/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-xlsxwriter/package.py b/var/spack/repos/builtin/packages/py-xlsxwriter/package.py
index 97170d76d5..af6dd10d7c 100644
--- a/var/spack/repos/builtin/packages/py-xlsxwriter/package.py
+++ b/var/spack/repos/builtin/packages/py-xlsxwriter/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-xmlrunner/package.py b/var/spack/repos/builtin/packages/py-xmlrunner/package.py
index 104d6113c0..aa469b6b40 100644
--- a/var/spack/repos/builtin/packages/py-xmlrunner/package.py
+++ b/var/spack/repos/builtin/packages/py-xmlrunner/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-xopen/package.py b/var/spack/repos/builtin/packages/py-xopen/package.py
index 4b6df42419..0d2121e855 100644
--- a/var/spack/repos/builtin/packages/py-xopen/package.py
+++ b/var/spack/repos/builtin/packages/py-xopen/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-xpyb/package.py b/var/spack/repos/builtin/packages/py-xpyb/package.py
index 60f69610c3..11e73d24b0 100644
--- a/var/spack/repos/builtin/packages/py-xpyb/package.py
+++ b/var/spack/repos/builtin/packages/py-xpyb/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-xvfbwrapper/package.py b/var/spack/repos/builtin/packages/py-xvfbwrapper/package.py
index 09c9f6da47..18b08b266f 100644
--- a/var/spack/repos/builtin/packages/py-xvfbwrapper/package.py
+++ b/var/spack/repos/builtin/packages/py-xvfbwrapper/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-yamlreader/package.py b/var/spack/repos/builtin/packages/py-yamlreader/package.py
new file mode 100644
index 0000000000..66c7be55ed
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-yamlreader/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyYamlreader(PythonPackage):
+    """Yamlreader merges YAML data from a directory, a list of files or a
+    file glob."""
+
+    homepage = "http://pyyaml.org/wiki/PyYAML"
+    url      = "https://pypi.io/packages/source/y/yamlreader/yamlreader-3.0.4.tar.gz"
+
+    version('3.0.4', '542179b5b5bedae941245b8b673119db')
+
+    depends_on('py-setuptools', type=('build', 'run'))
+    depends_on('py-pyyaml', type=('build', 'run'))
+    depends_on('py-six', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-yapf/package.py b/var/spack/repos/builtin/packages/py-yapf/package.py
index 76121cf2d2..1b71fbe2ba 100644
--- a/var/spack/repos/builtin/packages/py-yapf/package.py
+++ b/var/spack/repos/builtin/packages/py-yapf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-yt/package.py b/var/spack/repos/builtin/packages/py-yt/package.py
index 6c8aa1797f..9344fe7463 100644
--- a/var/spack/repos/builtin/packages/py-yt/package.py
+++ b/var/spack/repos/builtin/packages/py-yt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -35,24 +16,21 @@ class PyYt(PythonPackage):
        interdisciplinary community.
     """
     homepage = "http://yt-project.org"
-    url = "https://bitbucket.org/yt_analysis/yt"
+    url      = "https://github.com/yt-project/yt/archive/yt-3.4.0.tar.gz"
+    git      = "https://github.com/yt-project/yt.git"
+
+    version("develop", branch="master")
 
-    version("3.3.5", "2ad314ff3d3261e41825d15db027b0e7",
-            url="https://bitbucket.org/yt_analysis/yt/get/yt-3.3.5.tar.gz")
-    version("3.3.4", "3a84e56dfd82f9dd923f3fb8490e679c",
-            url="https://bitbucket.org/yt_analysis/yt/get/yt-3.3.4.tar.gz")
-    version("3.3.1", hg="https://bitbucket.org/yt_analysis/yt",
-            tag="yt-3.3.1", commit="9bc3d0e9b750c923d44d73c447df64fc431f5838")
-    version("3.2.3", hg="https://bitbucket.org/yt_analysis/yt",
-            tag="yt-3.2.3", commit="83d2c1e9313e7d83eb5b96888451ff2646fd8ff3")
-    version("3.1.0", hg="https://bitbucket.org/yt_analysis/yt",
-            tag="yt-3.1.0", commit="fd7cdc4836188a3badf81adb477bcc1b9632e485")
-    version("3.0.2", hg="https://bitbucket.org/yt_analysis/yt",
-            tag="yt-3.0.2", commit="511887af4c995a78fe606e58ce8162c88380ecdc")
-    version("2.6.3", hg="https://bitbucket.org/yt_analysis/yt",
-            tag="yt-2.6.3", commit="816186f16396a16853810ac9ebcde5057d8d5b1a")
-    version("development", hg="https://bitbucket.org/yt_analysis/yt",
-            branch="yt")
+    version('3.4.1', sha256='b9a73ade3726a8163fc992999c8c1010ca89473131901fe4d48b820ab2ced486')
+    version('3.4.0', sha256='2120793a76864cf3165b2b7290ef719e358fa57501ee8721941e7cfc434cfb2b')
+    version('3.3.5', sha256='2ebe4bbefd9f5367563ce4d7eb87d3f6ef0de1f97ed1c03106d9541e71b7e1ca')
+    version('3.3.4', sha256='2842bab891cfbf3269a3c4bd8f22fef23c9a15a790ba48c6490730cb51ce9b0e')
+    version('3.3.3', sha256='7b9244089e92b1d32cef791cd72760bb8c80b391eaec29672a5377c33f932d88')
+    version('3.3.2', sha256='d323419ad3919e86d2af1738c846021fd7f5b5dc5c06059cdf3a2bc63226466a')
+    version('3.3.1', sha256='7ac68d5e05e2b57fb3635f1027f3201094f3547d584e72ab55fedbfd3bc09a36')
+    version('3.3.0', sha256='e6be799c0d9a83a06649f0d77a61ad9c23b94b34f94e16724e2b18f5c7513c33')
+    version('3.2.3', sha256='96476d17e9ce35f0d4380b2ddb398fe729e39f1f3894602ff07e49844541e5ca')
+    version('3.2.2', sha256='498ed77b3dae8c54929602d4931f3c3e0a3420a9b500cbd870f50b1e0efea8c3')
 
     variant("astropy", default=True, description="enable astropy support")
     variant("h5py", default=True, description="enable h5py support")
diff --git a/var/spack/repos/builtin/packages/py-ytopt/package.py b/var/spack/repos/builtin/packages/py-ytopt/package.py
new file mode 100644
index 0000000000..ec70d6c06d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-ytopt/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyYtopt(PythonPackage):
+    """Ytopt package implements search using Random Forest (SuRF), an autotuning
+       search method developed within Y-Tune ECP project."""
+
+    homepage = "https://xgitlab.cels.anl.gov/pbalapra/ytopt"
+    url      = "https://xgitlab.cels.anl.gov/pbalapra/ytopt/raw/release/dist/ytopt-0.1.0.tar.gz"
+
+    version('0.1.0', sha256='c7081fe3585a5b7a25bcb84733cd2326b72de3bfc4f84d6ad110341f24c3e612')
+
+    depends_on('py-scikit-learn', type=('build', 'run'))
+    depends_on('py-scikit-optimize', type=('build', 'run'))	
+
+    def build_args(self, spec, prefix):
+        args = []
+        return args
diff --git a/var/spack/repos/builtin/packages/py-zmq/package.py b/var/spack/repos/builtin/packages/py-zmq/package.py
index d5734d8a33..51a13ddaf2 100644
--- a/var/spack/repos/builtin/packages/py-zmq/package.py
+++ b/var/spack/repos/builtin/packages/py-zmq/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-zope-event/package.py b/var/spack/repos/builtin/packages/py-zope-event/package.py
new file mode 100644
index 0000000000..a2f0e6ecc1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-zope-event/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyZopeEvent(PythonPackage):
+    """Very basic event publishing system."""
+
+    homepage = "http://github.com/zopefoundation/zope.event"
+    url      = "https://pypi.io/packages/source/z/zope.event/zope.event-4.3.0.tar.gz"
+
+    # FIXME: No idea why this import test fails.
+    # Maybe some kind of namespace issue?
+    # import_modules = ['zope.event']
+
+    version('4.3.0', '8ca737960741c6fd112972f3313303bd')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-zope-interface/package.py b/var/spack/repos/builtin/packages/py-zope-interface/package.py
new file mode 100644
index 0000000000..0fd1b3bee5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-zope-interface/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyZopeInterface(PythonPackage):
+    """This package provides an implementation of "object interfaces" for
+    Python. Interfaces are a mechanism for labeling objects as conforming to a
+    given API or contract. So, this package can be considered as implementation
+    of the Design By Contract methodology support in Python."""
+
+    homepage = "https://github.com/zopefoundation/zope.interface"
+    url      = "https://pypi.io/packages/source/z/zope.interface/zope.interface-4.5.0.tar.gz"
+
+    # FIXME: No idea why these import tests fail.
+    # Maybe some kind of namespace issue?
+    # import_modules = ['zope.interface', 'zope.interface.common']
+
+    version('4.5.0', '7b669cd692d817772c61d2e3ad0f1e71')
+
+    depends_on('python@2.7:2.8,3.4:', type=('build', 'run'))
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-zope-event', type='test')
+    depends_on('py-nose', type='test')
+    depends_on('py-coverage', type='test')
diff --git a/var/spack/repos/builtin/packages/pythia6/CMakeLists.txt b/var/spack/repos/builtin/packages/pythia6/CMakeLists.txt
new file mode 100644
index 0000000000..9362f03668
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pythia6/CMakeLists.txt
@@ -0,0 +1,115 @@
+# ======================================================================
+#  pythia6 main build file
+#
+#  setup cmake
+#  cd .../path/to/build/directory
+#  cmake [-DCMAKE_INSTALL_PREFIX=/install/path]
+#        [-DCMAKE_BUILD_TYPE=<RelWithDebInfo|Debug|Release|MinSizeRel> ]
+#        [-Drun_long_tests:BOOL=ON]
+#        .../path/to/pythia/source
+#  make
+#  make test
+#  make install
+# ======================================================================
+
+# use cmake 2.6 or later
+cmake_minimum_required (VERSION 2.6)
+
+project(pythia6 C Fortran)
+message(STATUS "pythia version is ${PYTHIA6_VERSION}")
+
+enable_testing()
+
+#build all libraries in a single directory to enable testing
+set(LIBRARY_OUTPUT_PATH ${PROJECT_BINARY_DIR}/lib)
+
+# set compiler flags
+# default GNU compiler flags:
+# DEBUG           -g
+# RELEASE         -O3 -DNDEBUG
+# MINSIZEREL      -Os -DNDEBUG
+# RELWITHDEBINFO  -O2 -g
+set( CMAKE_C_FLAGS_DEBUG "-g -O0" )
+set( CMAKE_C_FLAGS_RELWITHDEBINFO "-O3 -g -DNDEBUG -fno-omit-frame-pointer" )
+set( CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" )
+set( CMAKE_Fortran_FLAGS_DEBUG "-g -O0 -fno-second-underscore" )
+set( CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-O3 -g -DNDEBUG -fno-omit-frame-pointer -fno-second-underscore" )
+set( CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG -fno-second-underscore" )
+
+message(STATUS "CMAKE_Fortran_COMPILER_INIT = ${CMAKE_Fortran_COMPILER_INIT}")
+message(STATUS "CMAKE_Fortran_COMPILER_FULLPATH = ${CMAKE_Fortran_COMPILER_FULLPATH}")
+message(STATUS "CMAKE_Fortran_COMPILER = ${CMAKE_Fortran_COMPILER}")
+
+if(NOT CMAKE_BUILD_TYPE)
+  set(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING "" FORCE)
+endif()
+message(STATUS "cmake build type set to ${CMAKE_BUILD_TYPE}")
+
+message("ENV_FLAGS = $ENV{FFLAGS}")
+string(TOUPPER ${CMAKE_BUILD_TYPE} BTYPE_UC )
+if( ${BTYPE_UC} MATCHES "DEBUG")
+  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS_DEBUG}")
+  set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS_DEBUG}")
+elseif( ${BTYPE_UC} MATCHES "RELEASE")
+  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS_RELEASE}")
+  set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS_RELEASE}")
+elseif( ${BTYPE_UC} MATCHES "RELWITHDEBINFO")
+  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS_RELWITHDEBINFO}")
+  set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS_RELWITHDEBINFO}")
+endif()
+set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} $ENV{CFLAGS}")
+set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} $ENV{FFLAGS}")
+message("CMAKE_C_FLAGS = ${CMAKE_C_FLAGS}")
+message("CMAKE_Fortran_FLAGS = ${CMAKE_Fortran_FLAGS}")
+
+# source
+# shared library
+file(GLOB src_files *.c *.F *.f)
+add_library(Pythia6 SHARED ${src_files})
+
+# Installation:
+# Library.
+install(TARGETS Pythia6 DESTINATION lib)
+
+# Include-able file.
+install( FILES example/main60.f
+         DESTINATION include )
+
+# Documentation.
+install(DIRECTORY doc DESTINATION .)
+
+# Examples
+install(DIRECTORY example DESTINATION .)
+
+# tests
+macro( pythia_test testname )
+  set ( package_library_list ${PROJECT_BINARY_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}CLHEP-${PACKAGE}-${VERSION}${CMAKE_STATIC_LIBRARY_SUFFIX} )
+  link_libraries( Pythia6 )
+  message( STATUS "building ${testname} from ${CMAKE_CURRENT_SOURCE_DIR}/example in ${CMAKE_CURRENT_BINARY_DIR}" )
+  add_executable(${testname} example/${testname}.f)
+  add_test( ${testname} ${CMAKE_CURRENT_BINARY_DIR}/${testname} )
+endmacro( pythia_test )
+
+pythia_test( main61 )
+pythia_test( main63 )
+pythia_test( main66 )
+pythia_test( main67 )
+pythia_test( main68 )
+pythia_test( main69 )
+pythia_test( main71 )
+pythia_test( main72 )
+pythia_test( main73 )
+pythia_test( main75 )
+pythia_test( main77 )
+pythia_test( main78 )
+pythia_test( main81 )
+
+# these examples take a while to run
+if( run_long_tests )
+  pythia_test( main62 )
+  pythia_test( main64 )
+  pythia_test( main65 )
+  pythia_test( main70 )
+  pythia_test( main74 )
+  pythia_test( main79 )
+endif( run_long_tests )
diff --git a/var/spack/repos/builtin/packages/pythia6/package.py b/var/spack/repos/builtin/packages/pythia6/package.py
new file mode 100644
index 0000000000..800073bf41
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pythia6/package.py
@@ -0,0 +1,154 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import numbers
+import os
+from six import iteritems
+from six.moves.urllib.parse import urlparse
+
+
+def _is_integral(x):
+    """Accepts only integral values."""
+    try:
+        return isinstance(int(x), numbers.Integral) and \
+            (not isinstance(x, bool)) and \
+            int(x) == x
+    except ValueError:
+        return False
+
+
+class Pythia6(CMakePackage):
+    """PYTHIA is a program for the generation of high-energy physics events,
+    i.e. for the description of collisions at high energies between elementary
+    particles such as e+, e-, p and pbar in various combinations.
+
+    PYTHIA6 is a Fortran package which is no longer maintained: new
+    prospective users should use Pythia8 instead.
+
+    This recipe includes patches required to interoperate with Root.
+    """
+
+    homepage = 'https://pythiasix.hepforge.org/'
+    url = 'http://www.hepforge.org/archive/pythiasix/pythia-6.4.28.tgz'
+
+    version('6.4.28',
+            sha256='01cbff47e99365b5e46f6d62c1735d3cae1932c4710604850d59f538cb758020')
+
+    # Root's TPythia6 interface requires extra sources to be built into
+    # the Pythia6 library.
+    variant('root', default=False,
+            description='Build extra (non OEM) code to allow use by Root.')
+
+    # The maximum number of particles (NMXHEP) supported by the arrays
+    # in the /HEPEVT/ COMMON block may need tweaking if pythia6 is
+    # intended to be used with other code with different requirements.
+    variant('nmxhep', default=4000, values=_is_integral, description='Extent of particle arrays in the /HEPEVT/ COMMON block.')
+
+    # In the unlikely event of new versions >6.4.28,
+    # pythia6_common_address.c should be checked for accuracy against
+    # the definitions of the relevant COMMON blocks in the Pythia6
+    # Fortran source, and patched if necessaary.
+    resource(
+        name='root-pythia6-shim',
+        url='https://root.cern.ch/download/pythia6.tar.gz',
+        sha256='d613dcb27c905710e2f13a934913cc5545e3e5d0e477e580107385d9ef260056',
+        when='+root',
+        destination='.',
+        placement={'pythia6_common_address.c': 'pythia6_common_address.c',
+                   'tpythia6_called_from_cc.F': 'tpythia6_called_from_cc.F'}
+    )
+
+    # Download examples separately.
+    examples \
+        = {'main60.f':
+           'd713b8b267c4405cc9d31c58bba267ae3378902a26fa52393003bf35fd56902c',
+           'main61.f':
+           'e2a3d5524e43d16f60d9edc6e7198d41006d1ba127fb7b0e265aa509e13128b4',
+           'main62.f':
+           'dce822a72fe2d6cfb6d43c479ba98928fb0a39290a6ee26fdcacc66229313045',
+           'main63.f':
+           'b2dd343b3cd7969979b80c564d82b92e0d776d66bb19d346b52f2af27adeb62d',
+           'main64.f':
+           'a35f2f232e6e0d68d67fd350d4d46b0a353f5c7811de0c2db47ae16d17ed1843',
+           'main65.f':
+           '03c81e0bbd77710b0461e18265e80e3bd51360b9f416c86013401f882ac39a5e',
+           'main66.f':
+           '50dd9221a7e84ee7c5005db6758e5880d190eab8cce8a52e7c7b29e9fee8d3da',
+           'main67.f':
+           '1984aa90fe4e3d628c3bcceaa6fca1b08231d835158d975fa171337d55ca4a2f',
+           'main68.f':
+           'c8d6def1298477ffec6a1d98c7e02dcee0debe6badc7c63f752f9194b82f212d',
+           'main69.f':
+           'd14399d43f8c4b670907558849d3e5a4d7625d027de3c10002185c58b20b061a',
+           'main71.f':
+           '2e47af778003b0596e8999f0914033c6eda7335211b9e96ac3075d45a3cde12e',
+           'main72.f':
+           'e27ce2af68b40436c51c65767ebb5ff0955ab8dfdfc5fc5c217ae73cd53070da',
+           'main73.f':
+           '567db2d1a66896ce5103ffa7e10742442b0e934088883e91339536e0249772c4',
+           'main75.f':
+           'b850986c43a5af1e7d13b66d22b01584e3c68bb338be32eac39e31f971b80be4',
+           'main77.f':
+           '0679852c4f35719531ad38dc1dbb374b884181eb5e483c36d8867ccb449177a4',
+           'main78.f':
+           '5babc59fe6a0bd57d97ec398cf01745bc9b72ce6ce0711e934d53c7821e21912',
+           'main79.f':
+           '27ca84d6d0877f3605cbc1b865c3e1f571e7d2c9301094a4122e726a903dbead',
+           'main81.f':
+           'b02fecd1cd0f9ba16eaae53e9da0ba602569fdf0e46856cccdfb4c5b7ba33e8b',
+           'ttbar.lhe':
+           'fb0d43175cc392b19c2b6633dcf673d0b56229b60bec92df4aa782c7196b149c'}
+
+    for example, checksum in iteritems(examples):
+        resource(name=example,
+                 url='http://pythiasix.hepforge.org/examples/{0}'.
+                 format(example),
+                 sha256=checksum,
+                 expand=False,
+                 destination='example',
+                 placement={example: example}
+             )
+
+    # Docs.
+    docs \
+        = {'http://www.hepforge.org/archive/pythiasix/update_notes-6.4.28.txt':
+            'a229be4ba9a4eb65a9d53600a5f388b620038d56694c6cb4671c2be224b67751',
+           'http://home.thep.lu.se/~torbjorn/pythia6/lutp0613man2.pdf':
+           '03d637310ea80f0d7aea761492bd38452c602890d8cf913a1ec9edacd79fa43d',
+           'https://pythiasix.hepforge.org/pythia6-announcement.txt':
+           '2a52def41f0c93e32e0db58dbcf072b987ebfbd32e42ccfc1f9382fcf65f1271'}
+
+    for docurl, checksum in iteritems(docs):
+        doc = os.path.basename(urlparse(docurl).path)
+        resource(name=doc,
+                 url=docurl,
+                 sha256=checksum,
+                 expand=False,
+                 destination='doc',
+                 placement={doc: doc}
+             )
+
+    # The included patch customizes some routines provided in dummy form
+    # by the original source to be useful out of the box in the vast
+    # majority of cases. If your case is different, platform- or
+    # variant-based adjustments should be made.
+    patch('pythia6.patch', level=0)
+
+    def patch(self):
+        # Use our provided CMakeLists.txt. The Makefile provided with
+        # the source is GCC (gfortran) specific, and would have required
+        # additional patching for the +root variant.
+        llnl.util.filesystem.copy(os.path.join(os.path.dirname(__file__),
+                                               'CMakeLists.txt'),
+                                  self.stage.source_path)
+        # Apply the variant value at the relevant place in the source.
+        filter_file(r'^(\s+PARAMETER\s*\(\s*NMXHEP\s*=\s*)\d+',
+                    r'\1{0}'.format(self.spec.variants['nmxhep'].value),
+                    'pyhepc.f')
+
+    def cmake_args(self):
+        args = ['-DPYTHIA6_VERSION={0}'.format(self.version.dotted)]
+        return args
diff --git a/var/spack/repos/builtin/packages/pythia6/pythia6.patch b/var/spack/repos/builtin/packages/pythia6/pythia6.patch
new file mode 100644
index 0000000000..5d45541e07
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pythia6/pythia6.patch
@@ -0,0 +1,278 @@
+diff -Naur pytime.f pytime.f
+--- pytime.f	2018-08-23 11:24:27.000000000 -0500
++++ pytime.f	2018-08-23 11:46:08.189999826 -0500
+@@ -1,4 +1,3 @@
+- 
+ C*********************************************************************
+  
+ C...PYTIME
+@@ -59,17 +58,18 @@
+ C      IDATI(6)=ISEC
+  
+ C...Example 4: GNU LINUX libU77, SunOS.
+-C      CALL IDATE(IDTEMP)
+-C      IDATI(1)=IDTEMP(3)
+-C      IDATI(2)=IDTEMP(2)
+-C      IDATI(3)=IDTEMP(1)
+-C      CALL ITIME(IDTEMP)
+-C      IDATI(4)=IDTEMP(1)
+-C      IDATI(5)=IDTEMP(2)
+-C      IDATI(6)=IDTEMP(3)
++      CALL IDATE(IDTEMP)
++      IDATI(1)=IDTEMP(3)
++      IDATI(2)=IDTEMP(2)
++      IDATI(3)=IDTEMP(1)
++      CALL ITIME(IDTEMP)
++      IDATI(4)=IDTEMP(1)
++      IDATI(5)=IDTEMP(2)
++      IDATI(6)=IDTEMP(3)
+  
+ C...Common code to ensure right century.
+       IDATI(1)=2000+MOD(IDATI(1),100)
+  
+       RETURN
+       END
++ 
+diff -Naur upevnt.f upevnt.f
+--- upevnt.f	2018-08-23 11:24:27.000000000 -0500
++++ upevnt.f	2018-08-23 11:46:08.189999826 -0500
+@@ -1,56 +1,3 @@
+-
+-C...Old example: handles a simple Pythia 6.4 initialization file.
+- 
+-c      SUBROUTINE UPINIT
+- 
+-C...Double precision and integer declarations.
+-c      IMPLICIT DOUBLE PRECISION(A-H, O-Z)
+-c      IMPLICIT INTEGER(I-N)
+- 
+-C...Commonblocks.
+-c      COMMON/PYDAT1/MSTU(200),PARU(200),MSTJ(200),PARJ(200)
+-c      COMMON/PYPARS/MSTP(200),PARP(200),MSTI(200),PARI(200)
+-c      SAVE /PYDAT1/,/PYPARS/
+- 
+-C...User process initialization commonblock.
+-c      INTEGER MAXPUP
+-c      PARAMETER (MAXPUP=100)
+-c      INTEGER IDBMUP,PDFGUP,PDFSUP,IDWTUP,NPRUP,LPRUP
+-c      DOUBLE PRECISION EBMUP,XSECUP,XERRUP,XMAXUP
+-c      COMMON/HEPRUP/IDBMUP(2),EBMUP(2),PDFGUP(2),PDFSUP(2),
+-c     &IDWTUP,NPRUP,XSECUP(MAXPUP),XERRUP(MAXPUP),XMAXUP(MAXPUP),
+-c     &LPRUP(MAXPUP)
+-c      SAVE /HEPRUP/
+- 
+-C...Read info from file.
+-c      IF(MSTP(161).GT.0) THEN
+-c        READ(MSTP(161),*,END=110,ERR=110) IDBMUP(1),IDBMUP(2),EBMUP(1),
+-c     &  EBMUP(2),PDFGUP(1),PDFGUP(2),PDFSUP(1),PDFSUP(2),IDWTUP,NPRUP
+-c        DO 100 IPR=1,NPRUP
+-c          READ(MSTP(161),*,END=110,ERR=110) XSECUP(IPR),XERRUP(IPR),
+-c     &    XMAXUP(IPR),LPRUP(IPR)
+-c  100   CONTINUE
+-c        RETURN
+-C...Error or prematurely reached end of file.
+-c  110   WRITE(MSTU(11),5000)
+-c        STOP
+- 
+-C...Else not implemented.
+-c      ELSE
+-c        WRITE(MSTU(11),5100)
+-c        STOP
+-c      ENDIF
+- 
+-C...Format for error printout.
+-c 5000 FORMAT(1X,'Error: UPINIT routine failed to read information'/
+-c     &1X,'Execution stopped!')
+-c 5100 FORMAT(1X,'Error: You have not implemented UPINIT routine'/
+-c     &1X,'Dummy routine in PYTHIA file called instead.'/
+-c     &1X,'Execution stopped!')
+- 
+-c      RETURN
+-c      END
+- 
+ C*********************************************************************
+  
+ C...UPEVNT
+@@ -120,3 +67,54 @@
+  
+       RETURN
+       END
++
++C...Old example: handles a simple Pythia 6.4 event file.
++ 
++c      SUBROUTINE UPEVNT
++ 
++C...Double precision and integer declarations.
++c      IMPLICIT DOUBLE PRECISION(A-H, O-Z)
++c      IMPLICIT INTEGER(I-N)
++ 
++C...Commonblocks.
++c      COMMON/PYDAT1/MSTU(200),PARU(200),MSTJ(200),PARJ(200)
++c      COMMON/PYPARS/MSTP(200),PARP(200),MSTI(200),PARI(200)
++c      SAVE /PYDAT1/,/PYPARS/
++ 
++C...User process event common block.
++c      INTEGER MAXNUP
++c      PARAMETER (MAXNUP=500)
++c      INTEGER NUP,IDPRUP,IDUP,ISTUP,MOTHUP,ICOLUP
++c      DOUBLE PRECISION XWGTUP,SCALUP,AQEDUP,AQCDUP,PUP,VTIMUP,SPINUP
++c      COMMON/HEPEUP/NUP,IDPRUP,XWGTUP,SCALUP,AQEDUP,AQCDUP,IDUP(MAXNUP),
++c     &ISTUP(MAXNUP),MOTHUP(2,MAXNUP),ICOLUP(2,MAXNUP),PUP(5,MAXNUP),
++c     &VTIMUP(MAXNUP),SPINUP(MAXNUP)
++c      SAVE /HEPEUP/
++ 
++C...Read info from file.
++c      IF(MSTP(162).GT.0) THEN
++c        READ(MSTP(162),*,END=110,ERR=110) NUP,IDPRUP,XWGTUP,SCALUP,
++c     &  AQEDUP,AQCDUP
++c        DO 100 I=1,NUP
++c          READ(MSTP(162),*,END=110,ERR=110) IDUP(I),ISTUP(I),
++c     &    MOTHUP(1,I),MOTHUP(2,I),ICOLUP(1,I),ICOLUP(2,I),
++c     &    (PUP(J,I),J=1,5),VTIMUP(I),SPINUP(I)
++c  100   CONTINUE
++c        RETURN
++C...Special when reached end of file or other error.
++c  110   NUP=0
++ 
++C...Else not implemented.
++c      ELSE
++c        WRITE(MSTU(11),5000)
++c        STOP
++c      ENDIF
++ 
++C...Format for error printout.
++c 5000 FORMAT(1X,'Error: You have not implemented UPEVNT routine'/
++c     &1X,'Dummy routine in PYTHIA file called instead.'/
++c     &1X,'Execution stopped!')
++ 
++c      RETURN
++c      END
++ 
+diff -Naur upinit.f upinit.f
+--- upinit.f	2018-08-23 11:24:27.000000000 -0500
++++ upinit.f	2018-08-23 11:46:08.190999819 -0500
+@@ -1,4 +1,3 @@
+- 
+ C*********************************************************************
+  
+ C...UPINIT
+@@ -64,3 +63,56 @@
+  
+       RETURN
+       END
++
++C...Old example: handles a simple Pythia 6.4 initialization file.
++ 
++c      SUBROUTINE UPINIT
++ 
++C...Double precision and integer declarations.
++c      IMPLICIT DOUBLE PRECISION(A-H, O-Z)
++c      IMPLICIT INTEGER(I-N)
++ 
++C...Commonblocks.
++c      COMMON/PYDAT1/MSTU(200),PARU(200),MSTJ(200),PARJ(200)
++c      COMMON/PYPARS/MSTP(200),PARP(200),MSTI(200),PARI(200)
++c      SAVE /PYDAT1/,/PYPARS/
++ 
++C...User process initialization commonblock.
++c      INTEGER MAXPUP
++c      PARAMETER (MAXPUP=100)
++c      INTEGER IDBMUP,PDFGUP,PDFSUP,IDWTUP,NPRUP,LPRUP
++c      DOUBLE PRECISION EBMUP,XSECUP,XERRUP,XMAXUP
++c      COMMON/HEPRUP/IDBMUP(2),EBMUP(2),PDFGUP(2),PDFSUP(2),
++c     &IDWTUP,NPRUP,XSECUP(MAXPUP),XERRUP(MAXPUP),XMAXUP(MAXPUP),
++c     &LPRUP(MAXPUP)
++c      SAVE /HEPRUP/
++ 
++C...Read info from file.
++c      IF(MSTP(161).GT.0) THEN
++c        READ(MSTP(161),*,END=110,ERR=110) IDBMUP(1),IDBMUP(2),EBMUP(1),
++c     &  EBMUP(2),PDFGUP(1),PDFGUP(2),PDFSUP(1),PDFSUP(2),IDWTUP,NPRUP
++c        DO 100 IPR=1,NPRUP
++c          READ(MSTP(161),*,END=110,ERR=110) XSECUP(IPR),XERRUP(IPR),
++c     &    XMAXUP(IPR),LPRUP(IPR)
++c  100   CONTINUE
++c        RETURN
++C...Error or prematurely reached end of file.
++c  110   WRITE(MSTU(11),5000)
++c        STOP
++ 
++C...Else not implemented.
++c      ELSE
++c        WRITE(MSTU(11),5100)
++c        STOP
++c      ENDIF
++ 
++C...Format for error printout.
++c 5000 FORMAT(1X,'Error: UPINIT routine failed to read information'/
++c     &1X,'Execution stopped!')
++c 5100 FORMAT(1X,'Error: You have not implemented UPINIT routine'/
++c     &1X,'Dummy routine in PYTHIA file called instead.'/
++c     &1X,'Execution stopped!')
++ 
++c      RETURN
++c      END
++ 
+diff -Naur upveto.f upveto.f
+--- upveto.f	2018-08-23 11:24:27.000000000 -0500
++++ upveto.f	2018-08-23 11:46:08.190999819 -0500
+@@ -1,54 +1,3 @@
+-
+-C...Old example: handles a simple Pythia 6.4 event file.
+- 
+-c      SUBROUTINE UPEVNT
+- 
+-C...Double precision and integer declarations.
+-c      IMPLICIT DOUBLE PRECISION(A-H, O-Z)
+-c      IMPLICIT INTEGER(I-N)
+- 
+-C...Commonblocks.
+-c      COMMON/PYDAT1/MSTU(200),PARU(200),MSTJ(200),PARJ(200)
+-c      COMMON/PYPARS/MSTP(200),PARP(200),MSTI(200),PARI(200)
+-c      SAVE /PYDAT1/,/PYPARS/
+- 
+-C...User process event common block.
+-c      INTEGER MAXNUP
+-c      PARAMETER (MAXNUP=500)
+-c      INTEGER NUP,IDPRUP,IDUP,ISTUP,MOTHUP,ICOLUP
+-c      DOUBLE PRECISION XWGTUP,SCALUP,AQEDUP,AQCDUP,PUP,VTIMUP,SPINUP
+-c      COMMON/HEPEUP/NUP,IDPRUP,XWGTUP,SCALUP,AQEDUP,AQCDUP,IDUP(MAXNUP),
+-c     &ISTUP(MAXNUP),MOTHUP(2,MAXNUP),ICOLUP(2,MAXNUP),PUP(5,MAXNUP),
+-c     &VTIMUP(MAXNUP),SPINUP(MAXNUP)
+-c      SAVE /HEPEUP/
+- 
+-C...Read info from file.
+-c      IF(MSTP(162).GT.0) THEN
+-c        READ(MSTP(162),*,END=110,ERR=110) NUP,IDPRUP,XWGTUP,SCALUP,
+-c     &  AQEDUP,AQCDUP
+-c        DO 100 I=1,NUP
+-c          READ(MSTP(162),*,END=110,ERR=110) IDUP(I),ISTUP(I),
+-c     &    MOTHUP(1,I),MOTHUP(2,I),ICOLUP(1,I),ICOLUP(2,I),
+-c     &    (PUP(J,I),J=1,5),VTIMUP(I),SPINUP(I)
+-c  100   CONTINUE
+-c        RETURN
+-C...Special when reached end of file or other error.
+-c  110   NUP=0
+- 
+-C...Else not implemented.
+-c      ELSE
+-c        WRITE(MSTU(11),5000)
+-c        STOP
+-c      ENDIF
+- 
+-C...Format for error printout.
+-c 5000 FORMAT(1X,'Error: You have not implemented UPEVNT routine'/
+-c     &1X,'Dummy routine in PYTHIA file called instead.'/
+-c     &1X,'Execution stopped!')
+- 
+-c      RETURN
+-c      END
+- 
+ C*********************************************************************
+  
+ C...UPVETO
+@@ -98,3 +47,4 @@
+  
+       RETURN
+       END
++ 
diff --git a/var/spack/repos/builtin/packages/python/gcc-8-2.7.14.patch b/var/spack/repos/builtin/packages/python/gcc-8-2.7.14.patch
new file mode 100644
index 0000000000..72c879cdea
--- /dev/null
+++ b/var/spack/repos/builtin/packages/python/gcc-8-2.7.14.patch
@@ -0,0 +1,35 @@
+diff --git a/Include/objimpl.h b/Include/objimpl.h
+index 5f2868332955..cbf6bc3f8763 100644
+--- a/Include/objimpl.h
++++ b/Include/objimpl.h
+@@ -248,6 +248,20 @@ PyAPI_FUNC(PyVarObject *) _PyObject_GC_Resize(PyVarObject *, Py_ssize_t);
+ /* for source compatibility with 2.2 */
+ #define _PyObject_GC_Del PyObject_GC_Del
+ 
++/*
++ * Former over-aligned definition of PyGC_Head, used to compute the size of the
++ * padding for the new version below.
++ */
++union _gc_head;
++union _gc_head_old {
++    struct {
++        union _gc_head_old *gc_next;
++        union _gc_head_old *gc_prev;
++        Py_ssize_t gc_refs;
++    } gc;
++    long double dummy;
++};
++
+ /* GC information is stored BEFORE the object structure. */
+ typedef union _gc_head {
+     struct {
+@@ -255,7 +269,8 @@ typedef union _gc_head {
+         union _gc_head *gc_prev;
+         Py_ssize_t gc_refs;
+     } gc;
+-    long double dummy;  /* force worst-case alignment */
++    double dummy; /* Force at least 8-byte alignment. */
++    char dummy_padding[sizeof(union _gc_head_old)];
+ } PyGC_Head;
+ 
+ extern PyGC_Head *_PyGC_generation0;
diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index c77756a78f..6d8823cc64 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import ast
 import os
 import platform
@@ -30,12 +11,14 @@ import sys
 
 import llnl.util.tty as tty
 from llnl.util.lang import match_predicate
-from llnl.util.filesystem import force_remove
+from llnl.util.filesystem import (force_remove, get_filetype,
+                                  path_contains_subdirectory)
 
-import spack
-from spack import *
-from spack.util.prefix import Prefix
+import spack.store
 import spack.util.spack_json as sjson
+from spack.util.environment import is_system_path
+from spack.util.prefix import Prefix
+from spack import *
 
 
 class Python(AutotoolsPackage):
@@ -46,6 +29,10 @@ class Python(AutotoolsPackage):
     list_url = "https://www.python.org/downloads/"
     list_depth = 1
 
+    version('3.7.0', '41b6595deb4147a1ed517a7d9a580271')
+    version('3.6.5', 'ab25d24b1f8cc4990ade979f6dc37883')
+    version('3.6.4', '9de6494314ea199e3633211696735f65')
+    version('3.6.3', 'e9180c69ed9a878a4a8a3ab221e32fa9')
     version('3.6.2', 'e1a36bfffdd1d3a780b1825daf16e56c')
     version('3.6.1', '2d0fc9f3a5940707590e07f03ecb08b9')
     version('3.6.0', '3f7062ccf8be76491884d0e47ac8b251')
@@ -56,7 +43,8 @@ class Python(AutotoolsPackage):
     version('3.3.6', 'cdb3cd08f96f074b3f3994ccb51063e9')
     version('3.2.6', '23815d82ae706e9b781ca65865353d39')
     version('3.1.5', '02196d3fc7bc76bdda68aa36b0dd16ab')
-    version('2.7.14', 'cee2e4b33ad3750da77b2e85f2f8b724', preferred=True)
+    version('2.7.15', '045fb3440219a1f6923fefdabde63342', preferred=True)
+    version('2.7.14', 'cee2e4b33ad3750da77b2e85f2f8b724')
     version('2.7.13', '17add4bf0ad0ec2f08e0cae6d205c700')
     version('2.7.12', '88d61f82e3616a4be952828b3694109d')
     version('2.7.11', '6b6076ec9e93f05dd63e47eb9c15728b')
@@ -83,6 +71,18 @@ class Python(AutotoolsPackage):
     variant('pic', default=True,
             description='Produce position-independent code (for shared libs)')
 
+    variant('dbm', default=True, description='Provide support for dbm')
+    variant(
+        'optimizations',
+        default=False,
+        description='Enable expensive build-time optimizations, if available'
+    )
+    # See https://legacy.python.org/dev/peps/pep-0394/
+    variant('pythoncmd', default=True,
+            description="Symlink 'python3' executable to 'python' "
+            "(not PEP 394 compliant)")
+
+    depends_on("pkgconfig", type="build")
     depends_on("openssl")
     depends_on("bzip2")
     depends_on("readline")
@@ -91,6 +91,11 @@ class Python(AutotoolsPackage):
     depends_on("zlib")
     depends_on("tk", when="+tk")
     depends_on("tcl", when="+tk")
+    depends_on("gdbm", when='+dbm')
+
+    # https://docs.python.org/3/whatsnew/3.7.html#build-changes
+    depends_on("libffi", when="@3.7:")
+    depends_on("openssl@1.0.2:", when="@3.7:")
 
     # Patch does not work for Python 3.1
     patch('ncurses.patch', when='@:2.8,3.2:')
@@ -99,10 +104,25 @@ class Python(AutotoolsPackage):
     patch('cray-rpath-2.3.patch', when="@2.3:3.0.1 platform=cray")
     patch('cray-rpath-3.1.patch', when="@3.1:3.99  platform=cray")
 
+    # Fixes an alignment problem with more aggressive optimization in gcc8
+    # https://github.com/python/cpython/commit/0b91f8a668201fc58fa732b8acc496caedfdbae0
+    patch('gcc-8-2.7.14.patch', when="@2.7.14 %gcc@8:")
+
+    # For more information refer to this bug report:
+    # https://bugs.python.org/issue29712
+    conflicts(
+        '@:2.8 +shared',
+        when='+optimizations',
+        msg='+optimizations is incompatible with +shared in python@2.X'
+    )
+
     _DISTUTIL_VARS_TO_SAVE = ['LDSHARED']
     _DISTUTIL_CACHE_FILENAME = 'sysconfig.json'
     _distutil_vars = None
 
+    # An in-source build with --enable-optimizations fails for python@3.X
+    build_directory = 'spack-build'
+
     @when('@2.7:2.8,3.4:')
     def patch(self):
         # NOTE: Python's default installation procedure makes it possible for a
@@ -117,7 +137,6 @@ class Python(AutotoolsPackage):
 
     def setup_environment(self, spack_env, run_env):
         spec = self.spec
-        prefix = self.prefix
 
         # TODO: The '--no-user-cfg' option for Python installation is only in
         # Python v2.7 and v3.4+ (see https://bugs.python.org/issue1180) and
@@ -128,8 +147,6 @@ class Python(AutotoolsPackage):
                       'user configurations are present.').format(self.version))
 
         # Need this to allow python build to find the Python installation.
-        spack_env.set('PYTHONHOME', prefix)
-        spack_env.set('PYTHONPATH', prefix)
         spack_env.set('MACOSX_DEPLOYMENT_TARGET', platform.mac_ver()[0])
 
     def configure_args(self):
@@ -137,15 +154,45 @@ class Python(AutotoolsPackage):
 
         # setup.py needs to be able to read the CPPFLAGS and LDFLAGS
         # as it scans for the library and headers to build
-        dep_pfxs = [dspec.prefix for dspec in spec.dependencies('link')]
-        config_args = [
-            '--with-threads',
-            'CPPFLAGS=-I{0}'.format(' -I'.join(dp.include for dp in dep_pfxs)),
-            'LDFLAGS=-L{0}'.format(' -L'.join(dp.lib for dp in dep_pfxs)),
-        ]
+        link_deps = spec.dependencies('link')
+
+        # Header files are often included assuming they reside in a
+        # subdirectory of prefix.include, e.g. #include <openssl/ssl.h>,
+        # which is why we don't use HeaderList here. The header files of
+        # libffi reside in prefix.lib but the configure script of Python
+        # finds them using pkg-config.
+        cppflags = '-I' + ' -I'.join(dep.prefix.include
+                                     for dep in link_deps
+                                     if dep.name != 'libffi')
+
+        # Currently, the only way to get SpecBuildInterface wrappers of the
+        # dependencies (which we need to get their 'libs') is to get them
+        # using spec.__getitem__.
+        ldflags = ' '.join(spec[dep.name].libs.search_flags
+                           for dep in link_deps)
+
+        config_args = ['CPPFLAGS=' + cppflags, 'LDFLAGS=' + ldflags]
+
+        # https://docs.python.org/3/whatsnew/3.7.html#build-changes
+        if spec.satisfies('@:3.6'):
+            config_args.append('--with-threads')
+
+        if '^libffi' in spec:
+            config_args.append('--with-system-ffi')
+        else:
+            config_args.append('--without-system-ffi')
+
+        if spec.satisfies('@2.7.13:2.8,3.5.3:', strict=True) \
+                and '+optimizations' in spec:
+            config_args.append('--enable-optimizations')
+
         if spec.satisfies('%gcc platform=darwin'):
             config_args.append('--disable-toolbox-glue')
 
+        if spec.satisfies('%intel', strict=True) and \
+                spec.satisfies('@2.7.12:2.8,3.5.2:', strict=True):
+            config_args.append('--with-icc')
+
         if '+shared' in spec:
             config_args.append('--enable-shared')
         else:
@@ -202,6 +249,12 @@ class Python(AutotoolsPackage):
                 os.symlink(os.path.join(src, f),
                            os.path.join(dst, f))
 
+        if spec.satisfies('@3:') and spec.satisfies('+pythoncmd'):
+            os.symlink(os.path.join(prefix.bin, 'python3'),
+                       os.path.join(prefix.bin, 'python'))
+            os.symlink(os.path.join(prefix.bin, 'python3-config'),
+                       os.path.join(prefix.bin, 'python-config'))
+
     # TODO: Once better testing support is integrated, add the following tests
     # https://wiki.python.org/moin/TkInter
     #
@@ -352,37 +405,32 @@ class Python(AutotoolsPackage):
         on the version of Python and how it was installed.
 
         In general, Python 2 comes with ``python`` and ``python2`` commands,
-        while Python 3 only comes with a ``python3`` command.
+        while Python 3 only comes with a ``python3`` command. However, some
+        package managers will symlink ``python`` to ``python3``, while others
+        may contain ``python3.6``, ``python3.5``, and ``python3.4`` in the
+        same directory.
 
-        :returns: The Python command
-        :rtype: Executable
+        Returns:
+            Executable: the Python command
         """
         # We need to be careful here. If the user is using an externally
-        # installed python, all 3 commands could be in the same directory.
-
-        # Search for `python2` iff using Python 2
-        if (self.spec.satisfies('@:2') and
-                os.path.exists(os.path.join(self.prefix.bin, 'python2'))):
-            command = 'python2'
-        # Search for `python3` iff using Python 3
-        elif (self.spec.satisfies('@3:') and
-                os.path.exists(os.path.join(self.prefix.bin, 'python3'))):
-            command = 'python3'
-        # If neither were found, try `python`
-        elif os.path.exists(os.path.join(self.prefix.bin, 'python')):
-            command = 'python'
+        # installed python, several different commands could be located
+        # in the same directory. Be as specific as possible. Search for:
+        #
+        # * python3.6
+        # * python3
+        # * python
+        #
+        # in that order if using python@3.6.5, for example.
+        version = self.spec.version
+        for ver in [version.up_to(2), version.up_to(1), '']:
+            path = os.path.join(self.prefix.bin, 'python{0}'.format(ver))
+            if os.path.exists(path):
+                return Executable(path)
         else:
             msg = 'Unable to locate {0} command in {1}'
             raise RuntimeError(msg.format(self.name, self.prefix.bin))
 
-        # The python command may be a symlink if it was installed
-        # with Homebrew. Since some packages try to determine the
-        # location of libraries and headers based on the path,
-        # return the realpath
-        path = os.path.realpath(os.path.join(self.prefix.bin, command))
-
-        return Executable(path)
-
     def print_string(self, string):
         """Returns the appropriate print string depending on the
         version of Python.
@@ -461,7 +509,7 @@ class Python(AutotoolsPackage):
                 return LibraryList(os.path.join(frameworkprefix, ldlibrary))
             else:
                 msg = 'Unable to locate {0} libraries in {1}'
-                raise RuntimeError(msg.format(self.name, libdir))
+                raise RuntimeError(msg.format(ldlibrary, libdir))
         else:
             library = self.get_config_var('LIBRARY')
 
@@ -471,7 +519,7 @@ class Python(AutotoolsPackage):
                 return LibraryList(os.path.join(frameworkprefix, library))
             else:
                 msg = 'Unable to locate {0} libraries in {1}'
-                raise RuntimeError(msg.format(self.name, libdir))
+                raise RuntimeError(msg.format(library, libdir))
 
     @property
     def headers(self):
@@ -504,11 +552,19 @@ class Python(AutotoolsPackage):
         """Set PYTHONPATH to include the site-packages directory for the
         extension and any other python extensions it depends on."""
 
+        # If we set PYTHONHOME, we must also ensure that the corresponding
+        # python is found in the build environment. This to prevent cases
+        # where a system provided python is run against the standard libraries
+        # of a Spack built python. See issue #7128
         spack_env.set('PYTHONHOME', self.home)
 
+        path = os.path.dirname(self.command.path)
+        if not is_system_path(path):
+            spack_env.prepend_path('PATH', path)
+
         python_paths = []
         for d in dependent_spec.traverse(
-                deptype=('build', 'run'), deptype_query='run'):
+                deptype=('build', 'run', 'test')):
             if d.package.extends(self.spec):
                 python_paths.append(join_path(d.prefix,
                                               self.site_packages_dir))
@@ -628,33 +684,49 @@ class Python(AutotoolsPackage):
                         "sys.path[p:p]=new; "
                         "sys.__egginsert = p+len(new)\n")
 
-    def activate(self, ext_pkg, **args):
+    def activate(self, ext_pkg, view, **args):
         ignore = self.python_ignore(ext_pkg, args)
         args.update(ignore=ignore)
 
-        extensions_layout = args.get("extensions_layout",
-                                     spack.store.extensions)
-
-        super(Python, self).activate(ext_pkg, **args)
+        super(Python, self).activate(ext_pkg, view, **args)
 
+        extensions_layout = view.extensions_layout
         exts = extensions_layout.extension_map(self.spec)
         exts[ext_pkg.name] = ext_pkg.spec
 
-        self.write_easy_install_pth(
-            exts,
-            prefix=extensions_layout.extendee_target_directory(self))
+        self.write_easy_install_pth(exts, prefix=view.root)
 
-    def deactivate(self, ext_pkg, **args):
+    def deactivate(self, ext_pkg, view, **args):
         args.update(ignore=self.python_ignore(ext_pkg, args))
-        super(Python, self).deactivate(ext_pkg, **args)
 
-        extensions_layout = args.get("extensions_layout",
-                                     spack.store.extensions)
+        super(Python, self).deactivate(ext_pkg, view, **args)
 
+        extensions_layout = view.extensions_layout
         exts = extensions_layout.extension_map(self.spec)
         # Make deactivate idempotent
         if ext_pkg.name in exts:
             del exts[ext_pkg.name]
-            self.write_easy_install_pth(
-                exts,
-                prefix=extensions_layout.extendee_target_directory(self))
+            self.write_easy_install_pth(exts, prefix=view.root)
+
+    def add_files_to_view(self, view, merge_map):
+        bin_dir = self.spec.prefix.bin
+        for src, dst in merge_map.items():
+            if not path_contains_subdirectory(src, bin_dir):
+                view.link(src, dst)
+            elif not os.path.islink(src):
+                copy(src, dst)
+                if 'script' in get_filetype(src):
+                    filter_file(
+                        self.spec.prefix, os.path.abspath(view.root), dst)
+            else:
+                orig_link_target = os.path.realpath(src)
+                new_link_target = os.path.abspath(merge_map[orig_link_target])
+                view.link(new_link_target, dst)
+
+    def remove_files_from_view(self, view, merge_map):
+        bin_dir = self.spec.prefix.bin
+        for src, dst in merge_map.items():
+            if not path_contains_subdirectory(src, bin_dir):
+                view.remove_file(src, dst)
+            else:
+                os.remove(dst)
diff --git a/var/spack/repos/builtin/packages/qbank/package.py b/var/spack/repos/builtin/packages/qbank/package.py
index b56be62bad..30133052b4 100644
--- a/var/spack/repos/builtin/packages/qbank/package.py
+++ b/var/spack/repos/builtin/packages/qbank/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
diff --git a/var/spack/repos/builtin/packages/qbox/package.py b/var/spack/repos/builtin/packages/qbox/package.py
index 7945370997..0bd70f4445 100644
--- a/var/spack/repos/builtin/packages/qbox/package.py
+++ b/var/spack/repos/builtin/packages/qbox/package.py
@@ -1,29 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-import shutil
 from spack import *
 
 
@@ -88,6 +67,6 @@ class Qbox(MakefilePackage):
     def install(self, spec, prefix):
         mkdir(prefix.src)
         install('src/qb', prefix.src)
-        shutil.move('test', prefix)
-        shutil.move('xml', prefix)
-        shutil.move('util', prefix)
+        install_tree('test', prefix)
+        install_tree('xml', prefix)
+        install_tree('util', prefix)
diff --git a/var/spack/repos/builtin/packages/qhull/package.py b/var/spack/repos/builtin/packages/qhull/package.py
index 3e3e033025..9bdfcab341 100644
--- a/var/spack/repos/builtin/packages/qhull/package.py
+++ b/var/spack/repos/builtin/packages/qhull/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/qmcpack/package.py b/var/spack/repos/builtin/packages/qmcpack/package.py
index 360ae0a51d..0e9169a481 100644
--- a/var/spack/repos/builtin/packages/qmcpack/package.py
+++ b/var/spack/repos/builtin/packages/qmcpack/package.py
@@ -1,28 +1,10 @@
-##############################################################################
-# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
+import llnl.util.tty as tty
 
 
 class Qmcpack(CMakePackage):
@@ -31,16 +13,21 @@ class Qmcpack(CMakePackage):
 
     # Package information
     homepage = "http://www.qmcpack.org/"
-    url      = "https://github.com/QMCPACK/qmcpack.git"
-
-    # This download method is untrusted, and is not recommended
-    # by the Spack manual. However, it is easier to maintain
-    # because github hashes can occasionally change
-    version('3.2.0', git=url, tag='v3.2.0')
-    version('3.1.1', git=url, tag='v3.1.1')
-    version('3.1.0', git=url, tag='v3.1.0')
-    version('3.0.0', git=url, tag='v3.0.0')
-    version('develop', git=url)
+    git      = "https://github.com/QMCPACK/qmcpack.git"
+
+    tags = ['ecp', 'ecp-apps']
+
+    # This download method is untrusted, and is not recommended by the
+    # Spack manual. However, it is easier to maintain because github hashes
+    # can occasionally change.
+    # NOTE: 12/19/2017 QMCPACK 3.0.0 does not build properly with Spack.
+    version('develop')
+    version('3.5.0', tag='v3.5.0')
+    version('3.4.0', tag='v3.4.0')
+    version('3.3.0', tag='v3.3.0')
+    version('3.2.0', tag='v3.2.0')
+    version('3.1.1', tag='v3.1.1')
+    version('3.1.0', tag='v3.1.0')
 
     # These defaults match those in the QMCPACK manual
     variant('debug', default=False, description='Build debug version')
@@ -57,11 +44,13 @@ class Qmcpack(CMakePackage):
                         'Array-of-Structure code. Only for CPU code'
                         'and only in mixed precision')
     variant('timers', default=False,
-             description='Build with support for timers')
+            description='Build with support for timers')
     variant('da', default=False,
             description='Install with support for basic data analysis tools')
     variant('gui', default=False,
             description='Install with Matplotlib (long installation time)')
+    variant('qe', default=True,
+            description='Install with patched Quantum Espresso 6.3.0')
 
     # cuda variant implies mixed precision variant by default, but there is
     # no way to express this in variant syntax, need something like
@@ -72,7 +61,9 @@ class Qmcpack(CMakePackage):
     conflicts('^openblas+ilp64')
     conflicts('^intel-mkl+ilp64')
 
-    # Dependencies match those in the QMCPACK manual
+    # Dependencies match those in the QMCPACK manual.
+    # FIXME: once concretizer can unite unconditional and conditional
+    # dependencies the some of the '~mpi' will not be necessary.
     depends_on('cmake@3.4.3:', type='build')
     depends_on('mpi', when='+mpi')
     depends_on('libxml2')
@@ -90,23 +81,41 @@ class Qmcpack(CMakePackage):
     # qmcpack data analysis tools
     # basic command line tool based on Python and NumPy
     # blas and lapack patching fails often and so are disabled at this time
-    depends_on('py-numpy~blas~lapack', type='run', when='+da')
+    depends_on('py-numpy~blas~lapack', when='+da', type='run')
 
-    # GUI is optional fpr data anlysis
+    # GUI is optional for data anlysis
     # py-matplotlib leads to a long complex DAG for dependencies
-    depends_on('py-matplotlib', type='run', when='+gui')
+    depends_on('py-matplotlib', when='+gui', type='run')
 
     # B-spline basis calculation require a patched version of
-    # Quantum Espresso 5.3.0 (see QMCPACK manual)
-    patch_url = 'https://raw.githubusercontent.com/QMCPACK/qmcpack/develop/external_codes/quantum_espresso/add_pw2qmcpack_to_espresso-5.3.0.diff'
-    patch_checksum = '0d8d7ba805313ddd4c02ee32c96d2f12e7091e9e82e22671d3ad5a24247860c4'
-    depends_on('espresso@5.3.0~elpa',
-               patches=patch(patch_url, sha256=patch_checksum),
-               when='+mpi')
-
-    depends_on('espresso@5.3.0~elpa~scalapack~mpi',
-               patches=patch(patch_url, sha256=patch_checksum),
-               when='~mpi')
+    # Quantum Espresso 6.3 (see QMCPACK manual)
+    # Building explicitly without ELPA due to issues in Quantum Espresso
+    # Spack package
+    patch_url = 'https://raw.githubusercontent.com/QMCPACK/qmcpack/develop/external_codes/quantum_espresso/add_pw2qmcpack_to_qe-6.3.diff'
+    patch_checksum = '2ee346e24926479f5e96f8dc47812173a8847a58354bbc32cf2114af7a521c13'
+    depends_on('quantum-espresso@6.3~elpa+hdf5',
+               patches=patch(patch_url, sha256=patch_checksum, when='+qe'),
+                   when='+qe+mpi', type='run')
+
+    depends_on('quantum-espresso@6.3~elpa~scalapack~mpi+hdf5',
+               patches=patch(patch_url, sha256=patch_checksum, when='+qe'),
+                   when='+qe~mpi', type='run')
+
+    # Backport several patches from recent versions of QMCPACK
+    # The test_numerics unit test is broken prior to QMCPACK 3.3.0
+    patch_url = 'https://patch-diff.githubusercontent.com/raw/QMCPACK/qmcpack/pull/621.patch'
+    patch_checksum = 'e2ff7a6f0f006856085d4aab6d31f32f16353e41f760a33a7ef75f3ecce6a5d6'
+    patch(patch_url, sha256=patch_checksum, when='@3.1.0:3.3.0')
+
+    # FindMKL.cmake has an issues prior to QMCPACK 3.3.0
+    patch_url = 'https://patch-diff.githubusercontent.com/raw/QMCPACK/qmcpack/pull/623.patch'
+    patch_checksum = '3eb9dec05fd1a544318ff84cd8b5926cfc6b46b375c7f3b012ccf0b50cf617b7'
+    patch(patch_url, sha256=patch_checksum, when='@3.1.0:3.3.0')
+
+    # git-rev files for not git builds issues prior to QMCPACK 3.3.0
+    patch_url = 'https://patch-diff.githubusercontent.com/raw/QMCPACK/qmcpack/pull/643.patch'
+    patch_checksum = 'c066c79901a612cf8848135e0d544efb114534cca70b90bfccc8ed989d3d9dde'
+    patch(patch_url, sha256=patch_checksum, when='@3.1.0:3.3.0')
 
     def patch(self):
         # FindLibxml2QMC.cmake doesn't check the environment by default
@@ -116,22 +125,23 @@ class Qmcpack(CMakePackage):
                     'CMake/FindLibxml2QMC.cmake')
 
     def cmake_args(self):
+        spec = self.spec
         args = []
 
-        if '+mpi' in self.spec:
-            mpi = self.spec['mpi']
+        if '+mpi' in spec:
+            mpi = spec['mpi']
             args.append('-DCMAKE_C_COMPILER={0}'.format(mpi.mpicc))
             args.append('-DCMAKE_CXX_COMPILER={0}'.format(mpi.mpicxx))
             args.append('-DMPI_BASE_DIR:PATH={0}'.format(mpi.prefix))
 
         # Currently FFTW_HOME and LIBXML2_HOME are used by CMake.
         # Any CMake warnings about other variables are benign.
-        xml2_prefix = self.spec['libxml2'].prefix
+        xml2_prefix = spec['libxml2'].prefix
         args.append('-DLIBXML2_HOME={0}'.format(xml2_prefix))
         args.append('-DLibxml2_INCLUDE_DIRS={0}'.format(xml2_prefix.include))
         args.append('-DLibxml2_LIBRARY_DIRS={0}'.format(xml2_prefix.lib))
 
-        fftw_prefix = self.spec['fftw'].prefix
+        fftw_prefix = spec['fftw'].prefix
         args.append('-DFFTW_HOME={0}'.format(fftw_prefix))
         args.append('-DFFTW_INCLUDE_DIRS={0}'.format(fftw_prefix.include))
         args.append('-DFFTW_LIBRARY_DIRS={0}'.format(fftw_prefix.lib))
@@ -140,15 +150,15 @@ class Qmcpack(CMakePackage):
         args.append('-DHDF5_ROOT={0}'.format(self.spec['hdf5'].prefix))
 
         # Default is MPI, serial version is convenient for cases, e.g. laptops
-        if '+mpi' in self.spec:
+        if '+mpi' in spec:
             args.append('-DQMC_MPI=1')
-        elif '~mpi' in self.spec:
+        elif '~mpi' in spec:
             args.append('-DQMC_MPI=0')
 
         # Default is real-valued single particle orbitals
-        if '+complex' in self.spec:
+        if '+complex' in spec:
             args.append('-DQMC_COMPLEX=1')
-        elif '~complex' in self.spec:
+        elif '~complex' in spec:
             args.append('-DQMC_COMPLEX=0')
 
         # When '-DQMC_CUDA=1', CMake automatically sets:
@@ -157,44 +167,66 @@ class Qmcpack(CMakePackage):
         # There is a double-precision CUDA path, but it is not as well
         # tested.
 
-        if '+cuda' in self.spec:
+        if '+cuda' in spec:
             args.append('-DQMC_CUDA=1')
-        elif '~cuda' in self.spec:
+        elif '~cuda' in spec:
             args.append('-DQMC_CUDA=0')
 
         # Mixed-precision versues double-precision CPU and GPU code
-        if '+mixed' in self.spec:
+        if '+mixed' in spec:
             args.append('-DQMC_MIXED_PRECISION=1')
-        elif '~mixed' in self.spec:
+        elif '~mixed' in spec:
             args.append('-DQMC_MIXED_PRECISION=0')
 
         # New Structure-of-Array (SOA) code, much faster than default
         # Array-of-Structure (AOS) code.
         # No support for local atomic orbital basis.
-        if '+soa' in self.spec:
+        if '+soa' in spec:
             args.append('-DENABLE_SOA=1')
-        elif '~soa' in self.spec:
+        elif '~soa' in spec:
             args.append('-DENABLE_SOA=0')
 
         # Manual Timers
-        if '+timers' in self.spec:
+        if '+timers' in spec:
             args.append('-DENABLE_TIMERS=1')
-        elif '~timers' in self.spec:
+        elif '~timers' in spec:
             args.append('-DENABLE_TIMERS=0')
 
-    #     # Proper MKL detection not working.
-    #     # Include MKL flags
-    #     if 'intel-mkl' in self.spec:
-    #         args.append('-DBLA_VENDOR=Intel10_64lp_seq')
-    #         args.append('-DQMC_INCLUDE={0}'.format(join_path(env['MKLROOT'],'include')))
-        return args
+        # Proper detection of optimized BLAS and LAPACK.
+        # Based on the code from the deal II Spack package:
+        # https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/dealii/package.py
+        #
+        # Basically, we override CMake's auto-detection mechanism
+        # and use the Spack's interface instead
+        lapack_blas = spec['lapack'].libs + spec['blas'].libs
+        args.extend([
+            '-DLAPACK_FOUND=true',
+            '-DLAPACK_LIBRARIES=%s' % lapack_blas.joined(';')
+        ])
+
+        # Additionally, we need to pass the BLAS+LAPACK include directory for
+        # header files. This is to insure vectorized math and FFT libraries
+        # get properly detected. Intel MKL requires special case due to
+        # differences in Darwin vs. Linux $MKLROOT naming schemes. This section
+        # of code is intentionally redundant for backwards compatibility.
+        if 'intel-mkl' in self.spec:
+            lapack_dir = format(join_path(env['MKLROOT'], 'include'))
+            # Next two lines were introduced in QMCPACK 3.5.0 and later.
+            # Prior to v3.5.0, these lines should be benign.
+            args.append('-DENABLE_MKL=1')
+            args.append('-DMKL_ROOT=%s' % env['MKLROOT'])
+        else:
+            lapack_dir = ':'.join((
+                spec['lapack'].prefix.include,
+                spec['blas'].prefix.include
+            ))
+
+        args.extend([
+            '-DCMAKE_CXX_FLAGS=-I%s' % lapack_dir,
+            '-DCMAKE_C_FLAGS=-I%s' % lapack_dir
+        ])
 
-    # def setup_environment(self, spack_env, run_env):
-    #     # Add MKLROOT/lib to the CMAKE_PREFIX_PATH to enable CMake to find
-    #     # MKL libraries. MKLROOT environment variable must be defined for
-    #     # this to work properly.
-    #     if 'intel-mkl' in self.spec:
-    #         spack_env.append_path('CMAKE_PREFIX_PATH',format(join_path(env['MKLROOT'],'lib')))
+        return args
 
     def install(self, spec, prefix):
         """Make the install targets"""
@@ -228,7 +260,19 @@ class Qmcpack(CMakePackage):
     def check(self):
         """Run ctest after building binary.
         It can take over 24 hours to run all the regression tests, here we
-        only run the unit tests and short tests."""
+        only run the unit tests and short tests. If the unit tests fail,
+        the QMCPACK installation aborts. On the other hand, the short tests
+        are too strict and often fail, but are still useful to run. In the
+        future, the short tests will be more reasonable in terms of quality
+        assurance (i.e. they will not be so strict), but will be sufficient to
+        validate QMCPACK in production."""
+
         with working_dir(self.build_directory):
             ctest('-L', 'unit')
-            ctest('-R', 'short')
+            try:
+                ctest('-R', 'short')
+            except ProcessError:
+                warn  = 'Unit tests passed, but short tests have failed.\n'
+                warn += 'Please review failed tests before proceeding\n'
+                warn += 'with production calculations.\n'
+                tty.msg(warn)
diff --git a/var/spack/repos/builtin/packages/qmd-progress/package.py b/var/spack/repos/builtin/packages/qmd-progress/package.py
index a880609e76..ea87217689 100644
--- a/var/spack/repos/builtin/packages/qmd-progress/package.py
+++ b/var/spack/repos/builtin/packages/qmd-progress/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,10 +13,12 @@ class QmdProgress(CMakePackage):
     commonly used in quantum chemistry packages."""
 
     homepage = "https://github.com/lanl/qmd-progress"
-    url      = "https://github.com/lanl/qmd-progress"
+    url      = "https://github.com/lanl/qmd-progress/tarball/v1.1.0"
+    git      = "https://github.com/lanl/qmd-progress.git"
 
-    version('develop', git='https://github.com/lanl/qmd-progress', branch='master')
-    version('1.0.0', git='https://github.com/lanl/qmd-progress', tag='v1.0.0')
+    version('develop', branch='master')
+    version('1.1.0', 'dda155134f0925629bf116e562c0a4bd')
+    version('1.0.0', 'c950bead2719a47a78864e3376ba143e')
 
     variant('graphlib', default=False, description='Build with Metis Suppport')
     variant('mpi', default=True, description='Build with MPI Support')
diff --git a/var/spack/repos/builtin/packages/qorts/QoRTs.sh b/var/spack/repos/builtin/packages/qorts/QoRTs.sh
new file mode 100644
index 0000000000..d847e76e05
--- /dev/null
+++ b/var/spack/repos/builtin/packages/qorts/QoRTs.sh
@@ -0,0 +1,3 @@
+#!/bin/sh
+# convenience wrapper for the QoRTs jar file
+java -jar QoRTs.jar "$@"
diff --git a/var/spack/repos/builtin/packages/qorts/package.py b/var/spack/repos/builtin/packages/qorts/package.py
new file mode 100644
index 0000000000..5b1c811e5f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/qorts/package.py
@@ -0,0 +1,51 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os.path
+
+
+class Qorts(RPackage):
+    """The QoRTs software package is a fast, efficient, and portable
+    multifunction toolkit designed to assist in the analysis, quality
+    control, and data management of RNA-Seq and DNA-Seq datasets. Its
+    primary function is to aid in the detection and identification of
+    errors, biases, and artifacts produced by high-throughput sequencing
+    technology."""
+
+    homepage = "https://github.com/hartleys/QoRTs"
+    url      = "https://github.com/hartleys/QoRTs/releases/download/v1.2.42/QoRTs_1.2.42.tar.gz"
+
+    version('1.2.42', '7d46162327b0da70bfe483fe2f2b7829')
+
+    depends_on('java', type='run')
+
+    resource(
+        name='QoRTs.jar',
+        url='https://github.com/hartleys/QoRTs/releases/download/v1.2.42/QoRTs.jar',
+        md5='918df4291538218c12caa3ab98c535e9',
+        placement='jarfile',
+        expand=False
+    )
+
+    @run_after('install')
+    def install_jar(self):
+        install_tree(join_path(self.stage.source_path, 'jarfile'),
+                     self.prefix.bin)
+
+        # Set up a helper script to call java on the jar file,
+        # explicitly codes the path for java and the jar file.
+        script_sh = join_path(os.path.dirname(__file__), "QoRTs.sh")
+        script = self.prefix.bin.QoRTs
+        install(script_sh, script)
+        set_executable(script)
+
+        # Munge the helper script to explicitly point to java and the
+        # jar file.
+        java = self.spec['java'].prefix.bin.java
+        kwargs = {'backup': False}
+        filter_file('^java', java, script, **kwargs)
+        filter_file('QoRTs.jar', join_path(self.prefix.bin, 'QoRTs.jar'),
+                    script, **kwargs)
diff --git a/var/spack/repos/builtin/packages/qrupdate/package.py b/var/spack/repos/builtin/packages/qrupdate/package.py
index 0856a4efb0..915f6615e8 100644
--- a/var/spack/repos/builtin/packages/qrupdate/package.py
+++ b/var/spack/repos/builtin/packages/qrupdate/package.py
@@ -1,31 +1,14 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import os
+import sys
 from spack import *
 
 
-class Qrupdate(Package):
+class Qrupdate(MakefilePackage):
     """qrupdate is a Fortran library for fast updates of QR and
     Cholesky decompositions."""
 
@@ -37,7 +20,30 @@ class Qrupdate(Package):
     depends_on("blas")
     depends_on("lapack")
 
+    def edit(self, spec, prefix):
+        # BSD "install" does not understand GNU -D flag.
+        # We will create the parent directory ourselves.
+        makefile = FileFilter('src/Makefile')
+        if (sys.platform == 'darwin'):
+            makefile.filter('-D', '')
+        return
+
     def install(self, spec, prefix):
+        lapack_blas = spec['lapack'].libs + spec['blas'].libs
         # Build static and dynamic libraries
-        make("lib", "solib")
+        make('lib', 'solib',
+             'BLAS={0}'.format(lapack_blas.ld_flags),
+             'LAPACK={0}'.format(lapack_blas.ld_flags))
+        # "INSTALL" confuses "make install" on case-insensitive filesystems
+        if os.path.isfile("INSTALL"):
+            os.remove("INSTALL")
+        # create lib folder:
+        if (sys.platform == 'darwin'):
+            mkdirp(prefix.lib)
         make("install", "PREFIX=%s" % prefix)
+
+    @run_after('install')
+    def fix_darwin_install(self):
+        # The shared libraries are not installed correctly on Darwin:
+        if (sys.platform == 'darwin'):
+            fix_darwin_install_name(self.spec.prefix.lib)
diff --git a/var/spack/repos/builtin/packages/qt-creator/package.py b/var/spack/repos/builtin/packages/qt-creator/package.py
index c7484f9643..05581edae4 100644
--- a/var/spack/repos/builtin/packages/qt-creator/package.py
+++ b/var/spack/repos/builtin/packages/qt-creator/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py
index fe29ced8a9..f956d77219 100644
--- a/var/spack/repos/builtin/packages/qt/package.py
+++ b/var/spack/repos/builtin/packages/qt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import platform
 import os
@@ -36,6 +17,8 @@ class Qt(Package):
     list_url = 'http://download.qt.io/archive/qt/'
     list_depth = 3
 
+    version('5.11.2', 'c6104b840b6caee596fa9a35bc5f57f67ed5a99d6a36497b6fe66f990a53ca81')
+    version('5.10.0', 'c5e275ab0ed7ee61d0f4b82cd471770d')
     version('5.9.1',  '77b4af61c49a09833d4df824c806acaf')
     version('5.9.0',  '9c8bc8b828c2b56721980368266df9d9')
     version('5.8.0',  'a9f2494f75f966e2f22358ec367d8f41')
@@ -66,7 +49,13 @@ class Qt(Package):
     variant('opengl',     default=False,
             description="Build with OpenGL support.")
 
+    # fix installation of pkgconfig files
+    # see https://github.com/Homebrew/homebrew-core/pull/5951
+    patch('restore-pc-files.patch', when='@5.9: platform=darwin')
+
+    patch('qt3accept.patch', when='@3.3.8b')
     patch('qt3krell.patch', when='@3.3.8b+krellpatch')
+    patch('qt3ptrdiff.patch', when='@3.3.8b')
 
     # see https://bugreports.qt.io/browse/QTBUG-57656
     patch('QTBUG-57656.patch', when='@5.8.0')
@@ -83,6 +72,12 @@ class Qt(Package):
     patch('qt4-pcre-include-conflict.patch', when='@4')
     patch('qt4-el-capitan.patch', when='@4')
 
+    # Allow Qt's configure script to build the webkit option with more
+    # recent versions of gcc.
+    # https://github.com/spack/spack/issues/9205
+    # https://github.com/spack/spack/issues/9209
+    patch('qt4-gcc-and-webkit.patch', when='@4')
+
     # Use system openssl for security.
     depends_on("openssl")
     depends_on("glib", when='@4:')
@@ -96,21 +91,36 @@ class Qt(Package):
     depends_on("libmng")
     depends_on("jpeg")
     depends_on("icu4c")
-    depends_on("fontconfig")
+    depends_on("fontconfig", when=(sys.platform != 'darwin'))  # (Unix only)
     depends_on("freetype")
-    # FIXME:
-    # depends_on("freetype", when='@5.8:') and '-system-freetype'
-    # -system-harfbuzz
-    # -system-pcre
+
+    # Core options:
+    # -doubleconversion  [system/qt/no]
+    # -iconv             [posix/sun/gnu/no] (Unix only)
+    # -pcre              [system/qt]
+
+    # Gui, printing, widget options:
+    # -harfbuzz          [system/qt/no]
+    # -xkbcommon-x11     [system/qt/no]
+    # -system-xkbcommon
+
+    # Database options:
+    # -sqlite            [system/qt]
+
+    # Qt3D options:
+    # -assimp            [system/qt/no]
 
     # QtQml
     depends_on("python", when='@5.7.0:', type='build')
 
     # OpenGL hardware acceleration
-    depends_on("mesa", when='@4:+opengl')
+    depends_on("gl@3.2:", when='@4:+opengl')
     depends_on("libxcb", when=sys.platform != 'darwin')
     depends_on("libx11", when=sys.platform != 'darwin')
 
+    if sys.platform != 'darwin':
+        depends_on("libxext", when='@3:4.99')
+
     # Webkit
     depends_on("flex", when='+webkit', type='build')
     depends_on("bison", when='+webkit', type='build')
@@ -121,6 +131,17 @@ class Qt(Package):
     # depends_on("pulse", when='+multimedia')
     # depends_on("flac", when='+multimedia')
     # depends_on("ogg", when='+multimedia')
+    # -pulseaudio                [auto] (Unix only)
+    # -alsa                      [auto] (Unix only)
+
+    # Webengine options:
+    # -webengine-alsa            [auto] (Linux only)
+    # -webengine-pulseaudio      [auto] (Linux only)
+    # -webengine-embedded-build  [auto] (Linux only)
+    # -webengine-icu             [system/qt] (Linux only)
+    # -webengine-ffmpeg          [system/qt] (Linux only)
+    # -webengine-opus            [system/qt] (Linux only)
+    # -webengine-webp            [system/qt] (Linux only)
 
     use_xcode = True
 
@@ -146,7 +167,9 @@ class Qt(Package):
         elif version >= Version('2.1'):
             url += 'x11-'
 
-        if version >= Version('4.0'):
+        if version >= Version('5.10.0'):
+            url += 'src-'
+        elif version >= Version('4.0'):
             url += 'opensource-src-'
         elif version >= Version('3'):
             url += 'free-'
@@ -198,6 +221,7 @@ class Qt(Package):
 
     @property
     def common_config_args(self):
+        # incomplete list is here http://doc.qt.io/qt-5/configure-options.html
         config_args = [
             '-prefix', self.prefix,
             '-v',
@@ -208,12 +232,14 @@ class Qt(Package):
             '-confirm-license',
             '-openssl-linked',
             '-optimized-qmake',
-            '-fontconfig',
             '-system-freetype',
             '-I{0}/freetype2'.format(self.spec['freetype'].prefix.include),
             '-no-pch'
         ]
 
+        if sys.platform != 'darwin':
+            config_args.append('-fontconfig')
+
         if '@:5.7.1' in self.spec:
             config_args.append('-no-openvg')
         else:
@@ -243,7 +269,6 @@ class Qt(Package):
             config_args.append('-I%s/dbus-1.0/include' % dbus.lib)
             config_args.append('-I%s/dbus-1.0' % dbus.include)
             config_args.append('-L%s' % dbus.lib)
-            config_args.append('-ldbus-1')
         else:
             config_args.append('-no-dbus')
 
@@ -255,6 +280,8 @@ class Qt(Package):
                 '-no-alsa',
             ])
 
+        # FIXME: else: -system-xcb ?
+
         if '@4' in self.spec and sys.platform == 'darwin':
             config_args.append('-cocoa')
 
@@ -333,6 +360,17 @@ class Qt(Package):
                 '-skip', 'webengine',
             ])
 
+        if '~opengl' in self.spec and self.spec.satisfies('@5.10:'):
+            config_args.extend([
+                '-skip', 'webglplugin',
+            ])
+
+        if self.version > Version('5.8'):
+            # relies on a system installed wayland, i.e. no spack package yet
+            # https://wayland.freedesktop.org/ubuntu16.04.html
+            # https://wiki.qt.io/QtWayland
+            config_args.extend(['-skip', 'wayland'])
+
         configure('-no-eglfs',
                   '-no-directfb',
                   '-{0}gtk'.format('' if '+gtk' in self.spec else 'no-'),
diff --git a/var/spack/repos/builtin/packages/qt/qt3accept.patch b/var/spack/repos/builtin/packages/qt/qt3accept.patch
new file mode 100644
index 0000000000..32dfb9df08
--- /dev/null
+++ b/var/spack/repos/builtin/packages/qt/qt3accept.patch
@@ -0,0 +1,38 @@
+--- qt-x11-free-3.3.8b/configure	2008-01-15 13:09:15.000000000 -0600
++++ qt-x11-free-3.3.8b-fixes/configure	2015-07-08 15:49:03.379560633 -0500
+@@ -2339,7 +2339,7 @@
+         else
+             echo "Do you accept the terms of the $TheLicense? \c"
+         fi
+-        read acceptance
++        acceptance=yes
+         echo
+ 	if [ "$acceptance" = yes ]; then
+ 	    break
+@@ -2397,7 +2397,7 @@
+ 	else
+ 	    echo "Do you accept the terms of $affix license? \c"
+ 	fi
+-	read acceptance
++        acceptance=yes
+ 	echo
+ 	if [ "$acceptance" = "yes" ]; then
+ 	    break
+@@ -2443,7 +2443,7 @@
+ 	else
+ 	    echo "Do you accept the terms of the license? \c"
+ 	fi
+-	read acceptance
++        acceptance=yes
+ 	echo
+ 	if [ "$acceptance" = "yes" ]; then
+ 	    break
+@@ -2524,7 +2524,7 @@
+ 	else
+ 	    echo "Do you accept the terms of the $Platform License? \c"
+ 	fi
+-	read acceptance
++        acceptance=yes
+ 	echo
+ 	if [ "$acceptance" = "yes" ]; then
+ 	    break
diff --git a/var/spack/repos/builtin/packages/qt/qt3krell.patch b/var/spack/repos/builtin/packages/qt/qt3krell.patch
index 3333eeacd4..cee94b3cbc 100644
--- a/var/spack/repos/builtin/packages/qt/qt3krell.patch
+++ b/var/spack/repos/builtin/packages/qt/qt3krell.patch
@@ -1,23 +1,3 @@
---- qt-x11-free-3.3.8b/src/tools/qmap.h	2008-01-15 13:09:13.000000000 -0600
-+++ qt-x11-free-3.3.8b-fixes/src/tools/qmap.h	2015-07-08 15:47:34.757565247 -0500
-@@ -52,6 +52,7 @@
- #ifndef QT_NO_STL
- #include <iterator>
- #include <map>
-+#include <cstddef>
- #endif
- 
- //#define QT_CHECK_MAP_RANGE
---- qt-x11-free-3.3.8b/src/tools/qvaluelist.h	2008-01-15 13:09:13.000000000 -0600
-+++ qt-x11-free-3.3.8b-fixes/src/tools/qvaluelist.h	2015-07-08 15:47:34.758565247 -0500
-@@ -50,6 +50,7 @@
- #ifndef QT_NO_STL
- #include <iterator>
- #include <list>
-+#include <cstddef>
- #endif
- 
- //#define QT_CHECK_VALUELIST_RANGE
 --- qt-x11-free-3.3.8b/src/tools/qvaluevector.h	2008-01-15 13:09:13.000000000 -0600
 +++ qt-x11-free-3.3.8b-fixes/src/tools/qvaluevector.h	2015-07-08 15:47:34.758565247 -0500
 @@ -47,6 +47,7 @@
@@ -28,41 +8,3 @@
  #endif
  
  template <class T>
---- qt-x11-free-3.3.8b/configure	2008-01-15 13:09:15.000000000 -0600
-+++ qt-x11-free-3.3.8b-fixes/configure	2015-07-08 15:49:03.379560633 -0500
-@@ -2339,7 +2339,7 @@
-         else
-             echo "Do you accept the terms of the $TheLicense? \c"
-         fi
--        read acceptance
-+        acceptance=yes
-         echo
- 	if [ "$acceptance" = yes ]; then
- 	    break
-@@ -2397,7 +2397,7 @@
- 	else
- 	    echo "Do you accept the terms of $affix license? \c"
- 	fi
--	read acceptance
-+        acceptance=yes
- 	echo
- 	if [ "$acceptance" = "yes" ]; then
- 	    break
-@@ -2443,7 +2443,7 @@
- 	else
- 	    echo "Do you accept the terms of the license? \c"
- 	fi
--	read acceptance
-+        acceptance=yes
- 	echo
- 	if [ "$acceptance" = "yes" ]; then
- 	    break
-@@ -2524,7 +2524,7 @@
- 	else
- 	    echo "Do you accept the terms of the $Platform License? \c"
- 	fi
--	read acceptance
-+        acceptance=yes
- 	echo
- 	if [ "$acceptance" = "yes" ]; then
- 	    break
diff --git a/var/spack/repos/builtin/packages/qt/qt3ptrdiff.patch b/var/spack/repos/builtin/packages/qt/qt3ptrdiff.patch
new file mode 100644
index 0000000000..5043e4b5a8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/qt/qt3ptrdiff.patch
@@ -0,0 +1,20 @@
+--- a/src/tools/qmap.h	2008-01-16 06:09:13.000000000 +1100
++++ b/src/tools/qmap.h	2018-01-07 11:32:38.720893324 +1100
+@@ -52,6 +52,7 @@
+ #ifndef QT_NO_STL
+ #include <iterator>
+ #include <map>
++#include <stddef.h>
+ #endif
+ 
+ //#define QT_CHECK_MAP_RANGE
+--- a/src/tools/qvaluelist.h	2008-01-16 06:09:13.000000000 +1100
++++ b/src/tools/qvaluelist.h	2018-01-07 11:33:03.393206961 +1100
+@@ -50,6 +50,7 @@
+ #ifndef QT_NO_STL
+ #include <iterator>
+ #include <list>
++#include <stddef.h>
+ #endif
+ 
+ //#define QT_CHECK_VALUELIST_RANGE
diff --git a/var/spack/repos/builtin/packages/qt/qt4-corewlan-new-osx.patch b/var/spack/repos/builtin/packages/qt/qt4-corewlan-new-osx.patch
index 370edf7fa5..a4b652e401 100644
--- a/var/spack/repos/builtin/packages/qt/qt4-corewlan-new-osx.patch
+++ b/var/spack/repos/builtin/packages/qt/qt4-corewlan-new-osx.patch
@@ -1,16 +1,16 @@
 diff -Nr -U5 qt-everywhere-opensource-src-4.8.6/src/plugins/bearer/corewlan/corewlan.pro qt-everywhere-opensource-src-4.8.6.corewlan-new-osx/src/plugins/bearer/corewlan/corewlan.pro
 --- qt-everywhere-opensource-src-4.8.6/src/plugins/bearer/corewlan/corewlan.pro	2014-04-10 14:37:12.000000000 -0400
 +++ qt-everywhere-opensource-src-4.8.6.corewlan-new-osx/src/plugins/bearer/corewlan/corewlan.pro	2015-12-02 12:21:34.608585392 -0500
-@@ -3,11 +3,11 @@
- 
+@@ -3,9 +3,9 @@
+
  QT = core network
  LIBS += -framework Foundation -framework SystemConfiguration
- 
+
  contains(QT_CONFIG, corewlan) {
 -    isEmpty(QMAKE_MAC_SDK)|contains(QMAKE_MAC_SDK, "/Developer/SDKs/MacOSX10\.[67]\.sdk") {
-+    isEmpty(QMAKE_MAC_SDK)|contains(QMAKE_MAC_SDK, ".*MacOSX10\.([6789]|1[01])\.sdk") {
++    isEmpty(QMAKE_MAC_SDK)|contains(QMAKE_MAC_SDK, ".*MacOSX10\.([6789]|1[0123])\.sdk") {
           LIBS += -framework CoreWLAN -framework Security
      }
  }
- 
+
  HEADERS += qcorewlanengine.h \
diff --git a/var/spack/repos/builtin/packages/qt/qt4-gcc-and-webkit.patch b/var/spack/repos/builtin/packages/qt/qt4-gcc-and-webkit.patch
new file mode 100644
index 0000000000..38a1c350f3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/qt/qt4-gcc-and-webkit.patch
@@ -0,0 +1,20 @@
+--- a/configure.orig	2018-09-18 07:02:33.866633000 +1000
++++ b/configure	2018-09-18 07:05:21.935194000 +1000
+@@ -7708,7 +7708,7 @@
+ 
+ 	# Check gcc's version
+ 	case "$(${QMAKE_CONF_COMPILER} -dumpversion)" in
+-	    4*)
++	    [4-8]*)
+ 		;;
+ 	    3.4*)
+ 		canBuildQtXmlPatterns="no"
+@@ -7729,7 +7729,7 @@
+     *-g++*)
+ 	# Check gcc's version
+ 	case "$(${QMAKE_CONF_COMPILER} -dumpversion)" in
+-	    4*|3.4*)
++	    [4-8]*|3.4*)
+ 		;;
+             3.3*)
+                 canBuildWebKit="no"
diff --git a/var/spack/repos/builtin/packages/qt/restore-pc-files.patch b/var/spack/repos/builtin/packages/qt/restore-pc-files.patch
new file mode 100644
index 0000000000..35fbaddd43
--- /dev/null
+++ b/var/spack/repos/builtin/packages/qt/restore-pc-files.patch
@@ -0,0 +1,15 @@
+Partially reverts <https://codereview.qt-project.org/#/c/140954/>.
+
+diff --git i/qtbase/mkspecs/features/qt_module.prf w/qtbase/mkspecs/features/qt_module.prf
+index bb28af97..36bb6483 100644
+--- i/qtbase/mkspecs/features/qt_module.prf
++++ w/qtbase/mkspecs/features/qt_module.prf
+@@ -245,7 +245,7 @@ load(qt_installs)
+ load(qt_targets)
+
+ # this builds on top of qt_common
+-!internal_module:!lib_bundle:if(unix|mingw) {
++!internal_module:if(unix|mingw) {
+     CONFIG += create_pc
+     QMAKE_PKGCONFIG_DESTDIR = pkgconfig
+     host_build: \
diff --git a/var/spack/repos/builtin/packages/qtgraph/package.py b/var/spack/repos/builtin/packages/qtgraph/package.py
index 742b51dd1f..012bce84f2 100644
--- a/var/spack/repos/builtin/packages/qtgraph/package.py
+++ b/var/spack/repos/builtin/packages/qtgraph/package.py
@@ -1,45 +1,10 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-##############################################################################
-# Copyright (c) 2015-2017 Krell Institute. All Rights Reserved.
-#
-# This program is free software; you can redistribute it and/or modify it
-# under the terms of the GNU General Public License as published by the Free
-# Software Foundation; either version 2 of the License, or (at your option)
-# any later version.
-#
-# This program is distributed in the hope that it will be useful, but WITHOUT
-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
-# FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for
-# more details.
-#
-# You should have received a copy of the GNU General Public License along with
-# this program; if not, write to the Free Software Foundation, Inc., 59 Temple
-# Place, Suite 330, Boston, MA  02111-1307  USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
+import os
 
 
 class Qtgraph(QMakePackage):
@@ -49,25 +14,34 @@ class Qtgraph(QMakePackage):
        libgvc within the Qt Graphics View Framework."""
 
     homepage = "https://github.com/OpenSpeedShop/QtGraph"
+    git      = "https://github.com/OpenSpeedShop/QtGraph.git"
 
-    url      = "https://github.com/OpenSpeedShop/QtGraph.git"
-    version('1.0.0', branch='master',
-            git='https://github.com/OpenSpeedShop/QtGraph.git')
+    version('develop', branch='master')
+    version('1.0.0.0', branch='1.0.0.0')
 
     # qtgraph depends on these packages
-    depends_on('qt@4.8.6:')
-    depends_on('graphviz')
+    depends_on('qt@4.8.6:', when='@develop')
+    depends_on('qt@5.10.0', when='@1.0.0.0:')
+
+    depends_on("graphviz@2.40.1:", when='@develop')
+    depends_on("graphviz@2.40.1", when='@1.0.0.0:')
 
     def setup_environment(self, spack_env, run_env):
         """Set up the compile and runtime environments for a package."""
         spack_env.set('GRAPHVIZ_ROOT', self.spec['graphviz'].prefix)
         spack_env.set('INSTALL_ROOT', self.prefix)
 
+        # What library suffix should be used based on library existence
+        if os.path.isdir(self.prefix.lib64):
+            lib_dir = self.prefix.lib64
+        else:
+            lib_dir = self.prefix.lib
+
         # The implementor has set up the library and include paths in
         # a non-conventional way.  We reflect that here.
         run_env.prepend_path(
             'LD_LIBRARY_PATH', join_path(
-                self.prefix.lib64,
+                lib_dir,
                 '{0}'.format(self.spec['qt'].version.up_to(3))))
 
         run_env.prepend_path('CPATH', self.prefix.include.QtGraph)
diff --git a/var/spack/repos/builtin/packages/qthreads/package.py b/var/spack/repos/builtin/packages/qthreads/package.py
index b06e824681..f1796099aa 100644
--- a/var/spack/repos/builtin/packages/qthreads/package.py
+++ b/var/spack/repos/builtin/packages/qthreads/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/espresso/dspev_drv_elpa.patch b/var/spack/repos/builtin/packages/quantum-espresso/dspev_drv_elpa.patch
index 153bcf2ef5..153bcf2ef5 100644
--- a/var/spack/repos/builtin/packages/espresso/dspev_drv_elpa.patch
+++ b/var/spack/repos/builtin/packages/quantum-espresso/dspev_drv_elpa.patch
diff --git a/var/spack/repos/builtin/packages/espresso/package.py b/var/spack/repos/builtin/packages/quantum-espresso/package.py
index 23014710a1..7c1310ec31 100644
--- a/var/spack/repos/builtin/packages/espresso/package.py
+++ b/var/spack/repos/builtin/packages/quantum-espresso/package.py
@@ -1,34 +1,15 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import glob
 import os.path
 
 from spack import *
 
 
-class Espresso(Package):
+class QuantumEspresso(Package):
     """Quantum-ESPRESSO is an integrated suite of Open-Source computer codes
     for electronic-structure calculations and materials modeling at the
     nanoscale. It is based on density-functional theory, plane waves, and
@@ -36,20 +17,12 @@ class Espresso(Package):
     """
 
     homepage = 'http://quantum-espresso.org'
-    url = 'http://www.qe-forge.org/gf/download/frsrelease/204/912/espresso-5.3.0.tar.gz'
+    url      = 'https://github.com/QEF/q-e/archive/qe-6.2.0.tar.gz'
 
-    version(
-        '6.1.0',
-        'db398edcad76e085f8c8a3f6ecb7aaab',
-        url='http://www.qe-forge.org/gf/download/frsrelease/240/1075/qe-6.1.tar.gz'
-    )
-
-    version(
-        '5.4.0',
-        '8bb78181b39bd084ae5cb7a512c1cfe7',
-        url='http://www.qe-forge.org/gf/download/frsrelease/211/968/espresso-5.4.0.tar.gz'
-    )
-    version('5.3.0', '6848fcfaeb118587d6be36bd10b7f2c3')
+    version('6.2.0', '972176a58d16ae8cf0c9a308479e2b97')
+    version('6.1.0', '3fe861dcb5f6ec3d15f802319d5d801b')
+    version('5.4',   '085f7e4de0952e266957bbc79563c54e')
+    version('5.3',   'be3f8778e302cffb89258a5f936a7592')
 
     variant('mpi', default=True, description='Builds with mpi support')
     variant('openmp', default=False, description='Enables openMP support')
@@ -71,8 +44,8 @@ class Espresso(Package):
     depends_on('elpa~openmp', when='+elpa~openmp')
     depends_on('hdf5', when='+hdf5')
 
-    patch('dspev_drv_elpa.patch', when='@6.1 ^elpa@2016.05.004')
-    patch('dspev_drv_elpa.patch', when='@6.1 ^elpa@2016.05.003')
+    patch('dspev_drv_elpa.patch', when='@6.1.0:+elpa ^elpa@2016.05.004')
+    patch('dspev_drv_elpa.patch', when='@6.1.0:+elpa ^elpa@2016.05.003')
 
     # We can't ask for scalapack or elpa if we don't want MPI
     conflicts(
@@ -154,6 +127,24 @@ class Espresso(Package):
 
         configure(*options)
 
+        # Apparently the build system of QE is so broken that:
+        #
+        # 1. The variable reported on stdout as HDF5_LIBS is actually
+        #    called HDF5_LIB (singular)
+        # 2. The link flags omit a few `-L` from the line, and this
+        #    causes the linker to break
+        #
+        # Below we try to match the entire HDF5_LIB line and substitute
+        # with the list of libraries that needs to be linked.
+        if '+hdf5' in spec:
+            make_inc = join_path(self.stage.source_path, 'make.inc')
+            hdf5_libs = ' '.join(spec['hdf5:hl,fortran'].libs)
+            filter_file(
+                'HDF5_LIB([\s]*)=([\s\w\-\/.,]*)',
+                'HDF5_LIB = {0}'.format(hdf5_libs),
+                make_inc
+            )
+
         make('all')
 
         if 'platform=darwin' in spec:
diff --git a/var/spack/repos/builtin/packages/quinoa/package.py b/var/spack/repos/builtin/packages/quinoa/package.py
index 5a47d355d9..61a933b378 100644
--- a/var/spack/repos/builtin/packages/quinoa/package.py
+++ b/var/spack/repos/builtin/packages/quinoa/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -34,12 +15,12 @@ class Quinoa(CMakePackage):
     """
 
     homepage = "http://quinoacomputing.org"
-    url      = "https://github.com/quinoacomputing/quinoa/tarball/quinoa_v0.1"
+    git      = "https://github.com/quinoacomputing/quinoa.git"
 
-    version('develop', git='https://github.com/quinoacomputing/quinoa', branch='master')
+    version('develop', branch='master')
 
     depends_on('hdf5+mpi')
-    depends_on("charm backend=mpi")
+    depends_on("charmpp backend=mpi")
     depends_on("trilinos+exodus")
     depends_on("boost")
     depends_on("hypre~internal-superlu")
diff --git a/var/spack/repos/builtin/packages/qwt/package.py b/var/spack/repos/builtin/packages/qwt/package.py
index cef42d73e1..1d996a6246 100644
--- a/var/spack/repos/builtin/packages/qwt/package.py
+++ b/var/spack/repos/builtin/packages/qwt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-a4/package.py b/var/spack/repos/builtin/packages/r-a4/package.py
index 248e0c41f8..18b13c506e 100644
--- a/var/spack/repos/builtin/packages/r-a4/package.py
+++ b/var/spack/repos/builtin/packages/r-a4/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,9 @@ class RA4(RPackage):
     """Automated Affymetrix Array Analysis Umbrella Package."""
 
     homepage = "https://www.bioconductor.org/packages/a4/"
-    url      = "https://git.bioconductor.org/packages/a4"
-    list_url = homepage
-    version('1.24.0', git='https://git.bioconductor.org/packages/a4', commit='79b5143652176787c85a0d587b3bbfad6b4a19f4')
+    git      = "https://git.bioconductor.org/packages/a4.git"
+
+    version('1.24.0', commit='79b5143652176787c85a0d587b3bbfad6b4a19f4')
 
     depends_on('r@3.4.0:3.4.9', when='@1.24.0')
     depends_on('r-a4base', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-a4base/package.py b/var/spack/repos/builtin/packages/r-a4base/package.py
index bc18cae16d..0e76c245f3 100644
--- a/var/spack/repos/builtin/packages/r-a4base/package.py
+++ b/var/spack/repos/builtin/packages/r-a4base/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,9 @@ class RA4base(RPackage):
     """Automated Affymetrix Array Analysis."""
 
     homepage = "https://www.bioconductor.org/packages/a4Base/"
-    url      = "'https://git.bioconductor.org/packages/a4Base'"
-    list_url = homepage
-    version('1.24.0', git='https://git.bioconductor.org/packages/a4Base', commit='f674afe424a508df2c8ee6c87a06fbd4aa410ef6')
+    git      = "https://git.bioconductor.org/packages/a4Base.git"
+
+    version('1.24.0', commit='f674afe424a508df2c8ee6c87a06fbd4aa410ef6')
 
     depends_on('r@3.4.0:3.4.9', when='@1.24.0')
     depends_on('r-biobase', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-a4classif/package.py b/var/spack/repos/builtin/packages/r-a4classif/package.py
index 18a2e1b390..8a2a5c40f5 100644
--- a/var/spack/repos/builtin/packages/r-a4classif/package.py
+++ b/var/spack/repos/builtin/packages/r-a4classif/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,10 +10,9 @@ class RA4classif(RPackage):
     """Automated Affymetrix Array Analysis Classification Package."""
 
     homepage = "https://www.bioconductor.org/packages/a4Classif/"
-    url      = "https://git.bioconductor.org/packages/a4Classif"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/a4Classif.git"
 
-    version('1.24.0', git='https://git.bioconductor.org/packages/a4Classif', commit='ca06bf274c87a73fc12c29a6eea4b90289fe30b1')
+    version('1.24.0', commit='ca06bf274c87a73fc12c29a6eea4b90289fe30b1')
 
     depends_on('r@3.4.0:3.4.9', when='@1.24.0')
     depends_on('r-a4core', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-a4core/package.py b/var/spack/repos/builtin/packages/r-a4core/package.py
index d01514d499..df2142be36 100644
--- a/var/spack/repos/builtin/packages/r-a4core/package.py
+++ b/var/spack/repos/builtin/packages/r-a4core/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,9 @@ class RA4core(RPackage):
     """Automated Affymetrix Array Analysis Core Package."""
 
     homepage = "https://www.bioconductor.org/packages/a4Core/"
-    url      = "https://git.bioconductor.org/packages/a4Core"
+    git      = "https://git.bioconductor.org/packages/a4Core.git"
 
-    version('1.24.0', git='https://git.bioconductor.org/packages/a4Core', commit='c871faa3e1ab6be38a9ea3018816cf31b58b0ed3')
+    version('1.24.0', commit='c871faa3e1ab6be38a9ea3018816cf31b58b0ed3')
 
     depends_on('r@3.4.0:3.4.9', when='@1.24.0')
     depends_on('r-biobase', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-a4preproc/package.py b/var/spack/repos/builtin/packages/r-a4preproc/package.py
index 3410b0640b..08530cf7b4 100644
--- a/var/spack/repos/builtin/packages/r-a4preproc/package.py
+++ b/var/spack/repos/builtin/packages/r-a4preproc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,9 @@ class RA4preproc(RPackage):
     """Automated Affymetrix Array Analysis Preprocessing Package."""
 
     homepage = "https://www.bioconductor.org/packages/a4Preproc/"
-    url      = "https://git.bioconductor.org/packages/a4Preproc"
+    git      = "https://git.bioconductor.org/packages/a4Preproc.git"
 
-    version('1.24.0', git='https://git.bioconductor.org/packages/a4Preproc', commit='651014b8102807aea4f1274e34e083e70b5e7ee7')
+    version('1.24.0', commit='651014b8102807aea4f1274e34e083e70b5e7ee7')
 
     depends_on('r@3.4.0:3.4.9', when='@1.24.0')
     depends_on('r-annotationdbi', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-a4reporting/package.py b/var/spack/repos/builtin/packages/r-a4reporting/package.py
index 352d35b38a..f0f9f32065 100644
--- a/var/spack/repos/builtin/packages/r-a4reporting/package.py
+++ b/var/spack/repos/builtin/packages/r-a4reporting/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,9 @@ class RA4reporting(RPackage):
     """Automated Affymetrix Array Analysis Reporting Package."""
 
     homepage = "https://www.bioconductor.org/packages/a4Reporting"
-    url      = "https://git.bioconductor.org/packages/a4Reporting"
-    list_url = homepage
-    version('1.24.0', git='https://git.bioconductor.org/packages/a4Reporting', commit='bf22c4d50daf40fc9eaf8c476385bf4a24a5b5ce')
+    git      = "https://git.bioconductor.org/packages/a4Reporting.git"
+
+    version('1.24.0', commit='bf22c4d50daf40fc9eaf8c476385bf4a24a5b5ce')
 
     depends_on('r@3.4.0:3.4.9', when='@1.24.0')
     depends_on('r-annaffy', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-abadata/package.py b/var/spack/repos/builtin/packages/r-abadata/package.py
index 0d92e3e540..aa9796e383 100644
--- a/var/spack/repos/builtin/packages/r-abadata/package.py
+++ b/var/spack/repos/builtin/packages/r-abadata/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-abaenrichment/package.py b/var/spack/repos/builtin/packages/r-abaenrichment/package.py
index c3e903e248..c43a85c214 100644
--- a/var/spack/repos/builtin/packages/r-abaenrichment/package.py
+++ b/var/spack/repos/builtin/packages/r-abaenrichment/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -42,9 +23,9 @@ class RAbaenrichment(RPackage):
     user-defined brain regions."""
 
     homepage = "https://bioconductor.org/packages/ABAEnrichment/"
-    url      = "https://git.bioconductor.org/packages/ABAEnrichment"
+    git      = "https://git.bioconductor.org/packages/ABAEnrichment.git"
 
-    version('1.6.0', git='https://git.bioconductor.org/packages/ABAEnrichment', commit='d2a0467dcb7aa6e103e3b83dccd6510b0e142ac1')
+    version('1.6.0', commit='d2a0467dcb7aa6e103e3b83dccd6510b0e142ac1')
 
     depends_on('r@3.4.0:3.4.9', when='@1.6.0')
     depends_on('r-rcpp', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-abind/package.py b/var/spack/repos/builtin/packages/r-abind/package.py
index 768e930f4b..d9e7b2d821 100644
--- a/var/spack/repos/builtin/packages/r-abind/package.py
+++ b/var/spack/repos/builtin/packages/r-abind/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-absseq/package.py b/var/spack/repos/builtin/packages/r-absseq/package.py
index e3a094c97c..46bcf022f0 100644
--- a/var/spack/repos/builtin/packages/r-absseq/package.py
+++ b/var/spack/repos/builtin/packages/r-absseq/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,9 +13,9 @@ class RAbsseq(RPackage):
     of dispersion across expression level."""
 
     homepage = "https://www.bioconductor.org/packages/ABSSeq/"
-    url      = "https://git.bioconductor.org/packages/ABSSeq"
+    git      = "https://git.bioconductor.org/packages/ABSSeq.git"
 
-    version('1.22.8', git='https://git.bioconductor.org/packages/ABSSeq', commit='a67ba49bc156a4522092519644f3ec83d58ebd6a')
+    version('1.22.8', commit='a67ba49bc156a4522092519644f3ec83d58ebd6a')
 
     depends_on('r@3.4.0:3.4.9', when='@1.22.8')
     depends_on('r-locfit', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-acde/package.py b/var/spack/repos/builtin/packages/r-acde/package.py
index fd8677d42e..6abcd589ae 100644
--- a/var/spack/repos/builtin/packages/r-acde/package.py
+++ b/var/spack/repos/builtin/packages/r-acde/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-acepack/package.py b/var/spack/repos/builtin/packages/r-acepack/package.py
index be5d20f6ad..29a91b8a11 100644
--- a/var/spack/repos/builtin/packages/r-acepack/package.py
+++ b/var/spack/repos/builtin/packages/r-acepack/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-acgh/package.py b/var/spack/repos/builtin/packages/r-acgh/package.py
index f2e923ca3e..54db729af3 100644
--- a/var/spack/repos/builtin/packages/r-acgh/package.py
+++ b/var/spack/repos/builtin/packages/r-acgh/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,9 +13,9 @@ class RAcgh(RPackage):
     printing and plotting aCGH objects."""
 
     homepage = "https://www.bioconductor.org/packages/aCGH/"
-    url      = "https://git.bioconductor.org/packages/aCGH"
+    git      = "https://git.bioconductor.org/packages/aCGH.git"
 
-    version('1.54.0', git='https://git.bioconductor.org/packages/aCGH', commit='be2ed339449f55c8d218e10c435e4ad356683693')
+    version('1.54.0', commit='be2ed339449f55c8d218e10c435e4ad356683693')
 
     depends_on('r@3.4.0:3.4.9', when='@1.54.0')
     depends_on('r-cluster', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-acme/package.py b/var/spack/repos/builtin/packages/r-acme/package.py
index 168f2044d5..d4263bfcc8 100644
--- a/var/spack/repos/builtin/packages/r-acme/package.py
+++ b/var/spack/repos/builtin/packages/r-acme/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,9 +18,9 @@ class RAcme(RPackage):
     experiments quite easily with enough memory."""
 
     homepage = "https://www.bioconductor.org/packages/ACME/"
-    url      = "https://git.bioconductor.org/packages/ACME"
+    git      = "https://git.bioconductor.org/packages/ACME.git"
 
-    version('2.32.0', git='https://git.bioconductor.org/packages/ACME', commit='76372255d7714a0c8128a11c028bf70214dac407')
+    version('2.32.0', commit='76372255d7714a0c8128a11c028bf70214dac407')
 
     depends_on('r@3.4.0:3.4.9', when='@2.32.0')
     depends_on('r-biobase', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-ada/package.py b/var/spack/repos/builtin/packages/r-ada/package.py
index fbd4c0f167..eecb780fb0 100644
--- a/var/spack/repos/builtin/packages/r-ada/package.py
+++ b/var/spack/repos/builtin/packages/r-ada/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-adabag/package.py b/var/spack/repos/builtin/packages/r-adabag/package.py
index 407d0ad1ab..1e07829d5c 100644
--- a/var/spack/repos/builtin/packages/r-adabag/package.py
+++ b/var/spack/repos/builtin/packages/r-adabag/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-ade4/package.py b/var/spack/repos/builtin/packages/r-ade4/package.py
index 39b21c3373..b3acb086e9 100644
--- a/var/spack/repos/builtin/packages/r-ade4/package.py
+++ b/var/spack/repos/builtin/packages/r-ade4/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-adegenet/package.py b/var/spack/repos/builtin/packages/r-adegenet/package.py
index 64c475bc1f..754fb4ac22 100644
--- a/var/spack/repos/builtin/packages/r-adegenet/package.py
+++ b/var/spack/repos/builtin/packages/r-adegenet/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-adsplit/package.py b/var/spack/repos/builtin/packages/r-adsplit/package.py
index f862b1e581..d2a9f44352 100644
--- a/var/spack/repos/builtin/packages/r-adsplit/package.py
+++ b/var/spack/repos/builtin/packages/r-adsplit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,9 +13,9 @@ class RAdsplit(RPackage):
     significance of the supporting gene set is determined."""
 
     homepage = "https://www.bioconductor.org/packages/adSplit/"
-    url      = "https://git.bioconductor.org/packages/adSplit"
+    git      = "https://git.bioconductor.org/packages/adSplit.git"
 
-    version('1.46.0', git='https://git.bioconductor.org/packages/adSplit', commit='7e81a83f34d371447f491b3a146bf6851e260c7c')
+    version('1.46.0', commit='7e81a83f34d371447f491b3a146bf6851e260c7c')
 
     depends_on('r@3.4.0:3.4.9', when='@1.46.0')
     depends_on('r-annotationdbi', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-aer/package.py b/var/spack/repos/builtin/packages/r-aer/package.py
new file mode 100644
index 0000000000..830d4d74c6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-aer/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RAer(RPackage):
+    """Functions, data sets, examples, demos, and vignettes
+    for the book Christian Kleiber and Achim Zeileis (2008),
+    Applied Econometrics with R, Springer-Verlag, New York.
+    ISBN 978-0-387-77316-2."""
+
+    homepage = "https://cran.r-project.org/web/packages/AER/index.html"
+    url      = "https://cran.r-project.org/src/contrib/AER_1.2-5.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/AER"
+
+    version('1.2-5', '419df9dc8ee6e5edd79678fee06719ae')
+
+    depends_on('r@2.13.0:', type=('build', 'run'))
+    depends_on('r-car@2.10-19:', type=('build', 'run'))
+    depends_on('r-lmtest', type=('build', 'run'))
+    depends_on('r-sandwich', type=('build', 'run'))
+    depends_on('r-survival@2.37-5:', type=('build', 'run'))
+    depends_on('r-zoo', type=('build', 'run'))
+    depends_on('r-formula', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-affxparser/package.py b/var/spack/repos/builtin/packages/r-affxparser/package.py
index 1fd1dc5e85..79522cac96 100644
--- a/var/spack/repos/builtin/packages/r-affxparser/package.py
+++ b/var/spack/repos/builtin/packages/r-affxparser/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,9 +17,8 @@ class RAffxparser(RPackage):
     from a set of CEL files into a convenient list structure."""
 
     homepage = "https://www.bioconductor.org/packages/affxparser/"
-    url      = "https://git.bioconductor.org/packages/affxparser"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/affxparser.git"
 
-    version('1.48.0', git='https://git.bioconductor.org/packages/affxparser', commit='2461ea88f310b59c4a9a997a4b3dadedbd65a4aa')
+    version('1.48.0', commit='2461ea88f310b59c4a9a997a4b3dadedbd65a4aa')
 
     depends_on('r@3.4.0:3.4.9', when='@1.48.0')
diff --git a/var/spack/repos/builtin/packages/r-affy/package.py b/var/spack/repos/builtin/packages/r-affy/package.py
index 6be405c38b..eb361b1b95 100644
--- a/var/spack/repos/builtin/packages/r-affy/package.py
+++ b/var/spack/repos/builtin/packages/r-affy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,10 +12,9 @@ class RAffy(RPackage):
        functions. 'affy' is fully functional without it."""
 
     homepage = "https://bioconductor.org/packages/affy/"
-    url      = "https://git.bioconductor.org/packages/affy"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/affy.git"
 
-    version('1.54.0', git='https://git.bioconductor.org/packages/affy', commit='a815f02906fcf491b28ed0a356d6fce95a6bd20e')
+    version('1.54.0', commit='a815f02906fcf491b28ed0a356d6fce95a6bd20e')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-biobase', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-affycomp/package.py b/var/spack/repos/builtin/packages/r-affycomp/package.py
index 16593472ad..329ffe1ed2 100644
--- a/var/spack/repos/builtin/packages/r-affycomp/package.py
+++ b/var/spack/repos/builtin/packages/r-affycomp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,9 @@ class RAffycomp(RPackage):
     expression measures for Affymetrix Oligonucleotide Arrays."""
 
     homepage = "https://www.bioconductor.org/packages/affycomp/"
-    url      = "https://git.bioconductor.org/packages/affycomp"
+    git      = "https://git.bioconductor.org/packages/affycomp.git"
 
-    version('1.52.0', git='https://git.bioconductor.org/packages/affycomp', commit='1b97a1cb21ec93bf1e5c88d5d55b988059612790')
+    version('1.52.0', commit='1b97a1cb21ec93bf1e5c88d5d55b988059612790')
 
     depends_on('r@3.4.0:3.4.9', when='@1.52.0')
     depends_on('r-biobase', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-affycompatible/package.py b/var/spack/repos/builtin/packages/r-affycompatible/package.py
index 68f6f5c450..de43dc9f9b 100644
--- a/var/spack/repos/builtin/packages/r-affycompatible/package.py
+++ b/var/spack/repos/builtin/packages/r-affycompatible/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,9 +15,9 @@ class RAffycompatible(RPackage):
     (AGCC)-compatible sample annotation files."""
 
     homepage = "https://www.bioconductor.org/packages/AffyCompatible/"
-    url      = "https://git.bioconductor.org/packages/AffyCompatible"
+    git      = "https://git.bioconductor.org/packages/AffyCompatible.git"
 
-    version('1.36.0', 'https://git.bioconductor.org/packages/AffyCompatible', commit='dbbfd43a54ae1de6173336683a9461084ebf38c3')
+    version('1.36.0', commit='dbbfd43a54ae1de6173336683a9461084ebf38c3')
 
     depends_on('r@3.4.0:3.4.9', when=('@1.36.0'))
     depends_on('r-xml', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-affycontam/package.py b/var/spack/repos/builtin/packages/r-affycontam/package.py
index c2c08be3d6..f44105ce13 100644
--- a/var/spack/repos/builtin/packages/r-affycontam/package.py
+++ b/var/spack/repos/builtin/packages/r-affycontam/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,9 @@ class RAffycontam(RPackage):
     effectiveness."""
 
     homepage = "https://www.bioconductor.org/packages/affyContam/"
-    url      = "https://git.bioconductor.org/packages/affyContam"
+    git      = "https://git.bioconductor.org/packages/affyContam.git"
 
-    version('1.34.0', git='https://git.bioconductor.org/packages/affyContam', commit='03529f26d059c19e069cdda358dbf7789b6d4c40')
+    version('1.34.0', commit='03529f26d059c19e069cdda358dbf7789b6d4c40')
 
     depends_on('r@3.4.0:3.4.9', when=('@1.34.0'))
     depends_on('r-biobase', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-affycoretools/package.py b/var/spack/repos/builtin/packages/r-affycoretools/package.py
index 303b7255f8..b2023e7084 100644
--- a/var/spack/repos/builtin/packages/r-affycoretools/package.py
+++ b/var/spack/repos/builtin/packages/r-affycoretools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,9 @@ class RAffycoretools(RPackage):
     the more common analyses that a core Biostatistician might see."""
 
     homepage = "https://www.bioconductor.org/packages/affycoretools/"
-    url      = "https://git.bioconductor.org/packages/affycoretools"
+    git      = "https://git.bioconductor.org/packages/affycoretools.git"
 
-    version('1.48.0', git='https://git.bioconductor.org/packages/affycoretools', commit='e0d52e34eead1ac45d3e60c59efd940e4889eb99')
+    version('1.48.0', commit='e0d52e34eead1ac45d3e60c59efd940e4889eb99')
 
     depends_on('r@3.4.0:3.4.9', when='@1.48.0')
     depends_on('r-biobase', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-affydata/package.py b/var/spack/repos/builtin/packages/r-affydata/package.py
index 9fa647f282..ac720a1793 100644
--- a/var/spack/repos/builtin/packages/r-affydata/package.py
+++ b/var/spack/repos/builtin/packages/r-affydata/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-affyexpress/package.py b/var/spack/repos/builtin/packages/r-affyexpress/package.py
index 0e3a8f19d7..ec99f7bdce 100644
--- a/var/spack/repos/builtin/packages/r-affyexpress/package.py
+++ b/var/spack/repos/builtin/packages/r-affyexpress/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,9 +12,9 @@ class RAffyexpress(RPackage):
     expressed genes in the Affymetrix gene expression data."""
 
     homepage = "https://www.bioconductor.org/packages/AffyExpress/"
-    url      = "https://git.bioconductor.org/packages/AffyExpress"
+    git      = "https://git.bioconductor.org/packages/AffyExpress.git"
 
-    version('1.42.0', git='https://git.bioconductor.org/packages/AffyExpress', commit='f5c5cf6173f4419e25f4aeff5e6b705a40abc371')
+    version('1.42.0', commit='f5c5cf6173f4419e25f4aeff5e6b705a40abc371')
 
     depends_on('r@3.4.0:3.4.9', when='@1.42.0')
     depends_on('r-affy', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-affyilm/package.py b/var/spack/repos/builtin/packages/r-affyilm/package.py
index 7b854bc262..baa61ac6e0 100644
--- a/var/spack/repos/builtin/packages/r-affyilm/package.py
+++ b/var/spack/repos/builtin/packages/r-affyilm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,9 +14,9 @@ class RAffyilm(RPackage):
     of the Langmuir model."""
 
     homepage = "https://www.bioconductor.org/packages/affyILM/"
-    url      = "https://git.bioconductor.org/packages/affyILM"
+    git      = "https://git.bioconductor.org/packages/affyILM.git"
 
-    version('1.28.0', git='https://git.bioconductor.org/packages/affyILM', commit='307bee3ebc599e0ea4a1d6fa8d5511ccf8bef7de')
+    version('1.28.0', commit='307bee3ebc599e0ea4a1d6fa8d5511ccf8bef7de')
 
     depends_on('r@3.4.0:3.4.9', when='@1.28.0')
     depends_on('r-gcrma', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-affyio/package.py b/var/spack/repos/builtin/packages/r-affyio/package.py
index ed1f9ff265..973fdd757c 100644
--- a/var/spack/repos/builtin/packages/r-affyio/package.py
+++ b/var/spack/repos/builtin/packages/r-affyio/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,9 +12,9 @@ class RAffyio(RPackage):
        formats."""
 
     homepage = "https://bioconductor.org/packages/affyio/"
-    url      = "https://git.bioconductor.org/packages/affyio"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/affyio.git"
+
+    version('1.46.0', commit='977597f2772e08273d86579486f452170566c880')
 
-    version('1.46.0', git='https://git.bioconductor.org/packages/affyio', commit='977597f2772e08273d86579486f452170566c880')
     depends_on('r-zlibbioc', type=('build', 'run'))
     depends_on('r@3.4.0:3.4.9', when='@1.46.0')
diff --git a/var/spack/repos/builtin/packages/r-affypdnn/package.py b/var/spack/repos/builtin/packages/r-affypdnn/package.py
index 6fa1136468..f7cfaa20a6 100644
--- a/var/spack/repos/builtin/packages/r-affypdnn/package.py
+++ b/var/spack/repos/builtin/packages/r-affypdnn/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,9 @@ class RAffypdnn(RPackage):
     described by Li Zhang et al."""
 
     homepage = "https://www.bioconductor.org/packages/affypdnn/"
-    url      = "https://git.bioconductor.org/packages/affypdnn"
+    git      = "https://git.bioconductor.org/packages/affypdnn.git"
 
-    version('1.50.0', git='https://git.bioconductor.org/packages/affypdnn', commit='97ff68e9f51f31333c0330435ea23b212b3ed18a')
+    version('1.50.0', commit='97ff68e9f51f31333c0330435ea23b212b3ed18a')
 
     depends_on('r@3.4.0:3.4.9', when='@1.50.0')
     depends_on('r-affy', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-affyplm/package.py b/var/spack/repos/builtin/packages/r-affyplm/package.py
index f73b7ca19f..1690ce430b 100644
--- a/var/spack/repos/builtin/packages/r-affyplm/package.py
+++ b/var/spack/repos/builtin/packages/r-affyplm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,9 +14,9 @@ class RAffyplm(RPackage):
     PLM based quality assessment tools."""
 
     homepage = "https://www.bioconductor.org/packages/affyPLM/"
-    url      = "https://git.bioconductor.org/packages/affyPLM"
+    git      = "https://git.bioconductor.org/packages/affyPLM.git"
 
-    version('1.52.1', git='https://git.bioconductor.org/packages/affyPLM', commit='e8613a6018c4ee58045df6bf19128844f50a1f43')
+    version('1.52.1', commit='e8613a6018c4ee58045df6bf19128844f50a1f43')
 
     depends_on('r@3.4.0:3.4.9', when='@1.52.1')
     depends_on('r-biocgenerics', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-affyqcreport/package.py b/var/spack/repos/builtin/packages/r-affyqcreport/package.py
index a7b9f2aa3c..cb78a3d887 100644
--- a/var/spack/repos/builtin/packages/r-affyqcreport/package.py
+++ b/var/spack/repos/builtin/packages/r-affyqcreport/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,9 +12,9 @@ class RAffyqcreport(RPackage):
     quality of a set of arrays in an AffyBatch object."""
 
     homepage = "https://www.bioconductor.org/packages/affyQCReport/"
-    url      = "https://git.bioconductor.org/packages/affyQCReport"
+    git      = "https://git.bioconductor.org/packages/affyQCReport.git"
 
-    version('1.54.0', git='https://git.bioconductor.org/packages/affyQCReport', commit='5572e9981dc874b78b4adebf58080cac3fbb69e1')
+    version('1.54.0', commit='5572e9981dc874b78b4adebf58080cac3fbb69e1')
 
     depends_on('r@3.4.0:3.4.9', when='@1.54.0')
     depends_on('r-biobase', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-affyrnadegradation/package.py b/var/spack/repos/builtin/packages/r-affyrnadegradation/package.py
index 0a5d5f315c..b3cbabcc12 100644
--- a/var/spack/repos/builtin/packages/r-affyrnadegradation/package.py
+++ b/var/spack/repos/builtin/packages/r-affyrnadegradation/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,9 +15,9 @@ class RAffyrnadegradation(RPackage):
     by RNA degradation."""
 
     homepage = "https://www.bioconductor.org/packages/AffyRNADegradation/"
-    url      = "https://git.bioconductor.org/packages/AffyRNADegradation"
+    git      = "https://git.bioconductor.org/packages/AffyRNADegradation.git"
 
-    version('1.22.0', git='https://git.bioconductor.org/packages/AffyRNADegradation', commit='0fa78f8286494711a239ded0ba587b0de47c15d3')
+    version('1.22.0', commit='0fa78f8286494711a239ded0ba587b0de47c15d3')
 
     depends_on('r@3.4.0:3.4.9', when='@1.22.0')
     depends_on('r-affy', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-agdex/package.py b/var/spack/repos/builtin/packages/r-agdex/package.py
index 8abec46a01..85275712fb 100644
--- a/var/spack/repos/builtin/packages/r-agdex/package.py
+++ b/var/spack/repos/builtin/packages/r-agdex/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,9 @@ class RAgdex(RPackage):
     for cross-species genomics."""
 
     homepage = "http://bioconductor.org/packages/AGDEX/"
-    url      = "https://git.bioconductor.org/packages/AGDEX"
+    git      = "https://git.bioconductor.org/packages/AGDEX.git"
 
-    version('1.24.0', git='https://git.bioconductor.org/packages/AGDEX', commit='29c6bcfa6919a5c6d8bcb36b44e75145a60ce7b5')
+    version('1.24.0', commit='29c6bcfa6919a5c6d8bcb36b44e75145a60ce7b5')
 
     depends_on('r@3.4.0:3.4.9', when='@1.24.0')
     depends_on('r-biobase', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-agilp/package.py b/var/spack/repos/builtin/packages/r-agilp/package.py
index 15aba2cdce..9b90fca17a 100644
--- a/var/spack/repos/builtin/packages/r-agilp/package.py
+++ b/var/spack/repos/builtin/packages/r-agilp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,8 +10,8 @@ class RAgilp(RPackage):
     """Agilent expression array processing package."""
 
     homepage = "http://bioconductor.org/packages/agilp/"
-    url      = "https://git.bioconductor.org/packages/agilp"
+    git      = "https://git.bioconductor.org/packages/agilp.git"
 
-    version('3.8.0', git='https://git.bioconductor.org/packages/agilp', commit='c772a802af1b4c0741f2edd78053a0425160ea53')
+    version('3.8.0', commit='c772a802af1b4c0741f2edd78053a0425160ea53')
 
     depends_on('r@3.4.0:3.4.9', when='@3.8.0')
diff --git a/var/spack/repos/builtin/packages/r-agimicrorna/package.py b/var/spack/repos/builtin/packages/r-agimicrorna/package.py
index b672f784bc..c509634f77 100644
--- a/var/spack/repos/builtin/packages/r-agimicrorna/package.py
+++ b/var/spack/repos/builtin/packages/r-agimicrorna/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,9 @@ class RAgimicrorna(RPackage):
     """Processing and Analysis of Agilent microRNA data."""
 
     homepage = "https://www.bioconductor.org/packages/AgiMicroRna/"
-    url      = "https://git.bioconductor.org/packages/AgiMicroRna"
+    git      = "https://git.bioconductor.org/packages/AgiMicroRna.git"
 
-    version('2.26.0', git='https://git.bioconductor.org/packages/AgiMicroRna', commit='6dd74bae47986f2a23d03e3f1f9f78f701dd8053')
+    version('2.26.0', commit='6dd74bae47986f2a23d03e3f1f9f78f701dd8053')
 
     depends_on('r@3.4.0:3.4.9', when='@2.26.0')
     depends_on('r-affycoretools', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-aims/package.py b/var/spack/repos/builtin/packages/r-aims/package.py
index 4a724804ae..9d87e99052 100644
--- a/var/spack/repos/builtin/packages/r-aims/package.py
+++ b/var/spack/repos/builtin/packages/r-aims/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,9 +14,9 @@ class RAims(RPackage):
     as well as on dataset of gene expression data."""
 
     homepage = "http://bioconductor.org/packages/AIMS/"
-    url      = "https://git.bioconductor.org/packages/AIMS"
+    git      = "https://git.bioconductor.org/packages/AIMS.git"
 
-    version('1.8.0', git='https://git.bioconductor.org/packages/AIMS', commit='86b866c20e191047492c51b43e3f73082c3f8357')
+    version('1.8.0', commit='86b866c20e191047492c51b43e3f73082c3f8357')
 
     depends_on('r@3.4.0:3.4.9', when='@1.8.0')
     depends_on('r-e1071', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-aldex2/package.py b/var/spack/repos/builtin/packages/r-aldex2/package.py
index ab046f82ec..1a1912a32e 100644
--- a/var/spack/repos/builtin/packages/r-aldex2/package.py
+++ b/var/spack/repos/builtin/packages/r-aldex2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,9 +20,9 @@ class RAldex2(RPackage):
     and fdr values calculated by the Benjamini Hochberg correction."""
 
     homepage = "http://bioconductor.org/packages/ALDEx2/"
-    url      = "https://git.bioconductor.org/packages/ALDEx2"
+    git      = "https://git.bioconductor.org/packages/ALDEx2.git"
 
-    version('1.8.0', git='https://git.bioconductor.org/packages/ALDEx2', commit='24104824ca2402ad4f54fbf1ed9cee7fac2aaaf1')
+    version('1.8.0', commit='24104824ca2402ad4f54fbf1ed9cee7fac2aaaf1')
 
     depends_on('r@3.4.0:3.4.9', when='@1.8.0')
     depends_on('r-s4vectors', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-allelicimbalance/package.py b/var/spack/repos/builtin/packages/r-allelicimbalance/package.py
index f7e95e519c..6e5b2a4088 100644
--- a/var/spack/repos/builtin/packages/r-allelicimbalance/package.py
+++ b/var/spack/repos/builtin/packages/r-allelicimbalance/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,9 @@ class RAllelicimbalance(RPackage):
     investigation using RNA-seq data."""
 
     homepage = "http://bioconductor.org/packages/AllelicImbalance/"
-    url      = "https://git.bioconductor.org/packages/AllelicImbalance"
+    git      = "https://git.bioconductor.org/packages/AllelicImbalance.git"
 
-    version('1.14.0', git='https://git.bioconductor.org/packages/AllelicImbalance', commit='35958534945819baafde0e13d1eb4d05a514142c')
+    version('1.14.0', commit='35958534945819baafde0e13d1eb4d05a514142c')
 
     depends_on('r@3.4.0:3.4.9', when='@1.14.0')
     depends_on('r-genomicranges', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-alpine/package.py b/var/spack/repos/builtin/packages/r-alpine/package.py
index 9d28ec66e7..2d3666642e 100644
--- a/var/spack/repos/builtin/packages/r-alpine/package.py
+++ b/var/spack/repos/builtin/packages/r-alpine/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,9 @@ class RAlpine(RPackage):
     transcript abundance estimation."""
 
     homepage = "http://bioconductor.org/packages/alpine/"
-    url      = "https://git.bioconductor.org/packages/alpine"
+    git      = "https://git.bioconductor.org/packages/alpine.git"
 
-    version('1.2.0', git='https://git.bioconductor.org/packages/alpine', commit='896872e6071769e1ac2cf786974edb8b875c45eb')
+    version('1.2.0', commit='896872e6071769e1ac2cf786974edb8b875c45eb')
 
     depends_on('r@3.4.0:3.4.9', when='@1.2.0')
     depends_on('r-biostrings', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-als/package.py b/var/spack/repos/builtin/packages/r-als/package.py
index 12f1905614..9102e21b32 100644
--- a/var/spack/repos/builtin/packages/r-als/package.py
+++ b/var/spack/repos/builtin/packages/r-als/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-alsace/package.py b/var/spack/repos/builtin/packages/r-alsace/package.py
index 0573dde123..cc6eb65902 100644
--- a/var/spack/repos/builtin/packages/r-alsace/package.py
+++ b/var/spack/repos/builtin/packages/r-alsace/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,9 +16,9 @@ class RAlsace(RPackage):
     retention time correction, etcetera."""
 
     homepage = "https://www.bioconductor.org/packages/alsace/"
-    url      = "https://git.bioconductor.org/packages/alsace"
+    git      = "https://git.bioconductor.org/packages/alsace.git"
 
-    version('1.12.0', git='https://git.bioconductor.org/packages/alsace', commit='1364c65bbff05786d05c02799fd44fd57748fae3')
+    version('1.12.0', commit='1364c65bbff05786d05c02799fd44fd57748fae3')
 
     depends_on('r-als', type=('build', 'run'))
     depends_on('r-ptw', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-altcdfenvs/package.py b/var/spack/repos/builtin/packages/r-altcdfenvs/package.py
index 8f9770d68a..9853b0cda8 100644
--- a/var/spack/repos/builtin/packages/r-altcdfenvs/package.py
+++ b/var/spack/repos/builtin/packages/r-altcdfenvs/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,9 @@ class RAltcdfenvs(RPackage):
     """Convenience data structures and functions to handle cdfenvs."""
 
     homepage = "https://www.bioconductor.org/packages/altcdfenvs/"
-    url      = "https://git.bioconductor.org/packages/altcdfenvs"
+    git      = "https://git.bioconductor.org/packages/altcdfenvs.git"
 
-    version('2.38.0', git='https://git.bioconductor.org/packages/altcdfenvs', commit='2e92b9da76dbe50af4bf33c525134e29e9809291')
+    version('2.38.0', commit='2e92b9da76dbe50af4bf33c525134e29e9809291')
 
     depends_on('r@3.4.0:3.4.9', when='@2.38.0')
     depends_on('r-biocgenerics', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-amap/package.py b/var/spack/repos/builtin/packages/r-amap/package.py
new file mode 100644
index 0000000000..d783a8220a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-amap/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RAmap(RPackage):
+    """Tools for Clustering and Principal Component Analysis
+       (With robust methods, and parallelized functions)."""
+
+    homepage = "http://mulcyber.toulouse.inra.fr/projects/amap/"
+    url      = "https://cran.rstudio.com/src/contrib/amap_0.8-16.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/amap/"
+
+    version('0.8-16', sha256='d3775ad7f660581f7d2f070e426be95ae0d6743622943e6f5491988e5217d4e2')
+
+    depends_on('r@2.10.0:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-ampliqueso/package.py b/var/spack/repos/builtin/packages/r-ampliqueso/package.py
index a703caf19e..ec0ec337e1 100644
--- a/var/spack/repos/builtin/packages/r-ampliqueso/package.py
+++ b/var/spack/repos/builtin/packages/r-ampliqueso/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,9 @@ class RAmpliqueso(RPackage):
     amplicon sequencing panels, such as AmpliSeq."""
 
     homepage = "https://www.bioconductor.org/packages/ampliQueso/"
-    url      = "https://git.bioconductor.org/packages/ampliQueso"
+    git      = "https://git.bioconductor.org/packages/ampliQueso.git"
 
-    version('1.14.0', git='https://git.bioconductor.org/packages/ampliQueso', commit='9a4c26ec594171279aba8ab7fe59c4a2ea09b06b')
+    version('1.14.0', commit='9a4c26ec594171279aba8ab7fe59c4a2ea09b06b')
 
     depends_on('r@3.4.0:3.4.9', when='@1.14.0')
     depends_on('r-samr', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-analysispageserver/package.py b/var/spack/repos/builtin/packages/r-analysispageserver/package.py
index 4245dbed56..f37f3b0daa 100644
--- a/var/spack/repos/builtin/packages/r-analysispageserver/package.py
+++ b/var/spack/repos/builtin/packages/r-analysispageserver/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,9 @@ class RAnalysispageserver(RPackage):
     of customizable R analyses via the web."""
 
     homepage = "https://www.bioconductor.org/packages/AnalysisPageServer/"
-    url      = "https://git.bioconductor.org/packages/AnalysisPageServer"
+    git      = "https://git.bioconductor.org/packages/AnalysisPageServer.git"
 
-    version('1.10.0', git='https://git.bioconductor.org/packages/AnalysisPageServer', commit='876c87073be116fa15a1afdd407e21152eb80d50')
+    version('1.10.0', commit='876c87073be116fa15a1afdd407e21152eb80d50')
 
     depends_on('r@3.4.0:3.4.9', when='@1.10.0')
     depends_on('r-log4r', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-anaquin/package.py b/var/spack/repos/builtin/packages/r-anaquin/package.py
index 678084df09..2cf761c2b0 100644
--- a/var/spack/repos/builtin/packages/r-anaquin/package.py
+++ b/var/spack/repos/builtin/packages/r-anaquin/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,9 +14,9 @@ class RAnaquin(RPackage):
     modelling and visualization of spike-in controls."""
 
     homepage = "https://www.bioconductor.org/packages/Anaquin/"
-    url      = "https://git.bioconductor.org/packages/Anaquin"
+    git      = "https://git.bioconductor.org/packages/Anaquin.git"
 
-    version('1.2.0', git='https://git.bioconductor.org/packages/Anaquin', commit='584d1970cc9dc1d354f9a6d7c1306bd7e8567119')
+    version('1.2.0', commit='584d1970cc9dc1d354f9a6d7c1306bd7e8567119')
 
     depends_on('r@3.4.0:3.4.9', when='@1.2.0')
     depends_on('r-deseq2', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-aneufinder/package.py b/var/spack/repos/builtin/packages/r-aneufinder/package.py
index 6be07235a1..4123db13c5 100644
--- a/var/spack/repos/builtin/packages/r-aneufinder/package.py
+++ b/var/spack/repos/builtin/packages/r-aneufinder/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,9 @@ class RAneufinder(RPackage):
     export and analysis from whole-genome single cell sequencing data."""
 
     homepage = "https://www.bioconductor.org/packages/AneuFinder/"
-    url      = "https://git.bioconductor.org/packages/AneuFinder"
+    git      = "https://git.bioconductor.org/packages/AneuFinder.git"
 
-    version('1.4.0', git='https://git.bioconductor.org/packages/AneuFinder', commit='e5bdf4d5e4f84ee5680986826ffed636ed853b8e')
+    version('1.4.0', commit='e5bdf4d5e4f84ee5680986826ffed636ed853b8e')
 
     depends_on('r@3.4.0:3.4.9', when='@1.4.0')
     depends_on('r-genomicranges', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-aneufinderdata/package.py b/var/spack/repos/builtin/packages/r-aneufinderdata/package.py
index a61e7cd4cd..dde20609af 100644
--- a/var/spack/repos/builtin/packages/r-aneufinderdata/package.py
+++ b/var/spack/repos/builtin/packages/r-aneufinderdata/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,8 +11,8 @@ class RAneufinderdata(RPackage):
     purposes in the AneuFinder package."""
 
     homepage = "https://www.bioconductor.org/packages/AneuFinderData/"
-    url      = "https://git.bioconductor.org/packages/AneuFinderData"
+    git      = "https://git.bioconductor.org/packages/AneuFinderData.git"
 
-    version('1.4.0', git='https://git.bioconductor.org/packages/AneuFinderData', commit='55c8807ee4a37a2eb6d0defafaf843f980b22c40')
+    version('1.4.0', commit='55c8807ee4a37a2eb6d0defafaf843f980b22c40')
 
     depends_on('r@3.4.0:3.4.9', when='@1.4.0')
diff --git a/var/spack/repos/builtin/packages/r-animation/package.py b/var/spack/repos/builtin/packages/r-animation/package.py
new file mode 100644
index 0000000000..c0d592c518
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-animation/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RAnimation(RPackage):
+    """Provides functions for animations in statistics, covering topics
+    in probability theory, mathematical statistics, multivariate statistics,
+    non-parametric statistics, sampling survey, linear models, time series,
+    computational statistics, data mining and machine learning.
+    These functions maybe helpful in teaching statistics and data analysis."""
+
+    homepage = "https://cran.r-project.org/package=animation"
+    url = "https://cran.r-project.org/src/contrib/animation_2.5.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/animation"
+
+    version('2.5', sha256='b232fef1b318c79710e5e1923d87baba4c85ffe2c77ddb188130e0911d8cb55f')
+
+    extends('r')
+    depends_on('r', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-annaffy/package.py b/var/spack/repos/builtin/packages/r-annaffy/package.py
index f4bfd87d3e..af47b5f193 100644
--- a/var/spack/repos/builtin/packages/r-annaffy/package.py
+++ b/var/spack/repos/builtin/packages/r-annaffy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 #
 from spack import *
@@ -35,9 +16,9 @@ class RAnnaffy(RPackage):
     using various criteria."""
 
     homepage = "https://www.bioconductor.org/packages/annaffy/"
-    url      = "https://git.bioconductor.org/packages/annaffy"
+    git      = "https://git.bioconductor.org/packages/annaffy.git"
 
-    version('1.48.0', git='https://git.bioconductor.org/packages/annaffy', commit='89a03c64ac9df5d963ed60b87893a3fffa6798a0')
+    version('1.48.0', commit='89a03c64ac9df5d963ed60b87893a3fffa6798a0')
 
     depends_on('r@3.4.0:3.4.9', when='@1.48.0')
     depends_on('r-biobase', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-annotate/package.py b/var/spack/repos/builtin/packages/r-annotate/package.py
index 7c49849f01..09e367cb35 100644
--- a/var/spack/repos/builtin/packages/r-annotate/package.py
+++ b/var/spack/repos/builtin/packages/r-annotate/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,12 +10,14 @@ class RAnnotate(RPackage):
     """Using R enviroments for annotation."""
 
     homepage = "https://www.bioconductor.org/packages/annotate/"
-    url      = "https://git.bioconductor.org/packages/annotate"
-    list_url = homepage
-    version('1.54.0', git='https://git.bioconductor.org/packages/annotate', commit='860cc5b696795a31b18beaf4869f9c418d74549e')
+    git      = "https://git.bioconductor.org/packages/annotate.git"
+
+    version('1.58.0', commit='d1b5dd5feb8793f4f816d9a4aecbebb5ec7df7bc')
+    version('1.54.0', commit='860cc5b696795a31b18beaf4869f9c418d74549e')
 
-    depends_on('r@3.4.0:3.4.9', when='@1.54.0')
     depends_on('r-annotationdbi', type=('build', 'run'))
     depends_on('r-xml', type=('build', 'run'))
     depends_on('r-rcurl', type=('build', 'run'))
     depends_on('r-xtable', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@1.54.0', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@1.58.0', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-annotationdbi/package.py b/var/spack/repos/builtin/packages/r-annotationdbi/package.py
index 2b55b95a63..d6a66236ce 100644
--- a/var/spack/repos/builtin/packages/r-annotationdbi/package.py
+++ b/var/spack/repos/builtin/packages/r-annotationdbi/package.py
@@ -1,29 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-#
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,11 +11,13 @@ class RAnnotationdbi(RPackage):
     annotation data packages using SQLite data storage."""
 
     homepage = "https://www.bioconductor.org/packages/AnnotationDbi/"
-    url      = "https://git.bioconductor.org/packages/AnnotationDbi"
-    list_url = homepage
-    version('1.38.2', git='https://git.bioconductor.org/packages/AnnotationDbi', commit='67d46facba8c15fa5f0eb47c4e39b53dbdc67c36')
+    git      = "https://git.bioconductor.org/packages/AnnotationDbi.git"
+
+    version('1.42.1', commit='71085b47ea2e1ef929bebe8b17eb8e8a573f98e3')
+    version('1.38.2', commit='67d46facba8c15fa5f0eb47c4e39b53dbdc67c36')
 
-    depends_on('r@3.4.0:3.4.9', when='@1.38.2')
+    depends_on('r@3.4.0:3.4.9', when='@1.38.2', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@1.42.1', type=('build', 'run'))
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-biobase', type=('build', 'run'))
     depends_on('r-iranges', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-annotationfilter/package.py b/var/spack/repos/builtin/packages/r-annotationfilter/package.py
index ff82f8a3c0..b6c39cac1e 100644
--- a/var/spack/repos/builtin/packages/r-annotationfilter/package.py
+++ b/var/spack/repos/builtin/packages/r-annotationfilter/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,10 +13,9 @@ class RAnnotationfilter(RPackage):
        packages."""
 
     homepage = "https://bioconductor.org/packages/AnnotationFilter/"
-    url      = "https://git.bioconductor.org/packages/AnnotationFilter"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/AnnotationFilter.git"
 
-    version('1.0.0', git='https://git.bioconductor.org/packages/AnnotationFilter', commit='a9f79b26defe3021eea60abe16ce1fa379813ec9')
+    version('1.0.0', commit='a9f79b26defe3021eea60abe16ce1fa379813ec9')
 
     depends_on('r-genomicranges', type=('build', 'run'))
     depends_on('r-lazyeval', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-annotationforge/package.py b/var/spack/repos/builtin/packages/r-annotationforge/package.py
index 57a69306c3..41dfa85c25 100644
--- a/var/spack/repos/builtin/packages/r-annotationforge/package.py
+++ b/var/spack/repos/builtin/packages/r-annotationforge/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,9 +12,9 @@ class RAnnotationforge(RPackage):
     with AnnotationDbi."""
 
     homepage = "https://www.bioconductor.org/packages/AnnotationForge/"
-    url      = "https://git.bioconductor.org/packages/AnnotationForge"
+    git      = "https://git.bioconductor.org/packages/AnnotationForge.git"
 
-    version('1.18.2', git='https://git.bioconductor.org/packages/AnnotationForge', commit='44ca3d4ef9e9825c14725ffdbbaa57ea059532e1')
+    version('1.18.2', commit='44ca3d4ef9e9825c14725ffdbbaa57ea059532e1')
 
     depends_on('r@3.4.0:3.4.9', when='@1.18.2')
     depends_on('r-biocgenerics', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-annotationhub/package.py b/var/spack/repos/builtin/packages/r-annotationhub/package.py
index ccda18a203..92fe597a94 100644
--- a/var/spack/repos/builtin/packages/r-annotationhub/package.py
+++ b/var/spack/repos/builtin/packages/r-annotationhub/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,10 +17,9 @@ class RAnnotationhub(RPackage):
        quick and reproducible access."""
 
     homepage = "https://bioconductor.org/packages/AnnotationHub/"
-    url      = "https://git.bioconductor.org/packages/AnnotationHub"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/AnnotationHub.git"
 
-    version('2.8.3', git='https://git.bioconductor.org/packages/AnnotationHub', commit='8aa9c64262a8d708d2bf1c82f82dfc3d7d4ccc0c')
+    version('2.8.3', commit='8aa9c64262a8d708d2bf1c82f82dfc3d7d4ccc0c')
 
     depends_on('r-rsqlite', type=('build', 'run'))
     depends_on('r-biocinstaller', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-ape/package.py b/var/spack/repos/builtin/packages/r-ape/package.py
index 17a0f0ff23..63f1dfed6b 100644
--- a/var/spack/repos/builtin/packages/r-ape/package.py
+++ b/var/spack/repos/builtin/packages/r-ape/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -46,6 +27,10 @@ class RApe(RPackage):
     url      = "https://cran.r-project.org/src/contrib/ape_4.1.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/ape"
 
+    version('5.0', '82fd2786a502f070ca020797f7b19fa4')
     version('4.1', 'a9ed416d6d172d4b9682556cf692d7c2')
 
     depends_on('r@3.2:')
+    depends_on('r-nlme', type=('build', 'run'))
+    depends_on('r-lattice', type=('build', 'run'))
+    depends_on('r-rcpp', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-argparse/package.py b/var/spack/repos/builtin/packages/r-argparse/package.py
new file mode 100644
index 0000000000..c722eae792
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-argparse/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RArgparse(RPackage):
+    """A command line parser to be used with Rscript to write "#!"
+       shebang scripts that gracefully accept positional and optional
+       arguments and automatically generate usage."""
+
+    homepage = "https://github.com/trevorld/argparse"
+    url      = "https://cran.r-project.org/src/contrib/argparse_1.1.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/argparse"
+
+    version('1.1.1', sha256='441449f0816411a868fd1b15cf4b2bc45931bbd4b67d6592dbe48875905cf93b')
+
+    depends_on('r-proto@1:', type=('build', 'run'))
+    depends_on('r-findpython', type=('build', 'run'))
+    depends_on('r-getopt', type=('build', 'run'))
+    depends_on('r-jsonlite', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-assertthat/package.py b/var/spack/repos/builtin/packages/r-assertthat/package.py
index 37e0424d1a..331e13d887 100644
--- a/var/spack/repos/builtin/packages/r-assertthat/package.py
+++ b/var/spack/repos/builtin/packages/r-assertthat/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-backports/package.py b/var/spack/repos/builtin/packages/r-backports/package.py
index 02c0c6fc1b..97303b92da 100644
--- a/var/spack/repos/builtin/packages/r-backports/package.py
+++ b/var/spack/repos/builtin/packages/r-backports/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-bamsignals/package.py b/var/spack/repos/builtin/packages/r-bamsignals/package.py
index 29a7fda80d..78310f5f4c 100644
--- a/var/spack/repos/builtin/packages/r-bamsignals/package.py
+++ b/var/spack/repos/builtin/packages/r-bamsignals/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,9 +13,9 @@ class RBamsignals(RPackage):
     profiles. It also handles paired-end data."""
 
     homepage = "https://www.bioconductor.org/packages/bamsignals/"
-    url      = "https://git.bioconductor.org/packages/bamsignals"
+    git      = "https://git.bioconductor.org/packages/bamsignals.git"
 
-    version('1.8.0', git='https://git.bioconductor.org/packages/bamsignals', commit='b123b83e8e026c9ec91209d4498aff3e95a5de23')
+    version('1.8.0', commit='b123b83e8e026c9ec91209d4498aff3e95a5de23')
 
     depends_on('r@3.4.0:3.4.9', when='@1.8.0')
     depends_on('r-biocgenerics', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-base64/package.py b/var/spack/repos/builtin/packages/r-base64/package.py
index 6a693e12a7..6a599a62f0 100644
--- a/var/spack/repos/builtin/packages/r-base64/package.py
+++ b/var/spack/repos/builtin/packages/r-base64/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-base64enc/package.py b/var/spack/repos/builtin/packages/r-base64enc/package.py
index 3566baab7a..7424fefe8f 100644
--- a/var/spack/repos/builtin/packages/r-base64enc/package.py
+++ b/var/spack/repos/builtin/packages/r-base64enc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-bbmisc/package.py b/var/spack/repos/builtin/packages/r-bbmisc/package.py
new file mode 100644
index 0000000000..f8cee5cec6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-bbmisc/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RBbmisc(RPackage):
+    """Miscellaneous helper functions for and from B. Bischl and some other
+       guys, mainly for package development."""
+
+    homepage = "https://github.com/berndbischl/BBmisc"
+    url      = "https://cran.r-project.org/src/contrib/BBmisc_1.11.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/BBmisc"
+
+    version('1.11', '681642628037406beb6088d5f773473d')
+
+    depends_on('r-checkmate@1.8.0:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-beanplot/package.py b/var/spack/repos/builtin/packages/r-beanplot/package.py
index 3ddb95f59e..34760038fb 100644
--- a/var/spack/repos/builtin/packages/r-beanplot/package.py
+++ b/var/spack/repos/builtin/packages/r-beanplot/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-bh/package.py b/var/spack/repos/builtin/packages/r-bh/package.py
index bcf4f600a6..54ed774931 100644
--- a/var/spack/repos/builtin/packages/r-bh/package.py
+++ b/var/spack/repos/builtin/packages/r-bh/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-biasedurn/package.py b/var/spack/repos/builtin/packages/r-biasedurn/package.py
new file mode 100644
index 0000000000..258788ebdd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-biasedurn/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RBiasedurn(RPackage):
+    """Statistical models of biased sampling in the form of univariate and
+       multivariate noncentral hypergeometric distributions, including
+       Wallenius' noncentral hypergeometric distribution and Fisher's
+       noncentral hypergeometric distribution (also called extended
+       hypergeometric distribution). See vignette("UrnTheory") for
+       explanation of these distributions."""
+
+    homepage = "http://www.agner.org/random/"
+    url      = "https://cran.rstudio.com/src/contrib/BiasedUrn_1.07.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/BiasedUrn/"
+
+    version('1.07', sha256='2377c2e59d68e758a566452d7e07e88663ae61a182b9ee455d8b4269dda3228e')
diff --git a/var/spack/repos/builtin/packages/r-bindr/package.py b/var/spack/repos/builtin/packages/r-bindr/package.py
new file mode 100644
index 0000000000..e874ac264f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-bindr/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RBindr(RPackage):
+    """Provides a simple interface for creating active bindings where the
+       bound function accepts additional arguments."""
+
+    homepage = "https://github.com/krlmlr/bindr"
+    url      = "https://cran.r-project.org/src/contrib/bindr_0.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/bindr"
+
+    version('0.1', 'f3897a70cbad2d2981272772fa30bb59')
diff --git a/var/spack/repos/builtin/packages/r-bindrcpp/package.py b/var/spack/repos/builtin/packages/r-bindrcpp/package.py
new file mode 100644
index 0000000000..78d50af84e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-bindrcpp/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RBindrcpp(RPackage):
+    """Provides an easy way to fill an environment with active bindings that
+       call a C++ function."""
+
+    homepage = "https://github.com/krlmlr/bindrcpp"
+    url      = "https://cran.r-project.org/src/contrib/bindrcpp_0.2.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/bindrcpp"
+
+    version('0.2.2', '48130709eba9d133679a0e959e49a7b14acbce4f47c1e15c4ab46bd9e48ae467')
+    version('0.2', '2ed7f19fd9a12587f882d90060e7a343')
+
+    depends_on('r-rcpp', type=('build', 'run'))
+    depends_on('r-bindr', type=('build', 'run'))
+    depends_on('r-plogr', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-biobase/package.py b/var/spack/repos/builtin/packages/r-biobase/package.py
index 035d0ddcad..015522735c 100644
--- a/var/spack/repos/builtin/packages/r-biobase/package.py
+++ b/var/spack/repos/builtin/packages/r-biobase/package.py
@@ -1,40 +1,23 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 from spack import *
 
 
 class RBiobase(RPackage):
     """Functions that are needed by many other packages
- or which replace R functions."""
+    or which replace R functions."""
 
     homepage = "https://www.bioconductor.org/packages/Biobase/"
-    url      = "https://git.bioconductor.org/packages/Biobase"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/Biobase.git"
 
-    version('2.36.2', git='https://git.bioconductor.org/packages/Biobase', commit='15f50912f3fa08ccb15c33b7baebe6b8a59ce075')
+    version('2.40.0', commit='6555edbbcb8a04185ef402bfdea7ed8ac72513a5')
+    version('2.38.0', commit='83f89829e0278ac014b0bc6664e621ac147ba424')
+    version('2.36.2', commit='15f50912f3fa08ccb15c33b7baebe6b8a59ce075')
 
-    depends_on('r-biocgenerics', type=('build', 'run'))
-    depends_on('r@3.4.0:3.4.9', when='@2.36.2')
+    depends_on('r-biocgenerics@0.16.1:', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@2.36.2', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@2.40.0', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-biocgenerics/package.py b/var/spack/repos/builtin/packages/r-biocgenerics/package.py
index 2d101b09e1..b6758db358 100644
--- a/var/spack/repos/builtin/packages/r-biocgenerics/package.py
+++ b/var/spack/repos/builtin/packages/r-biocgenerics/package.py
@@ -1,37 +1,20 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class RBiocgenerics(RPackage):
     """S4 generic functions needed by many Bioconductor packages."""
+
     homepage = "https://www.bioconductor.org/packages/BiocGenerics/"
-    url      = "https://git.bioconductor.org/packages/BiocGenerics"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/BiocGenerics.git"
 
-    version('0.22.1', git='https://git.bioconductor.org/packages/BiocGenerics', commit='9c90bb8926885289d596a81ff318ee3745cbb6ad')
+    version('0.26.0', commit='5b2a6df639e48c3cd53789e0b174aec9dda6b67d')
+    version('0.24.0', commit='3db111e8c1f876267da89f4f0c5406a9d5c31cd1')
+    version('0.22.1', commit='9c90bb8926885289d596a81ff318ee3745cbb6ad')
 
-    depends_on('r@3.4.0:3.4.9', when='@0.22.1')
+    depends_on('r@3.4.0:3.4.9', when='@0.22.1', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@0.26.0', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-biocinstaller/package.py b/var/spack/repos/builtin/packages/r-biocinstaller/package.py
index b2248f87ac..a3cc8e471e 100644
--- a/var/spack/repos/builtin/packages/r-biocinstaller/package.py
+++ b/var/spack/repos/builtin/packages/r-biocinstaller/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,8 @@ class RBiocinstaller(RPackage):
     and (some) github packages."""
 
     homepage = "https://bioconductor.org/packages/BiocInstaller/"
-    url      = "https://git.bioconductor.org/packages/BiocInstaller"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/BiocInstaller.git"
 
-    version('1.26.1', git='https://git.bioconductor.org/packages/BiocInstaller', commit='9049b82a77aefa98e3f8e4dd7068317505d70e98')
+    version('1.26.1', commit='9049b82a77aefa98e3f8e4dd7068317505d70e98')
 
     depends_on('r@3.4.0:3.4.9', when='@1.26.1')
diff --git a/var/spack/repos/builtin/packages/r-biocparallel/package.py b/var/spack/repos/builtin/packages/r-biocparallel/package.py
index 769c8b9b16..37d0b93375 100644
--- a/var/spack/repos/builtin/packages/r-biocparallel/package.py
+++ b/var/spack/repos/builtin/packages/r-biocparallel/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,11 +12,13 @@ class RBiocparallel(RPackage):
        objects."""
 
     homepage = "https://bioconductor.org/packages/BiocParallel/"
-    url      = "https://git.bioconductor.org/packages/BiocParallel"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/BiocParallel.git"
 
-    version('1.10.1', git='https://git.bioconductor.org/packages/BiocParallel', commit='a76c58cf99fd585ba5ea33065649e68f1afe0a7d')
+    version('1.14.2', commit='1d5a44960b19e9dbbca04c7290c8c58b0a7fc299')
+    version('1.10.1', commit='a76c58cf99fd585ba5ea33065649e68f1afe0a7d')
 
     depends_on('r-futile-logger', type=('build', 'run'))
     depends_on('r-snow', type=('build', 'run'))
-    depends_on('r@3.4.0:3.4.9', when='@1.10.1')
+    depends_on('r-bh', type=('build', 'link', 'run'), when='@1.14.2:')
+    depends_on('r@3.4.0:3.4.9', when='@1.10.1', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@1.14.2', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-biocstyle/package.py b/var/spack/repos/builtin/packages/r-biocstyle/package.py
new file mode 100644
index 0000000000..411b2549fa
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-biocstyle/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RBiocstyle(RPackage):
+    """Provides standard formatting styles for Bioconductor PDF and HTML
+    documents. Package vignettes illustrate use and functionality."""
+
+    homepage = "https://www.bioconductor.org/packages/BiocStyle/"
+    git      = "https://git.bioconductor.org/packages/BiocStyle.git"
+
+    version('2.4.1', commit='ef10764b68ac23a3a7a8ec3b6a6436187309c138')
+
+    depends_on('r-bookdown', type=('build', 'run'))
+    depends_on('r-knitr@1.12:', type=('build', 'run'))
+    depends_on('r-rmarkdown@1.2:', type=('build', 'run'))
+    depends_on('r-yaml', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@2.4.1')
diff --git a/var/spack/repos/builtin/packages/r-biom-utils/package.py b/var/spack/repos/builtin/packages/r-biom-utils/package.py
new file mode 100644
index 0000000000..7bd3d2471d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-biom-utils/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RBiomUtils(RPackage):
+    """Provides utilities to facilitate import, export and computation with
+    the BIOM (Biological Observation Matrix) format (http://biom-format.org).
+    """
+
+    homepage = "https://github.com/braithwaite/BIOM.utils/"
+    url      = "https://cran.r-project.org/src/contrib/BIOM.utils_0.9.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/biom/"
+
+    version('0.9', sha256='e7024469fb38e275aa78fbfcce15b9a7661317f632a7e9b8124695e076839375')
+
+    depends_on('r@3:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-biomart/package.py b/var/spack/repos/builtin/packages/r-biomart/package.py
index d9c15151bd..b74a6794ba 100644
--- a/var/spack/repos/builtin/packages/r-biomart/package.py
+++ b/var/spack/repos/builtin/packages/r-biomart/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,11 +21,17 @@ class RBiomart(RPackage):
        online queries from gene annotation to database mining."""
 
     homepage = "https://bioconductor.org/packages/biomaRt/"
-    url      = "https://git.bioconductor.org/packages/biomaRt"
+    git      = "https://git.bioconductor.org/packages/biomaRt.git"
 
-    version('2.32.1', git='https://git.bioconductor.org/packages/biomaRt', commit='f84d74424fa599f6d08f8db4612ca09914a9087f')
+    version('2.36.1', commit='5634e57e20199f9dc1f8b927eb3893143fc02f4f')
+    version('2.34.2', commit='a7030915fbc6120cc6812aefdedba423a207459b')
+    version('2.32.1', commit='f84d74424fa599f6d08f8db4612ca09914a9087f')
 
     depends_on('r-xml', type=('build', 'run'))
     depends_on('r-rcurl', type=('build', 'run'))
     depends_on('r-annotationdbi', type=('build', 'run'))
-    depends_on('r@3.4.0:3.4.9', when='@2.32.1')
+    depends_on('r-progress', type=('build', 'run'), when='@2.34.2:')
+    depends_on('r-stringr', type=('build', 'run'), when='@2.34.2:')
+    depends_on('r-httr', type=('build', 'run'), when='@2.34.2:')
+    depends_on('r@3.4.0:3.4.9', when='@2.32.1:2.35.9', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@2.36.1', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-biomformat/package.py b/var/spack/repos/builtin/packages/r-biomformat/package.py
new file mode 100644
index 0000000000..29c1d4e75c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-biomformat/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RBiomformat(RPackage):
+    """This is an R package for interfacing with the BIOM format. This
+    package includes basic tools for reading biom-format files, accessing
+    and subsetting data tables from a biom object (which is more complex
+    than a single table), as well as limited support for writing a
+    biom-object back to a biom-format file. The design of this API is
+    intended to match the python API and other tools included with the
+    biom-format project, but with a decidedly "R flavor" that should be
+    familiar to R users. This includes S4 classes and methods, as well
+    as extensions of common core functions/methods."""
+
+    homepage = "https://www.bioconductor.org/packages/biomformat/"
+    git      = "https://git.bioconductor.org/packages/biomformat.git"
+
+    version('1.4.0', commit='83b4b1883bc56ea93a0a6ca90fc1b18712ef0f1a')
+
+    depends_on('r-plyr', type=('build', 'run'))
+    depends_on('r-jsonlite', type=('build', 'run'))
+    depends_on('r-matrix', type=('build', 'run'))
+    depends_on('r-rhdf5', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@1.4.0')
diff --git a/var/spack/repos/builtin/packages/r-biostrings/package.py b/var/spack/repos/builtin/packages/r-biostrings/package.py
index fee137c11b..b6337f29b8 100644
--- a/var/spack/repos/builtin/packages/r-biostrings/package.py
+++ b/var/spack/repos/builtin/packages/r-biostrings/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,13 +12,18 @@ class RBiostrings(RPackage):
        or sets of sequences."""
 
     homepage = "https://bioconductor.org/packages/Biostrings/"
-    url      = "https://git.bioconductor.org/packages/Biostrings"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/Biostrings.git"
 
-    version('2.44.2', git='https://git.bioconductor.org/packages/Biostrings', commit='e4a2b320fb21c5cab3ece7b3c6fecaedfb1e5200')
+    version('2.48.0', commit='aa3599a7d259d658014d087b86d71ab1deb5f12b')
+    version('2.44.2', commit='e4a2b320fb21c5cab3ece7b3c6fecaedfb1e5200')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.15.6:', when='@2.48.0', type=('build', 'run'))
     depends_on('r-s4vectors', type=('build', 'run'))
+    depends_on('r-s4vectors@0.17.25:', when='@2.48.0', type=('build', 'run'))
     depends_on('r-iranges', type=('build', 'run'))
+    depends_on('r-iranges@2.13.24:', when='@2.48.0', type=('build', 'run'))
     depends_on('r-xvector', type=('build', 'run'))
-    depends_on('r@3.4.0:3.4.9', when='@2.44.2')
+    depends_on('r-xvector@0.19.8:', when='@2.48.0', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@2.44.2', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@2.48.0', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-biovizbase/package.py b/var/spack/repos/builtin/packages/r-biovizbase/package.py
index ee87f87625..0535c052d9 100644
--- a/var/spack/repos/builtin/packages/r-biovizbase/package.py
+++ b/var/spack/repos/builtin/packages/r-biovizbase/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,9 +14,9 @@ class RBiovizbase(RPackage):
     and encourages consistency."""
 
     homepage = "http://bioconductor.org/packages/biovizBase/"
-    url      = "https://git.bioconductor.org/packages/biovizBase"
+    git      = "https://git.bioconductor.org/packages/biovizBase.git"
 
-    version('1.24.0', git='https://git.bioconductor.org/packages/biovizBase', commit='ae9cd2ff665b74a8f45ed9c1d17fc0a778b4af6c')
+    version('1.24.0', commit='ae9cd2ff665b74a8f45ed9c1d17fc0a778b4af6c')
 
     depends_on('r@3.4.0:3.4.9', when='@1.24.0')
     depends_on('r-scales', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-bit/package.py b/var/spack/repos/builtin/packages/r-bit/package.py
index aed6d724a6..0d178c10f8 100644
--- a/var/spack/repos/builtin/packages/r-bit/package.py
+++ b/var/spack/repos/builtin/packages/r-bit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-bit64/package.py b/var/spack/repos/builtin/packages/r-bit64/package.py
index 85c631e1ba..a8e8501f2f 100644
--- a/var/spack/repos/builtin/packages/r-bit64/package.py
+++ b/var/spack/repos/builtin/packages/r-bit64/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-bitops/package.py b/var/spack/repos/builtin/packages/r-bitops/package.py
index ec0b45f454..2d61f87d17 100644
--- a/var/spack/repos/builtin/packages/r-bitops/package.py
+++ b/var/spack/repos/builtin/packages/r-bitops/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/r-blob/package.py b/var/spack/repos/builtin/packages/r-blob/package.py
index b77399f775..85e33a1ac4 100644
--- a/var/spack/repos/builtin/packages/r-blob/package.py
+++ b/var/spack/repos/builtin/packages/r-blob/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-bookdown/package.py b/var/spack/repos/builtin/packages/r-bookdown/package.py
new file mode 100644
index 0000000000..94d2ed08fa
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-bookdown/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RBookdown(RPackage):
+    """Output formats and utilities for authoring books and technical
+    documents with R Markdown."""
+
+    homepage = "https://cran.r-project.org/package=bookdown"
+    url      = "https://cran.rstudio.com/src/contrib/bookdown_0.5.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/bookdown"
+
+    version('0.5', '7bad360948e2b22d28397870b9319f17')
+
+    depends_on('r-yaml@2.1.14:', type=('build', 'run'))
+    depends_on('r-rmarkdown@1.5:', type=('build', 'run'))
+    depends_on('r-knitr@1.16:', type=('build', 'run'))
+    depends_on('r-htmltools@0.3.6:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-boot/package.py b/var/spack/repos/builtin/packages/r-boot/package.py
index 2e2802893d..52df4caee5 100644
--- a/var/spack/repos/builtin/packages/r-boot/package.py
+++ b/var/spack/repos/builtin/packages/r-boot/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-brew/package.py b/var/spack/repos/builtin/packages/r-brew/package.py
index e3cf99a095..bf765a6627 100644
--- a/var/spack/repos/builtin/packages/r-brew/package.py
+++ b/var/spack/repos/builtin/packages/r-brew/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-broom/package.py b/var/spack/repos/builtin/packages/r-broom/package.py
new file mode 100644
index 0000000000..2daad5e49e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-broom/package.py
@@ -0,0 +1,30 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RBroom(RPackage):
+    """Convert statistical analysis objects from R into tidy data frames, so
+       that they can more easily be combined, reshaped and otherwise processed
+       with tools like 'dplyr', 'tidyr' and 'ggplot2'. The package provides
+       three S3 generics: tidy, which summarizes a model's statistical
+       findings such as coefficients of a regression; augment, which adds
+       columns to the original data such as predictions, residuals and cluster
+       assignments; and glance, which provides a one-row summary of
+       model-level statistics."""
+
+    homepage = "http://github.com/tidyverse/broom"
+    url      = "https://cran.r-project.org/src/contrib/broom_0.4.2.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/broom"
+    version('0.4.2', '6eabab1f2eaec10f93cf9aa56d6a61de')
+
+    depends_on('r-plyr', type=('build', 'run'))
+    depends_on('r-dplyr', type=('build', 'run'))
+    depends_on('r-tidyr', type=('build', 'run'))
+    depends_on('r-psych', type=('build', 'run'))
+    depends_on('r-stringr', type=('build', 'run'))
+    depends_on('r-reshape2', type=('build', 'run'))
+    depends_on('r-nlme', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-bsgenome/package.py b/var/spack/repos/builtin/packages/r-bsgenome/package.py
index 3758992266..3b2de6aeb7 100644
--- a/var/spack/repos/builtin/packages/r-bsgenome/package.py
+++ b/var/spack/repos/builtin/packages/r-bsgenome/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,18 +11,21 @@ class RBsgenome(RPackage):
        packages."""
 
     homepage = "https://www.bioconductor.org/packages/BSgenome/"
-    url      = "https://git.bioconductor.org/packages/BSgenome"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/BSgenome.git"
 
-    version('1.44.2', git='https://git.bioconductor.org/packages/BSgenome', commit='105b00588a758d5ec7c347a7dff2756aea4516a0')
+    version('1.46.0', commit='bdfbd6d09820993585b8231ddea5e11c99008dc5')
+    version('1.44.2', commit='105b00588a758d5ec7c347a7dff2756aea4516a0')
 
-    depends_on('r-biocgenerics', type=('build', 'run'))
-    depends_on('r-s4vectors', type=('build', 'run'))
-    depends_on('r-iranges', type=('build', 'run'))
-    depends_on('r-genomeinfodb', type=('build', 'run'))
-    depends_on('r-genomicranges', type=('build', 'run'))
-    depends_on('r-biostrings', type=('build', 'run'))
-    depends_on('r-rtracklayer', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.13.8:', type=('build', 'run'))
+    depends_on('r-s4vectors@0.9.36:', type=('build', 'run'))
+    depends_on('r-iranges@2.1.33:', type=('build', 'run'), when='@1.44.2')
+    depends_on('r-iranges@2.11.16:', type=('build', 'run'), when='@1.46.0')
+    depends_on('r-genomeinfodb@1.11.4:', type=('build', 'run'), when='@1.44.2')
+    depends_on('r-genomeinfodb@1.13.1:', type=('build', 'run'), when='@1.46.0')
+    depends_on('r-genomicranges@1.27.6:', type=('build', 'run'), when='@1.44.2')
+    depends_on('r-genomicranges@1.29.14:', type=('build', 'run'), when='@1.46.0')
+    depends_on('r-biostrings@2.35.3:', type=('build', 'run'))
+    depends_on('r-rtracklayer@1.25.8:', type=('build', 'run'))
     depends_on('r-rsamtools', type=('build', 'run'))
     depends_on('r-xvector', type=('build', 'run'))
-    depends_on('r@3.4.0:3.4.9', when='@1.44.2')
+    depends_on('r@3.4.0:3.4.9', when='@1.44.2:')
diff --git a/var/spack/repos/builtin/packages/r-bumphunter/package.py b/var/spack/repos/builtin/packages/r-bumphunter/package.py
index bc36a53485..8b952a7d97 100644
--- a/var/spack/repos/builtin/packages/r-bumphunter/package.py
+++ b/var/spack/repos/builtin/packages/r-bumphunter/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,10 +10,9 @@ class RBumphunter(RPackage):
     """Tools for finding bumps in genomic data"""
 
     homepage = "http://bioconductor.org/packages/bumphunter/"
-    url      = "https://git.bioconductor.org/packages/bumphunter"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/bumphunter.git"
 
-    version('1.16.0', git='https://git.bioconductor.org/packages/bumphunter', commit='1c3ab4d1fd2d75b1586ccef12665960b3602080a')
+    version('1.16.0', commit='1c3ab4d1fd2d75b1586ccef12665960b3602080a')
 
     depends_on('r-s4vectors', type=('build', 'run'))
     depends_on('r-iranges', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-c50/package.py b/var/spack/repos/builtin/packages/r-c50/package.py
index e5ee2d285a..6e4a6f6b77 100644
--- a/var/spack/repos/builtin/packages/r-c50/package.py
+++ b/var/spack/repos/builtin/packages/r-c50/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/r-callr/package.py b/var/spack/repos/builtin/packages/r-callr/package.py
index f69ed861ce..2cee5cd308 100644
--- a/var/spack/repos/builtin/packages/r-callr/package.py
+++ b/var/spack/repos/builtin/packages/r-callr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,5 +13,7 @@ class RCallr(RPackage):
 
     homepage = "https://github.com/MangoTheCat/callr"
     url      = "https://cran.r-project.org/src/contrib/callr_1.0.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/callr/"
 
+    version('3.0.0', sha256='e36361086c65660a6ecbbc09b5ecfcddee6b59caf75e983e48b21d3b8defabe7')
     version('1.0.0', 'd9af99bb95696310fa1e5d1cb7166c91')
diff --git a/var/spack/repos/builtin/packages/r-car/package.py b/var/spack/repos/builtin/packages/r-car/package.py
index aa5a776e37..e02a46e45e 100644
--- a/var/spack/repos/builtin/packages/r-car/package.py
+++ b/var/spack/repos/builtin/packages/r-car/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-caret/package.py b/var/spack/repos/builtin/packages/r-caret/package.py
index 89dcc691ea..95bcf03130 100644
--- a/var/spack/repos/builtin/packages/r-caret/package.py
+++ b/var/spack/repos/builtin/packages/r-caret/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-category/package.py b/var/spack/repos/builtin/packages/r-category/package.py
index 026f0c5987..0b2949ef25 100644
--- a/var/spack/repos/builtin/packages/r-category/package.py
+++ b/var/spack/repos/builtin/packages/r-category/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,9 @@ class RCategory(RPackage):
     """A collection of tools for performing category analysis."""
 
     homepage = "https://www.bioconductor.org/packages/Category/"
-    url      = "https://git.bioconductor.org/packages/Category"
+    git      = "https://git.bioconductor.org/packages/Category.git"
 
-    version('2.42.1', git='https://git.bioconductor.org/packages/Category', commit='382c817a2371671a72f8f949dfb4050361ebabcd')
+    version('2.42.1', commit='382c817a2371671a72f8f949dfb4050361ebabcd')
 
     depends_on('r@3.4.0:3.4.9', when='@2.42.1')
     depends_on('r-biocgenerics', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-catools/package.py b/var/spack/repos/builtin/packages/r-catools/package.py
index 2253b1e0ec..2c19850222 100644
--- a/var/spack/repos/builtin/packages/r-catools/package.py
+++ b/var/spack/repos/builtin/packages/r-catools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/r-cdcfluview/package.py b/var/spack/repos/builtin/packages/r-cdcfluview/package.py
new file mode 100644
index 0000000000..541441c38a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-cdcfluview/package.py
@@ -0,0 +1,32 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RCdcfluview(RPackage):
+    """The 'U.S.' Centers for Disease Control ('CDC') maintains a portal
+    <http://gis.cdc.gov/grasp/fluview/fluportaldashboard.html> for accessing
+    state, regional and national influenza statistics as well as Mortality
+    Surveillance Data. The web interface makes it difficult and time-consuming
+    to select and retrieve influenza data. Tools are provided to access the
+    data provided by the portal's underlying 'API'."""
+
+    homepage = "https://cran.r-project.org/package=cdcfluview"
+    url      = "https://cran.r-project.org/src/contrib/cdcfluview_0.7.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/cdcfluview"
+
+    version('0.7.0', 'd592606fab3da3536f39a15c0fdbcd17')
+
+    depends_on('r-httr', type=('build', 'run'))
+    depends_on('r-dplyr', type=('build', 'run'))
+    depends_on('r-jsonlite', type=('build', 'run'))
+    depends_on('r-sf', type=('build', 'run'))
+    depends_on('r-xml2', type=('build', 'run'))
+    depends_on('r-purrr', type=('build', 'run'))
+    depends_on('r-readr', type=('build', 'run'))
+    depends_on('r-mmwrweek', type=('build', 'run'))
+    depends_on('r-units@0.4-6:', type=('build', 'run'))
+    depends_on('r@3.2.0:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-cellranger/package.py b/var/spack/repos/builtin/packages/r-cellranger/package.py
index 5b57c221f9..ca5e60048d 100644
--- a/var/spack/repos/builtin/packages/r-cellranger/package.py
+++ b/var/spack/repos/builtin/packages/r-cellranger/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-checkmate/package.py b/var/spack/repos/builtin/packages/r-checkmate/package.py
index 278937335a..0aff1514d4 100644
--- a/var/spack/repos/builtin/packages/r-checkmate/package.py
+++ b/var/spack/repos/builtin/packages/r-checkmate/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-checkpoint/package.py b/var/spack/repos/builtin/packages/r-checkpoint/package.py
index 6d3d9cc830..517eed195a 100644
--- a/var/spack/repos/builtin/packages/r-checkpoint/package.py
+++ b/var/spack/repos/builtin/packages/r-checkpoint/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-chemometrics/package.py b/var/spack/repos/builtin/packages/r-chemometrics/package.py
new file mode 100644
index 0000000000..4bf7932e2b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-chemometrics/package.py
@@ -0,0 +1,31 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RChemometrics(RPackage):
+    """R companion to the book "Introduction to Multivariate Statistical Analysis
+    in Chemometrics" written by K. Varmuza and P. Filzmoser (2009)."""
+
+    homepage = "https://cran.r-project.org/web/packages/chemometrics/index.html"
+    url      = "https://cran.r-project.org/src/contrib/chemometrics_1.4.2.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/chemometrics"
+
+    version('1.4.2', '8137b0ca4004add9cc2ea81d2c54427f')
+    version('1.4.1', '1e5a89442bb4a61db0da884eedd74fc2')
+    version('1.3.9', '2b619791896db1513ca3d714acb68af3')
+    version('1.3.8', '7fad828bd094b5485fbf20bdf7d3d0d1')
+    version('1.3.7', 'a9e2f32efb1545421dd96185fd849184')
+
+    depends_on('r@2.10:', type=('build', 'run'))
+    depends_on('r-rpart', type=('build', 'run'))
+    depends_on('r-mclust', type=('build', 'run'))
+    depends_on('r-lars', type=('build', 'run'))
+    depends_on('r-robustbase', type=('build', 'run'))
+    depends_on('r-e1071', type=('build', 'run'))
+    depends_on('r-pls', type=('build', 'run'))
+    depends_on('r-som', type=('build', 'run'))
+    depends_on('r-pcapp', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-chron/package.py b/var/spack/repos/builtin/packages/r-chron/package.py
index 0a2566c0b1..b7fcc3777f 100644
--- a/var/spack/repos/builtin/packages/r-chron/package.py
+++ b/var/spack/repos/builtin/packages/r-chron/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-circlize/package.py b/var/spack/repos/builtin/packages/r-circlize/package.py
index 628c042d7d..5740e14d2b 100644
--- a/var/spack/repos/builtin/packages/r-circlize/package.py
+++ b/var/spack/repos/builtin/packages/r-circlize/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-class/package.py b/var/spack/repos/builtin/packages/r-class/package.py
index 3b35634302..a0cc01075c 100644
--- a/var/spack/repos/builtin/packages/r-class/package.py
+++ b/var/spack/repos/builtin/packages/r-class/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-classint/package.py b/var/spack/repos/builtin/packages/r-classint/package.py
new file mode 100644
index 0000000000..7009519294
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-classint/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RClassint(RPackage):
+    """Selected commonly used methods for choosing univariate class intervals
+       for mapping or other graphics purposes."""
+
+    homepage = "https://cran.r-project.org/package=classInt"
+    url      = "https://cran.r-project.org/src/contrib/classInt_0.1-24.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/classInt"
+
+    version('0.1-24', '45f1bde3ec7601ce17c99189be5c0fd5')
+
+    depends_on('r-e1071', type=('build', 'run'))
+    depends_on('r-class', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-cli/package.py b/var/spack/repos/builtin/packages/r-cli/package.py
new file mode 100644
index 0000000000..2b48e5fdb4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-cli/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RCli(RPackage):
+    """A suite of tools designed to build attractive command line interfaces
+       ('CLIs'). Includes tools for drawing rules, boxes, trees, and
+       'Unicode' symbols with 'ASCII' alternatives."""
+
+    homepage = "https://github.com/r-lib/cli#readme"
+    url      = "https://cran.r-project.org/src/contrib/cli_1.0.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/cli"
+
+    version('1.0.0', 'e6c4169541d394d6d435c4b430b1dd77')
+
+    depends_on('r-assertthat', type=('build', 'run'))
+    depends_on('r-crayon', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-clipr/package.py b/var/spack/repos/builtin/packages/r-clipr/package.py
index a5b6ce9993..c87ffa1f3c 100644
--- a/var/spack/repos/builtin/packages/r-clipr/package.py
+++ b/var/spack/repos/builtin/packages/r-clipr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-cluster/package.py b/var/spack/repos/builtin/packages/r-cluster/package.py
index e59a486434..cdde5da74f 100644
--- a/var/spack/repos/builtin/packages/r-cluster/package.py
+++ b/var/spack/repos/builtin/packages/r-cluster/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,9 +12,9 @@ class RCluster(RPackage):
     (1990) "Finding Groups in Data"."""
 
     homepage = "https://cran.r-project.org/web/packages/cluster/index.html"
-    url      = "https://cran.rstudio.com/src/contrib/cluster_2.0.6.tar.gz"
+    url      = "https://cran.rstudio.com/src/contrib/cluster_2.0.7-1.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/cluster"
 
-    version('2.0.6', 'e7d0660b05c65f4d886ebf7f046939ab')
+    version('2.0.7-1', 'a37add21b91d3e4f3883d005331e0d45')
     version('2.0.5', '7330f209ebce960bdee1a6d6679cb85a')
     version('2.0.4', 'bb4deceaafb1c42bb1278d5d0dc11e59')
diff --git a/var/spack/repos/builtin/packages/r-clusterprofiler/package.py b/var/spack/repos/builtin/packages/r-clusterprofiler/package.py
new file mode 100644
index 0000000000..5a1f51dc95
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-clusterprofiler/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RClusterprofiler(RPackage):
+    """This package implements methods to analyze and visualize functional
+    profiles (GO and KEGG) of gene and gene clusters."""
+
+    homepage = "https://www.bioconductor.org/packages/clusterProfiler/"
+    git      = "https://git.bioconductor.org/packages/clusterProfiler.git"
+
+    version('3.4.4', commit='b86b00e8405fe130e439362651a5567736e2d9d7')
+
+    depends_on('r@3.4.0:3.4.9', when='@3.4.4')
+    depends_on('r-tidyr', type=('build', 'run'))
+    depends_on('r-rvcheck', type=('build', 'run'))
+    depends_on('r-qvalue', type=('build', 'run'))
+    depends_on('r-plyr', type=('build', 'run'))
+    depends_on('r-magrittr', type=('build', 'run'))
+    depends_on('r-gosemsim', type=('build', 'run'))
+    depends_on('r-go-db', type=('build', 'run'))
+    depends_on('r-ggplot2', type=('build', 'run'))
+    depends_on('r-annotationdbi', type=('build', 'run'))
+    depends_on('r-dose', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-cner/package.py b/var/spack/repos/builtin/packages/r-cner/package.py
new file mode 100644
index 0000000000..8a96c0b086
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-cner/package.py
@@ -0,0 +1,37 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RCner(RPackage):
+    """"Large-scale identification and advanced visualization of sets of
+        conserved noncoding elements."""
+
+    homepage = "https://bioconductor.org/packages/CNEr/"
+    git      = "https://git.bioconductor.org/packages/CNEr.git"
+
+    version('1.14.0', commit='b8634d65c51728c815127e22b45eba7c9b9db897')
+
+    depends_on('r-biostrings@2.33.4:', type=('build', 'run'))
+    depends_on('r-dbi@0.7:', type=('build', 'run'))
+    depends_on('r-rsqlite@0.11.4:', type=('build', 'run'))
+    depends_on('r-genomeinfodb@1.1.3:', type=('build', 'run'))
+    depends_on('r-genomicranges@1.23.16:', type=('build', 'run'))
+    depends_on('r-rtracklayer@1.25.5:', type=('build', 'run'))
+    depends_on('r-xvector@0.5.4:', type=('build', 'run'))
+    depends_on('r-genomicalignments@1.1.9:', type=('build', 'run'))
+    depends_on('r-s4vectors@0.13.13:', type=('build', 'run'))
+    depends_on('r-iranges@2.5.27:', type=('build', 'run'))
+    depends_on('r-readr@0.2.2:', type=('build', 'run'))
+    depends_on('r-biocgenerics', type=('build', 'run'))
+    depends_on('r-reshape2@1.4.1:', type=('build', 'run'))
+    depends_on('r-ggplot2@2.1.0:', type=('build', 'run'))
+    depends_on('r-powerlaw@0.60.3:', type=('build', 'run'))
+    depends_on('r-annotate@1.50.0:', type=('build', 'run'))
+    depends_on('r-go-db@3.3.0:', type=('build', 'run'))
+    depends_on('r-keggrest@1.14.0:', type=('build', 'run'))
+    depends_on('r-utils@2.3.0:', type=('build', 'run'))
+    depends_on('r@3.4.3:3.4.9', when='@1.14.0')
diff --git a/var/spack/repos/builtin/packages/r-coda/package.py b/var/spack/repos/builtin/packages/r-coda/package.py
index 82c1887a32..de5e8e112f 100644
--- a/var/spack/repos/builtin/packages/r-coda/package.py
+++ b/var/spack/repos/builtin/packages/r-coda/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-codetools/package.py b/var/spack/repos/builtin/packages/r-codetools/package.py
index ce78dd590b..a32e9ddc77 100644
--- a/var/spack/repos/builtin/packages/r-codetools/package.py
+++ b/var/spack/repos/builtin/packages/r-codetools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-coin/package.py b/var/spack/repos/builtin/packages/r-coin/package.py
index 8c7a3a348e..f9688bbb86 100644
--- a/var/spack/repos/builtin/packages/r-coin/package.py
+++ b/var/spack/repos/builtin/packages/r-coin/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-colorspace/package.py b/var/spack/repos/builtin/packages/r-colorspace/package.py
index 70e3ea63a7..137f0441d2 100644
--- a/var/spack/repos/builtin/packages/r-colorspace/package.py
+++ b/var/spack/repos/builtin/packages/r-colorspace/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-complexheatmap/package.py b/var/spack/repos/builtin/packages/r-complexheatmap/package.py
index 04c88f8ef8..e4c0025f58 100644
--- a/var/spack/repos/builtin/packages/r-complexheatmap/package.py
+++ b/var/spack/repos/builtin/packages/r-complexheatmap/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,10 +13,9 @@ class RComplexheatmap(RPackage):
        multiple heatmaps and supports self-defined annotation graphics."""
 
     homepage = "https://bioconductor.org/packages/ComplexHeatmap/"
-    url      = "https://git.bioconductor.org/packages/ComplexHeatmap"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/ComplexHeatmap.git"
 
-    version('1.14.0', git='https://git.bioconductor.org/packages/ComplexHeatmap', commit='0acd8974fb5cedde8cd96efea6dfa39324d25b34')
+    version('1.14.0', commit='0acd8974fb5cedde8cd96efea6dfa39324d25b34')
 
     depends_on('r-circlize', type=('build', 'run'))
     depends_on('r-getoptlong', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-corpcor/package.py b/var/spack/repos/builtin/packages/r-corpcor/package.py
index b07e333ad7..2be6972de0 100644
--- a/var/spack/repos/builtin/packages/r-corpcor/package.py
+++ b/var/spack/repos/builtin/packages/r-corpcor/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-corrplot/package.py b/var/spack/repos/builtin/packages/r-corrplot/package.py
index 52408e5ae7..cf053e7733 100644
--- a/var/spack/repos/builtin/packages/r-corrplot/package.py
+++ b/var/spack/repos/builtin/packages/r-corrplot/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-covr/package.py b/var/spack/repos/builtin/packages/r-covr/package.py
index 5e3d8fff21..dc6430bafd 100644
--- a/var/spack/repos/builtin/packages/r-covr/package.py
+++ b/var/spack/repos/builtin/packages/r-covr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-cowplot/package.py b/var/spack/repos/builtin/packages/r-cowplot/package.py
index cb49c52acb..17a7d8f80e 100644
--- a/var/spack/repos/builtin/packages/r-cowplot/package.py
+++ b/var/spack/repos/builtin/packages/r-cowplot/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-crayon/package.py b/var/spack/repos/builtin/packages/r-crayon/package.py
index de1140df3b..d74f993f3e 100644
--- a/var/spack/repos/builtin/packages/r-crayon/package.py
+++ b/var/spack/repos/builtin/packages/r-crayon/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-crosstalk/package.py b/var/spack/repos/builtin/packages/r-crosstalk/package.py
new file mode 100644
index 0000000000..aa92cb027c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-crosstalk/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RCrosstalk(RPackage):
+    """Provides building blocks for allowing HTML widgets to communicate with
+    each other, with Shiny or without (i.e. static .html files)."""
+
+    homepage = "https://cran.r-project.org/web/packages/crosstalk/index.html"
+    url      = "https://cran.r-project.org/src/contrib/crosstalk_1.0.0.tar.gz"
+
+    version('1.0.0', 'c13c21b81af2154be3f08870fd3a7077')
+
+    depends_on('r@3.4.0:3.4.9')
+    depends_on('r-htmltools', type=('build', 'run'))
+    depends_on('r-jsonlite', type=('build', 'run'))
+    depends_on('r-lazyeval', type=('build', 'run'))
+    depends_on('r-ggplot2', type=('build', 'run'))
+    depends_on('r-shiny', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-ctc/package.py b/var/spack/repos/builtin/packages/r-ctc/package.py
new file mode 100644
index 0000000000..c4ceb4d471
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-ctc/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RCtc(RPackage):
+    """Tools for export and import classification trees and clusters
+       to other programs"""
+
+    homepage = "https://www.bioconductor.org/packages/release/bioc/html/ctc.html"
+    git      = "https://git.bioconductor.org/packages/ctc.git"
+
+    version('1.54.0', commit='0c3df81dfc8fabe12e11884bed44b64e11fd6d4e')
+
+    depends_on('r-amap', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@1.54.0:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-cubature/package.py b/var/spack/repos/builtin/packages/r-cubature/package.py
index 9f09069094..2701f470e4 100644
--- a/var/spack/repos/builtin/packages/r-cubature/package.py
+++ b/var/spack/repos/builtin/packages/r-cubature/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-cubist/package.py b/var/spack/repos/builtin/packages/r-cubist/package.py
index 8fd4639fc5..a5472f2965 100644
--- a/var/spack/repos/builtin/packages/r-cubist/package.py
+++ b/var/spack/repos/builtin/packages/r-cubist/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-curl/package.py b/var/spack/repos/builtin/packages/r-curl/package.py
index 0b53d436fd..3951059736 100644
--- a/var/spack/repos/builtin/packages/r-curl/package.py
+++ b/var/spack/repos/builtin/packages/r-curl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-data-table/package.py b/var/spack/repos/builtin/packages/r-data-table/package.py
index fad200eeb1..9726785a54 100644
--- a/var/spack/repos/builtin/packages/r-data-table/package.py
+++ b/var/spack/repos/builtin/packages/r-data-table/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,6 +16,7 @@ class RDataTable(RPackage):
     url      = "https://cran.r-project.org/src/contrib/data.table_1.10.0.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/data.table"
 
+    version('1.10.4-3', '081da241d06f30ae4a2bc60efb409893')
     version('1.10.4-2', '4a2d3541f241088d0979522b4083a765')
     version('1.10.0', 'f0e08dd5ba1b3f46c59dd1574fe497c1')
     version('1.9.6',  'b1c0c7cce490bdf42ab288541cc55372')
diff --git a/var/spack/repos/builtin/packages/r-dbi/package.py b/var/spack/repos/builtin/packages/r-dbi/package.py
index 00b38984e1..5c4c8493ab 100644
--- a/var/spack/repos/builtin/packages/r-dbi/package.py
+++ b/var/spack/repos/builtin/packages/r-dbi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-dbplyr/package.py b/var/spack/repos/builtin/packages/r-dbplyr/package.py
new file mode 100644
index 0000000000..7f0dcf7577
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-dbplyr/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RDbplyr(RPackage):
+    """A 'dplyr' back end for databases that allows you to work with remote
+       database tables as if they are in-memory data frames. Basic features
+       works with any database that has a 'DBI' back end; more advanced
+       features require 'SQL' translation to be provided by the package
+       author."""
+
+    homepage = "https://github.com/tidyverse/dbplyr"
+    url      = "https://cran.r-project.org/src/contrib/dbplyr_1.1.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/dbplyr"
+
+    version('1.1.0', 'a66a08d1046e3e44bfe17e65ce72a1d0')
+
+    depends_on('r-assertthat', type=('build', 'run'))
+    depends_on('r-dbi', type=('build', 'run'))
+    depends_on('r-dplyr', type=('build', 'run'))
+    depends_on('r-glue', type=('build', 'run'))
+    depends_on('r-purrr', type=('build', 'run'))
+    depends_on('r-rlang', type=('build', 'run'))
+    depends_on('r-tibble', type=('build', 'run'))
+    depends_on('r-r6', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-delayedarray/package.py b/var/spack/repos/builtin/packages/r-delayedarray/package.py
index 8cbeb0296b..c6c32aa888 100644
--- a/var/spack/repos/builtin/packages/r-delayedarray/package.py
+++ b/var/spack/repos/builtin/packages/r-delayedarray/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -43,13 +24,20 @@ class RDelayedarray(RPackage):
        frames."""
 
     homepage = "https://bioconductor.org/packages/DelayedArray/"
-    url      = "https://git.bioconductor.org/packages/DelayedArray"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/DelayedArray.git"
 
-    version('0.2.7', git='https://git.bioconductor.org/packages/DelayedArray', commit='909c2ce1665ebae2543172ead50abbe10bd42bc4')
+    version('0.6.5', commit='7d1cb6477cb024c38bf1ee0c9155e010249ed94e')
+    version('0.4.1', commit='ffe932ef8c255614340e4856fc6e0b44128a27a1')
+    version('0.2.7', commit='909c2ce1665ebae2543172ead50abbe10bd42bc4')
 
+    depends_on('r-biocparallel', when='@0.6.5:', type=('build', 'run'))
     depends_on('r-biocgenerics', type=('build', 'run'))
-    depends_on('r-s4vectors', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.25.1:', when='@0.6.5', type=('build', 'run'))
+    depends_on('r-s4vectors@0.14.3:', when='@0.2.7', type=('build', 'run'))
+    depends_on('r-s4vectors@0.15.3:', when='@0.4.1', type=('build', 'run'))
+    depends_on('r-s4vectors@0.17.43:', when='@0.6.5', type=('build', 'run'))
     depends_on('r-iranges', type=('build', 'run'))
+    depends_on('r-iranges@2.11.17:', when='@0.4.1:', type=('build', 'run'))
     depends_on('r-matrixstats', type=('build', 'run'))
-    depends_on('r@3.4.0:3.4.9', when='@0.2.7')
+    depends_on('r@3.4.0:3.4.9', when='@0.2.7', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@0.6.5', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-deldir/package.py b/var/spack/repos/builtin/packages/r-deldir/package.py
index d02ecb19ce..7a2a5c6de0 100644
--- a/var/spack/repos/builtin/packages/r-deldir/package.py
+++ b/var/spack/repos/builtin/packages/r-deldir/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-dendextend/package.py b/var/spack/repos/builtin/packages/r-dendextend/package.py
index 5d98e012fc..73f085b7b7 100644
--- a/var/spack/repos/builtin/packages/r-dendextend/package.py
+++ b/var/spack/repos/builtin/packages/r-dendextend/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-deoptim/package.py b/var/spack/repos/builtin/packages/r-deoptim/package.py
index 298b790693..7a4daac46b 100644
--- a/var/spack/repos/builtin/packages/r-deoptim/package.py
+++ b/var/spack/repos/builtin/packages/r-deoptim/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/r-deoptimr/package.py b/var/spack/repos/builtin/packages/r-deoptimr/package.py
index af95c081e0..e2ec25a988 100644
--- a/var/spack/repos/builtin/packages/r-deoptimr/package.py
+++ b/var/spack/repos/builtin/packages/r-deoptimr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-deseq/package.py b/var/spack/repos/builtin/packages/r-deseq/package.py
index 900c82499a..78886d4f03 100644
--- a/var/spack/repos/builtin/packages/r-deseq/package.py
+++ b/var/spack/repos/builtin/packages/r-deseq/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,9 +13,9 @@ class RDeseq(RPackage):
     distribution."""
 
     homepage = "https://www.bioconductor.org/packages/DESeq/"
-    url      = "https://git.bioconductor.org/packages/DESeq"
+    git      = "https://git.bioconductor.org/packages/DESeq.git"
 
-    version('1.28.0', git='https://git.bioconductor.org/packages/DESeq', commit='738371466e6ccf00179fd35b617c8ba0e1e91630')
+    version('1.28.0', commit='738371466e6ccf00179fd35b617c8ba0e1e91630')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-biobase', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-deseq2/package.py b/var/spack/repos/builtin/packages/r-deseq2/package.py
index 96a2426c4f..2a470b808d 100644
--- a/var/spack/repos/builtin/packages/r-deseq2/package.py
+++ b/var/spack/repos/builtin/packages/r-deseq2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,11 +13,12 @@ class RDeseq2(RPackage):
     distribution."""
 
     homepage = "https://www.bioconductor.org/packages/DESeq2/"
-    url      = "https://git.bioconductor.org/packages/DESeq2"
+    git      = "https://git.bioconductor.org/packages/DESeq2.git"
 
-    version('1.16.1', git='https://git.bioconductor.org/packages/DESeq2', commit='0a815574382704a08ef8b906eceb0296f81cded5')
+    version('1.20.0', commit='7e88ea5c5e68473824ce0af6e10f19e22374cb7c')
+    version('1.18.1', commit='ef65091d46436af68915124b752f5e1cc55e93a7')
+    version('1.16.1', commit='0a815574382704a08ef8b906eceb0296f81cded5')
 
-    depends_on('r@3.4.0:3.4.9', when='@1.16.1')
     depends_on("r-rcpparmadillo", type=('build', 'run'))
     depends_on('r-s4vectors', type=('build', 'run'))
     depends_on('r-iranges', type=('build', 'run'))
@@ -51,3 +33,5 @@ class RDeseq2(RPackage):
     depends_on('r-ggplot2', type=('build', 'run'))
     depends_on('r-hmisc', type=('build', 'run'))
     depends_on('r-rcpp', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@1.16.1:1.19', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@1.20.0', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-desolve/package.py b/var/spack/repos/builtin/packages/r-desolve/package.py
index bbcbebcd53..11642809e1 100644
--- a/var/spack/repos/builtin/packages/r-desolve/package.py
+++ b/var/spack/repos/builtin/packages/r-desolve/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-devtools/package.py b/var/spack/repos/builtin/packages/r-devtools/package.py
index 7b9b789eb3..68bb13ed76 100644
--- a/var/spack/repos/builtin/packages/r-devtools/package.py
+++ b/var/spack/repos/builtin/packages/r-devtools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-diagrammer/package.py b/var/spack/repos/builtin/packages/r-diagrammer/package.py
index 650ab64a3f..a5c7c58787 100644
--- a/var/spack/repos/builtin/packages/r-diagrammer/package.py
+++ b/var/spack/repos/builtin/packages/r-diagrammer/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-dicekriging/package.py b/var/spack/repos/builtin/packages/r-dicekriging/package.py
new file mode 100644
index 0000000000..6dcfddda69
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-dicekriging/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RDicekriging(RPackage):
+    """Estimation, validation and prediction of kriging models. Important
+       functions : km, print.km, plot.km, predict.km."""
+
+    homepage = "http://dice.emse.fr/"
+    url      = "https://cran.r-project.org/src/contrib/DiceKriging_1.5.5.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/DiceKriging"
+
+    version('1.5.5', 'ee3e2d7a91d4a712467ef4f0b69c2844')
diff --git a/var/spack/repos/builtin/packages/r-dichromat/package.py b/var/spack/repos/builtin/packages/r-dichromat/package.py
index b40cff31dd..1364e90113 100644
--- a/var/spack/repos/builtin/packages/r-dichromat/package.py
+++ b/var/spack/repos/builtin/packages/r-dichromat/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-diffusionmap/package.py b/var/spack/repos/builtin/packages/r-diffusionmap/package.py
new file mode 100644
index 0000000000..c4011ff844
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-diffusionmap/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RDiffusionmap(RPackage):
+    """Allows to display a progress bar in the R console for long running
+    computations taking place in c++ code, and support for interrupting those
+    computations even in multithreaded code, typically using OpenMP."""
+
+    homepage = "https://cran.r-project.org/web/packages/diffusionMap/index.html"
+    url      = "https://cran.r-project.org/src/contrib/diffusionMap_1.1-0.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/diffusionMap"
+
+    version('1.1-0', 'cc7d728087ba08d9299ae3a64a8d8919')
+    version('1.0-0', 'bca462e6efe45c5eaa48d38621f0bd6f')
+    version('0.0-2', 'b599f47ebf30127e34ce2219dc3e43ae')
+    version('0.0-1', '20c2cc2fffb5237d5c0216207016c2a1')
+
+    depends_on('r@3.4.0:3.4.9')
+    depends_on('r-matrix', type=('build', 'run'))
+    depends_on('r-scatterplot3d', type=('build', 'run'))
+    depends_on('r-igraph', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-digest/package.py b/var/spack/repos/builtin/packages/r-digest/package.py
index 78b96e03f4..db1678ed1e 100644
--- a/var/spack/repos/builtin/packages/r-digest/package.py
+++ b/var/spack/repos/builtin/packages/r-digest/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-diptest/package.py b/var/spack/repos/builtin/packages/r-diptest/package.py
index 96d9eea734..1afe05803b 100644
--- a/var/spack/repos/builtin/packages/r-diptest/package.py
+++ b/var/spack/repos/builtin/packages/r-diptest/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-dirichletmultinomial/package.py b/var/spack/repos/builtin/packages/r-dirichletmultinomial/package.py
new file mode 100644
index 0000000000..ce634abf12
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-dirichletmultinomial/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RDirichletmultinomial(RPackage):
+    """Dirichlet-multinomial mixture models can be used to describe
+    variability in microbial metagenomic data.
+
+    This package is an interface to code originally made available by
+    Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): 1-15, as discussed
+    further in the man page for this package, ?DirichletMultinomial."""
+
+    homepage = "https://bioconductor.org/packages/DirichletMultinomial/"
+    git      = "https://git.bioconductor.org/packages/DirichletMultinomial.git"
+
+    version('1.20.0', commit='251529f301da1482551142240aeb6baf8dab2272')
+
+    depends_on('r-s4vectors', type=('build', 'run'))
+    depends_on('r-iranges', type=('build', 'run'))
+    depends_on('gsl')
+    depends_on('r@3.4.0:')
diff --git a/var/spack/repos/builtin/packages/r-dismo/package.py b/var/spack/repos/builtin/packages/r-dismo/package.py
new file mode 100644
index 0000000000..db2db94130
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-dismo/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RDismo(RPackage):
+    """Functions for species distribution modeling, that is, predicting
+       entire geographic distributions form occurrences at a number of sites
+       and the environment at these sites."""
+
+    homepage = "https://cran.r-project.org/package=dismo"
+    url      = "https://cran.r-project.org/src/contrib/dismo_1.1-4.tar.gz"
+
+    version('1.1-4', sha256='f2110f716cd9e4cca5fd2b22130c6954658aaf61361d2fe688ba22bbfdfa97c8')
+
+    depends_on('r@3.2.0:', type=('build', 'run'))
+    depends_on('r-raster@2.5-2:', type=('build', 'run'))
+    depends_on('r-sp@1.2-0:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-dnacopy/package.py b/var/spack/repos/builtin/packages/r-dnacopy/package.py
index ade0424829..2f1900f361 100644
--- a/var/spack/repos/builtin/packages/r-dnacopy/package.py
+++ b/var/spack/repos/builtin/packages/r-dnacopy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,6 +12,6 @@ class RDnacopy(RPackage):
     with abnormal copy number."""
 
     homepage = "https://www.bioconductor.org/packages/DNAcopy/"
-    url      = "https://git.bioconductor.org/packages/DNAcopy"
+    git      = "https://git.bioconductor.org/packages/DNAcopy.git"
 
-    version('1.50.1', git='https://git.bioconductor.org/packages/DNAcopy', commit='a20153029e28c009df813dbaf13d9f519fafa4e8')
+    version('1.50.1', commit='a20153029e28c009df813dbaf13d9f519fafa4e8')
diff --git a/var/spack/repos/builtin/packages/r-do-db/package.py b/var/spack/repos/builtin/packages/r-do-db/package.py
new file mode 100644
index 0000000000..3dd7c8b258
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-do-db/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RDoDb(RPackage):
+    """A set of annotation maps describing the entire Disease
+    Ontology assembled using data from DO."""
+
+    homepage = "https://bioconductor.org/packages/DO.db/"
+    url      = "https://www.bioconductor.org/packages/3.5/data/annotation/src/contrib/DO.db_2.9.tar.gz"
+
+    version('2.9', '63dda6d46d2fe40c52a2e79260a7fb9d')
+
+    depends_on('r-annotationdbi', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-domc/package.py b/var/spack/repos/builtin/packages/r-domc/package.py
index 9ed4841520..2fd58884d5 100644
--- a/var/spack/repos/builtin/packages/r-domc/package.py
+++ b/var/spack/repos/builtin/packages/r-domc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-doparallel/package.py b/var/spack/repos/builtin/packages/r-doparallel/package.py
index 1690db07a7..06bc2bf0a7 100644
--- a/var/spack/repos/builtin/packages/r-doparallel/package.py
+++ b/var/spack/repos/builtin/packages/r-doparallel/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-dorng/package.py b/var/spack/repos/builtin/packages/r-dorng/package.py
index 7ac9556d9b..ba094688ad 100644
--- a/var/spack/repos/builtin/packages/r-dorng/package.py
+++ b/var/spack/repos/builtin/packages/r-dorng/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-dose/package.py b/var/spack/repos/builtin/packages/r-dose/package.py
new file mode 100644
index 0000000000..96bbf34451
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-dose/package.py
@@ -0,0 +1,33 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RDose(RPackage):
+    """This package implements five methods proposed by Resnik, Schlicker,
+    Jiang, Lin and Wang respectively for measuring semantic similarities
+    among DO terms and gene products. Enrichment analyses including
+    hypergeometric model and gene set enrichment analysis are also
+    implemented for discovering disease associations of high-throughput
+    biological data."""
+
+    homepage = "https://www.bioconductor.org/packages/DOSE/"
+    git      = "https://git.bioconductor.org/packages/DOSE.git"
+
+    version('3.2.0', commit='71f563fc39d02dfdf65184c94e0890a63b96b86b')
+
+    depends_on('r@3.4.0:3.4.9', when='@3.2.0')
+    depends_on('r-scales', type=('build', 'run'))
+    depends_on('r-s4vectors', type=('build', 'run'))
+    depends_on('r-reshape2', type=('build', 'run'))
+    depends_on('r-qvalue', type=('build', 'run'))
+    depends_on('r-igraph', type=('build', 'run'))
+    depends_on('r-gosemsim', type=('build', 'run'))
+    depends_on('r-ggplot2', type=('build', 'run'))
+    depends_on('r-fgsea', type=('build', 'run'))
+    depends_on('r-do-db', type=('build', 'run'))
+    depends_on('r-biocparallel', type=('build', 'run'))
+    depends_on('r-annotationdbi', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-downloader/package.py b/var/spack/repos/builtin/packages/r-downloader/package.py
index d71c17e304..6a0293b8c6 100644
--- a/var/spack/repos/builtin/packages/r-downloader/package.py
+++ b/var/spack/repos/builtin/packages/r-downloader/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-dplyr/package.py b/var/spack/repos/builtin/packages/r-dplyr/package.py
index fa68988692..72a34222cb 100644
--- a/var/spack/repos/builtin/packages/r-dplyr/package.py
+++ b/var/spack/repos/builtin/packages/r-dplyr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,18 +10,26 @@ class RDplyr(RPackage):
     """A fast, consistent tool for working with data frame like objects, both
     in memory and out of memory."""
 
-    homepage = "https://github.com/hadley/dplyr"
-    url      = "https://cran.rstudio.com/src/contrib/dplyr_0.7.3.tar.gz"
+    homepage = "https://cran.r-project.org/package=dplyr"
+    url      = "https://cran.r-project.org/src/contrib/dplyr_0.7.6.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/dplyr"
 
+    version('0.7.5', sha256='2fbd8f316a59670076d43a0fe854654621941ee5f621ea5f0185a3f5daafda50')
+    version('0.7.4', '9edee9b2db9831c2438054d0d2c1647d')
     version('0.7.3', 'f9760b796917747e9dcd927ebb531c7d')
     version('0.5.0', '1fcafcacca70806eea2e6d465cdb94ef')
 
+    depends_on('r-tidyselect@0.2.3', type=('build', 'run'))
     depends_on('r-assertthat', type=('build', 'run'))
+    depends_on('r-bindr@0.1.1', type=('build', 'run'))
     depends_on('r-r6', type=('build', 'run'))
     depends_on('r-rcpp', type=('build', 'run'))
     depends_on('r-tibble', type=('build', 'run'))
     depends_on('r-magrittr', type=('build', 'run'))
     depends_on('r-lazyeval', type=('build', 'run'))
     depends_on('r-dbi', type=('build', 'run'))
+    depends_on('r-bindrcpp', type=('build', 'run'))
+    depends_on('r-glue', type=('build', 'run'))
+    depends_on('r-pkgconfig', type=('build', 'run'))
+    depends_on('r-plogr', type=('build', 'run'))
     depends_on('r-bh', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-dt/package.py b/var/spack/repos/builtin/packages/r-dt/package.py
index a2d01900e1..3a68487f43 100644
--- a/var/spack/repos/builtin/packages/r-dt/package.py
+++ b/var/spack/repos/builtin/packages/r-dt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-dtw/package.py b/var/spack/repos/builtin/packages/r-dtw/package.py
new file mode 100644
index 0000000000..a752f202d6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-dtw/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RDtw(RPackage):
+    """A comprehensive implementation of dynamic time warping (DTW) algorithms
+    in R. DTW computes the optimal (least cumulative distance) alignment
+    between points of two time series."""
+
+    homepage = "https://cran.r-project.org/web/packages/dtw/index.html"
+    url      = "https://cran.r-project.org/src/contrib/dtw_1.18-1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/dtw"
+
+    version('1.18-1', '5e9995a198a62f28045c29461265d536')
+    version('1.17-1', 'e8be988fe528acd6b44afdf5aa06b745')
+    version('1.16',   '260bd22d9db429394eb39739db4a4686')
+    version('1.15',   'd3b6fdb0b866ff2e5b178c37bcfc7c55')
+    version('1.14-3', 'a7b878e8dda7a61df22356d0a81540c5')
+
+    depends_on('r@3.4.0:3.4.9')
+    depends_on('r-proxy', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-dygraphs/package.py b/var/spack/repos/builtin/packages/r-dygraphs/package.py
index 91e2dc5504..eeb0f08481 100644
--- a/var/spack/repos/builtin/packages/r-dygraphs/package.py
+++ b/var/spack/repos/builtin/packages/r-dygraphs/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-e1071/package.py b/var/spack/repos/builtin/packages/r-e1071/package.py
index 7be5264895..94b6a60ef9 100644
--- a/var/spack/repos/builtin/packages/r-e1071/package.py
+++ b/var/spack/repos/builtin/packages/r-e1071/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-edger/package.py b/var/spack/repos/builtin/packages/r-edger/package.py
index 2d9da861db..cc94490e97 100644
--- a/var/spack/repos/builtin/packages/r-edger/package.py
+++ b/var/spack/repos/builtin/packages/r-edger/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,11 +16,13 @@ class REdger(RPackage):
        SAGE and CAGE."""
 
     homepage = "https://bioconductor.org/packages/edgeR/"
-    url      = "https://git.bioconductor.org/packages/edgeR"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/edgeR.git"
 
-    version('3.18.1', git='https://git.bioconductor.org/packages/edgeR', commit='101106f3fdd9e2c45d4a670c88f64c12e97a0495')
+    version('3.22.3', commit='e82e54afc9398ac54dc4caba0f7ae5c43e572203')
+    version('3.18.1', commit='101106f3fdd9e2c45d4a670c88f64c12e97a0495')
 
     depends_on('r-limma', type=('build', 'run'))
     depends_on('r-locfit', type=('build', 'run'))
+    depends_on('r-rcpp', type=('build', 'link', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@3.22.3')
     depends_on('r@3.4.0:3.4.9', when='@3.18.1')
diff --git a/var/spack/repos/builtin/packages/r-ellipse/package.py b/var/spack/repos/builtin/packages/r-ellipse/package.py
index 52393ed66a..555e5cd985 100644
--- a/var/spack/repos/builtin/packages/r-ellipse/package.py
+++ b/var/spack/repos/builtin/packages/r-ellipse/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-ensembldb/package.py b/var/spack/repos/builtin/packages/r-ensembldb/package.py
index c6f424a855..c1e5b219ef 100644
--- a/var/spack/repos/builtin/packages/r-ensembldb/package.py
+++ b/var/spack/repos/builtin/packages/r-ensembldb/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,10 +18,9 @@ class REnsembldb(RPackage):
        region or transcript models of lincRNA genes."""
 
     homepage = "https://bioconductor.org/packages/ensembldb/"
-    url      = "https://git.bioconductor.org/packages/ensembldb"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/ensembldb.git"
 
-    version('2.0.4', git='https://git.bioconductor.org/packages/ensembldb', commit='514623d71e3cca7a4e547adb579b5a958702ef86')
+    version('2.0.4', commit='514623d71e3cca7a4e547adb579b5a958702ef86')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-genomicranges', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-ergm/package.py b/var/spack/repos/builtin/packages/r-ergm/package.py
index 419119e2b0..cea98327f7 100644
--- a/var/spack/repos/builtin/packages/r-ergm/package.py
+++ b/var/spack/repos/builtin/packages/r-ergm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-evaluate/package.py b/var/spack/repos/builtin/packages/r-evaluate/package.py
index d32bff7319..8edc12743e 100644
--- a/var/spack/repos/builtin/packages/r-evaluate/package.py
+++ b/var/spack/repos/builtin/packages/r-evaluate/package.py
@@ -1,28 +1,7 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/r-expm/package.py b/var/spack/repos/builtin/packages/r-expm/package.py
index 48080163de..2f68a851ab 100644
--- a/var/spack/repos/builtin/packages/r-expm/package.py
+++ b/var/spack/repos/builtin/packages/r-expm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-factoextra/package.py b/var/spack/repos/builtin/packages/r-factoextra/package.py
index 518f4d6a63..8bffeafbc9 100644
--- a/var/spack/repos/builtin/packages/r-factoextra/package.py
+++ b/var/spack/repos/builtin/packages/r-factoextra/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-factominer/package.py b/var/spack/repos/builtin/packages/r-factominer/package.py
index d2abf10ff7..f9aa8a7d77 100644
--- a/var/spack/repos/builtin/packages/r-factominer/package.py
+++ b/var/spack/repos/builtin/packages/r-factominer/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-fastcluster/package.py b/var/spack/repos/builtin/packages/r-fastcluster/package.py
new file mode 100644
index 0000000000..303219e630
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-fastcluster/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RFastcluster(RPackage):
+    """This is a two-in-one package which provides interfaces to both R
+       and 'Python'. It implements fast hierarchical, agglomerative
+       clustering routines. Part of the functionality is designed as drop-in
+       replacement for existing routines: linkage() in the 'SciPy' package
+       'scipy.cluster.hierarchy', hclust() in R's 'stats' package, and the
+       'flashClust' package. It provides the same functionality with the
+       benefit of a much faster implementation. Moreover, there are
+       memory-saving routines for clustering of vector data, which go beyond
+       what the existing packages provide. For information on how to install
+       the 'Python' files, see the file INSTALL in the source distribution."""
+
+    homepage = "http://danifold.net/fastcluster.html"
+    url      = "https://cran.r-project.org/src/contrib/fastcluster_1.1.25.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/fastcluster/"
+
+    version('1.1.25', sha256='f3661def975802f3dd3cec5b2a1379f3707eacff945cf448e33aec0da1ed4205')
+
+    depends_on('r@3.0.0:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-fastmatch/package.py b/var/spack/repos/builtin/packages/r-fastmatch/package.py
new file mode 100644
index 0000000000..73f849db91
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-fastmatch/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RFastmatch(RPackage):
+    """Package providing a fast match() replacement for cases that require
+       repeated look-ups. It is slightly faster that R's built-in match()
+       function on first match against a table, but extremely fast on any
+       subsequent lookup as it keeps the hash table in memory."""
+
+    homepage = "http://www.rforge.net/fastmatch"
+    url      = "https://cran.r-project.org/src/contrib/fastmatch_1.1-0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/fastmatch"
+
+    version('1.1-0', '900c2363c15059ac9d63c4c71ea2d6b2')
diff --git a/var/spack/repos/builtin/packages/r-ff/package.py b/var/spack/repos/builtin/packages/r-ff/package.py
index 1bb7250658..aa68be9562 100644
--- a/var/spack/repos/builtin/packages/r-ff/package.py
+++ b/var/spack/repos/builtin/packages/r-ff/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-fftwtools/package.py b/var/spack/repos/builtin/packages/r-fftwtools/package.py
new file mode 100644
index 0000000000..237d40035e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-fftwtools/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RFftwtools(RPackage):
+    """Provides a wrapper for several 'FFTW' functions. This package provides
+       access to the two-dimensional 'FFT', the multivariate 'FFT', and the
+       one-dimensional real to complex 'FFT' using the 'FFTW3' library. The
+       package includes the functions fftw() and mvfftw() which are designed
+       to mimic the functionality of the R functions fft() and mvfft().
+       The 'FFT' functions have a parameter that allows them to not return
+       the redundant complex conjugate when the input is real data."""
+
+    homepage = "https://github.com/krahim/fftwtools"
+    url      = "https://cran.r-project.org/src/contrib/fftwtools_0.9-8.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/fftwtools"
+
+    version('0.9-8', '2d1258fbaf0940b57ed61c8d6cd6694d')
+
+    depends_on('fftw')
diff --git a/var/spack/repos/builtin/packages/r-fgsea/package.py b/var/spack/repos/builtin/packages/r-fgsea/package.py
new file mode 100644
index 0000000000..938a15bf6f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-fgsea/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RFgsea(RPackage):
+    """The package implements an algorithm for fast gene set enrichment
+    analysis. Using the fast algorithm allows to make more permutations
+    and get more fine grained p-values, which allows to use accurate
+    stantard approaches to multiple hypothesis correction."""
+
+    homepage = "https://www.bioconductor.org/packages/fgsea/"
+    git      = "https://git.bioconductor.org/packages/fgsea.git"
+
+    version('1.2.1', commit='99b04eef664204d0dca4b9f8027cd7eefb006b72')
+
+    depends_on('r@3.4.0:3.4.9', when='@1.2.1')
+    depends_on('r-fastmatch', type=('build', 'run'))
+    depends_on('r-gridextra', type=('build', 'run'))
+    depends_on('r-ggplot2', type=('build', 'run'))
+    depends_on('r-biocparallel', type=('build', 'run'))
+    depends_on('r-data-table', type=('build', 'run'))
+    depends_on('r-rcpp', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-filehash/package.py b/var/spack/repos/builtin/packages/r-filehash/package.py
index b7cfbb19ce..0220fbc6bb 100644
--- a/var/spack/repos/builtin/packages/r-filehash/package.py
+++ b/var/spack/repos/builtin/packages/r-filehash/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-findpython/package.py b/var/spack/repos/builtin/packages/r-findpython/package.py
new file mode 100644
index 0000000000..e5a298b09a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-findpython/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RFindpython(RPackage):
+    """Package designed to find an acceptable python binary."""
+
+    homepage = "https://github.com/trevorld/findpython"
+    url      = "https://cran.r-project.org/src/contrib/findpython_1.0.3.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/findpython"
+
+    version('1.0.3', sha256='5486535ae2f0a123b630d8eabf93a61b730765f55dfcc8ef4f6e56e7c49408f8')
+
+    depends_on('python', type='run')
diff --git a/var/spack/repos/builtin/packages/r-fit-models/package.py b/var/spack/repos/builtin/packages/r-fit-models/package.py
new file mode 100644
index 0000000000..32c2b96f9e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-fit-models/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RFitModels(RPackage):
+    """Compare Fitted Models"""
+
+    homepage = "https://cran.r-project.org/package=fit.models"
+    url      = "https://cran.r-project.org/src/contrib/fit.models_0.5-14.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/fit.models"
+
+    version('0.5-14', '159b5c57953db4c917bc186ddacdff51')
+    version('0.5-13', 'c9ff87e98189bcc3be597e3833408497')
+
+    depends_on('r-lattice', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-flashclust/package.py b/var/spack/repos/builtin/packages/r-flashclust/package.py
index cfaee392db..c36ad50cf8 100644
--- a/var/spack/repos/builtin/packages/r-flashclust/package.py
+++ b/var/spack/repos/builtin/packages/r-flashclust/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-flexclust/package.py b/var/spack/repos/builtin/packages/r-flexclust/package.py
new file mode 100644
index 0000000000..338bfd4d07
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-flexclust/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RFlexclust(RPackage):
+    """The main function kcca implements a general framework for k-centroids
+    cluster analysis supporting arbitrary distance measures and centroid
+    computation. Further cluster methods include hard competitive learning,
+    neural gas, and QT clustering. There are numerous visualization methods for
+    cluster results (neighborhood graphs, convex cluster hulls, barcharts of
+    centroids, ...), and bootstrap methods for the analysis of cluster
+    stability."""
+
+    homepage = "https://cran.r-project.org/package=flexclust"
+    url      = "https://cran.rstudio.com/src/contrib/flexclust_1.3-5.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/flexclust"
+
+    version('1.3-5', '90226a0e3a4f256f392a278e9543f8f4')
+
+    depends_on('r-lattice', type=('build', 'run'))
+    depends_on('r-modeltools', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-flexmix/package.py b/var/spack/repos/builtin/packages/r-flexmix/package.py
index 82ea3f068a..f41e959b7c 100644
--- a/var/spack/repos/builtin/packages/r-flexmix/package.py
+++ b/var/spack/repos/builtin/packages/r-flexmix/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-fnn/package.py b/var/spack/repos/builtin/packages/r-fnn/package.py
new file mode 100644
index 0000000000..984024a5d0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-fnn/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RFnn(RPackage):
+    """Cover-tree and kd-tree fast k-nearest neighbor search algorithms and
+    related applications including KNN classification, regression and
+    information measures are implemented."""
+
+    homepage = "https://cran.r-project.org/web/packages/FNN/index.html"
+    url      = "https://cran.r-project.org/src/contrib/FNN_1.1.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/FNN"
+
+    version('1.1',   '8ba8f5b8be271785593e13eae7b8c393')
+    version('1.0',   'e9a47dc69d1ba55165be0877b8443fe0')
+    version('0.6-4', '1c105df9763ceb7b13989cdbcb542fcc')
+    version('0.6-3', 'f0f0184e50f9f30a36ed5cff24d6cff2')
+    version('0.6-2', '20648ba934ea32b1b00dafb75e1a830c')
+
+    depends_on('r@3.0.0:', type=('build', 'run'))
+    depends_on('r-mvtnorm', type=('build', 'run'))
+    depends_on('r-chemometrics', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-forcats/package.py b/var/spack/repos/builtin/packages/r-forcats/package.py
new file mode 100644
index 0000000000..3497da1f8b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-forcats/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RForcats(RPackage):
+    """Helpers for reordering factor levels (including moving specified levels
+       to front, ordering by first appearance, reversing, and randomly
+       shuffling), and tools for modifying factor levels (including collapsing
+       rare levels into other, 'anonymising', and manually 'recoding')."""
+
+    homepage = "http://forcats.tidyverse.org/"
+    url      = "https://cran.r-project.org/src/contrib/forcats_0.2.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/forcats"
+
+    version('0.2.0', 'e4ba2c0a59dcdfcc02274c519bf3dbfc')
+
+    depends_on('r-tibble', type=('build', 'run'))
+    depends_on('r-magrittr', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-foreach/package.py b/var/spack/repos/builtin/packages/r-foreach/package.py
index bf542efaea..b7ffbcc256 100644
--- a/var/spack/repos/builtin/packages/r-foreach/package.py
+++ b/var/spack/repos/builtin/packages/r-foreach/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-forecast/package.py b/var/spack/repos/builtin/packages/r-forecast/package.py
index e6549a30dd..d491a3bc20 100644
--- a/var/spack/repos/builtin/packages/r-forecast/package.py
+++ b/var/spack/repos/builtin/packages/r-forecast/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-foreign/package.py b/var/spack/repos/builtin/packages/r-foreign/package.py
index f43e0ad0e4..4974ec76d7 100644
--- a/var/spack/repos/builtin/packages/r-foreign/package.py
+++ b/var/spack/repos/builtin/packages/r-foreign/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-formatr/package.py b/var/spack/repos/builtin/packages/r-formatr/package.py
index e6fa3c6824..7e495ca821 100644
--- a/var/spack/repos/builtin/packages/r-formatr/package.py
+++ b/var/spack/repos/builtin/packages/r-formatr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/r-formula/package.py b/var/spack/repos/builtin/packages/r-formula/package.py
index 499ebfa8da..9f756f8917 100644
--- a/var/spack/repos/builtin/packages/r-formula/package.py
+++ b/var/spack/repos/builtin/packages/r-formula/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/r-fpc/package.py b/var/spack/repos/builtin/packages/r-fpc/package.py
index 4628970171..26901c8035 100644
--- a/var/spack/repos/builtin/packages/r-fpc/package.py
+++ b/var/spack/repos/builtin/packages/r-fpc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-fracdiff/package.py b/var/spack/repos/builtin/packages/r-fracdiff/package.py
index c5ed63b240..4666832c17 100644
--- a/var/spack/repos/builtin/packages/r-fracdiff/package.py
+++ b/var/spack/repos/builtin/packages/r-fracdiff/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-futile-logger/package.py b/var/spack/repos/builtin/packages/r-futile-logger/package.py
index 93d735f027..e2e3cf2667 100644
--- a/var/spack/repos/builtin/packages/r-futile-logger/package.py
+++ b/var/spack/repos/builtin/packages/r-futile-logger/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-futile-options/package.py b/var/spack/repos/builtin/packages/r-futile-options/package.py
index 9d0ee93d13..881d6f8ad1 100644
--- a/var/spack/repos/builtin/packages/r-futile-options/package.py
+++ b/var/spack/repos/builtin/packages/r-futile-options/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,5 +11,6 @@ class RFutileOptions(RPackage):
 
     homepage = "https://cran.rstudio.com/web/packages/futile.options/index.html"
     url      = "https://cran.rstudio.com/src/contrib/futile.options_1.0.0.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/futile.options"
 
     version('1.0.0', '8fd845774bbce56f41f7c43c3b4c13ba')
diff --git a/var/spack/repos/builtin/packages/r-gbm/package.py b/var/spack/repos/builtin/packages/r-gbm/package.py
index cddc0c77be..5309583922 100644
--- a/var/spack/repos/builtin/packages/r-gbm/package.py
+++ b/var/spack/repos/builtin/packages/r-gbm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-gcrma/package.py b/var/spack/repos/builtin/packages/r-gcrma/package.py
index b54315796a..8f9fe9ff1f 100644
--- a/var/spack/repos/builtin/packages/r-gcrma/package.py
+++ b/var/spack/repos/builtin/packages/r-gcrma/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,10 +10,9 @@ class RGcrma(RPackage):
     """Background adjustment using sequence information"""
 
     homepage = "https://bioconductor.org/packages/gcrma/"
-    url      = "https://git.bioconductor.org/packages/gcrma"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/gcrma.git"
 
-    version('2.48.0', git='https://git.bioconductor.org/packages/gcrma', commit='3ea0eb0b5c15ffb24df76620667ae7996ed715b4')
+    version('2.48.0', commit='3ea0eb0b5c15ffb24df76620667ae7996ed715b4')
 
     depends_on('r-affy', type=('build', 'run'))
     depends_on('r-biobase', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-gdata/package.py b/var/spack/repos/builtin/packages/r-gdata/package.py
index e07fc8d360..a093ae4485 100644
--- a/var/spack/repos/builtin/packages/r-gdata/package.py
+++ b/var/spack/repos/builtin/packages/r-gdata/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-gdsfmt/package.py b/var/spack/repos/builtin/packages/r-gdsfmt/package.py
new file mode 100644
index 0000000000..b2a98aa726
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-gdsfmt/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RGdsfmt(RPackage):
+    """This package provides a high-level R interface to CoreArray Genomic
+       Data Structure (GDS) data files, which are portable across platforms
+       with hierarchical structure to store multiple scalable array-oriented
+       data sets with metadata information. It is suited for large-scale
+       datasets, especially for data which are much larger than the available
+       random-access memory. The gdsfmt package offers the efficient
+       operations specifically designed for integers of less than 8 bits,
+       since a diploid genotype, like single-nucleotide polymorphism (SNP),
+       usually occupies fewer bits than a byte. Data compression and
+       decompression are available with relatively efficient random access.
+       It is also allowed to read a GDS file in parallel with multiple R
+       processes supported by the package parallel."""
+
+    homepage = "http://bioconductor.org/packages/gdsfmt/"
+    git      = "https://git.bioconductor.org/packages/gdsfmt.git"
+
+    version('1.14.1', commit='15743647b7eea5b82d3284858b4591fb6e59959d')
+
+    depends_on('r@3.4.0:3.4.9', when='@1.14.1')
diff --git a/var/spack/repos/builtin/packages/r-geiger/package.py b/var/spack/repos/builtin/packages/r-geiger/package.py
index c2ce69ef37..8bb6f8a3c7 100644
--- a/var/spack/repos/builtin/packages/r-geiger/package.py
+++ b/var/spack/repos/builtin/packages/r-geiger/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-genefilter/package.py b/var/spack/repos/builtin/packages/r-genefilter/package.py
index e5b631d778..afe1e1edf6 100644
--- a/var/spack/repos/builtin/packages/r-genefilter/package.py
+++ b/var/spack/repos/builtin/packages/r-genefilter/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,12 +10,14 @@ class RGenefilter(RPackage):
     """Some basic functions for filtering genes"""
 
     homepage = "https://bioconductor.org/packages/genefilter/"
-    url      = "https://git.bioconductor.org/packages/genefilter"
-    list_url = homepage
-    version('1.58.1', git='https://git.bioconductor.org/packages/genefilter', commit='ace2556049677f60882adfe91f8cc96791556fc2')
+    git      = "https://git.bioconductor.org/packages/genefilter.git"
+
+    version('1.62.0', commit='eb119894f015c759f93f458af7733bdb770a22ad')
+    version('1.58.1', commit='ace2556049677f60882adfe91f8cc96791556fc2')
 
-    depends_on('r@3.4.0:3.4.9', when='@1.58.1')
     depends_on('r-s4vectors', type=('build', 'run'))
     depends_on('r-annotationdbi', type=('build', 'run'))
     depends_on('r-annotate', type=('build', 'run'))
     depends_on('r-biobase', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@1.58.1', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@1.62.0', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-genelendatabase/package.py b/var/spack/repos/builtin/packages/r-genelendatabase/package.py
new file mode 100644
index 0000000000..003bc11e9d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-genelendatabase/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RGenelendatabase(RPackage):
+    """Length of mRNA transcripts for a number of genomes and gene ID
+       formats, largely based on UCSC table browser"""
+
+    homepage = "https://bioconductor.org/packages/release/data/experiment/html/geneLenDataBase.html"
+    git      = "https://git.bioconductor.org/packages/geneLenDataBase.git"
+
+    version('1.16.0', commit='c2a8b2359c6c59388853d6f6d15d71dffb17a198')
+
+    depends_on('r@3.5.0:3.5.9', when='@1.16.0:', type=('build', 'run'))
+    depends_on('r-rtracklayer', type=('build', 'run'))
+    depends_on('r-genomicfeatures@1.3.15:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-geneplotter/package.py b/var/spack/repos/builtin/packages/r-geneplotter/package.py
index 940c87e01f..46918c492a 100644
--- a/var/spack/repos/builtin/packages/r-geneplotter/package.py
+++ b/var/spack/repos/builtin/packages/r-geneplotter/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,14 +10,16 @@ class RGeneplotter(RPackage):
     """Functions for plotting genomic data."""
 
     homepage = "https://www.bioconductor.org/packages/geneplotter/"
-    url      = "https://git.bioconductor.org/packages/geneplotter"
+    git      = "https://git.bioconductor.org/packages/geneplotter.git"
 
-    version('1.54.0', git='https://git.bioconductor.org/packages/geneplotter', commit='efdd946e092e44e35fde1eb4bcc5ec1d52090940')
+    version('1.58.0', commit='2b3f44804d61a40cfe7eaedf74ac9f5a054f7fde')
+    version('1.54.0', commit='efdd946e092e44e35fde1eb4bcc5ec1d52090940')
 
-    depends_on('r@3.4.0:3.4.9', when='@1.54.0')
     depends_on('r-biobase', type=('build', 'run'))
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-lattice', type=('build', 'run'))
     depends_on('r-annotate', type=('build', 'run'))
     depends_on('r-annotationdbi', type=('build', 'run'))
     depends_on('r-rcolorbrewer', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@1.54.0', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@1.58.0', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-genie3/package.py b/var/spack/repos/builtin/packages/r-genie3/package.py
new file mode 100644
index 0000000000..b2942ffc89
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-genie3/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RGenie3(RPackage):
+    """This package implements the GENIE3 algorithm for inferring gene
+    regulatory networks from expression data."""
+
+    homepage = "https://bioconductor.org/packages/GENIE3/"
+    git      = "https://git.bioconductor.org/packages/GENIE3.git"
+
+    version('1.2.0', commit='cafe6a1a85095cda6cc3c812eb6f53501fcbaf93')
+
+    depends_on('r-reshape2', type=('build', 'run'))
+    depends_on('r@3.5.0:', when='@1.2.0')
diff --git a/var/spack/repos/builtin/packages/r-genomeinfodb/package.py b/var/spack/repos/builtin/packages/r-genomeinfodb/package.py
index 85a161a01b..a13b969c73 100644
--- a/var/spack/repos/builtin/packages/r-genomeinfodb/package.py
+++ b/var/spack/repos/builtin/packages/r-genomeinfodb/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,14 +13,19 @@ class RGenomeinfodb(RPackage):
        names in their natural, rather than lexicographic, order."""
 
     homepage = "https://bioconductor.org/packages/GenomeInfoDb/"
-    url      = "https://git.bioconductor.org/packages/GenomeInfoDb"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/GenomeInfoDb.git"
 
-    version('1.12.3', git='https://git.bioconductor.org/packages/GenomeInfoDb', commit='2deef3f0571b7f622483257bc22d2509ab5a0369')
+    version('1.16.0', commit='6543dad89bbc2c275010b329eb114b237fd712fa')
+    version('1.14.0', commit='4978308a57d887b764cc4ce83724ca1758f580f6')
+    version('1.12.3', commit='2deef3f0571b7f622483257bc22d2509ab5a0369')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.13.8:', when='@1.16.0', type=('build', 'run'))
     depends_on('r-s4vectors', type=('build', 'run'))
+    depends_on('r-s4vectors@0.17.25:', when='@1.16.0', type=('build', 'run'))
     depends_on('r-iranges', type=('build', 'run'))
+    depends_on('r-iranges@2.13.12:', when='@1.16.0', type=('build', 'run'))
     depends_on('r-rcurl', type=('build', 'run'))
     depends_on('r-genomeinfodbdata', type=('build', 'run'))
-    depends_on('r@3.4.0:3.4.9', when='@1.12.3')
+    depends_on('r@3.4.0:3.4.9', when='@1.12.3', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@1.16.0', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-genomeinfodbdata/package.py b/var/spack/repos/builtin/packages/r-genomeinfodbdata/package.py
index 8e231ac43c..cf74104950 100644
--- a/var/spack/repos/builtin/packages/r-genomeinfodbdata/package.py
+++ b/var/spack/repos/builtin/packages/r-genomeinfodbdata/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,8 +10,11 @@ class RGenomeinfodbdata(RPackage):
     """for mapping between NCBI taxonomy ID and species. Used by functions
        in the GenomeInfoDb package."""
 
-    homepage = "http://www.example.co://bioconductor.org/packages/3.5/data/annotation/html/GenomeInfoDbData.html"
+    homepage = "https://bioconductor.org/packages/GenomeInfoDbData/"
     url      = "https://bioconductor.org/packages/3.5/data/annotation/src/contrib/GenomeInfoDbData_0.99.0.tar.gz"
 
+    version('1.1.0', '6efdca22839c90d455843bdab7c0ecb5d48e3b6c2f7b4882d3210a6bbad4304c',
+            url='https://bioconductor.org/packages/release/data/annotation/src/contrib/GenomeInfoDbData_1.1.0.tar.gz')
     version('0.99.0', '85977b51061dd02a90153db887040d05')
-    depends_on('r@3.4.0:3.4.9', when='@0.99.0')
+    depends_on('r@3.4.0:3.4.9', when='@0.99.0', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@1.1.0', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-genomicalignments/package.py b/var/spack/repos/builtin/packages/r-genomicalignments/package.py
index 4a26b91538..9f66a1aba8 100644
--- a/var/spack/repos/builtin/packages/r-genomicalignments/package.py
+++ b/var/spack/repos/builtin/packages/r-genomicalignments/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,18 +13,29 @@ class RGenomicalignments(RPackage):
     detection, and working with the nucleotide content of the alignments."""
 
     homepage = "https://bioconductor.org/packages/GenomicAlignments/"
-    url      = "https://git.bioconductor.org/packages/GenomicAlignments"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/GenomicAlignments.git"
 
-    version('1.12.2', git='https://git.bioconductor.org/packages/GenomicAlignments', commit='b5d6f19e4a89b6c1c3e9e58e5ea4eb13870874ef')
+    version('1.16.0', commit='db032a459e5cf05a2a5c2059662a541827112974')
+    version('1.14.2', commit='57b0b35d8b36069d4d94af86af051f0129b28eef')
+    version('1.12.2', commit='b5d6f19e4a89b6c1c3e9e58e5ea4eb13870874ef')
 
-    depends_on('r-biocgenerics', type=('build', 'run'))
-    depends_on('r-s4vectors', type=('build', 'run'))
-    depends_on('r-iranges', type=('build', 'run'))
-    depends_on('r-genomeinfodb', type=('build', 'run'))
-    depends_on('r-genomicranges', type=('build', 'run'))
-    depends_on('r-summarizedexperiment', type=('build', 'run'))
-    depends_on('r-biostrings', type=('build', 'run'))
-    depends_on('r-rsamtools', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.15.3:', type=('build', 'run'))
+    depends_on('r-s4vectors@0.13.13:', type=('build', 'run'))
+    depends_on('r-s4vectors@0.17.28:', when='@1.16.0', type=('build', 'run'))
+    depends_on('r-iranges@2.5.36:', when='@1.12.2', type=('build', 'run'))
+    depends_on('r-iranges@2.11.16:', when='@1.14.2', type=('build', 'run'))
+    depends_on('r-iranges@2.13.25:', when='@1.16.0', type=('build', 'run'))
+    depends_on('r-genomeinfodb@1.11.5:', when='@1.12.2', type=('build', 'run'))
+    depends_on('r-genomeinfodb@1.13.1:', when='@1.14.2:', type=('build', 'run'))
+    depends_on('r-genomicranges@1.27.19:', when='@1.12.2', type=('build', 'run'))
+    depends_on('r-genomicranges@1.29.14:', when='@1.14.2', type=('build', 'run'))
+    depends_on('r-genomicranges@1.31.19:', when='@1.16.0', type=('build', 'run'))
+    depends_on('r-summarizedexperiment@1.5.3:', type=('build', 'run'))
+    depends_on('r-summarizedexperiment@1.9.13:', when='@1.16.0', type=('build', 'run'))
+    depends_on('r-biostrings@2.37.1:', type=('build', 'run'))
+    depends_on('r-biostrings@2.47.6:', when='@1.16.0', type=('build', 'run'))
+    depends_on('r-rsamtools@1.21.4:', type=('build', 'run'))
+    depends_on('r-rsamtools@1.31.2:', when='@1.16.0', type=('build', 'run'))
     depends_on('r-biocparallel', type=('build', 'run'))
-    depends_on('r@3.4.0:3.4.9', when='@1.12.2')
+    depends_on('r@3.4.0:3.4.9', when='@1.12.2:1.15.9', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@1.16.0', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-genomicfeatures/package.py b/var/spack/repos/builtin/packages/r-genomicfeatures/package.py
index a9e4bf5143..9531e36ccd 100644
--- a/var/spack/repos/builtin/packages/r-genomicfeatures/package.py
+++ b/var/spack/repos/builtin/packages/r-genomicfeatures/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,23 +17,34 @@ class RGenomicfeatures(RPackage):
        desired features in a convenient format."""
 
     homepage = "http://bioconductor.org/packages/GenomicFeatures/"
-    url      = "https://git.bioconductor.org/packages/GenomicFeatures"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/GenomicFeatures.git"
 
-    version('1.28.5', git='https://git.bioconductor.org/packages/GenomicFeatures', commit='ba92381ae93cb1392dad5e6acfab8f6c1d744834')
+    version('1.32.2', commit='8487aedc8be85a99f0c3fc90cd62430b3fec3a03')
+    version('1.28.5', commit='ba92381ae93cb1392dad5e6acfab8f6c1d744834')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-s4vectors', type=('build', 'run'))
+    depends_on('r-s4vectors@0.17.29:', when='@1.32.2', type=('build', 'run'))
     depends_on('r-iranges', type=('build', 'run'))
+    depends_on('r-iranges@2.13.23:', when='@1.32.2', type=('build', 'run'))
     depends_on('r-genomeinfodb', type=('build', 'run'))
+    depends_on('r-genomeinfodb@1.15.4:', when='@1.32.2', type=('build', 'run'))
     depends_on('r-genomicranges', type=('build', 'run'))
+    depends_on('r-genomicranges@1.31.17:', when='@1.32.2', type=('build', 'run'))
     depends_on('r-annotationdbi', type=('build', 'run'))
+    depends_on('r-annotationdbi@1.41.4:', when='@1.32.2', type=('build', 'run'))
     depends_on('r-dbi', type=('build', 'run'))
-    depends_on('r-rsqlite', type=('build', 'run'))
+    depends_on('r-rsqlite@2.0:', when='@1.28.5:', type=('build', 'run'))
     depends_on('r-rcurl', type=('build', 'run'))
     depends_on('r-xvector', type=('build', 'run'))
+    depends_on('r-xvector@0.19.7:', when='@1.32.2', type=('build', 'run'))
     depends_on('r-biostrings', type=('build', 'run'))
+    depends_on('r-biostrings@2.47.6:', when='@1.32.2', type=('build', 'run'))
     depends_on('r-rtracklayer', type=('build', 'run'))
+    depends_on('r-rtracklayer@1.39.7:', when='@1.32.2', type=('build', 'run'))
     depends_on('r-biomart', type=('build', 'run'))
+    depends_on('r-biomart@2.17.1:', when='@1.32.2', type=('build', 'run'))
     depends_on('r-biobase', type=('build', 'run'))
-    depends_on('r@3.4.0:3.4.9', when='@1.28.5')
+    depends_on('r-biobase@2.15.1:', when='@1.32.2', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@1.28.5', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@1.32.2', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-genomicranges/package.py b/var/spack/repos/builtin/packages/r-genomicranges/package.py
index bd3f685acd..d362b57909 100644
--- a/var/spack/repos/builtin/packages/r-genomicranges/package.py
+++ b/var/spack/repos/builtin/packages/r-genomicranges/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,14 +19,23 @@ class RGenomicranges(RPackage):
        infrastructure."""
 
     homepage = "https://bioconductor.org/packages/GenomicRanges/"
-    url      = "https://git.bioconductor.org/packages/GenomicRanges"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/GenomicRanges.git"
 
-    version('1.28.6', git='https://git.bioconductor.org/packages/GenomicRanges', commit='197472d618f3ed04c795dc6ed435500c29619563')
+    version('1.32.6', commit='31426be0fd6b76f7858971dc45aaf6e6d1dbac4e')
+    version('1.30.3', commit='e99979054bc50ed8c0109bc54563036c1b368997')
+    version('1.28.6', commit='197472d618f3ed04c795dc6ed435500c29619563')
 
-    depends_on('r-biocgenerics', type=('build', 'run'))
-    depends_on('r-s4vectors', type=('build', 'run'))
-    depends_on('r-iranges', type=('build', 'run'))
-    depends_on('r-genomeinfodb', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.21.2:', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.25.3:', when='@1.32.6', type=('build', 'run'))
+    depends_on('r-s4vectors@0.9.47:', type=('build', 'run'))
+    depends_on('r-s4vectors@0.17.32:', when='@1.32.6', type=('build', 'run'))
+    depends_on('r-iranges@2.9.11:', when='@1.28.6', type=('build', 'run'))
+    depends_on('r-iranges@2.11.16:', when='@1.30.3', type=('build', 'run'))
+    depends_on('r-iranges@2.14.4:', when='@1.32.6', type=('build', 'run'))
+    depends_on('r-genomeinfodb@1.11.5:', when='@1.28.6', type=('build', 'run'))
+    depends_on('r-genomeinfodb@1.13.1:', when='@1.30.3', type=('build', 'run'))
+    depends_on('r-genomeinfodb@1.15.2:', when='@1.32.6', type=('build', 'run'))
     depends_on('r-xvector', type=('build', 'run'))
-    depends_on('r@3.4.0:3.4.9', when='@1.28.6')
+    depends_on('r-xvector@0.19.8:', when='@1.32.6', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@1.28.6', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@1.32.6', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-geomorph/package.py b/var/spack/repos/builtin/packages/r-geomorph/package.py
index 1cb82c9d7e..cb9e3605de 100644
--- a/var/spack/repos/builtin/packages/r-geomorph/package.py
+++ b/var/spack/repos/builtin/packages/r-geomorph/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-geoquery/package.py b/var/spack/repos/builtin/packages/r-geoquery/package.py
index fd2c497430..af3629e5ed 100644
--- a/var/spack/repos/builtin/packages/r-geoquery/package.py
+++ b/var/spack/repos/builtin/packages/r-geoquery/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,10 +13,9 @@ class RGeoquery(RPackage):
        GEOquery is the bridge between GEO and BioConductor."""
 
     homepage = "https://bioconductor.org/packages/GEOquery/"
-    url      = "https://git.bioconductor.org/packages/GEOquery"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/GEOquery.git"
 
-    version('2.42.0', git='https://git.bioconductor.org/packages/GEOquery', commit='c26adef8d3ddbd6932a3170f2f84f6e4327641fb')
+    version('2.42.0', commit='c26adef8d3ddbd6932a3170f2f84f6e4327641fb')
 
     depends_on('r-biobase', type=('build', 'run'))
     depends_on('r-xml', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-geosphere/package.py b/var/spack/repos/builtin/packages/r-geosphere/package.py
index ee93217fb5..f6a3f233a1 100644
--- a/var/spack/repos/builtin/packages/r-geosphere/package.py
+++ b/var/spack/repos/builtin/packages/r-geosphere/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-getopt/package.py b/var/spack/repos/builtin/packages/r-getopt/package.py
new file mode 100644
index 0000000000..a1e1286b6c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-getopt/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RGetopt(RPackage):
+    """Package designed to be used with Rscript to write "#!" shebang scripts
+       that accept short and long flags/options. Many users will prefer using
+       instead the packages optparse or argparse which add extra features like
+       automatically generated help option and usage, support for default
+       values, positional argument support, etc."""
+
+    homepage = "https://github.com/trevorld/getopt"
+    url      = "https://cran.r-project.org/src/contrib/getopt_1.20.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/getopt"
+
+    version('1.20.1', '323cf2846e306f49236b8174bc3d4e47')
diff --git a/var/spack/repos/builtin/packages/r-getoptlong/package.py b/var/spack/repos/builtin/packages/r-getoptlong/package.py
index b4c4a8f4e6..61d6cb7977 100644
--- a/var/spack/repos/builtin/packages/r-getoptlong/package.py
+++ b/var/spack/repos/builtin/packages/r-getoptlong/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-ggally/package.py b/var/spack/repos/builtin/packages/r-ggally/package.py
index f06d8257d3..26dacf1378 100644
--- a/var/spack/repos/builtin/packages/r-ggally/package.py
+++ b/var/spack/repos/builtin/packages/r-ggally/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-ggbio/package.py b/var/spack/repos/builtin/packages/r-ggbio/package.py
index 8c5f27885a..30ebcf23d8 100644
--- a/var/spack/repos/builtin/packages/r-ggbio/package.py
+++ b/var/spack/repos/builtin/packages/r-ggbio/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,10 +18,9 @@ class RGgbio(RPackage):
        and several splicing summaries."""
 
     homepage = "http://bioconductor.org/packages/ggbio/"
-    url      = "https://git.bioconductor.org/packages/ggbio"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/ggbio.git"
 
-    version('1.24.1', git='https://git.bioconductor.org/packages/ggbio', commit='ef04c1bca1330f37152bcc21080cbde94849a094')
+    version('1.24.1', commit='ef04c1bca1330f37152bcc21080cbde94849a094')
 
     depends_on('r-gridextra', type=('build', 'run'))
     depends_on('r-scales', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-ggdendro/package.py b/var/spack/repos/builtin/packages/r-ggdendro/package.py
index e86180d4ac..d0b0562f39 100644
--- a/var/spack/repos/builtin/packages/r-ggdendro/package.py
+++ b/var/spack/repos/builtin/packages/r-ggdendro/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-ggjoy/package.py b/var/spack/repos/builtin/packages/r-ggjoy/package.py
new file mode 100644
index 0000000000..aa3ca2477b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-ggjoy/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RGgjoy(RPackage):
+    """Joyplots provide a convenient way of visualizing changes in distributions
+    over time or space."""
+
+    homepage = "https://cran.r-project.org/web/packages/ggjoy/index.html"
+    url      = "https://cran.r-project.org/src/contrib/ggjoy_0.4.0.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/ggjoy"
+
+    version('0.4.0', 'c63782e2395a9cfc435d08e078e6596b')
+    version('0.3.0', '59bd34a846270d43f2eeb1e90b03a127')
+    version('0.2.0', '8584cd154e228f8505b324e91d2e50d7')
+
+    depends_on('r@3.4.0:3.4.9')
+    depends_on('r-ggplot2', type=('build', 'run'))
+    depends_on('r-ggridges', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-ggmap/package.py b/var/spack/repos/builtin/packages/r-ggmap/package.py
index a3c16f7a45..4fe5a9e583 100644
--- a/var/spack/repos/builtin/packages/r-ggmap/package.py
+++ b/var/spack/repos/builtin/packages/r-ggmap/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-ggplot2/package.py b/var/spack/repos/builtin/packages/r-ggplot2/package.py
index c2c5e49832..0836103e41 100644
--- a/var/spack/repos/builtin/packages/r-ggplot2/package.py
+++ b/var/spack/repos/builtin/packages/r-ggplot2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-ggpubr/package.py b/var/spack/repos/builtin/packages/r-ggpubr/package.py
index ebc505bf5b..66f10d03f9 100644
--- a/var/spack/repos/builtin/packages/r-ggpubr/package.py
+++ b/var/spack/repos/builtin/packages/r-ggpubr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-ggrepel/package.py b/var/spack/repos/builtin/packages/r-ggrepel/package.py
index a44a22ee1e..075b081535 100644
--- a/var/spack/repos/builtin/packages/r-ggrepel/package.py
+++ b/var/spack/repos/builtin/packages/r-ggrepel/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-ggridges/package.py b/var/spack/repos/builtin/packages/r-ggridges/package.py
new file mode 100644
index 0000000000..c5f686282d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-ggridges/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RGgridges(RPackage):
+    """Ridgeline plots provide a convenient way of visualizing changes in
+    distributions over time or space."""
+
+    homepage = "https://cran.r-project.org/web/packages/ggridges/index.html"
+    url      = "https://cran.r-project.org/src/contrib/ggridges_0.4.1.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/ggridges"
+
+    version('0.4.1', '21d53b3f7263beb17f629f0ebfb7b67a')
+    version('0.4.0', 'da94ed1ee856a7fa5fb87712c84ec4c9')
+
+    depends_on('r@3.4.0:3.4.9')
+    depends_on('r-ggplot2', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-ggsci/package.py b/var/spack/repos/builtin/packages/r-ggsci/package.py
index 1fedf202ee..2cec0a6496 100644
--- a/var/spack/repos/builtin/packages/r-ggsci/package.py
+++ b/var/spack/repos/builtin/packages/r-ggsci/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-ggvis/package.py b/var/spack/repos/builtin/packages/r-ggvis/package.py
index c0dab6b8e4..6c2dffcc42 100644
--- a/var/spack/repos/builtin/packages/r-ggvis/package.py
+++ b/var/spack/repos/builtin/packages/r-ggvis/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-gistr/package.py b/var/spack/repos/builtin/packages/r-gistr/package.py
index 7cbe2ecafe..500d9cb0de 100644
--- a/var/spack/repos/builtin/packages/r-gistr/package.py
+++ b/var/spack/repos/builtin/packages/r-gistr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/r-git2r/package.py b/var/spack/repos/builtin/packages/r-git2r/package.py
index 3fa8baab7c..ad9545b6a2 100644
--- a/var/spack/repos/builtin/packages/r-git2r/package.py
+++ b/var/spack/repos/builtin/packages/r-git2r/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-glimma/package.py b/var/spack/repos/builtin/packages/r-glimma/package.py
new file mode 100644
index 0000000000..5fe40e6594
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-glimma/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RGlimma(RPackage):
+    """This package generates interactive visualisations for analysis of
+       RNA-sequencing data using output from limma, edgeR or DESeq2 packages
+       in an HTML page. The interactions are built on top of the popular
+       static representations of analysis results in order to provide
+       additional information."""
+
+    homepage = "https://bioconductor.org/packages/release/bioc/html/Glimma.html"
+    git      = "https://git.bioconductor.org/packages/Glimma.git"
+
+    version('1.8.2', commit='f4aa1f05c2890d04b01ad4c0ab27f2f729f2c969')
+
+    depends_on('r@3.5.0:3.5.9', when='@1.8.2:', type=('build', 'run'))
+    depends_on('r-edger', type=('build', 'run'))
+    depends_on('r-jsonlite', type=('build', 'run'))
+    depends_on('r-s4vectors', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-glmnet/package.py b/var/spack/repos/builtin/packages/r-glmnet/package.py
index 4e531165be..7f79e5f023 100644
--- a/var/spack/repos/builtin/packages/r-glmnet/package.py
+++ b/var/spack/repos/builtin/packages/r-glmnet/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-globaloptions/package.py b/var/spack/repos/builtin/packages/r-globaloptions/package.py
index 7785d4f3a1..3aef7c1f65 100644
--- a/var/spack/repos/builtin/packages/r-globaloptions/package.py
+++ b/var/spack/repos/builtin/packages/r-globaloptions/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-glue/package.py b/var/spack/repos/builtin/packages/r-glue/package.py
new file mode 100644
index 0000000000..bfd92fcdbd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-glue/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RGlue(RPackage):
+    """An implementation of interpreted string literals, inspired by Python's
+       Literal String Interpolation <https://www.python.org/dev/peps/pep-0498/>
+       and Docstrings <https://www.python.org/dev/peps/pep-0257/> and Julia's
+       Triple-Quoted String Literals <https://docs.julialang.org/en/stable/
+       manual/strings/#triple-quoted-string-literals>."""
+
+    homepage = "https://github.com/tidyverse/glue"
+    url      = "https://cran.r-project.org/src/contrib/glue_1.2.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/glue"
+
+    version('1.2.0', '77d06b6d86abc882fa1c0599e457c5e2')
diff --git a/var/spack/repos/builtin/packages/r-gmodels/package.py b/var/spack/repos/builtin/packages/r-gmodels/package.py
index ce4a8c9692..a9fd5541c0 100644
--- a/var/spack/repos/builtin/packages/r-gmodels/package.py
+++ b/var/spack/repos/builtin/packages/r-gmodels/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-gmp/package.py b/var/spack/repos/builtin/packages/r-gmp/package.py
index 18e394f1ac..6aaa8d683c 100644
--- a/var/spack/repos/builtin/packages/r-gmp/package.py
+++ b/var/spack/repos/builtin/packages/r-gmp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-go-db/package.py b/var/spack/repos/builtin/packages/r-go-db/package.py
index af5df1ce3b..61cd6d35dc 100644
--- a/var/spack/repos/builtin/packages/r-go-db/package.py
+++ b/var/spack/repos/builtin/packages/r-go-db/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-googlevis/package.py b/var/spack/repos/builtin/packages/r-googlevis/package.py
index 4d7cfbd259..ac12962998 100644
--- a/var/spack/repos/builtin/packages/r-googlevis/package.py
+++ b/var/spack/repos/builtin/packages/r-googlevis/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-goplot/package.py b/var/spack/repos/builtin/packages/r-goplot/package.py
new file mode 100644
index 0000000000..f9b86de5bd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-goplot/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+from spack import *
+
+
+class RGoplot(RPackage):
+    """Implementation of multilayered visualizations for enhanced graphical
+       representation of functional analysis data. It combines and integrates
+       omics data derived from expression and functional annotation enrichment
+       analyses. Its plotting functions have been developed with an
+       hierarchical structure in mind: starting from a general overview to
+       identify the most enriched categories (modified bar plot, bubble plot)
+       to a more detailed one displaying different types of relevant
+       information for the molecules in a given set of categories
+       (circle plot, chord plot, cluster plot, Venn diagram, heatmap)."""
+
+    homepage = "https://github.com/wencke/wencke.github.io/issues"
+    url      = "https://cran.r-project.org/src/contrib/GOplot_1.0.2.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/GOplot"
+
+    version('1.0.2', sha256='3ddaa2b6d1297ad6daad30d18af708adf43d86e8804b1b92fa29dfbf26d80df9')
+
+    depends_on('r@3.2.3:', type=('build', 'run'))
+    depends_on('r-ggplot2@2.0.0:', type=('build', 'run'))
+    depends_on('r-ggdendro@0.1-17:', type=('build', 'run'))
+    depends_on('r-gridextra@2.0.0:', type=('build', 'run'))
+    depends_on('r-rcolorbrewer@1.1-2:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-gosemsim/package.py b/var/spack/repos/builtin/packages/r-gosemsim/package.py
new file mode 100644
index 0000000000..b425445b0c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-gosemsim/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RGosemsim(RPackage):
+    """The semantic comparisons of Gene Ontology (GO) annotations provide
+    quantitative ways to compute similarities between genes and gene
+    groups, and have became important basis for many bioinformatics
+    analysis approaches. GOSemSim is an R package for semantic similarity
+    computation among GO terms, sets of GO terms, gene products and gene
+    clusters. GOSemSim implemented five methods proposed by Resnik,
+    Schlicker, Jiang, Lin and Wang respectively."""
+
+    homepage = "https://www.bioconductor.org/packages/GOSemSim/"
+    git      = "https://git.bioconductor.org/packages/GOSemSim.git"
+
+    version('2.2.0', commit='247434790e6c8cf99e5643f569390362b8c87c52')
+
+    depends_on('r@3.4.0:3.4.9', when='@2.2.0')
+    depends_on('r-annotationdbi', type=('build', 'run'))
+    depends_on('r-go-db', type=('build', 'run'))
+    depends_on('r-rcpp', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-goseq/package.py b/var/spack/repos/builtin/packages/r-goseq/package.py
new file mode 100644
index 0000000000..5801169f1f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-goseq/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RGoseq(RPackage):
+    """Detects Gene Ontology and/or other user defined categories which are
+       over/under represented in RNA-seq data"""
+
+    homepage = "https://bioconductor.org/packages/release/bioc/html/goseq.html"
+    git      = "https://git.bioconductor.org/packages/goseq.git"
+
+    version('1.32.0', commit='32fcbe647eea17d7d0d7a262610811502c421d36')
+
+    depends_on('r@3.5.0:3.5.9', when='@1.32.0:', type=('build', 'run'))
+    depends_on('r-biasedurn', type=('build', 'run'))
+    depends_on('r-genelendatabase@1.9.2:', type=('build', 'run'))
+    depends_on('r-mgcv', type=('build', 'run'))
+    depends_on('r-annotationdbi', type=('build', 'run'))
+    depends_on('r-go-db', type=('build', 'run'))
+    depends_on('r-biocgenerics', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-gostats/package.py b/var/spack/repos/builtin/packages/r-gostats/package.py
index ef4231fc7d..36ca8a63d0 100644
--- a/var/spack/repos/builtin/packages/r-gostats/package.py
+++ b/var/spack/repos/builtin/packages/r-gostats/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,9 +12,9 @@ class RGostats(RPackage):
     testing and other simple calculations."""
 
     homepage = "https://www.bioconductor.org/packages/GOstats/"
-    url      = "https://git.bioconductor.org/packages/GOstats"
+    git      = "https://git.bioconductor.org/packages/GOstats.git"
 
-    version('2.42.0', git='https://git.bioconductor.org/packages/GOstats', commit='8b29709064a3b66cf1d963b2be0c996fb48c873e')
+    version('2.42.0', commit='8b29709064a3b66cf1d963b2be0c996fb48c873e')
 
     depends_on('r@3.4.1:3.4.9', when='@2.42.0')
     depends_on('r-biobase', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-gplots/package.py b/var/spack/repos/builtin/packages/r-gplots/package.py
index 21c3738caa..ff81686ba3 100644
--- a/var/spack/repos/builtin/packages/r-gplots/package.py
+++ b/var/spack/repos/builtin/packages/r-gplots/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 #
 from spack import *
diff --git a/var/spack/repos/builtin/packages/r-graph/package.py b/var/spack/repos/builtin/packages/r-graph/package.py
index a7b6140de8..88760e05bc 100644
--- a/var/spack/repos/builtin/packages/r-graph/package.py
+++ b/var/spack/repos/builtin/packages/r-graph/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,9 @@ class RGraph(RPackage):
     """A package that implements some simple graph handling capabilities."""
 
     homepage = "https://www.bioconductor.org/packages/graph/"
-    url      = "https://git.bioconductor.org/packages/graph"
+    git      = "https://git.bioconductor.org/packages/graph.git"
 
-    version('1.54.0', git='https://git.bioconductor.org/packages/graph', commit='2a8b08520096241620421078fc1098f4569c7301')
+    version('1.54.0', commit='2a8b08520096241620421078fc1098f4569c7301')
 
     depends_on('r@3.4.0:3.4.9', when='@1.54.0')
     depends_on('r-biocgenerics', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-gridbase/package.py b/var/spack/repos/builtin/packages/r-gridbase/package.py
index 4353f16819..ed8e0b0267 100644
--- a/var/spack/repos/builtin/packages/r-gridbase/package.py
+++ b/var/spack/repos/builtin/packages/r-gridbase/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-gridextra/package.py b/var/spack/repos/builtin/packages/r-gridextra/package.py
index 2b64580c4e..27c66a10ba 100644
--- a/var/spack/repos/builtin/packages/r-gridextra/package.py
+++ b/var/spack/repos/builtin/packages/r-gridextra/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-gseabase/package.py b/var/spack/repos/builtin/packages/r-gseabase/package.py
index b02b16289b..6dbe982b5d 100644
--- a/var/spack/repos/builtin/packages/r-gseabase/package.py
+++ b/var/spack/repos/builtin/packages/r-gseabase/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,9 @@ class RGseabase(RPackage):
     Set Enrichment Analysis (GSEA)."""
 
     homepage = "https://www.bioconductor.org/packages/GSEABase/"
-    url      = "https://git.bioconductor.org/packages/GSEABase"
+    git      = "https://git.bioconductor.org/packages/GSEABase.git"
 
-    version('1.38.2', git='https://git.bioconductor.org/packages/GSEABase', commit='84c9f10c316163118ca990900a7a67555b96e75b')
+    version('1.38.2', commit='84c9f10c316163118ca990900a7a67555b96e75b')
 
     depends_on('r@3.4.0:3.4.9', when='@1.38.2')
     depends_on('r-biocgenerics', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-gss/package.py b/var/spack/repos/builtin/packages/r-gss/package.py
new file mode 100644
index 0000000000..9d65dd1d32
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-gss/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RGss(RPackage):
+    """A comprehensive package for structural multivariate function
+    estimation using smoothing splines."""
+
+    homepage = "https://cran.r-project.org/package=gss"
+    url      = "https://cran.rstudio.com/src/contrib/gss_2.1-7.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/gss"
+
+    version('2.1-7', '4a6bd96339d22b40c932895b64504fb2')
diff --git a/var/spack/repos/builtin/packages/r-gsubfn/package.py b/var/spack/repos/builtin/packages/r-gsubfn/package.py
index 858f7f2e39..ffe55f94a7 100644
--- a/var/spack/repos/builtin/packages/r-gsubfn/package.py
+++ b/var/spack/repos/builtin/packages/r-gsubfn/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-gtable/package.py b/var/spack/repos/builtin/packages/r-gtable/package.py
index 498e5ba2c3..e3400d641b 100644
--- a/var/spack/repos/builtin/packages/r-gtable/package.py
+++ b/var/spack/repos/builtin/packages/r-gtable/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-gtools/package.py b/var/spack/repos/builtin/packages/r-gtools/package.py
index 0c74d8449a..e42aae0220 100644
--- a/var/spack/repos/builtin/packages/r-gtools/package.py
+++ b/var/spack/repos/builtin/packages/r-gtools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-gtrellis/package.py b/var/spack/repos/builtin/packages/r-gtrellis/package.py
index 64526035db..a1558c9cbd 100644
--- a/var/spack/repos/builtin/packages/r-gtrellis/package.py
+++ b/var/spack/repos/builtin/packages/r-gtrellis/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,10 +15,9 @@ class RGtrellis(RPackage):
        graphics in the plot."""
 
     homepage = "https://bioconductor.org/packages/gtrellis/"
-    url      = "https://git.bioconductor.org/packages/gtrellis"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/gtrellis.git"
 
-    version('1.8.0', git='https://git.bioconductor.org/packages/gtrellis', commit='f813b420a008c459f63a2a13e5e64c5507c4c472')
+    version('1.8.0', commit='f813b420a008c459f63a2a13e5e64c5507c4c472')
 
     depends_on('r-iranges', type=('build', 'run'))
     depends_on('r-genomicranges', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-gviz/package.py b/var/spack/repos/builtin/packages/r-gviz/package.py
index ddb56cc681..23b886a34b 100644
--- a/var/spack/repos/builtin/packages/r-gviz/package.py
+++ b/var/spack/repos/builtin/packages/r-gviz/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,9 +16,9 @@ class RGviz(RPackage):
     together with your data."""
 
     homepage = "http://bioconductor.org/packages/Gviz/"
-    url      = "https://git.bioconductor.org/packages/Gviz"
+    git      = "https://git.bioconductor.org/packages/Gviz.git"
 
-    version('1.20.0', git='https://git.bioconductor.org/packages/Gviz', commit='299b8255e1b03932cebe287c3690d58c88f5ba5c')
+    version('1.20.0', commit='299b8255e1b03932cebe287c3690d58c88f5ba5c')
 
     depends_on('r@3.4.0:3.4.9', when='@1.20.0')
     depends_on('r-s4vectors', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-haven/package.py b/var/spack/repos/builtin/packages/r-haven/package.py
new file mode 100644
index 0000000000..dab9e486b5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-haven/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RHaven(RPackage):
+    """Import foreign statistical formats into R via the embedded 'ReadStat' C
+       library, <https://github.com/WizardMac/ReadStat>."""
+
+    homepage = "http://haven.tidyverse.org/"
+    url      = "https://cran.r-project.org/src/contrib/haven_1.1.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/haven"
+
+    version('1.1.0', '8edd4b7683f8c36b5bb68582ac1b8733')
+
+    depends_on('r-rcpp', type=('build', 'run'))
+    depends_on('r-readr', type=('build', 'run'))
+    depends_on('r-hms', type=('build', 'run'))
+    depends_on('r-tibble', type=('build', 'run'))
+    depends_on('r-forcats', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-hexbin/package.py b/var/spack/repos/builtin/packages/r-hexbin/package.py
index 179914fca3..8f71d729d4 100644
--- a/var/spack/repos/builtin/packages/r-hexbin/package.py
+++ b/var/spack/repos/builtin/packages/r-hexbin/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/r-highr/package.py b/var/spack/repos/builtin/packages/r-highr/package.py
index cc89cfd80b..fe8606ca59 100644
--- a/var/spack/repos/builtin/packages/r-highr/package.py
+++ b/var/spack/repos/builtin/packages/r-highr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/r-hmisc/package.py b/var/spack/repos/builtin/packages/r-hmisc/package.py
index 436c3279ec..11cc890764 100644
--- a/var/spack/repos/builtin/packages/r-hmisc/package.py
+++ b/var/spack/repos/builtin/packages/r-hmisc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,9 +15,10 @@ class RHmisc(RPackage):
     code, and recoding variables."""
 
     homepage = "http://biostat.mc.vanderbilt.edu/Hmisc"
-    url      = "https://cran.rstudio.com/src/contrib/Hmisc_4.0-3.tar.gz"
+    url      = "https://cran.rstudio.com/src/contrib/Hmisc_4.1-1.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/Hmisc"
 
+    version('4.1-1', 'd255611f2b108d3cc0212b8a98fef6e3')
     version('4.0-3', '7091924db1e473419d8116c3335f82da')
 
     depends_on('r-lattice', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-hms/package.py b/var/spack/repos/builtin/packages/r-hms/package.py
index cf3a4a88c3..caf95888d5 100644
--- a/var/spack/repos/builtin/packages/r-hms/package.py
+++ b/var/spack/repos/builtin/packages/r-hms/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-htmltable/package.py b/var/spack/repos/builtin/packages/r-htmltable/package.py
index f142a5221a..d2b832d151 100644
--- a/var/spack/repos/builtin/packages/r-htmltable/package.py
+++ b/var/spack/repos/builtin/packages/r-htmltable/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,13 +16,15 @@ class RHtmltable(RPackage):
     compatible with HTML/'LaTeX'."""
 
     homepage = "https://CRAN.R-project.org/package=htmlTable"
-    url      = "https://cran.rstudio.com/src/contrib/htmlTable_1.9.tar.gz"
+    url      = "https://cran.rstudio.com/src/contrib/htmlTable_1.11.2.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/htmlTable"
 
+    version('1.11.2', '473e6d486e7714f8dd7f16a31480c896')
     version('1.9', '08c62c19e1ffe570e7d8fa57db5094b9')
 
     depends_on('r-stringr', type=('build', 'run'))
-    depends_on('r-knitr', type=('build', 'run'))
-    depends_on('r-magrittr', type=('build', 'run'))
+    depends_on('r-knitr@1.6:', type=('build', 'run'))
+    depends_on('r-magrittr@1.5:', type=('build', 'run'))
     depends_on('r-checkmate', type=('build', 'run'))
     depends_on('r-htmlwidgets', type=('build', 'run'))
+    depends_on('r-rstudioapi@0.6:', type=('build', 'run'), when="@1.11.0:")
diff --git a/var/spack/repos/builtin/packages/r-htmltools/package.py b/var/spack/repos/builtin/packages/r-htmltools/package.py
index 865c2f79ae..4bedff2115 100644
--- a/var/spack/repos/builtin/packages/r-htmltools/package.py
+++ b/var/spack/repos/builtin/packages/r-htmltools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-htmlwidgets/package.py b/var/spack/repos/builtin/packages/r-htmlwidgets/package.py
index 1dcbbe5062..4416678974 100644
--- a/var/spack/repos/builtin/packages/r-htmlwidgets/package.py
+++ b/var/spack/repos/builtin/packages/r-htmlwidgets/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-httpuv/package.py b/var/spack/repos/builtin/packages/r-httpuv/package.py
index 59ba283621..ac2967c491 100644
--- a/var/spack/repos/builtin/packages/r-httpuv/package.py
+++ b/var/spack/repos/builtin/packages/r-httpuv/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-httr/package.py b/var/spack/repos/builtin/packages/r-httr/package.py
index a533f6cbd9..f3f5426fdd 100644
--- a/var/spack/repos/builtin/packages/r-httr/package.py
+++ b/var/spack/repos/builtin/packages/r-httr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-hwriter/package.py b/var/spack/repos/builtin/packages/r-hwriter/package.py
index df8a2129db..348dec8b56 100644
--- a/var/spack/repos/builtin/packages/r-hwriter/package.py
+++ b/var/spack/repos/builtin/packages/r-hwriter/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-hypergraph/package.py b/var/spack/repos/builtin/packages/r-hypergraph/package.py
index b6fc0df172..8da1131197 100644
--- a/var/spack/repos/builtin/packages/r-hypergraph/package.py
+++ b/var/spack/repos/builtin/packages/r-hypergraph/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,9 @@ class RHypergraph(RPackage):
     representing and manipulating hypergraphs."""
 
     homepage = "https://www.bioconductor.org/packages/hypergraph/"
-    url      = "https://git.bioconductor.org/packages/hypergraph"
+    git      = "https://git.bioconductor.org/packages/hypergraph.git"
 
-    version('1.48.0', git='https://git.bioconductor.org/packages/hypergraph', commit='a4c19ea0b5f15204f706a7bfdea5363706382820')
+    version('1.48.0', commit='a4c19ea0b5f15204f706a7bfdea5363706382820')
 
     depends_on('r@3.4.0:3.4.9', when='@1.48.0')
     depends_on('r-graph', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-ica/package.py b/var/spack/repos/builtin/packages/r-ica/package.py
new file mode 100644
index 0000000000..10e46c971e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-ica/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RIca(RPackage):
+    """Independent Component Analysis (ICA) using various algorithms: FastICA,
+    Information-Maximization (Infomax), and Joint Approximate Diagonalization
+    of Eigenmatrices (JADE)."""
+
+    homepage = "https://cran.r-project.org/web/packages/ica/index.html"
+    url      = "https://cran.r-project.org/src/contrib/ica_1.0-1.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/ica"
+
+    depends_on('r@3.4.0:3.4.9')
+    version('1.0-1', '15c8d5afeec2804beec55dd14abc585d')
+    version('1.0-0', '3ade2b3b00eb39c348d802f24d2afd1d')
diff --git a/var/spack/repos/builtin/packages/r-igraph/package.py b/var/spack/repos/builtin/packages/r-igraph/package.py
index b8a715b9ae..9d14815389 100644
--- a/var/spack/repos/builtin/packages/r-igraph/package.py
+++ b/var/spack/repos/builtin/packages/r-igraph/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,11 +15,12 @@ class RIgraph(RPackage):
     url      = "https://cran.r-project.org/src/contrib/igraph_1.0.1.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/igraph"
 
+    version('1.1.2', 'ca1617aea272852d2856c4661ad1c7d8')
     version('1.0.1', 'ea33495e49adf4a331e4ba60ba559065')
 
     depends_on('r-matrix', type=('build', 'run'))
     depends_on('r-magrittr', type=('build', 'run'))
-    depends_on('r-nmf', type=('build', 'run'))
+    depends_on('r-pkgconfig', type=('build', 'run'))
     depends_on('r-irlba', type=('build', 'run'))
     depends_on('gmp')
     depends_on('libxml2')
diff --git a/var/spack/repos/builtin/packages/r-illuminaio/package.py b/var/spack/repos/builtin/packages/r-illuminaio/package.py
index 9d0993fb8f..8e578421c6 100644
--- a/var/spack/repos/builtin/packages/r-illuminaio/package.py
+++ b/var/spack/repos/builtin/packages/r-illuminaio/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,10 +11,9 @@ class RIlluminaio(RPackage):
        IDAT."""
 
     homepage = "http://bioconductor.org/packages/illuminaio/"
-    url      = "https://git.bioconductor.org/packages/illuminaio"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/illuminaio.git"
 
-    version('0.18.0', git='https://git.bioconductor.org/packages/illuminaio', commit='e6b8ab1f8eacb760aebdb4828e9cfbf07da06eda')
+    version('0.18.0', commit='e6b8ab1f8eacb760aebdb4828e9cfbf07da06eda')
 
     depends_on('r-base64', type=('build', 'run'))
     depends_on('r@3.4.0:3.4.9', when='@0.18.0')
diff --git a/var/spack/repos/builtin/packages/r-impute/package.py b/var/spack/repos/builtin/packages/r-impute/package.py
index b8bf956ac1..76cfb9be9b 100644
--- a/var/spack/repos/builtin/packages/r-impute/package.py
+++ b/var/spack/repos/builtin/packages/r-impute/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,8 +10,8 @@ class RImpute(RPackage):
     """Imputation for microarray data (currently KNN only)."""
 
     homepage = "https://www.bioconductor.org/packages/impute/"
-    url      = "https://git.bioconductor.org/packages/impute"
+    git      = "https://git.bioconductor.org/packages/impute.git"
 
-    version('1.50.1', git='https://git.bioconductor.org/packages/impute', commit='31d1cc141797afdc83743e1d95aab8a90ee19b71')
+    version('1.50.1', commit='31d1cc141797afdc83743e1d95aab8a90ee19b71')
 
     depends_on('r@3.4.0:3.4.9', when='@1.50.1')
diff --git a/var/spack/repos/builtin/packages/r-influencer/package.py b/var/spack/repos/builtin/packages/r-influencer/package.py
index 53f1ba67a7..ded5558e98 100644
--- a/var/spack/repos/builtin/packages/r-influencer/package.py
+++ b/var/spack/repos/builtin/packages/r-influencer/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-inline/package.py b/var/spack/repos/builtin/packages/r-inline/package.py
index 235aacfe19..54e32607b3 100644
--- a/var/spack/repos/builtin/packages/r-inline/package.py
+++ b/var/spack/repos/builtin/packages/r-inline/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-interactivedisplaybase/package.py b/var/spack/repos/builtin/packages/r-interactivedisplaybase/package.py
index 8b64962096..8a5a6a038d 100644
--- a/var/spack/repos/builtin/packages/r-interactivedisplaybase/package.py
+++ b/var/spack/repos/builtin/packages/r-interactivedisplaybase/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,10 +12,9 @@ class RInteractivedisplaybase(RPackage):
        Bioconductor objects."""
 
     homepage = "https://bioconductor.org/packages/interactiveDisplayBase/"
-    url      = "https://git.bioconductor.org/packages/interactiveDisplayBase"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/interactiveDisplayBase.git"
 
-    version('1.14.0', git='https://git.bioconductor.org/packages/interactiveDisplayBase', commit='e2ccc7eefdd904e3b1032dc6b3f4a28d08c1cd40')
+    version('1.14.0', commit='e2ccc7eefdd904e3b1032dc6b3f4a28d08c1cd40')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-shiny', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-ipred/package.py b/var/spack/repos/builtin/packages/r-ipred/package.py
index 97d84f5361..825046560f 100644
--- a/var/spack/repos/builtin/packages/r-ipred/package.py
+++ b/var/spack/repos/builtin/packages/r-ipred/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-iranges/package.py b/var/spack/repos/builtin/packages/r-iranges/package.py
index c53b2773a7..5a79d0973b 100644
--- a/var/spack/repos/builtin/packages/r-iranges/package.py
+++ b/var/spack/repos/builtin/packages/r-iranges/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,10 +19,17 @@ class RIranges(RPackage):
     i.e., collections of atomic vectors and DataFrames."""
 
     homepage = "https://www.bioconductor.org/packages/IRanges/"
-    url      = "https://git.bioconductor.org/packages/IRanges"
-    list_url = homepage
-    version('2.10.5', git='https://git.bioconductor.org/packages/IRanges', commit='b00d1d5025e3c480d17c13100f0da5a0132b1614')
+    git      = "https://git.bioconductor.org/packages/IRanges.git"
+
+    version('2.14.10', commit='c76118a38e84c7c764141adbd66ee350d0882bc9')
+    version('2.12.0', commit='1b1748655a8529ba87ad0f223f035ef0c08e7fcd')
+    version('2.10.5', commit='b00d1d5025e3c480d17c13100f0da5a0132b1614')
 
-    depends_on('r-biocgenerics', type=('build', 'run'))
-    depends_on('r-s4vectors', type=('build', 'run'))
-    depends_on('r@3.4.0:3.4.9', when='@2.10.5')
+    depends_on('r-biocgenerics@0.21.1:', type=('build', 'run'), when='@2.10.5')
+    depends_on('r-biocgenerics@0.23.3:', type=('build', 'run'), when='@2.12.0')
+    depends_on('r-biocgenerics@0.25.3:', type=('build', 'run'), when='@2.14.10')
+    depends_on('r-s4vectors@0.13.17:', type=('build', 'run'), when='@2.10.5')
+    depends_on('r-s4vectors@0.15.5:', type=('build', 'run'), when='@2.12.0')
+    depends_on('r-s4vectors@0.18.2:', type=('build', 'run'), when='@2.14.10')
+    depends_on('r@3.4.0:3.4.9', when='@2.10.5', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@2.14.10', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-irdisplay/package.py b/var/spack/repos/builtin/packages/r-irdisplay/package.py
index 1edbf40c1a..293c0bc7c0 100644
--- a/var/spack/repos/builtin/packages/r-irdisplay/package.py
+++ b/var/spack/repos/builtin/packages/r-irdisplay/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/r-irkernel/package.py b/var/spack/repos/builtin/packages/r-irkernel/package.py
index 62daf2e0ca..2ab4c2d01e 100644
--- a/var/spack/repos/builtin/packages/r-irkernel/package.py
+++ b/var/spack/repos/builtin/packages/r-irkernel/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -30,10 +11,9 @@ class RIrkernel(RPackage):
     """R kernel for Jupyter"""
 
     homepage = "https://irkernel.github.io/"
+    git      = "https://github.com/IRkernel/IRkernel.git"
 
-    # Git repository
-    version('master', git='https://github.com/IRkernel/IRkernel.git',
-        tag='0.7')
+    version('master', tag='0.7')
 
     depends_on('r-repr', type=('build', 'run'))
     depends_on('r-irdisplay', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-irlba/package.py b/var/spack/repos/builtin/packages/r-irlba/package.py
index 21e3df5e9f..3062b2411d 100644
--- a/var/spack/repos/builtin/packages/r-irlba/package.py
+++ b/var/spack/repos/builtin/packages/r-irlba/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-iso/package.py b/var/spack/repos/builtin/packages/r-iso/package.py
index f4be39ee6e..bf9e428eb3 100644
--- a/var/spack/repos/builtin/packages/r-iso/package.py
+++ b/var/spack/repos/builtin/packages/r-iso/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-iterators/package.py b/var/spack/repos/builtin/packages/r-iterators/package.py
index 1e864864e3..3b337cfa29 100644
--- a/var/spack/repos/builtin/packages/r-iterators/package.py
+++ b/var/spack/repos/builtin/packages/r-iterators/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-janitor/package.py b/var/spack/repos/builtin/packages/r-janitor/package.py
new file mode 100644
index 0000000000..eeb66b3c41
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-janitor/package.py
@@ -0,0 +1,30 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RJanitor(RPackage):
+    """The main janitor functions can: perfectly format data.frame column
+       names; provide quick one- and two-variable tabulations (i.e., frequency
+       tables and crosstabs); and isolate duplicate records. Other janitor
+       functions nicely format the tabulation results. These
+       tabulate-and-report functions approximate popular features of SPSS and
+       Microsoft Excel. This package follows the principles of the "tidyverse"
+       and works well with the pipe function %>%. janitor was built with
+       beginning-to-intermediate R users in mind and is optimized for
+       user-friendliness. Advanced R users can already do everything covered
+       here, but with janitor they can do it faster and save their thinking
+       for the fun stuff."""
+
+    homepage = "https://github.com/sfirke/janitor"
+    url      = "https://cran.r-project.org/src/contrib/janitor_0.3.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/janitor"
+
+    version('0.3.0', '76036c54693b91aef19d468107ae066a')
+
+    depends_on('r-dplyr', type=('build', 'run'))
+    depends_on('r-tidyr', type=('build', 'run'))
+    depends_on('r-magrittr', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-jaspar2018/package.py b/var/spack/repos/builtin/packages/r-jaspar2018/package.py
new file mode 100644
index 0000000000..a2bd68de81
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-jaspar2018/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RJaspar2018(RPackage):
+    """Data package for JASPAR 2018. To search this databases,
+    please use the package TFBSTools (>= 1.15.6)."""
+
+    homepage = "http://jaspar.genereg.net/"
+    git      = "https://git.bioconductor.org/packages/JASPAR2018.git"
+
+    version('1.0.0', commit='4c84092b3737bb1c57ab56f4321f2f5e4b0efeaa')
+
+    depends_on('r@3.4.0:')
diff --git a/var/spack/repos/builtin/packages/r-jomo/package.py b/var/spack/repos/builtin/packages/r-jomo/package.py
new file mode 100644
index 0000000000..adc88c4ed5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-jomo/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RJomo(RPackage):
+    """Similarly to Schafer's package 'pan', 'jomo' is a package for multilevel
+    joint modelling multiple imputation (Carpenter and Kenward, 2013)
+    <doi:10.1002/9781119942283>. Novel aspects of 'jomo' are the possibility of
+    handling binary and categorical data through latent normal variables, the
+    option to use cluster-specific covariance matrices and to impute compatibly
+    with the substantive model.
+    """
+
+    homepage = "https://cran.r-project.org/package=jomo"
+    url      = "https://cran.r-project.org/src/contrib/jomo_2.6-2.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/jomo"
+
+    version('2.6-2', 'eff4a6c1a971708959d65b3224c98a25')
+
+    depends_on('r-lme4', type=('build', 'run'))
+    depends_on('r-survival', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-jpeg/package.py b/var/spack/repos/builtin/packages/r-jpeg/package.py
index 5a11610fc9..e8c379ce8d 100644
--- a/var/spack/repos/builtin/packages/r-jpeg/package.py
+++ b/var/spack/repos/builtin/packages/r-jpeg/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-jsonlite/package.py b/var/spack/repos/builtin/packages/r-jsonlite/package.py
index 13f3bcd0e2..2403ec762a 100644
--- a/var/spack/repos/builtin/packages/r-jsonlite/package.py
+++ b/var/spack/repos/builtin/packages/r-jsonlite/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-kegg-db/package.py b/var/spack/repos/builtin/packages/r-kegg-db/package.py
index e205b1d42a..db4f1ff9e7 100644
--- a/var/spack/repos/builtin/packages/r-kegg-db/package.py
+++ b/var/spack/repos/builtin/packages/r-kegg-db/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-kegggraph/package.py b/var/spack/repos/builtin/packages/r-kegggraph/package.py
new file mode 100644
index 0000000000..424ceca845
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-kegggraph/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RKegggraph(RPackage):
+    """KEGGGraph is an interface between KEGG pathway and graph object as
+    well as a collection of tools to analyze, dissect and visualize these
+    graphs. It parses the regularly updated KGML (KEGG XML) files into graph
+    models maintaining all essential pathway attributes. The package offers
+    functionalities including parsing, graph operation, visualization and
+    etc."""
+
+    homepage = "https://www.bioconductor.org/packages/KEGGgraph/"
+    git      = "https://git.bioconductor.org/packages/KEGGgraph.git"
+
+    version('1.38.1', commit='dd31665beb36d5aad8ed09ed56c603633b6b2292')
+
+    depends_on('r-graph', type=('build', 'run'))
+    depends_on('r-xml', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@1.38.1')
diff --git a/var/spack/repos/builtin/packages/r-keggrest/package.py b/var/spack/repos/builtin/packages/r-keggrest/package.py
index b9a6e6a291..d19446e9a2 100644
--- a/var/spack/repos/builtin/packages/r-keggrest/package.py
+++ b/var/spack/repos/builtin/packages/r-keggrest/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,11 +15,13 @@ class RKeggrest(RPackage):
        catalogue) are provided."""
 
     homepage = "http://bioconductor.org/packages/KEGGREST"
-    url      = "https://git.bioconductor.org/packages/KEGGREST"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/KEGGREST.git"
 
-    version('1.2.0', git='https://git.bioconductor.org/packages/KEGGREST', commit='ed48de0def57a909894e237fa4731c4a052d8849')
+    version('1.18.1', commit='f6e6f1987e4db9d977a75609fab0cb710be2e2e4')
+    version('1.2.0',  commit='ed48de0def57a909894e237fa4731c4a052d8849')
 
     depends_on('r-httr', type=('build', 'run'))
     depends_on('r-png', type=('build', 'run'))
     depends_on('r-biostrings', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@1.2.0')
+    depends_on('r@3.4.3:3.4.9', when='@1.18.1')
diff --git a/var/spack/repos/builtin/packages/r-kernlab/package.py b/var/spack/repos/builtin/packages/r-kernlab/package.py
index 9ff25832be..a2191441b0 100644
--- a/var/spack/repos/builtin/packages/r-kernlab/package.py
+++ b/var/spack/repos/builtin/packages/r-kernlab/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-kernsmooth/package.py b/var/spack/repos/builtin/packages/r-kernsmooth/package.py
index e6fd8512c2..c1ad34ec21 100644
--- a/var/spack/repos/builtin/packages/r-kernsmooth/package.py
+++ b/var/spack/repos/builtin/packages/r-kernsmooth/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-kknn/package.py b/var/spack/repos/builtin/packages/r-kknn/package.py
index 86d67fb4d4..8d07faf285 100644
--- a/var/spack/repos/builtin/packages/r-kknn/package.py
+++ b/var/spack/repos/builtin/packages/r-kknn/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-knitr/package.py b/var/spack/repos/builtin/packages/r-knitr/package.py
index 1e0e51a3f1..8b92234ce0 100644
--- a/var/spack/repos/builtin/packages/r-knitr/package.py
+++ b/var/spack/repos/builtin/packages/r-knitr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/r-ks/package.py b/var/spack/repos/builtin/packages/r-ks/package.py
new file mode 100644
index 0000000000..dca118bdf5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-ks/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RKs(RPackage):
+    """Kernel smoothers for univariate and multivariate data."""
+
+    homepage = "https://cran.r-project.org/package=ks"
+    url      = "https://cran.r-project.org/src/contrib/Archive/ks/ks_1.11.2.tar.gz"
+
+    version('1.11.2', sha256='9dfd485096e1e67abc7dfcb7b76a83de110dd15bcfeffe5c899605b3a5592961')
+
+    depends_on('r@2.10:', type=('build', 'run'))
+
+    depends_on('r-fnn@1.1:', type=('build', 'run'))
+    depends_on('r-kernlab', type=('build', 'run'))
+    depends_on('r-mclust', type=('build', 'run'))
+    depends_on('r-multicool', type=('build', 'run'))
+    depends_on('r-mvtnorm@1.0:', type=('build', 'run'))
+    depends_on('r-kernsmooth@2.22:', type=('build', 'run'))
+    depends_on('r-matrix', type=('build', 'run'))
+    depends_on('r-mgcv', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-labeling/package.py b/var/spack/repos/builtin/packages/r-labeling/package.py
index 02790fe88d..49c8c640dc 100644
--- a/var/spack/repos/builtin/packages/r-labeling/package.py
+++ b/var/spack/repos/builtin/packages/r-labeling/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-lambda-r/package.py b/var/spack/repos/builtin/packages/r-lambda-r/package.py
index 914826af97..d6a2b56c1e 100644
--- a/var/spack/repos/builtin/packages/r-lambda-r/package.py
+++ b/var/spack/repos/builtin/packages/r-lambda-r/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,5 +13,6 @@ class RLambdaR(RPackage):
 
     homepage = "https://cran.rstudio.com/web/packages/lambda.r/index.html"
     url      = "https://cran.rstudio.com/src/contrib/lambda.r_1.2.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/lambda.r"
 
     version('1.2', 'bda49898b85ad5902880a31f43b432e2')
diff --git a/var/spack/repos/builtin/packages/r-laplacesdemon/package.py b/var/spack/repos/builtin/packages/r-laplacesdemon/package.py
index 3af2665c3e..e255cb1e49 100644
--- a/var/spack/repos/builtin/packages/r-laplacesdemon/package.py
+++ b/var/spack/repos/builtin/packages/r-laplacesdemon/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-lars/package.py b/var/spack/repos/builtin/packages/r-lars/package.py
new file mode 100644
index 0000000000..8788aa715f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-lars/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RLars(RPackage):
+    """Efficient procedures for fitting an entire lasso sequence with the cost
+    of a single least squares fit."""
+
+    homepage = "https://cran.r-project.org/web/packages/lars/index.html"
+    url      = "https://cran.r-project.org/src/contrib/lars_1.2.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/lars"
+
+    version('1.2',   '2571bae325f6cba1ad0202ea61695b8c')
+    version('1.1',   'e94f6902aade09b13ec25ba2381384e5')
+    version('0.9-8', 'e6f9fffab2d83898f6d3d811f04d177f')
+
+    depends_on('r@2.10:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-lattice/package.py b/var/spack/repos/builtin/packages/r-lattice/package.py
index 170e99aa9d..80450bee59 100644
--- a/var/spack/repos/builtin/packages/r-lattice/package.py
+++ b/var/spack/repos/builtin/packages/r-lattice/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-latticeextra/package.py b/var/spack/repos/builtin/packages/r-latticeextra/package.py
index 86c9d93ed7..a337e26ed5 100644
--- a/var/spack/repos/builtin/packages/r-latticeextra/package.py
+++ b/var/spack/repos/builtin/packages/r-latticeextra/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-lava/package.py b/var/spack/repos/builtin/packages/r-lava/package.py
index ae4218e1db..deb37f9da7 100644
--- a/var/spack/repos/builtin/packages/r-lava/package.py
+++ b/var/spack/repos/builtin/packages/r-lava/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-lazyeval/package.py b/var/spack/repos/builtin/packages/r-lazyeval/package.py
index 3746851d00..035661c0cc 100644
--- a/var/spack/repos/builtin/packages/r-lazyeval/package.py
+++ b/var/spack/repos/builtin/packages/r-lazyeval/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-leaflet/package.py b/var/spack/repos/builtin/packages/r-leaflet/package.py
index ef6debbdbb..fd418c4dc8 100644
--- a/var/spack/repos/builtin/packages/r-leaflet/package.py
+++ b/var/spack/repos/builtin/packages/r-leaflet/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-leaps/package.py b/var/spack/repos/builtin/packages/r-leaps/package.py
index e27874ec27..056c84fea1 100644
--- a/var/spack/repos/builtin/packages/r-leaps/package.py
+++ b/var/spack/repos/builtin/packages/r-leaps/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-learnbayes/package.py b/var/spack/repos/builtin/packages/r-learnbayes/package.py
index 71904b3d24..731f6488d1 100644
--- a/var/spack/repos/builtin/packages/r-learnbayes/package.py
+++ b/var/spack/repos/builtin/packages/r-learnbayes/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-lhs/package.py b/var/spack/repos/builtin/packages/r-lhs/package.py
new file mode 100644
index 0000000000..c607d68124
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-lhs/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RLhs(RPackage):
+    """Provides a number of methods for creating and augmenting Latin Hypercube
+       Samples."""
+
+    homepage = "http://lhs.r-forge.r-project.org/"
+    url      = "https://cran.r-project.org/src/contrib/lhs_0.16.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/lhs"
+
+    version('0.16', '088e593e5283414951e7e541a50ec2d1')
diff --git a/var/spack/repos/builtin/packages/r-limma/package.py b/var/spack/repos/builtin/packages/r-limma/package.py
index 8c4df2b059..7de1463b5f 100644
--- a/var/spack/repos/builtin/packages/r-limma/package.py
+++ b/var/spack/repos/builtin/packages/r-limma/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,10 +11,12 @@ class RLimma(RPackage):
     for microarray data."""
 
     homepage = "https://www.bioconductor.org/packages/limma/"
-    url      = "https://git.bioconductor.org/packages/limma"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/limma.git"
 
-    version('3.32.10', git='https://git.bioconductor.org/packages/limma', commit='593edf28e21fe054d64137ae271b8a52ab05bc60')
-    version('3.32.6', 'df5dc2b85189a24e939efa3a8e6abc41')
+    version('3.36.2',  commit='0cd5c13e22565182226bd2937ffcf8c59de1ca59')
+    version('3.34.9',  commit='6755278a929f942a49e2441fb002a3ed393e1139')
+    version('3.32.10', commit='593edf28e21fe054d64137ae271b8a52ab05bc60')
 
+    depends_on('r@3.5.0:3.5.9', when='@3.36.2')
+    depends_on('r@3.4.2:3.4.9', when='@3.34.9')
     depends_on('r@3.4.0:3.4.9', when='@3.32.10')
diff --git a/var/spack/repos/builtin/packages/r-lme4/package.py b/var/spack/repos/builtin/packages/r-lme4/package.py
index c7565e381e..8ba8e92a12 100644
--- a/var/spack/repos/builtin/packages/r-lme4/package.py
+++ b/var/spack/repos/builtin/packages/r-lme4/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-lmtest/package.py b/var/spack/repos/builtin/packages/r-lmtest/package.py
index 160fd3669b..ad8dbaf468 100644
--- a/var/spack/repos/builtin/packages/r-lmtest/package.py
+++ b/var/spack/repos/builtin/packages/r-lmtest/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-locfit/package.py b/var/spack/repos/builtin/packages/r-locfit/package.py
index 99b7af6fcf..f08811d14b 100644
--- a/var/spack/repos/builtin/packages/r-locfit/package.py
+++ b/var/spack/repos/builtin/packages/r-locfit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-log4r/package.py b/var/spack/repos/builtin/packages/r-log4r/package.py
index c6719cbe30..28cd6314e7 100644
--- a/var/spack/repos/builtin/packages/r-log4r/package.py
+++ b/var/spack/repos/builtin/packages/r-log4r/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-lpsolve/package.py b/var/spack/repos/builtin/packages/r-lpsolve/package.py
index 996725f129..e3690b86f9 100644
--- a/var/spack/repos/builtin/packages/r-lpsolve/package.py
+++ b/var/spack/repos/builtin/packages/r-lpsolve/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-lsei/package.py b/var/spack/repos/builtin/packages/r-lsei/package.py
index a2de608256..5d23d10991 100644
--- a/var/spack/repos/builtin/packages/r-lsei/package.py
+++ b/var/spack/repos/builtin/packages/r-lsei/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-lubridate/package.py b/var/spack/repos/builtin/packages/r-lubridate/package.py
index bdb314e673..d156d2c776 100644
--- a/var/spack/repos/builtin/packages/r-lubridate/package.py
+++ b/var/spack/repos/builtin/packages/r-lubridate/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,9 +15,11 @@ class RLubridate(RPackage):
     fun."""
 
     homepage = "https://cran.r-project.org/web/packages/lubridate/index.html"
-    url      = "https://cran.r-project.org/src/contrib/lubridate_1.5.6.tar.gz"
+    url      = "https://cran.r-project.org/src/contrib/lubridate_1.7.1.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/lubridate"
 
+    version('1.7.1', '17dcb4c6a95189941bbdcffecf61b83b')
     version('1.5.6', 'a5dc44817548ee219d26a10bae92e611')
 
+    depends_on('r-rcpp@0.11:', type=('build', 'run'))
     depends_on('r-stringr', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-magic/package.py b/var/spack/repos/builtin/packages/r-magic/package.py
index b6cd78be63..7365cfc3dd 100644
--- a/var/spack/repos/builtin/packages/r-magic/package.py
+++ b/var/spack/repos/builtin/packages/r-magic/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-magrittr/package.py b/var/spack/repos/builtin/packages/r-magrittr/package.py
index 528fb7ff67..a52960890b 100644
--- a/var/spack/repos/builtin/packages/r-magrittr/package.py
+++ b/var/spack/repos/builtin/packages/r-magrittr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-makecdfenv/package.py b/var/spack/repos/builtin/packages/r-makecdfenv/package.py
index 8c74fc532b..fe307b5220 100644
--- a/var/spack/repos/builtin/packages/r-makecdfenv/package.py
+++ b/var/spack/repos/builtin/packages/r-makecdfenv/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,9 +14,9 @@ class RMakecdfenv(RPackage):
     that environment."""
 
     homepage = "https://www.bioconductor.org/packages/makecdfenv/"
-    url      = "https://git.bioconductor.org/packages/makecdfenv"
+    git      = "https://git.bioconductor.org/packages/makecdfenv.git"
 
-    version('1.52.0', git='https://git.bioconductor.org/packages/makecdfenv', commit='b88a3e93e3b7feeeca69eda7c1fc5a0826c81120')
+    version('1.52.0', commit='b88a3e93e3b7feeeca69eda7c1fc5a0826c81120')
 
     depends_on('r@3.4.0:3.4.9', when='@1.52.0')
     depends_on('r-affyio', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-maldiquant/package.py b/var/spack/repos/builtin/packages/r-maldiquant/package.py
index ad1e1bb95f..69ad9033b5 100644
--- a/var/spack/repos/builtin/packages/r-maldiquant/package.py
+++ b/var/spack/repos/builtin/packages/r-maldiquant/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-mapproj/package.py b/var/spack/repos/builtin/packages/r-mapproj/package.py
index d17ba5a8b3..689e175d67 100644
--- a/var/spack/repos/builtin/packages/r-mapproj/package.py
+++ b/var/spack/repos/builtin/packages/r-mapproj/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-maps/package.py b/var/spack/repos/builtin/packages/r-maps/package.py
index f9d6a487df..4895599fa0 100644
--- a/var/spack/repos/builtin/packages/r-maps/package.py
+++ b/var/spack/repos/builtin/packages/r-maps/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-maptools/package.py b/var/spack/repos/builtin/packages/r-maptools/package.py
index e84fc2ef70..6a7487cc94 100644
--- a/var/spack/repos/builtin/packages/r-maptools/package.py
+++ b/var/spack/repos/builtin/packages/r-maptools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-markdown/package.py b/var/spack/repos/builtin/packages/r-markdown/package.py
index d58e56548c..ff9175ae97 100644
--- a/var/spack/repos/builtin/packages/r-markdown/package.py
+++ b/var/spack/repos/builtin/packages/r-markdown/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-mass/package.py b/var/spack/repos/builtin/packages/r-mass/package.py
index 5767b10be1..9bcd7bf70b 100644
--- a/var/spack/repos/builtin/packages/r-mass/package.py
+++ b/var/spack/repos/builtin/packages/r-mass/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-matr/package.py b/var/spack/repos/builtin/packages/r-matr/package.py
new file mode 100644
index 0000000000..4f2c03d546
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-matr/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RMatr(RPackage):
+    """Package matR (Metagenomics Analysis Tools for R) is an analysis
+    client for the MG-RAST metagenome annotation engine, part of the US
+    Department of Energy (DOE) Systems Biology Knowledge Base (KBase).
+    Customized analysis and visualization tools securely access remote
+    data and metadata within the popular open source R language and
+    environment for statistical computing."""
+
+    homepage = "https://github.com/MG-RAST/matR"
+    url      = "https://cran.r-project.org/src/contrib/matR_0.9.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/matR/matR_0.9.tar.gz"
+
+    version('0.9.1', sha256='554aeff37b27d0f17ddeb62b2e1004aa1f29190300e4946b1bec1d7c2bde82e3')
+    version('0.9', 'e2be8734009f5c5b9c1f6b677a77220a')
+
+    depends_on('r-mgraster', type=('build', 'run'))
+    depends_on('r-biom-utils', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-matrix/package.py b/var/spack/repos/builtin/packages/r-matrix/package.py
index c2911c4211..533cece9ff 100644
--- a/var/spack/repos/builtin/packages/r-matrix/package.py
+++ b/var/spack/repos/builtin/packages/r-matrix/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,12 @@ class RMatrix(RPackage):
     using 'LAPACK' and 'SuiteSparse'."""
 
     homepage = "http://matrix.r-forge.r-project.org/"
-    url      = "https://cran.rstudio.com/src/contrib/Matrix_1.2-11.tar.gz"
+    url      = "https://cran.rstudio.com/src/contrib/Matrix_1.2-14.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/Matrix"
-    version('1.2-11', 'a8c1a893f36d7ea918ddbf8cb8d10b43')
+
+    version('1.2-14', 'b2babcf1515625196b75592c9b345bba')
+    version('1.2-12', '0ade6e374716f08650cc8b8da99a313c')
+    version('1.2-11', 'b7d2a639aa52228dfde7c3c3ee68b38e')
     version('1.2-8', '4a6406666bf97d3ec6b698eea5d9c0f5')
     version('1.2-6', 'f545307fb1284861e9266c4e9712c55e')
 
diff --git a/var/spack/repos/builtin/packages/r-matrixmodels/package.py b/var/spack/repos/builtin/packages/r-matrixmodels/package.py
index de309edbdd..02fc848414 100644
--- a/var/spack/repos/builtin/packages/r-matrixmodels/package.py
+++ b/var/spack/repos/builtin/packages/r-matrixmodels/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-matrixstats/package.py b/var/spack/repos/builtin/packages/r-matrixstats/package.py
index 177275267b..79001b6802 100644
--- a/var/spack/repos/builtin/packages/r-matrixstats/package.py
+++ b/var/spack/repos/builtin/packages/r-matrixstats/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-mclust/package.py b/var/spack/repos/builtin/packages/r-mclust/package.py
index 30e1200da0..c198d9905c 100644
--- a/var/spack/repos/builtin/packages/r-mclust/package.py
+++ b/var/spack/repos/builtin/packages/r-mclust/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-mcmcglmm/package.py b/var/spack/repos/builtin/packages/r-mcmcglmm/package.py
index 19bd61f746..edf11d4c55 100644
--- a/var/spack/repos/builtin/packages/r-mcmcglmm/package.py
+++ b/var/spack/repos/builtin/packages/r-mcmcglmm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-mco/package.py b/var/spack/repos/builtin/packages/r-mco/package.py
new file mode 100644
index 0000000000..eae3fe7a99
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-mco/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RMco(RPackage):
+    """Functions for multiple criteria optimization using genetic algorithms
+       and related test problems"""
+
+    homepage = "https://github.com/cran/mco"
+    url      = "https://cran.r-project.org/src/contrib/mco_1.0-15.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/mco"
+
+    version('1.0-15.1', '1768dea61d0561d71be2bbc6ac3dccfa')
+    version('1.0-15', '0b444e085c59d919611224e86b5637f8')
diff --git a/var/spack/repos/builtin/packages/r-mda/package.py b/var/spack/repos/builtin/packages/r-mda/package.py
index 492cc4fe13..f59f09844e 100644
--- a/var/spack/repos/builtin/packages/r-mda/package.py
+++ b/var/spack/repos/builtin/packages/r-mda/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-memoise/package.py b/var/spack/repos/builtin/packages/r-memoise/package.py
index 6bc766f0cd..e8a8b32e1b 100644
--- a/var/spack/repos/builtin/packages/r-memoise/package.py
+++ b/var/spack/repos/builtin/packages/r-memoise/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-mergemaid/package.py b/var/spack/repos/builtin/packages/r-mergemaid/package.py
index ae6ef977c5..ff4ae551f3 100644
--- a/var/spack/repos/builtin/packages/r-mergemaid/package.py
+++ b/var/spack/repos/builtin/packages/r-mergemaid/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,9 +19,9 @@ class RMergemaid(RPackage):
        cross-validate associations of gene expression data with survival."""
 
     homepage = "https://www.bioconductor.org/packages/MergeMaid/"
-    url      = "https://git.bioconductor.org/packages/MergeMaid"
+    git      = "https://git.bioconductor.org/packages/MergeMaid.git"
 
-    version('2.48.0', git='https://git.bioconductor.org/packages/MergeMaid', commit='aee89c523fcafff4c166ff3db4fff90df16a1ed4')
+    version('2.48.0', commit='aee89c523fcafff4c166ff3db4fff90df16a1ed4')
 
     depends_on('r-survival', type=('build', 'run'))
     depends_on('r-biobase', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-methodss3/package.py b/var/spack/repos/builtin/packages/r-methodss3/package.py
index 2c1768a1b1..d5793a73a0 100644
--- a/var/spack/repos/builtin/packages/r-methodss3/package.py
+++ b/var/spack/repos/builtin/packages/r-methodss3/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-mgcv/package.py b/var/spack/repos/builtin/packages/r-mgcv/package.py
index 0bf7563df1..22296ac36d 100644
--- a/var/spack/repos/builtin/packages/r-mgcv/package.py
+++ b/var/spack/repos/builtin/packages/r-mgcv/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,6 +16,12 @@ class RMgcv(RPackage):
     url      = "https://cran.r-project.org/src/contrib/mgcv_1.8-16.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/mgcv"
 
+    version('1.8-22', 'b42079b33b46de784f293a74c824b877')
+    version('1.8-21', 'aae8262a07c8698ca8d6213065c4983f')
+    version('1.8-20', '58eb94404aad7ff8a0cf11a2f098f8bf')
+    version('1.8-19', 'f9a4e29464f4d10b7b2cb9d0bec3fa9e')
+    version('1.8-18', 'c134fc2db253530233b95f2e36b56a2f')
+    version('1.8-17', '398582d0f999ac34749f4f5f1d103f75')
     version('1.8-16', '4c1d85e0f80b017bccb4b63395842911')
     version('1.8-13', '30607be3aaf44b13bd8c81fc32e8c984')
 
diff --git a/var/spack/repos/builtin/packages/r-mgraster/package.py b/var/spack/repos/builtin/packages/r-mgraster/package.py
new file mode 100644
index 0000000000..f3e3978860
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-mgraster/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RMgraster(RPackage):
+    """Convenience Functions for R Language Access to the v.1 API of the
+    MG-RAST Metagenome Annotation Server, part of the US Department of Energy
+    (DOE) Systems Biology Knowledge Base (KBase)."""
+
+    homepage = "https://github.com/braithwaite/MGRASTer/"
+    url      = "https://cran.r-project.org/src/contrib/MGRASTer_0.9.tar.gz"
+
+    version('0.9', '902c7ad4180b858d6b6428ea26d7652a')
+
+    depends_on('r@3:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-mice/package.py b/var/spack/repos/builtin/packages/r-mice/package.py
new file mode 100644
index 0000000000..e18a83c9a4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-mice/package.py
@@ -0,0 +1,38 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RMice(RPackage):
+    """Multiple imputation using Fully Conditional Specification (FCS)
+    implemented by the MICE algorithm as described in Van Buuren and
+    Groothuis-Oudshoorn (2011) <doi:10.18637/jss.v045.i03>.
+
+    Each variable has its own imputation model. Built-in imputation models are
+    provided for continuous data (predictive mean matching, normal), binary
+    data (logistic regression), unordered categorical data (polytomous logistic
+    regression) and ordered categorical data (proportional odds). MICE can
+    also impute continuous two-level data (normal model, pan, second-level
+    variables). Passive imputation can be used to maintain consistency between
+    variables. Various diagnostic plots are available to inspect the quality
+    of the imputations."""
+
+    homepage = "https://cran.r-project.org/package=mice"
+    url      = "https://cran.r-project.org/src/contrib/mice_3.0.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/mice"
+
+    version('3.0.0', 'fb54a29679536c474c756cca4538d7e3')
+
+    depends_on('r-broom', type=('build', 'run'))
+    depends_on('r-dplyr', type=('build', 'run'))
+    depends_on('r-mass', type=('build', 'run'))
+    depends_on('r-mitml', type=('build', 'run'))
+    depends_on('r-nnet', type=('build', 'run'))
+    depends_on('r-rcpp', type=('build', 'run'))
+    depends_on('r-rlang', type=('build', 'run'))
+    depends_on('r-rpart', type=('build', 'run'))
+    depends_on('r-survival', type=('build', 'run'))
+    depends_on('r-lattice', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-mime/package.py b/var/spack/repos/builtin/packages/r-mime/package.py
index bb235270d7..4d0dd95015 100644
--- a/var/spack/repos/builtin/packages/r-mime/package.py
+++ b/var/spack/repos/builtin/packages/r-mime/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-minfi/package.py b/var/spack/repos/builtin/packages/r-minfi/package.py
index 3621743aaa..06cfff4cef 100644
--- a/var/spack/repos/builtin/packages/r-minfi/package.py
+++ b/var/spack/repos/builtin/packages/r-minfi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,10 +10,9 @@ class RMinfi(RPackage):
     """Tools to analyze & visualize Illumina Infinium methylation arrays."""
 
     homepage = "https://bioconductor.org/packages/minfi/"
-    url      = "https://git.bioconductor.org/packages/minfi"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/minfi.git"
 
-    version('1.22.1', git='https://git.bioconductor.org/packages/minfi', commit='b2faf84bcbb291e32d470a0e029450093527545b')
+    version('1.22.1', commit='b2faf84bcbb291e32d470a0e029450093527545b')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-genomicranges', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-minqa/package.py b/var/spack/repos/builtin/packages/r-minqa/package.py
index 23fe7b5b5c..4b52bef0aa 100644
--- a/var/spack/repos/builtin/packages/r-minqa/package.py
+++ b/var/spack/repos/builtin/packages/r-minqa/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-misc3d/package.py b/var/spack/repos/builtin/packages/r-misc3d/package.py
new file mode 100644
index 0000000000..838b8bf738
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-misc3d/package.py
@@ -0,0 +1,16 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RMisc3d(RPackage):
+    """A collection of miscellaneous 3d plots, including isosurfaces."""
+
+    homepage = "https://cran.r-project.org/web/packages/misc3d/index.html"
+    url      = "https://cran.r-project.org/src/contrib/misc3d_0.8-4.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/misc3d"
+
+    version('0.8-4', 'aefa27e67a243c21a1046868540343fe')
diff --git a/var/spack/repos/builtin/packages/r-mitml/package.py b/var/spack/repos/builtin/packages/r-mitml/package.py
new file mode 100644
index 0000000000..4a0f91d65c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-mitml/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RMitml(RPackage):
+    """Provides tools for multiple imputation of missing data in multilevel
+    modeling. Includes a user-friendly interface to the packages 'pan' and
+    'jomo', and several functions for visualization, data management and the
+    analysis of multiply imputed data sets."""
+
+    homepage = "https://cran.r-project.org/package=mitml"
+    url      = "https://cran.r-project.org/src/contrib/mitml_0.3-5.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/mitml"
+    version('0.3-5', '6f8659c33696915bf510241287b2a34d')
+
+    depends_on('r-pan', type=('build', 'run'))
+    depends_on('r-jomo', type=('build', 'run'))
+    depends_on('r-haven', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-mixtools/package.py b/var/spack/repos/builtin/packages/r-mixtools/package.py
new file mode 100644
index 0000000000..3538113eb8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-mixtools/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RMixtools(RPackage):
+    """mixtools: Tools for Analyzing Finite Mixture Models
+
+    Analyzes finite mixture models for various parametric and semiparametric
+    settings."""
+
+    homepage = "https://cran.r-project.org/web/packages/mixtools/index.html"
+    url      = "https://cran.r-project.org/src/contrib/mixtools_1.1.0.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/mixtools"
+
+    version('1.1.0', 'c7d59110dd42964d40593a05b98acd5f')
+    version('1.0.4', 'c0e6ec44d16ec8914797fb74a651d3e5')
+
+    depends_on('r@3.4.0:3.4.9')
+    depends_on('r-mass', type=('build', 'run'))
+    depends_on('r-segmented', type=('build', 'run'))
+    depends_on('r-survival', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-mlbench/package.py b/var/spack/repos/builtin/packages/r-mlbench/package.py
index 9d450ced9e..c2eec7e418 100644
--- a/var/spack/repos/builtin/packages/r-mlbench/package.py
+++ b/var/spack/repos/builtin/packages/r-mlbench/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-mlinterfaces/package.py b/var/spack/repos/builtin/packages/r-mlinterfaces/package.py
index 9c83563b8f..79ea6ba809 100644
--- a/var/spack/repos/builtin/packages/r-mlinterfaces/package.py
+++ b/var/spack/repos/builtin/packages/r-mlinterfaces/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,9 @@ class RMlinterfaces(RPackage):
     code for data in R and Bioconductor containers."""
 
     homepage = "https://www.bioconductor.org/packages/MLInterfaces/"
-    url      = "https://git.bioconductor.org/packages/MLInterfaces"
+    git      = "https://git.bioconductor.org/packages/MLInterfaces.git"
 
-    version('1.56.0', git='https://git.bioconductor.org/packages/MLInterfaces', commit='31fe6fb20d859fcb01d5552f42bca6bab16cc67f')
+    version('1.56.0', commit='31fe6fb20d859fcb01d5552f42bca6bab16cc67f')
 
     depends_on('r@3.4.0:3.4.9', when='@1.56.0')
     depends_on('r-biocgenerics', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-mlr/package.py b/var/spack/repos/builtin/packages/r-mlr/package.py
new file mode 100644
index 0000000000..120c7adaa9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-mlr/package.py
@@ -0,0 +1,36 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RMlr(RPackage):
+    """Interface to a large number of classification and regression techniques,
+       including machine-readable parameter descriptions. There is also an
+       experimental extension for survival analysis, clustering and general,
+       example-specific cost-sensitive learning. Generic resampling,
+       including cross-validation, bootstrapping and subsampling.
+       Hyperparameter tuning with modern optimization techniques,
+       for single- and multi-objective problems. Filter and wrapper methods for
+       feature selection. Extension of basic learners with additional
+       operations common in machine learning, also allowing for easy nested
+       resampling. Most operations can be parallelized."""
+
+    homepage = "https://github.com/mlr-org/mlr/"
+    url      = "https://cran.r-project.org/src/contrib/mlr_2.12.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/mlr"
+
+    version('2.12.1', 'abddfc9dfe95f290a233ecd97969a4ec')
+    version('2.12', '94ee7495aeafb432c8af5a8bdd26c25f')
+
+    depends_on('r-paramhelpers@1.10:', type=('build', 'run'))
+    depends_on('r-bbmisc@1.11:', type=('build', 'run'))
+    depends_on('r-backports@1.1.0:', type=('build', 'run'))
+    depends_on('r-ggplot2', type=('build', 'run'))
+    depends_on('r-stringi', type=('build', 'run'))
+    depends_on('r-checkmate@1.8.2:', type=('build', 'run'))
+    depends_on('r-data-table', type=('build', 'run'))
+    depends_on('r-parallelmap@1.3:', type=('build', 'run'))
+    depends_on('r-xml', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-mlrmbo/package.py b/var/spack/repos/builtin/packages/r-mlrmbo/package.py
new file mode 100644
index 0000000000..3f789a869c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-mlrmbo/package.py
@@ -0,0 +1,39 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RMlrmbo(RPackage):
+    """Flexible and comprehensive R toolbox for model-based optimization
+       ('MBO'), also known as Bayesian optimization. It is designed for both
+       single- and multi-objective optimization with mixed continuous,
+       categorical and conditional parameters. The machine learning toolbox
+       'mlr' provide dozens of regression learners to model the performance of
+       the target algorithm with respect to the parameter settings. It provides
+       many different infill criteria to guide the search process. Additional
+       features include multi-point batch proposal, parallel execution as well
+       as visualization and sophisticated logging mechanisms, which is
+       especially useful for teaching and understanding of algorithm behavior.
+       'mlrMBO' is implemented in a modular fashion, such that single
+       components can be easily replaced or adapted by the user for specific
+       use cases."""
+
+    homepage = "https://github.com/mlr-org/mlrMBO/"
+    url      = "https://cran.r-project.org/src/contrib/mlrMBO_1.1.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/mlrMBO"
+
+    version('1.1.1', '9a35b41ceb8754111af294dee0ae76e0')
+    version('1.1.0', '9e27ff8498225d24863b8da758d2918e')
+
+    depends_on('r-mlr@2.10:', type=('build', 'run'))
+    depends_on('r-paramhelpers@1.10:', type=('build', 'run'))
+    depends_on('r-smoof@1.5.1:', type=('build', 'run'))
+    depends_on('r-backports@1.1.0:', type=('build', 'run'))
+    depends_on('r-bbmisc@1.11:', type=('build', 'run'))
+    depends_on('r-checkmate@1.8.2:', type=('build', 'run'))
+    depends_on('r-data-table', type=('build', 'run'))
+    depends_on('r-lhs', type=('build', 'run'))
+    depends_on('r-parallelmap@1.3:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-mmwrweek/package.py b/var/spack/repos/builtin/packages/r-mmwrweek/package.py
new file mode 100644
index 0000000000..f62bd6275c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-mmwrweek/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RMmwrweek(RPackage):
+    """The first day of any MMWR week is Sunday. MMWR week numbering is
+    sequential beginning with 1 and incrementing with each week to a maximum
+    of 52 or 53. MMWR week #1 of an MMWR year is the first week of the year
+    that has at least four days in the calendar year. This package provides
+    functionality to convert Dates to MMWR day, week, and year and the
+    reverse."""
+
+    homepage = "https://cran.r-project.org/package=MMWRweek"
+    url      = "https://cran.r-project.org/src/contrib/MMWRweek_0.1.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/MMWRweek"
+
+    version('0.1.1', 'a1245025126f8a96c72be8f7b06b0499')
diff --git a/var/spack/repos/builtin/packages/r-mnormt/package.py b/var/spack/repos/builtin/packages/r-mnormt/package.py
new file mode 100644
index 0000000000..34c88cf85a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-mnormt/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RMnormt(RPackage):
+    """Functions are provided for computing the density and the distribution
+       function of multivariate normal and "t" random variables, and for
+       generating random vectors sampled from these distributions.
+       Probabilities are computed via non-Monte Carlo methods; different
+       routines are used in the case d=1, d=2, d>2, if d denotes the number
+       of dimensions."""
+
+    homepage = "http://azzalini.stat.unipd.it/SW/Pkg-mnormt"
+    url      = "https://cran.r-project.org/src/contrib/mnormt_1.5-5.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/mnormt"
+
+    version('1.5-5', '19b5be2e9ed33b92d7a716bfcca6b2c7')
diff --git a/var/spack/repos/builtin/packages/r-modelmetrics/package.py b/var/spack/repos/builtin/packages/r-modelmetrics/package.py
index c3625e1e37..fd4648abd9 100644
--- a/var/spack/repos/builtin/packages/r-modelmetrics/package.py
+++ b/var/spack/repos/builtin/packages/r-modelmetrics/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-modelr/package.py b/var/spack/repos/builtin/packages/r-modelr/package.py
new file mode 100644
index 0000000000..2d9bf982ef
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-modelr/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RModelr(RPackage):
+    """Functions for modelling that help you seamlessly integrate modelling
+       into a pipeline of data manipulation and visualisation."""
+
+    homepage = "https://github.com/hadley/modelr"
+    url      = "https://cran.r-project.org/src/contrib/modelr_0.1.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/modelr"
+
+    version('0.1.1', 'ce5fd088fb7850228ab1e34d241a975d')
+
+    depends_on('r-magrittr', type=('build', 'run'))
+    depends_on('r-purrr', type=('build', 'run'))
+    depends_on('r-lazyeval', type=('build', 'run'))
+    depends_on('r-tibble', type=('build', 'run'))
+    depends_on('r-broom', type=('build', 'run'))
+    depends_on('r-dplyr', type=('build', 'run'))
+    depends_on('r-tidyr', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-modeltools/package.py b/var/spack/repos/builtin/packages/r-modeltools/package.py
index 1c0873dfae..5f8b660029 100644
--- a/var/spack/repos/builtin/packages/r-modeltools/package.py
+++ b/var/spack/repos/builtin/packages/r-modeltools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-mpm/package.py b/var/spack/repos/builtin/packages/r-mpm/package.py
index 78b21ab11b..7bf560cc8c 100644
--- a/var/spack/repos/builtin/packages/r-mpm/package.py
+++ b/var/spack/repos/builtin/packages/r-mpm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-msnbase/package.py b/var/spack/repos/builtin/packages/r-msnbase/package.py
index fddbffdcec..78f882ec53 100644
--- a/var/spack/repos/builtin/packages/r-msnbase/package.py
+++ b/var/spack/repos/builtin/packages/r-msnbase/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,9 @@ class RMsnbase(RPackage):
        proteomics data."""
 
     homepage = "https://www.bioconductor.org/packages/MSnbase/"
-    url      = "https://git.bioconductor.org/packages/MSnbase"
+    git      = "https://git.bioconductor.org/packages/MSnbase.git"
 
-    version('2.2.0', git='https://git.bioconductor.org/packages/MSnbase', commit='d6e8fb7f106d05096fa9074da0f829ac8f02c197')
+    version('2.2.0', commit='d6e8fb7f106d05096fa9074da0f829ac8f02c197')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-biobase', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-multcomp/package.py b/var/spack/repos/builtin/packages/r-multcomp/package.py
index 8b5b6deff7..d8eb6b6d5c 100644
--- a/var/spack/repos/builtin/packages/r-multcomp/package.py
+++ b/var/spack/repos/builtin/packages/r-multcomp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-multicool/package.py b/var/spack/repos/builtin/packages/r-multicool/package.py
new file mode 100644
index 0000000000..3bb41ac560
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-multicool/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RMulticool(RPackage):
+    """Permutations of multisets in cool-lex order."""
+
+    homepage = "https://cran.r-project.org/package=multicool"
+    url      = "https://cran.r-project.org/src/contrib/Archive/multicool/multicool_0.1-9.tar.gz"
+
+    version('0.1-9', sha256='bdf92571cef1b649952d155395a92b8683099ee13114f73a9d41fc5d7d49d329')
+
+    depends_on('r-rcpp@0.11.2:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-multtest/package.py b/var/spack/repos/builtin/packages/r-multtest/package.py
index 04030423ee..aa5e5a34a0 100644
--- a/var/spack/repos/builtin/packages/r-multtest/package.py
+++ b/var/spack/repos/builtin/packages/r-multtest/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,9 @@ class RMulttest(RPackage):
     """Resampling-based multiple hypothesis testing"""
 
     homepage = "https://www.bioconductor.org/packages/multtest/"
-    url      = "https://git.bioconductor.org/packages/multtest"
+    git      = "https://git.bioconductor.org/packages/multtest.git"
 
-    version('2.32.0', git='https://git.bioconductor.org/packages/multtest', commit='c5e890dfbffcc3a3f107303a24b6085614312f4a')
+    version('2.32.0', commit='c5e890dfbffcc3a3f107303a24b6085614312f4a')
 
     depends_on('r@3.4.0:3.4.9', when='@2.32.0')
     depends_on('r-biocgenerics', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-munsell/package.py b/var/spack/repos/builtin/packages/r-munsell/package.py
index de729c84ef..353e9ecd2c 100644
--- a/var/spack/repos/builtin/packages/r-munsell/package.py
+++ b/var/spack/repos/builtin/packages/r-munsell/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-mvtnorm/package.py b/var/spack/repos/builtin/packages/r-mvtnorm/package.py
index 9806c21cb5..e341a2e76e 100644
--- a/var/spack/repos/builtin/packages/r-mvtnorm/package.py
+++ b/var/spack/repos/builtin/packages/r-mvtnorm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-mzid/package.py b/var/spack/repos/builtin/packages/r-mzid/package.py
index cb23814ea8..ea9778ffcb 100644
--- a/var/spack/repos/builtin/packages/r-mzid/package.py
+++ b/var/spack/repos/builtin/packages/r-mzid/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,9 +14,9 @@ class RMzid(RPackage):
        supply an mzIdentML file so the problems can be fixed quickly."""
 
     homepage = "https://www.bioconductor.org/packages/mzID/"
-    url      = "https://git.bioconductor.org/packages/mzID"
+    git      = "https://git.bioconductor.org/packages/mzID.git"
 
-    version('1.14.0', git='https://git.bioconductor.org/packages/mzID', commit='1c53aa6523ae61d3ebb13381381fc119d6cc6115')
+    version('1.14.0', commit='1c53aa6523ae61d3ebb13381381fc119d6cc6115')
 
     depends_on('r-xml', type=('build', 'run'))
     depends_on('r-plyr', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-mzr/package.py b/var/spack/repos/builtin/packages/r-mzr/package.py
index 282962153b..19b5080037 100644
--- a/var/spack/repos/builtin/packages/r-mzr/package.py
+++ b/var/spack/repos/builtin/packages/r-mzr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,9 +15,9 @@ class RMzr(RPackage):
        reading code has previously been used in XCMS."""
 
     homepage = "https://www.bioconductor.org/packages/mzR/"
-    url      = "https://git.bioconductor.org/packages/mzR"
+    git      = "https://git.bioconductor.org/packages/mzR.git"
 
-    version('2.10.0', git='https://git.bioconductor.org/packages/mzR', commit='a6168b68e48c281e88de9647254a8db1e21df388')
+    version('2.10.0', commit='a6168b68e48c281e88de9647254a8db1e21df388')
 
     depends_on('r-biobase', type=('build', 'run'))
     depends_on('r-biocgenerics', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-nanotime/package.py b/var/spack/repos/builtin/packages/r-nanotime/package.py
new file mode 100644
index 0000000000..07c3d8830a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-nanotime/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RNanotime(RPackage):
+    """Full 64-bit resolution date and time support with resolution up to
+       nanosecond granularity is provided, with easy transition to and from
+       the standard 'POSIXct' type."""
+
+    homepage = "https://cran.r-project.org/package=nanotime"
+    url      = "https://cran.r-project.org/src/contrib/nanotime_0.2.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/nanotime"
+
+    version('0.2.0', '796b1f7d0bb43e2f3d98e3cc6f4b0657')
+
+    depends_on('r-bit64', type=('build', 'run'))
+    depends_on('r-rcppcctz', type=('build', 'run'))
+    depends_on('r-zoo', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-ncbit/package.py b/var/spack/repos/builtin/packages/r-ncbit/package.py
index c9bc90654c..3d66e92009 100644
--- a/var/spack/repos/builtin/packages/r-ncbit/package.py
+++ b/var/spack/repos/builtin/packages/r-ncbit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-ncdf4/package.py b/var/spack/repos/builtin/packages/r-ncdf4/package.py
index 8e24a0eba1..d38ba6d5b9 100644
--- a/var/spack/repos/builtin/packages/r-ncdf4/package.py
+++ b/var/spack/repos/builtin/packages/r-ncdf4/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-network/package.py b/var/spack/repos/builtin/packages/r-network/package.py
index 867fbf41f6..e586c6d030 100644
--- a/var/spack/repos/builtin/packages/r-network/package.py
+++ b/var/spack/repos/builtin/packages/r-network/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-networkd3/package.py b/var/spack/repos/builtin/packages/r-networkd3/package.py
index 4102dbefe4..45eada135f 100644
--- a/var/spack/repos/builtin/packages/r-networkd3/package.py
+++ b/var/spack/repos/builtin/packages/r-networkd3/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-nlme/package.py b/var/spack/repos/builtin/packages/r-nlme/package.py
index b50fa42c10..fac6a7c7f6 100644
--- a/var/spack/repos/builtin/packages/r-nlme/package.py
+++ b/var/spack/repos/builtin/packages/r-nlme/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-nloptr/package.py b/var/spack/repos/builtin/packages/r-nloptr/package.py
index 613900c799..d77d18f17f 100644
--- a/var/spack/repos/builtin/packages/r-nloptr/package.py
+++ b/var/spack/repos/builtin/packages/r-nloptr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -42,3 +23,13 @@ class RNloptr(RPackage):
     version('1.0.4', 'f2775dfb4f7f5552d46937a04c062b0d')
 
     depends_on('r-testthat', type=('build', 'run'))
+    depends_on('nlopt')
+
+    def configure_args(self):
+        include_flags = self.spec['nlopt'].headers.include_flags
+        libs = self.spec['nlopt'].libs.libraries[0]
+        args = [
+            '--with-nlopt-cflags={0}'.format(include_flags),
+            '--with-nlopt-libs={0}'.format(libs)
+        ]
+        return args
diff --git a/var/spack/repos/builtin/packages/r-nmf/package.py b/var/spack/repos/builtin/packages/r-nmf/package.py
index 8e2806efed..8be0914277 100644
--- a/var/spack/repos/builtin/packages/r-nmf/package.py
+++ b/var/spack/repos/builtin/packages/r-nmf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-nnet/package.py b/var/spack/repos/builtin/packages/r-nnet/package.py
index 5298b38abe..1326221ceb 100644
--- a/var/spack/repos/builtin/packages/r-nnet/package.py
+++ b/var/spack/repos/builtin/packages/r-nnet/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-nnls/package.py b/var/spack/repos/builtin/packages/r-nnls/package.py
index 44ea8174c2..3da3e20b63 100644
--- a/var/spack/repos/builtin/packages/r-nnls/package.py
+++ b/var/spack/repos/builtin/packages/r-nnls/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-nor1mix/package.py b/var/spack/repos/builtin/packages/r-nor1mix/package.py
index f02a70cc9b..9e4f27007b 100644
--- a/var/spack/repos/builtin/packages/r-nor1mix/package.py
+++ b/var/spack/repos/builtin/packages/r-nor1mix/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-np/package.py b/var/spack/repos/builtin/packages/r-np/package.py
index 6bb788e38d..1a32b6f71d 100644
--- a/var/spack/repos/builtin/packages/r-np/package.py
+++ b/var/spack/repos/builtin/packages/r-np/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-numderiv/package.py b/var/spack/repos/builtin/packages/r-numderiv/package.py
index 86887bb1a5..8e145d572f 100644
--- a/var/spack/repos/builtin/packages/r-numderiv/package.py
+++ b/var/spack/repos/builtin/packages/r-numderiv/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-oligoclasses/package.py b/var/spack/repos/builtin/packages/r-oligoclasses/package.py
index 85e221e275..86d72876fe 100644
--- a/var/spack/repos/builtin/packages/r-oligoclasses/package.py
+++ b/var/spack/repos/builtin/packages/r-oligoclasses/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,9 +12,9 @@ class ROligoclasses(RPackage):
     crlmm packages."""
 
     homepage = "https://www.bioconductor.org/packages/oligoClasses/"
-    url      = "https://git.bioconductor.org/packages/oligoClasses"
+    git      = "https://git.bioconductor.org/packages/oligoClasses.git"
 
-    version('1.38.0', git='https://git.bioconductor.org/packages/oligoClasses', commit='fe2bb7f02c7ed3cbd338254c27ceba6ff829a962')
+    version('1.38.0', commit='fe2bb7f02c7ed3cbd338254c27ceba6ff829a962')
 
     depends_on('r@3.4.0:3.4.9', when='@1.38.0')
     depends_on('r-biocgenerics', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-oo/package.py b/var/spack/repos/builtin/packages/r-oo/package.py
index 7f4a3e39d9..6cba9eb491 100644
--- a/var/spack/repos/builtin/packages/r-oo/package.py
+++ b/var/spack/repos/builtin/packages/r-oo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-openssl/package.py b/var/spack/repos/builtin/packages/r-openssl/package.py
index 4c038f29c9..4b228646ac 100644
--- a/var/spack/repos/builtin/packages/r-openssl/package.py
+++ b/var/spack/repos/builtin/packages/r-openssl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-org-hs-eg-db/package.py b/var/spack/repos/builtin/packages/r-org-hs-eg-db/package.py
new file mode 100644
index 0000000000..893c6618f7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-org-hs-eg-db/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class ROrgHsEgDb(RPackage):
+    """Genome wide annotation for Human, primarily based on mapping
+    using Entrez Gene identifiers."""
+
+    homepage = "https://bioconductor.org/packages/org.Hs.eg.db/"
+    url      = "https://www.bioconductor.org/packages/3.5/data/annotation/src/contrib/org.Hs.eg.db_3.4.1.tar.gz"
+
+    version('3.4.1', '0a987ef7d6167df70e91e6f48145e41c')
+
+    depends_on('r@3.4.0:3.4.9', when='@3.4.1')
+    depends_on('r-annotationdbi', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-organismdbi/package.py b/var/spack/repos/builtin/packages/r-organismdbi/package.py
index b299c5919b..e9cd3d499b 100644
--- a/var/spack/repos/builtin/packages/r-organismdbi/package.py
+++ b/var/spack/repos/builtin/packages/r-organismdbi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,10 +12,9 @@ class ROrganismdbi(RPackage):
        fact that each of these packages implements a select methods."""
 
     homepage = "https://bioconductor.org/packages/OrganismDbi/"
-    url      = "https://git.bioconductor.org/packages/OrganismDbi"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/OrganismDbi.git"
 
-    version('1.18.1', git='https://git.bioconductor.org/packages/OrganismDbi', commit='ba2d1237256805e935d9534a0c6f1ded07b42e95')
+    version('1.18.1', commit='ba2d1237256805e935d9534a0c6f1ded07b42e95')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-annotationdbi', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-packrat/package.py b/var/spack/repos/builtin/packages/r-packrat/package.py
index c87326cacb..7a8b002786 100644
--- a/var/spack/repos/builtin/packages/r-packrat/package.py
+++ b/var/spack/repos/builtin/packages/r-packrat/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-pacman/package.py b/var/spack/repos/builtin/packages/r-pacman/package.py
index c272904a2e..a419b520da 100644
--- a/var/spack/repos/builtin/packages/r-pacman/package.py
+++ b/var/spack/repos/builtin/packages/r-pacman/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-pamr/package.py b/var/spack/repos/builtin/packages/r-pamr/package.py
index 9e3de93ad6..3be3f2e4c3 100644
--- a/var/spack/repos/builtin/packages/r-pamr/package.py
+++ b/var/spack/repos/builtin/packages/r-pamr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-pan/package.py b/var/spack/repos/builtin/packages/r-pan/package.py
new file mode 100644
index 0000000000..db9bc7988d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-pan/package.py
@@ -0,0 +1,16 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RPan(RPackage):
+    """Multiple imputation for multivariate panel or clustered data."""
+
+    homepage = "https://cran.r-project.org/package=pan"
+    url      = "https://cran.r-project.org/src/contrib/pan_1.4.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/pan"
+
+    version('1.4', 'cdead963110561fc42dc544a60ac44ed')
diff --git a/var/spack/repos/builtin/packages/r-parallelmap/package.py b/var/spack/repos/builtin/packages/r-parallelmap/package.py
new file mode 100644
index 0000000000..cb7c10a028
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-parallelmap/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RParallelmap(RPackage):
+    """Unified parallelization framework for multiple back-end, designed for
+       internal package and interactive usage. The main operation is a parallel
+       "map" over lists. Supports local, multicore, mpi and BatchJobs mode.
+       Allows "tagging" of the parallel operation with a level name that can be
+       later selected by the user to switch on parallel execution for exactly
+       this operation."""
+
+    homepage = "https://github.com/berndbischl/parallelMap"
+    url      = "https://cran.r-project.org/src/contrib/parallelMap_1.3.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/parallelMap"
+
+    version('1.3', 'dd62866b395847b0bd5b13bed98c0081')
+
+    depends_on('r-bbmisc@1.8:', type=('build', 'run'))
+    depends_on('r-checkmate@1.5.1:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-paramhelpers/package.py b/var/spack/repos/builtin/packages/r-paramhelpers/package.py
new file mode 100644
index 0000000000..2fabb7954a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-paramhelpers/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RParamhelpers(RPackage):
+    """Functions for parameter descriptions and operations in black-box
+       optimization, tuning and machine learning. Parameters can be described
+       (type, constraints, defaults, etc.), combined to parameter sets and can
+       in general be programmed on. A useful OptPath object (archive) to log
+       function evaluations is also provided."""
+
+    homepage = "https://github.com/berndbischl/ParamHelpers"
+    url      = "https://cran.r-project.org/src/contrib/ParamHelpers_1.10.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/ParamHelpers"
+
+    version('1.10', '36e9060488ebd484d62cd991a4693332')
+
+    depends_on('r-bbmisc@1.10:', type=('build', 'run'))
+    depends_on('r-checkmate@1.8.1:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-party/package.py b/var/spack/repos/builtin/packages/r-party/package.py
index de9be7d79d..f0d5065d68 100644
--- a/var/spack/repos/builtin/packages/r-party/package.py
+++ b/var/spack/repos/builtin/packages/r-party/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-partykit/package.py b/var/spack/repos/builtin/packages/r-partykit/package.py
index 45ce019cad..680891ae0d 100644
--- a/var/spack/repos/builtin/packages/r-partykit/package.py
+++ b/var/spack/repos/builtin/packages/r-partykit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/r-pathview/package.py b/var/spack/repos/builtin/packages/r-pathview/package.py
new file mode 100644
index 0000000000..bedd4571f7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-pathview/package.py
@@ -0,0 +1,32 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RPathview(RPackage):
+    """Pathview is a tool set for pathway based data integration and
+    visualization. It maps and renders a wide variety of biological data on
+    relevant pathway graphs. All users need is to supply their data and
+    specify the target pathway. Pathview automatically downloads the pathway
+    graph data, parses the data file, maps user data to the pathway, and
+    render pathway graph with the mapped data. In addition, Pathview also
+    seamlessly integrates with pathway and gene set (enrichment) analysis
+    tools for large-scale and fully automated analysis."""
+
+    homepage = "https://www.bioconductor.org/packages/pathview/"
+    git      = "https://git.bioconductor.org/packages/pathview.git"
+
+    version('1.16.7', commit='fc560ed15ef7393a73d35e714716cc24dc835339')
+
+    depends_on('r-keggrest', type=('build', 'run'))
+    depends_on('r-png', type=('build', 'run'))
+    depends_on('r-annotationdbi', type=('build', 'run'))
+    depends_on('r-graph', type=('build', 'run'))
+    depends_on('r-rgraphviz', type=('build', 'run'))
+    depends_on('r-xml', type=('build', 'run'))
+    depends_on('r-kegggraph', type=('build', 'run'))
+    depends_on('r-org-hs-eg-db', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@1.16.7')
diff --git a/var/spack/repos/builtin/packages/r-pbapply/package.py b/var/spack/repos/builtin/packages/r-pbapply/package.py
new file mode 100644
index 0000000000..14d5d9a178
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-pbapply/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RPbapply(RPackage):
+    """A lightweight package that adds progress bar to vectorized R
+    apply functions."""
+
+    homepage = "https://cran.r-project.org/web/packages/pbapply/index.html"
+    url      = "https://cran.r-project.org/src/contrib/pbapply_1.3-3.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/pbapply"
+
+    version('1.3-3', '570db6795179a1439c174be881c77d18')
+    version('1.3-2', 'd72a777bfe4a28ba4e1585e31680f82e')
+    version('1.3-1', '13d64dead441426aa96a3bf3fde29daf')
+    version('1.3-0', 'a3f93cd05054657a01893a3817fa1f08')
+    version('1.2-2', '23e2bfe531c704b79308b0b5fbe1ace8')
+
+    depends_on('r@3.4.0:3.4.9')
diff --git a/var/spack/repos/builtin/packages/r-pbdzmq/package.py b/var/spack/repos/builtin/packages/r-pbdzmq/package.py
index 82adce3430..5ff32c0487 100644
--- a/var/spack/repos/builtin/packages/r-pbdzmq/package.py
+++ b/var/spack/repos/builtin/packages/r-pbdzmq/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/r-pbkrtest/package.py b/var/spack/repos/builtin/packages/r-pbkrtest/package.py
index 4d6ae727cc..1bb9f75f0b 100644
--- a/var/spack/repos/builtin/packages/r-pbkrtest/package.py
+++ b/var/spack/repos/builtin/packages/r-pbkrtest/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-pcamethods/package.py b/var/spack/repos/builtin/packages/r-pcamethods/package.py
index b43fac79d0..a0e9721e9d 100644
--- a/var/spack/repos/builtin/packages/r-pcamethods/package.py
+++ b/var/spack/repos/builtin/packages/r-pcamethods/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,9 +18,9 @@ class RPcamethods(RPackage):
        Physiology, Golm, Germany."""
 
     homepage = "http://bioconductor.org/packages/pcaMethods/"
-    url      = "https://git.bioconductor.org/packages/pcaMethods"
-    list_url = homepage
-    version('1.68.0', git='https://git.bioconductor.org/packages/pcaMethods', commit='c8d7c93dcaf7ef728f3d089ae5d55771b320bdab')
+    git      = "https://git.bioconductor.org/packages/pcaMethods.git"
+
+    version('1.68.0', commit='c8d7c93dcaf7ef728f3d089ae5d55771b320bdab')
 
     depends_on('r-biobase', type=('build', 'run'))
     depends_on('r-biocgenerics', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-pcapp/package.py b/var/spack/repos/builtin/packages/r-pcapp/package.py
new file mode 100644
index 0000000000..3fe6f2d745
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-pcapp/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RPcapp(RPackage):
+        """Provides functions for robust PCA by projection pursuit."""
+
+        homepage = "https://cran.r-project.org/web/packages/pcaPP/index.html"
+        url      = "https://cran.r-project.org/src/contrib/pcaPP_1.9-72.tar.gz"
+        list_url = "https://cran.rstudio.com/src/contrib/Archive/pcaPP"
+
+        version('1.9-72', '87c08f8ecab69311bba395c026bbc91c')
+        version('1.9-70', '3fcc809ec1cdc910f10e9ebf372888e8')
+        version('1.9-61', '1bd5bc3aff968b168493e8c523d726ea')
+        version('1.9-60', '23dd468abb9fedc11e40166446df1017')
+        version('1.9-50', 'be44f173404fd6e86ba0a5515711bfa3')
+
+        depends_on('r-mvtnorm', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-permute/package.py b/var/spack/repos/builtin/packages/r-permute/package.py
index 846028e0da..48f4197e5f 100644
--- a/var/spack/repos/builtin/packages/r-permute/package.py
+++ b/var/spack/repos/builtin/packages/r-permute/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-pfam-db/package.py b/var/spack/repos/builtin/packages/r-pfam-db/package.py
index ef580a84bb..c29bdad99c 100644
--- a/var/spack/repos/builtin/packages/r-pfam-db/package.py
+++ b/var/spack/repos/builtin/packages/r-pfam-db/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-phangorn/package.py b/var/spack/repos/builtin/packages/r-phangorn/package.py
new file mode 100644
index 0000000000..c20fd50fe4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-phangorn/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RPhangorn(RPackage):
+    """Package contains methods for estimation of phylogenetic trees and
+       networks using Maximum Likelihood, Maximum Parsimony, distance methods
+       and Hadamard conjugation. Allows to compare trees, models selection and
+       offers visualizations for trees and split networks."""
+
+    homepage = "https://cran.r-project.org/package=phangorn"
+    url      = "https://cran.r-project.org/src/contrib/phangorn_2.3.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/phangorn"
+
+    version('2.3.1', '85e7309900d061432508ab6f7e3e627e')
+
+    depends_on('r-ape@5.0:', type=('build', 'run'))
+    depends_on('r-quadprog', type=('build', 'run'))
+    depends_on('r-igraph@1.0:', type=('build', 'run'))
+    depends_on('r-matrix', type=('build', 'run'))
+    depends_on('r-fastmatch', type=('build', 'run'))
+    depends_on('r-magrittr', type=('build', 'run'))
+    depends_on('r-rcpp@0.12.0:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-phantompeakqualtools/package.py b/var/spack/repos/builtin/packages/r-phantompeakqualtools/package.py
new file mode 100644
index 0000000000..a40df310b9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-phantompeakqualtools/package.py
@@ -0,0 +1,30 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RPhantompeakqualtools(RPackage):
+    """Computes informative enrichment and quality measures for
+       ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. This is a modified version
+       of r-spp to be used in conjunction with the phantompeakqualtools
+       package."""
+
+    homepage = "https://github.com/kundajelab/phantompeakqualtools"
+    url      = "https://github.com/kundajelab/phantompeakqualtools/raw/master/spp_1.14.tar.gz"
+
+    version('1.14', '4de207d570999170c1bf45bcba8c6d2d')
+
+    depends_on('boost@1.41.0:')
+    depends_on('r-catools', type=('build', 'run'))
+    depends_on('r-snow', type=('build', 'run'))
+    depends_on('r-snowfall', type=('build', 'run'))
+    depends_on('r-bitops', type=('build', 'run'))
+    depends_on('r-rsamtools', type=('build', 'run'))
+
+    conflicts('%gcc@6:')
+
+    def setup_environment(self, spack_env, run_env):
+        spack_env.set('BOOST_ROOT', self.spec['boost'].prefix)
diff --git a/var/spack/repos/builtin/packages/r-phyloseq/package.py b/var/spack/repos/builtin/packages/r-phyloseq/package.py
new file mode 100644
index 0000000000..c2323c4209
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-phyloseq/package.py
@@ -0,0 +1,34 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RPhyloseq(RPackage):
+    """phyloseq provides a set of classes and tools to facilitate the import,
+    storage, analysis, and graphical display of microbiome census data."""
+
+    homepage = "https://www.bioconductor.org/packages/phyloseq/"
+    git      = "https://git.bioconductor.org/packages/phyloseq.git"
+
+    version('1.20.0', commit='107d1d5e3437a6e33982c06a548d3cc91df2a7e0')
+
+    depends_on('r@3.4.0:3.4.9', when='@1.20.0')
+    depends_on('r-biocgenerics', type=('build', 'run'))
+    depends_on('r-ade4', type=('build', 'run'))
+    depends_on('r-ape', type=('build', 'run'))
+    depends_on('r-biomformat', type=('build', 'run'))
+    depends_on('r-biostrings', type=('build', 'run'))
+    depends_on('r-cluster', type=('build', 'run'))
+    depends_on('r-data-table', type=('build', 'run'))
+    depends_on('r-foreach', type=('build', 'run'))
+    depends_on('r-ggplot2', type=('build', 'run'))
+    depends_on('r-igraph', type=('build', 'run'))
+    depends_on('r-multtest', type=('build', 'run'))
+    depends_on('r-plyr', type=('build', 'run'))
+    depends_on('r-reshape2', type=('build', 'run'))
+    depends_on('r-scales', type=('build', 'run'))
+    depends_on('r-vegan', type=('build', 'run'))
+    depends_on('r-biobase', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-picante/package.py b/var/spack/repos/builtin/packages/r-picante/package.py
new file mode 100644
index 0000000000..f967e5b19b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-picante/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RPicante(RPackage):
+    """R tools for integrating phylogenies and ecology"""
+
+    homepage = "https://cran.r-project.org/package=picante"
+    url      = "https://cran.r-project.org/src/contrib/picante_1.6-2.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/picante"
+
+    version('1.6-2', 'e3eba6ef254068d2cfa9e96760bcd7a3')
+    version('1.6-1', '73d86b90eceda582654e995d47236d6e')
+
+    depends_on('r-ape', type=('build', 'run'))
+    depends_on('r-nlme', type=('build', 'run'))
+    depends_on('r-vegan', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-pkgconfig/package.py b/var/spack/repos/builtin/packages/r-pkgconfig/package.py
index 56263cb210..b35d0e1383 100644
--- a/var/spack/repos/builtin/packages/r-pkgconfig/package.py
+++ b/var/spack/repos/builtin/packages/r-pkgconfig/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-pkgmaker/package.py b/var/spack/repos/builtin/packages/r-pkgmaker/package.py
index efb91262a4..8b0b1b7e1c 100644
--- a/var/spack/repos/builtin/packages/r-pkgmaker/package.py
+++ b/var/spack/repos/builtin/packages/r-pkgmaker/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-plogr/package.py b/var/spack/repos/builtin/packages/r-plogr/package.py
index 0f5e1319b7..e959c294a2 100644
--- a/var/spack/repos/builtin/packages/r-plogr/package.py
+++ b/var/spack/repos/builtin/packages/r-plogr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,7 +11,9 @@ class RPlogr(RPackage):
     'LinkingTo: plogr' to 'DESCRIPTION', and '#include <plogr.h>'
     in your C++ modules to use it."""
 
-    homepage = "https://cran.r-project.org/web/packages/plogr/index.html"
-    url      = "https://cran.r-project.org/src/contrib/plogr_0.1-1.tar.gz"
+    homepage = "https://cran.r-project.org/package=plogr"
+    url      = "https://cran.r-project.org/src/contrib/plogr_0.2.0.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/plogr"
+
+    version('0.2.0', sha256='0e63ba2e1f624005fe25c67cdd403636a912e063d682eca07f2f1d65e9870d29')
     version('0.1-1', '5ee46ed21b5c571d02900219098517c0')
diff --git a/var/spack/repos/builtin/packages/r-plot3d/package.py b/var/spack/repos/builtin/packages/r-plot3d/package.py
new file mode 100644
index 0000000000..74883c1f2f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-plot3d/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RPlot3d(RPackage):
+    """Functions for viewing 2-D and 3-D data, including perspective plots,
+       slice plots, surface plots, scatter plots, etc. Includes data sets from
+       oceanography."""
+
+    homepage = "https://CRAN.R-project.org/package=plot3D"
+    url      = "https://cran.r-project.org/src/contrib/plot3D_1.1.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/plot3D"
+
+    version('1.1.1', '5135aa1f3cf6106f2ded3f393a24e75d')
+
+    depends_on('r-misc3d', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-plotly/package.py b/var/spack/repos/builtin/packages/r-plotly/package.py
new file mode 100644
index 0000000000..414155d75b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-plotly/package.py
@@ -0,0 +1,34 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RPlotly(RPackage):
+    """Easily translate 'ggplot2' graphs to an interactive web-based version
+    and/or create custom web-based visualizations directly from R."""
+
+    homepage = "https://cran.r-project.org/web/packages/plotly/index.html"
+    url      = "https://cran.r-project.org/src/contrib/plotly_4.7.1.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/plotly"
+
+    version('4.7.1', '4799c8b429291d4c52fb904380806548')
+    version('4.7.0', '5bd52d515c01af7ff291c30a6cf23bec')
+    version('4.6.0', '27ff3de288bacfaad6e6694752ea2929')
+    version('4.5.6', 'e6e00177fa64dc6b1a199facfd73f585')
+    version('4.5.2', '7eb11b24a9faa9a572657fd89ed72fa5')
+
+    depends_on('r@3.4.0:3.4.9')
+    depends_on('r-ggplot2', type=('build', 'run'))
+    depends_on('r-httr', type=('build', 'run'))
+    depends_on('r-base64enc', type=('build', 'run'))
+    depends_on('r-htmltools', type=('build', 'run'))
+    depends_on('r-tidyr', type=('build', 'run'))
+    depends_on('r-dplyr', type=('build', 'run'))
+    depends_on('r-htmlwidgets', type=('build', 'run'))
+    depends_on('r-data-table', type=('build', 'run'))
+    depends_on('r-hexbin', type=('build', 'run'))
+    depends_on('r-purrr', type=('build', 'run'))
+    depends_on('r-crosstalk', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-plotrix/package.py b/var/spack/repos/builtin/packages/r-plotrix/package.py
index 018d68c498..0ab72642af 100644
--- a/var/spack/repos/builtin/packages/r-plotrix/package.py
+++ b/var/spack/repos/builtin/packages/r-plotrix/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-pls/package.py b/var/spack/repos/builtin/packages/r-pls/package.py
index b4d5c5c493..51c83e32a3 100644
--- a/var/spack/repos/builtin/packages/r-pls/package.py
+++ b/var/spack/repos/builtin/packages/r-pls/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-plyr/package.py b/var/spack/repos/builtin/packages/r-plyr/package.py
index 70a2659f95..bd2dc01429 100644
--- a/var/spack/repos/builtin/packages/r-plyr/package.py
+++ b/var/spack/repos/builtin/packages/r-plyr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-pmcmr/package.py b/var/spack/repos/builtin/packages/r-pmcmr/package.py
index 11d8d3edfb..5a2c5593ce 100644
--- a/var/spack/repos/builtin/packages/r-pmcmr/package.py
+++ b/var/spack/repos/builtin/packages/r-pmcmr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-png/package.py b/var/spack/repos/builtin/packages/r-png/package.py
index 6d65cc6476..d0cc9c24db 100644
--- a/var/spack/repos/builtin/packages/r-png/package.py
+++ b/var/spack/repos/builtin/packages/r-png/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-powerlaw/package.py b/var/spack/repos/builtin/packages/r-powerlaw/package.py
new file mode 100644
index 0000000000..9666f8fd09
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-powerlaw/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RPowerlaw(RPackage):
+    """An implementation of maximum likelihood estimators for a variety of
+       heavy tailed distributions, including both the discrete and continuous
+       power law distributions. Additionally, a goodness-of-fit based approach
+       is used to estimate the lower cut-off for the scaling region."""
+
+    homepage = "https://github.com/csgillespie/poweRlaw"
+    url      = "https://cran.rstudio.com/src/contrib/poweRlaw_0.70.1.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/poweRlaw"
+
+    version('0.70.1', '4117cb95c37f72441f320ea12f553065')
+
+    depends_on('r-vgam', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-prabclus/package.py b/var/spack/repos/builtin/packages/r-prabclus/package.py
index de5b5b7db9..688cd683cd 100644
--- a/var/spack/repos/builtin/packages/r-prabclus/package.py
+++ b/var/spack/repos/builtin/packages/r-prabclus/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-praise/package.py b/var/spack/repos/builtin/packages/r-praise/package.py
index f58ba04b06..06ae033e60 100644
--- a/var/spack/repos/builtin/packages/r-praise/package.py
+++ b/var/spack/repos/builtin/packages/r-praise/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-preprocesscore/package.py b/var/spack/repos/builtin/packages/r-preprocesscore/package.py
index 95ce33d8c3..d07e164a6d 100644
--- a/var/spack/repos/builtin/packages/r-preprocesscore/package.py
+++ b/var/spack/repos/builtin/packages/r-preprocesscore/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,8 @@ class RPreprocesscore(RPackage):
     """A library of core preprocessing routines"""
 
     homepage = "https://bioconductor.org/packages/preprocessCore/"
-    url      = "https://git.bioconductor.org/packages/preprocessCore"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/preprocessCore.git"
 
-    version('1.38.1', git='https://git.bioconductor.org/packages/preprocessCore', commit='c58cb4c720eda0f1c733b989b14912093a7c5fbc')
+    version('1.38.1', commit='c58cb4c720eda0f1c733b989b14912093a7c5fbc')
 
     depends_on('r@3.4.0:3.4.9', when='@1.38.1')
diff --git a/var/spack/repos/builtin/packages/r-prettyunits/package.py b/var/spack/repos/builtin/packages/r-prettyunits/package.py
index 0741d17411..fc5de8b0e1 100644
--- a/var/spack/repos/builtin/packages/r-prettyunits/package.py
+++ b/var/spack/repos/builtin/packages/r-prettyunits/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-processx/package.py b/var/spack/repos/builtin/packages/r-processx/package.py
new file mode 100644
index 0000000000..fec9bba0b1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-processx/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RProcessx(RPackage):
+    """Tools to run system processes in the background"""
+
+    homepage = "https://github.com/r-lib/processx"
+    url      = "https://cran.r-project.org/src/contrib/processx_3.2.0.tar.gz"
+    list_url      = "https://cran.r-project.org/src/contrib/Archive/processx/processx_3.1.0.tar.gz"
+
+    version('3.2.0', sha256='c4ba602fcbdc032ae9d94701b3e6b83a2dab1b53d0b4f9937b07a84eae22fddf')
+    version('3.1.0',   sha256='11ac120ab4e4aa0e99c9b2eda87d07bc683bab735f1761e95e5ddacd311b5972')
+    version('3.0.3',   sha256='53781dba3c538605a02e28b3b577e7de79e2064bfc502025f7ec0e5945e302bf')
+    version('2.0.0.1', sha256='8f61b2952d0f2d13c74465bfba174ce11eee559475c2f7b9be6bcb9e2e1d827b')
+    version('2.0.0',   sha256='8325b56a60a276909228756281523cda9256bc754c5f3ca03b41c5c17cc398ad')
+
+    depends_on('r-assertthat', type=('build', 'run'))
+    depends_on('r-crayon', type=('build', 'run'))
+    depends_on('r-ps', type=('build', 'run'))
+    depends_on('r-r6', type=('build', 'run'))
+    depends_on('r-utils', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-prodlim/package.py b/var/spack/repos/builtin/packages/r-prodlim/package.py
index b9721174d6..8cb3523f6d 100644
--- a/var/spack/repos/builtin/packages/r-prodlim/package.py
+++ b/var/spack/repos/builtin/packages/r-prodlim/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-progress/package.py b/var/spack/repos/builtin/packages/r-progress/package.py
index b5a909a73d..756b8cecff 100644
--- a/var/spack/repos/builtin/packages/r-progress/package.py
+++ b/var/spack/repos/builtin/packages/r-progress/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-protgenerics/package.py b/var/spack/repos/builtin/packages/r-protgenerics/package.py
index 7ec8fa8537..2b14314b29 100644
--- a/var/spack/repos/builtin/packages/r-protgenerics/package.py
+++ b/var/spack/repos/builtin/packages/r-protgenerics/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,8 @@ class RProtgenerics(RPackage):
     """S4 generic functions needed by Bioconductor proteomics packages."""
 
     homepage = "https://bioconductor.org/packages/ProtGenerics/"
-    url      = "https://git.bioconductor.org/packages/ProtGenerics"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/ProtGenerics.git"
 
-    version('1.8.0', git='https://git.bioconductor.org/packages/ProtGenerics', commit='b2b3bb0938e20f58fca905f6870de7dbc9dfd7a3')
+    version('1.8.0', commit='b2b3bb0938e20f58fca905f6870de7dbc9dfd7a3')
 
     depends_on('r@3.4.0:3.4.9', when='@1.8.0')
diff --git a/var/spack/repos/builtin/packages/r-proto/package.py b/var/spack/repos/builtin/packages/r-proto/package.py
index 412ad956e3..5fe325b834 100644
--- a/var/spack/repos/builtin/packages/r-proto/package.py
+++ b/var/spack/repos/builtin/packages/r-proto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,4 +14,5 @@ class RProto(RPackage):
     url      = "https://cran.r-project.org/src/contrib/proto_0.3-10.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/proto"
 
+    version('1.0.0', sha256='9294d9a3b2b680bb6fac17000bfc97453d77c87ef68cfd609b4c4eb6d11d04d1')
     version('0.3-10', 'd5523943a5be6ca2f0ab557c900f8212')
diff --git a/var/spack/repos/builtin/packages/r-proxy/package.py b/var/spack/repos/builtin/packages/r-proxy/package.py
index 5f6057c769..963568491c 100644
--- a/var/spack/repos/builtin/packages/r-proxy/package.py
+++ b/var/spack/repos/builtin/packages/r-proxy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-pryr/package.py b/var/spack/repos/builtin/packages/r-pryr/package.py
index b1e9ad4e9b..89142810ba 100644
--- a/var/spack/repos/builtin/packages/r-pryr/package.py
+++ b/var/spack/repos/builtin/packages/r-pryr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/r-ps/package.py b/var/spack/repos/builtin/packages/r-ps/package.py
new file mode 100644
index 0000000000..0973376a04
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-ps/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RPs(RPackage):
+    """Manipulate processes on Windows, Linux and MacOS"""
+
+    homepage = "https://github.com/r-lib/ps"
+    url      = "https://cran.r-project.org/src/contrib/ps_1.1.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/ps/ps_1.0.0.tar.gz"
+
+    version('1.1.0', sha256='5d5240d5bf1d48c721b3fdf47cfc9dbf878e388ea1f057b764db05bffdc4a9fe')
+    version('1.0.0', sha256='9bdaf64aaa44ae11866868402eb75bf56c2e3022100476d9b9dcd16ca784ffd8')
diff --git a/var/spack/repos/builtin/packages/r-psych/package.py b/var/spack/repos/builtin/packages/r-psych/package.py
new file mode 100644
index 0000000000..d000222e7a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-psych/package.py
@@ -0,0 +1,36 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RPsych(RPackage):
+    """A general purpose toolbox for personality, psychometric theory and
+       experimental psychology. Functions are primarily for multivariate
+       analysis and scale construction using factor analysis, principal
+       component analysis, cluster analysis and reliability analysis, although
+       others provide basic descriptive statistics. Item Response Theory is
+       done using factor analysis of tetrachoric and polychoric correlations.
+       Functions for analyzing data at multiple levels include within and
+       between group statistics, including correlations and factor analysis.
+       Functions for simulating and testing particular item and test structures
+       are included. Several functions serve as a useful front end for
+       structural equation modeling. Graphical displays of path diagrams,
+       factor analysis and structural equation models are created using basic
+       graphics. Some of the functions are written to support a book on
+       psychometric theory as well as publications in personality research.
+       For more information, see the <http://personality-project.org/r> web
+       page."""
+
+    homepage = "http://personality-project.org/r/psych"
+    url      = "https://cran.r-project.org/src/contrib/psych_1.7.8.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/psych"
+
+    version('1.7.8', 'db37f2f85ff5470ee40bbc0a58ebe22b')
+
+    depends_on('r-mnormt', type=('build', 'run'))
+    depends_on('r-foreign', type=('build', 'run'))
+    depends_on('r-lattice', type=('build', 'run'))
+    depends_on('r-nlme', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-ptw/package.py b/var/spack/repos/builtin/packages/r-ptw/package.py
index 38048bc2a7..dcb5fdedc0 100644
--- a/var/spack/repos/builtin/packages/r-ptw/package.py
+++ b/var/spack/repos/builtin/packages/r-ptw/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-purrr/package.py b/var/spack/repos/builtin/packages/r-purrr/package.py
index 4ef40d9480..73a422c0cb 100644
--- a/var/spack/repos/builtin/packages/r-purrr/package.py
+++ b/var/spack/repos/builtin/packages/r-purrr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-quadprog/package.py b/var/spack/repos/builtin/packages/r-quadprog/package.py
index dc35139a65..ad68a31a0d 100644
--- a/var/spack/repos/builtin/packages/r-quadprog/package.py
+++ b/var/spack/repos/builtin/packages/r-quadprog/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-quantmod/package.py b/var/spack/repos/builtin/packages/r-quantmod/package.py
index 749558f894..b9f0e063e8 100644
--- a/var/spack/repos/builtin/packages/r-quantmod/package.py
+++ b/var/spack/repos/builtin/packages/r-quantmod/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-quantreg/package.py b/var/spack/repos/builtin/packages/r-quantreg/package.py
index 6b33827526..e882ece170 100644
--- a/var/spack/repos/builtin/packages/r-quantreg/package.py
+++ b/var/spack/repos/builtin/packages/r-quantreg/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-quantro/package.py b/var/spack/repos/builtin/packages/r-quantro/package.py
index 05185abe8b..796685c40a 100644
--- a/var/spack/repos/builtin/packages/r-quantro/package.py
+++ b/var/spack/repos/builtin/packages/r-quantro/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,10 +15,9 @@ class RQuantro(RPackage):
        user-defined groups."""
 
     homepage = "https://www.bioconductor.org/packages/quantro/"
-    url      = "https://git.bioconductor.org/packages/quantro"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/quantro.git"
 
-    version('1.10.0', git='https://git.bioconductor.org/packages/quantro', commit='111337c0aba052aa49c3d2e2d3042794b28858c9')
+    version('1.10.0', commit='111337c0aba052aa49c3d2e2d3042794b28858c9')
 
     depends_on('r-biobase', type=('build', 'run'))
     depends_on('r-minfi', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-qvalue/package.py b/var/spack/repos/builtin/packages/r-qvalue/package.py
index f34f00c7e4..5deb42a748 100644
--- a/var/spack/repos/builtin/packages/r-qvalue/package.py
+++ b/var/spack/repos/builtin/packages/r-qvalue/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -41,10 +22,12 @@ class RQvalue(RPackage):
     and data mining."""
 
     homepage = "https://www.bioconductor.org/packages/qvalue/"
-    url      = "https://git.bioconductor.org/packages/qvalue"
+    git      = "https://git.bioconductor.org/packages/qvalue.git"
 
-    version('2.8.0', git='https://git.bioconductor.org/packages/qvalue', commit='c7bf3315619d42d800f57a36670c25a7495ded72')
+    version('2.12.0', commit='7df64ebfcbe69dcbf8b88cb6ef0068bf16979673')
+    version('2.8.0', commit='c7bf3315619d42d800f57a36670c25a7495ded72')
 
-    depends_on('r@3.4.0:3.4.9', when='@2.8.0')
     depends_on('r-ggplot2', type=('build', 'run'))
     depends_on('r-reshape2', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@2.8.0', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@2.12.0', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-r6/package.py b/var/spack/repos/builtin/packages/r-r6/package.py
index f424b1c8e1..fad58e9517 100644
--- a/var/spack/repos/builtin/packages/r-r6/package.py
+++ b/var/spack/repos/builtin/packages/r-r6/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-randomforest/package.py b/var/spack/repos/builtin/packages/r-randomforest/package.py
index 3fbb2a3d1e..1125e26d22 100644
--- a/var/spack/repos/builtin/packages/r-randomforest/package.py
+++ b/var/spack/repos/builtin/packages/r-randomforest/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-ranger/package.py b/var/spack/repos/builtin/packages/r-ranger/package.py
new file mode 100644
index 0000000000..0693fc0023
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-ranger/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RRanger(RPackage):
+    """A fast implementation of Random Forests, particularly suited for high
+    dimensional data."""
+
+    homepage = "https://cran.r-project.org/web/packages/ranger/index.html"
+    url      = "https://cran.r-project.org/src/contrib/ranger_0.8.0.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/ranger"
+
+    version('0.8.0', '1501380f418e784a6159bc1fb06fd32c')
+    version('0.7.0', 'c7fbcbab7c195bc8e65b1ceb3baeb87f')
+    version('0.6.0', '047ad26289c9b528b7476aa4811b4111')
+    version('0.5.0', 'd45001c8ff58d3078de7353971219927')
+    version('0.4.0', 'd404d8a9142372e3c77482b6b7dc469b')
+
+    depends_on('r@3.4.0:3.4.9')
+    depends_on('r-matrix', type=('build', 'run'))
+    depends_on('r-rcpp', type=('build', 'run'))
+    depends_on('r-rcppeigen', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-rappdirs/package.py b/var/spack/repos/builtin/packages/r-rappdirs/package.py
new file mode 100644
index 0000000000..b39a699690
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rappdirs/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RRappdirs(RPackage):
+    """An easy way to determine which directories on the users computer
+    you should use to save data, caches and logs. A port of Python's
+    'Appdirs' to R."""
+
+    homepage = "https://cran.r-project.org/package=rappdirs"
+    url      = "https://cran.rstudio.com/src/contrib/rappdirs_0.3.1.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/rappdirs"
+
+    version('0.3.1', 'fbbdceda2aa49374e61c7d387bf9ea21')
+
+    depends_on('r@2.14:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-raster/package.py b/var/spack/repos/builtin/packages/r-raster/package.py
index 917adfb7d6..0bcb424ea6 100644
--- a/var/spack/repos/builtin/packages/r-raster/package.py
+++ b/var/spack/repos/builtin/packages/r-raster/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-rbgl/package.py b/var/spack/repos/builtin/packages/r-rbgl/package.py
index 13cd4fb68e..87216adc55 100644
--- a/var/spack/repos/builtin/packages/r-rbgl/package.py
+++ b/var/spack/repos/builtin/packages/r-rbgl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,9 @@ class RRbgl(RPackage):
     algorithms contained in the BOOST library."""
 
     homepage = "https://www.bioconductor.org/packages/RBGL/"
-    url      = "https://git.bioconductor.org/packages/RBGL"
+    git      = "https://git.bioconductor.org/packages/RBGL.git"
 
-    version('1.52.0', git='https://git.bioconductor.org/packages/RBGL', commit='93e8fcfafec8f1cd5638fe30dc0f9506d15b49c0')
+    version('1.52.0', commit='93e8fcfafec8f1cd5638fe30dc0f9506d15b49c0')
 
     depends_on('r@3.4.0:3.4.9', when='@1.52.0')
     depends_on('r-graph', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-rbokeh/package.py b/var/spack/repos/builtin/packages/r-rbokeh/package.py
index ee254db179..22c421b16b 100644
--- a/var/spack/repos/builtin/packages/r-rbokeh/package.py
+++ b/var/spack/repos/builtin/packages/r-rbokeh/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py b/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py
index 6092e34163..7115d8b2b4 100644
--- a/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py
+++ b/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-rcpp/package.py b/var/spack/repos/builtin/packages/r-rcpp/package.py
index b95626020a..933cd294fb 100644
--- a/var/spack/repos/builtin/packages/r-rcpp/package.py
+++ b/var/spack/repos/builtin/packages/r-rcpp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,6 +21,8 @@ class RRcpp(RPackage):
     url      = "https://cran.rstudio.com/src/contrib/Rcpp_0.12.13.tar.gz"
     list_url = "https://cran.rstudio.com/src/contrib/Archive/Rcpp"
 
+    version('0.12.16', 'ab5107766c63d66065ed1a92a4cab1b7')
+    version('0.12.15', 'bebac0782862c15c2944764343e55582')
     version('0.12.14', '89a3dbad0aa3e345b9d0b862fa1fc56a')
     version('0.12.13', '5186d119132bfe07f66da74c50b190a4')
     version('0.12.12', '97b36a3b567e3438067c4a7d0075fd90')
diff --git a/var/spack/repos/builtin/packages/r-rcpparmadillo/package.py b/var/spack/repos/builtin/packages/r-rcpparmadillo/package.py
index dba1dfe93d..250e12ec2f 100644
--- a/var/spack/repos/builtin/packages/r-rcpparmadillo/package.py
+++ b/var/spack/repos/builtin/packages/r-rcpparmadillo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-rcppblaze/package.py b/var/spack/repos/builtin/packages/r-rcppblaze/package.py
new file mode 100644
index 0000000000..dfdcefa2b1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rcppblaze/package.py
@@ -0,0 +1,46 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RRcppblaze(RPackage):
+    """'Blaze' is an open-source, high-performance C++ math library for dense
+       and sparse arithmetic.
+
+       With its state-of-the-art Smart Expression Template implementation
+       'Blaze' combines the elegance and ease of use of a domain-specific
+       language with 'HPC'-grade performance, making it one of the most
+       intuitive and fastest C++ math libraries available. The 'Blaze'
+       library offers: - high performance through the integration of
+       'BLAS' libraries and manually tuned 'HPC' math kernels - vectorization
+       by 'SSE', 'SSE2', 'SSE3', 'SSSE3', 'SSE4', 'AVX', 'AVX2', 'AVX-512',
+       'FMA', and 'SVML' - parallel execution by 'OpenMP', C++11 threads and
+       'Boost' threads ('Boost' threads are disabled in 'RcppBlaze') - the
+       intuitive and easy to use API of a domain specific language - unified
+       arithmetic with dense and sparse vectors and matrices - thoroughly
+       tested matrix and vector arithmetic - completely portable, high quality
+       C++ source code. The 'RcppBlaze' package includes the header files from
+       the 'Blaze' library with disabling some functionalities related to link
+       to the thread and system libraries which make 'RcppBlaze' be a
+       header-only library. Therefore, users do not need to install 'Blaze'
+       and the dependency 'Boost'. 'Blaze' is licensed under the New (Revised)
+       BSD license, while 'RcppBlaze' (the 'Rcpp' bindings/bridge to 'Blaze')
+       is licensed under the GNU GPL version 2 or later, as is the rest of
+       'Rcpp'. Note that since 'Blaze' has committed to 'C++14' commit to
+       'C++14' which does not used by most R users from version 3.0, we will
+       use the version 2.6 of 'Blaze' which is 'C++98' compatible to support
+       the most compilers and system."""
+
+    homepage = "https://github.com/Chingchuan-chen/RcppBlaze"
+    url      = "https://cran.rstudio.com/src/contrib/RcppBlaze_0.2.2.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/RcppBlaze"
+
+    version('0.2.2', '22ecae73cf1bebce06ed6387d49f2c77')
+
+    depends_on('r-rcpp@0.11.0:', type=('build', 'run'))
+    depends_on('r-matrix@1.1-0:', type=('build', 'run'))
+    depends_on('r-bh@1.54.0-2:', type=('build', 'run'))
+    depends_on('r@3.0.2:')
diff --git a/var/spack/repos/builtin/packages/r-rcppcctz/package.py b/var/spack/repos/builtin/packages/r-rcppcctz/package.py
new file mode 100644
index 0000000000..5e454dd6dc
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rcppcctz/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RRcppcctz(RPackage):
+    """'Rcpp' Access to the 'CCTZ' timezone library is provided. 'CCTZ' is a
+       C++ library for translating between absolute and civil times using the
+       rules of a time zone. The 'CCTZ' source code, released under the
+       Apache 2.0 License, is included in this package. See
+       <https://github.com/google/cctz> for more details."""
+
+    homepage = "https://github.com/eddelbuettel/rcppcctz"
+    url      = "https://cran.r-project.org/src/contrib/RcppCCTZ_0.2.3.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/RcppCCTZ"
+
+    version('0.2.3', '7635014a1cc696a3f00a7619fb5d7008')
+
+    depends_on('r-rcpp', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-rcppcnpy/package.py b/var/spack/repos/builtin/packages/r-rcppcnpy/package.py
new file mode 100644
index 0000000000..ace5876f48
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rcppcnpy/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RRcppcnpy(RPackage):
+    """Rcpp bindings for NumPy files."""
+
+    homepage = "https://github.com/eddelbuettel/rcppcnpy"
+    url      = "https://cran.r-project.org/src/contrib/RcppCNPy_0.2.9.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/RcppCNPy"
+
+    version('0.2.9', '7f63354d15928b6716830c2975b3baf0')
+
+    depends_on('r@3.1.0:', type=('build', 'run'))
+    depends_on('cnpy')
+    depends_on('r-rcpp', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-rcppeigen/package.py b/var/spack/repos/builtin/packages/r-rcppeigen/package.py
index 47ce27e3f5..14d4e250ef 100644
--- a/var/spack/repos/builtin/packages/r-rcppeigen/package.py
+++ b/var/spack/repos/builtin/packages/r-rcppeigen/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -44,6 +25,7 @@ class RRcppeigen(RPackage):
     url      = "https://cran.r-project.org/src/contrib/RcppEigen_0.3.2.9.0.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/RcppEigen"
 
+    version('0.3.3.3.1', '1a5ae17828813e40e6b3e7400e408a2b')
     version('0.3.2.9.0', '14a7786882a5d9862d53c4b2217df318')
     version('0.3.2.8.1', '4146e06e4fdf7f4d08db7839069d479f')
 
diff --git a/var/spack/repos/builtin/packages/r-rcppprogress/package.py b/var/spack/repos/builtin/packages/r-rcppprogress/package.py
new file mode 100644
index 0000000000..d56b33f757
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rcppprogress/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RRcppprogress(RPackage):
+    """Allows to display a progress bar in the R console for long running
+    computations taking place in c++ code, and support for interrupting
+    those computations even in multithreaded code, typically using OpenMP."""
+
+    homepage = "https://cran.r-project.org/web/packages/RcppProgress/index.html"
+    url      = "https://cran.r-project.org/src/contrib/RcppProgress_0.3.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/RcppProgress"
+
+    version('0.3',   '3cd527af84bc6fcb3c77422e0ff09dba')
+    version('0.2.1', 'c9cd69759ff457acfee0b52353f9af1b')
+    version('0.2',   '9522c962ecddd4895b5636e7a499bda5')
+    version('0.1',   '34afefe0580ca42b6353533fe758d5bf')
+
+    depends_on('r@3.4.0:3.4.9')
+    depends_on('r-rcpp', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-rcurl/package.py b/var/spack/repos/builtin/packages/r-rcurl/package.py
index a60499330c..031c69e842 100644
--- a/var/spack/repos/builtin/packages/r-rcurl/package.py
+++ b/var/spack/repos/builtin/packages/r-rcurl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-rda/package.py b/var/spack/repos/builtin/packages/r-rda/package.py
index 614f6756ce..e8d455050a 100644
--- a/var/spack/repos/builtin/packages/r-rda/package.py
+++ b/var/spack/repos/builtin/packages/r-rda/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,6 +11,7 @@ class RRda(RPackage):
     classification purpose in high dimensional data."""
 
     homepage = "https://cran.r-project.org/web/packages/rda/index.html"
-    url      = "https://cran.r-project.org/src/contrib/rda_1.0.2-2.tar.gz"
+    url      = "https://cran.r-project.org/src/contrib/rda_1.0.2-1.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/rda"
+
     version('1.0.2-1', '78060c5e054a63a2df4ae4002d7247bc')
diff --git a/var/spack/repos/builtin/packages/r-readr/package.py b/var/spack/repos/builtin/packages/r-readr/package.py
index bec64a6ebd..bb9b862ac9 100644
--- a/var/spack/repos/builtin/packages/r-readr/package.py
+++ b/var/spack/repos/builtin/packages/r-readr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-readxl/package.py b/var/spack/repos/builtin/packages/r-readxl/package.py
index c70750ea69..3d19f6808e 100644
--- a/var/spack/repos/builtin/packages/r-readxl/package.py
+++ b/var/spack/repos/builtin/packages/r-readxl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,8 +14,10 @@ class RReadxl(RPackage):
     without external dependencies."""
 
     homepage = "http://readxl.tidyverse.org/"
-    url      = "https://cran.r-project.org/src/contrib/readxl_1.0.0.tar.gz"
+    url      = "https://cran.r-project.org/src/contrib/readxl_1.1.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/readxl/readxl_1.0.0.tar.gz"
 
+    version('1.1.0', sha256='b63d21fc6510acb373e96deaec45e966a523ec75cbec75a089529297ed443116')
     version('1.0.0', '030c47ae1af5dd4168087160c29131e4')
 
     depends_on('r-tibble', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-registry/package.py b/var/spack/repos/builtin/packages/r-registry/package.py
index da252a9681..f83c78f0e0 100644
--- a/var/spack/repos/builtin/packages/r-registry/package.py
+++ b/var/spack/repos/builtin/packages/r-registry/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-rematch/package.py b/var/spack/repos/builtin/packages/r-rematch/package.py
index 931f979c60..b4232fa1da 100644
--- a/var/spack/repos/builtin/packages/r-rematch/package.py
+++ b/var/spack/repos/builtin/packages/r-rematch/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-reordercluster/package.py b/var/spack/repos/builtin/packages/r-reordercluster/package.py
index 49ab521967..cc4af49952 100644
--- a/var/spack/repos/builtin/packages/r-reordercluster/package.py
+++ b/var/spack/repos/builtin/packages/r-reordercluster/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-reportingtools/package.py b/var/spack/repos/builtin/packages/r-reportingtools/package.py
index db5978248c..e093b019be 100644
--- a/var/spack/repos/builtin/packages/r-reportingtools/package.py
+++ b/var/spack/repos/builtin/packages/r-reportingtools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,9 +21,9 @@ class RReportingtools(RPackage):
     site: http:// research-pub.gene.com/ReportingTools."""
 
     homepage = "https://bioconductor.org/packages/ReportingTools/"
-    url      = "https://git.bioconductor.org/packages/ReportingTools"
+    git      = "https://git.bioconductor.org/packages/ReportingTools.git"
 
-    version('2.16.0', git='https://git.bioconductor.org/packages/ReportingTools', commit='b1aa0ea302da7f2993ce8087b1d09c11ddf03663')
+    version('2.16.0', commit='b1aa0ea302da7f2993ce8087b1d09c11ddf03663')
 
     depends_on('r@3.4.0:3.4.9', when='@2.16.0')
     depends_on('r-knitr', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-repr/package.py b/var/spack/repos/builtin/packages/r-repr/package.py
index 056e19aedc..0396cd79bb 100644
--- a/var/spack/repos/builtin/packages/r-repr/package.py
+++ b/var/spack/repos/builtin/packages/r-repr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/r-reprex/package.py b/var/spack/repos/builtin/packages/r-reprex/package.py
index a4fa82ed16..e87e70367b 100644
--- a/var/spack/repos/builtin/packages/r-reprex/package.py
+++ b/var/spack/repos/builtin/packages/r-reprex/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-reshape/package.py b/var/spack/repos/builtin/packages/r-reshape/package.py
index a4da7286ca..8364397fa2 100644
--- a/var/spack/repos/builtin/packages/r-reshape/package.py
+++ b/var/spack/repos/builtin/packages/r-reshape/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-reshape2/package.py b/var/spack/repos/builtin/packages/r-reshape2/package.py
index 204ccdee8a..ac424cd4f3 100644
--- a/var/spack/repos/builtin/packages/r-reshape2/package.py
+++ b/var/spack/repos/builtin/packages/r-reshape2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-rex/package.py b/var/spack/repos/builtin/packages/r-rex/package.py
index e39976644c..d8bb5841c2 100644
--- a/var/spack/repos/builtin/packages/r-rex/package.py
+++ b/var/spack/repos/builtin/packages/r-rex/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-rgdal/package.py b/var/spack/repos/builtin/packages/r-rgdal/package.py
new file mode 100644
index 0000000000..b2fbfee9dc
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rgdal/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RRgdal(RPackage):
+    """Provides bindings to the 'Geospatial' Data Abstraction Library
+    ('GDAL') (>= 1.6.3) and access to projection/transformation operations
+    from the 'PROJ.4' library. The 'GDAL' and 'PROJ.4' libraries are
+    external to the package, and, when installing the package from source,
+    must be correctly installed first. Both 'GDAL' raster and 'OGR' vector
+    map data can be imported into R, and 'GDAL' raster data and 'OGR'
+    vector data exported. Use is made of classes defined in the 'sp' package.
+    Windows and Mac Intel OS X binaries (including 'GDAL', 'PROJ.4' and
+    'Expat') are provided on 'CRAN'."""
+
+    homepage = "https://cran.r-project.org/package=rgdal"
+    url      = "https://cran.rstudio.com/src/contrib/rgdal_1.2-16.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/rgdal"
+
+    version('1.2-16', 'de83bf08519a53de68a7632ecb7f2dc9')
+
+    depends_on('r-sp', type=('build', 'run'))
+    depends_on('gdal')
+    depends_on('proj')
diff --git a/var/spack/repos/builtin/packages/r-rgenoud/package.py b/var/spack/repos/builtin/packages/r-rgenoud/package.py
new file mode 100644
index 0000000000..c2d7c517d4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rgenoud/package.py
@@ -0,0 +1,16 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RRgenoud(RPackage):
+    """A genetic algorithm plus derivative optimizer."""
+
+    homepage = "http://sekhon.berkeley.edu/rgenoud/"
+    url      = "https://cran.r-project.org/src/contrib/rgenoud_5.8-1.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/rgenoud"
+
+    version('5.8-1.0', '85801093d2f1e6789683b46ab4a7d70f')
diff --git a/var/spack/repos/builtin/packages/r-rgeos/package.py b/var/spack/repos/builtin/packages/r-rgeos/package.py
new file mode 100644
index 0000000000..2f55d523f6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rgeos/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RRgeos(RPackage):
+    """Interface to Geometry Engine - Open Source ('GEOS') using the C
+    'API' for topology operations on geometries. The 'GEOS' library is
+    external to the package, and, when installing the package from source,
+    must be correctly installed first. Windows and Mac Intel OS X binaries
+    are provided on 'CRAN'."""
+
+    homepage = "https://cran.r-project.org/package=rgeos"
+    url      = "https://cran.rstudio.com/src/contrib/rgeos_0.3-26.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/rgeos"
+
+    version('0.3-26', '7d10a28011b49f68c5817b6fbca132df')
+
+    depends_on('r-sp', type=('build', 'run'))
+    depends_on('geos')
diff --git a/var/spack/repos/builtin/packages/r-rgl/package.py b/var/spack/repos/builtin/packages/r-rgl/package.py
index 97f89ed092..261fbffa98 100644
--- a/var/spack/repos/builtin/packages/r-rgl/package.py
+++ b/var/spack/repos/builtin/packages/r-rgl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-rgooglemaps/package.py b/var/spack/repos/builtin/packages/r-rgooglemaps/package.py
index e1665fd991..b246f8f63f 100644
--- a/var/spack/repos/builtin/packages/r-rgooglemaps/package.py
+++ b/var/spack/repos/builtin/packages/r-rgooglemaps/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-rgraphviz/package.py b/var/spack/repos/builtin/packages/r-rgraphviz/package.py
new file mode 100644
index 0000000000..1f341b24b9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rgraphviz/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RRgraphviz(RPackage):
+    """Interfaces R with the AT and T graphviz library for plotting
+    R graph objects from the graph package."""
+
+    homepage = "http://bioconductor.org/packages/Rgraphviz/"
+    git      = "https://git.bioconductor.org/packages/Rgraphviz.git"
+
+    version('2.20.0', commit='eface6298150667bb22eac672f1a45e52fbf8c90')
+
+    depends_on('r@3.4.0:3.4.9', when='@2.20.0')
+    depends_on('r-graph', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-rhdf5/package.py b/var/spack/repos/builtin/packages/r-rhdf5/package.py
new file mode 100644
index 0000000000..7c4a3a9987
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rhdf5/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RRhdf5(RPackage):
+    """This R/Bioconductor package provides an interface between HDF5
+    and R. HDF5's main features are the ability to store and access very
+    large and/or complex datasets and a wide variety of metadata on mass
+    storage (disk) through a completely portable file format. The rhdf5
+    package is thus suited for the exchange of large and/or complex
+    datasets between R and other software package, and for letting R
+    applications work on datasets that are larger than the available RAM."""
+
+    homepage = "https://www.bioconductor.org/packages/rhdf5/"
+    git      = "https://git.bioconductor.org/packages/rhdf5.git"
+
+    version('2.20.0', commit='37b5165325062728bbec9167f89f5f4b794f30bc')
+
+    depends_on('r@3.4.0:3.4.9', when='@2.20.0')
+    depends_on('r-zlibbioc', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-rhtslib/package.py b/var/spack/repos/builtin/packages/r-rhtslib/package.py
index 4af0093830..e87164b5aa 100644
--- a/var/spack/repos/builtin/packages/r-rhtslib/package.py
+++ b/var/spack/repos/builtin/packages/r-rhtslib/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,9 +14,10 @@ class RRhtslib(RPackage):
     are in the vignette, vignette(package="Rhtslib", "Rhtslib")."""
 
     homepage = "https://www.bioconductor.org/packages/Rhtslib/"
-    url      = "https://git.bioconductor.org/packages/Rhtslib"
+    git      = "https://git.bioconductor.org/packages/Rhtslib.git"
 
-    version('1.8.0', git='https://git.bioconductor.org/packages/Rhtslib', commit='3b5493473bed42958614091c58c739932ffcfa79')
+    version('1.8.0', commit='3b5493473bed42958614091c58c739932ffcfa79')
 
     depends_on('r@3.4.0:3.4.9', when='@1.8.0')
     depends_on('r-zlibbioc', type=('build', 'run'))
+    depends_on('autoconf@2.67:', type='build')
diff --git a/var/spack/repos/builtin/packages/r-rinside/package.py b/var/spack/repos/builtin/packages/r-rinside/package.py
index 1d744db01d..bc7d48745a 100644
--- a/var/spack/repos/builtin/packages/r-rinside/package.py
+++ b/var/spack/repos/builtin/packages/r-rinside/package.py
@@ -1,27 +1,7 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack import *
 
@@ -43,9 +23,10 @@ class RRinside(RPackage):
     available at the 'RInside' website as well."""
 
     homepage = "http://dirk.eddelbuettel.com/code/rinside.html"
-    url      = "https://cran.r-project.org/src/contrib/RInside_0.2.13.tar.gz"
+    url      = "https://cran.r-project.org/src/contrib/RInside_0.2.14.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/RInside"
 
+    version('0.2.14', 'fc72761e22b1f597433eb53d6eb122ff')
     version('0.2.13', '2e3c35a7bd648e9bef98d0afcc02cf88')
 
-    depends_on('r-rcpp', type=('build', 'run'))
+    depends_on('r-rcpp@0.11.0:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-rjags/package.py b/var/spack/repos/builtin/packages/r-rjags/package.py
new file mode 100644
index 0000000000..1dae43af36
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rjags/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class RRjags(RPackage):
+    """Interface to the JAGS MCMC library.
+       Usage: $ spack load r-rjags """
+
+    homepage = "https://cran.r-project.org/web/packages/rjags/index.html"
+    url      = "https://cran.r-project.org/src/contrib/rjags_4-8.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/rjags/"
+
+    version('4-8', sha256='1529827ab11493fb5f05552e239d700ae2f818995d86d3c9e4c92523f594b59f')
+    version('4-6', 'c26b7cc8e8ddcdb55e14cba28df39f4c')
+
+    depends_on('jags', type=('link'))
+    depends_on('r-coda', type=('build', 'run'))
+
+    def configure_args(self):
+        args = ['--with-jags-lib=%s' % self.spec['jags'].prefix.lib,
+                '--with-jags-include=%s' % self.spec['jags'].prefix.include,
+                '--with-jags-modules=%s/JAGS/modules-4'
+                % self.spec['jags'].prefix.lib]
+        return args
diff --git a/var/spack/repos/builtin/packages/r-rjava/package.py b/var/spack/repos/builtin/packages/r-rjava/package.py
index a1e8003343..fc8c3850aa 100644
--- a/var/spack/repos/builtin/packages/r-rjava/package.py
+++ b/var/spack/repos/builtin/packages/r-rjava/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-rjson/package.py b/var/spack/repos/builtin/packages/r-rjson/package.py
index d22b7c780f..250c5171a8 100644
--- a/var/spack/repos/builtin/packages/r-rjson/package.py
+++ b/var/spack/repos/builtin/packages/r-rjson/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-rjsonio/package.py b/var/spack/repos/builtin/packages/r-rjsonio/package.py
index 064a50aea8..a8134aa6d6 100644
--- a/var/spack/repos/builtin/packages/r-rjsonio/package.py
+++ b/var/spack/repos/builtin/packages/r-rjsonio/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-rlang/package.py b/var/spack/repos/builtin/packages/r-rlang/package.py
index 86eb205b7c..cd179fcf57 100644
--- a/var/spack/repos/builtin/packages/r-rlang/package.py
+++ b/var/spack/repos/builtin/packages/r-rlang/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,11 @@ class RRlang(RPackage):
     """A toolbox for working with base types, core R features like the
        condition system, and core 'Tidyverse' features like tidy evaluation."""
 
-    homepage = "https://cran.r-project.org/web/packages/rlang/index.html"
-    url      = "https://cran.r-project.org/src/contrib/rlang_0.1.2.tar.gz"
+    homepage = "https://cran.r-project.org/package=rlang"
+    url      = "https://cran.r-project.org/src/contrib/rlang_0.2.2.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/rlang"
 
+    version('0.2.2', 'df2abf3a1936c503ed1edd4350ffb5f0')
+    version('0.1.4', 'daed5104d557c0cbfb4a654ec8ffb579')
     version('0.1.2', '170f8cf7b61898040643515a1746a53a')
     version('0.1.1', '38a51a0b8f8487eb52b4f3d986313682')
diff --git a/var/spack/repos/builtin/packages/r-rmarkdown/package.py b/var/spack/repos/builtin/packages/r-rmarkdown/package.py
index 1910aa043a..6258b03a6e 100644
--- a/var/spack/repos/builtin/packages/r-rmarkdown/package.py
+++ b/var/spack/repos/builtin/packages/r-rmarkdown/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -33,12 +14,17 @@ class RRmarkdown(RPackage):
     url      = "https://cran.r-project.org/src/contrib/rmarkdown_1.0.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/rmarkdown"
 
+    version('1.7', '477c50840581ba7947b3d905c67a511b')
     version('1.0', '264aa6a59e9680109e38df8270e14c58')
 
-    depends_on('r-knitr', type=('build', 'run'))
-    depends_on('r-yaml', type=('build', 'run'))
-    depends_on('r-htmltools', type=('build', 'run'))
-    depends_on('r-catools', type=('build', 'run'))
-    depends_on('r-evaluate', type=('build', 'run'))
+    depends_on('r-knitr@1.14:', type=('build', 'run'))
+    depends_on('r-yaml@2.1.5:', type=('build', 'run'))
+    depends_on('r-htmltools@0.3.5:', type=('build', 'run'))
+    depends_on('r-evaluate@0.8:', type=('build', 'run'))
     depends_on('r-base64enc', type=('build', 'run'))
     depends_on('r-jsonlite', type=('build', 'run'))
+    depends_on('r-rprojroot', type=('build', 'run'))
+    depends_on('r-mime', type=('build', 'run'))
+    depends_on('r-stringr@1.2.0:', type=('build', 'run'))
+    depends_on('r-catools', type=('build', 'run'))
+    depends_on('r@3.0:')
diff --git a/var/spack/repos/builtin/packages/r-rminer/package.py b/var/spack/repos/builtin/packages/r-rminer/package.py
index 2bd9147afb..758ac03fbe 100644
--- a/var/spack/repos/builtin/packages/r-rminer/package.py
+++ b/var/spack/repos/builtin/packages/r-rminer/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-rmpfr/package.py b/var/spack/repos/builtin/packages/r-rmpfr/package.py
index 1c2e5aafe3..eb6eb23e18 100644
--- a/var/spack/repos/builtin/packages/r-rmpfr/package.py
+++ b/var/spack/repos/builtin/packages/r-rmpfr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-rmpi/package.py b/var/spack/repos/builtin/packages/r-rmpi/package.py
index e7e2870975..c81e101f91 100644
--- a/var/spack/repos/builtin/packages/r-rmpi/package.py
+++ b/var/spack/repos/builtin/packages/r-rmpi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -51,13 +32,13 @@ class RRmpi(RPackage):
         # The type of MPI. Supported values are:
         # OPENMPI, LAM, MPICH, MPICH2, or CRAY
         if mpi_name == 'openmpi':
-            Rmpi_type = 'OPENMPI'
+            rmpi_type = 'OPENMPI'
         elif mpi_name == 'mpich':
-            Rmpi_type = 'MPICH2'
+            rmpi_type = 'MPICH2'
         else:
             raise InstallError('Unsupported MPI type')
 
         return [
-            '--with-Rmpi-type={0}'.format(Rmpi_type),
+            '--with-Rmpi-type={0}'.format(rmpi_type),
             '--with-mpi={0}'.format(spec['mpi'].prefix),
         ]
diff --git a/var/spack/repos/builtin/packages/r-rmysql/package.py b/var/spack/repos/builtin/packages/r-rmysql/package.py
index e34677652c..dc14ddde16 100644
--- a/var/spack/repos/builtin/packages/r-rmysql/package.py
+++ b/var/spack/repos/builtin/packages/r-rmysql/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-rngtools/package.py b/var/spack/repos/builtin/packages/r-rngtools/package.py
index a9b06161d7..6112485e4e 100644
--- a/var/spack/repos/builtin/packages/r-rngtools/package.py
+++ b/var/spack/repos/builtin/packages/r-rngtools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-robustbase/package.py b/var/spack/repos/builtin/packages/r-robustbase/package.py
index 1361e289fb..719a0045c1 100644
--- a/var/spack/repos/builtin/packages/r-robustbase/package.py
+++ b/var/spack/repos/builtin/packages/r-robustbase/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-rocr/package.py b/var/spack/repos/builtin/packages/r-rocr/package.py
index 9936d99dbf..1f2ca35c44 100644
--- a/var/spack/repos/builtin/packages/r-rocr/package.py
+++ b/var/spack/repos/builtin/packages/r-rocr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-rodbc/package.py b/var/spack/repos/builtin/packages/r-rodbc/package.py
index f7364b16fc..4f70634b62 100644
--- a/var/spack/repos/builtin/packages/r-rodbc/package.py
+++ b/var/spack/repos/builtin/packages/r-rodbc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,6 +11,7 @@ class RRodbc(RPackage):
 
     homepage = "https://cran.rstudio.com/web/packages/RODBC/"
     url      = "https://cran.rstudio.com/src/contrib/RODBC_1.3-13.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/RODBC/"
 
     version('1.3-13', 'c52ef9139c2ed85adc53ad6effa7d68e')
 
diff --git a/var/spack/repos/builtin/packages/r-rots/package.py b/var/spack/repos/builtin/packages/r-rots/package.py
new file mode 100644
index 0000000000..3c19b4d325
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rots/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RRots(RPackage):
+    """Calculates the Reproducibility-Optimized Test Statistic (ROTS)
+       for differential testing in omics data."""
+
+    homepage = "https://bioconductor.org/packages/release/bioc/html/ROTS.html"
+    git      = "https://git.bioconductor.org/packages/ROTS.git"
+
+    version('1.8.0', commit='02e3c6455bb1afe7c4cc59ad6d4d8bae7b01428b')
+
+    depends_on('r@3.5.0:3.5.9', when='@1.8.0:', type=('build', 'run'))
+    depends_on('r-rcpp', type=('build', 'run'))
+    depends_on('r-biobase', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-roxygen2/package.py b/var/spack/repos/builtin/packages/r-roxygen2/package.py
index 30e295fbad..60fd47687d 100644
--- a/var/spack/repos/builtin/packages/r-roxygen2/package.py
+++ b/var/spack/repos/builtin/packages/r-roxygen2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-rpart-plot/package.py b/var/spack/repos/builtin/packages/r-rpart-plot/package.py
index e7c1a09519..b531df7e3d 100644
--- a/var/spack/repos/builtin/packages/r-rpart-plot/package.py
+++ b/var/spack/repos/builtin/packages/r-rpart-plot/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-rpart/package.py b/var/spack/repos/builtin/packages/r-rpart/package.py
index adfbf3fdef..2c2f926d55 100644
--- a/var/spack/repos/builtin/packages/r-rpart/package.py
+++ b/var/spack/repos/builtin/packages/r-rpart/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-rpostgresql/package.py b/var/spack/repos/builtin/packages/r-rpostgresql/package.py
index 3c8d9f0798..9061ba3c1d 100644
--- a/var/spack/repos/builtin/packages/r-rpostgresql/package.py
+++ b/var/spack/repos/builtin/packages/r-rpostgresql/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-rprojroot/package.py b/var/spack/repos/builtin/packages/r-rprojroot/package.py
new file mode 100644
index 0000000000..617646350c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rprojroot/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RRprojroot(RPackage):
+    """Robust, reliable and flexible paths to files below a project root.
+    The 'root' of a project is defined as a directory that matches a
+    certain criterion, e.g., it contains a certain regular file."""
+
+    homepage = "https://cran.r-project.org/package=rprojroot"
+    url      = "https://cran.rstudio.com/src/contrib/rprojroot_1.2.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/rprojroot"
+
+    version('1.2', 'c1a0574aaac2a43a72f804abbaea19c3')
+
+    depends_on('r-backports', type=('build', 'run'))
+    depends_on('r@3.0.0:')
diff --git a/var/spack/repos/builtin/packages/r-rsamtools/package.py b/var/spack/repos/builtin/packages/r-rsamtools/package.py
index 41b08a95c7..d8062cc89b 100644
--- a/var/spack/repos/builtin/packages/r-rsamtools/package.py
+++ b/var/spack/repos/builtin/packages/r-rsamtools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,19 +13,27 @@ class RRsamtools(RPackage):
        indexed tab-delimited (tabix) files."""
 
     homepage = "https://bioconductor.org/packages/Rsamtools/"
-    url      = "https://git.bioconductor.org/packages/Rsamtools"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/Rsamtools.git"
 
-    version('1.28.0', git='https://git.bioconductor.org/packages/Rsamtools', commit='dfa5b6abef68175586f21add7927174786412472')
+    version('1.32.2', commit='2b3254ccdeb24dc6ad95a93c2eb527021631797e')
+    version('1.28.0', commit='dfa5b6abef68175586f21add7927174786412472')
 
     depends_on('r-genomeinfodb', type=('build', 'run'))
+    depends_on('r-genomeinfodb@1.1.3:', when='@1.32.2', type=('build', 'run'))
     depends_on('r-genomicranges', type=('build', 'run'))
+    depends_on('r-genomicranges@1.31.8:', when='@1.32.2', type=('build', 'run'))
     depends_on('r-biostrings', type=('build', 'run'))
+    depends_on('r-biostrings@2.47.6:', when='@1.32.2', type=('build', 'run'))
     depends_on('r-biocgenerics', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.25.1:', when='@1.32.2', type=('build', 'run'))
     depends_on('r-s4vectors', type=('build', 'run'))
+    depends_on('r-s4vectors@0.17.25:', when='@1.32.2', type=('build', 'run'))
     depends_on('r-iranges', type=('build', 'run'))
+    depends_on('r-iranges@2.13.12:', when='@1.32.2', type=('build', 'run'))
     depends_on('r-xvector', type=('build', 'run'))
+    depends_on('r-xvector@0.19.7:', when='@1.32.2', type=('build', 'run'))
     depends_on('r-zlibbioc', type=('build', 'run'))
     depends_on('r-bitops', type=('build', 'run'))
     depends_on('r-biocparallel', type=('build', 'run'))
-    depends_on('r@3.4.0:3.4.9', when='@1.28.0')
+    depends_on('r@3.4.0:3.4.9', when='@1.28.0', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@1.32.2', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-rsnns/package.py b/var/spack/repos/builtin/packages/r-rsnns/package.py
index 92b891bf1a..8de7a9b7a1 100644
--- a/var/spack/repos/builtin/packages/r-rsnns/package.py
+++ b/var/spack/repos/builtin/packages/r-rsnns/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/r-rsolnp/package.py b/var/spack/repos/builtin/packages/r-rsolnp/package.py
new file mode 100644
index 0000000000..db4ab24959
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rsolnp/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RRsolnp(RPackage):
+    """General Non-linear Optimization Using Augmented Lagrange Multiplier
+    Method."""
+
+    homepage = "https://cran.r-project.org/package=Rsolnp"
+    url      = "https://cran.rstudio.com/src/contrib/Rsolnp_1.16.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/Rsolnp"
+
+    version('1.16', '507e1e1a64f5f1d32b7e4e12ed19599f')
+
+    depends_on('r-truncnorm', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-rsqlite/package.py b/var/spack/repos/builtin/packages/r-rsqlite/package.py
index 50cd4df05d..61ba90e83c 100644
--- a/var/spack/repos/builtin/packages/r-rsqlite/package.py
+++ b/var/spack/repos/builtin/packages/r-rsqlite/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,8 +12,9 @@ class RRsqlite(RPackage):
     (version 3.8.6) is included."""
 
     homepage = "https://cran.rstudio.com/web/packages/RSQLite/index.html"
-    url      = "https://cran.r-project.org/src/contrib/RSQLite_1.0.0.tar.gz"
+    url      = "https://cran.r-project.org/src/contrib/RSQLite_2.0.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/RSQLite"
+
     version('2.0', '63842410e78ccdfc52d4ee97992521d5')
 
     depends_on('r-dbi', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-rstan/package.py b/var/spack/repos/builtin/packages/r-rstan/package.py
index 50c9dbb205..30b4166091 100644
--- a/var/spack/repos/builtin/packages/r-rstan/package.py
+++ b/var/spack/repos/builtin/packages/r-rstan/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,6 +21,7 @@ class RRstan(RPackage):
     url      = "https://cran.r-project.org/src/contrib/rstan_2.10.1.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/rstan"
 
+    version('2.17.2', '60f4a0284c58f5efc1b1cbf488d7edda')
     version('2.10.1', 'f5d212f6f8551bdb91fe713d05d4052a')
 
     depends_on('r-ggplot2', type=('build', 'run'))
@@ -48,4 +30,5 @@ class RRstan(RPackage):
     depends_on('r-gridextra', type=('build', 'run'))
     depends_on('r-rcpp', type=('build', 'run'))
     depends_on('r-rcppeigen', type=('build', 'run'))
+    depends_on('r-rcppeigen@0.3.3.3.0:', type=('build', 'run'), when='@2.17.2:')
     depends_on('r-bh', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-rstudioapi/package.py b/var/spack/repos/builtin/packages/r-rstudioapi/package.py
index a9d977f62e..5b51a050d8 100644
--- a/var/spack/repos/builtin/packages/r-rstudioapi/package.py
+++ b/var/spack/repos/builtin/packages/r-rstudioapi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,8 +11,9 @@ class RRstudioapi(RPackage):
     messages when it's not."""
 
     homepage = "https://cran.r-project.org/web/packages/rstudioapi/index.html"
-    url      = "https://cran.r-project.org/src/contrib/rstudioapi_0.5.tar.gz"
+    url      = "https://cran.r-project.org/src/contrib/rstudioapi_0.7.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/rstudioapi"
 
+    version('0.7', 'ee4ab567a7a9fdfac1a6fd01fe38de4a')
     version('0.6', 'fdb13bf46aab02421557e713fceab66b')
     version('0.5', '6ce1191da74e7bcbf06b61339486b3ba')
diff --git a/var/spack/repos/builtin/packages/r-rtracklayer/package.py b/var/spack/repos/builtin/packages/r-rtracklayer/package.py
index 11f604b72f..69a2d37c43 100644
--- a/var/spack/repos/builtin/packages/r-rtracklayer/package.py
+++ b/var/spack/repos/builtin/packages/r-rtracklayer/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,20 +15,31 @@ class RRtracklayer(RPackage):
        current viewport."""
 
     homepage = "http://bioconductor.org/packages/rtracklayer/"
-    url      = "https://git.bioconductor.org/packages/rtracklayer"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/rtracklayer.git"
 
-    version('1.36.6', git='https://git.bioconductor.org/packages/rtracklayer', commit='8c0ac7230f94e0c5a981acbb178c8de70e968131')
+    version('1.40.5', commit='4e5b06daccd0bca1ddcd93052deca896ade58fd6')
+    version('1.36.6', commit='8c0ac7230f94e0c5a981acbb178c8de70e968131')
 
     depends_on('r-xml', type=('build', 'run'))
     depends_on('r-biocgenerics', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.25.1:', when='@1.40.5', type=('build', 'run'))
     depends_on('r-s4vectors', type=('build', 'run'))
+    depends_on('r-s4vectors@0.17.25:', when='@1.40.5', type=('build', 'run'))
     depends_on('r-iranges', type=('build', 'run'))
+    depends_on('r-iranges@2.13.13:', when='@1.40.5', type=('build', 'run'))
     depends_on('r-xvector', type=('build', 'run'))
+    depends_on('r-xvector@0.19.7:', when='@1.40.5', type=('build', 'run'))
     depends_on('r-genomeinfodb', type=('build', 'run'))
+    depends_on('r-genomeinfodb@1.15.2:', when='@1.40.5', type=('build', 'run'))
     depends_on('r-biostrings', type=('build', 'run'))
+    depends_on('r-biostrings@2.47.6:', when='@1.40.5', type=('build', 'run'))
     depends_on('r-zlibbioc', type=('build', 'run'))
     depends_on('r-rcurl', type=('build', 'run'))
     depends_on('r-rsamtools', type=('build', 'run'))
+    depends_on('r-rsamtools@1.31.2:', when='@1.40.5', type=('build', 'run'))
     depends_on('r-genomicalignments', type=('build', 'run'))
-    depends_on('r@3.4.0:3.4.9', when='@1.36.6')
+    depends_on('r-genomicalignments@1.15.6:', when='@1.40.5', type=('build', 'run'))
+    depends_on('r-genomicranges@1.21.20:', when='@1.36.3', type=('build', 'run'))
+    depends_on('r-genomicranges@1.31.8:', when='@1.40.5', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@1.36.6', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@1.40.5', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-rtsne/package.py b/var/spack/repos/builtin/packages/r-rtsne/package.py
new file mode 100644
index 0000000000..2ec641f5eb
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rtsne/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RRtsne(RPackage):
+    """An R wrapper around the fast T-distributed Stochastic Neighbor
+    Embedding implementation."""
+
+    homepage = "https://CRAN.R-project.org/package=Rtsne"
+    url      = "https://cran.r-project.org/src/contrib/Rtsne_0.13.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/Rtsne"
+
+    version('0.13', 'ea1d2ef2bda16735bbf219ffda5b0661')
+    version('0.11', '9a1eaa9b71d67cc27a55780e6e9df733')
+    version('0.10', 'c587e1b76fdcea2629424f74c6e92340')
+
+    depends_on('r@3.4.0:3.4.9')
+    depends_on('r-rcpp', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-rvcheck/package.py b/var/spack/repos/builtin/packages/r-rvcheck/package.py
new file mode 100644
index 0000000000..25ba893d4f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rvcheck/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RRvcheck(RPackage):
+    """Check latest release version of R and R package (both in 'CRAN',
+    'Bioconductor' or 'Github')."""
+
+    homepage = "https://cran.r-project.org/package=rvcheck"
+    url      = "https://cran.rstudio.com/src/contrib/rvcheck_0.0.9.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/rvcheck"
+
+    version('0.0.9', '7e9821de754577f94fdcbf7b02a20edc')
diff --git a/var/spack/repos/builtin/packages/r-rvest/package.py b/var/spack/repos/builtin/packages/r-rvest/package.py
index d35e14ace7..837dd81a05 100644
--- a/var/spack/repos/builtin/packages/r-rvest/package.py
+++ b/var/spack/repos/builtin/packages/r-rvest/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-rzmq/package.py b/var/spack/repos/builtin/packages/r-rzmq/package.py
index 18ef9e04f2..77f1420d04 100644
--- a/var/spack/repos/builtin/packages/r-rzmq/package.py
+++ b/var/spack/repos/builtin/packages/r-rzmq/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/r-s4vectors/package.py b/var/spack/repos/builtin/packages/r-s4vectors/package.py
index 84ee43cdfe..71eb0a588b 100644
--- a/var/spack/repos/builtin/packages/r-s4vectors/package.py
+++ b/var/spack/repos/builtin/packages/r-s4vectors/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,10 +17,13 @@ class RS4vectors(RPackage):
        package and in other Bioconductor infrastructure packages)."""
 
     homepage = "https://bioconductor.org/packages/S4Vectors/"
-    url      = "https://git.bioconductor.org/packages/S4Vectors"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/S4Vectors.git"
 
-    version('0.14.7', git='https://git.bioconductor.org/packages/S4Vectors', commit='40af17fe0b8e93b6a72fc787540d2961773b8e23')
+    version('0.18.3', commit='d6804f94ad3663828440914920ac933b934aeff1')
+    version('0.16.0', commit='00fec03fcbcb7cff37917fab0da28d91fdf9dc3d')
+    version('0.14.7', commit='40af17fe0b8e93b6a72fc787540d2961773b8e23')
 
-    depends_on('r-biocgenerics', type=('build', 'run'))
-    depends_on('r@3.4.0:3.4.9', when='@0.14.7')
+    depends_on('r-biocgenerics@0.21.1:', type=('build', 'run'), when='@0.14.7')
+    depends_on('r-biocgenerics@0.23.3:', type=('build', 'run'), when='@0.16.0:')
+    depends_on('r@3.4.0:3.4.9', when='@0.14.7', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@0.18.3', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-samr/package.py b/var/spack/repos/builtin/packages/r-samr/package.py
index da575143e8..f24a731bfc 100644
--- a/var/spack/repos/builtin/packages/r-samr/package.py
+++ b/var/spack/repos/builtin/packages/r-samr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-sandwich/package.py b/var/spack/repos/builtin/packages/r-sandwich/package.py
index 5f7d66dd7a..5be31684c1 100644
--- a/var/spack/repos/builtin/packages/r-sandwich/package.py
+++ b/var/spack/repos/builtin/packages/r-sandwich/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-scales/package.py b/var/spack/repos/builtin/packages/r-scales/package.py
index ebe9798e86..eb1d75e7f4 100644
--- a/var/spack/repos/builtin/packages/r-scales/package.py
+++ b/var/spack/repos/builtin/packages/r-scales/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-scatterplot3d/package.py b/var/spack/repos/builtin/packages/r-scatterplot3d/package.py
index eedd61cc6e..a4c5a41ca1 100644
--- a/var/spack/repos/builtin/packages/r-scatterplot3d/package.py
+++ b/var/spack/repos/builtin/packages/r-scatterplot3d/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-sdmtools/package.py b/var/spack/repos/builtin/packages/r-sdmtools/package.py
new file mode 100644
index 0000000000..584a935eb4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-sdmtools/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RSdmtools(RPackage):
+    """Species Distribution Modelling Tools: Tools for processing data
+    associated with species distribution modelling exercises
+
+    This packages provides a set of tools for post processing the outcomes of
+    species distribution modeling exercises."""
+
+    homepage = "https://cran.r-project.org/web/packages/SDMTools/index.html"
+    url      = "https://cran.r-project.org/src/contrib/SDMTools_1.1-221.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/SDMTools"
+
+    version('1.1-221', '3604da1783d0c6081b62b29d35a32c3c')
+    version('1.1-20', '27cc8de63cfdd86d4ba9983012121c58')
+    version('1.1-13', '0d6a14d985988a81b9ff06c635675143')
+    version('1.1-12', 'a13d75e4024d908a57ea462112d8a437')
+    version('1.1-11', 'cb890ee06eb862f97141b73c7390a0a9')
+
+    depends_on('r@3.4.0:3.4.9')
+    depends_on('r-utils', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-segmented/package.py b/var/spack/repos/builtin/packages/r-segmented/package.py
index 784a9d55d5..bea89c1a27 100644
--- a/var/spack/repos/builtin/packages/r-segmented/package.py
+++ b/var/spack/repos/builtin/packages/r-segmented/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-selectr/package.py b/var/spack/repos/builtin/packages/r-selectr/package.py
index 321a7da099..601812dc19 100644
--- a/var/spack/repos/builtin/packages/r-selectr/package.py
+++ b/var/spack/repos/builtin/packages/r-selectr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-seqinr/package.py b/var/spack/repos/builtin/packages/r-seqinr/package.py
index a78e36ef74..8b7c566b87 100644
--- a/var/spack/repos/builtin/packages/r-seqinr/package.py
+++ b/var/spack/repos/builtin/packages/r-seqinr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-seqlogo/package.py b/var/spack/repos/builtin/packages/r-seqlogo/package.py
new file mode 100644
index 0000000000..b7864868c9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-seqlogo/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RSeqlogo(RPackage):
+    """seqLogo takes the position weight matrix of a DNA sequence motif and
+       plots the corresponding sequence logo as introduced by Schneider and
+       Stephens (1990)."""
+
+    homepage = "https://bioconductor.org/packages/seqLogo/"
+    git      = "https://git.bioconductor.org/packages/seqLogo.git"
+
+    version('1.44.0', commit='4cac14ff29f413d6de1a9944eb5d21bfe5045fac')
+
+    depends_on('r@3.4.3:3.4.9', when='@1.44.0')
diff --git a/var/spack/repos/builtin/packages/r-seurat/package.py b/var/spack/repos/builtin/packages/r-seurat/package.py
new file mode 100644
index 0000000000..8d9b06758a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-seurat/package.py
@@ -0,0 +1,54 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RSeurat(RPackage):
+    """Seurat is an R package designed for QC, analysis, and exploration of
+    single cell RNA-seq data."""
+
+    homepage = "http://satijalab.org/seurat/"
+    url      = "https://cran.r-project.org/src/contrib/Seurat_2.1.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/Seurat"
+
+    version('2.1.0', '46427837bb739883f9b7addd08fccee5')
+    version('2.0.1', 'a77794891e93b9fa1ef41735fe8424ea')
+
+    depends_on('r@3.4.0:3.4.9')
+    depends_on('r-ggplot2', type=('build', 'run'))
+    depends_on('r-gplots', type=('build', 'run'))
+    depends_on('r-reshape2', type=('build', 'run'))
+    depends_on('r-ape', type=('build', 'run'))
+    depends_on('r-tidyr', type=('build', 'run'))
+    depends_on('r-caret', type=('build', 'run'))
+    depends_on('r-gdata', type=('build', 'run'))
+    depends_on('r-glue', type=('build', 'run'))
+    depends_on('r-pkgconfig', type=('build', 'run'))
+    depends_on('r-plogr', type=('build', 'run'))
+    depends_on('r-gridextra', type=('build', 'run'))
+    depends_on('r-cowplot', type=('build', 'run'))
+    depends_on('r-rocr', type=('build', 'run'))
+    depends_on('r-hmisc', type=('build', 'run'))
+    depends_on('r-nmf', type=('build', 'run'))
+    depends_on('r-irlba', type=('build', 'run'))
+    depends_on('r-igraph', type=('build', 'run'))
+    depends_on('r-fpc', type=('build', 'run'))
+    depends_on('r-rcppprogress', type=('build', 'run'))
+    depends_on('r-lars', type=('build', 'run'))
+    depends_on('r-dtw', type=('build', 'run'))
+    depends_on('r-mixtools', type=('build', 'run'))
+    depends_on('r-ica', type=('build', 'run'))
+    depends_on('r-diffusionmap', type=('build', 'run'))
+    depends_on('r-tsne', type=('build', 'run'))
+    depends_on('r-rtsne', type=('build', 'run'))
+    depends_on('r-ranger', type=('build', 'run'))
+    depends_on('r-pbapply', type=('build', 'run'))
+    depends_on('r-ggjoy', type=('build', 'run'))
+    depends_on('r-plotly', type=('build', 'run'))
+    depends_on('r-sdmtools', type=('build', 'run'))
+    depends_on('r-tclust', type=('build', 'run'))
+    depends_on('r-fnn', type=('build', 'run'))
+    depends_on('r-vgam', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-sf/package.py b/var/spack/repos/builtin/packages/r-sf/package.py
new file mode 100644
index 0000000000..019feb1b18
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-sf/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RSf(RPackage):
+    """Support for simple features, a standardized way to encode spatial
+       vector data. Binds to GDAL for reading and writing data, to GEOS for
+       geometrical operations, and to Proj.4 for projection conversions and
+       datum transformations."""
+
+    homepage = "https://github.com/r-spatial/sf/"
+    url      = "https://cran.r-project.org/src/contrib/sf_0.5-5.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/sf"
+
+    version('0.5-5', '53ff32d0c9bf2844666c68ce7d75beb2')
+
+    depends_on('r-rcpp', type=('build', 'run'))
+    depends_on('r-dbi@0.5:', type=('build', 'run'))
+    depends_on('r-units@0.4-6:', type=('build', 'run'))
+    depends_on('r-classint', type=('build', 'run'))
+    depends_on('r-magrittr', type=('build', 'run'))
+    depends_on('gdal@2.0.0:')
+    depends_on('geos@3.3.0:')
+    depends_on('proj@4.8.0:')
diff --git a/var/spack/repos/builtin/packages/r-sfsmisc/package.py b/var/spack/repos/builtin/packages/r-sfsmisc/package.py
index d07abd3b44..c2bf1e540f 100644
--- a/var/spack/repos/builtin/packages/r-sfsmisc/package.py
+++ b/var/spack/repos/builtin/packages/r-sfsmisc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,6 +12,7 @@ class RSfsmisc(RPackage):
     some were ported from S-plus."""
 
     homepage = "https://cran.r-project.org/web/packages/sfsmisc/index.html"
-    url      = "https://cran.r-project.org/src/contrib/sfsmisc_1.1-1.tar.gz"
+    url      = "https://cran.r-project.org/src/contrib/sfsmisc_1.1-0.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/sfsmisc"
+
     version('1.1-0', '1ba4303076e2bbf018f7eecc7d04e178')
diff --git a/var/spack/repos/builtin/packages/r-shape/package.py b/var/spack/repos/builtin/packages/r-shape/package.py
index 8f07f842e0..18ab11de62 100644
--- a/var/spack/repos/builtin/packages/r-shape/package.py
+++ b/var/spack/repos/builtin/packages/r-shape/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-shiny/package.py b/var/spack/repos/builtin/packages/r-shiny/package.py
index 1d42d8df23..7165cd7af6 100644
--- a/var/spack/repos/builtin/packages/r-shiny/package.py
+++ b/var/spack/repos/builtin/packages/r-shiny/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-shinydashboard/package.py b/var/spack/repos/builtin/packages/r-shinydashboard/package.py
new file mode 100644
index 0000000000..b9b6406f9c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-shinydashboard/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RShinydashboard(RPackage):
+    """Create Dashboards with 'Shiny'"""
+
+    homepage = "https://cran.r-project.org/package=shinydashboard"
+    url      = "https://cran.r-project.org/src/contrib/shinydashboard_0.7.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/shinydashboard"
+
+    version('0.7.0', 'a572695884e3b45320b0ab5a7b364ffd')
+    version('0.6.1', '0f6ad0448237e10d53d4d27ade1c6863')
+
+    depends_on('r@3.3.0:', type=('build', 'run'))
+    depends_on('r-htmltools@0.2.6:', type=('build', 'run'))
+    depends_on('r-shiny@1.0.0:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-shortread/package.py b/var/spack/repos/builtin/packages/r-shortread/package.py
new file mode 100644
index 0000000000..81ed95b0b5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-shortread/package.py
@@ -0,0 +1,36 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RShortread(RPackage):
+    """This package implements sampling, iteration, and input of FASTQ
+    files. The package includes functions for filtering and trimming
+    reads, and for generating a quality assessment report. Data are
+    represented as DNAStringSet-derived objects, and easily manipulated
+    for a diversity of purposes. The package also contains legacy support
+    for early single-end, ungapped alignment formats."""
+
+    homepage = "https://www.bioconductor.org/packages/ShortRead/"
+    git      = "https://git.bioconductor.org/packages/ShortRead.git"
+
+    version('1.34.2', commit='25daac63b301df66a8ef6e98cc2977522c6786cd')
+
+    depends_on('r@3.4.0:3.4.9', when='@1.34.2')
+    depends_on('r-latticeextra', type=('build', 'run'))
+    depends_on('r-lattice', type=('build', 'run'))
+    depends_on('r-zlibbioc', type=('build', 'run'))
+    depends_on('r-hwriter', type=('build', 'run'))
+    depends_on('r-genomicranges', type=('build', 'run'))
+    depends_on('r-genomeinfodb', type=('build', 'run'))
+    depends_on('r-iranges', type=('build', 'run'))
+    depends_on('r-s4vectors', type=('build', 'run'))
+    depends_on('r-biobase', type=('build', 'run'))
+    depends_on('r-genomicalignments', type=('build', 'run'))
+    depends_on('r-rsamtools', type=('build', 'run'))
+    depends_on('r-biostrings', type=('build', 'run'))
+    depends_on('r-biocparallel', type=('build', 'run'))
+    depends_on('r-biocgenerics', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-siggenes/package.py b/var/spack/repos/builtin/packages/r-siggenes/package.py
index ec0809c9da..ec425f54bc 100644
--- a/var/spack/repos/builtin/packages/r-siggenes/package.py
+++ b/var/spack/repos/builtin/packages/r-siggenes/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,10 +13,9 @@ class RSiggenes(RPackage):
        (EBAM)."""
 
     homepage = "http://bioconductor.org/packages/siggenes/"
-    url      = "https://git.bioconductor.org/packages/siggenes"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/siggenes.git"
 
-    version('1.50.0', git='https://git.bioconductor.org/packages/siggenes', commit='b1818f26e1449005ffd971df6bda8da0303080bc')
+    version('1.50.0', commit='b1818f26e1449005ffd971df6bda8da0303080bc')
 
     depends_on('r-biobase', type=('build', 'run'))
     depends_on('r-multtest', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-simpleaffy/package.py b/var/spack/repos/builtin/packages/r-simpleaffy/package.py
index 36d616fa8c..c977569d5e 100644
--- a/var/spack/repos/builtin/packages/r-simpleaffy/package.py
+++ b/var/spack/repos/builtin/packages/r-simpleaffy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,10 +14,9 @@ class RSimpleaffy(RPackage):
        for generating high resolution journal figures..."""
 
     homepage = "http://bioconductor.org/packages/simpleaffy/"
-    url      = "https://git.bioconductor.org/packages/simpleaffy"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/simpleaffy.git"
 
-    version('2.52.0', git='https://git.bioconductor.org/packages/simpleaffy', commit='f2b43fb9b8e6fa4c03fe28b4efb3144a0a42a385')
+    version('2.52.0', commit='f2b43fb9b8e6fa4c03fe28b4efb3144a0a42a385')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-biobase', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-sm/package.py b/var/spack/repos/builtin/packages/r-sm/package.py
new file mode 100644
index 0000000000..e57ad8584b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-sm/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RSm(RPackage):
+    """This is software linked to the book 'Applied Smoothing Techniques for
+       Data Analysis - The Kernel Approach with S-Plus Illustrations'
+       Oxford University Press."""
+
+    homepage = "http://www.stats.gla.ac.uk/~adrian/sm"
+    url      = "https://cran.r-project.org/src/contrib/sm_2.2-5.5.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/sm"
+
+    version('2.2-5.5', sha256='43e212a14c364b98b10018b56fe0a619ccffe4bde1294e6c45b3eafe7caf82e7')
+
+    depends_on('r@3.1.0:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-smoof/package.py b/var/spack/repos/builtin/packages/r-smoof/package.py
new file mode 100644
index 0000000000..c980683109
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-smoof/package.py
@@ -0,0 +1,33 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RSmoof(RPackage):
+    """Provides generators for a high number of both single- and
+       multi- objective test functions which are frequently used for the
+       benchmarking of (numerical) optimization algorithms. Moreover, it offers
+       a set of convenient functions to generate, plot and work with objective
+       functions."""
+
+    homepage = "http://github.com/jakobbossek/smoof"
+    url      = "https://cran.r-project.org/src/contrib/smoof_1.5.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/smoof"
+
+    version('1.5.1', 'c3e3b5dafed34608f933ae255cf49054')
+    version('1.5', 'b371bde2724eade5a6d4d808fa3ad269')
+
+    depends_on('r-paramhelpers@1.8:', type=('build', 'run'))
+    depends_on('r-bbmisc@1.6:', type=('build', 'run'))
+    depends_on('r-checkmate@1.1:', type=('build', 'run'))
+    depends_on('r-ggplot2@2.2.1:', type=('build', 'run'))
+    depends_on('r-rcolorbrewer', type=('build', 'run'))
+    depends_on('r-plot3d', type=('build', 'run'))
+    depends_on('r-plotly', type=('build', 'run'))
+    depends_on('r-mco', type=('build', 'run'))
+    depends_on('r-rcpp@0.11.0:', type=('build', 'run'))
+    depends_on('r-rjsonio', type=('build', 'run'))
+    depends_on('r-rcpparmadillo', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-sn/package.py b/var/spack/repos/builtin/packages/r-sn/package.py
new file mode 100644
index 0000000000..9dbfced26a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-sn/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RSn(RPackage):
+    """Build and manipulate probability distributions of the skew-normal
+    family and some related ones, notably the skew-t family, and provide
+    related statistical methods for data fitting and diagnostics, in the
+    univariate and the multivariate case."""
+
+    homepage = "https://cran.r-project.org/web/packages/sn/index.html"
+    url      = "https://cran.r-project.org/src/contrib/sn_1.5-0.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/sn"
+
+    version('1.5-0', 'a3349773be950199d7f4c17954be56d1')
+    version('1.4-0', 'cfa604317ea54224b06abd1cec179375')
+    version('1.3-0', '84d02ba2ab5ca6f3644626013e7ce36d')
+    version('1.2-4', 'bf3a47b05016326e910fdb4cc4967e4d')
+    version('1.2-3', '290ae511d974a6beb4c3c79c0106858f')
+
+    depends_on('r@3.4.0:3.4.9')
+    depends_on('r-mnormt', type=('build', 'run'))
+    depends_on('r-numderiv', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-snow/package.py b/var/spack/repos/builtin/packages/r-snow/package.py
index 7be7d36018..73bdd4bcf5 100644
--- a/var/spack/repos/builtin/packages/r-snow/package.py
+++ b/var/spack/repos/builtin/packages/r-snow/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-snowfall/package.py b/var/spack/repos/builtin/packages/r-snowfall/package.py
new file mode 100644
index 0000000000..4ed0f934a6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-snowfall/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RSnowfall(RPackage):
+    """Usability wrapper around snow for easier development of parallel R
+       programs. This package offers e.g. extended error checks, and additional
+       functions. All functions work in sequential mode, too, if no cluster is
+       present or wished. Package is also designed as connector to the cluster
+       management tool sfCluster, but can also used without it."""
+
+    homepage = "https://cran.r-project.org/web/packages/snowfall/index.html"
+    url      = "https://cran.r-project.org/src/contrib/snowfall_1.84-6.1.tar.gz"
+
+    version('1.84-6.1', '5ec38116aa9cac237d56f59ba5bd60e3')
+
+    depends_on('r-snow', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-snprelate/package.py b/var/spack/repos/builtin/packages/r-snprelate/package.py
new file mode 100644
index 0000000000..f7a0d04fa9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-snprelate/package.py
@@ -0,0 +1,33 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RSnprelate(RPackage):
+    """Genome-wide association studies (GWAS) are widely used to investigate
+       the genetic basis of diseases and traits, but they pose many
+       computational challenges. We developed an R package SNPRelate to
+       provide a binary format for single-nucleotide polymorphism (SNP) data
+       in GWAS utilizing CoreArray Genomic Data Structure (GDS) data files.
+       The GDS format offers the efficient operations specifically designed
+       for integers with two bits, since a SNP could occupy only two bits.
+       SNPRelate is also designed to accelerate two key computations on SNP
+       data using parallel computing for multi-core symmetric multiprocessing
+       computer architectures: Principal Component Analysis (PCA) and
+       relatedness analysis using Identity-By-Descent measures. The SNP GDS
+       format is also used by the GWASTools package with the support of S4
+       classes and generic functions. The extended GDS format is implemented
+       in the SeqArray package to support the storage of single nucleotide
+       variations (SNVs), insertion/deletion polymorphism (indel) and
+       structural variation calls."""
+
+    homepage = "https://bioconductor.org/packages/SNPRelate"
+    git      = "https://git.bioconductor.org/packages/SNPRelate.git"
+
+    version('1.12.2', commit='dce2e2b6f36483a9f905bb5df6ae834a9f1136fe')
+
+    depends_on('r@3.4.0:3.4.9', when='@1.12.2')
+    depends_on('r-gdsfmt@1.8.3:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-som/package.py b/var/spack/repos/builtin/packages/r-som/package.py
new file mode 100644
index 0000000000..7a79e31f62
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-som/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RSom(RPackage):
+    """Self-Organizing Map (with application in gene clustering)."""
+
+    homepage = "https://cran.r-project.org/web/packages/som/index.html"
+    url      = "https://cran.r-project.org/src/contrib/som_0.3-5.1.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/som"
+
+    version('0.3-5.1', '802a5a80902579354ce3420faeeeb756')
+    version('0.3-5', '72717499794c7aa945a768b742af8895')
+    version('0.3-4', '1e25572e446409f5e32c5da5f1af98e6')
+    version('0.3-3', 'd4ac444be24f71d08b99974c2f4b96e5')
+    version('0.3-2', '4ce28f46df68fbb73905711ba2416fac')
+
+    depends_on('r@2.10:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-somaticsignatures/package.py b/var/spack/repos/builtin/packages/r-somaticsignatures/package.py
index 004023fd25..36fdd5e78e 100644
--- a/var/spack/repos/builtin/packages/r-somaticsignatures/package.py
+++ b/var/spack/repos/builtin/packages/r-somaticsignatures/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,10 +13,9 @@ class RSomaticsignatures(RPackage):
        flexibility in the matrix decomposition algorithms."""
 
     homepage = "https://bioconductor.org/packages/SomaticSignatures/"
-    url      = "https://git.bioconductor.org/packages/SomaticSignatures"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/SomaticSignatures.git"
 
-    version('2.12.1', git='https://git.bioconductor.org/packages/SomaticSignatures', commit='932298c6877d076004de5541cec85a14e819517a')
+    version('2.12.1', commit='932298c6877d076004de5541cec85a14e819517a')
 
     depends_on('r-variantannotation', type=('build', 'run'))
     depends_on('r-genomicranges', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-sourcetools/package.py b/var/spack/repos/builtin/packages/r-sourcetools/package.py
index 87f9dfc2c9..f0b08a0eef 100644
--- a/var/spack/repos/builtin/packages/r-sourcetools/package.py
+++ b/var/spack/repos/builtin/packages/r-sourcetools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-sp/package.py b/var/spack/repos/builtin/packages/r-sp/package.py
index c085aa1521..0212bb028e 100644
--- a/var/spack/repos/builtin/packages/r-sp/package.py
+++ b/var/spack/repos/builtin/packages/r-sp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-sparsem/package.py b/var/spack/repos/builtin/packages/r-sparsem/package.py
index 3aac221fd1..d5641178da 100644
--- a/var/spack/repos/builtin/packages/r-sparsem/package.py
+++ b/var/spack/repos/builtin/packages/r-sparsem/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-spdep/package.py b/var/spack/repos/builtin/packages/r-spdep/package.py
index f7b7a4671e..6fdd2e953b 100644
--- a/var/spack/repos/builtin/packages/r-spdep/package.py
+++ b/var/spack/repos/builtin/packages/r-spdep/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-speedglm/package.py b/var/spack/repos/builtin/packages/r-speedglm/package.py
index f520965da5..c653323f27 100644
--- a/var/spack/repos/builtin/packages/r-speedglm/package.py
+++ b/var/spack/repos/builtin/packages/r-speedglm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-spem/package.py b/var/spack/repos/builtin/packages/r-spem/package.py
new file mode 100644
index 0000000000..ee4a1a794c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-spem/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RSpem(RPackage):
+    """This package can optimize the parameter in S-system models given time
+    series data"""
+
+    homepage = "https://bioconductor.org/packages/SPEM/"
+    git      = "https://git.bioconductor.org/packages/SPEM.git"
+
+    version('1.18.0', commit='3ab425dd9889885eac328d26b73366a875cd250b')
+
+    depends_on('r-rsolnp', type=('build', 'run'))
+    depends_on('r-biobase', type=('build', 'run'))
+    depends_on('r@3.4.3:3.4.9', when='@1.18.0')
diff --git a/var/spack/repos/builtin/packages/r-splitstackshape/package.py b/var/spack/repos/builtin/packages/r-splitstackshape/package.py
new file mode 100644
index 0000000000..3bff263624
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-splitstackshape/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RSplitstackshape(RPackage):
+    """Stack and Reshape Datasets After Splitting Concatenated Values.
+
+    Online data collection tools like Google Forms often export
+    multiple-response questions with data concatenated in cells. The
+    concat.split (cSplit) family of functions splits such data into
+    separate cells. The package also includes functions to stack groups
+    of columns and to reshape wide data, even when the data are
+    "unbalanced" something which reshape (from base R) does not handle,
+    and which melt and dcast from reshape2 do not easily handle.
+    """
+
+    homepage = "http://github.com/mrdwab/splitstackshape"
+    url      = "https://cran.r-project.org/src/contrib/splitstackshape_1.4.4.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/splitstackshape"
+
+    version('1.4.4', '54d2554fe92dfc4670a000b45baacc28')
+
+    depends_on('r-data-table@1.9.4:', type=('build', 'run'))
+    depends_on('r@2.10:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-sqldf/package.py b/var/spack/repos/builtin/packages/r-sqldf/package.py
index c891891221..d0c90d4a14 100644
--- a/var/spack/repos/builtin/packages/r-sqldf/package.py
+++ b/var/spack/repos/builtin/packages/r-sqldf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-squash/package.py b/var/spack/repos/builtin/packages/r-squash/package.py
new file mode 100644
index 0000000000..e939b870e5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-squash/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RSquash(RPackage):
+    """Color-Based Plots for Multivariate Visualization"""
+
+    homepage = "https://cran.r-project.org/package=squash"
+    url      = "https://cran.r-project.org/src/contrib/squash_1.0.8.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/squash"
+
+    version('1.0.8', '50d5743d306fa11cfa1a3c4daa75e508')
+    version('1.0.7', '4ac381b17d4d7b77bdaa6f824fbb03ab')
diff --git a/var/spack/repos/builtin/packages/r-stanheaders/package.py b/var/spack/repos/builtin/packages/r-stanheaders/package.py
index 383eb82580..62e787197f 100644
--- a/var/spack/repos/builtin/packages/r-stanheaders/package.py
+++ b/var/spack/repos/builtin/packages/r-stanheaders/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -46,4 +27,5 @@ class RStanheaders(RPackage):
     url      = "https://cran.r-project.org/src/contrib/StanHeaders_2.10.0-2.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/StanHeaders"
 
+    version('2.17.1', '11d8770277dd18e563852852633c6c25')
     version('2.10.0-2', '9d09b1e9278f08768f7a988ad9082d57')
diff --git a/var/spack/repos/builtin/packages/r-statmod/package.py b/var/spack/repos/builtin/packages/r-statmod/package.py
index 7eb095aa92..df2fbc70a5 100644
--- a/var/spack/repos/builtin/packages/r-statmod/package.py
+++ b/var/spack/repos/builtin/packages/r-statmod/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-statnet-common/package.py b/var/spack/repos/builtin/packages/r-statnet-common/package.py
index 2c61f23f2e..d8f8413200 100644
--- a/var/spack/repos/builtin/packages/r-statnet-common/package.py
+++ b/var/spack/repos/builtin/packages/r-statnet-common/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-stringi/package.py b/var/spack/repos/builtin/packages/r-stringi/package.py
index 55dd10e378..af49c8aca2 100644
--- a/var/spack/repos/builtin/packages/r-stringi/package.py
+++ b/var/spack/repos/builtin/packages/r-stringi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-stringr/package.py b/var/spack/repos/builtin/packages/r-stringr/package.py
index 64b291adc5..28497c97d8 100644
--- a/var/spack/repos/builtin/packages/r-stringr/package.py
+++ b/var/spack/repos/builtin/packages/r-stringr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-strucchange/package.py b/var/spack/repos/builtin/packages/r-strucchange/package.py
index 4f0a2bf28a..1b0ae07613 100644
--- a/var/spack/repos/builtin/packages/r-strucchange/package.py
+++ b/var/spack/repos/builtin/packages/r-strucchange/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-subplex/package.py b/var/spack/repos/builtin/packages/r-subplex/package.py
index 66df912a5f..3adb487f9d 100644
--- a/var/spack/repos/builtin/packages/r-subplex/package.py
+++ b/var/spack/repos/builtin/packages/r-subplex/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-summarizedexperiment/package.py b/var/spack/repos/builtin/packages/r-summarizedexperiment/package.py
index 104a61cb8c..781db8fedc 100644
--- a/var/spack/repos/builtin/packages/r-summarizedexperiment/package.py
+++ b/var/spack/repos/builtin/packages/r-summarizedexperiment/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,16 +13,25 @@ class RSummarizedexperiment(RPackage):
        represent samples."""
 
     homepage = "https://bioconductor.org/packages/SummarizedExperiment/"
-    url      = "https://git.bioconductor.org/packages/SummarizedExperiment"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/SummarizedExperiment.git"
 
-    version('1.6.5', git='https://git.bioconductor.org/packages/SummarizedExperiment', commit='ec69cd5cfbccaef148a9f6abdfb3e22e888695d0')
+    version('1.10.0', commit='7ad2e991c8285bfc4b2e15b29d94cc86d07f8f2b')
+    version('1.8.1', commit='9d8a29aa9c78bbc7dcc6472537e13fc0d11dc1f7')
+    version('1.6.5', commit='ec69cd5cfbccaef148a9f6abdfb3e22e888695d0')
 
-    depends_on('r-genomicranges', type=('build', 'run'))
+    depends_on('r-genomicranges@1.27.22:', when='@1.6.5', type=('build', 'run'))
+    depends_on('r-genomicranges@1.29.14:', when='@1.8.1', type=('build', 'run'))
+    depends_on('r-genomicranges@1.31.17:', when='@1.10.0', type=('build', 'run'))
     depends_on('r-biobase', type=('build', 'run'))
-    depends_on('r-delayedarray', type=('build', 'run'))
+    depends_on('r-delayedarray@0.1.9:', when='@1.6.5', type=('build', 'run'))
+    depends_on('r-delayedarray@0.3.20:', when='@1.8.1:', type=('build', 'run'))
     depends_on('r-matrix', type=('build', 'run'))
     depends_on('r-s4vectors', type=('build', 'run'))
+    depends_on('r-s4vectors@0.17.25:', when='@1.10.0', type=('build', 'run'))
     depends_on('r-iranges', type=('build', 'run'))
+    depends_on('r-iranges@2.13.16:', when='@1.10.0', type=('build', 'run'))
     depends_on('r-genomeinfodb', type=('build', 'run'))
-    depends_on('r@3.4.0:3.4.9', when='@1.6.5')
+    depends_on('r-genomeinfodb@1.13.1:', when='@1.10.0', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.15.3:', when='@1.6.5:', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@1.6.5:1.9.9', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@1.10.0', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-survey/package.py b/var/spack/repos/builtin/packages/r-survey/package.py
index 62d21bb00b..cf0c11d4b0 100644
--- a/var/spack/repos/builtin/packages/r-survey/package.py
+++ b/var/spack/repos/builtin/packages/r-survey/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-survival/package.py b/var/spack/repos/builtin/packages/r-survival/package.py
index c63c2eb864..f4f8b4eed3 100644
--- a/var/spack/repos/builtin/packages/r-survival/package.py
+++ b/var/spack/repos/builtin/packages/r-survival/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-sva/package.py b/var/spack/repos/builtin/packages/r-sva/package.py
new file mode 100644
index 0000000000..3510a46b2a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-sva/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RSva(RPackage):
+    """Surrogate Variable Analysis."""
+
+    homepage = "https://www.bioconductor.org/packages/sva/"
+    git      = "https://git.bioconductor.org/packages/sva.git"
+
+    version('3.24.4', commit='ed2ebb6e33374dc9ec50e6ea97cc1d9aef836c73')
+
+    depends_on('r@3.4.0:3.4.9', when='@3.24.4')
+    depends_on('r-mgcv', type=('build', 'run'))
+    depends_on('r-genefilter', type=('build', 'run'))
+    depends_on('r-biocparallel', type=('build', 'run'))
+    depends_on('r-matrixstats', type=('build', 'run'))
+    depends_on('r-limma', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-tarifx/package.py b/var/spack/repos/builtin/packages/r-tarifx/package.py
index b58eb5194e..2fa7653d73 100644
--- a/var/spack/repos/builtin/packages/r-tarifx/package.py
+++ b/var/spack/repos/builtin/packages/r-tarifx/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-tclust/package.py b/var/spack/repos/builtin/packages/r-tclust/package.py
new file mode 100644
index 0000000000..0c07d18a56
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-tclust/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RTclust(RPackage):
+    """Provides functions for robust trimmed clustering."""
+
+    homepage = "https://cran.r-project.org/web/packages/tclust/index.html"
+    url      = "https://cran.r-project.org/src/contrib/tclust_1.3-1.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/tclust"
+
+    version('1.3-1',  '5415d74682588d4a6fb8ce166fc75661')
+    version('1.2-7',  'e32cd02819682cc944c7baaac3b6f2b7')
+    version('1.2-3',  '922abc1abd8da4c6ac9830e1f2f71e84')
+    version('1.1-03', 'f1cc9278bdb068acce4623a9d98b7b62')
+    version('1.1-02', '6f206501b0341fb5623208d145984f5a')
+
+    depends_on('r@3.4.0:3.4.9')
+    depends_on('r-cluster', type=('build', 'run'))
+    depends_on('r-mclust', type=('build', 'run'))
+    depends_on('r-mvtnorm', type=('build', 'run'))
+    depends_on('r-sn', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-tensora/package.py b/var/spack/repos/builtin/packages/r-tensora/package.py
index c19e3604fc..c999e3c759 100644
--- a/var/spack/repos/builtin/packages/r-tensora/package.py
+++ b/var/spack/repos/builtin/packages/r-tensora/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-testit/package.py b/var/spack/repos/builtin/packages/r-testit/package.py
index 7a5fb607e8..c349351975 100644
--- a/var/spack/repos/builtin/packages/r-testit/package.py
+++ b/var/spack/repos/builtin/packages/r-testit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/r-testthat/package.py b/var/spack/repos/builtin/packages/r-testthat/package.py
index 045f447df1..49d31da8c6 100644
--- a/var/spack/repos/builtin/packages/r-testthat/package.py
+++ b/var/spack/repos/builtin/packages/r-testthat/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-tfbstools/package.py b/var/spack/repos/builtin/packages/r-tfbstools/package.py
new file mode 100644
index 0000000000..1e4b224444
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-tfbstools/package.py
@@ -0,0 +1,49 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RTfbstools(RPackage):
+    """TFBSTools is a package for the analysis and manipulation of
+       transcription factor binding sites.
+
+       It includes matrices conversion between Position Frequency Matirx (PFM),
+       Position Weight Matirx (PWM) and Information Content Matrix (ICM). It
+       can also scan putative TFBS from sequence/alignment, query JASPAR
+       database and provides a wrapper of de novo motif discovery software.
+       TFBSTools is a package for the analysis and manipulation of
+       transcription factor binding sites. It includes matrices conversion
+       between Position Frequency Matirx (PFM), Position Weight Matirx (PWM)
+       and Information Content Matrix (ICM). It can also scan putative TFBS
+       from sequence/alignment, query JASPAR database and provides a wrapper
+       of de novo motif discovery software."""
+
+    homepage = "http://bioconductor.org/packages/TFBSTools/"
+    git      = "https://git.bioconductor.org/packages/TFBSTools.git"
+
+    version('1.16.0', commit='565436a5a674d4dea7279e796a20c5bd2034f65a')
+
+    depends_on('r-biobase@2.28:', type=('build', 'run'))
+    depends_on('r-biostrings@2.36.4:', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.14.0:', type=('build', 'run'))
+    depends_on('r-biocparallel@1.2.21:', type=('build', 'run'))
+    depends_on('r-bsgenome@1.36.3:', type=('build', 'run'))
+    depends_on('r-catools@1.17.1:', type=('build', 'run'))
+    depends_on('r-cner@1.4.0:', type=('build', 'run'))
+    depends_on('r-dirichletmultinomial@1.10.0:', type=('build', 'run'))
+    depends_on('r-genomeinfodb@1.6.1:', type=('build', 'run'))
+    depends_on('r-genomicranges@1.20.6:', type=('build', 'run'))
+    depends_on('r-gtools@3.5.0:', type=('build', 'run'))
+    depends_on('r-iranges@2.2.7:', type=('build', 'run'))
+    depends_on('r-dbi@0.6:', type=('build', 'run'))
+    depends_on('r-rsqlite@1.0.0:', type=('build', 'run'))
+    depends_on('r-rtracklayer@1.28.10:', type=('build', 'run'))
+    depends_on('r-seqlogo@1.34.0:', type=('build', 'run'))
+    depends_on('r-s4vectors@0.9.25:', type=('build', 'run'))
+    depends_on('r-tfmpvalue@0.0.5:', type=('build', 'run'))
+    depends_on('r-xml@3.98-1.3:', type=('build', 'run'))
+    depends_on('r-xvector@0.8.0:', type=('build', 'run'))
+    depends_on('r@3.4.3:3.4.9', when='@1.16.0')
diff --git a/var/spack/repos/builtin/packages/r-tfmpvalue/package.py b/var/spack/repos/builtin/packages/r-tfmpvalue/package.py
new file mode 100644
index 0000000000..d3304686b2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-tfmpvalue/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RTfmpvalue(RPackage):
+    """In putative Transcription Factor Binding Sites (TFBSs) identification
+       from sequence/alignments, we are interested in the significance of
+       certain match score. TFMPvalue provides the accurate calculation of
+       P-value with score threshold for Position Weight Matrices, or the score
+       with given P-value. This package is an interface to code originally
+       made available by Helene Touzet and Jean-Stephane Varre, 2007,
+       Algorithms Mol Biol:2, 15."""
+
+    homepage = "https://github.com/ge11232002/TFMPvalue"
+    url      = "https://cran.rstudio.com/src/contrib/TFMPvalue_0.0.6.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/TFMPvalue"
+
+    version('0.0.6', '69fdf4f9b9a0f408a5cee9ce34bea261')
+
+    depends_on('r-rcpp@0.11.1:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-th-data/package.py b/var/spack/repos/builtin/packages/r-th-data/package.py
index e5713ee9fc..ccbac55279 100644
--- a/var/spack/repos/builtin/packages/r-th-data/package.py
+++ b/var/spack/repos/builtin/packages/r-th-data/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-threejs/package.py b/var/spack/repos/builtin/packages/r-threejs/package.py
index f39ede0fb7..908cf9a283 100644
--- a/var/spack/repos/builtin/packages/r-threejs/package.py
+++ b/var/spack/repos/builtin/packages/r-threejs/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-tibble/package.py b/var/spack/repos/builtin/packages/r-tibble/package.py
index 66b9f9235a..af08f9b037 100644
--- a/var/spack/repos/builtin/packages/r-tibble/package.py
+++ b/var/spack/repos/builtin/packages/r-tibble/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-tidycensus/package.py b/var/spack/repos/builtin/packages/r-tidycensus/package.py
new file mode 100644
index 0000000000..70c180eac0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-tidycensus/package.py
@@ -0,0 +1,34 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RTidycensus(RPackage):
+    """An integrated R interface to the decennial US Census and American
+    Community Survey APIs and the US Census Bureau's geographic boundary
+    files. Allows R users to return Census and ACS data as tidyverse-ready
+    data frames, and optionally returns a list-column with feature
+    geometry for many geographies."""
+
+    homepage = "https://cran.r-project.org/package=tidycensus"
+    url      = "https://cran.rstudio.com/src/contrib/tidycensus_0.3.1.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/tidycensus"
+
+    version('0.3.1', '420d046b5a408d321e775c3d410e7699')
+
+    depends_on('r-httr', type=('build', 'run'))
+    depends_on('r-sf', type=('build', 'run'))
+    depends_on('r-dplyr', type=('build', 'run'))
+    depends_on('r-tigris', type=('build', 'run'))
+    depends_on('r-stringr', type=('build', 'run'))
+    depends_on('r-jsonlite', type=('build', 'run'))
+    depends_on('r-purrr', type=('build', 'run'))
+    depends_on('r-rvest', type=('build', 'run'))
+    depends_on('r-tidyr', type=('build', 'run'))
+    depends_on('r-rappdirs', type=('build', 'run'))
+    depends_on('r-readr', type=('build', 'run'))
+    depends_on('r-xml2', type=('build', 'run'))
+    depends_on('r-units', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-tidyr/package.py b/var/spack/repos/builtin/packages/r-tidyr/package.py
index 0e6973fd13..1897495eb2 100644
--- a/var/spack/repos/builtin/packages/r-tidyr/package.py
+++ b/var/spack/repos/builtin/packages/r-tidyr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,14 +12,18 @@ class RTidyr(RPackage):
     pipelines."""
 
     homepage = "https://github.com/hadley/tidyr"
-    url      = "https://cran.r-project.org/src/contrib/tidyr_0.5.1.tar.gz"
+    url      = "https://cran.r-project.org/src/contrib/tidyr_0.7.2.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/tidyr"
 
+    version('0.7.2', '42d723bf04c5c1c59e27a8be14f3a6b6')
     version('0.5.1', '3cadc869510c054ed93d374ab44120bd')
 
     depends_on('r-tibble', type=('build', 'run'))
-    depends_on('r-dplyr', type=('build', 'run'))
+    depends_on('r-dplyr@0.7.0:', type=('build', 'run'))
     depends_on('r-stringi', type=('build', 'run'))
-    depends_on('r-lazyeval', type=('build', 'run'))
     depends_on('r-magrittr', type=('build', 'run'))
+    depends_on('r-glue', type=('build', 'run'))
     depends_on('r-rcpp', type=('build', 'run'))
+    depends_on('r-purrr', type=('build', 'run'))
+    depends_on('r-tidyselect', type=('build', 'run'))
+    depends_on('r-rlang', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-tidyselect/package.py b/var/spack/repos/builtin/packages/r-tidyselect/package.py
new file mode 100644
index 0000000000..96ae53a11c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-tidyselect/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RTidyselect(RPackage):
+    """A backend for the selecting functions of the 'tidyverse'. It makes it
+       easy to implement select-like functions in your own packages in a way
+       that is consistent with other 'tidyverse' interfaces for selection."""
+
+    homepage = "https://cran.r-project.org/package=tidyselect"
+    url      = "https://cran.r-project.org/src/contrib/tidyselect_0.2.3.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/tidyselect"
+
+    version('0.2.3', 'c9dbd895ad7ce209bacfad6d19de91c9')
+
+    depends_on('r-glue', type=('build', 'run'))
+    depends_on('r-purrr', type=('build', 'run'))
+    depends_on('r-rlang@0.1:', type=('build', 'run'))
+    depends_on('r-rcpp@0.12.0:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-tidyverse/package.py b/var/spack/repos/builtin/packages/r-tidyverse/package.py
new file mode 100644
index 0000000000..f12e708308
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-tidyverse/package.py
@@ -0,0 +1,46 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RTidyverse(RPackage):
+    """The 'tidyverse' is a set of packages that work in harmony because they
+       share common data representations and 'API' design. This package is
+       designed to make it easy to install and load multiple 'tidyverse'
+       packages in a single step."""
+
+    homepage = "http://tidyverse.tidyverse.org/"
+    url      = "https://cran.r-project.org/src/contrib/tidyverse_1.2.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/tidyverse"
+
+    version('1.2.1', '7e2ca0b72ab668342c02fd0f52c082e1')
+
+    depends_on('r-broom@0.4.2:', type=('build', 'run'))
+    depends_on('r-cli@1.0.0:', type=('build', 'run'))
+    depends_on('r-crayon@1.3.4:', type=('build', 'run'))
+    depends_on('r-dplyr@0.7.4:', type=('build', 'run'))
+    depends_on('r-dbplyr@1.1.0:', type=('build', 'run'))
+    depends_on('r-forcats@0.2.0:', type=('build', 'run'))
+    depends_on('r-ggplot2@2.2.1:', type=('build', 'run'))
+    depends_on('r-haven@1.1.0:', type=('build', 'run'))
+    depends_on('r-hms@0.3:', type=('build', 'run'))
+    depends_on('r-httr@1.3.1:', type=('build', 'run'))
+    depends_on('r-jsonlite@1.5:', type=('build', 'run'))
+    depends_on('r-lubridate@1.7.1:', type=('build', 'run'))
+    depends_on('r-magrittr@1.5:', type=('build', 'run'))
+    depends_on('r-modelr@0.1.1:', type=('build', 'run'))
+    depends_on('r-purrr@0.2.4:', type=('build', 'run'))
+    depends_on('r-readr@1.1.1:', type=('build', 'run'))
+    depends_on('r-readxl@1.0.0:', type=('build', 'run'))
+    depends_on('r-reprex@0.1.1:', type=('build', 'run'))
+    depends_on('r-rlang@0.1.4:', type=('build', 'run'))
+    depends_on('r-rstudioapi@0.7:', type=('build', 'run'))
+    depends_on('r-rvest@0.3.2:', type=('build', 'run'))
+    depends_on('r-stringr@1.2.0:', type=('build', 'run'))
+    depends_on('r-tibble@1.3.4:', type=('build', 'run'))
+    depends_on('r-tidyr@0.7.2:', type=('build', 'run'))
+    depends_on('r-xml2@1.1.1:', type=('build', 'run'))
+    depends_on('r-rlang@0.1.4:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-tiff/package.py b/var/spack/repos/builtin/packages/r-tiff/package.py
index c751cb04e2..8dafca0a35 100644
--- a/var/spack/repos/builtin/packages/r-tiff/package.py
+++ b/var/spack/repos/builtin/packages/r-tiff/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-tigris/package.py b/var/spack/repos/builtin/packages/r-tigris/package.py
new file mode 100644
index 0000000000..a87409ac1e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-tigris/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RTigris(RPackage):
+    """Download TIGER/Line shapefiles from the United States Census Bureau
+    and load into R as 'SpatialDataFrame' or 'sf' objects."""
+
+    homepage = "https://cran.r-project.org/package=tigris"
+    url      = "https://cran.rstudio.com/src/contrib/tigris_0.5.3.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/tigris"
+
+    version('0.5.3', 'c11cb459bf134d3deb1a641a60c86413')
+
+    depends_on('r-stringr', type=('build', 'run'))
+    depends_on('r-magrittr', type=('build', 'run'))
+    depends_on('r-rgdal', type=('build', 'run'))
+    depends_on('r-rgeos', type=('build', 'run'))
+    depends_on('r-sp', type=('build', 'run'))
+    depends_on('r-rappdirs', type=('build', 'run'))
+    depends_on('r-maptools', type=('build', 'run'))
+    depends_on('r-httr', type=('build', 'run'))
+    depends_on('r-uuid', type=('build', 'run'))
+    depends_on('r-sf', type=('build', 'run'))
+    depends_on('r-dplyr', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-timedate/package.py b/var/spack/repos/builtin/packages/r-timedate/package.py
index d593b6c2bc..b55d61b881 100644
--- a/var/spack/repos/builtin/packages/r-timedate/package.py
+++ b/var/spack/repos/builtin/packages/r-timedate/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-tmixclust/package.py b/var/spack/repos/builtin/packages/r-tmixclust/package.py
new file mode 100644
index 0000000000..cbd49587b7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-tmixclust/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RTmixclust(RPackage):
+    """Implementation of a clustering method for time series gene expression
+    data based on mixed-effects models with Gaussian variables and
+    non-parametric cubic splines estimation. The method can robustly account
+    for the high levels of noise present in typical gene expression time
+    series datasets."""
+
+    homepage = "https://bioconductor.org/packages/TMixClust/"
+    git      = "https://git.bioconductor.org/packages/TMixClust.git"
+
+    version('1.0.1', commit='0ac800210e3eb9da911767a80fb5582ab33c0cad')
+
+    depends_on('r-gss', type=('build', 'run'))
+    depends_on('r-mvtnorm', type=('build', 'run'))
+    depends_on('r-zoo', type=('build', 'run'))
+    depends_on('r-cluster', type=('build', 'run'))
+    depends_on('r-biocparallel', type=('build', 'run'))
+    depends_on('r-flexclust', type=('build', 'run'))
+    depends_on('r-biobase', type=('build', 'run'))
+    depends_on('r-spem', type=('build', 'run'))
+    depends_on('r@3.4.3:3.4.9', when='@1.0.1')
diff --git a/var/spack/repos/builtin/packages/r-topgo/package.py b/var/spack/repos/builtin/packages/r-topgo/package.py
new file mode 100644
index 0000000000..1997f407c2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-topgo/package.py
@@ -0,0 +1,30 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RTopgo(RPackage):
+    """topGO package provides tools for testing GO terms while accounting
+    for the topology of the GO graph. Different test statistics and
+    different methods for eliminating local similarities and dependencies
+    between GO terms can be implemented and applied."""
+
+    homepage = "https://www.bioconductor.org/packages/topGO/"
+    git      = "https://git.bioconductor.org/packages/topGO.git"
+
+    version('2.30.1', commit='b1469ce1d198ccb73ef79ca22cab81659e16dbaa')
+    version('2.28.0', commit='066a975d460046cce33fb27e74e6a0ebc33fd716')
+
+    depends_on('r@3.4.0:3.4.9')
+    depends_on('r-dbi', type=('build', 'run'))
+    depends_on('r-matrixstats', type=('build', 'run'))
+    depends_on('r-lattice', type=('build', 'run'))
+    depends_on('r-sparsem@0.73:', type=('build', 'run'))
+    depends_on('r-annotationdbi@1.7.19:', type=('build', 'run'))
+    depends_on('r-go-db@2.3.0:', type=('build', 'run'))
+    depends_on('r-biobase@2.0.0:', type=('build', 'run'))
+    depends_on('r-graph@1.14.0:', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.13.6:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-trimcluster/package.py b/var/spack/repos/builtin/packages/r-trimcluster/package.py
index c7f6cdb179..e1ea58534d 100644
--- a/var/spack/repos/builtin/packages/r-trimcluster/package.py
+++ b/var/spack/repos/builtin/packages/r-trimcluster/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-truncnorm/package.py b/var/spack/repos/builtin/packages/r-truncnorm/package.py
new file mode 100644
index 0000000000..07cfb8716e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-truncnorm/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RTruncnorm(RPackage):
+    """Density, probability, quantile and random number generation functions
+    for the truncated normal distribution."""
+
+    homepage = "https://cran.r-project.org/package=truncnorm"
+    url      = "https://cran.rstudio.com/src/contrib/truncnorm_1.0-8.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/truncnorm"
+
+    version('1.0-8', 'c60cd6555be0dd2ea91e61757439282d')
diff --git a/var/spack/repos/builtin/packages/r-trust/package.py b/var/spack/repos/builtin/packages/r-trust/package.py
index e83d8ad2b3..e076cf5cfd 100644
--- a/var/spack/repos/builtin/packages/r-trust/package.py
+++ b/var/spack/repos/builtin/packages/r-trust/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-tseries/package.py b/var/spack/repos/builtin/packages/r-tseries/package.py
index e581a77596..8509b84944 100644
--- a/var/spack/repos/builtin/packages/r-tseries/package.py
+++ b/var/spack/repos/builtin/packages/r-tseries/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-tsne/package.py b/var/spack/repos/builtin/packages/r-tsne/package.py
new file mode 100644
index 0000000000..89dd259886
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-tsne/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RTsne(RPackage):
+    """A "pure R" implementation of the t-SNE algorithm."""
+
+    homepage = "https://cran.r-project.org/web/packages/tsne/index.html"
+    url      = "https://cran.r-project.org/src/contrib/tsne_0.1-3.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/tnse"
+
+    version('0.1-3', '00974d4b3fd5f1100d0ebd24e03b0af9')
+    version('0.1-2', 'd96d8dce6ffeda68e2b25ec1ff52ea61')
+    version('0.1-1', '8197e5c61dec916b7a31b74e658b632d')
+
+    depends_on('r@3.4.0:3.4.9')
diff --git a/var/spack/repos/builtin/packages/r-ttr/package.py b/var/spack/repos/builtin/packages/r-ttr/package.py
index abaac57c6f..8c30fe566b 100644
--- a/var/spack/repos/builtin/packages/r-ttr/package.py
+++ b/var/spack/repos/builtin/packages/r-ttr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-udunits2/package.py b/var/spack/repos/builtin/packages/r-udunits2/package.py
new file mode 100644
index 0000000000..23dd7d86a0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-udunits2/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RUdunits2(RPackage):
+    """Provides simple bindings to Unidata's udunits library."""
+
+    homepage = "https://github.com/pacificclimate/Rudunits2"
+    url      = "https://cran.r-project.org/src/contrib/udunits2_0.13.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/udunits2"
+
+    version('0.13', 'c8717808c740ef70eed7aea93c7c4c7d')
+
+    depends_on('udunits2')
diff --git a/var/spack/repos/builtin/packages/r-units/package.py b/var/spack/repos/builtin/packages/r-units/package.py
new file mode 100644
index 0000000000..9d3f41d0d8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-units/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RUnits(RPackage):
+    """Support for measurement units in R vectors, matrices and arrays:
+       automatic propagation, conversion, derivation and simplification of
+       units; raising errors in case of unit incompatibility. Compatible with
+       the POSIXct, Date and difftime classes. Uses the UNIDATA udunits
+       library and unit database for unit compatibility checking and
+       conversion."""
+
+    homepage = "https://github.com/edzer/units/"
+    url      = "https://cran.r-project.org/src/contrib/units_0.4-6.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/units"
+
+    version('0.4-6', '0bb90dde5dad7608fa6feb1599381bf2')
+
+    depends_on('r-udunits2', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-utils/package.py b/var/spack/repos/builtin/packages/r-utils/package.py
index bb39da3e60..5ea5e2d63c 100644
--- a/var/spack/repos/builtin/packages/r-utils/package.py
+++ b/var/spack/repos/builtin/packages/r-utils/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-uuid/package.py b/var/spack/repos/builtin/packages/r-uuid/package.py
index ff0c13cf10..461a11ff84 100644
--- a/var/spack/repos/builtin/packages/r-uuid/package.py
+++ b/var/spack/repos/builtin/packages/r-uuid/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/r-variantannotation/package.py b/var/spack/repos/builtin/packages/r-variantannotation/package.py
index 1b8e3da4d5..3063836f5a 100644
--- a/var/spack/repos/builtin/packages/r-variantannotation/package.py
+++ b/var/spack/repos/builtin/packages/r-variantannotation/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,10 +11,9 @@ class RVariantannotation(RPackage):
        outcomes."""
 
     homepage = "https://www.bioconductor.org/packages/VariantAnnotation/"
-    url      = "https://git.bioconductor.org/packages/VariantAnnotation"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/VariantAnnotation.git"
 
-    version('1.22.3', git='https://git.bioconductor.org/packages/VariantAnnotation', commit='3a91b6d4297aa416d5f056dec6f8925eb1a8eaee')
+    version('1.22.3', commit='3a91b6d4297aa416d5f056dec6f8925eb1a8eaee')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-genomeinfodb', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-varselrf/package.py b/var/spack/repos/builtin/packages/r-varselrf/package.py
index 7cfb3392cd..05a11ee0b9 100644
--- a/var/spack/repos/builtin/packages/r-varselrf/package.py
+++ b/var/spack/repos/builtin/packages/r-varselrf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-vcd/package.py b/var/spack/repos/builtin/packages/r-vcd/package.py
index c0ca50a605..07d7104686 100644
--- a/var/spack/repos/builtin/packages/r-vcd/package.py
+++ b/var/spack/repos/builtin/packages/r-vcd/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-vegan/package.py b/var/spack/repos/builtin/packages/r-vegan/package.py
index 51591ec41d..c571615d92 100644
--- a/var/spack/repos/builtin/packages/r-vegan/package.py
+++ b/var/spack/repos/builtin/packages/r-vegan/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-vgam/package.py b/var/spack/repos/builtin/packages/r-vgam/package.py
new file mode 100644
index 0000000000..f148239434
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-vgam/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RVgam(RPackage):
+    """An implementation of about 6 major classes of statistical regression
+    models."""
+
+    homepage = "https://cran.r-project.org/web/packages/VGAM/index.html"
+    url      = "https://cran.r-project.org/src/contrib/VGAM_1.0-4.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/VGAM"
+
+    version('1.0-4', '9d30736842db6d9dcec83df49f11d3c1')
+    version('1.0-3', 'a158cd0a6ff956b4bf21d610df361b18')
+    version('1.0-2', '813b303d5d956914cf8910db3fa1ba14')
+    version('1.0-1', '778182585c774036ac3d10240cf63b40')
+    version('1.0-0', '81da7b3a797b5e26b9e859dc2f373b7b')
+
+    depends_on('r@3.4.0:3.4.9')
+    depends_on('r-mass', type=('build', 'run'))
+    depends_on('r-mgcv', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-vipor/package.py b/var/spack/repos/builtin/packages/r-vipor/package.py
new file mode 100644
index 0000000000..79c1d0cfba
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-vipor/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RVipor(RPackage):
+    """Plot Categorical Data Using Quasirandom Noise and Density Estimates"""
+
+    homepage = "https://cran.r-project.org/package=vipor"
+    url      = "https://cran.r-project.org/src/contrib/vipor_0.4.5.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/vipor"
+
+    version('0.4.5', 'd08bc95b3aaf1574bf41b7eb41b67ce4')
+    version('0.4.4', '834212e3971787809ba9737744d54dee')
+
+    depends_on('r@3.0.0:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-viridis/package.py b/var/spack/repos/builtin/packages/r-viridis/package.py
index 627ba4ac39..d71d0654b0 100644
--- a/var/spack/repos/builtin/packages/r-viridis/package.py
+++ b/var/spack/repos/builtin/packages/r-viridis/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-viridislite/package.py b/var/spack/repos/builtin/packages/r-viridislite/package.py
index bfdd6c3bc5..d83c606dca 100644
--- a/var/spack/repos/builtin/packages/r-viridislite/package.py
+++ b/var/spack/repos/builtin/packages/r-viridislite/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-visnetwork/package.py b/var/spack/repos/builtin/packages/r-visnetwork/package.py
index 5cbc427c17..decbaa0f7d 100644
--- a/var/spack/repos/builtin/packages/r-visnetwork/package.py
+++ b/var/spack/repos/builtin/packages/r-visnetwork/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-vsn/package.py b/var/spack/repos/builtin/packages/r-vsn/package.py
index 649f42ea5d..27e7026b65 100644
--- a/var/spack/repos/builtin/packages/r-vsn/package.py
+++ b/var/spack/repos/builtin/packages/r-vsn/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,9 +21,9 @@ class RVsn(RPackage):
        differential transcription."""
 
     homepage = "https://www.bioconductor.org/packages/vsn/"
-    url      = "https://git.bioconductor.org/packages/vsn"
+    git      = "https://git.bioconductor.org/packages/vsn.git"
 
-    version('3.44.0', git='https://git.bioconductor.org/packages/vsn', commit='e54513fcdd07ccfb8094359e93cef145450f0ee0')
+    version('3.44.0', commit='e54513fcdd07ccfb8094359e93cef145450f0ee0')
 
     depends_on('r-biobase', type=('build', 'run'))
     depends_on('r-affy', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-whisker/package.py b/var/spack/repos/builtin/packages/r-whisker/package.py
index d22b1a5209..f54c9b4529 100644
--- a/var/spack/repos/builtin/packages/r-whisker/package.py
+++ b/var/spack/repos/builtin/packages/r-whisker/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-withr/package.py b/var/spack/repos/builtin/packages/r-withr/package.py
index 67afc532ae..cd9888c431 100644
--- a/var/spack/repos/builtin/packages/r-withr/package.py
+++ b/var/spack/repos/builtin/packages/r-withr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-xde/package.py b/var/spack/repos/builtin/packages/r-xde/package.py
index 5d4a686fb5..25598b44dc 100644
--- a/var/spack/repos/builtin/packages/r-xde/package.py
+++ b/var/spack/repos/builtin/packages/r-xde/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,9 @@ class RXde(RPackage):
        expression."""
 
     homepage = "https://www.bioconductor.org/packages/XDE/"
-    url      = "https://git.bioconductor.org/packages/XDE"
+    git      = "https://git.bioconductor.org/packages/XDE.git"
 
-    version('2.22.0', git='https://git.bioconductor.org/packages/XDE', commit='25bcec965ae42a410dd285a9db9be46d112d8e81')
+    version('2.22.0', commit='25bcec965ae42a410dd285a9db9be46d112d8e81')
 
     depends_on('r-biobase', type=('build', 'run'))
     depends_on('r-biocgenerics', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-xgboost/package.py b/var/spack/repos/builtin/packages/r-xgboost/package.py
index 22f87b5c54..ad7aac9f0e 100644
--- a/var/spack/repos/builtin/packages/r-xgboost/package.py
+++ b/var/spack/repos/builtin/packages/r-xgboost/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/r-xlconnect/package.py b/var/spack/repos/builtin/packages/r-xlconnect/package.py
index 6a388c14a5..49d468f539 100644
--- a/var/spack/repos/builtin/packages/r-xlconnect/package.py
+++ b/var/spack/repos/builtin/packages/r-xlconnect/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-xlconnectjars/package.py b/var/spack/repos/builtin/packages/r-xlconnectjars/package.py
index fd7913a296..a8f128cda1 100644
--- a/var/spack/repos/builtin/packages/r-xlconnectjars/package.py
+++ b/var/spack/repos/builtin/packages/r-xlconnectjars/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-xlsx/package.py b/var/spack/repos/builtin/packages/r-xlsx/package.py
index 988fa41157..82d36970be 100644
--- a/var/spack/repos/builtin/packages/r-xlsx/package.py
+++ b/var/spack/repos/builtin/packages/r-xlsx/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-xlsxjars/package.py b/var/spack/repos/builtin/packages/r-xlsxjars/package.py
index 8bd19f97c4..bb49a81b70 100644
--- a/var/spack/repos/builtin/packages/r-xlsxjars/package.py
+++ b/var/spack/repos/builtin/packages/r-xlsxjars/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-xmapbridge/package.py b/var/spack/repos/builtin/packages/r-xmapbridge/package.py
index 0836eb3951..07b410fc7f 100644
--- a/var/spack/repos/builtin/packages/r-xmapbridge/package.py
+++ b/var/spack/repos/builtin/packages/r-xmapbridge/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,8 @@ class RXmapbridge(RPackage):
        exports plotting files in a suitable format."""
 
     homepage = "https://www.bioconductor.org/packages/xmapbridge/"
-    url      = "https://git.bioconductor.org/packages/xmapbridge"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/xmapbridge.git"
 
-    version('1.34.0', git='https://git.bioconductor.org/packages/xmapbridge', commit='f162e1f72ead5f5a1aede69032d5771a6572d965')
+    version('1.34.0', commit='f162e1f72ead5f5a1aede69032d5771a6572d965')
 
     depends_on('r@3.4.0:3.4.9', when='@1.34.0')
diff --git a/var/spack/repos/builtin/packages/r-xml/package.py b/var/spack/repos/builtin/packages/r-xml/package.py
index aca86eade4..9ce222a351 100644
--- a/var/spack/repos/builtin/packages/r-xml/package.py
+++ b/var/spack/repos/builtin/packages/r-xml/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-xml2/package.py b/var/spack/repos/builtin/packages/r-xml2/package.py
index ffbe0f626f..9d5cc6f56d 100644
--- a/var/spack/repos/builtin/packages/r-xml2/package.py
+++ b/var/spack/repos/builtin/packages/r-xml2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-xtable/package.py b/var/spack/repos/builtin/packages/r-xtable/package.py
index 8f3cc65c0b..78a5833949 100644
--- a/var/spack/repos/builtin/packages/r-xtable/package.py
+++ b/var/spack/repos/builtin/packages/r-xtable/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-xts/package.py b/var/spack/repos/builtin/packages/r-xts/package.py
index 1c1184428a..1efa347f1c 100644
--- a/var/spack/repos/builtin/packages/r-xts/package.py
+++ b/var/spack/repos/builtin/packages/r-xts/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-xvector/package.py b/var/spack/repos/builtin/packages/r-xvector/package.py
index 4018422c18..bd9c8a7672 100644
--- a/var/spack/repos/builtin/packages/r-xvector/package.py
+++ b/var/spack/repos/builtin/packages/r-xvector/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,13 +11,17 @@ class RXvector(RPackage):
        an R external pointer, or on disk)."""
 
     homepage = "https://bioconductor.org/packages/XVector/"
-    url      = "https://git.bioconductor.org/packages/XVector"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/XVector.git"
 
-    version('0.16.0', git='https://git.bioconductor.org/packages/XVector', commit='54615888e1a559da4a81de33e934fc0f1c3ad99f')
+    version('0.20.0', commit='a83a7ea01f6a710f0ba7d9fb021cfa795b291cb4')
+    version('0.16.0', commit='54615888e1a559da4a81de33e934fc0f1c3ad99f')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.19.2:', when='@0.20.0', type=('build', 'run'))
     depends_on('r-s4vectors', type=('build', 'run'))
+    depends_on('r-s4vectors@0.17.24:', when='@0.20.0', type=('build', 'run'))
     depends_on('r-iranges', type=('build', 'run'))
+    depends_on('r-iranges@2.13.16:', when='@0.20.0', type=('build', 'run'))
     depends_on('r-zlibbioc', type=('build', 'run'))
-    depends_on('r@3.4.0:3.4.9', when='@0.16.0')
+    depends_on('r@3.4.0:3.4.9', when='@0.16.0', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@0.20.0', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-yaml/package.py b/var/spack/repos/builtin/packages/r-yaml/package.py
index 25e60cdd9a..4c582bee8f 100644
--- a/var/spack/repos/builtin/packages/r-yaml/package.py
+++ b/var/spack/repos/builtin/packages/r-yaml/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-yapsa/package.py b/var/spack/repos/builtin/packages/r-yapsa/package.py
index a69b745a7e..4e771bd199 100644
--- a/var/spack/repos/builtin/packages/r-yapsa/package.py
+++ b/var/spack/repos/builtin/packages/r-yapsa/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,10 +15,9 @@ class RYapsa(RPackage):
        catalogue) are provided."""
 
     homepage = "http://bioconductor.org/packages/YAPSA/"
-    url      = "https://git.bioconductor.org/packages/YAPSA"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/YAPSA.git"
 
-    version('1.2.0', git='https://git.bioconductor.org/packages/YAPSA', commit='320809b69e470e30a777a383f8341f93064ec24d')
+    version('1.2.0', commit='320809b69e470e30a777a383f8341f93064ec24d')
 
     depends_on('r-genomicranges', type=('build', 'run'))
     depends_on('r-ggplot2', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-yaqcaffy/package.py b/var/spack/repos/builtin/packages/r-yaqcaffy/package.py
index 1901990927..9ead0a9110 100644
--- a/var/spack/repos/builtin/packages/r-yaqcaffy/package.py
+++ b/var/spack/repos/builtin/packages/r-yaqcaffy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,10 +12,9 @@ class RYaqcaffy(RPackage):
        reference datasets."""
 
     homepage = "http://bioconductor.org/packages/yaqcaffy/"
-    url      = "https://git.bioconductor.org/packages/yaqcaffy"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/yaqcaffy.git"
 
-    version('1.36.0', git='https://git.bioconductor.org/packages/yaqcaffy', commit='4d46fe77b2c8de2230a77b0c07dd5dd726e3abd6')
+    version('1.36.0', commit='4d46fe77b2c8de2230a77b0c07dd5dd726e3abd6')
 
     depends_on('r-simpleaffy', type=('build', 'run'))
     depends_on('r@3.4.0:3.4.9', when='@1.36.0')
diff --git a/var/spack/repos/builtin/packages/r-yarn/package.py b/var/spack/repos/builtin/packages/r-yarn/package.py
index 5b0a76b476..bf181f5886 100644
--- a/var/spack/repos/builtin/packages/r-yarn/package.py
+++ b/var/spack/repos/builtin/packages/r-yarn/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,11 +14,10 @@ class RYarn(RPackage):
        and statistical techniques to account for the large heterogeneity and
        sparsity found in very large RNA-seq experiments."""
 
-    homepage = "http://www.example.co://www.bioconductor.org/packages/yarn/"
-    url      = "https://git.bioconductor.org/packages/yarn"
-    list_url = homepage
+    homepage = "https://bioconductor.org/packages/yarn/"
+    git      = "https://git.bioconductor.org/packages/yarn.git"
 
-    version('1.2.0', git='https://git.bioconductor.org/packages/yarn', commit='28af616ef8c27dcadf6568e276dea8465486a697')
+    version('1.2.0', commit='28af616ef8c27dcadf6568e276dea8465486a697')
 
     depends_on('r-biobase', type=('build', 'run'))
     depends_on('r-biomart', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-zlibbioc/package.py b/var/spack/repos/builtin/packages/r-zlibbioc/package.py
index 280c7da3de..b493b2a66f 100644
--- a/var/spack/repos/builtin/packages/r-zlibbioc/package.py
+++ b/var/spack/repos/builtin/packages/r-zlibbioc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,9 +13,11 @@ class RZlibbioc(RPackage):
        direct need for this package). See the vignette for instructions
        on use."""
 
-    homepage = "http://bioconductor.org/packages/release/bioc/html/Zlibbioc.html"
-    url      = "https://git.bioconductor.org/packages/zlibbioc"
-    list_url = homepage
+    homepage = "http://bioconductor.org/packages/release/bioc/html/zlibbioc.html"
+    git      = "https://git.bioconductor.org/packages/zlibbioc.git"
+
+    version('1.26.0', commit='2e3ab097caa09a5e3ddaa3469b13e19a7224da0d')
+    version('1.22.0', commit='30377f830af2bc1ff17bbf3fdd2cb6442015fea5')
 
-    version('1.22.0', git='https://git.bioconductor.org/packages/zlibbioc', commit='30377f830af2bc1ff17bbf3fdd2cb6442015fea5')
-    depends_on('r@3.4.0:3.4.9', when='@1.22.0')
+    depends_on('r@3.4.0:3.4.9', when='@1.22.0', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@1.26.0', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-zoo/package.py b/var/spack/repos/builtin/packages/r-zoo/package.py
index 33fa5d3353..c746c297b6 100644
--- a/var/spack/repos/builtin/packages/r-zoo/package.py
+++ b/var/spack/repos/builtin/packages/r-zoo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r/package.py b/var/spack/repos/builtin/packages/r/package.py
index 603a372861..6430e5b33f 100644
--- a/var/spack/repos/builtin/packages/r/package.py
+++ b/var/spack/repos/builtin/packages/r/package.py
@@ -1,28 +1,10 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-import shutil
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import os
+
 from spack import *
 
 
@@ -34,16 +16,22 @@ class R(AutotoolsPackage):
     Please consult the R project homepage for further information."""
 
     homepage = "https://www.r-project.org"
-    url = "https://cloud.r-project.org/src/base/R-3/R-3.4.0.tar.gz"
+    url = "https://cloud.r-project.org/src/base/R-3/R-3.4.3.tar.gz"
 
     extendable = True
 
+    version('3.5.1', sha256='0463bff5eea0f3d93fa071f79c18d0993878fd4f2e18ae6cf22c1639d11457ed')
+    version('3.5.0', 'c0455dbfa76ca807e4dfa93d49dcc817')
+    version('3.4.4', '9d6f73be072531e95884c7965ff80cd8')
+    version('3.4.3', 'bc55db54f992fda9049201ca62d2a584')
+    version('3.4.2', '1cd6d37850188e7f190f1eb94a24ca1f')
     version('3.4.1', '3a79c01dc0527c62e80ffb1c489297ea')
     version('3.4.0', '75083c23d507b9c16d5c6afbd7a827e7')
     version('3.3.3', '0ac211ec15e813a24f8f4a5a634029a4')
     version('3.3.2', '2437014ef40641cdc9673e89c040b7a8')
     version('3.3.1', 'f50a659738b73036e2f5635adbd229c5')
     version('3.3.0', '5a7506c8813432d1621c9725e86baf7a')
+    version('3.2.5', '7b23ee70cfb383be3bd4360e3c71d8c3')
     version('3.2.3', '1ba3dac113efab69e706902810cc2970')
     version('3.2.2', '57cef5c2e210a5454da1979562a10e5b')
     version('3.2.1', 'c2aac8b40f84e08e7f8c9068de9239a3')
@@ -55,12 +43,14 @@ class R(AutotoolsPackage):
             description='Links to externally installed BLAS/LAPACK')
     variant('X', default=False,
             description='Enable X11 support (call configure --with-x)')
+    variant('memory_profiling', default=False,
+            description='Enable memory profiling')
 
     # Virtual dependencies
     depends_on('blas', when='+external-lapack')
     depends_on('lapack', when='+external-lapack')
 
-    # Concrete dependencies
+    # Concrete dependencies.
     depends_on('readline')
     depends_on('ncurses')
     depends_on('icu4c')
@@ -86,6 +76,10 @@ class R(AutotoolsPackage):
 
     patch('zlib.patch', when='@:3.3.2')
 
+    filter_compiler_wrappers(
+        'Makeconf', relative_root=os.path.join('rlib', 'R', 'etc')
+    )
+
     @property
     def etcdir(self):
         return join_path(prefix, 'rlib', 'R', 'etc')
@@ -94,16 +88,21 @@ class R(AutotoolsPackage):
         spec   = self.spec
         prefix = self.prefix
 
+        tcl_config_path = join_path(spec['tcl'].prefix.lib, 'tclConfig.sh')
+        tk_config_path = join_path(spec['tk'].prefix.lib, 'tkConfig.sh')
+
         config_args = [
             '--libdir={0}'.format(join_path(prefix, 'rlib')),
             '--enable-R-shlib',
             '--enable-BLAS-shlib',
-            '--enable-R-framework=no'
+            '--enable-R-framework=no',
+            '--with-tcl-config={0}'.format(tcl_config_path),
+            '--with-tk-config={0}'.format(tk_config_path),
         ]
 
         if '+external-lapack' in spec:
             config_args.extend([
-                '--with-blas',
+                '--with-blas={0}'.format(spec['blas'].libs),
                 '--with-lapack'
             ])
 
@@ -112,6 +111,9 @@ class R(AutotoolsPackage):
         else:
             config_args.append('--without-x')
 
+        if '+memory_profiling' in spec:
+            config_args.append('--enable-memory-profiling')
+
         return config_args
 
     @run_after('install')
@@ -120,27 +122,7 @@ class R(AutotoolsPackage):
         # dependencies in Spack.
         src_makeconf = join_path(self.etcdir, 'Makeconf')
         dst_makeconf = join_path(self.etcdir, 'Makeconf.spack')
-        shutil.copy(src_makeconf, dst_makeconf)
-
-    @run_after('install')
-    def filter_compilers(self):
-        """Run after install to tell the configuration files and Makefiles
-        to use the compilers that Spack built the package with.
-
-        If this isn't done, they'll have CC and CXX set to Spack's generic
-        cc and c++. We want them to be bound to whatever compiler
-        they were built with."""
-
-        kwargs = {'ignore_absent': True, 'backup': False, 'string': True}
-
-        filter_file(env['CC'], self.compiler.cc,
-                    join_path(self.etcdir, 'Makeconf'), **kwargs)
-        filter_file(env['CXX'], self.compiler.cxx,
-                    join_path(self.etcdir, 'Makeconf'), **kwargs)
-        filter_file(env['F77'], self.compiler.f77,
-                    join_path(self.etcdir, 'Makeconf'), **kwargs)
-        filter_file(env['FC'], self.compiler.fc,
-                    join_path(self.etcdir, 'Makeconf'), **kwargs)
+        install(src_makeconf, dst_makeconf)
 
     # ========================================================================
     # Set up environment to make install easy for R extensions.
diff --git a/var/spack/repos/builtin/packages/racon/package.py b/var/spack/repos/builtin/packages/racon/package.py
new file mode 100644
index 0000000000..706d1f68c2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/racon/package.py
@@ -0,0 +1,32 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Racon(CMakePackage):
+    """Ultrafast consensus module for raw de novo genome assembly of long
+     uncorrected reads."""
+
+    homepage = "https://github.com/isovic/racon"
+    url      = "https://github.com/isovic/racon/releases/download/1.2.1/racon-v1.2.1.tar.gz"
+
+    version('1.3.0', 'e00d61f391bce2af20ebd2a3aee1e05a')
+    version('1.2.1', '7bf273b965a5bd0f41342a9ffe5c7639')
+
+    depends_on('cmake@3.2:', type='build')
+    depends_on('python', type='build')
+
+    conflicts('%gcc@:4.7')
+    conflicts('%clang@:3.1')
+
+    def cmake_args(self):
+        args = ['-Dracon_build_wrapper=ON']
+        return args
+
+    def install(self, spec, prefix):
+        install_tree('spack-build/bin', prefix.bin)
+        install_tree('spack-build/lib', prefix.lib)
diff --git a/var/spack/repos/builtin/packages/raft/package.py b/var/spack/repos/builtin/packages/raft/package.py
index a5cc1f0ced..44d4828b97 100644
--- a/var/spack/repos/builtin/packages/raft/package.py
+++ b/var/spack/repos/builtin/packages/raft/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -31,10 +12,11 @@ class Raft(CMakePackage):
        Toolbox under development at Brazilian Synchrotron Light Source."""
 
     homepage = "https://bitbucket.org/gill_martinez/raft_aps"
-    url = "https://bitbucket.org/gill_martinez/raft_aps/get/1.2.3.tar.gz"
+    url      = "https://bitbucket.org/gill_martinez/raft_aps/get/1.2.3.tar.gz"
+    git      = "https://bitbucket.org/gill_martinez/raft_aps.git"
 
+    version('develop', branch='master')
     version('1.2.3', '4d1b106d9b3493e63dde96f7dd44b834')
-    version('develop', git='https://bitbucket.org/gill_martinez/raft_aps.git')
 
     depends_on('mpi')
     depends_on('cmake', type='build')
diff --git a/var/spack/repos/builtin/packages/ragel/package.py b/var/spack/repos/builtin/packages/ragel/package.py
new file mode 100644
index 0000000000..90056223e4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ragel/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Ragel(AutotoolsPackage):
+    """Ragel State Machine Compiler
+    Ragel compiles executable finite state machines from regular
+    languages. Ragel targets C, C++ and ASM. Ragel state machines can
+    not only recognize byte sequences as regular expression machines
+    do, but can also execute code at arbitrary points in the
+    recognition of a regular language. Code embedding is done using
+    inline operators that do not disrupt the regular language syntax.
+    """
+    homepage = "http://www.colm.net/open-source/ragel"
+    git      = "git://colm.net/ragel.git"
+    url      = "http://www.colm.net/files/ragel/ragel-6.10.tar.gz"
+
+    version('6.10', '748cae8b50cffe9efcaa5acebc6abf0d')
+
+    depends_on('colm', type='build')
diff --git a/var/spack/repos/builtin/packages/raja/package.py b/var/spack/repos/builtin/packages/raja/package.py
index 18d2135991..eceaf277fc 100644
--- a/var/spack/repos/builtin/packages/raja/package.py
+++ b/var/spack/repos/builtin/packages/raja/package.py
@@ -1,34 +1,45 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class Raja(CMakePackage):
     """RAJA Parallel Framework."""
+
     homepage = "http://software.llnl.gov/RAJA/"
+    git      = "https://github.com/LLNL/RAJA.git"
+
+    version('develop', branch='develop', submodules='True')
+    version('master',  branch='master',  submodules='True')
+    version('0.5.3', tag='v0.5.3', submodules="True")
+    version('0.5.2', tag='v0.5.2', submodules="True")
+    version('0.5.1', tag='v0.5.1', submodules="True")
+    version('0.5.0', tag='v0.5.0', submodules="True")
+    version('0.4.1', tag='v0.4.1', submodules="True")
+    version('0.4.0', tag='v0.4.0', submodules="True")
 
-    version('develop', git='https://github.com/LLNL/RAJA.git', branch="master", submodules="True")
+    variant('cuda', default=False, description='Build with CUDA backend')
+    variant('openmp', default=True, description='Build OpenMP backend')
+
+    depends_on('cuda', when='+cuda')
 
     depends_on('cmake@3.3:', type='build')
+
+    def cmake_args(self):
+        spec = self.spec
+
+        options = []
+
+        if '+openmp' in spec:
+            options.extend([
+                '-DENABLE_OPENMP=On'])
+
+        if '+cuda' in spec:
+            options.extend([
+                '-DENABLE_CUDA=On',
+                '-DCUDA_TOOLKIT_ROOT_DIR=%s' % (spec['cuda'].prefix)])
+
+        return options
diff --git a/var/spack/repos/builtin/packages/randfold/package.py b/var/spack/repos/builtin/packages/randfold/package.py
index 5160840332..12f6b0e2fa 100644
--- a/var/spack/repos/builtin/packages/randfold/package.py
+++ b/var/spack/repos/builtin/packages/randfold/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/random123/package.py b/var/spack/repos/builtin/packages/random123/package.py
index 978467b457..0274adcc5d 100644
--- a/var/spack/repos/builtin/packages/random123/package.py
+++ b/var/spack/repos/builtin/packages/random123/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/randrproto/package.py b/var/spack/repos/builtin/packages/randrproto/package.py
index 24f6aaed41..151ada479e 100644
--- a/var/spack/repos/builtin/packages/randrproto/package.py
+++ b/var/spack/repos/builtin/packages/randrproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Randrproto(AutotoolsPackage):
 
     version('1.5.0', '863d6ee3e0b2708f75d968470ed31eb9')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/range-v3/package.py b/var/spack/repos/builtin/packages/range-v3/package.py
new file mode 100644
index 0000000000..e3d226a741
--- /dev/null
+++ b/var/spack/repos/builtin/packages/range-v3/package.py
@@ -0,0 +1,40 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RangeV3(CMakePackage):
+    """Range library for C++11/14/17"""
+
+    homepage = "https://github.com/ericniebler/range-v3"
+    url      = "https://github.com/ericniebler/range-v3/archive/0.3.6.tar.gz"
+    git      = "https://github.com/ericniebler/range-v3.git"
+
+    version('develop', branch='master')
+    version('0.3.6', sha256='ce6e80c6b018ca0e03df8c54a34e1fd04282ac1b068cd39e902e2e5201ac117f')
+    version('0.3.5', sha256='0a0094b450fe17e1454468bef5b6bf60e73ef100aebe1663daf6fbdf2c353836')
+    version('0.3.0', sha256='cc29fbed5b06b11e7f9a732f7e1211483ebbd3cfe29d86e40c93209014790d74')
+    version('0.2.6', sha256='b1b448ead59bd726248bcb607b4a47335a00bed1c74630e09d550da3ff72d02c')
+    version('0.2.5', sha256='4125089da83dec3f0ed676066f0cf583fe55dd9270bc62f1736907f57656ca7e')
+    version('0.2.4', sha256='6fc4f9e80ee8eb22302db45c5648c665817aeeeee7f99b7effdf6a38a1be9a75')
+    version('0.2.3', sha256='214a3f0ea70d479ca58f0af8938de49a9ed476564213431ab3b8e02a849b8098')
+    version('0.2.2', sha256='01a7bee222570a55a79c84a54b2997ed718dac06f43a82122ff0150a11477f9d')
+    version('0.2.1', sha256='25d5e3dad8052d668873e960bd78f068bebfba3bd28a278f805ea386f9438790')
+    version('0.2.0', sha256='49b1a62a7a36dab582521c8034d8e736a8922af664d007c1529d3162b1294331')
+
+    variant('cxxstd',
+            default='11',
+            values=('11', '14', '17'),
+            multi=False,
+            description='Use the specified C++ standard when building.')
+
+    depends_on('cmake@3.6:', type='build')
+
+    def cmake_args(self):
+        args = [
+            '-DRANGES_CXX_STD={0}'.format(self.spec.variants['cxxstd'].value)
+        ]
+        return args
diff --git a/var/spack/repos/builtin/packages/rankstr/package.py b/var/spack/repos/builtin/packages/rankstr/package.py
new file mode 100644
index 0000000000..3334b8deeb
--- /dev/null
+++ b/var/spack/repos/builtin/packages/rankstr/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Rankstr(CMakePackage):
+    """Assign one-to-one mapping of MPI ranks to strings"""
+
+    homepage = "https://github.com/ECP-VeloC/rankstr"
+    url      = "https://github.com/ECP-VeloC/rankstr/archive/v0.0.1.zip"
+    git      = "https://github.com/ecp-veloc/rankstr.git"
+
+    tags = ['ecp']
+
+    version('master', branch='master')
+    version('0.0.2', sha256='c16d53aa9bb79934cbe2dcd8612e2db7d59de80be500c104e39e8623d4eacd8e')
+
+    depends_on('mpi')
+
+    def cmake_args(self):
+        args = []
+        args.append("-DMPI_C_COMPILER=%s" % self.spec['mpi'].mpicc)
+        if self.spec.satisfies('platform=cray'):
+            args.append("-DRANKSTR_LINK_STATIC=ON")
+        return args
diff --git a/var/spack/repos/builtin/packages/rapidjson/package.py b/var/spack/repos/builtin/packages/rapidjson/package.py
new file mode 100644
index 0000000000..33d616cb2a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/rapidjson/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Rapidjson(CMakePackage):
+    """A fast JSON parser/generator for C++ with both SAX/DOM style API"""
+
+    homepage = "http://rapidjson.org"
+    url      = "https://github.com/Tencent/rapidjson/archive/v1.1.0.tar.gz"
+
+    version('1.1.0', 'badd12c511e081fec6c89c43a7027bce')
+    version('1.0.2', '97cc60d01282a968474c97f60714828c')
+    version('1.0.1', '48cc188df49617b859d13d31344a50b8')
+    version('1.0.0', '08247fbfa464d7f15304285f04b4b228')
diff --git a/var/spack/repos/builtin/packages/ravel/package.py b/var/spack/repos/builtin/packages/ravel/package.py
index 3f03444f76..7a2f53ea4d 100644
--- a/var/spack/repos/builtin/packages/ravel/package.py
+++ b/var/spack/repos/builtin/packages/ravel/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/raxml/package.py b/var/spack/repos/builtin/packages/raxml/package.py
index 96d6f7c95b..edb781eb80 100644
--- a/var/spack/repos/builtin/packages/raxml/package.py
+++ b/var/spack/repos/builtin/packages/raxml/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
 
@@ -51,6 +32,9 @@ class Raxml(Package):
     conflicts('%xl')
     conflicts('%xl_r')
 
+    # can't build multiple binaries in parallel without things breaking
+    parallel = False
+
     def install(self, spec, prefix):
         mkdirp(prefix.bin)
         files = glob.iglob("Makefile.*")
@@ -62,46 +46,45 @@ class Raxml(Package):
             make('-f', 'Makefile.AVX.HYBRID.gcc')
             install('raxmlHPC-HYBRID-AVX', prefix.bin)
 
-        elif '+mpi' and '+sse' and '+pthreads' in spec:
+        if '+mpi' and '+sse' and '+pthreads' in spec:
             make('-f', 'Makefile.SSE3.HYBRID.gcc')
             install('raxmlHPC-HYBRID-SSE3', prefix.bin)
 
-        elif '+mpi' and '+pthreads' in spec:
+        if '+mpi' and '+pthreads' in spec:
             make('-f', 'Makefile.HYBRID.gcc')
             install('raxmlHPC-HYBRID', prefix.bin)
 
-        elif '+mpi' and '+avx' in spec:
+        if '+mpi' and '+avx' in spec:
             make('-f', 'Makefile.AVX.MPI.gcc')
             install('raxmlHPC-MPI-AVX', prefix.bin)
 
-        elif '+mpi' and '+sse' in spec:
+        if '+mpi' and '+sse' in spec:
             make('-f', 'Makefile.SSE3.MPI.gcc')
             install('raxmlHPC-MPI-SSE3', prefix.bin)
 
-        elif '+mpi' in spec:
+        if '+mpi' in spec:
             make('-f', 'Makefile.MPI.gcc')
             install('raxmlHPC-MPI', prefix.bin)
 
-        elif '+pthreads' and '+avx' in spec:
+        if '+pthreads' and '+avx' in spec:
             make('-f', 'Makefile.AVX.PTHREADS.gcc')
             install('raxmlHPC-PTHREADS-AVX', prefix.bin)
 
-        elif '+pthreads' and '+sse' in spec:
+        if '+pthreads' and '+sse' in spec:
             make('-f', 'Makefile.SSE3.PTHREADS.gcc')
             install('raxmlHPC-PTHREADS-SSE3', prefix.bin)
 
-        elif '+pthreads' in spec:
+        if '+pthreads' in spec:
             make('-f', 'Makefile.PTHREADS.gcc')
             install('raxmlHPC-PTHREADS', prefix.bin)
 
-        elif '+sse' in spec:
+        if '+sse' in spec:
             make('-f', 'Makefile.SSE3.gcc')
             install('raxmlHPC-SSE3', prefix.bin)
 
-        elif '+avx' in spec:
+        if '+avx' in spec:
             make('-f', 'Makefile.AVX.gcc')
             install('raxmlHPC-AVX', prefix.bin)
 
-        else:
-            make('-f', 'Makefile.gcc')
-            install('raxmlHPC', prefix.bin)
+        make('-f', 'Makefile.gcc')
+        install('raxmlHPC', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/ray/package.py b/var/spack/repos/builtin/packages/ray/package.py
index 45e08c74ff..f8d3c0f1b1 100644
--- a/var/spack/repos/builtin/packages/ray/package.py
+++ b/var/spack/repos/builtin/packages/ray/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/rclone/package.py b/var/spack/repos/builtin/packages/rclone/package.py
new file mode 100644
index 0000000000..ae8a1d2c26
--- /dev/null
+++ b/var/spack/repos/builtin/packages/rclone/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Rclone(Package):
+    """Rclone is a command line program to sync files and directories
+       to and from various cloud storage providers"""
+
+    homepage = "http://rclone.org"
+    url      = "https://github.com/ncw/rclone/releases/download/v1.43/rclone-v1.43.tar.gz"
+
+    version('1.43', sha256='d30527b00cecb4e5e7188dddb78e5cec62d67cf2422dab82190db58512b5a4e3')
+
+    depends_on("go", type='build')
+
+    def install(self, spec, prefix):
+        go('build')
+        mkdirp(prefix.bin)
+        install('rclone', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/rdma-core/package.py b/var/spack/repos/builtin/packages/rdma-core/package.py
new file mode 100644
index 0000000000..37138e9203
--- /dev/null
+++ b/var/spack/repos/builtin/packages/rdma-core/package.py
@@ -0,0 +1,32 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RdmaCore(CMakePackage):
+    """RDMA core userspace libraries and daemons"""
+
+    homepage = "https://github.com/linux-rdma/rdma-core"
+    url      = "https://github.com/linux-rdma/rdma-core/releases/download/v17.1/rdma-core-17.1.tar.gz"
+
+    version('20', sha256='bc846989f807cd2b03643927d2b99fbf6f849cb1e766ab49bc9e81ce769d5421')
+    version('17.1', sha256='b47444b7c05d3906deb8771eec3e634984dd83f5e620d5e37d3a83f74f0cc1ba')
+    version('13', sha256='e5230fd7cda610753ad1252b40a28b1e9cf836423a10d8c2525b081527760d97')
+
+    depends_on('pkgconfig', type='build')
+    depends_on('libnl')
+    conflicts('platform=darwin', msg='rdma-core requires FreeBSD or Linux')
+    conflicts('%intel', msg='rdma-core cannot be built with intel (use gcc instead)')
+
+# NOTE: specify CMAKE_INSTALL_RUNDIR explicitly to prevent rdma-core from
+#       using the spack staging build dir (which may be a very long file
+#       system path) as a component in compile-time static strings such as
+#       IBACM_SERVER_PATH.
+    def cmake_args(self):
+        cmake_args = ["-DCMAKE_INSTALL_SYSCONFDIR=" +
+                      self.spec.prefix.etc,
+                      "-DCMAKE_INSTALL_RUNDIR=/var/run"]
+        return cmake_args
diff --git a/var/spack/repos/builtin/packages/rdp-classifier/package.py b/var/spack/repos/builtin/packages/rdp-classifier/package.py
index 637e490a17..b17e926066 100644
--- a/var/spack/repos/builtin/packages/rdp-classifier/package.py
+++ b/var/spack/repos/builtin/packages/rdp-classifier/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/re2c/package.py b/var/spack/repos/builtin/packages/re2c/package.py
new file mode 100644
index 0000000000..596c03cc29
--- /dev/null
+++ b/var/spack/repos/builtin/packages/re2c/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+#
+from spack import *
+
+
+class Re2c(AutotoolsPackage):
+    """re2c: a free and open-source lexer generator for C and C++"""
+
+    homepage = "http://re2c.org/index.html"
+    url      = "https://github.com/skvadrik/re2c/releases/download/1.0.3/re2c-1.0.3.tar.gz"
+
+    version('1.0.3', '8f575e2bf2efd3c685c87042f279ae4f')
+
+    def configure_args(self):
+        args = ['--disable-dependency-tracking']
+        return args
diff --git a/var/spack/repos/builtin/packages/readfq/package.py b/var/spack/repos/builtin/packages/readfq/package.py
new file mode 100644
index 0000000000..28ee9225aa
--- /dev/null
+++ b/var/spack/repos/builtin/packages/readfq/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Readfq(Package):
+    """Readfq is a collection of routines for parsing the FASTA/FASTQ format.
+    It seamlessly parses both FASTA and multi-line FASTQ with a simple
+    interface."""
+
+    homepage = "https://github.com/lh3/readfq"
+    git      = "https://github.com/lh3/readfq.git"
+
+    version('2013.04.10', commit='4fb766095d8f459e0f8025be70f9173673905d12')
+
+    def install(self, spec, prefix):
+        install_tree('.', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/readline/package.py b/var/spack/repos/builtin/packages/readline/package.py
index ccdea0aa0f..156a7d429b 100644
--- a/var/spack/repos/builtin/packages/readline/package.py
+++ b/var/spack/repos/builtin/packages/readline/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,7 +15,7 @@ class Readline(AutotoolsPackage):
     csh-like history expansion on previous commands."""
 
     homepage = "http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html"
-    url      = "https://ftp.gnu.org/gnu/readline/readline-7.0.tar.gz"
+    url      = "https://ftpmirror.gnu.org/readline/readline-7.0.tar.gz"
 
     version('7.0', '205b03a87fc83dab653b628c59b9fc91')
     version('6.3', '33c8fb279e981274f485fd91da77e94a')
diff --git a/var/spack/repos/builtin/packages/recordproto/package.py b/var/spack/repos/builtin/packages/recordproto/package.py
index dcbc0326e8..737d6e3ffb 100644
--- a/var/spack/repos/builtin/packages/recordproto/package.py
+++ b/var/spack/repos/builtin/packages/recordproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Recordproto(AutotoolsPackage):
 
     version('1.14.2', '868235e1e150e68916d5a316ebc4ccc4')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/redset/package.py b/var/spack/repos/builtin/packages/redset/package.py
new file mode 100644
index 0000000000..3514a9bbf1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/redset/package.py
@@ -0,0 +1,32 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Redset(CMakePackage):
+    """Create MPI communicators for disparate redundancy sets"""
+
+    homepage = "https://github.com/ECP-VeloC/redset"
+    url      = "https://github.com/ECP-VeloC/redset/archive/v0.0.2.zip"
+    git      = "https://github.com/ecp-veloc/redset.git"
+
+    tags = ['ecp']
+
+    version('master', branch='master')
+    version('0.0.3', sha256='f110c9b42209d65f84a8478b919b27ebe2d566839cb0cd0c86ccbdb1f51598f4')
+
+    depends_on('mpi')
+    depends_on('rankstr')
+    depends_on('kvtree+mpi')
+
+    def cmake_args(self):
+        args = []
+        args.append("-DMPI_C_COMPILER=%s" % self.spec['mpi'].mpicc)
+        if self.spec.satisfies('platform=cray'):
+            args.append("-DREDSET_LINK_STATIC=ON")
+        args.append("-DWITH_KVTREE_PREFIX=%s" % self.spec['kvtree'].prefix)
+        args.append("-DWITH_RANKSTR_PREFIX=%s" % self.spec['rankstr'].prefix)
+        return args
diff --git a/var/spack/repos/builtin/packages/redundans/package.py b/var/spack/repos/builtin/packages/redundans/package.py
index 71f83f623a..17aed51ee1 100644
--- a/var/spack/repos/builtin/packages/redundans/package.py
+++ b/var/spack/repos/builtin/packages/redundans/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,16 +17,22 @@ class Redundans(Package):
     depends_on('python', type=('build', 'run'))
     depends_on('py-pyscaf', type=('build', 'run'))
     depends_on('py-fastaindex', type=('build', 'run'))
+    depends_on('py-numpy', type=('build', 'run'))
     depends_on('perl', type=('build', 'run'))
     depends_on('sspace-standard')
     depends_on('bwa')
     depends_on('last')
     depends_on('gapcloser')
     depends_on('parallel')
-    depends_on('snap-berkeley')
+    depends_on('snap-berkeley@1.0beta.18:', type=('build', 'run'))
 
     def install(self, spec, prefix):
+        sspace_location = join_path(spec['sspace-standard'].prefix,
+                                    'SSPACE_Standard_v3.0.pl')
         mkdirp(prefix.bin)
+        filter_file(r'sspacebin = os.path.join(.*)$',
+                    'sspacebin = \'' + sspace_location + '\'',
+                    'redundans.py')
         install('redundans.py', prefix.bin)
         with working_dir('bin'):
             install('fasta2homozygous.py', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/regcm/package.py b/var/spack/repos/builtin/packages/regcm/package.py
new file mode 100644
index 0000000000..32fde4885b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/regcm/package.py
@@ -0,0 +1,73 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Regcm(AutotoolsPackage):
+    """RegCM ICTP Regional Climate Model."""
+
+    homepage = 'https://gforge.ictp.it/gf/project/regcm/'
+
+    version('4.7.0', sha256='456631c10dcb83d70e51c3babda2f7a1aa41ed9e60cb4209deb3764655267519',
+            url='https://gforge.ictp.it/gf/download/frsrelease/259/1845/RegCM-4.7.0.tar.gz')
+
+    variant('debug', default=False,
+            description='Build RegCM using debug options.')
+    variant('profile', default=False,
+            description='Build RegCM using profiling options.')
+    variant('singleprecision', default=False,
+            description='Build RegCM using single precision float type.')
+
+    # On Intel and PGI compilers, multiple archs can be built at the same time,
+    # producing a so-called fat binary. Unfortunately, gcc builds only the last
+    # architecture provided (in the configure), so we allow a single arch.
+    extensions = ('knl', 'skl', 'bdw', 'nhl')
+    variant('extension', default=None, values=extensions, multi=True,
+            description='Build extensions for a specific Intel architecture.')
+
+    depends_on('netcdf')
+    depends_on('netcdf-fortran')
+    depends_on('hdf5')
+    depends_on('mpi')
+
+    # 'make' sometimes crashes when compiling with more than 10-12 cores.
+    # Moreover, parallel compile time is ~ 1m 30s, while serial is ~ 50s.
+    parallel = False
+
+    def flag_handler(self, name, flags):
+        if name == 'fflags' and self.compiler.fc.endswith('gfortran'):
+            flags.extend(['-Wall', '-Wextra', '-Warray-temporaries',
+                          '-Wconversion', '-fimplicit-none', '-fbacktrace',
+                          '-ffree-line-length-0', '-finit-real=nan',
+                          '-ffpe-trap=zero,overflow,underflow', '-fcheck=all'])
+
+        elif name == 'ldlibs':
+            flags.extend(['-lnetcdff', '-lnetcdf'])
+            if self.compiler.fc.endswith('gfortran'):
+                flags.extend(['-lm', '-ldl'])
+            else:
+                flags.extend(['-lhdf5_hl', '-lhdf5', '-lz'])
+
+        return (None, None, flags)
+
+    def configure_args(self):
+        args = ['--enable-shared']
+
+        for opt in ('debug', 'profile', 'singleprecision'):
+            if '+{0}'.format(opt) in self.spec:
+                args.append('--enable-' + opt)
+
+        for ext in self.extensions:
+            if 'extension={0}'.format(ext) in self.spec:
+                args.append('--enable-' + ext)
+                break
+
+        # RegCM complains when compiled with gfortran, and unfortunately FFLAGS
+        # is ignored by the configure, so we need to set the option in FCFLAGS.
+        if self.compiler.fc.endswith('gfortran'):
+            args.append('FCFLAGS=-fno-range-check')
+
+        return args
diff --git a/var/spack/repos/builtin/packages/relion/package.py b/var/spack/repos/builtin/packages/relion/package.py
index ba006b9b43..eb092b6fa1 100644
--- a/var/spack/repos/builtin/packages/relion/package.py
+++ b/var/spack/repos/builtin/packages/relion/package.py
@@ -1,56 +1,59 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class Relion(CMakePackage):
+class Relion(CMakePackage, CudaPackage):
     """RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a
     stand-alone computer program that employs an empirical Bayesian approach to
     refinement of (multiple) 3D reconstructions or 2D class averages in
     electron cryo-microscopy (cryo-EM)."""
 
     homepage = "http://http://www2.mrc-lmb.cam.ac.uk/relion"
-    url      = "https://github.com/3dem/relion"
+    git      = "https://github.com/3dem/relion.git"
 
-    version('develop', git='https://github.com/3dem/relion.git')
+    version('3.0_beta',
+            git='https://bitbucket.org/scheres/relion-3.0_beta.git')
+    version('2.1', preferred='true', tag='2.1')
+    version('2.0.3', tag='2.0.3')
+    # relion has no develop branch though pulling from master
+    # should be considered the same as develop
+    version('develop', branch='master')
 
     variant('gui', default=True, description="build the gui")
-    variant('cuda', default=False, description="enable compute on gpu")
-    variant('double', default=False, description="double precision (cpu) code")
-    variant('double-gpu', default=False, description="double precision (gpu) code")
+    variant('cuda', default=True, description="enable compute on gpu")
+    variant('double', default=True, description="double precision (cpu) code")
+    variant('double-gpu', default=False, description="double precision gpu")
+    # if built with purpose=cluster then relion will link to gpfs libraries
+    # if that's not desirable then use purpose=desktop
+    variant('purpose', default='cluster', values=('cluster', 'desktop'),
+            description="build relion for use in cluster or desktop")
     variant('build_type', default='RelWithDebInfo',
             description='The build type to build',
             values=('Debug', 'Release', 'RelWithDebInfo',
                     'Profiling', 'Benchmarking'))
 
     depends_on('mpi')
+    # relion will not build with newer versions of cmake
+    # per https://github.com/3dem/relion/issues/380
+    depends_on('cmake@3:3.9.4', type='build')
     depends_on('fftw+float+double')
     depends_on('fltk', when='+gui')
-    depends_on('cuda@8.0:8.99', when='+cuda')
+    depends_on('libtiff')
+
+    # relion 3 supports cuda 9
+    # relion < 3 does not
+    depends_on('cuda', when='+cuda')
+    depends_on('cuda@9:', when='@3: +cuda')
+    depends_on('cuda@8.0:8.99', when='@:2 +cuda')
 
     def cmake_args(self):
+
+        carch = self.spec.variants['cuda_arch'].value[0]
+
         args = [
             '-DCMAKE_C_FLAGS=-g',
             '-DCMAKE_CXX_FLAGS=-g',
@@ -58,9 +61,18 @@ class Relion(CMakePackage):
             '-DDoublePrec_CPU=%s' % ('+double' in self.spec),
             '-DDoublePrec_GPU=%s' % ('+double-gpu' in self.spec),
         ]
+
         if '+cuda' in self.spec:
-            args += [
-                '-DCUDA=on',
-                '-DCUFFT=on',
-            ]
+            # relion+cuda requires selecting cuda_arch
+            if not carch:
+                raise ValueError("select cuda_arch when building with +cuda")
+            else:
+                args += ['-DCUDA=ON', '-DCudaTexture=ON',
+                         '-DCUDA_ARCH=%s' % (carch)]
+
+        # these new values were added in relion 3
+        # do not seem to cause problems with < 3
+        else:
+            args += ['-DMKLFFT=ON', '-DFORCE_OWN_TBB=ON', '-DALTCPU=ON']
+
         return args
diff --git a/var/spack/repos/builtin/packages/rempi/package.py b/var/spack/repos/builtin/packages/rempi/package.py
index f6e2a2f3e5..d3559fe6a0 100644
--- a/var/spack/repos/builtin/packages/rempi/package.py
+++ b/var/spack/repos/builtin/packages/rempi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,6 +11,7 @@ class Rempi(AutotoolsPackage):
     homepage = "https://github.com/PRUNERS/ReMPI"
     url      = "https://github.com/PRUNERS/ReMPI/releases/download/v1.0.0/ReMPI-1.0.0.tar.gz"
 
+    version("1.1.0", "05b872a6f3e2f49a2fc6112a844c7f43")
     version("1.0.0", "32c780a6a74627b5796bea161d4c4733")
 
     depends_on("mpi")
diff --git a/var/spack/repos/builtin/packages/rename/package.py b/var/spack/repos/builtin/packages/rename/package.py
index 01bc35f073..dfdaa31027 100644
--- a/var/spack/repos/builtin/packages/rename/package.py
+++ b/var/spack/repos/builtin/packages/rename/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/rendercheck/package.py b/var/spack/repos/builtin/packages/rendercheck/package.py
index 65fcc7a312..ea66f66c0b 100644
--- a/var/spack/repos/builtin/packages/rendercheck/package.py
+++ b/var/spack/repos/builtin/packages/rendercheck/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Rendercheck(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/renderproto/package.py b/var/spack/repos/builtin/packages/renderproto/package.py
index a6c91ab06b..ded178b5bb 100644
--- a/var/spack/repos/builtin/packages/renderproto/package.py
+++ b/var/spack/repos/builtin/packages/renderproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Renderproto(AutotoolsPackage):
 
     version('0.11.1', '9b103359123e375bb7760f7dbae3dece')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/repeatmasker/package.py b/var/spack/repos/builtin/packages/repeatmasker/package.py
index c9713c7892..63d680c2e1 100644
--- a/var/spack/repos/builtin/packages/repeatmasker/package.py
+++ b/var/spack/repos/builtin/packages/repeatmasker/package.py
@@ -1,30 +1,10 @@
-##############################################################################
-# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import inspect
-import distutils.dir_util
 
 
 class Repeatmasker(Package):
@@ -37,6 +17,7 @@ class Repeatmasker(Package):
     version('4.0.7', '4dcbd7c88c5343e02d819f4b3e6527c6')
 
     depends_on('perl', type=('build', 'run'))
+    depends_on('perl-text-soundex', type=('build', 'run'))
     depends_on('hmmer')
     depends_on('ncbi-rmblastn')
     depends_on('trf')
@@ -63,7 +44,7 @@ class Repeatmasker(Package):
         #    Repeatmasker? (Y/N)
         # Add a Search Engine: Done
 
-        config_answers = ['\n', '%s\n' % self.spec['perl'].prefix.bin.perl,
+        config_answers = ['\n', '%s\n' % self.spec['perl'].command.path,
                           '%s\n' % self.stage.source_path,
                           '%s\n' % self.spec['trf'].prefix.bin.trf, '2\n',
                           '%s\n' % self.spec['ncbi-rmblastn'].prefix.bin,
@@ -77,4 +58,4 @@ class Repeatmasker(Package):
         with open(config_answers_filename, 'r') as f:
             inspect.getmodule(self).perl('configure', input=f)
 
-        distutils.dir_util.copy_tree(".", prefix)
+        install_tree('.', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/resourceproto/package.py b/var/spack/repos/builtin/packages/resourceproto/package.py
index 4e58ae7f00..98f126f5d9 100644
--- a/var/spack/repos/builtin/packages/resourceproto/package.py
+++ b/var/spack/repos/builtin/packages/resourceproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Resourceproto(AutotoolsPackage):
 
     version('1.2.0', '33091d5358ec32dd7562a1aa225a70aa')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/revbayes/package.py b/var/spack/repos/builtin/packages/revbayes/package.py
index 1ebbec534b..9eb3674b39 100644
--- a/var/spack/repos/builtin/packages/revbayes/package.py
+++ b/var/spack/repos/builtin/packages/revbayes/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/rgb/package.py b/var/spack/repos/builtin/packages/rgb/package.py
index 2b09a2c4a5..f0aa44b75c 100644
--- a/var/spack/repos/builtin/packages/rgb/package.py
+++ b/var/spack/repos/builtin/packages/rgb/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/rhash/package.py b/var/spack/repos/builtin/packages/rhash/package.py
index c2191f1f07..6ea3a56a0b 100644
--- a/var/spack/repos/builtin/packages/rhash/package.py
+++ b/var/spack/repos/builtin/packages/rhash/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import glob
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/rlwrap/package.py b/var/spack/repos/builtin/packages/rlwrap/package.py
new file mode 100644
index 0000000000..6378e6b45d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/rlwrap/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Rlwrap(AutotoolsPackage):
+    """rlwrap is a 'readline wrapper', a small utility that uses the GNU
+    readline library to allow the editing of keyboard input for any command."""
+
+    homepage = "https://github.com/hanslub42/rlwrap"
+    url      = "https://github.com/hanslub42/rlwrap/releases/download/v0.43/rlwrap-0.43.tar.gz"
+
+    version('0.43', 'b993e83d3a292464de70719b32f83a34')
+
+    depends_on('readline@4.2:')
diff --git a/var/spack/repos/builtin/packages/rmats/package.py b/var/spack/repos/builtin/packages/rmats/package.py
new file mode 100644
index 0000000000..990d5a8f77
--- /dev/null
+++ b/var/spack/repos/builtin/packages/rmats/package.py
@@ -0,0 +1,32 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+from os import symlink
+
+
+class Rmats(Package):
+    """MATS is a computational tool to detect differential alternative
+       splicing events from RNA-Seq data."""
+
+    homepage = "https://rnaseq-mats.sourceforge.net/index.html"
+    url      = "https://downloads.sourceforge.net/project/rnaseq-mats/MATS/rMATS.4.0.2.tgz"
+
+    version('4.0.2', sha256='afab002a9ae836d396909aede96318f6dab6e5818078246419dd563624bf26d1')
+
+    depends_on('python@2.7:', type='run')
+    depends_on('py-numpy', type=('build', 'run'))
+    depends_on('openblas')
+
+    def install(self, spec, prefix):
+        # since the tool is a python script we install it to /usr/lib
+        install_tree('rMATS-turbo-Linux-UCS4', join_path(prefix.lib, 'rmats'))
+
+        # the script has an appropriate shebang so a quick symlink will do
+        set_executable(join_path(prefix.lib, 'rmats/rmats.py'))
+        mkdirp(prefix.bin)
+        symlink(join_path(prefix.lib, 'rmats/rmats.py'),
+                join_path(prefix.bin, 'rmats'))
diff --git a/var/spack/repos/builtin/packages/rmlab/package.py b/var/spack/repos/builtin/packages/rmlab/package.py
new file mode 100644
index 0000000000..5304bf0d09
--- /dev/null
+++ b/var/spack/repos/builtin/packages/rmlab/package.py
@@ -0,0 +1,38 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Rmlab(CMakePackage):
+    """C++ File API for the reMarkable tablet"""
+
+    homepage = "https://github.com/ax3l/lines-are-beautiful"
+    git      = "https://github.com/ax3l/lines-are-beautiful.git"
+
+    maintainers = ['ax3l']
+
+    version('develop', branch='develop')
+
+    variant('png', default=True,
+            description='Enable PNG conversion support')
+
+    # modern CMake
+    depends_on('cmake@3.7.0:', type='build')
+    # C++11
+    conflicts('%gcc@:4.7')
+    conflicts('%intel@:15')
+    conflicts('%pgi@:14')
+
+    depends_on('pngwriter@0.6.0:', when='+png')
+
+    def cmake_args(self):
+        spec = self.spec
+
+        args = [
+            '-DRmlab_USE_PNG={0}'.format(
+                'ON' if '+png' in spec else 'OFF')
+        ]
+        return args
diff --git a/var/spack/repos/builtin/packages/rna-seqc/package.py b/var/spack/repos/builtin/packages/rna-seqc/package.py
new file mode 100644
index 0000000000..38fbf7c474
--- /dev/null
+++ b/var/spack/repos/builtin/packages/rna-seqc/package.py
@@ -0,0 +1,43 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os.path
+
+
+class RnaSeqc(Package):
+    """RNA-SeQC is a java program which computes a series of quality control
+    metrics for RNA-seq data."""
+
+    homepage = "http://archive.broadinstitute.org/cancer/cga/rna-seqc"
+    url      = "http://www.broadinstitute.org/cancer/cga/tools/rnaseqc/RNA-SeQC_v1.1.8.jar"
+
+    version('1.1.8', '71d7b5d3b3dcc1893cdc7f6819185d41', expand=False)
+    version('1.1.7', '2d0b8ecac955af2f9bc1b185fdfb6b45', expand=False)
+    version('1.1.6', 'fa9c9885081ae2e47f285c7c0f596a14', expand=False)
+    version('1.1.5', '4b875671e906f708cbb8fd9bcf0e958d', expand=False)
+    version('1.1.4', 'b04d06947c48cb2dc1b0ba29c8232db5', expand=False)
+
+    depends_on('jdk@8:', type='run')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        jar_file = 'RNA-SeQC_v{0}.jar'.format(self.version.dotted)
+        install(jar_file, prefix.bin)
+
+        # Set up a helper script to call java on the jar file,
+        # explicitly codes the path for java and the jar file.
+        script_sh = join_path(os.path.dirname(__file__), "rna-seqc.sh")
+        script = join_path(prefix.bin, "rna-seqc")
+        install(script_sh, script)
+        set_executable(script)
+
+        # Munge the helper script to explicitly point to java and the
+        # jar file.
+        java = self.spec['jdk'].prefix.bin.java
+        kwargs = {'ignore_absent': False, 'backup': False, 'string': False}
+        filter_file('^java', java, script, **kwargs)
+        filter_file('RNA-SeQC_v{0}.jar', join_path(prefix.bin, jar_file),
+                    script, **kwargs)
diff --git a/var/spack/repos/builtin/packages/rna-seqc/rna-seqc.sh b/var/spack/repos/builtin/packages/rna-seqc/rna-seqc.sh
new file mode 100644
index 0000000000..c1d8d7c2e7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/rna-seqc/rna-seqc.sh
@@ -0,0 +1,3 @@
+#!/bin/sh
+# convenience wrapper for the rna-seqc jar file
+java $JAVA_ARGS $JAVA_OPTS -jar RNA-SeQC_v{}.jar "$@"
diff --git a/var/spack/repos/builtin/packages/rngstreams/package.py b/var/spack/repos/builtin/packages/rngstreams/package.py
new file mode 100644
index 0000000000..7168d0c400
--- /dev/null
+++ b/var/spack/repos/builtin/packages/rngstreams/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Rngstreams(AutotoolsPackage):
+    """Multiple independent streams of pseudo-random numbers."""
+
+    homepage = "http://statmath.wu.ac.at/software/RngStreams"
+    url      = "http://statmath.wu.ac.at/software/RngStreams/rngstreams-1.0.1.tar.gz"
+
+    version('1.0.1', '6d9d842247cd1d4e9e60440406858a69')
diff --git a/var/spack/repos/builtin/packages/rockstar/package.py b/var/spack/repos/builtin/packages/rockstar/package.py
index 2f8bfdc804..fc9a0fa76d 100644
--- a/var/spack/repos/builtin/packages/rockstar/package.py
+++ b/var/spack/repos/builtin/packages/rockstar/package.py
@@ -1,38 +1,16 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 import os
 from spack import *
-from distutils.dir_util import copy_tree
 
 
 class Rockstar(MakefilePackage):
     """The Rockstar Halo Finder"""
 
     homepage = "https://bitbucket.org/gfcstanford/rockstar"
-    url      = "https://bitbucket.org/gfcstanford/rockstar"
 
     version('develop', git='https://bitbucket.org/gfcstanford/rockstar.git')
     version('yt', hg='https://bitbucket.org/MatthewTurk/rockstar')
@@ -60,7 +38,7 @@ class Rockstar(MakefilePackage):
 
     def install(self, spec, prefix):
         # Install all files and directories
-        copy_tree(".", prefix)
+        install_tree('.', prefix)
 
         mkdir(prefix.bin)
         mkdir(prefix.lib)
diff --git a/var/spack/repos/builtin/packages/root/package.py b/var/spack/repos/builtin/packages/root/package.py
index a003d3d5e2..91da3fc582 100644
--- a/var/spack/repos/builtin/packages/root/package.py
+++ b/var/spack/repos/builtin/packages/root/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 import sys
@@ -53,7 +34,7 @@ class Root(CMakePackage):
     variant('graphviz', default=False, description='Enable graphviz support')
 
     depends_on('cmake@3.4.3:', type='build')
-    depends_on('pkg-config',   type='build')
+    depends_on('pkgconfig',   type='build')
 
     depends_on('binutils')
     depends_on('zlib')
diff --git a/var/spack/repos/builtin/packages/rose/package.py b/var/spack/repos/builtin/packages/rose/package.py
index 8a7f22cf97..537c30f2d4 100644
--- a/var/spack/repos/builtin/packages/rose/package.py
+++ b/var/spack/repos/builtin/packages/rose/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 # -----------------------------------------------------------------------------
 # Author: Justin Too <too1@llnl.gov>
 # -----------------------------------------------------------------------------
@@ -35,11 +16,11 @@ class Rose(Package):
        (Developed at Lawrence Livermore National Lab)"""
 
     homepage = "http://rosecompiler.org/"
-    url = "https://github.com/rose-compiler/rose/archive/v0.9.7.tar.gz"
+    url      = "https://github.com/rose-compiler/rose/archive/v0.9.7.tar.gz"
+    git      = "https://github.com/rose-compiler/rose.git"
 
+    version('master', branch='master')
     version('0.9.7', 'e14ce5250078df4b09f4f40559d46c75')
-    version('master', branch='master',
-            git='https://github.com/rose-compiler/rose.git')
 
     patch('add_spack_compiler_recognition.patch')
 
diff --git a/var/spack/repos/builtin/packages/ross/package.py b/var/spack/repos/builtin/packages/ross/package.py
new file mode 100644
index 0000000000..95b2f6a571
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ross/package.py
@@ -0,0 +1,30 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Ross(CMakePackage):
+    """Rensselaer Optimistic Simulation System"""
+
+    homepage = "http://carothersc.github.io/ROSS/"
+    git      = "https://github.com/carothersc/ROSS.git"
+
+    version('develop', branch='master')
+    version('7.0.0', tag='v7.0.0')
+
+    depends_on('mpi')
+
+    def cmake_args(self):
+        if 'x86_64' not in self.spec.architecture:
+            raise InstallError(
+                'This package currently only builds on x86_64 architectures')
+
+        args = ["-DBUILD_SHARED_LIBS=ON",
+                "-DARCH=x86_64",
+                "-DCMAKE_C_COMPILER=%s" % self.spec['mpi'].mpicc,
+                "-DCMAKE_CXX_COMPILER=%s" % self.spec['mpi'].mpicxx]
+
+        return args
diff --git a/var/spack/repos/builtin/packages/rr/package.py b/var/spack/repos/builtin/packages/rr/package.py
index 245744a6fa..2c5ed168a0 100644
--- a/var/spack/repos/builtin/packages/rr/package.py
+++ b/var/spack/repos/builtin/packages/rr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,8 +20,8 @@ class Rr(CMakePackage):
     depends_on('zlib')
     # depends_on('capnproto', when='@4.6:')  # not yet in spack
     # depends_on('libcapnp')    # needed for future releases
-    depends_on('pkg-config', type='build')
-    depends_on('py-pexpect', type='build')  # actually tests
+    depends_on('pkgconfig', type='build')
+    depends_on('py-pexpect', type='test')
 
     # rr needs architecture Nehalem and beyond, how can spack
     # test this?
diff --git a/var/spack/repos/builtin/packages/rsbench/package.py b/var/spack/repos/builtin/packages/rsbench/package.py
index 91c8d6f71b..6f1595c02b 100644
--- a/var/spack/repos/builtin/packages/rsbench/package.py
+++ b/var/spack/repos/builtin/packages/rsbench/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/rsem/package.py b/var/spack/repos/builtin/packages/rsem/package.py
index 2d29610b20..8212c11427 100644
--- a/var/spack/repos/builtin/packages/rsem/package.py
+++ b/var/spack/repos/builtin/packages/rsem/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,7 +13,7 @@ class Rsem(MakefilePackage):
     homepage = "http://deweylab.github.io/RSEM/"
     url      = "https://github.com/deweylab/RSEM/archive/v1.3.0.tar.gz"
 
-    version('1.3.0', '9728161625d339d022130e2428604bf5')
+    version('1.3.0', '273fd755e23d349cc38a079b81bb03b6')
 
     depends_on('r', type=('build', 'run'))
     depends_on('perl', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/rstart/package.py b/var/spack/repos/builtin/packages/rstart/package.py
index 2a0cf59e81..d819274a9c 100644
--- a/var/spack/repos/builtin/packages/rstart/package.py
+++ b/var/spack/repos/builtin/packages/rstart/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Rstart(AutotoolsPackage):
     version('1.0.5', '32db3625cb5e841e17d6bc696f21edfb')
 
     depends_on('xproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/rsync/package.py b/var/spack/repos/builtin/packages/rsync/package.py
index 642f702ac0..d1f4384b6a 100644
--- a/var/spack/repos/builtin/packages/rsync/package.py
+++ b/var/spack/repos/builtin/packages/rsync/package.py
@@ -1,34 +1,16 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class Rsync(AutotoolsPackage):
     """An open source utility that provides fast incremental file transfer."""
     homepage = "https://rsync.samba.org"
-    url      = "https://download.samba.org/pub/rsync/rsync-3.1.1.tar.gz"
+    url      = "https://download.samba.org/pub/rsync/src/rsync-3.1.2.tar.gz"
 
+    version('3.1.3', '1581a588fde9d89f6bc6201e8129afaf')
     version('3.1.2', '0f758d7e000c0f7f7d3792610fad70cb')
     version('3.1.1', '43bd6676f0b404326eee2d63be3cdcfe')
diff --git a/var/spack/repos/builtin/packages/rtags/package.py b/var/spack/repos/builtin/packages/rtags/package.py
index 8e1a962209..d7d9b313dd 100644
--- a/var/spack/repos/builtin/packages/rtags/package.py
+++ b/var/spack/repos/builtin/packages/rtags/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,16 +10,17 @@ class Rtags(CMakePackage):
     """RTags is a client/server application that indexes C/C++ code"""
 
     homepage = "https://github.com/Andersbakken/rtags/"
-    url      = "https://andersbakken.github.io/rtags-releases/rtags-2.12.tar.gz"
+    url      = "https://andersbakken.github.io/rtags-releases/rtags-2.17.tar.gz"
 
-    version('2.12', '84988aaff27915a79d4b4b57299f9a51')
+    version('2.17', '95b24d7729678645a027d83be114d624')
+    # version('2.12', '84988aaff27915a79d4b4b57299f9a51')  # no available
 
     depends_on("llvm@3.3: +clang")
     depends_on("zlib")
     depends_on("openssl")
     depends_on("lua@5.3:")
     depends_on("bash-completion")
-    depends_on("pkg-config", type='build')
+    depends_on("pkgconfig", type='build')
 
     patch("add_string_iterator_erase_compile_check.patch", when='@2.12')
 
diff --git a/var/spack/repos/builtin/packages/rtax/package.py b/var/spack/repos/builtin/packages/rtax/package.py
index 3e359d7346..ead8371499 100644
--- a/var/spack/repos/builtin/packages/rtax/package.py
+++ b/var/spack/repos/builtin/packages/rtax/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/ruby-gnuplot/package.py b/var/spack/repos/builtin/packages/ruby-gnuplot/package.py
new file mode 100644
index 0000000000..a947c001aa
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ruby-gnuplot/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RubyGnuplot(Package):
+    """Utility library to aid in interacting with gnuplot from ruby"""
+
+    homepage = "https://rubygems.org/gems/gnuplot/versions/2.6.2"
+    url      = "https://rubygems.org/downloads/gnuplot-2.6.2.gem"
+
+    version('2.6.2', 'ff36a37cf71b9cd6273fcd14bbfd82df', expand=False)
+
+    depends_on('gnuplot+X')
+
+    extends('ruby')
+
+    def install(self, spec, prefix):
+        gem('install', 'gnuplot-{0}.gem'.format(self.version))
diff --git a/var/spack/repos/builtin/packages/ruby-narray/package.py b/var/spack/repos/builtin/packages/ruby-narray/package.py
new file mode 100644
index 0000000000..52f1db091f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ruby-narray/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RubyNarray(Package):
+    """Numo::NArray is an Numerical N-dimensional Array class for fast
+       processing and easy manipulation of multi-dimensional numerical data,
+       similar to numpy.ndaray."""
+
+    homepage = "https://rubygems.org/gems/narray"
+    git      = "https://github.com/ruby-numo/narray.git"
+
+    version('0.9.0.9', commit='9cadbbccf1e01b6d1bc143c19d598cad1c420869')
+
+    extends('ruby')
+
+    def install(self, spec, prefix):
+        gem('build', 'numo-narray.gemspec')
+        gem('install', 'numo-narray-{0}.gem'.format(self.version))
diff --git a/var/spack/repos/builtin/packages/ruby-ronn/package.py b/var/spack/repos/builtin/packages/ruby-ronn/package.py
new file mode 100644
index 0000000000..2637bcfc6a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ruby-ronn/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RubyRonn(Package):
+    """Ronn builds manuals. It converts simple, human readable textfiles to
+    roff for terminal display, and also to HTML for the web."""
+
+    homepage = "https://rubygems.org/gems/ronn"
+    url      = "https://github.com/rtomayko/ronn/archive/0.7.3.tar.gz"
+
+    version('0.7.3', '90cdedb42920c8c2a74e2d177e9535b6')
+    version('0.7.0', '34ad78510a75e46904629631f5335e06')
+
+    extends('ruby')
+
+    def install(self, spec, prefix):
+        gem('build', 'ronn.gemspec')
+        gem('install', 'ronn-{0}.gem'.format(self.version))
diff --git a/var/spack/repos/builtin/packages/ruby-rubyinline/package.py b/var/spack/repos/builtin/packages/ruby-rubyinline/package.py
new file mode 100644
index 0000000000..f3ab0cd49b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ruby-rubyinline/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RubyRubyinline(Package):
+    """Inline allows you to write foreign code within your ruby code."""
+
+    homepage = "https://rubygems.org/gems/RubyInline"
+    url      = "https://rubygems.org/downloads/RubyInline-3.12.4.gem"
+
+    version('3.12.4', '3058f4c48e62baef811b127f4925ee70', expand=False)
+
+    extends('ruby')
+
+    def install(self, spec, prefix):
+        gem('install', 'RubyInline-{0}.gem'.format(self.version))
diff --git a/var/spack/repos/builtin/packages/ruby-svn2git/package.py b/var/spack/repos/builtin/packages/ruby-svn2git/package.py
new file mode 100644
index 0000000000..6373247051
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ruby-svn2git/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RubySvn2git(Package):
+    """svn2git is a tiny utility for migrating projects from Subversion to Git
+    while keeping the trunk, branches and tags where they should be. It uses
+    git-svn to clone an svn repository and does some clean-up to make sure
+    branches and tags are imported in a meaningful way, and that the code
+    checked into master ends up being what's currently in your svn trunk rather
+    than whichever svn branch your last commit was in."""
+
+    homepage = "https://github.com/nirvdrum/svn2git/"
+    url      = "https://github.com/nirvdrum/svn2git/archive/v2.4.0.tar.gz"
+
+    version('2.4.0', 'f19ac6eb0634aa1fed31a1e40a2aeaa2')
+
+    depends_on('git')
+    depends_on('subversion+perl')
+
+    extends('ruby')
+
+    def install(self, spec, prefix):
+        gem('build', 'svn2git.gemspec')
+        gem('install', 'svn2git-{0}.gem'.format(self.version))
diff --git a/var/spack/repos/builtin/packages/ruby-terminal-table/package.py b/var/spack/repos/builtin/packages/ruby-terminal-table/package.py
new file mode 100644
index 0000000000..083e20bb5c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ruby-terminal-table/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RubyTerminalTable(Package):
+    """Simple, feature rich ascii table generation library"""
+
+    homepage = "https://rubygems.org/gems/terminal-table"
+    url      = "https://rubygems.org/downloads/terminal-table-1.8.0.gem"
+
+    version('1.8.0', 'd78db9d71f70aaadd7e689641078e7e7', expand=False)
+
+    extends('ruby')
+
+    def install(self, spec, prefix):
+        gem('install', 'terminal-table-{0}.gem'.format(self.version))
diff --git a/var/spack/repos/builtin/packages/ruby/package.py b/var/spack/repos/builtin/packages/ruby/package.py
index 1e3934df76..f1ae31f177 100644
--- a/var/spack/repos/builtin/packages/ruby/package.py
+++ b/var/spack/repos/builtin/packages/ruby/package.py
@@ -1,56 +1,64 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class Ruby(Package):
+class Ruby(AutotoolsPackage):
     """A dynamic, open source programming language with a focus on
     simplicity and productivity."""
 
     homepage = "https://www.ruby-lang.org/"
     url      = "http://cache.ruby-lang.org/pub/ruby/2.2/ruby-2.2.0.tar.gz"
+    list_url = "http://cache.ruby-lang.org/pub/ruby/"
+    list_depth = 1
+
+    version('2.2.0', 'cd03b28fd0b555970f5c4fd481700852')
+
+    variant('openssl', default=True, description="Enable OpenSSL support")
+    variant('readline', default=False, description="Enable Readline support")
 
     extendable = True
 
-    version('2.2.0', 'cd03b28fd0b555970f5c4fd481700852')
+    depends_on('pkgconfig', type=('build'))
     depends_on('libffi')
     depends_on('zlib')
-    variant('openssl', default=False, description="Enable OpenSSL support")
+    depends_on('libx11')
+    depends_on('tcl')
+    depends_on('tk')
     depends_on('openssl', when='+openssl')
-    variant('readline', default=False, description="Enable Readline support")
     depends_on('readline', when='+readline')
 
-    def install(self, spec, prefix):
-        options = ["--prefix=%s" % prefix]
-        if '+openssl' in spec:
-            options.append("--with-openssl-dir=%s" % spec['openssl'].prefix)
-        if '+readline' in spec:
-            options.append("--with-readline-dir=%s" % spec['readline'].prefix)
-        configure(*options)
-        make()
-        make("install")
+    # gcc-7-based build requires patches (cf. https://bugs.ruby-lang.org/issues/13150)
+    patch('ruby_23_gcc7.patch', level=0, when='@2.2.0:2.2.999 %gcc@7:')
+    patch('ruby_23_gcc7.patch', level=0, when='@2.3.0:2.3.4 %gcc@7:')
+    patch('ruby_24_gcc7.patch', level=1, when='@2.4.0 %gcc@7:')
+
+    resource(
+        name='rubygems-updated-ssl-cert',
+        url='https://raw.githubusercontent.com/rubygems/rubygems/master/lib/rubygems/ssl_certs/index.rubygems.org/GlobalSignRootCA.pem',
+        sha256='df68841998b7fd098a9517fe971e97890be0fc93bbe1b2a1ef63ebdea3111c80',
+        when='+openssl',
+        destination='',
+        placement='rubygems-updated-ssl-cert',
+        expand=False
+    )
+
+    def url_for_version(self, version):
+        url = "http://cache.ruby-lang.org/pub/ruby/{0}/ruby-{1}.tar.gz"
+        return url.format(version.up_to(2), version)
+
+    def configure_args(self):
+        args = []
+        if '+openssl' in self.spec:
+            args.append("--with-openssl-dir=%s" % self.spec['openssl'].prefix)
+        if '+readline' in self.spec:
+            args.append("--with-readline-dir=%s"
+                        % self.spec['readline'].prefix)
+        args.append('--with-tk=%s' % self.spec['tk'].prefix)
+        return args
 
     def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
         # TODO: do this only for actual extensions.
@@ -76,3 +84,21 @@ class Ruby(Package):
         # Ruby extension builds have global ruby and gem functions
         module.ruby = Executable(join_path(self.spec.prefix.bin, 'ruby'))
         module.gem = Executable(join_path(self.spec.prefix.bin, 'gem'))
+
+    @run_after('install')
+    def post_install(self):
+        """ RubyGems updated their SSL certificates at some point, so
+        new certificates must be installed after Ruby is installed
+        in order to download gems; see
+        http://guides.rubygems.org/ssl-certificate-update/
+        for details.
+        """
+        rubygems_updated_cert_path = join_path(self.stage.source_path,
+                                               'rubygems-updated-ssl-cert',
+                                               'GlobalSignRootCA.pem')
+        rubygems_certs_path = join_path(self.spec.prefix.lib,
+                                        'ruby',
+                                        '{0}'.format(self.spec.version.dotted),
+                                        'rubygems',
+                                        'ssl_certs')
+        install(rubygems_updated_cert_path, rubygems_certs_path)
diff --git a/var/spack/repos/builtin/packages/ruby/ruby_23_gcc7.patch b/var/spack/repos/builtin/packages/ruby/ruby_23_gcc7.patch
new file mode 100644
index 0000000000..b7fdd530b7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ruby/ruby_23_gcc7.patch
@@ -0,0 +1,98 @@
+diff --git include/ruby/ruby.h include/ruby/ruby.h
+index 60cfb1174e..dccfdc763a 100644
+--- include/ruby/ruby.h
++++ include/ruby/ruby.h
+@@ -551,27 +551,23 @@ static inline int rb_type(VALUE obj);
+ 	((type) == RUBY_T_FLOAT) ? RB_FLOAT_TYPE_P(obj) : \
+ 	(!RB_SPECIAL_CONST_P(obj) && RB_BUILTIN_TYPE(obj) == (type)))
+ 
+-/* RB_GC_GUARD_PTR() is an intermediate macro, and has no effect by
+- * itself.  don't use it directly */
+ #ifdef __GNUC__
+-#define RB_GC_GUARD_PTR(ptr) \
+-    __extension__ ({volatile VALUE *rb_gc_guarded_ptr = (ptr); rb_gc_guarded_ptr;})
+-#else
+-#ifdef _MSC_VER
++#define RB_GC_GUARD(v) \
++    (*__extension__ ({ \
++	volatile VALUE *rb_gc_guarded_ptr = &(v); \
++	__asm__("" : : "m"(rb_gc_guarded_ptr)); \
++	rb_gc_guarded_ptr; \
++    }))
++#elif defined _MSC_VER
+ #pragma optimize("", off)
+ static inline volatile VALUE *rb_gc_guarded_ptr(volatile VALUE *ptr) {return ptr;}
+ #pragma optimize("", on)
++#define RB_GC_GUARD(v) (*rb_gc_guarded_ptr(&(v)))
+ #else
+ volatile VALUE *rb_gc_guarded_ptr_val(volatile VALUE *ptr, VALUE val);
+ #define HAVE_RB_GC_GUARDED_PTR_VAL 1
+ #define RB_GC_GUARD(v) (*rb_gc_guarded_ptr_val(&(v),(v)))
+ #endif
+-#define RB_GC_GUARD_PTR(ptr) rb_gc_guarded_ptr(ptr)
+-#endif
+-
+-#ifndef RB_GC_GUARD
+-#define RB_GC_GUARD(v) (*RB_GC_GUARD_PTR(&(v)))
+-#endif
+ 
+ #ifdef __GNUC__
+ #define RB_UNUSED_VAR(x) x __attribute__ ((unused))
+diff --git marshal.c marshal.c
+index c56de4af8d..b7274bf3c4 100644
+--- marshal.c
++++ marshal.c
+@@ -1022,7 +1022,7 @@ VALUE
+ rb_marshal_dump_limited(VALUE obj, VALUE port, int limit)
+ {
+     struct dump_arg *arg;
+-    VALUE wrapper; /* used to avoid memory leak in case of exception */
++    volatile VALUE wrapper; /* used to avoid memory leak in case of exception */
+ 
+     wrapper = TypedData_Make_Struct(rb_cData, struct dump_arg, &dump_arg_data, arg);
+     arg->dest = 0;
+@@ -1051,8 +1051,8 @@ rb_marshal_dump_limited(VALUE obj, VALUE port, int limit)
+ 	rb_io_write(arg->dest, arg->str);
+ 	rb_str_resize(arg->str, 0);
+     }
+-    clear_dump_arg(arg);
+-    RB_GC_GUARD(wrapper);
++    free_dump_arg(arg);
++    rb_gc_force_recycle(wrapper);
+ 
+     return port;
+ }
+@@ -2044,7 +2044,7 @@ rb_marshal_load_with_proc(VALUE port, VALUE proc)
+ {
+     int major, minor, infection = 0;
+     VALUE v;
+-    VALUE wrapper; /* used to avoid memory leak in case of exception */
++    volatile VALUE wrapper; /* used to avoid memory leak in case of exception */
+     struct load_arg *arg;
+ 
+     v = rb_check_string_type(port);
+@@ -2090,8 +2090,8 @@ rb_marshal_load_with_proc(VALUE port, VALUE proc)
+ 
+     if (!NIL_P(proc)) arg->proc = proc;
+     v = r_object(arg);
+-    clear_load_arg(arg);
+-    RB_GC_GUARD(wrapper);
++    free_load_arg(arg);
++    rb_gc_force_recycle(wrapper);
+ 
+     return v;
+ }
+diff --git test/ruby/test_marshal.rb test/ruby/test_marshal.rb
+index 6ac5c29991..dc2b8b30dc 100644
+--- test/ruby/test_marshal.rb
++++ test/ruby/test_marshal.rb
+@@ -645,6 +645,9 @@ def test_continuation
+     c = Bug9523.new
+     assert_raise_with_message(RuntimeError, /Marshal\.dump reentered at marshal_dump/) do
+       Marshal.dump(c)
++      GC.start
++      1000.times {"x"*1000}
++      GC.start
+       c.cc.call
+     end
+   end
diff --git a/var/spack/repos/builtin/packages/ruby/ruby_24_gcc7.patch b/var/spack/repos/builtin/packages/ruby/ruby_24_gcc7.patch
new file mode 100644
index 0000000000..4be26af7d6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ruby/ruby_24_gcc7.patch
@@ -0,0 +1,66 @@
+diff --git a/include/ruby/ruby.h b/include/ruby/ruby.h
+index 6144c672346d..4aa388849ba4 100644
+--- a/include/ruby/ruby.h
++++ b/include/ruby/ruby.h
+@@ -536,7 +536,11 @@ static inline int rb_type(VALUE obj);
+ 
+ #ifdef __GNUC__
+ #define RB_GC_GUARD(v) \
+-    (*__extension__ ({volatile VALUE *rb_gc_guarded_ptr = &(v); rb_gc_guarded_ptr;}))
++    (*__extension__ ({ \
++	volatile VALUE *rb_gc_guarded_ptr = &(v); \
++	__asm__("" : : "m"(rb_gc_guarded_ptr)); \
++	rb_gc_guarded_ptr; \
++    }))
+ #elif defined _MSC_VER
+ #pragma optimize("", off)
+ static inline volatile VALUE *rb_gc_guarded_ptr(volatile VALUE *ptr) {return ptr;}
+diff --git a/marshal.c b/marshal.c
+index a9926acf564e..7e16d0b024c4 100644
+--- a/marshal.c
++++ b/marshal.c
+@@ -1026,7 +1026,7 @@ rb_marshal_dump_limited(VALUE obj, VALUE port, int limit)
+     struct dump_arg *arg;
+     VALUE wrapper; /* used to avoid memory leak in case of exception */
+ 
+-    wrapper = TypedData_Make_Struct(rb_cData, struct dump_arg, &dump_arg_data, arg);
++    wrapper = TypedData_Make_Struct(0, struct dump_arg, &dump_arg_data, arg);
+     arg->dest = 0;
+     arg->symbols = st_init_numtable();
+     arg->data    = rb_init_identtable();
+@@ -2053,7 +2053,7 @@ rb_marshal_load_with_proc(VALUE port, VALUE proc)
+     else {
+ 	io_needed();
+     }
+-    wrapper = TypedData_Make_Struct(rb_cData, struct load_arg, &load_arg_data, arg);
++    wrapper = TypedData_Make_Struct(0, struct load_arg, &load_arg_data, arg);
+     arg->infection = infection;
+     arg->src = port;
+     arg->offset = 0;
+diff --git a/test/ruby/test_marshal.rb b/test/ruby/test_marshal.rb
+index bc22b5fd3ab8..bfc3f6df256f 100644
+--- a/test/ruby/test_marshal.rb
++++ b/test/ruby/test_marshal.rb
+@@ -644,6 +644,9 @@ def test_continuation
+     c = Bug9523.new
+     assert_raise_with_message(RuntimeError, /Marshal\.dump reentered at marshal_dump/) do
+       Marshal.dump(c)
++      GC.start
++      1000.times {"x"*1000}
++      GC.start
+       c.cc.call
+     end
+   end
+diff --git a/version.h b/version.h
+index 0a845df84416..39214c474439 100644
+--- a/version.h
++++ b/version.h
+@@ -1,6 +1,6 @@
+ #define RUBY_VERSION "2.4.0"
+ #define RUBY_RELEASE_DATE "2017-03-13"
+-#define RUBY_PATCHLEVEL 99
++#define RUBY_PATCHLEVEL 100
+ 
+ #define RUBY_RELEASE_YEAR 2017
+ #define RUBY_RELEASE_MONTH 3
+
diff --git a/var/spack/repos/builtin/packages/rust-bindgen/package.py b/var/spack/repos/builtin/packages/rust-bindgen/package.py
index 3c7e42ca8a..de0eda3fee 100644
--- a/var/spack/repos/builtin/packages/rust-bindgen/package.py
+++ b/var/spack/repos/builtin/packages/rust-bindgen/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
diff --git a/var/spack/repos/builtin/packages/rust/package.py b/var/spack/repos/builtin/packages/rust/package.py
index 219c82fa83..8c86ae4696 100644
--- a/var/spack/repos/builtin/packages/rust/package.py
+++ b/var/spack/repos/builtin/packages/rust/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
@@ -33,10 +14,11 @@ def get_submodules():
 
 class Rust(Package):
     """The rust programming language toolchain"""
+
     homepage = "http://www.rust-lang.org"
-    url = "https://github.com/rust-lang/rust"
+    git      = "https://github.com/rust-lang/rust.git"
 
-    version('1.8.0', tag='1.8.0', git="https://github.com/rust-lang/rust")
+    version('1.8.0', tag='1.8.0')
 
     resource(name='cargo',
              git="https://github.com/rust-lang/cargo.git",
diff --git a/var/spack/repos/builtin/packages/sabre/package.py b/var/spack/repos/builtin/packages/sabre/package.py
index b93b07be51..b1c7c8b81d 100644
--- a/var/spack/repos/builtin/packages/sabre/package.py
+++ b/var/spack/repos/builtin/packages/sabre/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -37,9 +18,9 @@ class Sabre(MakefilePackage):
     """
 
     homepage = "https://github.com/najoshi/sabre"
-    url = "https://github.com/najoshi/sabre"
+    git      = "https://github.com/najoshi/sabre.git"
 
-    version('2013-09-27', git='https://github.com/najoshi/sabre.git', commit='039a55e500ba07b7e6432ea6ec2ddcfb3471d949')
+    version('2013-09-27', commit='039a55e500ba07b7e6432ea6ec2ddcfb3471d949')
 
     depends_on('zlib')
 
diff --git a/var/spack/repos/builtin/packages/sailfish/package.py b/var/spack/repos/builtin/packages/sailfish/package.py
new file mode 100644
index 0000000000..1db70a05f5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/sailfish/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Sailfish(CMakePackage):
+    """Sailfish is a tool for transcript quantification from RNA-seq data."""
+
+    homepage = "http://www.cs.cmu.edu/~ckingsf/software/sailfish"
+    url      = "https://github.com/kingsfordgroup/sailfish/archive/v0.10.1.tar.gz"
+
+    version('0.10.1', 'e6dab4cf3a39f346df7c28f40eb58cad')
+
+    depends_on('boost@1.55:')
+    depends_on('tbb')
diff --git a/var/spack/repos/builtin/packages/salmon/package.py b/var/spack/repos/builtin/packages/salmon/package.py
index a323aa1dab..06bfd70324 100644
--- a/var/spack/repos/builtin/packages/salmon/package.py
+++ b/var/spack/repos/builtin/packages/salmon/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,9 +13,15 @@ class Salmon(CMakePackage):
     homepage = "http://combine-lab.github.io/salmon/"
     url      = "https://github.com/COMBINE-lab/salmon/archive/v0.8.2.tar.gz"
 
+    version('0.9.1', '1277b8ed65d2c6982ed176a496a2a1e3')
     version('0.8.2', 'ee512697bc44b13661a16d4e14cf0a00')
 
-    depends_on('boost')
+    depends_on('tbb')
+    depends_on('boost@:1.66.0')
+
+    def patch(self):
+        # remove static linking to libstdc++
+        filter_file('-static-libstdc++', '', 'CMakeLists.txt', string=True)
 
     def cmake_args(self):
         args = ['-DBOOST_ROOT=%s' % self.spec['boost'].prefix]
diff --git a/var/spack/repos/builtin/packages/sambamba/package.py b/var/spack/repos/builtin/packages/sambamba/package.py
index ad8c68547c..69ed5fd676 100644
--- a/var/spack/repos/builtin/packages/sambamba/package.py
+++ b/var/spack/repos/builtin/packages/sambamba/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,9 @@ class Sambamba(Package):
     """Sambamba: process your BAM data faster (bioinformatics)"""
 
     homepage = "http://lomereiter.github.io/sambamba/"
+    git      = "https://github.com/lomereiter/sambamba.git"
 
-    version('0.6.6', git='https://github.com/lomereiter/sambamba.git',
-            tag='v0.6.6', submodules=True)
+    version('0.6.6', tag='v0.6.6', submodules=True)
 
     depends_on('ldc~shared', type=('build', 'link'))
     depends_on('python', type='build')
diff --git a/var/spack/repos/builtin/packages/samblaster/package.py b/var/spack/repos/builtin/packages/samblaster/package.py
new file mode 100644
index 0000000000..d463fbea55
--- /dev/null
+++ b/var/spack/repos/builtin/packages/samblaster/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Samblaster(MakefilePackage):
+    """A tool to mark duplicates and extract discordant and split reads from
+    sam files."""
+
+    homepage = "https://github.com/GregoryFaust/samblaster"
+    url      = "https://github.com/GregoryFaust/samblaster/archive/v.0.1.24.tar.gz"
+
+    version('0.1.24', '885d5782cc277865dfb086fc0a20243e')
+    version('0.1.23', '95d33b6fcceaa38a9bd79014446b4545')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('samblaster', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/samrai/package.py b/var/spack/repos/builtin/packages/samrai/package.py
index 78b674213d..468531da1b 100644
--- a/var/spack/repos/builtin/packages/samrai/package.py
+++ b/var/spack/repos/builtin/packages/samrai/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,7 +18,12 @@ class Samrai(AutotoolsPackage):
     url      = "https://computation.llnl.gov/projects/samrai/download/SAMRAI-v3.11.2.tar.gz"
     list_url = homepage
 
+    version('3.12.0',     '07364f6e209284e45ac0e9caf1d610f6')
+    version('3.11.5',     '4359a03145c03501b230777f92b62104')
+    version('3.11.4',     '473d6796772f5926b1c0d1cf8f3f8c99')
+    # Version 3.11.3 permissions don't allow downloading
     version('3.11.2',     'd5f59f8efd755b23b797e46349428206')
+    version('3.11.1',     '19a2398a7448ec0f0f0c5e8fc6f80478')
     version('3.10.0',     'ff5f5b8b4a35b52a1b7e37a74166c65a')
     version('3.9.1',      '232d04d0c995f5abf20d94350befd0b2')
     version('3.8.0',      'c18fcffa706346bfa5828b36787ce5fe')
@@ -55,15 +41,23 @@ class Samrai(AutotoolsPackage):
     # and more print statements
     variant('debug', default=False,
             description='Compile with reduced optimization and debugging on')
+    variant('silo', default=False,
+            description='Compile with support for silo')
 
     depends_on('mpi')
     depends_on('zlib')
     depends_on('hdf5+mpi')
-    depends_on('boost')
     depends_on('m4', type='build')
+    depends_on('boost@:1.64.0', when='@3.0.0:3.11.99', type='build')
+    depends_on('silo+mpi', when='+silo')
 
-    # don't build tools with gcc
-    patch('no-tool-build.patch', when='%gcc')
+    # don't build SAMRAI 3+ with tools with gcc
+    patch('no-tool-build.patch', when='@3.0.0:%gcc')
+
+    # 2.4.4 needs a lot of patches to fix ADL and performance problems
+    patch('https://github.com/IBAMR/IBAMR/releases/download/v0.3.0/ibamr-samrai-fixes.patch',
+          sha256='1d088b6cca41377747fa0ae8970440c20cb68988bbc34f9032d5a4e6aceede47',
+          when='@2.4.4')
 
     def configure_args(self):
         options = []
@@ -74,13 +68,16 @@ class Samrai(AutotoolsPackage):
             '--with-F77=%s' % self.spec['mpi'].mpifc,
             '--with-M4=%s' % self.spec['m4'].prefix,
             '--with-hdf5=%s' % self.spec['hdf5'].prefix,
-            '--with-boost=%s' % self.spec['boost'].prefix,
             '--with-zlib=%s' % self.spec['zlib'].prefix,
             '--without-blas',
             '--without-lapack',
             '--with-hypre=no',
             '--with-petsc=no'])
 
+        # SAMRAI 2 used templates; enable implicit instantiation
+        if self.spec.satisfies('@:3'):
+            options.append('--enable-implicit-template-instantiation')
+
         if '+debug' in self.spec:
             options.extend([
                 '--disable-opt',
@@ -90,4 +87,14 @@ class Samrai(AutotoolsPackage):
                 '--enable-opt',
                 '--disable-debug'])
 
+        if '+silo' in self.spec:
+            options.append('--with-silo=%s' % self.spec['silo'].prefix)
+
+        if self.spec.satisfies('@3.0:3.11.99'):
+            options.append('--with-boost=%s' % self.spec['boost'].prefix)
+
         return options
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        if self.spec.satisfies('@3.12:'):
+            spack_env.append_flags('CXXFLAGS', self.compiler.cxx11_flag)
diff --git a/var/spack/repos/builtin/packages/samtools/package.py b/var/spack/repos/builtin/packages/samtools/package.py
index ae0acdde47..95949a86c6 100644
--- a/var/spack/repos/builtin/packages/samtools/package.py
+++ b/var/spack/repos/builtin/packages/samtools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,6 +14,9 @@ class Samtools(Package):
     homepage = "www.htslib.org"
     url = "https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2"
 
+    version('1.9', 'cca9a40d9b91b007af2ff905cb8b5924')
+    version('1.8', 'c6e981c92ca00a44656a708c4b52aba3')
+    version('1.7', '2240175242b5183bfa6baf1483f68023')
     version('1.6', 'b756f05fd5d1a7042074417edb8c9aea')
     version('1.4', '8cbd7d2a0ec16d834babcd6c6d85d691')
     version('1.3.1', 'a7471aa5a1eb7fc9cc4c6491d73c2d88')
@@ -40,9 +24,14 @@ class Samtools(Package):
 
     depends_on('ncurses')
     # htslib became standalone @1.3.1, must use corresponding version
+    depends_on('htslib@1.9',   when='@1.9')
+    depends_on('htslib@1.8',   when='@1.8')
+    depends_on('htslib@1.7',   when='@1.7')
     depends_on('htslib@1.6',   when='@1.6')
     depends_on('htslib@1.4',   when='@1.4')
     depends_on('htslib@1.3.1', when='@1.3.1')
+    depends_on('zlib', when='@1.7:')
+    depends_on('bzip2', when='@1.7:')
 
     def install(self, spec, prefix):
         if self.spec.version >= Version('1.3.1'):
@@ -53,3 +42,9 @@ class Samtools(Package):
         else:
             make("prefix=%s" % prefix)
             make("prefix=%s" % prefix, "install")
+        # Install dev headers and libs for legacy apps depending on them
+        mkdir(prefix.include)
+        mkdir(prefix.lib)
+        install('sam.h', prefix.include)
+        install('bam.h', prefix.include)
+        install('libbam.a', prefix.lib)
diff --git a/var/spack/repos/builtin/packages/sandbox/package.py b/var/spack/repos/builtin/packages/sandbox/package.py
index 58c6696243..d86222b0d9 100644
--- a/var/spack/repos/builtin/packages/sandbox/package.py
+++ b/var/spack/repos/builtin/packages/sandbox/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/sas/package.py b/var/spack/repos/builtin/packages/sas/package.py
index f6a1cf4101..d2d07bff0a 100644
--- a/var/spack/repos/builtin/packages/sas/package.py
+++ b/var/spack/repos/builtin/packages/sas/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/satsuma2/package.py b/var/spack/repos/builtin/packages/satsuma2/package.py
index 4859c97c0e..82dae616e4 100644
--- a/var/spack/repos/builtin/packages/satsuma2/package.py
+++ b/var/spack/repos/builtin/packages/satsuma2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,9 +14,9 @@ class Satsuma2(CMakePackage):
     """
 
     homepage = "https://github.com/bioinfologics/satsuma2"
-    url      = "https://github.com/bioinfologics/satsuma2"
+    git      = "https://github.com/bioinfologics/satsuma2.git"
 
-    version('2016-11-22', git='https://github.com/bioinfologics/satsuma2.git', commit='da694aeecf352e344b790bea4a7aaa529f5b69e6')
+    version('2016-11-22', commit='da694aeecf352e344b790bea4a7aaa529f5b69e6')
 
     def install(self, spec, prefix):
         install_tree(join_path('spack-build', 'bin'), prefix.bin)
diff --git a/var/spack/repos/builtin/packages/savanna/package.py b/var/spack/repos/builtin/packages/savanna/package.py
index af2cdf9ed8..5e49428f0c 100644
--- a/var/spack/repos/builtin/packages/savanna/package.py
+++ b/var/spack/repos/builtin/packages/savanna/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from distutils.dir_util import copy_tree
 
 
 class Savanna(MakefilePackage):
@@ -32,12 +12,10 @@ class Savanna(MakefilePackage):
     """
 
     homepage = "https://github.com/CODARcode/savanna"
-    url = "https://github.com/CODARcode/savanna/archive/v0.5.tar.gz"
+    git      = "https://github.com/CODARcode/savanna.git"
 
-    version('develop', git='https://github.com/CODARcode/savanna.git',
-            branch='master', submodules=True)
-    version('0.5', git='https://github.com/CODARcode/savanna.git',
-            tag='0.5', submodules=True)
+    version('develop', branch='master', submodules=True)
+    version('0.5', tag='0.5', submodules=True)
 
     variant('tau', default=False, description='Enable TAU profiling support')
 
@@ -48,4 +26,4 @@ class Savanna(MakefilePackage):
     depends_on('tau', when='+tau')
 
     def install(self, spec, prefix):
-        copy_tree('.', prefix)
+        install_tree('.', prefix)
diff --git a/var/spack/repos/builtin/packages/saws/package.py b/var/spack/repos/builtin/packages/saws/package.py
index bda54644c6..359258a1dd 100644
--- a/var/spack/repos/builtin/packages/saws/package.py
+++ b/var/spack/repos/builtin/packages/saws/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,7 +11,9 @@ class Saws(AutotoolsPackage):
        scientific or engineering application code into a webserver,
        allowing one to examine (and even modify) the state of the
        simulation with any browser from anywhere."""
+
     homepage = "https://bitbucket.org/saws/saws/wiki/Home"
+    git      = "https://bitbucket.org/saws/saws.git"
 
-    version('develop', git='https://bitbucket.org/saws/saws.git', tag='master')
-    version('0.1.0', git='https://bitbucket.org/saws/saws.git', tag='v0.1.0')
+    version('develop', tag='master')
+    version('0.1.0', tag='v0.1.0')
diff --git a/var/spack/repos/builtin/packages/sbt/package.py b/var/spack/repos/builtin/packages/sbt/package.py
index baa93fa93a..791d316ef2 100644
--- a/var/spack/repos/builtin/packages/sbt/package.py
+++ b/var/spack/repos/builtin/packages/sbt/package.py
@@ -1,41 +1,24 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-import shutil
 
 
 class Sbt(Package):
     """Scala Build Tool"""
 
-    homepage = "http://www.scala-sbt.org"
-    url      = "https://dl.bintray.com/sbt/native-packages/sbt/0.13.12/sbt-0.13.12.tgz"
+    homepage = 'http://www.scala-sbt.org'
+    url      = "https://github.com/sbt/sbt/releases/download/v1.1.4/sbt-1.1.4.tgz"
 
-    version('0.13.12', 'cec3071d46ef13334c8097cc3467ff28')
+    version('1.1.6', 'd307b131ed041c783ac5ed7bbb4768dc')
+    version('1.1.5', 'b771480feb07f98fa8cd6d787c8d4485')
+    version('1.1.4', 'c71e5fa846164d14d4cd450520d66c6a')
+    version('0.13.17', 'c52c6152cc7aadfd1f0736a1a5d0a5b8')
 
     depends_on('java')
 
     def install(self, spec, prefix):
-        shutil.copytree('bin', join_path(prefix, 'bin'), symlinks=True)
-        shutil.copytree('conf', join_path(prefix, 'conf'), symlinks=True)
+        install_tree('bin',  prefix.bin)
+        install_tree('conf', prefix.conf)
diff --git a/var/spack/repos/builtin/packages/scala/package.py b/var/spack/repos/builtin/packages/scala/package.py
index 8c36f9e981..263a62b956 100644
--- a/var/spack/repos/builtin/packages/scala/package.py
+++ b/var/spack/repos/builtin/packages/scala/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -36,9 +17,10 @@ class Scala(Package):
     homepage = "https://www.scala-lang.org/"
     url = "https://downloads.lightbend.com/scala/2.12.1/scala-2.12.1.tgz"
 
+    version('2.12.5', '25cf4989d061c585bd0a3fa357ccf0a6')
     version('2.12.1', '3eaecbce019b0fa3067503846e292b32')
     version('2.11.11', '3f5b76001f60cbc31111ddb81de5ea07')
-    version('2.20.6', 'd79dc9fdc627b73289306bdaec81ca98')
+    version('2.10.6', 'd79dc9fdc627b73289306bdaec81ca98')
 
     depends_on('java')
 
diff --git a/var/spack/repos/builtin/packages/scalasca/package.py b/var/spack/repos/builtin/packages/scalasca/package.py
index 21f50cf1fe..b2f68c5b81 100644
--- a/var/spack/repos/builtin/packages/scalasca/package.py
+++ b/var/spack/repos/builtin/packages/scalasca/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -38,14 +19,18 @@ class Scalasca(AutotoolsPackage):
     homepage = "http://www.scalasca.org"
     url = "http://apps.fz-juelich.de/scalasca/releases/scalasca/2.1/dist/scalasca-2.1.tar.gz"
 
+    version('2.4',   '4a895868258030f700a635eac93d36764f60c8c63673c7db419ea4bcc6b0b760')
     version('2.3.1', 'a83ced912b9d2330004cb6b9cefa7585')
     version('2.2.2', '2bafce988b0522d18072f7771e491ab9')
     version('2.1',   'bab9c2b021e51e2ba187feec442b96e6')
 
     depends_on("mpi")
 
+    # version 2.4
+    depends_on('cubew@4.4:', when='@2.4:')
+
     # version 2.3
-    depends_on('cube@4.3:', when='@2.3:')
+    depends_on('cube@4.3', when='@2.3:2.3.99')
     depends_on('otf2@2:', when='@2.3:')
 
     # version 2.1+
@@ -60,7 +45,11 @@ class Scalasca(AutotoolsPackage):
 
         config_args = ["--enable-shared"]
 
-        config_args.append("--with-cube=%s" % spec['cube'].prefix.bin)
+        if spec.satisfies('@2.4:'):
+            config_args.append("--with-cube=%s" % spec['cubew'].prefix.bin)
+        else:
+            config_args.append("--with-cube=%s" % spec['cube'].prefix.bin)
+
         config_args.append("--with-otf2=%s" % spec['otf2'].prefix.bin)
 
         if self.spec['mpi'].name == 'openmpi':
diff --git a/var/spack/repos/builtin/packages/scalpel/package.py b/var/spack/repos/builtin/packages/scalpel/package.py
index f7d2834732..a44106cb68 100644
--- a/var/spack/repos/builtin/packages/scalpel/package.py
+++ b/var/spack/repos/builtin/packages/scalpel/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/scan-for-matches/package.py b/var/spack/repos/builtin/packages/scan-for-matches/package.py
new file mode 100644
index 0000000000..54d5e285ec
--- /dev/null
+++ b/var/spack/repos/builtin/packages/scan-for-matches/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class ScanForMatches(Package):
+    """scan_for_matches is a utility written in C for locating patterns in DNA
+       or protein FASTA files."""
+
+    homepage = "http://blog.theseed.org/servers/2010/07/scan-for-matches.html"
+    url      = "http://www.theseed.org/servers/downloads/scan_for_matches.tgz"
+
+    version('2010-7-16', 'f64c9cfb385984ded2a7ad9ad2253d83')
+
+    def install(self, spec, prefix):
+        cc = Executable(self.compiler.cc)
+        cc('-O', '-o', 'scan_for_matches', 'ggpunit.c', 'scan_for_matches.c')
+        mkdirp(prefix.bin)
+        install('scan_for_matches', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/scons/package.py b/var/spack/repos/builtin/packages/scons/package.py
index 8bf6ceddcc..7dcae8c960 100644
--- a/var/spack/repos/builtin/packages/scons/package.py
+++ b/var/spack/repos/builtin/packages/scons/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,10 +10,14 @@ class Scons(PythonPackage):
     """SCons is a software construction tool"""
 
     homepage = "http://scons.org"
-    url      = "https://pypi.io/packages/source/s/scons/scons-2.5.1.tar.gz"
+    url      = "https://pypi.io/packages/source/s/scons/scons-3.0.1.tar.gz"
 
-    version('2.5.1', '3eac81e5e8206304a9b4683c57665aa4')
-    version('2.5.0', 'bda5530a70a41a7831d83c8b191c021e')
+    version('3.0.1', 'b6a292e251b34b82c203b56cfa3968b3',
+            url="https://pypi.python.org/packages/c1/0a/520a3c86ce5cff36e81af5e91d4dcd741ebc189c2f0f42d54cc12a8a7519/scons-3.0.1.tar.gz")
+    version('2.5.1', '3eac81e5e8206304a9b4683c57665aa4',
+            url="https://pypi.python.org/packages/2c/ee/a9601b958c94e93410e635a5d67ed95300998ffdc36127b16d322b054ff0/scons-2.5.1.tar.gz")
+    version('2.5.0', 'bda5530a70a41a7831d83c8b191c021e',
+            url="https://pypi.python.org/packages/17/f0/60464796a3fd16899a2cf54e22615c38bbe8124386cf3763c17ff367c2af/scons-2.5.0.tar.gz")
 
-    # Python 3 is not supported
-    depends_on('python@:2.8', type=('build', 'run'))
+    # Python 3 support was added in SCons 3.0.0
+    depends_on('python@:2', when='@:2', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/scorec-core/package.py b/var/spack/repos/builtin/packages/scorec-core/package.py
index e629a63ebe..ad6b5c1876 100644
--- a/var/spack/repos/builtin/packages/scorec-core/package.py
+++ b/var/spack/repos/builtin/packages/scorec-core/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,9 +12,9 @@ class ScorecCore(CMakePackage):
     """
 
     homepage = 'https://www.scorec.rpi.edu/'
-    url = 'https://github.com/SCOREC/core.git'
+    git      = 'https://github.com/SCOREC/core.git'
 
-    version('develop', git=url)
+    version('develop')
 
     depends_on('mpi')
     depends_on('zoltan')
diff --git a/var/spack/repos/builtin/packages/scorep/package.py b/var/spack/repos/builtin/packages/scorep/package.py
index fd7da69442..b5a1fa73cd 100644
--- a/var/spack/repos/builtin/packages/scorep/package.py
+++ b/var/spack/repos/builtin/packages/scorep/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,21 +15,34 @@ class Scorep(AutotoolsPackage):
     homepage = "http://www.vi-hps.org/projects/score-p"
     url      = "http://www.vi-hps.org/upload/packages/scorep/scorep-2.0.2.tar.gz"
 
+    version('4.1',   '7bb6c1eecdd699b4a3207caf202866778ee01f15ff39a9ec198fcd872578fe63')
+    version('4.0',   'f04478e0407d67eeb8c49c3c51d91e12')
     version('3.1',   '065bf8eb08398e8146c895718ddb9145')
     version('3.0',   '44da8beaa3f71436a5f6fe51938aab2f')
     version('2.0.2', '8f00e79e1b5b96e511c5ebecd10b2888')
     version('1.4.2', '3b9a042b13bdd5836452354e6567f71e')
     version('1.3',   '9db6f957b7f51fa01377a9537867a55c')
 
-    patch('gcc7.patch')
+    patch('gcc7.patch', when='@:3')
+
+    variant('mpi', default=True, description="Enable MPI support")
+    variant('papi', default=True, description="Enable PAPI")
+    variant('pdt', default=False, description="Enable PDT")
+    variant('shmem', default=False, description='Enable shmem tracing')
 
-    ##########
     # Dependencies for SCORE-P are quite tight. See the homepage for more
-    # information.
+    # information. Starting with scorep 4.0 / cube 4.4, Score-P only depends on
+    # two components of cube -- cubew and cubelib.
+
+    # SCOREP 4
+    depends_on('otf2@2.1:', when='@4:')
+    depends_on('opari2@2.0:', when='@4:')
+    depends_on('cubew@4.4:', when='@4:')
+    depends_on('cubelib@4.4:', when='@4:')
     # SCOREP 3
-    depends_on('otf2@2:', when='@3:')
-    depends_on('opari2@2:', when='@3:')
-    depends_on('cube@4.3:', when='@3:')
+    depends_on('otf2@2:', when='@3:3.99')
+    depends_on('opari2@2:', when='@3:3.99')
+    depends_on('cube@4.3:', when='@3:3.99')
     # SCOREP 2.0.2
     depends_on('otf2@2.0', when='@2.0.2')
     depends_on('opari2@2.0', when='@2.0.2')
@@ -61,13 +55,10 @@ class Scorep(AutotoolsPackage):
     depends_on("otf2@1.4", when='@1.3')
     depends_on("opari2@1.1.4", when='@1.3')
     depends_on("cube@4.2.3", when='@1.3')
-    ##########
 
-    depends_on("mpi")
-    depends_on("papi")
-    depends_on('pdt')
-
-    variant('shmem', default=False, description='Enable shmem tracing')
+    depends_on('mpi', when="+mpi")
+    depends_on('papi', when="+papi")
+    depends_on('pdt', when="+pdt")
 
     # Score-P requires a case-sensitive file system, and therefore
     # does not work on macOS
@@ -80,15 +71,29 @@ class Scorep(AutotoolsPackage):
         config_args = [
             "--with-otf2=%s" % spec['otf2'].prefix.bin,
             "--with-opari2=%s" % spec['opari2'].prefix.bin,
-            "--with-cube=%s" % spec['cube'].prefix.bin,
-            "--with-papi-header=%s" % spec['papi'].prefix.include,
-            "--with-papi-lib=%s" % spec['papi'].prefix.lib,
-            "--with-pdt=%s" % spec['pdt'].prefix.bin,
             "--enable-shared"]
 
         cname = spec.compiler.name
         config_args.append('--with-nocross-compiler-suite={0}'.format(cname))
 
+        if self.version >= Version('4.0'):
+            config_args.append("--with-cubew=%s" % spec['cubew'].prefix.bin)
+            config_args.append("--with-cubelib=%s" %
+                               spec['cubelib'].prefix.bin)
+        else:
+            config_args.append("--with-cube=%s" % spec['cube'].prefix.bin)
+
+        if "+papi" in spec:
+            config_args.append("--with-papi-header=%s" %
+                               spec['papi'].prefix.include)
+            config_args.append("--with-papi-lib=%s" % spec['papi'].prefix.lib)
+
+        if "+pdt" in spec:
+            config_args.append("--with-pdt=%s" % spec['pdt'].prefix.bin)
+
+        config_args += self.with_or_without('shmem')
+        config_args += self.with_or_without('mpi')
+
         if spec.satisfies('^intel-mpi'):
             config_args.append('--with-mpi=intel3')
         elif spec.satisfies('^mpich') or spec.satisfies('^mvapich2'):
@@ -96,16 +101,17 @@ class Scorep(AutotoolsPackage):
         elif spec.satisfies('^openmpi'):
             config_args.append('--with-mpi=openmpi')
 
-        if '~shmem' in spec:
-            config_args.append("--without-shmem")
-
         config_args.extend([
             'CFLAGS={0}'.format(self.compiler.pic_flag),
-            'CXXFLAGS={0}'.format(self.compiler.pic_flag),
-            'MPICC={0}'.format(spec['mpi'].mpicc),
-            'MPICXX={0}'.format(spec['mpi'].mpicxx),
-            'MPIF77={0}'.format(spec['mpi'].mpif77),
-            'MPIFC={0}'.format(spec['mpi'].mpifc)
+            'CXXFLAGS={0}'.format(self.compiler.pic_flag)
         ])
 
+        if "+mpi" in spec:
+            config_args.extend([
+                'MPICC={0}'.format(spec['mpi'].mpicc),
+                'MPICXX={0}'.format(spec['mpi'].mpicxx),
+                'MPIF77={0}'.format(spec['mpi'].mpif77),
+                'MPIFC={0}'.format(spec['mpi'].mpifc)
+            ])
+
         return config_args
diff --git a/var/spack/repos/builtin/packages/scotch/libscotchmetis-return-6.0.5a.patch b/var/spack/repos/builtin/packages/scotch/libscotchmetis-return-6.0.5a.patch
new file mode 100644
index 0000000000..7e124c6aac
--- /dev/null
+++ b/var/spack/repos/builtin/packages/scotch/libscotchmetis-return-6.0.5a.patch
@@ -0,0 +1,10 @@
+--- a/src/libscotchmetis/metis_graph_part.c	2018-07-13 14:25:50.000000000 -0500
++++ b/src/libscotchmetis/metis_graph_part.c	2018-07-13 14:21:08.000000000 -0500
+@@ -298,7 +298,7 @@
+
+     edgenbr = xadj[vertnbr] - baseval;
+     if ((edlotax = memAlloc (edgenbr * sizeof (SCOTCH_Num))) == NULL)
+-      return;
++      return (METIS_ERROR);
+     edlotax -= baseval;                           /* Base access to edlotax */
+     vsiztax  = vsize2 - baseval;
diff --git a/var/spack/repos/builtin/packages/scotch/metis-headers-6.0.4.patch b/var/spack/repos/builtin/packages/scotch/metis-headers-6.0.4.patch
new file mode 100644
index 0000000000..9c902a62b8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/scotch/metis-headers-6.0.4.patch
@@ -0,0 +1,634 @@
+--- A/src/libscotch/Makefile	2014-09-23 21:28:28.000000000 +0200
++++ B/src/libscotch/Makefile	2015-07-24 12:51:31.357132922 +0200
+@@ -60,7 +60,7 @@ scotch				:
+ 					libscotcherrexit$(LIB)
+ 
+ ptscotch			:	scotch
+-					$(MAKE) CFLAGS="$(CFLAGS) -DSCOTCH_PTSCOTCH" CC="$(CCP)"	\
++					$(MAKE) CFLAGS="$(CFLAGS) -DSCOTCH_PTSCOTCH" CC="$(CCP)" CCD="$(CCP)"	\
+ 					ptscotch.h							\
+ 					ptscotchf.h							\
+ 					libptscotch$(LIB)						\
+--- A/src/libscotchmetis/Makefile	2011-09-06 18:46:48.000000000 +0200
++++ B/src/libscotchmetis/Makefile	2015-08-25 13:37:31.424467916 +0200
+@@ -54,10 +54,12 @@ include ../Makefile.inc
+ 
+ scotch				:
+ 					$(MAKE) CC="$(CCS)" SCOTCHLIB=ptscotch						\
++					metis.h                                                                         \
+ 					libscotchmetis$(LIB)
+ 
+ ptscotch			:
+ 					$(MAKE) CFLAGS="$(CFLAGS) -DSCOTCH_PTSCOTCH" CC="$(CCP)" SCOTCHLIB=ptscotch	\
++					parmetis.h									\
+ 					libptscotchparmetis$(LIB)
+ 
+ install				:	scotch
+@@ -69,7 +71,7 @@ ptinstall			:	ptscotch
+ 					-$(CP) libptscotchparmetis$(LIB) $(libdir)
+ 
+ clean				:
+-					-$(RM) *~ *$(OBJ) lib*$(LIB)
++					-$(RM) *~ *$(OBJ) lib*$(LIB) metis.h parmetis.h
+ 
+ realclean			:	clean
+ 
+@@ -138,3 +140,10 @@ libscotchmetis$(LIB)		:	metis_graph_orde
+ 					metis_graph_part_f$(OBJ)
+ 					$(AR) $(ARFLAGS) $(@) $(^)
+ 					-$(RANLIB) $(@)
++metis.h				:	metis_skeleton.h			\
++					../libscotch/dummysizes
++					../libscotch/dummysizes metis_skeleton.h metis.h
++
++parmetis.h				:	parmetis_skeleton.h		\
++					../libscotch/dummysizes
++					../libscotch/dummysizes parmetis_skeleton.h parmetis.h
+--- A/src/libscotchmetis/metis.h	2012-09-13 17:43:52.000000000 +0200
++++ B/src/libscotchmetis/metis.h	1970-01-01 01:00:00.000000000 +0100
+@@ -1,97 +0,0 @@
+-/*********************************************************
+-**                                                      **
+-**  WARNING: THIS IS NOT THE ORIGINAL INCLUDE FILE OF   **
+-**  THE MeTiS SOFTWARE PACKAGE.                         **
+-**  This file is a compatibility include file provided  **
+-**  as part of the Scotch software distribution.        **
+-**  Preferably use the original MeTiS include file to   **
+-**  keep definitions of routines not overloaded by      **
+-**  the libScotchMeTiS library.                         **
+-**                                                      **
+-*********************************************************/
+-/* Copyright 2007,2010,2012 IPB, Universite de Bordeaux, INRIA & CNRS
+-**
+-** This file is part of the Scotch software package for static mapping,
+-** graph partitioning and sparse matrix ordering.
+-**
+-** This software is governed by the CeCILL-C license under French law
+-** and abiding by the rules of distribution of free software. You can
+-** use, modify and/or redistribute the software under the terms of the
+-** CeCILL-C license as circulated by CEA, CNRS and INRIA at the following
+-** URL: "http://www.cecill.info".
+-** 
+-** As a counterpart to the access to the source code and rights to copy,
+-** modify and redistribute granted by the license, users are provided
+-** only with a limited warranty and the software's author, the holder of
+-** the economic rights, and the successive licensors have only limited
+-** liability.
+-** 
+-** In this respect, the user's attention is drawn to the risks associated
+-** with loading, using, modifying and/or developing or reproducing the
+-** software by the user in light of its specific status of free software,
+-** that may mean that it is complicated to manipulate, and that also
+-** therefore means that it is reserved for developers and experienced
+-** professionals having in-depth computer knowledge. Users are therefore
+-** encouraged to load and test the software's suitability as regards
+-** their requirements in conditions enabling the security of their
+-** systems and/or data to be ensured and, more generally, to use and
+-** operate it in the same conditions as regards security.
+-** 
+-** The fact that you are presently reading this means that you have had
+-** knowledge of the CeCILL-C license and that you accept its terms.
+-*/
+-/************************************************************/
+-/**                                                        **/
+-/**   NAME       : metis.h                                 **/
+-/**                                                        **/
+-/**   AUTHOR     : Francois PELLEGRINI                     **/
+-/**                                                        **/
+-/**   FUNCTION   : Compatibility declaration file for the  **/
+-/**                MeTiS interface routines provided by    **/
+-/**                the Scotch project.                     **/
+-/**                                                        **/
+-/**   DATES      : # Version 5.0  : from : 08 sep 2006     **/
+-/**                                 to     07 jun 2007     **/
+-/**                # Version 5.1  : from : 30 jun 2010     **/
+-/**                                 to     30 jun 2010     **/
+-/**                # Version 6.0  : from : 13 sep 2012     **/
+-/**                                 to     13 sep 2012     **/
+-/**                                                        **/
+-/************************************************************/
+-
+-/*
+-**  The defines.
+-*/
+-
+-#ifdef SCOTCH_METIS_PREFIX
+-#define SCOTCH_METIS_PREFIXL        scotch_
+-#define SCOTCH_METIS_PREFIXU        SCOTCH_
+-#endif /* SCOTCH_METIS_PREFIX */
+-
+-#ifndef SCOTCH_METIS_PREFIXL
+-#define SCOTCH_METIS_PREFIXL
+-#endif /* SCOTCH_METIS_PREFIXL */
+-
+-#ifndef SCOTCH_METIS_PREFIXU
+-#define SCOTCH_METIS_PREFIXU
+-#endif /* SCOTCH_METIS_PREFIXU */
+-
+-#ifndef METISNAMEL
+-#define METISNAMEL(s)               METISNAME2(METISNAME3(SCOTCH_METIS_PREFIXL),s)
+-#define METISNAMEU(s)               METISNAME2(METISNAME3(SCOTCH_METIS_PREFIXU),s)
+-#define METISNAME2(p,s)             METISNAME4(p,s)
+-#define METISNAME3(s)               s
+-#define METISNAME4(p,s)             p##s
+-#endif /* METISNAMEL */
+-
+-/*
+-**  The function prototypes.
+-*/
+-
+-void                        METISNAMEU(METIS_EdgeND) (const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const);
+-void                        METISNAMEU(METIS_NodeND) (const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const);
+-void                        METISNAMEU(METIS_NodeWND) (const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const);
+-
+-void                        METISNAMEU(METIS_PartGraphKway) (const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const);
+-void                        METISNAMEU(METIS_PartGraphRecursive) (const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const);
+-void                        METISNAMEU(METIS_PartGraphVKway) (const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const);
+--- A/src/libscotchmetis/metis_skeleton.h	1970-01-01 01:00:00.000000000 +0100
++++ B/src/libscotchmetis/metis_skeleton.h	2015-08-25 13:27:07.224497875 +0200
+@@ -0,0 +1,103 @@
++/*********************************************************
++**                                                      **
++**  WARNING: THIS IS NOT THE ORIGINAL INCLUDE FILE OF   **
++**  THE MeTiS SOFTWARE PACKAGE.                         **
++**  This file is a compatibility include file provided  **
++**  as part of the Scotch software distribution.        **
++**  Preferably use the original MeTiS include file to   **
++**  keep definitions of routines not overloaded by      **
++**  the libScotchMeTiS library.                         **
++**                                                      **
++*********************************************************/
++/* Copyright 2007,2010,2012 IPB, Universite de Bordeaux, INRIA & CNRS
++**
++** This file is part of the Scotch software package for static mapping,
++** graph partitioning and sparse matrix ordering.
++**
++** This software is governed by the CeCILL-C license under French law
++** and abiding by the rules of distribution of free software. You can
++** use, modify and/or redistribute the software under the terms of the
++** CeCILL-C license as circulated by CEA, CNRS and INRIA at the following
++** URL: "http://www.cecill.info".
++** 
++** As a counterpart to the access to the source code and rights to copy,
++** modify and redistribute granted by the license, users are provided
++** only with a limited warranty and the software's author, the holder of
++** the economic rights, and the successive licensors have only limited
++** liability.
++** 
++** In this respect, the user's attention is drawn to the risks associated
++** with loading, using, modifying and/or developing or reproducing the
++** software by the user in light of its specific status of free software,
++** that may mean that it is complicated to manipulate, and that also
++** therefore means that it is reserved for developers and experienced
++** professionals having in-depth computer knowledge. Users are therefore
++** encouraged to load and test the software's suitability as regards
++** their requirements in conditions enabling the security of their
++** systems and/or data to be ensured and, more generally, to use and
++** operate it in the same conditions as regards security.
++** 
++** The fact that you are presently reading this means that you have had
++** knowledge of the CeCILL-C license and that you accept its terms.
++*/
++/************************************************************/
++/**                                                        **/
++/**   NAME       : metis.h                                 **/
++/**                                                        **/
++/**   AUTHOR     : Francois PELLEGRINI                     **/
++/**                                                        **/
++/**   FUNCTION   : Compatibility declaration file for the  **/
++/**                MeTiS interface routines provided by    **/
++/**                the Scotch project.                     **/
++/**                                                        **/
++/**   DATES      : # Version 5.0  : from : 08 sep 2006     **/
++/**                                 to     07 jun 2007     **/
++/**                # Version 5.1  : from : 30 jun 2010     **/
++/**                                 to     30 jun 2010     **/
++/**                # Version 6.0  : from : 13 sep 2012     **/
++/**                                 to     13 sep 2012     **/
++/**                                                        **/
++/************************************************************/
++
++#include<stdint.h>
++
++/*
++**  The defines.
++*/
++
++#ifdef SCOTCH_METIS_PREFIX
++#define SCOTCH_METIS_PREFIXL        scotch_
++#define SCOTCH_METIS_PREFIXU        SCOTCH_
++#endif /* SCOTCH_METIS_PREFIX */
++
++#ifndef SCOTCH_METIS_PREFIXL
++#define SCOTCH_METIS_PREFIXL
++#endif /* SCOTCH_METIS_PREFIXL */
++
++#ifndef SCOTCH_METIS_PREFIXU
++#define SCOTCH_METIS_PREFIXU
++#endif /* SCOTCH_METIS_PREFIXU */
++
++#ifndef METISNAMEL
++#define METISNAMEL(s)               METISNAME2(METISNAME3(SCOTCH_METIS_PREFIXL),s)
++#define METISNAMEU(s)               METISNAME2(METISNAME3(SCOTCH_METIS_PREFIXU),s)
++#define METISNAME2(p,s)             METISNAME4(p,s)
++#define METISNAME3(s)               s
++#define METISNAME4(p,s)             p##s
++#endif /* METISNAMEL */
++
++/*+ Integer type. +*/
++
++typedef DUMMYINT SCOTCH_Num;
++
++/*
++**  The function prototypes.
++*/
++
++void                        METISNAMEU(METIS_EdgeND) (const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const);
++void                        METISNAMEU(METIS_NodeND) (const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const);
++void                        METISNAMEU(METIS_NodeWND) (const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const);
++
++void                        METISNAMEU(METIS_PartGraphKway) (const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const);
++void                        METISNAMEU(METIS_PartGraphRecursive) (const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const);
++void                        METISNAMEU(METIS_PartGraphVKway) (const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const);
+--- A/src/libscotchmetis/parmetis.h	2012-09-13 17:41:21.000000000 +0200
++++ B/src/libscotchmetis/parmetis.h	1970-01-01 01:00:00.000000000 +0100
+@@ -1,100 +0,0 @@
+-/*********************************************************
+-**                                                      **
+-**  WARNING: THIS IS NOT THE ORIGINAL INCLUDE FILE OF   **
+-**  THE ParMeTiS SOFTWARE PACKAGE.                      **
+-**  This file is a compatibility include file provided  **
+-**  as part of the Scotch software distribution.        **
+-**  Preferably use the original ParMeTiS include file   **
+-**  to keep definitions of routines not overloaded by   **
+-**  the libPTScotchMeTiS library.                       **
+-**                                                      **
+-*********************************************************/
+-/* Copyright 2007,2008,2010,2012 IPB, Universite de Bordeaux, INRIA & CNRS
+-**
+-** This file is part of the Scotch software package for static mapping,
+-** graph partitioning and sparse matrix ordering.
+-**
+-** This software is governed by the CeCILL-C license under French law
+-** and abiding by the rules of distribution of free software. You can
+-** use, modify and/or redistribute the software under the terms of the
+-** CeCILL-C license as circulated by CEA, CNRS and INRIA at the following
+-** URL: "http://www.cecill.info".
+-** 
+-** As a counterpart to the access to the source code and rights to copy,
+-** modify and redistribute granted by the license, users are provided
+-** only with a limited warranty and the software's author, the holder of
+-** the economic rights, and the successive licensors have only limited
+-** liability.
+-** 
+-** In this respect, the user's attention is drawn to the risks associated
+-** with loading, using, modifying and/or developing or reproducing the
+-** software by the user in light of its specific status of free software,
+-** that may mean that it is complicated to manipulate, and that also
+-** therefore means that it is reserved for developers and experienced
+-** professionals having in-depth computer knowledge. Users are therefore
+-** encouraged to load and test the software's suitability as regards
+-** their requirements in conditions enabling the security of their
+-** systems and/or data to be ensured and, more generally, to use and
+-** operate it in the same conditions as regards security.
+-** 
+-** The fact that you are presently reading this means that you have had
+-** knowledge of the CeCILL-C license and that you accept its terms.
+-*/
+-/************************************************************/
+-/**                                                        **/
+-/**   NAME       : parmetis.h                              **/
+-/**                                                        **/
+-/**   AUTHOR     : Francois PELLEGRINI                     **/
+-/**                                                        **/
+-/**   FUNCTION   : Compatibility declaration file for the  **/
+-/**                MeTiS interface routines provided by    **/
+-/**                the Scotch project.                     **/
+-/**                                                        **/
+-/**   DATES      : # Version 5.0  : from : 17 oct 2007     **/
+-/**                                 to     18 oct 2007     **/
+-/**                # Version 5.1  : from : 19 jun 2008     **/
+-/**                                 to     30 jun 2010     **/
+-/**                # Version 6.0  : from : 13 sep 2012     **/
+-/**                                 to     13 sep 2012     **/
+-/**                                                        **/
+-/************************************************************/
+-
+-/*
+-**  The defines and includes.
+-*/
+-
+-#ifndef __parmetis_h__
+-#define __parmetis_h__
+-
+-#include <mpi.h>                                  /* Since ParMeTiS does it, do it too */
+-
+-#endif /* __parmetis_h__ */
+-
+-#ifdef SCOTCH_METIS_PREFIX
+-#define SCOTCH_METIS_PREFIXL        scotch_
+-#define SCOTCH_METIS_PREFIXU        SCOTCH_
+-#endif /* SCOTCH_METIS_PREFIX */
+-
+-#ifndef SCOTCH_METIS_PREFIXL
+-#define SCOTCH_METIS_PREFIXL
+-#endif /* SCOTCH_METIS_PREFIXL */
+-
+-#ifndef SCOTCH_METIS_PREFIXU
+-#define SCOTCH_METIS_PREFIXU
+-#endif /* SCOTCH_METIS_PREFIXU */
+-
+-#ifndef METISNAMEL
+-#define METISNAMEL(s)               METISNAME2(METISNAME3(SCOTCH_METIS_PREFIXL),s)
+-#define METISNAMEU(s)               METISNAME2(METISNAME3(SCOTCH_METIS_PREFIXU),s)
+-#define METISNAME2(p,s)             METISNAME4(p,s)
+-#define METISNAME3(s)               s
+-#define METISNAME4(p,s)             p##s
+-#endif /* METISNAMEL */
+-
+-/*
+-**  The function prototypes.
+-*/
+-
+-void                        METISNAMEU(ParMETIS_V3_NodeND) (const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, MPI_Comm * const);
+-void                        METISNAMEU(ParMETIS_V3_PartGeomKway) (const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const float * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const float * const, const float * const, const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, MPI_Comm * const);
+-void                        METISNAMEU(ParMETIS_V3_PartKway) (const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const float * const, const float * const, const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, MPI_Comm * const);
+--- A/src/libscotchmetis/parmetis_skeleton.h	1970-01-01 01:00:00.000000000 +0100
++++ B/src/libscotchmetis/parmetis_skeleton.h	2015-08-25 13:42:17.972454163 +0200
+@@ -0,0 +1,105 @@
++/*********************************************************
++**                                                      **
++**  WARNING: THIS IS NOT THE ORIGINAL INCLUDE FILE OF   **
++**  THE ParMeTiS SOFTWARE PACKAGE.                      **
++**  This file is a compatibility include file provided  **
++**  as part of the Scotch software distribution.        **
++**  Preferably use the original ParMeTiS include file   **
++**  to keep definitions of routines not overloaded by   **
++**  the libPTScotchMeTiS library.                       **
++**                                                      **
++*********************************************************/
++/* Copyright 2007,2008,2010,2012 IPB, Universite de Bordeaux, INRIA & CNRS
++**
++** This file is part of the Scotch software package for static mapping,
++** graph partitioning and sparse matrix ordering.
++**
++** This software is governed by the CeCILL-C license under French law
++** and abiding by the rules of distribution of free software. You can
++** use, modify and/or redistribute the software under the terms of the
++** CeCILL-C license as circulated by CEA, CNRS and INRIA at the following
++** URL: "http://www.cecill.info".
++** 
++** As a counterpart to the access to the source code and rights to copy,
++** modify and redistribute granted by the license, users are provided
++** only with a limited warranty and the software's author, the holder of
++** the economic rights, and the successive licensors have only limited
++** liability.
++** 
++** In this respect, the user's attention is drawn to the risks associated
++** with loading, using, modifying and/or developing or reproducing the
++** software by the user in light of its specific status of free software,
++** that may mean that it is complicated to manipulate, and that also
++** therefore means that it is reserved for developers and experienced
++** professionals having in-depth computer knowledge. Users are therefore
++** encouraged to load and test the software's suitability as regards
++** their requirements in conditions enabling the security of their
++** systems and/or data to be ensured and, more generally, to use and
++** operate it in the same conditions as regards security.
++** 
++** The fact that you are presently reading this means that you have had
++** knowledge of the CeCILL-C license and that you accept its terms.
++*/
++/************************************************************/
++/**                                                        **/
++/**   NAME       : parmetis.h                              **/
++/**                                                        **/
++/**   AUTHOR     : Francois PELLEGRINI                     **/
++/**                                                        **/
++/**   FUNCTION   : Compatibility declaration file for the  **/
++/**                MeTiS interface routines provided by    **/
++/**                the Scotch project.                     **/
++/**                                                        **/
++/**   DATES      : # Version 5.0  : from : 17 oct 2007     **/
++/**                                 to     18 oct 2007     **/
++/**                # Version 5.1  : from : 19 jun 2008     **/
++/**                                 to     30 jun 2010     **/
++/**                # Version 6.0  : from : 13 sep 2012     **/
++/**                                 to     13 sep 2012     **/
++/**                                                        **/
++/************************************************************/
++
++/*
++**  The defines and includes.
++*/
++
++#ifndef __parmetis_h__
++#define __parmetis_h__
++
++#include<stdint.h>
++#include <mpi.h>                                  /* Since ParMeTiS does it, do it too */
++
++#endif /* __parmetis_h__ */
++
++#ifdef SCOTCH_METIS_PREFIX
++#define SCOTCH_METIS_PREFIXL        scotch_
++#define SCOTCH_METIS_PREFIXU        SCOTCH_
++#endif /* SCOTCH_METIS_PREFIX */
++
++#ifndef SCOTCH_METIS_PREFIXL
++#define SCOTCH_METIS_PREFIXL
++#endif /* SCOTCH_METIS_PREFIXL */
++
++#ifndef SCOTCH_METIS_PREFIXU
++#define SCOTCH_METIS_PREFIXU
++#endif /* SCOTCH_METIS_PREFIXU */
++
++#ifndef METISNAMEL
++#define METISNAMEL(s)               METISNAME2(METISNAME3(SCOTCH_METIS_PREFIXL),s)
++#define METISNAMEU(s)               METISNAME2(METISNAME3(SCOTCH_METIS_PREFIXU),s)
++#define METISNAME2(p,s)             METISNAME4(p,s)
++#define METISNAME3(s)               s
++#define METISNAME4(p,s)             p##s
++#endif /* METISNAMEL */
++
++/*+ Integer type. +*/
++
++typedef DUMMYINT SCOTCH_Num;
++
++/*
++**  The function prototypes.
++*/
++
++void                        METISNAMEU(ParMETIS_V3_NodeND) (const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, MPI_Comm * const);
++void                        METISNAMEU(ParMETIS_V3_PartGeomKway) (const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const float * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const float * const, const float * const, const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, MPI_Comm * const);
++void                        METISNAMEU(ParMETIS_V3_PartKway) (const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const float * const, const float * const, const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, MPI_Comm * const);
+--- A/src/Makefile	2014-10-02 17:31:36.000000000 +0200
++++ B/src/Makefile	2015-08-25 13:00:50.288573562 +0200
+@@ -115,6 +115,7 @@ install				:	required	$(bindir)	$(includ
+ 					-$(CP) -f ../bin/[agm]*$(EXE) $(bindir)
+ 					-$(CP) -f ../bin/d[agm]*$(EXE) $(bindir)
+ 					-$(CP) -f ../include/*scotch*.h $(includedir)
++					-$(CP) -f ../include/*metis*.h $(includedir)
+ 					-$(CP) -f ../lib/*scotch*$(LIB) $(libdir)
+ 					-$(CP) -Rf ../man/* $(mandir)
+ 
+--- A/src/Makefile~	1970-01-01 01:00:00.000000000 +0100
++++ B/src/Makefile~	2014-10-02 17:31:36.000000000 +0200
+@@ -0,0 +1,134 @@
++## Copyright 2004,2007,2008,2010-2012,2014 IPB, Universite de Bordeaux, INRIA & CNRS
++##
++## This file is part of the Scotch software package for static mapping,
++## graph partitioning and sparse matrix ordering.
++##
++## This software is governed by the CeCILL-C license under French law
++## and abiding by the rules of distribution of free software. You can
++## use, modify and/or redistribute the software under the terms of the
++## CeCILL-C license as circulated by CEA, CNRS and INRIA at the following
++## URL: "http://www.cecill.info".
++## 
++## As a counterpart to the access to the source code and rights to copy,
++## modify and redistribute granted by the license, users are provided
++## only with a limited warranty and the software's author, the holder of
++## the economic rights, and the successive licensors have only limited
++## liability.
++## 
++## In this respect, the user's attention is drawn to the risks associated
++## with loading, using, modifying and/or developing or reproducing the
++## software by the user in light of its specific status of free software,
++## that may mean that it is complicated to manipulate, and that also
++## therefore means that it is reserved for developers and experienced
++## professionals having in-depth computer knowledge. Users are therefore
++## encouraged to load and test the software's suitability as regards
++## their requirements in conditions enabling the security of their
++## systems and/or data to be ensured and, more generally, to use and
++## operate it in the same conditions as regards security.
++## 
++## The fact that you are presently reading this means that you have had
++## knowledge of the CeCILL-C license and that you accept its terms.
++##
++
++VERSION	= 6
++RELEASE = 0
++PATCHLEVEL = 4
++
++.PHONY				:	clean	default	install	ptscotch	realclean	required	scotch
++
++default				:	scotch
++
++required			:	Makefile.inc	../bin	../include	../lib
++
++Makefile.inc			:
++					@echo "#####################################################################"
++			        	@echo "BEFORE COMPILING Scotch OR PT-Scotch, YOU SHOULD HAVE AN APPROPRIATE"
++					@echo "Makefile.inc FILE IN THIS DIRECTORY. PLEASE LOOK INTO DIRECTORY"
++	        			@echo " ./Make.inc FOR AN EXISTING Makefile.inc FILE THAT FITS YOUR NEED, OR"
++		        		@echo "USE THEM AS MODELS IN CASE YOU NEED TO BUILD A NEW ONE FOR YOUR"
++		        		@echo "PARTICULAR PLATFORM."
++			        	@echo "#####################################################################"
++			        	@echo "Then, type \"make scotch\" (default) for the sequential library"
++			        	@echo "and software, or \"make ptscotch\" for the parallel library and"
++			        	@echo "software."
++					@exit 1
++
++include Makefile.inc
++
++prefix		?= /usr/local
++bindir		?= $(prefix)/bin
++includedir	?= $(prefix)/include
++libdir		?= $(prefix)/lib
++datarootdir	?= $(prefix)/share
++mandir		?= $(datarootdir)/man
++
++../bin				:
++					-$(MKDIR) ../bin
++
++../include			:
++					-$(MKDIR) ../include
++
++../lib				:
++					-$(MKDIR) ../lib
++
++$(bindir)			:
++					-$(MKDIR) $(bindir)
++
++$(datarootdir)			:
++					-$(MKDIR) $(datarootdir)
++
++$(includedir)			:
++					-$(MKDIR) $(includedir)
++
++$(libdir)			:
++					-$(MKDIR) $(libdir)
++
++$(mandir)			:	$(datarootdir)
++					-$(MKDIR) $(mandir)
++
++$(mandir)/man1			:	$(mandir)
++					-$(MKDIR) $(mandir)/man1
++
++scotch				:	required
++					(cd libscotch ;      $(MAKE) VERSION=$(VERSION) RELEASE=$(RELEASE) PATCHLEVEL=$(PATCHLEVEL) scotch && $(MAKE) install)
++					(cd scotch ;         $(MAKE) VERSION=$(VERSION) RELEASE=$(RELEASE) PATCHLEVEL=$(PATCHLEVEL) scotch && $(MAKE) install)
++					(cd libscotchmetis ; $(MAKE)                                                                scotch && $(MAKE) install)
++
++ptscotch			:	required
++					(cd libscotch ;      $(MAKE) VERSION=$(VERSION) RELEASE=$(RELEASE) PATCHLEVEL=$(PATCHLEVEL) ptscotch && $(MAKE) ptinstall)
++					(cd scotch ;         $(MAKE) VERSION=$(VERSION) RELEASE=$(RELEASE) PATCHLEVEL=$(PATCHLEVEL) ptscotch && $(MAKE) ptinstall)
++					(cd libscotchmetis ; $(MAKE)                                                                ptscotch && $(MAKE) ptinstall)
++
++check				:	scotch
++					(cd check ; $(MAKE) check)
++
++ptcheck				:	ptscotch
++					(cd check ; $(MAKE) ptcheck)
++
++esmumps				:	scotch
++					(cd esmumps ; $(MAKE) scotch && $(MAKE) install)
++
++ptesmumps			:	ptscotch
++					(cd esmumps ; $(MAKE) ptscotch && $(MAKE) ptinstall)
++
++install				:	required	$(bindir)	$(includedir)	$(libdir)	$(mandir)/man1
++					-$(CP) -f ../bin/[agm]*$(EXE) $(bindir)
++					-$(CP) -f ../bin/d[agm]*$(EXE) $(bindir)
++					-$(CP) -f ../include/*scotch*.h $(includedir)
++					-$(CP) -f ../lib/*scotch*$(LIB) $(libdir)
++					-$(CP) -Rf ../man/* $(mandir)
++
++clean				:	required
++					(cd libscotch ;      $(MAKE) clean)
++					(cd scotch ;         $(MAKE) clean)
++					(cd libscotchmetis ; $(MAKE) clean)
++					(cd check ;          $(MAKE) clean)
++					(cd esmumps ;        $(MAKE) clean)
++
++realclean			:	required
++					(cd libscotch ;      $(MAKE) realclean)
++					(cd scotch ;         $(MAKE) realclean)
++					(cd libscotchmetis ; $(MAKE) realclean)
++					(cd check ;          $(MAKE) realclean)
++					(cd esmumps ;        $(MAKE) realclean)
++					-$(RM) ../bin/* ../include/* ../lib/*
+--- A/src/Make.inc/Makefile.inc.x86-64_pc_linux2~	1970-01-01 01:00:00.000000000 +0100
++++ B/src/Make.inc/Makefile.inc.x86-64_pc_linux2~	2015-08-25 13:09:33.984548426 +0200
+@@ -0,0 +1,21 @@
++EXE		=
++LIB		= .a
++OBJ		= .o
++
++MAKE		= make
++AR		= ar
++ARFLAGS		= -ruv
++CAT		= cat
++CCS		= gcc
++CCP		= mpicc
++CCD		= gcc
++CFLAGS		= -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -DSCOTCH_PTHREAD -Drestrict=__restrict -DIDXSIZE64 -DINT=int64_t
++CLIBFLAGS	=
++LDFLAGS		= -lz -lm -lrt -pthread
++CP		= cp
++LEX		= flex -Pscotchyy -olex.yy.c
++LN		= ln
++MKDIR		= mkdir
++MV		= mv
++RANLIB		= ranlib
++YACC		= bison -pscotchyy -y -b y
diff --git a/var/spack/repos/builtin/packages/scotch/package.py b/var/spack/repos/builtin/packages/scotch/package.py
index 48ae1490c8..e15696b54b 100644
--- a/var/spack/repos/builtin/packages/scotch/package.py
+++ b/var/spack/repos/builtin/packages/scotch/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,6 +14,8 @@ class Scotch(Package):
     url      = "http://gforge.inria.fr/frs/download.php/latestfile/298/scotch_6.0.4.tar.gz"
     list_url = "http://gforge.inria.fr/frs/?group_id=248"
 
+    version('6.0.6', 'ef676a3118b5590c416176e402fac248')
+    version('6.0.5a', '8430dff7175a1dfd5a3258e75260cf71')
     version('6.0.4', 'd58b825eb95e1db77efe8c6ff42d329f')
     version('6.0.3', '10b0cc0f184de2de99859eafaca83cfc')
     version('6.0.0', 'c50d6187462ba801f9a82133ee666e8e')
@@ -60,6 +43,9 @@ class Scotch(Package):
     # Version-specific patches
     patch('nonthreaded-6.0.4.patch', when='@6.0.4')
     patch('esmumps-ldflags-6.0.4.patch', when='@6.0.4')
+    patch('metis-headers-6.0.4.patch', when='@6.0.4')
+
+    patch('libscotchmetis-return-6.0.5a.patch', when='@6.0.5a')
 
     # NOTE: In cross-compiling environment parallel build
     # produces weird linker errors.
@@ -91,7 +77,7 @@ class Scotch(Package):
             libraries = ['libesmumps'] + libraries
 
         scotchlibs = find_libraries(
-            libraries, root=self.prefix, recurse=True, shared=shared
+            libraries, root=self.prefix, recursive=True, shared=shared
         )
         if '+compression' in self.spec:
             zlibs = self.spec['zlib'].libs
@@ -159,7 +145,7 @@ class Scotch(Package):
         if self.compiler.name == 'gcc':
             cflags.append('-Drestrict=__restrict')
         elif self.compiler.name == 'intel':
-            cflags.append('-restrict')
+            cflags.append('-Drestrict=')
 
         mpicc_path = self.spec['mpi'].mpicc if '+mpi' in self.spec else 'mpicc'
         makefile_inc.append('CCS       = $(CC)')
diff --git a/var/spack/repos/builtin/packages/scr/package.py b/var/spack/repos/builtin/packages/scr/package.py
index 1f49f34969..cffbcd8a12 100644
--- a/var/spack/repos/builtin/packages/scr/package.py
+++ b/var/spack/repos/builtin/packages/scr/package.py
@@ -1,31 +1,11 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 import os
-import shutil
 
 
 class Scr(CMakePackage):
@@ -34,13 +14,16 @@ class Scr(CMakePackage):
        capability for MPI codes"""
 
     homepage = "http://computation.llnl.gov/projects/scalable-checkpoint-restart-for-mpi"
+    url      = "https://github.com/LLNL/scr/archive/v1.2.0.tar.gz"
+    git      = "https://github.com/llnl/scr.git"
 
     # NOTE: scr-v1.1.8 is built with autotools and is not properly build here.
     # scr-v1.1.8 will be deprecated with the upcoming release of v1.2.0
     # url      = "https://github.com/LLNL/scr/releases/download/v1.1.8/scr-1.1.8.tar.gz"
     # version('1.1.8', '6a0f11ad18e27fcfc00a271ff587b06e')
 
-    version('master', git='https://github.com/llnl/scr.git', branch='master')
+    version('master', branch='master')
+    version('1.2.0', '060e9e9c7604c1765f3991f9cd6e9d2d')
 
     depends_on('pdsh+static_modules', type=('build', 'run'))
     depends_on('zlib')
@@ -89,6 +72,8 @@ class Scr(CMakePackage):
     variant('cntl_base', default='/tmp',
             description='Compile time default location for control directory.')
 
+    conflicts('platform=bgq')
+
     def get_abs_path_rel_prefix(self, path):
         # Return path if absolute, otherwise prepend prefix
         if os.path.isabs(path):
@@ -100,6 +85,9 @@ class Scr(CMakePackage):
         spec = self.spec
         args = []
 
+        if 'platform=cray' in spec:
+            args.append('-DSCR_LINK_STATIC=ON')
+
         args.append('-DENABLE_FORTRAN={0}'.format('+fortran' in spec))
 
         conf_path = self.get_abs_path_rel_prefix(
@@ -143,4 +131,4 @@ class Scr(CMakePackage):
         if spec.variants['copy_config'].value:
             dest_path = self.get_abs_path_rel_prefix(
                 spec.variants['scr_config'].value)
-            shutil.copyfile(spec.variants['copy_config'].value, dest_path)
+            install(spec.variants['copy_config'].value, dest_path)
diff --git a/var/spack/repos/builtin/packages/screen/package.py b/var/spack/repos/builtin/packages/screen/package.py
index 34bc952ec6..5094b34971 100644
--- a/var/spack/repos/builtin/packages/screen/package.py
+++ b/var/spack/repos/builtin/packages/screen/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,8 +12,9 @@ class Screen(AutotoolsPackage):
     """
 
     homepage = "https://www.gnu.org/software/screen/"
-    url      = "http://ftp.gnu.org/gnu/screen/screen-4.3.1.tar.gz"
+    url      = "https://ftpmirror.gnu.org/screen/screen-4.3.1.tar.gz"
 
+    version('4.6.2', 'a0f529d3333b128dfaa324d978ba73a8')
     version('4.3.1', '5bb3b0ff2674e29378c31ad3411170ad')
     version('4.3.0', 'f76d28eadc4caaf6cdff00685ae6ad46')
     version('4.2.1', '419a0594e2b25039239af8b90eda7d92')
diff --git a/var/spack/repos/builtin/packages/scripts/package.py b/var/spack/repos/builtin/packages/scripts/package.py
index ddd184b44f..5589169cc8 100644
--- a/var/spack/repos/builtin/packages/scripts/package.py
+++ b/var/spack/repos/builtin/packages/scripts/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,5 +16,5 @@ class Scripts(AutotoolsPackage):
 
     depends_on('libx11')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/scrnsaverproto/package.py b/var/spack/repos/builtin/packages/scrnsaverproto/package.py
index 71fe86abbc..6647763b6a 100644
--- a/var/spack/repos/builtin/packages/scrnsaverproto/package.py
+++ b/var/spack/repos/builtin/packages/scrnsaverproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Scrnsaverproto(AutotoolsPackage):
 
     version('1.2.2', '21704f1bad472d94abd22fea5704bb48')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/sctk/package.py b/var/spack/repos/builtin/packages/sctk/package.py
index e64d2c79aa..33fbb76d70 100644
--- a/var/spack/repos/builtin/packages/sctk/package.py
+++ b/var/spack/repos/builtin/packages/sctk/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from distutils.dir_util import copy_tree
 
 
 class Sctk(Package):
@@ -49,5 +29,4 @@ class Sctk(Package):
         make('config')
         make('all')
         make('install')
-        mkdirp(prefix.bin)
-        copy_tree('bin', prefix.bin)
+        install_tree('bin', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/sdl2-image/package.py b/var/spack/repos/builtin/packages/sdl2-image/package.py
index 3986c59c1e..6a28c37d40 100644
--- a/var/spack/repos/builtin/packages/sdl2-image/package.py
+++ b/var/spack/repos/builtin/packages/sdl2-image/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/sdl2/package.py b/var/spack/repos/builtin/packages/sdl2/package.py
index 272261f54c..5e831ebba3 100644
--- a/var/spack/repos/builtin/packages/sdl2/package.py
+++ b/var/spack/repos/builtin/packages/sdl2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/sed/package.py b/var/spack/repos/builtin/packages/sed/package.py
index 84c5c94ed9..19fd8b7c59 100644
--- a/var/spack/repos/builtin/packages/sed/package.py
+++ b/var/spack/repos/builtin/packages/sed/package.py
@@ -1,33 +1,14 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class Sed(AutotoolsPackage):
     """GNU implementation of the famous stream editor."""
     homepage = "http://www.gnu.org/software/sed/"
-    url      = "http://ftpmirror.gnu.org/sed/sed-4.2.2.tar.bz2"
+    url      = "https://ftpmirror.gnu.org/sed/sed-4.2.2.tar.bz2"
 
     version('4.2.2', '7ffe1c7cdc3233e1e0c4b502df253974')
diff --git a/var/spack/repos/builtin/packages/sentieon-genomics/package.py b/var/spack/repos/builtin/packages/sentieon-genomics/package.py
new file mode 100644
index 0000000000..e860a76bef
--- /dev/null
+++ b/var/spack/repos/builtin/packages/sentieon-genomics/package.py
@@ -0,0 +1,39 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import os.path
+from spack import *
+
+
+class SentieonGenomics(Package):
+    """Sentieon provides complete solutions for secondary DNA analysis.
+    Our software improves upon BWA, GATK, Mutect, and Mutect2 based pipelines.
+    The Sentieon tools are deployable on any CPU-based computing system.
+    Please set the path to the sentieon license server with:
+
+    export SENTIEON_LICENSE=[FQDN]:[PORT]
+
+    Note: A manual download is required.
+    Spack will search your current directory for the download file.
+    Alternatively, add this file to a mirror so that Spack can find it.
+    For instructions on how to set up a mirror, see
+    http://spack.readthedocs.io/en/latest/mirrors.html"""
+
+    homepage = "https://www.sentieon.com/"
+    url      = "file://{0}/sentieon-genomics-201808.01.tar.gz".format(os.getcwd())
+
+    version('201808.01', sha256='6d77bcd5a35539549b28eccae07b19a3b353d027720536e68f46dcf4b980d5f7')
+
+    # Licensing.
+    license_require = True
+    license_vars = ['SENTIEON_LICENSE']
+
+    def install(self, spec, prefix):
+        install_tree('bin', prefix.bin)
+        install_tree('doc', prefix.doc)
+        install_tree('etc', prefix.etc)
+        install_tree('lib', prefix.lib)
+        install_tree('libexec', prefix.libexec)
+        install_tree('share', prefix.share)
diff --git a/var/spack/repos/builtin/packages/seqan/package.py b/var/spack/repos/builtin/packages/seqan/package.py
new file mode 100644
index 0000000000..a13ed6d3b2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/seqan/package.py
@@ -0,0 +1,33 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Seqan(CMakePackage):
+    """SeqAn is an open source C++ library of efficient algorithms and data
+    structures for the analysis of sequences with the focus on biological data.
+    Our library applies a unique generic design that guarantees high
+    performance, generality, extensibility, and integration with other
+    libraries. SeqAn is easy to use and simplifies the development of new
+    software tools with a minimal loss of performance"""
+
+    homepage = "https://www.seqan.de"
+    url      = "https://github.com/seqan/seqan/archive/seqan-v2.4.0.tar.gz"
+
+    version('2.4.0', 'd899821e295fed0a22e08099f40cbc17')
+
+    depends_on('cmake@3.4.0:', type='build')
+    depends_on('python@2.7.0:', type='build')
+    depends_on('py-nose', type='build')
+    depends_on('py-sphinx', type='build')
+    depends_on('boost', type=('build', 'link'))
+    depends_on('zlib', type=('build', 'link'))
+    depends_on('bzip2', type=('build', 'link'))
+
+    conflicts('%intel@:16.0.4')
+    conflicts('%gcc@:4.9.4')
+    conflicts('%llvm@:3.5.1')
diff --git a/var/spack/repos/builtin/packages/seqprep/package.py b/var/spack/repos/builtin/packages/seqprep/package.py
index d4c75cc5fa..793c8e5985 100644
--- a/var/spack/repos/builtin/packages/seqprep/package.py
+++ b/var/spack/repos/builtin/packages/seqprep/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/seqtk/package.py b/var/spack/repos/builtin/packages/seqtk/package.py
index 6393d3e587..addaee78a3 100644
--- a/var/spack/repos/builtin/packages/seqtk/package.py
+++ b/var/spack/repos/builtin/packages/seqtk/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/serf/package.py b/var/spack/repos/builtin/packages/serf/package.py
index 5604b8b166..6135a4ecfa 100644
--- a/var/spack/repos/builtin/packages/serf/package.py
+++ b/var/spack/repos/builtin/packages/serf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -54,6 +35,19 @@ class Serf(SConsPackage):
             'ZLIB={0}'.format(spec['zlib'].prefix),
         ]
 
+        # ZLIB variable is ignored on non-Windows platforms before and
+        # including the version 1.3.9:
+        # https://www.mail-archive.com/dev@serf.apache.org/msg01359.html
+        # The issue is fixed in the trunk. Hopefully, the next stable version
+        # will work properly.
+        if '@:1.3.9' in self.spec:
+            zlib_spec = self.spec['zlib']
+            link_flags = [zlib_spec.libs.search_flags]
+            link_flags.extend([self.compiler.cc_rpath_arg + d
+                               for d in zlib_spec.libs.directories])
+            args.append('LINKFLAGS=' + ' '.join(link_flags))
+            args.append('CPPFLAGS=' + zlib_spec.headers.cpp_flags)
+
         if '+debug' in spec:
             args.append('DEBUG=yes')
         else:
diff --git a/var/spack/repos/builtin/packages/sessreg/package.py b/var/spack/repos/builtin/packages/sessreg/package.py
index af3f001e70..a93604ef09 100644
--- a/var/spack/repos/builtin/packages/sessreg/package.py
+++ b/var/spack/repos/builtin/packages/sessreg/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,7 +17,7 @@ class Sessreg(AutotoolsPackage):
     version('1.1.0', '5d7eb499043c7fdd8d53c5ba43660312')
 
     depends_on('xproto@7.0.25:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def patch(self):
diff --git a/var/spack/repos/builtin/packages/setxkbmap/package.py b/var/spack/repos/builtin/packages/setxkbmap/package.py
index 5a8a5ea345..1ed7903c8e 100644
--- a/var/spack/repos/builtin/packages/setxkbmap/package.py
+++ b/var/spack/repos/builtin/packages/setxkbmap/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Setxkbmap(AutotoolsPackage):
     depends_on('libxkbfile')
     depends_on('libx11')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/sga/package.py b/var/spack/repos/builtin/packages/sga/package.py
index 2c38244675..0349d86c13 100644
--- a/var/spack/repos/builtin/packages/sga/package.py
+++ b/var/spack/repos/builtin/packages/sga/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/shapeit/package.py b/var/spack/repos/builtin/packages/shapeit/package.py
index 4f0295cca1..0cb36d4cf6 100644
--- a/var/spack/repos/builtin/packages/shapeit/package.py
+++ b/var/spack/repos/builtin/packages/shapeit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/shared-mime-info/package.py b/var/spack/repos/builtin/packages/shared-mime-info/package.py
index 80880eebc1..e63f7b048b 100644
--- a/var/spack/repos/builtin/packages/shared-mime-info/package.py
+++ b/var/spack/repos/builtin/packages/shared-mime-info/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 from spack import *
 
@@ -32,6 +13,7 @@ class SharedMimeInfo(AutotoolsPackage):
     homepage = "https://freedesktop.org/wiki/Software/shared-mime-info"
     url      = "http://freedesktop.org/~hadess/shared-mime-info-1.8.tar.xz"
 
+    version('1.9', '45103889b91242850aa47f09325e798b')
     version('1.8', 'f6dcadce764605552fc956563efa058c')
 
     parallel = False
@@ -40,7 +22,7 @@ class SharedMimeInfo(AutotoolsPackage):
     depends_on('libxml2')
     depends_on('intltool', type='build')
     depends_on('gettext', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
 
     def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
         spack_env.prepend_path("XDG_DATA_DIRS",
diff --git a/var/spack/repos/builtin/packages/shiny-server/package.py b/var/spack/repos/builtin/packages/shiny-server/package.py
index 2edd966825..af306b0d98 100644
--- a/var/spack/repos/builtin/packages/shiny-server/package.py
+++ b/var/spack/repos/builtin/packages/shiny-server/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/shocklibs/package.py b/var/spack/repos/builtin/packages/shocklibs/package.py
new file mode 100644
index 0000000000..7cd90918cf
--- /dev/null
+++ b/var/spack/repos/builtin/packages/shocklibs/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Shocklibs(Package):
+    """The lib for shock: An object store for scientific data."""
+
+    homepage = "https://github.com/MG-RAST/Shock"
+    url      = "https://github.com/MG-RAST/Shock/archive/v0.9.24.tar.gz"
+
+    version('0.9.24', '98b2e91e2726c7165f75afaf0ca51a5b')
+
+    def install(self, spec, prefix):
+        install_tree('libs', prefix.libs)
diff --git a/var/spack/repos/builtin/packages/shoremap/package.py b/var/spack/repos/builtin/packages/shoremap/package.py
new file mode 100644
index 0000000000..cd4623ecaf
--- /dev/null
+++ b/var/spack/repos/builtin/packages/shoremap/package.py
@@ -0,0 +1,35 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Shoremap(MakefilePackage):
+    """SHOREmap is a computational tool implementing a method that enables
+       simple and straightforward mapping-by-sequencing analysis.
+
+       Whole genome resequencing of pools of recombinant mutant genomes allows
+       directly linking phenotypic traits to causal mutations. Such an
+       analysis, called mapping-by-sequencing, combines classical genetic
+       mapping and next generation sequencing by relying on selection-induced
+       patterns within genome-wide allele frequency in pooled genomes."""
+
+    homepage = "http://bioinfo.mpipz.mpg.de/shoremap/"
+    url      = "http://bioinfo.mpipz.mpg.de/shoremap/SHOREmap_v3.6.tar.gz"
+
+    version('3.6', 'ccc9331189705a139d50f2c161178cb1')
+
+    depends_on('dislin')
+
+    def edit(self, spec, prefix):
+        makefile = FileFilter('makefile')
+        makefile.filter(r'-L/usr/lib/',
+                        self.spec['libxt'].libs.search_flags)
+        makefile.filter(r'-L\./dislin.* -ldislin_d',
+                        self.spec['dislin:d'].libs.ld_flags)
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('SHOREmap', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/shortbred/package.py b/var/spack/repos/builtin/packages/shortbred/package.py
new file mode 100644
index 0000000000..6105e4e8f0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/shortbred/package.py
@@ -0,0 +1,32 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Shortbred(Package):
+    """ShortBRED is a system for profiling protein families of interest at
+    very high specificity in shotgun meta'omic sequencing data."""
+
+    homepage = "https://huttenhower.sph.harvard.edu/shortbred"
+    url      = "https://bitbucket.org/biobakery/shortbred/get/0.9.4.tar.gz"
+
+    version('0.9.4', 'ad3dff344cbea3713e78b384afad28fd')
+
+    depends_on('blast-plus@2.2.28:')
+    depends_on('cdhit@4.6:')
+    depends_on('muscle@3.8.31:')
+    depends_on('python@2.7.9:')
+    depends_on('py-biopython')
+    depends_on('usearch@6.0.307:')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('shortbred_identify.py', prefix.bin)
+        install('shortbred_quantify.py', prefix.bin)
+        install_tree('src', prefix.src)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PYTHONPATH', self.prefix)
diff --git a/var/spack/repos/builtin/packages/shortstack/package.py b/var/spack/repos/builtin/packages/shortstack/package.py
index 75d363e185..5f55022ec6 100644
--- a/var/spack/repos/builtin/packages/shortstack/package.py
+++ b/var/spack/repos/builtin/packages/shortstack/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/showfont/package.py b/var/spack/repos/builtin/packages/showfont/package.py
index 769c77f076..71c8b138d3 100644
--- a/var/spack/repos/builtin/packages/showfont/package.py
+++ b/var/spack/repos/builtin/packages/showfont/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Showfont(AutotoolsPackage):
 
     depends_on('libfs')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/shuffile/package.py b/var/spack/repos/builtin/packages/shuffile/package.py
new file mode 100644
index 0000000000..2bc1c28ca5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/shuffile/package.py
@@ -0,0 +1,30 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Shuffile(CMakePackage):
+    """Shuffle files between MPI ranks"""
+
+    homepage = "https://github.com/ECP-VeloC/shuffile"
+    url      = "https://github.com/ECP-VeloC/shuffile/archive/v0.0.2.zip"
+    git      = "https://github.com/ecp-veloc/shuffile.git"
+
+    tags = ['ecp']
+
+    version('master', branch='master')
+    version('0.0.3', sha256='6debdd9d6e6f1c4ec31015d7956e8b556acd61ce31f757e4d1fa5002029c75e2')
+
+    depends_on('mpi')
+    depends_on('kvtree')
+
+    def cmake_args(self):
+        args = []
+        args.append("-DMPI_C_COMPILER=%s" % self.spec['mpi'].mpicc)
+        if self.spec.satisfies('platform=cray'):
+            args.append("-DSHUFFILE_LINK_STATIC=ON")
+        args.append("-DWITH_KVTREE_PREFIX=%s" % self.spec['kvtree'].prefix)
+        return args
diff --git a/var/spack/repos/builtin/packages/sickle/package.py b/var/spack/repos/builtin/packages/sickle/package.py
index 248f1ef3b9..9b0a14ba3f 100644
--- a/var/spack/repos/builtin/packages/sickle/package.py
+++ b/var/spack/repos/builtin/packages/sickle/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/siesta/configure.patch b/var/spack/repos/builtin/packages/siesta/configure.patch
new file mode 100644
index 0000000000..577c77f529
--- /dev/null
+++ b/var/spack/repos/builtin/packages/siesta/configure.patch
@@ -0,0 +1,53 @@
+--- a/Src/configure	2017-11-23 12:42:40.909339915 +0100
++++ b/Src/configure	2017-11-23 12:42:59.911416449 +0100
+@@ -6000,7 +6000,7 @@
+   withval="$with_netcdf"
+ 
+ fi;
+-if test x$with_netcdf != xno; then
++if test "x$with_netcdf" != xno; then
+ 
+ tw_netcdf_ok=no
+ ac_ext=${FC_SRCEXT-f}
+@@ -6069,7 +6069,7 @@
+   LIBS="$save_LIBS"
+ fi
+ if test $tw_netcdf_ok = yes; then
+-  DEFS="$DEFS CDF";NETCDF_INTERFACE="libnetcdf_f90.a"
++  DEFS="$DEFS CDF";
+ else
+   NETCDF_LIBS="";tw_netcdf_ok=no;if test ! -z "$with_netcdf"; then { { echo "$as_me:$LINENO: error: Could not find NetCDF library." >&5
+ echo "$as_me: error: Could not find NetCDF library." >&2;}
+--- a/Util/TBTrans_rep/Makefile	2017-12-08 09:49:02.307877000 +0100
++++ b/Util/TBTrans_rep/Makefile	2017-12-08 09:49:44.385288000 +0100
+@@ -14,7 +14,7 @@
+ # Please see note about Linear-Algebra libraries below
+ #
+ 
+-default: what tbtrans 
++default: what tbtrans_rep 
+ 
+ VPATH:=$(shell pwd)/../../Src
+ OBJDIR=Obj
+@@ -91,16 +91,16 @@
+                           "ARCH_MAKE=../$(ARCH_MAKE)" \
+                           "INCFLAGS=$(LINALG_INCFLAGS)" "FFLAGS=$(FFLAGS:$(IPO_FLAG)=)" $(LINALG))
+ 
+-tbtrans: FPPFLAGS+=$(DEFS_PREFIX) -DTBTRANS
+-tbtrans: DEFS+=$(DEFS_PREFIX) -DTBTRANS
+-tbtrans: $(MPI_INTERFACE) $(FDF) $(TBTOBJS) $(SYSOBJ) $(LINALG)
+-	$(FC) $(FFLAGS) $(LDFLAGS) -o tbtrans \
++tbtrans_rep: FPPFLAGS+=$(DEFS_PREFIX) -DTBTRANS
++tbtrans_rep: DEFS+=$(DEFS_PREFIX) -DTBTRANS
++tbtrans_rep: $(MPI_INTERFACE) $(FDF) $(TBTOBJS) $(SYSOBJ) $(LINALG)
++	$(FC) $(FFLAGS) $(LDFLAGS) -o tbtrans_rep \
+               $(TBTOBJS) $(MPI_INTERFACE)  \
+               $(FDF) $(LIBS) $(LINALG)  || echo "***Please see top of Makefile"
+ 
+ clean: 
+ 	@echo "==> Cleaning object, library, and executable files"
+-	rm -f tbtrans *.o *.a *.mod
++	rm -f tbtrans_rep *.o *.a *.mod
+ 	rm -rf ./fdf
+ 	rm -rf ./MPI
+ 	rm -rf ./Libs
diff --git a/var/spack/repos/builtin/packages/siesta/package.py b/var/spack/repos/builtin/packages/siesta/package.py
new file mode 100644
index 0000000000..ec35aa9160
--- /dev/null
+++ b/var/spack/repos/builtin/packages/siesta/package.py
@@ -0,0 +1,77 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+import os
+
+
+class Siesta(Package):
+    """SIESTA performs electronic structure calculations and ab initio molecular
+       dynamics simulations of molecules and solids."""
+
+    homepage = "https://departments.icmab.es/leem/siesta/"
+
+    version('4.0.1', '5cb60ce068f2f6e84fa9184ffca94c08', url='https://launchpad.net/siesta/4.0/4.0.1/+download/siesta-4.0.1.tar.gz')
+    version('3.2-pl-5', '27a300c65eb2a25d107d910d26aaf81a', url='http://departments.icmab.es/leem/siesta/CodeAccess/Code/siesta-3.2-pl-5.tgz')
+
+    patch('configure.patch', when='@:4.0')
+
+    depends_on('mpi')
+    depends_on('blas')
+    depends_on('lapack')
+    depends_on('scalapack')
+    depends_on('netcdf')
+    depends_on('netcdf-fortran')
+
+    phases = ['configure', 'build', 'install']
+
+    def configure(self, spec, prefix):
+        sh = which('sh')
+        configure_args = ['--enable-mpi',
+                          '--with-blas=%s' % spec['blas'].libs,
+                          '--with-lapack=%s' % spec['lapack'].libs,
+                          # need to include BLAS below because Intel MKL's
+                          # BLACS depends on BLAS, otherwise the compiler
+                          # test fails
+                          '--with-blacs=%s' % (spec['scalapack'].libs +
+                                               spec['blas'].libs),
+                          '--with-scalapack=%s' % spec['scalapack'].libs,
+                          '--with-netcdf=%s' % (spec['netcdf-fortran'].libs +
+                                                spec['netcdf'].libs),
+                          # need to specify MPIFC explicitly below, otherwise
+                          # Intel's mpiifort is not found
+                          'MPIFC=%s' % spec['mpi'].mpifc
+                          ]
+        for d in ['Obj', 'Obj_trans']:
+            with working_dir(d, create=True):
+                sh('../Src/configure', *configure_args)
+                if spec.satisfies('@:4.0%intel'):
+                    with open('arch.make', 'a') as f:
+                        f.write('\natom.o: atom.F\n')
+                        f.write('\t$(FC) -c $(FFLAGS) -O1')
+                        f.write('$(INCFLAGS) $(FPPFLAGS) $<')
+                sh('../Src/obj_setup.sh')
+
+    def build(self, spec, prefix):
+        with working_dir('Obj'):
+            make(parallel=False)
+        with working_dir('Obj_trans'):
+            make('transiesta', parallel=False)
+        with working_dir('Util'):
+            sh = which('sh')
+            sh('build_all.sh')
+
+    def install(self, spec, prefix):
+        mkdir(prefix.bin)
+        with working_dir('Obj'):
+            install('siesta', prefix.bin)
+        with working_dir('Obj_trans'):
+            install('transiesta', prefix.bin)
+        for root, _, files in os.walk('Util'):
+            for fname in files:
+                fname = join_path(root, fname)
+                if os.access(fname, os.X_OK):
+                    install(fname, prefix.bin)
diff --git a/var/spack/repos/builtin/packages/signalp/package.py b/var/spack/repos/builtin/packages/signalp/package.py
index 95197badfc..cbb5126884 100644
--- a/var/spack/repos/builtin/packages/signalp/package.py
+++ b/var/spack/repos/builtin/packages/signalp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
diff --git a/var/spack/repos/builtin/packages/signify/package.py b/var/spack/repos/builtin/packages/signify/package.py
new file mode 100755
index 0000000000..7c98977c88
--- /dev/null
+++ b/var/spack/repos/builtin/packages/signify/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Signify(MakefilePackage):
+    """OpenBSD tool to signs and verify signatures on files."""
+
+    homepage = "https://github.com/aperezdc/signify"
+    url      = "https://github.com/aperezdc/signify/archive/v23.tar.gz"
+
+    version('23', '0552295572a172740ae8427eb018ede8')
+
+    depends_on('libbsd@0.8:')
+
+    def setup_environment(self, spack_env, run_env):
+        spack_env.set('PREFIX', self.prefix)
diff --git a/var/spack/repos/builtin/packages/silo/package.py b/var/spack/repos/builtin/packages/silo/package.py
index 763fc66383..fed4ea223e 100644
--- a/var/spack/repos/builtin/packages/silo/package.py
+++ b/var/spack/repos/builtin/packages/silo/package.py
@@ -1,38 +1,21 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class Silo(Package):
+class Silo(AutotoolsPackage):
     """Silo is a library for reading and writing a wide variety of scientific
        data to binary, disk files."""
 
     homepage = "http://wci.llnl.gov/simulation/computer-codes/silo"
     url      = "https://wci.llnl.gov/content/assets/docs/simulation/computer-codes/silo/silo-4.10.2/silo-4.10.2.tar.gz"
 
-    version('4.10.2', '9ceac777a2f2469ac8cef40f4fab49c8')
+    version('4.10.2', '9ceac777a2f2469ac8cef40f4fab49c8', preferred=True)
+    version('4.10.2-bsd', '60fef9ce373daf1e9cc8320cfa509bc5',
+            url="https://wci.llnl.gov/content/assets/docs/simulation/computer-codes/silo/silo-4.10.2/silo-4.10.2-bsd.tar.gz")
     version('4.9', 'a83eda4f06761a86726e918fc55e782a')
     version('4.8', 'b1cbc0e7ec435eb656dc4b53a23663c9')
 
@@ -42,14 +25,30 @@ class Silo(Package):
             description='Builds Silex, a GUI for viewing Silo files')
     variant('pic', default=True,
             description='Produce position-independent code (for shared libs)')
+    variant('mpi', default=True,
+            description='Compile with MPI Compatibility')
 
-    depends_on('hdf5')
+    depends_on('hdf5~mpi', when='~mpi')
+    depends_on('mpi', when='+mpi')
+    depends_on('hdf5+mpi', when='+mpi')
     depends_on('qt', when='+silex')
+    depends_on('zlib')
 
     patch('remove-mpiposix.patch', when='@4.8:4.10.2')
 
-    def install(self, spec, prefix):
+    def flag_handler(self, name, flags):
+        if name == 'ldflags' and self.spec['hdf5'].satisfies('~shared'):
+            flags.append('-ldl')
+        return (flags, None, None)
+
+    def configure_args(self):
+        spec = self.spec
         config_args = [
+            '--with-hdf5=%s,%s' % (spec['hdf5'].prefix.include,
+                                   spec['hdf5'].prefix.lib),
+            '--with-zlib=%s,%s' % (spec['zlib'].prefix.include,
+                                   spec['zlib'].prefix.lib),
+            '--enable-install-lite-headers',
             '--enable-fortran' if '+fortran' in spec else '--disable-fortran',
             '--enable-silex' if '+silex' in spec else '--disable-silex',
             '--enable-shared' if '+shared' in spec else '--disable-shared',
@@ -64,14 +63,9 @@ class Silo(Package):
                 'CXXFLAGS={0}'.format(self.compiler.pic_flag),
                 'FCFLAGS={0}'.format(self.compiler.pic_flag)]
 
-        configure(
-            '--prefix=%s' % prefix,
-            '--with-hdf5=%s,%s' % (spec['hdf5'].prefix.include,
-                                   spec['hdf5'].prefix.lib),
-            '--with-zlib=%s,%s' % (spec['zlib'].prefix.include,
-                                   spec['zlib'].prefix.lib),
-            '--enable-install-lite-headers',
-            *config_args)
+        if '+mpi' in spec:
+            config_args.append('CC=%s' % spec['mpi'].mpicc)
+            config_args.append('CXX=%s' % spec['mpi'].mpicxx)
+            config_args.append('FC=%s' % spec['mpi'].mpifc)
 
-        make()
-        make('install')
+        return config_args
diff --git a/var/spack/repos/builtin/packages/simplemoc/package.py b/var/spack/repos/builtin/packages/simplemoc/package.py
index 8f6759b019..49f91dc605 100644
--- a/var/spack/repos/builtin/packages/simplemoc/package.py
+++ b/var/spack/repos/builtin/packages/simplemoc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -33,9 +14,9 @@ class Simplemoc(MakefilePackage):
         light water reactor simulation."""
 
     homepage = "https://github.com/ANL-CESAR/SimpleMOC/"
-    url = "https://github.com/ANL-CESAR/SimpleMOC/archive/master.tar.gz"
+    url = "https://github.com/ANL-CESAR/SimpleMOC/archive/v4.tar.gz"
 
-    version('1.0', 'd8827221a4ae76e9766a32e16d143e60')
+    version('4', sha256='a39906014fdb234c43bf26e1919bdc8a13097788812e0b353a492b8e568816a6')
 
     tags = ['proxy-app']
 
diff --git a/var/spack/repos/builtin/packages/simul/package.py b/var/spack/repos/builtin/packages/simul/package.py
index 7ef8720dc9..e01f2d81da 100644
--- a/var/spack/repos/builtin/packages/simul/package.py
+++ b/var/spack/repos/builtin/packages/simul/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/simulationio/package.py b/var/spack/repos/builtin/packages/simulationio/package.py
index b027f49584..42d945dac0 100644
--- a/var/spack/repos/builtin/packages/simulationio/package.py
+++ b/var/spack/repos/builtin/packages/simulationio/package.py
@@ -1,40 +1,22 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
 
 class Simulationio(CMakePackage):
     """SimulationIO: Efficient and convenient I/O for large PDE simulations"""
+
     homepage = "https://github.com/eschnett/SimulationIO"
     url      = "https://github.com/eschnett/SimulationIO/archive/version/0.1.0.tar.gz"
+    git      = "https://github.com/eschnett/SimulationIO.git"
 
+    version('develop', branch='master')
     version('1.0.0', '5cbf1d0084eb436d861ffcdd297eaa08')
     version('0.1.0', '00f7dabc08ed1ab77858785ce0809f50')
-    version('develop',
-            git='https://github.com/eschnett/SimulationIO.git', branch='master')
 
     variant('julia', default=False)
     variant('python', default=True)
diff --git a/var/spack/repos/builtin/packages/singularity/package.py b/var/spack/repos/builtin/packages/singularity/package.py
index 810a811d39..838cfe6f3e 100644
--- a/var/spack/repos/builtin/packages/singularity/package.py
+++ b/var/spack/repos/builtin/packages/singularity/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,13 +10,23 @@ class Singularity(AutotoolsPackage):
     """Singularity is a container platform focused on supporting 'Mobility of
        Compute'"""
 
-    homepage = "http://singularity.lbl.gov/"
-    url      = "https://github.com/singularityware/singularity/archive/2.4.tar.gz"
+    homepage = "https://www.sylabs.io/singularity/"
+    url      = "https://github.com/singularityware/singularity/releases/download/2.5.2/singularity-2.5.2.tar.gz"
+    git      = "https://github.com/singularityware/singularity.git"
+
+    # Versions before 2.5.2 suffer from a serious security problem.
+    # https://nvd.nist.gov/vuln/detail/CVE-2018-12021
+    version('develop', branch='master')
+    version('2.6.0', sha256='7c425211a099f6fa6f74037e6e17be58fb5923b0bd11aea745e48ef83c488b49')
+    version('2.5.2', '2edc1a8ac9a4d7d26fba6244f1c5fd95')
 
-    version('2.4', 'd357ce68ef2f8149edd84155731531465dbe74148c37719f87f168fc39384377')
-    version('2.3.1', '292ff7fe3db09c854b8accf42f763f62')
+    depends_on('libarchive', when='@2.5.2:')
+    # these are only needed if we're grabbing the unreleased tree
+    depends_on('m4',       type='build', when='@develop')
+    depends_on('autoconf', type='build', when='@develop')
+    depends_on('automake', type='build', when='@develop')
+    depends_on('libtool',  type='build', when='@develop')
 
-    depends_on('m4',       type='build')
-    depends_on('autoconf', type='build')
-    depends_on('automake', type='build')
-    depends_on('libtool',  type='build')
+    # When installing as root, the copy has to run before chmod runs
+    def install(self, spec, prefix):
+        make('install', parallel=False)
diff --git a/var/spack/repos/builtin/packages/skilion-onedrive/package.py b/var/spack/repos/builtin/packages/skilion-onedrive/package.py
new file mode 100644
index 0000000000..a78d2c8ce5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/skilion-onedrive/package.py
@@ -0,0 +1,37 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class SkilionOnedrive(MakefilePackage):
+    """A complete tool to interact with OneDrive on Linux,
+    developed by Skilion, following the UNIX philosophy."""
+
+    homepage = "https://github.com/skilion/onedrive"
+    url      = "https://github.com/skilion/onedrive/archive/v1.1.1.tar.gz"
+
+    version('1.1.1', sha256='fb51c81ec95c28f3fe3b29e3b7f915e30161bd5f4b14bb53ae5c2233cc1e92e9')
+
+    depends_on('dmd')
+    depends_on('curl')
+    depends_on('sqlite')
+
+    def edit(self, spec, prefix):
+        makefile = FileFilter('Makefile')
+        # Generate the version file
+        makefile.filter('.git/HEAD .git/index', '', string=True)
+        makefile.filter('$(shell git describe --tags)',
+                        '{0}'.format(spec.version),
+                        string=True)
+        # Patch sqlite.d https://github.com/skilion/onedrive/issues/392
+        sqlited = FileFilter('src/sqlite.d')
+        sqlited.filter('std.c.stdlib', 'core.stdc.stdlib', String=True)
+
+    def build(self, spec, prefix):
+        make('onedrive', 'DESTDIR={0}'.format(prefix), 'PREFIX=/')
+
+    def install(self, spec, prefix):
+        make('install', 'DESTDIR={0}'.format(prefix), 'PREFIX=/')
diff --git a/var/spack/repos/builtin/packages/sleef/package.py b/var/spack/repos/builtin/packages/sleef/package.py
new file mode 100644
index 0000000000..2375766582
--- /dev/null
+++ b/var/spack/repos/builtin/packages/sleef/package.py
@@ -0,0 +1,16 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Sleef(CMakePackage):
+    """SIMD Library for Evaluating Elementary Functions,
+    vectorized libm and DFT."""
+
+    homepage = "http://sleef.org"
+    url      = "https://github.com/shibatch/sleef/archive/3.2.tar.gz"
+
+    version('3.2', '459215058f2c8d55cd2b644d56c8c4f0')
diff --git a/var/spack/repos/builtin/packages/slepc/package.py b/var/spack/repos/builtin/packages/slepc/package.py
index ac8df77d50..cb79b37acf 100644
--- a/var/spack/repos/builtin/packages/slepc/package.py
+++ b/var/spack/repos/builtin/packages/slepc/package.py
@@ -1,53 +1,43 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
+import sys
 from spack import *
 
 
 class Slepc(Package):
-    """
-    Scalable Library for Eigenvalue Problem Computations.
-    """
+    """Scalable Library for Eigenvalue Problem Computations."""
 
     homepage = "http://www.grycap.upv.es/slepc"
-    url = "http://slepc.upv.es/download/distrib/slepc-3.6.2.tar.gz"
+    url      = "http://slepc.upv.es/download/distrib/slepc-3.6.2.tar.gz"
+    git      = "https://bitbucket.org/slepc/slepc.git"
 
+    version('develop', branch='master')
+    version('3.10.1', 'f64787c8c2ab3d2f6db3c67d2bfe6ee84f741ce3dfde1d2f8221e131820a12a1')
+    version('3.10.0', '069d7a579995e0be1567c5bc869251e29c00044369a786933ca3040149d0412a')
+    version('3.9.2', '247585b3f8c10bf50b9464cb8ef7b5f22bead6f96524384897a37ec4146eb03e')
+    version('3.9.1', 'e174ea7c127d9161eef976b0288f0c56d443a58d6ab2dc8af1e8bd66f156ce17')
+    version('3.9.0', '1f3930db56b4065aaf214ea758ddff1a70bf19d45544cbdfd19d2787db4bfe0b')
+    version('3.8.2', '1e7d20d20eb26da307d36017461fe4a55f40e947e232739179dbe6412e22ed13')
     version('3.8.0', 'c58ccc4e852d1da01112466c48efa41f0839649f3a265925788237d76cd3d963')
     version('3.7.4', '2fb782844e3bc265a8d181c3c3e2632a4ca073111c874c654f1365d33ca2eb8a')
     version('3.7.3', '3ef9bcc645a10c1779d56b3500472ceb66df692e389d635087d30e7c46424df9')
     version('3.7.1', '670216f263e3074b21e0623c01bc0f562fdc0bffcd7bd42dd5d8edbe73a532c2')
     version('3.6.3', '384939d009546db37bc05ed81260c8b5ba451093bf891391d32eb7109ccff876')
     version('3.6.2', '2ab4311bed26ccf7771818665991b2ea3a9b15f97e29fd13911ab1293e8e65df')
-    version('develop', git='https://bitbucket.org/slepc/slepc.git')
 
     variant('arpack', default=True, description='Enables Arpack wrappers')
+    variant('blopex', default=False, description='Enables BLOPEX wrappers')
 
     # NOTE: make sure PETSc and SLEPc use the same python.
     depends_on('python@2.6:2.8', type='build')
     # Cannot mix release and development versions of SLEPc and PETSc:
     depends_on('petsc@develop', when='@develop')
+    depends_on('petsc@3.10:3.10.99', when='@3.10:3.10.99')
+    depends_on('petsc@3.9:3.9.99', when='@3.9:3.9.99')
     depends_on('petsc@3.8:3.8.99', when='@3.8:3.8.99')
     depends_on('petsc@3.7:3.7.7', when='@3.7.1:3.7.4')
     depends_on('petsc@3.6.3:3.6.4', when='@3.6.2:3.6.3')
@@ -59,6 +49,13 @@ class Slepc(Package):
     # Arpack can not be used with 64bit integers.
     conflicts('+arpack', when='^petsc+int64')
 
+    resource(name='blopex',
+             url='http://slepc.upv.es/download/external/blopex-1.1.2.tar.gz',
+             sha256='0081ee4c4242e635a8113b32f655910ada057c59043f29af4b613508a762f3ac',
+             destination=join_path('installed-arch-' + sys.platform + '-c-opt',
+                                   'externalpackages'),
+             when='+blopex')
+
     def install(self, spec, prefix):
         # set SLEPC_DIR for installation
         # Note that one should set the current (temporary) directory instead
@@ -80,6 +77,11 @@ class Slepc(Package):
                     '--with-arpack-flags=-lparpack,-larpack'
                 ])
 
+        # It isn't possible to install BLOPEX separately and link to it;
+        # BLOPEX has to be downloaded with SLEPc at configure time
+        if '+blopex' in spec:
+            options.append('--download-blopex')
+
         configure('--prefix=%s' % prefix, *options)
 
         make('MAKE_NP=%s' % make_jobs, parallel=False)
diff --git a/var/spack/repos/builtin/packages/slurm/package.py b/var/spack/repos/builtin/packages/slurm/package.py
index ac0d6f2610..afa3fc27db 100644
--- a/var/spack/repos/builtin/packages/slurm/package.py
+++ b/var/spack/repos/builtin/packages/slurm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -43,6 +24,8 @@ class Slurm(AutotoolsPackage):
     homepage = 'https://slurm.schedmd.com'
     url = 'https://github.com/SchedMD/slurm/archive/slurm-17-02-6-1.tar.gz'
 
+    version('18-08-0-1', sha256='62129d0f2949bc8a68ef86fe6f12e0715cbbf42f05b8da6ef7c3e7e7240b50d9')
+    version('17-11-9-2', sha256='6e34328ed68262e776f524f59cca79ac75bcd18030951d45ea545a7ba4c45906')
     version('17-02-6-1', '8edbb9ad41819464350d9de013367020')
 
     variant('gtk', default=False, description='Enable GTK+ support')
@@ -64,11 +47,11 @@ class Slurm(AutotoolsPackage):
     depends_on('lz4')
     depends_on('munge')
     depends_on('openssl')
-    depends_on('pkg-config', type='build')
-    depends_on('readline')
+    depends_on('pkgconfig', type='build')
+    depends_on('readline', when='+readline')
     depends_on('zlib')
 
-    depends_on('gtkplus+X', when='+gtk')
+    depends_on('gtkplus', when='+gtk')
     depends_on('hdf5', when='+hdf5')
     depends_on('hwloc', when='+hwloc')
     depends_on('mariadb', when='+mariadb')
@@ -89,9 +72,7 @@ class Slurm(AutotoolsPackage):
         if '~gtk' in spec:
             args.append('--disable-gtktest')
 
-        if '+readline' in spec:
-            args.append('--with-readline={0}'.format(spec['readline'].prefix))
-        else:
+        if '~readline' in spec:
             args.append('--without-readline')
 
         if '+hdf5' in spec:
diff --git a/var/spack/repos/builtin/packages/smalt/package.py b/var/spack/repos/builtin/packages/smalt/package.py
index 4c65afe20d..23466e0fd1 100644
--- a/var/spack/repos/builtin/packages/smalt/package.py
+++ b/var/spack/repos/builtin/packages/smalt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/smc/package.py b/var/spack/repos/builtin/packages/smc/package.py
deleted file mode 100644
index 353e5f46b9..0000000000
--- a/var/spack/repos/builtin/packages/smc/package.py
+++ /dev/null
@@ -1,83 +0,0 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-from spack import *
-import glob
-
-
-class Smc(MakefilePackage):
-    """A minimalist high-order finite difference algorithm
-    for combustion problems. It includes core discretizations
-    for advection, diffusive transport and chemical kinetics.
-    The models for computing diffusive transport coefficients
-    have been replaced by a simplified approximation
-    but the full structure of the discretization of
-    the diffusive terms have been preserved."""
-
-    homepage = "https://ccse.lbl.gov/ExaCT/index.html"
-    url      = "https://ccse.lbl.gov/ExaCT/SMC.tar.gz"
-    tags     = ['proxy-app']
-
-    version('master', '94a4ea94abbc5e61397c2a4d1fb56ed6')
-
-    variant(
-        'mpi', default=True,
-        description='Build with MPI support')
-    variant(
-        'openmp', default=True,
-        description='Build with OpenMP support')
-    variant(
-        'debug', default=False,
-        description='Build with debugging')
-#   variant(
-#       'mic', default=False,
-#       description='Compile for Intel Xeon Phi')
-    variant(
-        'k_use_automatic', default=True,
-        description='Some arrays in kernels.F90 will be automatic')
-
-    depends_on('mpi', when='+mpi')
-    depends_on('gmake', type='build')
-
-    def edit(self, spec, prefix):
-        makefile = FileFilter('GNUmakefile')
-        if '~mpi' in spec:
-            makefile.filter('MPI := t', '#')
-        if '~openmp' in spec:
-            makefile.filter('OMP := t', '#')
-        if '+debug' in spec:
-            makefile.filter('NDEBUG :=', '#')
-        if '~k_use_automatic' in spec:
-            makefile.filter('K_U.*:= t', '#')
-        if self.compiler.name == 'intel':
-            makefile.filter('COMP := .*', 'COMP := Intel')
-
-    def install(self, spec, prefix):
-        mkdirp(prefix.bin)
-        files = glob.glob(join_path(self.build_directory, '*.exe'))
-        for f in files:
-            install(f, prefix.bin)
-        install('inputs_SMC', prefix.bin)
-        install('README', prefix)
-        install('BoxLib.license.txt', prefix)
diff --git a/var/spack/repos/builtin/packages/smproxy/package.py b/var/spack/repos/builtin/packages/smproxy/package.py
index 571b25d4b6..bc4f943244 100644
--- a/var/spack/repos/builtin/packages/smproxy/package.py
+++ b/var/spack/repos/builtin/packages/smproxy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Smproxy(AutotoolsPackage):
     depends_on('libxt')
     depends_on('libxmu')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/snakemake/package.py b/var/spack/repos/builtin/packages/snakemake/package.py
index d97dc47442..3c55b55ec6 100644
--- a/var/spack/repos/builtin/packages/snakemake/package.py
+++ b/var/spack/repos/builtin/packages/snakemake/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/snap-berkeley/package.py b/var/spack/repos/builtin/packages/snap-berkeley/package.py
index a6b1e08c47..4f7865ceca 100644
--- a/var/spack/repos/builtin/packages/snap-berkeley/package.py
+++ b/var/spack/repos/builtin/packages/snap-berkeley/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/snap-korf/package.py b/var/spack/repos/builtin/packages/snap-korf/package.py
index 68fb4c61ae..840d2ccefb 100644
--- a/var/spack/repos/builtin/packages/snap-korf/package.py
+++ b/var/spack/repos/builtin/packages/snap-korf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
 
diff --git a/var/spack/repos/builtin/packages/snap/package.py b/var/spack/repos/builtin/packages/snap/package.py
index 7bc88b812f..8695a9efbf 100644
--- a/var/spack/repos/builtin/packages/snap/package.py
+++ b/var/spack/repos/builtin/packages/snap/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,10 +15,11 @@ class Snap(MakefilePackage):
     It is modeled off the Los Alamos National Laboratory code PARTISN."""
 
     homepage = "https://github.com/lanl/SNAP"
-    url      = ""
-    tags     = ['proxy-app']
+    git      = "https://github.com/lanl/SNAP.git"
+
+    tags = ['proxy-app']
 
-    version('master', git='https://github.com/lanl/SNAP.git')
+    version('master')
 
     variant('openmp', default=False, description='Build with OpenMP support')
     variant('opt', default=True, description='Build with debugging')
diff --git a/var/spack/repos/builtin/packages/snappy/link_gtest.patch b/var/spack/repos/builtin/packages/snappy/link_gtest.patch
new file mode 100644
index 0000000000..7a95b77036
--- /dev/null
+++ b/var/spack/repos/builtin/packages/snappy/link_gtest.patch
@@ -0,0 +1,11 @@
+--- a/CMakeLists.txt	2018-09-03 14:25:32.390110709 +0200
++++ b/CMakeLists.txt	2018-09-03 14:24:16.198182317 +0200
+@@ -118,7 +118,7 @@
+       "${PROJECT_SOURCE_DIR}/snappy-test.cc"
+   )
+   target_compile_definitions(snappy_unittest PRIVATE -DHAVE_CONFIG_H)
+-  target_link_libraries(snappy_unittest snappy ${GFLAGS_LIBRARIES})
++  target_link_libraries(snappy_unittest snappy ${GFLAGS_LIBRARIES} ${GTEST_LIBRARIES})
+ 
+   if(HAVE_LIBZ)
+     target_link_libraries(snappy_unittest z)
diff --git a/var/spack/repos/builtin/packages/snappy/package.py b/var/spack/repos/builtin/packages/snappy/package.py
index a023b2ee95..23845a4079 100644
--- a/var/spack/repos/builtin/packages/snappy/package.py
+++ b/var/spack/repos/builtin/packages/snappy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,6 +15,11 @@ class Snappy(CMakePackage):
     version('1.1.7', 'ee9086291c9ae8deb4dac5e0b85bf54a')
 
     variant('shared', default=True, description='Build shared libraries')
+    variant('pic', default=True, description='Build position independent code')
+
+    depends_on('googletest', type='test')
+
+    patch('link_gtest.patch')
 
     def cmake_args(self):
         spec = self.spec
@@ -42,11 +28,19 @@ class Snappy(CMakePackage):
             '-DCMAKE_INSTALL_LIBDIR:PATH={0}'.format(
                 self.prefix.lib),
             '-DBUILD_SHARED_LIBS:BOOL={0}'.format(
-                'ON' if '+shared' in spec else 'OFF')
+                'ON' if '+shared' in spec else 'OFF'),
+            '-DSNAPPY_BUILD_TESTS:BOOL={0}'.format(
+                'ON' if self.run_tests else 'OFF')
         ]
 
         return args
 
+    def flag_handler(self, name, flags):
+        flags = list(flags)
+        if '+pic' in self.spec and name in ('cflags', 'cxxflags'):
+            flags.append(self.compiler.pic_flag)
+        return (None, None, flags)
+
     @run_after('install')
     def install_pkgconfig(self):
         mkdirp(self.prefix.lib.pkgconfig)
diff --git a/var/spack/repos/builtin/packages/snbone/package.py b/var/spack/repos/builtin/packages/snbone/package.py
index eb493d9a16..8e112ebdba 100644
--- a/var/spack/repos/builtin/packages/snbone/package.py
+++ b/var/spack/repos/builtin/packages/snbone/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -31,9 +12,9 @@ class Snbone(MakefilePackage):
        continuous finite element based transport equation solver."""
 
     homepage = "https://github.com/ANL-CESAR/"
-    url = "https://github.com/ANL-CESAR/SNbone.git"
+    git      = "https://github.com/ANL-CESAR/SNbone.git"
 
-    version('develop', git='https://github.com/ANL-CESAR/SNbone.git')
+    version('develop')
 
     tags = ['proxy-app']
 
@@ -50,7 +31,9 @@ class Snbone(MakefilePackage):
                 elif self.compiler.name == 'intel':
                     make('COMPILER=intel', 'LDFLAGS=-lm')
                 else:
-                    make('COMPILER=gfortran', 'LDFLAGS=-lm')
+                    # older gcc need link libs after objs, but
+                    # LDFLAGS is in the front, so use IBMLIB instead
+                    make('COMPILER=gfortran', 'IBMLIB=-lm')
 
     def install(self, spec, prefix):
         mkdirp(prefix.bin.C)
diff --git a/var/spack/repos/builtin/packages/sniffles/package.py b/var/spack/repos/builtin/packages/sniffles/package.py
index caa6591a5e..0d498be646 100644
--- a/var/spack/repos/builtin/packages/sniffles/package.py
+++ b/var/spack/repos/builtin/packages/sniffles/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,6 +12,7 @@ class Sniffles(CMakePackage):
     homepage = "https://github.com/fritzsedlazeck/Sniffles/wiki"
     url      = "https://github.com/fritzsedlazeck/Sniffles/archive/v1.0.5.tar.gz"
 
+    version('1.0.7', '83bd93c5ab5dad3a6dc776f11d3a880e')
     version('1.0.5', 'c2f2350d00418ba4d82c074e7f0b1832')
 
     # the build process doesn't actually install anything, do it by hand
diff --git a/var/spack/repos/builtin/packages/snpeff/SnpSift.sh b/var/spack/repos/builtin/packages/snpeff/SnpSift.sh
new file mode 100644
index 0000000000..3422a77914
--- /dev/null
+++ b/var/spack/repos/builtin/packages/snpeff/SnpSift.sh
@@ -0,0 +1,3 @@
+#!/bin/sh
+# convenience wrapper for the SnpSift jar file
+java -jar SnpSift.jar "$@"
diff --git a/var/spack/repos/builtin/packages/snpeff/package.py b/var/spack/repos/builtin/packages/snpeff/package.py
new file mode 100644
index 0000000000..81e7147d20
--- /dev/null
+++ b/var/spack/repos/builtin/packages/snpeff/package.py
@@ -0,0 +1,42 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os.path
+
+
+class Snpeff(Package):
+    """SnpEff is a variant annotation and effect prediction tool. It
+    annotates and predicts the effects of genetic variants (such as
+    amino acid changes)."""
+
+    homepage = "http://snpeff.sourceforge.net/"
+    url      = "https://kent.dl.sourceforge.net/project/snpeff/snpEff_latest_core.zip"
+
+    version('2017-11-24', '1fa84a703580a423e27f1e14a945901c')
+
+    depends_on('jdk', type=('build', 'run'))
+
+    def install(self, spec, prefix):
+        install_tree('snpEff', prefix.bin)
+
+        # Set up a helper script to call java on the jar files,
+        # explicitly codes the path for java and the jar files.
+        scripts = ['snpEff', 'SnpSift']
+
+        for script in scripts:
+            script_sh = join_path(os.path.dirname(__file__), script + ".sh")
+            script_path = join_path(prefix.bin, script)
+            install(script_sh, script_path)
+            set_executable(script_path)
+
+            # Munge the helper script to explicitly point to java and the
+            # jar file.
+            java = self.spec['java'].prefix.bin.java
+            kwargs = {'backup': False}
+            filter_file('^java', java, script_path, **kwargs)
+            filter_file(script + '.jar',
+                        join_path(prefix.bin, script + '.jar'),
+                        script_path, **kwargs)
diff --git a/var/spack/repos/builtin/packages/snpeff/snpEff.sh b/var/spack/repos/builtin/packages/snpeff/snpEff.sh
new file mode 100644
index 0000000000..7bee480e2e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/snpeff/snpEff.sh
@@ -0,0 +1,3 @@
+#!/bin/sh
+# convenience wrapper for the snpEff jar file
+java -jar snpEff.jar "$@"
diff --git a/var/spack/repos/builtin/packages/snphylo/package.py b/var/spack/repos/builtin/packages/snphylo/package.py
new file mode 100644
index 0000000000..d249af2e65
--- /dev/null
+++ b/var/spack/repos/builtin/packages/snphylo/package.py
@@ -0,0 +1,37 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Snphylo(Package):
+    """A pipeline to generate a phylogenetic tree from huge SNP data"""
+
+    homepage = "http://chibba.pgml.uga.edu/snphylo/"
+    url      = "http://chibba.pgml.uga.edu/snphylo/snphylo.tar.gz"
+
+    version('2016-02-04', '467660814965bc9bed6c020c05c0d3a6')
+
+    depends_on('python', type=('build', 'run'))
+    depends_on('r', type=('build', 'run'))
+    depends_on('r-phangorn', type=('build', 'run'))
+    depends_on('r-gdsfmt', type=('build', 'run'))
+    depends_on('r-snprelate', type=('build', 'run'))
+    depends_on('r-getopt', type=('build', 'run'))
+    depends_on('muscle')
+    depends_on('phylip')
+
+    def install(self, spec, prefix):
+        install_answer = ['y', 'y', 'y', 'y']
+        install_answer_input = 'spack-config.in'
+        with open(install_answer_input, 'w') as f:
+            f.writelines(install_answer)
+        with open(install_answer_input, 'r') as f:
+            bash = which('bash')
+            bash('./setup.sh', input=f)
+            install_tree('.', prefix)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PATH', self.spec.prefix)
diff --git a/var/spack/repos/builtin/packages/snptest/package.py b/var/spack/repos/builtin/packages/snptest/package.py
index 57a49c5bec..a348c9fefd 100644
--- a/var/spack/repos/builtin/packages/snptest/package.py
+++ b/var/spack/repos/builtin/packages/snptest/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/soap2/package.py b/var/spack/repos/builtin/packages/soap2/package.py
index 9b34e35320..20b71eb57e 100644
--- a/var/spack/repos/builtin/packages/soap2/package.py
+++ b/var/spack/repos/builtin/packages/soap2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/soapdenovo-trans/package.py b/var/spack/repos/builtin/packages/soapdenovo-trans/package.py
new file mode 100644
index 0000000000..f837ce94ea
--- /dev/null
+++ b/var/spack/repos/builtin/packages/soapdenovo-trans/package.py
@@ -0,0 +1,33 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class SoapdenovoTrans(MakefilePackage):
+    """SOAPdenovo-Trans is a de novo transcriptome assembler basing on the
+       SOAPdenovo framework, adapt to alternative splicing and different
+       expression level among transcripts."""
+
+    homepage = "http://soap.genomics.org.cn/SOAPdenovo-Trans.html"
+    url      = "https://github.com/aquaskyline/SOAPdenovo-Trans/archive/1.0.4.tar.gz"
+
+    version('1.0.4', 'a3b00b0f743b96141c4d5f1b49f2918c')
+
+    build_directory = 'src'
+
+    def edit(self, spec, prefix):
+        with working_dir(self.build_directory):
+            makefile = FileFilter('Makefile')
+            makefile.filter('CFLAGS=         -O3 -fomit-frame-pointer -static',
+                            'CFLAGS=         -O3 -fomit-frame-pointer')
+
+    def build(self, spec, prefix):
+        with working_dir(self.build_directory):
+            make()
+            make('127mer=1', parallel=False)
+
+    def install(self, spec, prefix):
+        install_tree('.', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/soapdenovo2/package.py b/var/spack/repos/builtin/packages/soapdenovo2/package.py
new file mode 100644
index 0000000000..d64116e359
--- /dev/null
+++ b/var/spack/repos/builtin/packages/soapdenovo2/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Soapdenovo2(MakefilePackage):
+    """SOAPdenovo is a novel short-read assembly method that can build a de
+       novo draft assembly for the human-sized genomes. The program is
+       specially designed to assemble Illumina GA short reads. It creates
+       new opportunities for building reference sequences and carrying out
+       accurate analyses of unexplored genomes in a cost effective way."""
+
+    homepage = "https://github.com/aquaskyline/SOAPdenovo2"
+    url      = "https://github.com/aquaskyline/SOAPdenovo2/archive/r240.tar.gz"
+
+    version('240', '3bc6b63edf87bb47874bb6f126e43cd4')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('SOAPdenovo-63mer', prefix.bin)
+        install('SOAPdenovo-127mer', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/soapindel/package.py b/var/spack/repos/builtin/packages/soapindel/package.py
index 1a6bd4ff8d..56dafc5c12 100644
--- a/var/spack/repos/builtin/packages/soapindel/package.py
+++ b/var/spack/repos/builtin/packages/soapindel/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/soapsnp/package.py b/var/spack/repos/builtin/packages/soapsnp/package.py
index 34c56eebb2..6908ba491a 100644
--- a/var/spack/repos/builtin/packages/soapsnp/package.py
+++ b/var/spack/repos/builtin/packages/soapsnp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/sofa-c/package.py b/var/spack/repos/builtin/packages/sofa-c/package.py
new file mode 100644
index 0000000000..ec5d52c29b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/sofa-c/package.py
@@ -0,0 +1,31 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class SofaC(MakefilePackage):
+    "Standards of Fundamental Astronomy (SOFA) library for ANSI C."
+
+    homepage = "http://www.iausofa.org/current_C.html"
+    url      = "http://www.iausofa.org/2018_0130_C/sofa_c-20180130.tar.gz"
+
+    version('20180130', '9d6903c7690e84a788b622fba6f10146')
+
+    @property
+    def build_directory(self):
+        return join_path(self.version, 'c', 'src')
+
+    def edit(self, spec, prefix):
+        makefile = FileFilter(join_path(self.build_directory, 'makefile'))
+        makefile.filter('CCOMPC = gcc', 'CCOMPC = {0}'.format(spack_cc))
+
+    def install(self, spec, prefix):
+        with working_dir(self.build_directory):
+            mkdir(prefix.include)
+            install('sofa.h', prefix.include)
+            install('sofam.h', prefix.include)
+            mkdir(prefix.lib)
+            install('libsofa_c.a', prefix.lib)
diff --git a/var/spack/repos/builtin/packages/somatic-sniper/package.py b/var/spack/repos/builtin/packages/somatic-sniper/package.py
index 40c66af214..23c542bc52 100644
--- a/var/spack/repos/builtin/packages/somatic-sniper/package.py
+++ b/var/spack/repos/builtin/packages/somatic-sniper/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/sortmerna/package.py b/var/spack/repos/builtin/packages/sortmerna/package.py
index bd3136162b..a24d92eba8 100644
--- a/var/spack/repos/builtin/packages/sortmerna/package.py
+++ b/var/spack/repos/builtin/packages/sortmerna/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,9 @@ class Sortmerna(CMakePackage):
        reads in metatranscriptomic and metagenomic data"""
 
     homepage = "https://github.com/biocore/sortmerna"
-    url      = "https://github.com/biocore/sortmerna"
+    git      = "https://github.com/biocore/sortmerna.git"
 
-    version('2017-07-13', git='https://github.com/biocore/sortmerna.git', commit='8bde6fa113a5d99a23ae81b48eeea6760e966094')
+    version('2017-07-13', commit='8bde6fa113a5d99a23ae81b48eeea6760e966094')
 
     depends_on('zlib')
 
diff --git a/var/spack/repos/builtin/packages/sosflow/package.py b/var/spack/repos/builtin/packages/sosflow/package.py
index c3b99fd479..1100794493 100644
--- a/var/spack/repos/builtin/packages/sosflow/package.py
+++ b/var/spack/repos/builtin/packages/sosflow/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -31,12 +12,14 @@ class Sosflow(CMakePackage):
     observation, introspection, feedback, and control of HPC applications."""
 
     homepage = "https://github.com/cdwdirect/sos_flow/wiki"
-    url      = "https://github.com/cdwdirect/sos_flow.git"
+    git      = "https://github.com/cdwdirect/sos_flow.git"
 
-    version('spack', git='https://github.com/cdwdirect/sos_flow.git', tag='spack-build-v0.9901')
+    version('spack', tag='spack-build-v0.9901')
 
     depends_on('libevpath')
     depends_on('sqlite@3:')
+    depends_on('pkgconfig')
+    depends_on('mpi')
 
     def setup_environment(self, spack_env, run_env):
         spack_env.set('SOS_HOST_KNOWN_AS', 'SPACK-SOS-BUILD')
diff --git a/var/spack/repos/builtin/packages/sowing/package.py b/var/spack/repos/builtin/packages/sowing/package.py
index 668038255b..59ae89b841 100644
--- a/var/spack/repos/builtin/packages/sowing/package.py
+++ b/var/spack/repos/builtin/packages/sowing/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -34,6 +15,7 @@ class Sowing(AutotoolsPackage):
     homepage = "http://www.mcs.anl.gov/petsc/index.html"
     url = "http://ftp.mcs.anl.gov/pub/petsc/externalpackages/sowing-1.1.23-p1.tar.gz"
 
+    version('1.1.25-p1', 'fc5e5664b80e606ad71ba9b85f4c86b9')
     version('1.1.23-p1', '65aaf3ae2a4c0f30d532fec291702e16')
 
     def build(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/sox/package.py b/var/spack/repos/builtin/packages/sox/package.py
index 64c9803d52..d36222e23c 100644
--- a/var/spack/repos/builtin/packages/sox/package.py
+++ b/var/spack/repos/builtin/packages/sox/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/spades/package.py b/var/spack/repos/builtin/packages/spades/package.py
index 0748ef0618..ee96794523 100644
--- a/var/spack/repos/builtin/packages/spades/package.py
+++ b/var/spack/repos/builtin/packages/spades/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,12 +13,17 @@ class Spades(CMakePackage):
     homepage = "http://cab.spbu.ru/software/spades/"
     url      = "http://cab.spbu.ru/files/release3.10.1/SPAdes-3.10.1.tar.gz"
 
+    version('3.12.0', '15b48a3bcbbe6a8ad58fd04ba5d3f1015990fbfd9bdf4913042803b171853ac7')
+    version('3.11.1', '478677b560e2f98db025e8efd5245cdf')
     version('3.10.1', 'dcab7d145af81b59cc867562f27536c3')
 
     depends_on('python', type=('build', 'run'))
     depends_on('zlib')
     depends_on('bzip2')
 
-    conflicts('%gcc@7.1.0:')
+    # SPAdes will explicitly not compile with gcc < 5.3.0
+    conflicts('%gcc@:5.2.9')
+
+    conflicts('%gcc@7.1.0:', when='@:3.10.1')
 
     root_cmakelists_dir = 'src'
diff --git a/var/spack/repos/builtin/packages/span-lite/package.py b/var/spack/repos/builtin/packages/span-lite/package.py
new file mode 100644
index 0000000000..2ec1ede756
--- /dev/null
+++ b/var/spack/repos/builtin/packages/span-lite/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+from shutil import copytree
+
+
+class SpanLite(Package):
+    """
+    A single-file header-only version of a C++20-like span for C++98, C++11 and
+    later
+    """
+
+    homepage = "https://github.com/martinmoene/span-lite"
+    url      = "https://github.com/martinmoene/span-lite/archive/v0.3.0.tar.gz"
+
+    version('0.3.0', sha256='e083f368167fe632f866956edaa2c7a7d57a33ffb0d8def9b9f1a9daa47834bb')
+    version('0.2.0', sha256='6e3305fe868442410a00962a39fc59ed494cecc4f99fe2aff187e33932f06e46')
+    version('0.1.0', sha256='0a84b9369f86beba326e2160b683fd0922f416ce136437751a9ed70afcc67a1c')
+
+    def install(self, spec, prefix):
+        copytree('include', prefix.include)
diff --git a/var/spack/repos/builtin/packages/spark/package.py b/var/spack/repos/builtin/packages/spark/package.py
index 9d7f793803..4ccfbbf4cb 100644
--- a/var/spack/repos/builtin/packages/spark/package.py
+++ b/var/spack/repos/builtin/packages/spark/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import re
-import shutil
 
 from spack import *
 
@@ -42,6 +22,7 @@ class Spark(Package):
     depends_on('java', type=('build', 'run'))
     depends_on('hadoop', when='+hadoop', type=('build', 'run'))
 
+    version('2.3.0', 'db21021b8e877b219ab886097ef42344')
     version('2.1.0', '21d4471e78250775b1fa7c0e6c3a1326')
     version('2.0.2', '32110c1bb8f081359738742bd26bced1')
     version('2.0.0', '8a5307d973da6949a385aefb6ff747bb')
@@ -63,15 +44,12 @@ class Spark(Package):
         install_dir('yarn')
 
         # required for spark to recognize binary distribution
-        shutil.copy('RELEASE', prefix)
+        install('RELEASE', prefix)
 
     @when('+hadoop')
     def setup_environment(self, spack_env, run_env):
-
-        env['JAVA_HOME'] = self.spec['java'].prefix
-        # spack_env.set('JAVA_HOME', self.spec['jdk'].prefix)
-
         hadoop = self.spec['hadoop'].command
+        hadoop.add_default_env('JAVA_HOME', self.spec['java'].home)
         hadoop_classpath = hadoop('classpath', output=str)
 
         # Remove whitespaces, as they can compromise syntax in
diff --git a/var/spack/repos/builtin/packages/sparsehash/package.py b/var/spack/repos/builtin/packages/sparsehash/package.py
index 1d8b870bd5..6093db83b7 100644
--- a/var/spack/repos/builtin/packages/sparsehash/package.py
+++ b/var/spack/repos/builtin/packages/sparsehash/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/sparta/package.py b/var/spack/repos/builtin/packages/sparta/package.py
index cfe6658f3b..1b3bbfe55b 100644
--- a/var/spack/repos/builtin/packages/sparta/package.py
+++ b/var/spack/repos/builtin/packages/sparta/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/spdlog/package.py b/var/spack/repos/builtin/packages/spdlog/package.py
index 9d952728db..c669d99257 100644
--- a/var/spack/repos/builtin/packages/spdlog/package.py
+++ b/var/spack/repos/builtin/packages/spdlog/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,6 +12,20 @@ class Spdlog(CMakePackage):
     homepage = "https://github.com/gabime/spdlog"
     url = "https://github.com/gabime/spdlog/archive/v0.9.0.tar.gz"
 
+    version('1.2.1', sha256='867a4b7cedf9805e6f76d3ca41889679054f7e5a3b67722fe6d0eae41852a767')
+    version('1.2.0', sha256='0ba31b9e7f8e43a7be328ab0236d57810e5d4fc8a1a7842df665ae22d5cbd128')
+    version('1.1.0',  sha256='3dbcbfd8c07e25f5e0d662b194d3a7772ef214358c49ada23c044c4747ce8b19')
+    version('1.0.0',  sha256='90d5365121bcd2c41ce94dfe6a460e89507a2dfef6133fe5fad5bb35ac4ef0a1')
+    version('0.17.0', sha256='94f74fd1b3344733d1db3de2ec22e6cbeb769f93a8baa0d4a22b1f62dc7369f8')
+    version('0.16.3', sha256='b88d7be261d9089c817fc8cee6c000d69f349b357828e4c7f66985bc5d5360b8')
+    version('0.16.2', sha256='2081e5df5e87402398847431e16b87c71dd5c4d632314bb976ace8161f4d32de')
+    version('0.16.1', sha256='733260e1fbdcf1b3dc307fc585e4476240026de8be28eb905731d2ab0942deae')
+    version('0.16.0', sha256='9e64e3b10c2a3c54dfff63aa056057cf1db8a5fd506b3d9cf77207511820baac')
+    version('0.14.0', sha256='eb5beb4e53f4bfff5b32eb4db8588484bdc15a17b90eeefef3a9fc74fec1d83d')
+    version('0.13.0', sha256='d798a6ca19165f0a18a43938859359269f5a07fd8e0eb83ab8674739c9e8f361')
+    version('0.12.0', sha256='5cfd6a0b3182a88e1eb35bcb65a7ef9035140d7c73b16ba6095939dbf07325b9')
     version('0.11.0', '08232203f18a6f9ff47e083cc7a141a050805d3b')
     version('0.10.0', '57b471ef97a23cc29c38b62e00e89a411a87ea7f')
     version('0.9.0', 'dda741ef8e12d57d91f778d85e95a27d84a82ac4')
+
+    depends_on('cmake@3.1:', type='build')
diff --git a/var/spack/repos/builtin/packages/spectrum-mpi/package.py b/var/spack/repos/builtin/packages/spectrum-mpi/package.py
index c2b08c0086..c700f67285 100644
--- a/var/spack/repos/builtin/packages/spectrum-mpi/package.py
+++ b/var/spack/repos/builtin/packages/spectrum-mpi/package.py
@@ -1,38 +1,15 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at International Business Machines Corporation
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Serban Maerean, serban@us.ibm.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class SpectrumMpi(Package):
-    """
-    IBM MPI implementation from Spectrum MPI.
-
-    """
+    """IBM MPI implementation from Spectrum MPI."""
 
     homepage = "http://www-03.ibm.com/systems/spectrum-computing/products/mpi"
-    url = "http://www-03.ibm.com/systems/spectrum-computing/products/mpi"
 
     provides('mpi')
 
@@ -46,6 +23,11 @@ class SpectrumMpi(Package):
             self.spec.mpicxx = join_path(self.prefix.bin, 'mpixlC')
             self.spec.mpif77 = join_path(self.prefix.bin, 'mpixlf')
             self.spec.mpifc = join_path(self.prefix.bin, 'mpixlf')
+        elif '%pgi' in dependent_spec:
+            self.spec.mpicc = join_path(self.prefix.bin, 'mpipgicc')
+            self.spec.mpicxx = join_path(self.prefix.bin, 'mpipgic++')
+            self.spec.mpif77 = join_path(self.prefix.bin, 'mpipgifort')
+            self.spec.mpifc = join_path(self.prefix.bin, 'mpipgifort')
         else:
             self.spec.mpicc = join_path(self.prefix.bin, 'mpicc')
             self.spec.mpicxx = join_path(self.prefix.bin, 'mpicxx')
@@ -58,6 +40,11 @@ class SpectrumMpi(Package):
             spack_env.set('MPICXX', join_path(self.prefix.bin, 'mpixlC'))
             spack_env.set('MPIF77', join_path(self.prefix.bin, 'mpixlf'))
             spack_env.set('MPIF90', join_path(self.prefix.bin, 'mpixlf'))
+        elif '%pgi' in dependent_spec:
+            spack_env.set('MPICC', join_path(self.prefix.bin, 'mpipgicc'))
+            spack_env.set('MPICXX', join_path(self.prefix.bin, 'mpipgic++'))
+            spack_env.set('MPIF77', join_path(self.prefix.bin, 'mpipgifort'))
+            spack_env.set('MPIF90', join_path(self.prefix.bin, 'mpipgifort'))
         else:
             spack_env.set('MPICC', join_path(self.prefix.bin, 'mpicc'))
             spack_env.set('MPICXX', join_path(self.prefix.bin, 'mpic++'))
@@ -68,3 +55,5 @@ class SpectrumMpi(Package):
         spack_env.set('OMPI_CXX', spack_cxx)
         spack_env.set('OMPI_FC', spack_fc)
         spack_env.set('OMPI_F77', spack_f77)
+
+        spack_env.prepend_path('LD_LIBRARY_PATH', self.prefix.lib)
diff --git a/var/spack/repos/builtin/packages/speex/package.py b/var/spack/repos/builtin/packages/speex/package.py
index 6e0f50feec..51816e337a 100644
--- a/var/spack/repos/builtin/packages/speex/package.py
+++ b/var/spack/repos/builtin/packages/speex/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/spglib/fix_cmake_install.patch b/var/spack/repos/builtin/packages/spglib/fix_cmake_install.patch
new file mode 100644
index 0000000000..d7451460db
--- /dev/null
+++ b/var/spack/repos/builtin/packages/spglib/fix_cmake_install.patch
@@ -0,0 +1,25 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 3296d91..d18d26c 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -47,17 +47,17 @@ set(SOURCES ${PROJECT_SOURCE_DIR}/src/arithmetic.c
+ add_library(symspg SHARED ${SOURCES})
+ set_property(TARGET symspg PROPERTY VERSION ${serial})
+ set_property(TARGET symspg PROPERTY SOVERSION ${soserial})
+-install(TARGETS symspg LIBRARY DESTINATION ${PROJECT_SOURCE_DIR}/lib)
++install(TARGETS symspg LIBRARY DESTINATION ${CMAKE_INSTALL_PREFIX}/lib)
+ 
+ # Static link library
+ add_library(symspg_static STATIC ${SOURCES})
+ set_property(TARGET symspg_static PROPERTY VERSION ${serial})
+ set_property(TARGET symspg_static PROPERTY SOVERSION ${soserial})
+ set_property(TARGET symspg_static PROPERTY OUTPUT_NAME symspg)
+-install(TARGETS symspg_static ARCHIVE DESTINATION ${PROJECT_SOURCE_DIR}/lib)
++install(TARGETS symspg_static ARCHIVE DESTINATION ${CMAKE_INSTALL_PREFIX}/lib)
+ 
+ # Header file
+-install(FILES ${PROJECT_SOURCE_DIR}/src/spglib.h DESTINATION ${PROJECT_SOURCE_DIR}/include)
++install(FILES ${PROJECT_SOURCE_DIR}/src/spglib.h DESTINATION ${CMAKE_INSTALL_PREFIX}/include)
+ 
+ # make check
+ enable_testing()
diff --git a/var/spack/repos/builtin/packages/spglib/fix_cpp.patch b/var/spack/repos/builtin/packages/spglib/fix_cpp.patch
new file mode 100644
index 0000000000..9ab4c9bffe
--- /dev/null
+++ b/var/spack/repos/builtin/packages/spglib/fix_cpp.patch
@@ -0,0 +1,34 @@
+From a91ea68d6771ed7d6b03bcbffd891489dc77e574 Mon Sep 17 00:00:00 2001
+From: Krishnendu Ghosh
+Date: Thu, 22 Feb 2018 14:24:14 -0500
+Subject: [PATCH] added extern "C"
+
+---
+ src/spglib.h | 6 ++++++
+ 1 file changed, 6 insertions(+)
+
+diff --git a/src/spglib.h b/src/spglib.h
+index e1746b1..530dfa4 100644
+--- a/src/spglib.h
++++ b/src/spglib.h
+@@ -35,6 +35,9 @@
+ #ifndef __spglib_H__
+ #define __spglib_H__
+ 
++#ifdef __cplusplus
++extern "C" {
++#endif
+ /* SPGCONST is used instead of 'const' so to avoid gcc warning. */
+ /* However there should be better way than this way.... */
+ #ifndef SPGCONST
+@@ -481,4 +484,7 @@ void spg_get_neighboring_grid_points(int relative_grid_points[],
+ /* Return 0 if failed */
+ int spg_niggli_reduce(double lattice[3][3], const double symprec);
+ 
++#ifdef __cplusplus
++}
++#endif
+ #endif
+-- 
+2.7.4.1.g5468f9e
+
diff --git a/var/spack/repos/builtin/packages/spglib/package.py b/var/spack/repos/builtin/packages/spglib/package.py
new file mode 100644
index 0000000000..d68243c4b7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/spglib/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Spglib(CMakePackage):
+    """C library for finding and handling crystal symmetries."""
+
+    homepage = "https://atztogo.github.io/spglib/"
+    url      = "https://github.com/atztogo/spglib/archive/v1.10.3.tar.gz"
+
+    patch('fix_cmake_install.patch', when='@:1.10.3')
+    # patch by Krishnendu Ghosh
+    patch('fix_cpp.patch', when='@:1.10.3')
+
+    version('1.10.3', 'f6ef0554fa528ffa49d8eaee18a2b7b9')
+    version('1.10.0', '0ad9330ae8a511d25e2e26cb9bf02808')
diff --git a/var/spack/repos/builtin/packages/sph2pipe/package.py b/var/spack/repos/builtin/packages/sph2pipe/package.py
index 471461249a..f3e2e991e3 100644
--- a/var/spack/repos/builtin/packages/sph2pipe/package.py
+++ b/var/spack/repos/builtin/packages/sph2pipe/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/spherepack/package.py b/var/spack/repos/builtin/packages/spherepack/package.py
index 792853b51d..eabd1731ef 100644
--- a/var/spack/repos/builtin/packages/spherepack/package.py
+++ b/var/spack/repos/builtin/packages/spherepack/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/spindle/package.py b/var/spack/repos/builtin/packages/spindle/package.py
index 1b863689c3..905ef33cf2 100644
--- a/var/spack/repos/builtin/packages/spindle/package.py
+++ b/var/spack/repos/builtin/packages/spindle/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/spot/package.py b/var/spack/repos/builtin/packages/spot/package.py
index cd045dae68..1e74a0b2da 100644
--- a/var/spack/repos/builtin/packages/spot/package.py
+++ b/var/spack/repos/builtin/packages/spot/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/sqlite/package.py b/var/spack/repos/builtin/packages/sqlite/package.py
index de949df998..dc14a7b088 100644
--- a/var/spack/repos/builtin/packages/sqlite/package.py
+++ b/var/spack/repos/builtin/packages/sqlite/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 from spack import architecture
 
@@ -33,6 +14,12 @@ class Sqlite(AutotoolsPackage):
     """
     homepage = "www.sqlite.org"
 
+    version('3.23.1', '0edbfd75ececb95e8e6448d6ff33df82774c9646',
+            url='https://www.sqlite.org/2018/sqlite-autoconf-3230100.tar.gz')
+    version('3.22.0', '2fb24ec12001926d5209d2da90d252b9825366ac',
+            url='https://www.sqlite.org/2018/sqlite-autoconf-3220000.tar.gz')
+    version('3.21.0', '7913de4c3126ba3c24689cb7a199ea31',
+            url='https://www.sqlite.org/2017/sqlite-autoconf-3210000.tar.gz')
     version('3.20.0', 'e262a28b73cc330e7e83520c8ce14e4d',
             url='https://www.sqlite.org/2017/sqlite-autoconf-3200000.tar.gz')
     version('3.18.0', 'a6687a8ae1f66abc8df739aeadecfd0c',
@@ -48,7 +35,31 @@ class Sqlite(AutotoolsPackage):
     # defines a macro B0. Sqlite has a shell.c source file that declares a
     # variable named B0 and will fail to compile when the macro is found. The
     # following patch undefines the macro in shell.c
-    patch('sqlite_b0.patch', when='@3.18.0')
+    patch('sqlite_b0.patch', when='@3.18.0:3.21.0')
+
+    # Starting version 3.17.0, SQLite uses compiler built-ins
+    # __builtin_sub_overflow(), __builtin_add_overflow(), and
+    # __builtin_mul_overflow(), which are not supported by Intel compiler.
+    # Starting version 3.21.0 SQLite doesn't use the built-ins if Intel
+    # compiler is used.
+    patch('remove_overflow_builtins.patch', when='@3.17.0:3.20%intel')
+
+    variant('functions', default=False,
+            description='Provide mathematical and string extension functions '
+                        'for SQL queries using the loadable extensions '
+                        'mechanism.')
+
+    resource(name='extension-functions',
+             url='https://sqlite.org/contrib/download/extension-functions.c/download/extension-functions.c?get=25',
+             md5='3a32bfeace0d718505af571861724a43',
+             expand=False,
+             placement={'extension-functions.c?get=25':
+                        'extension-functions.c'},
+             when='+functions')
+
+    @property
+    def libs(self):
+        return find_libraries('libsqlite3', root=self.prefix.lib)
 
     def get_arch(self):
         arch = architecture.Arch()
@@ -62,3 +73,12 @@ class Sqlite(AutotoolsPackage):
             args.append('--build=powerpc64le-redhat-linux-gnu')
 
         return args
+
+    @run_after('install')
+    def build_libsqlitefunctions(self):
+        if '+functions' in self.spec:
+            libraryname = 'libsqlitefunctions.' + dso_suffix
+            cc = Executable(spack_cc)
+            cc(self.compiler.pic_flag, '-lm', '-shared',
+                'extension-functions.c', '-o', libraryname)
+            install(libraryname, self.prefix.lib)
diff --git a/var/spack/repos/builtin/packages/sqlite/remove_overflow_builtins.patch b/var/spack/repos/builtin/packages/sqlite/remove_overflow_builtins.patch
new file mode 100644
index 0000000000..a0a5d2e3da
--- /dev/null
+++ b/var/spack/repos/builtin/packages/sqlite/remove_overflow_builtins.patch
@@ -0,0 +1,48 @@
+diff --git a/sqlite3.c b/sqlite3.c
+index 4ec1271..8615169 100644
+--- a/sqlite3.c
++++ b/sqlite3.c
+@@ -29466,9 +29466,6 @@ SQLITE_PRIVATE int sqlite3SafetyCheckSickOrOk(sqlite3 *db){
+ ** overflow, leave *pA unchanged and return 1.
+ */
+ SQLITE_PRIVATE int sqlite3AddInt64(i64 *pA, i64 iB){
+-#if GCC_VERSION>=5004000
+-  return __builtin_add_overflow(*pA, iB, pA);
+-#else
+   i64 iA = *pA;
+   testcase( iA==0 ); testcase( iA==1 );
+   testcase( iB==-1 ); testcase( iB==0 );
+@@ -29483,12 +29480,8 @@ SQLITE_PRIVATE int sqlite3AddInt64(i64 *pA, i64 iB){
+   }
+   *pA += iB;
+   return 0; 
+-#endif
+ }
+ SQLITE_PRIVATE int sqlite3SubInt64(i64 *pA, i64 iB){
+-#if GCC_VERSION>=5004000
+-  return __builtin_sub_overflow(*pA, iB, pA);
+-#else
+   testcase( iB==SMALLEST_INT64+1 );
+   if( iB==SMALLEST_INT64 ){
+     testcase( (*pA)==(-1) ); testcase( (*pA)==0 );
+@@ -29498,12 +29491,8 @@ SQLITE_PRIVATE int sqlite3SubInt64(i64 *pA, i64 iB){
+   }else{
+     return sqlite3AddInt64(pA, -iB);
+   }
+-#endif
+ }
+ SQLITE_PRIVATE int sqlite3MulInt64(i64 *pA, i64 iB){
+-#if GCC_VERSION>=5004000
+-  return __builtin_mul_overflow(*pA, iB, pA);
+-#else
+   i64 iA = *pA;
+   if( iB>0 ){
+     if( iA>LARGEST_INT64/iB ) return 1;
+@@ -29519,7 +29508,6 @@ SQLITE_PRIVATE int sqlite3MulInt64(i64 *pA, i64 iB){
+   }
+   *pA = iA*iB;
+   return 0;
+-#endif
+ }
+ 
+ /*
diff --git a/var/spack/repos/builtin/packages/sqlitebrowser/package.py b/var/spack/repos/builtin/packages/sqlitebrowser/package.py
new file mode 100644
index 0000000000..5ec2d47707
--- /dev/null
+++ b/var/spack/repos/builtin/packages/sqlitebrowser/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Sqlitebrowser(CMakePackage):
+    """DB Browser for SQLite (DB4S) is a high quality, visual,
+    open source tool to create, design, and edit database files
+    compatible with SQLite."""
+
+    homepage = "https://sqlitebrowser.org"
+    url      = "https://github.com/sqlitebrowser/sqlitebrowser/archive/v3.10.1.tar.gz"
+
+    version('3.10.1', '66cbe41f9da5be80067942ed3816576c')
+
+    msg = 'sqlitebrowser requires C++11 support'
+    conflicts('%gcc@:4.8.0', msg=msg)
+    conflicts('%clang@:3.2', msg=msg)
+    conflicts('%intel@:12',  msg=msg)
+    conflicts('%xl@:13.0',   msg=msg)
+    conflicts('%xl_r@:13.0', msg=msg)
+
+    depends_on('sqlite@3:+functions')
+    depends_on('qt@5.5:')
diff --git a/var/spack/repos/builtin/packages/squid/package.py b/var/spack/repos/builtin/packages/squid/package.py
index 379aff577c..13a6bd32f4 100644
--- a/var/spack/repos/builtin/packages/squid/package.py
+++ b/var/spack/repos/builtin/packages/squid/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/sra-toolkit/package.py b/var/spack/repos/builtin/packages/sra-toolkit/package.py
index e1d5b54300..0726883afd 100644
--- a/var/spack/repos/builtin/packages/sra-toolkit/package.py
+++ b/var/spack/repos/builtin/packages/sra-toolkit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,13 +14,14 @@ class SraToolkit(Package):
     homepage = "https://trace.ncbi.nlm.nih.gov/Traces/sra"
     url      = "https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.8.2-1/sratoolkit.2.8.2-1-centos_linux64.tar.gz"
 
-    version('2.8.2-1', '3a2910754aea71aba5662804efff2a68')
+    version('2.9.2', sha256='17dbe13aa1ed7955d31e1e76e8b62786e80a77e9ed9d396631162dc3ad8b716d')
+    version('2.8.2-1', sha256='b053061aae7c6d00162fe0f514be4128a60365b4b2b5b36e7f4798b348b55cf5')
 
     def url_for_version(self, version):
         url = 'https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/{0}/sratoolkit.{0}-centos_linux64.tar.gz'
         return url.format(version)
 
     def install(self, spec, prefix):
-        install_tree('bin', prefix.bin)
+        install_tree('bin', prefix.bin, symlinks=True)
         install_tree('example', prefix.example)
         install_tree('schema', prefix.schema)
diff --git a/var/spack/repos/builtin/packages/ssht/package.py b/var/spack/repos/builtin/packages/ssht/package.py
new file mode 100644
index 0000000000..54d1d9684d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ssht/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Ssht(Package):
+    """The SSHT code provides functionality to perform fast and exact
+    spin spherical harmonic transforms."""
+
+    homepage = "https://astro-informatics.github.io/ssht/"
+    git      = "https://github.com/astro-informatics/ssht.git"
+
+    version('1.2b1', commit='7378ce8853897cbd1b08adebf7ec088c1e40f860')
+
+    depends_on('fftw')
+
+    def install(self, spec, prefix):
+        make('default')
+        install_tree('include/c', join_path(prefix, 'include'))
+        install_tree('doc/c', join_path(prefix, 'doc'))
+        install_tree('lib/c', join_path(prefix, 'lib'))
diff --git a/var/spack/repos/builtin/packages/sspace-longread/package.py b/var/spack/repos/builtin/packages/sspace-longread/package.py
index 4eac8cf177..bb6c05b112 100644
--- a/var/spack/repos/builtin/packages/sspace-longread/package.py
+++ b/var/spack/repos/builtin/packages/sspace-longread/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
diff --git a/var/spack/repos/builtin/packages/sspace-standard/package.py b/var/spack/repos/builtin/packages/sspace-standard/package.py
index 2724c1022f..9275b200ea 100644
--- a/var/spack/repos/builtin/packages/sspace-standard/package.py
+++ b/var/spack/repos/builtin/packages/sspace-standard/package.py
@@ -1,29 +1,11 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
+import glob
 
 
 class SspaceStandard(Package):
@@ -41,15 +23,29 @@ class SspaceStandard(Package):
 
     version('3.0', '7e171b4861b9d514e80aafc3d9cdf554')
 
-    depends_on('perl', type=('build', 'run'))
+    depends_on('perl+threads', type=('build', 'run'))
+    depends_on('perl-perl4-corelibs', type=('build', 'run'))
 
     def install(self, spec, prefix):
+        rootscript = 'SSPACE_Standard_v{0}.pl'.format(self.version)
+
+        scripts = [rootscript]
+        scripts.extend(glob.glob('tools/*.pl'))
+        scripts.extend(glob.glob('bwa/*.pl'))
+
+        for s in scripts:
+            filter_file('/usr/bin/perl', '/usr/bin/env perl',
+                        s, string=True)
+            filter_file('require "getopts.pl";', 'use Getopt::Std;',
+                        s, string=True)
+            filter_file('&Getopts(', 'getopts(', s, string=True)
+
         install_tree('bin', prefix.bin)
         install_tree('bowtie', prefix.bowtie)
         install_tree('bwa', prefix.bwa)
         install_tree('dotlib', prefix.dotlib)
         install_tree('tools', prefix.tools)
-        install('SSPACE_Standard_v{0}.pl'.format(self.version), prefix)
+        install(rootscript, prefix)
 
     def setup_environment(self, spack_env, run_env):
         run_env.set('SSPACE_HOME', prefix)
diff --git a/var/spack/repos/builtin/packages/sst-core/package.py b/var/spack/repos/builtin/packages/sst-core/package.py
new file mode 100644
index 0000000000..a64bc40753
--- /dev/null
+++ b/var/spack/repos/builtin/packages/sst-core/package.py
@@ -0,0 +1,44 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class SstCore(AutotoolsPackage):
+    """The Structural Simulation Toolkit (SST) was developed to explore
+    innovations in highly concurrent systems where the ISA, microarchitecture,
+    and memory interact with the programming model and communications system"""
+
+    homepage = "http://sst-simulator.org/"
+    url      = "https://github.com/sstsimulator/sst-core/releases/download/v8.0.0_Final/sstcore-8.0.0.tar.gz"
+    git      = "https://github.com/sstsimulator/sst-core.git"
+
+    version('develop', branch='devel')
+    version('8.0.0', sha256='34a62425c3209cf80b6bca99cb0dcc328b67fb84ed92d5e6d6c975ad9319ba8a')
+
+    variant('mpi', default=True, description='Support multi-node simulations using MPI')
+    variant('boost', default=False, description='Use boost')
+
+    depends_on('autoconf@1.68:', type='build', when='@develop')
+    depends_on('automake@1.11.1:', type='build', when='@develop')
+    depends_on('libtool@1.2.4:', type='build', when='@develop')
+    depends_on('m4', type='build', when='@develop')
+
+    depends_on('python@:2')
+    depends_on('zlib', type='build')
+    depends_on('mpi', when='+mpi')
+    depends_on('boost@1.56.0:', type='build', when='+boost')
+
+    def configure_args(self):
+        args = []
+        spec = self.spec
+
+        if '~mpi' in spec:
+            args.append('--disable-mpi')
+
+        if '+boost' in spec:
+            args.append('--with-boost=%s' % spec['boost'].prefix)
+
+        return args
diff --git a/var/spack/repos/builtin/packages/sst-dumpi/package.py b/var/spack/repos/builtin/packages/sst-dumpi/package.py
index 6422013871..96bbd6e3c7 100644
--- a/var/spack/repos/builtin/packages/sst-dumpi/package.py
+++ b/var/spack/repos/builtin/packages/sst-dumpi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 # Author: Samuel Knight <sknigh@sandia.gov>
 # Date: Feb 3, 2017
@@ -39,14 +20,12 @@ class SstDumpi(AutotoolsPackage):
 
     homepage = "http://sst.sandia.gov/about_dumpi.html"
     url      = "https://github.com/sstsimulator/sst-dumpi/archive/6.1.0.tar.gz"
+    git      = "https://github.com/sstsimulator/sst-dumpi.git"
+
+    version('master', branch='master')
+    version('6.1.0', '31c3f40a697dc85bf23dd34270982319')
 
     depends_on('autoconf@1.68:', type='build')
     depends_on('automake@1.11.1:', type='build')
     depends_on('libtool@1.2.4:', type='build')
     depends_on('m4', type='build')
-
-    version('master',
-          git='https://github.com/sstsimulator/sst-dumpi.git',
-          branch='master')
-
-    version('6.1.0', '31c3f40a697dc85bf23dd34270982319')
diff --git a/var/spack/repos/builtin/packages/sst-macro/package.py b/var/spack/repos/builtin/packages/sst-macro/package.py
index 3fade2694f..65c0e613e0 100644
--- a/var/spack/repos/builtin/packages/sst-macro/package.py
+++ b/var/spack/repos/builtin/packages/sst-macro/package.py
@@ -1,64 +1,87 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-#
-# Author: Samuel Knight <sknigh@sandia.gov>
-# Date: Feb 3, 2017
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class SstMacro(AutotoolsPackage):
-    """The SST/macro software package provides a simulator for large-scale
-    parallel computer architectures for the coarse-grained study of
-    distributed-memory applications. The simulator is driven from either a
+    """The Structural Simulation Toolkit Macroscale Element Library simulates
+    large-scale parallel computer architectures for the coarse-grained study
+    of distributed-memory applications. The simulator is driven from either a
     trace file or skeleton application. SST/macro's modular architecture can
-    be extended with additional network models, trace file formats,
-    software services, and processor models.
+    be extended with additional network models, trace file formats, software
+    services, and processor models.
     """
 
     homepage = "http://sst.sandia.gov/about_sstmacro.html"
     url      = "https://github.com/sstsimulator/sst-macro/releases/download/v6.1.0_Final/sstmacro-6.1.0.tar.gz"
+    git      = "https://github.com/sstsimulator/sst-macro.git"
+
+    version('develop', branch='devel')
+    version('8.0.0', sha256='8618a259e98ede9a1a2ce854edd4930628c7c5a770c3915858fa840556c1861f')
+    version('6.1.0', '98b737be6326b8bd711de832ccd94d14')
 
-    depends_on('boost@1.59:')
-    depends_on('autoconf@1.68:', type='build', when='@master')
-    depends_on('automake@1.11.1:', type='build', when='@master')
-    depends_on('libtool@1.2.4:', type='build', when='@master')
-    depends_on('m4', type='build', when='@master')
+    depends_on('boost@1.59:', when='@:6.1.0')
 
-    version('master',
-          git='https://github.com/sstsimulator/sst-macro.git',
-          branch='master')
+    depends_on('autoconf@1.68:', type='build', when='@develop')
+    depends_on('automake@1.11.1:', type='build', when='@develop')
+    depends_on('libtool@1.2.4:', type='build', when='@develop')
+    depends_on('m4', type='build', when='@develop')
 
-    version('6.1.0', '98b737be6326b8bd711de832ccd94d14',
-          url='https://github.com/sstsimulator/sst-macro/releases/download/v6.1.0_Final/sstmacro-6.1.0.tar.gz')
+    depends_on('binutils', type='build')
+    depends_on('zlib', type=('build', 'link'))
+    depends_on('otf2', when='+otf2')
+    depends_on('llvm+clang@:5.99.99', when='+skeletonizer')
+    depends_on('mpi', when='+mpi')
+    depends_on('sst-core@8.0.0', when='@8.0.0 +core')
+    depends_on('sst-core@develop', when='@develop +core')
+
+    variant('core', default=False, description='Use SST Core for PDES')
+    variant('mpi', default=True, description='Enable distributed PDES simulation')
+    variant('otf2', default=False, description='Enable OTF2 trace emission and replay support')
+    variant('shared', default=True, description='Build shared libraries')
+    variant('skeletonizer', default=False, description='Enable Clang source-to-source autoskeletonization')
+    variant('static', default=True, description='Build static libraries')
+    variant('threaded', default=False, description='Enable thread-parallel PDES simulation')
 
     @run_before('autoreconf')
     def bootstrap(self):
-        if '@master' in self.spec:
+        if '@develop' in self.spec:
             Executable('./bootstrap.sh')()
 
     def configure_args(self):
         args = ['--disable-regex']
+
+        # Set CFLAGS and CXXFLAGS so they won't automatically insert '-g'
+        env['CFLAGS'] = '-O2'
+        env['CXXFLAGS'] = '-O2'
+
+        spec = self.spec
+        args.append(
+            '--enable-static=%s' % ('yes' if '+static' in spec else 'no'))
+        args.append(
+            '--enable-shared=%s' % ('yes' if '+shared' in spec else 'no'))
+
+        if spec.satisfies("@8.0.0:"):
+            args.extend([
+                '--%sable-otf2' % ('en' if '+otf2' in spec else 'dis'),
+                '--%sable-multithread' % (
+                    'en' if '+threaded' in spec else 'dis')
+            ])
+
+            if '+skeletonizer' in spec:
+                args.append('--with-clang=' + spec['llvm'].prefix)
+
+        if '+core' in spec:
+            args.append('--with-sst-core=%s' % spec['sst-core'].prefix)
+
+        # Optional MPI support
+        if '+mpi' in spec:
+            env['CC'] = spec['mpi'].mpicc
+            env['CXX'] = spec['mpi'].mpicxx
+            env['F77'] = spec['mpi'].mpif77
+            env['FC'] = spec['mpi'].mpifc
+
         return args
diff --git a/var/spack/repos/builtin/packages/stacks/package.py b/var/spack/repos/builtin/packages/stacks/package.py
index 975e1c88b6..d156ec9f30 100644
--- a/var/spack/repos/builtin/packages/stacks/package.py
+++ b/var/spack/repos/builtin/packages/stacks/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/staden-io-lib/package.py b/var/spack/repos/builtin/packages/staden-io-lib/package.py
index 3cb82061aa..9ecb46fbbe 100644
--- a/var/spack/repos/builtin/packages/staden-io-lib/package.py
+++ b/var/spack/repos/builtin/packages/staden-io-lib/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/star-ccm-plus/package.py b/var/spack/repos/builtin/packages/star-ccm-plus/package.py
index cc230fe028..59d043fe65 100644
--- a/var/spack/repos/builtin/packages/star-ccm-plus/package.py
+++ b/var/spack/repos/builtin/packages/star-ccm-plus/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
 import os
@@ -35,7 +16,7 @@ class StarCcmPlus(Package):
 
     version('11.06.010_02', 'd349c6ac8293d8e6e7a53533d695588f')
 
-    variant('docs', default=False, description='Install the documentation')
+    variant('doc', default=False, description='Install the documentation')
 
     # Licensing
     license_required = True
diff --git a/var/spack/repos/builtin/packages/star/package.py b/var/spack/repos/builtin/packages/star/package.py
index 3a21e5806e..9f6d51c219 100644
--- a/var/spack/repos/builtin/packages/star/package.py
+++ b/var/spack/repos/builtin/packages/star/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,12 +10,21 @@ class Star(Package):
     """STAR is an ultrafast universal RNA-seq aligner."""
 
     homepage = "https://github.com/alexdobin/STAR"
-    url      = "https://github.com/alexdobin/STAR/archive/2.5.3a.tar.gz"
+    url      = "https://github.com/alexdobin/STAR/archive/2.6.1b.tar.gz"
+
+    version('2.6.1b', sha256='1bba5b26c1e6e9a7aca8473a99dbf37bad1dbdd0a589402448e278553bb6b3da')
+    version('2.6.1a', sha256='dc87357211432c05123ce49966aae712dec590cbe27c1fd0193c3aeb8d4abe4b')
+    version('2.6.0c', sha256='bebba6cc72da302429c44c20f3b07bdde6b0ddf33e538a99e297f1d342070387')
+    version('2.6.0b', sha256='1ebbecbb698a3de95990b35fe386189a2c00b07cd9d2d4e017ab8234e7dc042e')
+    version('2.6.0a', sha256='a6b0dd1918e1961eebec71e6c7c3c8e632f66d10e0620aa09c0710e2ab279179')
+    version('2.5.4b', sha256='bfa6ccd3b7b3878155a077a9c15eec5490dffad8e077ac93abe6f9bfa75bb2b4')
+    version('2.5.4a', sha256='17b02703cdd580c9fd426a14f20712ea252d32a4ded804eef759029b600e3afb')
+    version('2.5.3a', sha256='2a258e77cda103aa293e528f8597f25dc760cba188d0a7bc7c9452f4698e7c04')
+    version('2.5.2b', sha256='f88b992740807ab10f2ac3b83781bf56951617f210001fab523f6480d0b546d9')
+    version('2.5.2a', sha256='2a372d9bcab1dac8d35cbbed3f0ab58291e4fbe99d6c1842b094ba7449d55476')
+    version('2.4.2a', '8b9345f2685a5ec30731e0868e86d506', url='https://github.com/alexdobin/STAR/archive/STAR_2.4.2a.tar.gz')
 
-    version('2.5.3a', 'baf8d1b62a50482cfa13acb7652dc391',
-            url='https://github.com/alexdobin/STAR/archive/2.5.3a.tar.gz')
-    version('2.4.2a', '8b9345f2685a5ec30731e0868e86d506',
-            url='https://github.com/alexdobin/STAR/archive/STAR_2.4.2a.tar.gz')
+    depends_on('zlib')
 
     def install(self, spec, prefix):
         with working_dir('source'):
diff --git a/var/spack/repos/builtin/packages/startup-notification/package.py b/var/spack/repos/builtin/packages/startup-notification/package.py
new file mode 100644
index 0000000000..e10736253b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/startup-notification/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class StartupNotification(AutotoolsPackage):
+    """startup-notification contains a reference implementation of the
+    freedesktop startup notification protocol."""
+
+    homepage = "https://www.freedesktop.org/wiki/Software/startup-notification/"
+    url      = "http://www.freedesktop.org/software/startup-notification/releases/startup-notification-0.12.tar.gz"
+
+    version('0.12', '2cd77326d4dcaed9a5a23a1232fb38e9')
+
+    depends_on('libx11')
+    depends_on('libxcb')
+    depends_on('xcb-util')
diff --git a/var/spack/repos/builtin/packages/stat/package.py b/var/spack/repos/builtin/packages/stat/package.py
index f2733f8f61..3df3d04a61 100644
--- a/var/spack/repos/builtin/packages/stat/package.py
+++ b/var/spack/repos/builtin/packages/stat/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,8 +10,14 @@ class Stat(AutotoolsPackage):
     """Library to create, manipulate, and export graphs Graphlib."""
 
     homepage = "http://paradyn.org/STAT/STAT.html"
-    url      = "https://github.com/lee218llnl/stat/archive/v2.0.0.tar.gz"
+    url      = "https://github.com/LLNL/STAT/archive/v2.0.0.tar.gz"
+    git      = "https://github.com/llnl/stat.git"
 
+    version('develop', branch='develop')
+    version('4.0.1', '3e21b48e7932d9a4a9efb300f0b97fa2',
+            url='https://github.com/LLNL/STAT/files/2489327/stat-4.0.1.tar.gz')
+    version('4.0.0', 'b357160662ced251bc55cb1b884c3407',
+            url='https://github.com/LLNL/STAT/releases/download/v4.0.0/stat-4.0.0.tar.gz')
     version('3.0.1', 'dac6f23c3639a0b21f923dc6219ba385',
             url='https://github.com/LLNL/STAT/files/911503/stat-3.0.1.zip')
     version('3.0.0', 'a97cb235c266371c4a26329112de48a2',
@@ -42,20 +29,23 @@ class Stat(AutotoolsPackage):
     # TODO: dysect requires Dyninst patch for version 3.0.0b
     variant('dysect', default=False, description="enable DySectAPI")
     variant('examples', default=False, description="enable examples")
+    variant('fgfs', default=True, description="enable file broadcasting")
 
     depends_on('autoconf', type='build')
     depends_on('automake', type='build')
     depends_on('libtool', type='build')
-    depends_on('libdwarf')
     depends_on('dyninst', when='~dysect')
     depends_on('dyninst@8.2.1+stat_dysect', when='+dysect')
+    depends_on('fast-global-file-status', when='+fgfs')
     depends_on('graphlib@2.0.0', when='@2.0.0:2.2.0')
     depends_on('graphlib@3.0.0', when='@3:')
     depends_on('graphviz', type=('build', 'link', 'run'))
     depends_on('launchmon')
     depends_on('mrnet')
-    depends_on('python@:2.8')
-    depends_on('py-pygtk', type=('build', 'run'))
+    depends_on('python@:2.8', when='@:4.0.0')
+    depends_on('py-pygtk', type=('build', 'run'), when='@:4.0.0')
+    depends_on('py-enum34', type=('run'), when='@:4.0.0')
+    depends_on('py-xdot', when='@4.0.1:')
     depends_on('swig')
     depends_on('mpi', when='+examples')
 
@@ -68,9 +58,11 @@ class Stat(AutotoolsPackage):
             "--with-mrnet=%s"       % spec['mrnet'].prefix,
             "--with-graphlib=%s"    % spec['graphlib'].prefix,
             "--with-stackwalker=%s" % spec['dyninst'].prefix,
-            "--with-libdwarf=%s"    % spec['libdwarf'].prefix,
             "--with-python=%s"      % spec['python'].command.path,
         ]
+        if '+fgfs' in spec:
+            args.append('--with-fgfs=%s'
+                        % spec['fast-global-file-status'].prefix)
         if '+dysect' in spec:
             args.append('--enable-dysectapi')
         if '~examples' in spec:
diff --git a/var/spack/repos/builtin/packages/stc/package.py b/var/spack/repos/builtin/packages/stc/package.py
index 7a55b73873..7332d4843d 100644
--- a/var/spack/repos/builtin/packages/stc/package.py
+++ b/var/spack/repos/builtin/packages/stc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -30,13 +11,14 @@ class Stc(AutotoolsPackage):
     """STC: The Swift-Turbine Compiler"""
 
     homepage = 'http://swift-lang.org/Swift-T'
-    url      = 'http://swift-lang.github.io/swift-t-downloads/stc-0.7.3.tar.gz'
+    url      = 'http://swift-lang.github.io/swift-t-downloads/spack/stc-0.0.0.tar.gz'
 
-    version('0.7.3', '6bf769f406f6c33d1c134521373718d3')
+    version('0.8.2', '883b0657f1aac9b81158ef0a8989be4c')
 
-    depends_on('java')
-    depends_on('ant')
-    depends_on('turbine')
+    depends_on('java', type=('build', 'run'))
+    depends_on('ant', type='build')
+    depends_on('turbine', type=('build', 'run'))
+    depends_on('zsh', type=('build', 'run'))
 
     def configure_args(self):
         args = ['--with-turbine=' + self.spec['turbine'].prefix]
diff --git a/var/spack/repos/builtin/packages/steps/package.py b/var/spack/repos/builtin/packages/steps/package.py
new file mode 100644
index 0000000000..0831852f3c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/steps/package.py
@@ -0,0 +1,61 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Steps(CMakePackage):
+    """STochastic Engine for Pathway Simulation"""
+
+    homepage = "https://groups.oist.jp/cnu/software"
+    git      = "https://github.com/CNS-OIST/STEPS.git"
+
+    version("3.3.0", submodules=True)
+    version("3.2.0", submodules=True)
+    version("develop", branch="master", submodules=True)
+
+    variant("native", default=True, description="Generate non-portable arch-specific code")
+    variant("lapack", default=False, description="Use new BDSystem/Lapack code for E-Field solver")
+    variant("petsc", default=False, description="Use PETSc library for parallel E-Field solver")
+    variant("mpi", default=True, description="Use MPI for parallel solvers")
+
+    depends_on("blas")
+    depends_on("lapack", when="+lapack")
+    depends_on("mpi", when="+mpi")
+    depends_on("petsc~debug+int64", when="+petsc")
+    depends_on("python")
+    depends_on("py-cython")
+
+    def cmake_args(self):
+        args = []
+        spec = self.spec
+
+        if "+native" in spec:
+            args.append("-DTARGET_NATIVE_ARCH:BOOL=True")
+        else:
+            args.append("-DTARGET_NATIVE_ARCH:BOOL=False")
+
+        if "+lapack" in spec:
+            args.append("-DUSE_BDSYSTEM_LAPACK:BOOL=True")
+        else:
+            args.append("-DUSE_BDSYSTEM_LAPACK:BOOL=False")
+
+        if "+petsc" in spec:
+            args.append("-DUSE_PETSC:BOOL=True")
+        else:
+            args.append("-DUSE_PETSC:BOOL=False")
+
+        if "+mpi" in spec:
+            args.append("-DUSE_MPI:BOOL=True")
+        else:
+            args.append("-DUSE_MPI:BOOL=False")
+
+        args.append('-DBLAS_LIBRARIES=' + spec['blas'].libs.joined(";"))
+        return args
+
+    def setup_environment(self, spack_env, run_env):
+        # This recipe exposes a Python package from a C++ CMake project.
+        # This hook is required to reproduce what Spack PythonPackage does.
+        run_env.prepend_path('PYTHONPATH', self.prefix)
diff --git a/var/spack/repos/builtin/packages/stow/package.py b/var/spack/repos/builtin/packages/stow/package.py
new file mode 100644
index 0000000000..5861351441
--- /dev/null
+++ b/var/spack/repos/builtin/packages/stow/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Stow(AutotoolsPackage):
+    """GNU Stow: a symlink farm manager
+
+       GNU Stow is a symlink farm manager which takes distinct
+       packages of software and/or data located in separate
+       directories on the filesystem, and makes them appear to be
+       installed in the same place."""
+
+    homepage = "https://www.gnu.org/software/stow/"
+    url      = "https://ftpmirror.gnu.org/stow/stow-2.2.2.tar.bz2"
+
+    version('2.2.2', 'af1e1de9d973c835bee80c745b5ee849')
+    version('2.2.0', '5bb56592eff9aaf9dfb6c975b3004240')
+    version('2.1.3', '533651c25b29c3630f01d0be33849a7c')
+    version('2.1.2', '0b8154a2165e4004ddc9579e3499af98')
+    version('2.1.1', '882d2490d05723b4b78029c2973775d3')
+    version('2.1.0', 'aa3a2389b6cbf3bd555e15c80a0be6ab')
+
+    depends_on('perl@5.6.1:')
diff --git a/var/spack/repos/builtin/packages/strace/package.py b/var/spack/repos/builtin/packages/strace/package.py
new file mode 100644
index 0000000000..b43e2c4ef4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/strace/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Strace(AutotoolsPackage):
+    """Strace is a diagnostic, debugging and instructional userspace
+    utility for Linux. It is used to monitor and tamper with interactions
+    between processes and the Linux kernel, which include system calls,
+    signal deliveries, and changes of process state."""
+
+    homepage = "https://strace.io"
+    url      = "https://strace.io/files/4.21/strace-4.21.tar.xz"
+
+    conflicts('platform=darwin', msg='strace runs only on Linux.')
+
+    version('4.21', '785b679a75e9758ebeb66816f315b9fe')
diff --git a/var/spack/repos/builtin/packages/stream/package.py b/var/spack/repos/builtin/packages/stream/package.py
index 69ddfe5b07..45aad6da05 100644
--- a/var/spack/repos/builtin/packages/stream/package.py
+++ b/var/spack/repos/builtin/packages/stream/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,8 +12,9 @@ class Stream(MakefilePackage):
     computation rate for simple vector kernels."""
 
     homepage = "https://www.cs.virginia.edu/stream/ref.html"
+    git      = "https://github.com/jeffhammond/STREAM.git"
 
-    version('5.10', git='https://github.com/jeffhammond/STREAM.git')
+    version('5.10')
 
     variant('openmp', default=False, description='Build with OpenMP support')
 
diff --git a/var/spack/repos/builtin/packages/strelka/package.py b/var/spack/repos/builtin/packages/strelka/package.py
index 19c5de7dc8..fdd4b67434 100644
--- a/var/spack/repos/builtin/packages/strelka/package.py
+++ b/var/spack/repos/builtin/packages/strelka/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/stress/package.py b/var/spack/repos/builtin/packages/stress/package.py
index 497853f73b..0588cc36a2 100644
--- a/var/spack/repos/builtin/packages/stress/package.py
+++ b/var/spack/repos/builtin/packages/stress/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/string-view-lite/package.py b/var/spack/repos/builtin/packages/string-view-lite/package.py
new file mode 100644
index 0000000000..ab564b4880
--- /dev/null
+++ b/var/spack/repos/builtin/packages/string-view-lite/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+from shutil import copytree
+
+
+class StringViewLite(Package):
+    """
+    A single-file header-only version of a C++17-like string_view for C++98,
+    C++11 and later
+    """
+
+    homepage = "https://github.com/martinmoene/string-view-lite"
+    url      = "https://github.com/martinmoene/string-view-lite/archive/v1.0.0.tar.gz"
+
+    version('1.0.0', sha256='44e30dedd6f4777e646da26528f9d2d5cc96fd0fa79e2e5c0adc14817d048d63')
+    version('0.2.0', sha256='c8ae699dfd2ccd15c5835e9b1d246834135bbb91b82f7fc4211b8ac366bffd34')
+    version('0.1.0', sha256='7de87d6595230a6085655dab6145340bc423f2cf206263ef73c9b78f7b153340')
+
+    def install(self, spec, prefix):
+        copytree('include', prefix.include)
diff --git a/var/spack/repos/builtin/packages/stringtie/package.py b/var/spack/repos/builtin/packages/stringtie/package.py
index 9e5a690a5d..cb01647651 100644
--- a/var/spack/repos/builtin/packages/stringtie/package.py
+++ b/var/spack/repos/builtin/packages/stringtie/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,6 +13,7 @@ class Stringtie(MakefilePackage):
     homepage = "https://ccb.jhu.edu/software/stringtie"
     url      = "https://github.com/gpertea/stringtie/archive/v1.3.3b.tar.gz"
 
+    version('1.3.4a', '2a191ef6512242a3a5778cf7718bb6af')
     version('1.3.3b', '11a43260b18e4272182380e922445d88')
 
     depends_on('samtools')
diff --git a/var/spack/repos/builtin/packages/structure/package.py b/var/spack/repos/builtin/packages/structure/package.py
index cbfc1e9850..f0d04676be 100644
--- a/var/spack/repos/builtin/packages/structure/package.py
+++ b/var/spack/repos/builtin/packages/structure/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/strumpack/package.py b/var/spack/repos/builtin/packages/strumpack/package.py
new file mode 100644
index 0000000000..4bd4dac459
--- /dev/null
+++ b/var/spack/repos/builtin/packages/strumpack/package.py
@@ -0,0 +1,96 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Strumpack(CMakePackage):
+    """STRUMPACK -- STRUctured Matrix PACKage - provides linear solvers
+    for sparse matrices and for dense rank-structured matrices, i.e.,
+    matrices that exhibit some kind of low-rank property. It provides a
+    distributed memory fully algebraic sparse solver and
+    preconditioner. The preconditioner is mostly aimed at large sparse
+    linear systems which result from the discretization of a partial
+    differential equation, but is not limited to any particular type of
+    problem. STRUMPACK also provides preconditioned GMRES and BiCGStab
+    iterative solvers."""
+
+    homepage = "http://portal.nersc.gov/project/sparse/strumpack"
+    url      = "https://github.com/pghysels/STRUMPACK/archive/v3.0.3.tar.gz"
+    git      = "https://github.com/pghysels/STRUMPACK.git"
+
+    version('master', branch='master')
+    version('3.1.1', sha256='c1c3446ee023f7b24baa97b24907735e89ce4ae9f5ef516645dfe390165d1778')
+    version('3.1.0', sha256='b4f91b7d433955518b04538be1c726afc5de4bffb163e982ef8844d391b26fa7')
+    version('3.0.3', sha256='2bd2a40d9585b769ae4ba461de02c6e36433bf2b21827f824a50f2fdf73389f7')
+    version('3.0.2', sha256='828e5ec59019b2c74e008745b04ceebbb7ef1313fb4e3ac01fa8ff350799df38')
+    version('3.0.1', sha256='b4a4d870c589937e22e77a6c4b52a96fd808f0b564e363f826ae5ffc94b9d000')
+    version('3.0.0', sha256='7acd9b4653b8b11380de733c80b164348ca00f9226904f5dc166a8e3db88cd20')
+    version('2.2.0', sha256='8fe73875cbbb29ed1faf714e3bf13ad538eb062e39d7d5e73cb9c4aafb571e24')
+
+    variant('mpi', default=True, description='Use MPI')
+    variant('openmp', default=True,
+            description='Enable thread parallellism via tasking with OpenMP')
+    variant('parmetis', default=False,
+            description='Enable use of ParMetis')
+    variant('scotch', default=False,
+            description='Enable use of Scotch')
+    variant('c_interface', default=True,
+            description='Enable C interface')
+    variant('count_flops', default=False,
+            description='Build with flop counters')
+    variant('task_timers', default=False,
+            description='Build with timers for internal routines')
+    variant('build_dev_tests', default=False,
+            description='Build developer test routines')
+    variant('build_tests', default=False,
+            description='Build test routines')
+
+    depends_on('cmake@3.2:', type='build')
+    depends_on('mpi', when='+mpi')
+    depends_on('blas')
+    depends_on('lapack')
+    depends_on('scalapack', when='+mpi')
+    depends_on('metis')
+    depends_on('parmetis', when='+parmetis')
+    depends_on('scotch~metis', when='+scotch')
+    depends_on('scotch~metis+mpi', when='+scotch+mpi')
+
+    conflicts('+parmetis', when='~mpi')
+
+    def cmake_args(self):
+        spec = self.spec
+
+        def on_off(varstr):
+            return 'ON' if varstr in spec else 'OFF'
+
+        if '+mpi' in spec:
+            args = ['-DCMAKE_C_COMPILER=%s' % spec['mpi'].mpicc,
+                    '-DCMAKE_CXX_COMPILER=%s' % spec['mpi'].mpicxx,
+                    '-DCMAKE_Fortran_COMPILER=%s' % spec['mpi'].mpifc,
+                    '-DSTRUMPACK_USE_MPI=ON']
+        else:
+            args = ['-DSTRUMPACK_USE_MPI=OFF']
+
+        args.extend([
+            '-DSTRUMPACK_USE_OPENMP=%s' % on_off('+openmp'),
+            '-DSTRUMPACK_C_INTERFACE=%s' % on_off('+c_interface'),
+            '-DSTRUMPACK_COUNT_FLOPS=%s' % on_off('+count_flops'),
+            '-DSTRUMPACK_TASK_TIMERS=%s' % on_off('+task_timers'),
+            '-DSTRUMPACK_DEV_TESTING=%s' % on_off('+build_dev_tests'),
+            '-DSTRUMPACK_BUILD_TESTS=%s' % on_off('+build_tests')
+        ])
+
+        if spec.satisfies('@3.0.4:'):
+            args.extend([
+                '-DTPL_ENABLE_PARMETIS=%s' % on_off('+parmetis'),
+                '-DTPL_ENABLE_SCOTCH=%s' % on_off('+scotch')
+            ])
+        else:
+            args.extend([
+                '-DSTRUMPACK_USE_PARMETIS=%s' % on_off('+parmetis'),
+                '-DSTRUMPACK_USE_SCOTCH=%s' % on_off('+scotch')
+            ])
+        return args
diff --git a/var/spack/repos/builtin/packages/sublime-text/package.py b/var/spack/repos/builtin/packages/sublime-text/package.py
index e28aa04c94..403d5c42a8 100644
--- a/var/spack/repos/builtin/packages/sublime-text/package.py
+++ b/var/spack/repos/builtin/packages/sublime-text/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from distutils.dir_util import copy_tree
 
 
 class SublimeText(Package):
@@ -31,8 +11,9 @@ class SublimeText(Package):
     prose."""
 
     homepage = "http://www.sublimetext.com/"
-    url      = "https://download.sublimetext.com/sublime_text_3_build_3126_x64.tar.bz2"
+    url      = "https://download.sublimetext.com/sublime_text_3_build_3176_x64.tar.bz2"
 
+    version('3_build_3176', '7d4c8c5167224888d901e8cbafb6ec7f')
     version('3_build_3126', 'acc34252b0ea7dff1f581c5db1564dcb')
     version('2.0.2',        '699cd26d7fe0bada29eb1b2cd7b50e4b')
 
@@ -52,8 +33,8 @@ class SublimeText(Package):
         if version[0] == 2:
             return "https://download.sublimetext.com/Sublime%20Text%20{0}%20x64.tar.bz2".format(version)
         else:
-            return "https://download.sublimetext.com/sublime_text_3_build_{0}_x64.tar.bz2".format(version)
+            return "https://download.sublimetext.com/sublime_text_{0}_x64.tar.bz2".format(version)
 
     def install(self, spec, prefix):
         # Sublime text comes as a pre-compiled binary.
-        copy_tree('.', prefix)
+        install_tree('.', prefix)
diff --git a/var/spack/repos/builtin/packages/subread/package.py b/var/spack/repos/builtin/packages/subread/package.py
index 86c5efe42e..b6af49d745 100644
--- a/var/spack/repos/builtin/packages/subread/package.py
+++ b/var/spack/repos/builtin/packages/subread/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import sys
 
@@ -33,6 +14,8 @@ class Subread(MakefilePackage):
     homepage = "http://subread.sourceforge.net/"
     url      = "https://downloads.sourceforge.net/project/subread/subread-1.5.2/subread-1.5.2-source.tar.gz"
 
+    version('1.6.2', '70125531737fe9ba2be83622ca236e5e')
+    version('1.6.0', 'ed7e32c56bda1e769703e0a4db5a89a7')
     version('1.5.2', '817d2a46d87fcef885c8832475b8b247')
 
     depends_on('zlib')
@@ -41,6 +24,11 @@ class Subread(MakefilePackage):
         plat = sys.platform
         with working_dir('src'):
             if plat.startswith('linux'):
+                filter_file(
+                    'CC_EXEC = gcc',
+                    'CC_EXEC = {0}'.format(spack_cc),
+                    'Makefile.Linux'
+                )
                 make('-f', 'Makefile.Linux')
             elif plat.startswith('darwin'):
                 make('-f', 'Makefile.MacOS')
diff --git a/var/spack/repos/builtin/packages/subversion/package.py b/var/spack/repos/builtin/packages/subversion/package.py
index 5d4b998b32..8a041451b2 100644
--- a/var/spack/repos/builtin/packages/subversion/package.py
+++ b/var/spack/repos/builtin/packages/subversion/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,6 +11,8 @@ class Subversion(Package):
     homepage = 'https://subversion.apache.org/'
     url = 'http://archive.apache.org/dist/subversion/subversion-1.8.13.tar.gz'
 
+    version('1.9.7',     '1a5f48acf9d0faa60e8c7aea96a9b29ab1d4dcac')
+    version('1.9.6',     '89e1b3f9d79422c094ccb95769360d5fe7df2bb1')
     version('1.9.5',     'ac9f8ee235f1b667dd6506864af8035aaedfc2d9')
     version('1.9.3',     'a92bcfaec4e5038f82c74a7b5bbd2f46')
     version('1.8.17',    'd1f8d45f97168d6271c58c5b25421cc32954c81b')
diff --git a/var/spack/repos/builtin/packages/suite-sparse/graphblas_libm_dep.patch b/var/spack/repos/builtin/packages/suite-sparse/graphblas_libm_dep.patch
new file mode 100644
index 0000000000..441b0eff87
--- /dev/null
+++ b/var/spack/repos/builtin/packages/suite-sparse/graphblas_libm_dep.patch
@@ -0,0 +1,10 @@
+--- a/GraphBLAS/CMakeLists.txt
++++ b/GraphBLAS/CMakeLists.txt
+@@ -87,6 +87,7 @@
+     C_STANDARD_REQUIRED 11
+     PUBLIC_HEADER "Include/GraphBLAS.h" )
+ set_property ( TARGET graphblas PROPERTY C_STANDARD 11 )
++target_link_libraries ( graphblas m )
+
+ # create the static graphblas library.  Requires ANSI C11
+ add_library ( graphblas_static STATIC ${GRAPHBLAS_SOURCES} )
diff --git a/var/spack/repos/builtin/packages/suite-sparse/package.py b/var/spack/repos/builtin/packages/suite-sparse/package.py
index 429a7f0706..3ab4f06068 100644
--- a/var/spack/repos/builtin/packages/suite-sparse/package.py
+++ b/var/spack/repos/builtin/packages/suite-sparse/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,8 +11,11 @@ class SuiteSparse(Package):
     SuiteSparse is a suite of sparse matrix algorithms
     """
     homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html'
-    url = 'http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-4.5.1.tar.gz'
+    url = 'http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-5.2.0.tar.gz'
 
+    version('5.3.0', sha256='90e69713d8c454da5a95a839aea5d97d8d03d00cc1f667c4bdfca03f640f963d')
+    version('5.2.0', '8e625539dbeed061cc62fbdfed9be7cf')
+    version('5.1.0', '9c34d7c07ad5ce1624b8187faa132046')
     version('4.5.5', '0a5b38af0016f009409a9606d2f1b555')
     version('4.5.4', 'f6ab689442e64a1624a47aa220072d1b')
     version('4.5.3', '8ec57324585df3c6483ad7f556afccbd')
@@ -44,6 +28,7 @@ class SuiteSparse(Package):
 
     depends_on('blas')
     depends_on('lapack')
+    depends_on('cmake', when='@5.2.0:', type='build')
 
     depends_on('metis@5.1.0', when='@4.5.1:')
     # in @4.5.1. TBB support in SPQR seems to be broken as TBB-related linkng
@@ -57,6 +42,12 @@ class SuiteSparse(Package):
     # This patch removes unsupported flags for pgi compiler
     patch('pgi.patch', when='%pgi')
 
+    # This patch adds '-lm' when linking libgraphblas and when using clang.
+    # Fixes 'libgraphblas.so.2.0.1: undefined reference to `__fpclassify''
+    patch('graphblas_libm_dep.patch', when='@5.2.0:5.2.99%clang')
+
+    conflicts('%gcc@:4.8', when='@5.2.0:', msg='gcc version must be at least 4.9 for suite-sparse@5.2.0:')
+
     def install(self, spec, prefix):
         # The build system of SuiteSparse is quite old-fashioned.
         # It's basically a plain Makefile which include an header
@@ -94,10 +85,16 @@ class SuiteSparse(Package):
             # with the TCOV path of SparseSuite 4.5.1's Suitesparse_config.mk,
             # even though this fix is ugly
             'BLAS=%s' % (spec['blas'].libs.ld_flags + (
-                '-lstdc++' if '@4.5.1' in spec else '')),
+                ' -lstdc++' if '@4.5.1' in spec else '')),
             'LAPACK=%s' % spec['lapack'].libs.ld_flags,
         ]
 
+        # 64bit blas in UMFPACK:
+        if (spec.satisfies('^openblas+ilp64') or
+            spec.satisfies('^intel-mkl+ilp64') or
+            spec.satisfies('^intel-parallel-studio+mkl+ilp64')):
+            make_args.append('UMFPACK_CONFIG=-DLONGBLAS="long long"')
+
         # SuiteSparse defaults to using '-fno-common -fexceptions' in
         # CFLAGS, but not all compilers use the same flags for these
         # optimizations
@@ -107,7 +104,7 @@ class SuiteSparse(Package):
         elif '%pgi' in spec:
             make_args += ['CFLAGS+=--exceptions']
 
-        if '%xl' in spec or '%xl_r' in spec:
+        if spack_f77.endswith('xlf') or spack_f77.endswith('xlf_r'):
             make_args += ['CFLAGS+=-DBLAS_NO_UNDERSCORE']
 
         # Intel TBB in SuiteSparseQR
@@ -118,3 +115,22 @@ class SuiteSparse(Package):
             ]
 
         make('install', *make_args)
+
+    @property
+    def libs(self):
+        """Export the libraries of SuiteSparse.
+        Sample usage: spec['suite-sparse'].libs.ld_flags
+                      spec['suite-sparse:klu,btf'].libs.ld_flags
+        """
+        # Component libraries, ordered by dependency. Any missing components?
+        all_comps = ['klu', 'btf', 'umfpack', 'cholmod', 'colamd', 'amd',
+                     'camd', 'ccolamd', 'cxsparse', 'ldl', 'rbio', 'spqr',
+                     'suitesparseconfig']
+        query_parameters = self.spec.last_query.extra_parameters
+        comps = all_comps if not query_parameters else query_parameters
+        libs = find_libraries(['lib' + c for c in comps], root=self.prefix.lib,
+                              shared=True, recursive=False)
+        if not libs:
+            return None
+        libs += find_system_libraries('librt')
+        return libs
diff --git a/var/spack/repos/builtin/packages/sumaclust/package.py b/var/spack/repos/builtin/packages/sumaclust/package.py
index 923fb347b4..66f7820d59 100644
--- a/var/spack/repos/builtin/packages/sumaclust/package.py
+++ b/var/spack/repos/builtin/packages/sumaclust/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/sundials/package.py b/var/spack/repos/builtin/packages/sundials/package.py
index 16cbcbe34f..0002b3e376 100644
--- a/var/spack/repos/builtin/packages/sundials/package.py
+++ b/var/spack/repos/builtin/packages/sundials/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 import sys
@@ -33,16 +14,22 @@ class Sundials(CMakePackage):
 
     homepage = "https://computation.llnl.gov/projects/sundials"
     url = "https://computation.llnl.gov/projects/sundials/download/sundials-2.7.0.tar.gz"
-    maintainers = ['cswoodward', 'gardner48']
+    maintainers = ['cswoodward', 'gardner48', 'balos1']
 
     # ==========================================================================
     # Versions
     # ==========================================================================
-
-    version('3.1.0', '1a84ca41c7f71067e03d519ddbcd9dae')
-    version('3.0.0', '5163a44cedd7398bddda442ba00313b8')
-    version('2.7.0', 'c304631b9bc82877d7b0e9f4d4fd94d3')
-    version('2.6.2', '3deeb0ede9f514184c6bd83ecab77d95')
+    version('4.0.0-dev.2', sha256='124fc12f2a68d32210c20f5005510607e0833764afaef2a70b741bc922519984')
+    version('4.0.0-dev.1', sha256='6354e1d266b60c23766137b4ffa9bbde8bca97a562ccd94cab756b597ed753c1')
+    version('4.0.0-dev', sha256='50e526327461aebe463accf6ef56f9c6773df65025f3020b9ce68b83bbf5dd27')
+    version('3.2.1', sha256='47d94d977ab2382cdcdd02f72a25ebd4ba8ca2634bbb2f191fe1636e71c86808', preferred=True)
+    version('3.2.0', sha256='d2b690afecadf8b5a048bb27ab341de591d714605b98d3518985dfc2250e93f9')
+    version('3.1.2', sha256='a8985bb1e851d90e24260450667b134bc13d71f5c6effc9e1d7183bd874fe116')
+    version('3.1.1', sha256='a24d643d31ed1f31a25b102a1e1759508ce84b1e4739425ad0e18106ab471a24')
+    version('3.1.0', sha256='18d52f8f329626f77b99b8bf91e05b7d16b49fde2483d3a0ea55496ce4cdd43a')
+    version('3.0.0', sha256='28b8e07eecfdef66e2c0d0ea0cb1b91af6e4e94d71008abfe80c27bf39f63fde')
+    version('2.7.0', sha256='d39fcac7175d701398e4eb209f7e92a5b30a78358d4a0c0fcc23db23c11ba104')
+    version('2.6.2', sha256='d8ed0151509dd2b0f317b318a4175f8b95a174340fc3080b8c20617da8aa4d2f')
 
     # ==========================================================================
     # Variants
@@ -164,6 +151,9 @@ class Sundials(CMakePackage):
 
     # Build dependencies
     depends_on('cmake@2.8.1:', type='build')
+    depends_on('cmake@2.8.12:', type='build', when='@3.1.2')
+    depends_on('cmake@3.0.2:', type='build', when='@4.0.0-dev.1')
+    depends_on('cmake@3.1.3:', type='build', when='@3.2.0,4.0.0-dev.2')
 
     # MPI related dependencies
     depends_on('mpi', when='+mpi')
@@ -215,10 +205,10 @@ class Sundials(CMakePackage):
             return 'ON' if varstr in self.spec else 'OFF'
 
         fortran_flag = self.compiler.pic_flag
-        if spec.satisfies('%clang platform=darwin'):
-            mpif77 = Executable(self.spec['mpi'].mpif77)
-            libgfortran = LibraryList(mpif77('--print-file-name',
-                                             'libgfortran.a', output=str))
+        if (spec.satisfies('%clang platform=darwin')) and ('+fcmix' in spec):
+            f77 = Executable(self.compiler.f77)
+            libgfortran = LibraryList(f77('--print-file-name',
+                                          'libgfortran.a', output=str))
             fortran_flag += ' ' + libgfortran.ld_flags
 
         # List of CMake arguments
@@ -325,6 +315,12 @@ class Sundials(CMakePackage):
                 '-DPETSC_LIBRARY_DIR=%s' % spec['petsc'].prefix.lib
             ])
 
+        # Building with RAJA
+        if '+raja' in spec:
+            args.extend([
+                '-DRAJA_DIR=%s' % spec['raja'].prefix.share.raja.cmake
+            ])
+
         # Examples
         if spec.satisfies('@3.0.0:'):
             args.extend([
@@ -374,6 +370,8 @@ class Sundials(CMakePackage):
         Spack's generic cc and f77. We want them to be bound to
         whatever compiler they were built with."""
 
+        spec = self.spec
+
         kwargs = {'ignore_absent': True, 'backup': False, 'string': True}
         dirname = os.path.join(self.prefix, 'examples')
 
@@ -469,10 +467,46 @@ class Sundials(CMakePackage):
             filter_file(r'^CPP\s*=.*', self.compiler.cc,
                         os.path.join(dirname, filename), **kwargs)
 
-        for filename in f77_files:
-            filter_file(os.environ['F77'], self.compiler.f77,
-                        os.path.join(dirname, filename), **kwargs)
-
-        for filename in f90_files:
-            filter_file(os.environ['FC'], self.compiler.fc,
-                        os.path.join(dirname, filename), **kwargs)
+        if ('+fcmix' in spec) and ('+examples-f77' in spec):
+            for filename in f77_files:
+                filter_file(os.environ['F77'], self.compiler.f77,
+                            os.path.join(dirname, filename), **kwargs)
+
+        if ('+fcmix' in spec) and ('+examples-f90' in spec):
+            for filename in f90_files:
+                filter_file(os.environ['FC'], self.compiler.fc,
+                            os.path.join(dirname, filename), **kwargs)
+
+    @property
+    def headers(self):
+        """Export the headers and defines of SUNDIALS.
+           Sample usage: spec['sundials'].headers.cpp_flags
+        """
+        # SUNDIALS headers are inside subdirectories, so we use a fake header
+        # in the include directory.
+        hdr = find(self.prefix.include.nvector, 'nvector_serial.h',
+                   recursive=False)
+        return HeaderList(join_path(self.spec.prefix.include, 'fake.h')) \
+            if hdr else None
+
+    @property
+    def libs(self):
+        """Export the libraries of SUNDIALS.
+           Sample usage: spec['sundials'].libs.ld_flags
+                         spec['sundials:arkode,cvode'].libs.ld_flags
+        """
+        query_parameters = self.spec.last_query.extra_parameters
+        if not query_parameters:
+            sun_libs = 'libsundials_*[!0-9]'
+            # Q: should the result be ordered by dependency?
+        else:
+            sun_libs = ['libsundials_' + p for p in query_parameters]
+        search_paths = [[self.prefix.lib, False], [self.prefix.lib64, False],
+                        [self.prefix, True]]
+        is_shared = '+shared' in self.spec
+        for path, recursive in search_paths:
+            libs = find_libraries(sun_libs, root=path, shared=is_shared,
+                                  recursive=recursive)
+            if libs:
+                return libs
+        return None  # Raise an error
diff --git a/var/spack/repos/builtin/packages/superlu-dist/package.py b/var/spack/repos/builtin/packages/superlu-dist/package.py
index cc7058236a..122b706b42 100644
--- a/var/spack/repos/builtin/packages/superlu-dist/package.py
+++ b/var/spack/repos/builtin/packages/superlu-dist/package.py
@@ -1,54 +1,33 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-import glob
-import os
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class SuperluDist(Package):
+class SuperluDist(CMakePackage):
     """A general purpose library for the direct solution of large, sparse,
     nonsymmetric systems of linear equations on high performance machines."""
+
     homepage = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
-    url = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/superlu_dist_4.1.tar.gz"
+    url      = "https://github.com/xiaoyeli/superlu_dist/archive/v6.0.0.tar.gz"
+    git      = "https://github.com/xiaoyeli/superlu_dist.git"
 
-    version('develop', git='https://github.com/xiaoyeli/superlu_dist', tag='master')
-    version('xsdk-0.2.0', git='https://github.com/xiaoyeli/superlu_dist', tag='xsdk-0.2.0')
-    version('5.2.2', 'a685ef7fb7859b24c8c9d5d5f121a8a5')
-    version('5.2.1', 'af857778ffeb04aea02aa4843e6e8e1d')
-    version('5.1.3', '3a9e88a8469aa7f319f0364364b8da35')
-    version('5.1.1', '12638c631733a27dcbd87110e9f9cb1e')
-    version('5.1.0', '6bb86e630bd4bd8650243aed8fd92eb9')
-    version('5.0.0', '2b53baf1b0ddbd9fcf724992577f0670')
-    version('4.3', 'ee66c84e37b4f7cc557771ccc3dc43ae')
-    version('4.2', 'ae9fafae161f775fbac6eba11e530a65')
-    version('4.1', '4edee38cc29f687bd0c8eb361096a455')
-    version('4.0', 'c0b98b611df227ae050bc1635c6940e0')
-    version('3.3', 'f4805659157d93a962500902c219046b')
+    version('develop', branch='master')
+    version('xsdk-0.2.0', tag='xsdk-0.2.0')
+    version('6.0.0', 'ff6cdfa0263d595708bbb6d11fb780915d8cfddab438db651e246ea292f37ee4')
+    version('5.4.0', '3ac238fe082106a2c4dbaf0c22af1ff1247308ffa8f053de9d78c3ec7dd0d801')
+    version('5.3.0', '49ed110bdef1e284a0181d6c7dd1fae3aa110cb45f67c6aa5cb791070304d670')
+    version('5.2.2', '65cfb9ace9a81f7affac4ad92b9571badf0f10155b3468531b0fffde3bd8e727')
+    version('5.2.1', '67cf3c46cbded4cee68e2a9d601c30ab13b08091c8cdad95b0a8e018b6d5d1f1')
+    version('5.1.3', '58e3dfdb4ae6f8e3f6f3d5ee5e851af59b967c4483cdb3b15ccd1dbdf38f44f9')
+    version('5.1.2', 'e34865ad6696ee6a6d178b4a01c8e19103a7d241ba9de043603970d63b0ee1e2')
+    version('5.1.0', '73f292ab748b590b6dd7469e6986aeb95d279b8b8b3da511c695a396bdbc996c')
+    version('5.0.0', '78d1d6460ff16b3f71e4bcd7306397574d54d421249553ccc26567f00a10bfc6')
 
-    variant('int64', default=False,
-            description="Use 64bit integers")
+    variant('int64', default=False, description='Build with 64 bit integers')
+    variant('shared', default=True, description='Build shared libraries')
 
     depends_on('mpi')
     depends_on('blas')
@@ -56,61 +35,35 @@ class SuperluDist(Package):
     depends_on('parmetis')
     depends_on('metis@5:')
 
-    def install(self, spec, prefix):
+    def cmake_args(self):
+        spec = self.spec
         lapack_blas = spec['lapack'].libs + spec['blas'].libs
-        makefile_inc = []
-        makefile_inc.extend([
-            'PLAT         = _mac_x',
-            'DSuperLUroot = %s' % self.stage.source_path,
-            'DSUPERLULIB  = $(DSuperLUroot)/lib/libsuperlu_dist.a',
-            'BLASDEF      = -DUSE_VENDOR_BLAS',
-            'BLASLIB      = %s' % lapack_blas.ld_flags,
-            'METISLIB     = %s' % spec['metis'].libs.ld_flags,
-            'PARMETISLIB  = %s' % spec['parmetis'].libs.ld_flags,
-            'FLIBS        =',
-            'LIBS         = $(DSUPERLULIB) $(BLASLIB) $(PARMETISLIB) $(METISLIB)',  # noqa
-            'ARCH         = ar',
-            'ARCHFLAGS    = cr',
-            'RANLIB       = true',
-            'CC           = {0}'.format(self.spec['mpi'].mpicc),
-            'CFLAGS       = %s %s -O2 %s %s %s' % (
-                self.compiler.pic_flag,
-                '' if '%pgi' in spec else '-std=c99',
-                spec['parmetis'].headers.cpp_flags,
-                spec['metis'].headers.cpp_flags,
-                '-D_LONGINT' if '+int64' in spec and not
-                self.spec.satisfies('@5.2.0:') else ''),
-            'XSDK_INDEX_SIZE = %s' % ('64' if '+int64' in spec else '32'),
-            'NOOPTS       = %s -std=c99' % (
-                self.compiler.pic_flag),
-            'FORTRAN      = {0}'.format(self.spec['mpi'].mpif77),
-            'F90FLAGS     = -O2',
-            'LOADER       = {0}'.format(self.spec['mpi'].mpif77),
-            'LOADOPTS     =',
-            'CDEFS        = %s' % ("-DNoChange"
-                                       if '%xl' in spec or '%xl_r' in spec
-                                       else "-DAdd_")
-        ])
-
-        with open('make.inc', 'w') as fh:
-            fh.write('\n'.join(makefile_inc))
-
-        mkdirp(os.path.join(self.stage.source_path, 'lib'))
-        make("lib", parallel=False)
-
-        # FIXME:
-        # cd "EXAMPLE" do
-        # system "make"
+        args = [
+            '-DCMAKE_C_COMPILER=%s' % spec['mpi'].mpicc,
+            '-DCMAKE_CXX_COMPILER=%s' % spec['mpi'].mpicxx,
+            '-DCMAKE_INSTALL_LIBDIR:STRING=%s' % self.prefix.lib,
+            '-DTPL_BLAS_LIBRARIES=%s' % lapack_blas.ld_flags,
+            '-DUSE_XSDK_DEFAULTS=YES',
+            '-DTPL_PARMETIS_LIBRARIES=%s' % spec['parmetis'].libs.ld_flags +
+            ';' + spec['metis'].libs.ld_flags,
+            '-DTPL_PARMETIS_INCLUDE_DIRS=%s' % spec['parmetis'].prefix.include
+        ]
 
-        # need to install by hand
-        headers_location = self.prefix.include
-        mkdirp(headers_location)
-        mkdirp(prefix.lib)
+        if '+int64' in spec:
+            args.append('-DXSDK_INDEX_SIZE=64')
+        else:
+            args.append('-DXSDK_INDEX_SIZE=32')
 
-        headers = glob.glob(join_path(self.stage.source_path, 'SRC', '*.h'))
-        for h in headers:
-            install(h, headers_location)
+        if '+shared' in spec:
+            args.append('-DBUILD_SHARED_LIBS:BOOL=ON')
+        else:
+            args.append('-DBUILD_SHARED_LIBS:BOOL=OFF')
+        return args
 
-        superludist_lib = join_path(self.stage.source_path,
-                                    'lib/libsuperlu_dist.a')
-        install(superludist_lib, self.prefix.lib)
+    def flag_handler(self, name, flags):
+        flags = list(flags)
+        if name == 'cxxflags':
+            flags.append(self.compiler.cxx11_flag)
+        if name == 'cflags' and '%pgi' not in self.spec:
+            flags.append('-std=c99')
+        return (None, None, flags)
diff --git a/var/spack/repos/builtin/packages/superlu-mt/package.py b/var/spack/repos/builtin/packages/superlu-mt/package.py
index 99ecdcc642..fa663b9395 100644
--- a/var/spack/repos/builtin/packages/superlu-mt/package.py
+++ b/var/spack/repos/builtin/packages/superlu-mt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
 import os
diff --git a/var/spack/repos/builtin/packages/superlu/package.py b/var/spack/repos/builtin/packages/superlu/package.py
index 72f13ffde7..bb657b780f 100644
--- a/var/spack/repos/builtin/packages/superlu/package.py
+++ b/var/spack/repos/builtin/packages/superlu/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
 import os
diff --git a/var/spack/repos/builtin/packages/supernova/package.py b/var/spack/repos/builtin/packages/supernova/package.py
new file mode 100644
index 0000000000..ed7b85405d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/supernova/package.py
@@ -0,0 +1,45 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class Supernova(Package):
+    """Supernova is a software package for de novo assembly from Chromium
+    Linked-Reads that are made from a single whole-genome library from an
+    individual DNA source.
+
+    A key feature of Supernova is that it creates diploid assemblies, thus
+    separately representing maternal and paternal chromosomes over very long
+    distances. Almost all other methods instead merge homologous chromosomes
+    into single incorrect 'consensus' sequences. Supernova is the only
+    practical method for creating diploid assemblies of large genomes.
+
+    To install this package, you will need to go to the supernova download
+    page of supernova, register with your email address and download
+    supernova yourself. Spack will search your current directory for the
+    download file. Alternatively, add this file yo a mirror so that Spack
+    can find it. For instructions on how to set up a mirror, see
+    http://spack.readthedocs.io/en/latest/mirrors.html"""
+
+    homepage = "https://support.10xgenomics.com/de-novo-assembly/software/overview/latest/welcome"
+
+    version('2.0.1', '3697ce043c798fcb672fe0a66c56d6f0')
+
+    depends_on('bcl2fastq2')
+
+    def url_for_version(self, version):
+        return "file://{0}/supernova-{1}.tar.gz".format(os.getcwd(), version)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PATH', self.prefix)
+
+    def install(self, spec, prefix):
+        rm = which('rm')
+        # remove the broken symlinks
+        rm('anaconda-cs/2.2.0-anaconda-cs-c7/lib/libtcl.so',
+            'anaconda-cs/2.2.0-anaconda-cs-c7/lib/libtk.so')
+        install_tree('.', prefix)
diff --git a/var/spack/repos/builtin/packages/sw4lite/package.py b/var/spack/repos/builtin/packages/sw4lite/package.py
index 868fc88ec2..379eedd6bf 100644
--- a/var/spack/repos/builtin/packages/sw4lite/package.py
+++ b/var/spack/repos/builtin/packages/sw4lite/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
 
@@ -34,9 +15,10 @@ class Sw4lite(MakefilePackage):
 
     homepage = "https://geodynamics.org/cig/software/sw4"
     url      = "https://github.com/geodynamics/sw4lite/archive/v1.0.zip"
+    git      = "https://github.com/geodynamics/sw4lite.git"
 
-    version('develop', git='https://github.com/geodynamics/sw4lite',
-            branch='master')
+    version('develop', branch='master')
+    version('1.1', sha256='34b5f7b56f9e40474c14abebcaa024192de018de6beb6dafee53d3db5b07c6d3')
     version('1.0', '3d911165f4f2ff6d5f9c1bd56ab6723f')
 
     variant('openmp', default=True, description='Build with OpenMP support')
diff --git a/var/spack/repos/builtin/packages/swap-assembler/package.py b/var/spack/repos/builtin/packages/swap-assembler/package.py
new file mode 100644
index 0000000000..938bb4c71d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/swap-assembler/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class SwapAssembler(MakefilePackage):
+    """A scalable and fully parallelized genome assembler."""
+
+    homepage = "https://sourceforge.net/projects/swapassembler/"
+    url      = "https://sourceforge.net/projects/swapassembler/files/SWAP_Assembler-0.4.tar.bz2/download"
+
+    version('0.4', '944f2aeae4f451be81160bb625304fc3')
+
+    depends_on('mpich')
+
+    def edit(self, spec, prefix):
+        makefile = FileFilter('Makefile')
+        makefile.filter('$(CC) -O2', '$(CC) -pthread -O2', string=True)
+
+    def install(self, spec, prefix):
+        install_tree('.', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/swarm/package.py b/var/spack/repos/builtin/packages/swarm/package.py
index 0f52b9774e..277a10974f 100644
--- a/var/spack/repos/builtin/packages/swarm/package.py
+++ b/var/spack/repos/builtin/packages/swarm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/swfft/package.py b/var/spack/repos/builtin/packages/swfft/package.py
index aeb7e00293..4297933639 100644
--- a/var/spack/repos/builtin/packages/swfft/package.py
+++ b/var/spack/repos/builtin/packages/swfft/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -30,19 +11,29 @@ class Swfft(MakefilePackage):
     """A stand-alone version of HACC's distributed-memory, pencil-decomposed,
     parallel 3D FFT."""
 
-    homepage = 'https://xgitlab.cels.anl.gov/hacc/SWFFT'
-
-    url = "https://xgitlab.cels.anl.gov/hacc/SWFFT/repository/v1.0/archive.tar.gz"
+    homepage = "https://xgitlab.cels.anl.gov/hacc/SWFFT"
+    url      = "https://xgitlab.cels.anl.gov/api/v4/projects/hacc%2FSWFFT/repository/archive.tar.gz?sha=v1.0"
+    git      = "https://xgitlab.cels.anl.gov/hacc/SWFFT.git"
 
     version('1.0', '0fbc34544b97ba9c3fb19ef2d7a0f076')
-    version('develop', git='https://xgitlab.cels.anl.gov/hacc/SWFFT',
-            branch='master')
+    version('develop', branch='master')
 
     depends_on('mpi')
     depends_on('fftw')
 
     tags = ['proxy-app', 'ecp-proxy-app']
 
+    @property
+    def build_targets(self):
+        targets = []
+        spec = self.spec
+
+        targets.append('DFFT_MPI_CC=%s' % spec['mpi'].mpicc)
+        targets.append('DFFT_MPI_CXX=%s' % spec['mpi'].mpicxx)
+        targets.append('DFFT_MPI_F90=%s' % spec['mpi'].mpifc)
+
+        return targets
+
     def install(self, spec, prefix):
         mkdir(prefix.bin)
         install('build/CheckDecomposition', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/swiftsim/package.py b/var/spack/repos/builtin/packages/swiftsim/package.py
index 4f094c561f..494d92c1d7 100644
--- a/var/spack/repos/builtin/packages/swiftsim/package.py
+++ b/var/spack/repos/builtin/packages/swiftsim/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import llnl.util.tty as tty
 
@@ -33,10 +14,10 @@ class Swiftsim(AutotoolsPackage):
     """
 
     homepage = 'http://icc.dur.ac.uk/swift/'
-    url = 'http://gitlab.cosma.dur.ac.uk/swift/swiftsim/repository/archive.tar.gz?ref=v0.3.0'
+    url = 'https://gitlab.cosma.dur.ac.uk/api/v4/projects/swift%2Fswiftsim/repository/archive.tar.gz?sha=v0.3.0'
 
-    version('0.3.0', git='https://gitlab.cosma.dur.ac.uk/swift/swiftsim.git',
-            commit='254cc1b563b2f88ddcf437b1f71da123bb9db733')
+    version('0.7.0', '1c703d7e20a31a3896e1c291bddd71ab')
+    version('0.3.0', '162ec2bdfdf44a31a08b3fcee23a886a')
 
     variant('mpi', default=True,
             description='Enable distributed memory parallelism')
diff --git a/var/spack/repos/builtin/packages/swig/package.py b/var/spack/repos/builtin/packages/swig/package.py
index e9148333de..0d4c97a58f 100644
--- a/var/spack/repos/builtin/packages/swig/package.py
+++ b/var/spack/repos/builtin/packages/swig/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 
 
diff --git a/var/spack/repos/builtin/packages/symengine/package.py b/var/spack/repos/builtin/packages/symengine/package.py
index 844e0c2e5e..b0bbd61e37 100644
--- a/var/spack/repos/builtin/packages/symengine/package.py
+++ b/var/spack/repos/builtin/packages/symengine/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import sys
 
@@ -31,11 +12,12 @@ class Symengine(CMakePackage):
 
     homepage = "https://github.com/symengine/symengine"
     url      = "https://github.com/symengine/symengine/archive/v0.2.0.tar.gz"
+    git      = "https://github.com/symengine/symengine.git"
 
+    version('develop', branch='master')
     version('0.3.0', 'e61d7513cca4963cd062616891de54c6')
     version('0.2.0', '45401561add36a13c1f0b0c5f8d7422d')
     version('0.1.0', '41ad7daed61fc5a77c285eb6c7303425')
-    version('develop', git='https://github.com/symengine/symengine.git')
 
     variant('boostmp',      default=False,
             description='Compile with Boost multi-precision integer library')
diff --git a/var/spack/repos/builtin/packages/sympol/package.py b/var/spack/repos/builtin/packages/sympol/package.py
index 215c23ae98..ca69920323 100644
--- a/var/spack/repos/builtin/packages/sympol/package.py
+++ b/var/spack/repos/builtin/packages/sympol/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/sz/package.py b/var/spack/repos/builtin/packages/sz/package.py
index 5ff44d18b2..f9d1c0f2a6 100644
--- a/var/spack/repos/builtin/packages/sz/package.py
+++ b/var/spack/repos/builtin/packages/sz/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -30,10 +11,20 @@ class Sz(AutotoolsPackage):
     """Error-bounded Lossy Compressor for HPC Data."""
 
     homepage = "https://collab.cels.anl.gov/display/ESR/SZ"
-    url      = "https://github.com/disheng222/SZ/archive/v1.4.11.0.tar.gz"
+    url      = "https://github.com/disheng222/SZ/archive/v2.0.2.0.tar.gz"
+
+    git      = "https://github.com/disheng222/SZ.git"
 
-    version('develop', git='https://github.com/disheng222/SZ.git',
-            branch='master')
+    version('develop', branch='master')
+    version('2.0.2.0',  sha256='176c65b421bdec8e91010ffbc9c7bf7852c799972101d6b66d2a30d9702e59b0')
+    version('1.4.13.5', sha256='b5e37bf3c377833eed0a7ca0471333c96cd2a82863abfc73893561aaba5f18b9')
+    version('1.4.13.4', sha256='c99b95793c48469cac60e6cf82f921babf732ca8c50545a719e794886289432b')
+    version('1.4.13.3', sha256='9d80390f09816bf01b7a817e07339030d596026b00179275616af55ed3c1af98')
+    version('1.4.13.2', sha256='bc45329bf54876ed0f721998940855dbd5fda54379ef35dad8463325488ea4c6')
+    version('1.4.13.0', sha256='baaa7fa740a47e152c319b8d7b9a69fe96b4fea5360621cdc96cb250635f946f')
+    version('1.4.12.3', sha256='c1413e1c260fac7a48cb11c6dd705730525f134b9f9b244af59885d564ac7a6f')
+    version('1.4.12.1', sha256='98289d75481a6e407e4027b5e23013ae83b4aed88b3f150327ea711322cd54b6')
+    version('1.4.11.1', sha256='6cbc5b233a3663a166055f1874f17c96ba29aa5a496d352707ab508288baa65c')
     version('1.4.11.0', '10dee28b3503821579ce35a50e352cc6')
     version('1.4.10.0', '82e23dc5a51bcce1f70ba7e3b68a5965')
     version('1.4.9.2',  '028ce90165b7a4c4051d4c0189f193c0')
diff --git a/var/spack/repos/builtin/packages/tabix/package.py b/var/spack/repos/builtin/packages/tabix/package.py
index 85c1b03e59..c35d15c1e8 100644
--- a/var/spack/repos/builtin/packages/tabix/package.py
+++ b/var/spack/repos/builtin/packages/tabix/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,9 @@ class Tabix(MakefilePackage):
     """Generic indexer for TAB-delimited genome position files"""
 
     homepage = "https://github.com/samtools/tabix"
-    url      = "https://github.com/samtools/tabix"
+    git      = "https://github.com/samtools/tabix.git"
 
-    version('2013-12-16', git='https://github.com/samtools/tabix.git', commit='1ae158ac79b459f5feeed7490c67519b14ce9f35')
+    version('2013-12-16', commit='1ae158ac79b459f5feeed7490c67519b14ce9f35')
 
     depends_on('perl', type=('build', 'run'))
     depends_on('python', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/talass/package.py b/var/spack/repos/builtin/packages/talass/package.py
new file mode 100644
index 0000000000..94e0a10b28
--- /dev/null
+++ b/var/spack/repos/builtin/packages/talass/package.py
@@ -0,0 +1,58 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Talass(CMakePackage):
+    """TALASS: Topological Analysis of Large-Scale Simulations
+    This package compiles the talass tool chain thar implements
+    various topological algorithms to analyze large scale data.
+    The package is organized hierarchical FileFormat < Statistics
+    < StreamingTopology and any of the subsets can be build stand-
+    alone."""
+
+    homepage = "http://www.cedmav.org/research/project/16-talass.html"
+    git      = "git@bitbucket.org:cedmav/talass.git"
+
+    version('2018-09-21', commit='bf7da9bb54a026d8cb575b5be28b9c88095cb307')
+
+    # The default precision and index space sizes
+    variant('precision', default='32', values=('32', '64'),
+            description='Precision of the function values')
+    variant('global', default='32', values=('16', '32', '64'),
+            description='Number of bits used for the global index space')
+    variant('local', default='32', values=('16', '32', '64'),
+            description='Number of bits used for the local index space')
+
+    root_cmakelists_dir = 'StreamingTopology'
+
+    def cmake_args(self):
+        variants = self.spec.variants
+
+        args = []
+
+        if int(variants['local'].value) > int(variants['global'].value):
+            raise InstallError('The global index space (%d bits) must be at least as large\
+ as the local index space (% bits)' % (variants['global'].value,
+                                       variants['local'].value))
+
+        if variants['precision'].value == '32':
+            args.append('-DFUNCTION_TYPE=float')
+        elif variants['precision'].value == '64':
+            args.append('-DFUNCTION_TYPE=double')
+
+        # Set global index space
+        args.append('-DGLOBAL_INDEX_TYPE=uint{0}_t'.format(
+            variants['global'].value))
+
+        # Set local index space
+        args.append('-DLOCAL_INDEX_TYPE=uint{0}_t'.format(
+            variants['local'].value))
+
+        # Deal with the PROJECT_INSTALL_PREFIX to enable Talass super builds
+        args.append('-DPROJECT_INSTALL_PREFIX=%s' % self.prefix)
+
+        return args
diff --git a/var/spack/repos/builtin/packages/talloc/package.py b/var/spack/repos/builtin/packages/talloc/package.py
index b2d7160a00..2fec8da46b 100644
--- a/var/spack/repos/builtin/packages/talloc/package.py
+++ b/var/spack/repos/builtin/packages/talloc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/tantan/package.py b/var/spack/repos/builtin/packages/tantan/package.py
new file mode 100644
index 0000000000..df183d07d9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/tantan/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Tantan(MakefilePackage):
+    """tantan is a tool to mask simple regions (low complexity and
+    short-period tandem repeats) in DNA, RNA, and protein sequences."""
+
+    homepage = "http://cbrc3.cbrc.jp/~martin/tantan"
+    url      = "http://cbrc3.cbrc.jp/~martin/tantan/tantan-13.zip"
+
+    version('13', '90a30284a7d0cd04d797527d47bc8bd0')
+
+    def install(self, spec, prefix):
+        make('prefix={0}'.format(self.prefix), 'install')
diff --git a/var/spack/repos/builtin/packages/tar/package.py b/var/spack/repos/builtin/packages/tar/package.py
index d6b660016a..3f491a5cfc 100644
--- a/var/spack/repos/builtin/packages/tar/package.py
+++ b/var/spack/repos/builtin/packages/tar/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,8 +11,9 @@ class Tar(AutotoolsPackage):
     other kinds of manipulation."""
 
     homepage = "https://www.gnu.org/software/tar/"
-    url = "https://ftp.gnu.org/gnu/tar/tar-1.29.tar.gz"
+    url      = "https://ftpmirror.gnu.org/tar/tar-1.29.tar.gz"
 
+    version('1.30', 'e0c5ed59e4dd33d765d6c90caadd3c73')
     version('1.29', 'cae466e6e58c7292355e7080248f244db3a4cf755f33f4fa25ca7f9a7ed09af0')
     version('1.28', '6ea3dbea1f2b0409b234048e021a9fd7')
 
diff --git a/var/spack/repos/builtin/packages/targetp/package.py b/var/spack/repos/builtin/packages/targetp/package.py
index 5b7fde557c..8fa33e7b9d 100644
--- a/var/spack/repos/builtin/packages/targetp/package.py
+++ b/var/spack/repos/builtin/packages/targetp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
diff --git a/var/spack/repos/builtin/packages/task/package.py b/var/spack/repos/builtin/packages/task/package.py
index b4fdd020de..93c58bc6eb 100644
--- a/var/spack/repos/builtin/packages/task/package.py
+++ b/var/spack/repos/builtin/packages/task/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,6 +11,7 @@ class Task(CMakePackage):
     homepage = "http://www.taskwarrior.org"
     url      = "http://taskwarrior.org/download/task-2.4.4.tar.gz"
 
+    version('2.5.1', 'bcd984a00d6d1eb6b40faf567419f784')
     version('2.4.4', '517450c4a23a5842df3e9905b38801b3')
 
     depends_on('cmake@2.8:', type='build')
diff --git a/var/spack/repos/builtin/packages/taskd/package.py b/var/spack/repos/builtin/packages/taskd/package.py
index 56adbf619f..43f6a8b7df 100644
--- a/var/spack/repos/builtin/packages/taskd/package.py
+++ b/var/spack/repos/builtin/packages/taskd/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/tasmanian/package.py b/var/spack/repos/builtin/packages/tasmanian/package.py
new file mode 100644
index 0000000000..908841bce9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/tasmanian/package.py
@@ -0,0 +1,125 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Tasmanian(CMakePackage):
+    """The Toolkit for Adaptive Stochastic Modeling and Non-Intrusive
+    ApproximatioN is a robust library for high dimensional integration and
+    interpolation as well as parameter calibration."""
+
+    homepage = 'http://tasmanian.ornl.gov'
+    url      = 'https://github.com/ORNL/TASMANIAN/archive/v6.0.tar.gz'
+    git      = 'https://github.com/ORNL/TASMANIAN.git'
+
+    version('develop', branch='master')
+
+    version('6.0', '43dcb1d2bcb2f2c829ad046d0e91e83d')  # use for xsdk-0.4.0
+    version('5.1', '5d904029a24470a6acf4a87d3339846e')
+
+    version('5.0', '4bf131841d786033863d271739be0f7a',
+            url='http://tasmanian.ornl.gov/documents/Tasmanian_v5.0.zip')
+
+    variant('xsdkflags', default=False,
+            description='enable XSDK defaults for Tasmanian')
+
+    variant('openmp', default=True,
+            description='add OpenMP support to Tasmanian')
+    # tested with OpenMP 3.1 (clang4) through 4.0-4.5 (gcc 5 - 8)
+
+    variant('blas', default=False,
+            description='add BLAS support to Tasmanian')
+
+    variant('mpi', default=False,
+            description='add MPI support to Tasmanian')
+
+    variant('cuda', default=False,
+            description='add CUDA support to Tasmanian')
+
+    variant('magma', default=False,
+            description='add UTK MAGMA support to Tasmanian')
+
+    variant('python', default=False,
+            description='add Python binding for Tasmanian')
+
+    variant('fortran', default=False,
+            description='add Fortran 90/95 interface to Tasmanian')
+
+    variant('build_type', default='Release',
+            description='CMake build type',
+            values=('Debug', 'Release'))
+
+    depends_on('cmake@3.5.1:', type='build')
+
+    depends_on('python@2.7:', when='+python', type=('build', 'run'))
+    depends_on('py-numpy', when='+python', type=('build', 'run'))
+
+    extends('python', when='+python', type=('build', 'run'))
+
+    depends_on('mpi', when="+mpi", type=('build', 'run'))  # openmpi 2 and 3 tested
+
+    depends_on('blas', when="+blas", type=('build', 'run'))  # openblas 0.2.18 or newer
+
+    depends_on('cuda@8.0.61:', when='+cuda', type=('build', 'run'))
+    depends_on('cuda@8.0.61:', when='+magma', type=('build', 'run'))
+
+    depends_on('magma@2.4.0:', when='+magma', type=('build', 'run'))
+
+    conflicts('-cuda', when='+magma')  # currently MAGMA only works with CUDA
+
+    # old versions
+    conflicts('+magma', when='@:5.1')  # magma does not work prior to 6.0
+    conflicts('+mpi', when='@:5.1')    # MPI is broken prior to 6.0
+    conflicts('+xsdkflags', when='@:5.1')  # 6.0 is the first version included in xSDK
+
+    def cmake_args(self):
+        spec = self.spec
+
+        if '+xsdkflags' in spec:
+            args = [
+                '-DUSE_XSDK_DEFAULTS:BOOL=ON',
+                '-DXSDK_ENABLE_PYTHON:BOOL={0}'.format(
+                    'ON' if '+python' in spec else 'OFF'),
+                '-DTasmanian_ENABLE_MPI:BOOL={0}'.format(
+                    'ON' if '+mpi' in spec else 'OFF'),
+                '-DXSDK_ENABLE_OPENMP:BOOL={0}'.format(
+                    'ON' if '+openmp' in spec else 'OFF'),
+                '-DTPL_ENABLE_BLAS:BOOL={0}'.format(
+                    'ON' if '+blas' in spec else 'OFF'),
+                '-DXSDK_ENABLE_CUDA:BOOL={0}'.format(
+                    'ON' if '+cuda' in spec else 'OFF'),
+                '-DTPL_ENABLE_MAGMA:BOOL={0}'.format(
+                    'ON' if '+magma' in spec else 'OFF'),
+                '-DXSDK_ENABLE_FORTRAN:BOOL={0}'.format(
+                    'ON' if '+fortran' in spec else 'OFF'), ]
+        else:
+            args = [
+                '-DTasmanian_ENABLE_OPENMP:BOOL={0}'.format(
+                    'ON' if '+openmp' in spec else 'OFF'),
+                '-DTasmanian_ENABLE_BLAS:BOOL={0}'.format(
+                    'ON' if '+blas' in spec else 'OFF'),
+                '-DTasmanian_ENABLE_PYTHON:BOOL={0}'.format(
+                    'ON' if '+python' in spec else 'OFF'),
+                '-DTasmanian_ENABLE_MPI:BOOL={0}'.format(
+                    'ON' if '+mpi' in spec else 'OFF'),
+                '-DTasmanian_ENABLE_CUDA:BOOL={0}'.format(
+                    'ON' if '+cuda' in spec else 'OFF'),
+                '-DTasmanian_ENABLE_MAGMA:BOOL={0}'.format(
+                    'ON' if '+magma' in spec else 'OFF'),
+                '-DTasmanian_ENABLE_FORTRAN:BOOL={0}'.format(
+                    'ON' if '+fortran' in spec else 'OFF'), ]
+
+        if spec.satisfies('+python'):
+            args.append('-DPYTHON_EXECUTABLE:FILEPATH={0}'.format(
+                self.spec['python'].command.path))
+
+        # _CUBLAS and _CUDA were separate options prior to 6.0
+        # skipping _CUBLAS leads to peformance regression
+        if spec.satisfies('@:5.1'):
+            args.append('-DTasmanian_ENABLE_CUBLAS={0}'.format(
+                        'ON' if '+cuda' in spec else 'OFF'))
+
+        return args
diff --git a/var/spack/repos/builtin/packages/tassel/package.py b/var/spack/repos/builtin/packages/tassel/package.py
index eb48897e0e..5a568cc0f4 100644
--- a/var/spack/repos/builtin/packages/tassel/package.py
+++ b/var/spack/repos/builtin/packages/tassel/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,10 +11,9 @@ class Tassel(Package):
        evolutionary patterns, and linkage disequilibrium."""
 
     homepage = "http://www.maizegenetics.net/tassel"
-    url      = "https://bitbucket.org/tasseladmin/tassel-5-source/get/master.tar.gz"
+    git      = "https://bitbucket.org/tasseladmin/tassel-5-standalone.git"
 
-    version('2017-07-22', git='https://bitbucket.org/tasseladmin/tassel-5-standalone.git',
-            commit='ae96ae75c3c9a9e8026140b6c775fa4685bdf531')
+    version('2017-07-22', commit='ae96ae75c3c9a9e8026140b6c775fa4685bdf531')
 
     depends_on('java', type=('build', 'run'))
     depends_on('perl', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/tau/package.py b/var/spack/repos/builtin/packages/tau/package.py
index 26b1e38b27..9aa29297e4 100644
--- a/var/spack/repos/builtin/packages/tau/package.py
+++ b/var/spack/repos/builtin/packages/tau/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 import glob
@@ -37,6 +18,9 @@ class Tau(Package):
     homepage = "http://www.cs.uoregon.edu/research/tau"
     url      = "https://www.cs.uoregon.edu/research/tau/tau_releases/tau-2.25.tar.gz"
 
+    version('2.27.1', '4f98ff67ae5ab1ff2712f694bdec1fa9')
+    version('2.27',   '76602d35fc96f546b5b9dcaf09158651')
+    version('2.26.3', '4ec14e85b8f3560b58628512c7b49e17')
     version('2.25', '46cd48fa3f3c4ce0197017b3158a2b43')
     version('2.24.1', '6635ece6d1f08215b02f5d0b3c1e971b')
     version('2.24', '57ce33539c187f2e5ec68f0367c76db4')
diff --git a/var/spack/repos/builtin/packages/tcl-itcl/package.py b/var/spack/repos/builtin/packages/tcl-itcl/package.py
new file mode 100644
index 0000000000..0b0d842fe3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/tcl-itcl/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class TclItcl(AutotoolsPackage):
+    """[incr Tcl] is the most widely used O-O system for Tcl. The name is a
+    play on C++, and [incr Tcl] provides a similar object model, including
+    multiple inheritence and public and private classes and variables."""
+
+    homepage = "https://sourceforge.net/projects/incrtcl/"
+    url      = "https://sourceforge.net/projects/incrtcl/files/%5Bincr%20Tcl_Tk%5D-4-source/itcl%204.0.4/itcl4.0.4.tar.gz"
+
+    version('4.0.4', 'c9c52afdd9435490e2db17c3c6c95ab4')
+
+    extends('tcl')
+
+    def configure_args(self):
+        args = [
+            '--enable-shared',
+            '--enable-threads',
+            '--with-tcl=' + self.spec['tcl'].tcl_lib_dir,
+        ]
+        return args
diff --git a/var/spack/repos/builtin/packages/tcl-tcllib/package.py b/var/spack/repos/builtin/packages/tcl-tcllib/package.py
new file mode 100644
index 0000000000..46ec7b6d46
--- /dev/null
+++ b/var/spack/repos/builtin/packages/tcl-tcllib/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class TclTcllib(AutotoolsPackage):
+    """Tcllib is a collection of utility modules for Tcl. These modules provide
+    a wide variety of functionality, from implementations of standard data
+    structures to implementations of common networking protocols. The intent is
+    to collect commonly used function into a single library, which users can
+    rely on to be available and stable."""
+
+    homepage   = "http://www.tcl.tk/software/tcllib"
+    url        = "https://sourceforge.net/projects/tcllib/files/tcllib/1.19/tcllib-1.19.tar.gz"
+    list_url   = "https://sourceforge.net/projects/tcllib/files/tcllib/"
+    list_depth = 1
+
+    version('1.19', '8d3990d01e3fb66480d441d18a7a7d0d')
+    version('1.18', '219361e6bdf9d9c0d79edbd1ab3e8080')
+    version('1.17', '4c75fbfbb518f8990fcd4686b976bd70')
+    version('1.16', 'e65e91f5ca188648019fdbe15fbfb9bf')
+    version('1.15', '7a0525912e8863f8d4360ab10e5450f8')
+    version('1.14', '55bac9afce54c3328f368918cc2d7a4b')
+
+    extends('tcl')
diff --git a/var/spack/repos/builtin/packages/tcl-tclxml/package.py b/var/spack/repos/builtin/packages/tcl-tclxml/package.py
new file mode 100644
index 0000000000..4f50a86809
--- /dev/null
+++ b/var/spack/repos/builtin/packages/tcl-tclxml/package.py
@@ -0,0 +1,39 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class TclTclxml(AutotoolsPackage):
+    """TclXML is an API for parsing XML documents using the Tcl scripting
+    language. It is also a package including a DOM implementation (TclDOM) and
+    XSL Transformations (TclXSLT). These allow Tcl scripts to read, manipulate
+    and write XML documents."""
+
+    homepage   = "http://tclxml.sourceforge.net/tclxml.html"
+    url        = "https://sourceforge.net/projects/tclxml/files/TclXML/3.2/tclxml-3.2.tar.gz"
+    list_url   = "https://sourceforge.net/projects/tclxml/files/TclXML/"
+    list_depth = 1
+
+    version('3.2', '9d1605246c899eff7db591bca3c23200')
+    version('3.1', '35de63a4ceba7a6fdb85dd1a62f2e881')
+
+    extends('tcl')
+
+    depends_on('tcl-tcllib')
+    depends_on('libxml2')
+    depends_on('libxslt')
+
+    def configure_args(self):
+        return [
+            '--exec-prefix={0}'.format(
+                self.prefix),
+            '--with-tcl={0}/lib'.format(
+                self.spec['tcl'].prefix),
+            '--with-xml2-config={0}/bin/xml2-config'.format(
+                self.spec['libxml2'].prefix),
+            '--with-xslt-config={0}/bin/xslt-config'.format(
+                self.spec['libxslt'].prefix),
+        ]
diff --git a/var/spack/repos/builtin/packages/tcl/package.py b/var/spack/repos/builtin/packages/tcl/package.py
index 219c63e62b..7e2d57c764 100644
--- a/var/spack/repos/builtin/packages/tcl/package.py
+++ b/var/spack/repos/builtin/packages/tcl/package.py
@@ -1,27 +1,11 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import os
+
+from spack.util.environment import is_system_path
 from spack import *
 
 
@@ -36,12 +20,15 @@ class Tcl(AutotoolsPackage):
     homepage = "http://www.tcl.tk"
     url      = "http://prdownloads.sourceforge.net/tcl/tcl8.6.5-src.tar.gz"
 
+    version('8.6.8', '81656d3367af032e0ae6157eff134f89')
     version('8.6.6', '5193aea8107839a79df8ac709552ecb7')
     version('8.6.5', '0e6426a4ca9401825fbc6ecf3d89a326')
     version('8.6.4', 'd7cbb91f1ded1919370a30edd1534304')
     version('8.6.3', 'db382feca91754b7f93da16dc4cdad1f')
     version('8.5.19', '0e6426a4ca9401825fbc6ecf3d89a326')
 
+    extendable = True
+
     depends_on('zlib')
 
     configure_directory = 'unix'
@@ -49,17 +36,103 @@ class Tcl(AutotoolsPackage):
     def setup_environment(self, spack_env, run_env):
         # When using Tkinter from within spack provided python+tk, python
         # will not be able to find Tcl/Tk unless TCL_LIBRARY is set.
-        run_env.set('TCL_LIBRARY', join_path(self.prefix.lib, 'tcl{0}'.format(
-            self.spec.version.up_to(2))))
+        run_env.set('TCL_LIBRARY', join_path(self.prefix, self.tcl_lib_dir))
 
     def install(self, spec, prefix):
         with working_dir(self.build_directory):
             make('install')
 
+            # http://wiki.tcl.tk/17463
+            if self.spec.satisfies('@8.6:'):
+                make('install-headers')
+
             # Some applications like Expect require private Tcl headers.
             make('install-private-headers')
 
+            # Copy source to install tree
+            # A user-provided install option might re-do this
+            # https://github.com/spack/spack/pull/4102/files
+            installed_src = join_path(
+                self.spec.prefix, 'share', self.name, 'src')
+            stage_src = os.path.realpath(self.stage.source_path)
+            install_tree(stage_src, installed_src)
+
+            # Replace stage dir -> installed src dir in tclConfig
+            filter_file(
+                stage_src, installed_src,
+                join_path(self.spec.prefix, 'lib', 'tclConfig.sh'))
+
+        # Don't install binaries in src/ tree
+        with working_dir(join_path(installed_src, self.configure_directory)):
+            make('clean')
+
     @run_after('install')
     def symlink_tclsh(self):
         with working_dir(self.prefix.bin):
             symlink('tclsh{0}'.format(self.version.up_to(2)), 'tclsh')
+
+    # ========================================================================
+    # Set up environment to make install easy for tcl extensions.
+    # ========================================================================
+
+    @property
+    def libs(self):
+        return LibraryList([])
+
+    @property
+    def command(self):
+        """Returns the tclsh command.
+
+        :returns: The tclsh command
+        :rtype: Executable
+        """
+        return Executable(os.path.realpath(self.prefix.bin.tclsh))
+
+    @property
+    def tcl_lib_dir(self):
+        """The Tcl version-specific library directory where all extensions are
+        installed."""
+        return 'lib'
+
+    @property
+    def tcl_builtin_lib_dir(self):
+        """The Tcl version-specific library directory where all builtin
+        extensions are installed."""
+        return join_path(self.tcl_lib_dir,
+                         'tcl{0}'.format(self.version.up_to(2)))
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        """Set TCLLIBPATH to include the tcl-shipped directory for
+        extensions and any other tcl extension it depends on.
+        For further info see: https://wiki.tcl.tk/1787"""
+
+        # If we set TCLLIBPATH, we must also ensure that the corresponding
+        # tcl is found in the build environment. This to prevent cases
+        # where a system provided tcl is run against the standard libraries
+        # of a Spack built tcl. See issue #7128 that relates to python but
+        # it boils down to the same situation we have here.
+        path = os.path.dirname(self.command.path)
+        if not is_system_path(path):
+            spack_env.prepend_path('PATH', path)
+
+        tcl_paths = [join_path(self.prefix, self.tcl_builtin_lib_dir)]
+
+        for d in dependent_spec.traverse(deptype=('build', 'run', 'test')):
+            if d.package.extends(self.spec):
+                tcl_paths.append(join_path(d.prefix, self.tcl_lib_dir))
+
+        # WARNING: paths in $TCLLIBPATH must be *space* separated,
+        # its value is meant to be a Tcl list, *not* an env list
+        # as explained here: https://wiki.tcl.tk/1787:
+        # "TCLLIBPATH is a Tcl list, not some platform-specific
+        # colon-separated or semi-colon separated format"
+        tcllibpath = ' '.join(tcl_paths)
+        spack_env.set('TCLLIBPATH', tcllibpath)
+
+        # For run time environment set only the path for
+        # dependent_spec and prepend it to TCLLIBPATH
+        if dependent_spec.package.extends(self.spec):
+            dependent_tcllibpath = join_path(dependent_spec.prefix,
+                                             self.tcl_lib_dir)
+            run_env.prepend_path('TCLLIBPATH', dependent_tcllibpath,
+                                 separator=' ')
diff --git a/var/spack/repos/builtin/packages/tclap/package.py b/var/spack/repos/builtin/packages/tclap/package.py
new file mode 100644
index 0000000000..ab067f4e3e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/tclap/package.py
@@ -0,0 +1,16 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Tclap(AutotoolsPackage):
+    """Templatized C++ Command Line Parser"""
+
+    homepage = "http://tclap.sourceforge.net"
+    url      = "https://downloads.sourceforge.net/project/tclap/tclap-1.2.2.tar.gz"
+
+    version('1.2.2', '6f35665814dca292eceda007d7e13bcb')
+    version('1.2.1', 'eb0521d029bf3b1cc0dcaa7e42abf82a')
diff --git a/var/spack/repos/builtin/packages/tcoffee/package.py b/var/spack/repos/builtin/packages/tcoffee/package.py
index 667f876dd9..2b2ed2d95e 100644
--- a/var/spack/repos/builtin/packages/tcoffee/package.py
+++ b/var/spack/repos/builtin/packages/tcoffee/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,9 @@ class Tcoffee(MakefilePackage):
     """T-Coffee is a multiple sequence alignment program."""
 
     homepage = "http://www.tcoffee.org/"
-    url      = "https://github.com/cbcrg/tcoffee"
+    git      = "https://github.com/cbcrg/tcoffee.git"
 
-    version('2017-08-17', git='https://github.com/cbcrg/tcoffee.git', commit='f389b558e91d0f82e7db934d9a79ce285f853a71')
+    version('2017-08-17', commit='f389b558e91d0f82e7db934d9a79ce285f853a71')
 
     depends_on('perl', type=('build', 'run'))
     depends_on('blast-plus')
diff --git a/var/spack/repos/builtin/packages/tcptrace/package.py b/var/spack/repos/builtin/packages/tcptrace/package.py
new file mode 100644
index 0000000000..dcb7dcd7f4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/tcptrace/package.py
@@ -0,0 +1,40 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+from os.path import join
+
+
+class Tcptrace(AutotoolsPackage):
+    """tcptrace is a tool written by Shawn Ostermann at Ohio University for
+       analysis of TCP dump files. It can take as input the files produced by
+       several popular packet-capture programs, including tcpdump, snoop,
+       etherpeek, HP Net Metrix, and WinDump."""
+
+    homepage = "http://www.tcptrace.org/"
+    url      = "http://www.tcptrace.org/download/tcptrace-6.6.7.tar.gz"
+
+    version('6.6.7', '68128dc1817b866475e2f048e158f5b9')
+
+    depends_on('bison', type='build')
+    depends_on('flex', type='build')
+    depends_on('libpcap')
+
+    # Fixes incorrect API access in libpcap.
+    # See https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=545595
+    patch('tcpdump.patch')
+
+    @run_after('configure')
+    def patch_makefile(self):
+        # see https://github.com/blitz/tcptrace/blob/master/README.linux
+        makefile = FileFilter('Makefile')
+        makefile.filter(
+            "PCAP_LDLIBS = -lpcap",
+            "DEFINES += -D_BSD_SOURCE\nPCAP_LDLIBS = -lpcap")
+
+    def install(self, spec, prefix):
+        # The build system has trouble creating directories
+        mkdirp(prefix.bin)
+        install('tcptrace', join(prefix.bin, 'tcptrace'))
diff --git a/var/spack/repos/builtin/packages/tcptrace/tcpdump.patch b/var/spack/repos/builtin/packages/tcptrace/tcpdump.patch
new file mode 100644
index 0000000000..107d3a8af6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/tcptrace/tcpdump.patch
@@ -0,0 +1,37 @@
+--- a/tcpdump.c
++++ b/tcpdump.c
+@@ -68,9 +68,6 @@
+ 
+ 
+ 
+-/* external ref, in case missing in older version */
+-extern int pcap_offline_read(void *, int, pcap_handler, u_char *);
+-
+ /* global pointer, the pcap info header */
+ static pcap_t *pcap;
+ 
+@@ -248,9 +245,12 @@
+     void		**pplast)
+ {
+     int ret;
++    struct pcap_pkthdr *pkt_header;
++    const u_char *pkt_data;
+ 
+     while (1) {
+-	if ((ret = pcap_offline_read(pcap,1,(pcap_handler)callback,0)) != 1) {
++       ret = pcap_next_ex(pcap, &pkt_header, &pkt_data);
++       if (ret != 1) {
+ 	    /* prob EOF */
+ 
+ 	    if (ret == -1) {
+@@ -265,6 +265,10 @@
+ 	    return(0);
+ 	}
+ 
++   if (callback(0, pkt_header, (char *)pkt_data)) {
++      continue;
++   }
++
+ 	/* at least one tcpdump implementation (AIX) seems to be */
+ 	/* storing NANOseconds in the usecs field of the timestamp. */
+ 	/* This confuses EVERYTHING.  Try to compensate. */
diff --git a/var/spack/repos/builtin/packages/tcsh/package.py b/var/spack/repos/builtin/packages/tcsh/package.py
index 84d0ed28b0..876957b150 100644
--- a/var/spack/repos/builtin/packages/tcsh/package.py
+++ b/var/spack/repos/builtin/packages/tcsh/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class Tcsh(AutotoolsPackage):
 
     version('6.20.00', '59d40ef40a68e790d95e182069431834')
 
-    def fedora_patch(commit, file, **kwargs):
+    def fedora_patch(commit, file, **kwargs):  # noqa
         prefix = 'https://src.fedoraproject.org/rpms/tcsh/raw/{0}/f/'.format(commit)
         patch('{0}{1}'.format(prefix, file), **kwargs)
 
diff --git a/var/spack/repos/builtin/packages/tealeaf/package.py b/var/spack/repos/builtin/packages/tealeaf/package.py
index c5031e9bd4..208d11ccc7 100644
--- a/var/spack/repos/builtin/packages/tealeaf/package.py
+++ b/var/spack/repos/builtin/packages/tealeaf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 import glob
 
diff --git a/var/spack/repos/builtin/packages/templight-tools/package.py b/var/spack/repos/builtin/packages/templight-tools/package.py
new file mode 100644
index 0000000000..d15db66459
--- /dev/null
+++ b/var/spack/repos/builtin/packages/templight-tools/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class TemplightTools(CMakePackage):
+    """Supporting tools for the Templight Profiler"""
+
+    homepage = "https://github.com/mikael-s-persson/templight-tools"
+    git      = "https://github.com/mikael-s-persson/templight-tools.git"
+
+    version('develop', branch='master')
+
+    depends_on('cmake @2.8.7:', type='build')
+    depends_on('boost @1.48.1: +filesystem +graph +program_options +test')
diff --git a/var/spack/repos/builtin/packages/templight/develop-20180720.patch b/var/spack/repos/builtin/packages/templight/develop-20180720.patch
new file mode 100644
index 0000000000..986d6a7783
--- /dev/null
+++ b/var/spack/repos/builtin/packages/templight/develop-20180720.patch
@@ -0,0 +1,44 @@
+--- a/templight_driver.cpp	2018-07-20 17:32:51.064430826 +0200
++++ b/templight_driver.cpp	2018-07-20 17:33:58.476431081 +0200
+@@ -57,6 +57,9 @@
+ #include "llvm/Support/TargetSelect.h"
+ #include "llvm/Support/Timer.h"
+ #include "llvm/Support/raw_ostream.h"
++#ifdef _WIN32
++#include "Windows/WindowsSupport.h"
++#endif
+ 
+ #include "TemplightAction.h"
+ 
+@@ -475,7 +478,21 @@
+ 
+ }
+ 
+-
++// llvm::sys::Process::GetArgumentVector was renamed as of rL330216
++// https://reviews.llvm.org/rL330216
++// This aims to preserves compatibility, but the better way to do it would
++// be to let InitLLVM do the job
++std::error_code GetArgumentVector(
++    SmallVectorImpl<const char *> &ArgsOut, ArrayRef<const char *> ArgsIn,
++    SpecificBumpPtrAllocator<char> &ArgAllocator) {
++#ifdef _WIN32
++  return windows::GetCommandLineArguments(ArgsOut, ArgAllocator);
++#else
++  ArgsOut.append(ArgsIn.begin(), ArgsIn.end());
++  (void)ArgAllocator;
++  return std::error_code();
++#endif
++}
+ 
+ int main(int argc_, const char **argv_) {
+   llvm::sys::PrintStackTraceOnErrorSignal(argv_[0]);
+@@ -486,7 +503,7 @@
+ 
+   SmallVector<const char *, 256> argv;
+   llvm::SpecificBumpPtrAllocator<char> ArgAllocator;
+-  std::error_code EC = llvm::sys::Process::GetArgumentVector(
++  std::error_code EC = GetArgumentVector(
+       argv, llvm::makeArrayRef(argv_, argc_), ArgAllocator);
+   if (EC) {
+     llvm::errs() << "error: couldn't get arguments: " << EC.message() << '\n';
diff --git a/var/spack/repos/builtin/packages/templight/package.py b/var/spack/repos/builtin/packages/templight/package.py
new file mode 100644
index 0000000000..15264e6d22
--- /dev/null
+++ b/var/spack/repos/builtin/packages/templight/package.py
@@ -0,0 +1,147 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class Templight(CMakePackage):
+    """Templight is a Clang-based tool to profile the time and memory
+       consumption of template instantiations and to perform interactive
+       debugging sessions to gain introspection into the template
+       instantiation process."""
+
+    homepage = "https://github.com/mikael-s-persson/templight"
+    git      = "https://github.com/mikael-s-persson/templight.git"
+    llvm_svn = "http://llvm.org/svn/llvm-project/{0}/trunk"
+
+    family = 'compiler'  # Used by lmod
+
+    # Templight is a patch to clang, so we have three versions to care about:
+    # - The one that will be used in Spack specifications
+    # - The git branch that we need to fetch from in the templight repo
+    # - The svn tag that we need to fetch from in the LLVM repos
+    version('develop', branch='master')
+    resource(name='llvm-trunk',
+             svn=llvm_svn.format('llvm'),
+             destination='.',
+             placement='llvm',
+             when='@develop')
+    resource(name='clang-trunk',
+             svn=llvm_svn.format('cfe'),
+             destination='llvm/tools',
+             placement='clang',
+             when='@develop')
+
+    # Templight has no stable release yet, and is supposed to be built against
+    # the LLVM trunk. As this is a brittle combination, I decided to
+    # artificially create a stable release based on what works today. Please
+    # feel free to remove this version once templight has stabilized.
+    version('2018.07.20', commit='91589f95427620dd0a2346bd69ba922f374aa42a')
+    resource(name='llvm-r337566',
+             svn=llvm_svn.format('llvm'),
+             revision=337566,
+             destination='.',
+             placement='llvm',
+             when='@2018.07.20')
+    resource(name='clang-r337566',
+             svn=llvm_svn.format('cfe'),
+             revision=337566,
+             destination='llvm/tools',
+             placement='clang',
+             when='@2018.07.20')
+    patch('develop-20180720.patch', when='@2018.07.20')
+
+    # Clang debug builds can be _huge_ (20+ GB), make sure you know what you
+    # are doing before switching to them
+    variant('build_type', default='Release',
+            description='CMake build type',
+            values=('Debug', 'Release', 'RelWithDebInfo', 'MinSizeRel'))
+
+    # NOTE: LLVM has many configurable tweaks and optional tools/extensions.
+    #       I did not think that  propagating all of these to a debugging and
+    #       performance analysis tool was worth the maintenance burden. But
+    #       if you disagree, the llvm package can be used for inspiration.
+
+    depends_on('cmake@3.4.3:', type='build')
+    depends_on('python')
+    depends_on('py-lit', type=('build', 'run'))
+
+    def patch(self):
+        # We start with the templight source tree and an "llvm" subdir.
+        # But we actually need an llvm source tree with a "templight" subdir.
+        # Let's flip the directory organization around
+        templight_files = os.listdir('.')
+        templight_files.remove('llvm')
+        templight_dir = 'llvm/tools/clang/tools/templight'
+        os.mkdir(templight_dir)
+        for name in templight_files:
+            os.rename(name, os.path.join(templight_dir, name))
+        for name in os.listdir('llvm'):
+            os.rename(os.path.join('llvm', name), name)
+        os.rmdir('llvm')
+
+        # Tell the clang build system that it needs to build templight
+        with open("tools/clang/tools/CMakeLists.txt", "a") as cmake_lists:
+            cmake_lists.write("add_clang_subdirectory(templight)")
+
+    def setup_environment(self, spack_env, run_env):
+        spack_env.append_flags('CXXFLAGS', self.compiler.cxx11_flag)
+        run_env.set('CC', join_path(self.spec.prefix.bin, 'templight'))
+        run_env.set('CXX', join_path(self.spec.prefix.bin, 'templight++'))
+
+    def cmake_args(self):
+        spec = self.spec
+
+        # Templight is a debugging tool, not a production compiler, so we only
+        # need a very bare-bones build of clang
+        #
+        # Minimal build config ideas were taken from the llvm package, with
+        # the templight-specific assumption that we will always be building
+        # for LLVM / Clang 5.0+ and can safely ignore older tricks.
+        #
+        cmake_args = [
+            '-DLLVM_REQUIRES_RTTI:BOOL=ON',
+            '-DCLANG_DEFAULT_OPENMP_RUNTIME:STRING=libomp',
+            '-DPYTHON_EXECUTABLE:PATH={0}'.format(spec['python'].command.path),
+            '-DLLVM_EXTERNAL_POLLY_BUILD:Bool=OFF',
+            '-DLLVM_TOOL_POLLY_BUILD:Bool=OFF',
+            '-DLLVM_POLLY_BUILD:Bool=OFF',
+            '-DLLVM_POLLY_LINK_INTO_TOOLS:Bool=OFF',
+            '-DLLVM_EXTERNAL_LLDB_BUILD:Bool=OFF',
+            '-DLLVM_TOOL_LLDB_BUILD:Bool=OFF',
+            '-DLLVM_TOOL_LLD_BUILD:Bool=OFF',
+            '-DLLVM_EXTERNAL_LIBUNWIND_BUILD:Bool=OFF',
+            '-DLLVM_EXTERNAL_LIBCXX_BUILD:Bool=OFF',
+            '-DLLVM_EXTERNAL_LIBCXXABI_BUILD:Bool=OFF',
+            '-DLLVM_EXTERNAL_COMPILER_RT_BUILD:Bool=OFF',
+        ]
+
+        targets = ['NVPTX', 'AMDGPU']
+
+        if 'x86' in spec.architecture.target.lower():
+            targets.append('X86')
+        elif 'arm' in spec.architecture.target.lower():
+            targets.append('ARM')
+        elif 'aarch64' in spec.architecture.target.lower():
+            targets.append('AArch64')
+        elif 'sparc' in spec.architecture.target.lower():
+            targets.append('Sparc')
+        elif ('ppc' in spec.architecture.target.lower() or
+              'power' in spec.architecture.target.lower()):
+            targets.append('PowerPC')
+
+        cmake_args.append(
+            '-DLLVM_TARGETS_TO_BUILD:Bool=' + ';'.join(targets))
+
+        if spec.satisfies('platform=linux'):
+            cmake_args.append('-DCMAKE_BUILD_WITH_INSTALL_RPATH=1')
+
+        return cmake_args
+
+    @run_after('install')
+    def post_install(self):
+        with working_dir(self.build_directory):
+            install_tree('bin', self.prefix.libexec.llvm)
diff --git a/var/spack/repos/builtin/packages/tetgen/package.py b/var/spack/repos/builtin/packages/tetgen/package.py
index b7091c097c..3a23ec2902 100644
--- a/var/spack/repos/builtin/packages/tetgen/package.py
+++ b/var/spack/repos/builtin/packages/tetgen/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 import glob
diff --git a/var/spack/repos/builtin/packages/tethex/package.py b/var/spack/repos/builtin/packages/tethex/package.py
index 4ebe564522..75994e27e6 100644
--- a/var/spack/repos/builtin/packages/tethex/package.py
+++ b/var/spack/repos/builtin/packages/tethex/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,11 +15,12 @@ class Tethex(CMakePackage):
 
     homepage = "https://github.com/martemyev/tethex"
     url      = "https://github.com/martemyev/tethex/archive/v0.0.7.tar.gz"
+    git      = "https://github.com/martemyev/tethex.git"
 
     maintainers = ['davydden']
 
+    version('develop', branch='master')
     version('0.0.7', '6c9e4a18a6637deb4400c6d77ec03184')
-    version('develop', git='https://github.com/martemyev/tethex.git')
 
     variant('build_type', default='Release',
             description='The build type to build',
diff --git a/var/spack/repos/builtin/packages/texinfo/package.py b/var/spack/repos/builtin/packages/texinfo/package.py
index 47d65bcc80..b78f1e0b35 100644
--- a/var/spack/repos/builtin/packages/texinfo/package.py
+++ b/var/spack/repos/builtin/packages/texinfo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -34,10 +15,13 @@ class Texinfo(AutotoolsPackage):
     of the time. It is used by many non-GNU projects as well."""
 
     homepage = "https://www.gnu.org/software/texinfo/"
-    url      = "http://ftp.gnu.org/gnu/texinfo/texinfo-6.0.tar.gz"
+    url      = "https://ftpmirror.gnu.org/texinfo/texinfo-6.0.tar.gz"
 
+    version('6.5', '94e8f7149876793030e5518dd8d6e956')
     version('6.3', '9b08daca9bf8eccae9b0f884aba41f9e')
     version('6.0', 'e1a2ef5dce5018b53f0f6eed45b247a7')
     version('5.2', '1b8f98b80a8e6c50422125e07522e8db')
     version('5.1', '54e250014fe698fb4832016158747c03')
     version('5.0', '918432285abe6fe96c98355594c5656a')
+
+    depends_on('perl')
diff --git a/var/spack/repos/builtin/packages/texlive/package.py b/var/spack/repos/builtin/packages/texlive/package.py
index 3b26d2de94..4216be091e 100644
--- a/var/spack/repos/builtin/packages/texlive/package.py
+++ b/var/spack/repos/builtin/packages/texlive/package.py
@@ -1,29 +1,11 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
+import platform
 
 
 class Texlive(Package):
@@ -44,8 +26,8 @@ class Texlive(Package):
     # itself is stable.  Don't let that fool you though, it's still
     # installing TeX **LIVE** from e.g. ctan.math.... below, which is
     # not reproducible.
-    version('live', '8f8fc301514c08a89a2e97197369c648',
-            url='ftp://tug.org/historic/systems/texlive/2017/install-tl-unx.tar.gz')
+    version('live', '946701aa28ca1f93e55e8310ce63fbf8',
+            url='ftp://tug.org/historic/systems/texlive/2018/install-tl-unx.tar.gz')
 
     # There does not seem to be a complete list of schemes.
     # Examples include:
@@ -65,6 +47,10 @@ class Texlive(Package):
 
     depends_on('perl', type='build')
 
+    def setup_environment(self, spack_env, run_env):
+        suffix = "%s-%s" % (platform.machine(), platform.system().lower())
+        run_env.prepend_path('PATH', join_path(self.prefix.bin, suffix))
+
     def install(self, spec, prefix):
         # Using texlive's mirror system leads to mysterious problems,
         # in lieu of being able to specify a repository as a variant, hardwire
diff --git a/var/spack/repos/builtin/packages/the-platinum-searcher/package.py b/var/spack/repos/builtin/packages/the-platinum-searcher/package.py
index 212bc0d75e..e10c899600 100644
--- a/var/spack/repos/builtin/packages/the-platinum-searcher/package.py
+++ b/var/spack/repos/builtin/packages/the-platinum-searcher/package.py
@@ -1,45 +1,22 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-import os
-import shutil
 
 
 class ThePlatinumSearcher(Package):
     """Fast parallel recursive grep alternative"""
-    homepage = "https://github.com/monochromegane/the_platinum_searcher"
-    url = "https://github.com/monochromegane/the_platinum_searcher"
 
-    package = 'github.com/monochromegane/the_platinum_searcher/...'
+    homepage = "https://github.com/monochromegane/the_platinum_searcher"
+    go       = "github.com/monochromegane/the_platinum_searcher/..."
 
-    version('head', go=package)
+    version('head')
 
     extends("go", deptypes='build')
 
     def install(self, spec, prefix):
-        env = os.environ
         env['GOPATH'] = self.stage.source_path + ':' + env['GOPATH']
         go('install', self.package, env=env)
-        shutil.copytree('bin', os.path.join(prefix, 'bin'))
+        install_tree('bin', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/the-silver-searcher/package.py b/var/spack/repos/builtin/packages/the-silver-searcher/package.py
index 31b269e286..e3ed85d41f 100644
--- a/var/spack/repos/builtin/packages/the-silver-searcher/package.py
+++ b/var/spack/repos/builtin/packages/the-silver-searcher/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,4 +19,4 @@ class TheSilverSearcher(AutotoolsPackage):
     depends_on('pcre')
     depends_on('xz')
     depends_on('zlib')
-    depends_on('pkg-config', type='build')
+    depends_on('pkgconfig', type='build')
diff --git a/var/spack/repos/builtin/packages/thornado-mini/package.py b/var/spack/repos/builtin/packages/thornado-mini/package.py
new file mode 100644
index 0000000000..dc96f2a4b2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/thornado-mini/package.py
@@ -0,0 +1,77 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+import os
+
+
+class ThornadoMini(MakefilePackage):
+    """Code to solve the equation of radiative transfer in the
+    multi-group two-moment approximation"""
+
+    tags = ['proxy-app', 'ecp-proxy-app']
+
+    homepage = "https://sites.google.com/lbl.gov/exastar/home"
+    url      = "https://github.com/ECP-Astro/thornado_mini/archive/v1.0.tar.gz"
+    git      = "https://github.com/ECP-Astro/thornado_mini.git"
+
+    version('1.0', sha256='8a9f97acc823d374cce567831270cfcc50fa968949e49159c7e3442b93a2827d')
+
+    depends_on('mpi')
+    depends_on('hdf5+fortran')
+    depends_on('lapack')
+
+    parallel = False
+
+    def edit(self, spec, prefix):
+        os.environ['THORNADO_MACHINE'] = 'mymachine'
+        os.environ['THORNADO_DIR'] = os.getcwd()
+
+        file = open('Makefile', 'w')
+
+        file.write('FORTRAN_mymachine = %s %s\n' % (self.spec['mpi'].mpifc,
+                                                    self.compiler.openmp_flag))
+        file.write('FLINKER_mymachine = %s %s\n' % (self.spec['mpi'].mpifc,
+                                                    self.compiler.openmp_flag))
+        file.write('DEBUG_mymachine = -g -ffpe-trap=invalid,zero \
+        -fcheck=bounds\n')
+        file.write('OPTIMIZE_mymachine = -O2\n')
+        file.write('INCLUDE_HDF5_mymachine = \n')
+        file.write('INCLUDE_LAPACK_mymachine = \n')
+        file.write('LIBRARIES_HDF5_mymachine = \n')
+        file.write('LIBRARIES_LAPACK_mymachine = \n')
+        file.write('export FORTRAN_mymachine FLINKER_mymachine \
+        DEBUG_mymachine OPTIMIZE_mymachine\n')
+
+        file.write('all:\n')
+        file.write('\t@$(MAKE) -C $(THORNADO_DIR)/DeleptonizationProblem/Executables \
+        -f Makefile\n')
+
+        file.close()
+
+    @property
+    def build_targets(self):
+        targets = []
+
+        targets.append('INCLUDE_HDF5_mymachine = -I{0}'
+                       .format(self.spec['hdf5'].prefix.include))
+        targets.append('INCLUDE_LAPACK_mymachine = -I{0}'
+                       .format(self.spec['lapack'].prefix.include))
+        targets.append('LIBRARIES_HDF5_mymachine = {0} -lhdf5_fortran'
+                       .format(self.spec['hdf5'].libs.ld_flags))
+        targets.append('LIBRARIES_LAPACK_mymachine = {0}'
+                       .format(self.spec['lapack'].libs.ld_flags))
+
+        return targets
+
+    def install(self, spec, prefix):
+        install_tree('Documents', prefix.docs)
+        install('README.md', prefix.docs)
+
+        mkdirp(prefix.bin)
+        install('DeleptonizationProblem/Executables/'
+                'DeleptonizationProblem1D_%s' %
+                os.environ['THORNADO_MACHINE'], prefix.bin)
diff --git a/var/spack/repos/builtin/packages/thrift/package.py b/var/spack/repos/builtin/packages/thrift/package.py
index 9e296123fd..35d3a897e9 100644
--- a/var/spack/repos/builtin/packages/thrift/package.py
+++ b/var/spack/repos/builtin/packages/thrift/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,6 +19,7 @@ class Thrift(Package):
     homepage = "http://thrift.apache.org"
     url      = "http://apache.mirrors.ionfish.org/thrift/0.9.2/thrift-0.9.2.tar.gz"
 
+    version('0.11.0', '0be59730ebce071eceaf6bfdb8d3a20e')
     version('0.10.0', '795c5dd192e310ffff38cfd9430d6b29')
     version('0.9.3', '88d667a8ae870d5adeca8cb7d6795442')
     version('0.9.2', '89f63cc4d0100912f4a1f8a9dee63678')
@@ -45,6 +27,8 @@ class Thrift(Package):
     # Currently only support for c-family and python
     variant('c', default=True,
             description="Build support for C-family languages")
+    variant('pic', default=True,
+            description='Build position independent code')
     variant('python', default=True,
             description="Build support for python")
 
@@ -63,9 +47,13 @@ class Thrift(Package):
     depends_on('zlib', when='+c')
     depends_on('libevent', when='+c')
 
+    def setup_environment(self, spack_env, run_env):
+        if '+pic' in self.spec:
+            spack_env.append_flags('CFLAGS', self.compiler.pic_flag)
+            spack_env.append_flags('CXXFLAGS', self.compiler.pic_flag)
+
     def install(self, spec, prefix):
         env['PY_PREFIX'] = prefix
-        env['JAVA_HOME'] = spec['java'].prefix
 
         # configure options
         options = ['--prefix=%s' % prefix]
@@ -73,6 +61,7 @@ class Thrift(Package):
         options.append('--with-boost=%s' % spec['boost'].prefix)
         options.append('--enable-tests=no')
 
+        options.append('--with-nodejs=no')
         options.append('--with-c=%s' % ('yes' if '+c' in spec else 'no'))
         options.append('--with-python=%s' %
                        ('yes' if '+python' in spec else 'no'))
diff --git a/var/spack/repos/builtin/packages/thrust/package.py b/var/spack/repos/builtin/packages/thrust/package.py
index c3d7c8dadb..4870f828be 100644
--- a/var/spack/repos/builtin/packages/thrust/package.py
+++ b/var/spack/repos/builtin/packages/thrust/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/tig/package.py b/var/spack/repos/builtin/packages/tig/package.py
index 18c0597c46..58f07a011f 100644
--- a/var/spack/repos/builtin/packages/tig/package.py
+++ b/var/spack/repos/builtin/packages/tig/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/tinyxml/CMakeLists.txt b/var/spack/repos/builtin/packages/tinyxml/CMakeLists.txt
index 93f124d716..32db119762 100644
--- a/var/spack/repos/builtin/packages/tinyxml/CMakeLists.txt
+++ b/var/spack/repos/builtin/packages/tinyxml/CMakeLists.txt
@@ -1,17 +1,21 @@
 cmake_minimum_required(VERSION 2.6)
 
 project(TinyXml)
+
 OPTION(TIXML_USE_STL "Use STL with TIXML" ON)
+OPTION(BUILD_SHARED_LIBS "build as shared library" ON)
+
 if(TIXML_USE_STL)
 	add_definitions(-DTIXML_USE_STL)
 endif(TIXML_USE_STL)
-add_library(
-	tinyxml
-	tinyxml.cpp
-	tinystr.cpp
-	tinyxmlerror.cpp
-	tinyxmlparser.cpp
-)
 
-INSTALL( FILES tinyxml.h tinystr.h DESTINATION include )
-INSTALL( TARGETS tinyxml ARCHIVE DESTINATION lib )
+if(BUILD_SHARED_LIBS)
+  add_library(tinyxml SHARED tinyxml.cpp tinystr.cpp tinyxmlerror.cpp tinyxmlparser.cpp)
+  install(TARGETS tinyxml LIBRARY DESTINATION lib)
+else()
+  add_library(tinyxml_static STATIC tinyxml.cpp tinystr.cpp tinyxmlerror.cpp tinyxmlparser.cpp)
+  set_target_properties(tinyxml_static PROPERTIES OUTPUT_NAME tinyxml)
+  install(TARGETS tinyxml_static ARCHIVE DESTINATION lib)
+endif(BUILD_SHARED_LIBS)
+
+install(FILES tinyxml.h tinystr.h DESTINATION include)
diff --git a/var/spack/repos/builtin/packages/tinyxml/package.py b/var/spack/repos/builtin/packages/tinyxml/package.py
index 46f3c32a75..a7962a1253 100644
--- a/var/spack/repos/builtin/packages/tinyxml/package.py
+++ b/var/spack/repos/builtin/packages/tinyxml/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from shutil import copyfile
 import os.path
 
 
@@ -35,10 +15,17 @@ class Tinyxml(CMakePackage):
 
     version('2.6.2', 'cba3f50dd657cb1434674a03b21394df9913d764')
 
+    variant('shared', default=True, description='Build a shared library')
+
     def url_for_version(self, version):
         url = "https://sourceforge.net/projects/tinyxml/files/tinyxml/{0}/tinyxml_{1}.tar.gz"
         return url.format(version.dotted, version.underscored)
 
     def patch(self):
-        copyfile(join_path(os.path.dirname(__file__),
-                           "CMakeLists.txt"), "CMakeLists.txt")
+        copy(join_path(os.path.dirname(__file__),
+             "CMakeLists.txt"), "CMakeLists.txt")
+
+    def cmake_args(self):
+        spec = self.spec
+        return [
+            '-DBUILD_SHARED_LIBS=%s' % ('YES' if '+shared' in spec else 'NO')]
diff --git a/var/spack/repos/builtin/packages/tinyxml2/package.py b/var/spack/repos/builtin/packages/tinyxml2/package.py
index d54418e099..06f2e7b673 100644
--- a/var/spack/repos/builtin/packages/tinyxml2/package.py
+++ b/var/spack/repos/builtin/packages/tinyxml2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/tioga/package.py b/var/spack/repos/builtin/packages/tioga/package.py
new file mode 100644
index 0000000000..89ea1923e6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/tioga/package.py
@@ -0,0 +1,41 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Tioga(CMakePackage):
+    """Topology Independent Overset Grid Assembly (TIOGA)"""
+
+    homepage = "https://github.com/jsitaraman/tioga"
+    git      = "https://github.com/jsitaraman/tioga.git"
+
+    # The master branch doesn't support CMake
+    version('develop', branch='nalu-api')
+
+    variant('shared', default=True,
+            description="Enable building shared libraries")
+    variant('pic', default=True,
+            description="Position independent code")
+
+    depends_on('mpi')
+
+    # Tioga has the fortran module file problem with parallel builds
+    parallel = False
+
+    def cmake_args(self):
+        spec = self.spec
+
+        options = [
+            '-DBUILD_SHARED_LIBS:BOOL=%s' % (
+                'ON' if '+shared' in spec else 'OFF'),
+            '-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=%s' % (
+                'ON' if '+pic' in spec else 'OFF'),
+            '-DMPI_CXX_COMPILER:PATH=%s' % spec['mpi'].mpicxx,
+            '-DMPI_C_COMPILER:PATH=%s' % spec['mpi'].mpicc,
+            '-DMPI_Fortran_COMPILER:PATH=%s' % spec['mpi'].mpifc
+        ]
+
+        return options
diff --git a/var/spack/repos/builtin/packages/tk/package.py b/var/spack/repos/builtin/packages/tk/package.py
index b03d07013a..6b5c2cfbc1 100644
--- a/var/spack/repos/builtin/packages/tk/package.py
+++ b/var/spack/repos/builtin/packages/tk/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,15 +16,22 @@ class Tk(AutotoolsPackage):
     homepage = "http://www.tcl.tk"
     url      = "http://prdownloads.sourceforge.net/tcl/tk8.6.5-src.tar.gz"
 
+    version('8.6.8', '5e0faecba458ee1386078fb228d008ba')
     version('8.6.6', 'dd7dbb3a6523c42d05f6ab6e86096e99')
     version('8.6.5', '11dbbd425c3e0201f20d6a51482ce6c4')
     version('8.6.3', '85ca4dbf4dcc19777fd456f6ee5d0221')
 
-    depends_on('tcl')
+    extends('tcl')
+
+    depends_on('tcl@8.6:')
     depends_on('libx11')
 
     configure_directory = 'unix'
 
+    @property
+    def libs(self):
+        return LibraryList([])
+
     def setup_environment(self, spack_env, run_env):
         # When using Tkinter from within spack provided python+tk, python
         # will not be able to find Tcl/Tk unless TK_LIBRARY is set.
diff --git a/var/spack/repos/builtin/packages/tldd/package.py b/var/spack/repos/builtin/packages/tldd/package.py
new file mode 100644
index 0000000000..7db26422e7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/tldd/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Tldd(MakefilePackage):
+    """A program similar to ldd(1) but showing the output as a tree."""
+
+    homepage = "https://gitlab.com/miscripts/tldd"
+    git      = "https://gitlab.com/miscripts/tldd.git"
+
+    version('2018-10-05', commit='61cb512cc992ea6cbb7239e99ec7ac92ea072507')
+    version('master', branch='master')
+
+    depends_on('pstreams@0.8.0:')
+
+    def patch(self):
+        filter_file(
+            r'#include <pstreams/pstream.h>',
+            r'#include <pstream.h>',
+            'tldd.cc')
+
+    @property
+    def install_targets(self):
+        return ['install', 'PREFIX={0}'.format(self.prefix)]
diff --git a/var/spack/repos/builtin/packages/tmalign/package.py b/var/spack/repos/builtin/packages/tmalign/package.py
index ac7df4fb15..877caa929f 100644
--- a/var/spack/repos/builtin/packages/tmalign/package.py
+++ b/var/spack/repos/builtin/packages/tmalign/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/tmhmm/package.py b/var/spack/repos/builtin/packages/tmhmm/package.py
index 2fe2517444..32a34ec0e8 100644
--- a/var/spack/repos/builtin/packages/tmhmm/package.py
+++ b/var/spack/repos/builtin/packages/tmhmm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
diff --git a/var/spack/repos/builtin/packages/tmux/package.py b/var/spack/repos/builtin/packages/tmux/package.py
index 52c6c530d1..d2a39eab0e 100644
--- a/var/spack/repos/builtin/packages/tmux/package.py
+++ b/var/spack/repos/builtin/packages/tmux/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,8 +15,10 @@ class Tmux(AutotoolsPackage):
     """
 
     homepage = "http://tmux.github.io"
-    url = "https://github.com/tmux/tmux/releases/download/2.2/tmux-2.2.tar.gz"
+    url = "https://github.com/tmux/tmux/releases/download/2.6/tmux-2.6.tar.gz"
 
+    version('2.7', 'bcdfcf910c94c3e02ce6b1c035880306')
+    version('2.6', 'd541ff392249f94c4f3635793556f827')
     version('2.5', '4a5d73d96d8f11b0bdf9b6f15ab76d15')
     version('2.4', '6165d3aca811a3225ef8afbd1afcf1c5')
     version('2.3', 'fcfd1611d705d8b31df3c26ebc93bd3e')
diff --git a/var/spack/repos/builtin/packages/tmuxinator/package.py b/var/spack/repos/builtin/packages/tmuxinator/package.py
index 0f79d1f5bf..358d90965e 100644
--- a/var/spack/repos/builtin/packages/tmuxinator/package.py
+++ b/var/spack/repos/builtin/packages/tmuxinator/package.py
@@ -1,38 +1,18 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class Tmuxinator(Package):
     """A session configuration creator and manager for tmux"""
+
     homepage = "https://github.com/tmuxinator/tmuxinator"
-    url      = "https://github.com/tmuxinator/tmuxinator"
+    git      = "https://github.com/tmuxinator/tmuxinator.git"
 
-    version('0.6.11',
-            git='https://github.com/tmuxinator/tmuxinator',
-            tag='v0.6.11')
+    version('0.6.11', tag='v0.6.11')
 
     extends('ruby')
 
diff --git a/var/spack/repos/builtin/packages/tophat/package.py b/var/spack/repos/builtin/packages/tophat/package.py
index 682e9581eb..3dcf571f87 100644
--- a/var/spack/repos/builtin/packages/tophat/package.py
+++ b/var/spack/repos/builtin/packages/tophat/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,10 +12,15 @@ class Tophat(AutotoolsPackage):
     homepage = "http://ccb.jhu.edu/software/tophat/index.shtml"
     url      = "https://github.com/infphilo/tophat/archive/v2.1.1.tar.gz"
 
+    version('2.1.2', 'db844fd7f53c519e716cd6222e6195b2')
     version('2.1.1', 'ffd18de2f893a95eb7e9d0c5283d241f')
 
     depends_on('autoconf', type='build')
-    depends_on('automake', type='build')
+    # 2.1.1 only builds with automake@1.15.1.  There's a patch here:
+    # https://github.com/spack/spack/pull/8244, which was incorporated
+    # upstream in 2.1.2, which is known to build with 1.16.1 and 1.15.1.
+    depends_on('automake',                        type='build')
+    depends_on('automake@1.15.1', when='@:2.1.1', type='build')
     depends_on('libtool',  type='build')
     depends_on('m4',       type='build')
 
diff --git a/var/spack/repos/builtin/packages/tppred/package.py b/var/spack/repos/builtin/packages/tppred/package.py
index 15bf756f7a..75f5209c9f 100644
--- a/var/spack/repos/builtin/packages/tppred/package.py
+++ b/var/spack/repos/builtin/packages/tppred/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/tracer/package.py b/var/spack/repos/builtin/packages/tracer/package.py
new file mode 100644
index 0000000000..9fc7777596
--- /dev/null
+++ b/var/spack/repos/builtin/packages/tracer/package.py
@@ -0,0 +1,39 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Tracer(MakefilePackage):
+    """Trace Replay and Network Simulation Framework"""
+
+    homepage = "https://tracer-codes.readthedocs.io"
+    git      = "https://github.com/LLNL/tracer.git"
+
+    maintainers = ['bhatele']
+
+    version('develop', branch='master')
+
+    variant('otf2', default=True, description='Use OTF2 traces for simulation')
+
+    depends_on('mpi')
+    depends_on('codes')
+    depends_on('otf2', when='+otf2')
+
+    build_directory = 'tracer'
+
+    @property
+    def build_targets(self):
+        targets = []
+
+        targets.append('CXX = {0}'.format(self.spec['mpi'].mpicxx))
+        if "+otf2" in self.spec:
+            targets.append('SELECT_TRACE = -DTRACER_OTF_TRACES=1')
+
+        return targets
+
+    def install(self, spec, prefix):
+        with working_dir(self.build_directory):
+            make('PREFIX={0}'.format(prefix), 'install')
diff --git a/var/spack/repos/builtin/packages/transabyss/package.py b/var/spack/repos/builtin/packages/transabyss/package.py
index 32a266f9f2..c14bff0de7 100644
--- a/var/spack/repos/builtin/packages/transabyss/package.py
+++ b/var/spack/repos/builtin/packages/transabyss/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/transdecoder/package.py b/var/spack/repos/builtin/packages/transdecoder/package.py
index 022f205d67..76fa35a0f3 100644
--- a/var/spack/repos/builtin/packages/transdecoder/package.py
+++ b/var/spack/repos/builtin/packages/transdecoder/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,6 +18,7 @@ class Transdecoder(MakefilePackage):
     version('3.0.1', 'f62b86a15fcb78b1dada9f80cc25f300')
 
     depends_on('perl', type=('build', 'run'))
+    depends_on('perl-uri-escape', type='run')
 
     def install(self, spec, prefix):
         mkdirp(prefix.bin)
diff --git a/var/spack/repos/builtin/packages/transposome/package.py b/var/spack/repos/builtin/packages/transposome/package.py
index 63e7d47f41..ad7e83d536 100644
--- a/var/spack/repos/builtin/packages/transposome/package.py
+++ b/var/spack/repos/builtin/packages/transposome/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/transset/package.py b/var/spack/repos/builtin/packages/transset/package.py
index 52f83c6edf..9b5693ed56 100644
--- a/var/spack/repos/builtin/packages/transset/package.py
+++ b/var/spack/repos/builtin/packages/transset/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Transset(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/trapproto/package.py b/var/spack/repos/builtin/packages/trapproto/package.py
index c7b2f3727d..8718e15b28 100644
--- a/var/spack/repos/builtin/packages/trapproto/package.py
+++ b/var/spack/repos/builtin/packages/trapproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/tree/package.py b/var/spack/repos/builtin/packages/tree/package.py
index 339ce2c139..978b3b5ae6 100644
--- a/var/spack/repos/builtin/packages/tree/package.py
+++ b/var/spack/repos/builtin/packages/tree/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import sys
 
diff --git a/var/spack/repos/builtin/packages/treesub/package.py b/var/spack/repos/builtin/packages/treesub/package.py
new file mode 100644
index 0000000000..99feceddf8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/treesub/package.py
@@ -0,0 +1,41 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class Treesub(Package):
+    """A small program (which glues together other programs) that
+       allows a user to input a codon alignment in FASTA format and
+       produce an annotated phylogenetic tree showing which substitutions
+       occurred on a given branch. Originally written for colleagues at
+       the MRC NIMR."""
+
+    homepage = "https:/github.com/tamuri/treesub"
+    url      = "https://github.com/tamuri/treesub/archive/v0.2.tar.gz"
+
+    version('0.2', sha256='58b0d2638cf9ae1ad8705df26a57c32b52a69f50e7954debbd678c82772fdc56')
+    version('0.1', sha256='c083ecc5f7e9f11645a7e768f6a09fefcbb254b526212003527b4b8dd14723f1')
+
+    depends_on('jdk', type='run')
+    depends_on('ant', type='build')
+    depends_on('paml', type='run')
+    depends_on('raxml', type='run')
+    depends_on('figtree', type='run')
+
+    def install(self, spec, prefix):
+        ant = self.spec['ant'].command
+        ant('jar')
+
+        mkdirp(prefix.bin)
+        install_tree('dist', prefix.bin)
+
+        mkdirp(prefix.lib)
+        install_tree('lib', prefix.lib)
+
+        execscript = join_path(self.package_dir, 'treesub')
+        os.chmod(execscript, 0o775)
+        install(execscript, prefix.bin)
diff --git a/var/spack/repos/builtin/packages/treesub/treesub b/var/spack/repos/builtin/packages/treesub/treesub
new file mode 100755
index 0000000000..8be7cb73e6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/treesub/treesub
@@ -0,0 +1,2 @@
+#!/bin/sh
+java -jar $(dirname $0)/treesub.jar
diff --git a/var/spack/repos/builtin/packages/trf/package.py b/var/spack/repos/builtin/packages/trf/package.py
index f02e30302d..c429ccc33d 100644
--- a/var/spack/repos/builtin/packages/trf/package.py
+++ b/var/spack/repos/builtin/packages/trf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
@@ -44,3 +25,5 @@ class Trf(Package):
     def install(self, spec, prefix):
         mkdirp(prefix.bin)
         install('trf409.linux64', prefix.bin.trf)
+        chmod = which('chmod')
+        chmod('+x', prefix.bin.trf)
diff --git a/var/spack/repos/builtin/packages/triangle/package.py b/var/spack/repos/builtin/packages/triangle/package.py
index 9e20a4d964..ad6a775116 100644
--- a/var/spack/repos/builtin/packages/triangle/package.py
+++ b/var/spack/repos/builtin/packages/triangle/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index db0b1b3ba6..2170bc4d6d 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -1,31 +1,12 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 import sys
 from spack import *
-from spack.operating_systems.mac_os import macOS_version
+from spack.operating_systems.mac_os import macos_version
 
 # Trilinos is complicated to build, as an inspiration a couple of links to
 # other repositories which build it:
@@ -45,137 +26,215 @@ class Trilinos(CMakePackage):
     """
     homepage = "https://trilinos.org/"
     url      = "https://github.com/trilinos/Trilinos/archive/trilinos-release-12-12-1.tar.gz"
+    git      = "https://github.com/trilinos/Trilinos.git"
 
     maintainers = ['aprokop']
 
     # ###################### Versions ##########################
 
-    version('xsdk-0.2.0',
-            git='https://github.com/trilinos/Trilinos.git', tag='xsdk-0.2.0')
-    version('develop',
-            git='https://github.com/trilinos/Trilinos.git', tag='develop')
-    version('master',
-            git='https://github.com/trilinos/Trilinos.git', tag='master')
+    version('xsdk-0.2.0', tag='xsdk-0.2.0')
+    version('develop', branch='develop')
+    version('master', branch='master')
     version('12.12.1', 'ecd4606fa332212433c98bf950a69cc7')
     version('12.10.1', '667333dbd7c0f031d47d7c5511fd0810')
-    version('12.8.1', '01c0026f1e2050842857db941060ecd5')
-    version('12.6.4', 'c2ea7b5aa0d10bcabdb9b9a6e3bac3ea')
-    version('12.6.3', '8de5cc00981a0ca0defea6199b2fe4c1')
-    version('12.6.2', 'dc7f9924872778798149ecadd81605a5')
-    version('12.6.1', '8aecea78546e7558f63ecc9a3b2949da')
-    version('12.4.2', '4c25a757d86bde3531090bd900a2cea8')
-    version('12.2.1', '85d011f7f99a776a9c6c2625e8cb721c')
-    version('12.0.1', 'bcb3fdefd14d05dd6aa65ba4c5b9aa0e')
-    version('11.14.3', 'dea62e57ebe51a886bee0b10a2176969')
-    version('11.14.2', 'e7c3cdbbfe3279a8a68838b873ad6d51')
-    version('11.14.1', 'b7760b142eef66c79ed13de7c9560f81')
+    version('12.8.1', '9f37f683ee2b427b5540db8a20ed6b15')
+    version('12.6.4', 'e11fff717d0e4565779f75a47feecbb2')
+    version('12.6.3', '9ce30b6ab956bfc41730479a9ef05d05')
+    version('12.6.2', '0237d32feedd979a6fbb139aa5df8500')
+    version('12.6.1', '14ab8f7e74b66c33d5731cbf68b8cb82')
+    version('12.4.2', '98880f414752220e60feaeb36b023f60')
+    version('12.2.1', '8b344a9e9e533126dfd96db58ce69dde')
+    version('12.0.1', 'b8263f7037f7c688091d0da19d169709')
+    version('11.14.3', 'ff31ad49d633ab28369c228784055c85')
+    version('11.14.2', '1fdf15a5b4494f832b414f9c447ab685')
+    version('11.14.1', '478d0438d935294a7c94347c94a7c8cb')
 
     # ###################### Variants ##########################
 
-    variant('alloptpkgs',   default=False,
-            description='Compile with all optional packages')
-    variant('xsdkflags',    default=False,
-            description='Compile using the default xSDK configuration')
-    variant('metis',        default=True,
-            description='Compile with METIS and ParMETIS')
-    variant('mumps',        default=True,
-            description='Compile with support for MUMPS solvers')
-    variant('superlu-dist', default=True,
-            description='Compile with SuperluDist solvers')
-    variant('superlu',      default=False,
-            description='Compile with SuperLU solvers')
-    variant('hypre',        default=True,
-            description='Compile with Hypre preconditioner')
-    variant('hdf5',         default=True,
-            description='Compile with HDF5')
-    variant('suite-sparse', default=True,
-            description='Compile with SuiteSparse solvers')
+    # Other
     # not everyone has py-numpy activated, keep it disabled by default to avoid
     # configure errors
     variant('python',       default=False,
             description='Build python wrappers')
+
+    # Build options
+    variant('complex', default=False,
+            description='Enable complex numbers in Trilinos')
+    variant('explicit_template_instantiation',  default=True,
+            description='Enable explicit template instantiation (ETI)')
+    variant('float', default=False,
+            description='Enable single precision (float) numbers in Trilinos')
+    variant('fortran',      default=True,
+            description='Compile with Fortran support')
+    variant('openmp',       default=False,
+            description='Enable OpenMP')
     variant('shared',       default=True,
             description='Enables the build of shared libraries')
+    variant('xsdkflags',    default=False,
+            description='Compile using the default xSDK configuration')
+
+    # TPLs (alphabet order)
     variant('boost',        default=True,
             description='Compile with Boost')
-    variant('tpetra',       default=True,
-            description='Compile with Tpetra')
-    variant('epetra',       default=True,
-            description='Compile with Epetra')
-    variant('epetraext',    default=True,
-            description='Compile with EpetraExt')
+    variant('cgns',         default=False,
+            description='Enable CGNS')
     variant('exodus',       default=True,
             description='Compile with Exodus from SEACAS')
+    variant('gtest',        default=True,
+            description='Compile with Gtest')
+    variant('hdf5',         default=True,
+            description='Compile with HDF5')
+    variant('hypre',        default=True,
+            description='Compile with Hypre preconditioner')
+    variant('metis',        default=True,
+            description='Compile with METIS and ParMETIS')
+    variant('mumps',        default=True,
+            description='Compile with support for MUMPS solvers')
     variant('pnetcdf',      default=False,
             description='Compile with parallel-netcdf')
+    variant('suite-sparse', default=True,
+            description='Compile with SuiteSparse solvers')
+    variant('superlu-dist', default=False,
+            description='Compile with SuperluDist solvers')
+    variant('superlu',      default=False,
+            description='Compile with SuperLU solvers')
+    variant('x11',          default=False,
+            description='Compile with X11')
     variant('zlib',         default=False,
             description='Compile with zlib')
-    variant('stk',          default=False,
-            description='Compile with STK')
-    variant('teuchos',      default=True,
-            description='Compile with Teuchos')
-    variant('belos',        default=True,
-            description='Compile with Belos')
-    variant('zoltan',       default=True,
-            description='Compile with Zoltan')
-    variant('zoltan2',      default=True,
-            description='Compile with Zoltan2')
+
+    # Package options (alphabet order)
+    variant('alloptpkgs',   default=False,
+            description='Compile with all optional packages')
     variant('amesos',       default=True,
             description='Compile with Amesos')
     variant('amesos2',      default=True,
             description='Compile with Amesos2')
-    variant('anasazi',       default=True,
+    variant('anasazi',      default=True,
             description='Compile with Anasazi')
+    variant('aztec',        default=True,
+            description='Compile with Aztec')
+    variant('belos',        default=True,
+            description='Compile with Belos')
+    variant('epetra',       default=True,
+            description='Compile with Epetra')
+    variant('epetraext',    default=True,
+            description='Compile with EpetraExt')
     variant('ifpack',       default=True,
             description='Compile with Ifpack')
     variant('ifpack2',      default=True,
             description='Compile with Ifpack2')
-    variant('muelu',        default=True,
-            description='Compile with Muelu')
-    variant('fortran',      default=True,
-            description='Compile with Fortran support')
+    variant('intrepid',     default=False,
+            description='Enable Intrepid')
+    variant('intrepid2',    default=False,
+            description='Enable Intrepid2')
+    variant('isorropia',    default=False,
+            description='Compile with Isorropia')
+    variant('kokkos',       default=True,
+            description='Compile with Kokkos')
     variant('ml',           default=True,
             description='Compile with ML')
-    variant('gtest',        default=True,
-            description='Compile with Gtest')
-    variant('aztec',        default=True,
-            description='Compile with Aztec')
+    variant('minitensor',   default=False,
+            description='Compile with MiniTensor')
+    variant('muelu',        default=True,
+            description='Compile with Muelu')
+    variant('nox',          default=False,
+            description='Compile with NOX')
+    variant('piro',         default=False,
+            description='Compile with Piro')
+    variant('phalanx',      default=False,
+            description='Compile with Phalanx')
+    variant('rol',          default=False,
+            description='Compile with ROL')
+    variant('rythmos',      default=False,
+            description='Compile with Rythmos')
     variant('sacado',       default=True,
             description='Compile with Sacado')
-    variant('x11',          default=False,
-            description='Compile with X11')
-    variant('instantiate',  default=True,
-            description='Compile with explicit instantiation')
-    variant('instantiate_cmplx', default=False,
-            description='Compile with explicit instantiation for complex')
+    variant('stk',          default=False,
+            description='Compile with STK')
+    variant('shards',       default=False,
+            description='Compile with Shards')
+    variant('teko',         default=False,
+            description='Compile with Teko')
+    variant('tempus',       default=False,
+            description='Compile with Tempus')
+    variant('teuchos',      default=True,
+            description='Compile with Teuchos')
+    variant('tpetra',       default=True,
+            description='Compile with Tpetra')
+    variant('zoltan',       default=True,
+            description='Compile with Zoltan')
+    variant('zoltan2',      default=True,
+            description='Compile with Zoltan2')
+
+    # External package options
     variant('dtk',          default=False,
             description='Enable DataTransferKit')
     variant('fortrilinos',  default=False,
             description='Enable ForTrilinos')
-    variant('openmp',       default=False,
-            description='Enable OpenMP')
-    variant('rol',          default=False,
-            description='Enable ROL')
-    variant('nox',          default=False,
-            description='Enable NOX')
-    variant('shards',       default=False,
-            description='Enable Shards')
-    variant('intrepid',     default=False,
-            description='Enable Intrepid')
-    variant('intrepid2',     default=False,
-            description='Enable Intrepid2')
 
     resource(name='dtk',
-             git='https://github.com/ornl-cees/DataTransferKit',
+             git='https://github.com/ornl-cees/DataTransferKit.git',
              tag='master',
              placement='DataTransferKit',
              when='+dtk')
     resource(name='fortrilinos',
-             git='https://github.com/trilinos/ForTrilinos',
+             git='https://github.com/trilinos/ForTrilinos.git',
              tag='develop',
              placement='packages/ForTrilinos',
              when='+fortrilinos')
 
+    conflicts('+amesos2', when='~teuchos')
+    conflicts('+amesos2', when='~tpetra')
+    conflicts('+amesos', when='~epetra')
+    conflicts('+amesos', when='~teuchos')
+    conflicts('+anasazi', when='~teuchos')
+    conflicts('+belos', when='~teuchos')
+    conflicts('+epetraext', when='~epetra')
+    conflicts('+epetraext', when='~teuchos')
+    conflicts('+ifpack2', when='~belos')
+    conflicts('+ifpack2', when='~teuchos')
+    conflicts('+ifpack2', when='~tpetra')
+    conflicts('+ifpack', when='~epetra')
+    conflicts('+ifpack', when='~teuchos')
+    conflicts('+intrepid2', when='~kokkos')
+    conflicts('+intrepid2', when='~shards')
+    conflicts('+intrepid2', when='~teuchos')
+    conflicts('+intrepid', when='~sacado')
+    conflicts('+intrepid', when='~shards')
+    conflicts('+intrepid', when='~teuchos')
+    conflicts('+isorropia', when='~epetra')
+    conflicts('+isorropia', when='~epetraext')
+    conflicts('+isorropia', when='~teuchos')
+    conflicts('+isorropia', when='~zoltan')
+    conflicts('+muelu', when='~teuchos')
+    conflicts('+muelu', when='~xpetra')
+    conflicts('+nox', when='~teuchos')
+    conflicts('+phalanx', when='~kokkos')
+    conflicts('+phalanx', when='~sacado')
+    conflicts('+phalanx', when='~teuchos')
+    conflicts('+piro', when='~teuchos')
+    conflicts('+rol', when='~teuchos')
+    conflicts('+rythmos', when='~teuchos')
+    conflicts('+teko', when='~amesos')
+    conflicts('+teko', when='~anasazi')
+    conflicts('+teko', when='~aztec')
+    conflicts('+teko', when='~ifpack')
+    conflicts('+teko', when='~ml')
+    conflicts('+teko', when='~teuchos')
+    conflicts('+teko', when='~tpetra')
+    conflicts('+tempus', when='~nox')
+    conflicts('+tempus', when='~teuchos')
+    conflicts('+tpetra', when='~kokkos')
+    conflicts('+tpetra', when='~teuchos')
+    conflicts('+zoltan2', when='~teuchos')
+    conflicts('+zoltan2', when='~tpetra')
+    conflicts('+zoltan2', when='~xpetra')
+    conflicts('+zoltan2', when='~zoltan')
+
+    conflicts('+dtk', when='~intrepid2')
+    conflicts('+dtk', when='~kokkos')
+    conflicts('+dtk', when='~teuchos')
     conflicts('+dtk', when='~tpetra')
     conflicts('+fortrilinos', when='~fortran')
     conflicts('+fortrilinos', when='@:99')
@@ -185,8 +244,21 @@ class Trilinos(CMakePackage):
     # For Trilinos v11 we need to force SuperLUDist=OFF, since only the
     # deprecated SuperLUDist v3.3 together with an Amesos patch is working.
     conflicts('+superlu-dist', when='@11.4.1:11.14.3')
+    # see https://github.com/trilinos/Trilinos/issues/3566
+    conflicts('+superlu-dist', when='+float+amesos2+explicit_template_instantiation^superlu-dist@5.3.0:')
+    # Amesos, conflicting types of double and complex SLU_D
+    # see
+    # https://trilinos.org/pipermail/trilinos-users/2015-March/004731.html
+    # and
+    # https://trilinos.org/pipermail/trilinos-users/2015-March/004802.html
+    conflicts('+superlu-dist', when='+complex+amesos2')
     # PnetCDF was only added after v12.10.1
     conflicts('+pnetcdf', when='@0:12.10.1')
+    # https://github.com/trilinos/Trilinos/issues/2994
+    conflicts(
+        '+shared', when='+stk platform=darwin',
+        msg='Cannot build Trilinos with STK as a shared library on Darwin.'
+    )
 
     # ###################### Dependencies ##########################
 
@@ -205,7 +277,9 @@ class Trilinos(CMakePackage):
     depends_on('mpi')
     depends_on('netcdf+mpi', when="~pnetcdf")
     depends_on('netcdf+mpi+parallel-netcdf', when="+pnetcdf@master,12.12.1:")
+    depends_on('parallel-netcdf', when="+pnetcdf@master,12.12.1:")
     depends_on('parmetis', when='+metis')
+    depends_on('cgns', when='+cgns')
     # Trilinos' Tribits config system is limited which makes it very tricky to
     # link Amesos with static MUMPS, see
     # https://trilinos.org/docs/dev/packages/amesos2/doc/html/classAmesos2_1_1MUMPS.html
@@ -217,6 +291,7 @@ class Trilinos(CMakePackage):
     depends_on('scalapack', when='+mumps')
     depends_on('superlu-dist', when='+superlu-dist')
     depends_on('superlu-dist@:4.3', when='@:12.6.1+superlu-dist')
+    depends_on('superlu-dist@4.4:5.3', when='@12.6.2:12.12.1+superlu-dist')
     depends_on('superlu-dist@develop', when='@develop+superlu-dist')
     depends_on('superlu-dist@xsdk-0.2.0', when='@xsdk-0.2.0+superlu-dist')
     depends_on('superlu+pic@4.3', when='+superlu')
@@ -224,15 +299,19 @@ class Trilinos(CMakePackage):
     depends_on('hypre~internal-superlu~int64', when='+hypre')
     depends_on('hypre@xsdk-0.2.0~internal-superlu', when='@xsdk-0.2.0+hypre')
     depends_on('hypre@develop~internal-superlu', when='@develop+hypre')
-    # FIXME: concretizer bug? 'hl' req by netcdf is affecting this code.
+    # We need hdf5+hl to match with netcdf during concretization
     depends_on('hdf5+hl+mpi', when='+hdf5')
     depends_on('python', when='+python')
     depends_on('py-numpy', when='+python', type=('build', 'run'))
     depends_on('swig', when='+python')
 
     patch('umfpack_from_suitesparse.patch', when='@11.14.1:12.8.1')
-    patch('xlf_seacas.patch', when='@12.10.1%xl')
-    patch('xlf_seacas.patch', when='@12.10.1%xl_r')
+    patch('xlf_seacas.patch', when='@12.10.1:12.12.1 %xl')
+    patch('xlf_seacas.patch', when='@12.10.1:12.12.1 %xl_r')
+    patch('xlf_seacas.patch', when='@12.10.1:12.12.1 %clang')
+    patch('xlf_tpetra.patch', when='@12.12.1%xl')
+    patch('xlf_tpetra.patch', when='@12.12.1%xl_r')
+    patch('xlf_tpetra.patch', when='@12.12.1%clang')
 
     def url_for_version(self, version):
         url = "https://github.com/trilinos/Trilinos/archive/trilinos-release-{0}.tar.gz"
@@ -278,50 +357,66 @@ class Trilinos(CMakePackage):
         options.extend([
             '-DTrilinos_ENABLE_ALL_OPTIONAL_PACKAGES:BOOL=%s' % (
                 'ON' if '+alloptpkgs' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_Tpetra:BOOL=%s' % (
-                'ON' if '+tpetra' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_Epetra:BOOL=%s' % (
-                'ON' if '+epetra' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_EpetraExt:BOOL=%s' % (
-                'ON' if '+epetraext' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_ML:BOOL=%s' % (
-                'ON' if '+ml' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_AztecOO:BOOL=%s' % (
-                'ON' if '+aztec' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_Sacado:BOOL=%s' % (
-                'ON' if '+sacado' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_Belos:BOOL=%s' % (
-                'ON' if '+belos' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_Zoltan:BOOL=%s' % (
-                'ON' if '+zoltan' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_Zoltan2:BOOL=%s' % (
-                'ON' if '+zoltan2' in spec else 'OFF'),
             '-DTrilinos_ENABLE_Amesos:BOOL=%s' % (
                 'ON' if '+amesos' in spec else 'OFF'),
             '-DTrilinos_ENABLE_Amesos2:BOOL=%s' % (
                 'ON' if '+amesos2' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_MueLu:BOOL=%s' % (
-                'ON' if '+muelu' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Anasazi:BOOL=%s' % (
+                'ON' if '+anasazi' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_AztecOO:BOOL=%s' % (
+                'ON' if '+aztec' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Belos:BOOL=%s' % (
+                'ON' if '+belos' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Epetra:BOOL=%s' % (
+                'ON' if '+epetra' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_EpetraExt:BOOL=%s' % (
+                'ON' if '+epetraext' in spec else 'OFF'),
             '-DTrilinos_ENABLE_Ifpack:BOOL=%s' % (
                 'ON' if '+ifpack' in spec else 'OFF'),
             '-DTrilinos_ENABLE_Ifpack2:BOOL=%s' % (
                 'ON' if '+ifpack2' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_Gtest:BOOL=%s' % (
-                'ON' if '+gtest' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_Teuchos:BOOL=%s' % (
-                'ON' if '+teuchos' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_Anasazi:BOOL=%s' % (
-                'ON' if '+anasazi' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_ROL:BOOL=%s' % (
-                'ON' if '+rol' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_NOX:BOOL=%s' % (
-                'ON' if '+nox' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_Shards=%s' % (
-                'ON' if '+shards' in spec else 'OFF'),
             '-DTrilinos_ENABLE_Intrepid=%s' % (
                 'ON' if '+intrepid' in spec else 'OFF'),
             '-DTrilinos_ENABLE_Intrepid2=%s' % (
                 'ON' if '+intrepid2' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Isorropia=%s' % (
+                'ON' if '+isorropia' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Kokkos:BOOL=%s' % (
+                'ON' if '+kokkos' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_MiniTensor=%s' % (
+                'ON' if '+minitensor' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_ML:BOOL=%s' % (
+                'ON' if '+ml' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_MueLu:BOOL=%s' % (
+                'ON' if '+muelu' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_NOX:BOOL=%s' % (
+                'ON' if '+nox' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Piro:BOOL=%s' % (
+                'ON' if '+piro' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Phalanx=%s' % (
+                'ON' if '+phalanx' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_PyTrilinos:BOOL=%s' % (
+                'ON' if '+python' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_ROL:BOOL=%s' % (
+                'ON' if '+rol' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Rythmos=%s' % (
+                'ON' if '+rythmos' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Sacado:BOOL=%s' % (
+                'ON' if '+sacado' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Shards=%s' % (
+                'ON' if '+shards' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Teko=%s' % (
+                'ON' if '+teko' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Tempus=%s' % (
+                'ON' if '+tempus' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Teuchos:BOOL=%s' % (
+                'ON' if '+teuchos' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Tpetra:BOOL=%s' % (
+                'ON' if '+tpetra' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Zoltan:BOOL=%s' % (
+                'ON' if '+zoltan' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Zoltan2:BOOL=%s' % (
+                'ON' if '+zoltan2' in spec else 'OFF'),
         ])
 
         if '+xsdkflags' in spec:
@@ -332,6 +427,7 @@ class Trilinos(CMakePackage):
             # They can likely change when necessary in the future
             options.extend([
                 '-DTrilinos_ENABLE_STKMesh:BOOL=ON',
+                '-DTrilinos_ENABLE_STKNGP:BOOL=ON',
                 '-DTrilinos_ENABLE_STKSimd:BOOL=ON',
                 '-DTrilinos_ENABLE_STKIO:BOOL=ON',
                 '-DTrilinos_ENABLE_STKTransfer:BOOL=ON',
@@ -340,7 +436,8 @@ class Trilinos(CMakePackage):
                 '-DTrilinos_ENABLE_STKTopology:BOOL=ON',
                 '-DTrilinos_ENABLE_STKUnit_tests:BOOL=ON',
                 '-DTrilinos_ENABLE_STKUnit_test_utils:BOOL=ON',
-                '-DTrilinos_ENABLE_STKClassic:BOOL=OFF'
+                '-DTrilinos_ENABLE_STKClassic:BOOL=OFF',
+                '-DTrilinos_ENABLE_STKExprEval:BOOL=ON'
             ])
 
         if '+dtk' in spec:
@@ -384,8 +481,8 @@ class Trilinos(CMakePackage):
             '-DNetCDF_ROOT:PATH=%s' % spec['netcdf'].prefix,
             '-DTPL_ENABLE_X11:BOOL=%s' % (
                 'ON' if '+x11' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_PyTrilinos:BOOL=%s' % (
-                'ON' if '+python' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Gtest:BOOL=%s' % (
+                'ON' if '+gtest' in spec else 'OFF'),
         ])
 
         if '+hypre' in spec:
@@ -447,8 +544,9 @@ class Trilinos(CMakePackage):
                 '-DParMETIS_LIBRARY_DIRS=%s;%s' % (
                     spec['parmetis'].prefix.lib, spec['metis'].prefix.lib),
                 '-DParMETIS_LIBRARY_NAMES=parmetis;metis',
-                '-DTPL_ParMETIS_INCLUDE_DIRS=%s' % (
-                    spec['parmetis'].prefix.include)
+                '-DTPL_ParMETIS_INCLUDE_DIRS=%s;%s' % (
+                    spec['parmetis'].prefix.include,
+                    spec['metis'].prefix.include)
             ])
         else:
             options.extend([
@@ -479,13 +577,7 @@ class Trilinos(CMakePackage):
             ])
 
         if '+superlu-dist' in spec:
-            # Amesos, conflicting types of double and complex SLU_D
-            # see
-            # https://trilinos.org/pipermail/trilinos-users/2015-March/004731.html
-            # and
-            # https://trilinos.org/pipermail/trilinos-users/2015-March/004802.html
             options.extend([
-                '-DTeuchos_ENABLE_COMPLEX:BOOL=OFF',
                 '-DKokkosTSQR_ENABLE_Complex:BOOL=OFF'
             ])
             options.extend([
@@ -539,6 +631,17 @@ class Trilinos(CMakePackage):
                 '-DTPL_ENABLE_Zlib:BOOL=OFF'
             ])
 
+        if '+cgns' in spec:
+            options.extend([
+                '-DTPL_ENABLE_CGNS:BOOL=ON',
+                '-DCGNS_INCLUDE_DIRS:PATH=%s' % spec['cgns'].prefix.include,
+                '-DCGNS_LIBRARY_DIRS:PATH=%s' % spec['cgns'].prefix.lib
+            ])
+        else:
+            options.extend([
+                '-DTPL_ENABLE_CGNS:BOOL=OFF'
+            ])
+
         # ################# Miscellaneous Stuff ######################
 
         # OpenMP
@@ -564,19 +667,34 @@ class Trilinos(CMakePackage):
                     '-DTrilinos_ENABLE_Fortran=ON'
                 ])
 
-        # Explicit instantiation
-        if '+instantiate' in spec:
+        float_s = 'ON' if '+float' in spec else 'OFF'
+        complex_s = 'ON' if '+complex' in spec else 'OFF'
+        complex_float_s = 'ON' if ('+complex' in spec and
+                                   '+float' in spec) else 'OFF'
+        if '+teuchos' in spec:
             options.extend([
-                '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON'
+                '-DTeuchos_ENABLE_COMPLEX=%s' % complex_s,
+                '-DTeuchos_ENABLE_FLOAT=%s' % float_s
+            ])
+
+        # Explicit Template Instantiation (ETI) in Tpetra
+        # NOTE: Trilinos will soon move to fixed std::uint64_t for GO and
+        # std::int32_t or std::int64_t for local.
+        options.append(
+            '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=%s' % (
+                'ON' if '+explicit_template_instantiation' in spec else 'OFF'
+            )
+        )
+
+        if '+explicit_template_instantiation' in spec and '+tpetra' in spec:
+            options.extend([
+                '-DTpetra_INST_DOUBLE:BOOL=ON',
+                '-DTpetra_INST_INT_LONG:BOOL=ON',
+                '-DTpetra_INST_COMPLEX_DOUBLE=%s' % complex_s,
+                '-DTpetra_INST_COMPLEX_FLOAT=%s' % complex_float_s,
+                '-DTpetra_INST_FLOAT=%s' % float_s,
+                '-DTpetra_INST_SERIAL=ON'
             ])
-            if '+tpetra' in spec:
-                options.extend([
-                    '-DTpetra_INST_DOUBLE:BOOL=ON',
-                    '-DTpetra_INST_INT_LONG:BOOL=ON'
-                    '-DTpetra_INST_COMPLEX_DOUBLE=%s' % (
-                        'ON' if '+instantiate_cmplx' in spec else 'OFF'
-                    )
-                ])
 
         # disable due to compiler / config errors:
         if spec.satisfies('%xl') or spec.satisfies('%xl_r'):
@@ -590,11 +708,12 @@ class Trilinos(CMakePackage):
                 '-DTrilinos_ENABLE_FEI=OFF'
             ])
 
-        if sys.platform == 'darwin' and macOS_version() >= Version('10.12'):
+        if sys.platform == 'darwin' and macos_version() >= Version('10.12'):
             # use @rpath on Sierra due to limit of dynamic loader
             options.append('-DCMAKE_MACOSX_RPATH=ON')
         else:
-            options.append('-DCMAKE_INSTALL_NAME_DIR:PATH=%s' % prefix.lib)
+            options.append('-DCMAKE_INSTALL_NAME_DIR:PATH=%s' %
+                           self.prefix.lib)
 
         if spec.satisfies('%intel') and spec.satisfies('@12.6.2'):
             # Panzer uses some std:chrono that is not recognized by Intel
diff --git a/var/spack/repos/builtin/packages/trilinos/xlf_tpetra.patch b/var/spack/repos/builtin/packages/trilinos/xlf_tpetra.patch
new file mode 100644
index 0000000000..364bd28cb0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/trilinos/xlf_tpetra.patch
@@ -0,0 +1,289 @@
+--- a/packages/tpetra/core/src/Tpetra_Details_libGemm.cpp
++++ b/packages/tpetra/core/src/Tpetra_Details_libGemm.cpp
+@@ -108,19 +108,19 @@
+ namespace Impl {
+ 
+ void
+-cgemm (const char transA,
+-       const char transB,
+-       const int m,
+-       const int n,
+-       const int k,
+-       const ::Kokkos::complex<float>& alpha,
+-       const ::Kokkos::complex<float> A[],
+-       const int lda,
+-       const ::Kokkos::complex<float> B[],
+-       const int ldb,
+-       const ::Kokkos::complex<float>& beta,
+-       ::Kokkos::complex<float> C[],
+-       const int ldc)
++cgemm_fwrap (const char transA,
++             const char transB,
++             const int m,
++             const int n,
++             const int k,
++             const ::Kokkos::complex<float>& alpha,
++             const ::Kokkos::complex<float> A[],
++             const int lda,
++             const ::Kokkos::complex<float> B[],
++             const int ldb,
++             const ::Kokkos::complex<float>& beta,
++             ::Kokkos::complex<float> C[],
++             const int ldc)
+ {
+ #ifdef HAVE_TPETRA_INST_COMPLEX_FLOAT
+   TPETRACORE_CGEMM (&transA, &transB, &m, &n, &k, &alpha, A, &lda, B, &ldb, &beta, C, &ldc);
+@@ -131,55 +131,55 @@
+ }
+ 
+ void
+-dgemm (const char transA,
+-       const char transB,
+-       const int m,
+-       const int n,
+-       const int k,
+-       const double alpha,
+-       const double A[],
+-       const int lda,
+-       const double B[],
+-       const int ldb,
+-       const double beta,
+-       double C[],
+-       const int ldc)
++dgemm_fwrap (const char transA,
++             const char transB,
++             const int m,
++             const int n,
++             const int k,
++             const double alpha,
++             const double A[],
++             const int lda,
++             const double B[],
++             const int ldb,
++             const double beta,
++             double C[],
++             const int ldc)
+ {
+   TPETRACORE_DGEMM (&transA, &transB, &m, &n, &k, &alpha, A, &lda, B, &ldb, &beta, C, &ldc);
+ }
+ 
+ void
+-sgemm (const char transA,
+-       const char transB,
+-       const int m,
+-       const int n,
+-       const int k,
+-       const float alpha,
+-       const float A[],
+-       const int lda,
+-       const float B[],
+-       const int ldb,
+-       const float beta,
+-       float C[],
+-       const int ldc)
++sgemm_fwrap (const char transA,
++             const char transB,
++             const int m,
++             const int n,
++             const int k,
++             const float alpha,
++             const float A[],
++             const int lda,
++             const float B[],
++             const int ldb,
++             const float beta,
++             float C[],
++             const int ldc)
+ {
+   TPETRACORE_SGEMM (&transA, &transB, &m, &n, &k, &alpha, A, &lda, B, &ldb, &beta, C, &ldc);
+ }
+ 
+ void
+-zgemm (const char transA,
+-       const char transB,
+-       const int m,
+-       const int n,
+-       const int k,
+-       const ::Kokkos::complex<double>& alpha,
+-       const ::Kokkos::complex<double> A[],
+-       const int lda,
+-       const ::Kokkos::complex<double> B[],
+-       const int ldb,
+-       const ::Kokkos::complex<double>& beta,
+-       ::Kokkos::complex<double> C[],
+-       const int ldc)
++zgemm_fwrap (const char transA,
++             const char transB,
++             const int m,
++             const int n,
++             const int k,
++             const ::Kokkos::complex<double>& alpha,
++             const ::Kokkos::complex<double> A[],
++             const int lda,
++             const ::Kokkos::complex<double> B[],
++             const int ldb,
++             const ::Kokkos::complex<double>& beta,
++             ::Kokkos::complex<double> C[],
++             const int ldc)
+ {
+ #ifdef HAVE_TPETRA_INST_COMPLEX_DOUBLE
+   TPETRACORE_ZGEMM (&transA, &transB, &m, &n, &k, &alpha, A, &lda, B, &ldb, &beta, C, &ldc);
+ 
+--- a/packages/tpetra/core/src/Tpetra_Details_libGemm.hpp
++++ b/packages/tpetra/core/src/Tpetra_Details_libGemm.hpp
+@@ -99,67 +99,67 @@
+ 
+ /// \brief Wrapped version of the BLAS library's cgemm.
+ void
+-cgemm (const char char_transA,
+-       const char char_transB,
+-       const int m,
+-       const int n,
+-       const int k,
+-       const ::Kokkos::complex<float>& alpha,
+-       const ::Kokkos::complex<float> A[],
+-       const int lda,
+-       const ::Kokkos::complex<float> B[],
+-       const int ldb,
+-       const ::Kokkos::complex<float>& beta,
+-       ::Kokkos::complex<float> C[],
+-       const int ldc);
++cgemm_fwrap (const char char_transA,
++             const char char_transB,
++             const int m,
++             const int n,
++             const int k,
++             const ::Kokkos::complex<float>& alpha,
++             const ::Kokkos::complex<float> A[],
++             const int lda,
++             const ::Kokkos::complex<float> B[],
++             const int ldb,
++             const ::Kokkos::complex<float>& beta,
++             ::Kokkos::complex<float> C[],
++             const int ldc);
+ 
+ /// \brief Wrapped version of the BLAS library's dgemm.
+ void
+-dgemm (const char char_transA,
+-       const char char_transB,
+-       const int m,
+-       const int n,
+-       const int k,
+-       const double alpha,
+-       const double A[],
+-       const int lda,
+-       const double B[],
+-       const int ldb,
+-       const double beta,
+-       double C[],
+-       const int ldc);
++dgemm_fwrap (const char char_transA,
++             const char char_transB,
++             const int m,
++             const int n,
++             const int k,
++             const double alpha,
++             const double A[],
++             const int lda,
++             const double B[],
++             const int ldb,
++             const double beta,
++             double C[],
++             const int ldc);
+ 
+ /// \brief Wrapped version of the BLAS library's sgemm.
+ void
+-sgemm (const char char_transA,
+-       const char char_transB,
+-       const int m,
+-       const int n,
+-       const int k,
+-       const float alpha,
+-       const float A[],
+-       const int lda,
+-       const float B[],
+-       const int ldb,
+-       const float beta,
+-       float C[],
+-       const int ldc);
++sgemm_fwrap (const char char_transA,
++             const char char_transB,
++             const int m,
++             const int n,
++             const int k,
++             const float alpha,
++             const float A[],
++             const int lda,
++             const float B[],
++             const int ldb,
++             const float beta,
++             float C[],
++             const int ldc);
+ 
+ /// \brief Wrapped version of the BLAS library's zgemm.
+ void
+-zgemm (const char char_transA,
+-       const char char_transB,
+-       const int m,
+-       const int n,
+-       const int k,
+-       const ::Kokkos::complex<double>& alpha,
+-       const ::Kokkos::complex<double> A[],
+-       const int lda,
+-       const ::Kokkos::complex<double> B[],
+-       const int ldb,
+-       const ::Kokkos::complex<double>& beta,
+-       ::Kokkos::complex<double> C[],
+-       const int ldc);
++zgemm_fwrap (const char char_transA,
++             const char char_transB,
++             const int m,
++             const int n,
++             const int k,
++             const ::Kokkos::complex<double>& alpha,
++             const ::Kokkos::complex<double> A[],
++             const int lda,
++             const ::Kokkos::complex<double> B[],
++             const int ldb,
++             const ::Kokkos::complex<double>& beta,
++             ::Kokkos::complex<double> C[],
++             const int ldc);
+ 
+ /// \brief Wrapper for the above wrappers, templated on scalar type
+ ///   (the type of each entry in the matrices).
+@@ -184,7 +184,7 @@
+         scalar_type C[],
+         const int ldc)
+   {
+-    return cgemm (transA, transB, m, n, k, alpha, A, lda, B, ldb, beta, C, ldc);
++    return cgemm_fwrap (transA, transB, m, n, k, alpha, A, lda, B, ldb, beta, C, ldc);
+   }
+ };
+ 
+@@ -207,7 +207,7 @@
+         scalar_type C[],
+         const int ldc)
+   {
+-    return dgemm (transA, transB, m, n, k, alpha, A, lda, B, ldb, beta, C, ldc);
++    return dgemm_fwrap (transA, transB, m, n, k, alpha, A, lda, B, ldb, beta, C, ldc);
+   }
+ };
+ 
+@@ -230,7 +230,7 @@
+         scalar_type C[],
+         const int ldc)
+   {
+-    return sgemm (transA, transB, m, n, k, alpha, A, lda, B, ldb, beta, C, ldc);
++    return sgemm_fwrap (transA, transB, m, n, k, alpha, A, lda, B, ldb, beta, C, ldc);
+   }
+ };
+ 
+@@ -253,7 +253,7 @@
+         scalar_type C[],
+         const int ldc)
+   {
+-    return zgemm (transA, transB, m, n, k, alpha, A, lda, B, ldb, beta, C, ldc);
++    return zgemm_fwrap (transA, transB, m, n, k, alpha, A, lda, B, ldb, beta, C, ldc);
+   }
+ };
+ 
diff --git a/var/spack/repos/builtin/packages/trimal/package.py b/var/spack/repos/builtin/packages/trimal/package.py
new file mode 100644
index 0000000000..68d9efc6af
--- /dev/null
+++ b/var/spack/repos/builtin/packages/trimal/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Trimal(MakefilePackage):
+    """A tool for automated alignment trimming in large-scale
+       phylogenetic analyses"""
+
+    homepage = "https://github.com/scapella/trimal"
+    url      = "https://github.com/scapella/trimal/archive/v1.4.1.tar.gz"
+
+    version('1.4.1', sha256='cb8110ca24433f85c33797b930fa10fe833fa677825103d6e7f81dd7551b9b4e')
+
+    build_directory = 'source'
+
+    def install(self, sinstall_treepec, prefix):
+        mkdirp(prefix.bin)
+        binaries = ['trimal', 'readal', 'statal']
+        with working_dir(self.build_directory):
+            for b in binaries:
+                install(b, prefix.bin)
diff --git a/var/spack/repos/builtin/packages/trimgalore/package.py b/var/spack/repos/builtin/packages/trimgalore/package.py
index e1dca34f43..81cee833be 100644
--- a/var/spack/repos/builtin/packages/trimgalore/package.py
+++ b/var/spack/repos/builtin/packages/trimgalore/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,6 +14,7 @@ class Trimgalore(Package):
     homepage = "https://github.com/FelixKrueger/TrimGalore"
     url      = "https://github.com/FelixKrueger/TrimGalore/archive/0.4.4.tar.gz"
 
+    version('0.4.5', 'c71756042b2a65c34d483533a29dc206')
     version('0.4.4', 'aae1b807b48e38bae7074470203997bb')
 
     depends_on('perl', type=('build', 'run'))
@@ -40,5 +22,7 @@ class Trimgalore(Package):
     depends_on('fastqc')
 
     def install(self, spec, prefix):
+        filter_file(r'#!/usr/bin/perl', '#!/usr/bin/env perl', 'trim_galore')
+
         mkdirp(prefix.bin)
         install('trim_galore', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/trimmomatic/package.py b/var/spack/repos/builtin/packages/trimmomatic/package.py
index da741d5017..0f04596cf8 100644
--- a/var/spack/repos/builtin/packages/trimmomatic/package.py
+++ b/var/spack/repos/builtin/packages/trimmomatic/package.py
@@ -1,30 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from distutils.dir_util import copy_tree
-from shutil import copyfile
 import os.path
 
 
@@ -47,18 +26,18 @@ class Trimmomatic(Package):
         install(jar_file, prefix.bin)
 
         # Put the adapter files someplace sensible
-        copy_tree('adapters', join_path(self.prefix.share, 'adapters'))
+        install_tree('adapters', prefix.share.adapters)
 
         # Set up a helper script to call java on the jar file,
         # explicitly codes the path for java and the jar file.
         script_sh = join_path(os.path.dirname(__file__), "trimmomatic.sh")
-        script = join_path(prefix.bin, "trimmomatic")
-        copyfile(script_sh, script)
+        script = prefix.bin.trimmomatic
+        install(script_sh, script)
         set_executable(script)
 
         # Munge the helper script to explicitly point to java and the
         # jar file.
-        java = join_path(self.spec['java'].prefix, 'bin', 'java')
+        java = self.spec['java'].prefix.bin.java
         kwargs = {'ignore_absent': False, 'backup': False, 'string': False}
         filter_file('^java', java, script, **kwargs)
         filter_file('trimmomatic.jar', join_path(prefix.bin, jar_file),
diff --git a/var/spack/repos/builtin/packages/trinity/package.py b/var/spack/repos/builtin/packages/trinity/package.py
new file mode 100644
index 0000000000..8e198113d7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/trinity/package.py
@@ -0,0 +1,91 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Trinity(MakefilePackage):
+    """Trinity, developed at the Broad Institute and the Hebrew University of
+       Jerusalem, represents a novel method for the efficient and robust de
+       novo reconstruction of transcriptomes from RNA-seq data. Trinity
+       combines three independent software modules: Inchworm, Chrysalis, and
+       Butterfly, applied sequentially to process large volumes of RNA-seq
+       reads. Trinity partitions the sequence data into many individual de
+       Bruijn graphs, each representing the transcriptional complexity at a
+       given gene or locus, and then processes each graph independently to
+       extract full-length splicing isoforms and to tease apart transcripts
+       derived from paralogous genes.
+    """
+
+    homepage = "http://trinityrnaseq.github.io/"
+    url      = "https://github.com/trinityrnaseq/trinityrnaseq/archive/Trinity-v2.6.6.tar.gz"
+
+    version('2.6.6', 'b7472e98ab36655a6d9296d965471a56')
+
+    depends_on("java@8:", type=("build", "run"))
+    depends_on("bowtie2")
+    depends_on("jellyfish")
+    depends_on("salmon")
+    depends_on("perl+threads", type=("build", "run"))
+    depends_on("autoconf", type="build")
+    depends_on("automake", type="build")
+    depends_on("libtool", type="build")
+
+    # There is no documented list of these deps, but they're in the Dockerfile
+    #  and we have runtime errors without them
+    # https://github.com/trinityrnaseq/trinityrnaseq/blob/master/Docker/Dockerfile
+    depends_on("blast-plus", type="run")
+    depends_on("bowtie", type="run")
+    depends_on("r", type="run")
+    depends_on("r-tidyverse", type="run")
+    depends_on("r-edger", type="run")
+    depends_on("r-deseq2", type="run")
+    depends_on("r-ape", type="run")
+    depends_on("r-gplots", type="run")
+    depends_on("r-biobase", type="run")
+    depends_on("r-qvalue", type="run")
+    depends_on("rsem", type="run")
+    depends_on("kallisto", type="run")
+    depends_on("fastqc", type="run")
+    depends_on("samtools", type="run")
+    depends_on("py-numpy", type="run")
+    depends_on("express", type="run")
+    depends_on("perl-dbfile", type="run")
+    depends_on("perl-uri-escape", type="run")
+    depends_on("r-fastcluster", type="run")
+    depends_on("r-ctc", type="run")
+    depends_on("r-goseq", type="run")
+    depends_on("r-glimma", type="run")
+    depends_on("r-rots", type="run")
+    depends_on("r-goplot", type="run")
+    depends_on("r-argparse", type="run")
+    depends_on("r-sm", type="run")
+
+    def build(self, spec, prefix):
+        make()
+        make("trinity_essentials")
+        make("plugins")
+
+    def install(self, spec, prefix):
+        install_tree('.', prefix.bin)
+        force_remove(join_path(prefix.bin, '.gitmodules'))
+        force_remove(join_path(prefix.bin, 'Butterfly', '.err'))
+        force_remove(join_path(prefix.bin, 'Butterfly', 'src', '.classpath'))
+        force_remove(join_path(prefix.bin, 'Butterfly', 'src', '.err'))
+        force_remove(join_path(prefix.bin, 'Butterfly', 'src', '.project'))
+        remove_linked_tree(join_path(prefix.bin, 'Butterfly', 'src',
+                                     '.settings'))
+        remove_linked_tree(join_path(prefix.bin, 'Inchworm', 'src', '.deps'))
+        remove_linked_tree(join_path(prefix.bin, 'trinity-plugins',
+                                     'ParaFly-0.1.0', 'src', '.deps'))
+        force_remove(join_path(prefix.bin, 'trinity-plugins',
+                               'seqtk-trinity-0.0.2', '.gitignore'))
+        force_remove(join_path(prefix.bin, 'trinity-plugins', 'slclust', 'bin',
+                               '.hidden'))
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.set('TRINITY_HOME', self.prefix.bin)
+        run_env.prepend_path('PATH', self.prefix.bin.util)
+        spack_env.append_flags('CXXFLAGS', self.compiler.openmp_flag)
diff --git a/var/spack/repos/builtin/packages/trinotate/package.py b/var/spack/repos/builtin/packages/trinotate/package.py
new file mode 100644
index 0000000000..718a061ba8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/trinotate/package.py
@@ -0,0 +1,42 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class Trinotate(Package):
+    """Trinotate is a comprehensive annotation suite designed for
+       automatic functional annotation of transcriptomes, particularly
+       de novo assembled transcriptomes, from model or non-model organisms"""
+
+    homepage = "https://trinotate.github.io/"
+    url      = "https://github.com/Trinotate/Trinotate/archive/Trinotate-v3.1.1.tar.gz"
+
+    version('3.1.1', sha256='f8af0fa5dbeaaf5a085132cd4ac4f4206b05cc4630f0a17a672c586691f03843')
+
+    depends_on('trinity', type='run')
+    depends_on('transdecoder', type='run')
+    depends_on('sqlite', type='run')
+    depends_on('ncbi-rmblastn', type='run')
+    depends_on('hmmer', type='run')
+    depends_on('perl', type='run')
+    depends_on('lighttpd', type='run')
+    depends_on('perl-dbi', type='run')
+    depends_on('perl-dbd-mysql', type='run')
+    depends_on('perl-cgi', type='run')
+
+    def install(self, spec, prefix):
+        # most of the perl modules have local deps, install the whole tree
+        mkdirp(prefix.lib)
+        install_tree('.', join_path(prefix.lib, 'trinotate'))
+
+        mkdirp(prefix.bin)
+        os.symlink(join_path(prefix.lib, 'trinotate/Trinotate'),
+                   join_path(prefix.bin, 'Trinotate'))
+
+        os.symlink(join_path(prefix.lib,
+                             'trinotate/run_TrinotateWebserver.pl'),
+                   join_path(prefix.bin, 'run_TrinotateWebserver.pl'))
diff --git a/var/spack/repos/builtin/packages/trnascan-se/package.py b/var/spack/repos/builtin/packages/trnascan-se/package.py
new file mode 100644
index 0000000000..fcd2a3affd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/trnascan-se/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class TrnascanSe(AutotoolsPackage):
+    """Seaching for tRNA genes in genomic sequence"""
+
+    homepage = "http://lowelab.ucsc.edu/tRNAscan-SE/"
+    url      = "http://trna.ucsc.edu/software/trnascan-se-2.0.0.tar.gz"
+
+    version('2.0.0',    '36d2b53bcb281efbae09e0305346e544')
diff --git a/var/spack/repos/builtin/packages/turbine/package.py b/var/spack/repos/builtin/packages/turbine/package.py
index d12fa0a41c..7c4a2d7172 100644
--- a/var/spack/repos/builtin/packages/turbine/package.py
+++ b/var/spack/repos/builtin/packages/turbine/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -30,17 +11,41 @@ class Turbine(AutotoolsPackage):
     """Turbine: The Swift/T runtime"""
 
     homepage = 'http://swift-lang.org/Swift-T'
-    url      = 'http://swift-lang.github.io/swift-t-downloads/turbine-1.0.0.tar.gz'
+    url      = 'http://swift-lang.github.io/swift-t-downloads/spack/turbine-0.0.0.tar.gz'
 
-    version('1.0.0', '7ed56d65d6db0bfe15a439d818b4259e')
+    version('1.2.3', 'f2e393c292c4248b4e77a19f8272ae88')
+    version('1.2.1', 'c8976b22849aafe02a8fb4259dfed434')
+    version('1.1.0', '9a347cf16df02707cb529f96c265a082')
 
+    variant('python', default=False,
+            description='Enable calling python')
+    variant('r', default=False,
+            description='Enable calling R')
+    depends_on('adlbx@:0.8.0', when='@:1.1.0')
+    depends_on('adlbx', when='@1.2.1:')
     depends_on('adlbx')
-    depends_on('tcl')
-    depends_on('zsh', type='run')
+    depends_on('tcl', type=('build', 'run'))
+    depends_on('zsh', type=('build', 'run'))
+    depends_on('swig', type='build')
+    depends_on('python', when='+python')
+    depends_on('r', when='+r')
+
+    def setup_environment(self, spack_env, run_env):
+        spec = self.spec
+
+        spack_env.set('CC', spec['mpi'].mpicc)
+        spack_env.set('CXX', spec['mpi'].mpicxx)
+        spack_env.set('CXXLD', spec['mpi'].mpicxx)
 
     def configure_args(self):
         args = ['--with-c-utils=' + self.spec['exmcutils'].prefix,
                 '--with-adlb='    + self.spec['adlbx'].prefix,
                 '--with-tcl='     + self.spec['tcl'].prefix,
                 '--with-mpi='     + self.spec['mpi'].prefix]
+        if '+python' in self.spec:
+            args.append('--with-python-exe={0}'.format(
+                        self.spec['python'].command.path))
+        if '+r' in self.spec:
+            args.append('--with-r={0}/rlib/R'.format(
+                        self.spec['r'].prefix))
         return args
diff --git a/var/spack/repos/builtin/packages/turbomole/package.py b/var/spack/repos/builtin/packages/turbomole/package.py
index 14af3e4bdf..dfa424055f 100644
--- a/var/spack/repos/builtin/packages/turbomole/package.py
+++ b/var/spack/repos/builtin/packages/turbomole/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 import subprocess
diff --git a/var/spack/repos/builtin/packages/tut/package.py b/var/spack/repos/builtin/packages/tut/package.py
index c0d2bbcc8f..f39d83807e 100644
--- a/var/spack/repos/builtin/packages/tut/package.py
+++ b/var/spack/repos/builtin/packages/tut/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,6 +14,8 @@ class Tut(WafPackage):
 
     version('2016-12-19', '8b1967fa295ae1ce4d4431c2f811e521')
 
+    patch('python3-octal.patch', when='@2016-12-19')
+
     def build_args(self):
         args = []
 
diff --git a/var/spack/repos/builtin/packages/tut/python3-octal.patch b/var/spack/repos/builtin/packages/tut/python3-octal.patch
new file mode 100644
index 0000000000..d6d9b14273
--- /dev/null
+++ b/var/spack/repos/builtin/packages/tut/python3-octal.patch
@@ -0,0 +1,11 @@
+--- a/waftools/gcov.py	2016-12-19 04:55:44.000000000 -0600
++++ b/waftools/gcov.py	2018-03-28 10:42:53.000000000 -0500
+@@ -13,7 +13,7 @@
+     wrapper = NamedTemporaryFile(delete=False)
+     wrapper.write(script)
+     wrapper.close()
+-    os.chmod(wrapper.name, 0777)
++    os.chmod(wrapper.name, 0o777)
+ 
+     yield wrapper.name
+ 
diff --git a/var/spack/repos/builtin/packages/twm/package.py b/var/spack/repos/builtin/packages/twm/package.py
index b467420c82..34facb6666 100644
--- a/var/spack/repos/builtin/packages/twm/package.py
+++ b/var/spack/repos/builtin/packages/twm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -46,5 +27,5 @@ class Twm(AutotoolsPackage):
     depends_on('xproto@7.0.17:', type='build')
     depends_on('bison', type='build')
     depends_on('flex', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/tycho2/package.py b/var/spack/repos/builtin/packages/tycho2/package.py
index 0f54c2e661..5ac7bc3bb7 100644
--- a/var/spack/repos/builtin/packages/tycho2/package.py
+++ b/var/spack/repos/builtin/packages/tycho2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -31,9 +12,9 @@ class Tycho2(MakefilePackage):
        on unstructured, 3D tetrahedral meshes.
     """
     homepage = "https://github.com/lanl/tycho2"
-    url      = "https://github.com/lanl/tycho2/tarball/v0.1"
+    git      = "https://github.com/lanl/tycho2.git"
 
-    version('develop', git='https://github.com/lanl/tycho2', branch='master')
+    version('develop', branch='master')
 
     depends_on("mpi")
 
diff --git a/var/spack/repos/builtin/packages/typhon/package.py b/var/spack/repos/builtin/packages/typhon/package.py
new file mode 100644
index 0000000000..3de1bf4344
--- /dev/null
+++ b/var/spack/repos/builtin/packages/typhon/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Typhon(CMakePackage):
+    """
+    Typhon is a distributed communications library for unstructured mesh
+    applications.
+    """
+
+    homepage = "https://github.com/UK-MAC/Typhon"
+    url      = "https://github.com/UK-MAC/Typhon/archive/v3.0.tar.gz"
+    git      = "https://github.com/UK-MAC/Typhon.git"
+
+    version('develop', branch='develop')
+
+    version('3.0.2', sha256='28087eb07bf91d23792900214728b5eea61b5e81aa33df28c032dadd6d89b76e')
+    version('3.0.1', '89045decfba5fd468ef05ad4c924df8c')
+    version('3.0', 'ec67cd1aa585ce2410d4fa50514a916f')
+
+    depends_on('mpi')
diff --git a/var/spack/repos/builtin/packages/typhonio/package.py b/var/spack/repos/builtin/packages/typhonio/package.py
index 35fe269fd6..7b7285106f 100644
--- a/var/spack/repos/builtin/packages/typhonio/package.py
+++ b/var/spack/repos/builtin/packages/typhonio/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/llnl/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,19 +12,19 @@ class Typhonio(CMakePackage):
 
     homepage = "http://uk-mac.github.io/typhonio/"
     url      = "https://github.com/UK-MAC/typhonio/archive/v1.6_CMake.tar.gz"
+    git      = "https://github.com/UK-MAC/typhonio.git"
 
+    version('develop', branch='cmake_build')
     version('1.6_CMake', '8e8b2940a57874205e6d451856db5c2755884bf9')
-    version('develop', git='https://github.com/UK-MAC/typhonio.git',
-            branch='cmake_build')
 
     variant('build_type', default='Release', description='The build type to build',
         values=('Debug', 'Release'))
     variant('fortran', default=False, description='Enable Fortran support')
     variant('shared', default=False, description='Build shared libraries')
-    variant('docs', default=False, description='Build user guide and doxygen documentation')
+    variant('doc', default=False, description='Build user guide and doxygen documentation')
 
     depends_on('mpi')
-    depends_on('hdf5')
+    depends_on('hdf5+hl')
 
     def cmake_args(self):
         spec = self.spec
diff --git a/var/spack/repos/builtin/packages/uberftp/package.py b/var/spack/repos/builtin/packages/uberftp/package.py
index 040434f1b1..85a908c1df 100644
--- a/var/spack/repos/builtin/packages/uberftp/package.py
+++ b/var/spack/repos/builtin/packages/uberftp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/ucx/package.py b/var/spack/repos/builtin/packages/ucx/package.py
new file mode 100644
index 0000000000..7e85b65194
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ucx/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Ucx(AutotoolsPackage):
+    """a communication library implementing high-performance messaging for
+    MPI/PGAS frameworks"""
+
+    homepage = "http://www.openucx.org"
+    url      = "https://github.com/openucx/ucx/releases/download/v1.3.1/ucx-1.3.1.tar.gz"
+    # Current
+    version('1.3.1', '443ffdd64dc0e912b672a0ccb37ff666')
+
+    # Still supported
+    version('1.3.0', '2fdc3028eac3ef3ee1b1b523d170c071')
+    version('1.2.2', 'ff3fe65e4ebe78408fc3151a9ce5d286')
+    version('1.2.1', '697c2fd7912614fb5a1dadff3bfa485c')
+
+    depends_on('numactl')
+    depends_on('rdma-core')
diff --git a/var/spack/repos/builtin/packages/udunits2/package.py b/var/spack/repos/builtin/packages/udunits2/package.py
index 0e273f60ab..0b71b5f76c 100644
--- a/var/spack/repos/builtin/packages/udunits2/package.py
+++ b/var/spack/repos/builtin/packages/udunits2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/ufo-core/package.py b/var/spack/repos/builtin/packages/ufo-core/package.py
new file mode 100644
index 0000000000..eeaf19c473
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ufo-core/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class UfoCore(CMakePackage):
+    """The UFO data processing framework is a C library suited to build general
+    purpose streams data processing on heterogeneous architectures such as
+    CPUs, GPUs or clusters. This package contains the run-time system and
+    development files."""
+
+    homepage = "https://ufo.kit.edu"
+    url      = "https://github.com/ufo-kit/ufo-core/archive/v0.14.0.tar.gz"
+
+    version('0.14.0', '3bd94d10d0f589953aba11821a8295f3')
+
+    depends_on('glib')
+    depends_on('json-glib')
diff --git a/var/spack/repos/builtin/packages/ufo-filters/package.py b/var/spack/repos/builtin/packages/ufo-filters/package.py
new file mode 100644
index 0000000000..4cfd0c7527
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ufo-filters/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class UfoFilters(CMakePackage):
+    """The UFO data processing framework is a C library suited to build general
+    purpose streams data processing on heterogeneous architectures such as
+    CPUs, GPUs or clusters. This package contains filter plugins."""
+
+    homepage = "https://ufo.kit.edu"
+    url      = "https://github.com/ufo-kit/ufo-filters/archive/v0.14.1.tar.gz"
+
+    version('0.14.1', 'f2a81f5d38cfa71de58cbb5279782297')
+
+    depends_on('ufo-core')
diff --git a/var/spack/repos/builtin/packages/umpire/package.py b/var/spack/repos/builtin/packages/umpire/package.py
new file mode 100644
index 0000000000..d3d31f6cd6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/umpire/package.py
@@ -0,0 +1,43 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Umpire(CMakePackage):
+    """An application-focused API for memory management on NUMA & GPU
+    architectures"""
+
+    homepage = 'https://github.com/LLNL/Umpire'
+    git      = 'https://github.com/LLNL/Umpire.git'
+
+    version('develop', branch='develop', submodules='True')
+    version('master', branch='master', submodules='True')
+    version('0.1.4', tag='v0.1.4', submodules='True')
+    version('0.1.3', tag='v0.1.3', submodules='True')
+
+    variant('cuda', default=False, description='Build with CUDA support')
+    variant('fortran', default=False, description='Build C/Fortran API')
+
+    depends_on('cuda', when='+cuda')
+    depends_on('cmake@3.3:', type='build')
+
+    def cmake_args(self):
+        spec = self.spec
+
+        options = []
+
+        if '+cuda' in spec:
+            options.extend([
+                '-DENABLE_CUDA=On',
+                '-DCUDA_TOOLKIT_ROOT_DIR=%s' % (spec['cuda'].prefix)])
+        else:
+            options.append('-DENABLE_CUDA=Off')
+
+        if '+fortran' in spec:
+            options.append('-DENABLE_FORTRAN=On')
+
+        return options
diff --git a/var/spack/repos/builtin/packages/unblur/package.py b/var/spack/repos/builtin/packages/unblur/package.py
new file mode 100644
index 0000000000..2ca644f658
--- /dev/null
+++ b/var/spack/repos/builtin/packages/unblur/package.py
@@ -0,0 +1,53 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Unblur(AutotoolsPackage):
+    """Unblur is used to align the frames of movies recorded on an electron
+    microscope to reduce image blurring due to beam-induced motion."""
+
+    homepage = "http://grigoriefflab.janelia.org/unblur"
+    url      = "http://grigoriefflab.janelia.org/sites/default/files/unblur_1.0.2.tar.gz"
+
+    version('1.0.2', 'b6e367061cd0cef1b62a391a6289f681')
+
+    variant('openmp', default=True, description='Enable OpenMP support')
+    variant('shared', default=True, description='Dynamic linking')
+
+    depends_on('zlib')
+    depends_on('jpeg')
+    depends_on('libtiff')
+    depends_on('gsl')
+    depends_on('jbigkit')
+    depends_on('fftw@3:')
+    # Requires Intel Fortran compiler
+    conflicts('%gcc')
+    conflicts('%pgi')
+    conflicts('%clang')
+    conflicts('%cce')
+    conflicts('%xl')
+    conflicts('%xl_r')
+    conflicts('%nag')
+
+    configure_directory = 'src'
+
+    def patch(self):
+        filter_file(r'<<<<<<<.*', '', 'src/missing')
+
+    def configure_args(self):
+        spec = self.spec
+        return ['FC=ifort',
+                'F77=ifort',
+                '--enable-static={0}'
+                .format('yes' if '~shared' in spec else 'no'),
+                '--enable-openmp={0}'
+                .format('yes' if '+openmp' in spec else 'no'),
+                '--enable-optimisations=yes']
+
+    def build(self, spec, prefix):
+        with working_dir('src'):
+            make(parallel=False)
diff --git a/var/spack/repos/builtin/packages/uncrustify/package.py b/var/spack/repos/builtin/packages/uncrustify/package.py
index fdd7a49ec7..6222951641 100644
--- a/var/spack/repos/builtin/packages/uncrustify/package.py
+++ b/var/spack/repos/builtin/packages/uncrustify/package.py
@@ -1,34 +1,31 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class Uncrustify(AutotoolsPackage):
+class Uncrustify(Package):
     """Source Code Beautifier for C, C++, C#, ObjectiveC, Java, and others."""
 
     homepage = "http://uncrustify.sourceforge.net/"
     url      = "http://downloads.sourceforge.net/project/uncrustify/uncrustify/uncrustify-0.61/uncrustify-0.61.tar.gz"
 
+    version('0.67', '0c9a08366e5c97cd02ae766064e957de41827611')
     version('0.61', 'b6140106e74c64e831d0b1c4b6cf7727')
+
+    depends_on('cmake', type='build', when='@0.64:')
+
+    @when('@0.64:')
+    def install(self, spec, prefix):
+        with working_dir('spack-build', create=True):
+            cmake('..', *std_cmake_args)
+            make()
+            make('install')
+
+    @when('@:0.62')
+    def install(self, spec, prefix):
+        configure('--prefix={0}'.format(self.prefix))
+        make()
+        make('install')
diff --git a/var/spack/repos/builtin/packages/unibilium/package.py b/var/spack/repos/builtin/packages/unibilium/package.py
index 74cea8c8e2..dd1d1514ed 100644
--- a/var/spack/repos/builtin/packages/unibilium/package.py
+++ b/var/spack/repos/builtin/packages/unibilium/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/unifycr/package.py b/var/spack/repos/builtin/packages/unifycr/package.py
new file mode 100644
index 0000000000..17feb65e7a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/unifycr/package.py
@@ -0,0 +1,95 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+from spack import *
+
+
+class Unifycr(AutotoolsPackage):
+    """User level file system that enables applications to use node-local
+    storage as burst buffers for shared files. Supports scalable and efficient
+    aggregation of I/O bandwidth from burst buffers while having the same life
+    cycle as a batch-submitted job.
+    UnifyCR is designed to support common I/O workloads, including
+    checkpoint/restart. While primarily designed for N-N write/read, UnifyCR
+    compliments its functionality with the support for N-1 write/read."""
+
+    homepage = "https://github.com/LLNL/UnifyCR"
+    git      = "https://github.com/LLNL/UnifyCR.git"
+
+    version('develop', branch='dev', preferred=True)
+    version('0.1.1', tag='v0.1.1')
+
+    variant('debug', default='False', description='Enable debug build options')
+    variant('hdf5', default='False', description='Build with parallel HDF5 (install with `^hdf5~mpi` for serial)')
+    variant('numa', default='False', description='Build with NUMA')
+
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool',  type='build')
+    depends_on('m4',       type='build')
+
+    # Required dependencies
+    # Latest version of GOTCHA has API changes that break UnifyCR.
+    # Updates to UnifyCR are coming in order to fix this.
+    depends_on('gotcha@0.0.2')
+    depends_on('leveldb')
+    depends_on('mpi')
+    depends_on('pkg-config@0.9.0:')
+
+    # Optional dependencies
+
+    # UnifyCR's integration with HDF5 is still a WIP and is currently
+    # configured for serial only. HDF5 is parallel by default.
+    #
+    # To build with serial HDF5, use `spack install unifycr+hdf5 ^hdf5~mpi`
+    #
+    # Once UnifyCR is compatible with parallel HDF5, excluding `^hdf5~mpi` from
+    # the install line will build UnifyCR with parallel HDF5.
+
+    # v0.1.1 not HDF5 compatible; can change when v0.1.1 is no longer supported
+    depends_on('hdf5', when='@0.1.2: +hdf5')
+    depends_on('numactl',  when='+numa')
+
+    # we depend on numactl, which does't currently build on darwin
+    conflicts('platform=darwin', when='+numa')
+    conflicts('+hdf5', when='@:0.1.1')
+
+    # Parallel disabled to prevent tests from being run out-of-order when
+    # installed with the --test={root, all} option. Can potentially change if
+    # we add a +test configure option and variant.
+    parallel = False
+    build_directory = 'spack-build'
+
+    def configure_args(self):
+        spec = self.spec
+        args = []
+
+        if spec.satisfies('@0.1.1'):
+            env['CC'] = spec['mpi'].mpicc
+
+        # UnifyCR's configure requires the exact path for HDF5
+        def hdf5_compiler_path(name):
+            if '~mpi' in spec[name]:  # serial HDF5
+                return spec[name].prefix.bin.h5cc
+            else:  # parallel HDF5
+                return spec[name].prefix.bin.h5pcc
+
+        args.extend(self.with_or_without('numa',
+                                         lambda x: spec['numactl'].prefix))
+        args.extend(self.with_or_without('hdf5', hdf5_compiler_path))
+
+        if '+debug' in spec:
+            args.append('--enable-debug')
+
+        if spack.config.get('config:debug'):
+            args.append('--disable-silent-rules')
+        else:
+            args.append('--enable-silent-rules')
+
+        return args
+
+#    @when('@develop') TODO: uncomment when we `make dist` a stable release
+    def autoreconf(self, spec, prefix):
+        bash = which('bash')
+        bash('./autogen.sh')
diff --git a/var/spack/repos/builtin/packages/unison/package.py b/var/spack/repos/builtin/packages/unison/package.py
index 3d94ca7f49..55977a23c6 100644
--- a/var/spack/repos/builtin/packages/unison/package.py
+++ b/var/spack/repos/builtin/packages/unison/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/units/package.py b/var/spack/repos/builtin/packages/units/package.py
index 502dc999b7..f9e85f98a7 100644
--- a/var/spack/repos/builtin/packages/units/package.py
+++ b/var/spack/repos/builtin/packages/units/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,7 +10,7 @@ class Units(AutotoolsPackage):
     """GNU units converts between different systems of units"""
 
     homepage = "https://www.gnu.org/software/units/"
-    url      = "https://ftp.gnu.org/gnu/units/units-2.13.tar.gz"
+    url      = "https://ftpmirror.gnu.org/units/units-2.13.tar.gz"
 
     version('2.13', '5cbf2a6af76e94ba0ac55fc8d99d5a3e')
 
diff --git a/var/spack/repos/builtin/packages/unixodbc/package.py b/var/spack/repos/builtin/packages/unixodbc/package.py
index 30a771cdf2..488c91b553 100644
--- a/var/spack/repos/builtin/packages/unixodbc/package.py
+++ b/var/spack/repos/builtin/packages/unixodbc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/unuran/package.py b/var/spack/repos/builtin/packages/unuran/package.py
new file mode 100644
index 0000000000..2708882c6e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/unuran/package.py
@@ -0,0 +1,41 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Unuran(AutotoolsPackage):
+    """Universal Non-Uniform Random number generator."""
+
+    homepage = "http://statmath.wu.ac.at/unuran"
+    url      = "http://statmath.wu.ac.at/unuran/unuran-1.8.1.tar.gz"
+
+    version('1.8.1', 'a5885baab53a2608c1d85517bf5d06a5')
+
+    variant('shared', default=True,
+        description="Enable the build of shared libraries")
+    variant('rngstreams', default=True,
+        description="Use RNGSTREAM library for uniform random generation")
+    variant('gsl',      default=False,
+        description="Use random number generators from GNU Scientific Library")
+
+    depends_on('gsl',        when="+gsl")
+    depends_on('rngstreams', when="+rngstreams")
+
+    def configure_args(self):
+
+        spec = self.spec
+
+        args = [
+            '--%s-shared' % ('enable' if '+shared' in spec else 'disable'),
+            '--with-urgn-default=%s' % (
+                'rngstream' if '+rngstreams' in spec else 'builtin'),
+            '--%s-urng-gsl' % (
+                'with' if '+gsl' in spec else 'without'),
+            '--%s-urng-rngstreams' % (
+                'with' if '+rngstreams' in spec else 'without')
+        ]
+
+        return args
diff --git a/var/spack/repos/builtin/packages/unzip/package.py b/var/spack/repos/builtin/packages/unzip/package.py
new file mode 100644
index 0000000000..de9cc39c2e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/unzip/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Unzip(MakefilePackage):
+    """Unzip is a compression and file packaging/archive utility."""
+
+    homepage = 'http://www.info-zip.org/Zip.html'
+    url      = 'http://downloads.sourceforge.net/infozip/unzip60.tar.gz'
+
+    version('6.0', '62b490407489521db863b523a7f86375')
+
+    conflicts('platform=cray', msg='Unzip does not currently build on Cray')
+
+    make_args = ['-f', 'unix/Makefile']
+    build_targets = make_args + ['generic']
+
+    def url_for_version(self, version):
+        return 'http://downloads.sourceforge.net/infozip/unzip{0}.tar.gz'.format(version.joined)
+
+    @property
+    def install_targets(self):
+        return self.make_args + ['prefix={0}'.format(self.prefix), 'install']
diff --git a/var/spack/repos/builtin/packages/usearch/package.py b/var/spack/repos/builtin/packages/usearch/package.py
index b426376404..9ff833b907 100644
--- a/var/spack/repos/builtin/packages/usearch/package.py
+++ b/var/spack/repos/builtin/packages/usearch/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
diff --git a/var/spack/repos/builtin/packages/util-linux/package.py b/var/spack/repos/builtin/packages/util-linux/package.py
index f013737347..58b26abd5e 100644
--- a/var/spack/repos/builtin/packages/util-linux/package.py
+++ b/var/spack/repos/builtin/packages/util-linux/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/util-macros/package.py b/var/spack/repos/builtin/packages/util-macros/package.py
index e49987a57f..2ab1899ce1 100644
--- a/var/spack/repos/builtin/packages/util-macros/package.py
+++ b/var/spack/repos/builtin/packages/util-macros/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/uuid/package.py b/var/spack/repos/builtin/packages/uuid/package.py
index 5ad2e75341..0c6757e6c1 100644
--- a/var/spack/repos/builtin/packages/uuid/package.py
+++ b/var/spack/repos/builtin/packages/uuid/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/valgrind/package.py b/var/spack/repos/builtin/packages/valgrind/package.py
index b950e1cffd..3f9b7f39eb 100644
--- a/var/spack/repos/builtin/packages/valgrind/package.py
+++ b/var/spack/repos/builtin/packages/valgrind/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import sys
 
@@ -35,22 +16,34 @@ class Valgrind(AutotoolsPackage):
 
     Valgrind is Open Source / Free Software, and is freely available
     under the GNU General Public License, version 2.
-
     """
     homepage = "http://valgrind.org/"
-    url = "http://valgrind.org/downloads/valgrind-3.11.0.tar.bz2"
+    url      = "https://sourceware.org/pub/valgrind/valgrind-3.13.0.tar.bz2"
+    git      = "git://sourceware.org/git/valgrind.git"
 
+    version('develop', branch='master')
+    version('3.14.0', '74175426afa280184b62591b58c671b3')
+    version('3.13.0', '817dd08f1e8a66336b9ff206400a5369')
     version('3.12.0', '6eb03c0c10ea917013a7622e483d61bb')
     version('3.11.0', '4ea62074da73ae82e0162d6550d3f129')
     version('3.10.1', '60ddae962bc79e7c95cfc4667245707f')
     version('3.10.0', '7c311a72a20388aceced1aa5573ce970')
-    version('develop', svn='svn://svn.valgrind.org/valgrind/trunk')
 
     variant('mpi', default=True,
             description='Activates MPI support for valgrind')
     variant('boost', default=True,
             description='Activates boost support for valgrind')
+    variant('only64bit', default=True,
+            description='Sets --enable-only64bit option for valgrind')
+    variant('ubsan', default=True,
+            description='Activates ubsan support for valgrind')
 
+    conflicts('+ubsan', when='platform=darwin %clang',
+              msg="""
+Cannot build libubsan with clang on macOS.
+Otherwise with (Apple's) clang there is a linker error:
+clang: error: unknown argument: '-static-libubsan'
+""")
     depends_on('mpi', when='+mpi')
     depends_on('boost', when='+boost')
 
@@ -65,14 +58,11 @@ class Valgrind(AutotoolsPackage):
     def configure_args(self):
         spec = self.spec
         options = []
-        if not (spec.satisfies('%clang') and sys.platform == 'darwin'):
-            # Otherwise with (Apple's) clang there is a linker error:
-            # clang: error: unknown argument: '-static-libubsan'
+        if spec.satisfies('+ubsan'):
             options.append('--enable-ubsan')
+        if spec.satisfies('+only64bit'):
+            options.append('--enable-only64bit')
 
         if sys.platform == 'darwin':
-            options.extend([
-                '--build=amd64-darwin',
-                '--enable-only64bit'
-            ])
+            options.append('--build=amd64-darwin')
         return options
diff --git a/var/spack/repos/builtin/packages/vampirtrace/package.py b/var/spack/repos/builtin/packages/vampirtrace/package.py
index bc53cc6008..19d37118fd 100644
--- a/var/spack/repos/builtin/packages/vampirtrace/package.py
+++ b/var/spack/repos/builtin/packages/vampirtrace/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/vardictjava/package.py b/var/spack/repos/builtin/packages/vardictjava/package.py
index 66745a6a58..0168e7921c 100644
--- a/var/spack/repos/builtin/packages/vardictjava/package.py
+++ b/var/spack/repos/builtin/packages/vardictjava/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
 
@@ -34,6 +15,7 @@ class Vardictjava(Package):
     url      = "https://github.com/AstraZeneca-NGS/VarDictJava/releases/download/v1.5.1/VarDict-1.5.1.tar"
 
     version('1.5.1', '8c0387bcc1f7dc696b04e926c48b27e6')
+    version('1.4.4', '6b2d7e1e5502b875760fc9938a0fe5e0')
 
     depends_on('java@8:', type='run')
 
diff --git a/var/spack/repos/builtin/packages/varscan/package.py b/var/spack/repos/builtin/packages/varscan/package.py
index 0ce5c6b634..4793c15fe3 100644
--- a/var/spack/repos/builtin/packages/varscan/package.py
+++ b/var/spack/repos/builtin/packages/varscan/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os.path
 
diff --git a/var/spack/repos/builtin/packages/vc/package.py b/var/spack/repos/builtin/packages/vc/package.py
index 048955205b..49b4add8e2 100644
--- a/var/spack/repos/builtin/packages/vc/package.py
+++ b/var/spack/repos/builtin/packages/vc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/vcftools/package.py b/var/spack/repos/builtin/packages/vcftools/package.py
index f62702a0eb..09ac1cb37b 100644
--- a/var/spack/repos/builtin/packages/vcftools/package.py
+++ b/var/spack/repos/builtin/packages/vcftools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -55,8 +36,7 @@ class Vcftools(AutotoolsPackage):
 
         with working_dir('src/perl'):
             match = '^#!/usr/bin/env perl'
-            perl = join_path(self.spec['perl'].prefix.bin, 'perl')
-            substitute = "#!{perl}".format(perl=perl)
+            substitute = "#!{perl}".format(perl=self.spec['perl'].command.path)
             # tab-to-vcf added in 0.1.15
             files = ['fill-aa', 'fill-an-ac', 'fill-fs',
                      'fill-ref-md5', 'tab-to-vcf', 'vcf-annotate',
diff --git a/var/spack/repos/builtin/packages/vcsh/package.py b/var/spack/repos/builtin/packages/vcsh/package.py
index 76cdaf3b7b..bcc21caa66 100644
--- a/var/spack/repos/builtin/packages/vcsh/package.py
+++ b/var/spack/repos/builtin/packages/vcsh/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/vdt/package.py b/var/spack/repos/builtin/packages/vdt/package.py
index 1ff2d014e3..7c2fc4eebd 100644
--- a/var/spack/repos/builtin/packages/vdt/package.py
+++ b/var/spack/repos/builtin/packages/vdt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/vecgeom/package.py b/var/spack/repos/builtin/packages/vecgeom/package.py
index 05c1519220..c4ba864f8b 100644
--- a/var/spack/repos/builtin/packages/vecgeom/package.py
+++ b/var/spack/repos/builtin/packages/vecgeom/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 import platform
@@ -32,9 +13,22 @@ class Vecgeom(CMakePackage):
     (toolkits)."""
 
     homepage = "https://gitlab.cern.ch/VecGeom/VecGeom"
-
-    version('0.3.rc', git='https://gitlab.cern.ch/VecGeom/VecGeom.git',
-            tag='v0.3.rc')
+    url = "https://gitlab.cern.ch/api/v4/projects/VecGeom%2FVecGeom/repository/archive.tar.gz?sha=v0.3.rc"
+
+    version('01.00.00', git='https://gitlab.cern.ch/VecGeom/VecGeom.git', tag='v01.00.00')
+    version('00.05.00', git='https://gitlab.cern.ch/VecGeom/VecGeom.git', tag='v00.05.00', preferred=True)
+    version('0.3.rc', 'c1f5d620f655f3c0610a44e7735203b5')
+
+    variant('cxxstd',
+            default='17',
+            values=('14', '17'),
+            multi=False,
+            description='Use the specified C++ standard when building.')
+    variant('vector',
+             default='native',
+             values=('sse3', 'sse4.2', 'native'),
+             multi=False,
+             description='Specify the instruction set for vectorization.')
 
     depends_on('cmake@3.5:', type='build')
 
@@ -43,12 +37,16 @@ class Vecgeom(CMakePackage):
             '-DBACKEND=Scalar',
             '-DGEANT4=OFF',
             '-DUSOLIDS=ON',
-            '-DUSOLIDS_VECGEOM=ON'
-        ]
-
+            '-DUSOLIDS_VECGEOM=ON',
+            '-DROOT=OFF',
+            '-DNO_SPECIALIZATION=ON',
+            '-DCMAKE_VERBOSE_MAKEFILE=TRUE']
+        options.append('-DCMAKE_CXX_STANDARD={0}'.
+                       format(self.spec.variants['cxxstd'].value))
         arch = platform.machine()
         if arch == 'x86_64':
-            options.append('-DVECGEOM_VECTOR=sse4.2')
+            options.append('-DVECGEOM_VECTOR={0}'.
+                           format(self.spec.variants['vector'].value))
         else:
             options.append('-DVECGEOM_VECTOR=' + arch)
         return options
diff --git a/var/spack/repos/builtin/packages/veclibfort/package.py b/var/spack/repos/builtin/packages/veclibfort/package.py
index e57384fd2c..988e59adf3 100644
--- a/var/spack/repos/builtin/packages/veclibfort/package.py
+++ b/var/spack/repos/builtin/packages/veclibfort/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import sys
 
@@ -33,9 +14,10 @@ class Veclibfort(Package):
 
     homepage = "https://github.com/mcg1969/vecLibFort"
     url      = "https://github.com/mcg1969/vecLibFort/archive/0.4.2.tar.gz"
+    git      = "https://github.com/mcg1969/vecLibFort.git"
 
+    version('develop', branch='master')
     version('0.4.2', '83395ffcbe8a2122c3f726a5c3a7cf93')
-    version('develop', git='https://github.com/mcg1969/vecLibFort.git')
 
     variant('shared', default=True,
             description="Build shared libraries as well as static libs.")
@@ -48,7 +30,7 @@ class Veclibfort(Package):
     def libs(self):
         shared = True if '+shared' in self.spec else False
         return find_libraries(
-            'libvecLibFort', root=self.prefix, shared=shared, recurse=True
+            'libvecLibFort', root=self.prefix, shared=shared, recursive=True
         )
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/vegas2/package.py b/var/spack/repos/builtin/packages/vegas2/package.py
index ad452b3384..d6d4e7f6cf 100644
--- a/var/spack/repos/builtin/packages/vegas2/package.py
+++ b/var/spack/repos/builtin/packages/vegas2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/veloc/package.py b/var/spack/repos/builtin/packages/veloc/package.py
new file mode 100644
index 0000000000..72b1ff746e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/veloc/package.py
@@ -0,0 +1,51 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Veloc(CMakePackage):
+    """Very-Low Overhead Checkpointing System. VELOC is a multi-level
+    checkpoint-restart runtime for HPC supercomputing infrastructures"""
+
+    homepage = "https://github.com/ECP-VeloC/VELOC"
+    url      = "https://github.com/ECP-VeloC/VELOC/archive/veloc-1.0rc1.zip"
+    git      = "https://github.com/ecp-veloc/veloc.git"
+
+    tags = ['ecp']
+
+    version('master', branch='master')
+    version('1.0',    '98fe2d9abd2a1b53d7a52267dab91fae', preferred=True)
+    version('1.0rc1', 'c6db0de56b5b865183b1fa719ac74c1d')
+
+    depends_on('boost~atomic~chrono~clanglibcpp~date_time~debug~exception'
+               '~filesystem~graph~icu~iostreams~locale~log~math~mpi'
+               '~multithreaded~numpy~program_options~python~random~regex'
+               '~serialization~shared~signals~singlethreaded~system'
+               '~taggedlayout~test~thread~timer~versionedlayout~wave')
+    depends_on('libpthread-stubs')
+    depends_on('mpi')
+    depends_on('er')
+    depends_on('axl')
+    depends_on('cmake@3.9:', type='build')
+
+    conflicts('%gcc@:4.9.3')
+
+    # requires C++11
+    def flag_handler(self, name, flags):
+        flags = list(flags)
+        if name == 'cxxflags':
+            flags.append(self.compiler.cxx11_flag)
+        return (None, None, flags)
+
+    def cmake_args(self):
+        args = [
+            "-DWITH_AXL_PREFIX=%s" % self.spec['axl'].prefix,
+            "-DWITH_ER_PREFIX=%s" % self.spec['er'].prefix,
+            "-DBOOST_ROOT=%s" % self.spec['boost'].prefix,
+            "-DMPI_CXX_COMPILER=%s" % self.spec['mpi'].mpicxx
+        ]
+
+        return args
diff --git a/var/spack/repos/builtin/packages/velvet/package.py b/var/spack/repos/builtin/packages/velvet/package.py
index 45e10f4ce2..8813cfe16c 100644
--- a/var/spack/repos/builtin/packages/velvet/package.py
+++ b/var/spack/repos/builtin/packages/velvet/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/verilator/package.py b/var/spack/repos/builtin/packages/verilator/package.py
new file mode 100644
index 0000000000..b993071266
--- /dev/null
+++ b/var/spack/repos/builtin/packages/verilator/package.py
@@ -0,0 +1,62 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Verilator(AutotoolsPackage):
+    """Verilator is the fastest free Verilog HDL simulator.
+
+    It compiles synthesizable Verilog (not test-bench code!), plus some PSL,
+    SystemVerilog and Synthesis assertions into C++ or SystemC code. It is
+    designed for large projects where fast simulation performance is of primary
+    concern, and is especially well suited to generate executable models of
+    CPUs for embedded software design teams.
+
+    Please do not download this program if you are expecting a full featured
+    replacement for NC-Verilog, VCS or another commercial Verilog simulator
+    or Verilog compiler for a little project! (Try Icarus instead.) However, if
+    you are looking for a path to migrate synthesizable Verilog to C++ or
+    SystemC, and writing just a touch of C code and Makefiles doesn't scare you
+    off, this is the free Verilog compiler for you.
+
+    Verilator supports the synthesis subset of Verilog, plus initial
+    statements, proper blocking/non-blocking assignments, functions, tasks,
+    multi-dimensional arrays, and signed numbers. It also supports very simple
+    forms of SystemVerilog assertions and coverage analysis. Verilator supports
+    the more important Verilog 2005 constructs, and some SystemVerilog
+    features, with additional constructs being added as users request them.
+
+    Verilator has been used to simulate many very large multi-million gate
+    designs with thousands of modules."""
+
+    homepage = "https://www.veripool.org/projects/verilator"
+    url      = "https://www.veripool.org/ftp/verilator-3.920.tgz"
+
+    version('3.920', '71de7b9ddb27a72e96ed2a04e5ccf933')
+    version('3.904', '7d4dc8e61d5e0e564c3016a06f0b9d07')
+
+    depends_on('bison', type='build')
+    depends_on('flex',  type='build')
+    depends_on('perl',  type=('build', 'run'))
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('VERILATOR_ROOT', self.prefix)
+
+    # verilator requires access to its shipped scripts (bin) and include
+    # but the standard make doesn't put it in the correct places
+    @run_before('install')
+    def install_include(self):
+        install_tree('include', prefix.include)
+        install_tree('bin', prefix.bin)
+
+    # we need to fix the CXX and LINK paths, as they point to the spack
+    # wrapper scripts which aren't usable without spack
+    @run_after('install')
+    def patch_cxx(self):
+        filter_file(r'^CXX\s*=.*', 'CXX = {0}'.format(self.compiler.cxx),
+                    join_path(self.prefix.include, 'verilated.mk'))
+        filter_file(r'^LINK\s*=.*', 'LINK = {0}'.format(self.compiler.cxx),
+                    join_path(self.prefix.include, 'verilated.mk'))
diff --git a/var/spack/repos/builtin/packages/verrou/package.py b/var/spack/repos/builtin/packages/verrou/package.py
new file mode 100644
index 0000000000..d0cde05339
--- /dev/null
+++ b/var/spack/repos/builtin/packages/verrou/package.py
@@ -0,0 +1,86 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import glob
+import os
+import sys
+
+
+class Verrou(AutotoolsPackage):
+    """A floating-point error checker.
+
+    Verrou helps you look for floating-point round-off errors in programs. It
+    implements a stochastic floating-point arithmetic based on random rounding:
+    all floating-point operations are perturbed by randomly switching rounding
+    modes. This can be seen as an asynchronous variant of the CESTAC method, or
+    a subset of Monte Carlo Arithmetic, performing only output randomization
+    through random rounding.
+    """
+
+    homepage = "https://github.com/edf-hpc/verrou"
+    url      = "https://github.com/edf-hpc/verrou/archive/v2.0.0.tar.gz"
+    git      = "https://github.com/edf-hpc/verrou.git"
+
+    version('develop', branch='master')
+    version('2.0.0', '388d493df3f253c9b049ce0ceae55fd6')
+    version('1.1.0', '9752d776fb534890e5e29f9721ee6125')
+
+    resource(name='valgrind-3.13.0',
+             url='https://sourceware.org/pub/valgrind/valgrind-3.13.0.tar.bz2',
+             sha256='d76680ef03f00cd5e970bbdcd4e57fb1f6df7d2e2c071635ef2be74790190c3b',
+             when='@1.1.0:')
+
+    variant('fma', default=True,
+            description='Activates fused multiply-add support for Verrou')
+
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool', type='build')
+    depends_on('m4', type='build')
+
+    def patch(self):
+        # We start with the verrou source tree and a "valgrind-x.y.z" subdir.
+        # But we actually need a valgrind source tree with a "verrou" subdir.
+        # First, let's locate the valgrind sources...
+        valgrind_dirs = glob.glob('valgrind-*')
+        assert len(valgrind_dirs) == 1
+        valgrind_dir = valgrind_dirs[0]
+
+        # ...then we can flip the directory organization around
+        verrou_files = os.listdir('.')
+        verrou_files.remove(valgrind_dir)
+        os.mkdir('verrou')
+        for name in verrou_files:
+            os.rename(name, os.path.join('verrou', name))
+        for name in os.listdir(valgrind_dir):
+            os.rename(os.path.join(valgrind_dir, name), name)
+        os.rmdir(valgrind_dir)
+
+        # Once this is done, we can patch valgrind
+        which('patch')('-p0', '--input=verrou/valgrind.diff')
+
+        # Autogenerated perl path may be too long, need to fix this here
+        # because these files are used during the build.
+        for link_tool_in in glob.glob('coregrind/link_tool_exe_*.in'):
+            filter_file('^#! @PERL@',
+                        '#! /usr/bin/env perl',
+                        link_tool_in)
+
+    def autoreconf(self, spec, prefix):
+        # Needed because we patched valgrind
+        which("bash")("autogen.sh")
+
+    def configure_args(self):
+        spec = self.spec
+        options = [
+            '--enable-only64bit',
+            '--{0}able-verrou-fma'.format('en' if '+fma' in spec else 'dis')
+        ]
+
+        if sys.platform == 'darwin':
+            options.append('--build=amd64-darwin')
+
+        return options
diff --git a/var/spack/repos/builtin/packages/videoproto/package.py b/var/spack/repos/builtin/packages/videoproto/package.py
index 21a40f98ff..4f093034b5 100644
--- a/var/spack/repos/builtin/packages/videoproto/package.py
+++ b/var/spack/repos/builtin/packages/videoproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Videoproto(AutotoolsPackage):
 
     version('2.3.3', 'd984100603ee2420072f27bb491f4b7d')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/viennarna/package.py b/var/spack/repos/builtin/packages/viennarna/package.py
index c3fad661db..d96d32ec64 100644
--- a/var/spack/repos/builtin/packages/viennarna/package.py
+++ b/var/spack/repos/builtin/packages/viennarna/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,8 +13,9 @@ class Viennarna(AutotoolsPackage):
     """
 
     homepage = "https://www.tbi.univie.ac.at/RNA/"
-    url      = "https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_3_x/ViennaRNA-2.3.5.tar.gz"
+    url      = "https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_4_x/ViennaRNA-2.4.3.tar.gz"
 
+    version('2.4.3', '41be2fd36a5323a35ed50debfc7bd118')
     version('2.3.5', '4542120adae9b7abb605e2304c2a1326')
 
     variant('sse', default=True, description='Enable SSE in order to substantially speed up execution')
@@ -54,6 +36,8 @@ class Viennarna(AutotoolsPackage):
         args = self.enable_or_disable('sse')
         args += self.with_or_without('python')
         args += self.with_or_without('perl')
+        if self.spec.satisfies('@2.4.3:'):
+            args.append('--without-swig')
 
         if 'python@3:' in self.spec:
             args.append('--with-python3')
diff --git a/var/spack/repos/builtin/packages/viewres/package.py b/var/spack/repos/builtin/packages/viewres/package.py
index 0929dace52..06108c46ca 100644
--- a/var/spack/repos/builtin/packages/viewres/package.py
+++ b/var/spack/repos/builtin/packages/viewres/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Viewres(AutotoolsPackage):
     depends_on('libxmu')
     depends_on('libxt')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/vim/package.py b/var/spack/repos/builtin/packages/vim/package.py
index d216cb0aed..84c6372ab9 100644
--- a/var/spack/repos/builtin/packages/vim/package.py
+++ b/var/spack/repos/builtin/packages/vim/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,8 +16,11 @@ class Vim(AutotoolsPackage):
     """
 
     homepage = "http://www.vim.org"
-    url      = "https://github.com/vim/vim/archive/v8.0.0134.tar.gz"
+    url      = "https://github.com/vim/vim/archive/v8.1.0338.tar.gz"
 
+    version('8.1.0338', '94191b4141245a5deb4955c4a80359bb')
+    version('8.1.0001', 'edb6f5c67cb3100ea9e3966a43b9c9da')
+    version('8.0.1376', '62855881a2d96d48956859d74cfb8a3b')
     version('8.0.0503', '82b77bd5cb38b70514bed47cfe033b8c')
     version('8.0.0454', '4030bf677bdfbd14efb588e4d9a24128')
     version('8.0.0134', 'c74668d25c2acc85d655430dd60886cd')
@@ -65,6 +49,11 @@ class Vim(AutotoolsPackage):
     # support for auto/no/gtk2/gnome2/gtk3/motif/athena/neXtaw/photon/carbon
     variant('gui', default=False, description="build with gui (gvim)")
     variant('x', default=False, description="use the X Window System")
+    depends_on('libx11', when="+x")
+    depends_on('libsm', when="+x")
+    depends_on('libxpm', when="+x")
+    depends_on('libxt', when="+x")
+    depends_on('libxtst', when="+x")
 
     depends_on('ncurses', when="@7.4:")
 
@@ -95,9 +84,14 @@ class Vim(AutotoolsPackage):
         configure_args.append("--with-features=" + feature_set)
 
         if '+python' in spec:
-            configure_args.append("--enable-pythoninterp=yes")
+            if 'python@3:' in self.spec:
+                configure_args.append("--enable-python3interp=yes")
+                configure_args.append("--enable-pythoninterp=no")
+            else:
+                configure_args.append("--enable-python3interp=no")
+                configure_args.append("--enable-pythoninterp=yes")
         else:
-            configure_args.append("--enable-pythoninterp=no")
+            configure_args.append("--enable-python3interp=no")
 
         if '+ruby' in spec:
             configure_args.append("--enable-rubyinterp=yes")
@@ -130,6 +124,10 @@ class Vim(AutotoolsPackage):
 
         return configure_args
 
+    # Tests must be run in serial
+    def check(self):
+        make('test', parallel=False)
+
     # Run the install phase with -j 1.  There seems to be a problem with
     # parallel builds that results in the creation of the links (e.g. view)
     # to the vim binary silently failing.
diff --git a/var/spack/repos/builtin/packages/virtualgl/package.py b/var/spack/repos/builtin/packages/virtualgl/package.py
index c80eea5345..9ccef35acb 100644
--- a/var/spack/repos/builtin/packages/virtualgl/package.py
+++ b/var/spack/repos/builtin/packages/virtualgl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/visit/package.py b/var/spack/repos/builtin/packages/visit/package.py
index 56dec99eec..47d93c3a7b 100644
--- a/var/spack/repos/builtin/packages/visit/package.py
+++ b/var/spack/repos/builtin/packages/visit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,31 +12,72 @@ class Visit(CMakePackage):
     homepage = "https://wci.llnl.gov/simulation/computer-codes/visit/"
     url = "http://portal.nersc.gov/project/visit/releases/2.10.1/visit2.10.1.tar.gz"
 
+    version('2.13.0', '716644b8e78a00ff82691619d4d1e7a914965b6535884890b667b97ba08d6a0f')
+    version('2.12.3', '2dd351a291ee3e79926bc00391ca89b202cfa4751331b0fdee1b960c7922161f')
     version('2.12.2', '355779b1dbf440cdd548526eecd77b60')
     version('2.10.3', 'a1082a6f6dab3e2dcb58993603456c2b')
     version('2.10.2', '253de0837a9d69fb689befc98ea4d068')
     version('2.10.1', '3cbca162fdb0249f17c4456605c4211e')
 
+    variant('gui',    default=True, description='Enable VisIt\'s GUI')
+    variant('hdf5',   default=True, description='Enable HDF5 file format')
+    variant('silo',   default=True, description='Enable Silo file format')
+    variant('python', default=True, description='Enable Python support')
+    variant('mpi',    default=True, description='Enable parallel engine')
+
     depends_on('cmake@3.0:', type='build')
-    depends_on('vtk@6.1.0~opengl2')
-    depends_on('qt@4.8.6')
-    depends_on('python')
-    depends_on('silo+shared')
-    depends_on('hdf5~mpi')
+    depends_on('vtk@6.1.0~opengl2~mpi')
+    depends_on('qt@4.8.6', when='+gui')
+    depends_on('qwt', when='+gui')
+    depends_on('python', when='+python')
+    depends_on('silo+shared', when='+silo')
+    depends_on('hdf5', when='+hdf5')
+    depends_on('mpi', when='+mpi')
+
+    conflicts('+hdf5', when='~gui')
+    conflicts('+silo', when='~gui')
 
     root_cmakelists_dir = 'src'
 
     def cmake_args(self):
         spec = self.spec
-        qt_bin = spec['qt'].prefix.bin
 
-        return [
+        args = [
             '-DVTK_MAJOR_VERSION={0}'.format(spec['vtk'].version[0]),
             '-DVTK_MINOR_VERSION={0}'.format(spec['vtk'].version[1]),
-            '-DVISIT_USE_GLEW=OFF',
-            '-DVISIT_LOC_QMAKE_EXE:FILEPATH={0}/qmake-qt4'.format(qt_bin),
-            '-DPYTHON_DIR:PATH={0}'.format(spec['python'].home),
-            '-DVISIT_SILO_DIR:PATH={0}'.format(spec['silo'].prefix),
-            '-DVISIT_HDF5_DIR:PATH={0}'.format(spec['hdf5'].prefix),
             '-DVISIT_VTK_DIR:PATH={0}'.format(spec['vtk'].prefix),
+            '-DVISIT_USE_GLEW=OFF',
+            '-DCMAKE_CXX_FLAGS=-fPIC',
+            '-DCMAKE_C_FLAGS=-fPIC'
         ]
+
+        if(spec.variants['python'].value):
+            args.append('-DPYTHON_DIR:PATH={0}'.format(spec['python'].home))
+
+        if(spec.variants['gui'].value):
+            qt_bin = spec['qt'].prefix.bin
+            args.append(
+                '-DVISIT_LOC_QMAKE_EXE:FILEPATH={0}/qmake-qt4'.format(qt_bin))
+            args.append('-DVISIT_QWT_DIR:PATH={0}'.format(spec['qwt'].prefix))
+        else:
+            args.append('-DVISIT_SERVER_COMPONENTS_ONLY=ON')
+            args.append('-DVISIT_ENGINE_ONLY=ON')
+
+        if(spec.variants['hdf5'].value):
+            args.append(
+                '-DVISIT_HDF5_DIR:PATH={0}'.format(spec['hdf5'].prefix))
+            if spec.satisfies('^hdf5+mpi', strict=True):
+                args.append('-DVISIT_HDF5_MPI_DIR:PATH={0}'.format(
+                    spec['hdf5'].prefix))
+
+        if(spec.variants['silo'].value):
+            args.append(
+                '-DVISIT_SILO_DIR:PATH={0}'.format(spec['silo'].prefix))
+
+        if(spec.variants['mpi'].value):
+            args.append('-DVISIT_PARALLEL=ON')
+            args.append('-DVISIT_C_COMPILER={0}'.format(spec['mpi'].mpicc))
+            args.append('-DVISIT_CXX_COMPILER={0}'.format(spec['mpi'].mpicxx))
+            args.append('-DVISIT_MPI_COMPILER={0}'.format(spec['mpi'].mpicxx))
+
+        return args
diff --git a/var/spack/repos/builtin/packages/vizglow/package.py b/var/spack/repos/builtin/packages/vizglow/package.py
index b35af35164..4a8db820e6 100644
--- a/var/spack/repos/builtin/packages/vizglow/package.py
+++ b/var/spack/repos/builtin/packages/vizglow/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
 import os
diff --git a/var/spack/repos/builtin/packages/vmatch/package.py b/var/spack/repos/builtin/packages/vmatch/package.py
index e58f9fbb22..62b38a8667 100644
--- a/var/spack/repos/builtin/packages/vmatch/package.py
+++ b/var/spack/repos/builtin/packages/vmatch/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/voropp/package.py b/var/spack/repos/builtin/packages/voropp/package.py
index e88c20d864..e0a63f6f8e 100644
--- a/var/spack/repos/builtin/packages/voropp/package.py
+++ b/var/spack/repos/builtin/packages/voropp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/votca-csg/package.py b/var/spack/repos/builtin/packages/votca-csg/package.py
index 5c827ad36d..ca2f1b39b3 100644
--- a/var/spack/repos/builtin/packages/votca-csg/package.py
+++ b/var/spack/repos/builtin/packages/votca-csg/package.py
@@ -1,26 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, The VOTCA Development Team (http://www.votca.org)
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -35,8 +17,9 @@ class VotcaCsg(CMakePackage):
     """
     homepage = "http://www.votca.org"
     url      = "https://github.com/votca/csg/tarball/v1.4"
+    git      = "https://github.com/votca/csg.git"
 
-    version('develop', git='https://github.com/votca/csg', branch='master')
+    version('develop', branch='master')
     version('1.4', 'd009e761e5e3afd51eed89c420610a67')
     version('1.4.1', 'e4195d69db2036e9d76f22115ae31f81')
 
@@ -44,3 +27,4 @@ class VotcaCsg(CMakePackage):
     depends_on("votca-tools@1.4:1.4.999", when='@1.4:1.4.999')
     depends_on("votca-tools@develop", when='@develop')
     depends_on("gromacs~mpi@5.1:")
+    depends_on("hdf5~mpi")
diff --git a/var/spack/repos/builtin/packages/votca-ctp/package.py b/var/spack/repos/builtin/packages/votca-ctp/package.py
index f02c7eb564..3cbd2e0c9f 100644
--- a/var/spack/repos/builtin/packages/votca-ctp/package.py
+++ b/var/spack/repos/builtin/packages/votca-ctp/package.py
@@ -1,26 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, The VOTCA Development Team (http://www.votca.org)
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -34,12 +16,11 @@ class VotcaCtp(CMakePackage):
        This package contains the VOTCA charge transport engine.
     """
     homepage = "http://www.votca.org"
-    # No release yet
-    # url      = "https://github.com/votca/ctp/tarball/v1.4"
+    git      = "https://github.com/votca/ctp.git"
 
-    version('develop', git='https://github.com/votca/ctp', branch='master')
+    version('develop', branch='master')
 
     depends_on("cmake@2.8:", type='build')
     depends_on("votca-tools@develop", when='@develop')
     depends_on("votca-csg@develop", when='@develop')
-    depends_on("votca-moo@develop", when='@develop')
+    depends_on("gsl")
diff --git a/var/spack/repos/builtin/packages/votca-moo/package.py b/var/spack/repos/builtin/packages/votca-moo/package.py
deleted file mode 100644
index 308d28aab1..0000000000
--- a/var/spack/repos/builtin/packages/votca-moo/package.py
+++ /dev/null
@@ -1,43 +0,0 @@
-#############################################################################
-# Copyright (c) 2017, The VOTCA Development Team (http://www.votca.org)
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-
-from spack import *
-
-
-class VotcaMoo(CMakePackage):
-    """Versatile Object-oriented Toolkit for Coarse-graining
-       Applications (VOTCA) is a package intended to reduce the amount of
-       routine work when doing systematic coarse-graining of various
-       systems. The core is written in C++.
-
-       This package contains the VOTCA molecular orbital module.
-    """
-    homepage = "http://www.votca.org"
-    # No release yet
-    # url      = "https://github.com/votca/moo/tarball/v1.4"
-
-    version('develop', git='https://github.com/votca/moo', branch='master')
-
-    depends_on("cmake@2.8:", type='build')
-    depends_on("votca-tools@develop", when='@develop')
diff --git a/var/spack/repos/builtin/packages/votca-tools/package.py b/var/spack/repos/builtin/packages/votca-tools/package.py
index 9eb7fd147a..1f0a67ee3e 100644
--- a/var/spack/repos/builtin/packages/votca-tools/package.py
+++ b/var/spack/repos/builtin/packages/votca-tools/package.py
@@ -1,26 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, The VOTCA Development Team (http://www.votca.org)
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -35,14 +17,22 @@ class VotcaTools(CMakePackage):
     """
     homepage = "http://www.votca.org"
     url      = "https://github.com/votca/tools/tarball/v1.4"
+    git      = "https://github.com/votca/tools.git"
 
-    version('develop', git='https://github.com/votca/tools', branch='master')
+    version('develop', branch='master')
     version('1.4', 'cd47868e9f28e2c7b9d01f95aa0185ca')
     version('1.4.1', '3176b72f8a41ec053cc740a5398e7dc4')
 
     depends_on("cmake@2.8:", type='build')
     depends_on("expat")
     depends_on("fftw")
-    depends_on("gsl")
+    depends_on("gsl", when="@:1.4.9999")
+    depends_on("eigen@3.3:", when="@1.5:")
     depends_on("boost")
     depends_on("sqlite")
+
+    def cmake_args(self):
+        args = [
+            '-DWITH_RC_FILES=OFF'
+        ]
+        return args
diff --git a/var/spack/repos/builtin/packages/votca-xtp/package.py b/var/spack/repos/builtin/packages/votca-xtp/package.py
index e2b8ee059e..14a323de71 100644
--- a/var/spack/repos/builtin/packages/votca-xtp/package.py
+++ b/var/spack/repos/builtin/packages/votca-xtp/package.py
@@ -1,26 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, The VOTCA Development Team (http://www.votca.org)
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -34,9 +16,10 @@ class VotcaXtp(CMakePackage):
        This package contains the VOTCA exciton transport engine.
     """
     homepage = "http://www.votca.org"
-    url      = "https://github.com/votca/xtp/tarball/v1.4"
+    url      = "https://github.com/votca/xtp/tarball/v1.4.1"
+    git      = "https://github.com/votca/xtp.git"
 
-    version('develop', git='https://github.com/votca/xtp', branch='master')
+    version('develop', branch='master')
     version('1.4.1', '31a2dbd8bd48bf337bc88b20ab312050')
 
     depends_on("cmake@2.8:", type='build')
@@ -45,4 +28,5 @@ class VotcaXtp(CMakePackage):
     depends_on("votca-csg@develop", when='@develop')
     depends_on("votca-csg@1.4:1.4.999", when='@1.4:1.4.999')
     depends_on("votca-ctp@develop", when='@develop')
-    depends_on("votca-moo@develop", when='@develop')
+    depends_on("libxc", when='@1.5:')
+    depends_on("ceres-solver", when='@1.5:')
diff --git a/var/spack/repos/builtin/packages/vpfft/package.py b/var/spack/repos/builtin/packages/vpfft/package.py
index 1de6bdcfe4..0d58430d7d 100644
--- a/var/spack/repos/builtin/packages/vpfft/package.py
+++ b/var/spack/repos/builtin/packages/vpfft/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,10 +16,11 @@ class Vpfft(MakefilePackage):
     """
 
     homepage = "http://www.exmatex.org/vpfft.html"
-    url      = "https://github.com/exmatex/VPFFT/archive/master.tar.gz"
-    tag      = ['proxy-app']
+    git      = "https://github.com/exmatex/VPFFT.git"
+
+    tag = ['proxy-app']
 
-    version('develop', git='https://github.com/exmatex/VPFFT.git')
+    version('develop')
 
     depends_on('eigen')
     depends_on('fftw')
diff --git a/var/spack/repos/builtin/packages/vpic/package.py b/var/spack/repos/builtin/packages/vpic/package.py
index b5be3c6b82..5be359be28 100644
--- a/var/spack/repos/builtin/packages/vpic/package.py
+++ b/var/spack/repos/builtin/packages/vpic/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -36,9 +17,9 @@ class Vpic(CMakePackage):
        order finite-difference-time-domain (FDTD) solve.
     """
     homepage = "https://github.com/lanl/vpic"
-    url      = "https://github.com/lanl/vpic/tarball/v1.0"
+    git      = "https://github.com/lanl/vpic.git"
 
-    version('develop', git='https://github.com/lanl/vpic', branch='master', submodules=True)
+    version('develop', branch='master', submodules=True)
 
     depends_on("cmake@3.1:", type='build')
     depends_on('mpi')
diff --git a/var/spack/repos/builtin/packages/vsearch/package.py b/var/spack/repos/builtin/packages/vsearch/package.py
index 8a69123d17..892dcfb9ec 100644
--- a/var/spack/repos/builtin/packages/vsearch/package.py
+++ b/var/spack/repos/builtin/packages/vsearch/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/vt/package.py b/var/spack/repos/builtin/packages/vt/package.py
new file mode 100644
index 0000000000..b3b8305a9c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/vt/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Vt(MakefilePackage):
+    """A tool set for short variant discovery in genetic sequence data."""
+
+    homepage = "http://genome.sph.umich.edu/wiki/vt"
+    url      = "https://github.com/atks/vt/archive/0.577.tar.gz"
+
+    version('0.577',  '59807456022bcecf978314c93254fe15')
+
+    def install(self, spec, spack):
+        mkdirp(prefix.bin)
+        install('vt', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/vtk/package.py b/var/spack/repos/builtin/packages/vtk/package.py
index 0ab9a1a131..9cc75f3a8b 100644
--- a/var/spack/repos/builtin/packages/vtk/package.py
+++ b/var/spack/repos/builtin/packages/vtk/package.py
@@ -1,28 +1,10 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+
+import os
 from spack import *
 
 
@@ -32,74 +14,250 @@ class Vtk(CMakePackage):
     processing and visualization. """
 
     homepage = "http://www.vtk.org"
-    url      = "http://www.vtk.org/files/release/7.1/VTK-7.1.0.tar.gz"
+    url      = "http://www.vtk.org/files/release/8.0/VTK-8.0.1.tar.gz"
     list_url = "http://www.vtk.org/download/"
 
+    version('8.1.1', sha256='71a09b4340f0a9c58559fe946dc745ab68a866cf20636a41d97b6046cb736324')
+    version('8.0.1', '692d09ae8fadc97b59d35cab429b261a')
     version('7.1.0', 'a7e814c1db503d896af72458c2d0228f')
     version('7.0.0', '5fe35312db5fb2341139b8e4955c367d')
     version('6.3.0', '0231ca4840408e9dd60af48b314c5b6d')
     version('6.1.0', '25e4dfb3bad778722dcaec80cd5dab7d')
 
     # VTK7 defaults to OpenGL2 rendering backend
-    variant('opengl2', default=True, description='Build with OpenGL2 instead of OpenGL as rendering backend')
-    variant('python', default=False, description='Build the python modules')
+    variant('opengl2', default=True, description='Enable OpenGL2 backend')
+    variant('osmesa', default=False, description='Enable OSMesa support')
+    variant('python', default=False, description='Enable Python support')
+    variant('qt', default=False, description='Build with support for Qt')
+    variant('xdmf', default=False, description='Build XDMF file support')
+    variant('ffmpeg', default=False, description='Build with FFMPEG support')
+    variant('mpi', default=True, description='Enable MPI support')
+
+    # Haru causes trouble on Fedora and Ubuntu in v8.1.1
+    # See https://bugzilla.redhat.com/show_bug.cgi?id=1460059#c13
+    variant('haru', default=True, description='Enable libharu')
 
     patch('gcc.patch', when='@6.1.0')
 
-    depends_on('qt')
+    # At the moment, we cannot build with both osmesa and qt, but as of
+    # VTK 8.1, that should change
+    conflicts('+osmesa', when='+qt')
+
+    depends_on('python', when='+python')
+    depends_on('py-mpi4py', when='+mpi +python', type='run')
+    extends('python', when='+python')
+    # python3.7 compatibility patch backported from upstream
+    # https://gitlab.kitware.com/vtk/vtk/commit/706f1b397df09a27ab8981ab9464547028d0c322
+    patch('python3.7-const-char.patch', when='@:8.1.1 ^python@3.7:')
+
+    # The use of the OpenGL2 backend requires at least OpenGL Core Profile
+    # version 3.2 or higher.
+    depends_on('gl@3.2:', when='+opengl2')
+
+    # If you didn't ask for osmesa, then hw rendering using vendor-specific
+    # drivers is faster, but it must be done externally.
+    depends_on('opengl', when='~osmesa')
+
+    # Note: it is recommended to use mesa+llvm, if possible.
+    # mesa default is software rendering, llvm makes it faster
+    depends_on('mesa', when='+osmesa')
+
+    # VTK will need Qt5OpenGL, and qt needs '-opengl' for that
+    depends_on('qt+opengl', when='+qt')
+
+    depends_on('mpi', when='+mpi')
+
+    depends_on('libharu', when='+haru')
+
+    depends_on('boost', when='+xdmf')
+    depends_on('boost+mpi', when='+xdmf +mpi')
+
+    depends_on('mpi', when='+mpi')
+
+    depends_on('ffmpeg', when='+ffmpeg')
+
+    depends_on('expat')
+    depends_on('freetype')
+    depends_on('glew')
     depends_on('hdf5')
+    depends_on('libjpeg')
+    depends_on('jsoncpp')
+    depends_on('libxml2')
+    depends_on('lz4')
     depends_on('netcdf')
     depends_on('netcdf-cxx')
-
-    extends('python', when='+python')
+    depends_on('libpng')
+    depends_on('libtiff')
+    depends_on('zlib')
 
     def url_for_version(self, version):
         url = "http://www.vtk.org/files/release/{0}/VTK-{1}.tar.gz"
         return url.format(version.up_to(2), version)
 
+    def setup_environment(self, spack_env, run_env):
+        # VTK has some trouble finding freetype unless it is set in
+        # the environment
+        spack_env.set('FREETYPE_DIR', self.spec['freetype'].prefix)
+
     def cmake_args(self):
         spec = self.spec
 
         opengl_ver = 'OpenGL{0}'.format('2' if '+opengl2' in spec else '')
-        qt_ver = spec['qt'].version.up_to(1)
-        qt_bin = spec['qt'].prefix.bin
 
-        cmake_args = std_cmake_args[:]
-        cmake_args.extend([
+        cmake_args = [
             '-DBUILD_SHARED_LIBS=ON',
             '-DVTK_RENDERING_BACKEND:STRING={0}'.format(opengl_ver),
-            '-DVTK_USE_SYSTEM_HDF5=ON',
-            '-DVTK_USE_SYSTEM_NETCDF=ON',
+
+            '-DVTK_USE_SYSTEM_LIBHARU=%s' % (
+                'ON' if '+haru' in spec else 'OFF'),
+
+            # In general, we disable use of VTK "ThirdParty" libs, preferring
+            # spack-built versions whenever possible
+            '-DVTK_USE_SYSTEM_LIBRARIES:BOOL=ON',
+
+            # However, in a few cases we can't do without them yet
+            '-DVTK_USE_SYSTEM_GL2PS:BOOL=OFF',
+            '-DVTK_USE_SYSTEM_LIBPROJ4:BOOL=OFF',
+            '-DVTK_USE_SYSTEM_OGGTHEORA:BOOL=OFF',
+
             '-DNETCDF_DIR={0}'.format(spec['netcdf'].prefix),
             '-DNETCDF_C_ROOT={0}'.format(spec['netcdf'].prefix),
             '-DNETCDF_CXX_ROOT={0}'.format(spec['netcdf-cxx'].prefix),
 
-            # Enable/Disable wrappers for Python.
-            '-DVTK_WRAP_PYTHON={0}'.format(
-                'ON' if '+python' in spec else 'OFF'),
-
             # Disable wrappers for other languages.
             '-DVTK_WRAP_JAVA=OFF',
             '-DVTK_WRAP_TCL=OFF',
+        ]
+
+        if '+mpi' in spec:
+            cmake_args.extend([
+                '-DVTK_Group_MPI:BOOL=ON',
+                '-DVTK_USE_SYSTEM_DIY2:BOOL=OFF',
+            ])
 
-            # Enable Qt support here.
-            '-DVTK_QT_VERSION:STRING={0}'.format(qt_ver),
-            '-DQT_QMAKE_EXECUTABLE:PATH={0}/qmake'.format(qt_bin),
-            '-DVTK_Group_Qt:BOOL=ON',
-        ])
+        if '+ffmpeg' in spec:
+            cmake_args.extend(['-DModule_vtkIOFFMPEG:BOOL=ON'])
 
-        # NOTE: The following definitions are required in order to allow
-        # VTK to build with qt~webkit versions (see the documentation for
-        # more info: http://www.vtk.org/Wiki/VTK/Tutorials/QtSetup).
-        if '~webkit' in spec['qt']:
+        # Enable/Disable wrappers for Python.
+        if '+python' in spec:
             cmake_args.extend([
-                '-DVTK_Group_Qt:BOOL=OFF',
-                '-DModule_vtkGUISupportQt:BOOL=ON',
-                '-DModule_vtkGUISupportQtOpenGL:BOOL=ON',
+                '-DVTK_WRAP_PYTHON=ON',
+                '-DPYTHON_EXECUTABLE={0}'.format(spec['python'].command.path),
+                '-DVTK_USE_SYSTEM_MPI4PY:BOOL=ON'
+            ])
+        else:
+            cmake_args.append('-DVTK_WRAP_PYTHON=OFF')
+
+        if 'darwin' in spec.architecture:
+            cmake_args.extend([
+                '-DCMAKE_MACOSX_RPATH=ON'
+            ])
+
+        if '+qt' in spec:
+            qt_ver = spec['qt'].version.up_to(1)
+            qt_bin = spec['qt'].prefix.bin
+            qmake_exe = os.path.join(qt_bin, 'qmake')
+
+            cmake_args.extend([
+                # Enable Qt support here.
+                '-DVTK_QT_VERSION:STRING={0}'.format(qt_ver),
+                '-DQT_QMAKE_EXECUTABLE:PATH={0}'.format(qmake_exe),
+                '-DVTK_Group_Qt:BOOL=ON',
+            ])
+
+            # NOTE: The following definitions are required in order to allow
+            # VTK to build with qt~webkit versions (see the documentation for
+            # more info: http://www.vtk.org/Wiki/VTK/Tutorials/QtSetup).
+            if '~webkit' in spec['qt']:
+                cmake_args.extend([
+                    '-DVTK_Group_Qt:BOOL=OFF',
+                    '-DModule_vtkGUISupportQt:BOOL=ON',
+                    '-DModule_vtkGUISupportQtOpenGL:BOOL=ON',
+                ])
+
+        if '+xdmf' in spec:
+            if spec.satisfies('^cmake@3.12:'):
+                # This policy exists only for CMake >= 3.12
+                cmake_args.extend(["-DCMAKE_POLICY_DEFAULT_CMP0074=NEW"])
+
+            cmake_args.extend([
+                # Enable XDMF Support here
+                "-DModule_vtkIOXdmf2:BOOL=ON",
+                "-DModule_vtkIOXdmf3:BOOL=ON",
+                "-DBOOST_ROOT={0}".format(spec['boost'].prefix),
+                "-DBOOST_LIBRARY_DIR={0}".format(spec['boost'].prefix.lib),
+                "-DBOOST_INCLUDE_DIR={0}".format(spec['boost'].prefix.include),
+                "-DBOOST_NO_SYSTEM_PATHS:BOOL=ON",
+                # This is needed because VTK has multiple FindBoost
+                # and they stick to system boost if there's a system boost
+                # installed with CMake
+                "-DBoost_NO_BOOST_CMAKE:BOOL=ON",
+                "-DHDF5_ROOT={0}".format(spec['hdf5'].prefix),
+                # The xdmf project does not export any CMake file...
+                "-DVTK_USE_SYSTEM_XDMF3:BOOL=OFF",
+                "-DVTK_USE_SYSTEM_XDMF2:BOOL=OFF"
+            ])
+
+            if '+mpi' in spec:
+                cmake_args.extend(["-DModule_vtkIOParallelXdmf3:BOOL=ON"])
+
+        if '+osmesa' in spec:
+            prefix = spec['mesa'].prefix
+            osmesa_include_dir = prefix.include
+            osmesa_library = os.path.join(prefix.lib, 'libOSMesa.so')
+
+            use_param = 'VTK_USE_X'
+            if 'darwin' in spec.architecture:
+                use_param = 'VTK_USE_COCOA'
+
+            cmake_args.extend([
+                '-D{0}:BOOL=OFF'.format(use_param),
+                '-DVTK_OPENGL_HAS_OSMESA:BOOL=ON',
+                '-DOSMESA_INCLUDE_DIR:PATH={0}'.format(osmesa_include_dir),
+                '-DOSMESA_LIBRARY:FILEPATH={0}'.format(osmesa_library),
+            ])
+        else:
+            prefix = spec['opengl'].prefix
+
+            opengl_include_dir = prefix.include
+            opengl_library = os.path.join(prefix.lib, 'libGL.so')
+            if 'darwin' in spec.architecture:
+                opengl_include_dir = prefix
+                opengl_library = prefix
+
+            cmake_args.extend([
+                '-DOPENGL_INCLUDE_DIR:PATH={0}'.format(opengl_include_dir),
+                '-DOPENGL_gl_LIBRARY:FILEPATH={0}'.format(opengl_library)
             ])
 
         if spec.satisfies('@:6.1.0'):
-            cmake_args.append('-DCMAKE_C_FLAGS=-DGLX_GLXEXT_LEGACY')
-            cmake_args.append('-DCMAKE_CXX_FLAGS=-DGLX_GLXEXT_LEGACY')
+            cmake_args.extend([
+                '-DCMAKE_C_FLAGS=-DGLX_GLXEXT_LEGACY',
+                '-DCMAKE_CXX_FLAGS=-DGLX_GLXEXT_LEGACY'
+            ])
+
+            # VTK 6.1.0 (and possibly earlier) does not use
+            # NETCDF_CXX_ROOT to detect NetCDF C++ bindings, so
+            # NETCDF_CXX_INCLUDE_DIR and NETCDF_CXX_LIBRARY must be
+            # used instead to detect these bindings
+            netcdf_cxx_lib = spec['netcdf-cxx'].libs.joined()
+            cmake_args.extend([
+                '-DNETCDF_CXX_INCLUDE_DIR={0}'.format(
+                    spec['netcdf-cxx'].prefix.include),
+                '-DNETCDF_CXX_LIBRARY={0}'.format(netcdf_cxx_lib),
+            ])
+
+            # Garbage collection is unsupported in Xcode starting with
+            # version 5.1; if the Apple clang version of the compiler
+            # is 5.1.0 or later, unset the required Objective-C flags
+            # to remove the garbage collection flags.  Versions of VTK
+            # after 6.1.0 set VTK_REQUIRED_OBJCXX_FLAGS to the empty
+            # string. This fix was recommended on the VTK mailing list
+            # in March 2014 (see
+            # https://public.kitware.com/pipermail/vtkusers/2014-March/083368.html)
+            if (self.spec.satisfies('%clang') and
+                self.compiler.is_apple and
+                self.compiler.version >= Version('5.1.0')):
+                cmake_args.extend(['-DVTK_REQUIRED_OBJCXX_FLAGS=""'])
 
         return cmake_args
diff --git a/var/spack/repos/builtin/packages/vtk/python3.7-const-char.patch b/var/spack/repos/builtin/packages/vtk/python3.7-const-char.patch
new file mode 100644
index 0000000000..80dbc78530
--- /dev/null
+++ b/var/spack/repos/builtin/packages/vtk/python3.7-const-char.patch
@@ -0,0 +1,27 @@
+diff --git a/Wrapping/PythonCore/vtkPythonArgs.cxx b/Wrapping/PythonCore/vtkPythonArgs.cxx
+index 1a82af0802..b733458975 100644
+--- a/Wrapping/PythonCore/vtkPythonArgs.cxx
++++ b/Wrapping/PythonCore/vtkPythonArgs.cxx
+@@ -95,13 +95,21 @@ bool vtkPythonGetStringValue(PyObject *o, T *&a, const char *exctext)
+ {
+   if (PyBytes_Check(o))
+   {
++#if PY_VERSION_HEX >= 0x03070000
++    a = const_cast<char *>(PyBytes_AS_STRING(o));
++    return true;
++#else
+     a = PyBytes_AS_STRING(o);
+     return true;
++#endif
+   }
+ #ifdef Py_USING_UNICODE
+   else if (PyUnicode_Check(o))
+   {
+-#if PY_VERSION_HEX >= 0x03030000
++#if PY_VERSION_HEX >= 0x03070000
++    a = const_cast<char *>(PyUnicode_AsUTF8(o));
++    return true;
++#elif PY_VERSION_HEX >= 0x03030000
+     a = PyUnicode_AsUTF8(o);
+     return true;
+ #else
diff --git a/var/spack/repos/builtin/packages/vtkh/package.py b/var/spack/repos/builtin/packages/vtkh/package.py
index 9073c1f6f3..f42322332a 100644
--- a/var/spack/repos/builtin/packages/vtkh/package.py
+++ b/var/spack/repos/builtin/packages/vtkh/package.py
@@ -1,29 +1,11 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
+import os
 
 
 class Vtkh(Package):
@@ -32,12 +14,9 @@ class Vtkh(Package):
     and DIY2 to provide a toolkit with hybrid parallel capabilities."""
 
     homepage = "https://github.com/Alpine-DAV/vtk-h"
-    url      = "https://github.com/Alpine-DAV/vtk-h"
+    git      = "https://github.com/Alpine-DAV/vtk-h.git"
 
-    version('master',
-            git='https://github.com/Alpine-DAV/vtk-h.git',
-            branch='master',
-            submodules=True)
+    version('master', branch='master', submodules=True)
 
     maintainers = ['cyrush']
 
@@ -67,7 +46,9 @@ class Vtkh(Package):
                 mpicxx = spec['mpi'].mpicxx
                 cmake_args.extend(["-DMPI_C_COMPILER={0}".format(mpicc),
                                    "-DMPI_CXX_COMPILER={0}".format(mpicxx)])
-
+                mpiexe_bin = join_path(spec['mpi'].prefix.bin, 'mpiexec')
+                if os.path.isfile(mpiexe_bin):
+                    cmake_args.append("-DMPIEXEC={0}".format(mpiexe_bin))
             # tbb support
             if "+tbb" in spec:
                 cmake_args.append("-DTBB_DIR={0}".format(spec["tbb"].prefix))
diff --git a/var/spack/repos/builtin/packages/vtkm/package.py b/var/spack/repos/builtin/packages/vtkm/package.py
index c1bc968f85..ded4a551ac 100644
--- a/var/spack/repos/builtin/packages/vtkm/package.py
+++ b/var/spack/repos/builtin/packages/vtkm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 import os
@@ -36,14 +17,12 @@ class Vtkm(Package):
     architectures."""
 
     homepage = "https://m.vtk.org/"
-    url      = "https://gitlab.kitware.com/vtk/vtk-m/repository/v1.1.0/archive.tar.gz"
+    url      = "https://gitlab.kitware.com/api/v4/projects/vtk%2Fvtk-m/repository/archive.tar.gz?sha=v1.1.0"
+    git      = "https://gitlab.kitware.com/vtk/vtk-m.git"
 
+    version('master', branch='master')
     version('1.1.0', "6aab1c0885f6ffaaffcf07930873d0df")
 
-    version('master',
-            git='https://gitlab.kitware.com/vtk/vtk-m.git',
-            branch='master')
-
     variant("cuda", default=False, description="build cuda support")
     variant("tbb", default=True, description="build TBB support")
 
diff --git a/var/spack/repos/builtin/packages/wannier90/package.py b/var/spack/repos/builtin/packages/wannier90/package.py
index c940d6c171..ec8a47620c 100644
--- a/var/spack/repos/builtin/packages/wannier90/package.py
+++ b/var/spack/repos/builtin/packages/wannier90/package.py
@@ -1,30 +1,10 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import inspect
 import os.path
-import shutil
 
 from spack import *
 
@@ -77,7 +57,7 @@ class Wannier90(MakefilePackage):
             'make.sys'
         )
 
-        shutil.copy(template, self.makefile_name)
+        copy(template, self.makefile_name)
         for key, value in substitutions.items():
             filter_file(key, value, self.makefile_name)
 
diff --git a/var/spack/repos/builtin/packages/warpx/package.py b/var/spack/repos/builtin/packages/warpx/package.py
new file mode 100644
index 0000000000..bfbcd7fa3a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/warpx/package.py
@@ -0,0 +1,84 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Warpx(MakefilePackage):
+    """WarpX is an advanced electromagnetic Particle-In-Cell code. It supports
+    many features including Perfectly-Matched Layers (PML) and mesh refinement.
+    In addition, WarpX is a highly-parallel and highly-optimized code and
+    features hybrid OpenMP/MPI parallelization, advanced vectorization
+    techniques and load balancing capabilities.
+    """
+
+    homepage = "https://ecp-warpx.github.io/index.html"
+    url      = "https://github.com/ECP-WarpX/WarpX"
+
+    version('master', git='https://github.com/ECP-WarpX/WarpX.git', tag='master')
+    version('dev', git='https://github.com/ECP-WarpX/WarpX.git', tag='dev')
+
+    depends_on('mpi')
+
+    variant('dims',
+            default='3',
+            values=('1', '2', '3'),
+            multi=False,
+            description='Number of spatial dimensions')
+
+    variant('psatd', default=False, description='Enable PSATD solver')
+    variant('do_electrostatic', default=False, description='Include electrostatic solver')
+    variant('debug', default=False, description='Enable debugging features')
+    variant('tprof', default=False, description='Enable tiny profiling features')
+    variant('openmp', default=True, description='Enable OpenMP features')
+
+    resource(name='amrex',
+             git='https://github.com/AMReX-Codes/amrex.git',
+             tag='development',
+             destination='.')
+
+    resource(name='picsar',
+             git='https://bitbucket.org/berkeleylab/picsar.git',
+             tag='master',
+             destination='.')
+
+    def edit(self, spec, prefix):
+
+        comp = 'gcc'
+        vendors = {'%gcc': 'gcc', '%intel': 'intel'}
+        for key, value in vendors.items():
+            if self.spec.satisfies(key):
+                comp = value
+
+        def torf(s):
+            "Returns the string TRUE or FALSE"
+            return repr(s in spec).upper()
+
+        makefile = FileFilter('GNUmakefile')
+        makefile.filter('AMREX_HOME .*', 'AMREX_HOME = amrex')
+        makefile.filter('PICSAR_HOME .*', 'PICSAR_HOME = picsar')
+        makefile.filter('COMP .*', 'COMP = {0}'.format(comp))
+        makefile.filter('DIM .*',
+                        'DIM = {0}'.format(int(spec.variants['dims'].value)))
+        makefile.filter('USE_PSATD .*',
+                        'USE_PSATD = {0}'.format(torf('+psatd')))
+        makefile.filter('DO_ELECTROSTATIC .*',
+                        'DO_ELECTROSTATIC = %s' % torf('+do_electrostatic'))
+        makefile.filter('USE_OMP .*',
+                        'USE_OMP = {0}'.format(torf('+openmp')))
+        makefile.filter('DEBUG .*',
+                        'DEBUG = {0}'.format(torf('+debug')))
+        makefile.filter('TINY_PROFILE .*',
+                        'TINY_PROFILE = {0}'.format(torf('+tprof')))
+        makefile.filter('EBASE .*', 'EBASE = warpx')
+
+    def setup_environment(self, spack_env, run_env):
+        # --- Fool the compiler into using the "unknown" configuration.
+        # --- With this, it will use the spack provided mpi.
+        spack_env.set('HOSTNAME', 'unknown')
+        spack_env.set('NERSC_HOST', 'unknown')
+
+    def install(self, spec, prefix):
+        make('WarpxBinDir = {0}'.format(prefix.bin), 'all')
diff --git a/var/spack/repos/builtin/packages/wcslib/package.py b/var/spack/repos/builtin/packages/wcslib/package.py
new file mode 100644
index 0000000000..a3b5a56a68
--- /dev/null
+++ b/var/spack/repos/builtin/packages/wcslib/package.py
@@ -0,0 +1,48 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Wcslib(AutotoolsPackage):
+    """WCSLIB a C implementation of the coordinate transformations
+    defined in the FITS WCS papers."""
+
+    homepage = "http://www.atnf.csiro.au/people/mcalabre/WCS/wcslib/"
+    url      = "ftp://ftp.atnf.csiro.au/pub/software/wcslib/wcslib-5.18.tar.bz2"
+
+    version('5.18', '67a78354be74eca4f17d3e0853d5685f')
+
+    variant('cfitsio', default=False, description='Include CFITSIO support')
+    variant('x',       default=False, description='Use the X Window System')
+
+    depends_on('gmake', type='build')
+    depends_on('flex@2.5.9:', type='build')
+    depends_on('cfitsio', when='+cfitsio')
+    depends_on('libx11', when='+x')
+
+    def configure_args(self):
+        spec = self.spec
+
+        # TODO: Add PGPLOT package
+        args = ['--without-pgplot']
+
+        if '+cfitsio' in spec:
+            args.extend([
+                '--with-cfitsio',
+                '--with-cfitsiolib={0}'.format(
+                    spec['cfitsio'].libs.directories[0]),
+                '--with-cfitsioinc={0}'.format(
+                    spec['cfitsio'].headers.directories[0]),
+            ])
+        else:
+            args.append('--without-cfitsio')
+
+        if '+x' in spec:
+            args.append('--with-x')
+        else:
+            args.append('--without-x')
+
+        return args
diff --git a/var/spack/repos/builtin/packages/wget/package.py b/var/spack/repos/builtin/packages/wget/package.py
index 03e0c86cf3..2ee6ea4171 100644
--- a/var/spack/repos/builtin/packages/wget/package.py
+++ b/var/spack/repos/builtin/packages/wget/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,7 +13,7 @@ class Wget(AutotoolsPackage):
     cron jobs, terminals without X-Windows support, etc."""
 
     homepage = "http://www.gnu.org/software/wget/"
-    url      = "http://ftp.gnu.org/gnu/wget/wget-1.19.1.tar.gz"
+    url      = "https://ftpmirror.gnu.org/wget/wget-1.19.1.tar.gz"
 
     version('1.19.1', '87cea36b7161fd43e3fd51a4e8b89689')
     version('1.17',   'c4c4727766f24ac716936275014a0536')
@@ -60,10 +41,9 @@ class Wget(AutotoolsPackage):
     depends_on('pcre', when='+pcre')
 
     depends_on('perl@5.12.0:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
 
-    # TODO: Add a 'test' deptype
-    # depends_on('valgrind', type='test')
+    depends_on('valgrind', type='test')
 
     build_directory = 'spack-build'
 
diff --git a/var/spack/repos/builtin/packages/wgsim/package.py b/var/spack/repos/builtin/packages/wgsim/package.py
new file mode 100644
index 0000000000..7caa098346
--- /dev/null
+++ b/var/spack/repos/builtin/packages/wgsim/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Wgsim(Package):
+    """Wgsim is a small tool for simulating sequence reads from a reference
+    genome.
+
+    It is able to simulate diploid genomes with SNPs and insertion/deletion
+    (INDEL) polymorphisms, and simulate reads with uniform substitution
+    sequencing errors. It does not generate INDEL sequencing errors, but this
+    can be partly compensated by simulating INDEL polymorphisms."""
+
+    homepage = "https://github.com/lh3/wgsim"
+    git      = "https://github.com/lh3/wgsim.git"
+
+    version('2011.10.17', commit='a12da3375ff3b51a5594d4b6fa35591173ecc229')
+
+    depends_on('zlib')
+
+    def install(self, spec, prefix):
+        cc = Executable(spack_cc)
+        cc('-g', '-O2', '-Wall', '-o', 'wgsim', 'wgsim.c', '-lz', '-lm')
+
+        install_tree(self.stage.source_path, prefix.bin)
diff --git a/var/spack/repos/builtin/packages/windowswmproto/package.py b/var/spack/repos/builtin/packages/windowswmproto/package.py
index 70f1aae995..d893604996 100644
--- a/var/spack/repos/builtin/packages/windowswmproto/package.py
+++ b/var/spack/repos/builtin/packages/windowswmproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/wireshark/package.py b/var/spack/repos/builtin/packages/wireshark/package.py
new file mode 100644
index 0000000000..73640dc246
--- /dev/null
+++ b/var/spack/repos/builtin/packages/wireshark/package.py
@@ -0,0 +1,117 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import glob
+
+
+class Wireshark(CMakePackage):
+    """Graphical network analyzer and capture tool"""
+
+    homepage = "https://www.wireshark.org"
+    url      = "https://www.wireshark.org/download/src/all-versions/wireshark-2.6.0.tar.xz"
+
+    version('2.6.0', 'd9f9e206977da14427bfd66b582601ae')
+
+    variant('smi',      default=False, description='Build with libsmi')
+    variant('libssh',   default=False, description='Build with libssh')
+    variant('nghttp2',  default=False, description='Build with nghttp2')
+    variant('qt',       default=False, description='Build with qt')
+    variant('gtk3',     default=False, description='Build with gtk3')
+    variant('gtk',      default=False, description='Build with gtk')
+    variant('headers',  default=True, description='Install headers')
+
+    depends_on('bison',     type='build')
+    depends_on('cares')
+    depends_on('doxygen',   type='build')
+    depends_on('flex',      type='build')
+    depends_on('git',       type='build')
+    depends_on('glib')
+    depends_on('gnutls')
+    depends_on('libgcrypt@1.4.2:')
+    depends_on('libmaxminddb')
+    depends_on('libtool@2.2.2:', type='build')
+    depends_on('libpcap')
+    depends_on('lua@5.0.0:5.2.99')
+    depends_on('krb5')
+    depends_on('pkgconfig', type='build')
+    depends_on('libsmi',    when='+smi')
+    depends_on('libssh',    when='+libssh')
+    depends_on('nghttp2',   when='+nghttp2')
+    depends_on('portaudio', when='+gtk')
+    depends_on('portaudio', when='+gtk3')
+    depends_on('qt@4.8:',   when='+qt')
+    depends_on('gtkplus3',  when='+gtk3')
+    depends_on('gtkplus',   when='+gtk')
+    depends_on('adwaita-icon-theme', when='+gtk3')
+
+    def cmake_args(self):
+        args = ['-DENEABLE_CARES=ON',
+                '-DENABLE_GNUTLS=ON',
+                '-DENABLE_LUA=ON',
+                '-DENABLE_MAXMINDDB=ON',
+                '-DYACC_EXECUTABLE=' + self.spec['bison'].prefix.bin.yacc,
+                '-DGIT_EXECUTABLE=' + self.spec['git'].prefix.bin.git,
+                '-DPCAP_INCLUDE_DIR=' + self.spec['libpcap'].prefix.include,
+                '-DPCAP_LIB=' + str(self.spec['libpcap'].libs),
+                '-DLUA_INCLUDE_DIR=' + self.spec['lua'].prefix.include,
+                '-DLUA_LIBRARY=' + str(self.spec['lua'].libs)
+                ]
+        if self.spec.satisfies('+qt'):
+            args.append('-DBUILD_wireshark=ON')
+            args.append('-DENABLE_APPLICATION_BUNDLE=ON')
+            if self.spec['qt'].version >= Version(5):
+                args.append('-DENABLE_QT5=ON')
+            else:
+                args.append('-DENABLE_QT5=OFF')
+        else:
+            args.append('-DBUILD_wireshark=OFF')
+            args.append('-DENABLE_APPLICATION_BUNDLE=OFF')
+            args.append('-DENABLE_QT5=OFF')
+
+        if self.spec.satisfies('+gtk3') or self.spec.satisfies('+gtk'):
+            args.append('-DBUILD_wireshark_gtk=ON')
+            args.append('-DENABLE_PORTAUDIO=ON')
+        else:
+            args.append('-DBUILD_wireshark_gtk=OFF')
+            args.append('-DENABLE_PORTAUDIO=OFF')
+        if self.spec.satisfies('+gtk3'):
+            args.append('-DENABLE_GTK3=ON')
+
+        if self.spec.satisfies('+libssh'):
+            args.append('-DBUILD_sshdump=ON')
+            args.append('-DBUILD_ciscodump=ON')
+        else:
+            args.append('-DBUILD_sshdump=OFF')
+            args.append('-DBUILD_ciscodump=OFF')
+
+        if self.spec.satisfies('+smi'):
+            args.append('-DBUILD_SMI=ON')
+        else:
+            args.append('-DBUILD_SMI=OFF')
+
+        if self.spec.satisfies('+nghttp2'):
+            args.append('-DBUILD_NGHTTP2=ON')
+        else:
+            args.append('-DBUILD_NGHTTP2=OFF')
+
+        return args
+
+    @run_after('install')
+    def symlink(self):
+        if self.spec.satisfies('platform=darwin'):
+            link(join_path(self.prefix,
+                           'Wireshark.app/Contents/MacOS/Wireshark'),
+                 self.prefix.bin.wireshark)
+
+    @run_after('install')
+    def install_headers(self):
+        if self.spec.satisfies('+headers'):
+            folders = ['.', 'epan/crypt', 'epan/dfilter', 'epan/dissectors',
+                       'epan/ftypes', 'epan/wmem', 'wiretap', 'wsutil']
+            for folder in folders:
+                headers = glob.glob(join_path(folder, '*.h'))
+                for h in headers:
+                    install(h, join_path(prefix.include, 'wireshark', folder))
diff --git a/var/spack/repos/builtin/packages/workrave/add_time_header.patch b/var/spack/repos/builtin/packages/workrave/add_time_header.patch
new file mode 100644
index 0000000000..535b7356fe
--- /dev/null
+++ b/var/spack/repos/builtin/packages/workrave/add_time_header.patch
@@ -0,0 +1,12 @@
+diff --git a/backend/src/TimePred.hh b/backend/src/TimePred.hh
+index 187f0fc..99bf48c 100644
+--- a/backend/src/TimePred.hh
++++ b/backend/src/TimePred.hh
+@@ -26,6 +26,7 @@
+ #else
+ # if HAVE_SYS_TIME_H
+ #  include <sys/time.h>
++#  include <time.h>
+ # else
+ #  include <time.h>
+ # endif
diff --git a/var/spack/repos/builtin/packages/workrave/dont_get_widget.patch b/var/spack/repos/builtin/packages/workrave/dont_get_widget.patch
new file mode 100644
index 0000000000..de8076748c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/workrave/dont_get_widget.patch
@@ -0,0 +1,22 @@
+diff --git a/frontend/plugin/statistics/gtkmm/src/StatisticsDialog.cc b/frontend/plugin/statistics/gtkmm/src/StatisticsDialog.cc
+index ee7d56f..608fddb 100644
+--- a/frontend/plugin/statistics/gtkmm/src/StatisticsDialog.cc
++++ b/frontend/plugin/statistics/gtkmm/src/StatisticsDialog.cc
+@@ -604,7 +604,7 @@ StatisticsDialog::on_history_delete_all()
+         );
+     Gtk::MessageDialog mb_ask( *this, msg, true, Gtk::MESSAGE_WARNING, Gtk::BUTTONS_YES_NO, false );
+     mb_ask.set_title( _("Warning") );
+-    mb_ask.get_widget_for_response( Gtk::RESPONSE_NO )->grab_default();
++    //mb_ask.get_widget_for_response( Gtk::RESPONSE_NO )->grab_default();
+     if( mb_ask.run() == Gtk::RESPONSE_YES )
+     {
+         mb_ask.hide();
+@@ -630,7 +630,7 @@ StatisticsDialog::on_history_delete_all()
+                 );
+             Gtk::MessageDialog mb_error( *this, msg, true, Gtk::MESSAGE_ERROR, Gtk::BUTTONS_YES_NO, false );
+             mb_error.set_title( _("Error") );
+-            mb_error.get_widget_for_response( Gtk::RESPONSE_NO )->grab_default();
++            //mb_error.get_widget_for_response( Gtk::RESPONSE_NO )->grab_default();
+             if( mb_error.run() != Gtk::RESPONSE_YES )
+                 break;
+         }
diff --git a/var/spack/repos/builtin/packages/workrave/no_gettext.patch b/var/spack/repos/builtin/packages/workrave/no_gettext.patch
new file mode 100644
index 0000000000..ab440c0e11
--- /dev/null
+++ b/var/spack/repos/builtin/packages/workrave/no_gettext.patch
@@ -0,0 +1,29 @@
+diff --git a/configure.ac b/configure.ac
+index a8a437f..6128cd2 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -949,8 +949,8 @@ dnl
+ dnl Internationalization
+ dnl
+ 
+-AM_GNU_GETTEXT_VERSION([0.17])
+-AM_GNU_GETTEXT([external])
++dnl AM_GNU_GETTEXT_VERSION([0.17])
++dnl AM_GNU_GETTEXT([external])
+ 
+ dnl Hack because windows gettext package is SEVERELY broken...
+ if test "x$platform_os_win32" = "xyes"
+@@ -963,9 +963,10 @@ then
+         BUILD_INCLUDED_LIBINTL=no
+ fi
+ 
+-GETTEXT_PACKAGE=workrave
+-AC_SUBST(GETTEXT_PACKAGE)
+-AC_DEFINE_UNQUOTED(GETTEXT_PACKAGE, "$GETTEXT_PACKAGE", [Define to the gettext domain name.])
++dnl GETTEXT_PACKAGE=workrave
++dnl AC_SUBST(GETTEXT_PACKAGE)
++dnl AC_DEFINE_UNQUOTED(GETTEXT_PACKAGE, "$GETTEXT_PACKAGE", [Define to the gettext domain name.])
++AC_DEFINE_UNQUOTED(GETTEXT_PACKAGE,"$GETTEXT_PACKAGE", [Gettext package])
+ IT_PROG_INTLTOOL([0.40.0])
+ 
+ 
diff --git a/var/spack/repos/builtin/packages/workrave/package.py b/var/spack/repos/builtin/packages/workrave/package.py
new file mode 100644
index 0000000000..fdbc2607c1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/workrave/package.py
@@ -0,0 +1,85 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Workrave(AutotoolsPackage):
+    """Workrave is a program that assists in the recovery and prevention of
+       Repetitive Strain Injury (RSI). The program frequently alerts you to
+       take micro-pauses, rest breaks and restricts you to your daily limit.
+       The program runs on GNU/Linux and Microsoft Windows.
+    """
+
+    homepage = "http://www.workrave.org/"
+    url      = "https://github.com/rcaelers/workrave/archive/v1_10_20.tar.gz"
+
+    version('1_10_20', '095567c10311bd2c1a52f98035cc8590')
+    version('1_10_19', 'a87ed53d5b321133e8b6b98fd715507b')
+    version('1_10_18', 'd36c2aba0485116b831d5b36a862f343')
+    version('1_10_17', 'ba829bb2c0ec999b3194b4d845549c39')
+    version('1_10_16', 'b9bf77bfe0c909fff56759e7dda40f9d')
+    version('1_10_15', '4a70c2e325503249d1a40fcc236d6802')
+    version('1_10_14', '67108d993719d9438a1b69f0cb8fc9b8')
+    version('1_10_13', 'd5e7110dfb0b0a31c909405913ac2a75')
+    version('1_10_12', '0bfbaa1dc35901ffa8f1a3676421a992')
+    version('1_10_10', 'cf827672c8a1ece074f8ddfcf73d0fe2')
+
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool',  type='build')
+    depends_on('m4',       type='build')
+
+    depends_on('libx11')
+    depends_on('py-cheetah')
+    depends_on('glib')
+    depends_on('glibmm')
+    depends_on('gtkplus')
+    depends_on('gtkmm@2.17.1')
+    depends_on('libsigcpp')
+
+    # adds #include <time.h> to a workrave test
+    patch('add_time_header.patch')
+
+    # removes call to missing gtkmm api function
+    patch('dont_get_widget.patch')
+
+    # removes gettext which canot be use with intltool
+    # https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=724555
+    # https://bugzilla.gnome.org/show_bug.cgi?id=708673#c4
+    patch('no_gettext.patch')
+
+    # add a couple m4 macros used during autoreconf
+    # https://github.com/rcaelers/workrave/issues/95
+    m4files = ['ax_cxx_compile_stdcxx_11', 'ax_cxx_compile_stdcxx']
+    resource(name=m4files[0],
+             url='http://git.savannah.gnu.org/gitweb/?p=autoconf-archive.git;a=blob_plain;f=m4/ax_cxx_compile_stdcxx_11.m4',
+             sha256='d75fc9fe4502eea02e8c5bfb61b88a04cd08aa6d5bd757fe66e9a9a1e4781b46',
+             expand=False,
+             destination='',
+             placement=m4files[0])
+    resource(name=m4files[1],
+             url='http://git.savannah.gnu.org/gitweb/?p=autoconf-archive.git;a=blob_plain;f=m4/ax_cxx_compile_stdcxx.m4',
+             sha256='0c08d2f64147f65eb7e255019102c1042ab695c60fd49add19793951a1279a1a',
+             expand=False,
+             destination='',
+             placement=m4files[1])
+
+    def setup_environment(self, build_env, run_env):
+        # unset PYTHONHOME to let system python script with explict
+        # system python sbangs like glib-mkenums work, see #6968
+        # Without this, we will get
+        # ImportError: No module named site
+        # during build phase when make runs glib-mkenums
+        build_env.unset('PYTHONHOME')
+
+    @run_before('autoreconf')
+    def extra_m4(self):
+        # move m4 macros, which we added with the resource() directive,
+        # to the m4 directory, where aclocal will pick them up
+        for fname in self.m4files:
+            src = '%s/%s/%s.m4' % (self.stage.source_path, fname, fname)
+            dest = '%s/m4/%s.m4' % (self.stage.source_path, fname)
+            copy(src, dest)
diff --git a/var/spack/repos/builtin/packages/wt/package.py b/var/spack/repos/builtin/packages/wt/package.py
index 36eefdf2c0..991a3fdc9f 100644
--- a/var/spack/repos/builtin/packages/wt/package.py
+++ b/var/spack/repos/builtin/packages/wt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,11 +12,11 @@ class Wt(CMakePackage):
     Wt is a C++ library for developing web applications."""
 
     homepage = "http://www.webtoolkit.eu/wt"
-    url = "https://github.com/emweb/wt/archive/3.3.7.tar.gz"
+    url      = "https://github.com/emweb/wt/archive/3.3.7.tar.gz"
+    git      = "https://github.com/emweb/wt.git"
 
+    version('master', branch='master')
     version('3.3.7', '09858901f2dcf5c3d36a9237daba3e3f')
-    version('master', branch='master',
-            git='https://github.com/emweb/wt.git')
 
     # wt builds in parallel, but requires more than 5 GByte RAM per -j <njob>
     # which most machines do not provide and crash the build
diff --git a/var/spack/repos/builtin/packages/wx/math_include.patch b/var/spack/repos/builtin/packages/wx/math_include.patch
new file mode 100644
index 0000000000..152f095d18
--- /dev/null
+++ b/var/spack/repos/builtin/packages/wx/math_include.patch
@@ -0,0 +1,12 @@
+diff --git a/src/stc/scintilla/src/Editor.cxx b/src/stc/scintilla/src/Editor.cxx
+index cd72953ae7..8c19154313 100644
+--- a/src/stc/scintilla/src/Editor.cxx
++++ b/src/stc/scintilla/src/Editor.cxx
+@@ -10,6 +10,7 @@
+ #include <stdio.h>
+ #include <ctype.h>
+ #include <assert.h>
++#include <math.h>
+
+ #include <string>
+ #include <vector>
diff --git a/var/spack/repos/builtin/packages/wx/package.py b/var/spack/repos/builtin/packages/wx/package.py
index fc42b5153f..284dab072c 100644
--- a/var/spack/repos/builtin/packages/wx/package.py
+++ b/var/spack/repos/builtin/packages/wx/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import sys
 
@@ -35,16 +16,19 @@ class Wx(AutotoolsPackage):
        native look and feel because it uses the platform's native API
        rather than emulating the GUI. It's also extensive, free,
        open-source and mature."""
+
     homepage = "http://www.wxwidgets.org/"
     url      = "https://github.com/wxWidgets/wxWidgets/releases/download/v3.1.0/wxWidgets-3.1.0.tar.bz2"
+    git      = "https://github.com/wxWidgets/wxWidgets.git"
 
+    version('develop', branch='master')
     version('3.1.0', '2170839cfa9d9322e8ee8368b21a15a2497b4f11')
     version('3.0.2', '6461eab4428c0a8b9e41781b8787510484dea800')
     version('3.0.1', '73e58521d6871c9f4d1e7974c6e3a81629fddcf8')
 
-    version('develop', git='https://github.com/wxWidgets/wxWidgets.git', branch='master')
+    patch('math_include.patch', when='@3.0.1:3.0.2')
 
-    depends_on('pkg-config', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('gtkplus')
 
     @when('@:3.0.2')
diff --git a/var/spack/repos/builtin/packages/wxpropgrid/package.py b/var/spack/repos/builtin/packages/wxpropgrid/package.py
index 7df30895fc..090655f67a 100644
--- a/var/spack/repos/builtin/packages/wxpropgrid/package.py
+++ b/var/spack/repos/builtin/packages/wxpropgrid/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/x11perf/package.py b/var/spack/repos/builtin/packages/x11perf/package.py
index b5a2e9344b..a52dcfc90b 100644
--- a/var/spack/repos/builtin/packages/x11perf/package.py
+++ b/var/spack/repos/builtin/packages/x11perf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class X11perf(AutotoolsPackage):
     depends_on('libxft')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xapian-core/package.py b/var/spack/repos/builtin/packages/xapian-core/package.py
index 8ea340a55a..c36e4e61fc 100644
--- a/var/spack/repos/builtin/packages/xapian-core/package.py
+++ b/var/spack/repos/builtin/packages/xapian-core/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/xauth/package.py b/var/spack/repos/builtin/packages/xauth/package.py
index ac02ba48b9..d247edc968 100644
--- a/var/spack/repos/builtin/packages/xauth/package.py
+++ b/var/spack/repos/builtin/packages/xauth/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,7 +21,7 @@ class Xauth(AutotoolsPackage):
     depends_on('libxmu')
 
     depends_on('xproto@7.0.17:')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     # TODO: add package for cmdtest test dependency
diff --git a/var/spack/repos/builtin/packages/xbacklight/package.py b/var/spack/repos/builtin/packages/xbacklight/package.py
index 2f4057ee80..e2cc57cb17 100644
--- a/var/spack/repos/builtin/packages/xbacklight/package.py
+++ b/var/spack/repos/builtin/packages/xbacklight/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Xbacklight(AutotoolsPackage):
     depends_on('libxcb')
     depends_on('xcb-util')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xbiff/package.py b/var/spack/repos/builtin/packages/xbiff/package.py
index 7d85e59fbf..19315e792b 100644
--- a/var/spack/repos/builtin/packages/xbiff/package.py
+++ b/var/spack/repos/builtin/packages/xbiff/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -41,5 +22,5 @@ class Xbiff(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xbitmaps', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xbitmaps/package.py b/var/spack/repos/builtin/packages/xbitmaps/package.py
index 6282ce7041..86823338b7 100644
--- a/var/spack/repos/builtin/packages/xbitmaps/package.py
+++ b/var/spack/repos/builtin/packages/xbitmaps/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,5 +15,5 @@ class Xbitmaps(AutotoolsPackage):
 
     version('1.1.1', '288bbe310db67280a9e2e5ebc5602595')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xbraid/package.py b/var/spack/repos/builtin/packages/xbraid/package.py
new file mode 100644
index 0000000000..81d85c401a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/xbraid/package.py
@@ -0,0 +1,54 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import glob
+import os.path
+
+
+class Xbraid(MakefilePackage):
+    """XBraid: Parallel time integration with Multigrid"""
+
+    homepage = "https://computation.llnl.gov/projects/parallel-time-integration-multigrid/software"
+    url      = "https://computation.llnl.gov/projects/parallel-time-integration-multigrid/download/braid_2.2.0.tar.gz"
+
+    version('2.2.0', '0a9c2fc3eb8f605f73cce78ab0d8a7d9')
+
+    depends_on('mpi')
+
+    def build(self, spec, prefix):
+        make('libbraid.a')
+
+    # XBraid doesn't have a real install target, so it has to be done
+    # manually
+    def install(self, spec, prefix):
+        # Install headers
+        mkdirp(prefix.include)
+        headers = glob.glob('*.h')
+        for f in headers:
+            install(f, join_path(prefix.include, os.path.basename(f)))
+
+        # Install library
+        mkdirp(prefix.lib)
+        library = 'libbraid.a'
+        install(library, join_path(prefix.lib, library))
+
+        # Install other material (e.g., examples, tests, docs)
+        mkdirp(prefix.share)
+        install('makefile.inc', prefix.share)
+        install_tree('examples', prefix.share.examples)
+        install_tree('drivers', prefix.share.drivers)
+
+        # TODO: Some of the scripts in 'test' are useful, even for
+        # users; some could be deleted from an installation because
+        # they're not useful to users
+        install_tree('test', prefix.share.test)
+        install_tree('user_utils', prefix.share.user_utils)
+        install_tree('docs', prefix.share.docs)
+
+    @property
+    def libs(self):
+        return find_libraries('libbraid', root=self.prefix,
+                              shared=False, recursive=True)
diff --git a/var/spack/repos/builtin/packages/xcalc/package.py b/var/spack/repos/builtin/packages/xcalc/package.py
index 5218ecac99..2ee66d7b98 100644
--- a/var/spack/repos/builtin/packages/xcalc/package.py
+++ b/var/spack/repos/builtin/packages/xcalc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Xcalc(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xcb-demo/package.py b/var/spack/repos/builtin/packages/xcb-demo/package.py
index 7a2c2f65f4..421d97dbb7 100644
--- a/var/spack/repos/builtin/packages/xcb-demo/package.py
+++ b/var/spack/repos/builtin/packages/xcb-demo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class XcbDemo(AutotoolsPackage):
     depends_on('xcb-util-image')
     depends_on('xcb-util-wm')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
 
     # FIXME: crashes with the following error message
     # X11/XCB/xcb.h: No such file or directory
diff --git a/var/spack/repos/builtin/packages/xcb-proto/package.py b/var/spack/repos/builtin/packages/xcb-proto/package.py
index 9cb2480b17..ed9667f7c1 100644
--- a/var/spack/repos/builtin/packages/xcb-proto/package.py
+++ b/var/spack/repos/builtin/packages/xcb-proto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,12 +11,14 @@ class XcbProto(AutotoolsPackage):
     generate the majority of its code and API."""
 
     homepage = "http://xcb.freedesktop.org/"
-    url      = "http://xcb.freedesktop.org/dist/xcb-proto-1.11.tar.gz"
+    url      = "http://xcb.freedesktop.org/dist/xcb-proto-1.13.tar.gz"
 
+    version('1.13', '0cc0294eb97e4af3a743e470e6a9d910')
     version('1.12', '5ee1ec124ea8d56bd9e83b8e9e0b84c4')
     version('1.11', 'c8c6cb72c84f58270f4db1f39607f66a')
 
     # TODO: uncomment once build deps can be resolved separately
+    # See #7646, #4145, #4063, and #2548 for details
     # extends('python')
 
     patch('xcb-proto-1.12-schema-1.patch', when='@1.12')
diff --git a/var/spack/repos/builtin/packages/xcb-util-cursor/package.py b/var/spack/repos/builtin/packages/xcb-util-cursor/package.py
index 64faa37207..2e79d358ac 100644
--- a/var/spack/repos/builtin/packages/xcb-util-cursor/package.py
+++ b/var/spack/repos/builtin/packages/xcb-util-cursor/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -42,4 +23,4 @@ class XcbUtilCursor(AutotoolsPackage):
     depends_on('xcb-util-renderutil')
     depends_on('xcb-util-image')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
diff --git a/var/spack/repos/builtin/packages/xcb-util-errors/package.py b/var/spack/repos/builtin/packages/xcb-util-errors/package.py
index 07aa424ddc..ca2b68af00 100644
--- a/var/spack/repos/builtin/packages/xcb-util-errors/package.py
+++ b/var/spack/repos/builtin/packages/xcb-util-errors/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -41,4 +22,4 @@ class XcbUtilErrors(AutotoolsPackage):
     depends_on('libxcb@1.4:')
 
     depends_on('xcb-proto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
diff --git a/var/spack/repos/builtin/packages/xcb-util-image/package.py b/var/spack/repos/builtin/packages/xcb-util-image/package.py
index a9f2f2263a..99eaea5d9b 100644
--- a/var/spack/repos/builtin/packages/xcb-util-image/package.py
+++ b/var/spack/repos/builtin/packages/xcb-util-image/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -42,4 +23,4 @@ class XcbUtilImage(AutotoolsPackage):
     depends_on('xcb-util')
 
     depends_on('xproto@7.0.8:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
diff --git a/var/spack/repos/builtin/packages/xcb-util-keysyms/package.py b/var/spack/repos/builtin/packages/xcb-util-keysyms/package.py
index 3901624e9a..11becf0611 100644
--- a/var/spack/repos/builtin/packages/xcb-util-keysyms/package.py
+++ b/var/spack/repos/builtin/packages/xcb-util-keysyms/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -41,4 +22,4 @@ class XcbUtilKeysyms(AutotoolsPackage):
     depends_on('libxcb@1.4:')
 
     depends_on('xproto@7.0.8:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
diff --git a/var/spack/repos/builtin/packages/xcb-util-renderutil/package.py b/var/spack/repos/builtin/packages/xcb-util-renderutil/package.py
index e9a325e83c..66500d4e6a 100644
--- a/var/spack/repos/builtin/packages/xcb-util-renderutil/package.py
+++ b/var/spack/repos/builtin/packages/xcb-util-renderutil/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,4 +21,4 @@ class XcbUtilRenderutil(AutotoolsPackage):
 
     depends_on('libxcb@1.4:')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
diff --git a/var/spack/repos/builtin/packages/xcb-util-wm/package.py b/var/spack/repos/builtin/packages/xcb-util-wm/package.py
index 5d9a5e3932..65e7a1de8a 100644
--- a/var/spack/repos/builtin/packages/xcb-util-wm/package.py
+++ b/var/spack/repos/builtin/packages/xcb-util-wm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,4 +21,4 @@ class XcbUtilWm(AutotoolsPackage):
 
     depends_on('libxcb@1.4:')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
diff --git a/var/spack/repos/builtin/packages/xcb-util-xrm/package.py b/var/spack/repos/builtin/packages/xcb-util-xrm/package.py
new file mode 100644
index 0000000000..ceb6aec837
--- /dev/null
+++ b/var/spack/repos/builtin/packages/xcb-util-xrm/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class XcbUtilXrm(AutotoolsPackage):
+    """XCB util-xrm module provides the 'xrm' library, i.e.  utility functions
+    for the X resource manager."""
+
+    homepage = "https://github.com/Airblader/xcb-util-xrm"
+    git      = "https://github.com/Airblader/xcb-util-xrm.git"
+
+    # This GitHub project includes some git submodules, which must be fetched
+    # in order to build it.
+    version('1.2', tag='v1.2', submodules=True)
+
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool',  type='build')
+    depends_on('m4',       type='build')
+    depends_on('pkgconfig', type='build')
+
+    depends_on('libxcb@1.4:')
diff --git a/var/spack/repos/builtin/packages/xcb-util/package.py b/var/spack/repos/builtin/packages/xcb-util/package.py
index c8ac0d40ab..e8526b962f 100644
--- a/var/spack/repos/builtin/packages/xcb-util/package.py
+++ b/var/spack/repos/builtin/packages/xcb-util/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,4 +21,4 @@ class XcbUtil(AutotoolsPackage):
 
     depends_on('libxcb@1.4:')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
diff --git a/var/spack/repos/builtin/packages/xclip/package.py b/var/spack/repos/builtin/packages/xclip/package.py
index d685d1f07c..a18a8bf7ae 100644
--- a/var/spack/repos/builtin/packages/xclip/package.py
+++ b/var/spack/repos/builtin/packages/xclip/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,9 +15,9 @@ class Xclip(AutotoolsPackage):
        which can then be redirected to a file or another program."""
 
     homepage = "https://github.com/astrand/xclip"
-    url      = "https://github.com/astrand/xclip"
+    git      = "https://github.com/astrand/xclip.git"
 
-    version('0.13', git='https://github.com/astrand/xclip', commit='9aa7090c3b8b437c6489edca32ae43d82e0c1281')
+    version('0.13', commit='9aa7090c3b8b437c6489edca32ae43d82e0c1281')
 
     depends_on('libxmu')
     depends_on('libx11')
diff --git a/var/spack/repos/builtin/packages/xclipboard/package.py b/var/spack/repos/builtin/packages/xclipboard/package.py
index bad81a9a96..a4917f3055 100644
--- a/var/spack/repos/builtin/packages/xclipboard/package.py
+++ b/var/spack/repos/builtin/packages/xclipboard/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -43,5 +24,5 @@ class Xclipboard(AutotoolsPackage):
     depends_on('libxkbfile')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xclock/package.py b/var/spack/repos/builtin/packages/xclock/package.py
index 47614e50e1..15cbcc2ba4 100644
--- a/var/spack/repos/builtin/packages/xclock/package.py
+++ b/var/spack/repos/builtin/packages/xclock/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -44,5 +25,5 @@ class Xclock(AutotoolsPackage):
     depends_on('libxt')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xcmiscproto/package.py b/var/spack/repos/builtin/packages/xcmiscproto/package.py
index 92c1b886a5..f478a2fe9f 100644
--- a/var/spack/repos/builtin/packages/xcmiscproto/package.py
+++ b/var/spack/repos/builtin/packages/xcmiscproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Xcmiscproto(AutotoolsPackage):
 
     version('1.2.2', 'ded6cd23fb2800df93ebf2b3f3b01119')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xcmsdb/package.py b/var/spack/repos/builtin/packages/xcmsdb/package.py
index b59a254262..0be4808cd8 100644
--- a/var/spack/repos/builtin/packages/xcmsdb/package.py
+++ b/var/spack/repos/builtin/packages/xcmsdb/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Xcmsdb(AutotoolsPackage):
 
     depends_on('libx11')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xcompmgr/package.py b/var/spack/repos/builtin/packages/xcompmgr/package.py
index dc8aa398b1..3af77c565a 100644
--- a/var/spack/repos/builtin/packages/xcompmgr/package.py
+++ b/var/spack/repos/builtin/packages/xcompmgr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -41,5 +22,5 @@ class Xcompmgr(AutotoolsPackage):
     depends_on('libxrender')
     depends_on('libxext')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xconsole/package.py b/var/spack/repos/builtin/packages/xconsole/package.py
index 2c130091d3..519d7447b5 100644
--- a/var/spack/repos/builtin/packages/xconsole/package.py
+++ b/var/spack/repos/builtin/packages/xconsole/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,5 +21,5 @@ class Xconsole(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xproto@7.0.17:')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xcursor-themes/package.py b/var/spack/repos/builtin/packages/xcursor-themes/package.py
index 112d63c274..4b0eaa7234 100644
--- a/var/spack/repos/builtin/packages/xcursor-themes/package.py
+++ b/var/spack/repos/builtin/packages/xcursor-themes/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class XcursorThemes(Package):
     depends_on('libxcursor')
 
     depends_on('xcursorgen', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/xcursorgen/package.py b/var/spack/repos/builtin/packages/xcursorgen/package.py
index c2b808b0af..5751365007 100644
--- a/var/spack/repos/builtin/packages/xcursorgen/package.py
+++ b/var/spack/repos/builtin/packages/xcursorgen/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Xcursorgen(AutotoolsPackage):
     depends_on('libxcursor')
     depends_on('libpng@1.2.0:')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xdbedizzy/package.py b/var/spack/repos/builtin/packages/xdbedizzy/package.py
index 9e21e54ca6..053c7e9954 100644
--- a/var/spack/repos/builtin/packages/xdbedizzy/package.py
+++ b/var/spack/repos/builtin/packages/xdbedizzy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Xdbedizzy(AutotoolsPackage):
     depends_on('libx11')
     depends_on('libxext')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xditview/package.py b/var/spack/repos/builtin/packages/xditview/package.py
index 5111de58af..c8c5294df1 100644
--- a/var/spack/repos/builtin/packages/xditview/package.py
+++ b/var/spack/repos/builtin/packages/xditview/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Xditview(AutotoolsPackage):
     depends_on('libxt')
     depends_on('libx11')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xdm/package.py b/var/spack/repos/builtin/packages/xdm/package.py
index 8f1b544f6d..90cdaeb0a6 100644
--- a/var/spack/repos/builtin/packages/xdm/package.py
+++ b/var/spack/repos/builtin/packages/xdm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -44,5 +25,5 @@ class Xdm(AutotoolsPackage):
     depends_on('libxt')
     depends_on('libxext')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xdpyinfo/package.py b/var/spack/repos/builtin/packages/xdpyinfo/package.py
index ab5935b474..bc4259a1ba 100644
--- a/var/spack/repos/builtin/packages/xdpyinfo/package.py
+++ b/var/spack/repos/builtin/packages/xdpyinfo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -47,5 +28,5 @@ class Xdpyinfo(AutotoolsPackage):
     depends_on('recordproto', type='build')
     depends_on('inputproto', type='build')
     depends_on('fixesproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xdriinfo/package.py b/var/spack/repos/builtin/packages/xdriinfo/package.py
index 86645072c0..ed58cdb505 100644
--- a/var/spack/repos/builtin/packages/xdriinfo/package.py
+++ b/var/spack/repos/builtin/packages/xdriinfo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -42,5 +23,5 @@ class Xdriinfo(AutotoolsPackage):
     depends_on('pcre')
 
     depends_on('glproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xedit/package.py b/var/spack/repos/builtin/packages/xedit/package.py
index 752fbf61d5..de2a345cfb 100644
--- a/var/spack/repos/builtin/packages/xedit/package.py
+++ b/var/spack/repos/builtin/packages/xedit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Xedit(AutotoolsPackage):
     depends_on('libxt@1.0:')
     depends_on('libx11')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xerces-c/package.py b/var/spack/repos/builtin/packages/xerces-c/package.py
index 3e832784f8..a316e14d30 100644
--- a/var/spack/repos/builtin/packages/xerces-c/package.py
+++ b/var/spack/repos/builtin/packages/xerces-c/package.py
@@ -1,28 +1,10 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
+import sys
 
 
 class XercesC(AutotoolsPackage):
@@ -33,9 +15,58 @@ class XercesC(AutotoolsPackage):
     APIs."""
 
     homepage = "https://xerces.apache.org/xerces-c"
-    url      = "https://archive.apache.org/dist/xerces/c/3/sources/xerces-c-3.1.4.tar.bz2"
+    url      = "https://archive.apache.org/dist/xerces/c/3/sources/xerces-c-3.2.1.tar.bz2"
 
+    version('3.2.2', '4c395216ecbef3c88a756ff4090e6f7e')
+    version('3.2.1', '8f98a81a3589bbc2dad9837452f7d319')
     version('3.1.4', 'd04ae9d8b2dee2157c6db95fa908abfd')
 
+    # It's best to be explicit about the transcoder or else xerces may
+    # choose another value.
+    if sys.platform == 'darwin':
+        default_transcoder = 'macos'
+    elif sys.platform.startswith('win') or sys.platform == 'cygwin':
+        default_transcoder = 'windows'
+    else:
+        default_transcoder = 'gnuiconv'
+
+    variant('transcoder', default=default_transcoder,
+            values=('gnuiconv', 'iconv', 'icu', 'macos', 'windows'),
+            multi=False,
+            description='Use the specified transcoder')
+
+    depends_on('libiconv', type='link', when='transcoder=gnuiconv')
+    depends_on('icu4c',    type='link', when='transcoder=icu')
+
+    # Pass flags to configure.  This is necessary for CXXFLAGS or else
+    # the xerces default will override the spack wrapper.
+    def flag_handler(self, name, flags):
+        spec = self.spec
+
+        # There is no --with-pkg for gnuiconv.
+        if name == 'ldflags' and 'transcoder=gnuiconv' in spec:
+            flags.append(spec['libiconv'].libs.ld_flags)
+
+        return (None, None, flags)
+
     def configure_args(self):
-        return ['--disable-network']
+        spec = self.spec
+        args = ['--disable-network']
+
+        if 'transcoder=gnuiconv' in spec:
+            args.append('--enable-transcoder-gnuiconv')
+
+        if 'transcoder=iconv' in spec:
+            args.append('--enable-transcoder-iconv')
+
+        if 'transcoder=icu' in spec:
+            args.append('--enable-transcoder-icu')
+            args.append('--with-icu=%s' % spec['icu4c'].prefix)
+
+        if 'transcoder=macos' in spec:
+            args.append('--enable-transcoder-macosunicodeconverter')
+
+        if 'transcoder=windows' in spec:
+            args.append('--enable-transcoder-windows')
+
+        return args
diff --git a/var/spack/repos/builtin/packages/xeus/cmake_find_cryptopp_and_check_cxx_compatibility.patch b/var/spack/repos/builtin/packages/xeus/cmake_find_cryptopp_and_check_cxx_compatibility.patch
new file mode 100644
index 0000000000..da19f84134
--- /dev/null
+++ b/var/spack/repos/builtin/packages/xeus/cmake_find_cryptopp_and_check_cxx_compatibility.patch
@@ -0,0 +1,52 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 810d5d1..d6ba3e9 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -49,7 +49,33 @@ message(STATUS "xeus binary version: v${XEUS_BINARY_VERSION}")
+ find_package(nlohmann_json 3.2.0 REQUIRED)
+ find_package(xtl 0.4 REQUIRED)
+ find_package(cppzmq 4.3.0 REQUIRED)
+-find_package(cryptopp REQUIRED)
++
++# cryptopp isn't built with cmake, find it manually
++find_path(cryptopp_ROOT_DIR
++  NAMES include/cryptopp/cryptlib.h
++  PATHS ENV cryptopp_ROOT)
++
++find_path(cryptopp_INCLUDE_DIR
++  NAMES cryptopp/cryptlib.h
++  HINTS ${cryptopp_ROOT_DIR}
++  PATH_SUFFIXES include)
++
++find_library(cryptopp_STATIC_LIB
++  NAMES libcryptopp.a
++  HINTS ${cryptopp_ROOT_DIR}
++  PATH_SUFFIXES lib)
++
++if (NOT cryptopp_INCLUDE_DIR OR NOT cryptopp_STATIC_LIB)
++  message(FATAL_ERROR "cannot find cryptopp, missing include dir or static lib")
++else()
++  message("Found cryptopp: ${cryptopp_ROOT_DIR}")
++endif()
++
++add_library(cryptopp-static STATIC IMPORTED)
++set_target_properties(cryptopp-static
++  PROPERTIES
++    IMPORTED_LOCATION ${cryptopp_STATIC_LIB}
++    INTERFACE_INCLUDE_DIRECTORIES ${cryptopp_INCLUDE_DIR})
+ 
+ # On Unix platforms, ZeroMQ is built with autotools and pkg-config is
+ # required to locate it.
+@@ -157,10 +183,11 @@ get_target_property(cryptopp_INCLUDE_DIR cryptopp-static INTERFACE_INCLUDE_DIREC
+ get_target_property(cryptopp_LIBRARY cryptopp-static LOCATION)
+ set(CMAKE_REQUIRED_LIBRARIES ${cryptopp_LIBRARY})
+ set(CMAKE_REQUIRED_INCLUDES ${cryptopp_INCLUDE_DIR})
++set(CMAKE_REQUIRED_FLAGS "--std=c++11")
+ check_cxx_source_compiles("
+ #include \"cryptopp/config.h\"
+ int main(){
+-  [[maybe_unused]] CryptoPP::byte b = CryptoPP::byte{0x36};
++  CryptoPP::byte b = CryptoPP::byte{0x36};
+ }" HAVE_CRYPTOPP_BYTE_T)
+ 
+ cmake_pop_check_state()
diff --git a/var/spack/repos/builtin/packages/xeus/package.py b/var/spack/repos/builtin/packages/xeus/package.py
new file mode 100644
index 0000000000..1b1286666c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/xeus/package.py
@@ -0,0 +1,44 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Xeus(CMakePackage):
+    """QuantStack C++ implementation of Jupyter kernel protocol"""
+
+    homepage = "https://xeus.readthedocs.io/en/latest/"
+    url      = "https://github.com/QuantStack/xeus/archive/0.14.1.tar.gz"
+    git      = "https://github.com/QuantStack/xeus.git"
+
+    version('develop', branch='master')
+    version('0.15.0', sha256='bc99235b24d5757dc129f3ed531501fb0d0667913927ed39ee24281952649183')
+    version('0.14.1', sha256='a6815845d4522ec279f142d3b4e92ef52cd80847b512146a65f256a77e058cfe')
+
+    variant('examples', default=False, description="Build examples")
+
+    conflicts('%gcc@:4.8')
+    conflicts('%clang@:3.6')
+    conflicts('%intel@:17')
+
+    depends_on('zeromq@4.2.5:-libsodium')
+    depends_on('cppzmq@4.3.0:')
+    depends_on('cryptopp@7.0.0:')
+    depends_on('xtl@0.4.0:')
+    depends_on('nlohmann-json@3.2.0', when='@develop@0.15.0:')
+    depends_on('nlohmann-json@3.1.1', when='@0.14.1')
+    depends_on('libuuid')
+
+    # finds cryptopp not built with cmake, removes c++17 attribute
+    # in check_cxx_source_compiles
+    patch('cmake_find_cryptopp_and_check_cxx_compatibility.patch')
+
+    def cmake_args(self):
+        args = [
+            '-DBUILD_EXAMPLES:BOOL=%s' % (
+                'ON' if '+examples' in self.spec else 'OFF')
+        ]
+
+        return args
diff --git a/var/spack/repos/builtin/packages/xev/package.py b/var/spack/repos/builtin/packages/xev/package.py
index fbccb0e103..94b7802885 100644
--- a/var/spack/repos/builtin/packages/xev/package.py
+++ b/var/spack/repos/builtin/packages/xev/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -43,5 +24,5 @@ class Xev(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xextproto/package.py b/var/spack/repos/builtin/packages/xextproto/package.py
index d02c1935c2..dbb83e13dc 100644
--- a/var/spack/repos/builtin/packages/xextproto/package.py
+++ b/var/spack/repos/builtin/packages/xextproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,7 +14,7 @@ class Xextproto(AutotoolsPackage):
 
     version('7.3.0', '37b700baa8c8ea7964702d948dd13821')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     parallel = False
diff --git a/var/spack/repos/builtin/packages/xeyes/package.py b/var/spack/repos/builtin/packages/xeyes/package.py
index 232f46212b..2487ecf8df 100644
--- a/var/spack/repos/builtin/packages/xeyes/package.py
+++ b/var/spack/repos/builtin/packages/xeyes/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Xeyes(AutotoolsPackage):
     depends_on('libxmu')
     depends_on('libxrender@0.4:')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xf86bigfontproto/package.py b/var/spack/repos/builtin/packages/xf86bigfontproto/package.py
index 4a1315b617..212c8a9072 100644
--- a/var/spack/repos/builtin/packages/xf86bigfontproto/package.py
+++ b/var/spack/repos/builtin/packages/xf86bigfontproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/xf86dga/package.py b/var/spack/repos/builtin/packages/xf86dga/package.py
index 3768fced15..ec4ff65565 100644
--- a/var/spack/repos/builtin/packages/xf86dga/package.py
+++ b/var/spack/repos/builtin/packages/xf86dga/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Xf86dga(AutotoolsPackage):
     depends_on('libx11')
     depends_on('libxxf86dga@1.1:')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xf86dgaproto/package.py b/var/spack/repos/builtin/packages/xf86dgaproto/package.py
index 88cd07c286..b42c3bdb8d 100644
--- a/var/spack/repos/builtin/packages/xf86dgaproto/package.py
+++ b/var/spack/repos/builtin/packages/xf86dgaproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/xf86driproto/package.py b/var/spack/repos/builtin/packages/xf86driproto/package.py
index 4877440649..16403e2b93 100644
--- a/var/spack/repos/builtin/packages/xf86driproto/package.py
+++ b/var/spack/repos/builtin/packages/xf86driproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Xf86driproto(AutotoolsPackage):
 
     version('2.1.1', '3ba16a48d8d9f9f746f9bd281ba8fb3f')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xf86miscproto/package.py b/var/spack/repos/builtin/packages/xf86miscproto/package.py
index 60e1db78bf..67c46f15f3 100644
--- a/var/spack/repos/builtin/packages/xf86miscproto/package.py
+++ b/var/spack/repos/builtin/packages/xf86miscproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/xf86rushproto/package.py b/var/spack/repos/builtin/packages/xf86rushproto/package.py
index 6b29e07c6a..3c9b0cf66c 100644
--- a/var/spack/repos/builtin/packages/xf86rushproto/package.py
+++ b/var/spack/repos/builtin/packages/xf86rushproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/xf86vidmodeproto/package.py b/var/spack/repos/builtin/packages/xf86vidmodeproto/package.py
index f8ce028474..993d203ecc 100644
--- a/var/spack/repos/builtin/packages/xf86vidmodeproto/package.py
+++ b/var/spack/repos/builtin/packages/xf86vidmodeproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Xf86vidmodeproto(AutotoolsPackage):
 
     version('2.3.1', '99016d0fe355bae0bb23ce00fb4d4a2c')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xfd/package.py b/var/spack/repos/builtin/packages/xfd/package.py
index 024f8ce141..ddec96e7a7 100644
--- a/var/spack/repos/builtin/packages/xfd/package.py
+++ b/var/spack/repos/builtin/packages/xfd/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -42,5 +23,5 @@ class Xfd(AutotoolsPackage):
     depends_on('libxt')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xfindproxy/package.py b/var/spack/repos/builtin/packages/xfindproxy/package.py
index fc12753133..d01aaf633b 100644
--- a/var/spack/repos/builtin/packages/xfindproxy/package.py
+++ b/var/spack/repos/builtin/packages/xfindproxy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -43,5 +24,5 @@ class Xfindproxy(AutotoolsPackage):
 
     depends_on('xproto', type='build')
     depends_on('xproxymanagementprotocol', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xfontsel/package.py b/var/spack/repos/builtin/packages/xfontsel/package.py
index 2a615216d5..babdee0cf7 100644
--- a/var/spack/repos/builtin/packages/xfontsel/package.py
+++ b/var/spack/repos/builtin/packages/xfontsel/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,5 +21,5 @@ class Xfontsel(AutotoolsPackage):
     depends_on('libxt')
     depends_on('libx11')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xfs/package.py b/var/spack/repos/builtin/packages/xfs/package.py
index 6846c320e2..f831cdf2b4 100644
--- a/var/spack/repos/builtin/packages/xfs/package.py
+++ b/var/spack/repos/builtin/packages/xfs/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Xfs(AutotoolsPackage):
     depends_on('xproto@7.0.17:', type='build')
     depends_on('fontsproto', type='build')
     depends_on('xtrans', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xfsinfo/package.py b/var/spack/repos/builtin/packages/xfsinfo/package.py
index 8f8ec13247..cf318828c2 100644
--- a/var/spack/repos/builtin/packages/xfsinfo/package.py
+++ b/var/spack/repos/builtin/packages/xfsinfo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,5 +21,5 @@ class Xfsinfo(AutotoolsPackage):
     depends_on('libfs')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xfwp/package.py b/var/spack/repos/builtin/packages/xfwp/package.py
index b0c8fa9158..da418e6396 100644
--- a/var/spack/repos/builtin/packages/xfwp/package.py
+++ b/var/spack/repos/builtin/packages/xfwp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,7 +18,7 @@ class Xfwp(AutotoolsPackage):
 
     depends_on('xproto', type='build')
     depends_on('xproxymanagementprotocol', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     # FIXME: fails with the error message:
diff --git a/var/spack/repos/builtin/packages/xgamma/package.py b/var/spack/repos/builtin/packages/xgamma/package.py
index b417a47c1c..bb0bf65211 100644
--- a/var/spack/repos/builtin/packages/xgamma/package.py
+++ b/var/spack/repos/builtin/packages/xgamma/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Xgamma(AutotoolsPackage):
     depends_on('libxxf86vm')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xgc/package.py b/var/spack/repos/builtin/packages/xgc/package.py
index 0b507332da..8c9dbdc084 100644
--- a/var/spack/repos/builtin/packages/xgc/package.py
+++ b/var/spack/repos/builtin/packages/xgc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Xgc(AutotoolsPackage):
 
     depends_on('flex', type='build')
     depends_on('bison', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xhmm/package.py b/var/spack/repos/builtin/packages/xhmm/package.py
new file mode 100644
index 0000000000..3538641da6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/xhmm/package.py
@@ -0,0 +1,31 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Xhmm(MakefilePackage):
+    """The XHMM C++ software suite was written to
+    call copy number variation (CNV) from next-generation
+    sequencing projects, where exome capture was used
+    (or targeted sequencing, more generally)."""
+
+    homepage = "http://atgu.mgh.harvard.edu/xhmm/index.shtml"
+    git      = "https://bitbucket.org/statgen/xhmm.git"
+
+    version('20160104', commit='cc14e528d90932f059ac4fe94e869e81221fd732')
+
+    depends_on('lapack')
+
+    def edit(self, spec, prefix):
+        filter_file('GCC', 'CC', 'sources/hmm++/config_rules.Makefile')
+        filter_file('GCC =gcc', '', 'sources/hmm++/config_defs.Makefile')
+
+    def build(self, spec, prefix):
+        make('LAPACK_LIBS=%s' % ''.join(spec['lapack'].libs.names))
+
+    def install(self, spec, prefix):
+        mkdir(prefix.bin)
+        install('xhmm', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/xhost/package.py b/var/spack/repos/builtin/packages/xhost/package.py
index 072a5a29b1..5affa15df6 100644
--- a/var/spack/repos/builtin/packages/xhost/package.py
+++ b/var/spack/repos/builtin/packages/xhost/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Xhost(AutotoolsPackage):
     depends_on('libxau')
 
     depends_on('xproto@7.0.22:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xineramaproto/package.py b/var/spack/repos/builtin/packages/xineramaproto/package.py
index b05e26254b..7a6e341bdd 100644
--- a/var/spack/repos/builtin/packages/xineramaproto/package.py
+++ b/var/spack/repos/builtin/packages/xineramaproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Xineramaproto(AutotoolsPackage):
 
     version('1.2.1', 'e0e148b11739e144a546b8a051b17dde')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xinit/package.py b/var/spack/repos/builtin/packages/xinit/package.py
index 03487e44a2..66a61f33e0 100644
--- a/var/spack/repos/builtin/packages/xinit/package.py
+++ b/var/spack/repos/builtin/packages/xinit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Xinit(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xinput/package.py b/var/spack/repos/builtin/packages/xinput/package.py
index 2a441d545d..88adddf090 100644
--- a/var/spack/repos/builtin/packages/xinput/package.py
+++ b/var/spack/repos/builtin/packages/xinput/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -43,5 +24,5 @@ class Xinput(AutotoolsPackage):
     depends_on('fixesproto', type='build')
     depends_on('randrproto', type='build')
     depends_on('xineramaproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xios/bld_extern_1.0.patch b/var/spack/repos/builtin/packages/xios/bld_extern_1.0.patch
new file mode 100644
index 0000000000..cf2aeaaa4e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/xios/bld_extern_1.0.patch
@@ -0,0 +1,27 @@
+--- a/bld.cfg	2017-12-23 11:41:14.000000000 +1100
++++ b/bld.cfg	2017-12-23 15:34:53.914024629 +1100
+@@ -24,9 +24,6 @@
+ 
+ search_src           true
+ src::zzz .
+-src::date $PWD/extern/boost/src/date_time
+-src::blitz $PWD/extern/blitz/src
+-src::netcdf $PWD/extern/netcdf4
+ bld::lib xios
+ bld::target libxios.a
+ #bld::target generate_fortran_interface.exe 
+@@ -37,11 +34,11 @@
+ bld::tool::fc        %FCOMPILER
+ bld::tool::fpp       %FPP
+ bld::tool::cpp       %CPP
+-bld::tool::cppflags  %CBASE_INC -I${PWD}/extern/src_netcdf -I${PWD}/extern/boost/include -I${PWD}/extern/rapidxml/include -I${PWD}/extern/blitz/include 
+-bld::tool::fppflags  %BASE_INC -I${PWD}/extern/boost/include -I${PWD}/extern/rapidxml/include 
++bld::tool::cppflags  %CBASE_INC -I${PWD}/extern/rapidxml/include
++bld::tool::fppflags  %BASE_INC -I${PWD}/extern/rapidxml/include 
+ bld::tool::ld        %LINKER
+ bld::tool::ldflags   %LD_FLAGS 
+-bld::tool::cflags    %CFLAGS %CBASE_INC -I${PWD}/extern/src_netcdf -I${PWD}/extern/boost/include -I${PWD}/extern/rapidxml/include -I${PWD}/extern/blitz/include 
++bld::tool::cflags    %CFLAGS %CBASE_INC -I${PWD}/extern/rapidxml/include
+ bld::tool::fflags    %FFLAGS %FBASE_INC 
+ bld::tool::cppkeys   %CPP_KEY
+ bld::tool::fppkeys   %CPP_KEY
diff --git a/var/spack/repos/builtin/packages/xios/bld_extern_1.x.patch b/var/spack/repos/builtin/packages/xios/bld_extern_1.x.patch
new file mode 100644
index 0000000000..fe52da1192
--- /dev/null
+++ b/var/spack/repos/builtin/packages/xios/bld_extern_1.x.patch
@@ -0,0 +1,27 @@
+--- a/bld.cfg	2017-12-23 15:21:01.458603785 +1100
++++ b/bld.cfg	2017-12-23 15:36:36.667684136 +1100
+@@ -24,9 +24,6 @@
+ 
+ search_src           true
+ src::zzz .
+-src::date $PWD/extern/boost/src/date_time
+-src::blitz $PWD/extern/blitz/src
+-src::netcdf $PWD/extern/netcdf4
+ src::remap $PWD/extern/remap/src
+ bld::lib xios
+ bld::target libxios.a 
+@@ -46,11 +43,11 @@
+ bld::tool::fc        %FCOMPILER
+ bld::tool::fpp       %FPP
+ bld::tool::cpp       %CPP
+-bld::tool::cppflags  %CBASE_INC -I${PWD}/extern/src_netcdf -I${PWD}/extern/boost/include -I${PWD}/extern/rapidxml/include -I${PWD}/extern/blitz/include 
+-bld::tool::fppflags  %BASE_INC -I${PWD}/extern/boost/include -I${PWD}/extern/rapidxml/include 
++bld::tool::cppflags  %CBASE_INC -I${PWD}/extern/rapidxml/include
++bld::tool::fppflags  %BASE_INC -I${PWD}/extern/rapidxml/include
+ bld::tool::ld        %LINKER
+ bld::tool::ldflags   %LD_FLAGS 
+-bld::tool::cflags    %CFLAGS %CBASE_INC -I${PWD}/extern/src_netcdf -I${PWD}/extern/boost/include -I${PWD}/extern/rapidxml/include -I${PWD}/extern/blitz/include 
++bld::tool::cflags    %CFLAGS %CBASE_INC -I${PWD}/extern/rapidxml/include
+ bld::tool::fflags    %FFLAGS %FBASE_INC 
+ bld::tool::cppkeys   %CPP_KEY
+ bld::tool::fppkeys   %CPP_KEY
diff --git a/var/spack/repos/builtin/packages/xios/llvm_bug_17782.patch b/var/spack/repos/builtin/packages/xios/llvm_bug_17782.patch
new file mode 100644
index 0000000000..9eb5c21950
--- /dev/null
+++ b/var/spack/repos/builtin/packages/xios/llvm_bug_17782.patch
@@ -0,0 +1,11 @@
+--- a/src/duration.cpp	2017-12-28 10:45:09.000000000 +1100
++++ b/src/duration.cpp	2017-12-28 11:01:40.000000000 +1100
+@@ -43,7 +43,7 @@
+       StdIStream& operator>>(StdIStream& in , CDuration& duration)
+       {
+         duration = NoneDu;
+-        double v = 1.0;
++        int v = 1;
+         char   c = '/';
+         bool   invalidUnit = false;
+         CDuration sentinel = NoneDu;
diff --git a/var/spack/repos/builtin/packages/xios/package.py b/var/spack/repos/builtin/packages/xios/package.py
new file mode 100644
index 0000000000..90ea16b10e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/xios/package.py
@@ -0,0 +1,204 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+#
+from spack import *
+import os
+
+
+class Xios(Package):
+    """XML-IO-SERVER library for IO management of climate models."""
+
+    homepage = "https://forge.ipsl.jussieu.fr/ioserver/wiki"
+
+    version('1.0', revision=910,
+            svn='http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-1.0')
+    version('develop', svn='http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/trunk')
+
+    variant('mode', values=('debug', 'dev', 'prod'), default='dev',
+            description='Build for debugging, development or production')
+    # NOTE: oasis coupler could be supported with a variant
+
+    # Use spack versions of blitz and netcdf for compatibility
+    # with recent compilers and optimised platform libraries:
+    patch('bld_extern_1.0.patch', when='@:1.0')
+    patch('bld_extern_1.x.patch', when='@1.1:')
+
+    # Workaround bug #17782 in llvm, where reading a double
+    # followed by a character is broken (e.g. duration '1d'):
+    patch('llvm_bug_17782.patch', when='@1.1: %clang')
+
+    depends_on('netcdf+mpi')
+    depends_on('netcdf-fortran')
+    depends_on('hdf5+mpi')
+    depends_on('mpi')
+    depends_on('boost')
+    depends_on('blitz')
+    depends_on('perl', type='build')
+    depends_on('perl-uri-escape', type='build')
+    depends_on('gmake', type='build')
+
+    @when('%clang')
+    def patch(self):
+        """Fix type references that are ambiguous for clang."""
+        for dirpath, dirnames, filenames in os.walk('src'):
+            for filename in filenames:
+                filepath = os.path.join(dirpath, filename)
+                # Use boost definition of type shared_ptr:
+                filter_file(r'([^:/])shared_ptr<',
+                            r'\1boost::shared_ptr<', filepath)
+                # Use type long for position in output stream:
+                filter_file(r'oss.tellp\(\) *- *startPos',
+                            r'(long)oss.tellp() - startPos', filepath)
+
+    def xios_env(self):
+        file = join_path('arch', 'arch-SPACK.env')
+        touch(file)
+
+    def xios_path(self):
+        file = join_path('arch', 'arch-SPACK.path')
+        spec = self.spec
+        paths = {'NETCDF_INC_DIR': spec['netcdf'].prefix.include,
+                 'NETCDF_LIB_DIR': spec['netcdf'].prefix.lib,
+                 'HDF5_INC_DIR': spec['hdf5'].prefix.include,
+                 'HDF5_LIB_DIR': spec['hdf5'].prefix.lib}
+        text = r"""
+NETCDF_INCDIR="-I {NETCDF_INC_DIR}"
+NETCDF_LIBDIR="-L {NETCDF_LIB_DIR}"
+NETCDF_LIB="-lnetcdff -lnetcdf"
+
+MPI_INCDIR=""
+MPI_LIBDIR=""
+MPI_LIB=""
+
+HDF5_INCDIR="-I {HDF5_INC_DIR}"
+HDF5_LIBDIR="-L {HDF5_LIB_DIR}"
+HDF5_LIB="-lhdf5_hl -lhdf5"
+
+OASIS_INCDIR=""
+OASIS_LIBDIR=""
+OASIS_LIB=""
+"""
+        with open(file, 'w') as f:
+            f.write(text.format(**paths))
+
+    def xios_fcm(self):
+        file = join_path('arch', 'arch-SPACK.fcm')
+        spec = self.spec
+        param = dict()
+        param['MPICXX'] = spec['mpi'].mpicxx
+        param['MPIFC'] = spec['mpi'].mpifc
+        param['CC'] = self.compiler.cc
+        param['FC'] = self.compiler.fc
+        param['BOOST_INC_DIR'] = spec['boost'].prefix.include
+        param['BOOST_LIB_DIR'] = spec['boost'].prefix.lib
+        param['BLITZ_INC_DIR'] = spec['blitz'].prefix.include
+        param['BLITZ_LIB_DIR'] = spec['blitz'].prefix.lib
+        if spec.satisfies('%clang platform=darwin'):
+            param['LIBCXX'] = '-lc++'
+        else:
+            param['LIBCXX'] = '-lstdc++'
+
+        if any(map(spec.satisfies, ('%gcc', '%intel', '%clang'))):
+            text = r"""
+%CCOMPILER      {MPICXX}
+%FCOMPILER      {MPIFC}
+%LINKER         {MPIFC}
+
+%BASE_CFLAGS    -ansi -w -D_GLIBCXX_USE_CXX11_ABI=0 \
+                -I{BOOST_INC_DIR} -I{BLITZ_INC_DIR}
+%PROD_CFLAGS    -O3 -DBOOST_DISABLE_ASSERTS
+%DEV_CFLAGS     -g -O2
+%DEBUG_CFLAGS   -g
+
+%BASE_FFLAGS    -D__NONE__
+%PROD_FFLAGS    -O3
+%DEV_FFLAGS     -g -O2
+%DEBUG_FFLAGS   -g
+
+%BASE_INC       -D__NONE__
+%BASE_LD        -L{BOOST_LIB_DIR} -L{BLITZ_LIB_DIR} -lblitz {LIBCXX}
+
+%CPP            {CC} -E
+%FPP            {CC} -E -P -x c
+%MAKE           gmake
+""".format(**param)
+        elif spec.satisfies('%cce'):
+            # In the CC compiler prior to cce/8.3.7,
+            # optimisation must be reduced to avoid a bug,
+            # as reported by Mike Rezny at the UK Met Office:
+            if spec.satisfies('%cce@8.3.7:'):
+                param.update({'CC_OPT_DEV': '-O2', 'CC_OPT_PROD': '-O3'})
+            else:
+                param.update({'CC_OPT_DEV': '-O1', 'CC_OPT_PROD': '-O1'})
+
+            text = r"""
+%CCOMPILER      {MPICXX}
+%FCOMPILER      {MPIFC}
+%LINKER         {MPIFC}
+
+%BASE_CFLAGS    -DMPICH_SKIP_MPICXX -h msglevel_4 -h zero -h gnu \
+                -I{BOOST_INC_DIR} -I{BLITZ_INC_DIR}
+%PROD_CFLAGS    {CC_OPT_PROD} -DBOOST_DISABLE_ASSERTS
+%DEV_CFLAGS     {CC_OPT_DEV}
+%DEBUG_CFLAGS   -g
+
+%BASE_FFLAGS    -em -m 4 -e0 -eZ
+%PROD_FFLAGS    -O3
+%DEV_FFLAGS     -G2
+%DEBUG_FFLAGS   -g
+
+%BASE_INC       -D__NONE__
+%BASE_LD        -D__NONE__ -L{BOOST_LIB_DIR} -L{BLITZ_LIB_DIR} -lblitz
+
+%CPP            cpp
+%FPP            cpp -P -CC
+%MAKE           gmake
+""".format(**param)
+        else:
+            raise InstallError('Unsupported compiler.')
+
+        with open(file, 'w') as f:
+            f.write(text)
+
+    def install(self, spec, prefix):
+        env['CC'] = spec['mpi'].mpicc
+        env['CXX'] = spec['mpi'].mpicxx
+        env['F77'] = spec['mpi'].mpif77
+        env['FC'] = spec['mpi'].mpifc
+
+        options = ['--full',
+                   '--%s' % spec.variants['mode'].value,
+                   '--arch', 'SPACK',
+                   '--netcdf_lib', 'netcdf4_par',
+                   '--job', str(make_jobs)]
+
+        self.xios_env()
+        self.xios_path()
+        self.xios_fcm()
+
+        make_xios = Executable('./make_xios')
+        make_xios(*options)
+
+        mkdirp(spec.prefix)
+        install_tree('bin', spec.prefix.bin)
+        install_tree('lib', spec.prefix.lib)
+        install_tree('inc', spec.prefix.include)
+        install_tree('etc', spec.prefix.etc)
+        install_tree('cfg', spec.prefix.cfg)
+
+    @run_after('install')
+    @on_package_attributes(run_tests=True)
+    def check_build(self):
+        mpirun = os.getenv('MPIRUN')
+        if mpirun is None:
+            mpirun = 'mpiexec'
+        mpiexec = Executable(mpirun)
+        with working_dir('inputs'):
+            try:
+                mpiexec('-n', '2', join_path('..', 'bin', 'test_client.exe'))
+            except Exception:
+                raise InstallError(
+                    'Test failed; defining MPIRUN variable may help.')
diff --git a/var/spack/repos/builtin/packages/xkbcomp/package.py b/var/spack/repos/builtin/packages/xkbcomp/package.py
index 2385bb75e9..ee858b4427 100644
--- a/var/spack/repos/builtin/packages/xkbcomp/package.py
+++ b/var/spack/repos/builtin/packages/xkbcomp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -43,5 +24,5 @@ class Xkbcomp(AutotoolsPackage):
 
     depends_on('xproto@7.0.17:', type='build')
     depends_on('bison', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xkbdata/package.py b/var/spack/repos/builtin/packages/xkbdata/package.py
index cb35f1ae3a..d937e91815 100644
--- a/var/spack/repos/builtin/packages/xkbdata/package.py
+++ b/var/spack/repos/builtin/packages/xkbdata/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/xkbevd/package.py b/var/spack/repos/builtin/packages/xkbevd/package.py
index 8ca91494b1..a0bef99bad 100644
--- a/var/spack/repos/builtin/packages/xkbevd/package.py
+++ b/var/spack/repos/builtin/packages/xkbevd/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Xkbevd(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('bison', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xkbprint/package.py b/var/spack/repos/builtin/packages/xkbprint/package.py
index 8d5205843f..3af59469a2 100644
--- a/var/spack/repos/builtin/packages/xkbprint/package.py
+++ b/var/spack/repos/builtin/packages/xkbprint/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Xkbprint(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xkbutils/package.py b/var/spack/repos/builtin/packages/xkbutils/package.py
index c4f604407a..ccf31b1512 100644
--- a/var/spack/repos/builtin/packages/xkbutils/package.py
+++ b/var/spack/repos/builtin/packages/xkbutils/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,5 +21,5 @@ class Xkbutils(AutotoolsPackage):
 
     depends_on('xproto@7.0.17:', type='build')
     depends_on('inputproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xkeyboard-config/package.py b/var/spack/repos/builtin/packages/xkeyboard-config/package.py
index 5995a7eae7..3e572148d5 100644
--- a/var/spack/repos/builtin/packages/xkeyboard-config/package.py
+++ b/var/spack/repos/builtin/packages/xkeyboard-config/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class XkeyboardConfig(AutotoolsPackage):
     depends_on('libx11@1.4.3:')
 
     depends_on('libxslt', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('intltool@0.30:', type='build')
     depends_on('xproto@7.0.20:', type='build')
 
diff --git a/var/spack/repos/builtin/packages/xkill/package.py b/var/spack/repos/builtin/packages/xkill/package.py
index 37ee488071..562f88f578 100644
--- a/var/spack/repos/builtin/packages/xkill/package.py
+++ b/var/spack/repos/builtin/packages/xkill/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Xkill(AutotoolsPackage):
     depends_on('libxmu')
 
     depends_on('xproto@7.0.22:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xload/package.py b/var/spack/repos/builtin/packages/xload/package.py
index cda2ab21a7..5326b9bd57 100644
--- a/var/spack/repos/builtin/packages/xload/package.py
+++ b/var/spack/repos/builtin/packages/xload/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,5 +21,5 @@ class Xload(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xlogo/package.py b/var/spack/repos/builtin/packages/xlogo/package.py
index aca6a47df8..5b5401fcf1 100644
--- a/var/spack/repos/builtin/packages/xlogo/package.py
+++ b/var/spack/repos/builtin/packages/xlogo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -43,5 +24,5 @@ class Xlogo(AutotoolsPackage):
     depends_on('libxrender')
     depends_on('libxt')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xlsatoms/package.py b/var/spack/repos/builtin/packages/xlsatoms/package.py
index b85fac8660..d27bc3e574 100644
--- a/var/spack/repos/builtin/packages/xlsatoms/package.py
+++ b/var/spack/repos/builtin/packages/xlsatoms/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Xlsatoms(AutotoolsPackage):
     depends_on('libxcb', when='@1.1:')
     depends_on('libx11', when='@:1.0')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xlsclients/package.py b/var/spack/repos/builtin/packages/xlsclients/package.py
index 6deb2c88e8..bc99dc1352 100644
--- a/var/spack/repos/builtin/packages/xlsclients/package.py
+++ b/var/spack/repos/builtin/packages/xlsclients/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Xlsclients(AutotoolsPackage):
     depends_on('libxcb@1.6:', when='@1.1:')
     depends_on('libx11', when='@:1.0')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xlsfonts/package.py b/var/spack/repos/builtin/packages/xlsfonts/package.py
index 15761e2d9f..177b434604 100644
--- a/var/spack/repos/builtin/packages/xlsfonts/package.py
+++ b/var/spack/repos/builtin/packages/xlsfonts/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Xlsfonts(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xmag/package.py b/var/spack/repos/builtin/packages/xmag/package.py
index 5a8ae6e961..bdbf014494 100644
--- a/var/spack/repos/builtin/packages/xmag/package.py
+++ b/var/spack/repos/builtin/packages/xmag/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Xmag(AutotoolsPackage):
     depends_on('libxt')
     depends_on('libx11')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xman/package.py b/var/spack/repos/builtin/packages/xman/package.py
index df11504f69..484f3b75ae 100644
--- a/var/spack/repos/builtin/packages/xman/package.py
+++ b/var/spack/repos/builtin/packages/xman/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Xman(AutotoolsPackage):
     depends_on('libxt')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xmessage/package.py b/var/spack/repos/builtin/packages/xmessage/package.py
index dee5d86e21..48b1ce61c8 100644
--- a/var/spack/repos/builtin/packages/xmessage/package.py
+++ b/var/spack/repos/builtin/packages/xmessage/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Xmessage(AutotoolsPackage):
     depends_on('libxaw')
     depends_on('libxt')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xmh/package.py b/var/spack/repos/builtin/packages/xmh/package.py
index 65873360c2..096c0b7cc8 100644
--- a/var/spack/repos/builtin/packages/xmh/package.py
+++ b/var/spack/repos/builtin/packages/xmh/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -41,5 +22,5 @@ class Xmh(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xbitmaps@1.1.0:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xmlf90/package.py b/var/spack/repos/builtin/packages/xmlf90/package.py
new file mode 100644
index 0000000000..09091adcfb
--- /dev/null
+++ b/var/spack/repos/builtin/packages/xmlf90/package.py
@@ -0,0 +1,35 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Xmlf90(AutotoolsPackage):
+    """xmlf90 is a suite of libraries to handle XML in Fortran."""
+
+    homepage = "https://launchpad.net/xmlf90"
+    url      = "https://launchpad.net/xmlf90/trunk/1.5/+download/xmlf90-1.5.2.tgz"
+
+    version('1.5.2', '324fdcba7dafce83db26e72aab9f6656')
+
+    depends_on('autoconf@2.69:', type='build')
+    depends_on('automake@1.14:', type='build')
+    depends_on('libtool@2.4.2:', type='build')
+    depends_on('m4',             type='build')
+
+    def autoreconf(self, spec, prefix):
+        sh = which('sh')
+        sh('autogen.sh')
+
+    def configure_args(self):
+        if self.spec.satisfies('%gcc'):
+            return ['FCFLAGS=-ffree-line-length-none']
+        return []
+
+    @run_after('install')
+    def fix_mk(self):
+        install(join_path(self.prefix, 'share', 'org.siesta-project',
+                          'xmlf90.mk'), prefix)
diff --git a/var/spack/repos/builtin/packages/xmlto/package.py b/var/spack/repos/builtin/packages/xmlto/package.py
index b1122d8ef6..af70c2f70d 100644
--- a/var/spack/repos/builtin/packages/xmlto/package.py
+++ b/var/spack/repos/builtin/packages/xmlto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/xmodmap/package.py b/var/spack/repos/builtin/packages/xmodmap/package.py
index 62582df6f2..13a8527bb8 100644
--- a/var/spack/repos/builtin/packages/xmodmap/package.py
+++ b/var/spack/repos/builtin/packages/xmodmap/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,5 +21,5 @@ class Xmodmap(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xproto@7.0.25:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xmore/package.py b/var/spack/repos/builtin/packages/xmore/package.py
index 0b76828999..597d7c0e8b 100644
--- a/var/spack/repos/builtin/packages/xmore/package.py
+++ b/var/spack/repos/builtin/packages/xmore/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Xmore(AutotoolsPackage):
     depends_on('libxaw')
     depends_on('libxt')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xorg-cf-files/package.py b/var/spack/repos/builtin/packages/xorg-cf-files/package.py
index edeba12f0e..ef1befcb4b 100644
--- a/var/spack/repos/builtin/packages/xorg-cf-files/package.py
+++ b/var/spack/repos/builtin/packages/xorg-cf-files/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,4 +17,4 @@ class XorgCfFiles(AutotoolsPackage):
 
     version('1.0.6', 'c0ce98377c70d95fb48e1bd856109bf8')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
diff --git a/var/spack/repos/builtin/packages/xorg-docs/package.py b/var/spack/repos/builtin/packages/xorg-docs/package.py
index bb67538f0a..0a0b94fc90 100644
--- a/var/spack/repos/builtin/packages/xorg-docs/package.py
+++ b/var/spack/repos/builtin/packages/xorg-docs/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,7 +17,7 @@ class XorgDocs(AutotoolsPackage):
 
     version('1.7.1', 'ca689ccbf8ebc362afbe5cc5792a4abd')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
     depends_on('xorg-sgml-doctools@1.8:', type='build')
     depends_on('xmlto', type='build')
diff --git a/var/spack/repos/builtin/packages/xorg-gtest/package.py b/var/spack/repos/builtin/packages/xorg-gtest/package.py
index 594ba2a3bd..49953792b6 100644
--- a/var/spack/repos/builtin/packages/xorg-gtest/package.py
+++ b/var/spack/repos/builtin/packages/xorg-gtest/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class XorgGtest(AutotoolsPackage):
     depends_on('libxi')
     depends_on('xorg-server')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     # TODO: may be missing evemu package?
diff --git a/var/spack/repos/builtin/packages/xorg-server/package.py b/var/spack/repos/builtin/packages/xorg-server/package.py
index 6b616bfe43..14d885a997 100644
--- a/var/spack/repos/builtin/packages/xorg-server/package.py
+++ b/var/spack/repos/builtin/packages/xorg-server/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,7 +20,7 @@ class XorgServer(AutotoolsPackage):
     depends_on('libxshmfence@1.1:')
     depends_on('libdrm@2.3.0:')
     depends_on('libx11')
-    # depends_on('gl@9.2.0:')
+    depends_on('mesa+hwrender', type='build')
 
     depends_on('dri2proto@2.8:', type='build')
     depends_on('dri3proto@1.0:', type='build')
@@ -47,56 +28,33 @@ class XorgServer(AutotoolsPackage):
 
     depends_on('flex', type='build')
     depends_on('bison', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
-
-    # TODO: add missing dependencies
-    # $LIBSELINUX $REQUIRED_MODULES $REQUIRED_LIBS
-    # $LIBPCIACCESS $DGAPROTO $XORG_MODULES epoxy xdmcp xau xfixes x11-xcb
-    # xcb-aux xcb-image xcb-ewmh xcb-icccm $WINDOWSWMPROTO windowsdriproto
-    # khronos-opengl-registry
-    # $APPLEWMPROTO $LIBAPPLEWM xfixes $LIBDMX $LIBXEXT $LIBDMX xmu $LIBXEXT
-    # $LIBDMX $LIBXI $LIBXEXT $LIBXTST $LIBXEXT xres $LIBXEXT $LIBXEXT
-    # $XEPHYR_REQUIRED_LIBS
-
-    # VIDEOPROTO="videoproto"
-    # COMPOSITEPROTO="compositeproto >= 0.4"
-    # RECORDPROTO="recordproto >= 1.13.99.1"
-    # SCRNSAVERPROTO="scrnsaverproto >= 1.1"
-    # RESOURCEPROTO="resourceproto >= 1.2.0"
-    # DRIPROTO="xf86driproto >= 2.1.0"
-    # XINERAMAPROTO="xineramaproto"
-    # BIGFONTPROTO="xf86bigfontproto >= 1.2.0"
-    # DGAPROTO="xf86dgaproto >= 2.0.99.1"
-    # DMXPROTO="dmxproto >= 2.2.99.1"
-    # VIDMODEPROTO="xf86vidmodeproto >= 2.2.99.1"
-    # WINDOWSWMPROTO="windowswmproto"
-    # APPLEWMPROTO="applewmproto >= 1.4"
-
-    # XPROTO="xproto >= 7.0.28"
-    # RANDRPROTO="randrproto >= 1.5.0"
-    # RENDERPROTO="renderproto >= 0.11"
-    # XEXTPROTO="xextproto >= 7.2.99.901"
-    # INPUTPROTO="inputproto >= 2.3"
-    # KBPROTO="kbproto >= 1.0.3"
-    # FONTSPROTO="fontsproto >= 2.1.3"
-    # FIXESPROTO="fixesproto >= 5.0"
-    # DAMAGEPROTO="damageproto >= 1.1"
-    # XCMISCPROTO="xcmiscproto >= 1.2.0"
-    # BIGREQSPROTO="bigreqsproto >= 1.1.0"
-    # XTRANS="xtrans >= 1.3.5"
-    # PRESENTPROTO="presentproto >= 1.0"
-
-    # LIBAPPLEWM="applewm >= 1.4"
-    # LIBDMX="dmx >= 1.0.99.1"
-    # LIBDRI="dri >= 7.8.0"
-    # LIBEGL="egl"
-    # LIBGBM="gbm >= 10.2.0"
-    # LIBXEXT="xext >= 1.0.99.4"
-    # LIBXFONT="xfont2 >= 2.0.0"
-    # LIBXI="xi >= 1.2.99.1"
-    # LIBXTST="xtst >= 1.0.99.2"
-    # LIBPCIACCESS="pciaccess >= 0.12.901"
-    # LIBUDEV="libudev >= 143"
-    # LIBSELINUX="libselinux >= 2.0.86"
-    # LIBDBUS="dbus-1 >= 1.0"
+    depends_on('fixesproto@5.0:')
+    depends_on('damageproto@1.1:')
+    depends_on('xcmiscproto@1.2.0:')
+    depends_on('xtrans@1.3.5:')
+    depends_on('bigreqsproto@1.1.0:')
+    depends_on('xproto@7.0.28:')
+    depends_on('randrproto@1.5.0:')
+    depends_on('renderproto@0.11:')
+    depends_on('xextproto@7.2.99.901:')
+    depends_on('inputproto@2.3:')
+    depends_on('kbproto@1.0.3:')
+    depends_on('fontsproto@2.1.3:')
+    depends_on('pixman@0.27.2:')
+    depends_on('videoproto')
+    depends_on('compositeproto@0.4:')
+    depends_on('recordproto@1.13.99.1:')
+    depends_on('scrnsaverproto@1.1:')
+    depends_on('resourceproto@1.2.0:')
+    depends_on('xf86driproto@2.1.0:')
+    depends_on('glproto@1.4.17:')
+    depends_on('presentproto@1.0:')
+    depends_on('xineramaproto')
+    depends_on('libxkbfile')
+    depends_on('libxfont2')
+    depends_on('libxext')
+    depends_on('libxdamage')
+    depends_on('libxfixes')
+    depends_on('libepoxy')
diff --git a/var/spack/repos/builtin/packages/xorg-sgml-doctools/package.py b/var/spack/repos/builtin/packages/xorg-sgml-doctools/package.py
index 1adc06dc41..53f2425dc5 100644
--- a/var/spack/repos/builtin/packages/xorg-sgml-doctools/package.py
+++ b/var/spack/repos/builtin/packages/xorg-sgml-doctools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,5 +16,5 @@ class XorgSgmlDoctools(AutotoolsPackage):
 
     version('1.11', '51cf4c6b476e2b98a068fea6975b9b21')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xphelloworld/package.py b/var/spack/repos/builtin/packages/xphelloworld/package.py
index 10f9be36df..c6ac5d62ee 100644
--- a/var/spack/repos/builtin/packages/xphelloworld/package.py
+++ b/var/spack/repos/builtin/packages/xphelloworld/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -44,5 +25,5 @@ class Xphelloworld(AutotoolsPackage):
     # It looks like xprint support was removed from libxaw at some point.
     # But even the oldest version of libxaw doesn't build libxaw8.
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xplor-nih/package.py b/var/spack/repos/builtin/packages/xplor-nih/package.py
index 3be84ebf22..bdfd68b1b2 100644
--- a/var/spack/repos/builtin/packages/xplor-nih/package.py
+++ b/var/spack/repos/builtin/packages/xplor-nih/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
diff --git a/var/spack/repos/builtin/packages/xplsprinters/package.py b/var/spack/repos/builtin/packages/xplsprinters/package.py
index 0757de82ba..5347c9a9e9 100644
--- a/var/spack/repos/builtin/packages/xplsprinters/package.py
+++ b/var/spack/repos/builtin/packages/xplsprinters/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Xplsprinters(AutotoolsPackage):
     depends_on('libxprintutil')
     depends_on('libx11')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xpr/package.py b/var/spack/repos/builtin/packages/xpr/package.py
index 5d246e957a..a5de719915 100644
--- a/var/spack/repos/builtin/packages/xpr/package.py
+++ b/var/spack/repos/builtin/packages/xpr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Xpr(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xprehashprinterlist/package.py b/var/spack/repos/builtin/packages/xprehashprinterlist/package.py
index 65701b180f..bc934a7391 100644
--- a/var/spack/repos/builtin/packages/xprehashprinterlist/package.py
+++ b/var/spack/repos/builtin/packages/xprehashprinterlist/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Xprehashprinterlist(AutotoolsPackage):
     depends_on('libxp')
     depends_on('libx11')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xprop/package.py b/var/spack/repos/builtin/packages/xprop/package.py
index 359ed6d6f1..6414b9784c 100644
--- a/var/spack/repos/builtin/packages/xprop/package.py
+++ b/var/spack/repos/builtin/packages/xprop/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Xprop(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xproto/package.py b/var/spack/repos/builtin/packages/xproto/package.py
index 2396e2966f..bd45c4cf8a 100644
--- a/var/spack/repos/builtin/packages/xproto/package.py
+++ b/var/spack/repos/builtin/packages/xproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -41,7 +22,7 @@ class Xproto(AutotoolsPackage):
     version('7.0.31', '04b925bf9e472c80f9212615cd684f1e')
     version('7.0.29', '16a78dd2c5ad73011105c96235f6a0af')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/xproxymanagementprotocol/package.py b/var/spack/repos/builtin/packages/xproxymanagementprotocol/package.py
index 2f70146e00..4a35b33993 100644
--- a/var/spack/repos/builtin/packages/xproxymanagementprotocol/package.py
+++ b/var/spack/repos/builtin/packages/xproxymanagementprotocol/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/xqilla/package.py b/var/spack/repos/builtin/packages/xqilla/package.py
index 0c63fa6c3f..2949dcda73 100644
--- a/var/spack/repos/builtin/packages/xqilla/package.py
+++ b/var/spack/repos/builtin/packages/xqilla/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/xrandr/package.py b/var/spack/repos/builtin/packages/xrandr/package.py
index 4aeb34d020..2a5544df8d 100644
--- a/var/spack/repos/builtin/packages/xrandr/package.py
+++ b/var/spack/repos/builtin/packages/xrandr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,7 +18,8 @@ class Xrandr(AutotoolsPackage):
     depends_on('libxrandr@1.5:')
     depends_on('libxrender')
     depends_on('libx11')
+    depends_on('randrproto')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xrdb/package.py b/var/spack/repos/builtin/packages/xrdb/package.py
index 075e04e9dc..a3ae50cc95 100644
--- a/var/spack/repos/builtin/packages/xrdb/package.py
+++ b/var/spack/repos/builtin/packages/xrdb/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Xrdb(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xrefresh/package.py b/var/spack/repos/builtin/packages/xrefresh/package.py
index 76a094779e..c4a97f718f 100644
--- a/var/spack/repos/builtin/packages/xrefresh/package.py
+++ b/var/spack/repos/builtin/packages/xrefresh/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Xrefresh(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xrootd/package.py b/var/spack/repos/builtin/packages/xrootd/package.py
index 94ee3eda46..8a14be9905 100644
--- a/var/spack/repos/builtin/packages/xrootd/package.py
+++ b/var/spack/repos/builtin/packages/xrootd/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -32,10 +13,49 @@ class Xrootd(CMakePackage):
     homepage = "http://xrootd.org"
     url      = "http://xrootd.org/download/v4.6.0/xrootd-4.6.0.tar.gz"
 
+    version('4.8.3', 'bb6302703ffc123f7f9141ddb589435e')
+    version('4.8.2', '531b632191b59c2cf76ab8d31af4a866')
+    version('4.8.1', 'a307973f7f43b0cc2688dfe502e17709')
+    version('4.8.0', '4349e7f664e686b72855e894b49063ad')
+    version('4.7.1', '4006422bcf99e0a19996ace4ebb99175')
+    version('4.7.0', '2a92ba483f574c6ba6a9ff061878af22')
+    version('4.6.1', '70c6f6e1f5f2b4eeb3c7d2c41a36bb2c')
     version('4.6.0', '5d60aade2d995b68fe0c46896bc4a5d1')
     version('4.5.0', 'd485df3d4a991e1c35efa4bf9ef663d7')
     version('4.4.1', '72b0842f802ccc94dede4ac5ab2a589e')
     version('4.4.0', '58f55e56801d3661d753ff5fd33dbcc9')
     version('4.3.0', '39c2fab9f632f35e12ff607ccaf9e16c')
 
+    variant('http', default=True,
+            description='Build with HTTP support')
+
+    variant('python', default=False,
+            description='Build pyxroot Python extension')
+
+    variant('readline', default=True,
+            description='Use readline')
+
+    depends_on('bzip2')
     depends_on('cmake@2.6:', type='build')
+    depends_on('libxml2', when='+http')
+    depends_on('openssl')
+    depends_on('python', when='+python')
+    depends_on('readline', when='+readline')
+    depends_on('xz')
+    depends_on('zlib')
+
+    extends('python', when='+python')
+    patch('python-support.patch', level=1, when='+python')
+
+    def cmake_args(self):
+        spec = self.spec
+        options = [
+            '-DENABLE_HTTP:BOOL={0}'.
+            format('ON' if '+http' in spec else 'OFF'),
+            '-DENABLE_PYTHON:BOOL={0}'.
+            format('ON' if '+python' in spec else 'OFF'),
+            '-DENABLE_READLINE:BOOL={0}'.
+            format('ON' if '+readline' in spec else 'OFF'),
+            '-DENABLE_CEPH:BOOL=OFF'
+        ]
+        return options
diff --git a/var/spack/repos/builtin/packages/xrootd/python-support.patch b/var/spack/repos/builtin/packages/xrootd/python-support.patch
new file mode 100644
index 0000000000..eef580641c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/xrootd/python-support.patch
@@ -0,0 +1,30 @@
+diff -Naur xrootd-4.8.0/bindings/python/setup.py.in xrootd-4.8.0/bindings/python/setup.py.in
+--- xrootd-4.8.0/bindings/python/setup.py.in	2017-12-13 11:28:52.000000000 -0600
++++ xrootd-4.8.0/bindings/python/setup.py.in	2017-12-21 17:47:51.378701139 -0600
+@@ -16,6 +16,13 @@
+ py_cflags = cfg_vars["PY_CFLAGS"]
+ cfg_vars["PY_CFLAGS"] = " ".join( flag for flag in py_cflags.split() if flag not in ['-Wstrict-prototypes' ${CLANG_PROHIBITED} ] )
+ 
++ccl=cfg_vars["CC"].split()
++ccl[0]="${CMAKE_C_COMPILER}"
++cfg_vars["CC"] = " ".join(ccl)
++cxxl=cfg_vars["CXX"].split()
++cxxl[0]="${CMAKE_CXX_COMPILER}"
++cfg_vars["CXX"] = " ".join(cxxl)
++cfg_vars["PY_CXXFLAGS"] = "${CMAKE_CXX_FLAGS}"
+ 
+ sources = list()
+ depends = list()
+diff -Naur xrootd-4.8.0/cmake/XRootDFindLibs.cmake xrootd-4.8.0/cmake/XRootDFindLibs.cmake
+--- xrootd-4.8.0/cmake/XRootDFindLibs.cmake	2017-12-13 11:28:52.000000000 -0600
++++ xrootd-4.8.0/cmake/XRootDFindLibs.cmake	2017-12-21 17:47:51.379701131 -0600
+@@ -85,8 +85,8 @@
+ endif()
+ 
+ if( ENABLE_PYTHON AND (Linux OR APPLE) )
+-  find_package( PythonLibs ${XRD_PYTHON_REQ_VERSION} )
+   find_package( PythonInterp ${XRD_PYTHON_REQ_VERSION} )
++  find_package( PythonLibs ${XRD_PYTHON_REQ_VERSION} )
+   if( PYTHONINTERP_FOUND AND PYTHONLIBS_FOUND )
+     set( BUILD_PYTHON TRUE )
+     set( PYTHON_FOUND TRUE )
diff --git a/var/spack/repos/builtin/packages/xrx/package.py b/var/spack/repos/builtin/packages/xrx/package.py
index fba6a88df1..3b1a3f6a4f 100644
--- a/var/spack/repos/builtin/packages/xrx/package.py
+++ b/var/spack/repos/builtin/packages/xrx/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -47,5 +28,5 @@ class Xrx(AutotoolsPackage):
 
     depends_on('xtrans', type='build')
     depends_on('xproxymanagementprotocol', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xsbench/package.py b/var/spack/repos/builtin/packages/xsbench/package.py
index 345d566bc0..e8010c135e 100644
--- a/var/spack/repos/builtin/packages/xsbench/package.py
+++ b/var/spack/repos/builtin/packages/xsbench/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -37,10 +18,12 @@ class Xsbench(MakefilePackage):
 
     tags = ['proxy-app', 'ecp-proxy-app']
 
+    version('18', sha256='a9a544eeacd1be8d687080d2df4eeb701c04eda31d3806e7c3ea1ff36c26f4b0')
     version('14', '94d5d28eb031fd4ef35507c9c1862169')
     version('13', '72a92232d2f5777fb52f5ea4082aff37')
 
-    variant('mpi', default=False, description='Build with MPI support')
+    variant('mpi', default=True, description='Build with MPI support')
+    variant('openmp', default=True, description='Build with OpenMP support')
 
     depends_on('mpi', when='+mpi')
 
@@ -54,8 +37,11 @@ class Xsbench(MakefilePackage):
         cflags = '-std=gnu99'
         if '+mpi' in self.spec:
             targets.append('CC={0}'.format(self.spec['mpi'].mpicc))
+        else:
+            targets.append('CC={0}'.format(self.compiler.cxx))
 
-        cflags += ' ' + self.compiler.openmp_flag
+        if '+openmp' in self.spec:
+            cflags += ' ' + self.compiler.openmp_flag
         targets.append('CFLAGS={0}'.format(cflags))
         targets.append('LDFLAGS=-lm')
 
diff --git a/var/spack/repos/builtin/packages/xscope/package.py b/var/spack/repos/builtin/packages/xscope/package.py
index c851fcf5f3..bea4a1d73f 100644
--- a/var/spack/repos/builtin/packages/xscope/package.py
+++ b/var/spack/repos/builtin/packages/xscope/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,5 +16,5 @@ class Xscope(AutotoolsPackage):
 
     depends_on('xproto@7.0.17:', type='build')
     depends_on('xtrans', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xsd/package.py b/var/spack/repos/builtin/packages/xsd/package.py
new file mode 100644
index 0000000000..3fb1a74dcd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/xsd/package.py
@@ -0,0 +1,33 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Xsd(MakefilePackage):
+    """CodeSynthesis XSD is an open-source, cross-platform W3C XML Schema
+    to C++ data binding compiler. It support in-memory and event-driven XML
+    processing models and is available for a wide range of C++ compilers
+    and platforms."""
+
+    homepage = "https://www.codesynthesis.com"
+    url      = "https://www.codesynthesis.com/download/xsd/4.0/xsd-4.0.0+dep.tar.bz2"
+
+    version('4.0.0', 'ad3de699eb140e747a0a214462d95fc81a21b494')
+
+    depends_on('xerces-c')
+    depends_on('libtool', type='build')
+
+    def install(self, spec, prefix):
+        make('install', 'install_prefix=' + prefix)
+
+    def setup_environment(self, spack_env, run_env):
+        xercesc_lib_flags = self.spec['xerces-c'].libs.search_flags
+        spack_env.append_flags('LDFLAGS', xercesc_lib_flags)
+
+    def url_for_version(self, version):
+        url = "https://www.codesynthesis.com/download/xsd/{0}/xsd-{1}+dep.tar.bz2"
+        return url.format(version.up_to(2), version)
diff --git a/var/spack/repos/builtin/packages/xsdk/package.py b/var/spack/repos/builtin/packages/xsdk/package.py
index 901613f77d..21f71b9abd 100644
--- a/var/spack/repos/builtin/packages/xsdk/package.py
+++ b/var/spack/repos/builtin/packages/xsdk/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 import os
 from spack import *
@@ -37,40 +18,75 @@ class Xsdk(Package):
 
     # Dummy url since Spack complains if I don't list something, will be
     # removed when metapackage is available
-    url      = 'https://bitbucket.org/saws/saws/get/master.tar.gz'
+    url      = 'http://ftp.mcs.anl.gov/pub/petsc/externalpackages/xsdk.tar.gz'
 
     version('develop', 'a52dc710c744afa0b71429b8ec9425bc')
+    version('0.3.0', 'a52dc710c744afa0b71429b8ec9425bc', preferred=True)
     version('xsdk-0.2.0', 'a52dc710c744afa0b71429b8ec9425bc')
 
-    depends_on('hypre@xsdk-0.2.0~internal-superlu', when='@xsdk-0.2.0')
+    variant('debug', default=False, description='Compile in debug mode')
+    variant('cuda', default=False, description='Enable CUDA dependent packages')
+
     depends_on('hypre@develop~internal-superlu', when='@develop')
+    depends_on('hypre@2.12.1~internal-superlu', when='@0.3.0')
+    depends_on('hypre@xsdk-0.2.0~internal-superlu', when='@xsdk-0.2.0')
+
+    depends_on('mfem@develop+mpi+hypre+superlu-dist+petsc+sundials+examples+miniapps', when='@develop')
+    depends_on('mfem@3.3.2+mpi+hypre+superlu-dist+petsc+sundials+examples+miniapps', when='@0.3.0')
 
-    depends_on('superlu-dist@xsdk-0.2.0', when='@xsdk-0.2.0')
     depends_on('superlu-dist@develop', when='@develop')
+    depends_on('superlu-dist@5.2.2', when='@0.3.0')
+    depends_on('superlu-dist@xsdk-0.2.0', when='@xsdk-0.2.0')
 
+    depends_on('trilinos@develop+hypre+superlu-dist+metis+hdf5~mumps+boost~suite-sparse+tpetra+nox+ifpack2+zoltan2+amesos2~exodus',
+               when='@develop')
+    depends_on('trilinos@12.12.1+hypre+superlu-dist+metis+hdf5~mumps+boost~suite-sparse~tpetra~ifpack2~zoltan2~amesos2~exodus',
+               when='@0.3.0')
     depends_on('trilinos@xsdk-0.2.0+hypre+superlu-dist+metis+hdf5~mumps+boost~suite-sparse~tpetra~ifpack2~zoltan2~amesos2~exodus',
                when='@xsdk-0.2.0')
-    depends_on('trilinos@develop+xsdkflags+hypre+superlu-dist+metis+hdf5~mumps+boost~suite-sparse~tpetra~ifpack2~zoltan2~amesos2~exodus',
-               when='@develop')
 
-    depends_on('petsc@xsdk-0.2.0+trilinos+mpi+hypre+superlu-dist+metis+hdf5~mumps~boost+double~int64',
-               when='@xsdk-0.2.0')
-    depends_on('petsc@develop+trilinos+mpi+hypre+superlu-dist+metis+hdf5~mumps~boost+double~int64',
+    depends_on('petsc@develop+trilinos+mpi+hypre+superlu-dist+metis+hdf5~mumps+double~int64',
                when='@develop')
+    depends_on('petsc@3.8.2+trilinos+mpi+hypre+superlu-dist+metis+hdf5~mumps+double~int64',
+               when='@0.3.0')
+    depends_on('petsc@xsdk-0.2.0+trilinos+mpi+hypre+superlu-dist+metis+hdf5~mumps+double~int64',
+               when='@xsdk-0.2.0')
+
+    depends_on('dealii@develop~assimp~python~doc~slepc~gmsh+petsc+mpi+trilinos~int64+hdf5~netcdf+metis', when='@develop')
 
-    depends_on('pflotran@xsdk-0.2.0', when='@xsdk-0.2.0')
     depends_on('pflotran@develop', when='@develop')
+    depends_on('pflotran@xsdk-0.3.0', when='@0.3.0')
+    depends_on('pflotran@xsdk-0.2.0', when='@xsdk-0.2.0')
 
-    depends_on('alquimia@xsdk-0.2.0', when='@xsdk-0.2.0')
     depends_on('alquimia@develop', when='@develop')
+    depends_on('alquimia@xsdk-0.3.0', when='@0.3.0')
+    depends_on('alquimia@xsdk-0.2.0', when='@xsdk-0.2.0')
+
+    depends_on('sundials@3.1.0~int64+hypre', when='@develop')
+    depends_on('sundials@3.1.0~int64+hypre', when='@0.3.0')
+
+    depends_on('plasma@17.2:', when='@develop %gcc@6.0:')
+
+    depends_on('magma@2.2.0', when='@develop +cuda')
+    depends_on('magma@2.2.0', when='@0.3.0 +cuda')
+
+    depends_on('amrex@develop', when='@develop %intel')
+    depends_on('amrex@develop', when='@develop %gcc')
+
+    depends_on('slepc@develop', when='@develop')
+
+    # the Fortran 2003 bindings of phist require python@3:, but this
+    # creates a conflict with other packages like petsc@develop. Actually
+    # these are type='build' dependencies, but spack reports a conflict anyway.
+    # This will be fixed once the new concretizer becomes available
+    # (says @adamjsteward)
+    depends_on('phist@develop kernel_lib=tpetra ~fortran ~scamac ~openmp', when='@develop')
 
     # xSDKTrilinos depends on the version of Trilinos built with
     # +tpetra which is turned off for faster xSDK
     # depends_on('xsdktrilinos@xsdk-0.2.0', when='@xsdk-0.2.0')
     # depends_on('xsdktrilinos@develop', when='@develop')
 
-    variant('debug', default=False, description='Compile in debug mode')
-
     # How do we propagate debug flag to all depends on packages ?
     # If I just do spack install xsdk+debug will that propogate it down?
 
diff --git a/var/spack/repos/builtin/packages/xsdktrilinos/package.py b/var/spack/repos/builtin/packages/xsdktrilinos/package.py
index cc75589937..66de6cef0c 100644
--- a/var/spack/repos/builtin/packages/xsdktrilinos/package.py
+++ b/var/spack/repos/builtin/packages/xsdktrilinos/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
@@ -33,9 +14,10 @@ class Xsdktrilinos(CMakePackage):
     """
     homepage = "https://trilinos.org/"
     url      = "https://github.com/trilinos/xSDKTrilinos/archive/trilinos-release-12-8-1.tar.gz"
+    git      = "https://github.com/trilinos/xSDKTrilinos.git"
 
-    version('develop', git='https://github.com/trilinos/xSDKTrilinos.git', tag='master')
-    version('xsdk-0.2.0', git='https://github.com/trilinos/xSDKTrilinos.git', tag='xsdk-0.2.0')
+    version('develop', tag='master')
+    version('xsdk-0.2.0', tag='xsdk-0.2.0')
     version('12.8.1', '9cc338ded17d1e10ea6c0dc18b22dcd4')
     version('12.6.4', '44c4c54ccbac73bb8939f68797b9454a')
 
diff --git a/var/spack/repos/builtin/packages/xset/package.py b/var/spack/repos/builtin/packages/xset/package.py
index 8488ded70c..93260d65ec 100644
--- a/var/spack/repos/builtin/packages/xset/package.py
+++ b/var/spack/repos/builtin/packages/xset/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Xset(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xsetmode/package.py b/var/spack/repos/builtin/packages/xsetmode/package.py
index e4d9b1a6a0..e1eb7dc33d 100644
--- a/var/spack/repos/builtin/packages/xsetmode/package.py
+++ b/var/spack/repos/builtin/packages/xsetmode/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Xsetmode(AutotoolsPackage):
     depends_on('libxi')
     depends_on('libx11')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xsetpointer/package.py b/var/spack/repos/builtin/packages/xsetpointer/package.py
index 296dae801b..66d91bbc04 100644
--- a/var/spack/repos/builtin/packages/xsetpointer/package.py
+++ b/var/spack/repos/builtin/packages/xsetpointer/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Xsetpointer(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('inputproto@1.4:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xsetroot/package.py b/var/spack/repos/builtin/packages/xsetroot/package.py
index 1468aa7e2e..43b61bd41c 100644
--- a/var/spack/repos/builtin/packages/xsetroot/package.py
+++ b/var/spack/repos/builtin/packages/xsetroot/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Xsetroot(AutotoolsPackage):
 
     depends_on('xbitmaps', type='build')
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xsimd/package.py b/var/spack/repos/builtin/packages/xsimd/package.py
new file mode 100644
index 0000000000..a7d1f8474a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/xsimd/package.py
@@ -0,0 +1,36 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Xsimd(CMakePackage):
+    """C++ wrappers for SIMD intrinsics"""
+
+    homepage = "http://quantstack.net/xsimd"
+    url      = "https://github.com/QuantStack/xsimd/archive/3.1.0.tar.gz"
+    git      = "https://github.com/QuantStack/xsimd.git"
+
+    maintainers = ['ax3l']
+
+    version('develop', branch='master')
+    version('4.0.0', '4186ec94985daa3fc284d9d0d4aa03e8')
+    version('3.1.0', '29c1c525116cbda28f610e2bf24a827e')
+
+    depends_on('googletest', type='test')
+
+    # C++14 support
+    conflicts('%gcc@:4.8')
+    conflicts('%clang@:3.6')
+    # untested: conflicts('%intel@:15')
+    # untested: conflicts('%pgi@:14')
+
+    def cmake_args(self):
+        args = [
+            '-DBUILD_TESTS:BOOL={0}'.format(
+                'ON' if self.run_tests else 'OFF')
+        ]
+
+        return args
diff --git a/var/spack/repos/builtin/packages/xsm/package.py b/var/spack/repos/builtin/packages/xsm/package.py
index 0bbd3ec805..eb1a3417dc 100644
--- a/var/spack/repos/builtin/packages/xsm/package.py
+++ b/var/spack/repos/builtin/packages/xsm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Xsm(AutotoolsPackage):
     depends_on('libsm')
     depends_on('libxaw')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xstdcmap/package.py b/var/spack/repos/builtin/packages/xstdcmap/package.py
index 9b8d4a1641..3f9ae0960b 100644
--- a/var/spack/repos/builtin/packages/xstdcmap/package.py
+++ b/var/spack/repos/builtin/packages/xstdcmap/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,5 +21,5 @@ class Xstdcmap(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xtensor-python/package.py b/var/spack/repos/builtin/packages/xtensor-python/package.py
new file mode 100644
index 0000000000..5bf808ff5e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/xtensor-python/package.py
@@ -0,0 +1,38 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class XtensorPython(CMakePackage):
+    """Python bindings for the xtensor C++ multi-dimensional array library"""
+
+    homepage = "https://xtensor-python.readthedocs.io"
+    url      = "https://github.com/QuantStack/xtensor-python/archive/0.17.0.tar.gz"
+    git      = "https://github.com/QuantStack/xtensor-python.git"
+
+    maintainers = ['ax3l']
+
+    version('develop', branch='master')
+    version('0.17.0', '51d22e42909a81201c3421d9e119eed0')
+
+    depends_on('xtensor@0.15.1:0.15.99', when='@0.17.0:')
+    depends_on('xtl@0.4.0:0.4.99', when='@0.17.0:')
+    depends_on('py-pybind11@2.2.1', when='@0.17.0:')
+
+    depends_on('py-numpy')
+    depends_on('python', type=('build', 'link', 'run'))
+
+    extends('python')
+
+    def cmake_args(self):
+        spec = self.spec
+
+        python_exe = spec['python'].command.path
+
+        args = [
+            '-DPYTHON_EXECUTABLE={0}'.format(python_exe)
+        ]
+        return args
diff --git a/var/spack/repos/builtin/packages/xtensor/package.py b/var/spack/repos/builtin/packages/xtensor/package.py
new file mode 100644
index 0000000000..9ba3dcda16
--- /dev/null
+++ b/var/spack/repos/builtin/packages/xtensor/package.py
@@ -0,0 +1,35 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Xtensor(CMakePackage):
+    """Multi-dimensional arrays with broadcasting and lazy computing"""
+
+    homepage = "http://quantstack.net/xtensor"
+    url      = "https://github.com/QuantStack/xtensor/archive/0.13.1.tar.gz"
+    git      = "https://github.com/QuantStack/xtensor.git"
+
+    maintainers = ['ax3l']
+
+    version('develop', branch='master')
+    version('0.15.1', 'c24ecc406003bd1ac22291f1f7cac29a')
+    version('0.13.1', '80e7e33f05066d17552bf0f8b582dcc5')
+
+    variant('xsimd', default=True,
+            description='Enable SIMD intrinsics')
+
+    depends_on('xtl')
+    depends_on('xtl@0.4.0:0.4.99', when='@0.15.1:')
+    depends_on('xtl@0.3.3:0.3.99', when='@0.13.1')
+    depends_on('xsimd@4.0.0', when='@0.15.1 +xsimd')
+    depends_on('xsimd@3.1.0', when='@0.13.1 +xsimd')
+
+    # C++14 support
+    conflicts('%gcc@:4.8')
+    conflicts('%clang@:3.5')
+    # untested: conflicts('%intel@:15')
+    # untested: conflicts('%pgi@:14')
diff --git a/var/spack/repos/builtin/packages/xterm/package.py b/var/spack/repos/builtin/packages/xterm/package.py
index 8c24931d7a..8ecd6eb64f 100644
--- a/var/spack/repos/builtin/packages/xterm/package.py
+++ b/var/spack/repos/builtin/packages/xterm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,7 +12,7 @@ class Xterm(AutotoolsPackage):
     that can't use the window system directly."""
 
     homepage = "http://invisible-island.net/xterm/"
-    url      = "http://invisible-island.net/xterm/xterm-327.tgz"
+    url      = "ftp://ftp.invisible-island.net/xterm/xterm-327.tgz"
 
     version('327', '3c32e931adcad44e64e57892e75d9e02')
 
@@ -52,4 +33,4 @@ class Xterm(AutotoolsPackage):
     depends_on('libxau')
     depends_on('bzip2')
 
-    depends_on('pkg-config', type='build')
+    depends_on('pkgconfig', type='build')
diff --git a/var/spack/repos/builtin/packages/xtl/package.py b/var/spack/repos/builtin/packages/xtl/package.py
new file mode 100644
index 0000000000..b73ec8fa10
--- /dev/null
+++ b/var/spack/repos/builtin/packages/xtl/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Xtl(CMakePackage):
+    """QuantStack tools library"""
+
+    homepage = "https://github.com/QuantStack/xtl"
+    url      = "https://github.com/QuantStack/xtl/archive/0.3.4.tar.gz"
+    git      = "https://github.com/QuantStack/xtl.git"
+
+    maintainers = ['ax3l']
+
+    version('develop', branch='master')
+    version('0.4.0', '48c76b63ab12e497a53fb147c41ae747')
+    version('0.3.4', 'b76548a55f1e171a9c849e5ed543e8b3')
+    version('0.3.3', '09b6d9611e460d9280bf1156bcca20f5')
+
+    # C++14 support
+    conflicts('%gcc@:4.8')
+    conflicts('%clang@:3.6')
+    # untested: conflicts('%intel@:15')
+    # untested: conflicts('%pgi@:14')
diff --git a/var/spack/repos/builtin/packages/xtrans/package.py b/var/spack/repos/builtin/packages/xtrans/package.py
index 186e3587e6..508483c358 100644
--- a/var/spack/repos/builtin/packages/xtrans/package.py
+++ b/var/spack/repos/builtin/packages/xtrans/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Xtrans(AutotoolsPackage):
 
     version('1.3.5', '6e4eac1b7c6591da0753052e1eccfb58')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xtrap/package.py b/var/spack/repos/builtin/packages/xtrap/package.py
index ef297e9e6d..e78aab7b66 100644
--- a/var/spack/repos/builtin/packages/xtrap/package.py
+++ b/var/spack/repos/builtin/packages/xtrap/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Xtrap(AutotoolsPackage):
     depends_on('libx11')
     depends_on('libxtrap')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xts/package.py b/var/spack/repos/builtin/packages/xts/package.py
index 985a35bd5a..f8e6038d50 100644
--- a/var/spack/repos/builtin/packages/xts/package.py
+++ b/var/spack/repos/builtin/packages/xts/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/xvidtune/package.py b/var/spack/repos/builtin/packages/xvidtune/package.py
index 573c027627..37cbc8a1d5 100644
--- a/var/spack/repos/builtin/packages/xvidtune/package.py
+++ b/var/spack/repos/builtin/packages/xvidtune/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,5 +21,5 @@ class Xvidtune(AutotoolsPackage):
     depends_on('libxmu')
     depends_on('libx11')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xvinfo/package.py b/var/spack/repos/builtin/packages/xvinfo/package.py
index 358573dcbe..7dd8670ce5 100644
--- a/var/spack/repos/builtin/packages/xvinfo/package.py
+++ b/var/spack/repos/builtin/packages/xvinfo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Xvinfo(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xproto@7.0.25:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xwd/package.py b/var/spack/repos/builtin/packages/xwd/package.py
index 0b992365be..ba5b693fbf 100644
--- a/var/spack/repos/builtin/packages/xwd/package.py
+++ b/var/spack/repos/builtin/packages/xwd/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Xwd(AutotoolsPackage):
     depends_on('libxkbfile')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xwininfo/package.py b/var/spack/repos/builtin/packages/xwininfo/package.py
index bba7088166..86473d401c 100644
--- a/var/spack/repos/builtin/packages/xwininfo/package.py
+++ b/var/spack/repos/builtin/packages/xwininfo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Xwininfo(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xwud/package.py b/var/spack/repos/builtin/packages/xwud/package.py
index b4b92cd214..dd13f44ced 100644
--- a/var/spack/repos/builtin/packages/xwud/package.py
+++ b/var/spack/repos/builtin/packages/xwud/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Xwud(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xxhash/package.py b/var/spack/repos/builtin/packages/xxhash/package.py
new file mode 100644
index 0000000000..990e6ed3e3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/xxhash/package.py
@@ -0,0 +1,30 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Xxhash(MakefilePackage):
+    """xxHash is an Extremely fast Hash algorithm, running at RAM speed
+    limits. It successfully completes the SMHasher test suite which
+    evaluates collision, dispersion and randomness qualities of hash
+    functions. Code is highly portable, and hashes are identical on all
+    platforms (little / big endian).
+    """
+
+    homepage = "https://github.com/Cyan4973/xxHash"
+    url      = "https://github.com/Cyan4973/xxHash/archive/v0.6.5.tar.gz"
+
+    version('0.6.5', '6af3a964f3c2accebce66e54b44b6446')
+    version('0.6.4', '3c071c95e31bd601cca149cc354e6f19')
+    version('0.6.3', 'f2ec1497317c0eb89addd7f333c83228')
+    version('0.6.2', 'b2d12d99094b824e0a5f3ab63abc6c58')
+    version('0.6.1', 'f4ced3767aad8384b1ecb73bd5f992ca')
+    version('0.6.0', 'e0fd163b07ab0038f389a180dc263cf2')
+    version('0.5.1', '9417fd8a4d88204b680e21a60f0ccada')
+    version('0.5.0', '42e9a31a2cfc2f626fde17e84a0b6bb7')
+
+    def install(self, spec, prefix):
+        make('prefix={0}'.format(prefix), 'install')
diff --git a/var/spack/repos/builtin/packages/xz/package.py b/var/spack/repos/builtin/packages/xz/package.py
index 04d91c76ac..9f2f9f9d83 100644
--- a/var/spack/repos/builtin/packages/xz/package.py
+++ b/var/spack/repos/builtin/packages/xz/package.py
@@ -1,39 +1,22 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class Xz(AutotoolsPackage):
     """XZ Utils is free general-purpose data compression software with
-       high compression ratio. XZ Utils were written for POSIX-like
-       systems, but also work on some not-so-POSIX systems. XZ Utils are
-       the successor to LZMA Utils."""
+    high compression ratio. XZ Utils were written for POSIX-like systems,
+    but also work on some not-so-POSIX systems. XZ Utils are the successor
+    to LZMA Utils."""
+
     homepage = "http://tukaani.org/xz/"
-    url      = "http://tukaani.org/xz/xz-5.2.0.tar.bz2"
+    url      = "http://tukaani.org/xz/xz-5.2.4.tar.bz2"
     list_url = "http://tukaani.org/xz/old.html"
 
+    version('5.2.4', 'b3264b15ab1db04c8c428dc81838d4eb')
     version('5.2.3', '1592e7ca3eece099b03b35f4d9179e7c')
     version('5.2.2', 'f90c9a0c8b259aee2234c4e0d7fd70af')
     version('5.2.0', '867cc8611760240ebf3440bd6e170bb9')
diff --git a/var/spack/repos/builtin/packages/yajl/package.py b/var/spack/repos/builtin/packages/yajl/package.py
index 604144c6e5..e26616bb05 100644
--- a/var/spack/repos/builtin/packages/yajl/package.py
+++ b/var/spack/repos/builtin/packages/yajl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,6 +11,7 @@ class Yajl(CMakePackage):
 
     homepage = "http://lloyd.github.io/yajl/"
     url      = "https://github.com/lloyd/yajl/archive/2.1.0.zip"
+    git      = "https://github.com/lloyd/yajl.git"
 
-    version('develop', git='https://github.com/lloyd/yajl.git', branch='master')
+    version('develop', branch='master')
     version('2.1.0', '5eb9c16539bf354b937fcb20e263d1eb')
diff --git a/var/spack/repos/builtin/packages/yambo/package.py b/var/spack/repos/builtin/packages/yambo/package.py
new file mode 100644
index 0000000000..ddb5964233
--- /dev/null
+++ b/var/spack/repos/builtin/packages/yambo/package.py
@@ -0,0 +1,151 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Yambo(AutotoolsPackage):
+    """Yambo is a FORTRAN/C code for Many-Body calculations in solid
+    state and molecular physics.
+
+    Yambo relies on the Kohn-Sham wavefunctions generated by two DFT
+    public codes: abinit, and PWscf. The code was originally developed
+    in the Condensed Matter Theoretical Group of the Physics Department
+    at the University of Rome "Tor Vergata" by Andrea Marini. Previous
+    to its release under the GPL license, yambo was known as SELF.
+    """
+
+    homepage = "http://www.yambo-code.org/index.php"
+    url = "https://github.com/yambo-code/yambo/archive/4.2.2.tar.gz"
+
+    version('4.2.2', '97f3513bd726141be5e18072118b6fb5')
+    version('4.2.1', '99027014192c0f0f4b5d9b48414ad85d')
+    version('4.2.0', '0cbb4d7c9790596d163ebe872d95bd30')
+
+    variant('dp', default=False, description='Enable double precision')
+    variant(
+        'profile',
+        values=('time', 'memory'),
+        default='',
+        description='Activate profiling of specific sections',
+        multi=True
+    )
+
+    variant(
+        'io',
+        values=('iotk', 'etsf-io'),
+        default='',
+        description='Activate support for different io formats (requires network access)',  # noqa
+        multi=True
+    )
+
+    # MPI + OpenMP parallelism
+    variant('mpi', default=True, description='Enable MPI support')
+    variant('openmp', default=False, description='Enable OpenMP support')
+
+    depends_on('blas')
+    depends_on('lapack')
+
+    # MPI dependencies are forced, until we have proper forwarding of variants
+    #
+    # Note that yambo is used as an application, and not linked as a library,
+    # thus there will be no case where another package pulls-in e.g. netcdf+mpi
+    # and wants to depend on yambo~mpi.
+    depends_on('mpi', when='+mpi')
+    depends_on('netcdf+mpi', when='+mpi')
+    depends_on('hdf5+mpi', when='+mpi')
+    depends_on('fftw+mpi', when='+mpi')
+    depends_on('scalapack', when='+mpi')
+
+    depends_on('netcdf~mpi', when='~mpi')
+    depends_on('hdf5~mpi', when='~mpi')
+    depends_on('fftw~mpi', when='~mpi')
+
+    depends_on('hdf5+fortran')
+    depends_on('netcdf')
+    depends_on('netcdf-fortran')
+    depends_on('libxc@2.0.3:')
+
+    build_targets = ['all']
+
+    parallel = False
+
+    # The configure in the package has the string 'cat config/report'
+    # hard-coded, which causes a failure at configure time due to the
+    # current working directory in Spack. Fix this by using the absolute
+    # path to the file.
+    @run_before('configure')
+    def filter_configure(self):
+        report_abspath = join_path(self.build_directory, 'config', 'report')
+        filter_file('config/report', report_abspath, 'configure')
+
+    def enable_or_disable_time(self, activated):
+        return '--enable-time-profile' if activated else '--disable-time-profile'  # noqa: E501
+
+    def enable_or_disable_memory(self, activated):
+        return '--enable-memory-profile' if activated else '--disable-memory-profile'  # noqa: E501
+
+    def enable_or_disable_openmp(self, activated):
+        return '--enable-open-mp' if activated else '--disable-open-mp'
+
+    def configure_args(self):
+
+        args = [
+            # As of version 4.2.1 there are hard-coded paths that make
+            # the build process fail if the target prefix is not the
+            # configure directory
+            '--prefix={0}'.format(self.stage.source_path),
+            '--disable-keep-objects',
+            '--with-editor=none'
+        ]
+        spec = self.spec
+
+        # Double precision
+        args.extend(self.enable_or_disable('dp'))
+
+        # Application profiling
+        args.extend(self.enable_or_disable('profile'))
+
+        # MPI + threading
+        args.extend(self.enable_or_disable('mpi'))
+        args.extend(self.enable_or_disable('openmp'))
+
+        # LAPACK
+        if '+mpi' in spec:
+            args.append('--with-scalapack-libs={0}'.format(
+                spec['scalapack'].libs +
+                spec['lapack'].libs +
+                spec['blas'].libs
+            ))
+
+        args.extend([
+            '--with-blas-libs={0}'.format(spec['blas'].libs),
+            '--with-lapack-libs={0}'.format(spec['lapack'].libs)
+        ])
+
+        # Netcdf
+        args.extend([
+            '--enable-netcdf-hdf5',
+            '--enable-hdf5-compression',
+            '--with-hdf5-libs={0}'.format(spec['hdf5'].libs),
+            '--with-netcdf-path={0}'.format(spec['netcdf'].prefix),
+            '--with-netcdff-path={0}'.format(spec['netcdf-fortran'].prefix)
+        ])
+
+        args.extend(self.enable_or_disable('io'))
+
+        # Other dependencies
+        args.append('--with-fft-path={0}'.format(spec['fftw'].prefix))
+        args.append('--with-libxc-path={0}'.format(spec['libxc'].prefix))
+
+        return args
+
+    def install(self, spec, prefix):
+        # As of version 4.2.1 an 'install' target is advertized,
+        # but not present
+        install_tree('bin', prefix.bin)
+        install_tree('lib', prefix.lib)
+        install_tree('include', prefix.include)
+        install_tree('driver', prefix.driver)
diff --git a/var/spack/repos/builtin/packages/yaml-cpp/package.py b/var/spack/repos/builtin/packages/yaml-cpp/package.py
index aaf6ab0a53..95df4da774 100644
--- a/var/spack/repos/builtin/packages/yaml-cpp/package.py
+++ b/var/spack/repos/builtin/packages/yaml-cpp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,16 +11,27 @@ class YamlCpp(CMakePackage):
 
     homepage = "https://github.com/jbeder/yaml-cpp"
     url      = "https://github.com/jbeder/yaml-cpp/archive/yaml-cpp-0.5.3.tar.gz"
+    git      = "https://github.com/jbeder/yaml-cpp.git"
 
-    version('0.5.3', '4e47733d98266e46a1a73ae0a72954eb')
-    version('develop', git='https://github.com/jbeder/yaml-cpp', branch='master')
+    version('develop', branch='master')
+    version('0.6.2', '5b943e9af0060d0811148b037449ef82')
+    version('0.5.3', '2bba14e6a7f12c7272f87d044e4a7211')
 
     variant('shared', default=True,
             description='Enable build of shared libraries')
     variant('pic',   default=True,
             description='Build with position independent code')
 
-    depends_on('boost', when='@:0.5.3')
+    depends_on('boost@:1.66.99', when='@:0.5.3')
+
+    conflicts('%gcc@:4.7', when='@0.6.0:', msg="versions 0.6.0: require c++11 support")
+    conflicts('%clang@:3.3.0', when='@0.6.0:', msg="versions 0.6.0: require c++11 support")
+    # currently we can't check for apple-clang's version
+    # conflicts('%clang@:4.0.0-apple', when='@0.6.0:',
+    # msg="versions 0.6.0: require c++11 support")
+    conflicts('%intel@:11.1', when='@0.6.0:', msg="versions 0.6.0: require c++11 support")
+    conflicts('%xl@:13.1', when='@0.6.0:', msg="versions 0.6.0: require c++11 support")
+    conflicts('%xl_r@:13.1', when='@0.6.0:', msg="versions 0.6.0: require c++11 support")
 
     def cmake_args(self):
         spec = self.spec
diff --git a/var/spack/repos/builtin/packages/yasm/package.py b/var/spack/repos/builtin/packages/yasm/package.py
index 0d35e41e04..0f6bb70744 100644
--- a/var/spack/repos/builtin/packages/yasm/package.py
+++ b/var/spack/repos/builtin/packages/yasm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,7 +11,15 @@ class Yasm(AutotoolsPackage):
        supports the x86 and AMD64 instruction sets, accepts NASM and
        GAS assembler syntaxes and outputs binary, ELF32 and ELF64
        object formats."""
+
     homepage = "http://yasm.tortall.net"
     url      = "http://www.tortall.net/projects/yasm/releases/yasm-1.3.0.tar.gz"
+    git      = "https://github.com/yasm/yasm.git"
 
+    version('develop', branch='master')
     version('1.3.0', 'fc9e586751ff789b34b1f21d572d96af')
+
+    depends_on('autoconf', when='@develop')
+    depends_on('automake', when='@develop')
+    depends_on('libtool', when='@develop')
+    depends_on('m4', when='@develop')
diff --git a/var/spack/repos/builtin/packages/yorick/package.py b/var/spack/repos/builtin/packages/yorick/package.py
index c30f9ca4ed..45f767a7ba 100644
--- a/var/spack/repos/builtin/packages/yorick/package.py
+++ b/var/spack/repos/builtin/packages/yorick/package.py
@@ -1,31 +1,10 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
-import shutil
-import glob
 
 
 class Yorick(Package):
@@ -40,12 +19,11 @@ class Yorick(Package):
 
     homepage = "http://dhmunro.github.io/yorick-doc/"
     url      = "https://github.com/dhmunro/yorick/archive/y_2_2_04.tar.gz"
+    git      = "https://github.com/dhmunro/yorick.git"
 
+    version('master', branch='master')
     version('2.2.04', '1b5b0da6ad81b2d9dba64d991ec17939')
-    version('master', branch='master',
-            git='https://github.com/dhmunro/yorick.git')
-    version('f90-plugin', branch='f90-plugin',
-            git='https://github.com/trmwzm/yorick.git')
+    version('f90-plugin', branch='f90-plugin')
 
     variant('X', default=False, description='Enable X11 support')
 
@@ -75,13 +53,4 @@ class Yorick(Package):
         make()
         make("install")
 
-        try:
-            os.makedirs(prefix)
-        except OSError:
-            pass
-        os.chdir("relocate")
-        for f in glob.glob('*'):
-            if os.path.isdir(f):
-                shutil.copytree(f, os.path.join(prefix, f))
-            else:
-                shutil.copy2(f, os.path.join(prefix, f))
+        install_tree('relocate', prefix)
diff --git a/var/spack/repos/builtin/packages/z3/package.py b/var/spack/repos/builtin/packages/z3/package.py
index 2234b7e596..131ebba39a 100644
--- a/var/spack/repos/builtin/packages/z3/package.py
+++ b/var/spack/repos/builtin/packages/z3/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/zeromq/package.py b/var/spack/repos/builtin/packages/zeromq/package.py
index f48e868891..57ed8fd1fc 100644
--- a/var/spack/repos/builtin/packages/zeromq/package.py
+++ b/var/spack/repos/builtin/packages/zeromq/package.py
@@ -1,39 +1,22 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class Zeromq(AutotoolsPackage):
-    """ The ZMQ networking/concurrency library and core API """
+    """The ZMQ networking/concurrency library and core API"""
+
     homepage = "http://zguide.zeromq.org/"
     url      = "http://download.zeromq.org/zeromq-4.1.2.tar.gz"
+    git      = "https://github.com/zeromq/libzmq.git"
 
-    version('develop', branch='master',
-            git='https://github.com/zeromq/libzmq.git')
-    version('4.2.2', '52499909b29604c1e47a86f1cb6a9115',
-            url='https://github.com/zeromq/libzmq/releases/download/v4.2.2/zeromq-4.2.2.tar.gz')
+    version('develop', branch='master')
+    version('4.2.5', 'a1c95b34384257e986842f4d006957b8',
+            url='https://github.com/zeromq/libzmq/releases/download/v4.2.5/zeromq-4.2.5.tar.gz')
+    version('4.2.2', '52499909b29604c1e47a86f1cb6a9115')
     version('4.1.4', 'a611ecc93fffeb6d058c0e6edf4ad4fb')
     version('4.1.2', '159c0c56a895472f02668e692d122685')
     version('4.1.1', '0a4b44aa085644f25c177f79dc13f253')
@@ -41,13 +24,17 @@ class Zeromq(AutotoolsPackage):
     version('4.0.6', 'd47dd09ed7ae6e7fd6f9a816d7f5fdf6')
     version('4.0.5', '73c39f5eb01b9d7eaf74a5d899f1d03d')
 
-    depends_on("libsodium")
-    depends_on("libsodium@:1.0.3", when='@:4.1.2')
+    variant("libsodium", default=True, description="Build with libsodium support")
+
+    depends_on("libsodium", when='+libsodium')
+    depends_on("libsodium@:1.0.3", when='+libsodium@:4.1.2')
 
     depends_on('autoconf', type='build', when='@develop')
     depends_on('automake', type='build', when='@develop')
     depends_on('libtool', type='build', when='@develop')
-    depends_on('pkg-config', type='build', when='@develop')
+    depends_on('pkgconfig', type='build')
+
+    conflicts('%gcc@8:', when='@:4.2.2')
 
     @when('@develop')
     def autoreconf(self, spec, prefix):
@@ -55,7 +42,9 @@ class Zeromq(AutotoolsPackage):
         bash('./autogen.sh')
 
     def configure_args(self):
-        config_args = ['--with-libsodium']
+        config_args = []
+        if '+libsodium' in self.spec:
+            config_args.append('--with-libsodium')
         if 'clang' in self.compiler.cc:
             config_args.append("CFLAGS=-Wno-gnu")
             config_args.append("CXXFLAGS=-Wno-gnu")
diff --git a/var/spack/repos/builtin/packages/zfp/package.py b/var/spack/repos/builtin/packages/zfp/package.py
index 704dc9dc72..447bbf4d2a 100644
--- a/var/spack/repos/builtin/packages/zfp/package.py
+++ b/var/spack/repos/builtin/packages/zfp/package.py
@@ -1,43 +1,21 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class Zfp(MakefilePackage):
-    """zfp is an open source C library for compressed floating-point arrays
-       that supports very high throughput read and write random acces,
-       target error bounds or bit rates.  Although bit-for-bit lossless
-       compression is not always possible, zfp is usually accurate to
-       within machine epsilon in near-lossless mode, and is often orders
-       of magnitude more accurate than other lossy compressors. Versions
-       of zfp 0.5.1 or newer also support compression of integer data.
+    """zfp is an open source C/C++ library for high-fidelity, high-throughput
+       lossy compression of floating-point and integer multi-dimensional
+       arrays.
     """
 
     homepage = 'http://computation.llnl.gov/projects/floating-point-compression'
-    url      = 'http://computation.llnl.gov/projects/floating-point-compression/download/zfp-0.5.1.tar.gz'
+    url      = 'http://computation.llnl.gov/projects/floating-point-compression/download/zfp-0.5.2.tar.gz'
 
+    version('0.5.2', '2f0a77aa34087219a6e10b8b7d031e77')
     version('0.5.1', '0ed7059a9b480635e0dd33745e213d17')
     version('0.5.0', '2ab29a852e65ad85aae38925c5003654')
 
diff --git a/var/spack/repos/builtin/packages/zip/package.py b/var/spack/repos/builtin/packages/zip/package.py
index 255f254dee..139e503c87 100644
--- a/var/spack/repos/builtin/packages/zip/package.py
+++ b/var/spack/repos/builtin/packages/zip/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/zlib/package.py b/var/spack/repos/builtin/packages/zlib/package.py
index 4898bf2b77..eb34730906 100644
--- a/var/spack/repos/builtin/packages/zlib/package.py
+++ b/var/spack/repos/builtin/packages/zlib/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -54,7 +35,7 @@ class Zlib(Package):
     def libs(self):
         shared = '+shared' in self.spec
         return find_libraries(
-            ['libz'], root=self.prefix, recurse=True, shared=shared
+            ['libz'], root=self.prefix, recursive=True, shared=shared
         )
 
     def setup_environment(self, spack_env, run_env):
diff --git a/var/spack/repos/builtin/packages/zoltan/package.py b/var/spack/repos/builtin/packages/zoltan/package.py
index eb393d3990..3fd29e17c3 100644
--- a/var/spack/repos/builtin/packages/zoltan/package.py
+++ b/var/spack/repos/builtin/packages/zoltan/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 import re
@@ -33,7 +14,7 @@ class Zoltan(Package):
     """The Zoltan library is a toolkit of parallel combinatorial algorithms
        for parallel, unstructured, and/or adaptive scientific
        applications.  Zoltan's largest component is a suite of dynamic
-       load-balancing and paritioning algorithms that increase
+       load-balancing and partitioning algorithms that increase
        applications' parallel performance by reducing idle time.  Zoltan
        also has graph coloring and graph ordering algorithms, which are
        useful in task schedulers and parallel preconditioners.
@@ -53,9 +34,15 @@ class Zoltan(Package):
 
     variant('fortran', default=True, description='Enable Fortran support.')
     variant('mpi', default=True, description='Enable MPI support.')
+    variant('parmetis', default=False, description='Enable ParMETIS support.')
 
     depends_on('mpi', when='+mpi')
 
+    depends_on('parmetis@4:', when='+parmetis')
+    depends_on('metis', when='+parmetis')
+
+    conflicts('+parmetis', when='~mpi')
+
     def install(self, spec, prefix):
         # FIXME: The older Zoltan versions fail to compile the F90 MPI wrappers
         # because of some complicated generic type problem.
@@ -70,7 +57,7 @@ class Zoltan(Package):
         ]
         config_cflags = [
             '-O0' if '+debug' in spec else '-O3',
-            '-g' if '+debug' in spec else '-g0',
+            '-g' if '+debug' in spec else '',
         ]
 
         if '+shared' in spec:
@@ -78,7 +65,20 @@ class Zoltan(Package):
             config_args.append('--with-ar=$(CXX) -shared $(LDFLAGS) -o')
             config_cflags.append(self.compiler.pic_flag)
             if spec.satisfies('%gcc'):
-                config_args.append('--with-libs={0}'.format('-lgfortran'))
+                config_args.append('--with-libs=-lgfortran')
+            if spec.satisfies('%intel'):
+                config_args.append('--with-libs=-lifcore')
+
+        if '+parmetis' in spec:
+            config_args.append('--with-parmetis')
+            config_args.append('--with-parmetis-libdir={0}'
+                               .format(spec['parmetis'].prefix.lib))
+            config_args.append('--with-parmetis-incdir={0}'
+                               .format(spec['parmetis'].prefix.include))
+            config_args.append('--with-incdirs=-I{0}'
+                               .format(spec['metis'].prefix.include))
+            config_args.append('--with-ldflags=-L{0}'
+                               .format(spec['metis'].prefix.lib))
 
         if '+mpi' in spec:
             config_args.append('CC={0}'.format(spec['mpi'].mpicc))
diff --git a/var/spack/repos/builtin/packages/zsh/package.py b/var/spack/repos/builtin/packages/zsh/package.py
index 53b3c7d536..b03eb1f74e 100644
--- a/var/spack/repos/builtin/packages/zsh/package.py
+++ b/var/spack/repos/builtin/packages/zsh/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,10 +13,11 @@ class Zsh(AutotoolsPackage):
     """
 
     homepage = "http://www.zsh.org"
-    url = "http://downloads.sourceforge.net/project/zsh/zsh/5.1.1/zsh-5.1.1.tar.gz"
+    url = "http://downloads.sourceforge.net/project/zsh/zsh/5.4.2/zsh-5.4.2.tar.gz"
 
-    version('5.3.1', checksum='d583fbca0c2410bf9542ce8a651c26ca')
-    version('5.1.1', checksum='8ba28a9ef82e40c3a271602f18343b2f')
+    version('5.4.2', sha256='957bcdb2c57f64c02f673693ea5a7518ef24b6557aeb3a4ce222cefa6d74acc9')
+    version('5.3.1', sha256='3d94a590ff3c562ecf387da78ac356d6bea79b050a9ef81e3ecb9f8ee513040e')
+    version('5.1.1', sha256='94ed5b412023761bc8d2f03c173f13d625e06e5d6f0dff2c7a6e140c3fa55087')
 
     # Testing for terminal related things causes failures in e.g. Jenkins.
     # See e.g. https://www.zsh.org/mla/users/2003/msg00845.html,
diff --git a/var/spack/repos/builtin/packages/zstd/package.py b/var/spack/repos/builtin/packages/zstd/package.py
index 9387311fbb..1382aebb72 100644
--- a/var/spack/repos/builtin/packages/zstd/package.py
+++ b/var/spack/repos/builtin/packages/zstd/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,11 @@ class Zstd(MakefilePackage):
     version('1.3.0', '888660a850e33c2dcc7c4f9d0b04d347')
     version('1.1.2', '4c57a080d194bdaac83f2d3251fc7ffc')
 
+    variant('pic', default=True, description='Build position independent code')
+
+    def setup_environment(self, spack_env, run_env):
+        if '+pic' in self.spec:
+            spack_env.append_flags('CFLAGS', self.compiler.pic_flag)
+
     def install(self, spec, prefix):
         make('install', 'PREFIX={0}'.format(prefix))
diff --git a/var/spack/repos/tutorial/packages/armadillo/package.py b/var/spack/repos/tutorial/packages/armadillo/package.py
new file mode 100644
index 0000000000..d95a61f67d
--- /dev/null
+++ b/var/spack/repos/tutorial/packages/armadillo/package.py
@@ -0,0 +1,62 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Armadillo(CMakePackage):
+    """Armadillo is a high quality linear algebra library (matrix maths)
+    for the C++ language, aiming towards a good balance between speed and
+    ease of use.
+    """
+
+    homepage = "http://arma.sourceforge.net/"
+    url = "http://sourceforge.net/projects/arma/files/armadillo-7.200.1.tar.xz"
+
+    version('8.100.1', 'd9762d6f097e0451d0cfadfbda295e7c')
+    version('7.950.1', 'c06eb38b12cae49cab0ce05f96147147')
+    version('7.900.1', '5ef71763bd429a3d481499878351f3be')
+    version('7.500.0', '7d316fdf3c3c7ea92b64704180ae315d')
+    version('7.200.2', 'b21585372d67a8876117fd515d8cf0a2')
+    version('7.200.1', 'ed86d6df0058979e107502e1fe3e469e')
+
+    variant('hdf5', default=False, description='Include HDF5 support')
+
+    depends_on('cmake@2.8.12:', type='build')
+    depends_on('arpack-ng')  # old arpack causes undefined symbols
+    depends_on('blas')
+    depends_on('lapack')
+    depends_on('superlu@5.2:')
+    depends_on('hdf5', when='+hdf5')
+
+    patch('undef_linux.patch', when='platform=linux')
+
+    def cmake_args(self):
+        spec = self.spec
+
+        # TUTORIAL: fix the lines below by adding the appropriate query to
+        # the right dependency. To ask a dependency, e.g. `blas`, for the
+        # list of libraries it provides it suffices to access its `libs`
+        # attribute:
+        #
+        #    blas_libs = spec['blas'].libs
+        #
+        # The CMake variables below require a semicolon separated list:
+        #
+        #    blas_libs.joined(';')
+
+        return [
+            # ARPACK support
+            '-DARPACK_LIBRARY={0}'.format('FIXME: arpack-ng'),
+            # BLAS support
+            '-DBLAS_LIBRARY={0}'.format('FIXME: blas'),
+            # LAPACK support
+            '-DLAPACK_LIBRARY={0}'.format('FIXME: lapack'),
+            # SuperLU support
+            '-DSuperLU_INCLUDE_DIR={0}'.format(spec['superlu'].prefix.include),
+            '-DSuperLU_LIBRARY={0}'.format('FIXME: superlu'),
+            # HDF5 support
+            '-DDETECT_HDF5={0}'.format('ON' if '+hdf5' in spec else 'OFF')
+        ]
diff --git a/var/spack/repos/tutorial/packages/armadillo/undef_linux.patch b/var/spack/repos/tutorial/packages/armadillo/undef_linux.patch
new file mode 100644
index 0000000000..68b434dca8
--- /dev/null
+++ b/var/spack/repos/tutorial/packages/armadillo/undef_linux.patch
@@ -0,0 +1,4 @@
+--- a/include/armadillo_bits/compiler_setup.hpp
++++ b/include/armadillo_bits/compiler_setup.hpp
+@@ -0,0 +1 @@
++#undef linux
diff --git a/var/spack/repos/tutorial/packages/elpa/package.py b/var/spack/repos/tutorial/packages/elpa/package.py
new file mode 100644
index 0000000000..386295eea9
--- /dev/null
+++ b/var/spack/repos/tutorial/packages/elpa/package.py
@@ -0,0 +1,78 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Elpa(AutotoolsPackage):
+    """Eigenvalue solvers for Petaflop-Applications (ELPA)"""
+
+    homepage = 'http://elpa.mpcdf.mpg.de/'
+    url = 'http://elpa.mpcdf.mpg.de/elpa-2015.11.001.tar.gz'
+
+    version('2018.05.001.rc1', 'ccd77bd8036988ee624f43c04992bcdd')
+    version('2017.11.001', '4a437be40cc966efb07aaab84c20cd6e', preferred=True)
+    version('2017.05.003', '7c8e5e58cafab212badaf4216695700f')
+    version('2017.05.002', 'd0abc1ac1f493f93bf5e30ec8ab155dc')
+    version('2016.11.001.pre', '5656fd066cf0dcd071dbcaf20a639b37')
+    version('2016.05.004', 'c0dd3a53055536fc3a2a221e78d8b376')
+    version('2016.05.003', '88a9f3f3bfb63e16509dd1be089dcf2c')
+    version('2015.11.001', 'de0f35b7ee7c971fd0dca35c900b87e6')
+
+    variant('openmp', default=False, description='Activates OpenMP support')
+    variant('optflags', default=True, description='Build with optimization flags')
+
+    depends_on('mpi')
+    depends_on('blas')
+    depends_on('lapack')
+    depends_on('scalapack')
+
+    def url_for_version(self, version):
+        t = 'http://elpa.mpcdf.mpg.de/html/Releases/{0}/elpa-{0}.tar.gz'
+        if version < Version('2016.05.003'):
+            t = 'http://elpa.mpcdf.mpg.de/elpa-{0}.tar.gz'
+        return t.format(str(version))
+
+    @property
+    def libs(self):
+        libname = 'libelpa_openmp' if '+openmp' in self.spec else 'libelpa'
+        return find_libraries(
+            libname, root=self.prefix, shared=True, recursive=True
+        )
+
+    build_directory = 'spack-build'
+
+    def setup_environment(self, spack_env, run_env):
+        # TUTORIAL: set the following environment variables:
+        #
+        # CC=spec['mpi'].mpicc
+        # FC=spec['mpi'].mpifc
+        # CXX=spec['mpi'].mpicxx
+        # SCALAPACK_LDFLAGS=spec['scalapack'].libs.joined()
+        #
+        # and append the following flags:
+        #
+        # LDFLAGS -> spec['lapack'].libs.search_flags
+        # LIBS -> spec['lapack'].libs.link_flags
+        pass
+
+    def configure_args(self):
+        # TODO: set optimum flags for platform+compiler combo, see
+        # https://github.com/hfp/xconfigure/tree/master/elpa
+        # also see:
+        # https://src.fedoraproject.org/cgit/rpms/elpa.git/
+        # https://packages.qa.debian.org/e/elpa.html
+        options = []
+        # without -march=native there is configure error for 2017.05.02
+        # Could not compile test program, try with --disable-sse, or
+        # adjust the C compiler or CFLAGS
+        if '+optflags' in self.spec:
+            options.extend([
+                'FCFLAGS=-O2 -march=native -ffree-line-length-none',
+                'CFLAGS=-O2 -march=native'
+            ])
+        if '+openmp' in self.spec:
+            options.append('--enable-openmp')
+        return options
diff --git a/var/spack/repos/tutorial/packages/hdf5/h5f90global-mult-obj-same-equivalence-same-common-block.patch b/var/spack/repos/tutorial/packages/hdf5/h5f90global-mult-obj-same-equivalence-same-common-block.patch
new file mode 100644
index 0000000000..8bf5c142e9
--- /dev/null
+++ b/var/spack/repos/tutorial/packages/hdf5/h5f90global-mult-obj-same-equivalence-same-common-block.patch
@@ -0,0 +1,16 @@
+diff --git a/fortran/src/H5f90global.F90 b/fortran/src/H5f90global.F90
+index dd2b171..629418a 100644
+--- a/fortran/src/H5f90global.F90
++++ b/fortran/src/H5f90global.F90
+@@ -142,10 +142,7 @@ MODULE H5GLOBAL
+
+   INTEGER(HID_T), DIMENSION(PREDEF_TYPES_LEN) :: predef_types
+   EQUIVALENCE (predef_types(1), H5T_NATIVE_INTEGER_KIND(1))
+-  EQUIVALENCE (predef_types(2), H5T_NATIVE_INTEGER_KIND(2))
+-  EQUIVALENCE (predef_types(3), H5T_NATIVE_INTEGER_KIND(3))
+-  EQUIVALENCE (predef_types(4), H5T_NATIVE_INTEGER_KIND(4))
+-  EQUIVALENCE (predef_types(5), H5T_NATIVE_INTEGER_KIND(5))
++  ! EQUIVALENCE predef_types(2:5) are unnecessary and violate the standard
+   EQUIVALENCE (predef_types(6), H5T_NATIVE_INTEGER)
+   EQUIVALENCE (predef_types(7), H5T_NATIVE_REAL)
+   EQUIVALENCE (predef_types(8), H5T_NATIVE_DOUBLE)
diff --git a/var/spack/repos/tutorial/packages/hdf5/package.py b/var/spack/repos/tutorial/packages/hdf5/package.py
new file mode 100644
index 0000000000..b879d81f1c
--- /dev/null
+++ b/var/spack/repos/tutorial/packages/hdf5/package.py
@@ -0,0 +1,307 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import shutil
+import sys
+
+from spack import *
+
+
+class Hdf5(AutotoolsPackage):
+    """HDF5 is a data model, library, and file format for storing and managing
+    data. It supports an unlimited variety of datatypes, and is designed for
+    flexible and efficient I/O and for high volume and complex data.
+    """
+
+    homepage = "https://support.hdfgroup.org/HDF5/"
+    url      = "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.1/src/hdf5-1.10.1.tar.gz"
+    list_url = "https://support.hdfgroup.org/ftp/HDF5/releases"
+    list_depth = 3
+
+    version('1.10.4', '8f60dc4dd6ab5fcd23c750d1dc5bca3d0453bdce5c8cdaf0a4a61a9d1122adb2')
+    version('1.10.3', 'b600d7c914cfa80ae127cd1a1539981213fee9994ac22ebec9e3845e951d9b39')
+    version('1.10.2', '8d4eae84e533efa57496638fd0dca8c3')
+    version('1.10.1', '43a2f9466702fb1db31df98ae6677f15')
+    version('1.10.0-patch1', '9180ff0ef8dc2ef3f61bd37a7404f295')
+    version('1.10.0', 'bdc935337ee8282579cd6bc4270ad199')
+    version('1.8.19', '7f568e2464d4ab0a74d16b23956d900b')
+    version('1.8.18', 'dd2148b740713ca0295442ec683d7b1c')
+    version('1.8.17', '7d572f8f3b798a628b8245af0391a0ca')
+    version('1.8.16', 'b8ed9a36ae142317f88b0c7ef4b9c618')
+    version('1.8.15', '03cccb5b33dbe975fdcd8ae9dc021f24')
+    version('1.8.14', 'a482686e733514a51cde12d6fe5c5d95')
+    version('1.8.13', 'c03426e9e77d7766944654280b467289')
+    version('1.8.12', 'd804802feb99b87fc668a90e6fa34411')
+    version('1.8.10', '710aa9fb61a51d61a7e2c09bf0052157')
+
+    variant('debug', default=False,
+            description='Builds a debug version of the library')
+    variant('shared', default=True,
+            description='Builds a shared version of the library')
+
+    variant('hl', default=False, description='Enable the high-level library')
+    variant('cxx', default=False, description='Enable C++ support')
+    variant('fortran', default=False, description='Enable Fortran support')
+    variant('threadsafe', default=False,
+            description='Enable thread-safe capabilities')
+
+    variant('mpi', default=True, description='Enable MPI support')
+    variant('szip', default=False, description='Enable szip support')
+    variant('pic', default=True,
+            description='Produce position-independent code (for shared libs)')
+
+    depends_on('mpi', when='+mpi')
+    # numactl does not currently build on darwin
+    if sys.platform != 'darwin':
+        depends_on('numactl', when='+mpi+fortran')
+    depends_on('szip', when='+szip')
+    depends_on('zlib@1.1.2:')
+
+    # There are several officially unsupported combinations of the features:
+    # 1. Thread safety is not guaranteed via high-level C-API but in some cases
+    #    it works.
+    # conflicts('+threadsafe+hl')
+
+    # 2. Thread safety is not guaranteed via Fortran (CXX) API, but it's
+    #    possible for a dependency tree to contain a package that uses Fortran
+    #    (CXX) API in a single thread and another one that uses low-level C-API
+    #    in multiple threads. To allow for such scenarios, we don't specify the
+    #    following conflicts.
+    # conflicts('+threadsafe+cxx')
+    # conflicts('+threadsafe+fortran')
+
+    # 3. Parallel features are not supported via CXX API, but for the reasons
+    #    described in #2 we allow for such combination.
+    # conflicts('+mpi+cxx')
+
+    # There are known build failures with intel@18.0.1. This issue is
+    # discussed and patch is provided at
+    # https://software.intel.com/en-us/forums/intel-fortran-compiler-for-linux-and-mac-os-x/topic/747951.
+    patch('h5f90global-mult-obj-same-equivalence-same-common-block.patch',
+          when='@1.10.1%intel@18')
+
+    # Turn line comments into block comments to conform with pre-C99 language
+    # standards. Versions of hdf5 after 1.8.10 don't require this patch,
+    # either because they conform to pre-C99 or neglect to ask for pre-C99
+    # language standards from their compiler. The hdf5 build system adds
+    # the -ansi cflag (run 'man gcc' for info on -ansi) for some versions
+    # of some compilers (see hdf5-1.8.10/config/gnu-flags). The hdf5 build
+    # system does not provide an option to disable -ansi, but since the
+    # pre-C99 code is restricted to just five lines of line comments in
+    # three src files, this patch accomplishes the simple task of patching the
+    # three src files and leaves the hdf5 build system alone.
+    patch('pre-c99-comments.patch', when='@1.8.10')
+
+    # There are build errors with GCC 8, see
+    # https://forum.hdfgroup.org/t/1-10-2-h5detect-compile-error-gcc-8-1-0-on-centos-7-2-solved/4441
+    patch('https://salsa.debian.org/debian-gis-team/hdf5/raw/bf94804af5f80f662cad80a5527535b3c6537df6/debian/patches/gcc-8.patch', sha256='57cee5ff1992b4098eda079815c36fc2da9b10e00a9056df054f2384c4fc7523', when='@1.10.2%gcc@8:')
+
+    filter_compiler_wrappers('h5cc', 'h5c++', 'h5fc', relative_root='bin')
+
+    def url_for_version(self, version):
+        url = "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-{0}/hdf5-{1}/src/hdf5-{1}.tar.gz"
+        return url.format(version.up_to(2), version)
+
+    @property
+    def libs(self):
+        """HDF5 can be queried for the following parameters:
+
+        - "hl": high-level interface
+        - "cxx": C++ APIs
+        - "fortran": Fortran APIs
+
+        :return: list of matching libraries
+        """
+        # This map contains a translation from query_parameters
+        # to the libraries needed
+        query2libraries = {  # noqa: F841
+            tuple(): ['libhdf5'],
+            ('cxx', 'fortran', 'hl'): [
+                'libhdf5hl_fortran',
+                'libhdf5_hl_cpp',
+                'libhdf5_hl',
+                'libhdf5_fortran',
+                'libhdf5',
+            ],
+            ('cxx', 'hl'): [
+                'libhdf5_hl_cpp',
+                'libhdf5_hl',
+                'libhdf5',
+            ],
+            ('fortran', 'hl'): [
+                'libhdf5hl_fortran',
+                'libhdf5_hl',
+                'libhdf5_fortran',
+                'libhdf5',
+            ],
+            ('hl',): [
+                'libhdf5_hl',
+                'libhdf5',
+            ],
+            ('cxx', 'fortran'): [
+                'libhdf5_fortran',
+                'libhdf5_cpp',
+                'libhdf5',
+            ],
+            ('cxx',): [
+                'libhdf5_cpp',
+                'libhdf5',
+            ],
+            ('fortran',): [
+                'libhdf5_fortran',
+                'libhdf5',
+            ]
+        }
+
+        # TUTORIAL: you need to fix the implementation below, and
+        # return the correct list of libraries according to the
+        # query parameters your dependency has used.
+        #
+        # You can retrieve the query parameters by doing
+        #
+        # query_parameters = self.spec.last_query.extra_parameters
+        #
+        # and use the map above to query the list of libraries you need
+        # to search.
+        #
+        # Finally uncomment the lines below to return a LibraryList
+        #
+        # shared = '+shared' in self.spec
+        # return find_libraries(
+        #     libraries, root=self.prefix, shared=shared, recursive=True
+        # )
+        return []
+
+    @run_before('configure')
+    def fortran_check(self):
+        if '+fortran' in self.spec and not self.compiler.fc:
+            msg = 'cannot build a Fortran variant without a Fortran compiler'
+            raise RuntimeError(msg)
+
+    def configure_args(self):
+        # Always enable this option. This does not actually enable any
+        # features: it only *allows* the user to specify certain
+        # combinations of other arguments. Enabling it just skips a
+        # sanity check in configure, so this doesn't merit a variant.
+        extra_args = ['--enable-unsupported']
+        extra_args += self.enable_or_disable('threadsafe')
+        extra_args += self.enable_or_disable('cxx')
+        extra_args += self.enable_or_disable('hl')
+        extra_args += self.enable_or_disable('fortran')
+
+        if '+szip' in self.spec:
+            extra_args.append('--with-szlib=%s' % self.spec['szip'].prefix)
+        else:
+            extra_args.append('--without-szlib')
+
+        if self.spec.satisfies('@1.10:'):
+            if '+debug' in self.spec:
+                extra_args.append('--enable-build-mode=debug')
+            else:
+                extra_args.append('--enable-build-mode=production')
+        else:
+            if '+debug' in self.spec:
+                extra_args.append('--enable-debug=all')
+            else:
+                extra_args.append('--enable-production')
+
+            # '--enable-fortran2003' no longer exists as of version 1.10.0
+            if '+fortran' in self.spec:
+                extra_args.append('--enable-fortran2003')
+            else:
+                extra_args.append('--disable-fortran2003')
+
+        if '+shared' in self.spec:
+            extra_args.append('--enable-shared')
+        else:
+            extra_args.append('--disable-shared')
+            extra_args.append('--enable-static-exec')
+
+        if '+pic' in self.spec:
+            extra_args += ['%s=%s' % (f, self.compiler.pic_flag)
+                           for f in ['CFLAGS', 'CXXFLAGS', 'FCFLAGS']]
+
+        if '+mpi' in self.spec:
+            # The HDF5 configure script warns if cxx and mpi are enabled
+            # together. There doesn't seem to be a real reason for this, except
+            # that parts of the MPI interface are not accessible via the C++
+            # interface. Since they are still accessible via the C interface,
+            # this is not actually a problem.
+            extra_args += ['--enable-parallel',
+                           'CC=%s' % self.spec['mpi'].mpicc]
+
+            if '+cxx' in self.spec:
+                extra_args.append('CXX=%s' % self.spec['mpi'].mpicxx)
+
+            if '+fortran' in self.spec:
+                extra_args.append('FC=%s' % self.spec['mpi'].mpifc)
+
+        extra_args.append('--with-zlib=%s' % self.spec['zlib'].prefix)
+
+        return extra_args
+
+    @run_after('configure')
+    def patch_postdeps(self):
+        if '@:1.8.14' in self.spec:
+            # On Ubuntu14, HDF5 1.8.12 (and maybe other versions)
+            # mysteriously end up with "-l -l" in the postdeps in the
+            # libtool script.  Patch this by removing the spurious -l's.
+            filter_file(
+                r'postdeps="([^"]*)"',
+                lambda m: 'postdeps="%s"' % ' '.join(
+                    arg for arg in m.group(1).split(' ') if arg != '-l'),
+                'libtool')
+
+    @run_after('install')
+    @on_package_attributes(run_tests=True)
+    def check_install(self):
+        # Build and run a small program to test the installed HDF5 library
+        spec = self.spec
+        print("Checking HDF5 installation...")
+        checkdir = "spack-check"
+        with working_dir(checkdir, create=True):
+            source = r"""
+#include <hdf5.h>
+#include <assert.h>
+#include <stdio.h>
+int main(int argc, char **argv) {
+  unsigned majnum, minnum, relnum;
+  herr_t herr = H5get_libversion(&majnum, &minnum, &relnum);
+  assert(!herr);
+  printf("HDF5 version %d.%d.%d %u.%u.%u\n", H5_VERS_MAJOR, H5_VERS_MINOR,
+         H5_VERS_RELEASE, majnum, minnum, relnum);
+  return 0;
+}
+"""
+            expected = """\
+HDF5 version {version} {version}
+""".format(version=str(spec.version.up_to(3)))
+            with open("check.c", 'w') as f:
+                f.write(source)
+            if '+mpi' in spec:
+                cc = Executable(spec['mpi'].mpicc)
+            else:
+                cc = Executable(self.compiler.cc)
+            cc(*(['-c', "check.c"] + spec['hdf5'].headers.cpp_flags.split()))
+            cc(*(['-o', "check",
+                  "check.o"] + spec['hdf5'].libs.ld_flags.split()))
+            try:
+                check = Executable('./check')
+                output = check(output=str)
+            except ProcessError:
+                output = ""
+            success = output == expected
+            if not success:
+                print("Produced output does not match expected output.")
+                print("Expected output:")
+                print('-' * 80)
+                print(expected)
+                print('-' * 80)
+                print("Produced output:")
+                print('-' * 80)
+                print(output)
+                print('-' * 80)
+                raise RuntimeError("HDF5 install check failed")
+        shutil.rmtree(checkdir)
diff --git a/var/spack/repos/tutorial/packages/hdf5/pre-c99-comments.patch b/var/spack/repos/tutorial/packages/hdf5/pre-c99-comments.patch
new file mode 100644
index 0000000000..97743e8fa5
--- /dev/null
+++ b/var/spack/repos/tutorial/packages/hdf5/pre-c99-comments.patch
@@ -0,0 +1,43 @@
+diff --git a/test/th5s.c b/test/th5s.c
+index 462bc36..8e18fad 100644
+--- a/test/th5s.c
++++ b/test/th5s.c
+@@ -730,8 +730,8 @@ test_h5s_zero_dim(void)
+         ret = H5Pset_chunk(plist_id, SPACE1_RANK, chunk_dims);
+         CHECK(ret, FAIL, "H5Pset_chunk");
+ 
+-        // ret = H5Pset_alloc_time(plist_id, alloc_time);
+-        // CHECK(ret, FAIL, "H5Pset_alloc_time");
++        /* ret = H5Pset_alloc_time(plist_id, alloc_time); */
++        /* CHECK(ret, FAIL, "H5Pset_alloc_time"); */
+ 
+         dset1 = H5Dcreate2(fid1, BASICDATASET1, H5T_NATIVE_INT, sid_chunk, H5P_DEFAULT, plist_id, H5P_DEFAULT);
+         CHECK(dset1, FAIL, "H5Dcreate2");
+diff --git a/tools/h5dump/h5dump_ddl.c b/tools/h5dump/h5dump_ddl.c
+index ee6de5e..3ed6045 100644
+--- a/tools/h5dump/h5dump_ddl.c
++++ b/tools/h5dump/h5dump_ddl.c
+@@ -1341,8 +1341,8 @@ handle_attributes(hid_t fid, const char *attr, void UNUSED * data, int UNUSED pe
+     string_dataformat.do_escape = display_escape;
+     outputformat = &string_dataformat;
+ 
+-    //attr_name = attr + j + 1;
+-	// need to replace escape characters
++    /* attr_name = attr + j + 1; */
++	/* need to replace escape characters */
+ 	attr_name = h5tools_str_replace(attr + j + 1, "\\/", "/");
+ 
+ 
+diff --git a/tools/lib/h5tools_str.c b/tools/lib/h5tools_str.c
+index 9ce3524..3b4e5e7 100644
+--- a/tools/lib/h5tools_str.c
++++ b/tools/lib/h5tools_str.c
+@@ -632,7 +632,7 @@ h5tools_str_indent(h5tools_str_t *str, const h5tool_format_t *info,
+         h5tools_str_append(str, "%s", OPT(info->line_indent, ""));
+     }
+ 
+-//    ctx->need_prefix = 0;
++/*    ctx->need_prefix = 0; */
+ }
+ 
+ /*-------------------------------------------------------------------------
diff --git a/var/spack/repos/tutorial/packages/mpich/mpich32_clang.patch b/var/spack/repos/tutorial/packages/mpich/mpich32_clang.patch
new file mode 100644
index 0000000000..01243072f7
--- /dev/null
+++ b/var/spack/repos/tutorial/packages/mpich/mpich32_clang.patch
@@ -0,0 +1,13 @@
+diff --git a/src/include/mpiimpl.h b/src/include/mpiimpl.h
+index e705e5d..3bfcbee 100644
+--- a/src/include/mpiimpl.h
++++ b/src/include/mpiimpl.h
+@@ -1528,7 +1528,7 @@ typedef struct MPID_Request {
+ #ifdef MPID_DEV_REQUEST_DECL
+     MPID_DEV_REQUEST_DECL
+ #endif
+-} MPID_Request ATTRIBUTE((__aligned__(32)));
++} ATTRIBUTE((__aligned__(32))) MPID_Request;
+ 
+ extern MPIU_Object_alloc_t MPID_Request_mem;
+ /* Preallocated request objects */
diff --git a/var/spack/repos/tutorial/packages/mpich/package.py b/var/spack/repos/tutorial/packages/mpich/package.py
new file mode 100644
index 0000000000..c3e0b8a54b
--- /dev/null
+++ b/var/spack/repos/tutorial/packages/mpich/package.py
@@ -0,0 +1,155 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class Mpich(AutotoolsPackage):
+    """MPICH is a high performance and widely portable implementation of
+    the Message Passing Interface (MPI) standard."""
+
+    homepage = "http://www.mpich.org"
+    url      = "http://www.mpich.org/static/downloads/3.0.4/mpich-3.0.4.tar.gz"
+    git      = "https://github.com/pmodels/mpich.git"
+    list_url = "http://www.mpich.org/static/downloads/"
+    list_depth = 1
+
+    version('develop', submodules=True)
+    version('3.2.1', 'e175452f4d61646a52c73031683fc375')
+    version('3.2',   'f414cfa77099cd1fa1a5ae4e22db508a')
+    version('3.1.4', '2ab544607986486562e076b83937bba2')
+    version('3.1.3', '93cb17f91ac758cbf9174ecb03563778')
+    version('3.1.2', '7fbf4b81dcb74b07ae85939d1ceee7f1')
+    version('3.1.1', '40dc408b1e03cc36d80209baaa2d32b7')
+    version('3.1',   '5643dd176499bfb7d25079aaff25f2ec')
+    version('3.0.4', '9c5d5d4fe1e17dd12153f40bc5b6dbc0')
+
+    variant('hydra', default=True,  description='Build the hydra process manager')
+    variant('pmi',   default=True,  description='Build with PMI support')
+    variant('romio', default=True,  description='Enable ROMIO MPI I/O implementation')
+    variant('verbs', default=False, description='Build support for OpenFabrics verbs.')
+    variant(
+        'device',
+        default='ch3',
+        description='''Abstract Device Interface (ADI)
+implementation. The ch4 device is currently in experimental state''',
+        values=('ch3', 'ch4'),
+        multi=False
+    )
+    variant(
+        'netmod',
+        default='tcp',
+        description='''Network module. Only single netmod builds are
+supported. For ch3 device configurations, this presumes the
+ch3:nemesis communication channel. ch3:sock is not supported by this
+spack package at this time.''',
+        values=('tcp', 'mxm', 'ofi', 'ucx'),
+        multi=False
+    )
+
+    provides('mpi')
+    provides('mpi@:3.0', when='@3:')
+    provides('mpi@:1.3', when='@1:')
+
+    filter_compiler_wrappers(
+        'mpicc', 'mpicxx', 'mpif77', 'mpif90', 'mpifort', relative_root='bin'
+    )
+
+    # fix MPI_Barrier segmentation fault
+    # see https://lists.mpich.org/pipermail/discuss/2016-May/004764.html
+    # and https://lists.mpich.org/pipermail/discuss/2016-June/004768.html
+    patch('mpich32_clang.patch', when='@3.2:3.2.0%clang')
+
+    depends_on('findutils', type='build')
+
+    depends_on('libfabric', when='netmod=ofi')
+
+    conflicts('device=ch4', when='@:3.2')
+    conflicts('netmod=ofi', when='@:3.1.4')
+    conflicts('netmod=ucx', when='device=ch3')
+    conflicts('netmod=mxm', when='device=ch4')
+    conflicts('netmod=mxm', when='@:3.1.3')
+    conflicts('netmod=tcp', when='device=ch4')
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        # TUTORIAL: set the following variables for dependents:
+        #
+        # MPICC=join_path(self.prefix.bin, 'mpicc')
+        # MPICXX=join_path(self.prefix.bin, 'mpic++')
+        # MPIF77=join_path(self.prefix.bin, 'mpif77')
+        # MPIF90=join_path(self.prefix.bin, 'mpif90')
+        # MPICH_CC=spack_cc
+        # MPICH_CXX=spack_cxx
+        # MPICH_F77=spack_f77
+        # MPICH_F90=spack_fc
+        # MPICH_FC=spack_fc
+        pass
+
+    def setup_dependent_package(self, module, dependent_spec):
+        if 'platform=cray' in self.spec:
+            self.spec.mpicc = spack_cc
+            self.spec.mpicxx = spack_cxx
+            self.spec.mpifc = spack_fc
+            self.spec.mpif77 = spack_f77
+        else:
+            self.spec.mpicc = join_path(self.prefix.bin, 'mpicc')
+            self.spec.mpicxx = join_path(self.prefix.bin, 'mpic++')
+            self.spec.mpifc = join_path(self.prefix.bin, 'mpif90')
+            self.spec.mpif77 = join_path(self.prefix.bin, 'mpif77')
+
+        self.spec.mpicxx_shared_libs = [
+            join_path(self.prefix.lib, 'libmpicxx.{0}'.format(dso_suffix)),
+            join_path(self.prefix.lib, 'libmpi.{0}'.format(dso_suffix))
+        ]
+
+    def autoreconf(self, spec, prefix):
+        """Not needed usually, configure should be already there"""
+        # If configure exists nothing needs to be done
+        if os.path.exists(self.configure_abs_path):
+            return
+        # Else bootstrap with autotools
+        bash = which('bash')
+        bash('./autogen.sh')
+
+    @run_before('autoreconf')
+    def die_without_fortran(self):
+        # Until we can pass variants such as +fortran through virtual
+        # dependencies depends_on('mpi'), require Fortran compiler to
+        # avoid delayed build errors in dependents.
+        if (self.compiler.f77 is None) or (self.compiler.fc is None):
+            raise InstallError(
+                'Mpich requires both C and Fortran compilers!'
+            )
+
+    def configure_args(self):
+        spec = self.spec
+        config_args = [
+            '--enable-shared',
+            '--with-pm={0}'.format('hydra' if '+hydra' in spec else 'no'),
+            '--with-pmi={0}'.format('yes' if '+pmi' in spec else 'no'),
+            '--{0}-romio'.format('enable' if '+romio' in spec else 'disable'),
+            '--{0}-ibverbs'.format('with' if '+verbs' in spec else 'without')
+        ]
+
+        # setup device configuration
+        device_config = ''
+        if 'device=ch4' in spec:
+            device_config = '--with-device=ch4:'
+        elif 'device=ch3' in spec:
+            device_config = '--with-device=ch3:nemesis:'
+
+        if 'netmod=ucx' in spec:
+            device_config += 'ucx'
+        elif 'netmod=ofi' in spec:
+            device_config += 'ofi'
+        elif 'netmod=mxm' in spec:
+            device_config += 'mxm'
+        elif 'netmod=tcp' in spec:
+            device_config += 'tcp'
+
+        config_args.append(device_config)
+
+        return config_args
diff --git a/var/spack/repos/tutorial/packages/netlib-lapack/ibm-xl.patch b/var/spack/repos/tutorial/packages/netlib-lapack/ibm-xl.patch
new file mode 100644
index 0000000000..c6fba2a028
--- /dev/null
+++ b/var/spack/repos/tutorial/packages/netlib-lapack/ibm-xl.patch
@@ -0,0 +1,42 @@
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -62,7 +62,7 @@
+     set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fp-model strict")
+   endif()
+   if("${CMAKE_Fortran_COMPILER}" MATCHES "xlf")
+-    set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -qnosave -qstrict=none")
++    set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -qnosave -qstrict")
+   endif()
+ # Delete libmtsk in linking sequence for Sun/Oracle Fortran Compiler.
+ # This library is not present in the Sun package SolarisStudio12.3-linux-x86-bin
+
+--- a/CMAKE/CheckLAPACKCompilerFlags.cmake
++++ b/CMAKE/CheckLAPACKCompilerFlags.cmake
+@@ -43,12 +43,6 @@
+   if( "${CMAKE_Fortran_FLAGS}" MATCHES "-qflttrap=[a-zA-Z:]:enable" )
+     set( FPE_EXIT TRUE )
+   endif()
+-
+-  if( NOT ("${CMAKE_Fortran_FLAGS}" MATCHES "-qfixed") )
+-    message( STATUS "Enabling fixed format F90/F95 with -qfixed" )
+-    set( CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -qfixed"
+-         CACHE STRING "Flags for Fortran compiler." FORCE )
+-  endif()
+ 
+ # HP Fortran
+ elseif( CMAKE_Fortran_COMPILER_ID STREQUAL "HP" )
+
+--- a/CBLAS/CMakeLists.txt
++++ b/CBLAS/CMakeLists.txt
+@@ -12,8 +12,8 @@
+                          SYMBOL_NAMESPACE "F77_")
+ if(NOT FortranCInterface_GLOBAL_FOUND OR NOT FortranCInterface_MODULE_FOUND)
+   message(WARNING "Reverting to pre-defined include/lapacke_mangling.h")
+-  configure_file(include/lapacke_mangling_with_flags.h.in
+-                 ${LAPACK_BINARY_DIR}/include/lapacke_mangling.h)
++  configure_file(include/cblas_mangling_with_flags.h.in
++                 ${LAPACK_BINARY_DIR}/include/cblas_mangling.h)
+ endif()
+ 
+ include_directories(include ${LAPACK_BINARY_DIR}/include)
+
diff --git a/var/spack/repos/tutorial/packages/netlib-lapack/package.py b/var/spack/repos/tutorial/packages/netlib-lapack/package.py
new file mode 100644
index 0000000000..ef43b8a2e0
--- /dev/null
+++ b/var/spack/repos/tutorial/packages/netlib-lapack/package.py
@@ -0,0 +1,186 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class NetlibLapack(CMakePackage):
+    """LAPACK version 3.X is a comprehensive FORTRAN library that does
+    linear algebra operations including matrix inversions, least squared
+    solutions to linear sets of equations, eigenvector analysis, singular
+    value decomposition, etc. It is a very comprehensive and reputable
+    package that has found extensive use in the scientific community.
+
+    """
+    homepage = "http://www.netlib.org/lapack/"
+    url = "http://www.netlib.org/lapack/lapack-3.5.0.tgz"
+
+    version('3.8.0', '96591affdbf58c450d45c1daa540dbd2',
+            url='http://www.netlib.org/lapack/lapack-3.8.0.tar.gz')
+    version('3.7.1', 'dcdeeed73de152c4643ccc5b1aeb453c')
+    version('3.7.0', '697bb8d67c7d336a0f339cc9dd0fa72f')
+    version('3.6.1', '421b2cb72e15f237e144428f9c460ee0')
+    version('3.6.0', 'f2f6c67134e851fe189bb3ca1fbb5101')
+    version('3.5.0', 'b1d3e3e425b2e44a06760ff173104bdf')
+    version('3.4.2', '61bf1a8a4469d4bdb7604f5897179478')
+    version('3.4.1', '44c3869c38c8335c2b9c2a8bb276eb55')
+    version('3.4.0', '02d5706ec03ba885fc246e5fa10d8c70')
+    version('3.3.1', 'd0d533ec9a5b74933c2a1e84eedc58b4')
+
+    variant('shared', default=True, description="Build shared library version")
+    variant('external-blas', default=False,
+            description='Build lapack with an external blas')
+
+    variant('lapacke', default=True,
+            description='Activates the build of the LAPACKE C interface')
+    variant('xblas', default=False,
+            description='Builds extended precision routines using XBLAS')
+
+    patch('ibm-xl.patch', when='@3.7: %xl')
+    patch('ibm-xl.patch', when='@3.7: %xl_r')
+
+    # https://github.com/Reference-LAPACK/lapack/issues/228
+    # TODO: update 'when' once the version of lapack
+    # containing the fix is released and added to Spack.
+    patch('undefined_declarations.patch', when='@3.8.0:')
+
+    # https://github.com/Reference-LAPACK/lapack/pull/268
+    # TODO: update 'when' once the version of lapack
+    # containing the fix is released and added to Spack.
+    patch('testing.patch', when='@3.7.0:')
+
+    # virtual dependency
+    provides('blas', when='~external-blas')
+    provides('lapack')
+
+    depends_on('blas', when='+external-blas')
+    depends_on('netlib-xblas+fortran+plain_blas', when='+xblas')
+    depends_on('python@2.7:', type='test')
+
+    # We need to run every phase twice in order to get static and shared
+    # versions of the libraries. When ~shared, we run the default
+    # implementations of the CMakePackage's phases and get only one building
+    # directory 'spack-build-static' with -DBUILD_SHARED_LIBS:BOOL=OFF (see
+    # implementations of self.build_directory and self.cmake_args() below).
+    # When +shared, we run the overridden methods for the phases, each
+    # running the default implementation twice with different values for
+    # self._building_shared. As a result, we get two building directories:
+    # 'spack-build-static' with -DBUILD_SHARED_LIBS:BOOL=OFF and
+    # 'spack-build-shared' with -DBUILD_SHARED_LIBS:BOOL=ON.
+    _building_shared = False
+
+    def patch(self):
+        # Fix cblas CMakeLists.txt -- has wrong case for subdirectory name.
+        if self.spec.satisfies('@3.6.0:'):
+            filter_file(
+                '${CMAKE_CURRENT_SOURCE_DIR}/CMAKE/',
+                '${CMAKE_CURRENT_SOURCE_DIR}/cmake/',
+                'CBLAS/CMakeLists.txt', string=True)
+
+    @property
+    def blas_libs(self):
+        shared = True if '+shared' in self.spec else False
+        query_parameters = self.spec.last_query.extra_parameters
+        query2libraries = {
+            tuple(): ['libblas'],
+            ('c', 'fortran'): [
+                'libcblas',
+                'libblas',
+            ],
+            ('c',): [
+                'libcblas',
+            ],
+            ('fortran',): [
+                'libblas',
+            ]
+        }
+        key = tuple(sorted(query_parameters))
+        libraries = query2libraries[key]
+        return find_libraries(
+            libraries, root=self.prefix, shared=shared, recursive=True
+        )
+
+    # TUTORIAL: add a proper `lapack_lib` property, along the lines
+    # of the `blas_lib` property above. The library that provides
+    # the lapack API is called `liblapack`.
+
+    @property
+    def headers(self):
+        include_dir = self.spec.prefix.include
+        cblas_h = join_path(include_dir, 'cblas.h')
+        lapacke_h = join_path(include_dir, 'lapacke.h')
+        return HeaderList([cblas_h, lapacke_h])
+
+    @property
+    def build_directory(self):
+        return join_path(self.stage.source_path,
+                         'spack-build-shared' if self._building_shared
+                         else 'spack-build-static')
+
+    def cmake_args(self):
+        args = ['-DBUILD_SHARED_LIBS:BOOL=' +
+                ('ON' if self._building_shared else 'OFF')]
+
+        if self.spec.satisfies('+lapacke'):
+            args.extend(['-DLAPACKE:BOOL=ON', '-DLAPACKE_WITH_TMG:BOOL=ON'])
+        else:
+            args.extend(['-DLAPACKE:BOOL=OFF', '-DLAPACKE_WITH_TMG:BOOL=OFF'])
+
+        if self.spec.satisfies('@3.6.0:'):
+            args.append('-DCBLAS=ON')  # always build CBLAS
+
+        if self.spec.satisfies('%intel'):
+            # Intel compiler finds serious syntax issues when trying to
+            # build CBLAS and LapackE
+            args.extend(['-DCBLAS=OFF', '-DLAPACKE:BOOL=OFF'])
+
+        if self.spec.satisfies('%xl') or self.spec.satisfies('%xl_r'):
+            # use F77 compiler if IBM XL
+            args.extend(['-DCMAKE_Fortran_COMPILER=' + self.compiler.f77,
+                         '-DCMAKE_Fortran_FLAGS=' +
+                         (' '.join(self.spec.compiler_flags['fflags'])) +
+                         " -O3 -qnohot"])
+
+        # deprecated routines are commonly needed by, for example, suitesparse
+        # Note that OpenBLAS spack is built with deprecated routines
+        args.append('-DBUILD_DEPRECATED:BOOL=ON')
+
+        if self.spec.satisfies('+external-blas'):
+            args.extend(['-DUSE_OPTIMIZED_BLAS:BOOL=ON',
+                         '-DBLAS_LIBRARIES:PATH=' +
+                         self.spec['blas'].libs.joined(';')])
+
+        if self.spec.satisfies('+xblas'):
+            args.extend(['-DXBLAS_INCLUDE_DIR=' +
+                         self.spec['netlib-xblas'].prefix.include,
+                         '-DXBLAS_LIBRARY=' +
+                         self.spec['netlib-xblas'].libs.joined(';')])
+
+        args.append('-DBUILD_TESTING:BOOL=' +
+                    ('ON' if self.run_tests else 'OFF'))
+
+        return args
+
+    # Build, install, and check both static and shared versions of the
+    # libraries when +shared
+    @when('+shared')
+    def cmake(self, spec, prefix):
+        for self._building_shared in (False, True):
+            super(NetlibLapack, self).cmake(spec, prefix)
+
+    @when('+shared')
+    def build(self, spec, prefix):
+        for self._building_shared in (False, True):
+            super(NetlibLapack, self).build(spec, prefix)
+
+    @when('+shared')
+    def install(self, spec, prefix):
+        for self._building_shared in (False, True):
+            super(NetlibLapack, self).install(spec, prefix)
+
+    @when('+shared')
+    def check(self):
+        for self._building_shared in (False, True):
+            super(NetlibLapack, self).check()
diff --git a/var/spack/repos/tutorial/packages/netlib-lapack/testing.patch b/var/spack/repos/tutorial/packages/netlib-lapack/testing.patch
new file mode 100644
index 0000000000..fce18548c4
--- /dev/null
+++ b/var/spack/repos/tutorial/packages/netlib-lapack/testing.patch
@@ -0,0 +1,13 @@
+diff --git a/TESTING/LIN/alahd.f b/TESTING/LIN/alahd.f
+index 8f4cd58d..6a4946e0 100644
+--- a/TESTING/LIN/alahd.f
++++ b/TESTING/LIN/alahd.f
+@@ -1036,7 +1036,7 @@
+  9929 FORMAT( ' Test ratios (1-3: ', A1, 'TZRZF):' )
+  9920 FORMAT( 3X, ' 7-10: same as 3-6', 3X, ' 11-14: same as 3-6' )
+  9921 FORMAT( ' Test ratios:', / '    (1-2: ', A1, 'GELS, 3-6: ', A1,
+-     $      'GELSY, 7-10: ', A1, 'GELSS, 11-14: ', A1, 'GELSD, 15-16: '
++     $      'GELSY, 7-10: ', A1, 'GELSS, 11-14: ', A1, 'GELSD, 15-16: ',
+      $        A1, 'GETSLS)')
+  9928 FORMAT( 7X, 'where ALPHA = ( 1 + SQRT( 17 ) ) / 8' )
+  9927 FORMAT( 3X, I2, ': ABS( Largest element in L )', / 12X,
diff --git a/var/spack/repos/tutorial/packages/netlib-lapack/undefined_declarations.patch b/var/spack/repos/tutorial/packages/netlib-lapack/undefined_declarations.patch
new file mode 100644
index 0000000000..9dac2562f7
--- /dev/null
+++ b/var/spack/repos/tutorial/packages/netlib-lapack/undefined_declarations.patch
@@ -0,0 +1,26 @@
+diff --git a/SRC/dsytrf_aa_2stage.f b/SRC/dsytrf_aa_2stage.f
+index 2991305..f5f06cc 100644
+--- a/SRC/dsytrf_aa_2stage.f
++++ b/SRC/dsytrf_aa_2stage.f
+@@ -191,7 +191,7 @@
+       EXTERNAL           LSAME, ILAENV
+ *     ..
+ *     .. External Subroutines ..
+-      EXTERNAL           XERBLA, DCOPY, DLACGV, DLACPY,
++      EXTERNAL           XERBLA, DCOPY, DLACPY,
+      $                   DLASET, DGBTRF, DGEMM,  DGETRF, 
+      $                   DSYGST, DSWAP, DTRSM 
+ *     ..
+diff --git a/SRC/ssytrf_aa_2stage.f b/SRC/ssytrf_aa_2stage.f
+index be6809d..a929749 100644
+--- a/SRC/ssytrf_aa_2stage.f
++++ b/SRC/ssytrf_aa_2stage.f
+@@ -191,7 +191,7 @@
+       EXTERNAL           LSAME, ILAENV
+ *     ..
+ *     .. External Subroutines ..
+-      EXTERNAL           XERBLA, SCOPY, SLACGV, SLACPY,
++      EXTERNAL           XERBLA, SCOPY, SLACPY,
+      $                   SLASET, SGBTRF, SGEMM,  SGETRF, 
+      $                   SSYGST, SSWAP, STRSM 
+ *     ..
diff --git a/var/spack/repos/tutorial/repo.yaml b/var/spack/repos/tutorial/repo.yaml
new file mode 100644
index 0000000000..b43f511136
--- /dev/null
+++ b/var/spack/repos/tutorial/repo.yaml
@@ -0,0 +1,2 @@
+repo:
+  namespace: tutorial